add hasStudy to Condition

.gitignore

@@ -140,7 +140,6 @@ dmypy.json
 #cogs
 .cogs/
 
-#pierrette's stuff
 config.yml
 great_expectations/
 harmonized_data/

project/graphql/include_schema.graphql

@@ -1,99 +1,95 @@
-type Aliquot
-  {
-  }
-
-type Assay
-  {
-    usesBiospecimen: Biospecimen
-    hasOutput: DataFile
-  }
-
 type Biospecimen
   {
+    hasStudy: Study
+    hasParticipant: Participant
+    sampleId: String!
+    sampleType: String!
     ageAtBiospecimenCollection: Integer
-    biospecimenStorage: String
+    parentSampleId: String
+    parentSampleType: String
     collectionId: String
     collectionSampleType: String
     containerId: String
-    hasDatafile: DataFile
-    hasParticipant: Participant
-    hasStudy: Study
-    laboratoryProcedure: String
-    parentSampleId: String
-    parentSampleType: String
-    sampleAvailability: EnumSampleAvailability
-    sampleId: String!
-    sampleType: String!
     volume: Float
     volumeUnit: String
-    hasAliquot: Aliquot
+    laboratoryProcedure: String
+    biospecimenStorage: String
+    sampleAvailability: EnumSampleAvailability
   }
 
 type Condition
   {
+    hasStudy: Study
     hasParticipant: Participant
+    eventId: String
+    eventType: String
+    conditionSourceText: String
     ageAtConditionObservation: Integer
-    mondoLabel: String
-    mondoCode: String
     conditionInterpretation: EnumConditionInterpretation
+    conditionStatus: EnumConditionStatus
     conditionDataSource: EnumConditionDataSource
     hpoLabel: String
     hpoCode: String
+    mondoLabel: String
+    mondoCode: String
     maxoLabel: String
     maxoCode: String
     otherLabel: String
     otherCode: String
+    measureType: String
+    measureValue: Integer
+    measureUnit: String
+    ageAtMeasurement: Integer
   }
 
 type DataFile
   {
-    accessUrl: Uriorcurie
-    collectionId: String
+    hasStudy: Study
+    hasParticipant: Participant
+    hasBiospecimen: Biospecimen
+    fileId: String
+    fileName: String!
+    fileHash: String
     dataAccess: EnumDataAccess
     dataCategory: String!
     dataType: String
     experimentalStrategy: String
-    fileId: String
-    fileName: String!
-    format: String!
-    hasBiospecimen: Biospecimen
-    hasParticipant: Participant
-    hasStudy: Study
-    participantId: String!
-    size: String
-    originalFileName: String!
-  }
-
-type FamilyGroup
-  {
-    hasParticipant: Participant
+    experimentalPlatform: String
+    fileFormat: String!
+    fileSize: Integer
+    fileSizeUnit: String
+    accessUrl: Uriorcurie
+    publicationDoi: String
   }
 
 type Participant
   {
-    ageAtLastVitalStatus: Integer
-    downSyndromeStatus: EnumDownSyndromeStatus!
-    ethnicity: EnumEthnicity!
-    externalId: String!
+    hasStudy: Study
+    participantId: String
+    participantExternalId: String!
     familyId: String
-    familyRelationship: Participant
     familyType: EnumFamilyType!
     fatherId: String
-    hasDatafile: DataFile
-    hasStudy: Study
     motherId: String
-    outcomesVitalStatus: EnumVitalStatus
-    participantId: String!
-    race: EnumRace!
+    siblingId: String
+    otherFamilyMemberId: String
+    familyRelationship: EnumFamilyRelationship
     sex: EnumSex!
+    race: EnumRace!
+    ethnicity: EnumEthnicity!
+    downSyndromeStatus: EnumDownSyndromeStatus!
+    ageAtFirstPatientEngagement: Integer!
+    firstPatientEngagementEvent: String!
+    outcomesVitalStatus: EnumVitalStatus
+    ageAtLastVitalStatus: Integer
   }
 
 type Study
   {
-    dbgap: String
-    program: EnumProgram!
     studyCode: EnumStudyCode!
     studyName: String!
+    program: EnumProgram!
+    dbgap: String
   }
 
 type Thing

project/jsonld/include_schema.context.jsonld

@@ -1,93 +1,113 @@
 {
-   "_comments": "Auto generated from include_schema.yaml by jsonldcontextgen.py version: 0.1.1\n    Generation date: 2022-11-09T12:04:48\n    Schema: include-schema\n    metamodel version: 1.7.0\n    model version: None\n    \n    id: https://w3id.org/include\n    description: \n    license: https://creativecommons.org/publicdomain/zero/1.0/\n    ",
+   "comments": {
+      "description": "Auto generated by LinkML jsonld context generator",
+      "generation_date": "2023-03-03T10:38:26",
+      "source": "include_schema.yaml"
+   },
    "@context": {
       "include": "https://w3id.org/include/",
       "linkml": "https://w3id.org/linkml/",
       "schema": "http://schema.org/",
       "skos": "http://www.w3.org/2004/02/skos/core#",
       "@vocab": "https://w3id.org/include/",
-      "access_url": {
+      "accessUrl": {
          "@type": "@id"
       },
-      "age_at_biospecimen_collection": {
+      "ageAtBiospecimenCollection": {
          "@type": "xsd:integer"
       },
-      "age_at_condition_observation": {
+      "ageAtConditionObservation": {
          "@type": "xsd:integer"
       },
-      "age_at_last_vital_status": {
+      "ageAtFirstPatientEngagement": {
          "@type": "xsd:integer"
       },
-      "condition_data_source": {
+      "ageAtLastVitalStatus": {
+         "@type": "xsd:integer"
+      },
+      "ageAtMeasurement": {
+         "@type": "xsd:integer"
+      },
+      "conditionDataSource": {
          "@context": {
             "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
          }
       },
-      "condition_interpretation": {
+      "conditionInterpretation": {
          "@context": {
             "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
          }
       },
-      "data_access": {
+      "conditionStatus": {
          "@context": {
             "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
          }
       },
-      "down_syndrome_status": {
+      "dataAccess": {
          "@context": {
             "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
          }
       },
-      "ethnicity": {
+      "downSyndromeStatus": {
          "@context": {
             "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
          }
       },
-      "family_relationship": {
-         "@type": "@id"
+      "ethnicity": {
+         "@context": {
+            "@vocab": "@null",
+            "text": "skos:notation",
+            "description": "skos:prefLabel",
+            "meaning": "@id"
+         }
       },
-      "family_type": {
+      "familyRelationship": {
          "@context": {
             "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
          }
       },
-      "has_aliquot": {
-         "@type": "@id"
+      "familyType": {
+         "@context": {
+            "@vocab": "@null",
+            "text": "skos:notation",
+            "description": "skos:prefLabel",
+            "meaning": "@id"
+         }
       },
-      "has_biospecimen": {
-         "@type": "@id"
+      "fileSize": {
+         "@type": "xsd:integer"
       },
-      "has_datafile": {
+      "hasBiospecimen": {
          "@type": "@id"
       },
-      "has_output": {
+      "hasParticipant": {
          "@type": "@id"
       },
-      "has_participant": {
+      "hasStudy": {
          "@type": "@id"
       },
-      "has_study": {
-         "@type": "@id"
+      "measureValue": {
+         "@type": "xsd:integer"
       },
-      "outcomes_vital_status": {
+      "outcomesVitalStatus": {
          "@context": {
             "@vocab": "@null",
             "text": "skos:notation",
@@ -111,7 +131,7 @@
             "meaning": "@id"
          }
       },
-      "sample_availability": {
+      "sampleAvailability": {
          "@context": {
             "@vocab": "@null",
             "text": "skos:notation",
@@ -127,17 +147,14 @@
             "meaning": "@id"
          }
       },
-      "study_code": {
+      "studyCode": {
          "@context": {
             "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
          }
       },
-      "uses_biospecimen": {
-         "@type": "@id"
-      },
       "volume": {
          "@type": "xsd:float"
       }