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[SCHEMATIC-214] change data model and component #1556

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Merged
thomasyu888 merged 5 commits into from
Dec 11, 2024
Merged

[SCHEMATIC-214] change data model and component #1556

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0af61ad
add valid values to Patient attributes
SageGJ Dec 11, 2024
85c6e69
update data model
SageGJ Dec 11, 2024
bb7e34c
add test manifests
SageGJ Dec 11, 2024
dee2694
update test for new model
SageGJ Dec 11, 2024
a0e8218
update test for new valid value
SageGJ Dec 11, 2024
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6 changes: 3 additions & 3 deletions tests/data/example.model.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -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,,,
Expand All @@ -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]
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20 changes: 20 additions & 0 deletions tests/data/example.model.jsonld
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Expand Up @@ -540,6 +540,9 @@
},
{
"@id": "bts:Malignant"
},
{
"@id": "bts:None"
}
],
"sms:displayName": "Tissue Status",
Expand All @@ -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",
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6 changes: 6 additions & 0 deletions tests/data/mock_manifests/Invalid_none_value_test_manifest.csv
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Original file line number Diff line number Diff line change
@@ -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
6 changes: 6 additions & 0 deletions tests/data/mock_manifests/Valid_none_value_test_manifest.csv
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@@ -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
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