diff --git a/tests/data/example_test_nones.model.csv b/tests/data/example_test_nones.model.csv index 77afc1f3c..bb691c793 100644 --- a/tests/data/example_test_nones.model.csv +++ b/tests/data/example_test_nones.model.csv @@ -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,, diff --git a/tests/data/example_test_nones.model.jsonld b/tests/data/example_test_nones.model.jsonld index c47804236..07a01596b 100644 --- a/tests/data/example_test_nones.model.jsonld +++ b/tests/data/example_test_nones.model.jsonld @@ -309,6 +309,9 @@ }, { "@id": "bts:Skin" + }, + { + "@id": "bts:None" } ], "sms:displayName": "Cancer Type", @@ -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", @@ -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" }, @@ -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" @@ -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" @@ -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]" @@ -1343,7 +1550,13 @@ "rdfs:label": "Ab", "rdfs:subClassOf": [ { - "@id": "bts:CheckList" + "@id": "bts:CheckListEnum" + }, + { + "@id": "bts:CheckListLikeEnum" + }, + { + "@id": "bts:CheckListEnumStrict" } ], "schema:isPartOf": { @@ -1360,7 +1573,13 @@ "rdfs:label": "Cd", "rdfs:subClassOf": [ { - "@id": "bts:CheckList" + "@id": "bts:CheckListEnum" + }, + { + "@id": "bts:CheckListLikeEnum" + }, + { + "@id": "bts:CheckListEnumStrict" } ], "schema:isPartOf": { @@ -1377,7 +1596,13 @@ "rdfs:label": "Ef", "rdfs:subClassOf": [ { - "@id": "bts:CheckList" + "@id": "bts:CheckListEnum" + }, + { + "@id": "bts:CheckListLikeEnum" + }, + { + "@id": "bts:CheckListEnumStrict" } ], "schema:isPartOf": { @@ -1394,7 +1619,13 @@ "rdfs:label": "Gh", "rdfs:subClassOf": [ { - "@id": "bts:CheckList" + "@id": "bts:CheckListEnum" + }, + { + "@id": "bts:CheckListLikeEnum" + }, + { + "@id": "bts:CheckListEnumStrict" } ], "schema:isPartOf": { diff --git a/tests/data/mock_manifests/Invalid_Test_Manifest_with_nones.csv b/tests/data/mock_manifests/Invalid_Test_Manifest_with_nones.csv new file mode 100644 index 000000000..aeab9e410 --- /dev/null +++ b/tests/data/mock_manifests/Invalid_Test_Manifest_with_nones.csv @@ -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 \ No newline at end of file