[SCHEMATIC-214] change data model and component

tests/data/example.model.csv

@@ -10,7 +10,7 @@ Cancer Type,,"Breast, Colorectal, Lung, Prostate, Skin",,,TRUE,DataProperty,,,
 Family History,,"Breast, Colorectal, Lung, Prostate, Skin",,,TRUE,DataProperty,,,list strict
 Biospecimen,,,"Sample ID, Patient ID, Tissue Status, Component",,FALSE,DataType,Patient,,
 Sample ID,,,,,TRUE,DataProperty,,,
-Tissue Status,,"Healthy, Malignant",,,TRUE,DataProperty,,,
+Tissue Status,,"Healthy, Malignant, None",,,TRUE,DataProperty,,,
 Bulk RNA-seq Assay,,,"Filename, Sample ID, File Format, Component",,FALSE,DataType,Biospecimen,,
 Filename,,,,,TRUE,DataProperty,,,#MockFilename filenameExists^^
 File Format,,"FASTQ, BAM, CRAM, CSV/TSV",,,TRUE,DataProperty,,,
@@ -24,8 +24,8 @@ Check List,,,,,TRUE,DataProperty,,,list
 Check List Enum,,"ab, cd, ef, gh",,,TRUE,DataProperty,,,list
 Check List Like,,,,,TRUE,DataProperty,,,list like
 Check List Like Enum,,"ab, cd, ef, gh",,,TRUE,DataProperty,,,list like
-Check List Strict,,,,,TRUE,DataProperty,,,list strict 
-Check List Enum Strict,,"ab, cd, ef, gh",,,TRUE,DataProperty,,,list strict 
+Check List Strict,,,,,TRUE,DataProperty,,,list strict
+Check List Enum Strict,,"ab, cd, ef, gh",,,TRUE,DataProperty,,,list strict
 Check Regex List,,,,,TRUE,DataProperty,,,list::regex match [a-f]
 Check Regex List Strict,,,,,TRUE,DataProperty,,,list strict::regex match [a-f]
 Check Regex List Like,,,,,TRUE,DataProperty,,,list like::regex match [a-f]

tests/data/example.model.jsonld

@@ -540,6 +540,9 @@
                 },
                 {
                     "@id": "bts:Malignant"
+                },
+                {
+                    "@id": "bts:None"
                 }
             ],
             "sms:displayName": "Tissue Status",
@@ -563,6 +566,23 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:None",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "None",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:TissueStatus"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "None",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:BulkRNA-seqAssay",
             "@type": "rdfs:Class",

tests/data/mock_manifests/Invalid_none_value_test_manifest.csv

@@ -0,0 +1,6 @@
+Sample ID,Patient ID,Tissue Status,Component
+1,1,Healthy,Biospecimen
+2,2,Malignant,Biospecimen
+3,3,None,Biospecimen
+4,4,None,Biospecimen
+5,5,InvalidValue,Biospecimen

tests/data/mock_manifests/Valid_none_value_test_manifest.csv

@@ -0,0 +1,6 @@
+Sample ID,Patient ID,Tissue Status,Component
+1,1,Healthy,Biospecimen
+2,2,Malignant,Biospecimen
+3,3,None,Biospecimen
+4,4,None,Biospecimen
+5,5,None,Biospecimen

tests/integration/test_commands.py

@@ -339,7 +339,7 @@ def test_generate_empty_google_sheet_manifests(
             assert False, f"Unexpected data validation found: {dv}"
         assert tissue_status_validation is not None
         assert tissue_status_validation.type == "list"
-        assert tissue_status_validation.formula1 == "Sheet2!$C$2:$C$3"
+        assert tissue_status_validation.formula1 == "Sheet2!$C$2:$C$4"
 
         # required fields are marked as “light blue”, while other non-required fields are marked as white.
         for col in ["Sample ID", "Patient ID", "Tissue Status", "Component"]:

tests/test_schemas.py

@@ -462,7 +462,7 @@ def test_generate_data_model_graph(self, helpers, data_model, data_model_labels)
         )
 
         # Check Edge directions
-        assert 4 == (len(graph.out_edges("TissueStatus")))
+        assert 6 == (len(graph.out_edges("TissueStatus")))
         assert 2 == (len(graph.in_edges("TissueStatus")))