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Feature improve tests #368

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65d2e72
Test: removed extra elements from test table
wbari Nov 24, 2017
a094191
Test: news tests for Ch38
wbari Nov 28, 2017
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4 changes: 2 additions & 2 deletions ...itnesse/FitNesseRoot/CellBase/CellBaseCompleteSuite/GeneralTests/MetaTests.wiki
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14 changes: 1 addition & 13 deletions ...se/FitNesseRoot/CellBase/CellBaseCompleteSuite/HSapiensTests/ClinicalTests.wiki
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
---
Prune
Test
---
!define TEST_SYSTEM {slim}
Expand All @@ -7,19 +8,6 @@ Test
| Table: Rest Fixture |$baseURL_hsapiens|isPresent.js|
|GET|/feature/clinical/search?limit=1|200|Content-Type : application/json|jsonbody.response[0].numTotalResults == '4597100'|

!3 Get Clinical Var Set (Phenotype Alzheimer)
| Table: Rest Fixture |$baseURL_hsapiens|isPresent.js|
|GET|/feature/clinical/search?include=clinvarSet.referenceClinVarAssertion.clinVarAccession.acc&limit=30&phenotype=alzheimer|200|Content-Type : application/json| !- /* javascript */
var isPresent = false;
for(count = 0; count < jsonbody.response[0].numResults; count++){
if ('RCV000019769' == jsonbody.response[0].result[count].clinvarSet.referenceClinVarAssertion.clinVarAccession.acc){
isPresent = true;
break;
}
}
isPresent && jsonbody.response[0].numTotalResults == 89 && jsonbody.response[0].numResults == 30;
-!|

!3 Get Clinical Var Set (Phenotype Alzheimer)
| Table: Rest Fixture |$baseURL_hsapiens|isPresent.js|
|GET|/feature/clinical/search?include=clinvarSet.referenceClinVarAssertion.clinVarAccession.acc&limit=30&phenotype=myelofibrosis|200|Content-Type : application/json| jsonbody.response[0].numTotalResults == 7739 && jsonbody.response[0].numResults == 30|
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4 changes: 2 additions & 2 deletions ...tnesse/FitNesseRoot/CellBase/CellBaseCompleteSuite/HSapiensTests/GeneTests.wiki
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2 changes: 1 addition & 1 deletion ...sse/FitNesseRoot/CellBase/CellBaseCompleteSuite/HSapiensTests/ProteinTests.wiki
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2 changes: 1 addition & 1 deletion ...esse/FitNesseRoot/CellBase/CellBaseCompleteSuite/HSapiensTests/RegionTests.wiki
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ Test
| Table: Rest Fixture |$baseURL_hsapiens|with-compareJSON.js|
|GET|/genomic/region/model|200|Content-Type : application/json| !- /* javascript */
var desiredResult = [{"id":"urn:jsonschema:org:opencb:biodata:models:core:Region","properties":{"chromosome":{"type":"string"},"start":{"type":"integer"},"end":{"type":"integer"}}}];
compareJSON(jsonbody.response,desiredResult);
compareJSON(jsonbody.response[0].result,desiredResult);
-!|


4 changes: 2 additions & 2 deletions ...tnesse/FitNesseRoot/CellBase/CellBaseCompleteSuite/HSapiensTests/TFBSTests.wiki
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Expand Up @@ -19,7 +19,7 @@ compareJSON(jsonbody.response[0].result,desiredResult);
!3 Get All Regulatory Elements
| Table: Rest Fixture |$baseURL_hsapiens|with-compareJSON.js|
|GET|/regulation/tf/search?limit=10|200|Content-Type : application/json| !- /* javascript */
var desiredResult = [{"chromosome":"22","source":"ccat_histone","featureType":"H3K36_trimethylation_site","start":16049880,"end":16050140,"score":".","strand":".","frame":".","name":"H3K36me3","featureClass":"Histone","alias":"DND-41_H3K36me3_ENCODE_Broad_ccat_histone","cellTypes":["DND-41"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16049900,"end":16050340,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"HepG2_H3K27me3_ENCODE_Broad_ccat_histone","cellTypes":["HepG2"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16049960,"end":16050300,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"A549_H3K27me3_ENCODE_Broad_ccat_histone","cellTypes":["A549"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16050540,"end":16050920,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"A549_H3K27me3_ENCODE_Broad_ccat_histone","cellTypes":["A549"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16050980,"end":16051140,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"A549_H3K27me3_ENCODE_Broad_ccat_histone","cellTypes":["A549"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K36_trimethylation_site","start":16051380,"end":16051680,"score":".","strand":".","frame":".","name":"H3K36me3","featureClass":"Histone","alias":"DND-41_H3K36me3_ENCODE_Broad_ccat_histone","cellTypes":["DND-41"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16052360,"end":16052600,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"A549_H3K27me3_ENCODE_Broad_ccat_histone","cellTypes":["A549"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16052980,"end":16053120,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"A549_H3K27me3_ENCODE_Broad_ccat_histone","cellTypes":["A549"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16053260,"end":16053700,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"K562_H3K27me3_ENCODE_YALE_ccat_histone","cellTypes":["K562"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16053740,"end":16054040,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"K562_H3K27me3_ENCODE_YALE_ccat_histone","cellTypes":["K562"]}];
var desiredResult = [{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16392020,"end":16393020,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"A549_H3K27me3_ENCODE_Broad_ccat_histone","cellTypes":["A549"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16392320,"end":16392680,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"DND-41_H3K27me3_ENCODE_Broad_ccat_histone","cellTypes":["DND-41"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16392800,"end":16392980,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"DND-41_H3K27me3_ENCODE_Broad_ccat_histone","cellTypes":["DND-41"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16393140,"end":16394080,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"A549_H3K27me3_ENCODE_Broad_ccat_histone","cellTypes":["A549"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16393980,"end":16394440,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"K562_H3K27me3_ENCODE_YALE_ccat_histone","cellTypes":["K562"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16394100,"end":16394400,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"A549_H3K27me3_ENCODE_Broad_ccat_histone","cellTypes":["A549"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16394440,"end":16394740,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"A549_H3K27me3_ENCODE_Broad_ccat_histone","cellTypes":["A549"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16394480,"end":16395780,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"K562_H3K27me3_ENCODE_YALE_ccat_histone","cellTypes":["K562"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16394900,"end":16396600,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"A549_H3K27me3_ENCODE_Broad_ccat_histone","cellTypes":["A549"]},{"chromosome":"22","source":"ccat_histone","featureType":"H3K27_trimethylation_site","start":16395480,"end":16395720,"score":".","strand":".","frame":".","name":"H3K27me3","featureClass":"Histone","alias":"DND-41_H3K27me3_ENCODE_Broad_ccat_histone","cellTypes":["DND-41"]}];
compareJSON(jsonbody.response[0].result,desiredResult);
-!|

Expand All @@ -33,6 +33,6 @@ compareJSON(jsonbody.response[0].result,desiredResult);
!3 Get TBFS Objects (CTCF)
| Table: Rest Fixture |$baseURL_hsapiens|with-compareJSON.js|
|GET|/regulation/tf/CTCF/tfbs?limit=10|200|Content-Type : application/json| !- /* javascript */
var desiredResult = [{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16084114,"end":16084562,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"K562_CTCF_ENCODE_Uw_SWEmbl_R0005_IDR","cellTypes":["K562"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16084179,"end":16084579,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"K562_CTCF_ENCODE_Broad_SWEmbl_R0005_IDR","cellTypes":["K562"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16084186,"end":16084630,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"DND-41_CTCF_ENCODE_Broad_SWEmbl_R0005_IDR","cellTypes":["DND-41"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16084186,"end":16084542,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"K562_CTCF_ENCODE_Uta_SWEmbl_R0005_IDR","cellTypes":["K562"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16084195,"end":16084542,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"HepG2_CTCF_ENCODE_Uta_SWEmbl_R0005_IDR","cellTypes":["HepG2"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16084248,"end":16084470,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"H1ESC_CTCF_ENCODE_Hudsonalpha_SWEmbl_R0005_IDR","cellTypes":["H1ESC"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16404444,"end":16404825,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"K562_CTCF_ENCODE_Uw_SWEmbl_R0005_IDR","cellTypes":["K562"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16156836,"end":16157242,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"HeLa-S3_CTCF_ENCODE_Uw_SWEmbl_R0005_IDR","cellTypes":["HeLa-S3"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16156837,"end":16157234,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"HepG2_CTCF_ENCODE_Uw_SWEmbl_R0005_IDR","cellTypes":["HepG2"]},{"chromosome":"22","source":"SWEmbl_R015","featureType":"TF_binding_site","start":16156872,"end":16157156,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"H1ESC_CTCF_ENCODE_Uta_SWEmbl_R015","cellTypes":["H1ESC"]}];
var desiredResult = [{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16404444,"end":16404825,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"K562_CTCF_ENCODE_Uw_SWEmbl_R0005_IDR","cellTypes":["K562"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16433994,"end":16434449,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"K562_CTCF_ENCODE_Broad_SWEmbl_R0005_IDR","cellTypes":["K562"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16434019,"end":16434329,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"K562_CTCF_ENCODE_Uta_SWEmbl_R0005_IDR","cellTypes":["K562"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16434024,"end":16434340,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"HepG2_CTCF_ENCODE_Uta_SWEmbl_R0005_IDR","cellTypes":["HepG2"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16466878,"end":16467525,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"HepG2_CTCF_ENCODE_Uta_SWEmbl_R0005_IDR","cellTypes":["HepG2"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16466878,"end":16467450,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"H1ESC_CTCF_ENCODE_Hudsonalpha_SWEmbl_R0005_IDR","cellTypes":["H1ESC"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16467120,"end":16467607,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"K562_CTCF_ENCODE_Broad_SWEmbl_R0005_IDR","cellTypes":["K562"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16467124,"end":16467589,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"A549_CTCF_ENCODE_Broad_SWEmbl_R0005_IDR","cellTypes":["A549"]},{"chromosome":"22","source":"SWEmbl_R015","featureType":"TF_binding_site","start":16467182,"end":16467452,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"HMEC_CTCF_ENCODE_Uw_SWEmbl_R015","cellTypes":["HMEC"]},{"chromosome":"22","source":"SWEmbl_R0005_IDR","featureType":"TF_binding_site","start":16848375,"end":16848656,"score":".","strand":".","frame":".","name":"CTCF","featureClass":"Transcription Factor","alias":"H1ESC_CTCF_ENCODE_Hudsonalpha_SWEmbl_R0005_IDR","cellTypes":["H1ESC"]}];
compareJSON(jsonbody.response[0].result,desiredResult);
-!|
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