From 97d2436e8b57b34d4ce53fc54939227d04f98fda Mon Sep 17 00:00:00 2001 From: Calvin Lu <59149377+calvinlu3@users.noreply.github.com> Date: Fri, 18 Apr 2025 11:50:03 -0400 Subject: [PATCH 1/3] Add preview component --- .../app/pages/curation/CurationPage.tsx | 2 +- .../collapsible/CancerTypeCollapsible.tsx | 12 ++-- .../collapsible/MutationCollapsible.tsx | 6 +- .../collapsible/TherapyCollapsible.tsx | 4 +- .../pages/curation/tooltip/CPLHelpTooltip.tsx | 44 ++++++++++++ .../firebase/input/RealtimeBasicInput.tsx | 11 ++- .../shared/firebase/input/RealtimeInputs.tsx | 46 +++++++++++- .../webapp/app/shared/tab/TabsContainer.tsx | 55 +++++++++++++++ .../webapp/app/shared/tab/tabs-container.scss | 70 +++++++++++++++++++ 9 files changed, 235 insertions(+), 15 deletions(-) create mode 100644 src/main/webapp/app/pages/curation/tooltip/CPLHelpTooltip.tsx create mode 100644 src/main/webapp/app/shared/tab/TabsContainer.tsx create mode 100644 src/main/webapp/app/shared/tab/tabs-container.scss diff --git a/src/main/webapp/app/pages/curation/CurationPage.tsx b/src/main/webapp/app/pages/curation/CurationPage.tsx index 55a29c91c..4544244fb 100644 --- a/src/main/webapp/app/pages/curation/CurationPage.tsx +++ b/src/main/webapp/app/pages/curation/CurationPage.tsx @@ -13,7 +13,7 @@ import OncoKBSidebar from 'app/components/sidebar/OncoKBSidebar'; import CurationHistoryTab from 'app/components/tabs/CurationHistoryTab'; import CurationToolsTab from 'app/components/tabs/CurationToolsTab'; import Tabs from 'app/components/tabs/tabs'; -import { RealtimeCheckedInputGroup, RealtimeTextAreaInput } from 'app/shared/firebase/input/RealtimeInputs'; +import { RealtimeCheckedInputGroup, RealtimeMultiTabTextAreaInput, RealtimeTextAreaInput } from 'app/shared/firebase/input/RealtimeInputs'; import GeneHeader from './header/GeneHeader'; import VusTable from 'app/shared/table/VusTable'; import * as styles from './styles.module.scss'; diff --git a/src/main/webapp/app/pages/curation/collapsible/CancerTypeCollapsible.tsx b/src/main/webapp/app/pages/curation/collapsible/CancerTypeCollapsible.tsx index 56a56e6ae..8a6207891 100644 --- a/src/main/webapp/app/pages/curation/collapsible/CancerTypeCollapsible.tsx +++ b/src/main/webapp/app/pages/curation/collapsible/CancerTypeCollapsible.tsx @@ -12,7 +12,7 @@ import ModifyCancerTypeModal from 'app/shared/modal/ModifyCancerTypeModal'; import { notifyError } from 'app/oncokb-commons/components/util/NotificationUtils'; import { getLevelDropdownOptions } from 'app/shared/util/firebase/firebase-level-utils'; import { DIAGNOSTIC_LEVELS_ORDERING, READABLE_FIELD, PROGNOSTIC_LEVELS_ORDERING } from 'app/config/constants/firebase'; -import { RealtimeTextAreaInput } from 'app/shared/firebase/input/RealtimeInputs'; +import { RealtimeMultiTabTextAreaInput, RealtimeTextAreaInput } from 'app/shared/firebase/input/RealtimeInputs'; import RealtimeLevelDropdownInput, { LevelOfEvidenceType } from 'app/shared/firebase/input/RealtimeLevelDropdownInput'; import CommentIcon from 'app/shared/icons/CommentIcon'; import { DeleteSectionButton } from '../button/DeleteSectionButton'; @@ -141,7 +141,7 @@ function CancerTypeCollapsible({ badge={} isPendingDelete={cancerTypesReview?.removed || false} > - - - - - - )} - - + + + OCPL Code + Output of Code from API + Example of output in an annotation + + + + {tableData.map((row, index) => ( + + +
{row[0]}
+ + {row[1]} + {row[2]} + + ))} + + + } + > + {props.children} + + ); +} diff --git a/src/main/webapp/app/shared/firebase/input/RealtimeBasicInput.tsx b/src/main/webapp/app/shared/firebase/input/RealtimeBasicInput.tsx index fa7f823b6..2e97e70dd 100644 --- a/src/main/webapp/app/shared/firebase/input/RealtimeBasicInput.tsx +++ b/src/main/webapp/app/shared/firebase/input/RealtimeBasicInput.tsx @@ -15,6 +15,7 @@ export enum RealtimeInputType { TEXT = 'text', INLINE_TEXT = 'inline_text', TEXTAREA = 'textarea', + MULTI_TAB_TEXTAREA = 'multi_tab_textarea', CHECKBOX = 'checkbox', RADIO = 'radio', DROPDOWN = 'dropdown', @@ -60,6 +61,7 @@ export interface IRealtimeBasicInput extends React.InputHTMLAttributes = (props: IRealtimeBasicInput) => { @@ -86,6 +88,7 @@ const RealtimeBasicInput: React.FunctionComponent = (props: disabledMessage, onMouseDown, labelOnClick, + hideLabel, ...otherProps } = props; @@ -144,7 +147,7 @@ const RealtimeBasicInput: React.FunctionComponent = (props: }; }, [inputValueLoaded]); - const labelComponent = label && ( + const labelComponent = label && !hideLabel && ( ); @@ -232,7 +235,11 @@ const RealtimeBasicInput: React.FunctionComponent = (props: {inputComponent} )} -
{parseRefs && !!inputValue ? : undefined}
+ {parseRefs && !!inputValue ? ( +
+ +
+ ) : undefined} ); }; diff --git a/src/main/webapp/app/shared/firebase/input/RealtimeInputs.tsx b/src/main/webapp/app/shared/firebase/input/RealtimeInputs.tsx index a6ff59bae..90e977d66 100644 --- a/src/main/webapp/app/shared/firebase/input/RealtimeInputs.tsx +++ b/src/main/webapp/app/shared/firebase/input/RealtimeInputs.tsx @@ -1,5 +1,8 @@ import React, { MouseEventHandler } from 'react'; -import RealtimeBasicInput, { IRealtimeBasicInput, RealtimeInputType } from './RealtimeBasicInput'; +import RealtimeBasicInput, { IRealtimeBasicInput, RealtimeBasicLabel, RealtimeInputType } from './RealtimeBasicInput'; +import TabsContainer, { ITabsContainer } from 'app/shared/tab/TabsContainer'; +import CPLHelpTooltip from 'app/pages/curation/tooltip/CPLHelpTooltip'; +import { IoHelpCircleOutline } from 'react-icons/io5'; /** * Text inputs @@ -15,6 +18,47 @@ export const RealtimeTextAreaInput = (props: Omit) return ; }; +export const RealtimeMultiTabTextAreaInput = (props: Omit) => { + const labelComponent = props.label && ( + + ); + + return ( +
+ {labelComponent} + , + key: `${props.firebasePath}-write`, + }, + { + title: 'Preview', + getContent: () => , + key: `${props.firebasePath}-preview`, + }, + ]} + toolbars={{ + default: ( + + ), + }} + > +
+ ); +}; + /** * Checkbox and Radio inputs */ diff --git a/src/main/webapp/app/shared/tab/TabsContainer.tsx b/src/main/webapp/app/shared/tab/TabsContainer.tsx new file mode 100644 index 000000000..98bdc2359 --- /dev/null +++ b/src/main/webapp/app/shared/tab/TabsContainer.tsx @@ -0,0 +1,55 @@ +import React, { useMemo, useState } from 'react'; +import './tabs-container.scss'; + +export type Tabs = { + title: string; + getContent: () => JSX.Element; + key: string; +}[]; + +export type ToolbarMap = { + [K in T[number]['key']]?: React.ReactNode; +} & { + // Toolbar shown on all tabs if no specific key matches + default?: React.ReactNode; +}; + +export interface ITabsContainer { + tabs: Tabs; + toolbars?: ToolbarMap; +} + +export default function TabsContainer({ tabs, toolbars }: ITabsContainer) { + const [selectedTab, setSelectedTab] = useState(tabs[0].key); + + const activeToolbar = useMemo(() => { + if (toolbars?.[selectedTab]) { + return toolbars[selectedTab]; + } + if (toolbars?.default) { + return toolbars.default; + } + return <>; + }, []); + + const activeTabIndex = tabs.findIndex(value => value.key === selectedTab); + + return ( +
+
+
    + {tabs.map(tab => ( +
  • + +
  • + ))} +
+
{activeToolbar}
+
+ +
{activeTabIndex > -1 ? tabs[activeTabIndex].getContent() : <>}
+
+ ); +} diff --git a/src/main/webapp/app/shared/tab/tabs-container.scss b/src/main/webapp/app/shared/tab/tabs-container.scss new file mode 100644 index 000000000..c249c3758 --- /dev/null +++ b/src/main/webapp/app/shared/tab/tabs-container.scss @@ -0,0 +1,70 @@ +.comment-box { + background-color: #ffffff; + border: 1px solid #d0d7de; + border-radius: 6px; + + .nav-tabs { + margin-bottom: 0; + + .nav-link { + border: none; + border-bottom: 2px solid transparent; + color: #57606a; + font-weight: 500; + + &.active { + color: #24292f; + border-bottom-color: #0969da; + background-color: transparent; + } + + &:hover { + color: #1f2328; + } + } + } + + .toolbar { + button { + padding: 2px 4px; + font-size: 23px; + line-height: 1.5; + border-radius: 6px; + height: 32px; + width: 32px; + display: flex; + align-items: center; + justify-content: center; + + &:hover { + background-color: #f3f4f6; + } + } + } + + .preview { + background-color: #ffffff; + border: 1px solid #d0d7de; + border-radius: 6px; + min-height: 10rem; + + p { + margin-bottom: 0.5rem; + } + } + + .btn-primary { + background-color: #2da44e; + border-color: #2da44e; + + &:hover { + background-color: #218739; + border-color: #1f7a32; + } + + &:disabled { + background-color: #94d3a2; + border-color: #94d3a2; + } + } +} From 8755f9972aa7824523919f1cabcf8b3d69a912e1 Mon Sep 17 00:00:00 2001 From: Calvin Lu <59149377+calvinlu3@users.noreply.github.com> Date: Tue, 29 Apr 2025 16:20:33 -0400 Subject: [PATCH 2/3] Add textarea preview --- .../security/SecurityConfigurationOAuth.java | 1 + .../oncokb/curation/web/rest/ApiProxy.java | 2 +- .../collapsible/CancerTypeCollapsible.tsx | 10 + .../collapsible/MutationCollapsible.tsx | 2 + .../collapsible/TherapyCollapsible.tsx | 2 + src/main/webapp/app/shared/api/clients.ts | 3 + .../api/generated/defaultCore/.gitignore | 4 + .../api/generated/defaultCore/.npmignore | 1 + .../defaultCore/.openapi-generator-ignore | 23 + .../defaultCore/.openapi-generator/FILES | 61 + .../defaultCore/.openapi-generator/VERSION | 1 + .../shared/api/generated/defaultCore/api.ts | 5902 +++++++++++++++++ .../shared/api/generated/defaultCore/base.ts | 91 + .../api/generated/defaultCore/common.ts | 148 + .../generated/defaultCore/configuration.ts | 122 + .../generated/defaultCore/docs/Alteration.md | 35 + .../AnnotateMutationByGenomicChangeQuery.md | 27 + .../docs/AnnotateMutationByHGVSgQuery.md | 27 + .../defaultCore/docs/AnnotatedVariant.md | 45 + .../defaultCore/docs/ApiHttpError.md | 27 + .../api/generated/defaultCore/docs/Article.md | 41 + .../defaultCore/docs/ArticleAbstract.md | 21 + .../defaultCore/docs/BiologicalVariant.md | 33 + .../defaultCore/docs/CancerTypeCount.md | 21 + .../generated/defaultCore/docs/Citations.md | 21 + .../defaultCore/docs/ClinicalVariant.md | 41 + .../defaultCore/docs/CplAnnotationRequest.md | 27 + .../defaultCore/docs/DownloadAvailability.md | 31 + .../api/generated/defaultCore/docs/Drug.md | 21 + .../generated/defaultCore/docs/DrugSynonym.md | 23 + .../generated/defaultCore/docs/DrugsApi.md | 58 + .../generated/defaultCore/docs/EnsemblGene.md | 31 + .../defaultCore/docs/EnsemblTranscript.md | 39 + .../generated/defaultCore/docs/Evidence.md | 55 + .../api/generated/defaultCore/docs/Exon.md | 29 + .../api/generated/defaultCore/docs/Gene.md | 37 + .../generated/defaultCore/docs/GeneNumber.md | 33 + .../api/generated/defaultCore/docs/Geneset.md | 25 + .../docs/GenomeNexusAnnotatedVariantInfo.md | 37 + .../generated/defaultCore/docs/Implication.md | 29 + .../docs/IndicatorQueryTreatment.md | 37 + .../generated/defaultCore/docs/LevelNumber.md | 21 + .../generated/defaultCore/docs/MainNumber.md | 27 + .../defaultCore/docs/MainNumberLevel.md | 21 + .../generated/defaultCore/docs/MainType.md | 25 + .../defaultCore/docs/MatchVariant.md | 21 + .../defaultCore/docs/MatchVariantRequest.md | 21 + .../defaultCore/docs/MatchVariantResult.md | 21 + .../defaultCore/docs/MutationEffectResp.md | 23 + .../defaultCore/docs/PfamDomainRange.md | 23 + .../defaultCore/docs/PortalAlteration.md | 33 + .../api/generated/defaultCore/docs/Query.md | 47 + .../docs/RelevantCancerTypeQuery.md | 21 + .../generated/defaultCore/docs/SearchApi.md | 262 + .../defaultCore/docs/TranscriptApi.md | 212 + .../docs/TranscriptCoverageFilterResult.md | 21 + .../defaultCore/docs/TranscriptResult.md | 23 + .../generated/defaultCore/docs/Treatment.md | 23 + .../defaultCore/docs/TreatmentDrug.md | 21 + .../defaultCore/docs/TreatmentDrugId.md | 19 + .../generated/defaultCore/docs/TumorType.md | 35 + .../defaultCore/docs/TypeaheadSearchResp.md | 43 + .../defaultCore/docs/UntranslatedRegion.md | 25 + .../generated/defaultCore/docs/UtilsApi.md | 1394 ++++ .../defaultCore/docs/VariantAnnotation.md | 73 + .../docs/VariantAnnotationTumorType.md | 23 + .../defaultCore/docs/VariantConsequence.md | 23 + .../api/generated/defaultCore/git_push.sh | 57 + .../shared/api/generated/defaultCore/index.ts | 16 + .../shared/firebase/input/PreviewTextArea.tsx | 87 + .../firebase/input/RealtimeBasicInput.tsx | 6 +- .../shared/firebase/input/RealtimeInputs.tsx | 9 +- src/main/webapp/app/shared/util/utils.tsx | 5 + webpack/webpack.dev.js | 2 +- 74 files changed, 9898 insertions(+), 9 deletions(-) create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/.gitignore create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/.npmignore create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/.openapi-generator-ignore create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/.openapi-generator/FILES create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/.openapi-generator/VERSION create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/api.ts create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/base.ts create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/common.ts create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/configuration.ts create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/Alteration.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/AnnotateMutationByGenomicChangeQuery.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/AnnotateMutationByHGVSgQuery.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/AnnotatedVariant.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/ApiHttpError.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/Article.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/ArticleAbstract.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/BiologicalVariant.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/CancerTypeCount.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/Citations.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/ClinicalVariant.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/CplAnnotationRequest.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/DownloadAvailability.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/Drug.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/DrugSynonym.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/DrugsApi.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/EnsemblGene.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/EnsemblTranscript.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/Evidence.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/Exon.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/Gene.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/GeneNumber.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/Geneset.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/GenomeNexusAnnotatedVariantInfo.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/Implication.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/IndicatorQueryTreatment.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/LevelNumber.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/MainNumber.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/MainNumberLevel.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/MainType.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/MatchVariant.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/MatchVariantRequest.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/MatchVariantResult.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/MutationEffectResp.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/PfamDomainRange.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/PortalAlteration.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/Query.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/RelevantCancerTypeQuery.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/SearchApi.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/TranscriptApi.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/TranscriptCoverageFilterResult.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/TranscriptResult.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/Treatment.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/TreatmentDrug.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/TreatmentDrugId.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/TumorType.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/TypeaheadSearchResp.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/UntranslatedRegion.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/UtilsApi.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/VariantAnnotation.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/VariantAnnotationTumorType.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/docs/VariantConsequence.md create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/git_push.sh create mode 100644 src/main/webapp/app/shared/api/generated/defaultCore/index.ts create mode 100644 src/main/webapp/app/shared/firebase/input/PreviewTextArea.tsx diff --git a/src/main/java/org/mskcc/oncokb/curation/config/security/SecurityConfigurationOAuth.java b/src/main/java/org/mskcc/oncokb/curation/config/security/SecurityConfigurationOAuth.java index 2ada4ec46..764dddf49 100644 --- a/src/main/java/org/mskcc/oncokb/curation/config/security/SecurityConfigurationOAuth.java +++ b/src/main/java/org/mskcc/oncokb/curation/config/security/SecurityConfigurationOAuth.java @@ -94,6 +94,7 @@ public SecurityFilterChain oauthFilterChain(HttpSecurity http, MvcRequestMatcher .requestMatchers(mvc.pattern("/websocket/**")).hasAnyAuthority(AuthoritiesConstants.CURATOR, AuthoritiesConstants.USER) .requestMatchers(mvc.pattern("/api/**")).hasAnyAuthority(AuthoritiesConstants.CURATOR, AuthoritiesConstants.USER, AuthoritiesConstants.ADMIN) .requestMatchers(mvc.pattern("/legacy-api/**")).hasAnyAuthority(AuthoritiesConstants.CURATOR, AuthoritiesConstants.USER, AuthoritiesConstants.ADMIN) + .requestMatchers(mvc.pattern("/core/**")).hasAnyAuthority(AuthoritiesConstants.CURATOR, AuthoritiesConstants.USER, AuthoritiesConstants.ADMIN) .requestMatchers(mvc.pattern("/v3/api-docs/**")).hasAuthority(AuthoritiesConstants.ADMIN) .requestMatchers(mvc.pattern("/management/**")).hasAuthority(AuthoritiesConstants.ADMIN) ) diff --git a/src/main/java/org/mskcc/oncokb/curation/web/rest/ApiProxy.java b/src/main/java/org/mskcc/oncokb/curation/web/rest/ApiProxy.java index 27105face..99318a97c 100644 --- a/src/main/java/org/mskcc/oncokb/curation/web/rest/ApiProxy.java +++ b/src/main/java/org/mskcc/oncokb/curation/web/rest/ApiProxy.java @@ -20,7 +20,7 @@ import org.springframework.web.server.ResponseStatusException; @RestController -@RequestMapping({ "/legacy-api" }) +@RequestMapping({ "/legacy-api", "/api/v1/utils" }) public class ApiProxy { private final ApiProxyService apiProxyService; diff --git a/src/main/webapp/app/pages/curation/collapsible/CancerTypeCollapsible.tsx b/src/main/webapp/app/pages/curation/collapsible/CancerTypeCollapsible.tsx index 8a6207891..2f5824fb1 100644 --- a/src/main/webapp/app/pages/curation/collapsible/CancerTypeCollapsible.tsx +++ b/src/main/webapp/app/pages/curation/collapsible/CancerTypeCollapsible.tsx @@ -146,6 +146,8 @@ function CancerTypeCollapsible({ firebasePath={`${cancerTypePath}/summary`} inputClass={styles.summaryTextarea} label="Therapeutic Summary (Optional)" + mutationName={mutationName} + cancerTypeName={cancerTypeName} labelIcon={ @@ -260,6 +268,8 @@ function CancerTypeCollapsible({ firebasePath={`${cancerTypePath}/prognostic/description`} inputClass={styles.textarea} label="Description of Evidence" + mutationName={mutationName} + cancerTypeName={cancerTypeName} name="evidenceDescription" parseRefs /> diff --git a/src/main/webapp/app/pages/curation/collapsible/MutationCollapsible.tsx b/src/main/webapp/app/pages/curation/collapsible/MutationCollapsible.tsx index 920c6c018..082fd4524 100644 --- a/src/main/webapp/app/pages/curation/collapsible/MutationCollapsible.tsx +++ b/src/main/webapp/app/pages/curation/collapsible/MutationCollapsible.tsx @@ -359,6 +359,7 @@ const MutationCollapsible = ({ firebasePath={`${mutationPath}/summary`} inputClass={styles.summaryTextarea} label="Mutation Summary (Optional)" + mutationName={mutationName} labelIcon={ } + * @memberof Alteration + */ + referenceGenomes?: Array; + /** + * + * @type {string} + * @memberof Alteration + */ + variantResidues?: string; +} + +export const AlterationReferenceGenomesEnum = { + Grch37: 'GRCh37', + Grch38: 'GRCh38', +} as const; + +export type AlterationReferenceGenomesEnum = (typeof AlterationReferenceGenomesEnum)[keyof typeof AlterationReferenceGenomesEnum]; + +/** + * + * @export + * @interface AnnotateMutationByGenomicChangeQuery + */ +export interface AnnotateMutationByGenomicChangeQuery { + /** + * + * @type {Array} + * @memberof AnnotateMutationByGenomicChangeQuery + */ + evidenceTypes?: Array; + /** + * + * @type {string} + * @memberof AnnotateMutationByGenomicChangeQuery + */ + genomicLocation?: string; + /** + * + * @type {string} + * @memberof AnnotateMutationByGenomicChangeQuery + */ + id?: string; + /** + * + * @type {string} + * @memberof AnnotateMutationByGenomicChangeQuery + */ + referenceGenome?: AnnotateMutationByGenomicChangeQueryReferenceGenomeEnum; + /** + * + * @type {string} + * @memberof AnnotateMutationByGenomicChangeQuery + */ + tumorType?: string; +} + +export const AnnotateMutationByGenomicChangeQueryEvidenceTypesEnum = { + GeneSummary: 'GENE_SUMMARY', + MutationSummary: 'MUTATION_SUMMARY', + TumorTypeSummary: 'TUMOR_TYPE_SUMMARY', + GeneTumorTypeSummary: 'GENE_TUMOR_TYPE_SUMMARY', + PrognosticSummary: 'PROGNOSTIC_SUMMARY', + DiagnosticSummary: 'DIAGNOSTIC_SUMMARY', + GeneBackground: 'GENE_BACKGROUND', + Oncogenic: 'ONCOGENIC', + MutationEffect: 'MUTATION_EFFECT', + Vus: 'VUS', + PrognosticImplication: 'PROGNOSTIC_IMPLICATION', + DiagnosticImplication: 'DIAGNOSTIC_IMPLICATION', + StandardTherapeuticImplicationsForDrugSensitivity: 'STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY', + StandardTherapeuticImplicationsForDrugResistance: 'STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE', + InvestigationalTherapeuticImplicationsDrugSensitivity: 'INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY', + InvestigationalTherapeuticImplicationsDrugResistance: 'INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE', +} as const; + +export type AnnotateMutationByGenomicChangeQueryEvidenceTypesEnum = + (typeof AnnotateMutationByGenomicChangeQueryEvidenceTypesEnum)[keyof typeof AnnotateMutationByGenomicChangeQueryEvidenceTypesEnum]; +export const AnnotateMutationByGenomicChangeQueryReferenceGenomeEnum = { + Grch37: 'GRCh37', + Grch38: 'GRCh38', +} as const; + +export type AnnotateMutationByGenomicChangeQueryReferenceGenomeEnum = + (typeof AnnotateMutationByGenomicChangeQueryReferenceGenomeEnum)[keyof typeof AnnotateMutationByGenomicChangeQueryReferenceGenomeEnum]; + +/** + * + * @export + * @interface AnnotateMutationByHGVSgQuery + */ +export interface AnnotateMutationByHGVSgQuery { + /** + * + * @type {Array} + * @memberof AnnotateMutationByHGVSgQuery + */ + evidenceTypes?: Array; + /** + * + * @type {string} + * @memberof AnnotateMutationByHGVSgQuery + */ + hgvsg?: string; + /** + * + * @type {string} + * @memberof AnnotateMutationByHGVSgQuery + */ + id?: string; + /** + * + * @type {string} + * @memberof AnnotateMutationByHGVSgQuery + */ + referenceGenome?: AnnotateMutationByHGVSgQueryReferenceGenomeEnum; + /** + * + * @type {string} + * @memberof AnnotateMutationByHGVSgQuery + */ + tumorType?: string; +} + +export const AnnotateMutationByHGVSgQueryEvidenceTypesEnum = { + GeneSummary: 'GENE_SUMMARY', + MutationSummary: 'MUTATION_SUMMARY', + TumorTypeSummary: 'TUMOR_TYPE_SUMMARY', + GeneTumorTypeSummary: 'GENE_TUMOR_TYPE_SUMMARY', + PrognosticSummary: 'PROGNOSTIC_SUMMARY', + DiagnosticSummary: 'DIAGNOSTIC_SUMMARY', + GeneBackground: 'GENE_BACKGROUND', + Oncogenic: 'ONCOGENIC', + MutationEffect: 'MUTATION_EFFECT', + Vus: 'VUS', + PrognosticImplication: 'PROGNOSTIC_IMPLICATION', + DiagnosticImplication: 'DIAGNOSTIC_IMPLICATION', + StandardTherapeuticImplicationsForDrugSensitivity: 'STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY', + StandardTherapeuticImplicationsForDrugResistance: 'STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE', + InvestigationalTherapeuticImplicationsDrugSensitivity: 'INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY', + InvestigationalTherapeuticImplicationsDrugResistance: 'INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE', +} as const; + +export type AnnotateMutationByHGVSgQueryEvidenceTypesEnum = + (typeof AnnotateMutationByHGVSgQueryEvidenceTypesEnum)[keyof typeof AnnotateMutationByHGVSgQueryEvidenceTypesEnum]; +export const AnnotateMutationByHGVSgQueryReferenceGenomeEnum = { + Grch37: 'GRCh37', + Grch38: 'GRCh38', +} as const; + +export type AnnotateMutationByHGVSgQueryReferenceGenomeEnum = + (typeof AnnotateMutationByHGVSgQueryReferenceGenomeEnum)[keyof typeof AnnotateMutationByHGVSgQueryReferenceGenomeEnum]; + +/** + * + * @export + * @interface AnnotatedVariant + */ +export interface AnnotatedVariant { + /** + * + * @type {string} + * @memberof AnnotatedVariant + */ + description?: string; + /** + * + * @type {number} + * @memberof AnnotatedVariant + */ + entrezGeneId?: number; + /** + * + * @type {string} + * @memberof AnnotatedVariant + */ + gene?: string; + /** + * + * @type {string} + * @memberof AnnotatedVariant + */ + grch37Isoform?: string; + /** + * + * @type {string} + * @memberof AnnotatedVariant + */ + grch37RefSeq?: string; + /** + * + * @type {string} + * @memberof AnnotatedVariant + */ + grch38Isoform?: string; + /** + * + * @type {string} + * @memberof AnnotatedVariant + */ + grch38RefSeq?: string; + /** + * + * @type {string} + * @memberof AnnotatedVariant + */ + mutationEffect?: string; + /** + * + * @type {string} + * @memberof AnnotatedVariant + */ + mutationEffectAbstracts?: string; + /** + * + * @type {string} + * @memberof AnnotatedVariant + */ + mutationEffectPmids?: string; + /** + * + * @type {string} + * @memberof AnnotatedVariant + */ + oncogenicity?: string; + /** + * + * @type {string} + * @memberof AnnotatedVariant + */ + proteinChange?: string; + /** + * + * @type {string} + * @memberof AnnotatedVariant + */ + referenceGenome?: string; + /** + * + * @type {string} + * @memberof AnnotatedVariant + */ + variant?: string; +} +/** + * + * @export + * @interface ApiHttpError + */ +export interface ApiHttpError { + /** + * + * @type {string} + * @memberof ApiHttpError + */ + detail?: string; + /** + * + * @type {string} + * @memberof ApiHttpError + */ + message?: string; + /** + * + * @type {string} + * @memberof ApiHttpError + */ + path?: string; + /** + * + * @type {number} + * @memberof ApiHttpError + */ + status?: number; + /** + * + * @type {string} + * @memberof ApiHttpError + */ + title?: string; +} +/** + * + * @export + * @interface Article + */ +export interface Article { + /** + * + * @type {string} + * @memberof Article + */ + abstract?: string; + /** + * + * @type {string} + * @memberof Article + */ + authors?: string; + /** + * + * @type {string} + * @memberof Article + */ + elocationId?: string; + /** + * + * @type {string} + * @memberof Article + */ + issue?: string; + /** + * + * @type {string} + * @memberof Article + */ + journal?: string; + /** + * + * @type {string} + * @memberof Article + */ + link?: string; + /** + * + * @type {string} + * @memberof Article + */ + pages?: string; + /** + * + * @type {string} + * @memberof Article + */ + pmid?: string; + /** + * + * @type {string} + * @memberof Article + */ + pubDate?: string; + /** + * + * @type {string} + * @memberof Article + */ + reference?: string; + /** + * + * @type {string} + * @memberof Article + */ + title?: string; + /** + * + * @type {string} + * @memberof Article + */ + volume?: string; +} +/** + * + * @export + * @interface ArticleAbstract + */ +export interface ArticleAbstract { + /** + * + * @type {string} + * @memberof ArticleAbstract + */ + abstract?: string; + /** + * + * @type {string} + * @memberof ArticleAbstract + */ + link?: string; +} +/** + * + * @export + * @interface BiologicalVariant + */ +export interface BiologicalVariant { + /** + * + * @type {string} + * @memberof BiologicalVariant + */ + mutationEffect?: string; + /** + * + * @type {Array} + * @memberof BiologicalVariant + */ + mutationEffectAbstracts?: Array; + /** + * + * @type {string} + * @memberof BiologicalVariant + */ + mutationEffectDescription?: string; + /** + * + * @type {Array} + * @memberof BiologicalVariant + */ + mutationEffectPmids?: Array; + /** + * + * @type {string} + * @memberof BiologicalVariant + */ + oncogenic?: string; + /** + * + * @type {Array} + * @memberof BiologicalVariant + */ + oncogenicAbstracts?: Array; + /** + * + * @type {Array} + * @memberof BiologicalVariant + */ + oncogenicPmids?: Array; + /** + * + * @type {Alteration} + * @memberof BiologicalVariant + */ + variant?: Alteration; +} +/** + * + * @export + * @interface CancerTypeCount + */ +export interface CancerTypeCount { + /** + * + * @type {string} + * @memberof CancerTypeCount + */ + cancerType?: string; + /** + * + * @type {number} + * @memberof CancerTypeCount + */ + count?: number; +} +/** + * + * @export + * @interface Citations + */ +export interface Citations { + /** + * Set of Abstract sources + * @type {Array} + * @memberof Citations + */ + abstracts?: Array; + /** + * Set of PubMed article ids + * @type {Array} + * @memberof Citations + */ + pmids?: Array; +} +/** + * + * @export + * @interface ClinicalVariant + */ +export interface ClinicalVariant { + /** + * + * @type {Array} + * @memberof ClinicalVariant + */ + cancerTypes?: Array; + /** + * + * @type {Array} + * @memberof ClinicalVariant + */ + drug?: Array; + /** + * + * @type {Array} + * @memberof ClinicalVariant + */ + drugAbstracts?: Array; + /** + * + * @type {string} + * @memberof ClinicalVariant + */ + drugDescription?: string; + /** + * + * @type {Array} + * @memberof ClinicalVariant + */ + drugPmids?: Array; + /** + * + * @type {Array} + * @memberof ClinicalVariant + */ + excludedCancerTypes?: Array; + /** + * + * @type {string} + * @memberof ClinicalVariant + */ + fdaLevel?: string; + /** + * + * @type {string} + * @memberof ClinicalVariant + */ + level?: string; + /** + * + * @type {string} + * @memberof ClinicalVariant + */ + liquidPropagationLevel?: string; + /** + * + * @type {string} + * @memberof ClinicalVariant + */ + oncogenic?: string; + /** + * + * @type {string} + * @memberof ClinicalVariant + */ + solidPropagationLevel?: string; + /** + * + * @type {Alteration} + * @memberof ClinicalVariant + */ + variant?: Alteration; +} +/** + * + * @export + * @interface CplAnnotationRequest + */ +export interface CplAnnotationRequest { + /** + * + * @type {string} + * @memberof CplAnnotationRequest + */ + alteration?: string; + /** + * + * @type {string} + * @memberof CplAnnotationRequest + */ + cancerType?: string; + /** + * + * @type {string} + * @memberof CplAnnotationRequest + */ + hugoSymbol?: string; + /** + * + * @type {string} + * @memberof CplAnnotationRequest + */ + referenceGenome?: CplAnnotationRequestReferenceGenomeEnum; + /** + * + * @type {string} + * @memberof CplAnnotationRequest + */ + template?: string; +} + +export const CplAnnotationRequestReferenceGenomeEnum = { + Grch37: 'GRCh37', + Grch38: 'GRCh38', +} as const; + +export type CplAnnotationRequestReferenceGenomeEnum = + (typeof CplAnnotationRequestReferenceGenomeEnum)[keyof typeof CplAnnotationRequestReferenceGenomeEnum]; + +/** + * + * @export + * @interface DownloadAvailability + */ +export interface DownloadAvailability { + /** + * + * @type {boolean} + * @memberof DownloadAvailability + */ + hasAllActionableVariants?: boolean; + /** + * + * @type {boolean} + * @memberof DownloadAvailability + */ + hasAllAnnotatedVariants?: boolean; + /** + * + * @type {boolean} + * @memberof DownloadAvailability + */ + hasAllCuratedGenes?: boolean; + /** + * + * @type {boolean} + * @memberof DownloadAvailability + */ + hasCancerGeneList?: boolean; + /** + * + * @type {boolean} + * @memberof DownloadAvailability + */ + hasReadme?: boolean; + /** + * + * @type {boolean} + * @memberof DownloadAvailability + */ + hasSqlDump?: boolean; + /** + * + * @type {string} + * @memberof DownloadAvailability + */ + version?: string; +} +/** + * + * @export + * @interface Drug + */ +export interface Drug { + /** + * + * @type {string} + * @memberof Drug + */ + drugName?: string; + /** + * + * @type {string} + * @memberof Drug + */ + ncitCode?: string; +} +/** + * + * @export + * @interface DrugSynonym + */ +export interface DrugSynonym { + /** + * + * @type {Drug} + * @memberof DrugSynonym + */ + drug?: Drug; + /** + * + * @type {number} + * @memberof DrugSynonym + */ + id?: number; + /** + * + * @type {string} + * @memberof DrugSynonym + */ + name?: string; +} +/** + * + * @export + * @interface EnsemblGene + */ +export interface EnsemblGene { + /** + * + * @type {boolean} + * @memberof EnsemblGene + */ + canonical?: boolean; + /** + * + * @type {string} + * @memberof EnsemblGene + */ + chromosome?: string; + /** + * + * @type {number} + * @memberof EnsemblGene + */ + end?: number; + /** + * + * @type {string} + * @memberof EnsemblGene + */ + ensemblGeneId?: string; + /** + * + * @type {string} + * @memberof EnsemblGene + */ + referenceGenome?: string; + /** + * + * @type {number} + * @memberof EnsemblGene + */ + start?: number; + /** + * + * @type {number} + * @memberof EnsemblGene + */ + strand?: number; +} +/** + * + * @export + * @interface EnsemblTranscript + */ +export interface EnsemblTranscript { + /** + * Consensus CDS (CCDS) ID + * @type {string} + * @memberof EnsemblTranscript + */ + ccdsId?: string; + /** + * Exon information + * @type {Array} + * @memberof EnsemblTranscript + */ + exons?: Array; + /** + * Ensembl gene id + * @type {string} + * @memberof EnsemblTranscript + */ + geneId: string; + /** + * Hugo symbols + * @type {Array} + * @memberof EnsemblTranscript + */ + hugoSymbols?: Array; + /** + * Pfam domains + * @type {Array} + * @memberof EnsemblTranscript + */ + pfamDomains?: Array; + /** + * Ensembl protein id + * @type {string} + * @memberof EnsemblTranscript + */ + proteinId: string; + /** + * Length of protein + * @type {number} + * @memberof EnsemblTranscript + */ + proteinLength?: number; + /** + * RefSeq mRNA ID + * @type {string} + * @memberof EnsemblTranscript + */ + refseqMrnaId?: string; + /** + * Ensembl transcript id + * @type {string} + * @memberof EnsemblTranscript + */ + transcriptId: string; + /** + * + * @type {string} + * @memberof EnsemblTranscript + */ + uniprotId?: string; + /** + * UTR information + * @type {Array} + * @memberof EnsemblTranscript + */ + utrs?: Array; +} +/** + * + * @export + * @interface Evidence + */ +export interface Evidence { + /** + * + * @type {string} + * @memberof Evidence + */ + additionalInfo?: string; + /** + * + * @type {Array} + * @memberof Evidence + */ + alterations?: Array; + /** + * + * @type {Array
} + * @memberof Evidence + */ + articles?: Array
; + /** + * + * @type {Array} + * @memberof Evidence + */ + cancerTypes?: Array; + /** + * + * @type {string} + * @memberof Evidence + */ + description?: string; + /** + * + * @type {string} + * @memberof Evidence + */ + evidenceType?: EvidenceEvidenceTypeEnum; + /** + * + * @type {Array} + * @memberof Evidence + */ + excludedCancerTypes?: Array; + /** + * + * @type {string} + * @memberof Evidence + */ + fdaLevel?: EvidenceFdaLevelEnum; + /** + * + * @type {Gene} + * @memberof Evidence + */ + gene?: Gene; + /** + * + * @type {number} + * @memberof Evidence + */ + id?: number; + /** + * + * @type {string} + * @memberof Evidence + */ + knownEffect?: string; + /** + * + * @type {string} + * @memberof Evidence + */ + lastEdit?: string; + /** + * + * @type {string} + * @memberof Evidence + */ + lastReview?: string; + /** + * + * @type {string} + * @memberof Evidence + */ + levelOfEvidence?: EvidenceLevelOfEvidenceEnum; + /** + * + * @type {string} + * @memberof Evidence + */ + liquidPropagationLevel?: EvidenceLiquidPropagationLevelEnum; + /** + * + * @type {Array} + * @memberof Evidence + */ + relevantCancerTypes?: Array; + /** + * + * @type {string} + * @memberof Evidence + */ + solidPropagationLevel?: EvidenceSolidPropagationLevelEnum; + /** + * + * @type {Array} + * @memberof Evidence + */ + treatments?: Array; + /** + * + * @type {string} + * @memberof Evidence + */ + uuid?: string; +} + +export const EvidenceEvidenceTypeEnum = { + GeneSummary: 'GENE_SUMMARY', + MutationSummary: 'MUTATION_SUMMARY', + TumorTypeSummary: 'TUMOR_TYPE_SUMMARY', + GeneTumorTypeSummary: 'GENE_TUMOR_TYPE_SUMMARY', + PrognosticSummary: 'PROGNOSTIC_SUMMARY', + DiagnosticSummary: 'DIAGNOSTIC_SUMMARY', + GeneBackground: 'GENE_BACKGROUND', + Oncogenic: 'ONCOGENIC', + MutationEffect: 'MUTATION_EFFECT', + Vus: 'VUS', + PrognosticImplication: 'PROGNOSTIC_IMPLICATION', + DiagnosticImplication: 'DIAGNOSTIC_IMPLICATION', + StandardTherapeuticImplicationsForDrugSensitivity: 'STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY', + StandardTherapeuticImplicationsForDrugResistance: 'STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE', + InvestigationalTherapeuticImplicationsDrugSensitivity: 'INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY', + InvestigationalTherapeuticImplicationsDrugResistance: 'INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE', +} as const; + +export type EvidenceEvidenceTypeEnum = (typeof EvidenceEvidenceTypeEnum)[keyof typeof EvidenceEvidenceTypeEnum]; +export const EvidenceFdaLevelEnum = { + Level1: 'LEVEL_1', + Level2: 'LEVEL_2', + Level3A: 'LEVEL_3A', + Level3B: 'LEVEL_3B', + Level4: 'LEVEL_4', + LevelR1: 'LEVEL_R1', + LevelR2: 'LEVEL_R2', + LevelPx1: 'LEVEL_Px1', + LevelPx2: 'LEVEL_Px2', + LevelPx3: 'LEVEL_Px3', + LevelDx1: 'LEVEL_Dx1', + LevelDx2: 'LEVEL_Dx2', + LevelDx3: 'LEVEL_Dx3', + LevelFda1: 'LEVEL_Fda1', + LevelFda2: 'LEVEL_Fda2', + LevelFda3: 'LEVEL_Fda3', + No: 'NO', +} as const; + +export type EvidenceFdaLevelEnum = (typeof EvidenceFdaLevelEnum)[keyof typeof EvidenceFdaLevelEnum]; +export const EvidenceLevelOfEvidenceEnum = { + Level1: 'LEVEL_1', + Level2: 'LEVEL_2', + Level3A: 'LEVEL_3A', + Level3B: 'LEVEL_3B', + Level4: 'LEVEL_4', + LevelR1: 'LEVEL_R1', + LevelR2: 'LEVEL_R2', + LevelPx1: 'LEVEL_Px1', + LevelPx2: 'LEVEL_Px2', + LevelPx3: 'LEVEL_Px3', + LevelDx1: 'LEVEL_Dx1', + LevelDx2: 'LEVEL_Dx2', + LevelDx3: 'LEVEL_Dx3', + LevelFda1: 'LEVEL_Fda1', + LevelFda2: 'LEVEL_Fda2', + LevelFda3: 'LEVEL_Fda3', + No: 'NO', +} as const; + +export type EvidenceLevelOfEvidenceEnum = (typeof EvidenceLevelOfEvidenceEnum)[keyof typeof EvidenceLevelOfEvidenceEnum]; +export const EvidenceLiquidPropagationLevelEnum = { + Level1: 'LEVEL_1', + Level2: 'LEVEL_2', + Level3A: 'LEVEL_3A', + Level3B: 'LEVEL_3B', + Level4: 'LEVEL_4', + LevelR1: 'LEVEL_R1', + LevelR2: 'LEVEL_R2', + LevelPx1: 'LEVEL_Px1', + LevelPx2: 'LEVEL_Px2', + LevelPx3: 'LEVEL_Px3', + LevelDx1: 'LEVEL_Dx1', + LevelDx2: 'LEVEL_Dx2', + LevelDx3: 'LEVEL_Dx3', + LevelFda1: 'LEVEL_Fda1', + LevelFda2: 'LEVEL_Fda2', + LevelFda3: 'LEVEL_Fda3', + No: 'NO', +} as const; + +export type EvidenceLiquidPropagationLevelEnum = + (typeof EvidenceLiquidPropagationLevelEnum)[keyof typeof EvidenceLiquidPropagationLevelEnum]; +export const EvidenceSolidPropagationLevelEnum = { + Level1: 'LEVEL_1', + Level2: 'LEVEL_2', + Level3A: 'LEVEL_3A', + Level3B: 'LEVEL_3B', + Level4: 'LEVEL_4', + LevelR1: 'LEVEL_R1', + LevelR2: 'LEVEL_R2', + LevelPx1: 'LEVEL_Px1', + LevelPx2: 'LEVEL_Px2', + LevelPx3: 'LEVEL_Px3', + LevelDx1: 'LEVEL_Dx1', + LevelDx2: 'LEVEL_Dx2', + LevelDx3: 'LEVEL_Dx3', + LevelFda1: 'LEVEL_Fda1', + LevelFda2: 'LEVEL_Fda2', + LevelFda3: 'LEVEL_Fda3', + No: 'NO', +} as const; + +export type EvidenceSolidPropagationLevelEnum = (typeof EvidenceSolidPropagationLevelEnum)[keyof typeof EvidenceSolidPropagationLevelEnum]; + +/** + * + * @export + * @interface Exon + */ +export interface Exon { + /** + * End position of exon + * @type {number} + * @memberof Exon + */ + exonEnd: number; + /** + * Exon id + * @type {string} + * @memberof Exon + */ + exonId: string; + /** + * Start position of exon + * @type {number} + * @memberof Exon + */ + exonStart: number; + /** + * Number of exon in transcript + * @type {number} + * @memberof Exon + */ + rank: number; + /** + * Strand exon is on, -1 for - and 1 for + + * @type {number} + * @memberof Exon + */ + strand: number; + /** + * Exon version + * @type {number} + * @memberof Exon + */ + version: number; +} +/** + * + * @export + * @interface Gene + */ +export interface Gene { + /** + * + * @type {number} + * @memberof Gene + */ + entrezGeneId?: number; + /** + * + * @type {Array} + * @memberof Gene + */ + geneAliases?: Array; + /** + * + * @type {Array} + * @memberof Gene + */ + genesets?: Array; + /** + * + * @type {string} + * @memberof Gene + */ + grch37Isoform?: string; + /** + * + * @type {string} + * @memberof Gene + */ + grch37RefSeq?: string; + /** + * + * @type {string} + * @memberof Gene + */ + grch38Isoform?: string; + /** + * + * @type {string} + * @memberof Gene + */ + grch38RefSeq?: string; + /** + * + * @type {string} + * @memberof Gene + */ + hugoSymbol?: string; + /** + * + * @type {boolean} + * @memberof Gene + */ + oncogene?: boolean; + /** + * + * @type {boolean} + * @memberof Gene + */ + tsg?: boolean; +} +/** + * + * @export + * @interface GeneNumber + */ +export interface GeneNumber { + /** + * + * @type {number} + * @memberof GeneNumber + */ + alteration?: number; + /** + * + * @type {Gene} + * @memberof GeneNumber + */ + gene?: Gene; + /** + * + * @type {string} + * @memberof GeneNumber + */ + highestDiagnosticImplicationLevel?: string; + /** + * + * @type {string} + * @memberof GeneNumber + */ + highestFdaLevel?: string; + /** + * + * @type {string} + * @memberof GeneNumber + */ + highestPrognosticImplicationLevel?: string; + /** + * + * @type {string} + * @memberof GeneNumber + */ + highestResistanceLevel?: string; + /** + * + * @type {string} + * @memberof GeneNumber + */ + highestSensitiveLevel?: string; + /** + * + * @type {number} + * @memberof GeneNumber + */ + tumorType?: number; +} +/** + * + * @export + * @interface Geneset + */ +export interface Geneset { + /** + * + * @type {Array} + * @memberof Geneset + */ + genes?: Array; + /** + * + * @type {number} + * @memberof Geneset + */ + id?: number; + /** + * + * @type {string} + * @memberof Geneset + */ + name?: string; + /** + * + * @type {string} + * @memberof Geneset + */ + uuid?: string; +} +/** + * + * @export + * @interface GenomeNexusAnnotatedVariantInfo + */ +export interface GenomeNexusAnnotatedVariantInfo { + /** + * + * @type {string} + * @memberof GenomeNexusAnnotatedVariantInfo + */ + consequenceTerms?: string; + /** + * + * @type {number} + * @memberof GenomeNexusAnnotatedVariantInfo + */ + entrezGeneId?: number; + /** + * + * @type {string} + * @memberof GenomeNexusAnnotatedVariantInfo + */ + genomicLocation?: string; + /** + * + * @type {string} + * @memberof GenomeNexusAnnotatedVariantInfo + */ + hgvsg?: string; + /** + * + * @type {string} + * @memberof GenomeNexusAnnotatedVariantInfo + */ + hgvspShort?: string; + /** + * + * @type {string} + * @memberof GenomeNexusAnnotatedVariantInfo + */ + hugoSymbol?: string; + /** + * + * @type {string} + * @memberof GenomeNexusAnnotatedVariantInfo + */ + originalVariantQuery?: string; + /** + * + * @type {number} + * @memberof GenomeNexusAnnotatedVariantInfo + */ + proteinEnd?: number; + /** + * + * @type {number} + * @memberof GenomeNexusAnnotatedVariantInfo + */ + proteinStart?: number; + /** + * + * @type {string} + * @memberof GenomeNexusAnnotatedVariantInfo + */ + referenceGenome?: GenomeNexusAnnotatedVariantInfoReferenceGenomeEnum; +} + +export const GenomeNexusAnnotatedVariantInfoReferenceGenomeEnum = { + Grch37: 'GRCh37', + Grch38: 'GRCh38', +} as const; + +export type GenomeNexusAnnotatedVariantInfoReferenceGenomeEnum = + (typeof GenomeNexusAnnotatedVariantInfoReferenceGenomeEnum)[keyof typeof GenomeNexusAnnotatedVariantInfoReferenceGenomeEnum]; + +/** + * + * @export + * @interface Implication + */ +export interface Implication { + /** + * List of abstracts cited to support the level of evidence. Defaulted to empty list + * @type {Array} + * @memberof Implication + */ + abstracts?: Array; + /** + * List of alterations associated with implication + * @type {Array} + * @memberof Implication + */ + alterations?: Array; + /** + * DEPRECATED + * @type {string} + * @memberof Implication + */ + description?: string; + /** + * Level associated with implication + * @type {string} + * @memberof Implication + */ + levelOfEvidence?: ImplicationLevelOfEvidenceEnum; + /** + * List of PubMed IDs cited to support the level of evidence. Defaulted to empty list + * @type {Array} + * @memberof Implication + */ + pmids?: Array; + /** + * + * @type {TumorType} + * @memberof Implication + */ + tumorType?: TumorType; +} + +export const ImplicationLevelOfEvidenceEnum = { + Level1: 'LEVEL_1', + Level2: 'LEVEL_2', + Level3A: 'LEVEL_3A', + Level3B: 'LEVEL_3B', + Level4: 'LEVEL_4', + LevelR1: 'LEVEL_R1', + LevelR2: 'LEVEL_R2', + LevelPx1: 'LEVEL_Px1', + LevelPx2: 'LEVEL_Px2', + LevelPx3: 'LEVEL_Px3', + LevelDx1: 'LEVEL_Dx1', + LevelDx2: 'LEVEL_Dx2', + LevelDx3: 'LEVEL_Dx3', + LevelFda1: 'LEVEL_Fda1', + LevelFda2: 'LEVEL_Fda2', + LevelFda3: 'LEVEL_Fda3', + No: 'NO', +} as const; + +export type ImplicationLevelOfEvidenceEnum = (typeof ImplicationLevelOfEvidenceEnum)[keyof typeof ImplicationLevelOfEvidenceEnum]; + +/** + * + * @export + * @interface IndicatorQueryTreatment + */ +export interface IndicatorQueryTreatment { + /** + * List of abstracts cited in the treatment description. Defaulted to empty list + * @type {Array} + * @memberof IndicatorQueryTreatment + */ + abstracts?: Array; + /** + * List of alterations associated with therapeutic implication + * @type {Array} + * @memberof IndicatorQueryTreatment + */ + alterations?: Array; + /** + * DEPRECATED + * @type {Array} + * @memberof IndicatorQueryTreatment + */ + approvedIndications?: Array; + /** + * Treatment description. Defaulted to \"\" + * @type {string} + * @memberof IndicatorQueryTreatment + */ + description?: string; + /** + * List of drugs associated with therapeutic implication + * @type {Array} + * @memberof IndicatorQueryTreatment + */ + drugs?: Array; + /** + * FDA level associated with implication + * @type {string} + * @memberof IndicatorQueryTreatment + */ + fdaLevel?: IndicatorQueryTreatmentFdaLevelEnum; + /** + * Therapeutic level associated with implication + * @type {string} + * @memberof IndicatorQueryTreatment + */ + level?: IndicatorQueryTreatmentLevelEnum; + /** + * + * @type {TumorType} + * @memberof IndicatorQueryTreatment + */ + levelAssociatedCancerType?: TumorType; + /** + * Excluded cancer types. Defaulted to empty list + * @type {Array} + * @memberof IndicatorQueryTreatment + */ + levelExcludedCancerTypes?: Array; + /** + * List of PubMed IDs cited in the treatment description. Defaulted to empty list + * @type {Array} + * @memberof IndicatorQueryTreatment + */ + pmids?: Array; +} + +export const IndicatorQueryTreatmentFdaLevelEnum = { + Level1: 'LEVEL_1', + Level2: 'LEVEL_2', + Level3A: 'LEVEL_3A', + Level3B: 'LEVEL_3B', + Level4: 'LEVEL_4', + LevelR1: 'LEVEL_R1', + LevelR2: 'LEVEL_R2', + LevelPx1: 'LEVEL_Px1', + LevelPx2: 'LEVEL_Px2', + LevelPx3: 'LEVEL_Px3', + LevelDx1: 'LEVEL_Dx1', + LevelDx2: 'LEVEL_Dx2', + LevelDx3: 'LEVEL_Dx3', + LevelFda1: 'LEVEL_Fda1', + LevelFda2: 'LEVEL_Fda2', + LevelFda3: 'LEVEL_Fda3', + No: 'NO', +} as const; + +export type IndicatorQueryTreatmentFdaLevelEnum = + (typeof IndicatorQueryTreatmentFdaLevelEnum)[keyof typeof IndicatorQueryTreatmentFdaLevelEnum]; +export const IndicatorQueryTreatmentLevelEnum = { + Level1: 'LEVEL_1', + Level2: 'LEVEL_2', + Level3A: 'LEVEL_3A', + Level3B: 'LEVEL_3B', + Level4: 'LEVEL_4', + LevelR1: 'LEVEL_R1', + LevelR2: 'LEVEL_R2', + LevelPx1: 'LEVEL_Px1', + LevelPx2: 'LEVEL_Px2', + LevelPx3: 'LEVEL_Px3', + LevelDx1: 'LEVEL_Dx1', + LevelDx2: 'LEVEL_Dx2', + LevelDx3: 'LEVEL_Dx3', + LevelFda1: 'LEVEL_Fda1', + LevelFda2: 'LEVEL_Fda2', + LevelFda3: 'LEVEL_Fda3', + No: 'NO', +} as const; + +export type IndicatorQueryTreatmentLevelEnum = (typeof IndicatorQueryTreatmentLevelEnum)[keyof typeof IndicatorQueryTreatmentLevelEnum]; + +/** + * + * @export + * @interface LevelNumber + */ +export interface LevelNumber { + /** + * + * @type {Array} + * @memberof LevelNumber + */ + genes?: Array; + /** + * + * @type {string} + * @memberof LevelNumber + */ + level?: LevelNumberLevelEnum; +} + +export const LevelNumberLevelEnum = { + Level1: 'LEVEL_1', + Level2: 'LEVEL_2', + Level3A: 'LEVEL_3A', + Level3B: 'LEVEL_3B', + Level4: 'LEVEL_4', + LevelR1: 'LEVEL_R1', + LevelR2: 'LEVEL_R2', + LevelPx1: 'LEVEL_Px1', + LevelPx2: 'LEVEL_Px2', + LevelPx3: 'LEVEL_Px3', + LevelDx1: 'LEVEL_Dx1', + LevelDx2: 'LEVEL_Dx2', + LevelDx3: 'LEVEL_Dx3', + LevelFda1: 'LEVEL_Fda1', + LevelFda2: 'LEVEL_Fda2', + LevelFda3: 'LEVEL_Fda3', + No: 'NO', +} as const; + +export type LevelNumberLevelEnum = (typeof LevelNumberLevelEnum)[keyof typeof LevelNumberLevelEnum]; + +/** + * + * @export + * @interface MainNumber + */ +export interface MainNumber { + /** + * + * @type {number} + * @memberof MainNumber + */ + alteration?: number; + /** + * + * @type {number} + * @memberof MainNumber + */ + drug?: number; + /** + * + * @type {number} + * @memberof MainNumber + */ + gene?: number; + /** + * + * @type {Array} + * @memberof MainNumber + */ + level?: Array; + /** + * + * @type {number} + * @memberof MainNumber + */ + tumorType?: number; +} +/** + * + * @export + * @interface MainNumberLevel + */ +export interface MainNumberLevel { + /** + * + * @type {string} + * @memberof MainNumberLevel + */ + level?: string; + /** + * + * @type {number} + * @memberof MainNumberLevel + */ + number?: number; +} +/** + * OncoTree Cancer Type + * @export + * @interface MainType + */ +export interface MainType { + /** + * + * @type {number} + * @memberof MainType + */ + id?: number; + /** + * + * @type {string} + * @memberof MainType + */ + name?: string; + /** + * + * @type {string} + * @memberof MainType + */ + tumorForm?: MainTypeTumorFormEnum; +} + +export const MainTypeTumorFormEnum = { + Solid: 'SOLID', + Liquid: 'LIQUID', + Mixed: 'MIXED', +} as const; + +export type MainTypeTumorFormEnum = (typeof MainTypeTumorFormEnum)[keyof typeof MainTypeTumorFormEnum]; + +/** + * + * @export + * @interface MatchVariant + */ +export interface MatchVariant { + /** + * + * @type {string} + * @memberof MatchVariant + */ + alteration?: string; + /** + * + * @type {string} + * @memberof MatchVariant + */ + hugoSymbol?: string; +} +/** + * + * @export + * @interface MatchVariantRequest + */ +export interface MatchVariantRequest { + /** + * + * @type {Array} + * @memberof MatchVariantRequest + */ + oncokbVariants?: Array; + /** + * + * @type {Array} + * @memberof MatchVariantRequest + */ + queries?: Array; +} +/** + * + * @export + * @interface MatchVariantResult + */ +export interface MatchVariantResult { + /** + * + * @type {Query} + * @memberof MatchVariantResult + */ + query?: Query; + /** + * + * @type {Array} + * @memberof MatchVariantResult + */ + result?: Array; +} +/** + * + * @export + * @interface MutationEffectResp + */ +export interface MutationEffectResp { + /** + * + * @type {Citations} + * @memberof MutationEffectResp + */ + citations?: Citations; + /** + * A brief overview of the biological and oncogenic effect of the variant. Defaulted to \"\" + * @type {string} + * @memberof MutationEffectResp + */ + description?: string; + /** + * Indicates the effect of the mutation on the gene. Defaulted to \"\" + * @type {string} + * @memberof MutationEffectResp + */ + knownEffect?: MutationEffectRespKnownEffectEnum; +} + +export const MutationEffectRespKnownEffectEnum = { + GainOfFunction: 'Gain-of-function', + Inconclusive: 'Inconclusive', + LossOfFunction: 'Loss-of-function', + LikelyLossOfFunction: 'Likely Loss-of-function', + LikelyGainOfFunction: 'Likely Gain-of-function', + Neutral: 'Neutral', + Unknown: 'Unknown', + LikelySwitchOfFunction: 'Likely Switch-of-function', + SwitchOfFunction: 'Switch-of-function', + LikelyNeutral: 'Likely Neutral', +} as const; + +export type MutationEffectRespKnownEffectEnum = (typeof MutationEffectRespKnownEffectEnum)[keyof typeof MutationEffectRespKnownEffectEnum]; + +/** + * + * @export + * @interface PfamDomainRange + */ +export interface PfamDomainRange { + /** + * Pfam domain end amino acid + * @type {number} + * @memberof PfamDomainRange + */ + pfamDomainEnd: number; + /** + * Pfam domain id + * @type {string} + * @memberof PfamDomainRange + */ + pfamDomainId: string; + /** + * Pfam domain start amino acid + * @type {number} + * @memberof PfamDomainRange + */ + pfamDomainStart: number; +} +/** + * + * @export + * @interface PortalAlteration + */ +export interface PortalAlteration { + /** + * + * @type {string} + * @memberof PortalAlteration + */ + alterationType?: string; + /** + * + * @type {string} + * @memberof PortalAlteration + */ + cancerStudy?: string; + /** + * + * @type {string} + * @memberof PortalAlteration + */ + cancerType?: string; + /** + * + * @type {Gene} + * @memberof PortalAlteration + */ + gene?: Gene; + /** + * + * @type {string} + * @memberof PortalAlteration + */ + proteinChange?: string; + /** + * + * @type {number} + * @memberof PortalAlteration + */ + proteinEndPosition?: number; + /** + * + * @type {number} + * @memberof PortalAlteration + */ + proteinStartPosition?: number; + /** + * + * @type {string} + * @memberof PortalAlteration + */ + sampleId?: string; +} +/** + * Enriched user annotation query + * @export + * @interface Query + */ +export interface Query { + /** + * (Nullable) Alteration from original query or the resolved alteration from HGVS variant + * @type {string} + * @memberof Query + */ + alteration?: string; + /** + * (Nullable) Alteration type + * @type {string} + * @memberof Query + */ + alterationType?: QueryAlterationTypeEnum; + /** + * (Nullable) The OncoKB canonical transcript. See https://www.oncokb.org/cancer-genes + * @type {string} + * @memberof Query + */ + canonicalTranscript?: string; + /** + * (Nullable) Variant consequence term from Ensembl. See https://useast.ensembl.org/info/genome/variation/prediction/predicted_data.html + * @type {string} + * @memberof Query + */ + consequence?: string; + /** + * (Nullable) Unique gene identifiers from NCBI. May be null if omitted from original query, otherwise filled in by OncoKB + * @type {number} + * @memberof Query + */ + entrezGeneId?: number; + /** + * (Nullable) The hgvsg or genomic location from original query + * @type {string} + * @memberof Query + */ + hgvs?: string; + /** + * (Nullable) Additional message for \"hgvs\" field. May indicate reason for failed hgvs annotation. + * @type {string} + * @memberof Query + */ + hgvsInfo?: string; + /** + * (Nullable) The gene symbol used in Human Genome Organisation + * @type {string} + * @memberof Query + */ + hugoSymbol?: string; + /** + * (Nullable) The id passed in request for the user to distinguish the query. + * @type {string} + * @memberof Query + */ + id?: string; + /** + * (Nullable) Protein end position + * @type {number} + * @memberof Query + */ + proteinEnd?: number; + /** + * (Nullable) Protein start position + * @type {number} + * @memberof Query + */ + proteinStart?: number; + /** + * Reference genome build version. Defaulted to GRCh37 + * @type {string} + * @memberof Query + */ + referenceGenome?: QueryReferenceGenomeEnum; + /** + * (Nullable) Structural variant type + * @type {string} + * @memberof Query + */ + svType?: QuerySvTypeEnum; + /** + * (Nullable) Oncotree tumor type name, code, or main type. + * @type {string} + * @memberof Query + */ + tumorType?: string; +} + +export const QueryAlterationTypeEnum = { + Mutation: 'MUTATION', + CopyNumberAlteration: 'COPY_NUMBER_ALTERATION', + StructuralVariant: 'STRUCTURAL_VARIANT', +} as const; + +export type QueryAlterationTypeEnum = (typeof QueryAlterationTypeEnum)[keyof typeof QueryAlterationTypeEnum]; +export const QueryReferenceGenomeEnum = { + Grch37: 'GRCh37', + Grch38: 'GRCh38', +} as const; + +export type QueryReferenceGenomeEnum = (typeof QueryReferenceGenomeEnum)[keyof typeof QueryReferenceGenomeEnum]; +export const QuerySvTypeEnum = { + Deletion: 'DELETION', + Translocation: 'TRANSLOCATION', + Duplication: 'DUPLICATION', + Insertion: 'INSERTION', + Inversion: 'INVERSION', + Fusion: 'FUSION', + Unknown: 'UNKNOWN', +} as const; + +export type QuerySvTypeEnum = (typeof QuerySvTypeEnum)[keyof typeof QuerySvTypeEnum]; + +/** + * + * @export + * @interface RelevantCancerTypeQuery + */ +export interface RelevantCancerTypeQuery { + /** + * + * @type {string} + * @memberof RelevantCancerTypeQuery + */ + code?: string; + /** + * + * @type {string} + * @memberof RelevantCancerTypeQuery + */ + mainType?: string; +} +/** + * + * @export + * @interface TranscriptCoverageFilterResult + */ +export interface TranscriptCoverageFilterResult { + /** + * + * @type {boolean} + * @memberof TranscriptCoverageFilterResult + */ + isCovered?: boolean; + /** + * + * @type {string} + * @memberof TranscriptCoverageFilterResult + */ + variant?: string; +} +/** + * + * @export + * @interface TranscriptResult + */ +export interface TranscriptResult { + /** + * + * @type {EnsemblTranscript} + * @memberof TranscriptResult + */ + grch37Transcript?: EnsemblTranscript; + /** + * + * @type {EnsemblTranscript} + * @memberof TranscriptResult + */ + grch38Transcript?: EnsemblTranscript; + /** + * + * @type {string} + * @memberof TranscriptResult + */ + note?: string; +} +/** + * + * @export + * @interface Treatment + */ +export interface Treatment { + /** + * + * @type {Array} + * @memberof Treatment + */ + approvedIndications?: Array; + /** + * + * @type {Array} + * @memberof Treatment + */ + drugs?: Array; + /** + * + * @type {number} + * @memberof Treatment + */ + priority?: number; +} +/** + * + * @export + * @interface TreatmentDrug + */ +export interface TreatmentDrug { + /** + * + * @type {number} + * @memberof TreatmentDrug + */ + priority?: number; + /** + * + * @type {TreatmentDrugId} + * @memberof TreatmentDrug + */ + treatmentDrugId?: TreatmentDrugId; +} +/** + * + * @export + * @interface TreatmentDrugId + */ +export interface TreatmentDrugId { + /** + * + * @type {Drug} + * @memberof TreatmentDrugId + */ + drug?: Drug; +} +/** + * OncoTree Detailed Cancer Type + * @export + * @interface TumorType + */ +export interface TumorType { + /** + * + * @type {string} + * @memberof TumorType + */ + code?: string; + /** + * + * @type {string} + * @memberof TumorType + */ + color?: string; + /** + * + * @type {number} + * @memberof TumorType + */ + id?: number; + /** + * + * @type {number} + * @memberof TumorType + */ + level?: number; + /** + * + * @type {string} + * @memberof TumorType + */ + mainType?: string; + /** + * + * @type {string} + * @memberof TumorType + */ + subtype?: string; + /** + * + * @type {string} + * @memberof TumorType + */ + tissue?: string; + /** + * + * @type {string} + * @memberof TumorType + */ + tumorForm?: TumorTypeTumorFormEnum; +} + +export const TumorTypeTumorFormEnum = { + Solid: 'SOLID', + Liquid: 'LIQUID', + Mixed: 'MIXED', +} as const; + +export type TumorTypeTumorFormEnum = (typeof TumorTypeTumorFormEnum)[keyof typeof TumorTypeTumorFormEnum]; + +/** + * + * @export + * @interface TypeaheadSearchResp + */ +export interface TypeaheadSearchResp { + /** + * + * @type {string} + * @memberof TypeaheadSearchResp + */ + annotation?: string; + /** + * + * @type {{ [key: string]: string; }} + * @memberof TypeaheadSearchResp + */ + annotationByLevel?: { [key: string]: string }; + /** + * + * @type {Drug} + * @memberof TypeaheadSearchResp + */ + drug?: Drug; + /** + * + * @type {Gene} + * @memberof TypeaheadSearchResp + */ + gene?: Gene; + /** + * + * @type {string} + * @memberof TypeaheadSearchResp + */ + highestResistanceLevel?: string; + /** + * + * @type {string} + * @memberof TypeaheadSearchResp + */ + highestSensitiveLevel?: string; + /** + * + * @type {string} + * @memberof TypeaheadSearchResp + */ + link?: string; + /** + * + * @type {string} + * @memberof TypeaheadSearchResp + */ + oncogenicity?: string; + /** + * + * @type {string} + * @memberof TypeaheadSearchResp + */ + queryType?: TypeaheadSearchRespQueryTypeEnum; + /** + * + * @type {Array} + * @memberof TypeaheadSearchResp + */ + tumorTypes?: Array; + /** + * + * @type {boolean} + * @memberof TypeaheadSearchResp + */ + variantExist?: boolean; + /** + * + * @type {Array} + * @memberof TypeaheadSearchResp + */ + variants?: Array; + /** + * + * @type {boolean} + * @memberof TypeaheadSearchResp + */ + vus?: boolean; +} + +export const TypeaheadSearchRespQueryTypeEnum = { + Gene: 'GENE', + Variant: 'VARIANT', + Drug: 'DRUG', + Text: 'TEXT', + Genomic: 'GENOMIC', + CancerType: 'CANCER_TYPE', +} as const; + +export type TypeaheadSearchRespQueryTypeEnum = (typeof TypeaheadSearchRespQueryTypeEnum)[keyof typeof TypeaheadSearchRespQueryTypeEnum]; + +/** + * + * @export + * @interface UntranslatedRegion + */ +export interface UntranslatedRegion { + /** + * End position of UTR + * @type {number} + * @memberof UntranslatedRegion + */ + end: number; + /** + * Start position of UTR + * @type {number} + * @memberof UntranslatedRegion + */ + start: number; + /** + * Strand UTR is on, -1 for - and 1 for + + * @type {number} + * @memberof UntranslatedRegion + */ + strand: number; + /** + * UTR Type + * @type {string} + * @memberof UntranslatedRegion + */ + type: string; +} +/** + * + * @export + * @interface VariantAnnotation + */ +export interface VariantAnnotation { + /** + * Indicates whether the alternate allele has been curated. See SOP Protocol 9.1 + * @type {boolean} + * @memberof VariantAnnotation + */ + alleleExist?: boolean; + /** + * + * @type {string} + * @memberof VariantAnnotation + */ + background?: string; + /** + * OncoKB data version. See www.oncokb.org/news + * @type {string} + * @memberof VariantAnnotation + */ + dataVersion?: string; + /** + * List of diagnostic implications. Defaulted to empty list + * @type {Array} + * @memberof VariantAnnotation + */ + diagnosticImplications?: Array; + /** + * Diagnostic summary. Defaulted to \"\" + * @type {string} + * @memberof VariantAnnotation + */ + diagnosticSummary?: string; + /** + * Indicates whether the gene is curated by OncoKB + * @type {boolean} + * @memberof VariantAnnotation + */ + geneExist?: boolean; + /** + * Gene summary. Defaulted to \"\" + * @type {string} + * @memberof VariantAnnotation + */ + geneSummary?: string; + /** + * (Nullable) The highest diagnostic level from a list of diagnostic evidences. + * @type {string} + * @memberof VariantAnnotation + */ + highestDiagnosticImplicationLevel?: VariantAnnotationHighestDiagnosticImplicationLevelEnum; + /** + * (Nullable) The highest FDA level from a list of therapeutic evidences. + * @type {string} + * @memberof VariantAnnotation + */ + highestFdaLevel?: VariantAnnotationHighestFdaLevelEnum; + /** + * (Nullable) The highest prognostic level from a list of prognostic evidences. + * @type {string} + * @memberof VariantAnnotation + */ + highestPrognosticImplicationLevel?: VariantAnnotationHighestPrognosticImplicationLevelEnum; + /** + * (Nullable) The highest resistance level from a list of therapeutic evidences. + * @type {string} + * @memberof VariantAnnotation + */ + highestResistanceLevel?: VariantAnnotationHighestResistanceLevelEnum; + /** + * (Nullable) The highest sensitivity level from a list of therapeutic evidences. + * @type {string} + * @memberof VariantAnnotation + */ + highestSensitiveLevel?: VariantAnnotationHighestSensitiveLevelEnum; + /** + * Whether variant is recurrently found in cancer with statistical significance, as defined in Chang et al. (2017). See SOP Protocol 9.2 + * @type {boolean} + * @memberof VariantAnnotation + */ + hotspot?: boolean; + /** + * OncoKB data release date. Formatted as MM/DD/YYYY + * @type {string} + * @memberof VariantAnnotation + */ + lastUpdate?: string; + /** + * + * @type {MutationEffectResp} + * @memberof VariantAnnotation + */ + mutationEffect?: MutationEffectResp; + /** + * The oncogenicity status of the variant. Defaulted to \"Unknown\". + * @type {string} + * @memberof VariantAnnotation + */ + oncogenic?: VariantAnnotationOncogenicEnum; + /** + * DEPRECATED + * @type {Array} + * @memberof VariantAnnotation + */ + otherSignificantResistanceLevels?: Array; + /** + * DEPRECATED + * @type {Array} + * @memberof VariantAnnotation + */ + otherSignificantSensitiveLevels?: Array; + /** + * List of prognostic implications. Defaulted to empty list + * @type {Array} + * @memberof VariantAnnotation + */ + prognosticImplications?: Array; + /** + * Prognostic summary. Defaulted to \"\" + * @type {string} + * @memberof VariantAnnotation + */ + prognosticSummary?: string; + /** + * + * @type {Query} + * @memberof VariantAnnotation + */ + query?: Query; + /** + * List of therapeutic implications implications. Defaulted to empty list + * @type {Array} + * @memberof VariantAnnotation + */ + treatments?: Array; + /** + * Tumor type summary. Defaulted to \"\" + * @type {string} + * @memberof VariantAnnotation + */ + tumorTypeSummary?: string; + /** + * + * @type {Array} + * @memberof VariantAnnotation + */ + tumorTypes?: Array; + /** + * Indicates whether an exact match for the queried variant is curated + * @type {boolean} + * @memberof VariantAnnotation + */ + variantExist?: boolean; + /** + * Variant summary. Defaulted to \"\" + * @type {string} + * @memberof VariantAnnotation + */ + variantSummary?: string; + /** + * + * @type {boolean} + * @memberof VariantAnnotation + */ + vue?: boolean; + /** + * + * @type {boolean} + * @memberof VariantAnnotation + */ + vus?: boolean; +} + +export const VariantAnnotationHighestDiagnosticImplicationLevelEnum = { + LevelDx1: 'LEVEL_Dx1', + LevelDx2: 'LEVEL_Dx2', + LevelDx3: 'LEVEL_Dx3.', +} as const; + +export type VariantAnnotationHighestDiagnosticImplicationLevelEnum = + (typeof VariantAnnotationHighestDiagnosticImplicationLevelEnum)[keyof typeof VariantAnnotationHighestDiagnosticImplicationLevelEnum]; +export const VariantAnnotationHighestFdaLevelEnum = { + LevelFda1: 'LEVEL_Fda1', + LevelFda2: 'LEVEL_Fda2', + LevelFda3: 'LEVEL_Fda3', +} as const; + +export type VariantAnnotationHighestFdaLevelEnum = + (typeof VariantAnnotationHighestFdaLevelEnum)[keyof typeof VariantAnnotationHighestFdaLevelEnum]; +export const VariantAnnotationHighestPrognosticImplicationLevelEnum = { + LevelPx1: 'LEVEL_Px1', + LevelPx2: 'LEVEL_Px2', + LevelPx3: 'LEVEL_Px3', +} as const; + +export type VariantAnnotationHighestPrognosticImplicationLevelEnum = + (typeof VariantAnnotationHighestPrognosticImplicationLevelEnum)[keyof typeof VariantAnnotationHighestPrognosticImplicationLevelEnum]; +export const VariantAnnotationHighestResistanceLevelEnum = { + LevelR1: 'LEVEL_R1', + LevelR2: 'LEVEL_R2', +} as const; + +export type VariantAnnotationHighestResistanceLevelEnum = + (typeof VariantAnnotationHighestResistanceLevelEnum)[keyof typeof VariantAnnotationHighestResistanceLevelEnum]; +export const VariantAnnotationHighestSensitiveLevelEnum = { + Level1: 'LEVEL_1', + Level2: 'LEVEL_2', + Level3A: 'LEVEL_3A', + Level3B: 'LEVEL_3B', + Level4: 'LEVEL_4', +} as const; + +export type VariantAnnotationHighestSensitiveLevelEnum = + (typeof VariantAnnotationHighestSensitiveLevelEnum)[keyof typeof VariantAnnotationHighestSensitiveLevelEnum]; +export const VariantAnnotationOncogenicEnum = { + Oncogenic: 'Oncogenic', + LikelyOncogenic: 'Likely Oncogenic', + LikelyNeutral: 'Likely Neutral', + Inconclusive: 'Inconclusive', + Resistance: 'Resistance', + Unknown: 'Unknown', +} as const; + +export type VariantAnnotationOncogenicEnum = (typeof VariantAnnotationOncogenicEnum)[keyof typeof VariantAnnotationOncogenicEnum]; +export const VariantAnnotationOtherSignificantResistanceLevelsEnum = { + Level1: 'LEVEL_1', + Level2: 'LEVEL_2', + Level3A: 'LEVEL_3A', + Level3B: 'LEVEL_3B', + Level4: 'LEVEL_4', + LevelR1: 'LEVEL_R1', + LevelR2: 'LEVEL_R2', + LevelPx1: 'LEVEL_Px1', + LevelPx2: 'LEVEL_Px2', + LevelPx3: 'LEVEL_Px3', + LevelDx1: 'LEVEL_Dx1', + LevelDx2: 'LEVEL_Dx2', + LevelDx3: 'LEVEL_Dx3', + LevelFda1: 'LEVEL_Fda1', + LevelFda2: 'LEVEL_Fda2', + LevelFda3: 'LEVEL_Fda3', + No: 'NO', +} as const; + +export type VariantAnnotationOtherSignificantResistanceLevelsEnum = + (typeof VariantAnnotationOtherSignificantResistanceLevelsEnum)[keyof typeof VariantAnnotationOtherSignificantResistanceLevelsEnum]; +export const VariantAnnotationOtherSignificantSensitiveLevelsEnum = { + Level1: 'LEVEL_1', + Level2: 'LEVEL_2', + Level3A: 'LEVEL_3A', + Level3B: 'LEVEL_3B', + Level4: 'LEVEL_4', + LevelR1: 'LEVEL_R1', + LevelR2: 'LEVEL_R2', + LevelPx1: 'LEVEL_Px1', + LevelPx2: 'LEVEL_Px2', + LevelPx3: 'LEVEL_Px3', + LevelDx1: 'LEVEL_Dx1', + LevelDx2: 'LEVEL_Dx2', + LevelDx3: 'LEVEL_Dx3', + LevelFda1: 'LEVEL_Fda1', + LevelFda2: 'LEVEL_Fda2', + LevelFda3: 'LEVEL_Fda3', + No: 'NO', +} as const; + +export type VariantAnnotationOtherSignificantSensitiveLevelsEnum = + (typeof VariantAnnotationOtherSignificantSensitiveLevelsEnum)[keyof typeof VariantAnnotationOtherSignificantSensitiveLevelsEnum]; + +/** + * + * @export + * @interface VariantAnnotationTumorType + */ +export interface VariantAnnotationTumorType { + /** + * + * @type {Array} + * @memberof VariantAnnotationTumorType + */ + evidences?: Array; + /** + * + * @type {boolean} + * @memberof VariantAnnotationTumorType + */ + relevantTumorType?: boolean; + /** + * + * @type {TumorType} + * @memberof VariantAnnotationTumorType + */ + tumorType?: TumorType; +} +/** + * + * @export + * @interface VariantConsequence + */ +export interface VariantConsequence { + /** + * + * @type {string} + * @memberof VariantConsequence + */ + description?: string; + /** + * + * @type {boolean} + * @memberof VariantConsequence + */ + isGenerallyTruncating?: boolean; + /** + * + * @type {string} + * @memberof VariantConsequence + */ + term?: string; +} + +/** + * DrugsApi - axios parameter creator + * @export + */ +export const DrugsApiAxiosParamCreator = function (configuration?: Configuration) { + return { + /** + * Find NCIT matches based on blur query. This is not for search OncoKB curated drugs. Please use drugs/lookup for that purpose. + * @summary searchDrugGet + * @param {string} query The search query, it could be drug name, NCIT code + * @param {number} [limit] The limit of returned result. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + searchDrugGetUsingGET: async (query: string, limit?: number, options: RawAxiosRequestConfig = {}): Promise => { + // verify required parameter 'query' is not null or undefined + assertParamExists('searchDrugGetUsingGET', 'query', query); + const localVarPath = `/search/ncitDrugs`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (query !== undefined) { + localVarQueryParameter['query'] = query; + } + + if (limit !== undefined) { + localVarQueryParameter['limit'] = limit; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + }; +}; + +/** + * DrugsApi - functional programming interface + * @export + */ +export const DrugsApiFp = function (configuration?: Configuration) { + const localVarAxiosParamCreator = DrugsApiAxiosParamCreator(configuration); + return { + /** + * Find NCIT matches based on blur query. This is not for search OncoKB curated drugs. Please use drugs/lookup for that purpose. + * @summary searchDrugGet + * @param {string} query The search query, it could be drug name, NCIT code + * @param {number} [limit] The limit of returned result. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async searchDrugGetUsingGET( + query: string, + limit?: number, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.searchDrugGetUsingGET(query, limit, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = operationServerMap['DrugsApi.searchDrugGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + }; +}; + +/** + * DrugsApi - factory interface + * @export + */ +export const DrugsApiFactory = function (configuration?: Configuration, basePath?: string, axios?: AxiosInstance) { + const localVarFp = DrugsApiFp(configuration); + return { + /** + * Find NCIT matches based on blur query. This is not for search OncoKB curated drugs. Please use drugs/lookup for that purpose. + * @summary searchDrugGet + * @param {string} query The search query, it could be drug name, NCIT code + * @param {number} [limit] The limit of returned result. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + searchDrugGetUsingGET(query: string, limit?: number, options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.searchDrugGetUsingGET(query, limit, options).then(request => request(axios, basePath)); + }, + }; +}; + +/** + * DrugsApi - object-oriented interface + * @export + * @class DrugsApi + * @extends {BaseAPI} + */ +export class DrugsApi extends BaseAPI { + /** + * Find NCIT matches based on blur query. This is not for search OncoKB curated drugs. Please use drugs/lookup for that purpose. + * @summary searchDrugGet + * @param {string} query The search query, it could be drug name, NCIT code + * @param {number} [limit] The limit of returned result. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof DrugsApi + */ + public searchDrugGetUsingGET(query: string, limit?: number, options?: RawAxiosRequestConfig) { + return DrugsApiFp(this.configuration) + .searchDrugGetUsingGET(query, limit, options) + .then(request => request(this.axios, this.basePath)); + } +} + +/** + * SearchApi - axios parameter creator + * @export + */ +export const SearchApiAxiosParamCreator = function (configuration?: Configuration) { + return { + /** + * Find NCIT matches based on blur query. This is not for search OncoKB curated drugs. Please use drugs/lookup for that purpose. + * @summary searchDrugGet + * @param {string} query The search query, it could be drug name, NCIT code + * @param {number} [limit] The limit of returned result. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + searchDrugGetUsingGET: async (query: string, limit?: number, options: RawAxiosRequestConfig = {}): Promise => { + // verify required parameter 'query' is not null or undefined + assertParamExists('searchDrugGetUsingGET', 'query', query); + const localVarPath = `/search/ncitDrugs`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (query !== undefined) { + localVarQueryParameter['query'] = query; + } + + if (limit !== undefined) { + localVarQueryParameter['limit'] = limit; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Search to find treatments. + * @summary searchTreatmentsGet + * @param {string} gene The search query, it could be hugoSymbol or entrezGeneId. + * @param {string} [level] The level of evidence. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + searchTreatmentsGetUsingGET: async (gene: string, level?: string, options: RawAxiosRequestConfig = {}): Promise => { + // verify required parameter 'gene' is not null or undefined + assertParamExists('searchTreatmentsGetUsingGET', 'gene', gene); + const localVarPath = `/search/treatments`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (gene !== undefined) { + localVarQueryParameter['gene'] = gene; + } + + if (level !== undefined) { + localVarQueryParameter['level'] = level; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Find matches based on blur query. + * @summary searchTypeAheadGet + * @param {string} query The search query, it could be hugoSymbol, entrezGeneId, variant, or cancer type. At least two characters. Maximum two keywords are supported, separated by space + * @param {number} [limit] The limit of returned result. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + searchTypeAheadGetUsingGET: async (query: string, limit?: number, options: RawAxiosRequestConfig = {}): Promise => { + // verify required parameter 'query' is not null or undefined + assertParamExists('searchTypeAheadGetUsingGET', 'query', query); + const localVarPath = `/search/typeahead`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (query !== undefined) { + localVarQueryParameter['query'] = query; + } + + if (limit !== undefined) { + localVarQueryParameter['limit'] = limit; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get annotated variants information for specified gene. + * @summary searchVariantsBiologicalGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + searchVariantsBiologicalGetUsingGET: async (hugoSymbol?: string, options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/search/variants/biological`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (hugoSymbol !== undefined) { + localVarQueryParameter['hugoSymbol'] = hugoSymbol; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get list of variant clinical information for specified gene. + * @summary searchVariantsClinicalGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + searchVariantsClinicalGetUsingGET: async (hugoSymbol?: string, options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/search/variants/clinical`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (hugoSymbol !== undefined) { + localVarQueryParameter['hugoSymbol'] = hugoSymbol; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + }; +}; + +/** + * SearchApi - functional programming interface + * @export + */ +export const SearchApiFp = function (configuration?: Configuration) { + const localVarAxiosParamCreator = SearchApiAxiosParamCreator(configuration); + return { + /** + * Find NCIT matches based on blur query. This is not for search OncoKB curated drugs. Please use drugs/lookup for that purpose. + * @summary searchDrugGet + * @param {string} query The search query, it could be drug name, NCIT code + * @param {number} [limit] The limit of returned result. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async searchDrugGetUsingGET( + query: string, + limit?: number, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.searchDrugGetUsingGET(query, limit, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = operationServerMap['SearchApi.searchDrugGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Search to find treatments. + * @summary searchTreatmentsGet + * @param {string} gene The search query, it could be hugoSymbol or entrezGeneId. + * @param {string} [level] The level of evidence. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async searchTreatmentsGetUsingGET( + gene: string, + level?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.searchTreatmentsGetUsingGET(gene, level, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['SearchApi.searchTreatmentsGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Find matches based on blur query. + * @summary searchTypeAheadGet + * @param {string} query The search query, it could be hugoSymbol, entrezGeneId, variant, or cancer type. At least two characters. Maximum two keywords are supported, separated by space + * @param {number} [limit] The limit of returned result. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async searchTypeAheadGetUsingGET( + query: string, + limit?: number, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.searchTypeAheadGetUsingGET(query, limit, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['SearchApi.searchTypeAheadGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get annotated variants information for specified gene. + * @summary searchVariantsBiologicalGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async searchVariantsBiologicalGetUsingGET( + hugoSymbol?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.searchVariantsBiologicalGetUsingGET(hugoSymbol, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['SearchApi.searchVariantsBiologicalGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get list of variant clinical information for specified gene. + * @summary searchVariantsClinicalGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async searchVariantsClinicalGetUsingGET( + hugoSymbol?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.searchVariantsClinicalGetUsingGET(hugoSymbol, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['SearchApi.searchVariantsClinicalGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + }; +}; + +/** + * SearchApi - factory interface + * @export + */ +export const SearchApiFactory = function (configuration?: Configuration, basePath?: string, axios?: AxiosInstance) { + const localVarFp = SearchApiFp(configuration); + return { + /** + * Find NCIT matches based on blur query. This is not for search OncoKB curated drugs. Please use drugs/lookup for that purpose. + * @summary searchDrugGet + * @param {string} query The search query, it could be drug name, NCIT code + * @param {number} [limit] The limit of returned result. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + searchDrugGetUsingGET(query: string, limit?: number, options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.searchDrugGetUsingGET(query, limit, options).then(request => request(axios, basePath)); + }, + /** + * Search to find treatments. + * @summary searchTreatmentsGet + * @param {string} gene The search query, it could be hugoSymbol or entrezGeneId. + * @param {string} [level] The level of evidence. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + searchTreatmentsGetUsingGET(gene: string, level?: string, options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.searchTreatmentsGetUsingGET(gene, level, options).then(request => request(axios, basePath)); + }, + /** + * Find matches based on blur query. + * @summary searchTypeAheadGet + * @param {string} query The search query, it could be hugoSymbol, entrezGeneId, variant, or cancer type. At least two characters. Maximum two keywords are supported, separated by space + * @param {number} [limit] The limit of returned result. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + searchTypeAheadGetUsingGET(query: string, limit?: number, options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.searchTypeAheadGetUsingGET(query, limit, options).then(request => request(axios, basePath)); + }, + /** + * Get annotated variants information for specified gene. + * @summary searchVariantsBiologicalGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + searchVariantsBiologicalGetUsingGET(hugoSymbol?: string, options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.searchVariantsBiologicalGetUsingGET(hugoSymbol, options).then(request => request(axios, basePath)); + }, + /** + * Get list of variant clinical information for specified gene. + * @summary searchVariantsClinicalGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + searchVariantsClinicalGetUsingGET(hugoSymbol?: string, options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.searchVariantsClinicalGetUsingGET(hugoSymbol, options).then(request => request(axios, basePath)); + }, + }; +}; + +/** + * SearchApi - object-oriented interface + * @export + * @class SearchApi + * @extends {BaseAPI} + */ +export class SearchApi extends BaseAPI { + /** + * Find NCIT matches based on blur query. This is not for search OncoKB curated drugs. Please use drugs/lookup for that purpose. + * @summary searchDrugGet + * @param {string} query The search query, it could be drug name, NCIT code + * @param {number} [limit] The limit of returned result. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof SearchApi + */ + public searchDrugGetUsingGET(query: string, limit?: number, options?: RawAxiosRequestConfig) { + return SearchApiFp(this.configuration) + .searchDrugGetUsingGET(query, limit, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Search to find treatments. + * @summary searchTreatmentsGet + * @param {string} gene The search query, it could be hugoSymbol or entrezGeneId. + * @param {string} [level] The level of evidence. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof SearchApi + */ + public searchTreatmentsGetUsingGET(gene: string, level?: string, options?: RawAxiosRequestConfig) { + return SearchApiFp(this.configuration) + .searchTreatmentsGetUsingGET(gene, level, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Find matches based on blur query. + * @summary searchTypeAheadGet + * @param {string} query The search query, it could be hugoSymbol, entrezGeneId, variant, or cancer type. At least two characters. Maximum two keywords are supported, separated by space + * @param {number} [limit] The limit of returned result. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof SearchApi + */ + public searchTypeAheadGetUsingGET(query: string, limit?: number, options?: RawAxiosRequestConfig) { + return SearchApiFp(this.configuration) + .searchTypeAheadGetUsingGET(query, limit, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get annotated variants information for specified gene. + * @summary searchVariantsBiologicalGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof SearchApi + */ + public searchVariantsBiologicalGetUsingGET(hugoSymbol?: string, options?: RawAxiosRequestConfig) { + return SearchApiFp(this.configuration) + .searchVariantsBiologicalGetUsingGET(hugoSymbol, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get list of variant clinical information for specified gene. + * @summary searchVariantsClinicalGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof SearchApi + */ + public searchVariantsClinicalGetUsingGET(hugoSymbol?: string, options?: RawAxiosRequestConfig) { + return SearchApiFp(this.configuration) + .searchVariantsClinicalGetUsingGET(hugoSymbol, options) + .then(request => request(this.axios, this.basePath)); + } +} + +/** + * TranscriptApi - axios parameter creator + * @export + */ +export const TranscriptApiAxiosParamCreator = function (configuration?: Configuration) { + return { + /** + * cache Genome Nexus variant info + * @summary cacheGenomeNexusVariantInfoPost + * @param {Array} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + cacheGenomeNexusVariantInfoPostUsingPOST: async ( + body: Array, + options: RawAxiosRequestConfig = {}, + ): Promise => { + // verify required parameter 'body' is not null or undefined + assertParamExists('cacheGenomeNexusVariantInfoPostUsingPOST', 'body', body); + const localVarPath = `/cacheGnVariantInfo`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'POST', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + localVarHeaderParameter['Content-Type'] = 'application/json'; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + localVarRequestOptions.data = serializeDataIfNeeded(body, localVarRequestOptions, configuration); + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Fetch Genome Nexus variant info by genomic change + * @summary fetchGenomeNexusVariantInfoByGenomicChangePost + * @param {Array} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + fetchGenomeNexusVariantInfoByGenomicChangePostUsingPOST: async ( + body: Array, + options: RawAxiosRequestConfig = {}, + ): Promise => { + // verify required parameter 'body' is not null or undefined + assertParamExists('fetchGenomeNexusVariantInfoByGenomicChangePostUsingPOST', 'body', body); + const localVarPath = `/fetchGnVariants/byGenomicChange`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'POST', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + localVarHeaderParameter['Content-Type'] = 'application/json'; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + localVarRequestOptions.data = serializeDataIfNeeded(body, localVarRequestOptions, configuration); + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Fetch Genome Nexus variant info by HGVSg + * @summary fetchGenomeNexusVariantInfoByHGVSgPost + * @param {Array} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + fetchGenomeNexusVariantInfoByHGVSgPostUsingPOST: async ( + body: Array, + options: RawAxiosRequestConfig = {}, + ): Promise => { + // verify required parameter 'body' is not null or undefined + assertParamExists('fetchGenomeNexusVariantInfoByHGVSgPostUsingPOST', 'body', body); + const localVarPath = `/fetchGnVariants/byHGVSg`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'POST', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + localVarHeaderParameter['Content-Type'] = 'application/json'; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + localVarRequestOptions.data = serializeDataIfNeeded(body, localVarRequestOptions, configuration); + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get transcript info in both GRCh37 and 38. + * @summary getTranscript + * @param {string} hugoSymbol hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + getTranscriptUsingGET: async (hugoSymbol: string, options: RawAxiosRequestConfig = {}): Promise => { + // verify required parameter 'hugoSymbol' is not null or undefined + assertParamExists('getTranscriptUsingGET', 'hugoSymbol', hugoSymbol); + const localVarPath = `/transcripts/{hugoSymbol}`.replace(`{${'hugoSymbol'}}`, encodeURIComponent(String(hugoSymbol))); + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + }; +}; + +/** + * TranscriptApi - functional programming interface + * @export + */ +export const TranscriptApiFp = function (configuration?: Configuration) { + const localVarAxiosParamCreator = TranscriptApiAxiosParamCreator(configuration); + return { + /** + * cache Genome Nexus variant info + * @summary cacheGenomeNexusVariantInfoPost + * @param {Array} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async cacheGenomeNexusVariantInfoPostUsingPOST( + body: Array, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise> { + const localVarAxiosArgs = await localVarAxiosParamCreator.cacheGenomeNexusVariantInfoPostUsingPOST(body, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['TranscriptApi.cacheGenomeNexusVariantInfoPostUsingPOST']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Fetch Genome Nexus variant info by genomic change + * @summary fetchGenomeNexusVariantInfoByGenomicChangePost + * @param {Array} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async fetchGenomeNexusVariantInfoByGenomicChangePostUsingPOST( + body: Array, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.fetchGenomeNexusVariantInfoByGenomicChangePostUsingPOST(body, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['TranscriptApi.fetchGenomeNexusVariantInfoByGenomicChangePostUsingPOST']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Fetch Genome Nexus variant info by HGVSg + * @summary fetchGenomeNexusVariantInfoByHGVSgPost + * @param {Array} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async fetchGenomeNexusVariantInfoByHGVSgPostUsingPOST( + body: Array, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.fetchGenomeNexusVariantInfoByHGVSgPostUsingPOST(body, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['TranscriptApi.fetchGenomeNexusVariantInfoByHGVSgPostUsingPOST']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get transcript info in both GRCh37 and 38. + * @summary getTranscript + * @param {string} hugoSymbol hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async getTranscriptUsingGET( + hugoSymbol: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise> { + const localVarAxiosArgs = await localVarAxiosParamCreator.getTranscriptUsingGET(hugoSymbol, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['TranscriptApi.getTranscriptUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + }; +}; + +/** + * TranscriptApi - factory interface + * @export + */ +export const TranscriptApiFactory = function (configuration?: Configuration, basePath?: string, axios?: AxiosInstance) { + const localVarFp = TranscriptApiFp(configuration); + return { + /** + * cache Genome Nexus variant info + * @summary cacheGenomeNexusVariantInfoPost + * @param {Array} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + cacheGenomeNexusVariantInfoPostUsingPOST( + body: Array, + options?: RawAxiosRequestConfig, + ): AxiosPromise { + return localVarFp.cacheGenomeNexusVariantInfoPostUsingPOST(body, options).then(request => request(axios, basePath)); + }, + /** + * Fetch Genome Nexus variant info by genomic change + * @summary fetchGenomeNexusVariantInfoByGenomicChangePost + * @param {Array} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + fetchGenomeNexusVariantInfoByGenomicChangePostUsingPOST( + body: Array, + options?: RawAxiosRequestConfig, + ): AxiosPromise> { + return localVarFp.fetchGenomeNexusVariantInfoByGenomicChangePostUsingPOST(body, options).then(request => request(axios, basePath)); + }, + /** + * Fetch Genome Nexus variant info by HGVSg + * @summary fetchGenomeNexusVariantInfoByHGVSgPost + * @param {Array} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + fetchGenomeNexusVariantInfoByHGVSgPostUsingPOST( + body: Array, + options?: RawAxiosRequestConfig, + ): AxiosPromise> { + return localVarFp.fetchGenomeNexusVariantInfoByHGVSgPostUsingPOST(body, options).then(request => request(axios, basePath)); + }, + /** + * Get transcript info in both GRCh37 and 38. + * @summary getTranscript + * @param {string} hugoSymbol hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + getTranscriptUsingGET(hugoSymbol: string, options?: RawAxiosRequestConfig): AxiosPromise { + return localVarFp.getTranscriptUsingGET(hugoSymbol, options).then(request => request(axios, basePath)); + }, + }; +}; + +/** + * TranscriptApi - object-oriented interface + * @export + * @class TranscriptApi + * @extends {BaseAPI} + */ +export class TranscriptApi extends BaseAPI { + /** + * cache Genome Nexus variant info + * @summary cacheGenomeNexusVariantInfoPost + * @param {Array} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof TranscriptApi + */ + public cacheGenomeNexusVariantInfoPostUsingPOST(body: Array, options?: RawAxiosRequestConfig) { + return TranscriptApiFp(this.configuration) + .cacheGenomeNexusVariantInfoPostUsingPOST(body, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Fetch Genome Nexus variant info by genomic change + * @summary fetchGenomeNexusVariantInfoByGenomicChangePost + * @param {Array} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof TranscriptApi + */ + public fetchGenomeNexusVariantInfoByGenomicChangePostUsingPOST( + body: Array, + options?: RawAxiosRequestConfig, + ) { + return TranscriptApiFp(this.configuration) + .fetchGenomeNexusVariantInfoByGenomicChangePostUsingPOST(body, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Fetch Genome Nexus variant info by HGVSg + * @summary fetchGenomeNexusVariantInfoByHGVSgPost + * @param {Array} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof TranscriptApi + */ + public fetchGenomeNexusVariantInfoByHGVSgPostUsingPOST(body: Array, options?: RawAxiosRequestConfig) { + return TranscriptApiFp(this.configuration) + .fetchGenomeNexusVariantInfoByHGVSgPostUsingPOST(body, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get transcript info in both GRCh37 and 38. + * @summary getTranscript + * @param {string} hugoSymbol hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof TranscriptApi + */ + public getTranscriptUsingGET(hugoSymbol: string, options?: RawAxiosRequestConfig) { + return TranscriptApiFp(this.configuration) + .getTranscriptUsingGET(hugoSymbol, options) + .then(request => request(this.axios, this.basePath)); + } +} + +/** + * UtilsApi - axios parameter creator + * @export + */ +export const UtilsApiAxiosParamCreator = function (configuration?: Configuration) { + return { + /** + * Annotate a string using CPL + * @summary utilAnnotateCPL + * @param {CplAnnotationRequest} cplRequest CPL Request + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilAnnotateCPLUsingPOST: async (cplRequest: CplAnnotationRequest, options: RawAxiosRequestConfig = {}): Promise => { + // verify required parameter 'cplRequest' is not null or undefined + assertParamExists('utilAnnotateCPLUsingPOST', 'cplRequest', cplRequest); + const localVarPath = `/utils/annotateCPL`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'POST', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + localVarHeaderParameter['Content-Type'] = 'application/json'; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + localVarRequestOptions.data = serializeDataIfNeeded(cplRequest, localVarRequestOptions, configuration); + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get information about what files are available by data version + * @summary utilDataAvailabilityGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilDataAvailabilityGetUsingGET: async (options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/data/availability`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get readme info for specific data release version + * @summary utilDataReadmeGet + * @param {string} [version] version + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilDataReadmeGetUsingGET: async (version?: string, options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/data/readme`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (version !== undefined) { + localVarQueryParameter['version'] = version; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * + * @summary utilDataSqlDumpGet + * @param {string} [version] version + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilDataSqlDumpGetUsingGET: async (version?: string, options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/data/sqlDump`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (version !== undefined) { + localVarQueryParameter['version'] = version; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * + * @summary utilDataTranscriptSqlDump + * @param {string} [version] version + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilDataTranscriptSqlDumpUsingGET: async (version?: string, options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/data/transcriptSqlDump`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (version !== undefined) { + localVarQueryParameter['version'] = version; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Filter genomic change based on oncokb coverage + * @summary utilFilterGenomicChangeBasedOnCoveragePost + * @param {Array} body List of queries. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilFilterGenomicChangeBasedOnCoveragePostUsingPOST: async ( + body: Array, + options: RawAxiosRequestConfig = {}, + ): Promise => { + // verify required parameter 'body' is not null or undefined + assertParamExists('utilFilterGenomicChangeBasedOnCoveragePostUsingPOST', 'body', body); + const localVarPath = `/utils/filterGenomicChangeBasedOnCoverage`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'POST', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + localVarHeaderParameter['Content-Type'] = 'application/json'; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + localVarRequestOptions.data = serializeDataIfNeeded(body, localVarRequestOptions, configuration); + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Filter HGVSg based on oncokb coverage + * @summary utilFilterHgvsgBasedOnCoveragePost + * @param {Array} body List of queries. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilFilterHgvsgBasedOnCoveragePostUsingPOST: async ( + body: Array, + options: RawAxiosRequestConfig = {}, + ): Promise => { + // verify required parameter 'body' is not null or undefined + assertParamExists('utilFilterHgvsgBasedOnCoveragePostUsingPOST', 'body', body); + const localVarPath = `/utils/filterHgvsgBasedOnCoverage`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'POST', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + localVarHeaderParameter['Content-Type'] = 'application/json'; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + localVarRequestOptions.data = serializeDataIfNeeded(body, localVarRequestOptions, configuration); + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * + * @summary utilMutationMapperDataGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilMutationMapperDataGetUsingGET: async (hugoSymbol?: string, options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/mutationMapperData`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (hugoSymbol !== undefined) { + localVarQueryParameter['hugoSymbol'] = hugoSymbol; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * + * @summary utilPortalAlterationSampleCountGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilPortalAlterationSampleCountGetUsingGET: async (hugoSymbol?: string, options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/portalAlterationSampleCount`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (hugoSymbol !== undefined) { + localVarQueryParameter['hugoSymbol'] = hugoSymbol; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get the list of relevant alterations + * @summary utilRelevantAlterationsGet + * @param {string} [referenceGenome] Reference genome, either GRCh37 or GRCh38. The default is GRCh37 + * @param {number} [entrezGeneId] alteration + * @param {string} [alteration] alteration + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilRelevantAlterationsGetUsingGET: async ( + referenceGenome?: string, + entrezGeneId?: number, + alteration?: string, + options: RawAxiosRequestConfig = {}, + ): Promise => { + const localVarPath = `/utils/relevantAlterations`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (referenceGenome !== undefined) { + localVarQueryParameter['referenceGenome'] = referenceGenome; + } + + if (entrezGeneId !== undefined) { + localVarQueryParameter['entrezGeneId'] = entrezGeneId; + } + + if (alteration !== undefined) { + localVarQueryParameter['alteration'] = alteration; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get the list of relevant tumor types. + * @summary utilRelevantCancerTypesPost + * @param {Array} body List of queries. + * @param {UtilRelevantCancerTypesPostUsingPOSTLevelOfEvidenceEnum} [levelOfEvidence] Level of Evidence + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilRelevantCancerTypesPostUsingPOST: async ( + body: Array, + levelOfEvidence?: UtilRelevantCancerTypesPostUsingPOSTLevelOfEvidenceEnum, + options: RawAxiosRequestConfig = {}, + ): Promise => { + // verify required parameter 'body' is not null or undefined + assertParamExists('utilRelevantCancerTypesPostUsingPOST', 'body', body); + const localVarPath = `/utils/relevantCancerTypes`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'POST', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (levelOfEvidence !== undefined) { + localVarQueryParameter['levelOfEvidence'] = levelOfEvidence; + } + + localVarHeaderParameter['Content-Type'] = 'application/json'; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + localVarRequestOptions.data = serializeDataIfNeeded(body, localVarRequestOptions, configuration); + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get the list of relevant tumor types. + * @summary utilRelevantTumorTypesGet + * @param {string} [tumorType] OncoTree tumor type name/main type/code + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilRelevantTumorTypesGetUsingGET: async (tumorType?: string, options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/relevantTumorTypes`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (tumorType !== undefined) { + localVarQueryParameter['tumorType'] = tumorType; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * + * @summary utilUpdateTranscriptGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {number} [entrezGeneId] entrezGeneId + * @param {string} [grch37Isoform] grch37Isoform + * @param {string} [grch37RefSeq] grch37RefSeq + * @param {string} [grch38Isoform] grch38Isoform + * @param {string} [grch38RefSeq] grch38RefSeq + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilUpdateTranscriptGetUsingGET: async ( + hugoSymbol?: string, + entrezGeneId?: number, + grch37Isoform?: string, + grch37RefSeq?: string, + grch38Isoform?: string, + grch38RefSeq?: string, + options: RawAxiosRequestConfig = {}, + ): Promise => { + const localVarPath = `/utils/updateTranscript`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (hugoSymbol !== undefined) { + localVarQueryParameter['hugoSymbol'] = hugoSymbol; + } + + if (entrezGeneId !== undefined) { + localVarQueryParameter['entrezGeneId'] = entrezGeneId; + } + + if (grch37Isoform !== undefined) { + localVarQueryParameter['grch37Isoform'] = grch37Isoform; + } + + if (grch37RefSeq !== undefined) { + localVarQueryParameter['grch37RefSeq'] = grch37RefSeq; + } + + if (grch38Isoform !== undefined) { + localVarQueryParameter['grch38Isoform'] = grch38Isoform; + } + + if (grch38RefSeq !== undefined) { + localVarQueryParameter['grch38RefSeq'] = grch38RefSeq; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * + * @summary utilValidateTranscriptUpdateGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {number} [entrezGeneId] entrezGeneId + * @param {string} [grch37Isoform] grch37Isoform + * @param {string} [grch38Isoform] grch38Isoform + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilValidateTranscriptUpdateGetUsingGET: async ( + hugoSymbol?: string, + entrezGeneId?: number, + grch37Isoform?: string, + grch38Isoform?: string, + options: RawAxiosRequestConfig = {}, + ): Promise => { + const localVarPath = `/utils/validateTranscriptUpdate`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (hugoSymbol !== undefined) { + localVarQueryParameter['hugoSymbol'] = hugoSymbol; + } + + if (entrezGeneId !== undefined) { + localVarQueryParameter['entrezGeneId'] = entrezGeneId; + } + + if (grch37Isoform !== undefined) { + localVarQueryParameter['grch37Isoform'] = grch37Isoform; + } + + if (grch38Isoform !== undefined) { + localVarQueryParameter['grch38Isoform'] = grch38Isoform; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get all the info for the query + * @summary utilVariantAnnotationGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {number} [entrezGeneId] entrezGeneId + * @param {string} [referenceGenome] Reference genome, either GRCh37 or GRCh38. The default is GRCh37 + * @param {string} [alteration] Alteration + * @param {string} [hgvsg] HGVS genomic format. Example: 7:g.140453136A>T + * @param {string} [genomicChange] Genomic change format. Example: 7,140453136,140453136,A,T + * @param {string} [tumorType] OncoTree tumor type name/main type/code + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilVariantAnnotationGetUsingGET: async ( + hugoSymbol?: string, + entrezGeneId?: number, + referenceGenome?: string, + alteration?: string, + hgvsg?: string, + genomicChange?: string, + tumorType?: string, + options: RawAxiosRequestConfig = {}, + ): Promise => { + const localVarPath = `/utils/variantAnnotation`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (hugoSymbol !== undefined) { + localVarQueryParameter['hugoSymbol'] = hugoSymbol; + } + + if (entrezGeneId !== undefined) { + localVarQueryParameter['entrezGeneId'] = entrezGeneId; + } + + if (referenceGenome !== undefined) { + localVarQueryParameter['referenceGenome'] = referenceGenome; + } + + if (alteration !== undefined) { + localVarQueryParameter['alteration'] = alteration; + } + + if (hgvsg !== undefined) { + localVarQueryParameter['hgvsg'] = hgvsg; + } + + if (genomicChange !== undefined) { + localVarQueryParameter['genomicChange'] = genomicChange; + } + + if (tumorType !== undefined) { + localVarQueryParameter['tumorType'] = tumorType; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get the list of Ensembl genes. + * @summary utilsEnsemblGenesGet + * @param {number} entrezGeneId Gene entrez id + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsEnsemblGenesGetUsingGET: async (entrezGeneId: number, options: RawAxiosRequestConfig = {}): Promise => { + // verify required parameter 'entrezGeneId' is not null or undefined + assertParamExists('utilsEnsemblGenesGetUsingGET', 'entrezGeneId', entrezGeneId); + const localVarPath = `/utils/ensembleGenes`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (entrezGeneId !== undefined) { + localVarQueryParameter['entrezGeneId'] = entrezGeneId; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get the list of evidences by levels. + * @summary utilsEvidencesByLevelsGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsEvidencesByLevelsGetUsingGET: async (options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/evidences/levels`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Determine whether variant is hotspot mutation. + * @summary utilsHotspotMutationGet + * @param {string} [hugoSymbol] Gene hugo symbol + * @param {string} [variant] Variant name + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsHotspotMutationGetUsingGET: async ( + hugoSymbol?: string, + variant?: string, + options: RawAxiosRequestConfig = {}, + ): Promise => { + const localVarPath = `/utils/isHotspot`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (hugoSymbol !== undefined) { + localVarQueryParameter['hugoSymbol'] = hugoSymbol; + } + + if (variant !== undefined) { + localVarQueryParameter['variant'] = variant; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get gene related numbers + * @summary utilsNumbersGeneGet + * @param {string} hugoSymbol The gene symbol used in Human Genome Organisation. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsNumbersGeneGetUsingGET: async (hugoSymbol: string, options: RawAxiosRequestConfig = {}): Promise => { + // verify required parameter 'hugoSymbol' is not null or undefined + assertParamExists('utilsNumbersGeneGetUsingGET', 'hugoSymbol', hugoSymbol); + const localVarPath = `/utils/numbers/gene/{hugoSymbol}`.replace(`{${'hugoSymbol'}}`, encodeURIComponent(String(hugoSymbol))); + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get gene related numbers of all genes. This is for main page word cloud. + * @summary utilsNumbersGenesGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsNumbersGenesGetUsingGET: async (options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/numbers/genes/`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get gene related numbers of all genes. This is for main page word cloud. + * @summary utilsNumbersLevelsGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsNumbersLevelsGetUsingGET: async (options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/numbers/levels/`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get numbers served for the main page dashboard. + * @summary utilsNumbersMainGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsNumbersMainGetUsingGET: async (options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/numbers/main/`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get All Suggested Variants. + * @summary utilsSuggestedVariantsGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsSuggestedVariantsGetUsingGET: async (options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/suggestedVariants`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Get the full list of TumorTypes. + * @summary utilsTumorTypesGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsTumorTypesGetUsingGET: async (options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/tumorTypes`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Check if clinical trials are valid or not by nctId. + * @summary validateTrials + * @param {Array} [nctIds] NCTID list + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + validateTrialsUsingGET: async (nctIds?: Array, options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/validation/trials`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + if (nctIds) { + localVarQueryParameter['nctIds'] = nctIds; + } + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Check if the genomic example will be mapped to OncoKB variant. + * @summary validateVariantExampleGet + * @param {string} [examples] The genomic examples. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + validateVariantExampleGetUsingGET: async (examples?: string, options: RawAxiosRequestConfig = {}): Promise => { + const localVarPath = `/utils/match/variant`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'GET', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + localVarHeaderParameter['Content-Type'] = 'application/json'; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + localVarRequestOptions.data = serializeDataIfNeeded(examples, localVarRequestOptions, configuration); + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + /** + * Check which OncoKB variants can be mapped on genomic examples. + * @summary validateVariantExamplePost + * @param {MatchVariantRequest} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + validateVariantExamplePostUsingPOST: async (body: MatchVariantRequest, options: RawAxiosRequestConfig = {}): Promise => { + // verify required parameter 'body' is not null or undefined + assertParamExists('validateVariantExamplePostUsingPOST', 'body', body); + const localVarPath = `/utils/match/variant`; + // use dummy base URL string because the URL constructor only accepts absolute URLs. + const localVarUrlObj = new URL(localVarPath, DUMMY_BASE_URL); + let baseOptions; + if (configuration) { + baseOptions = configuration.baseOptions; + } + + const localVarRequestOptions = { method: 'POST', ...baseOptions, ...options }; + const localVarHeaderParameter = {} as any; + const localVarQueryParameter = {} as any; + + localVarHeaderParameter['Content-Type'] = 'application/json'; + + setSearchParams(localVarUrlObj, localVarQueryParameter); + let headersFromBaseOptions = baseOptions && baseOptions.headers ? baseOptions.headers : {}; + localVarRequestOptions.headers = { ...localVarHeaderParameter, ...headersFromBaseOptions, ...options.headers }; + localVarRequestOptions.data = serializeDataIfNeeded(body, localVarRequestOptions, configuration); + + return { + url: toPathString(localVarUrlObj), + options: localVarRequestOptions, + }; + }, + }; +}; + +/** + * UtilsApi - functional programming interface + * @export + */ +export const UtilsApiFp = function (configuration?: Configuration) { + const localVarAxiosParamCreator = UtilsApiAxiosParamCreator(configuration); + return { + /** + * Annotate a string using CPL + * @summary utilAnnotateCPL + * @param {CplAnnotationRequest} cplRequest CPL Request + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilAnnotateCPLUsingPOST( + cplRequest: CplAnnotationRequest, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilAnnotateCPLUsingPOST(cplRequest, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = operationServerMap['UtilsApi.utilAnnotateCPLUsingPOST']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get information about what files are available by data version + * @summary utilDataAvailabilityGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilDataAvailabilityGetUsingGET( + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilDataAvailabilityGetUsingGET(options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilDataAvailabilityGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get readme info for specific data release version + * @summary utilDataReadmeGet + * @param {string} [version] version + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilDataReadmeGetUsingGET( + version?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilDataReadmeGetUsingGET(version, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = operationServerMap['UtilsApi.utilDataReadmeGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * + * @summary utilDataSqlDumpGet + * @param {string} [version] version + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilDataSqlDumpGetUsingGET( + version?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilDataSqlDumpGetUsingGET(version, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilDataSqlDumpGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * + * @summary utilDataTranscriptSqlDump + * @param {string} [version] version + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilDataTranscriptSqlDumpUsingGET( + version?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilDataTranscriptSqlDumpUsingGET(version, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilDataTranscriptSqlDumpUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Filter genomic change based on oncokb coverage + * @summary utilFilterGenomicChangeBasedOnCoveragePost + * @param {Array} body List of queries. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilFilterGenomicChangeBasedOnCoveragePostUsingPOST( + body: Array, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilFilterGenomicChangeBasedOnCoveragePostUsingPOST(body, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilFilterGenomicChangeBasedOnCoveragePostUsingPOST']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Filter HGVSg based on oncokb coverage + * @summary utilFilterHgvsgBasedOnCoveragePost + * @param {Array} body List of queries. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilFilterHgvsgBasedOnCoveragePostUsingPOST( + body: Array, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilFilterHgvsgBasedOnCoveragePostUsingPOST(body, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilFilterHgvsgBasedOnCoveragePostUsingPOST']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * + * @summary utilMutationMapperDataGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilMutationMapperDataGetUsingGET( + hugoSymbol?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilMutationMapperDataGetUsingGET(hugoSymbol, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilMutationMapperDataGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * + * @summary utilPortalAlterationSampleCountGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilPortalAlterationSampleCountGetUsingGET( + hugoSymbol?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilPortalAlterationSampleCountGetUsingGET(hugoSymbol, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilPortalAlterationSampleCountGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get the list of relevant alterations + * @summary utilRelevantAlterationsGet + * @param {string} [referenceGenome] Reference genome, either GRCh37 or GRCh38. The default is GRCh37 + * @param {number} [entrezGeneId] alteration + * @param {string} [alteration] alteration + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilRelevantAlterationsGetUsingGET( + referenceGenome?: string, + entrezGeneId?: number, + alteration?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilRelevantAlterationsGetUsingGET( + referenceGenome, + entrezGeneId, + alteration, + options, + ); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilRelevantAlterationsGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get the list of relevant tumor types. + * @summary utilRelevantCancerTypesPost + * @param {Array} body List of queries. + * @param {UtilRelevantCancerTypesPostUsingPOSTLevelOfEvidenceEnum} [levelOfEvidence] Level of Evidence + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilRelevantCancerTypesPostUsingPOST( + body: Array, + levelOfEvidence?: UtilRelevantCancerTypesPostUsingPOSTLevelOfEvidenceEnum, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilRelevantCancerTypesPostUsingPOST(body, levelOfEvidence, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilRelevantCancerTypesPostUsingPOST']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get the list of relevant tumor types. + * @summary utilRelevantTumorTypesGet + * @param {string} [tumorType] OncoTree tumor type name/main type/code + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilRelevantTumorTypesGetUsingGET( + tumorType?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilRelevantTumorTypesGetUsingGET(tumorType, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilRelevantTumorTypesGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * + * @summary utilUpdateTranscriptGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {number} [entrezGeneId] entrezGeneId + * @param {string} [grch37Isoform] grch37Isoform + * @param {string} [grch37RefSeq] grch37RefSeq + * @param {string} [grch38Isoform] grch38Isoform + * @param {string} [grch38RefSeq] grch38RefSeq + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilUpdateTranscriptGetUsingGET( + hugoSymbol?: string, + entrezGeneId?: number, + grch37Isoform?: string, + grch37RefSeq?: string, + grch38Isoform?: string, + grch38RefSeq?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilUpdateTranscriptGetUsingGET( + hugoSymbol, + entrezGeneId, + grch37Isoform, + grch37RefSeq, + grch38Isoform, + grch38RefSeq, + options, + ); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilUpdateTranscriptGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * + * @summary utilValidateTranscriptUpdateGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {number} [entrezGeneId] entrezGeneId + * @param {string} [grch37Isoform] grch37Isoform + * @param {string} [grch38Isoform] grch38Isoform + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilValidateTranscriptUpdateGetUsingGET( + hugoSymbol?: string, + entrezGeneId?: number, + grch37Isoform?: string, + grch38Isoform?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilValidateTranscriptUpdateGetUsingGET( + hugoSymbol, + entrezGeneId, + grch37Isoform, + grch38Isoform, + options, + ); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilValidateTranscriptUpdateGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get all the info for the query + * @summary utilVariantAnnotationGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {number} [entrezGeneId] entrezGeneId + * @param {string} [referenceGenome] Reference genome, either GRCh37 or GRCh38. The default is GRCh37 + * @param {string} [alteration] Alteration + * @param {string} [hgvsg] HGVS genomic format. Example: 7:g.140453136A>T + * @param {string} [genomicChange] Genomic change format. Example: 7,140453136,140453136,A,T + * @param {string} [tumorType] OncoTree tumor type name/main type/code + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilVariantAnnotationGetUsingGET( + hugoSymbol?: string, + entrezGeneId?: number, + referenceGenome?: string, + alteration?: string, + hgvsg?: string, + genomicChange?: string, + tumorType?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilVariantAnnotationGetUsingGET( + hugoSymbol, + entrezGeneId, + referenceGenome, + alteration, + hgvsg, + genomicChange, + tumorType, + options, + ); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilVariantAnnotationGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get the list of Ensembl genes. + * @summary utilsEnsemblGenesGet + * @param {number} entrezGeneId Gene entrez id + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilsEnsemblGenesGetUsingGET( + entrezGeneId: number, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilsEnsemblGenesGetUsingGET(entrezGeneId, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilsEnsemblGenesGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get the list of evidences by levels. + * @summary utilsEvidencesByLevelsGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilsEvidencesByLevelsGetUsingGET( + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilsEvidencesByLevelsGetUsingGET(options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilsEvidencesByLevelsGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Determine whether variant is hotspot mutation. + * @summary utilsHotspotMutationGet + * @param {string} [hugoSymbol] Gene hugo symbol + * @param {string} [variant] Variant name + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilsHotspotMutationGetUsingGET( + hugoSymbol?: string, + variant?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilsHotspotMutationGetUsingGET(hugoSymbol, variant, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilsHotspotMutationGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get gene related numbers + * @summary utilsNumbersGeneGet + * @param {string} hugoSymbol The gene symbol used in Human Genome Organisation. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilsNumbersGeneGetUsingGET( + hugoSymbol: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilsNumbersGeneGetUsingGET(hugoSymbol, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilsNumbersGeneGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get gene related numbers of all genes. This is for main page word cloud. + * @summary utilsNumbersGenesGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilsNumbersGenesGetUsingGET( + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilsNumbersGenesGetUsingGET(options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilsNumbersGenesGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get gene related numbers of all genes. This is for main page word cloud. + * @summary utilsNumbersLevelsGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilsNumbersLevelsGetUsingGET( + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilsNumbersLevelsGetUsingGET(options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilsNumbersLevelsGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get numbers served for the main page dashboard. + * @summary utilsNumbersMainGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilsNumbersMainGetUsingGET( + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilsNumbersMainGetUsingGET(options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilsNumbersMainGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get All Suggested Variants. + * @summary utilsSuggestedVariantsGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilsSuggestedVariantsGetUsingGET( + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilsSuggestedVariantsGetUsingGET(options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilsSuggestedVariantsGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Get the full list of TumorTypes. + * @summary utilsTumorTypesGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async utilsTumorTypesGetUsingGET( + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.utilsTumorTypesGetUsingGET(options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.utilsTumorTypesGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Check if clinical trials are valid or not by nctId. + * @summary validateTrials + * @param {Array} [nctIds] NCTID list + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async validateTrialsUsingGET( + nctIds?: Array, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise> { + const localVarAxiosArgs = await localVarAxiosParamCreator.validateTrialsUsingGET(nctIds, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = operationServerMap['UtilsApi.validateTrialsUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Check if the genomic example will be mapped to OncoKB variant. + * @summary validateVariantExampleGet + * @param {string} [examples] The genomic examples. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async validateVariantExampleGetUsingGET( + examples?: string, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise> { + const localVarAxiosArgs = await localVarAxiosParamCreator.validateVariantExampleGetUsingGET(examples, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.validateVariantExampleGetUsingGET']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + /** + * Check which OncoKB variants can be mapped on genomic examples. + * @summary validateVariantExamplePost + * @param {MatchVariantRequest} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + async validateVariantExamplePostUsingPOST( + body: MatchVariantRequest, + options?: RawAxiosRequestConfig, + ): Promise<(axios?: AxiosInstance, basePath?: string) => AxiosPromise>> { + const localVarAxiosArgs = await localVarAxiosParamCreator.validateVariantExamplePostUsingPOST(body, options); + const localVarOperationServerIndex = configuration?.serverIndex ?? 0; + const localVarOperationServerBasePath = + operationServerMap['UtilsApi.validateVariantExamplePostUsingPOST']?.[localVarOperationServerIndex]?.url; + return (axios, basePath) => + createRequestFunction(localVarAxiosArgs, globalAxios, BASE_PATH, configuration)(axios, localVarOperationServerBasePath || basePath); + }, + }; +}; + +/** + * UtilsApi - factory interface + * @export + */ +export const UtilsApiFactory = function (configuration?: Configuration, basePath?: string, axios?: AxiosInstance) { + const localVarFp = UtilsApiFp(configuration); + return { + /** + * Annotate a string using CPL + * @summary utilAnnotateCPL + * @param {CplAnnotationRequest} cplRequest CPL Request + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilAnnotateCPLUsingPOST(cplRequest: CplAnnotationRequest, options?: RawAxiosRequestConfig): AxiosPromise { + return localVarFp.utilAnnotateCPLUsingPOST(cplRequest, options).then(request => request(axios, basePath)); + }, + /** + * Get information about what files are available by data version + * @summary utilDataAvailabilityGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilDataAvailabilityGetUsingGET(options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.utilDataAvailabilityGetUsingGET(options).then(request => request(axios, basePath)); + }, + /** + * Get readme info for specific data release version + * @summary utilDataReadmeGet + * @param {string} [version] version + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilDataReadmeGetUsingGET(version?: string, options?: RawAxiosRequestConfig): AxiosPromise { + return localVarFp.utilDataReadmeGetUsingGET(version, options).then(request => request(axios, basePath)); + }, + /** + * + * @summary utilDataSqlDumpGet + * @param {string} [version] version + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilDataSqlDumpGetUsingGET(version?: string, options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.utilDataSqlDumpGetUsingGET(version, options).then(request => request(axios, basePath)); + }, + /** + * + * @summary utilDataTranscriptSqlDump + * @param {string} [version] version + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilDataTranscriptSqlDumpUsingGET(version?: string, options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.utilDataTranscriptSqlDumpUsingGET(version, options).then(request => request(axios, basePath)); + }, + /** + * Filter genomic change based on oncokb coverage + * @summary utilFilterGenomicChangeBasedOnCoveragePost + * @param {Array} body List of queries. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilFilterGenomicChangeBasedOnCoveragePostUsingPOST( + body: Array, + options?: RawAxiosRequestConfig, + ): AxiosPromise> { + return localVarFp.utilFilterGenomicChangeBasedOnCoveragePostUsingPOST(body, options).then(request => request(axios, basePath)); + }, + /** + * Filter HGVSg based on oncokb coverage + * @summary utilFilterHgvsgBasedOnCoveragePost + * @param {Array} body List of queries. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilFilterHgvsgBasedOnCoveragePostUsingPOST( + body: Array, + options?: RawAxiosRequestConfig, + ): AxiosPromise> { + return localVarFp.utilFilterHgvsgBasedOnCoveragePostUsingPOST(body, options).then(request => request(axios, basePath)); + }, + /** + * + * @summary utilMutationMapperDataGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilMutationMapperDataGetUsingGET(hugoSymbol?: string, options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.utilMutationMapperDataGetUsingGET(hugoSymbol, options).then(request => request(axios, basePath)); + }, + /** + * + * @summary utilPortalAlterationSampleCountGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilPortalAlterationSampleCountGetUsingGET(hugoSymbol?: string, options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.utilPortalAlterationSampleCountGetUsingGET(hugoSymbol, options).then(request => request(axios, basePath)); + }, + /** + * Get the list of relevant alterations + * @summary utilRelevantAlterationsGet + * @param {string} [referenceGenome] Reference genome, either GRCh37 or GRCh38. The default is GRCh37 + * @param {number} [entrezGeneId] alteration + * @param {string} [alteration] alteration + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilRelevantAlterationsGetUsingGET( + referenceGenome?: string, + entrezGeneId?: number, + alteration?: string, + options?: RawAxiosRequestConfig, + ): AxiosPromise> { + return localVarFp + .utilRelevantAlterationsGetUsingGET(referenceGenome, entrezGeneId, alteration, options) + .then(request => request(axios, basePath)); + }, + /** + * Get the list of relevant tumor types. + * @summary utilRelevantCancerTypesPost + * @param {Array} body List of queries. + * @param {UtilRelevantCancerTypesPostUsingPOSTLevelOfEvidenceEnum} [levelOfEvidence] Level of Evidence + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilRelevantCancerTypesPostUsingPOST( + body: Array, + levelOfEvidence?: UtilRelevantCancerTypesPostUsingPOSTLevelOfEvidenceEnum, + options?: RawAxiosRequestConfig, + ): AxiosPromise> { + return localVarFp.utilRelevantCancerTypesPostUsingPOST(body, levelOfEvidence, options).then(request => request(axios, basePath)); + }, + /** + * Get the list of relevant tumor types. + * @summary utilRelevantTumorTypesGet + * @param {string} [tumorType] OncoTree tumor type name/main type/code + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilRelevantTumorTypesGetUsingGET(tumorType?: string, options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.utilRelevantTumorTypesGetUsingGET(tumorType, options).then(request => request(axios, basePath)); + }, + /** + * + * @summary utilUpdateTranscriptGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {number} [entrezGeneId] entrezGeneId + * @param {string} [grch37Isoform] grch37Isoform + * @param {string} [grch37RefSeq] grch37RefSeq + * @param {string} [grch38Isoform] grch38Isoform + * @param {string} [grch38RefSeq] grch38RefSeq + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilUpdateTranscriptGetUsingGET( + hugoSymbol?: string, + entrezGeneId?: number, + grch37Isoform?: string, + grch37RefSeq?: string, + grch38Isoform?: string, + grch38RefSeq?: string, + options?: RawAxiosRequestConfig, + ): AxiosPromise { + return localVarFp + .utilUpdateTranscriptGetUsingGET(hugoSymbol, entrezGeneId, grch37Isoform, grch37RefSeq, grch38Isoform, grch38RefSeq, options) + .then(request => request(axios, basePath)); + }, + /** + * + * @summary utilValidateTranscriptUpdateGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {number} [entrezGeneId] entrezGeneId + * @param {string} [grch37Isoform] grch37Isoform + * @param {string} [grch38Isoform] grch38Isoform + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilValidateTranscriptUpdateGetUsingGET( + hugoSymbol?: string, + entrezGeneId?: number, + grch37Isoform?: string, + grch38Isoform?: string, + options?: RawAxiosRequestConfig, + ): AxiosPromise { + return localVarFp + .utilValidateTranscriptUpdateGetUsingGET(hugoSymbol, entrezGeneId, grch37Isoform, grch38Isoform, options) + .then(request => request(axios, basePath)); + }, + /** + * Get all the info for the query + * @summary utilVariantAnnotationGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {number} [entrezGeneId] entrezGeneId + * @param {string} [referenceGenome] Reference genome, either GRCh37 or GRCh38. The default is GRCh37 + * @param {string} [alteration] Alteration + * @param {string} [hgvsg] HGVS genomic format. Example: 7:g.140453136A>T + * @param {string} [genomicChange] Genomic change format. Example: 7,140453136,140453136,A,T + * @param {string} [tumorType] OncoTree tumor type name/main type/code + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilVariantAnnotationGetUsingGET( + hugoSymbol?: string, + entrezGeneId?: number, + referenceGenome?: string, + alteration?: string, + hgvsg?: string, + genomicChange?: string, + tumorType?: string, + options?: RawAxiosRequestConfig, + ): AxiosPromise { + return localVarFp + .utilVariantAnnotationGetUsingGET(hugoSymbol, entrezGeneId, referenceGenome, alteration, hgvsg, genomicChange, tumorType, options) + .then(request => request(axios, basePath)); + }, + /** + * Get the list of Ensembl genes. + * @summary utilsEnsemblGenesGet + * @param {number} entrezGeneId Gene entrez id + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsEnsemblGenesGetUsingGET(entrezGeneId: number, options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.utilsEnsemblGenesGetUsingGET(entrezGeneId, options).then(request => request(axios, basePath)); + }, + /** + * Get the list of evidences by levels. + * @summary utilsEvidencesByLevelsGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsEvidencesByLevelsGetUsingGET(options?: RawAxiosRequestConfig): AxiosPromise { + return localVarFp.utilsEvidencesByLevelsGetUsingGET(options).then(request => request(axios, basePath)); + }, + /** + * Determine whether variant is hotspot mutation. + * @summary utilsHotspotMutationGet + * @param {string} [hugoSymbol] Gene hugo symbol + * @param {string} [variant] Variant name + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsHotspotMutationGetUsingGET(hugoSymbol?: string, variant?: string, options?: RawAxiosRequestConfig): AxiosPromise { + return localVarFp.utilsHotspotMutationGetUsingGET(hugoSymbol, variant, options).then(request => request(axios, basePath)); + }, + /** + * Get gene related numbers + * @summary utilsNumbersGeneGet + * @param {string} hugoSymbol The gene symbol used in Human Genome Organisation. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsNumbersGeneGetUsingGET(hugoSymbol: string, options?: RawAxiosRequestConfig): AxiosPromise { + return localVarFp.utilsNumbersGeneGetUsingGET(hugoSymbol, options).then(request => request(axios, basePath)); + }, + /** + * Get gene related numbers of all genes. This is for main page word cloud. + * @summary utilsNumbersGenesGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsNumbersGenesGetUsingGET(options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.utilsNumbersGenesGetUsingGET(options).then(request => request(axios, basePath)); + }, + /** + * Get gene related numbers of all genes. This is for main page word cloud. + * @summary utilsNumbersLevelsGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsNumbersLevelsGetUsingGET(options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.utilsNumbersLevelsGetUsingGET(options).then(request => request(axios, basePath)); + }, + /** + * Get numbers served for the main page dashboard. + * @summary utilsNumbersMainGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsNumbersMainGetUsingGET(options?: RawAxiosRequestConfig): AxiosPromise { + return localVarFp.utilsNumbersMainGetUsingGET(options).then(request => request(axios, basePath)); + }, + /** + * Get All Suggested Variants. + * @summary utilsSuggestedVariantsGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsSuggestedVariantsGetUsingGET(options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.utilsSuggestedVariantsGetUsingGET(options).then(request => request(axios, basePath)); + }, + /** + * Get the full list of TumorTypes. + * @summary utilsTumorTypesGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + utilsTumorTypesGetUsingGET(options?: RawAxiosRequestConfig): AxiosPromise> { + return localVarFp.utilsTumorTypesGetUsingGET(options).then(request => request(axios, basePath)); + }, + /** + * Check if clinical trials are valid or not by nctId. + * @summary validateTrials + * @param {Array} [nctIds] NCTID list + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + validateTrialsUsingGET(nctIds?: Array, options?: RawAxiosRequestConfig): AxiosPromise { + return localVarFp.validateTrialsUsingGET(nctIds, options).then(request => request(axios, basePath)); + }, + /** + * Check if the genomic example will be mapped to OncoKB variant. + * @summary validateVariantExampleGet + * @param {string} [examples] The genomic examples. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + validateVariantExampleGetUsingGET(examples?: string, options?: RawAxiosRequestConfig): AxiosPromise { + return localVarFp.validateVariantExampleGetUsingGET(examples, options).then(request => request(axios, basePath)); + }, + /** + * Check which OncoKB variants can be mapped on genomic examples. + * @summary validateVariantExamplePost + * @param {MatchVariantRequest} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + */ + validateVariantExamplePostUsingPOST( + body: MatchVariantRequest, + options?: RawAxiosRequestConfig, + ): AxiosPromise> { + return localVarFp.validateVariantExamplePostUsingPOST(body, options).then(request => request(axios, basePath)); + }, + }; +}; + +/** + * UtilsApi - object-oriented interface + * @export + * @class UtilsApi + * @extends {BaseAPI} + */ +export class UtilsApi extends BaseAPI { + /** + * Annotate a string using CPL + * @summary utilAnnotateCPL + * @param {CplAnnotationRequest} cplRequest CPL Request + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilAnnotateCPLUsingPOST(cplRequest: CplAnnotationRequest, options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilAnnotateCPLUsingPOST(cplRequest, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get information about what files are available by data version + * @summary utilDataAvailabilityGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilDataAvailabilityGetUsingGET(options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilDataAvailabilityGetUsingGET(options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get readme info for specific data release version + * @summary utilDataReadmeGet + * @param {string} [version] version + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilDataReadmeGetUsingGET(version?: string, options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilDataReadmeGetUsingGET(version, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * + * @summary utilDataSqlDumpGet + * @param {string} [version] version + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilDataSqlDumpGetUsingGET(version?: string, options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilDataSqlDumpGetUsingGET(version, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * + * @summary utilDataTranscriptSqlDump + * @param {string} [version] version + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilDataTranscriptSqlDumpUsingGET(version?: string, options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilDataTranscriptSqlDumpUsingGET(version, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Filter genomic change based on oncokb coverage + * @summary utilFilterGenomicChangeBasedOnCoveragePost + * @param {Array} body List of queries. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilFilterGenomicChangeBasedOnCoveragePostUsingPOST( + body: Array, + options?: RawAxiosRequestConfig, + ) { + return UtilsApiFp(this.configuration) + .utilFilterGenomicChangeBasedOnCoveragePostUsingPOST(body, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Filter HGVSg based on oncokb coverage + * @summary utilFilterHgvsgBasedOnCoveragePost + * @param {Array} body List of queries. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilFilterHgvsgBasedOnCoveragePostUsingPOST(body: Array, options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilFilterHgvsgBasedOnCoveragePostUsingPOST(body, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * + * @summary utilMutationMapperDataGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilMutationMapperDataGetUsingGET(hugoSymbol?: string, options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilMutationMapperDataGetUsingGET(hugoSymbol, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * + * @summary utilPortalAlterationSampleCountGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilPortalAlterationSampleCountGetUsingGET(hugoSymbol?: string, options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilPortalAlterationSampleCountGetUsingGET(hugoSymbol, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get the list of relevant alterations + * @summary utilRelevantAlterationsGet + * @param {string} [referenceGenome] Reference genome, either GRCh37 or GRCh38. The default is GRCh37 + * @param {number} [entrezGeneId] alteration + * @param {string} [alteration] alteration + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilRelevantAlterationsGetUsingGET( + referenceGenome?: string, + entrezGeneId?: number, + alteration?: string, + options?: RawAxiosRequestConfig, + ) { + return UtilsApiFp(this.configuration) + .utilRelevantAlterationsGetUsingGET(referenceGenome, entrezGeneId, alteration, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get the list of relevant tumor types. + * @summary utilRelevantCancerTypesPost + * @param {Array} body List of queries. + * @param {UtilRelevantCancerTypesPostUsingPOSTLevelOfEvidenceEnum} [levelOfEvidence] Level of Evidence + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilRelevantCancerTypesPostUsingPOST( + body: Array, + levelOfEvidence?: UtilRelevantCancerTypesPostUsingPOSTLevelOfEvidenceEnum, + options?: RawAxiosRequestConfig, + ) { + return UtilsApiFp(this.configuration) + .utilRelevantCancerTypesPostUsingPOST(body, levelOfEvidence, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get the list of relevant tumor types. + * @summary utilRelevantTumorTypesGet + * @param {string} [tumorType] OncoTree tumor type name/main type/code + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilRelevantTumorTypesGetUsingGET(tumorType?: string, options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilRelevantTumorTypesGetUsingGET(tumorType, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * + * @summary utilUpdateTranscriptGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {number} [entrezGeneId] entrezGeneId + * @param {string} [grch37Isoform] grch37Isoform + * @param {string} [grch37RefSeq] grch37RefSeq + * @param {string} [grch38Isoform] grch38Isoform + * @param {string} [grch38RefSeq] grch38RefSeq + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilUpdateTranscriptGetUsingGET( + hugoSymbol?: string, + entrezGeneId?: number, + grch37Isoform?: string, + grch37RefSeq?: string, + grch38Isoform?: string, + grch38RefSeq?: string, + options?: RawAxiosRequestConfig, + ) { + return UtilsApiFp(this.configuration) + .utilUpdateTranscriptGetUsingGET(hugoSymbol, entrezGeneId, grch37Isoform, grch37RefSeq, grch38Isoform, grch38RefSeq, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * + * @summary utilValidateTranscriptUpdateGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {number} [entrezGeneId] entrezGeneId + * @param {string} [grch37Isoform] grch37Isoform + * @param {string} [grch38Isoform] grch38Isoform + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilValidateTranscriptUpdateGetUsingGET( + hugoSymbol?: string, + entrezGeneId?: number, + grch37Isoform?: string, + grch38Isoform?: string, + options?: RawAxiosRequestConfig, + ) { + return UtilsApiFp(this.configuration) + .utilValidateTranscriptUpdateGetUsingGET(hugoSymbol, entrezGeneId, grch37Isoform, grch38Isoform, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get all the info for the query + * @summary utilVariantAnnotationGet + * @param {string} [hugoSymbol] hugoSymbol + * @param {number} [entrezGeneId] entrezGeneId + * @param {string} [referenceGenome] Reference genome, either GRCh37 or GRCh38. The default is GRCh37 + * @param {string} [alteration] Alteration + * @param {string} [hgvsg] HGVS genomic format. Example: 7:g.140453136A>T + * @param {string} [genomicChange] Genomic change format. Example: 7,140453136,140453136,A,T + * @param {string} [tumorType] OncoTree tumor type name/main type/code + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilVariantAnnotationGetUsingGET( + hugoSymbol?: string, + entrezGeneId?: number, + referenceGenome?: string, + alteration?: string, + hgvsg?: string, + genomicChange?: string, + tumorType?: string, + options?: RawAxiosRequestConfig, + ) { + return UtilsApiFp(this.configuration) + .utilVariantAnnotationGetUsingGET(hugoSymbol, entrezGeneId, referenceGenome, alteration, hgvsg, genomicChange, tumorType, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get the list of Ensembl genes. + * @summary utilsEnsemblGenesGet + * @param {number} entrezGeneId Gene entrez id + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilsEnsemblGenesGetUsingGET(entrezGeneId: number, options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilsEnsemblGenesGetUsingGET(entrezGeneId, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get the list of evidences by levels. + * @summary utilsEvidencesByLevelsGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilsEvidencesByLevelsGetUsingGET(options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilsEvidencesByLevelsGetUsingGET(options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Determine whether variant is hotspot mutation. + * @summary utilsHotspotMutationGet + * @param {string} [hugoSymbol] Gene hugo symbol + * @param {string} [variant] Variant name + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilsHotspotMutationGetUsingGET(hugoSymbol?: string, variant?: string, options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilsHotspotMutationGetUsingGET(hugoSymbol, variant, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get gene related numbers + * @summary utilsNumbersGeneGet + * @param {string} hugoSymbol The gene symbol used in Human Genome Organisation. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilsNumbersGeneGetUsingGET(hugoSymbol: string, options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilsNumbersGeneGetUsingGET(hugoSymbol, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get gene related numbers of all genes. This is for main page word cloud. + * @summary utilsNumbersGenesGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilsNumbersGenesGetUsingGET(options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilsNumbersGenesGetUsingGET(options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get gene related numbers of all genes. This is for main page word cloud. + * @summary utilsNumbersLevelsGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilsNumbersLevelsGetUsingGET(options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilsNumbersLevelsGetUsingGET(options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get numbers served for the main page dashboard. + * @summary utilsNumbersMainGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilsNumbersMainGetUsingGET(options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilsNumbersMainGetUsingGET(options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get All Suggested Variants. + * @summary utilsSuggestedVariantsGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilsSuggestedVariantsGetUsingGET(options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilsSuggestedVariantsGetUsingGET(options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Get the full list of TumorTypes. + * @summary utilsTumorTypesGet + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public utilsTumorTypesGetUsingGET(options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .utilsTumorTypesGetUsingGET(options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Check if clinical trials are valid or not by nctId. + * @summary validateTrials + * @param {Array} [nctIds] NCTID list + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public validateTrialsUsingGET(nctIds?: Array, options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .validateTrialsUsingGET(nctIds, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Check if the genomic example will be mapped to OncoKB variant. + * @summary validateVariantExampleGet + * @param {string} [examples] The genomic examples. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public validateVariantExampleGetUsingGET(examples?: string, options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .validateVariantExampleGetUsingGET(examples, options) + .then(request => request(this.axios, this.basePath)); + } + + /** + * Check which OncoKB variants can be mapped on genomic examples. + * @summary validateVariantExamplePost + * @param {MatchVariantRequest} body List of queries. Please see swagger.json for request body format. + * @param {*} [options] Override http request option. + * @throws {RequiredError} + * @memberof UtilsApi + */ + public validateVariantExamplePostUsingPOST(body: MatchVariantRequest, options?: RawAxiosRequestConfig) { + return UtilsApiFp(this.configuration) + .validateVariantExamplePostUsingPOST(body, options) + .then(request => request(this.axios, this.basePath)); + } +} + +/** + * @export + */ +export const UtilRelevantCancerTypesPostUsingPOSTLevelOfEvidenceEnum = { + Level1: 'LEVEL_1', + Level2: 'LEVEL_2', + Level3A: 'LEVEL_3A', + Level3B: 'LEVEL_3B', + Level4: 'LEVEL_4', + LevelR1: 'LEVEL_R1', + LevelR2: 'LEVEL_R2', + LevelPx1: 'LEVEL_Px1', + LevelPx2: 'LEVEL_Px2', + LevelPx3: 'LEVEL_Px3', + LevelDx1: 'LEVEL_Dx1', + LevelDx2: 'LEVEL_Dx2', + LevelDx3: 'LEVEL_Dx3', + LevelFda1: 'LEVEL_Fda1', + LevelFda2: 'LEVEL_Fda2', + LevelFda3: 'LEVEL_Fda3', + No: 'NO', +} as const; +export type UtilRelevantCancerTypesPostUsingPOSTLevelOfEvidenceEnum = + (typeof UtilRelevantCancerTypesPostUsingPOSTLevelOfEvidenceEnum)[keyof typeof UtilRelevantCancerTypesPostUsingPOSTLevelOfEvidenceEnum]; diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/base.ts b/src/main/webapp/app/shared/api/generated/defaultCore/base.ts new file mode 100644 index 000000000..e52ae36ee --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/base.ts @@ -0,0 +1,91 @@ +/* tslint:disable */ +/* eslint-disable */ +/** + * OncoKB APIs + * OncoKB, a comprehensive and curated precision oncology knowledge base, offers oncologists detailed, evidence-based information about individual somatic mutations and structural alterations present in patient tumors with the goal of supporting optimal treatment decisions. + * + * The version of the OpenAPI document: v1.5.0 + * Contact: contact@oncokb.org + * + * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech). + * https://openapi-generator.tech + * Do not edit the class manually. + */ + +import type { Configuration } from './configuration'; +// Some imports not used depending on template conditions +// @ts-ignore +import type { AxiosPromise, AxiosInstance, RawAxiosRequestConfig } from 'axios'; +import globalAxios from 'axios'; + +export const BASE_PATH = 'http://localhost:8080/app/api/v1'.replace(/\/+$/, ''); + +/** + * + * @export + */ +export const COLLECTION_FORMATS = { + csv: ',', + ssv: ' ', + tsv: '\t', + pipes: '|', +}; + +/** + * + * @export + * @interface RequestArgs + */ +export interface RequestArgs { + url: string; + options: RawAxiosRequestConfig; +} + +/** + * + * @export + * @class BaseAPI + */ +export class BaseAPI { + protected configuration: Configuration | undefined; + + constructor( + configuration?: Configuration, + protected basePath: string = BASE_PATH, + protected axios: AxiosInstance = globalAxios, + ) { + if (configuration) { + this.configuration = configuration; + this.basePath = configuration.basePath ?? basePath; + } + } +} + +/** + * + * @export + * @class RequiredError + * @extends {Error} + */ +export class RequiredError extends Error { + constructor( + public field: string, + msg?: string, + ) { + super(msg); + this.name = 'RequiredError'; + } +} + +interface ServerMap { + [key: string]: { + url: string; + description: string; + }[]; +} + +/** + * + * @export + */ +export const operationServerMap: ServerMap = {}; diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/common.ts b/src/main/webapp/app/shared/api/generated/defaultCore/common.ts new file mode 100644 index 000000000..262d94391 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/common.ts @@ -0,0 +1,148 @@ +/* tslint:disable */ +/* eslint-disable */ +/** + * OncoKB APIs + * OncoKB, a comprehensive and curated precision oncology knowledge base, offers oncologists detailed, evidence-based information about individual somatic mutations and structural alterations present in patient tumors with the goal of supporting optimal treatment decisions. + * + * The version of the OpenAPI document: v1.5.0 + * Contact: contact@oncokb.org + * + * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech). + * https://openapi-generator.tech + * Do not edit the class manually. + */ + +import type { Configuration } from './configuration'; +import type { RequestArgs } from './base'; +import type { AxiosInstance, AxiosResponse } from 'axios'; +import { RequiredError } from './base'; + +/** + * + * @export + */ +export const DUMMY_BASE_URL = 'https://example.com'; + +/** + * + * @throws {RequiredError} + * @export + */ +export const assertParamExists = function (functionName: string, paramName: string, paramValue: unknown) { + if (paramValue === null || paramValue === undefined) { + throw new RequiredError(paramName, `Required parameter ${paramName} was null or undefined when calling ${functionName}.`); + } +}; + +/** + * + * @export + */ +export const setApiKeyToObject = async function (object: any, keyParamName: string, configuration?: Configuration) { + if (configuration && configuration.apiKey) { + const localVarApiKeyValue = + typeof configuration.apiKey === 'function' ? await configuration.apiKey(keyParamName) : await configuration.apiKey; + object[keyParamName] = localVarApiKeyValue; + } +}; + +/** + * + * @export + */ +export const setBasicAuthToObject = function (object: any, configuration?: Configuration) { + if (configuration && (configuration.username || configuration.password)) { + object['auth'] = { username: configuration.username, password: configuration.password }; + } +}; + +/** + * + * @export + */ +export const setBearerAuthToObject = async function (object: any, configuration?: Configuration) { + if (configuration && configuration.accessToken) { + const accessToken = + typeof configuration.accessToken === 'function' ? await configuration.accessToken() : await configuration.accessToken; + object['Authorization'] = 'Bearer ' + accessToken; + } +}; + +/** + * + * @export + */ +export const setOAuthToObject = async function (object: any, name: string, scopes: string[], configuration?: Configuration) { + if (configuration && configuration.accessToken) { + const localVarAccessTokenValue = + typeof configuration.accessToken === 'function' ? await configuration.accessToken(name, scopes) : await configuration.accessToken; + object['Authorization'] = 'Bearer ' + localVarAccessTokenValue; + } +}; + +function setFlattenedQueryParams(urlSearchParams: URLSearchParams, parameter: any, key: string = ''): void { + if (parameter == null) return; + if (typeof parameter === 'object') { + if (Array.isArray(parameter)) { + (parameter as any[]).forEach(item => setFlattenedQueryParams(urlSearchParams, item, key)); + } else { + Object.keys(parameter).forEach(currentKey => + setFlattenedQueryParams(urlSearchParams, parameter[currentKey], `${key}${key !== '' ? '.' : ''}${currentKey}`), + ); + } + } else { + if (urlSearchParams.has(key)) { + urlSearchParams.append(key, parameter); + } else { + urlSearchParams.set(key, parameter); + } + } +} + +/** + * + * @export + */ +export const setSearchParams = function (url: URL, ...objects: any[]) { + const searchParams = new URLSearchParams(url.search); + setFlattenedQueryParams(searchParams, objects); + url.search = searchParams.toString(); +}; + +/** + * + * @export + */ +export const serializeDataIfNeeded = function (value: any, requestOptions: any, configuration?: Configuration) { + const nonString = typeof value !== 'string'; + const needsSerialization = + nonString && configuration && configuration.isJsonMime ? configuration.isJsonMime(requestOptions.headers['Content-Type']) : nonString; + return needsSerialization ? JSON.stringify(value !== undefined ? value : {}) : value || ''; +}; + +/** + * + * @export + */ +export const toPathString = function (url: URL) { + return url.pathname + url.search + url.hash; +}; + +/** + * + * @export + */ +export const createRequestFunction = function ( + axiosArgs: RequestArgs, + globalAxios: AxiosInstance, + BASE_PATH: string, + configuration?: Configuration, +) { + return >(axios: AxiosInstance = globalAxios, basePath: string = BASE_PATH) => { + const axiosRequestArgs = { + ...axiosArgs.options, + url: (axios.defaults.baseURL ? '' : configuration?.basePath ?? basePath) + axiosArgs.url, + }; + return axios.request(axiosRequestArgs); + }; +}; diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/configuration.ts b/src/main/webapp/app/shared/api/generated/defaultCore/configuration.ts new file mode 100644 index 000000000..9be3ecd7b --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/configuration.ts @@ -0,0 +1,122 @@ +/* tslint:disable */ +/* eslint-disable */ +/** + * OncoKB APIs + * OncoKB, a comprehensive and curated precision oncology knowledge base, offers oncologists detailed, evidence-based information about individual somatic mutations and structural alterations present in patient tumors with the goal of supporting optimal treatment decisions. + * + * The version of the OpenAPI document: v1.5.0 + * Contact: contact@oncokb.org + * + * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech). + * https://openapi-generator.tech + * Do not edit the class manually. + */ + +export interface ConfigurationParameters { + apiKey?: string | Promise | ((name: string) => string) | ((name: string) => Promise); + username?: string; + password?: string; + accessToken?: + | string + | Promise + | ((name?: string, scopes?: string[]) => string) + | ((name?: string, scopes?: string[]) => Promise); + basePath?: string; + serverIndex?: number; + baseOptions?: any; + formDataCtor?: new () => any; +} + +export class Configuration { + /** + * parameter for apiKey security + * @param name security name + * @memberof Configuration + */ + apiKey?: string | Promise | ((name: string) => string) | ((name: string) => Promise); + /** + * parameter for basic security + * + * @type {string} + * @memberof Configuration + */ + username?: string; + /** + * parameter for basic security + * + * @type {string} + * @memberof Configuration + */ + password?: string; + /** + * parameter for oauth2 security + * @param name security name + * @param scopes oauth2 scope + * @memberof Configuration + */ + accessToken?: + | string + | Promise + | ((name?: string, scopes?: string[]) => string) + | ((name?: string, scopes?: string[]) => Promise); + /** + * override base path + * + * @type {string} + * @memberof Configuration + */ + basePath?: string; + /** + * override server index + * + * @type {number} + * @memberof Configuration + */ + serverIndex?: number; + /** + * base options for axios calls + * + * @type {any} + * @memberof Configuration + */ + baseOptions?: any; + /** + * The FormData constructor that will be used to create multipart form data + * requests. You can inject this here so that execution environments that + * do not support the FormData class can still run the generated client. + * + * @type {new () => FormData} + */ + formDataCtor?: new () => any; + + constructor(param: ConfigurationParameters = {}) { + this.apiKey = param.apiKey; + this.username = param.username; + this.password = param.password; + this.accessToken = param.accessToken; + this.basePath = param.basePath; + this.serverIndex = param.serverIndex; + this.baseOptions = { + ...param.baseOptions, + headers: { + ...param.baseOptions?.headers, + }, + }; + this.formDataCtor = param.formDataCtor; + } + + /** + * Check if the given MIME is a JSON MIME. + * JSON MIME examples: + * application/json + * application/json; charset=UTF8 + * APPLICATION/JSON + * application/vnd.company+json + * @param mime - MIME (Multipurpose Internet Mail Extensions) + * @return True if the given MIME is JSON, false otherwise. + */ + public isJsonMime(mime: string): boolean { + const jsonMime: RegExp = new RegExp('^(application/json|[^;/ \t]+/[^;/ \t]+[+]json)[ \t]*(;.*)?$', 'i'); + return mime !== null && (jsonMime.test(mime) || mime.toLowerCase() === 'application/json-patch+json'); + } +} diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/Alteration.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Alteration.md new file mode 100644 index 000000000..a15bb18f9 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Alteration.md @@ -0,0 +1,35 @@ +# Alteration + +## Properties + +| Name | Type | Description | Notes | +| -------------------- | ----------------------------------------------- | ----------- | --------------------------------- | +| **alteration** | **string** | | [optional] [default to undefined] | +| **consequence** | [**VariantConsequence**](VariantConsequence.md) | | [optional] [default to undefined] | +| **gene** | [**Gene**](Gene.md) | | [optional] [default to undefined] | +| **name** | **string** | | [optional] [default to undefined] | +| **proteinEnd** | **number** | | [optional] [default to undefined] | +| **proteinStart** | **number** | | [optional] [default to undefined] | +| **refResidues** | **string** | | [optional] [default to undefined] | +| **referenceGenomes** | **Array<string>** | | [optional] [default to undefined] | +| **variantResidues** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { Alteration } from './api'; + +const instance: Alteration = { + alteration, + consequence, + gene, + name, + proteinEnd, + proteinStart, + refResidues, + referenceGenomes, + variantResidues, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/AnnotateMutationByGenomicChangeQuery.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/AnnotateMutationByGenomicChangeQuery.md new file mode 100644 index 000000000..54bf297c0 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/AnnotateMutationByGenomicChangeQuery.md @@ -0,0 +1,27 @@ +# AnnotateMutationByGenomicChangeQuery + +## Properties + +| Name | Type | Description | Notes | +| ------------------- | ----------------------- | ----------- | --------------------------------- | +| **evidenceTypes** | **Array<string>** | | [optional] [default to undefined] | +| **genomicLocation** | **string** | | [optional] [default to undefined] | +| **id** | **string** | | [optional] [default to undefined] | +| **referenceGenome** | **string** | | [optional] [default to undefined] | +| **tumorType** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { AnnotateMutationByGenomicChangeQuery } from './api'; + +const instance: AnnotateMutationByGenomicChangeQuery = { + evidenceTypes, + genomicLocation, + id, + referenceGenome, + tumorType, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/AnnotateMutationByHGVSgQuery.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/AnnotateMutationByHGVSgQuery.md new file mode 100644 index 000000000..30bed80cb --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/AnnotateMutationByHGVSgQuery.md @@ -0,0 +1,27 @@ +# AnnotateMutationByHGVSgQuery + +## Properties + +| Name | Type | Description | Notes | +| ------------------- | ----------------------- | ----------- | --------------------------------- | +| **evidenceTypes** | **Array<string>** | | [optional] [default to undefined] | +| **hgvsg** | **string** | | [optional] [default to undefined] | +| **id** | **string** | | [optional] [default to undefined] | +| **referenceGenome** | **string** | | [optional] [default to undefined] | +| **tumorType** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { AnnotateMutationByHGVSgQuery } from './api'; + +const instance: AnnotateMutationByHGVSgQuery = { + evidenceTypes, + hgvsg, + id, + referenceGenome, + tumorType, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/AnnotatedVariant.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/AnnotatedVariant.md new file mode 100644 index 000000000..93005b500 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/AnnotatedVariant.md @@ -0,0 +1,45 @@ +# AnnotatedVariant + +## Properties + +| Name | Type | Description | Notes | +| --------------------------- | ---------- | ----------- | --------------------------------- | +| **description** | **string** | | [optional] [default to undefined] | +| **entrezGeneId** | **number** | | [optional] [default to undefined] | +| **gene** | **string** | | [optional] [default to undefined] | +| **grch37Isoform** | **string** | | [optional] [default to undefined] | +| **grch37RefSeq** | **string** | | [optional] [default to undefined] | +| **grch38Isoform** | **string** | | [optional] [default to undefined] | +| **grch38RefSeq** | **string** | | [optional] [default to undefined] | +| **mutationEffect** | **string** | | [optional] [default to undefined] | +| **mutationEffectAbstracts** | **string** | | [optional] [default to undefined] | +| **mutationEffectPmids** | **string** | | [optional] [default to undefined] | +| **oncogenicity** | **string** | | [optional] [default to undefined] | +| **proteinChange** | **string** | | [optional] [default to undefined] | +| **referenceGenome** | **string** | | [optional] [default to undefined] | +| **variant** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { AnnotatedVariant } from './api'; + +const instance: AnnotatedVariant = { + description, + entrezGeneId, + gene, + grch37Isoform, + grch37RefSeq, + grch38Isoform, + grch38RefSeq, + mutationEffect, + mutationEffectAbstracts, + mutationEffectPmids, + oncogenicity, + proteinChange, + referenceGenome, + variant, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/ApiHttpError.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/ApiHttpError.md new file mode 100644 index 000000000..116068b26 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/ApiHttpError.md @@ -0,0 +1,27 @@ +# ApiHttpError + +## Properties + +| Name | Type | Description | Notes | +| ----------- | ---------- | ----------- | --------------------------------- | +| **detail** | **string** | | [optional] [default to undefined] | +| **message** | **string** | | [optional] [default to undefined] | +| **path** | **string** | | [optional] [default to undefined] | +| **status** | **number** | | [optional] [default to undefined] | +| **title** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { ApiHttpError } from './api'; + +const instance: ApiHttpError = { + detail, + message, + path, + status, + title, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/Article.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Article.md new file mode 100644 index 000000000..0e69ebc11 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Article.md @@ -0,0 +1,41 @@ +# Article + +## Properties + +| Name | Type | Description | Notes | +| --------------- | ---------- | ----------- | --------------------------------- | +| **\_abstract** | **string** | | [optional] [default to undefined] | +| **authors** | **string** | | [optional] [default to undefined] | +| **elocationId** | **string** | | [optional] [default to undefined] | +| **issue** | **string** | | [optional] [default to undefined] | +| **journal** | **string** | | [optional] [default to undefined] | +| **link** | **string** | | [optional] [default to undefined] | +| **pages** | **string** | | [optional] [default to undefined] | +| **pmid** | **string** | | [optional] [default to undefined] | +| **pubDate** | **string** | | [optional] [default to undefined] | +| **reference** | **string** | | [optional] [default to undefined] | +| **title** | **string** | | [optional] [default to undefined] | +| **volume** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { Article } from './api'; + +const instance: Article = { + _abstract, + authors, + elocationId, + issue, + journal, + link, + pages, + pmid, + pubDate, + reference, + title, + volume, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/ArticleAbstract.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/ArticleAbstract.md new file mode 100644 index 000000000..ef050c7cc --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/ArticleAbstract.md @@ -0,0 +1,21 @@ +# ArticleAbstract + +## Properties + +| Name | Type | Description | Notes | +| -------------- | ---------- | ----------- | --------------------------------- | +| **\_abstract** | **string** | | [optional] [default to undefined] | +| **link** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { ArticleAbstract } from './api'; + +const instance: ArticleAbstract = { + _abstract, + link, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/BiologicalVariant.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/BiologicalVariant.md new file mode 100644 index 000000000..23d874599 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/BiologicalVariant.md @@ -0,0 +1,33 @@ +# BiologicalVariant + +## Properties + +| Name | Type | Description | Notes | +| ----------------------------- | ------------------------------------------------------ | ----------- | --------------------------------- | +| **mutationEffect** | **string** | | [optional] [default to undefined] | +| **mutationEffectAbstracts** | [**Array<ArticleAbstract>**](ArticleAbstract.md) | | [optional] [default to undefined] | +| **mutationEffectDescription** | **string** | | [optional] [default to undefined] | +| **mutationEffectPmids** | **Array<string>** | | [optional] [default to undefined] | +| **oncogenic** | **string** | | [optional] [default to undefined] | +| **oncogenicAbstracts** | [**Array<ArticleAbstract>**](ArticleAbstract.md) | | [optional] [default to undefined] | +| **oncogenicPmids** | **Array<string>** | | [optional] [default to undefined] | +| **variant** | [**Alteration**](Alteration.md) | | [optional] [default to undefined] | + +## Example + +```typescript +import { BiologicalVariant } from './api'; + +const instance: BiologicalVariant = { + mutationEffect, + mutationEffectAbstracts, + mutationEffectDescription, + mutationEffectPmids, + oncogenic, + oncogenicAbstracts, + oncogenicPmids, + variant, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/CancerTypeCount.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/CancerTypeCount.md new file mode 100644 index 000000000..43bca76c4 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/CancerTypeCount.md @@ -0,0 +1,21 @@ +# CancerTypeCount + +## Properties + +| Name | Type | Description | Notes | +| -------------- | ---------- | ----------- | --------------------------------- | +| **cancerType** | **string** | | [optional] [default to undefined] | +| **count** | **number** | | [optional] [default to undefined] | + +## Example + +```typescript +import { CancerTypeCount } from './api'; + +const instance: CancerTypeCount = { + cancerType, + count, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/Citations.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Citations.md new file mode 100644 index 000000000..75c30aa7c --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Citations.md @@ -0,0 +1,21 @@ +# Citations + +## Properties + +| Name | Type | Description | Notes | +| ------------- | ------------------------------------------------------ | ------------------------- | --------------------------------- | +| **abstracts** | [**Array<ArticleAbstract>**](ArticleAbstract.md) | Set of Abstract sources | [optional] [default to undefined] | +| **pmids** | **Array<string>** | Set of PubMed article ids | [optional] [default to undefined] | + +## Example + +```typescript +import { Citations } from './api'; + +const instance: Citations = { + abstracts, + pmids, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/ClinicalVariant.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/ClinicalVariant.md new file mode 100644 index 000000000..85d53835b --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/ClinicalVariant.md @@ -0,0 +1,41 @@ +# ClinicalVariant + +## Properties + +| Name | Type | Description | Notes | +| -------------------------- | ------------------------------------------------------ | ----------- | --------------------------------- | +| **cancerTypes** | [**Array<TumorType>**](TumorType.md) | | [optional] [default to undefined] | +| **drug** | **Array<string>** | | [optional] [default to undefined] | +| **drugAbstracts** | [**Array<ArticleAbstract>**](ArticleAbstract.md) | | [optional] [default to undefined] | +| **drugDescription** | **string** | | [optional] [default to undefined] | +| **drugPmids** | **Array<string>** | | [optional] [default to undefined] | +| **excludedCancerTypes** | [**Array<TumorType>**](TumorType.md) | | [optional] [default to undefined] | +| **fdaLevel** | **string** | | [optional] [default to undefined] | +| **level** | **string** | | [optional] [default to undefined] | +| **liquidPropagationLevel** | **string** | | [optional] [default to undefined] | +| **oncogenic** | **string** | | [optional] [default to undefined] | +| **solidPropagationLevel** | **string** | | [optional] [default to undefined] | +| **variant** | [**Alteration**](Alteration.md) | | [optional] [default to undefined] | + +## Example + +```typescript +import { ClinicalVariant } from './api'; + +const instance: ClinicalVariant = { + cancerTypes, + drug, + drugAbstracts, + drugDescription, + drugPmids, + excludedCancerTypes, + fdaLevel, + level, + liquidPropagationLevel, + oncogenic, + solidPropagationLevel, + variant, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/CplAnnotationRequest.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/CplAnnotationRequest.md new file mode 100644 index 000000000..411fe426d --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/CplAnnotationRequest.md @@ -0,0 +1,27 @@ +# CplAnnotationRequest + +## Properties + +| Name | Type | Description | Notes | +| ------------------- | ---------- | ----------- | --------------------------------- | +| **alteration** | **string** | | [optional] [default to undefined] | +| **cancerType** | **string** | | [optional] [default to undefined] | +| **hugoSymbol** | **string** | | [optional] [default to undefined] | +| **referenceGenome** | **string** | | [optional] [default to undefined] | +| **template** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { CplAnnotationRequest } from './api'; + +const instance: CplAnnotationRequest = { + alteration, + cancerType, + hugoSymbol, + referenceGenome, + template, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/DownloadAvailability.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/DownloadAvailability.md new file mode 100644 index 000000000..15685e1d9 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/DownloadAvailability.md @@ -0,0 +1,31 @@ +# DownloadAvailability + +## Properties + +| Name | Type | Description | Notes | +| ---------------------------- | ----------- | ----------- | --------------------------------- | +| **hasAllActionableVariants** | **boolean** | | [optional] [default to undefined] | +| **hasAllAnnotatedVariants** | **boolean** | | [optional] [default to undefined] | +| **hasAllCuratedGenes** | **boolean** | | [optional] [default to undefined] | +| **hasCancerGeneList** | **boolean** | | [optional] [default to undefined] | +| **hasReadme** | **boolean** | | [optional] [default to undefined] | +| **hasSqlDump** | **boolean** | | [optional] [default to undefined] | +| **version** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { DownloadAvailability } from './api'; + +const instance: DownloadAvailability = { + hasAllActionableVariants, + hasAllAnnotatedVariants, + hasAllCuratedGenes, + hasCancerGeneList, + hasReadme, + hasSqlDump, + version, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/Drug.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Drug.md new file mode 100644 index 000000000..6e9b8ab85 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Drug.md @@ -0,0 +1,21 @@ +# Drug + +## Properties + +| Name | Type | Description | Notes | +| ------------ | ---------- | ----------- | --------------------------------- | +| **drugName** | **string** | | [optional] [default to undefined] | +| **ncitCode** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { Drug } from './api'; + +const instance: Drug = { + drugName, + ncitCode, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/DrugSynonym.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/DrugSynonym.md new file mode 100644 index 000000000..c036b8326 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/DrugSynonym.md @@ -0,0 +1,23 @@ +# DrugSynonym + +## Properties + +| Name | Type | Description | Notes | +| -------- | ------------------- | ----------- | --------------------------------- | +| **drug** | [**Drug**](Drug.md) | | [optional] [default to undefined] | +| **id** | **number** | | [optional] [default to undefined] | +| **name** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { DrugSynonym } from './api'; + +const instance: DrugSynonym = { + drug, + id, + name, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/DrugsApi.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/DrugsApi.md new file mode 100644 index 000000000..9b3040464 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/DrugsApi.md @@ -0,0 +1,58 @@ +# DrugsApi + +All URIs are relative to _http://localhost:8080/app/api/v1_ + +| Method | HTTP request | Description | +| --------------------------------------------------- | ------------------------- | ------------- | +| [**searchDrugGetUsingGET**](#searchdruggetusingget) | **GET** /search/ncitDrugs | searchDrugGet | + +# **searchDrugGetUsingGET** + +> Array searchDrugGetUsingGET() + +Find NCIT matches based on blur query. This is not for search OncoKB curated drugs. Please use drugs/lookup for that purpose. + +### Example + +```typescript +import { DrugsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new DrugsApi(configuration); + +let query: string; //The search query, it could be drug name, NCIT code (default to undefined) +let limit: number; //The limit of returned result. (optional) (default to 5) + +const { status, data } = await apiInstance.searchDrugGetUsingGET(query, limit); +``` + +### Parameters + +| Name | Type | Description | Notes | +| --------- | ------------ | -------------------------------------------------- | ------------------------ | +| **query** | [**string**] | The search query, it could be drug name, NCIT code | defaults to undefined | +| **limit** | [**number**] | The limit of returned result. | (optional) defaults to 5 | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/EnsemblGene.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/EnsemblGene.md new file mode 100644 index 000000000..c3abbf14c --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/EnsemblGene.md @@ -0,0 +1,31 @@ +# EnsemblGene + +## Properties + +| Name | Type | Description | Notes | +| ------------------- | ----------- | ----------- | --------------------------------- | +| **canonical** | **boolean** | | [optional] [default to undefined] | +| **chromosome** | **string** | | [optional] [default to undefined] | +| **end** | **number** | | [optional] [default to undefined] | +| **ensemblGeneId** | **string** | | [optional] [default to undefined] | +| **referenceGenome** | **string** | | [optional] [default to undefined] | +| **start** | **number** | | [optional] [default to undefined] | +| **strand** | **number** | | [optional] [default to undefined] | + +## Example + +```typescript +import { EnsemblGene } from './api'; + +const instance: EnsemblGene = { + canonical, + chromosome, + end, + ensemblGeneId, + referenceGenome, + start, + strand, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/EnsemblTranscript.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/EnsemblTranscript.md new file mode 100644 index 000000000..7e294b96c --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/EnsemblTranscript.md @@ -0,0 +1,39 @@ +# EnsemblTranscript + +## Properties + +| Name | Type | Description | Notes | +| ----------------- | ------------------------------------------------------------ | ----------------------- | --------------------------------- | +| **ccdsId** | **string** | Consensus CDS (CCDS) ID | [optional] [default to undefined] | +| **exons** | [**Array<Exon>**](Exon.md) | Exon information | [optional] [default to undefined] | +| **geneId** | **string** | Ensembl gene id | [default to undefined] | +| **hugoSymbols** | **Array<string>** | Hugo symbols | [optional] [default to undefined] | +| **pfamDomains** | [**Array<PfamDomainRange>**](PfamDomainRange.md) | Pfam domains | [optional] [default to undefined] | +| **proteinId** | **string** | Ensembl protein id | [default to undefined] | +| **proteinLength** | **number** | Length of protein | [optional] [default to undefined] | +| **refseqMrnaId** | **string** | RefSeq mRNA ID | [optional] [default to undefined] | +| **transcriptId** | **string** | Ensembl transcript id | [default to undefined] | +| **uniprotId** | **string** | | [optional] [default to undefined] | +| **utrs** | [**Array<UntranslatedRegion>**](UntranslatedRegion.md) | UTR information | [optional] [default to undefined] | + +## Example + +```typescript +import { EnsemblTranscript } from './api'; + +const instance: EnsemblTranscript = { + ccdsId, + exons, + geneId, + hugoSymbols, + pfamDomains, + proteinId, + proteinLength, + refseqMrnaId, + transcriptId, + uniprotId, + utrs, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/Evidence.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Evidence.md new file mode 100644 index 000000000..6be3a64de --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Evidence.md @@ -0,0 +1,55 @@ +# Evidence + +## Properties + +| Name | Type | Description | Notes | +| -------------------------- | -------------------------------------------- | ----------- | --------------------------------- | +| **additionalInfo** | **string** | | [optional] [default to undefined] | +| **alterations** | [**Array<Alteration>**](Alteration.md) | | [optional] [default to undefined] | +| **articles** | [**Array<Article>**](Article.md) | | [optional] [default to undefined] | +| **cancerTypes** | [**Array<TumorType>**](TumorType.md) | | [optional] [default to undefined] | +| **description** | **string** | | [optional] [default to undefined] | +| **evidenceType** | **string** | | [optional] [default to undefined] | +| **excludedCancerTypes** | [**Array<TumorType>**](TumorType.md) | | [optional] [default to undefined] | +| **fdaLevel** | **string** | | [optional] [default to undefined] | +| **gene** | [**Gene**](Gene.md) | | [optional] [default to undefined] | +| **id** | **number** | | [optional] [default to undefined] | +| **knownEffect** | **string** | | [optional] [default to undefined] | +| **lastEdit** | **string** | | [optional] [default to undefined] | +| **lastReview** | **string** | | [optional] [default to undefined] | +| **levelOfEvidence** | **string** | | [optional] [default to undefined] | +| **liquidPropagationLevel** | **string** | | [optional] [default to undefined] | +| **relevantCancerTypes** | [**Array<TumorType>**](TumorType.md) | | [optional] [default to undefined] | +| **solidPropagationLevel** | **string** | | [optional] [default to undefined] | +| **treatments** | [**Array<Treatment>**](Treatment.md) | | [optional] [default to undefined] | +| **uuid** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { Evidence } from './api'; + +const instance: Evidence = { + additionalInfo, + alterations, + articles, + cancerTypes, + description, + evidenceType, + excludedCancerTypes, + fdaLevel, + gene, + id, + knownEffect, + lastEdit, + lastReview, + levelOfEvidence, + liquidPropagationLevel, + relevantCancerTypes, + solidPropagationLevel, + treatments, + uuid, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/Exon.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Exon.md new file mode 100644 index 000000000..b186b216c --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Exon.md @@ -0,0 +1,29 @@ +# Exon + +## Properties + +| Name | Type | Description | Notes | +| ------------- | ---------- | --------------------------------------- | ---------------------- | +| **exonEnd** | **number** | End position of exon | [default to undefined] | +| **exonId** | **string** | Exon id | [default to undefined] | +| **exonStart** | **number** | Start position of exon | [default to undefined] | +| **rank** | **number** | Number of exon in transcript | [default to undefined] | +| **strand** | **number** | Strand exon is on, -1 for - and 1 for + | [default to undefined] | +| **version** | **number** | Exon version | [default to undefined] | + +## Example + +```typescript +import { Exon } from './api'; + +const instance: Exon = { + exonEnd, + exonId, + exonStart, + rank, + strand, + version, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/Gene.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Gene.md new file mode 100644 index 000000000..d8f2ee06a --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Gene.md @@ -0,0 +1,37 @@ +# Gene + +## Properties + +| Name | Type | Description | Notes | +| ----------------- | -------------------------------------- | ----------- | --------------------------------- | +| **entrezGeneId** | **number** | | [optional] [default to undefined] | +| **geneAliases** | **Array<string>** | | [optional] [default to undefined] | +| **genesets** | [**Array<Geneset>**](Geneset.md) | | [optional] [default to undefined] | +| **grch37Isoform** | **string** | | [optional] [default to undefined] | +| **grch37RefSeq** | **string** | | [optional] [default to undefined] | +| **grch38Isoform** | **string** | | [optional] [default to undefined] | +| **grch38RefSeq** | **string** | | [optional] [default to undefined] | +| **hugoSymbol** | **string** | | [optional] [default to undefined] | +| **oncogene** | **boolean** | | [optional] [default to undefined] | +| **tsg** | **boolean** | | [optional] [default to undefined] | + +## Example + +```typescript +import { Gene } from './api'; + +const instance: Gene = { + entrezGeneId, + geneAliases, + genesets, + grch37Isoform, + grch37RefSeq, + grch38Isoform, + grch38RefSeq, + hugoSymbol, + oncogene, + tsg, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/GeneNumber.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/GeneNumber.md new file mode 100644 index 000000000..97a2f766b --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/GeneNumber.md @@ -0,0 +1,33 @@ +# GeneNumber + +## Properties + +| Name | Type | Description | Notes | +| ------------------------------------- | ------------------- | ----------- | --------------------------------- | +| **alteration** | **number** | | [optional] [default to undefined] | +| **gene** | [**Gene**](Gene.md) | | [optional] [default to undefined] | +| **highestDiagnosticImplicationLevel** | **string** | | [optional] [default to undefined] | +| **highestFdaLevel** | **string** | | [optional] [default to undefined] | +| **highestPrognosticImplicationLevel** | **string** | | [optional] [default to undefined] | +| **highestResistanceLevel** | **string** | | [optional] [default to undefined] | +| **highestSensitiveLevel** | **string** | | [optional] [default to undefined] | +| **tumorType** | **number** | | [optional] [default to undefined] | + +## Example + +```typescript +import { GeneNumber } from './api'; + +const instance: GeneNumber = { + alteration, + gene, + highestDiagnosticImplicationLevel, + highestFdaLevel, + highestPrognosticImplicationLevel, + highestResistanceLevel, + highestSensitiveLevel, + tumorType, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/Geneset.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Geneset.md new file mode 100644 index 000000000..41957a4fb --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Geneset.md @@ -0,0 +1,25 @@ +# Geneset + +## Properties + +| Name | Type | Description | Notes | +| --------- | -------------------------------- | ----------- | --------------------------------- | +| **genes** | [**Array<Gene>**](Gene.md) | | [optional] [default to undefined] | +| **id** | **number** | | [optional] [default to undefined] | +| **name** | **string** | | [optional] [default to undefined] | +| **uuid** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { Geneset } from './api'; + +const instance: Geneset = { + genes, + id, + name, + uuid, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/GenomeNexusAnnotatedVariantInfo.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/GenomeNexusAnnotatedVariantInfo.md new file mode 100644 index 000000000..49f25277d --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/GenomeNexusAnnotatedVariantInfo.md @@ -0,0 +1,37 @@ +# GenomeNexusAnnotatedVariantInfo + +## Properties + +| Name | Type | Description | Notes | +| ------------------------ | ---------- | ----------- | --------------------------------- | +| **consequenceTerms** | **string** | | [optional] [default to undefined] | +| **entrezGeneId** | **number** | | [optional] [default to undefined] | +| **genomicLocation** | **string** | | [optional] [default to undefined] | +| **hgvsg** | **string** | | [optional] [default to undefined] | +| **hgvspShort** | **string** | | [optional] [default to undefined] | +| **hugoSymbol** | **string** | | [optional] [default to undefined] | +| **originalVariantQuery** | **string** | | [optional] [default to undefined] | +| **proteinEnd** | **number** | | [optional] [default to undefined] | +| **proteinStart** | **number** | | [optional] [default to undefined] | +| **referenceGenome** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { GenomeNexusAnnotatedVariantInfo } from './api'; + +const instance: GenomeNexusAnnotatedVariantInfo = { + consequenceTerms, + entrezGeneId, + genomicLocation, + hgvsg, + hgvspShort, + hugoSymbol, + originalVariantQuery, + proteinEnd, + proteinStart, + referenceGenome, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/Implication.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Implication.md new file mode 100644 index 000000000..99027c22a --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Implication.md @@ -0,0 +1,29 @@ +# Implication + +## Properties + +| Name | Type | Description | Notes | +| ------------------- | ------------------------------------------------------ | ---------------------------------------------------------------------------------- | --------------------------------- | +| **abstracts** | [**Array<ArticleAbstract>**](ArticleAbstract.md) | List of abstracts cited to support the level of evidence. Defaulted to empty list | [optional] [default to undefined] | +| **alterations** | **Array<string>** | List of alterations associated with implication | [optional] [default to undefined] | +| **description** | **string** | DEPRECATED | [optional] [default to undefined] | +| **levelOfEvidence** | **string** | Level associated with implication | [optional] [default to undefined] | +| **pmids** | **Array<string>** | List of PubMed IDs cited to support the level of evidence. Defaulted to empty list | [optional] [default to undefined] | +| **tumorType** | [**TumorType**](TumorType.md) | | [optional] [default to undefined] | + +## Example + +```typescript +import { Implication } from './api'; + +const instance: Implication = { + abstracts, + alterations, + description, + levelOfEvidence, + pmids, + tumorType, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/IndicatorQueryTreatment.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/IndicatorQueryTreatment.md new file mode 100644 index 000000000..ab8e551d5 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/IndicatorQueryTreatment.md @@ -0,0 +1,37 @@ +# IndicatorQueryTreatment + +## Properties + +| Name | Type | Description | Notes | +| ----------------------------- | ------------------------------------------------------ | ------------------------------------------------------------------------------ | --------------------------------- | +| **abstracts** | [**Array<ArticleAbstract>**](ArticleAbstract.md) | List of abstracts cited in the treatment description. Defaulted to empty list | [optional] [default to undefined] | +| **alterations** | **Array<string>** | List of alterations associated with therapeutic implication | [optional] [default to undefined] | +| **approvedIndications** | **Array<string>** | DEPRECATED | [optional] [default to undefined] | +| **description** | **string** | Treatment description. Defaulted to \"\" | [optional] [default to undefined] | +| **drugs** | [**Array<Drug>**](Drug.md) | List of drugs associated with therapeutic implication | [optional] [default to undefined] | +| **fdaLevel** | **string** | FDA level associated with implication | [optional] [default to undefined] | +| **level** | **string** | Therapeutic level associated with implication | [optional] [default to undefined] | +| **levelAssociatedCancerType** | [**TumorType**](TumorType.md) | | [optional] [default to undefined] | +| **levelExcludedCancerTypes** | [**Array<TumorType>**](TumorType.md) | Excluded cancer types. Defaulted to empty list | [optional] [default to undefined] | +| **pmids** | **Array<string>** | List of PubMed IDs cited in the treatment description. Defaulted to empty list | [optional] [default to undefined] | + +## Example + +```typescript +import { IndicatorQueryTreatment } from './api'; + +const instance: IndicatorQueryTreatment = { + abstracts, + alterations, + approvedIndications, + description, + drugs, + fdaLevel, + level, + levelAssociatedCancerType, + levelExcludedCancerTypes, + pmids, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/LevelNumber.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/LevelNumber.md new file mode 100644 index 000000000..b7541ce08 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/LevelNumber.md @@ -0,0 +1,21 @@ +# LevelNumber + +## Properties + +| Name | Type | Description | Notes | +| --------- | -------------------------------- | ----------- | --------------------------------- | +| **genes** | [**Array<Gene>**](Gene.md) | | [optional] [default to undefined] | +| **level** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { LevelNumber } from './api'; + +const instance: LevelNumber = { + genes, + level, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/MainNumber.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/MainNumber.md new file mode 100644 index 000000000..6b6137089 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/MainNumber.md @@ -0,0 +1,27 @@ +# MainNumber + +## Properties + +| Name | Type | Description | Notes | +| -------------- | ------------------------------------------------------ | ----------- | --------------------------------- | +| **alteration** | **number** | | [optional] [default to undefined] | +| **drug** | **number** | | [optional] [default to undefined] | +| **gene** | **number** | | [optional] [default to undefined] | +| **level** | [**Array<MainNumberLevel>**](MainNumberLevel.md) | | [optional] [default to undefined] | +| **tumorType** | **number** | | [optional] [default to undefined] | + +## Example + +```typescript +import { MainNumber } from './api'; + +const instance: MainNumber = { + alteration, + drug, + gene, + level, + tumorType, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/MainNumberLevel.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/MainNumberLevel.md new file mode 100644 index 000000000..a02a52ba3 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/MainNumberLevel.md @@ -0,0 +1,21 @@ +# MainNumberLevel + +## Properties + +| Name | Type | Description | Notes | +| ---------- | ---------- | ----------- | --------------------------------- | +| **level** | **string** | | [optional] [default to undefined] | +| **number** | **number** | | [optional] [default to undefined] | + +## Example + +```typescript +import { MainNumberLevel } from './api'; + +const instance: MainNumberLevel = { + level, + number, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/MainType.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/MainType.md new file mode 100644 index 000000000..781764985 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/MainType.md @@ -0,0 +1,25 @@ +# MainType + +OncoTree Cancer Type + +## Properties + +| Name | Type | Description | Notes | +| ------------- | ---------- | ----------- | --------------------------------- | +| **id** | **number** | | [optional] [default to undefined] | +| **name** | **string** | | [optional] [default to undefined] | +| **tumorForm** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { MainType } from './api'; + +const instance: MainType = { + id, + name, + tumorForm, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/MatchVariant.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/MatchVariant.md new file mode 100644 index 000000000..eacd9b8ba --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/MatchVariant.md @@ -0,0 +1,21 @@ +# MatchVariant + +## Properties + +| Name | Type | Description | Notes | +| -------------- | ---------- | ----------- | --------------------------------- | +| **alteration** | **string** | | [optional] [default to undefined] | +| **hugoSymbol** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { MatchVariant } from './api'; + +const instance: MatchVariant = { + alteration, + hugoSymbol, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/MatchVariantRequest.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/MatchVariantRequest.md new file mode 100644 index 000000000..64a4af422 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/MatchVariantRequest.md @@ -0,0 +1,21 @@ +# MatchVariantRequest + +## Properties + +| Name | Type | Description | Notes | +| ------------------ | ------------------------------------------------ | ----------- | --------------------------------- | +| **oncokbVariants** | [**Array<MatchVariant>**](MatchVariant.md) | | [optional] [default to undefined] | +| **queries** | [**Array<Query>**](Query.md) | | [optional] [default to undefined] | + +## Example + +```typescript +import { MatchVariantRequest } from './api'; + +const instance: MatchVariantRequest = { + oncokbVariants, + queries, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/MatchVariantResult.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/MatchVariantResult.md new file mode 100644 index 000000000..e0f4bc0c3 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/MatchVariantResult.md @@ -0,0 +1,21 @@ +# MatchVariantResult + +## Properties + +| Name | Type | Description | Notes | +| ---------- | ------------------------------------------------ | ----------- | --------------------------------- | +| **query** | [**Query**](Query.md) | | [optional] [default to undefined] | +| **result** | [**Array<MatchVariant>**](MatchVariant.md) | | [optional] [default to undefined] | + +## Example + +```typescript +import { MatchVariantResult } from './api'; + +const instance: MatchVariantResult = { + query, + result, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/MutationEffectResp.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/MutationEffectResp.md new file mode 100644 index 000000000..a42cc797e --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/MutationEffectResp.md @@ -0,0 +1,23 @@ +# MutationEffectResp + +## Properties + +| Name | Type | Description | Notes | +| --------------- | ----------------------------- | --------------------------------------------------------------------------------------------------- | --------------------------------- | +| **citations** | [**Citations**](Citations.md) | | [optional] [default to undefined] | +| **description** | **string** | A brief overview of the biological and oncogenic effect of the variant. Defaulted to \"\" | [optional] [default to undefined] | +| **knownEffect** | **string** | Indicates the effect of the mutation on the gene. Defaulted to \"\" | [optional] [default to undefined] | + +## Example + +```typescript +import { MutationEffectResp } from './api'; + +const instance: MutationEffectResp = { + citations, + description, + knownEffect, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/PfamDomainRange.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/PfamDomainRange.md new file mode 100644 index 000000000..40179b650 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/PfamDomainRange.md @@ -0,0 +1,23 @@ +# PfamDomainRange + +## Properties + +| Name | Type | Description | Notes | +| ------------------- | ---------- | ---------------------------- | ---------------------- | +| **pfamDomainEnd** | **number** | Pfam domain end amino acid | [default to undefined] | +| **pfamDomainId** | **string** | Pfam domain id | [default to undefined] | +| **pfamDomainStart** | **number** | Pfam domain start amino acid | [default to undefined] | + +## Example + +```typescript +import { PfamDomainRange } from './api'; + +const instance: PfamDomainRange = { + pfamDomainEnd, + pfamDomainId, + pfamDomainStart, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/PortalAlteration.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/PortalAlteration.md new file mode 100644 index 000000000..0d6e1fc72 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/PortalAlteration.md @@ -0,0 +1,33 @@ +# PortalAlteration + +## Properties + +| Name | Type | Description | Notes | +| ------------------------ | ------------------- | ----------- | --------------------------------- | +| **alterationType** | **string** | | [optional] [default to undefined] | +| **cancerStudy** | **string** | | [optional] [default to undefined] | +| **cancerType** | **string** | | [optional] [default to undefined] | +| **gene** | [**Gene**](Gene.md) | | [optional] [default to undefined] | +| **proteinChange** | **string** | | [optional] [default to undefined] | +| **proteinEndPosition** | **number** | | [optional] [default to undefined] | +| **proteinStartPosition** | **number** | | [optional] [default to undefined] | +| **sampleId** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { PortalAlteration } from './api'; + +const instance: PortalAlteration = { + alterationType, + cancerStudy, + cancerType, + gene, + proteinChange, + proteinEndPosition, + proteinStartPosition, + sampleId, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/Query.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Query.md new file mode 100644 index 000000000..ef47b93da --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Query.md @@ -0,0 +1,47 @@ +# Query + +Enriched user annotation query + +## Properties + +| Name | Type | Description | Notes | +| ----------------------- | ---------- | ------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------- | +| **alteration** | **string** | (Nullable) Alteration from original query or the resolved alteration from HGVS variant | [optional] [default to undefined] | +| **alterationType** | **string** | (Nullable) Alteration type | [optional] [default to undefined] | +| **canonicalTranscript** | **string** | (Nullable) The OncoKB canonical transcript. See https://www.oncokb.org/cancer-genes | [optional] [default to undefined] | +| **consequence** | **string** | (Nullable) Variant consequence term from Ensembl. See https://useast.ensembl.org/info/genome/variation/prediction/predicted_data.html | [optional] [default to undefined] | +| **entrezGeneId** | **number** | (Nullable) Unique gene identifiers from NCBI. May be null if omitted from original query, otherwise filled in by OncoKB | [optional] [default to undefined] | +| **hgvs** | **string** | (Nullable) The hgvsg or genomic location from original query | [optional] [default to undefined] | +| **hgvsInfo** | **string** | (Nullable) Additional message for \"hgvs\" field. May indicate reason for failed hgvs annotation. | [optional] [default to undefined] | +| **hugoSymbol** | **string** | (Nullable) The gene symbol used in Human Genome Organisation | [optional] [default to undefined] | +| **id** | **string** | (Nullable) The id passed in request for the user to distinguish the query. | [optional] [default to undefined] | +| **proteinEnd** | **number** | (Nullable) Protein end position | [optional] [default to undefined] | +| **proteinStart** | **number** | (Nullable) Protein start position | [optional] [default to undefined] | +| **referenceGenome** | **string** | Reference genome build version. Defaulted to GRCh37 | [optional] [default to undefined] | +| **svType** | **string** | (Nullable) Structural variant type | [optional] [default to undefined] | +| **tumorType** | **string** | (Nullable) Oncotree tumor type name, code, or main type. | [optional] [default to undefined] | + +## Example + +```typescript +import { Query } from './api'; + +const instance: Query = { + alteration, + alterationType, + canonicalTranscript, + consequence, + entrezGeneId, + hgvs, + hgvsInfo, + hugoSymbol, + id, + proteinEnd, + proteinStart, + referenceGenome, + svType, + tumorType, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/RelevantCancerTypeQuery.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/RelevantCancerTypeQuery.md new file mode 100644 index 000000000..69cc50c5d --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/RelevantCancerTypeQuery.md @@ -0,0 +1,21 @@ +# RelevantCancerTypeQuery + +## Properties + +| Name | Type | Description | Notes | +| ------------ | ---------- | ----------- | --------------------------------- | +| **code** | **string** | | [optional] [default to undefined] | +| **mainType** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { RelevantCancerTypeQuery } from './api'; + +const instance: RelevantCancerTypeQuery = { + code, + mainType, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/SearchApi.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/SearchApi.md new file mode 100644 index 000000000..8d8279aae --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/SearchApi.md @@ -0,0 +1,262 @@ +# SearchApi + +All URIs are relative to _http://localhost:8080/app/api/v1_ + +| Method | HTTP request | Description | +| ------------------------------------------------------------------------------- | ----------------------------------- | --------------------------- | +| [**searchDrugGetUsingGET**](#searchdruggetusingget) | **GET** /search/ncitDrugs | searchDrugGet | +| [**searchTreatmentsGetUsingGET**](#searchtreatmentsgetusingget) | **GET** /search/treatments | searchTreatmentsGet | +| [**searchTypeAheadGetUsingGET**](#searchtypeaheadgetusingget) | **GET** /search/typeahead | searchTypeAheadGet | +| [**searchVariantsBiologicalGetUsingGET**](#searchvariantsbiologicalgetusingget) | **GET** /search/variants/biological | searchVariantsBiologicalGet | +| [**searchVariantsClinicalGetUsingGET**](#searchvariantsclinicalgetusingget) | **GET** /search/variants/clinical | searchVariantsClinicalGet | + +# **searchDrugGetUsingGET** + +> Array searchDrugGetUsingGET() + +Find NCIT matches based on blur query. This is not for search OncoKB curated drugs. Please use drugs/lookup for that purpose. + +### Example + +```typescript +import { SearchApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new SearchApi(configuration); + +let query: string; //The search query, it could be drug name, NCIT code (default to undefined) +let limit: number; //The limit of returned result. (optional) (default to 5) + +const { status, data } = await apiInstance.searchDrugGetUsingGET(query, limit); +``` + +### Parameters + +| Name | Type | Description | Notes | +| --------- | ------------ | -------------------------------------------------- | ------------------------ | +| **query** | [**string**] | The search query, it could be drug name, NCIT code | defaults to undefined | +| **limit** | [**number**] | The limit of returned result. | (optional) defaults to 5 | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **searchTreatmentsGetUsingGET** + +> Array searchTreatmentsGetUsingGET() + +Search to find treatments. + +### Example + +```typescript +import { SearchApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new SearchApi(configuration); + +let gene: string; //The search query, it could be hugoSymbol or entrezGeneId. (default to undefined) +let level: string; //The level of evidence. (optional) (default to 'false') + +const { status, data } = await apiInstance.searchTreatmentsGetUsingGET(gene, level); +``` + +### Parameters + +| Name | Type | Description | Notes | +| --------- | ------------ | --------------------------------------------------------- | ------------------------------ | +| **gene** | [**string**] | The search query, it could be hugoSymbol or entrezGeneId. | defaults to undefined | +| **level** | [**string**] | The level of evidence. | (optional) defaults to 'false' | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **searchTypeAheadGetUsingGET** + +> Array searchTypeAheadGetUsingGET() + +Find matches based on blur query. + +### Example + +```typescript +import { SearchApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new SearchApi(configuration); + +let query: string; //The search query, it could be hugoSymbol, entrezGeneId, variant, or cancer type. At least two characters. Maximum two keywords are supported, separated by space (default to undefined) +let limit: number; //The limit of returned result. (optional) (default to 5) + +const { status, data } = await apiInstance.searchTypeAheadGetUsingGET(query, limit); +``` + +### Parameters + +| Name | Type | Description | Notes | +| --------- | ------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------ | +| **query** | [**string**] | The search query, it could be hugoSymbol, entrezGeneId, variant, or cancer type. At least two characters. Maximum two keywords are supported, separated by space | defaults to undefined | +| **limit** | [**number**] | The limit of returned result. | (optional) defaults to 5 | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **searchVariantsBiologicalGetUsingGET** + +> Array searchVariantsBiologicalGetUsingGET() + +Get annotated variants information for specified gene. + +### Example + +```typescript +import { SearchApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new SearchApi(configuration); + +let hugoSymbol: string; //hugoSymbol (optional) (default to undefined) + +const { status, data } = await apiInstance.searchVariantsBiologicalGetUsingGET(hugoSymbol); +``` + +### Parameters + +| Name | Type | Description | Notes | +| -------------- | ------------ | ----------- | -------------------------------- | +| **hugoSymbol** | [**string**] | hugoSymbol | (optional) defaults to undefined | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **searchVariantsClinicalGetUsingGET** + +> Array searchVariantsClinicalGetUsingGET() + +Get list of variant clinical information for specified gene. + +### Example + +```typescript +import { SearchApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new SearchApi(configuration); + +let hugoSymbol: string; //hugoSymbol (optional) (default to undefined) + +const { status, data } = await apiInstance.searchVariantsClinicalGetUsingGET(hugoSymbol); +``` + +### Parameters + +| Name | Type | Description | Notes | +| -------------- | ------------ | ----------- | -------------------------------- | +| **hugoSymbol** | [**string**] | hugoSymbol | (optional) defaults to undefined | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/TranscriptApi.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/TranscriptApi.md new file mode 100644 index 000000000..003ea961a --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/TranscriptApi.md @@ -0,0 +1,212 @@ +# TranscriptApi + +All URIs are relative to _http://localhost:8080/app/api/v1_ + +| Method | HTTP request | Description | +| ----------------------------------------------------------------------------------------------------------------------- | ----------------------------------------- | ---------------------------------------------- | +| [**cacheGenomeNexusVariantInfoPostUsingPOST**](#cachegenomenexusvariantinfopostusingpost) | **POST** /cacheGnVariantInfo | cacheGenomeNexusVariantInfoPost | +| [**fetchGenomeNexusVariantInfoByGenomicChangePostUsingPOST**](#fetchgenomenexusvariantinfobygenomicchangepostusingpost) | **POST** /fetchGnVariants/byGenomicChange | fetchGenomeNexusVariantInfoByGenomicChangePost | +| [**fetchGenomeNexusVariantInfoByHGVSgPostUsingPOST**](#fetchgenomenexusvariantinfobyhgvsgpostusingpost) | **POST** /fetchGnVariants/byHGVSg | fetchGenomeNexusVariantInfoByHGVSgPost | +| [**getTranscriptUsingGET**](#gettranscriptusingget) | **GET** /transcripts/{hugoSymbol} | getTranscript | + +# **cacheGenomeNexusVariantInfoPostUsingPOST** + +> cacheGenomeNexusVariantInfoPostUsingPOST(body) + +cache Genome Nexus variant info + +### Example + +```typescript +import { TranscriptApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new TranscriptApi(configuration); + +let body: Array; //List of queries. Please see swagger.json for request body format. + +const { status, data } = await apiInstance.cacheGenomeNexusVariantInfoPostUsingPOST(body); +``` + +### Parameters + +| Name | Type | Description | Notes | +| -------- | ------------------------------------------ | ----------------------------------------------------------------- | ----- | +| **body** | **Array** | List of queries. Please see swagger.json for request body format. | | + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: application/json +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ----------------------------------- | ---------------- | +| **200** | OK | - | +| **201** | Created | - | +| **400** | Error, error message will be given. | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **fetchGenomeNexusVariantInfoByGenomicChangePostUsingPOST** + +> Array fetchGenomeNexusVariantInfoByGenomicChangePostUsingPOST(body) + +Fetch Genome Nexus variant info by genomic change + +### Example + +```typescript +import { TranscriptApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new TranscriptApi(configuration); + +let body: Array; //List of queries. Please see swagger.json for request body format. + +const { status, data } = await apiInstance.fetchGenomeNexusVariantInfoByGenomicChangePostUsingPOST(body); +``` + +### Parameters + +| Name | Type | Description | Notes | +| -------- | ----------------------------------------------- | ----------------------------------------------------------------- | ----- | +| **body** | **Array** | List of queries. Please see swagger.json for request body format. | | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: application/json +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ----------------------------------- | ---------------- | +| **200** | OK | - | +| **201** | Created | - | +| **400** | Error, error message will be given. | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **fetchGenomeNexusVariantInfoByHGVSgPostUsingPOST** + +> Array fetchGenomeNexusVariantInfoByHGVSgPostUsingPOST(body) + +Fetch Genome Nexus variant info by HGVSg + +### Example + +```typescript +import { TranscriptApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new TranscriptApi(configuration); + +let body: Array; //List of queries. Please see swagger.json for request body format. + +const { status, data } = await apiInstance.fetchGenomeNexusVariantInfoByHGVSgPostUsingPOST(body); +``` + +### Parameters + +| Name | Type | Description | Notes | +| -------- | --------------------------------------- | ----------------------------------------------------------------- | ----- | +| **body** | **Array** | List of queries. Please see swagger.json for request body format. | | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: application/json +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ----------------------------------- | ---------------- | +| **200** | OK | - | +| **201** | Created | - | +| **400** | Error, error message will be given. | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **getTranscriptUsingGET** + +> TranscriptResult getTranscriptUsingGET() + +Get transcript info in both GRCh37 and 38. + +### Example + +```typescript +import { TranscriptApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new TranscriptApi(configuration); + +let hugoSymbol: string; //hugoSymbol (default to undefined) + +const { status, data } = await apiInstance.getTranscriptUsingGET(hugoSymbol); +``` + +### Parameters + +| Name | Type | Description | Notes | +| -------------- | ------------ | ----------- | --------------------- | +| **hugoSymbol** | [**string**] | hugoSymbol | defaults to undefined | + +### Return type + +**TranscriptResult** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/TranscriptCoverageFilterResult.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/TranscriptCoverageFilterResult.md new file mode 100644 index 000000000..c4f5c3a45 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/TranscriptCoverageFilterResult.md @@ -0,0 +1,21 @@ +# TranscriptCoverageFilterResult + +## Properties + +| Name | Type | Description | Notes | +| ------------- | ----------- | ----------- | --------------------------------- | +| **isCovered** | **boolean** | | [optional] [default to undefined] | +| **variant** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { TranscriptCoverageFilterResult } from './api'; + +const instance: TranscriptCoverageFilterResult = { + isCovered, + variant, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/TranscriptResult.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/TranscriptResult.md new file mode 100644 index 000000000..bbe9ff22a --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/TranscriptResult.md @@ -0,0 +1,23 @@ +# TranscriptResult + +## Properties + +| Name | Type | Description | Notes | +| -------------------- | --------------------------------------------- | ----------- | --------------------------------- | +| **grch37Transcript** | [**EnsemblTranscript**](EnsemblTranscript.md) | | [optional] [default to undefined] | +| **grch38Transcript** | [**EnsemblTranscript**](EnsemblTranscript.md) | | [optional] [default to undefined] | +| **note** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { TranscriptResult } from './api'; + +const instance: TranscriptResult = { + grch37Transcript, + grch38Transcript, + note, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/Treatment.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Treatment.md new file mode 100644 index 000000000..33673243c --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/Treatment.md @@ -0,0 +1,23 @@ +# Treatment + +## Properties + +| Name | Type | Description | Notes | +| ----------------------- | -------------------------------------------------- | ----------- | --------------------------------- | +| **approvedIndications** | **Array<string>** | | [optional] [default to undefined] | +| **drugs** | [**Array<TreatmentDrug>**](TreatmentDrug.md) | | [optional] [default to undefined] | +| **priority** | **number** | | [optional] [default to undefined] | + +## Example + +```typescript +import { Treatment } from './api'; + +const instance: Treatment = { + approvedIndications, + drugs, + priority, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/TreatmentDrug.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/TreatmentDrug.md new file mode 100644 index 000000000..cc9018149 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/TreatmentDrug.md @@ -0,0 +1,21 @@ +# TreatmentDrug + +## Properties + +| Name | Type | Description | Notes | +| ------------------- | ----------------------------------------- | ----------- | --------------------------------- | +| **priority** | **number** | | [optional] [default to undefined] | +| **treatmentDrugId** | [**TreatmentDrugId**](TreatmentDrugId.md) | | [optional] [default to undefined] | + +## Example + +```typescript +import { TreatmentDrug } from './api'; + +const instance: TreatmentDrug = { + priority, + treatmentDrugId, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/TreatmentDrugId.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/TreatmentDrugId.md new file mode 100644 index 000000000..8f0a90b3e --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/TreatmentDrugId.md @@ -0,0 +1,19 @@ +# TreatmentDrugId + +## Properties + +| Name | Type | Description | Notes | +| -------- | ------------------- | ----------- | --------------------------------- | +| **drug** | [**Drug**](Drug.md) | | [optional] [default to undefined] | + +## Example + +```typescript +import { TreatmentDrugId } from './api'; + +const instance: TreatmentDrugId = { + drug, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/TumorType.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/TumorType.md new file mode 100644 index 000000000..9a98ea45a --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/TumorType.md @@ -0,0 +1,35 @@ +# TumorType + +OncoTree Detailed Cancer Type + +## Properties + +| Name | Type | Description | Notes | +| ------------- | ---------- | ----------- | --------------------------------- | +| **code** | **string** | | [optional] [default to undefined] | +| **color** | **string** | | [optional] [default to undefined] | +| **id** | **number** | | [optional] [default to undefined] | +| **level** | **number** | | [optional] [default to undefined] | +| **mainType** | **string** | | [optional] [default to undefined] | +| **subtype** | **string** | | [optional] [default to undefined] | +| **tissue** | **string** | | [optional] [default to undefined] | +| **tumorForm** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { TumorType } from './api'; + +const instance: TumorType = { + code, + color, + id, + level, + mainType, + subtype, + tissue, + tumorForm, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/TypeaheadSearchResp.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/TypeaheadSearchResp.md new file mode 100644 index 000000000..b9ff80048 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/TypeaheadSearchResp.md @@ -0,0 +1,43 @@ +# TypeaheadSearchResp + +## Properties + +| Name | Type | Description | Notes | +| -------------------------- | -------------------------------------------- | ----------- | --------------------------------- | +| **annotation** | **string** | | [optional] [default to undefined] | +| **annotationByLevel** | **{ [key: string]: string; }** | | [optional] [default to undefined] | +| **drug** | [**Drug**](Drug.md) | | [optional] [default to undefined] | +| **gene** | [**Gene**](Gene.md) | | [optional] [default to undefined] | +| **highestResistanceLevel** | **string** | | [optional] [default to undefined] | +| **highestSensitiveLevel** | **string** | | [optional] [default to undefined] | +| **link** | **string** | | [optional] [default to undefined] | +| **oncogenicity** | **string** | | [optional] [default to undefined] | +| **queryType** | **string** | | [optional] [default to undefined] | +| **tumorTypes** | [**Array<TumorType>**](TumorType.md) | | [optional] [default to undefined] | +| **variantExist** | **boolean** | | [optional] [default to undefined] | +| **variants** | [**Array<Alteration>**](Alteration.md) | | [optional] [default to undefined] | +| **vus** | **boolean** | | [optional] [default to undefined] | + +## Example + +```typescript +import { TypeaheadSearchResp } from './api'; + +const instance: TypeaheadSearchResp = { + annotation, + annotationByLevel, + drug, + gene, + highestResistanceLevel, + highestSensitiveLevel, + link, + oncogenicity, + queryType, + tumorTypes, + variantExist, + variants, + vus, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/UntranslatedRegion.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/UntranslatedRegion.md new file mode 100644 index 000000000..652a1e39b --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/UntranslatedRegion.md @@ -0,0 +1,25 @@ +# UntranslatedRegion + +## Properties + +| Name | Type | Description | Notes | +| ---------- | ---------- | -------------------------------------- | ---------------------- | +| **end** | **number** | End position of UTR | [default to undefined] | +| **start** | **number** | Start position of UTR | [default to undefined] | +| **strand** | **number** | Strand UTR is on, -1 for - and 1 for + | [default to undefined] | +| **type** | **string** | UTR Type | [default to undefined] | + +## Example + +```typescript +import { UntranslatedRegion } from './api'; + +const instance: UntranslatedRegion = { + end, + start, + strand, + type, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/UtilsApi.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/UtilsApi.md new file mode 100644 index 000000000..5d528a3f7 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/UtilsApi.md @@ -0,0 +1,1394 @@ +# UtilsApi + +All URIs are relative to _http://localhost:8080/app/api/v1_ + +| Method | HTTP request | Description | +| --------------------------------------------------------------------------------------------------------------- | -------------------------------------------------- | ------------------------------------------ | +| [**utilAnnotateCPLUsingPOST**](#utilannotatecplusingpost) | **POST** /utils/annotateCPL | utilAnnotateCPL | +| [**utilDataAvailabilityGetUsingGET**](#utildataavailabilitygetusingget) | **GET** /utils/data/availability | utilDataAvailabilityGet | +| [**utilDataReadmeGetUsingGET**](#utildatareadmegetusingget) | **GET** /utils/data/readme | utilDataReadmeGet | +| [**utilDataSqlDumpGetUsingGET**](#utildatasqldumpgetusingget) | **GET** /utils/data/sqlDump | utilDataSqlDumpGet | +| [**utilDataTranscriptSqlDumpUsingGET**](#utildatatranscriptsqldumpusingget) | **GET** /utils/data/transcriptSqlDump | utilDataTranscriptSqlDump | +| [**utilFilterGenomicChangeBasedOnCoveragePostUsingPOST**](#utilfiltergenomicchangebasedoncoveragepostusingpost) | **POST** /utils/filterGenomicChangeBasedOnCoverage | utilFilterGenomicChangeBasedOnCoveragePost | +| [**utilFilterHgvsgBasedOnCoveragePostUsingPOST**](#utilfilterhgvsgbasedoncoveragepostusingpost) | **POST** /utils/filterHgvsgBasedOnCoverage | utilFilterHgvsgBasedOnCoveragePost | +| [**utilMutationMapperDataGetUsingGET**](#utilmutationmapperdatagetusingget) | **GET** /utils/mutationMapperData | utilMutationMapperDataGet | +| [**utilPortalAlterationSampleCountGetUsingGET**](#utilportalalterationsamplecountgetusingget) | **GET** /utils/portalAlterationSampleCount | utilPortalAlterationSampleCountGet | +| [**utilRelevantAlterationsGetUsingGET**](#utilrelevantalterationsgetusingget) | **GET** /utils/relevantAlterations | utilRelevantAlterationsGet | +| [**utilRelevantCancerTypesPostUsingPOST**](#utilrelevantcancertypespostusingpost) | **POST** /utils/relevantCancerTypes | utilRelevantCancerTypesPost | +| [**utilRelevantTumorTypesGetUsingGET**](#utilrelevanttumortypesgetusingget) | **GET** /utils/relevantTumorTypes | utilRelevantTumorTypesGet | +| [**utilUpdateTranscriptGetUsingGET**](#utilupdatetranscriptgetusingget) | **GET** /utils/updateTranscript | utilUpdateTranscriptGet | +| [**utilValidateTranscriptUpdateGetUsingGET**](#utilvalidatetranscriptupdategetusingget) | **GET** /utils/validateTranscriptUpdate | utilValidateTranscriptUpdateGet | +| [**utilVariantAnnotationGetUsingGET**](#utilvariantannotationgetusingget) | **GET** /utils/variantAnnotation | utilVariantAnnotationGet | +| [**utilsEnsemblGenesGetUsingGET**](#utilsensemblgenesgetusingget) | **GET** /utils/ensembleGenes | utilsEnsemblGenesGet | +| [**utilsEvidencesByLevelsGetUsingGET**](#utilsevidencesbylevelsgetusingget) | **GET** /utils/evidences/levels | utilsEvidencesByLevelsGet | +| [**utilsHotspotMutationGetUsingGET**](#utilshotspotmutationgetusingget) | **GET** /utils/isHotspot | utilsHotspotMutationGet | +| [**utilsNumbersGeneGetUsingGET**](#utilsnumbersgenegetusingget) | **GET** /utils/numbers/gene/{hugoSymbol} | utilsNumbersGeneGet | +| [**utilsNumbersGenesGetUsingGET**](#utilsnumbersgenesgetusingget) | **GET** /utils/numbers/genes/ | utilsNumbersGenesGet | +| [**utilsNumbersLevelsGetUsingGET**](#utilsnumberslevelsgetusingget) | **GET** /utils/numbers/levels/ | utilsNumbersLevelsGet | +| [**utilsNumbersMainGetUsingGET**](#utilsnumbersmaingetusingget) | **GET** /utils/numbers/main/ | utilsNumbersMainGet | +| [**utilsSuggestedVariantsGetUsingGET**](#utilssuggestedvariantsgetusingget) | **GET** /utils/suggestedVariants | utilsSuggestedVariantsGet | +| [**utilsTumorTypesGetUsingGET**](#utilstumortypesgetusingget) | **GET** /utils/tumorTypes | utilsTumorTypesGet | +| [**validateTrialsUsingGET**](#validatetrialsusingget) | **GET** /utils/validation/trials | validateTrials | +| [**validateVariantExampleGetUsingGET**](#validatevariantexamplegetusingget) | **GET** /utils/match/variant | validateVariantExampleGet | +| [**validateVariantExamplePostUsingPOST**](#validatevariantexamplepostusingpost) | **POST** /utils/match/variant | validateVariantExamplePost | + +# **utilAnnotateCPLUsingPOST** + +> string utilAnnotateCPLUsingPOST(cplRequest) + +Annotate a string using CPL + +### Example + +```typescript +import { UtilsApi, Configuration, CplAnnotationRequest } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let cplRequest: CplAnnotationRequest; //CPL Request + +const { status, data } = await apiInstance.utilAnnotateCPLUsingPOST(cplRequest); +``` + +### Parameters + +| Name | Type | Description | Notes | +| -------------- | ------------------------ | ----------- | ----- | +| **cplRequest** | **CplAnnotationRequest** | CPL Request | | + +### Return type + +**string** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: application/json +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ----------------------------------- | ---------------- | +| **200** | OK | - | +| **201** | Created | - | +| **400** | Error, error message will be given. | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilDataAvailabilityGetUsingGET** + +> Array utilDataAvailabilityGetUsingGET() + +Get information about what files are available by data version + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +const { status, data } = await apiInstance.utilDataAvailabilityGetUsingGET(); +``` + +### Parameters + +This endpoint does not have any parameters. + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------------- | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | +| **503** | Service Unavailable | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilDataReadmeGetUsingGET** + +> string utilDataReadmeGetUsingGET() + +Get readme info for specific data release version + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let version: string; //version (optional) (default to undefined) + +const { status, data } = await apiInstance.utilDataReadmeGetUsingGET(version); +``` + +### Parameters + +| Name | Type | Description | Notes | +| ----------- | ------------ | ----------- | -------------------------------- | +| **version** | [**string**] | version | (optional) defaults to undefined | + +### Return type + +**string** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: text/plain + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------------- | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | +| **503** | Service Unavailable | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilDataSqlDumpGetUsingGET** + +> Array utilDataSqlDumpGetUsingGET() + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let version: string; //version (optional) (default to undefined) + +const { status, data } = await apiInstance.utilDataSqlDumpGetUsingGET(version); +``` + +### Parameters + +| Name | Type | Description | Notes | +| ----------- | ------------ | ----------- | -------------------------------- | +| **version** | [**string**] | version | (optional) defaults to undefined | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/gz + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilDataTranscriptSqlDumpUsingGET** + +> Array utilDataTranscriptSqlDumpUsingGET() + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let version: string; //version (optional) (default to undefined) + +const { status, data } = await apiInstance.utilDataTranscriptSqlDumpUsingGET(version); +``` + +### Parameters + +| Name | Type | Description | Notes | +| ----------- | ------------ | ----------- | -------------------------------- | +| **version** | [**string**] | version | (optional) defaults to undefined | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/gz + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilFilterGenomicChangeBasedOnCoveragePostUsingPOST** + +> Array utilFilterGenomicChangeBasedOnCoveragePostUsingPOST(body) + +Filter genomic change based on oncokb coverage + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let body: Array; //List of queries. + +const { status, data } = await apiInstance.utilFilterGenomicChangeBasedOnCoveragePostUsingPOST(body); +``` + +### Parameters + +| Name | Type | Description | Notes | +| -------- | ----------------------------------------------- | ---------------- | ----- | +| **body** | **Array** | List of queries. | | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: application/json +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ----------------------------------- | ---------------- | +| **200** | OK | - | +| **201** | Created | - | +| **400** | Error, error message will be given. | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilFilterHgvsgBasedOnCoveragePostUsingPOST** + +> Array utilFilterHgvsgBasedOnCoveragePostUsingPOST(body) + +Filter HGVSg based on oncokb coverage + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let body: Array; //List of queries. + +const { status, data } = await apiInstance.utilFilterHgvsgBasedOnCoveragePostUsingPOST(body); +``` + +### Parameters + +| Name | Type | Description | Notes | +| -------- | --------------------------------------- | ---------------- | ----- | +| **body** | **Array** | List of queries. | | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: application/json +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ----------------------------------- | ---------------- | +| **200** | OK | - | +| **201** | Created | - | +| **400** | Error, error message will be given. | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilMutationMapperDataGetUsingGET** + +> Array utilMutationMapperDataGetUsingGET() + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let hugoSymbol: string; //hugoSymbol (optional) (default to undefined) + +const { status, data } = await apiInstance.utilMutationMapperDataGetUsingGET(hugoSymbol); +``` + +### Parameters + +| Name | Type | Description | Notes | +| -------------- | ------------ | ----------- | -------------------------------- | +| **hugoSymbol** | [**string**] | hugoSymbol | (optional) defaults to undefined | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilPortalAlterationSampleCountGetUsingGET** + +> Array utilPortalAlterationSampleCountGetUsingGET() + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let hugoSymbol: string; //hugoSymbol (optional) (default to undefined) + +const { status, data } = await apiInstance.utilPortalAlterationSampleCountGetUsingGET(hugoSymbol); +``` + +### Parameters + +| Name | Type | Description | Notes | +| -------------- | ------------ | ----------- | -------------------------------- | +| **hugoSymbol** | [**string**] | hugoSymbol | (optional) defaults to undefined | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilRelevantAlterationsGetUsingGET** + +> Array utilRelevantAlterationsGetUsingGET() + +Get the list of relevant alterations + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let referenceGenome: string; //Reference genome, either GRCh37 or GRCh38. The default is GRCh37 (optional) (default to 'GRCh37') +let entrezGeneId: number; //alteration (optional) (default to undefined) +let alteration: string; //alteration (optional) (default to undefined) + +const { status, data } = await apiInstance.utilRelevantAlterationsGetUsingGET(referenceGenome, entrezGeneId, alteration); +``` + +### Parameters + +| Name | Type | Description | Notes | +| ------------------- | ------------ | ---------------------------------------------------------------- | -------------------------------- | +| **referenceGenome** | [**string**] | Reference genome, either GRCh37 or GRCh38. The default is GRCh37 | (optional) defaults to 'GRCh37' | +| **entrezGeneId** | [**number**] | alteration | (optional) defaults to undefined | +| **alteration** | [**string**] | alteration | (optional) defaults to undefined | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilRelevantCancerTypesPostUsingPOST** + +> Array utilRelevantCancerTypesPostUsingPOST(body) + +Get the list of relevant tumor types. + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let body: Array; //List of queries. +let levelOfEvidence: + | 'LEVEL_1' + | 'LEVEL_2' + | 'LEVEL_3A' + | 'LEVEL_3B' + | 'LEVEL_4' + | 'LEVEL_R1' + | 'LEVEL_R2' + | 'LEVEL_Px1' + | 'LEVEL_Px2' + | 'LEVEL_Px3' + | 'LEVEL_Dx1' + | 'LEVEL_Dx2' + | 'LEVEL_Dx3' + | 'LEVEL_Fda1' + | 'LEVEL_Fda2' + | 'LEVEL_Fda3' + | 'NO'; //Level of Evidence (optional) (default to undefined) + +const { status, data } = await apiInstance.utilRelevantCancerTypesPostUsingPOST(body, levelOfEvidence); +``` + +### Parameters + +| Name | Type | Description | Notes | +| ------------------- | ---------------------------------- | ----------------- | ------------------ | ------------------ | ----------------- | ------------------ | ------------------ | ------------------- | ------------------- | ------------------- | ------------------- | ------------------- | ------------------- | -------------------- | -------------------- | -------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------- | -------------------------------- | +| **body** | **Array** | List of queries. | | +| **levelOfEvidence** | [\*\*'LEVEL_1' | 'LEVEL_2' | 'LEVEL_3A' | 'LEVEL_3B' | 'LEVEL_4' | 'LEVEL_R1' | 'LEVEL_R2' | 'LEVEL_Px1' | 'LEVEL_Px2' | 'LEVEL_Px3' | 'LEVEL_Dx1' | 'LEVEL_Dx2' | 'LEVEL_Dx3' | 'LEVEL_Fda1' | 'LEVEL_Fda2' | 'LEVEL_Fda3' | 'NO'**]**Array<'LEVEL_1' | 'LEVEL_2' | 'LEVEL_3A' | 'LEVEL_3B' | 'LEVEL_4' | 'LEVEL_R1' | 'LEVEL_R2' | 'LEVEL_Px1' | 'LEVEL_Px2' | 'LEVEL_Px3' | 'LEVEL_Dx1' | 'LEVEL_Dx2' | 'LEVEL_Dx3' | 'LEVEL_Fda1' | 'LEVEL_Fda2' | 'LEVEL_Fda3' | 'NO'>\*\* | Level of Evidence | (optional) defaults to undefined | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: application/json +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **201** | Created | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilRelevantTumorTypesGetUsingGET** + +> Array utilRelevantTumorTypesGetUsingGET() + +Get the list of relevant tumor types. + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let tumorType: string; //OncoTree tumor type name/main type/code (optional) (default to undefined) + +const { status, data } = await apiInstance.utilRelevantTumorTypesGetUsingGET(tumorType); +``` + +### Parameters + +| Name | Type | Description | Notes | +| ------------- | ------------ | --------------------------------------- | -------------------------------- | +| **tumorType** | [**string**] | OncoTree tumor type name/main type/code | (optional) defaults to undefined | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilUpdateTranscriptGetUsingGET** + +> utilUpdateTranscriptGetUsingGET() + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let hugoSymbol: string; //hugoSymbol (optional) (default to undefined) +let entrezGeneId: number; //entrezGeneId (optional) (default to undefined) +let grch37Isoform: string; //grch37Isoform (optional) (default to undefined) +let grch37RefSeq: string; //grch37RefSeq (optional) (default to undefined) +let grch38Isoform: string; //grch38Isoform (optional) (default to undefined) +let grch38RefSeq: string; //grch38RefSeq (optional) (default to undefined) + +const { status, data } = await apiInstance.utilUpdateTranscriptGetUsingGET( + hugoSymbol, + entrezGeneId, + grch37Isoform, + grch37RefSeq, + grch38Isoform, + grch38RefSeq, +); +``` + +### Parameters + +| Name | Type | Description | Notes | +| ----------------- | ------------ | ------------- | -------------------------------- | +| **hugoSymbol** | [**string**] | hugoSymbol | (optional) defaults to undefined | +| **entrezGeneId** | [**number**] | entrezGeneId | (optional) defaults to undefined | +| **grch37Isoform** | [**string**] | grch37Isoform | (optional) defaults to undefined | +| **grch37RefSeq** | [**string**] | grch37RefSeq | (optional) defaults to undefined | +| **grch38Isoform** | [**string**] | grch38Isoform | (optional) defaults to undefined | +| **grch38RefSeq** | [**string**] | grch38RefSeq | (optional) defaults to undefined | + +### Return type + +void (empty response body) + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: Not defined + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilValidateTranscriptUpdateGetUsingGET** + +> string utilValidateTranscriptUpdateGetUsingGET() + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let hugoSymbol: string; //hugoSymbol (optional) (default to undefined) +let entrezGeneId: number; //entrezGeneId (optional) (default to undefined) +let grch37Isoform: string; //grch37Isoform (optional) (default to undefined) +let grch38Isoform: string; //grch38Isoform (optional) (default to undefined) + +const { status, data } = await apiInstance.utilValidateTranscriptUpdateGetUsingGET(hugoSymbol, entrezGeneId, grch37Isoform, grch38Isoform); +``` + +### Parameters + +| Name | Type | Description | Notes | +| ----------------- | ------------ | ------------- | -------------------------------- | +| **hugoSymbol** | [**string**] | hugoSymbol | (optional) defaults to undefined | +| **entrezGeneId** | [**number**] | entrezGeneId | (optional) defaults to undefined | +| **grch37Isoform** | [**string**] | grch37Isoform | (optional) defaults to undefined | +| **grch38Isoform** | [**string**] | grch38Isoform | (optional) defaults to undefined | + +### Return type + +**string** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: text/plain + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilVariantAnnotationGetUsingGET** + +> VariantAnnotation utilVariantAnnotationGetUsingGET() + +Get all the info for the query + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let hugoSymbol: string; //hugoSymbol (optional) (default to undefined) +let entrezGeneId: number; //entrezGeneId (optional) (default to undefined) +let referenceGenome: string; //Reference genome, either GRCh37 or GRCh38. The default is GRCh37 (optional) (default to 'GRCh37') +let alteration: string; //Alteration (optional) (default to undefined) +let hgvsg: string; //HGVS genomic format. Example: 7:g.140453136A>T (optional) (default to undefined) +let genomicChange: string; //Genomic change format. Example: 7,140453136,140453136,A,T (optional) (default to undefined) +let tumorType: string; //OncoTree tumor type name/main type/code (optional) (default to undefined) + +const { status, data } = await apiInstance.utilVariantAnnotationGetUsingGET( + hugoSymbol, + entrezGeneId, + referenceGenome, + alteration, + hgvsg, + genomicChange, + tumorType, +); +``` + +### Parameters + +| Name | Type | Description | Notes | +| ------------------- | ------------ | ---------------------------------------------------------------- | -------------------------------- | +| **hugoSymbol** | [**string**] | hugoSymbol | (optional) defaults to undefined | +| **entrezGeneId** | [**number**] | entrezGeneId | (optional) defaults to undefined | +| **referenceGenome** | [**string**] | Reference genome, either GRCh37 or GRCh38. The default is GRCh37 | (optional) defaults to 'GRCh37' | +| **alteration** | [**string**] | Alteration | (optional) defaults to undefined | +| **hgvsg** | [**string**] | HGVS genomic format. Example: 7:g.140453136A>T | (optional) defaults to undefined | +| **genomicChange** | [**string**] | Genomic change format. Example: 7,140453136,140453136,A,T | (optional) defaults to undefined | +| **tumorType** | [**string**] | OncoTree tumor type name/main type/code | (optional) defaults to undefined | + +### Return type + +**VariantAnnotation** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilsEnsemblGenesGetUsingGET** + +> Array utilsEnsemblGenesGetUsingGET() + +Get the list of Ensembl genes. + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let entrezGeneId: number; //Gene entrez id (default to undefined) + +const { status, data } = await apiInstance.utilsEnsemblGenesGetUsingGET(entrezGeneId); +``` + +### Parameters + +| Name | Type | Description | Notes | +| ---------------- | ------------ | -------------- | --------------------- | +| **entrezGeneId** | [**number**] | Gene entrez id | defaults to undefined | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilsEvidencesByLevelsGetUsingGET** + +> object utilsEvidencesByLevelsGetUsingGET() + +Get the list of evidences by levels. + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +const { status, data } = await apiInstance.utilsEvidencesByLevelsGetUsingGET(); +``` + +### Parameters + +This endpoint does not have any parameters. + +### Return type + +**object** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilsHotspotMutationGetUsingGET** + +> boolean utilsHotspotMutationGetUsingGET() + +Determine whether variant is hotspot mutation. + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let hugoSymbol: string; //Gene hugo symbol (optional) (default to undefined) +let variant: string; //Variant name (optional) (default to undefined) + +const { status, data } = await apiInstance.utilsHotspotMutationGetUsingGET(hugoSymbol, variant); +``` + +### Parameters + +| Name | Type | Description | Notes | +| -------------- | ------------ | ---------------- | -------------------------------- | +| **hugoSymbol** | [**string**] | Gene hugo symbol | (optional) defaults to undefined | +| **variant** | [**string**] | Variant name | (optional) defaults to undefined | + +### Return type + +**boolean** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilsNumbersGeneGetUsingGET** + +> GeneNumber utilsNumbersGeneGetUsingGET() + +Get gene related numbers + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let hugoSymbol: string; //The gene symbol used in Human Genome Organisation. (default to undefined) + +const { status, data } = await apiInstance.utilsNumbersGeneGetUsingGET(hugoSymbol); +``` + +### Parameters + +| Name | Type | Description | Notes | +| -------------- | ------------ | -------------------------------------------------- | --------------------- | +| **hugoSymbol** | [**string**] | The gene symbol used in Human Genome Organisation. | defaults to undefined | + +### Return type + +**GeneNumber** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilsNumbersGenesGetUsingGET** + +> Array utilsNumbersGenesGetUsingGET() + +Get gene related numbers of all genes. This is for main page word cloud. + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +const { status, data } = await apiInstance.utilsNumbersGenesGetUsingGET(); +``` + +### Parameters + +This endpoint does not have any parameters. + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilsNumbersLevelsGetUsingGET** + +> Array utilsNumbersLevelsGetUsingGET() + +Get gene related numbers of all genes. This is for main page word cloud. + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +const { status, data } = await apiInstance.utilsNumbersLevelsGetUsingGET(); +``` + +### Parameters + +This endpoint does not have any parameters. + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilsNumbersMainGetUsingGET** + +> MainNumber utilsNumbersMainGetUsingGET() + +Get numbers served for the main page dashboard. + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +const { status, data } = await apiInstance.utilsNumbersMainGetUsingGET(); +``` + +### Parameters + +This endpoint does not have any parameters. + +### Return type + +**MainNumber** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilsSuggestedVariantsGetUsingGET** + +> Array utilsSuggestedVariantsGetUsingGET() + +Get All Suggested Variants. + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +const { status, data } = await apiInstance.utilsSuggestedVariantsGetUsingGET(); +``` + +### Parameters + +This endpoint does not have any parameters. + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **utilsTumorTypesGetUsingGET** + +> Array utilsTumorTypesGetUsingGET() + +Get the full list of TumorTypes. + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +const { status, data } = await apiInstance.utilsTumorTypesGetUsingGET(); +``` + +### Parameters + +This endpoint does not have any parameters. + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **validateTrialsUsingGET** + +> object validateTrialsUsingGET() + +Check if clinical trials are valid or not by nctId. + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let nctIds: Array; //NCTID list (optional) (default to undefined) + +const { status, data } = await apiInstance.validateTrialsUsingGET(nctIds); +``` + +### Parameters + +| Name | Type | Description | Notes | +| ---------- | ----------------------- | ----------- | -------------------------------- | +| **nctIds** | **Array<string>** | NCTID list | (optional) defaults to undefined | + +### Return type + +**object** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: Not defined +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **validateVariantExampleGetUsingGET** + +> object validateVariantExampleGetUsingGET() + +Check if the genomic example will be mapped to OncoKB variant. + +### Example + +```typescript +import { UtilsApi, Configuration } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let examples: string; //The genomic examples. (optional) + +const { status, data } = await apiInstance.validateVariantExampleGetUsingGET(examples); +``` + +### Parameters + +| Name | Type | Description | Notes | +| ------------ | ---------- | --------------------- | ----- | +| **examples** | **string** | The genomic examples. | | + +### Return type + +**object** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: application/json +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) + +# **validateVariantExamplePostUsingPOST** + +> Array validateVariantExamplePostUsingPOST(body) + +Check which OncoKB variants can be mapped on genomic examples. + +### Example + +```typescript +import { UtilsApi, Configuration, MatchVariantRequest } from './api'; + +const configuration = new Configuration(); +const apiInstance = new UtilsApi(configuration); + +let body: MatchVariantRequest; //List of queries. Please see swagger.json for request body format. + +const { status, data } = await apiInstance.validateVariantExamplePostUsingPOST(body); +``` + +### Parameters + +| Name | Type | Description | Notes | +| -------- | ----------------------- | ----------------------------------------------------------------- | ----- | +| **body** | **MatchVariantRequest** | List of queries. Please see swagger.json for request body format. | | + +### Return type + +**Array** + +### Authorization + +No authorization required + +### HTTP request headers + +- **Content-Type**: application/json +- **Accept**: application/json + +### HTTP response details + +| Status code | Description | Response headers | +| ----------- | ------------ | ---------------- | +| **200** | OK | - | +| **201** | Created | - | +| **401** | Unauthorized | - | +| **403** | Forbidden | - | +| **404** | Not Found | - | + +[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/VariantAnnotation.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/VariantAnnotation.md new file mode 100644 index 000000000..11ecdfa0f --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/VariantAnnotation.md @@ -0,0 +1,73 @@ +# VariantAnnotation + +## Properties + +| Name | Type | Description | Notes | +| ------------------------------------- | ---------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------- | +| **alleleExist** | **boolean** | Indicates whether the alternate allele has been curated. See SOP Protocol 9.1 | [optional] [default to undefined] | +| **background** | **string** | | [optional] [default to undefined] | +| **dataVersion** | **string** | OncoKB data version. See www.oncokb.org/news | [optional] [default to undefined] | +| **diagnosticImplications** | [**Array<Implication>**](Implication.md) | List of diagnostic implications. Defaulted to empty list | [optional] [default to undefined] | +| **diagnosticSummary** | **string** | Diagnostic summary. Defaulted to \"\" | [optional] [default to undefined] | +| **geneExist** | **boolean** | Indicates whether the gene is curated by OncoKB | [optional] [default to undefined] | +| **geneSummary** | **string** | Gene summary. Defaulted to \"\" | [optional] [default to undefined] | +| **highestDiagnosticImplicationLevel** | **string** | (Nullable) The highest diagnostic level from a list of diagnostic evidences. | [optional] [default to undefined] | +| **highestFdaLevel** | **string** | (Nullable) The highest FDA level from a list of therapeutic evidences. | [optional] [default to undefined] | +| **highestPrognosticImplicationLevel** | **string** | (Nullable) The highest prognostic level from a list of prognostic evidences. | [optional] [default to undefined] | +| **highestResistanceLevel** | **string** | (Nullable) The highest resistance level from a list of therapeutic evidences. | [optional] [default to undefined] | +| **highestSensitiveLevel** | **string** | (Nullable) The highest sensitivity level from a list of therapeutic evidences. | [optional] [default to undefined] | +| **hotspot** | **boolean** | Whether variant is recurrently found in cancer with statistical significance, as defined in Chang et al. (2017). See SOP Protocol 9.2 | [optional] [default to undefined] | +| **lastUpdate** | **string** | OncoKB data release date. Formatted as MM/DD/YYYY | [optional] [default to undefined] | +| **mutationEffect** | [**MutationEffectResp**](MutationEffectResp.md) | | [optional] [default to undefined] | +| **oncogenic** | **string** | The oncogenicity status of the variant. Defaulted to \"Unknown\". | [optional] [default to undefined] | +| **otherSignificantResistanceLevels** | **Array<string>** | DEPRECATED | [optional] [default to undefined] | +| **otherSignificantSensitiveLevels** | **Array<string>** | DEPRECATED | [optional] [default to undefined] | +| **prognosticImplications** | [**Array<Implication>**](Implication.md) | List of prognostic implications. Defaulted to empty list | [optional] [default to undefined] | +| **prognosticSummary** | **string** | Prognostic summary. Defaulted to \"\" | [optional] [default to undefined] | +| **query** | [**Query**](Query.md) | | [optional] [default to undefined] | +| **treatments** | [**Array<IndicatorQueryTreatment>**](IndicatorQueryTreatment.md) | List of therapeutic implications implications. Defaulted to empty list | [optional] [default to undefined] | +| **tumorTypeSummary** | **string** | Tumor type summary. Defaulted to \"\" | [optional] [default to undefined] | +| **tumorTypes** | [**Array<VariantAnnotationTumorType>**](VariantAnnotationTumorType.md) | | [optional] [default to undefined] | +| **variantExist** | **boolean** | Indicates whether an exact match for the queried variant is curated | [optional] [default to undefined] | +| **variantSummary** | **string** | Variant summary. Defaulted to \"\" | [optional] [default to undefined] | +| **vue** | **boolean** | | [optional] [default to undefined] | +| **vus** | **boolean** | | [optional] [default to undefined] | + +## Example + +```typescript +import { VariantAnnotation } from './api'; + +const instance: VariantAnnotation = { + alleleExist, + background, + dataVersion, + diagnosticImplications, + diagnosticSummary, + geneExist, + geneSummary, + highestDiagnosticImplicationLevel, + highestFdaLevel, + highestPrognosticImplicationLevel, + highestResistanceLevel, + highestSensitiveLevel, + hotspot, + lastUpdate, + mutationEffect, + oncogenic, + otherSignificantResistanceLevels, + otherSignificantSensitiveLevels, + prognosticImplications, + prognosticSummary, + query, + treatments, + tumorTypeSummary, + tumorTypes, + variantExist, + variantSummary, + vue, + vus, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/VariantAnnotationTumorType.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/VariantAnnotationTumorType.md new file mode 100644 index 000000000..df169c67e --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/VariantAnnotationTumorType.md @@ -0,0 +1,23 @@ +# VariantAnnotationTumorType + +## Properties + +| Name | Type | Description | Notes | +| --------------------- | ---------------------------------------- | ----------- | --------------------------------- | +| **evidences** | [**Array<Evidence>**](Evidence.md) | | [optional] [default to undefined] | +| **relevantTumorType** | **boolean** | | [optional] [default to undefined] | +| **tumorType** | [**TumorType**](TumorType.md) | | [optional] [default to undefined] | + +## Example + +```typescript +import { VariantAnnotationTumorType } from './api'; + +const instance: VariantAnnotationTumorType = { + evidences, + relevantTumorType, + tumorType, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/docs/VariantConsequence.md b/src/main/webapp/app/shared/api/generated/defaultCore/docs/VariantConsequence.md new file mode 100644 index 000000000..515b3b8d2 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/docs/VariantConsequence.md @@ -0,0 +1,23 @@ +# VariantConsequence + +## Properties + +| Name | Type | Description | Notes | +| ------------------------- | ----------- | ----------- | --------------------------------- | +| **description** | **string** | | [optional] [default to undefined] | +| **isGenerallyTruncating** | **boolean** | | [optional] [default to undefined] | +| **term** | **string** | | [optional] [default to undefined] | + +## Example + +```typescript +import { VariantConsequence } from './api'; + +const instance: VariantConsequence = { + description, + isGenerallyTruncating, + term, +}; +``` + +[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/git_push.sh b/src/main/webapp/app/shared/api/generated/defaultCore/git_push.sh new file mode 100644 index 000000000..f53a75d4f --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/git_push.sh @@ -0,0 +1,57 @@ +#!/bin/sh +# ref: https://help.github.com/articles/adding-an-existing-project-to-github-using-the-command-line/ +# +# Usage example: /bin/sh ./git_push.sh wing328 openapi-petstore-perl "minor update" "gitlab.com" + +git_user_id=$1 +git_repo_id=$2 +release_note=$3 +git_host=$4 + +if [ "$git_host" = "" ]; then + git_host="github.com" + echo "[INFO] No command line input provided. Set \$git_host to $git_host" +fi + +if [ "$git_user_id" = "" ]; then + git_user_id="GIT_USER_ID" + echo "[INFO] No command line input provided. Set \$git_user_id to $git_user_id" +fi + +if [ "$git_repo_id" = "" ]; then + git_repo_id="GIT_REPO_ID" + echo "[INFO] No command line input provided. Set \$git_repo_id to $git_repo_id" +fi + +if [ "$release_note" = "" ]; then + release_note="Minor update" + echo "[INFO] No command line input provided. Set \$release_note to $release_note" +fi + +# Initialize the local directory as a Git repository +git init + +# Adds the files in the local repository and stages them for commit. +git add . + +# Commits the tracked changes and prepares them to be pushed to a remote repository. +git commit -m "$release_note" + +# Sets the new remote +git_remote=$(git remote) +if [ "$git_remote" = "" ]; then # git remote not defined + + if [ "$GIT_TOKEN" = "" ]; then + echo "[INFO] \$GIT_TOKEN (environment variable) is not set. Using the git credential in your environment." + git remote add origin https://${git_host}/${git_user_id}/${git_repo_id}.git + else + git remote add origin https://${git_user_id}:"${GIT_TOKEN}"@${git_host}/${git_user_id}/${git_repo_id}.git + fi + +fi + +git pull origin master + +# Pushes (Forces) the changes in the local repository up to the remote repository +echo "Git pushing to https://${git_host}/${git_user_id}/${git_repo_id}.git" +git push origin master 2>&1 | grep -v 'To https' diff --git a/src/main/webapp/app/shared/api/generated/defaultCore/index.ts b/src/main/webapp/app/shared/api/generated/defaultCore/index.ts new file mode 100644 index 000000000..3ae0e28d4 --- /dev/null +++ b/src/main/webapp/app/shared/api/generated/defaultCore/index.ts @@ -0,0 +1,16 @@ +/* tslint:disable */ +/* eslint-disable */ +/** + * OncoKB APIs + * OncoKB, a comprehensive and curated precision oncology knowledge base, offers oncologists detailed, evidence-based information about individual somatic mutations and structural alterations present in patient tumors with the goal of supporting optimal treatment decisions. + * + * The version of the OpenAPI document: v1.5.0 + * Contact: contact@oncokb.org + * + * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech). + * https://openapi-generator.tech + * Do not edit the class manually. + */ + +export * from './api'; +export * from './configuration'; diff --git a/src/main/webapp/app/shared/firebase/input/PreviewTextArea.tsx b/src/main/webapp/app/shared/firebase/input/PreviewTextArea.tsx new file mode 100644 index 000000000..83f7fc3f1 --- /dev/null +++ b/src/main/webapp/app/shared/firebase/input/PreviewTextArea.tsx @@ -0,0 +1,87 @@ +import { SentryError } from 'app/config/sentry-error'; +import LoadingIndicator, { LoaderSize } from 'app/oncokb-commons/components/loadingIndicator/LoadingIndicator'; +import { utilsClient } from 'app/shared/api/clients'; +import { parseFirebaseGenePath } from 'app/shared/util/firebase/firebase-path-utils'; +import { IRootStore } from 'app/stores'; +import { onValue, ref } from 'firebase/database'; +import { inject } from 'mobx-react'; +import React, { useEffect, useRef, useState } from 'react'; +import { Input } from 'reactstrap'; + +export interface IPreviewTextAreaProps extends React.HTMLAttributes, StoreProps { + firebasePath: string; // firebase path that component needs to listen to + className?: string; + mutationName?: string; + cancerTypeName?: string; +} + +const PreviewTextArea: React.FunctionComponent = (props: IPreviewTextAreaProps) => { + const { db, firebasePath, className, ...otherProps } = props; + + const [inputValue, setInputValue] = useState(undefined); + const [inputValueLoaded, setInputValueLoaded] = useState(false); + const [previewText, setPreviewText] = useState(null); + const [isLoading, setIsLoading] = useState(false); + + const inputRef = useRef(null); + + useEffect(() => { + if (!db) { + return; + } + const unsubscribe = onValue(ref(db, firebasePath), snapshot => { + setInputValue(snapshot.val()); + setInputValueLoaded(true); + }); + + return () => { + unsubscribe(); + }; + }, [firebasePath, db]); + + useEffect(() => { + if (inputValueLoaded && inputValue) { + fetchAnnotatedText(inputValue); + } + }, [inputValue, inputValueLoaded]); + + const fetchAnnotatedText = async (text: string) => { + setIsLoading(true); + try { + const parseRes = parseFirebaseGenePath(firebasePath); + if (!parseRes?.hugoSymbol) { + throw new Error(); + } + const response = await utilsClient.utilAnnotateCPLUsingPOST({ + template: text, + hugoSymbol: parseRes.hugoSymbol, + alteration: props.mutationName ?? '', + cancerType: props.cancerTypeName ?? '', + }); + setPreviewText(response.data); + } catch (error) { + setPreviewText(null); + throw new SentryError('Cannot preview text', { firebasePath, previewText }); + } finally { + setIsLoading(false); + } + }; + + if (isLoading) { + return ; + } + + return ( +
+ +
+ ); +}; + +const mapStoreToProps = ({ firebaseAppStore }: IRootStore) => ({ + db: firebaseAppStore.firebaseDb, +}); + +type StoreProps = Partial>; + +export default inject(mapStoreToProps)(PreviewTextArea); diff --git a/src/main/webapp/app/shared/firebase/input/RealtimeBasicInput.tsx b/src/main/webapp/app/shared/firebase/input/RealtimeBasicInput.tsx index 2e97e70dd..0d167e9da 100644 --- a/src/main/webapp/app/shared/firebase/input/RealtimeBasicInput.tsx +++ b/src/main/webapp/app/shared/firebase/input/RealtimeBasicInput.tsx @@ -10,6 +10,7 @@ import { FormFeedback, Input, Label, LabelProps } from 'reactstrap'; import { InputType } from 'reactstrap/types/lib/Input'; import * as styles from './styles.module.scss'; import { Unsubscribe } from 'firebase/database'; +import { resizeTextArea } from 'app/shared/util/utils'; export enum RealtimeInputType { TEXT = 'text', @@ -178,11 +179,6 @@ const RealtimeBasicInput: React.FunctionComponent = (props: return label === RADIO_OPTION_NONE; } - function resizeTextArea(textArea: HTMLInputElement | HTMLTextAreaElement) { - textArea.style.height = 'auto'; - textArea.style.height = `${textArea.scrollHeight}px`; - } - const inputStyle: React.CSSProperties | undefined = isCheckType ? { marginRight: '0.25rem', ...style } : undefined; const inputComponent = ( <> diff --git a/src/main/webapp/app/shared/firebase/input/RealtimeInputs.tsx b/src/main/webapp/app/shared/firebase/input/RealtimeInputs.tsx index 90e977d66..616c9f160 100644 --- a/src/main/webapp/app/shared/firebase/input/RealtimeInputs.tsx +++ b/src/main/webapp/app/shared/firebase/input/RealtimeInputs.tsx @@ -3,6 +3,7 @@ import RealtimeBasicInput, { IRealtimeBasicInput, RealtimeBasicLabel, RealtimeIn import TabsContainer, { ITabsContainer } from 'app/shared/tab/TabsContainer'; import CPLHelpTooltip from 'app/pages/curation/tooltip/CPLHelpTooltip'; import { IoHelpCircleOutline } from 'react-icons/io5'; +import PreviewTextArea from './PreviewTextArea'; /** * Text inputs @@ -18,7 +19,9 @@ export const RealtimeTextAreaInput = (props: Omit) return ; }; -export const RealtimeMultiTabTextAreaInput = (props: Omit) => { +export const RealtimeMultiTabTextAreaInput = ( + props: Omit & { mutationName?: string; cancerTypeName?: string }, +) => { const labelComponent = props.label && ( , + getContent: () => ( + + ), key: `${props.firebasePath}-preview`, }, ]} diff --git a/src/main/webapp/app/shared/util/utils.tsx b/src/main/webapp/app/shared/util/utils.tsx index d42ed107e..1dba14d96 100644 --- a/src/main/webapp/app/shared/util/utils.tsx +++ b/src/main/webapp/app/shared/util/utils.tsx @@ -431,3 +431,8 @@ export function shortenTextByCharacters(text: string, cutoff: number) { return words.join(separator); } } + +export function resizeTextArea(textArea: HTMLInputElement | HTMLTextAreaElement) { + textArea.style.height = 'auto'; + textArea.style.height = `${textArea.scrollHeight}px`; +} diff --git a/webpack/webpack.dev.js b/webpack/webpack.dev.js index 3f3140023..0f9513326 100644 --- a/webpack/webpack.dev.js +++ b/webpack/webpack.dev.js @@ -70,7 +70,7 @@ module.exports = async options => context: [ '/websocket', '/api', - '/legacy-api', + '/api/v1/utils', '/services', '/management', '/v3/api-docs', From a241f9ddc133d8a2f426efda53e3b649dde60e1a Mon Sep 17 00:00:00 2001 From: Calvin Lu <59149377+calvinlu3@users.noreply.github.com> Date: Tue, 29 Apr 2025 16:20:44 -0400 Subject: [PATCH 3/3] Update package.json --- package.json | 1 + 1 file changed, 1 insertion(+) diff --git a/package.json b/package.json index 9591b0180..6328f7327 100644 --- a/package.json +++ b/package.json @@ -61,6 +61,7 @@ "test:watch": "yarn run jest -- --watch", "updateAPI": "openapi-generator-cli generate -i http://localhost:9090/v3/api-docs -g typescript-axios -o src/main/webapp/app/shared/api/generated/curation --type-mappings set=Array", "updateCoreAPI": "curl http://localhost:8000/oncokb/api/v1/v2/api-docs?group=Private%20APIs | jq '.definitions.ResponseEntity.properties.statusCode.enum |= unique' > /tmp/updateCoreAPI.json && openapi-generator-cli generate -i /tmp/updateCoreAPI.json -g typescript-axios -o src/main/webapp/app/shared/api/generated/core --type-mappings List=any", + "updateDefaultCoreAPI": "curl 'http://localhost:8080/app/api/v1/v2/api-docs?group=default' > /tmp/updateDefaultCoreAPI.json && openapi-generator-cli generate -i /tmp/updateDefaultCoreAPI.json -g typescript-axios -o src/main/webapp/app/shared/api/generated/defaultCore --type-mappings List=any", "wdio": "cross-env TS_NODE_PROJECT=src/test/javascript/tsconfig.json wdio run ./wdio.conf.ts", "webapp:build": "yarn run clean-www && yarn run webapp:build:dev --", "webapp:build:dev": "webpack --config webpack/webpack.dev.js --env stats=minimal",