💄 add family module diagram (#94)

NIH-NCPI · Jan 6, 2025 · abb361d · abb361d
1 parent bfd7fcb
commit abb361d
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Showing 10 changed files with 449 additions and 146 deletions.
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,7 @@
+{
+    "cSpell.words": [
+        "biospecimen",
+        "FHIR",
+        "NCPI"
+    ]
+}
diff --git a/fsh-generated/fsh-index.json b/fsh-generated/fsh-index.json
@@ -4,16 +4,16 @@
     "fshName": "AdaptorTrimmedCS",
     "fshType": "CodeSystem",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 54,
-    "endLine": 60
+    "startLine": 72,
+    "endLine": 78
   },
   {
     "outputFile": "CodeSystem-assay-strategy-cs.json",
     "fshName": "AssayStrategyCS",
     "fshType": "CodeSystem",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 18,
-    "endLine": 23
+    "startLine": 36,
+    "endLine": 41
   },
   {
     "outputFile": "CodeSystem-biospecimen-availability.json",
@@ -60,32 +60,32 @@
     "fshName": "HashTypeCS",
     "fshType": "CodeSystem",
     "fshFile": "modules/files.fsh",
-    "startLine": 28,
-    "endLine": 38
+    "startLine": 25,
+    "endLine": 35
   },
   {
     "outputFile": "CodeSystem-library-prep-cs.json",
     "fshName": "LibraryPrepCS",
     "fshType": "CodeSystem",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 32,
-    "endLine": 37
+    "startLine": 50,
+    "endLine": 55
   },
   {
     "outputFile": "CodeSystem-library-selection-cs.json",
     "fshName": "LibrarySelectionCS",
     "fshType": "CodeSystem",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 39,
-    "endLine": 44
+    "startLine": 57,
+    "endLine": 62
   },
   {
     "outputFile": "CodeSystem-metadata-elements.json",
     "fshName": "MetadataElements",
     "fshType": "CodeSystem",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 1,
-    "endLine": 16
+    "startLine": 19,
+    "endLine": 34
   },
   {
     "outputFile": "CodeSystem-ncpi-family-types.json",
@@ -108,24 +108,24 @@
     "fshName": "PlatformInstrumentCS",
     "fshType": "CodeSystem",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 25,
-    "endLine": 30
+    "startLine": 43,
+    "endLine": 48
   },
   {
     "outputFile": "CodeSystem-reference-genome-cs.json",
     "fshName": "ReferenceGenomeCS",
     "fshType": "CodeSystem",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 78,
-    "endLine": 86
+    "startLine": 96,
+    "endLine": 104
   },
   {
     "outputFile": "CodeSystem-related-file-type-code-system.json",
     "fshName": "RelatedFileTypeCS",
     "fshType": "CodeSystem",
     "fshFile": "modules/files.fsh",
-    "startLine": 40,
-    "endLine": 48
+    "startLine": 37,
+    "endLine": 45
   },
   {
     "outputFile": "CodeSystem-research-data-access-code.json",
@@ -156,8 +156,8 @@
     "fshName": "StrandednessCS",
     "fshType": "CodeSystem",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 46,
-    "endLine": 52
+    "startLine": 64,
+    "endLine": 70
   },
   {
     "outputFile": "CodeSystem-study-name-type.json",
@@ -180,16 +180,16 @@
     "fshName": "WorkflowToolCS",
     "fshType": "CodeSystem",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 70,
-    "endLine": 76
+    "startLine": 88,
+    "endLine": 94
   },
   {
     "outputFile": "CodeSystem-workflow-type-cs.json",
     "fshName": "WorkflowTypeCS",
     "fshType": "CodeSystem",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 62,
-    "endLine": 68
+    "startLine": 80,
+    "endLine": 86
   },
   {
     "outputFile": "Consent-gregor-gru-consent.json",
@@ -517,7 +517,15 @@
     "fshType": "Logical",
     "fshFile": "modules/files.fsh",
     "startLine": 5,
-    "endLine": 24
+    "endLine": 21
+  },
+  {
+    "outputFile": "StructureDefinition-SharedDataModelFileMetadata.json",
+    "fshName": "CdmFileMetadata",
+    "fshType": "Logical",
+    "fshFile": "modules/file-metadata.fsh",
+    "startLine": 1,
+    "endLine": 17
   },
   {
     "outputFile": "StructureDefinition-SharedDataModelPerson.json",
@@ -684,8 +692,8 @@
     "fshName": "ContentVersion",
     "fshType": "Extension",
     "fshFile": "modules/files.fsh",
-    "startLine": 80,
-    "endLine": 86
+    "startLine": 77,
+    "endLine": 83
   },
   {
     "outputFile": "StructureDefinition-description.json",
@@ -716,40 +724,40 @@
     "fshName": "FileFormat",
     "fshType": "Extension",
     "fshFile": "modules/files.fsh",
-    "startLine": 56,
-    "endLine": 62
+    "startLine": 53,
+    "endLine": 59
   },
   {
     "outputFile": "StructureDefinition-file-size.json",
     "fshName": "FileSize",
     "fshType": "Extension",
     "fshFile": "modules/files.fsh",
-    "startLine": 72,
-    "endLine": 78
+    "startLine": 69,
+    "endLine": 75
   },
   {
     "outputFile": "StructureDefinition-hash-extension.json",
     "fshName": "HashExtension",
     "fshType": "Extension",
     "fshFile": "modules/files.fsh",
-    "startLine": 104,
-    "endLine": 112
+    "startLine": 101,
+    "endLine": 109
   },
   {
     "outputFile": "StructureDefinition-hash-type.json",
     "fshName": "HashType",
     "fshType": "Extension",
     "fshFile": "modules/files.fsh",
-    "startLine": 96,
-    "endLine": 102
+    "startLine": 93,
+    "endLine": 99
   },
   {
     "outputFile": "StructureDefinition-hash-value.json",
     "fshName": "HashValue",
     "fshType": "Extension",
     "fshFile": "modules/files.fsh",
-    "startLine": 88,
-    "endLine": 94
+    "startLine": 85,
+    "endLine": 91
   },
   {
     "outputFile": "StructureDefinition-label-extension.json",
@@ -764,8 +772,8 @@
     "fshName": "LocationAccess",
     "fshType": "Extension",
     "fshFile": "modules/files.fsh",
-    "startLine": 64,
-    "endLine": 70
+    "startLine": 61,
+    "endLine": 67
   },
   {
     "outputFile": "StructureDefinition-ncpi-Study-Participant.json",
@@ -780,8 +788,8 @@
     "fshName": "NcpiBAMCRAM",
     "fshType": "Profile",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 162,
-    "endLine": 209
+    "startLine": 180,
+    "endLine": 227
   },
   {
     "outputFile": "StructureDefinition-ncpi-collected-sample.json",
@@ -799,6 +807,22 @@
     "startLine": 123,
     "endLine": 181
   },
+  {
+    "outputFile": "StructureDefinition-ncpi-drs-attachment.json",
+    "fshName": "DRSAttachment",
+    "fshType": "Profile",
+    "fshFile": "modules/files.fsh",
+    "startLine": 116,
+    "endLine": 123
+  },
+  {
+    "outputFile": "StructureDefinition-ncpi-drs-file.json",
+    "fshName": "NcpiDRSFile",
+    "fshType": "Profile",
+    "fshFile": "modules/files.fsh",
+    "startLine": 155,
+    "endLine": 169
+  },
   {
     "outputFile": "StructureDefinition-ncpi-family-relationship.json",
     "fshName": "NcpiFamilyRelationship",
@@ -812,40 +836,40 @@
     "fshName": "NcpiFASTQ",
     "fshType": "Profile",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 113,
-    "endLine": 160
+    "startLine": 131,
+    "endLine": 178
   },
   {
     "outputFile": "StructureDefinition-ncpi-file-metadata.json",
     "fshName": "NcpiFileMetadata",
     "fshType": "Profile",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 88,
-    "endLine": 95
+    "startLine": 106,
+    "endLine": 113
   },
   {
     "outputFile": "StructureDefinition-ncpi-file.json",
     "fshName": "NcpiFile",
     "fshType": "Profile",
     "fshFile": "modules/files.fsh",
-    "startLine": 116,
-    "endLine": 142
+    "startLine": 127,
+    "endLine": 153
   },
   {
     "outputFile": "StructureDefinition-ncpi-gene-fusion-expression.json",
     "fshName": "NcpiGeneFusionOrExpression",
     "fshType": "Profile",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 309,
-    "endLine": 356
+    "startLine": 327,
+    "endLine": 374
   },
   {
     "outputFile": "StructureDefinition-ncpi-maf.json",
     "fshName": "NcpiMAF",
     "fshType": "Profile",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 260,
-    "endLine": 307
+    "startLine": 278,
+    "endLine": 325
   },
   {
     "outputFile": "StructureDefinition-ncpi-non-collected-sample.json",
@@ -876,8 +900,8 @@
     "fshName": "NcpiProteomics",
     "fshType": "Profile",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 358,
-    "endLine": 405
+    "startLine": 376,
+    "endLine": 423
   },
   {
     "outputFile": "StructureDefinition-ncpi-research-access-policy.json",
@@ -916,8 +940,8 @@
     "fshName": "NcpiSpecimenCollection",
     "fshType": "Profile",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 97,
-    "endLine": 103
+    "startLine": 115,
+    "endLine": 121
   },
   {
     "outputFile": "StructureDefinition-ncpi-study-family.json",
@@ -932,8 +956,8 @@
     "fshName": "NcpiVCF",
     "fshType": "Profile",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 211,
-    "endLine": 258
+    "startLine": 229,
+    "endLine": 276
   },
   {
     "outputFile": "StructureDefinition-research-age-at-last-vital-status.json",
@@ -1020,8 +1044,8 @@
     "fshName": "SpecimenCollection",
     "fshType": "Extension",
     "fshFile": "modules/file-metadata.fsh",
-    "startLine": 105,
-    "endLine": 111
+    "startLine": 123,
+    "endLine": 129
   },
   {
     "outputFile": "StructureDefinition-study-family-focus.json",
@@ -1092,8 +1116,8 @@
     "fshName": "EDAMOntologyTerms",
     "fshType": "ValueSet",
     "fshFile": "modules/files.fsh",
-    "startLine": 50,
-    "endLine": 54
+    "startLine": 47,
+    "endLine": 51
   },
   {
     "outputFile": "ValueSet-mesh-terms.json",