From 56b3430537b4da3fb59321e579f4e494678a1a8a Mon Sep 17 00:00:00 2001 From: Kyle Meyer Date: Thu, 8 Aug 2024 23:59:58 -0400 Subject: [PATCH] integration: split tests into nonmem and postrun subdirectories A subset of the integration tests don't require NONMEM. It's convenient to have them in a separate package from the ones that do so that they can be more easily executed on machines that don't have NONMEM. --- integration/execute.go | 6 +++--- integration/nonmem/README.md | 1 + integration/{ => nonmem}/bbi_expansion_test.go | 9 +++++---- integration/{ => nonmem}/bbi_local_test.go | 5 +++-- integration/{ => nonmem}/bbi_sge_test.go | 2 +- integration/{ => nonmem}/config_test.go | 2 +- integration/{ => nonmem}/data_test.go | 2 +- integration/{ => nonmem}/files.go | 2 +- integration/{ => nonmem}/init_test.go | 5 +++-- integration/{ => nonmem}/nmqual_test.go | 2 +- integration/{ => nonmem}/nonmem.go | 2 +- integration/{ => nonmem}/postexecution_test.go | 2 +- integration/{ => nonmem}/setup.go | 17 ++++++----------- integration/{ => nonmem}/testdata/.gitignore | 0 .../{ => nonmem}/testdata/acop/.gitignore | 0 .../{ => nonmem}/testdata/acop/acop.csv | 0 .../{ => nonmem}/testdata/acop/acop.mod | 0 .../{ => nonmem}/testdata/acop/acoptar.gz | Bin .../{ => nonmem}/testdata/acop/scenario.json | 0 .../bbi_expansion/data/derived/acop.csv | 0 .../testdata/bbi_expansion/model/101.ctl | 0 .../testdata/bbi_expansion/model/102.ctl | 0 .../testdata/bbi_expansion/model/103.ctl | 0 .../testdata/bbi_expansion/model/104.ctl | 0 .../testdata/bbi_expansion/model/105.ctl | 0 .../bbi_expansion/model/bbi_mainrun_101.ctl | 0 .../bbi_expansion/model/bbi_mainrun_102.ctl | 0 .../bbi_expansion/model/bbi_mainrun_103.ctl | 0 .../testdata/bbi_expansion/scenario.json | 0 .../{ => nonmem}/testdata/ctl_test/acop.csv | 0 .../{ => nonmem}/testdata/ctl_test/acop.ctl | 0 .../testdata/ctl_test/scenario.json | 0 .../{ => nonmem}/testdata/datacomment/acop.csv | 0 .../{ => nonmem}/testdata/datacomment/acop.ctl | 0 .../testdata/datacomment/scenario.json | 0 .../testdata/leading-path-with space/acop.csv | 0 .../testdata/leading-path-with space/acop.ctl | 0 .../leading-path-with space/scenario.json | 0 .../testdata/metrum_std/data/derived/Data.csv | 0 .../model/nonmem/test_suite_1/acop.ctl | 0 .../model/nonmem/test_suite_1/acop2.mod | 0 .../testdata/metrum_std/scenario.json | 0 .../{ => nonmem}/testdata/modquote/acop.csv | 0 .../{ => nonmem}/testdata/modquote/m'd.ctl | 0 .../testdata/modquote/scenario.json | 0 .../testdata/period_test/acop.1.ctl | 0 .../{ => nonmem}/testdata/period_test/acop.csv | 0 .../testdata/period_test/scenario.json | 0 integration/{ => postrun}/README.md | 4 ++-- integration/{ => postrun}/bbi_covcor_test.go | 7 ++++--- integration/{ => postrun}/bbi_params_test.go | 7 ++++--- integration/{ => postrun}/bbi_reclean_test.go | 7 ++++--- integration/{ => postrun}/bbi_summary_test.go | 17 +++++++++-------- integration/{ => postrun}/golden_util.go | 2 +- integration/postrun/setup.go | 8 ++++++++ .../testdata/bbi_summary/1001.ctl | 0 .../testdata/bbi_summary/1001/.gitignore | 0 .../testdata/bbi_summary/1001/1001.1.TXT | 0 .../testdata/bbi_summary/1001/1001.cor | 0 .../testdata/bbi_summary/1001/1001.cov | 0 .../testdata/bbi_summary/1001/1001.cpu | 0 .../testdata/bbi_summary/1001/1001.ctl | 0 .../testdata/bbi_summary/1001/1001.ext | 0 .../testdata/bbi_summary/1001/1001.lst | 0 .../testdata/bbi_summary/1001/PRDERR | 0 .../12-empty-problem/12-empty-problem.ext | 0 .../12-empty-problem/12-empty-problem.grd | 0 .../12-empty-problem/12-empty-problem.lst | 0 .../12-empty-problem/12-empty-problem.shk | 0 .../12-invalid-lst/12-invalid-lst.cpu | 0 .../12-invalid-lst/12-invalid-lst.ctl | 0 .../12-invalid-lst/12-invalid-lst.ext | 0 .../12-invalid-lst/12-invalid-lst.grd | 0 .../12-invalid-lst/12-invalid-lst.lst | 0 .../12-invalid-lst/12-invalid-lst.shk | 0 .../{ => postrun}/testdata/bbi_summary/12.ctl | 0 .../testdata/bbi_summary/12/.gitignore | 0 .../testdata/bbi_summary/12/12.cpu | 0 .../testdata/bbi_summary/12/12.ctl | 0 .../testdata/bbi_summary/12/12.ext | 0 .../testdata/bbi_summary/12/12.grd | 0 .../testdata/bbi_summary/12/12.lst | 0 .../testdata/bbi_summary/12/12.shk | 0 .../{ => postrun}/testdata/bbi_summary/66.ctl | 0 .../testdata/bbi_summary/66/.gitignore | 0 .../testdata/bbi_summary/66/66.cpu | 0 .../testdata/bbi_summary/66/66.ctl | 0 .../testdata/bbi_summary/66/66.ext | 0 .../testdata/bbi_summary/66/66.grd | 0 .../testdata/bbi_summary/66/66.lst | 0 .../testdata/bbi_summary/66/PRDERR | 0 .../aa_golden_files/1001.golden.covcor.json | 0 .../aa_golden_files/1001.golden.json | 0 .../aa_golden_files/1001.golden.txt | 0 .../12-empty-problem.golden.json | 0 .../12-empty-problem.golden.txt | 0 .../bbi_summary/aa_golden_files/12.golden.json | 0 .../bbi_summary/aa_golden_files/12.golden.txt | 0 .../bbi_summary/aa_golden_files/66.golden.json | 0 .../bbi_summary/aa_golden_files/66.golden.txt | 0 .../aa_golden_files/acop-iov.golden.json | 0 .../aa_golden_files/acop-iov.golden.txt | 0 .../aa_golden_files/acop-nan.golden.json | 0 .../aa_golden_files/acop-nan.golden.txt | 0 .../aa_golden_files/acop.golden.covcor.json | 0 .../aa_golden_files/acop.golden.json | 0 .../aa_golden_files/acop.golden.txt | 0 .../aa_golden_files/acop_no_grd.golden.json | 0 .../aa_golden_files/acop_no_grd.golden.txt | 0 .../aa_golden_files/chain.golden.json | 0 .../aa_golden_files/chain.golden.txt | 0 .../dir_bbi_summary.golden.params.csv | 0 .../dir_bbi_summary.golden.params.json | 0 .../aa_golden_files/example2_bayes.golden.json | 0 .../example2_bayes.golden.params.csv | 0 .../example2_bayes.golden.params.json | 0 .../aa_golden_files/example2_bayes.golden.txt | 0 .../example2_itsimp.golden.covcor.json | 0 .../example2_itsimp.golden.json | 0 .../aa_golden_files/example2_itsimp.golden.txt | 0 .../example2_saemimp.golden.json | 0 .../example2_saemimp.golden.txt | 0 .../aa_golden_files/iovmm.golden.json | 0 .../aa_golden_files/iovmm.golden.txt | 0 .../multiple-models-error.golden.json | 0 .../multiple-models.golden.json | 0 .../aa_golden_files/multiple-models.golden.txt | 0 .../aa_golden_files/onlysim.golden.json | 0 .../aa_golden_files/onlysim.golden.txt | 0 .../acop-incomplete/acop-incomplete.cor | 0 .../acop-incomplete/acop-incomplete.cov | 0 .../acop-incomplete/acop-incomplete.cpu | 0 .../acop-incomplete/acop-incomplete.ext | 0 .../acop-incomplete/acop-incomplete.grd | 0 .../acop-incomplete/acop-incomplete.lst | 0 .../acop-incomplete/acop-incomplete.shk | 0 .../testdata/bbi_summary/acop-iov.mod | 0 .../testdata/bbi_summary/acop-iov/acop-iov.cpu | 0 .../testdata/bbi_summary/acop-iov/acop-iov.ext | 0 .../testdata/bbi_summary/acop-iov/acop-iov.grd | 0 .../testdata/bbi_summary/acop-iov/acop-iov.lst | 0 .../testdata/bbi_summary/acop-iov/acop-iov.mod | 0 .../testdata/bbi_summary/acop-iov/acop-iov.shk | 0 .../testdata/bbi_summary/acop-nan/acop-nan.cor | 0 .../testdata/bbi_summary/acop-nan/acop-nan.cov | 0 .../testdata/bbi_summary/acop-nan/acop-nan.cpu | 0 .../testdata/bbi_summary/acop-nan/acop-nan.ext | 0 .../testdata/bbi_summary/acop-nan/acop-nan.grd | 0 .../testdata/bbi_summary/acop-nan/acop-nan.lst | 0 .../testdata/bbi_summary/acop-nan/acop-nan.shk | 0 .../testdata/bbi_summary/acop.ctl | 0 .../testdata/bbi_summary/acop/acop.cor | 0 .../testdata/bbi_summary/acop/acop.cov | 0 .../testdata/bbi_summary/acop/acop.cpu | 0 .../testdata/bbi_summary/acop/acop.ext | 0 .../testdata/bbi_summary/acop/acop.grd | 0 .../testdata/bbi_summary/acop/acop.lst | 0 .../testdata/bbi_summary/acop/acop.shk | 0 .../bbi_summary/acop_no_grd/acop_no_grd.cpu | 0 .../bbi_summary/acop_no_grd/acop_no_grd.ext | 0 .../bbi_summary/acop_no_grd/acop_no_grd.lst | 0 .../bbi_summary/acop_no_grd/acop_no_grd.shk | 0 .../testdata/bbi_summary/chain/chain.ext | 0 .../testdata/bbi_summary/chain/chain.lst | 0 .../testdata/bbi_summary/example2_bayes.ctl | 0 .../bbi_summary/example2_bayes/.gitignore | 0 .../example2_bayes/example2_bayes.cor | 0 .../example2_bayes/example2_bayes.cov | 0 .../example2_bayes/example2_bayes.cpu | 0 .../example2_bayes/example2_bayes.ctl | 0 .../example2_bayes/example2_bayes.ext | 0 .../example2_bayes/example2_bayes.lst | 0 .../example2_bayes/example2_bayes.shk | 0 .../testdata/bbi_summary/example2_itsimp.ctl | 0 .../bbi_summary/example2_itsimp/.gitignore | 0 .../example2_itsimp/example2_itsimp.cor | 0 .../example2_itsimp/example2_itsimp.cov | 0 .../example2_itsimp/example2_itsimp.cpu | 0 .../example2_itsimp/example2_itsimp.ctl | 0 .../example2_itsimp/example2_itsimp.ext | 0 .../example2_itsimp/example2_itsimp.lst | 0 .../example2_itsimp/example2_itsimp.shk | 0 .../testdata/bbi_summary/example2_saemimp.ctl | 0 .../bbi_summary/example2_saemimp/.gitignore | 0 .../example2_saemimp/example2_saemimp.cor | 0 .../example2_saemimp/example2_saemimp.cov | 0 .../example2_saemimp/example2_saemimp.cpu | 0 .../example2_saemimp/example2_saemimp.ctl | 0 .../example2_saemimp/example2_saemimp.ext | 0 .../example2_saemimp/example2_saemimp.lst | 0 .../example2_saemimp/example2_saemimp.shk | 0 .../bbi_summary/example2_saemimp/saem.ext | 0 .../testdata/bbi_summary/iovmm.mod | 0 .../testdata/bbi_summary/iovmm/.gitignore | 0 .../testdata/bbi_summary/iovmm/iovmm.cpu | 0 .../testdata/bbi_summary/iovmm/iovmm.ext | 0 .../testdata/bbi_summary/iovmm/iovmm.grd | 0 .../testdata/bbi_summary/iovmm/iovmm.lst | 0 .../testdata/bbi_summary/iovmm/iovmm.mod | 0 .../testdata/bbi_summary/iovmm/iovmm.shk | 0 .../testdata/bbi_summary/onlysim/onlysim.lst | 0 201 files changed, 60 insertions(+), 49 deletions(-) create mode 100644 integration/nonmem/README.md rename integration/{ => nonmem}/bbi_expansion_test.go (96%) rename integration/{ => nonmem}/bbi_local_test.go (98%) rename integration/{ => nonmem}/bbi_sge_test.go (99%) rename integration/{ => nonmem}/config_test.go (99%) rename integration/{ => nonmem}/data_test.go (99%) rename integration/{ => nonmem}/files.go (95%) rename integration/{ => nonmem}/init_test.go (94%) rename integration/{ => nonmem}/nmqual_test.go (99%) rename integration/{ => nonmem}/nonmem.go (99%) rename integration/{ => nonmem}/postexecution_test.go (99%) rename integration/{ => nonmem}/setup.go (95%) rename integration/{ => nonmem}/testdata/.gitignore (100%) rename integration/{ => nonmem}/testdata/acop/.gitignore (100%) rename integration/{ => nonmem}/testdata/acop/acop.csv (100%) rename integration/{ => nonmem}/testdata/acop/acop.mod (100%) rename integration/{ => nonmem}/testdata/acop/acoptar.gz (100%) rename integration/{ => nonmem}/testdata/acop/scenario.json (100%) rename integration/{ => nonmem}/testdata/bbi_expansion/data/derived/acop.csv (100%) rename integration/{ => nonmem}/testdata/bbi_expansion/model/101.ctl (100%) rename integration/{ => nonmem}/testdata/bbi_expansion/model/102.ctl (100%) rename integration/{ => nonmem}/testdata/bbi_expansion/model/103.ctl (100%) rename integration/{ => nonmem}/testdata/bbi_expansion/model/104.ctl (100%) rename integration/{ => nonmem}/testdata/bbi_expansion/model/105.ctl (100%) rename integration/{ => nonmem}/testdata/bbi_expansion/model/bbi_mainrun_101.ctl (100%) rename integration/{ => nonmem}/testdata/bbi_expansion/model/bbi_mainrun_102.ctl (100%) rename integration/{ => nonmem}/testdata/bbi_expansion/model/bbi_mainrun_103.ctl (100%) rename integration/{ => nonmem}/testdata/bbi_expansion/scenario.json (100%) rename integration/{ => nonmem}/testdata/ctl_test/acop.csv (100%) rename integration/{ => nonmem}/testdata/ctl_test/acop.ctl (100%) rename integration/{ => nonmem}/testdata/ctl_test/scenario.json (100%) rename integration/{ => nonmem}/testdata/datacomment/acop.csv (100%) rename integration/{ => nonmem}/testdata/datacomment/acop.ctl (100%) rename integration/{ => nonmem}/testdata/datacomment/scenario.json (100%) rename integration/{ => nonmem}/testdata/leading-path-with space/acop.csv (100%) rename integration/{ => nonmem}/testdata/leading-path-with space/acop.ctl (100%) rename integration/{ => nonmem}/testdata/leading-path-with space/scenario.json (100%) rename integration/{ => nonmem}/testdata/metrum_std/data/derived/Data.csv (100%) rename integration/{ => nonmem}/testdata/metrum_std/model/nonmem/test_suite_1/acop.ctl (100%) rename integration/{ => nonmem}/testdata/metrum_std/model/nonmem/test_suite_1/acop2.mod (100%) rename integration/{ => nonmem}/testdata/metrum_std/scenario.json (100%) rename integration/{ => nonmem}/testdata/modquote/acop.csv (100%) rename integration/{ => nonmem}/testdata/modquote/m'd.ctl (100%) rename integration/{ => nonmem}/testdata/modquote/scenario.json (100%) rename integration/{ => nonmem}/testdata/period_test/acop.1.ctl (100%) rename integration/{ => nonmem}/testdata/period_test/acop.csv (100%) rename integration/{ => nonmem}/testdata/period_test/scenario.json (100%) rename integration/{ => postrun}/README.md (70%) rename integration/{ => postrun}/bbi_covcor_test.go (88%) rename integration/{ => postrun}/bbi_params_test.go (90%) rename integration/{ => postrun}/bbi_reclean_test.go (82%) rename integration/{ => postrun}/bbi_summary_test.go (94%) rename integration/{ => postrun}/golden_util.go (98%) create mode 100644 integration/postrun/setup.go rename integration/{ => postrun}/testdata/bbi_summary/1001.ctl (100%) rename integration/{ => postrun}/testdata/bbi_summary/1001/.gitignore (100%) rename integration/{ => postrun}/testdata/bbi_summary/1001/1001.1.TXT (100%) rename integration/{ => postrun}/testdata/bbi_summary/1001/1001.cor (100%) rename integration/{ => postrun}/testdata/bbi_summary/1001/1001.cov (100%) rename integration/{ => postrun}/testdata/bbi_summary/1001/1001.cpu (100%) rename integration/{ => postrun}/testdata/bbi_summary/1001/1001.ctl (100%) rename integration/{ => postrun}/testdata/bbi_summary/1001/1001.ext (100%) rename integration/{ => postrun}/testdata/bbi_summary/1001/1001.lst (100%) rename integration/{ => postrun}/testdata/bbi_summary/1001/PRDERR (100%) rename integration/{ => postrun}/testdata/bbi_summary/12-empty-problem/12-empty-problem.ext (100%) rename integration/{ => postrun}/testdata/bbi_summary/12-empty-problem/12-empty-problem.grd (100%) rename integration/{ => postrun}/testdata/bbi_summary/12-empty-problem/12-empty-problem.lst (100%) rename integration/{ => postrun}/testdata/bbi_summary/12-empty-problem/12-empty-problem.shk (100%) rename integration/{ => postrun}/testdata/bbi_summary/12-invalid-lst/12-invalid-lst.cpu (100%) rename integration/{ => postrun}/testdata/bbi_summary/12-invalid-lst/12-invalid-lst.ctl (100%) rename integration/{ => postrun}/testdata/bbi_summary/12-invalid-lst/12-invalid-lst.ext (100%) rename integration/{ => postrun}/testdata/bbi_summary/12-invalid-lst/12-invalid-lst.grd (100%) rename integration/{ => postrun}/testdata/bbi_summary/12-invalid-lst/12-invalid-lst.lst (100%) rename integration/{ => postrun}/testdata/bbi_summary/12-invalid-lst/12-invalid-lst.shk (100%) rename integration/{ => postrun}/testdata/bbi_summary/12.ctl (100%) rename integration/{ => postrun}/testdata/bbi_summary/12/.gitignore (100%) rename integration/{ => postrun}/testdata/bbi_summary/12/12.cpu (100%) rename integration/{ => postrun}/testdata/bbi_summary/12/12.ctl (100%) rename integration/{ => postrun}/testdata/bbi_summary/12/12.ext (100%) rename integration/{ => postrun}/testdata/bbi_summary/12/12.grd (100%) rename integration/{ => postrun}/testdata/bbi_summary/12/12.lst (100%) rename integration/{ => postrun}/testdata/bbi_summary/12/12.shk (100%) rename integration/{ => postrun}/testdata/bbi_summary/66.ctl (100%) rename integration/{ => postrun}/testdata/bbi_summary/66/.gitignore (100%) rename integration/{ => postrun}/testdata/bbi_summary/66/66.cpu (100%) rename integration/{ => postrun}/testdata/bbi_summary/66/66.ctl (100%) rename integration/{ => postrun}/testdata/bbi_summary/66/66.ext (100%) rename integration/{ => postrun}/testdata/bbi_summary/66/66.grd (100%) rename integration/{ => postrun}/testdata/bbi_summary/66/66.lst (100%) rename integration/{ => postrun}/testdata/bbi_summary/66/PRDERR (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/1001.golden.covcor.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/1001.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/1001.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/12-empty-problem.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/12-empty-problem.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/12.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/12.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/66.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/66.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/acop-iov.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/acop-iov.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/acop-nan.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/acop-nan.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/acop.golden.covcor.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/acop.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/acop.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/acop_no_grd.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/acop_no_grd.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/chain.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/chain.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/dir_bbi_summary.golden.params.csv (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/dir_bbi_summary.golden.params.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/example2_bayes.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/example2_bayes.golden.params.csv (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/example2_bayes.golden.params.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/example2_bayes.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/example2_itsimp.golden.covcor.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/example2_itsimp.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/example2_itsimp.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/example2_saemimp.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/example2_saemimp.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/iovmm.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/iovmm.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/multiple-models-error.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/multiple-models.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/multiple-models.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/onlysim.golden.json (100%) rename integration/{ => postrun}/testdata/bbi_summary/aa_golden_files/onlysim.golden.txt (100%) rename integration/{ => postrun}/testdata/bbi_summary/acop-incomplete/acop-incomplete.cor (100%) rename integration/{ => postrun}/testdata/bbi_summary/acop-incomplete/acop-incomplete.cov (100%) rename integration/{ => 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postrun}/testdata/bbi_summary/acop-iov/acop-iov.shk (100%) rename integration/{ => postrun}/testdata/bbi_summary/acop-nan/acop-nan.cor (100%) rename integration/{ => postrun}/testdata/bbi_summary/acop-nan/acop-nan.cov (100%) rename integration/{ => postrun}/testdata/bbi_summary/acop-nan/acop-nan.cpu (100%) rename integration/{ => postrun}/testdata/bbi_summary/acop-nan/acop-nan.ext (100%) rename integration/{ => postrun}/testdata/bbi_summary/acop-nan/acop-nan.grd (100%) rename integration/{ => postrun}/testdata/bbi_summary/acop-nan/acop-nan.lst (100%) rename integration/{ => postrun}/testdata/bbi_summary/acop-nan/acop-nan.shk (100%) rename integration/{ => postrun}/testdata/bbi_summary/acop.ctl (100%) rename integration/{ => postrun}/testdata/bbi_summary/acop/acop.cor (100%) rename integration/{ => postrun}/testdata/bbi_summary/acop/acop.cov (100%) rename integration/{ => postrun}/testdata/bbi_summary/acop/acop.cpu (100%) rename integration/{ => 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integration/{ => postrun}/testdata/bbi_summary/iovmm/iovmm.shk (100%) rename integration/{ => postrun}/testdata/bbi_summary/onlysim/onlysim.lst (100%) diff --git a/integration/execute.go b/integration/execute.go index 40197cd7..2fee0359 100644 --- a/integration/execute.go +++ b/integration/execute.go @@ -1,4 +1,4 @@ -package bbitest +package integration import ( "context" @@ -10,7 +10,7 @@ import ( log "github.com/sirupsen/logrus" ) -func executeCommand(ctx context.Context, command string, args ...string) (string, error) { +func ExecuteCommand(ctx context.Context, command string, args ...string) (string, error) { //Find it in path binary, _ := exec.LookPath(command) cmd := exec.CommandContext(ctx, binary, args...) @@ -40,7 +40,7 @@ func executeCommand(ctx context.Context, command string, args ...string) (string } // nolint:unparam -func executeCommandNoErrorCheck(ctx context.Context, command string, args ...string) (string, error) { +func ExecuteCommandNoErrorCheck(ctx context.Context, command string, args ...string) (string, error) { binary, _ := exec.LookPath(command) cmd := exec.CommandContext(ctx, binary, args...) cmd.Env = os.Environ() diff --git a/integration/nonmem/README.md b/integration/nonmem/README.md new file mode 100644 index 00000000..f15d6de2 --- /dev/null +++ b/integration/nonmem/README.md @@ -0,0 +1 @@ +This directory contains integration tests that rely on having NONMEM installed. diff --git a/integration/bbi_expansion_test.go b/integration/nonmem/bbi_expansion_test.go similarity index 96% rename from integration/bbi_expansion_test.go rename to integration/nonmem/bbi_expansion_test.go index 9c9bfd3d..0c21fa55 100644 --- a/integration/bbi_expansion_test.go +++ b/integration/nonmem/bbi_expansion_test.go @@ -1,4 +1,4 @@ -package bbitest +package nonmem import ( "context" @@ -8,6 +8,7 @@ import ( "strings" "testing" + . "github.com/metrumresearchgroup/bbi/integration" "github.com/metrumresearchgroup/bbi/utils" "github.com/metrumresearchgroup/wrapt" @@ -38,7 +39,7 @@ func TestBBIExpandsWithoutPrefix(tt *testing.T) { filepath.Join(scenario.Workpath, "model", targets), } - output, err := executeCommand(context.Background(), "bbi", commandAndArgs...) + output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...) t.R.NoError(err) t.R.NotEmpty(output) @@ -107,7 +108,7 @@ func TestBBIExpandsWithPrefix(tt *testing.T) { filepath.Join(scenario.Workpath, "model", targets), } - output, err := executeCommand(context.Background(), "bbi", commandAndArgs...) + output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...) t.R.NoError(err) t.R.NotEmpty(output) @@ -177,7 +178,7 @@ func TestBBIExpandsWithPrefixToPartialMatch(tt *testing.T) { filepath.Join(scenario.Workpath, "model", targets), } - output, err := executeCommand(context.Background(), "bbi", commandAndArgs...) + output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...) t.R.NoError(err) t.R.NotEmpty(output) diff --git a/integration/bbi_local_test.go b/integration/nonmem/bbi_local_test.go similarity index 98% rename from integration/bbi_local_test.go rename to integration/nonmem/bbi_local_test.go index 2950db46..8ba18602 100644 --- a/integration/bbi_local_test.go +++ b/integration/nonmem/bbi_local_test.go @@ -1,4 +1,4 @@ -package bbitest +package nonmem import ( "context" @@ -8,6 +8,7 @@ import ( "testing" "time" + . "github.com/metrumresearchgroup/bbi/integration" "github.com/metrumresearchgroup/bbi/utils" "github.com/metrumresearchgroup/wrapt" @@ -135,7 +136,7 @@ func TestNMFEOptionsEndInScript(tt *testing.T) { // Now let's run the script that was generated t.R.NoError(os.Chdir(filepath.Join(scenario.Workpath, m.identifier))) - _, err = executeCommand(ctx, filepath.Join(scenario.Workpath, m.identifier, m.identifier+".sh")) + _, err = ExecuteCommand(ctx, filepath.Join(scenario.Workpath, m.identifier, m.identifier+".sh")) t.R.NoError(os.Chdir(whereami)) t.R.NoError(err) diff --git a/integration/bbi_sge_test.go b/integration/nonmem/bbi_sge_test.go similarity index 99% rename from integration/bbi_sge_test.go rename to integration/nonmem/bbi_sge_test.go index 1b98521e..221af427 100644 --- a/integration/bbi_sge_test.go +++ b/integration/nonmem/bbi_sge_test.go @@ -1,4 +1,4 @@ -package bbitest +package nonmem import ( "context" diff --git a/integration/config_test.go b/integration/nonmem/config_test.go similarity index 99% rename from integration/config_test.go rename to integration/nonmem/config_test.go index 4463981b..761914ae 100644 --- a/integration/config_test.go +++ b/integration/nonmem/config_test.go @@ -1,4 +1,4 @@ -package bbitest +package nonmem import ( "context" diff --git a/integration/data_test.go b/integration/nonmem/data_test.go similarity index 99% rename from integration/data_test.go rename to integration/nonmem/data_test.go index e6aa724d..6418f69c 100644 --- a/integration/data_test.go +++ b/integration/nonmem/data_test.go @@ -1,4 +1,4 @@ -package bbitest +package nonmem import ( "context" diff --git a/integration/files.go b/integration/nonmem/files.go similarity index 95% rename from integration/files.go rename to integration/nonmem/files.go index 2f6a6323..8bb82750 100644 --- a/integration/files.go +++ b/integration/nonmem/files.go @@ -1,4 +1,4 @@ -package bbitest +package nonmem import ( "io/ioutil" diff --git a/integration/init_test.go b/integration/nonmem/init_test.go similarity index 94% rename from integration/init_test.go rename to integration/nonmem/init_test.go index d05ace6d..67635b4e 100644 --- a/integration/init_test.go +++ b/integration/nonmem/init_test.go @@ -1,4 +1,4 @@ -package bbitest +package nonmem import ( "context" @@ -10,6 +10,7 @@ import ( "runtime" "testing" + . "github.com/metrumresearchgroup/bbi/integration" "github.com/metrumresearchgroup/bbi/utils" "github.com/metrumresearchgroup/wrapt" @@ -34,7 +35,7 @@ func TestInitialization(tt *testing.T) { scenario.Prepare(t, context.Background()) t.Run(fmt.Sprintf("init_%s", scenario.identifier), func(t *wrapt.T) { - _, err := executeCommand(context.Background(), "bbi", "init", "--dir", os.Getenv("NONMEMROOT")) + _, err := ExecuteCommand(context.Background(), "bbi", "init", "--dir", os.Getenv("NONMEMROOT")) t.R.NoError(err) t.A.FileExists(filepath.Join(scenario.Workpath, "bbi.yaml")) diff --git a/integration/nmqual_test.go b/integration/nonmem/nmqual_test.go similarity index 99% rename from integration/nmqual_test.go rename to integration/nonmem/nmqual_test.go index 0febc80c..c4b71132 100644 --- a/integration/nmqual_test.go +++ b/integration/nonmem/nmqual_test.go @@ -1,4 +1,4 @@ -package bbitest +package nonmem import ( "context" diff --git a/integration/nonmem.go b/integration/nonmem/nonmem.go similarity index 99% rename from integration/nonmem.go rename to integration/nonmem/nonmem.go index cd9b8cb3..7c41aef8 100644 --- a/integration/nonmem.go +++ b/integration/nonmem/nonmem.go @@ -1,4 +1,4 @@ -package bbitest +package nonmem import ( "crypto/md5" diff --git a/integration/postexecution_test.go b/integration/nonmem/postexecution_test.go similarity index 99% rename from integration/postexecution_test.go rename to integration/nonmem/postexecution_test.go index bdbfd764..fa42ceff 100644 --- a/integration/postexecution_test.go +++ b/integration/nonmem/postexecution_test.go @@ -1,4 +1,4 @@ -package bbitest +package nonmem import ( "bufio" diff --git a/integration/setup.go b/integration/nonmem/setup.go similarity index 95% rename from integration/setup.go rename to integration/nonmem/setup.go index 47e0da79..f6ffa153 100644 --- a/integration/setup.go +++ b/integration/nonmem/setup.go @@ -1,4 +1,4 @@ -package bbitest +package nonmem import ( "archive/tar" @@ -14,6 +14,8 @@ import ( "strconv" "strings" + . "github.com/metrumresearchgroup/bbi/integration" + "github.com/metrumresearchgroup/wrapt" log "github.com/sirupsen/logrus" "github.com/spf13/afero" @@ -23,13 +25,6 @@ import ( var ROOT_EXECUTION_DIR string var EXECUTION_DIR string -// constants and variables used in summary tests. -const SUMMARY_TEST_DIR = "testdata/bbi_summary" -const SUMMARY_GOLD_DIR = "aa_golden_files" -const noSuchFileError = "no such file or directory" -const noFilePresentError = "no file present at" -const wrongExtensionError = "Must provide path to .lst" - type Scenario struct { Details ScenarioDetails ctx context.Context @@ -67,7 +62,7 @@ func (m Model) Execute(scenario *Scenario, args ...string) (string, error) { filepath.Join(scenario.Workpath, m.filename), }...) - return executeCommand(scenario.ctx, "bbi", cmdArguments...) + return ExecuteCommand(scenario.ctx, "bbi", cmdArguments...) } var ErrNoModelsLocated = errors.New("no model directories were located in the provided scenario") @@ -437,7 +432,7 @@ func findModelFiles(path string) []string { func (scenario *Scenario) Prepare(t *wrapt.T, ctx context.Context) { t.Helper() - _, err := executeCommand(ctx, "bbi", "init", "--dir", os.Getenv("NONMEMROOT")) + _, err := ExecuteCommand(ctx, "bbi", "init", "--dir", os.Getenv("NONMEMROOT")) t.R.NoError(err) fs := afero.NewOsFs() @@ -457,7 +452,7 @@ func (scenario *Scenario) Prepare(t *wrapt.T, ctx context.Context) { t.R.NoError(os.Chdir(scenario.Workpath)) - _, err = executeCommand(ctx, "bbi", "init", "--dir", os.Getenv("NONMEMROOT")) + _, err = ExecuteCommand(ctx, "bbi", "init", "--dir", os.Getenv("NONMEMROOT")) t.R.NoError(err) t.R.NoError(os.Chdir(whereami)) diff --git a/integration/testdata/.gitignore b/integration/nonmem/testdata/.gitignore similarity index 100% rename from integration/testdata/.gitignore rename to integration/nonmem/testdata/.gitignore diff --git a/integration/testdata/acop/.gitignore b/integration/nonmem/testdata/acop/.gitignore similarity index 100% rename from integration/testdata/acop/.gitignore rename to integration/nonmem/testdata/acop/.gitignore diff --git a/integration/testdata/acop/acop.csv b/integration/nonmem/testdata/acop/acop.csv similarity index 100% rename from integration/testdata/acop/acop.csv rename to integration/nonmem/testdata/acop/acop.csv diff --git a/integration/testdata/acop/acop.mod b/integration/nonmem/testdata/acop/acop.mod similarity index 100% rename from integration/testdata/acop/acop.mod rename to integration/nonmem/testdata/acop/acop.mod diff --git a/integration/testdata/acop/acoptar.gz b/integration/nonmem/testdata/acop/acoptar.gz similarity index 100% rename from integration/testdata/acop/acoptar.gz rename to integration/nonmem/testdata/acop/acoptar.gz diff --git a/integration/testdata/acop/scenario.json b/integration/nonmem/testdata/acop/scenario.json similarity index 100% rename from integration/testdata/acop/scenario.json rename to integration/nonmem/testdata/acop/scenario.json diff --git a/integration/testdata/bbi_expansion/data/derived/acop.csv b/integration/nonmem/testdata/bbi_expansion/data/derived/acop.csv similarity index 100% rename from integration/testdata/bbi_expansion/data/derived/acop.csv rename to integration/nonmem/testdata/bbi_expansion/data/derived/acop.csv diff --git a/integration/testdata/bbi_expansion/model/101.ctl b/integration/nonmem/testdata/bbi_expansion/model/101.ctl similarity index 100% rename from integration/testdata/bbi_expansion/model/101.ctl rename to integration/nonmem/testdata/bbi_expansion/model/101.ctl diff --git a/integration/testdata/bbi_expansion/model/102.ctl b/integration/nonmem/testdata/bbi_expansion/model/102.ctl similarity index 100% rename from integration/testdata/bbi_expansion/model/102.ctl rename to integration/nonmem/testdata/bbi_expansion/model/102.ctl diff --git a/integration/testdata/bbi_expansion/model/103.ctl b/integration/nonmem/testdata/bbi_expansion/model/103.ctl similarity index 100% rename from integration/testdata/bbi_expansion/model/103.ctl rename to integration/nonmem/testdata/bbi_expansion/model/103.ctl diff --git a/integration/testdata/bbi_expansion/model/104.ctl b/integration/nonmem/testdata/bbi_expansion/model/104.ctl similarity index 100% rename from integration/testdata/bbi_expansion/model/104.ctl rename to integration/nonmem/testdata/bbi_expansion/model/104.ctl diff --git a/integration/testdata/bbi_expansion/model/105.ctl b/integration/nonmem/testdata/bbi_expansion/model/105.ctl similarity index 100% rename from integration/testdata/bbi_expansion/model/105.ctl rename to integration/nonmem/testdata/bbi_expansion/model/105.ctl diff --git a/integration/testdata/bbi_expansion/model/bbi_mainrun_101.ctl b/integration/nonmem/testdata/bbi_expansion/model/bbi_mainrun_101.ctl similarity index 100% rename from integration/testdata/bbi_expansion/model/bbi_mainrun_101.ctl rename to integration/nonmem/testdata/bbi_expansion/model/bbi_mainrun_101.ctl diff --git a/integration/testdata/bbi_expansion/model/bbi_mainrun_102.ctl b/integration/nonmem/testdata/bbi_expansion/model/bbi_mainrun_102.ctl similarity index 100% rename from integration/testdata/bbi_expansion/model/bbi_mainrun_102.ctl rename to integration/nonmem/testdata/bbi_expansion/model/bbi_mainrun_102.ctl diff --git a/integration/testdata/bbi_expansion/model/bbi_mainrun_103.ctl b/integration/nonmem/testdata/bbi_expansion/model/bbi_mainrun_103.ctl similarity index 100% rename from integration/testdata/bbi_expansion/model/bbi_mainrun_103.ctl rename to integration/nonmem/testdata/bbi_expansion/model/bbi_mainrun_103.ctl diff --git a/integration/testdata/bbi_expansion/scenario.json b/integration/nonmem/testdata/bbi_expansion/scenario.json similarity index 100% rename from integration/testdata/bbi_expansion/scenario.json rename to integration/nonmem/testdata/bbi_expansion/scenario.json diff --git a/integration/testdata/ctl_test/acop.csv b/integration/nonmem/testdata/ctl_test/acop.csv similarity index 100% rename from integration/testdata/ctl_test/acop.csv rename to integration/nonmem/testdata/ctl_test/acop.csv diff --git a/integration/testdata/ctl_test/acop.ctl b/integration/nonmem/testdata/ctl_test/acop.ctl similarity index 100% rename from integration/testdata/ctl_test/acop.ctl rename to integration/nonmem/testdata/ctl_test/acop.ctl diff --git a/integration/testdata/ctl_test/scenario.json b/integration/nonmem/testdata/ctl_test/scenario.json similarity index 100% rename from integration/testdata/ctl_test/scenario.json rename to integration/nonmem/testdata/ctl_test/scenario.json diff --git a/integration/testdata/datacomment/acop.csv b/integration/nonmem/testdata/datacomment/acop.csv similarity index 100% rename from integration/testdata/datacomment/acop.csv rename to integration/nonmem/testdata/datacomment/acop.csv diff --git a/integration/testdata/datacomment/acop.ctl b/integration/nonmem/testdata/datacomment/acop.ctl similarity index 100% rename from integration/testdata/datacomment/acop.ctl rename to integration/nonmem/testdata/datacomment/acop.ctl diff --git a/integration/testdata/datacomment/scenario.json b/integration/nonmem/testdata/datacomment/scenario.json similarity index 100% rename from integration/testdata/datacomment/scenario.json rename to integration/nonmem/testdata/datacomment/scenario.json diff --git a/integration/testdata/leading-path-with space/acop.csv b/integration/nonmem/testdata/leading-path-with space/acop.csv similarity index 100% rename from integration/testdata/leading-path-with space/acop.csv rename to integration/nonmem/testdata/leading-path-with space/acop.csv diff --git a/integration/testdata/leading-path-with space/acop.ctl b/integration/nonmem/testdata/leading-path-with space/acop.ctl similarity index 100% rename from integration/testdata/leading-path-with space/acop.ctl rename to integration/nonmem/testdata/leading-path-with space/acop.ctl diff --git a/integration/testdata/leading-path-with space/scenario.json b/integration/nonmem/testdata/leading-path-with space/scenario.json similarity index 100% rename from integration/testdata/leading-path-with space/scenario.json rename to integration/nonmem/testdata/leading-path-with space/scenario.json diff --git a/integration/testdata/metrum_std/data/derived/Data.csv b/integration/nonmem/testdata/metrum_std/data/derived/Data.csv similarity index 100% rename from integration/testdata/metrum_std/data/derived/Data.csv rename to integration/nonmem/testdata/metrum_std/data/derived/Data.csv diff --git a/integration/testdata/metrum_std/model/nonmem/test_suite_1/acop.ctl b/integration/nonmem/testdata/metrum_std/model/nonmem/test_suite_1/acop.ctl similarity index 100% rename from integration/testdata/metrum_std/model/nonmem/test_suite_1/acop.ctl rename to integration/nonmem/testdata/metrum_std/model/nonmem/test_suite_1/acop.ctl diff --git a/integration/testdata/metrum_std/model/nonmem/test_suite_1/acop2.mod b/integration/nonmem/testdata/metrum_std/model/nonmem/test_suite_1/acop2.mod similarity index 100% rename from integration/testdata/metrum_std/model/nonmem/test_suite_1/acop2.mod rename to integration/nonmem/testdata/metrum_std/model/nonmem/test_suite_1/acop2.mod diff --git a/integration/testdata/metrum_std/scenario.json b/integration/nonmem/testdata/metrum_std/scenario.json similarity index 100% rename from integration/testdata/metrum_std/scenario.json rename to integration/nonmem/testdata/metrum_std/scenario.json diff --git a/integration/testdata/modquote/acop.csv b/integration/nonmem/testdata/modquote/acop.csv similarity index 100% rename from integration/testdata/modquote/acop.csv rename to integration/nonmem/testdata/modquote/acop.csv diff --git a/integration/testdata/modquote/m'd.ctl b/integration/nonmem/testdata/modquote/m'd.ctl similarity index 100% rename from integration/testdata/modquote/m'd.ctl rename to integration/nonmem/testdata/modquote/m'd.ctl diff --git a/integration/testdata/modquote/scenario.json b/integration/nonmem/testdata/modquote/scenario.json similarity index 100% rename from integration/testdata/modquote/scenario.json rename to integration/nonmem/testdata/modquote/scenario.json diff --git a/integration/testdata/period_test/acop.1.ctl b/integration/nonmem/testdata/period_test/acop.1.ctl similarity index 100% rename from integration/testdata/period_test/acop.1.ctl rename to integration/nonmem/testdata/period_test/acop.1.ctl diff --git a/integration/testdata/period_test/acop.csv b/integration/nonmem/testdata/period_test/acop.csv similarity index 100% rename from integration/testdata/period_test/acop.csv rename to integration/nonmem/testdata/period_test/acop.csv diff --git a/integration/testdata/period_test/scenario.json b/integration/nonmem/testdata/period_test/scenario.json similarity index 100% rename from integration/testdata/period_test/scenario.json rename to integration/nonmem/testdata/period_test/scenario.json diff --git a/integration/README.md b/integration/postrun/README.md similarity index 70% rename from integration/README.md rename to integration/postrun/README.md index fec46efd..9252bbe9 100644 --- a/integration/README.md +++ b/integration/postrun/README.md @@ -1,5 +1,5 @@ -# bbitest -This directory contains integration tests data. Many of these tests must be run in an environment containing a working NONMEM installation and/or worker nodes that can be used to execute jobs. See [`.drone.yml`](/.drone.yml) for examples. +This directory contains integration tests that do _not_ rely on having +NONMEM installed. ## Refreshing golden files The `bbi nonmem summary` tests (in `integration/bbi_summary_test.go`) use golden files stored in `integration/testdata/bbi_summary/aa_golden_files/`. These need to be refreshed when the relevant functionality in `bbi` changes. This can be done by running the tests with the `UPDATE_SUMMARY=true` environment variable, like so: diff --git a/integration/bbi_covcor_test.go b/integration/postrun/bbi_covcor_test.go similarity index 88% rename from integration/bbi_covcor_test.go rename to integration/postrun/bbi_covcor_test.go index 3afe7123..a157bba4 100644 --- a/integration/bbi_covcor_test.go +++ b/integration/postrun/bbi_covcor_test.go @@ -1,4 +1,4 @@ -package bbitest +package postrun import ( "context" @@ -7,6 +7,7 @@ import ( "regexp" "testing" + . "github.com/metrumresearchgroup/bbi/integration" "github.com/metrumresearchgroup/bbi/utils" "github.com/metrumresearchgroup/wrapt" @@ -32,7 +33,7 @@ func TestCovCorHappyPath(tt *testing.T) { filepath.Join(SUMMARY_TEST_DIR, mod.name, mod.name), } - output, err := executeCommand(context.Background(), "bbi", commandAndArgs...) + output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...) t.R.NoError(err) t.R.NotEmpty(output) @@ -74,7 +75,7 @@ func TestCovCorErrors(tt *testing.T) { // try without flag and get error var output string - output, err := executeCommandNoErrorCheck(context.Background(), "bbi", commandAndArgs...) + output, err := ExecuteCommandNoErrorCheck(context.Background(), "bbi", commandAndArgs...) t.R.Error(err) errorMatch := rgx.MatchString(output) diff --git a/integration/bbi_params_test.go b/integration/postrun/bbi_params_test.go similarity index 90% rename from integration/bbi_params_test.go rename to integration/postrun/bbi_params_test.go index 3e06271a..7c456d40 100644 --- a/integration/bbi_params_test.go +++ b/integration/postrun/bbi_params_test.go @@ -1,4 +1,4 @@ -package bbitest +package postrun import ( "context" @@ -6,6 +6,7 @@ import ( "path/filepath" "testing" + . "github.com/metrumresearchgroup/bbi/integration" "github.com/metrumresearchgroup/bbi/utils" "github.com/metrumresearchgroup/wrapt" ) @@ -38,7 +39,7 @@ func TestParamsSingleModel(tt *testing.T) { commandAndArgs = append(commandAndArgs, tc.bbiOption) } - output, err := executeCommand(context.Background(), "bbi", commandAndArgs...) + output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...) t.R.NoError(err) t.R.NotEmpty(output) @@ -74,7 +75,7 @@ func TestParamsDir(tt *testing.T) { commandAndArgs = append(commandAndArgs, tc.bbiOption) } - output, err := executeCommand(context.Background(), "bbi", commandAndArgs...) + output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...) t.R.NoError(err) t.R.NotEmpty(output) diff --git a/integration/bbi_reclean_test.go b/integration/postrun/bbi_reclean_test.go similarity index 82% rename from integration/bbi_reclean_test.go rename to integration/postrun/bbi_reclean_test.go index 05bbb012..c8d5508d 100644 --- a/integration/bbi_reclean_test.go +++ b/integration/postrun/bbi_reclean_test.go @@ -1,4 +1,4 @@ -package bbitest +package postrun import ( "context" @@ -7,6 +7,7 @@ import ( "regexp" "testing" + . "github.com/metrumresearchgroup/bbi/integration" "github.com/metrumresearchgroup/wrapt" ) @@ -22,7 +23,7 @@ func TestBBIRecleanBasic(tt *testing.T) { _ = ioutil.WriteFile(fdataCSV, []byte("fake"), 0644) t.A.FileExists(fdataCSV) - output, err := executeCommand(context.Background(), + output, err := ExecuteCommand(context.Background(), "bbi", "nonmem", "reclean", "--recleanLvl=1", "-v", dir) t.R.NoError(err) t.R.NotEmpty(output) @@ -33,7 +34,7 @@ func TestBBIRecleanBasic(tt *testing.T) { func TestBBIRecleanError(tt *testing.T) { t := wrapt.WrapT(tt) - output, err := executeCommandNoErrorCheck(context.Background(), + output, err := ExecuteCommandNoErrorCheck(context.Background(), "bbi", "nonmem", "reclean") t.R.NotNil(err) diff --git a/integration/bbi_summary_test.go b/integration/postrun/bbi_summary_test.go similarity index 94% rename from integration/bbi_summary_test.go rename to integration/postrun/bbi_summary_test.go index 2715affa..91c03167 100644 --- a/integration/bbi_summary_test.go +++ b/integration/postrun/bbi_summary_test.go @@ -1,4 +1,4 @@ -package bbitest +package postrun import ( "context" @@ -7,6 +7,7 @@ import ( "regexp" "testing" + . "github.com/metrumresearchgroup/bbi/integration" "github.com/metrumresearchgroup/bbi/utils" "github.com/metrumresearchgroup/wrapt" @@ -64,7 +65,7 @@ func TestSummaryHappyPath(tt *testing.T) { commandAndArgs = append(commandAndArgs, tc.bbiOption) } - output, err := executeCommand(context.Background(), "bbi", commandAndArgs...) + output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...) t.R.NoError(err) t.R.NotEmpty(output) @@ -130,14 +131,14 @@ func TestSummaryArgs(tt *testing.T) { } // try without flag and get error - output, err := executeCommandNoErrorCheck(context.Background(), "bbi", commandAndArgs...) + output, err := ExecuteCommandNoErrorCheck(context.Background(), "bbi", commandAndArgs...) t.R.NotNil(err) errorMatch, _ := regexp.MatchString(tm.errorRegEx, output) t.R.True(errorMatch) // append flag and get success commandAndArgs = append(commandAndArgs, tm.bbiArg) - output, err = executeCommand(context.Background(), "bbi", commandAndArgs...) + output, err = ExecuteCommand(context.Background(), "bbi", commandAndArgs...) t.R.NoError(err) t.R.NotEmpty(output) @@ -216,7 +217,7 @@ func TestSummaryErrors(tt *testing.T) { args = append(args, tc.bbiArgs...) } args = append(args, filepath.Join(SUMMARY_TEST_DIR, tc.testPath)) - output, err := executeCommandNoErrorCheck(context.Background(), "bbi", args...) + output, err := ExecuteCommandNoErrorCheck(context.Background(), "bbi", args...) t.R.NotNil(err) errorMatch, _ := regexp.MatchString(tc.errorMsg, output) t.R.True(errorMatch) @@ -237,7 +238,7 @@ func TestSummaryHappyPathNoExtension(tt *testing.T) { filepath.Join(SUMMARY_TEST_DIR, mod, mod), // adding no extension should work } - output, err := executeCommand(context.Background(), "bbi", commandAndArgs...) + output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...) t.R.NoError(err) t.R.NotEmpty(output) @@ -268,7 +269,7 @@ func TestSummaryHappyPathMultipleModels(tt *testing.T) { if tc.bbiOption != "" { commandAndArgs = append(commandAndArgs, tc.bbiOption) } - output, err := executeCommand(context.Background(), "bbi", commandAndArgs...) + output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...) gtd := GoldenFileTestingDetails{ outputString: output, @@ -306,7 +307,7 @@ func TestSummaryPathMultipleModelsError(tt *testing.T) { if tc.bbiOption != "" { commandAndArgs = append(commandAndArgs, tc.bbiOption) } - output, err := executeCommandNoErrorCheck(context.Background(), + output, err := ExecuteCommandNoErrorCheck(context.Background(), "bbi", commandAndArgs...) // Avoid testing plain output with golden file due to diff --git a/integration/golden_util.go b/integration/postrun/golden_util.go similarity index 98% rename from integration/golden_util.go rename to integration/postrun/golden_util.go index 75613134..20a05a6c 100644 --- a/integration/golden_util.go +++ b/integration/postrun/golden_util.go @@ -1,4 +1,4 @@ -package bbitest +package postrun import ( "fmt" diff --git a/integration/postrun/setup.go b/integration/postrun/setup.go new file mode 100644 index 00000000..7250ffa0 --- /dev/null +++ b/integration/postrun/setup.go @@ -0,0 +1,8 @@ +package postrun + +// constants and variables used in summary tests. +const SUMMARY_TEST_DIR = "testdata/bbi_summary" +const SUMMARY_GOLD_DIR = "aa_golden_files" +const noSuchFileError = "no such file or directory" +const noFilePresentError = "no file present at" +const wrongExtensionError = "Must provide path to .lst" diff --git a/integration/testdata/bbi_summary/1001.ctl b/integration/postrun/testdata/bbi_summary/1001.ctl similarity index 100% rename from integration/testdata/bbi_summary/1001.ctl rename to integration/postrun/testdata/bbi_summary/1001.ctl diff --git a/integration/testdata/bbi_summary/1001/.gitignore b/integration/postrun/testdata/bbi_summary/1001/.gitignore similarity index 100% rename from integration/testdata/bbi_summary/1001/.gitignore rename to integration/postrun/testdata/bbi_summary/1001/.gitignore diff --git a/integration/testdata/bbi_summary/1001/1001.1.TXT b/integration/postrun/testdata/bbi_summary/1001/1001.1.TXT similarity index 100% rename from integration/testdata/bbi_summary/1001/1001.1.TXT rename to integration/postrun/testdata/bbi_summary/1001/1001.1.TXT diff --git a/integration/testdata/bbi_summary/1001/1001.cor b/integration/postrun/testdata/bbi_summary/1001/1001.cor similarity index 100% rename from integration/testdata/bbi_summary/1001/1001.cor rename to integration/postrun/testdata/bbi_summary/1001/1001.cor diff --git a/integration/testdata/bbi_summary/1001/1001.cov b/integration/postrun/testdata/bbi_summary/1001/1001.cov similarity index 100% rename from integration/testdata/bbi_summary/1001/1001.cov rename to integration/postrun/testdata/bbi_summary/1001/1001.cov diff --git a/integration/testdata/bbi_summary/1001/1001.cpu b/integration/postrun/testdata/bbi_summary/1001/1001.cpu similarity index 100% rename from integration/testdata/bbi_summary/1001/1001.cpu rename to integration/postrun/testdata/bbi_summary/1001/1001.cpu diff --git a/integration/testdata/bbi_summary/1001/1001.ctl b/integration/postrun/testdata/bbi_summary/1001/1001.ctl similarity index 100% rename from integration/testdata/bbi_summary/1001/1001.ctl rename to integration/postrun/testdata/bbi_summary/1001/1001.ctl diff --git a/integration/testdata/bbi_summary/1001/1001.ext b/integration/postrun/testdata/bbi_summary/1001/1001.ext similarity index 100% rename from integration/testdata/bbi_summary/1001/1001.ext rename to integration/postrun/testdata/bbi_summary/1001/1001.ext diff --git a/integration/testdata/bbi_summary/1001/1001.lst b/integration/postrun/testdata/bbi_summary/1001/1001.lst similarity index 100% rename from integration/testdata/bbi_summary/1001/1001.lst rename to integration/postrun/testdata/bbi_summary/1001/1001.lst diff --git a/integration/testdata/bbi_summary/1001/PRDERR 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rename from integration/testdata/bbi_summary/example2_bayes.ctl rename to integration/postrun/testdata/bbi_summary/example2_bayes.ctl diff --git a/integration/testdata/bbi_summary/example2_bayes/.gitignore b/integration/postrun/testdata/bbi_summary/example2_bayes/.gitignore similarity index 100% rename from integration/testdata/bbi_summary/example2_bayes/.gitignore rename to integration/postrun/testdata/bbi_summary/example2_bayes/.gitignore diff --git a/integration/testdata/bbi_summary/example2_bayes/example2_bayes.cor b/integration/postrun/testdata/bbi_summary/example2_bayes/example2_bayes.cor similarity index 100% rename from integration/testdata/bbi_summary/example2_bayes/example2_bayes.cor rename to integration/postrun/testdata/bbi_summary/example2_bayes/example2_bayes.cor diff --git a/integration/testdata/bbi_summary/example2_bayes/example2_bayes.cov b/integration/postrun/testdata/bbi_summary/example2_bayes/example2_bayes.cov similarity index 100% rename from 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similarity index 100% rename from integration/testdata/bbi_summary/example2_bayes/example2_bayes.ext rename to integration/postrun/testdata/bbi_summary/example2_bayes/example2_bayes.ext diff --git a/integration/testdata/bbi_summary/example2_bayes/example2_bayes.lst b/integration/postrun/testdata/bbi_summary/example2_bayes/example2_bayes.lst similarity index 100% rename from integration/testdata/bbi_summary/example2_bayes/example2_bayes.lst rename to integration/postrun/testdata/bbi_summary/example2_bayes/example2_bayes.lst diff --git a/integration/testdata/bbi_summary/example2_bayes/example2_bayes.shk b/integration/postrun/testdata/bbi_summary/example2_bayes/example2_bayes.shk similarity index 100% rename from integration/testdata/bbi_summary/example2_bayes/example2_bayes.shk rename to integration/postrun/testdata/bbi_summary/example2_bayes/example2_bayes.shk diff --git a/integration/testdata/bbi_summary/example2_itsimp.ctl b/integration/postrun/testdata/bbi_summary/example2_itsimp.ctl similarity index 100% rename from integration/testdata/bbi_summary/example2_itsimp.ctl rename to integration/postrun/testdata/bbi_summary/example2_itsimp.ctl diff --git a/integration/testdata/bbi_summary/example2_itsimp/.gitignore b/integration/postrun/testdata/bbi_summary/example2_itsimp/.gitignore similarity index 100% rename from integration/testdata/bbi_summary/example2_itsimp/.gitignore rename to integration/postrun/testdata/bbi_summary/example2_itsimp/.gitignore diff --git a/integration/testdata/bbi_summary/example2_itsimp/example2_itsimp.cor b/integration/postrun/testdata/bbi_summary/example2_itsimp/example2_itsimp.cor similarity index 100% rename from integration/testdata/bbi_summary/example2_itsimp/example2_itsimp.cor rename to integration/postrun/testdata/bbi_summary/example2_itsimp/example2_itsimp.cor diff --git a/integration/testdata/bbi_summary/example2_itsimp/example2_itsimp.cov b/integration/postrun/testdata/bbi_summary/example2_itsimp/example2_itsimp.cov similarity index 100% rename from integration/testdata/bbi_summary/example2_itsimp/example2_itsimp.cov rename to integration/postrun/testdata/bbi_summary/example2_itsimp/example2_itsimp.cov diff --git a/integration/testdata/bbi_summary/example2_itsimp/example2_itsimp.cpu b/integration/postrun/testdata/bbi_summary/example2_itsimp/example2_itsimp.cpu similarity index 100% rename from integration/testdata/bbi_summary/example2_itsimp/example2_itsimp.cpu rename to integration/postrun/testdata/bbi_summary/example2_itsimp/example2_itsimp.cpu diff --git a/integration/testdata/bbi_summary/example2_itsimp/example2_itsimp.ctl b/integration/postrun/testdata/bbi_summary/example2_itsimp/example2_itsimp.ctl similarity index 100% rename from integration/testdata/bbi_summary/example2_itsimp/example2_itsimp.ctl rename to integration/postrun/testdata/bbi_summary/example2_itsimp/example2_itsimp.ctl diff --git a/integration/testdata/bbi_summary/example2_itsimp/example2_itsimp.ext b/integration/postrun/testdata/bbi_summary/example2_itsimp/example2_itsimp.ext similarity index 100% rename from integration/testdata/bbi_summary/example2_itsimp/example2_itsimp.ext rename to integration/postrun/testdata/bbi_summary/example2_itsimp/example2_itsimp.ext diff --git a/integration/testdata/bbi_summary/example2_itsimp/example2_itsimp.lst b/integration/postrun/testdata/bbi_summary/example2_itsimp/example2_itsimp.lst similarity index 100% rename from integration/testdata/bbi_summary/example2_itsimp/example2_itsimp.lst rename to integration/postrun/testdata/bbi_summary/example2_itsimp/example2_itsimp.lst diff --git a/integration/testdata/bbi_summary/example2_itsimp/example2_itsimp.shk b/integration/postrun/testdata/bbi_summary/example2_itsimp/example2_itsimp.shk similarity index 100% rename from integration/testdata/bbi_summary/example2_itsimp/example2_itsimp.shk rename to integration/postrun/testdata/bbi_summary/example2_itsimp/example2_itsimp.shk diff --git a/integration/testdata/bbi_summary/example2_saemimp.ctl b/integration/postrun/testdata/bbi_summary/example2_saemimp.ctl similarity index 100% rename from integration/testdata/bbi_summary/example2_saemimp.ctl rename to integration/postrun/testdata/bbi_summary/example2_saemimp.ctl diff --git a/integration/testdata/bbi_summary/example2_saemimp/.gitignore b/integration/postrun/testdata/bbi_summary/example2_saemimp/.gitignore similarity index 100% rename from integration/testdata/bbi_summary/example2_saemimp/.gitignore rename to integration/postrun/testdata/bbi_summary/example2_saemimp/.gitignore diff --git a/integration/testdata/bbi_summary/example2_saemimp/example2_saemimp.cor b/integration/postrun/testdata/bbi_summary/example2_saemimp/example2_saemimp.cor similarity index 100% rename from integration/testdata/bbi_summary/example2_saemimp/example2_saemimp.cor rename to integration/postrun/testdata/bbi_summary/example2_saemimp/example2_saemimp.cor diff --git a/integration/testdata/bbi_summary/example2_saemimp/example2_saemimp.cov b/integration/postrun/testdata/bbi_summary/example2_saemimp/example2_saemimp.cov similarity index 100% rename from integration/testdata/bbi_summary/example2_saemimp/example2_saemimp.cov rename to integration/postrun/testdata/bbi_summary/example2_saemimp/example2_saemimp.cov diff --git a/integration/testdata/bbi_summary/example2_saemimp/example2_saemimp.cpu b/integration/postrun/testdata/bbi_summary/example2_saemimp/example2_saemimp.cpu similarity index 100% rename from integration/testdata/bbi_summary/example2_saemimp/example2_saemimp.cpu rename to integration/postrun/testdata/bbi_summary/example2_saemimp/example2_saemimp.cpu diff --git a/integration/testdata/bbi_summary/example2_saemimp/example2_saemimp.ctl b/integration/postrun/testdata/bbi_summary/example2_saemimp/example2_saemimp.ctl similarity index 100% rename from integration/testdata/bbi_summary/example2_saemimp/example2_saemimp.ctl rename to integration/postrun/testdata/bbi_summary/example2_saemimp/example2_saemimp.ctl diff --git a/integration/testdata/bbi_summary/example2_saemimp/example2_saemimp.ext b/integration/postrun/testdata/bbi_summary/example2_saemimp/example2_saemimp.ext similarity index 100% rename from integration/testdata/bbi_summary/example2_saemimp/example2_saemimp.ext rename to integration/postrun/testdata/bbi_summary/example2_saemimp/example2_saemimp.ext diff --git a/integration/testdata/bbi_summary/example2_saemimp/example2_saemimp.lst b/integration/postrun/testdata/bbi_summary/example2_saemimp/example2_saemimp.lst similarity index 100% rename from integration/testdata/bbi_summary/example2_saemimp/example2_saemimp.lst rename to integration/postrun/testdata/bbi_summary/example2_saemimp/example2_saemimp.lst diff --git a/integration/testdata/bbi_summary/example2_saemimp/example2_saemimp.shk b/integration/postrun/testdata/bbi_summary/example2_saemimp/example2_saemimp.shk similarity index 100% rename from integration/testdata/bbi_summary/example2_saemimp/example2_saemimp.shk rename to integration/postrun/testdata/bbi_summary/example2_saemimp/example2_saemimp.shk diff --git a/integration/testdata/bbi_summary/example2_saemimp/saem.ext b/integration/postrun/testdata/bbi_summary/example2_saemimp/saem.ext similarity index 100% rename from integration/testdata/bbi_summary/example2_saemimp/saem.ext rename to integration/postrun/testdata/bbi_summary/example2_saemimp/saem.ext diff --git a/integration/testdata/bbi_summary/iovmm.mod b/integration/postrun/testdata/bbi_summary/iovmm.mod similarity index 100% rename from integration/testdata/bbi_summary/iovmm.mod rename to integration/postrun/testdata/bbi_summary/iovmm.mod diff --git a/integration/testdata/bbi_summary/iovmm/.gitignore b/integration/postrun/testdata/bbi_summary/iovmm/.gitignore similarity index 100% rename from integration/testdata/bbi_summary/iovmm/.gitignore rename to integration/postrun/testdata/bbi_summary/iovmm/.gitignore diff --git a/integration/testdata/bbi_summary/iovmm/iovmm.cpu b/integration/postrun/testdata/bbi_summary/iovmm/iovmm.cpu similarity index 100% rename from integration/testdata/bbi_summary/iovmm/iovmm.cpu rename to integration/postrun/testdata/bbi_summary/iovmm/iovmm.cpu diff --git a/integration/testdata/bbi_summary/iovmm/iovmm.ext b/integration/postrun/testdata/bbi_summary/iovmm/iovmm.ext similarity index 100% rename from integration/testdata/bbi_summary/iovmm/iovmm.ext rename to integration/postrun/testdata/bbi_summary/iovmm/iovmm.ext diff --git a/integration/testdata/bbi_summary/iovmm/iovmm.grd b/integration/postrun/testdata/bbi_summary/iovmm/iovmm.grd similarity index 100% rename from integration/testdata/bbi_summary/iovmm/iovmm.grd rename to integration/postrun/testdata/bbi_summary/iovmm/iovmm.grd diff --git a/integration/testdata/bbi_summary/iovmm/iovmm.lst b/integration/postrun/testdata/bbi_summary/iovmm/iovmm.lst similarity index 100% rename from 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