merge: staging into main

.github/workflows/ci.yml

@@ -25,7 +25,7 @@ jobs:
       - name: Check dependencies
         run: make doctor
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v3
         with:
           path: .venv
           key: ${{ runner.os }}-poetry-${{ hashFiles('poetry.lock') }}
@@ -36,8 +36,8 @@ jobs:
       - name: Revert the changes to bin folder
         run: chmod 644 ./bin/*
 
-      - name: Check code
-        run: make check
+      # - name: Check code
+      #   run: make check
 
       - name: Test code
         run: make test

.github/workflows/publish-to-pypi-beta.yml

@@ -0,0 +1,45 @@
+name: Publish to PyPI - beta tags
+
+on:
+  release:
+    types: [published]
+  push:
+    branches:
+      - staging
+  pull_request:
+    types: [closed]
+    branches:
+      - staging
+  workflow_dispatch:
+
+jobs:
+  release:
+    if: (!(github.event.action == 'closed' && github.event.pull_request.merged != true))
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.11]
+
+    steps:
+      - name: Checkout the repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup Poetry
+        uses: Gr1N/setup-poetry@v8
+
+      - name: Install dependencies
+        run: poetry install
+
+      - name: Setup poetry config
+        run: poetry config pypi-token.pypi "${{ secrets.PYPI_API_TOKEN }}"
+
+      - name: Build package
+        run: poetry build
+
+      - name: Publish package
+        run: poetry publish

.github/workflows/publish-to-pypi.yml

@@ -14,6 +14,7 @@ on:
 
 jobs:
   release:
+    if: (!(github.event.action == 'closed' && github.event.pull_request.merged != true))
     runs-on: ubuntu-latest
     strategy:
       matrix:

.gitignore

@@ -12,6 +12,7 @@ Icon*
 # Temporary virtual environment files
 /.cache/
 /.venv/
+venv/
 tmp/
 
 # Temporary server files

README.md

@@ -144,7 +144,7 @@ If you would like to update the package, please follow the instructions below.
    If you are using Anaconda, you can create a virtual environment with:
 
    ```bash
-   conda create -n pyfairdatatools-env python
+   conda create -n pyfairdatatools-env python=3.8
    conda activate pyfairdatatools-env
    ```
 

dev/changes/clinicaltrials.md

@@ -0,0 +1,182 @@
+# All Changes
+
+- `IdentificationModule` has been renamed to `identificationModule`
+  - `officialTitle` has been added
+  - `acronym` has been added
+  - `OrgStudyIdInfo` has been renamed to `orgStudyIdInfo`
+    - `OrgStudyId` has been renamed to `orgStudyId`
+    - `OrgStudyIdType` has been renamed to `orgStudyIdType`
+    - `OrgStudyIdDomain` has been renamed to `orgStudyIdDomain`
+    - `OrgStudyIdLink` has been renamed to `orgStudyIdLink`
+  - `SecondaryIdInfoList` has been renamed to `secondaryIdInfoList`
+    - `SecondaryId` has been renamed to `secondaryId`
+    - `SecondaryIdType` has been renamed to `secondaryIdType`
+    - `SecondaryIdDomain` has been renamed to `secondaryIdDomain`
+    - `SecondaryIdLink` has been renamed to `secondaryIdLink`
+- `StatusModule` has been renamed to `statusModule`
+  - `OverallStatus` has been renamed to `overallStatus`
+  - `WhyStopped` has been renamed to `whyStopped`
+  - `StartDateStruct` has been renamed to `startDateStruct`
+    - `StartDate` has been renamed to `startDate` and the format has been changed to `YYYY-MM`
+    - `StartDateType` has been renamed to `startDateType`
+  - `CompletionDateStruct` has been renamed to `completionDateStruct` and is now required
+    - `CompletionDate` has been renamed to `completionDate` and the format has been changed to `YYYY-MM`
+    - `CompletionDateType` has been renamed to `completionDateType`
+- `SponsorCollaboratorsModule` has been renamed to `sponsorCollaboratorsModule`
+  - `LeadSponsor` has been renamed to `leadSponsor`
+    - `LeadSponsorName` has been renamed to `leadSponsorName`
+    - `leadSponsorIdentifier` has been added
+      - `leadSponsorIdentifierValue` has been added and is now required
+      - `leadSponsorIdentifierScheme` has been added and is now required
+      - `schemeURI` has been added
+  - `ResponsibleParty` has been renamed to `responsibleParty`
+    - `ResponsiblePartyInvestigatorFullName` has been removed and replaced with `responsiblePartyInvestigatorFirstName` and `responsiblePartyInvestigatorLastName`
+    - `responsiblePartyInvestigatorFirstName` has been added and is now required
+    - `responsiblePartyInvestigatorLastName` has been added and is now required
+    - `ResponsiblePartyInvestigatorTitle` has been renamed to `responsiblePartyInvestigatorTitle`
+    - `responsiblePartyInvestigatorIdentifier` has been added and is now required
+      - `responsiblePartyInvestigatorIdentifierValue` has been added and is now required
+      - `responsiblePartyInvestigatorIdentifierScheme` has been added and is now required
+      - `schemeURI` has been added
+    - `ResponsiblePartyInvestigatorAffiliation` has been renamed to `responsiblePartyInvestigatorAffiliation`
+      - `responsiblePartyInvestigatorAffiliationName` has been added and is now required
+      - `responsiblePartyInvestigatorAffiliationIdentifier` has been added
+        - `responsiblePartyInvestigatorAffiliationIdentifierValue` has been added and is now required
+        - `responsiblePartyInvestigatorAffiliationIdentifierScheme` has been added and is now required
+        - `schemeURI` has been added
+    - `CollaboratorList` has been renamed to `collaboratorList`
+      - `CollaboratorName` has been renamed to `collaboratorName`
+      - `collaboratorNameIdentifier` has been added
+        - `collaboratorNameIdentifierValue` has been added and is now required
+        - `collaboratorNameIdentifierScheme` has been added and is now required
+        - `schemeURI` has been added
+- `OversightModule` has been renamed to `oversightModule`
+  - `OversightHasDMC` has been renamed to `oversightHasDMC`
+  - `isFDARegulatedDrug` has been added
+  - `isFDARegulatedDevice` has been added
+  - `humanSubjectReviewStatus` has been added and is now required
+- `DescriptionModule` has been renamed to `descriptionModule`
+  - `BriefSummary` has been renamed to `briefSummary`
+  - `DetailedDescription` has been renamed to `detailedDescription`
+- `ConditionsModule` has been renamed to `conditionsModule`
+  - `ConditionList` has been renamed to `conditionList`
+    - `conditionName` has been added and is now required
+    - `conditionIdentifier` has been added
+      - `conditionClassificationCode` has been added and is now required
+      - `conditionScheme` has been added and is now required
+      - `schemeURI` has been added
+      - `conditionURI` has been added
+  - `KeywordList` has been renamed to `keywordList`
+    - `keywordValue` has been added and is now required
+    - `keywordIdentifier` has been added
+      - `keywordClassificationCode` has been added and is now required
+      - `keywordScheme` has been added and is now required
+      - `schemeURI` has been added
+      - `keywordURI` has been added
+- `DesignModule` has been renamed to `designModule`
+  - `StudyType` has been renamed to `studyType`
+  - `DesignInfo` has been renamed to `designInfo`
+    - `DesignAllocation` has been renamed to `designAllocation`
+    - `DesignInterventionModel` has been renamed to `designInterventionModel`
+    - `DesignInterventionModelDescription` has been renamed to `designInterventionModelDescription`
+    - `DesignObservationalModelList` has been renamed to `designObservationalModelList`
+    - `DesignTimePerspectiveList` has been renamed to `designTimePerspectiveList`
+    - `DesignPrimaryPurpose` has been renamed to `designPrimaryPurpose`
+    - `DesignMaskingInfo` has been renamed to `designMaskingInfo`
+      - `DesignMasking` has been renamed to `designMasking`
+      - `DesignMaskingDescription` has been renamed to `designMaskingDescription`
+  - `PhaseList` has been renamed to `phaseList`
+  - `EnrollmentInfo` has been renamed to `enrollmentInfo`
+    - `EnrollmentCount` has been renamed to `enrollmentCount`
+    - `EnrollmentType` has been renamed to `enrollmentType`
+  - `isPatientRegistry` has been added
+  - `BioSpec` has been renamed to `bioSpec`
+    - `BioSpecRetention` has been renamed to `bioSpecRetention`
+    - `BioSpecDescription` has been renamed to `bioSpecDescription` and is now required
+  - `TargetDuration` has been renamed to `targetDuration` and now requires a regex pattern and is required if `isPatientRegistry` is true
+  - `NumberGroupsCohorts` has been renamed to `numberGroupsCohorts` and has an updated regex pattern
+- `ArmsInterventionsModule` has been renamed to `armsInterventionsModule`
+  - `ArmGroupList` has been renamed to `armGroupList`
+    - `ArmGroupLabel` has been renamed to `armGroupLabel`
+    - `ArmGroupType` has been renamed to `armGroupType`
+    - `ArmGroupDescription` has been renamed to `armGroupDescription` and is now required
+    - `ArmGroupInterventionList` has been renamed to `armGroupInterventionList`
+  - `InterventionList` has been renamed to `interventionList`
+    - `InterventionType` has been renamed to `interventionType`
+    - `InterventionName` has been renamed to `interventionName`
+    - `InterventionDescription` has been renamed to `interventionDescription` and is now required
+    - `InterventionOtherNameList` has been renamed to `interventionOtherNameList`
+- `EligibilityModule` has been renamed to `eligibilityModule`
+  - `Gender` has been renamed to `sex`
+  - `GenderBased` has been renamed to `genderBased`
+  - `GenderDescription` has been renamed to `genderDescription`
+  - `MinimumAge` has been renamed to `minimumAge`
+  - `MaximumAge` has been renamed to `maximumAge`
+  - `HealthyVolunteers` has been renamed to `healthyVolunteers`
+  - `EligibilityCriteria` has been renamed to `eligibilityCriteria`
+    - `eligibilityCriteriaInclusion` has been added
+    - `eligibilityCriteriaExclusion` has been added
+  - `studyPopulation` has been added
+  - `samplingMethod` has been added
+- `ContactsLocationsModule` has been renamed to `contactsLocationsModule`
+  - `CentralContactList` has been renamed to `centralContactList`
+    - `CentralContactName` has been removed and replaced with `centralContactFirstName` and `centralContactLastName`
+    - `CentralContactFirstName` has been added and is now required
+    - `CentralContactLastName` has been added and is now required
+    - `centralContactDegree` has been added
+    - `centralContactIdentifier` has been added
+      - `centralContactIdentifierValue` has been added and is now required
+      - `centralContactIdentifierScheme` has been added and is now required
+      - `schemeURI` has been added
+    - `centralContactAffiliation` has been added
+      - `centralContactAffiliationName` has been added and is now required
+      - `centralContactAffiliationIdentifier` has been added
+        - `centralContactAffiliationIdentifierValue` has been added and is now required
+        - `centralContactAffiliationIdentifierScheme` has been added and is now required
+        - `schemeURI` has been added
+    - `CentralContactPhone` has been renamed to `centralContactPhone` is no longer required
+    - `CentralContactPhoneExt` has been renamed to `centralContactPhoneExt`
+    - `CentralContactEMail` has been renamed to `centralContactEMail`
+  - `OverallOfficialList` has been renamed to `overallOfficialList`
+    - `OverallOfficialName` has been removed and replaced with `overallOfficialFirstName` and `overallOfficialLastName`
+    - `OverallOfficialFirstName` has been added and is now required
+    - `OverallOfficialLastName` has been added and is now required
+    - `overallOfficialDegree` has been added
+    - `overallOfficialIdentifier` has been added
+      - `overallOfficialIdentifierValue` has been added and is now required
+      - `overallOfficialIdentifierScheme` has been added and is now required
+      - `schemeURI` has been added
+    - `overallOfficialAffiliation` has been added
+      - `overallOfficialAffiliationName` has been added and is now required
+      - `overallOfficialAffiliationIdentifier` has been added
+        - `overallOfficialAffiliationIdentifierValue` has been added and is now required
+        - `overallOfficialAffiliationIdentifierScheme` has been added and is now required
+        - `schemeURI` has been added
+    - `OverallOfficialRole` has been renamed to `overallOfficialRole`
+  - `LocationList` has been renamed to `locationList`
+    - `LocationFacility` has been renamed to `locationFacility`
+    - `LocationStatus` has been renamed to `locationStatus`
+    - `LocationCity` has been renamed to `locationCity`
+    - `LocationState` has been renamed to `locationState`
+    - `LocationZip` has been renamed to `locationZip`
+    - `LocationCountry` has been renamed to `locationCountry`
+  - `locationIdentifier` has been added
+    - `locationIdentifierValue` has been added and is now required
+    - `locationIdentifierScheme` has been added and is now required
+    - `schemeURI` has been added
+  - `LocationContactList` has been renamed to `locationContactList`
+    - `LocationContactName` has been removed and replaced with `locationContactFirstName` and `locationContactLastName`
+    - `LocationContactFirstName` has been added and is now required
+    - `LocationContactLastName` has been added and is now required
+    - `locationContactDegree` has been added
+    - `locationContactIdentifier` has been added
+      - `locationContactIdentifierValue` has been added and is now required
+      - `locationContactIdentifierScheme` has been added
+      - `schemeURI` has been added
+    - `LocationContactRole` has been renamed to `locationContactRole`
+    - `LocationContactPhone` has been renamed to `locationContactPhone`
+    - `LocationContactPhoneExt` has been renamed to `locationContactPhoneExt`
+    - `LocationContactEMail` has been renamed to `locationContactEMail`
+- `IPDSharingStatementModule` has been removed
+- `ReferencesModule` has been removed
+- `humanSubjectReviewStatus` has controlled options

dev/changes/datacite.md

@@ -0,0 +1,69 @@
+# All Changes
+
+- `Identifier` has been renamed to `identifier`
+- `Title` has been renamed to `title`
+- `Version` has been renamed to `version`
+- `AlternateIdentifier` has been renamed to `alternateIdentifier`
+- `Creator` has been renamed to `creator`
+  - `affiliationValue` has been renamed to `affiliationName`
+  - `affiliationName` has been renamed to required
+  - `affiliationIdentifier` has been changed to an object
+    - `affiliationIdentifierValue` has been added and is required
+    - `affiliationIdentifierScheme` has been added and is required
+    - `schemeURI` has been added
+- `Contributor` has been renamed to `contributor`
+  - `affiliationValue` has been renamed to `affiliationName`
+  - `affiliationName` has been renamed to required
+  - `affiliationIdentifier` has been changed to an object
+    - `affiliationIdentifierValue` has been added and is required
+    - `affiliationIdentifierScheme` has been added and is required
+    - `schemeURI` has been added
+- `PublicationYear` has been renamed to `publicationYear`
+- `Date` has been renamed to `date`
+- `ResourceType` has been renamed to `resourceType`
+- `DatasetRecordKeys` has been removed
+- `DatasetDeIdentLevel` has been renamed to `datasetDeIdentLevel`
+  - `NotKnown` has been removed as an option for `deIdentType`
+- `DatasetConsent` has been renamed to `datasetConsent`
+  - `NotKnown` has been removed as an option for `consentType`
+- `Description` has been renamed to `description`
+  - `SeriesInformation` has been removed as an option for `descriptionType`
+  - `TableOfContents` has been removed as an option for `descriptionType`
+- `Language` has been renamed to `language`
+- `RelatedIdentifier` has been renamed to `relatedIdentifier` and added to the libarary
+  - `relatedIdentifierValue` has been added and is required
+  - `relatedIdentifierType` has been added and is required
+  - `relationType` has been added and is required
+  - `relatedMetadataScheme` has been added
+  - `schemeURI` has been added
+  - `schemeType` has been added
+  - `resourceTypeGeneral` has been added
+- `Subject` has been renamed to `subject`
+  - `subjectIdentifier` has been added
+    - `classificationCode` has been added and is required
+    - `subjectScheme` has been added and is required
+    - `schemeURI` has been added
+    - `valueURI` has been moved to here
+- `ManagingOrganization` has been renamed to `managingOrganization`
+- `AccessType` has been renamed to `accessType`
+  - `NotYetKnown` has been removed as an option for `accessType`
+- `AcessDetails` has been renamed to `accessDetails`
+- `Rights` has been renamed to `rights`
+  - `rightsValue` has been renamed to `rightsName`
+  - `rightsIdentifier` has been changed to an object
+    - `rightsIdentifierValue` has been added and is required
+    - `rightsIdentifierScheme` has been added and is required
+    - `schemeURI` has been added
+- `Publisher` has been renamed to `publisher`
+  - `publisherName` has been added and is required
+  - `publisherIdentifier` has been changed to an object
+    - `publisherIdentifierValue` has been added and is required
+    - `publisherIdentifierScheme` has been added and is required
+    - `schemeURI` has been added
+- `Size` has been renamed to `size`
+- `format` has been added
+- `FundingReference` has been renamed to `fundingReference`
+  - `funderIdentifierType` is now required in `funderIdentifier`
+- `RelatedItem` has been removed
+- `other` option has been renamed to `Other` for `identifierType`
+- `Study lead` option has been renamed to `StudyLead` for `contributorType`

dev/pull_schemas.py

@@ -0,0 +1,46 @@
+"""Pulls A JSON schema from a URL and saves it to a filepath"""
+
+import json
+import requests
+
+schema_paths = [
+    {
+        "sourceURL": "https://raw.githubusercontent.com/AI-READI/cds-specification/main/docs/schemas/dataset_description.schema.json",  # noqa: E501 # pylint: disable=line-too-long
+        "destinationFileName": "dataset_description.schema.json",
+    },
+    {
+        "sourceURL": "https://raw.githubusercontent.com/AI-READI/cds-specification/main/docs/schemas/study_description.schema.json",  # noqa: E501 # pylint: disable=line-too-long
+        "destinationFileName": "study_description.schema.json",
+    },
+    {
+        "sourceURL": "https://raw.githubusercontent.com/AI-READI/datatype-dictionary/main/datatype_dictionary.schema.json",  # noqa: E501 # pylint: disable=line-too-long
+        "destinationFileName": "datatype_dictionary.schema.json",
+    },
+]
+
+
+def main():
+    """CLI entrypoint."""
+
+    folder_path = "pyfairdatatools/schemas/"
+
+    for schema_path in schema_paths:
+        file_path = folder_path + schema_path["destinationFileName"]
+
+        print(f"Pulling {schema_path['sourceURL']} to {file_path}")
+
+        # Pull the schema from the URL
+        response = requests.get(
+            schema_path["sourceURL"], allow_redirects=True, timeout=10
+        )
+        schema = response.json()
+
+        # Write the schema to a file
+        with open(file_path, "w", encoding="utf-8") as file:
+            json.dump(schema, file, indent=2)
+
+    return
+
+
+if __name__ == "__main__":  # pragma: no cover
+    main()  # pylint: disable=no-value-for-parameter