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[SCHEMATIC-210] Add attribute to nones data model (#1555)
Update example_test_nones.model.csv component and add new invalid manifest with nones
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-6
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3 files changed

+242
-6
lines changed

‎tests/data/example_test_nones.model.csv‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ CRAM,,,,"Genome Build, Genome FASTA",,FALSE,ValidValue,,
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CSV/TSV,,,,Genome Build,,FALSE,ValidValue,,
2020
Genome Build,,,"GRCh37, GRCh38, GRCm38, GRCm39",,,TRUE,DataProperty,,
2121
Genome FASTA,,,,,,TRUE,DataProperty,,
22-
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,,
22+
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,,
2323
Check List,list,,,,,FALSE,DataProperty,,
2424
Check List Enum,list,,"ab, cd, ef, gh",,,FALSE,DataProperty,,
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Check List Like,list like,,,,,FALSE,DataProperty,,

‎tests/data/example_test_nones.model.jsonld‎

Lines changed: 236 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -309,6 +309,9 @@
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},
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{
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"@id": "bts:Skin"
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},
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{
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"@id": "bts:None"
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}
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],
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"sms:displayName": "Cancer Type",
@@ -468,6 +471,23 @@
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:None",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "None",
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"rdfs:subClassOf": [
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{
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"@id": "bts:CancerType"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "None",
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"sms:required": "sms:false",
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"sms:validationRules": []
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},
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{
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"@id": "bts:Biospecimen",
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"@type": "rdfs:Class",
@@ -877,12 +897,36 @@
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{
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"@id": "bts:Component"
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},
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{
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"@id": "bts:CancerType"
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},
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{
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"@id": "bts:CheckList"
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},
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{
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"@id": "bts:CheckListEnum"
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},
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{
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"@id": "bts:CheckListLike"
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},
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{
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"@id": "bts:CheckListLikeEnum"
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},
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{
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"@id": "bts:CheckListStrict"
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},
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{
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"@id": "bts:CheckListEnumStrict"
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},
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{
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"@id": "bts:CheckRegexList"
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},
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{
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"@id": "bts:CheckRegexListLike"
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},
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{
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"@id": "bts:CheckRegexListStrict"
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},
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{
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"@id": "bts:CheckRegexSingle"
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},
@@ -953,6 +997,25 @@
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "Check List",
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"sms:required": "sms:false",
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"sms:validationRules": [
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"list"
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]
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},
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{
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"@id": "bts:CheckListEnum",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "CheckListEnum",
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"rdfs:subClassOf": [
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{
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"@id": "bts:DataProperty"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"schema:rangeIncludes": [
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{
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"@id": "bts:Ab"
@@ -967,7 +1030,111 @@
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"@id": "bts:Gh"
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}
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],
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"sms:displayName": "Check List",
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"sms:displayName": "Check List Enum",
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"sms:required": "sms:false",
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"sms:validationRules": [
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"list"
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]
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},
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{
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"@id": "bts:CheckListLike",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "CheckListLike",
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"rdfs:subClassOf": [
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{
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"@id": "bts:DataProperty"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "Check List Like",
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"sms:required": "sms:false",
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"sms:validationRules": [
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"list like"
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]
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},
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{
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"@id": "bts:CheckListLikeEnum",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "CheckListLikeEnum",
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"rdfs:subClassOf": [
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{
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"@id": "bts:DataProperty"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"schema:rangeIncludes": [
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{
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"@id": "bts:Ab"
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},
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{
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"@id": "bts:Cd"
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},
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{
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"@id": "bts:Ef"
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},
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{
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"@id": "bts:Gh"
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}
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],
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"sms:displayName": "Check List Like Enum",
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"sms:required": "sms:false",
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"sms:validationRules": [
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"list like"
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]
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},
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{
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"@id": "bts:CheckListStrict",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "CheckListStrict",
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"rdfs:subClassOf": [
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{
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"@id": "bts:DataProperty"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "Check List Strict",
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"sms:required": "sms:false",
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"sms:validationRules": [
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"list strict"
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]
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},
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{
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"@id": "bts:CheckListEnumStrict",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "CheckListEnumStrict",
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"rdfs:subClassOf": [
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{
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"@id": "bts:DataProperty"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"schema:rangeIncludes": [
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{
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"@id": "bts:Ab"
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},
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{
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"@id": "bts:Cd"
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},
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{
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"@id": "bts:Ef"
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},
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{
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"@id": "bts:Gh"
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}
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],
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"sms:displayName": "Check List Enum Strict",
9711138
"sms:required": "sms:false",
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"sms:validationRules": [
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"list strict"
@@ -988,6 +1155,46 @@
9881155
},
9891156
"sms:displayName": "Check Regex List",
9901157
"sms:required": "sms:false",
1158+
"sms:validationRules": [
1159+
"list",
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"regex match [a-f]"
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]
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},
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{
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"@id": "bts:CheckRegexListLike",
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"@type": "rdfs:Class",
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"rdfs:comment": "TBD",
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"rdfs:label": "CheckRegexListLike",
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"rdfs:subClassOf": [
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{
1170+
"@id": "bts:DataProperty"
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}
1172+
],
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"schema:isPartOf": {
1174+
"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "Check Regex List Like",
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"sms:required": "sms:false",
1178+
"sms:validationRules": [
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"list like",
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"regex match [a-f]"
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]
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},
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{
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"@id": "bts:CheckRegexListStrict",
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"@type": "rdfs:Class",
1186+
"rdfs:comment": "TBD",
1187+
"rdfs:label": "CheckRegexListStrict",
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"rdfs:subClassOf": [
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{
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"@id": "bts:DataProperty"
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}
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],
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"schema:isPartOf": {
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"@id": "http://schema.biothings.io"
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},
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"sms:displayName": "Check Regex List Strict",
1197+
"sms:required": "sms:false",
9911198
"sms:validationRules": [
9921199
"list strict",
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"regex match [a-f]"
@@ -1343,7 +1550,13 @@
13431550
"rdfs:label": "Ab",
13441551
"rdfs:subClassOf": [
13451552
{
1346-
"@id": "bts:CheckList"
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"@id": "bts:CheckListEnum"
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},
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{
1556+
"@id": "bts:CheckListLikeEnum"
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},
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{
1559+
"@id": "bts:CheckListEnumStrict"
13471560
}
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],
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"schema:isPartOf": {
@@ -1360,7 +1573,13 @@
13601573
"rdfs:label": "Cd",
13611574
"rdfs:subClassOf": [
13621575
{
1363-
"@id": "bts:CheckList"
1576+
"@id": "bts:CheckListEnum"
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},
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{
1579+
"@id": "bts:CheckListLikeEnum"
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},
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{
1582+
"@id": "bts:CheckListEnumStrict"
13641583
}
13651584
],
13661585
"schema:isPartOf": {
@@ -1377,7 +1596,13 @@
13771596
"rdfs:label": "Ef",
13781597
"rdfs:subClassOf": [
13791598
{
1380-
"@id": "bts:CheckList"
1599+
"@id": "bts:CheckListEnum"
1600+
},
1601+
{
1602+
"@id": "bts:CheckListLikeEnum"
1603+
},
1604+
{
1605+
"@id": "bts:CheckListEnumStrict"
13811606
}
13821607
],
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"schema:isPartOf": {
@@ -1394,7 +1619,13 @@
13941619
"rdfs:label": "Gh",
13951620
"rdfs:subClassOf": [
13961621
{
1397-
"@id": "bts:CheckList"
1622+
"@id": "bts:CheckListEnum"
1623+
},
1624+
{
1625+
"@id": "bts:CheckListLikeEnum"
1626+
},
1627+
{
1628+
"@id": "bts:CheckListEnumStrict"
13981629
}
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],
14001631
"schema:isPartOf": {

‎tests/data/mock_manifests/Invalid_Test_Manifest_with_nones.csv‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
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
2+
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
3+
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
4+
MockComponent,None,,,,,,,,,,b,,683902,,,,,,,,,,present,,,,,
5+
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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