Merge pull request #41 from mc2-center/data-models-dev

24-1 model updates

.gitignore

@@ -38,3 +38,6 @@ vignettes/*.pdf
 # R Environment Variables
 .Renviron
 .venv/
+
+# schematic-related files
+great_expectations/

all_valid_values.csv

@@ -235,7 +235,7 @@ tumorGrade,Not Applicable
 specimenComp,Primary Tumor
 specimenComp,Metastatic Tumor
 specimenComp,Normal Tissue
-specimenComp,Mixed
+specimenComp,Tumor-adjacent Normal Tissue
 specimenComp,Not Applicable
 diseaseStatus,Distant met recurrence/progression
 diseaseStatus,Loco-regional recurrence/progression
@@ -1624,6 +1624,7 @@ tool_format,CSV
 tool_format,Chemical Data Format
 tool_format,Cytoband Format
 tool_format,Cytoscape Input File Format
+tool_format,DCC
 tool_format,DCD
 tool_format,DSV
 tool_format,Database Hits (Sequence) Format 
@@ -1871,6 +1872,7 @@ institution_name,Massachusetts Institute of Technology
 institution_name,Mayo Clinic
 institution_name,Memorial Sloan Kettering Cancer Center
 institution_name,Moffitt Cancer Center
+institution_name,Northeastern University
 institution_name,New York University
 institution_name,Northwestern University
 institution_name,Oregon Health & Science University

dca_config/dca-template-config.json

@@ -0,0 +1,56 @@
+{
+  "manifest_schemas": [
+    {
+      "display_name": "Dataset View",
+      "schema_name": "DatasetView",
+      "type": "record"
+    },
+    {
+      "display_name": "Educational Resource",
+      "schema_name": "EducationalResource",
+      "type": "record"
+    },
+    {
+      "display_name": "Publication View",
+      "schema_name": "PublicationView",
+      "type": "record"
+    },
+    {
+      "display_name": "Tool View",
+      "schema_name": "ToolView",
+      "type": "record"
+    },
+    {
+      "display_name": "Biospecimen",
+      "schema_name": "Biospecimen",
+      "type": "record"
+    },
+    {
+      "display_name": "NanoString GeoMx DSP Level 1",
+      "schema_name": "NanoStringGeoMxDSPLevel1",
+      "type": "record"
+    },
+    {
+      "display_name": "NanoString GeoMx DSP Level 2",
+      "schema_name": "NanoStringGeoMxDSPLevel2",
+      "type": "record"
+    },
+    {
+      "display_name": "NanoString GeoMx DSP Level 3",
+      "schema_name": "NanoStringGeoMxDSPLevel3",
+      "type": "record"
+    },
+    {
+      "display_name": "NanoString GeoMX ROI Segment Annotation",
+      "schema_name": "NanoStringGeoMXROISegmentAnnotation",
+      "type": "record"
+    },
+    {
+      "display_name": "NanoString GeoMx DSP Imaging Level 2",
+      "schema_name": "NanoStringGeoMxDSPImagingLevel2",
+      "type": "record"
+    }
+  ],
+  "service_version": "v23.8.1",
+  "schema_version": ""
+}