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Added new test suite cases for version check
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‎gpunit_functionality/version_check/invalid_mix_species1_test.yml‎

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# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved.
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#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00317:7
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module: GSEAPreranked
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name: GSEAPreranked invalid_mix_species1_test
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description: Test the GSEA version check with files of mixed species no collapsing; expect an error. Note that we need to use remote files to trigger the check.
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params:
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ranked.list: "<%gpunit.testData%>gpunit/GSEAPreranked/v7/input/Diabetes_collapsed_symbols.rnk"
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gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt",
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"https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Mm/m1.all.v2022.1.Mm.symbols.gmt" ]
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number.of.permutations: "10"
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collapse.dataset: "No_Collapse"
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chip.platform.file: ""
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omit.features.with.no.symbol.match: "true"
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collapsing.mode.for.probe.sets.with.more.than.one.match: "Max_probe"
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output.file.name: "<ranked.list_basename>.zip"
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scoring.scheme: "weighted"
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max.gene.set.size: "500"
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min.gene.set.size: "15"
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normalization.mode: "meandiv"
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randomization.mode: "no_balance"
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# Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results
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random.seed: "149"
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create.svgs: "false"
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num.top.sets: "20"
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make.detailed.gene.set.report: "false"
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selected.gene.sets: ""
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dev.mode: "true"
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alt.delim: ""
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create.zip: "false"
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assertions:
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jobStatus: fail
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files:
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"stderr.txt":
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diffCmd: ../grepMessages.sh
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/invalid_mix_species1_test/stderrMatches.txt"

‎gpunit_functionality/version_check/invalid_mix_species2_test.yml‎

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# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved.
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#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00317:7
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module: GSEAPreranked
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name: GSEAPreranked invalid_mix_species2_test
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description: Test the GSEAPreranked version check with files of mixed species no collapsing; expect an error. Note that we need to use remote files to trigger the check.
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params:
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ranked.list: "<%gpunit.testData%>gpunit/GSEAPreranked/v7/input/Diabetes_faked_ranking_for_test.rnk"
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gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt" ]
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number.of.permutations: "10"
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collapse.dataset: "Collapse"
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chip.platform.file: "https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations/mouse/Human_AFFY_HG_U133_Mouse_Orthologs_MSigDB.v2022.1.Mm.chip"
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# Changing the output.file.name for ease of testing
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output.file.name: "<ranked.list_basename>_collapsed.zip"
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scoring.scheme: "weighted"
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max.gene.set.size: "500"
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min.gene.set.size: "15"
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collapsing.mode.for.probe.sets.with.more.than.one.match: "Mean_of_probes"
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normalization.mode: "meandiv"
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randomization.mode: "no_balance"
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omit.features.with.no.symbol.match: "true"
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# Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results
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random.seed: "149"
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create.svgs: "false"
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num.top.sets: "20"
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make.detailed.gene.set.report: "false"
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selected.gene.sets: ""
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dev.mode: "true"
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alt.delim: ""
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create.zip: "true"
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assertions:
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jobStatus: fail
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files:
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"stderr.txt":
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diffCmd: ../grepMessages.sh
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/invalid_mix_species2_test/stderrMatches.txt"

‎gpunit_functionality/version_check/valid_same_vers_with_chip_test.yml‎

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# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved.
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#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00317:7
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module: GSEAPreranked
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name: GSEAPreranked valid_same_vers_with_chip_test
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description: Test the GSEAPreranked version check with files of matching version with collapsing. Note that we need to use remote files to trigger the check.
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params:
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ranked.list: "<%gpunit.testData%>gpunit/GSEAPreranked/v7/input/Diabetes_faked_ranking_for_test.rnk"
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gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt" ]
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number.of.permutations: "10"
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collapse.dataset: "Collapse"
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chip.platform.file: "https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations/human/Human_AFFY_HG_U133_MSigDB.v2022.1.Hs.chip"
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# Changing the output.file.name for ease of testing
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output.file.name: "<ranked.list_basename>_collapsed.zip"
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scoring.scheme: "weighted"
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max.gene.set.size: "500"
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min.gene.set.size: "15"
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collapsing.mode.for.probe.sets.with.more.than.one.match: "Mean_of_probes"
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normalization.mode: "meandiv"
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randomization.mode: "no_balance"
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omit.features.with.no.symbol.match: "true"
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# Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results
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random.seed: "149"
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create.svgs: "false"
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num.top.sets: "20"
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make.detailed.gene.set.report: "false"
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selected.gene.sets: ""
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dev.mode: "true"
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alt.delim: ""
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create.zip: "true"
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assertions:
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jobStatus: success
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files:
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"results.edb":
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diffCmd: diff -q --strip-trailing-cr
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/valid_same_vers_with_chip_test/results.edb"
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"gene_sets.gmt":
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diffCmd: diff -q --strip-trailing-cr
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/valid_same_vers_with_chip_test/gene_sets.gmt"

‎gpunit_functionality/version_check/valid_same_version_test.yml‎

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# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved.
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#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00317:7
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module: GSEAPreranked
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name: GSEAPreranked valid_same_version_test
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description: Test the GSEAPreranked version check with files of matching version and no collapsing. Note that we need to use remote files to trigger the check.
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params:
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ranked.list: "<%gpunit.testData%>gpunit/GSEAPreranked/v7/input/Diabetes_collapsed_symbols.rnk"
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gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt",
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"https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/c1.all.v2022.1.Hs.symbols.gmt" ]
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number.of.permutations: "10"
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collapse.dataset: "No_Collapse"
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chip.platform.file: ""
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omit.features.with.no.symbol.match: "true"
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collapsing.mode.for.probe.sets.with.more.than.one.match: "Max_probe"
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output.file.name: "<ranked.list_basename>.zip"
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scoring.scheme: "weighted"
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max.gene.set.size: "500"
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min.gene.set.size: "15"
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normalization.mode: "meandiv"
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randomization.mode: "no_balance"
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# Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results
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random.seed: "149"
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create.svgs: "false"
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num.top.sets: "20"
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make.detailed.gene.set.report: "false"
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selected.gene.sets: ""
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dev.mode: "true"
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alt.delim: ""
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create.zip: "false"
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assertions:
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jobStatus: success
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files:
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"results.edb":
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diffCmd: diff -q --strip-trailing-cr
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/valid_same_version_test/results.edb"
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"gene_sets.gmt":
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diffCmd: diff -q --strip-trailing-cr
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/valid_same_version_test/gene_sets.gmt"

‎gpunit_functionality/version_check/valid_warn_mix_vers_with_chip1_test.yml‎

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# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved.
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#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00317:7
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module: GSEAPreranked
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name: GSEAPreranked valid_warn_mix_vers_with_chip1_test
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description: Test the GSEAPreranked version check with files of matching version with collapsing. Note that we need to use remote files to trigger the check.
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params:
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ranked.list: "<%gpunit.testData%>gpunit/GSEAPreranked/v7/input/Diabetes_faked_ranking_for_test.rnk"
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gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/7.5.1/h.all.v7.5.1.symbols.gmt",
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"https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/c1.all.v2022.1.Hs.symbols.gmt" ]
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number.of.permutations: "10"
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collapse.dataset: "Collapse"
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chip.platform.file: "https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations/human/Human_AFFY_HG_U133_MSigDB.v2022.1.Hs.chip"
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# Changing the output.file.name for ease of testing
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output.file.name: "<ranked.list_basename>_collapsed.zip"
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scoring.scheme: "weighted"
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max.gene.set.size: "500"
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min.gene.set.size: "15"
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collapsing.mode.for.probe.sets.with.more.than.one.match: "Mean_of_probes"
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normalization.mode: "meandiv"
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randomization.mode: "no_balance"
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omit.features.with.no.symbol.match: "true"
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# Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results
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random.seed: "149"
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create.svgs: "false"
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num.top.sets: "20"
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make.detailed.gene.set.report: "false"
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selected.gene.sets: ""
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dev.mode: "true"
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alt.delim: ""
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create.zip: "true"
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assertions:
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jobStatus: success
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files:
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"results.edb":
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diffCmd: diff -q --strip-trailing-cr
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/valid_warn_mix_vers_with_chip1_test/results.edb"
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"gene_sets.gmt":
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diffCmd: diff -q --strip-trailing-cr
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/valid_warn_mix_vers_with_chip1_test/gene_sets.gmt"
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"stdout.txt":
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diffCmd: ../grepMessages.sh
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/valid_warn_mix_vers_with_chip1_test/stdoutMatches.txt"

‎gpunit_functionality/version_check/valid_warn_mix_vers_with_chip2_test.yml‎

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# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved.
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#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00317:7
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module: GSEAPreranked
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name: GSEAPreranked valid_warn_mix_vers_with_chip2_test
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description: Test the GSEAPreranked version check with files of mixed versions with collapsing; should warn but complete. Note that we need to use remote files to trigger the check.
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params:
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ranked.list: "<%gpunit.testData%>gpunit/GSEAPreranked/v7/input/Diabetes_faked_ranking_for_test.rnk"
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gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt",
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"https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/c1.all.v2022.1.Hs.symbols.gmt" ]
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number.of.permutations: "10"
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collapse.dataset: "Collapse"
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chip.platform.file: "https://data.broadinstitute.org/gsea-msigdb/msigdb/annotations/human/Human_AFFY_HG_U133_MSigDB.v7.5.1.chip"
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# Changing the output.file.name for ease of testing
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output.file.name: "<ranked.list_basename>_collapsed.zip"
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scoring.scheme: "weighted"
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max.gene.set.size: "500"
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min.gene.set.size: "15"
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collapsing.mode.for.probe.sets.with.more.than.one.match: "Mean_of_probes"
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normalization.mode: "meandiv"
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randomization.mode: "no_balance"
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omit.features.with.no.symbol.match: "true"
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# Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results
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random.seed: "149"
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create.svgs: "false"
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num.top.sets: "20"
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make.detailed.gene.set.report: "false"
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selected.gene.sets: ""
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dev.mode: "true"
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alt.delim: ""
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create.zip: "true"
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assertions:
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jobStatus: success
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files:
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"results.edb":
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diffCmd: diff -q --strip-trailing-cr
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/valid_warn_mix_vers_with_chip2_test/results.edb"
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"gene_sets.gmt":
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diffCmd: diff -q --strip-trailing-cr
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/valid_warn_mix_vers_with_chip2_test/gene_sets.gmt"
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"stdout.txt":
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diffCmd: ../grepMessages.sh
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/valid_warn_mix_vers_with_chip2_test/stdoutMatches.txt"

‎gpunit_functionality/version_check/valid_warn_mix_version_test.yml‎

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# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved.
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#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00317:7
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module: GSEAPreranked
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name: GSEAPreranked valid_warn_mix_version_test
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description: Test the GSEAPreranked version check with files of mixed versions and no collapsing; should warn but complete. Note that we need to use remote files to trigger the check.
6+
params:
7+
ranked.list: "<%gpunit.testData%>gpunit/GSEAPreranked/v7/input/Diabetes_collapsed_symbols.rnk"
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gene.sets.database: [ "https://data.broadinstitute.org/gsea-msigdb/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt",
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"https://data.broadinstitute.org/gsea-msigdb/msigdb/release/7.5.1/c1.all.v7.5.1.symbols.gmt" ]
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number.of.permutations: "10"
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collapse.dataset: "No_Collapse"
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chip.platform.file: ""
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omit.features.with.no.symbol.match: "true"
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collapsing.mode.for.probe.sets.with.more.than.one.match: "Max_probe"
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output.file.name: "<ranked.list_basename>.zip"
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scoring.scheme: "weighted"
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max.gene.set.size: "500"
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min.gene.set.size: "15"
19+
normalization.mode: "meandiv"
20+
randomization.mode: "no_balance"
21+
# Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results
22+
random.seed: "149"
23+
create.svgs: "false"
24+
num.top.sets: "20"
25+
make.detailed.gene.set.report: "false"
26+
selected.gene.sets: ""
27+
dev.mode: "true"
28+
alt.delim: ""
29+
create.zip: "false"
30+
assertions:
31+
jobStatus: success
32+
files:
33+
"results.edb":
34+
diffCmd: diff -q --strip-trailing-cr
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/valid_warn_mix_version_test/results.edb"
36+
"gene_sets.gmt":
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diffCmd: diff -q --strip-trailing-cr
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/valid_warn_mix_version_test/gene_sets.gmt"
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"stdout.txt":
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diffCmd: ../grepMessages.sh
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diff: "<%gpunit.resultData%>gpunit/GSEAPreranked/v7/output/version_check/valid_warn_mix_version_test/stdoutMatches.txt"

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