Merge pull request #239 from include-dcc/2024-12-30_PL

2024 12 30 pl

Author: lopierra

src/data_validation/validate_study.py

@@ -20,15 +20,15 @@ def validate_study_entry(row):
             researchDomain = row['research domain'].split('|') if handle_nan(row['research domain']) else [],
             participantLifespanStage = row['participant lifespan stage'].split('|') if handle_nan(row['participant lifespan stage']) else [],
             selectionCriteria = handle_nan(row['selection criteria']),
-            studyDesign = handle_nan(row['study design']),
+            studyDesign = row['study design'].split('|') if handle_nan(row['study design']) else [],
             clinicalDataSourceType = row['clinical data source type'].split('|') if handle_nan(row['clinical data source type']) else [],
             dataCategory = row['data category'].split('|') if handle_nan(row['data category']) else [],
             studyWebsite = handle_nan(row['study website']),
             dbgap = row['dbgap'].split('|') if handle_nan(row['dbgap']) else [],
             publication = str(row['publication']).split('|') if handle_nan(row['publication']) else [],
             expectedNumberOfParticipants = handle_nan(row['expected number of participants']),
             guidType = row['guid type'],
-            guidMapped = bool(row['guids mapped?']),
+            guidMapped = bool(row['guid mapped']),
             acknowledgments = row['acknowledgments'].split('|') if handle_nan(row['acknowledgments']) else [],
             citationStatement = row['citation statement'].split('|') if handle_nan(row['citation statement']) else []
         )

src/linkml/include_assay.yaml

@@ -88,8 +88,8 @@ classes:
     - sampleExternalId #usage of this field in multi-sample files is TBD
     - fileName
     - fileGlobalId
-    - fileS3Location
     - fileUploadLocation
+    - fileS3Location
     - drsUri
     - fileHash
     - dataAccess

src/linkml/include_participant.yaml

@@ -52,21 +52,12 @@ classes:
     - firstPatientEngagementEvent
     - outcomesVitalStatus
     - ageAtLastVitalStatus
-  # FamilyGroup:
-  #   name: FamilyGroup
-  #   definition_uri: include:FamilyGroup
-  #   annotations:
-  #     required:
-  #       tag: required
-  #       value: 'False'
-  #     requires_component:
-  #       tag: requires_component
-  #       value: Study,Participant
-  #   description: A group of Participants in the same Study
-  #   title: FamilyGroup
-  #   is_a: Thing
-  #   slots:
-  #   - has_member # add this slot later
+    slot_usage:
+      studyCode:
+        multivalued: true
+      participantExternalId:
+        multivalued: true
+
   Condition:
     title: Condition
     annotations:

src/linkml/include_study.yaml

@@ -224,6 +224,7 @@ slots:
     title: Study Design
     range: enum_studyDesign 
     required: true
+    multivalued: true
   clinicalDataSourceType: 
     definition_uri: include:clinicalDataSourceType
     description: Source(s) of data collected from study participants; pipe-separated if multiple
@@ -389,6 +390,9 @@ enums:
       bri_dsr:
         text: bri_dsr
         title: BRI-DSR
+      ccds:
+        text: ccds
+        title: CCDS
       child_ds:
         text: child_ds
         title: CHILD-DS
@@ -398,6 +402,9 @@ enums:
       decidas:
         text: decidas
         title: DECIDAS
+      ds_arc:
+        text: ds_arc
+        title: DS-ARC
       ds_brain:
         text: ds_brain
         title: DS-Brain
@@ -437,6 +444,9 @@ enums:
       dsc:
         text: dsc
         title: DSC
+      dsrrs:
+        text: dsrrs
+        title: DSRRS
       ecods:
         text: ecods
         title: ECODS
@@ -594,9 +604,9 @@ enums:
       cognitive_behavioral:
         text: cognitive_behavioral
         title: Cognitive/Behavioral
-      immune_maps:
-        text: immune_maps
-        title: Immune Maps
+      immune_profiling:
+        text: immune_profiling
+        title: Immune Profiling
       imaging:
         text: imaging
         title: Imaging