Fix #168 Update Model per STS01 and OSA04 requirements - polish

model-desc/icdc-model-props.yml

@@ -149,15 +149,15 @@ PropDefinitions:
       - 'Yes'
       - 'No'
       - Not Applicable # accommodates situations where an adverse event is not attributed to any therapeutic agent and cannot therefore be limiting in terms of dosage
-    Req: 'Yes'
+    Req: Preferred # preferred instead of required accommodates siutations where the source data simply doesn't have any values, but if values are available, they must be compliant with the controlled vocabulary defined above
   unexpected_adverse_event:
     Desc: An indication as to whether any given adverse event observed during the clinical trial is completely unanticipated and therefore considered novel.
     Src: Data Owner(s)
     Enum:
       - 'Yes'
       - 'No'
       - Undefined # accommodates situations where there is any ambiguity in terms of an adverse event being expected or not
-    Req: 'Yes'
+    Req: Preferred # preferred instead of required accommodates siutations where the source data simply doesn't have any values, but if values are available, they must be compliant with the controlled vocabulary defined above 
   # agent props
   document_number:
     Desc: S/N of the executed CRF
@@ -1038,24 +1038,24 @@ PropDefinitions:
     Desc: An indication as to the nature of the file in terms of its content, i.e. what type of information the file contains, as opposed to the file's format.
     Src: Data Owner(s)
     Enum:
-      - Study Protocol
-      - Supplemental Data File
-      - Pathology Report
-      - Image File
-      - RNA Sequence File
-      - Whole Genome Sequence File
-      - Whole Exome Sequence File
+      - Affymetrix GeneChip Analysis File
+      - Array CGH Analysis File # required for the MGT01 study
+      - Data Analysis Whitepaper # for any document detailing a data analysis pipeline and/or methodology
       - DNA Methylation Analysis File
+      - Image File
       - Index File
-      - Array CGH Analysis File # required for the MGT01 study
-      - Variant Call File # for raw .vcf files
       - Mutation Annotation File # for annotated .maf files
-      - Variant Report # for reports detailing validated variants
-      - Data Analysis Whitepaper # for any document detailing a data analysis pipeline and/or methodology
-      - Affymetrix GeneChip Analysis File
+      - Pathology Report
+      - RNA Sequence File
       - scATAC Sequence File # required for the OSA04 study
       - scH5 Matrix File # required for the OSA04 study
       - scRNA Sequence File # required for the OSA04 study
+      - Study Protocol
+      - Supplemental Data File
+      - Variant Call File # for raw .vcf files
+      - Variant Report # for reports detailing validated variants
+      - Whole Exome Sequence File
+      - Whole Genome Sequence File
     Req: 'Yes'
     Tags:
        Labeled: File Type

model-desc/icdc-model.yml

@@ -594,6 +594,7 @@ Relationships:
         Mul: one_to_one
       - Src: diagnosis
         Dst: case
+        Mul: one_to_one # changed form many_to_one to one_to_one given that thus far, we've only ever needed to define a single primary  diagnosis, and as elegant as supporting multiple diagnoses might appear, it is becoming more trouble than it's worth
       - Src: cycle
         Dst: case
       - Src: follow_up