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Refactor gradle test so that we can run smoke tests separately from o…
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…ther tests by running: (#1265)

gradle test -PnonSmokeTests

or

gradle test -PsmokeTests
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@rtaylorzfin
rtaylorzfin authored Dec 17, 2024
1 parent 03332e2 commit 521e10d
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230 changes: 64 additions & 166 deletions build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -219,122 +219,6 @@ def translateVariableSet = [
'WEBHOST_FASTA_FILE_PATH',
]

//These are the only files that need to be searched and replaced (<!--|KEY|-->)
//Let's whittle this list down over time
//Other

def whitelistTemplateFiles = [
'cgi-bin/send_request.perl',
'cgi-bin/merge_markers.pl',
'server_apps/DB_maintenance/backupBlastDbsAndRsyncAlmostBlastDbs.sh',
'server_apps/DB_maintenance/checkVarcharOctetLength.pl',
'server_apps/DB_maintenance/check_undefined_environment.pl',
'server_apps/DB_maintenance/disable_updates.pl',
'server_apps/DB_maintenance/extentMonitoring/dailyExtentCheck.sh',
'server_apps/DB_maintenance/fx_permission_check.pl',
'server_apps/DB_maintenance/loadExternalNotes.pl',
'server_apps/DB_maintenance/loadExternalNotes.sql',
'server_apps/DB_maintenance/loadUp/README_loadUp',
'server_apps/DB_maintenance/loadUp/rsync.pl',
'server_apps/DB_maintenance/orphanChecks.pl',
'server_apps/DB_maintenance/postgres/compareTables.groovy',
'server_apps/DB_maintenance/pushDataToPublic.sh',
'server_apps/DB_maintenance/queryMonitoring/dailyQueryCostCheck.sh',
'server_apps/DB_maintenance/rotateInformixLog.sh',
'server_apps/DB_maintenance/set_unload_timestamp.sql',
'server_apps/DB_maintenance/warehouse/chromosomeMartPostgres/runChromosomeMart.sh',
'server_apps/DB_maintenance/warehouse/expressionMart/runExpressionMart.sh',
'server_apps/DB_maintenance/warehouse/phenotypeMart/runPhenotypeMart.sh',
'server_apps/DB_maintenance/warehouse/regenChromosomeMart.sh',
'server_apps/DB_maintenance/warehouse/regenExpressionMart.sh',
'server_apps/DB_maintenance/warehouse/regenPhenotypeMart.sh',
'server_apps/DB_maintenance/warehouse/switch.sh',
'server_apps/DB_maintenance/warehouse/who_is.sh',
'server_apps/DB_maintenance/warehouse/who_is_not.sh',
'server_apps/Reports/AnnualStats/runStats.sh',
'server_apps/Reports/BetterFish/betterFish.sql',
'server_apps/Reports/PubTracking/runAverageTimeInBinsCumulative.sh',
'server_apps/Reports/PubTracking/runLongestBinResidents.sh',
'server_apps/Reports/PubTracking/runMonthlyBinLengthReport.sh',
'server_apps/Reports/PubTracking/runPaperlessPubTrackingDailyIndexedMetrics.sh',
'server_apps/Reports/elsevier_report.pl',
'server_apps/Reports/reportPubsForGeneAndFeature.pl',
'server_apps/WebSiteTools/gen-jobs-rss.r',
'server_apps/WebSiteTools/gen-meetings-rss.r',
'server_apps/WebSiteTools/gen-news-rss.r',
'server_apps/WebSiteTools/signsoflife.sh',
'server_apps/apache/inc-redirect',
'server_apps/cron/crontab.production',
'server_apps/data_transfer/Downloads/GFF3/E_unload_ensembl_contig.sql',
'server_apps/data_transfer/Downloads/generateStagedAnatomy.pl',
'server_apps/data_transfer/Ensembl/fetch_ensdarT_dbacc.sh',
'server_apps/data_transfer/Ensembl/fetch_ensdarg.sh',
'server_apps/data_transfer/Ensembl/fetch_ensdargOttdargTable.sh',
'server_apps/data_transfer/Ensembl/fetch_ensembl_agp.sh',
'server_apps/data_transfer/Ensembl/fetch_sangerMutantInfo.sh',
'server_apps/data_transfer/Ensembl/notifyStaleIds.sh',
'server_apps/data_transfer/Ensembl/pullFromBioMart.pl',
'server_apps/data_transfer/Ensembl/reportEnsembleStatistics.sh',
'server_apps/data_transfer/ExternalSearch/CreateMarkerSearchPage.pl',
'server_apps/data_transfer/ExternalSearch/CreateMarkerSearchPage.sql',
'server_apps/data_transfer/GO/go.pl',
'server_apps/data_transfer/GO/gofile.sql',
'server_apps/data_transfer/GO/gofile2.sql',
'server_apps/data_transfer/GO/gofile2_all.sql',
'server_apps/data_transfer/GO/gp2protein.pl',
'server_apps/data_transfer/GO/gpad.pl',
'server_apps/data_transfer/GO/gpad2.0.sql',
'server_apps/data_transfer/GO/validateUniprotIDsZFIN.pl',
'server_apps/data_transfer/Genbank/gbaccession.pl',
'server_apps/data_transfer/Load/ReNo/Nomenclature/generate_special_Sanger_uniprot_nomenclature_run.sh',
'server_apps/data_transfer/Load/ReNo/load_run_report_hit.sh',
'server_apps/data_transfer/Load/blast_withdrawn.pl',
'server_apps/data_transfer/LoadOntology/parseHeader.pl',
'server_apps/data_transfer/LoadOntology/parseObo.pl',
'server_apps/data_transfer/MEOW/meow.pl',
'server_apps/data_transfer/NCBIStartEnd/NCBIStartEnd.pl',
'server_apps/data_transfer/OMIM/OMIM.pl',
'server_apps/data_transfer/OMIM/loadOMIM.sql',
'server_apps/data_transfer/ORTHO/downloadFiles.pl',
'server_apps/data_transfer/ORTHO/emailOrthologyReports.pl',
'server_apps/data_transfer/ORTHO/loadAndUpdateNCBIOrthologs.sql',
'server_apps/data_transfer/ORTHO/loadHumanSynonyms.sql',
'server_apps/data_transfer/ORTHO/parseHumanData.pl',
'server_apps/data_transfer/ORTHO/parseOrthoFile.pl',
'server_apps/data_transfer/ORTHO/reportOrthoNameChanges.pl',
'server_apps/data_transfer/ORTHO/runOrthology.pl',
'server_apps/data_transfer/ORTHO/updateZebrafishGeneNames.pl',
'server_apps/data_transfer/ORTHO/updateZebrafishGeneNames.sql',
'server_apps/data_transfer/PUBMED/Journal/checkAndUpdateJournals.sql',
'server_apps/data_transfer/PUBMED/Journal/insertJournalAlias.sql',
'server_apps/data_transfer/PUBMED/addMeshTermsToAllPubs.groovy',
'server_apps/data_transfer/PUBMED/addPMCidsToAllPubs.groovy',
'server_apps/data_transfer/PUBMED/loadNewPubs.sql',
'server_apps/data_transfer/PUBMED/load_complete_author_names.sql',
'server_apps/data_transfer/PUBMED/pubActivation.groovy',
'server_apps/data_transfer/PUBMED/updatePublicationDate.groovy',
'server_apps/data_transfer/RNACentral/loadTranscriptSequences.sql',
'server_apps/data_transfer/RNACentral/loadTscriptSeq.pl',
'server_apps/data_transfer/RNACentral/preLoadTranscriptSequence.sql',
'server_apps/data_transfer/RNACentral/runTscriptSequenceLoad.pl',
'server_apps/data_transfer/ResourceCenters/pullFromEZRC.pl',
'server_apps/data_transfer/ResourceCenters/pullFromZIRC.pl',
'server_apps/data_transfer/ResourceCenters/pushToZirc.pl',
'server_apps/data_transfer/ResourceCenters/pushToZirc.sql',
'server_apps/data_transfer/SNP/addNewClonesJSmith.pl',
'server_apps/data_transfer/SNP/addTalbotSNPAttr.sql',
'server_apps/data_transfer/SNP/dbSNP.pl',
'server_apps/data_transfer/SNP/loadNewSNPAttrs.sql',
'server_apps/data_transfer/SNP/loadNewSNPs.sql',
'server_apps/data_transfer/eco_go_mapping/insert_eco_go_map.sql',
'server_apps/data_transfer/maintainTermDisplay/checkRNAConsequenceTerm.groovy',
'server_apps/data_transfer/zfishbook/preprocess_zfishbook.pl',
'server_apps/data_transfer/zfishbook/zfishbook.pl',
'server_apps/data_transfer/zfishbook/zfishbook.sh',
]

project.ext.set("whitelistTemplateFiles", whitelistTemplateFiles)

// load properties into gradle
task setup {
project.ext.ttNameMap = new Properties()
Expand Down Expand Up @@ -855,77 +739,91 @@ test {
testLogging {
//showStandardStreams = true
}

def includeSmokeTests = project.hasProperty('smokeTests')
def includeNonSmokeTests = project.hasProperty('nonSmokeTests')
if (!includeSmokeTests && !includeNonSmokeTests) {
//if neither flag is set, run all tests
includeSmokeTests = true
includeNonSmokeTests = true
}

filter {
includeTestsMatching "org.zfin.UnitTests"
//spock tests

includeTestsMatching "org.zfin.publication.MeshHeadingSpec"
if (includeNonSmokeTests) {
includeTestsMatching "org.zfin.UnitTests"
//spock tests

includeTestsMatching "org.zfin.publication.presentation.PublicationValidatorSpec"
includeTestsMatching "org.zfin.publication.repository.PublicationRepositorySpec"
includeTestsMatching "org.zfin.feature.service.MutationDetailsConversionServiceSpec"
includeTestsMatching "org.zfin.util.ReportGeneratorSpec"
includeTestsMatching "org.zfin.search.service.SolrServiceSpec"
includeTestsMatching "org.zfin.search.service.SolrQueryFacadeSpec"
includeTestsMatching "org.zfin.search.service.MarkerSearchServiceSpec"
includeTestsMatching "org.zfin.search.service.SearchSuggestionServiceSpec"
includeTestsMatching "org.zfin.publication.MeshHeadingSpec"

includeTestsMatching "org.zfin.ontology.service.RibbonServiceIntegrationSpec"
includeTestsMatching "org.zfin.uniquery.RelatedLinksSpec"
includeTestsMatching "org.zfin.publication.presentation.PublicationValidatorSpec"
includeTestsMatching "org.zfin.publication.repository.PublicationRepositorySpec"
includeTestsMatching "org.zfin.feature.service.MutationDetailsConversionServiceSpec"
includeTestsMatching "org.zfin.util.ReportGeneratorSpec"
includeTestsMatching "org.zfin.search.service.SolrServiceSpec"
includeTestsMatching "org.zfin.search.service.SolrQueryFacadeSpec"
includeTestsMatching "org.zfin.search.service.MarkerSearchServiceSpec"
includeTestsMatching "org.zfin.search.service.SearchSuggestionServiceSpec"

includeTestsMatching "org.zfin.ontology.service.RibbonServiceIntegrationSpec"
includeTestsMatching "org.zfin.uniquery.RelatedLinksSpec"

// Failing tests that we may want to bring back: (ZFIN-8271)
// includeTestsMatching "org.zfin.uniquery.CategoriesAndFacetsSpec"
// includeTestsMatching "org.zfin.uniquery.QuerySpec"
// includeTestsMatching "org.zfin.uniquery.ResultAttributesSpec"
includeTestsMatching "org.zfin.sequence.repository.SequenceRepositorySpec"
includeTestsMatching "org.zfin.feature.FeatureServiceSpec"
includeTestsMatching "org.zfin.curation.service.CurationDTOConversionServiceSpec"
includeTestsMatching "org.zfin.expression.ExpressionSearchSpec"
includeTestsMatching "org.zfin.marker.presentation.GeneAddFormBeanValidatorSpec"
includeTestsMatching "org.zfin.marker.presentation.MarkerGoServiceIntegrationSpec"
includeTestsMatching "org.zfin.marker.presentation.SequenceTargetingReagentAddBeanValidatorSpec"
includeTestsMatching "org.zfin.figure.repository.FigureRepositorySpec"
includeTestsMatching "org.zfin.gbrowse.presentation.GBrowseImageSpec"
includeTestsMatching "org.zfin.figure.service.ImageServiceSpec"

/*need to figure out ..all tests fail here

includeTestsMatching "org.zfin.sequence.repository.SequenceRepositorySpec"
includeTestsMatching "org.zfin.feature.FeatureServiceSpec"
includeTestsMatching "org.zfin.curation.service.CurationDTOConversionServiceSpec"
includeTestsMatching "org.zfin.expression.ExpressionSearchSpec"
includeTestsMatching "org.zfin.marker.presentation.GeneAddFormBeanValidatorSpec"
includeTestsMatching "org.zfin.marker.presentation.MarkerGoServiceIntegrationSpec"
includeTestsMatching "org.zfin.marker.presentation.SequenceTargetingReagentAddBeanValidatorSpec"
includeTestsMatching "org.zfin.figure.repository.FigureRepositorySpec"
includeTestsMatching "org.zfin.gbrowse.presentation.GBrowseImageSpec"
includeTestsMatching "org.zfin.figure.service.ImageServiceSpec"

/*need to figure out ..all tests fail here
includeTestsMatching "org.zfin.figure.service.FigureViewServiceSpec"*/

//includeTestsMatching "org.zfin.publication.PublicationServiceSpec"
// PublicationServiceSpec > #authorString should bring back #author FAILED
//org.spockframework.runtime.SpockAssertionError at UnrollIterationNameProvider.java:80
//includeTestsMatching "org.zfin.publication.PublicationServiceSpec"
// PublicationServiceSpec > #authorString should bring back #author FAILED
//org.spockframework.runtime.SpockAssertionError at UnrollIterationNameProvider.java:80


/*includeTestsMatching "org.zfin.figure.service.ImageServiceSpec" (needs fixing..null pointer here: tempDir.newFolder(ZfinPropertiesEnum.IMAGE_LOAD.toString(), "medium"))
/*includeTestsMatching "org.zfin.figure.service.ImageServiceSpec" (needs fixing..null pointer here: tempDir.newFolder(ZfinPropertiesEnum.IMAGE_LOAD.toString(), "medium"))
includeTestsMatching "org.zfin.figure.service.VideoServiceSpec"*/

/*//following use geb..likely not to fix
/*//following use geb..likely not to fix
includeTestsMatching "org.zfin.figure.presentation.FigureViewWebSpec" (geb test)
includeTestsMatching "org.zfin.marker.MarkerselectWebSpec" (geb test)
includeTestsMatching "org.zfin.framework.GroovyWebSpec"(geb test)
includeTestsMatching "org.zfin.ontology.service.RibbonServiceIntegrationSpec"(geb test)*/

// db unit tests
includeTestsMatching "org.zfin.DbUnitTests"
includeTestsMatching "org.zfin.infrastructure.EnumValidationTest"
includeTestsMatching "org.zfin.DbControllerTests"
includeTestsMatching "org.zfin.ThirdPartyServiceTests"

includeTestsMatching "org.zfin.anatomy.AnatomySmokeTest"
includeTestsMatching "org.zfin.antibody.smoketest.AntibodySmokeTest"
includeTestsMatching "org.zfin.sequence.blast.smoketest.BlastSmokeTest"
includeTestsMatching "org.zfin.datatransfer.smoketests.DownloadSmokeTest"
includeTestsMatching "org.zfin.feature.presentation.FeatureDetailSmokeTest"
includeTestsMatching "org.zfin.feature.presentation.GenotypeDetailSmokeTest"
includeTestsMatching "org.zfin.expression.presentation.FigureSummarySmokeTest"
includeTestsMatching "org.zfin.fish.smoketest.FishSmokeTest"
includeTestsMatching "org.zfin.fish.smoketest.PhenotypeSummarySmokeTest"
includeTestsMatching "org.zfin.httpunittest.MarkerViewSmokeTest"
includeTestsMatching "org.zfin.sebservice.MarkerRestSmokeTest"
//include specific method in any of the tests
// includeTestsMatching "*ActiveDataTest"
// db unit tests
includeTestsMatching "org.zfin.DbUnitTests"
includeTestsMatching "org.zfin.infrastructure.EnumValidationTest"
includeTestsMatching "org.zfin.DbControllerTests"
includeTestsMatching "org.zfin.ThirdPartyServiceTests"
}

if (includeSmokeTests) {
includeTestsMatching "org.zfin.anatomy.AnatomySmokeTest"
includeTestsMatching "org.zfin.antibody.smoketest.AntibodySmokeTest"
includeTestsMatching "org.zfin.sequence.blast.smoketest.BlastSmokeTest"
includeTestsMatching "org.zfin.datatransfer.smoketests.DownloadSmokeTest"
includeTestsMatching "org.zfin.feature.presentation.FeatureDetailSmokeTest"
includeTestsMatching "org.zfin.feature.presentation.GenotypeDetailSmokeTest"
includeTestsMatching "org.zfin.expression.presentation.FigureSummarySmokeTest"
includeTestsMatching "org.zfin.fish.smoketest.FishSmokeTest"
includeTestsMatching "org.zfin.fish.smoketest.PhenotypeSummarySmokeTest"
includeTestsMatching "org.zfin.httpunittest.MarkerViewSmokeTest"
includeTestsMatching "org.zfin.sebservice.MarkerRestSmokeTest"
//include specific method in any of the tests
// includeTestsMatching "*ActiveDataTest"
}
}

reports {
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