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Add mrgvalidate Test Id's to any tests that are missing them #246

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seth127 opened this issue Sep 23, 2021 · 2 comments · Fixed by #251
Closed

Add mrgvalidate Test Id's to any tests that are missing them #246

seth127 opened this issue Sep 23, 2021 · 2 comments · Fixed by #251
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Move validation p...

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@seth127
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seth127 commented Sep 23, 2021

As described in https://metrumresearchgroup.github.io/mrgvalprep/articles/basic_usage.html#test-ids

Some should have already been added from #239 and #233 but there will surely be some left that still need them.

This will also involve mapping these to the updated requirements and stories in googlesheets or whatever end up using for #238
@seth127 seth127 mentioned this issue Sep 28, 2021
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@seth127
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seth127 commented Sep 30, 2021

These is the current list of tests we need to tag (none of them have tags yet)

$ grep -rn '^func Test' .
./cmd/nonmem_test.go:16:func Test_doesDirectoryContainOutputFiles(tt *testing.T) {
./cmd/nonmem_test.go:72:func Test_processNMFEOptions(tt *testing.T) {
./cmd/nonmem_test.go:166:func Test_modelDataFile(tt *testing.T) {
./cmd/nonmem_test.go:213:func Test_dataFileIsPresent(tt *testing.T) {
./cmd/sge_test.go:9:func Test_gridengineJobName(t *testing.T) {
./parsers/nmparser/set_missing_values_to_default_test.go:10:func TestSetMissingValuesToDefaultParameterDataMethod(tt *testing.T) {
./parsers/nmparser/set_missing_values_to_default_test.go:41:func TestSetMissingValuesToDefaultParameterDataStdErrDimension(tt *testing.T) {
./parsers/nmparser/set_missing_values_to_default_test.go:72:func TestSetMissingValuesToDefaultParameterDataRESDDimension(tt *testing.T) {
./parsers/nmparser/set_missing_values_to_default_test.go:102:func TestSetMissingValuesToDefaultParameterDataValues(tt *testing.T) {
./parsers/nmparser/set_missing_values_to_default_test.go:138:func TestSetMissingValuesToDefaultParameterNameValues(tt *testing.T) {
./parsers/nmparser/utils_test.go:9:func TestCreateDiagonalBlock(tt *testing.T) {
./parsers/nmparser/parse_block_result_test.go:9:func TestParseBlockResults(tt *testing.T) {
./parsers/nmparser/parse_block_structure_test.go:9:func TestParseParameterBlock(tt *testing.T) {
./parsers/nmparser/format_theta_test.go:9:func TestFormattingThetaBlock(tt *testing.T) {
./parsers/nmparser/parse_theta_results_test.go:9:func TestParseThetaResultsBlock(tt *testing.T) {
./parsers/nmparser/parameter_names_test.go:9:func TestDefaultParameterNames(tt *testing.T) {
./parsers/nmparser/read_cov_test.go:9:func TestReadParseCovLines(tt *testing.T) {
./parsers/nmparser/add_path_level_test.go:11:func TestAddingPathLevel(tt *testing.T) {
./parsers/nmparser/consts_test.go:10:func TestOmega(tt *testing.T) {
./parsers/nmparser/parse_parameter_structure_test.go:11:func TestParseParameterStructure(tt *testing.T) {
./parsers/nmparser/parse_parameter_structure_test.go:36:func TestParseParameterStructures(tt *testing.T) {
./parsers/nmparser/parse_final_parameter_estimates_test.go:9:func TestParseFinalParameterEstimatesFromLst(tt *testing.T) {
./parsers/nmparser/read_ext_test.go:9:func TestReadExt(tt *testing.T) {
./parsers/nmparser/parse_lst_file_test.go:11:func TestParseOBJV(tt *testing.T) {
./parsers/nmparser/parse_lst_file_test.go:34:func TestParTestParseOBJV2(tt *testing.T) {
./parsers/nmparser/parse_lst_file_test.go:57:func TestParTestParseOBJV3(tt *testing.T) {
./parsers/nmparser/parse_lst_file_test.go:79:func TestParseGradient(tt *testing.T) {
./parsers/nmparser/parse_lst_file_test.go:137:func TestConditionNumber(tt *testing.T) {
./parsers/nmparser/parse_lst_file_test.go:230:func TestSetCorrelationsOk(tt *testing.T) {
./parsers/nmparser/parse_lst_file_test.go:538:func TestCheckMatrix(tt *testing.T) {
./parsers/nmparser/parse_lst_file_test.go:573:func TestSetCov(tt *testing.T) {
./parsers/nmparser/parse_lst_file_test.go:667:func TestGetGradientLine(tt *testing.T) {
./parsers/nmparser/clean_theta_test.go:72:func TestCleaningThetaBlock(tt *testing.T) {
./parsers/nmparser/read_shk_test.go:11:func TestReadParseShkLines(tt *testing.T) {
./parsers/nmparser/read_shk_test.go:111:func TestReadParseShkLines2(tt *testing.T) {
./parsers/nmparser/diagonal_elements_test.go:9:func TestGetDiagonalIndices(tt *testing.T) {
./parsers/nmparser/diagonal_elements_test.go:57:func TestGetDiagonalIndices2(tt *testing.T) {
./parsers/nmparser/diagonal_elements_test.go:110:func TestGetBlockParameterNames(tt *testing.T) {
./parsers/nmparser/read_grd_test.go:12:func TestReadParseGrdLines(tt *testing.T) {
./parsers/nmparser/parse_run_details_test.go:30:func TestParseRunDetails(tt *testing.T) {
./parsers/nmparser/parse_run_details_test.go:131:func TestParseRunDetailsFromFile(t *testing.T) {
./integration/bbi_local_test.go:15:func TestBbiCompletesLocalExecution(tt *testing.T) {
./integration/bbi_local_test.go:71:func TestNMFEOptionsEndInScript(tt *testing.T) {
./integration/bbi_local_test.go:139:func TestBbiParallelExecution(tt *testing.T) {
./integration/bbi_local_test.go:201:func TestDefaultConfigLoaded(tt *testing.T) {
./integration/bbi_local_test.go:245:func TestSpecifiedConfigByAbsPathLoaded(tt *testing.T) {
./integration/bbi_local_test.go:314:func TestSpecifiedConfigByRelativePathLoaded(tt *testing.T) {
./integration/bbi_covcor_test.go:13:func TestCovCorHappyPath(tt *testing.T) {
./integration/bbi_covcor_test.go:51:func TestCovCorErrors(tt *testing.T) {
./integration/bbi_expansion_test.go:15:func TestBBIExpandsWithoutPrefix(tt *testing.T) {
./integration/bbi_expansion_test.go:80:func TestBBIExpandsWithPrefix(tt *testing.T) {
./integration/bbi_expansion_test.go:142:func TestBBIExpandsWithPrefixToPartialMatch(tt *testing.T) {
./integration/nmqual_test.go:13:func TestNMQUALExecutionSucceeds(tt *testing.T) {
./integration/nmqual_test.go:56:func TestHashingForNMQualWorksWithOriginalModFile(tt *testing.T) {
./integration/bbi_sge_test.go:16:func TestBbiCompletesSGEExecution(tt *testing.T) {
./integration/bbi_sge_test.go:71:func TestBbiCompletesParallelSGEExecution(tt *testing.T) {
./integration/data_test.go:16:func TestHasValidDataPathForCTL(tt *testing.T) {
./integration/data_test.go:49:func TestHasInvalidDataPath(tt *testing.T) {
./integration/data_test.go:105:func TestHasValidComplexPathCTLAndMod(tt *testing.T) {
./integration/init_test.go:17:func TestInitialization(tt *testing.T) {
./integration/bbi_summary_test.go:35:func TestSummaryHappyPath(tt *testing.T) {
./integration/bbi_summary_test.go:88:func TestSummaryArgs(tt *testing.T) {
./integration/bbi_summary_test.go:154:func TestSummaryErrors(tt *testing.T) {
./integration/bbi_summary_test.go:200:func TestSummaryHappyPathNoExtension(tt *testing.T) {
./integration/config_test.go:18:func TestBBIConfigJSONCreated(tt *testing.T) {
./integration/config_test.go:82:func TestConfigValuesAreCorrectInWrittenFile(tt *testing.T) {
./integration/postexecution_test.go:50:func TestKVPExpansion(tt *testing.T) {
./integration/postexecution_test.go:63:func TestPostExecutionSucceeds(tt *testing.T) {
./runner/consts_test.go:28:func TestEstOutputFilesByRun(tt *testing.T) {
./runner/prepare_to_execute_test.go:10:func TestPrepareForExecution(tt *testing.T) {
./runner/estimate_model_test.go:9:func TestDefaultEstimateModel(tt *testing.T) {
./runner/estimate_model_test.go:23:func TestCustomEstimateModel(tt *testing.T) {
./runner/estimate_model_test.go:38:func TestLogiclessTemplateForEstimateModel(tt *testing.T) {
./runner/read_copied_files_test.go:10:func TestReadCopiedFiles(tt *testing.T) {
./runner/read_copied_files_test.go:34:func TestGetCopiedFilenames(tt *testing.T) {
./utils/utils_test.go:12:func TestDirExists(tt *testing.T) {
./utils/utils_test.go:96:func TestIsDir(tt *testing.T) {
./utils/utils_test.go:135:func TestFileAndExt(tt *testing.T) {
./utils/list_matches_test.go:11:func TestListMatchesByRegex(tt *testing.T) {
./utils/list_matches_test.go:74:func TestListMatchesByGlob(tt *testing.T) {
./utils/list_model_files_test.go:9:func TestListModelFiles(tt *testing.T) {
./utils/expand_sequence_test.go:9:func TestExpandSequence(tt *testing.T) {
./utils/io_test.go:10:func TestReadExt(tt *testing.T) {
./utils/io_test.go:42:func TestHasZero(tt *testing.T) {
./utils/left_pad_test.go:9:func TestPadNum(tt *testing.T) {

@seth127 seth127 mentioned this issue Sep 30, 2021
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@seth127
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seth127 commented Sep 30, 2021

Proposed Test Id's (the output from previous comment, annotated and rearranged a little)

UNIT-CMD-001 ./cmd/nonmem_test.go:16:func Test_doesDirectoryContainOutputFiles(tt *testing.T) {
UNIT-CMD-002 ./cmd/nonmem_test.go:72:func Test_processNMFEOptions(tt *testing.T) {
UNIT-CMD-003 ./cmd/nonmem_test.go:166:func Test_modelDataFile(tt *testing.T) {
UNIT-CMD-004 ./cmd/nonmem_test.go:213:func Test_dataFileIsPresent(tt *testing.T) {
UNIT-CMD-005 ./cmd/sge_test.go:9:func Test_gridengineJobName(t *testing.T) {

UNIT-NMP-001 ./parsers/nmparser/set_missing_values_to_default_test.go:10:func TestSetMissingValuesToDefaultParameterDataMethod(tt *testing.T) {
UNIT-NMP-002 ./parsers/nmparser/set_missing_values_to_default_test.go:41:func TestSetMissingValuesToDefaultParameterDataStdErrDimension(tt *testing.T) {
UNIT-NMP-003 ./parsers/nmparser/set_missing_values_to_default_test.go:72:func TestSetMissingValuesToDefaultParameterDataRESDDimension(tt *testing.T) {
UNIT-NMP-004 ./parsers/nmparser/set_missing_values_to_default_test.go:102:func TestSetMissingValuesToDefaultParameterDataValues(tt *testing.T) {
UNIT-NMP-005 ./parsers/nmparser/set_missing_values_to_default_test.go:138:func TestSetMissingValuesToDefaultParameterNameValues(tt *testing.T) {
UNIT-NMP-006 ./parsers/nmparser/utils_test.go:9:func TestCreateDiagonalBlock(tt *testing.T) {
UNIT-NMP-007 ./parsers/nmparser/parse_block_result_test.go:9:func TestParseBlockResults(tt *testing.T) {
UNIT-NMP-008 ./parsers/nmparser/parse_block_structure_test.go:9:func TestParseParameterBlock(tt *testing.T) {
UNIT-NMP-009 ./parsers/nmparser/format_theta_test.go:9:func TestFormattingThetaBlock(tt *testing.T) {
UNIT-NMP-010 ./parsers/nmparser/parse_theta_results_test.go:9:func TestParseThetaResultsBlock(tt *testing.T) {
UNIT-NMP-011 ./parsers/nmparser/parameter_names_test.go:9:func TestDefaultParameterNames(tt *testing.T) {
UNIT-NMP-012 ./parsers/nmparser/read_cov_test.go:9:func TestReadParseCovLines(tt *testing.T) {
UNIT-NMP-013 ./parsers/nmparser/add_path_level_test.go:11:func TestAddingPathLevel(tt *testing.T) {
UNIT-NMP-014 ./parsers/nmparser/consts_test.go:10:func TestOmega(tt *testing.T) {
UNIT-NMP-015 ./parsers/nmparser/parse_parameter_structure_test.go:11:func TestParseParameterStructure(tt *testing.T) {
UNIT-NMP-016 ./parsers/nmparser/parse_parameter_structure_test.go:36:func TestParseParameterStructures(tt *testing.T) {
UNIT-NMP-017 ./parsers/nmparser/parse_final_parameter_estimates_test.go:9:func TestParseFinalParameterEstimatesFromLst(tt *testing.T) {
UNIT-NMP-018 ./parsers/nmparser/read_ext_test.go:9:func TestReadExt(tt *testing.T) {
UNIT-NMP-019 ./parsers/nmparser/parse_lst_file_test.go:11:func TestParseOBJV(tt *testing.T) {
UNIT-NMP-020 ./parsers/nmparser/parse_lst_file_test.go:34:func TestParTestParseOBJV2(tt *testing.T) {
UNIT-NMP-021 ./parsers/nmparser/parse_lst_file_test.go:57:func TestParTestParseOBJV3(tt *testing.T) {
UNIT-NMP-022 ./parsers/nmparser/parse_lst_file_test.go:79:func TestParseGradient(tt *testing.T) {
UNIT-NMP-023 ./parsers/nmparser/parse_lst_file_test.go:137:func TestConditionNumber(tt *testing.T) {
UNIT-NMP-024 ./parsers/nmparser/parse_lst_file_test.go:230:func TestSetCorrelationsOk(tt *testing.T) {
UNIT-NMP-025 ./parsers/nmparser/parse_lst_file_test.go:538:func TestCheckMatrix(tt *testing.T) {
UNIT-NMP-026 ./parsers/nmparser/parse_lst_file_test.go:573:func TestSetCov(tt *testing.T) {
UNIT-NMP-027 ./parsers/nmparser/parse_lst_file_test.go:667:func TestGetGradientLine(tt *testing.T) {
UNIT-NMP-028 ./parsers/nmparser/clean_theta_test.go:72:func TestCleaningThetaBlock(tt *testing.T) {
UNIT-NMP-029 ./parsers/nmparser/read_shk_test.go:11:func TestReadParseShkLines(tt *testing.T) {
UNIT-NMP-030 ./parsers/nmparser/read_shk_test.go:111:func TestReadParseShkLines2(tt *testing.T) {
UNIT-NMP-031 ./parsers/nmparser/diagonal_elements_test.go:9:func TestGetDiagonalIndices(tt *testing.T) {
UNIT-NMP-032 ./parsers/nmparser/diagonal_elements_test.go:57:func TestGetDiagonalIndices2(tt *testing.T) {
UNIT-NMP-033 ./parsers/nmparser/diagonal_elements_test.go:110:func TestGetBlockParameterNames(tt *testing.T) {
UNIT-NMP-034 ./parsers/nmparser/read_grd_test.go:12:func TestReadParseGrdLines(tt *testing.T) {
UNIT-NMP-035 ./parsers/nmparser/parse_run_details_test.go:30:func TestParseRunDetails(tt *testing.T) {
UNIT-NMP-036 ./parsers/nmparser/parse_run_details_test.go:131:func TestParseRunDetailsFromFile(t *testing.T) {

UNIT-RUN-001 ./runner/consts_test.go:28:func TestEstOutputFilesByRun(tt *testing.T) {
UNIT-RUN-002 ./runner/prepare_to_execute_test.go:10:func TestPrepareForExecution(tt *testing.T) {
UNIT-RUN-003 ./runner/estimate_model_test.go:9:func TestDefaultEstimateModel(tt *testing.T) {
UNIT-RUN-004 ./runner/estimate_model_test.go:23:func TestCustomEstimateModel(tt *testing.T) {
UNIT-RUN-005 ./runner/estimate_model_test.go:38:func TestLogiclessTemplateForEstimateModel(tt *testing.T) {
UNIT-RUN-006 ./runner/read_copied_files_test.go:10:func TestReadCopiedFiles(tt *testing.T) {
UNIT-RUN-007 ./runner/read_copied_files_test.go:34:func TestGetCopiedFilenames(tt *testing.T) {

UNIT-UTL-001 ./utils/utils_test.go:12:func TestDirExists(tt *testing.T) {
UNIT-UTL-002 ./utils/utils_test.go:96:func TestIsDir(tt *testing.T) {
UNIT-UTL-003 ./utils/utils_test.go:135:func TestFileAndExt(tt *testing.T) {
UNIT-UTL-004 ./utils/list_matches_test.go:11:func TestListMatchesByRegex(tt *testing.T) {
UNIT-UTL-005 ./utils/list_matches_test.go:74:func TestListMatchesByGlob(tt *testing.T) {
UNIT-UTL-006 ./utils/list_model_files_test.go:9:func TestListModelFiles(tt *testing.T) {
UNIT-UTL-007 ./utils/expand_sequence_test.go:9:func TestExpandSequence(tt *testing.T) {
UNIT-UTL-008 ./utils/io_test.go:10:func TestReadExt(tt *testing.T) {
UNIT-UTL-009 ./utils/io_test.go:42:func TestHasZero(tt *testing.T) {
UNIT-UTL-010 ./utils/left_pad_test.go:9:func TestPadNum(tt *testing.T) {

INT-LOCAL-001 ./integration/bbi_local_test.go:15:func TestBbiCompletesLocalExecution(tt *testing.T) {
INT-LOCAL-002 ./integration/bbi_local_test.go:71:func TestNMFEOptionsEndInScript(tt *testing.T) {
INT-LOCAL-003 ./integration/bbi_local_test.go:139:func TestBbiParallelExecution(tt *testing.T) {
INT-LOCAL-004 ./integration/bbi_local_test.go:201:func TestDefaultConfigLoaded(tt *testing.T) {
INT-LOCAL-005 ./integration/bbi_local_test.go:245:func TestSpecifiedConfigByAbsPathLoaded(tt *testing.T) {
INT-LOCAL-006 ./integration/bbi_local_test.go:314:func TestSpecifiedConfigByRelativePathLoaded(tt *testing.T) {
INT-COVCOR-001 ./integration/bbi_covcor_test.go:13:func TestCovCorHappyPath(tt *testing.T) {
INT-COVCOR-002 ./integration/bbi_covcor_test.go:51:func TestCovCorErrors(tt *testing.T) {
INT-EXP-001 ./integration/bbi_expansion_test.go:15:func TestBBIExpandsWithoutPrefix(tt *testing.T) {
INT-EXP-002 ./integration/bbi_expansion_test.go:80:func TestBBIExpandsWithPrefix(tt *testing.T) {
INT-EXP-003 ./integration/bbi_expansion_test.go:142:func TestBBIExpandsWithPrefixToPartialMatch(tt *testing.T) {
INT-NMQ-001 ./integration/nmqual_test.go:13:func TestNMQUALExecutionSucceeds(tt *testing.T) {
INT-NMQ-002 ./integration/nmqual_test.go:56:func TestHashingForNMQualWorksWithOriginalModFile(tt *testing.T) {
INT-SGE-001 ./integration/bbi_sge_test.go:16:func TestBbiCompletesSGEExecution(tt *testing.T) {
INT-SGE-002 ./integration/bbi_sge_test.go:71:func TestBbiCompletesParallelSGEExecution(tt *testing.T) {
INT-DATA-001 ./integration/data_test.go:16:func TestHasValidDataPathForCTL(tt *testing.T) {
INT-DATA-002 ./integration/data_test.go:49:func TestHasInvalidDataPath(tt *testing.T) {
INT-DATA-003 ./integration/data_test.go:105:func TestHasValidComplexPathCTLAndMod(tt *testing.T) {
INT-INIT-001 ./integration/init_test.go:17:func TestInitialization(tt *testing.T) {
INT-SUM-001 ./integration/bbi_summary_test.go:35:func TestSummaryHappyPath(tt *testing.T) {
INT-SUM-002 ./integration/bbi_summary_test.go:88:func TestSummaryArgs(tt *testing.T) {
INT-SUM-003 ./integration/bbi_summary_test.go:154:func TestSummaryErrors(tt *testing.T) {
INT-SUM-004 ./integration/bbi_summary_test.go:200:func TestSummaryHappyPathNoExtension(tt *testing.T) {
INT-CFG-001 ./integration/config_test.go:18:func TestBBIConfigJSONCreated(tt *testing.T) {
INT-CFG-002 ./integration/config_test.go:82:func TestConfigValuesAreCorrectInWrittenFile(tt *testing.T) {
INT-POSTEX-001 ./integration/postexecution_test.go:50:func TestKVPExpansion(tt *testing.T) {
INT-POSTEX-002 ./integration/postexecution_test.go:63:func TestPostExecutionSucceeds(tt *testing.T) {

@seth127 seth127 mentioned this issue Oct 1, 2021
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Move validation process to mrgval*
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Adding mrgvalidate style Test Id's metrumresearchgroup/bbi
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@seth127