[DT-2527] Fix data collection failure

DEVNOTES.md

@@ -59,7 +59,7 @@ Or, if not using docker:
 java -jar /path/to/consent.jar server /path/to/config/file
 ```
 
-Visit local swagger page: https://local.dsde-dev.broadinstitute.org:27443/swagger/
+Visit local swagger page: https://local.dsde-dev.broadinstitute.org:27443
 
 ### Debugging
 

src/main/java/org/broadinstitute/consent/http/models/DataAccessRequest.java

@@ -353,7 +353,7 @@ public static DataAccessRequest populateProgressReportFromJsonString(
     originalDataCopy.setExternalCollaborators(newData.getExternalCollaborators());
     originalDataCopy.setLabCollaborators(newData.getLabCollaborators());
     originalDataCopy.setProgressReportSummary(newData.getProgressReportSummary());
-    originalDataCopy.setIntellectualProperties(newData.getIntellectualProperties());
+    originalDataCopy.setIntellectualProperty(newData.getIntellectualProperty());
     originalDataCopy.setPublications(newData.getPublications());
     originalDataCopy.setPresentations(newData.getPresentations());
     originalDataCopy.setDmi(newData.getDmi());

src/main/java/org/broadinstitute/consent/http/models/DataAccessRequestData.java

@@ -124,7 +124,7 @@ public class DataAccessRequestData {
 
   // Progress Report/Closeout Fields
   private String progressReportSummary;
-  private List<IntellectualProperty> intellectualProperties;
+  private List<IntellectualProperty> intellectualProperty;
   private List<Publication> publications;
   private List<Presentation> presentations;
   private DataManagementIncident dmi;
@@ -709,12 +709,12 @@ public void setProgressReportSummary(String progressReportSummary) {
     this.progressReportSummary = progressReportSummary;
   }
 
-  public List<IntellectualProperty> getIntellectualProperties() {
-    return intellectualProperties;
+  public List<IntellectualProperty> getIntellectualProperty() {
+    return intellectualProperty;
   }
 
-  public void setIntellectualProperties(List<IntellectualProperty> intellectualProperties) {
-    this.intellectualProperties = intellectualProperties;
+  public void setIntellectualProperty(List<IntellectualProperty> intellectualProperty) {
+    this.intellectualProperty = intellectualProperty;
   }
 
   public List<Publication> getPublications() {

src/main/resources/assets/schemas/Author.yaml

@@ -0,0 +1,9 @@
+type: object
+description: An Author object.
+properties:
+  name:
+    type: string
+    description: The author's name.
+  orcId:
+    type: string
+    description: The author's ORCID identifier.

src/main/resources/assets/schemas/DataAccessRequest.yaml

@@ -233,9 +233,11 @@ properties:
   progressReportSummary:
     type: string
     description: A Progress Report Summary.
-  intellectualPropertySummary:
-    type: string
-    description: An Intellectual Property Summary.
+  intellectualProperty:
+    type: array
+    description: An array of intellectual property.
+    items:
+      $ref: './IntellectualProperty.yaml'
   publications:
     type: array
     description: An array of publications.

src/main/resources/assets/schemas/IntellectualProperty.yaml

@@ -0,0 +1,41 @@
+type: object
+description: An Intellectual Property object.
+properties:
+  type:
+    type: string
+    description: The type of intellectual property.
+  title:
+    type: string
+    description: The title of the intellectual property.
+  date:
+    type: string
+    description: The date associated with the intellectual property.
+  assignee:
+    type: string
+    description: The assignee of the intellectual property.
+  patentNumber:
+    type: string
+    description: The patent number.
+  filingDate:
+    type: boolean
+    description: The filing date indicator.
+  status:
+    type: string
+    description: The status of the intellectual property.
+  url:
+    type: string
+    description: The URL associated with the intellectual property.
+  contact:
+    type: string
+    description: The contact information for the intellectual property.
+  ipId:
+    type: string
+    description: The unique identifier for the intellectual property.
+  studyId:
+    type: string
+    description: The study ID associated with the intellectual property.
+  tags:
+    type: array
+    items:
+      type: string
+    description: Tags associated with the intellectual property.

src/main/resources/assets/schemas/Presentation.yaml

@@ -4,12 +4,11 @@ properties:
   title:
     type: string
     description: The title of the presentation.
-  link:
+  url:
     type: string
-    description: The link to the presentation.
+    description: The URL to the presentation.
   date:
     type: string
-    format: date
     description: The presentation date.
   authors:
     type: string
@@ -20,3 +19,30 @@ properties:
   citation:
     type: boolean
     description: Indicates if the dataset(s) were cited in the Presentation.
+  presentationId:
+    type: string
+    description: The unique identifier for the presentation.
+  studyId:
+    type: string
+    description: The study ID associated with the presentation.
+  presenter:
+    allOf:
+      - $ref: './Presenter.yaml'
+      - description: The presenter information.
+  event:
+    type: string
+    description: The event name.
+  location:
+    type: string
+    description: The location of the presentation.
+  format:
+    type: string
+    description: The format of the presentation.
+  access:
+    type: string
+    description: The access level of the presentation.
+  tags:
+    type: array
+    items:
+      type: string
+    description: Tags associated with the presentation.

src/main/resources/assets/schemas/Presenter.yaml

@@ -0,0 +1,9 @@
+type: object
+description: A Presenter object.
+properties:
+  name:
+    type: string
+    description: The presenter's name.
+  email:
+    type: string
+    description: The presenter's email address.

src/main/resources/assets/schemas/Publication.yaml

@@ -7,12 +7,13 @@ properties:
   pubmedId:
     type: string
     description: The PubMed ID of the publication.
-  date:
+  publishedDate:
     type: string
-    format: date
     description: The publication date.
   authors:
-    type: string
+    type: array
+    items:
+      $ref: './Author.yaml'
     description: The authors of the publication.
   bibliographicCitation:
     type: string
@@ -23,3 +24,26 @@ properties:
   citation:
     type: boolean
     description: Indicates if the dataset(s) were cited in the Publication.
+  publicationId:
+    type: string
+    description: The unique identifier for the publication.
+  studyId:
+    type: string
+    description: The study ID associated with the publication.
+  journal:
+    type: string
+    description: The journal name.
+  doi:
+    type: string
+    description: The Digital Object Identifier.
+  url:
+    type: string
+    description: The URL to the publication.
+  access:
+    type: string
+    description: The access level of the publication.
+  tags:
+    type: array
+    items:
+      type: string
+    description: Tags associated with the publication.

src/main/resources/changelog-master.xml

@@ -214,4 +214,6 @@
            relativeToChangelogFile="true" />
   <include file="changesets/changelog-consent-2025-12-02-alter-dataset-name-column.xml"
     relativeToChangelogFile="true" />
+  <include file="changesets/changelog-consent-2025-12-05-migrate-ip-presentations-publications.xml"
+           relativeToChangelogFile="true" />
 </databaseChangeLog>

src/main/resources/changesets/changelog-consent-2025-12-05-migrate-ip-presentations-publications.xml

@@ -0,0 +1,95 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog
+         https://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.1.xsd">
+  <changeSet id="changelog-consent-2025-12-05-migrate-intellectual-property-summary" author="kevinmarete">
+    <comment>
+      Migrate intellectualPropertySummary to intellectualProperty array format.
+      Transforms the summary field into an array with a title object.
+    </comment>
+    <sql>
+      UPDATE data_access_request
+      SET data = jsonb_set(
+        data #- '{intellectualPropertySummary}',
+        '{intellectualProperty}',
+        jsonb_build_array(
+          jsonb_build_object('title', data -> 'intellectualPropertySummary')
+        )
+                 )
+      WHERE parent_id IS NOT NULL
+        AND data -> 'intellectualPropertySummary' IS NOT NULL
+        AND data -> 'ipId' IS NULL;
+    </sql>
+  </changeSet>
+
+  <changeSet id="changelog-consent-2025-12-05-migrate-presentations-link-to-url" author="kevinmarete">
+    <comment>
+      Migrate presentations link field to url field in data_access_request table.
+      Removes the link field and sets the url field with the link value.
+    </comment>
+    <sql>
+      UPDATE data_access_request
+      SET data = jsonb_set(
+        data #- '{presentations,0,link}',
+        '{presentations,0,url}',
+        data -> 'presentations' -> 0 -> 'link'
+                 )
+      WHERE parent_id IS NOT NULL
+        AND jsonb_typeof(data -> 'presentations') = 'array'
+        AND data -> 'presentations' -> 0 -> 'link' IS NOT NULL
+        AND data -> 'presentations' -> 0 -> 'url' IS NULL;
+    </sql>
+  </changeSet>
+
+  <changeSet id="changelog-consent-2025-12-05-migrate-publications-authors-and-dates" author="kevinmarete">
+    <comment>
+      Migrate publications authors from string to array format and rename date to publishedDate.
+      Splits comma-separated authors into individual author objects.
+    </comment>
+    <sql splitStatements="false">
+      UPDATE data_access_request
+      SET data = jsonb_set(
+        data,
+        '{publications}',
+        (
+          SELECT jsonb_agg(
+                   CASE
+                     WHEN jsonb_typeof(pub -&gt; 'authors') = 'string'
+                       THEN (
+                       pub
+                         || jsonb_build_object(
+                         'authors',
+                         (
+                           SELECT jsonb_agg(jsonb_build_object('name', author_name))
+                           FROM regexp_split_to_table(pub -&gt;&gt; 'authors', ',') AS author_name
+                         )
+                            )
+                         || (CASE WHEN pub -&gt; 'date' IS NOT NULL AND pub -&gt; 'publishedDate' IS NULL
+                                    THEN jsonb_build_object('publishedDate', pub -&gt; 'date')
+                                  ELSE '{}'::jsonb END)
+                         #- (CASE WHEN pub -&gt; 'date' IS NOT NULL AND pub -&gt; 'publishedDate' IS NULL
+                                  THEN '{date}'::text[]
+                                  ELSE '{}'::text[] END)
+                       )
+                     ELSE pub
+                       || (CASE WHEN pub -&gt; 'date' IS NOT NULL AND pub -&gt; 'publishedDate' IS NULL
+                                  THEN jsonb_build_object('publishedDate', pub -&gt; 'date')
+                                ELSE '{}'::jsonb END)
+                       #- (CASE WHEN pub -&gt; 'date' IS NOT NULL AND pub -&gt; 'publishedDate' IS NULL
+                                THEN '{date}'::text[]
+                                ELSE '{}'::text[] END)
+                     END
+                 )
+          FROM jsonb_array_elements(data -&gt; 'publications') AS pub
+        )
+                 )
+      WHERE parent_id IS NOT NULL
+        AND jsonb_typeof(data -&gt; 'publications') = 'array'
+        AND EXISTS (
+        SELECT 1 FROM jsonb_array_elements(data -&gt; 'publications') AS pub
+        WHERE jsonb_typeof(pub -&gt; 'authors') = 'string'
+           OR (pub -&gt; 'date' IS NOT NULL AND pub -&gt; 'publishedDate' IS NULL)
+      );
+    </sql>
+  </changeSet>
+</databaseChangeLog>

src/test/java/org/broadinstitute/consent/http/service/DataAccessRequestServiceTest.java

@@ -901,7 +901,7 @@ private DataAccessRequest generateProgressReport() {
     progressReport.getData().setProgressReportSummary("Progress Report Summary");
     progressReport
         .getData()
-        .setIntellectualProperties(
+        .setIntellectualProperty(
             List.of(
                 new IntellectualProperty(
                     "Patent",