Replace definitions with $defs in JSON Schema artifact

Pipfile

@@ -7,32 +7,29 @@ name = "pypi"
 # For LinkML, we use the `ccdh-dev` branch, which we manually keep in sync with LinkML's main branch
 # as well as some additional changes required for CRDCH generation.
 linkml = {editable = true, ref = "ccdh-dev", git = "https://github.com/cancerDHC/linkml.git"}
-
 # Since we use the development version of LinkML, we also use the development version of linkml-runtime.
 # This may sometimes cause issues between this and LinkML.
 linkml-runtime = {editable = true, git = "https://github.com/linkml/linkml-runtime.git"}
-
 pyparsing = "<=2.4.7"
 rdflib-pyld-compat = "*" # resinstating after removal by migration to linkml model template
 
 [dev-packages]
 pyyaml = "*"            # For reading and writing YAML files.
-
 # Packages needed for testing.
 pytest = "~=6.2.4"
 tox = "*"
 typing_extensions = "*" # This is a tox prereq for Python 3.7, but not installed by Pipenv.
 twine = "*" # should this go in make-venv/Pipfile ?
-
 # Packages needed by sheet2linkml.
 black = "==v21.5b1"     # Used for code linting.
 requests = "*"          # For making HTTP requests.
 pygsheets = "*"         # For accessing Google Sheets.
 python-dotenv = "*"     # For reading .env files.
-
 # Packages needed for building and publishing documentation.
 mike = "*"
 mkdocs-material = "*"
+assertpy = "*"
+jsonschema = "*"
 
 [pipenv]
 allow_prereleases = true # added by migration to linkml model template

crdch_model/csv/crdch_model.csv

@@ -45,7 +45,7 @@ SpecimenTransportActivity,,An activity through which a specimen is transported b
 Subject,,Demographics and other administrative information about an individual or animal receiving care or other health-related services.
 Substance,,"A type of material substance, or instance thereof,  as used in a particular application. May include information about the role the substance played in a particular application."
 TimePeriod,,A period of time between a start and end time point.
-TimePoint,,"A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, or specification in terms of offset from a defined index."
+TimePoint,,"A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred."
 TobaccoExposureObservation,,"A structured object that describes a single data item about an individual's exposure to tobacco, as generated through a point-in-time observation, measurement, or interpretation."
 Treatment,,Represent medication administration or other treatment types.
 

crdch_model/graphql/crdch_model.graphql

@@ -82,10 +82,12 @@ type CodeableConcept
 type Coding
   {
     code: CrdchString!
+    label: CrdchString
     system: CrdchString!
-    systemURL: CrdchString
     systemVersion: CrdchString
-    label: CrdchString
+    valueSet: CrdchString
+    valueSetVersion: CrdchString
+    tag: [CrdchString]
   }
 
 type Diagnosis
@@ -94,7 +96,7 @@ type Diagnosis
     identifier: [Identifier]
     subject: Subject
     ageAtDiagnosis: Quantity
-    yearAtDiagnosis: CrdchInteger
+    diagnosisDate: TimePoint
     condition: EnumCRDCHDiagnosisCondition
     primarySite: [BodySite]
     metastaticSite: [BodySite]
@@ -325,8 +327,8 @@ type Specimen
     qualityMeasure: [SpecimenQualityObservation]
     cellularCompositionType: EnumCRDCHSpecimenCellularCompositionType
     histologicalCompositionMeasures: [HistologicalCompositionObservationSet]
-    generalTissueMorphology: EnumCRDCHSpecimenGeneralTissueMorphology
-    specificTissueMorphology: EnumCRDCHSpecimenSpecificTissueMorphology
+    generalTissuePathology: EnumCRDCHSpecimenGeneralTissuePathology
+    specificTissuePathology: EnumCRDCHSpecimenSpecificTissuePathology
     preinvasiveTissueMorphology: EnumCRDCHSpecimenPreinvasiveTissueMorphology
     morphologyPathologicallyConfirmed: CrdchBoolean
     morphologyAssessorRole: EnumCRDCHSpecimenMorphologyAssessorRole

crdch_model/shex/crdch_model.shex

@@ -163,10 +163,12 @@ linkml:Nodeidentifier NONLITERAL
     (  $<Coding_tes> (  &<Entity_tes> ;
           rdf:type [ <Entity> ] ? ;
           <code> @<CrdchString> ;
+          <label> @<CrdchString> ? ;
           <system> @<CrdchString> ;
-          <systemURL> @<CrdchString> ? ;
-          <systemVersion> @<CrdchString> ? ;
-          <label> @<CrdchString> ?
+          <system_version> @<CrdchString> ? ;
+          <value_set> @<CrdchString> ? ;
+          <value_set_version> @<CrdchString> ? ;
+          <tag> @<CrdchString> *
        ) ;
        rdf:type [ <Coding> ] ?
     )
@@ -179,7 +181,7 @@ linkml:Nodeidentifier NONLITERAL
           <identifier> @<Identifier> * ;
           <subject> @<Subject> ? ;
           <age_at_diagnosis> @<Quantity> ? ;
-          <year_at_diagnosis> @<CrdchInteger> ? ;
+          <diagnosis_date> @<TimePoint> ? ;
           <condition> @<EnumCRDCHDiagnosisCondition> ? ;
           <primary_site> @<BodySite> * ;
           <metastatic_site> @<BodySite> * ;
@@ -490,8 +492,8 @@ linkml:Nodeidentifier NONLITERAL
           <quality_measure> @<SpecimenQualityObservation> * ;
           <cellular_composition_type> @<EnumCRDCHSpecimenCellularCompositionType> ? ;
           <histological_composition_measures> @<HistologicalCompositionObservationSet> * ;
-          <general_tissue_morphology> @<EnumCRDCHSpecimenGeneralTissueMorphology> ? ;
-          <specific_tissue_morphology> @<EnumCRDCHSpecimenSpecificTissueMorphology> ? ;
+          <general_tissue_pathology> @<EnumCRDCHSpecimenGeneralTissuePathology> ? ;
+          <specific_tissue_pathology> @<EnumCRDCHSpecimenSpecificTissuePathology> ? ;
           <preinvasive_tissue_morphology> @<EnumCRDCHSpecimenPreinvasiveTissueMorphology> ? ;
           <morphology_pathologically_confirmed> @<CrdchBoolean> ? ;
           <morphology_assessor_role> @<EnumCRDCHSpecimenMorphologyAssessorRole> ? ;

crdch_model/shex/crdch_model.shexj

@@ -797,6 +797,13 @@
                         "min": 1,
                         "max": 1
                      },
+                     {
+                        "type": "TripleConstraint",
+                        "predicate": "https://example.org/crdch/label",
+                        "valueExpr": "https://example.org/crdch/CrdchString",
+                        "min": 0,
+                        "max": 1
+                     },
                      {
                         "type": "TripleConstraint",
                         "predicate": "https://example.org/crdch/system",
@@ -806,24 +813,31 @@
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/systemURL",
+                        "predicate": "https://example.org/crdch/system_version",
                         "valueExpr": "https://example.org/crdch/CrdchString",
                         "min": 0,
                         "max": 1
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/systemVersion",
+                        "predicate": "https://example.org/crdch/value_set",
                         "valueExpr": "https://example.org/crdch/CrdchString",
                         "min": 0,
                         "max": 1
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/label",
+                        "predicate": "https://example.org/crdch/value_set_version",
                         "valueExpr": "https://example.org/crdch/CrdchString",
                         "min": 0,
                         "max": 1
+                     },
+                     {
+                        "type": "TripleConstraint",
+                        "predicate": "https://example.org/crdch/tag",
+                        "valueExpr": "https://example.org/crdch/CrdchString",
+                        "min": 0,
+                        "max": -1
                      }
                   ]
                },
@@ -894,8 +908,8 @@
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/year_at_diagnosis",
-                        "valueExpr": "https://example.org/crdch/CrdchInteger",
+                        "predicate": "https://example.org/crdch/diagnosis_date",
+                        "valueExpr": "https://example.org/crdch/TimePoint",
                         "min": 0,
                         "max": 1
                      },
@@ -2743,15 +2757,15 @@
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/general_tissue_morphology",
-                        "valueExpr": "https://example.org/crdch/EnumCRDCHSpecimenGeneralTissueMorphology",
+                        "predicate": "https://example.org/crdch/general_tissue_pathology",
+                        "valueExpr": "https://example.org/crdch/EnumCRDCHSpecimenGeneralTissuePathology",
                         "min": 0,
                         "max": 1
                      },
                      {
                         "type": "TripleConstraint",
-                        "predicate": "https://example.org/crdch/specific_tissue_morphology",
-                        "valueExpr": "https://example.org/crdch/EnumCRDCHSpecimenSpecificTissueMorphology",
+                        "predicate": "https://example.org/crdch/specific_tissue_pathology",
+                        "valueExpr": "https://example.org/crdch/EnumCRDCHSpecimenSpecificTissuePathology",
                         "min": 0,
                         "max": 1
                      },