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[SCHEMATIC-210] Add attribute to nones data model #1555

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Merged
GiaJordan merged 2 commits into from
Dec 9, 2024
Merged

[SCHEMATIC-210] Add attribute to nones data model #1555

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7e90a19
update test nones data model
SageGJ Dec 9, 2024
d12e60f
add invalid test nones manifest
SageGJ Dec 9, 2024
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2 changes: 1 addition & 1 deletion tests/data/example_test_nones.model.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ CRAM,,,,"Genome Build, Genome FASTA",,FALSE,ValidValue,,
CSV/TSV,,,,Genome Build,,FALSE,ValidValue,,
Genome Build,,,"GRCh37, GRCh38, GRCm38, GRCm39",,,TRUE,DataProperty,,
Genome FASTA,,,,,,TRUE,DataProperty,,
MockComponent,,,,"Component, Check List, Check List Enum, Check List Like, Check List Like Enum, Check List Strict, Check List Enum Strict, Check Regex List, Check Regex List Like, Check Regex List Strict, Check Regex Single, Check Regex Format, Check Regex Integer, Check Num, Check Float, Check Int, Check String, Check URL,Check Match at Least, Check Match at Least values, Check Match Exactly, Check Match Exactly values, Check Recommended, Check Ages, Check Unique, Check Range, Check Date, Check NA",,FALSE,DataType,,
MockComponent,,,,"Component, Cancer Type, Check List, Check List Enum, Check List Like, Check List Like Enum, Check List Strict, Check List Enum Strict, Check Regex List, Check Regex List Like, Check Regex List Strict, Check Regex Single, Check Regex Format, Check Regex Integer, Check Num, Check Float, Check Int, Check String, Check URL,Check Match at Least, Check Match at Least values, Check Match Exactly, Check Match Exactly values, Check Recommended, Check Ages, Check Unique, Check Range, Check Date, Check NA",,FALSE,DataType,,
Check List,list,,,,,FALSE,DataProperty,,
Check List Enum,list,,"ab, cd, ef, gh",,,FALSE,DataProperty,,
Check List Like,list like,,,,,FALSE,DataProperty,,
Expand Down
241 changes: 236 additions & 5 deletions tests/data/example_test_nones.model.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -309,6 +309,9 @@
},
{
"@id": "bts:Skin"
},
{
"@id": "bts:None"
}
],
"sms:displayName": "Cancer Type",
Expand Down Expand Up @@ -468,6 +471,23 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:None",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "None",
"rdfs:subClassOf": [
{
"@id": "bts:CancerType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "None",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Biospecimen",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -877,12 +897,36 @@
{
"@id": "bts:Component"
},
{
"@id": "bts:CancerType"
},
{
"@id": "bts:CheckList"
},
{
"@id": "bts:CheckListEnum"
},
{
"@id": "bts:CheckListLike"
},
{
"@id": "bts:CheckListLikeEnum"
},
{
"@id": "bts:CheckListStrict"
},
{
"@id": "bts:CheckListEnumStrict"
},
{
"@id": "bts:CheckRegexList"
},
{
"@id": "bts:CheckRegexListLike"
},
{
"@id": "bts:CheckRegexListStrict"
},
{
"@id": "bts:CheckRegexSingle"
},
Expand Down Expand Up @@ -953,6 +997,25 @@
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Check List",
"sms:required": "sms:false",
"sms:validationRules": [
"list"
]
},
{
"@id": "bts:CheckListEnum",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "CheckListEnum",
"rdfs:subClassOf": [
{
"@id": "bts:DataProperty"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"schema:rangeIncludes": [
{
"@id": "bts:Ab"
Expand All @@ -967,7 +1030,111 @@
"@id": "bts:Gh"
}
],
"sms:displayName": "Check List",
"sms:displayName": "Check List Enum",
"sms:required": "sms:false",
"sms:validationRules": [
"list"
]
},
{
"@id": "bts:CheckListLike",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "CheckListLike",
"rdfs:subClassOf": [
{
"@id": "bts:DataProperty"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Check List Like",
"sms:required": "sms:false",
"sms:validationRules": [
"list like"
]
},
{
"@id": "bts:CheckListLikeEnum",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "CheckListLikeEnum",
"rdfs:subClassOf": [
{
"@id": "bts:DataProperty"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"schema:rangeIncludes": [
{
"@id": "bts:Ab"
},
{
"@id": "bts:Cd"
},
{
"@id": "bts:Ef"
},
{
"@id": "bts:Gh"
}
],
"sms:displayName": "Check List Like Enum",
"sms:required": "sms:false",
"sms:validationRules": [
"list like"
]
},
{
"@id": "bts:CheckListStrict",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "CheckListStrict",
"rdfs:subClassOf": [
{
"@id": "bts:DataProperty"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Check List Strict",
"sms:required": "sms:false",
"sms:validationRules": [
"list strict"
]
},
{
"@id": "bts:CheckListEnumStrict",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "CheckListEnumStrict",
"rdfs:subClassOf": [
{
"@id": "bts:DataProperty"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"schema:rangeIncludes": [
{
"@id": "bts:Ab"
},
{
"@id": "bts:Cd"
},
{
"@id": "bts:Ef"
},
{
"@id": "bts:Gh"
}
],
"sms:displayName": "Check List Enum Strict",
"sms:required": "sms:false",
"sms:validationRules": [
"list strict"
Expand All @@ -988,6 +1155,46 @@
},
"sms:displayName": "Check Regex List",
"sms:required": "sms:false",
"sms:validationRules": [
"list",
"regex match [a-f]"
]
},
{
"@id": "bts:CheckRegexListLike",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "CheckRegexListLike",
"rdfs:subClassOf": [
{
"@id": "bts:DataProperty"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Check Regex List Like",
"sms:required": "sms:false",
"sms:validationRules": [
"list like",
"regex match [a-f]"
]
},
{
"@id": "bts:CheckRegexListStrict",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "CheckRegexListStrict",
"rdfs:subClassOf": [
{
"@id": "bts:DataProperty"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Check Regex List Strict",
"sms:required": "sms:false",
"sms:validationRules": [
"list strict",
"regex match [a-f]"
Expand Down Expand Up @@ -1343,7 +1550,13 @@
"rdfs:label": "Ab",
"rdfs:subClassOf": [
{
"@id": "bts:CheckList"
"@id": "bts:CheckListEnum"
},
{
"@id": "bts:CheckListLikeEnum"
},
{
"@id": "bts:CheckListEnumStrict"
}
],
"schema:isPartOf": {
Expand All @@ -1360,7 +1573,13 @@
"rdfs:label": "Cd",
"rdfs:subClassOf": [
{
"@id": "bts:CheckList"
"@id": "bts:CheckListEnum"
},
{
"@id": "bts:CheckListLikeEnum"
},
{
"@id": "bts:CheckListEnumStrict"
}
],
"schema:isPartOf": {
Expand All @@ -1377,7 +1596,13 @@
"rdfs:label": "Ef",
"rdfs:subClassOf": [
{
"@id": "bts:CheckList"
"@id": "bts:CheckListEnum"
},
{
"@id": "bts:CheckListLikeEnum"
},
{
"@id": "bts:CheckListEnumStrict"
}
],
"schema:isPartOf": {
Expand All @@ -1394,7 +1619,13 @@
"rdfs:label": "Gh",
"rdfs:subClassOf": [
{
"@id": "bts:CheckList"
"@id": "bts:CheckListEnum"
},
{
"@id": "bts:CheckListLikeEnum"
},
{
"@id": "bts:CheckListEnumStrict"
}
],
"schema:isPartOf": {
Expand Down
5 changes: 5 additions & 0 deletions tests/data/mock_manifests/Invalid_Test_Manifest_with_nones.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
Component,Cancer Type,Check List,Check List Enum,Check List Like,Check List Like Enum,Check List Strict,Check List Enum Strict,Check Regex List,Check Regex List Like,Check Regex List Strict,Check Regex Single,Check Regex Format,Check Regex Integer,Check Num,Check Float,Check Int,Check String,Check URL,Check Match at Least,Check Match at Least values,Check Match Exactly,Check Match Exactly values,Check Recommended,Check Ages,Check Unique,Check Range,Check Date,Check NA
MockComponent,None,"ab,cd","ab,cd",ab,ab,"ab,cd","ab,cd","a,c,f",a,"a,c,f",a,a,,6,99.65,7,valid,https://www.google.com/,1738,1738,8085,8085,,6571,str1,75,10/21/2022,Not Applicable
MockComponent,None,"ab,cd","ab,cd",,,"ab,cd","ab,cd","a,c,f","a,c,f","a,c,f",,b,1234,71,58.4,3,valid,https://www.google.com/,9965,9965,9965,9965,,6571,str2,80,October 21 2022,8
MockComponent,None,,,,,,,,,,b,,683902,,,,,,,,,,present,,,,,
MockComponent,InvalidValue,"ab,cd","ab,cd","ab,cd","ab,cd","ab,cd","ab,cd","b,d,f","b,d,f","b,d,f",b,c,0,6.5,62.3,2,valid,https://www.google.com/,79,79,7,7,,32849,str4,55,21/10/2022,695
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