Patch/issues 486 492

modules/Assay/Assay.yaml

@@ -206,6 +206,8 @@ enums:
       cell count:
         description: A procedure to determine the number of cells in a sample. Also used to mean the result of such a procedure.
         meaning: http://purl.obolibrary.org/obo/NCIT_C48938
+      cell painting:
+        source: https://www.nature.com/articles/nprot.2016.105
       cell proliferation:
         description: A cellular assay that allows for the measurement of the multiplication or reproduction of cells, resulting in the expansion of a cell population.
         meaning: http://purl.obolibrary.org/obo/ERO_0000636

modules/Assay/Platform.yaml

@@ -290,3 +290,7 @@ enums:
       Zeno Electronic Walkway:
         description: System for gait analysis.
         source: https://pubmed.ncbi.nlm.nih.gov/29286982/
+      ZetaView:
+        source: https://particle-metrix.com/zetaview/
+
+

modules/Template/Data.yaml

@@ -118,6 +118,7 @@ classes:
     - dissociationMethod
     - runType
     - libraryStrand
+    - libraryKitID
     - libraryPrep
     - libraryPreparationMethod
     - readPair

modules/props.yaml

@@ -578,9 +578,9 @@ slots:
     range: PresenceEnum
     required: false
     title: Leukemia
-  libraryID:
-    description: ''
-    required: false
+  libraryKitID:
+    description: Library kit ID.
+    required: true
   libraryPrep:
     description: The general strategy by which the library was prepared
     range: LibraryPrepEnum

registered-json-schemas/Dataset.json

@@ -29,6 +29,7 @@
         "CAPP-seq",
         "cell competition",
         "cell count",
+        "cell painting",
         "cell proliferation",
         "cell viability assay",
         "Child Behavior Checklist for Ages 1.5-5",

registered-json-schemas/PortalDataset.json

@@ -79,6 +79,7 @@
           "calcium retention capacity assay",
           "cell competition",
           "cell count",
+          "cell painting",
           "cell proliferation",
           "cell viability assay",
           "clinical data",
@@ -196,7 +197,10 @@
         "items": {
           "type": "string"
         },
-        "type": "array"
+        "type": [
+          "array",
+          "null"
+        ]
       },
       "creator": {
         "type": "string"
@@ -250,7 +254,10 @@
         "title": "dataType"
       },
       "description": {
-        "type": "string"
+        "type": [
+          "string",
+          "null"
+        ]
       },
       "diseaseFocus": {
         "items": {
@@ -333,11 +340,17 @@
           "title": "ManifestationEnum",
           "type": "string"
         },
-        "type": "array",
+        "type": [
+          "array",
+          "null"
+        ],
         "title": "manifestation"
       },
       "series": {
-        "type": "string"
+        "type": [
+          "string",
+          "null"
+        ]
       },
       "species": {
         "items": {
@@ -358,7 +371,10 @@
           "title": "SpeciesEnum",
           "type": "string"
         },
-        "type": "array",
+        "type": [
+          "array",
+          "null"
+        ],
         "title": "species"
       },
       "studyId": {
@@ -371,13 +387,22 @@
         "items": {
           "type": "string"
         },
-        "type": "array"
+        "type": [
+          "array",
+          "null"
+        ]
       },
       "yearProcessed": {
-        "type": "integer"
+        "type": [
+          "integer",
+          "null"
+        ]
       },
       "yearPublished": {
-        "type": "integer"
+        "type": [
+          "integer",
+          "null"
+        ]
       }
     },
     "required": [

registered-json-schemas/PortalStudy.json

@@ -4,10 +4,16 @@
     "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-portalstudy",
     "properties": {
       "accessRequirements": {
-        "type": "string"
+        "type": [
+          "string",
+          "null"
+        ]
       },
       "acknowledgementStatements": {
-        "type": "string"
+        "type": [
+          "string",
+          "null"
+        ]
       },
       "dataStatus": {
         "description": "",
@@ -67,7 +73,10 @@
           "title": "Data",
           "type": "string"
         },
-        "type": "array"
+        "type": [
+          "array",
+          "null"
+        ]
       },
       "diseaseFocus": {
         "items": {
@@ -85,7 +94,10 @@
           "title": "DiseaseFocusEnum",
           "type": "string"
         },
-        "type": "array"
+        "type": [
+          "array",
+          "null"
+        ]
       },
       "fundingAgency": {
         "type": "string"
@@ -94,7 +106,10 @@
         "items": {
           "type": "string"
         },
-        "type": "array"
+        "type": [
+          "array",
+          "null"
+        ]
       },
       "initiative": {
         "type": "string"
@@ -436,13 +451,19 @@
         "items": {
           "type": "string"
         },
-        "type": "array"
+        "type": [
+          "array",
+          "null"
+        ]
       },
       "relatedStudies": {
         "items": {
           "type": "string"
         },
-        "type": "array"
+        "type": [
+          "array",
+          "null"
+        ]
       },
       "studyFileviewId": {
         "type": "string"

registered-json-schemas/Superdataset.json

@@ -29,6 +29,7 @@
         "CAPP-seq",
         "cell competition",
         "cell count",
+        "cell painting",
         "cell proliferation",
         "cell viability assay",
         "Child Behavior Checklist for Ages 1.5-5",

tests/validate/ScRNASeqTemplate_0.csv

@@ -1,5 +1,5 @@
-Component,Filename,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,species,sex,age,ageUnit,diagnosis,nf1Genotype,nf2Genotype,modelSystemName,parentSpecimenID,specimenID,aliquotID,tumorType,platform,nucleicAcidSource,specimenPreparationMethod,cellType,isCellLine,cellID,dissociationMethod,runType,libraryStrand,libraryPrep,libraryPreparationMethod,readPair,readLength,readDepth,targetDepth,batchID,auxiliaryAsset
-ScRNASeqTemplate,a,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,A,Homo sapiens,,,,Neurofibromatosis type 1,,,,,A1,A1-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,Not Applicable,,10x,,,,,,
-ScRNASeqTemplate,b,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,B,Homo sapiens,,,,Neurofibromatosis type 1,,,,,B2,B2-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,Not Applicable,,10x,,,,,,
-ScRNASeqTemplate,c,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,C,Homo sapiens,,,,Neurofibromatosis type 1,,,,,C3,C3-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,Not Applicable,,10x,,,,,,
-ScRNASeqTemplate,d,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,D,Homo sapiens,,,,Neurofibromatosis type 1,,,,,D4,D4-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,Not Applicable,,10x,,,,,,
+Component,Filename,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,species,sex,age,ageUnit,diagnosis,nf1Genotype,nf2Genotype,modelSystemName,parentSpecimenID,specimenID,aliquotID,tumorType,platform,nucleicAcidSource,specimenPreparationMethod,cellType,isCellLine,cellID,dissociationMethod,runType,libraryStrand,libraryPrep,libraryKitID,libraryPreparationMethod,readPair,readLength,readDepth,targetDepth,batchID,auxiliaryAsset
+ScRNASeqTemplate,a,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,A,Homo sapiens,,,,Neurofibromatosis type 1,,,,,A1,A1-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,Not Applicable,,"Chromium NextGEM Single Cell 3′ Reagent Kit, CG000204 Rev D (10X Genomics, Inc.)",10x,,,,,,
+ScRNASeqTemplate,b,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,B,Homo sapiens,,,,Neurofibromatosis type 1,,,,,B2,B2-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,Not Applicable,,"Chromium NextGEM Single Cell 3′ Reagent Kit, CG000204 Rev D (10X Genomics, Inc.)",10x,,,,,,
+ScRNASeqTemplate,c,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,C,Homo sapiens,,,,Neurofibromatosis type 1,,,,,C3,C3-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,Not Applicable,,"Chromium NextGEM Single Cell 3′ Reagent Kit, CG000204 Rev D (10X Genomics, Inc.)",10x,,,,,,
+ScRNASeqTemplate,d,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,D,Homo sapiens,,,,Neurofibromatosis type 1,,,,,D4,D4-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,Not Applicable,,"Chromium NextGEM Single Cell 3′ Reagent Kit, CG000204 Rev D (10X Genomics, Inc.)",10x,,,,,,

tests/validate/ScRNASeqTemplate_1.csv

@@ -1,5 +1,5 @@
-Component,Filename,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,species,sex,age,ageUnit,diagnosis,nf1Genotype,nf2Genotype,modelSystemName,parentSpecimenID,specimenID,aliquotID,tumorType,platform,nucleicAcidSource,specimenPreparationMethod,cellType,isCellLine,cellID,dissociationMethod,runType,libraryStrand,libraryPrep,libraryPreparationMethod,readPair,readLength,readDepth,targetDepth,batchID,auxiliaryAsset
-ScRNASeqTemplate,a,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,A,Homo sapiens,,,,Neurofibromatosis type 1,,,,,A1,A1-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,,,10x,,,,,,
-ScRNASeqTemplate,b,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,B,Homo sapiens,,,,Neurofibromatosis type 1,,,,,B2,B2-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,,,10x,,,,,,
-ScRNASeqTemplate,c,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,C,Homo sapiens,,,,Neurofibromatosis type 1,,,,,C3,C3-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,,,10x,,,,,,
-ScRNASeqTemplate,d,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,D,Homo sapiens,,,,Neurofibromatosis type 1,,,,,D4,D4-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,,,10x,,,,,,
+Component,Filename,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,species,sex,age,ageUnit,diagnosis,nf1Genotype,nf2Genotype,modelSystemName,parentSpecimenID,specimenID,aliquotID,tumorType,platform,nucleicAcidSource,specimenPreparationMethod,cellType,isCellLine,cellID,dissociationMethod,runType,libraryStrand,libraryKitID,libraryPrep,libraryPreparationMethod,readPair,readLength,readDepth,targetDepth,batchID,auxiliaryAsset
+ScRNASeqTemplate,a,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,A,Homo sapiens,,,,Neurofibromatosis type 1,,,,,A1,A1-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,,"Chromium NextGEM Single Cell 3′ Reagent Kit, CG000204 Rev D (10X Genomics, Inc.)",,10x,,,,,,
+ScRNASeqTemplate,b,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,B,Homo sapiens,,,,Neurofibromatosis type 1,,,,,B2,B2-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,,"Chromium NextGEM Single Cell 3′ Reagent Kit, CG000204 Rev D (10X Genomics, Inc.)",,10x,,,,,,
+ScRNASeqTemplate,c,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,C,Homo sapiens,,,,Neurofibromatosis type 1,,,,,C3,C3-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,,"Chromium NextGEM Single Cell 3′ Reagent Kit, CG000204 Rev D (10X Genomics, Inc.)",,10x,,,,,,
+ScRNASeqTemplate,d,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,D,Homo sapiens,,,,Neurofibromatosis type 1,,,,,D4,D4-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,,"Chromium NextGEM Single Cell 3′ Reagent Kit, CG000204 Rev D (10X Genomics, Inc.)",,10x,,,,,,