From 25b3bc5c6cc097a56c563f123dbe851cac5443cb Mon Sep 17 00:00:00 2001 From: rfm-targa Date: Fri, 12 Apr 2024 17:13:15 +0100 Subject: [PATCH] Created file with test arguments. --- CHEWBBACA/tests/test_allelecall.py | 53 ++--- CHEWBBACA/tests/test_allelecall_evaluator.py | 5 +- CHEWBBACA/tests/test_arguments.py | 215 +++++++++++++++++++ CHEWBBACA/tests/test_basic_messages.py | 66 +++--- CHEWBBACA/tests/test_createschema.py | 17 +- CHEWBBACA/tests/test_prepexternalschema.py | 15 +- CHEWBBACA/tests/test_schema_evaluator.py | 15 +- CHEWBBACA/utils/constants.py | 199 ----------------- 8 files changed, 303 insertions(+), 282 deletions(-) create mode 100644 CHEWBBACA/tests/test_arguments.py diff --git a/CHEWBBACA/tests/test_allelecall.py b/CHEWBBACA/tests/test_allelecall.py index 9c1205d6..c3e9ba24 100644 --- a/CHEWBBACA/tests/test_allelecall.py +++ b/CHEWBBACA/tests/test_allelecall.py @@ -13,6 +13,7 @@ from CHEWBBACA import chewBBACA from CHEWBBACA.utils import constants as ct +from CHEWBBACA.tests import test_arguments as ta # Use the tmp_path fixture to create a tmp directory for each test @@ -29,20 +30,20 @@ def args_fixture(request, tmp_path): @pytest.mark.parametrize( "args_fixture", [ - (ct.ALLELECALL_TEST_DEFAULT, 'data/allelecall_data/test_results/mode4'), - (ct.ALLELECALL_TEST_MODE1, 'data/allelecall_data/test_results/mode1'), - (ct.ALLELECALL_TEST_MODE2, 'data/allelecall_data/test_results/mode2'), - (ct.ALLELECALL_TEST_MODE3, 'data/allelecall_data/test_results/mode3'), - (ct.ALLELECALL_TEST_MODE4, 'data/allelecall_data/test_results/mode4'), - (ct.ALLELECALL_TEST_CDS_DEFAULT, 'data/allelecall_data/test_results/cds_input_mode4'), - (ct.ALLELECALL_TEST_CDS_MODE1, 'data/allelecall_data/test_results/cds_input_mode1'), - (ct.ALLELECALL_TEST_CDS_MODE2, 'data/allelecall_data/test_results/cds_input_mode2'), - (ct.ALLELECALL_TEST_CDS_MODE3, 'data/allelecall_data/test_results/cds_input_mode3'), - (ct.ALLELECALL_TEST_CDS_MODE4, 'data/allelecall_data/test_results/cds_input_mode4'), - (ct.ALLELECALL_TEST_GENOME_LIST, 'data/allelecall_data/test_results/mode4'), - (ct.ALLELECALL_TEST_LOCI_IDS_EXTENSION, 'data/allelecall_data/test_genes_list/test_genes_results'), - (ct.ALLELECALL_TEST_LOCI_IDS_NOEXTENSION, 'data/allelecall_data/test_genes_list/test_genes_results'), - (ct.ALLELECALL_TEST_LOCI_PATHS, 'data/allelecall_data/test_genes_list/test_genes_results'), + (ta.ALLELECALL_TEST_DEFAULT, 'data/allelecall_data/test_results/mode4'), + (ta.ALLELECALL_TEST_MODE1, 'data/allelecall_data/test_results/mode1'), + (ta.ALLELECALL_TEST_MODE2, 'data/allelecall_data/test_results/mode2'), + (ta.ALLELECALL_TEST_MODE3, 'data/allelecall_data/test_results/mode3'), + (ta.ALLELECALL_TEST_MODE4, 'data/allelecall_data/test_results/mode4'), + (ta.ALLELECALL_TEST_CDS_DEFAULT, 'data/allelecall_data/test_results/cds_input_mode4'), + (ta.ALLELECALL_TEST_CDS_MODE1, 'data/allelecall_data/test_results/cds_input_mode1'), + (ta.ALLELECALL_TEST_CDS_MODE2, 'data/allelecall_data/test_results/cds_input_mode2'), + (ta.ALLELECALL_TEST_CDS_MODE3, 'data/allelecall_data/test_results/cds_input_mode3'), + (ta.ALLELECALL_TEST_CDS_MODE4, 'data/allelecall_data/test_results/cds_input_mode4'), + (ta.ALLELECALL_TEST_GENOME_LIST, 'data/allelecall_data/test_results/mode4'), + (ta.ALLELECALL_TEST_LOCI_IDS_EXTENSION, 'data/allelecall_data/test_genes_list/test_genes_results'), + (ta.ALLELECALL_TEST_LOCI_IDS_NOEXTENSION, 'data/allelecall_data/test_genes_list/test_genes_results'), + (ta.ALLELECALL_TEST_LOCI_PATHS, 'data/allelecall_data/test_genes_list/test_genes_results'), ], indirect=True # Pass parameters through args_fixture fixture ) @@ -78,10 +79,10 @@ def test_allelecall_valid_input(monkeypatch, args_fixture): @pytest.mark.parametrize( "args_fixture", [ - (ct.ALLELECALL_TEST_EMPTY_DIR, ct.MISSING_FASTAS_EXCEPTION), - (ct.ALLELECALL_TEST_EMPTY_FILES, ct.MISSING_FASTAS_EXCEPTION), - (ct.ALLELECALL_TEST_ZERO_BYTES, ct.MISSING_FASTAS_EXCEPTION), - (ct.ALLELECALL_TEST_FAKE_PATH, ct.INVALID_INPUT_PATH) + (ta.ALLELECALL_TEST_EMPTY_DIR, ct.MISSING_FASTAS_EXCEPTION), + (ta.ALLELECALL_TEST_EMPTY_FILES, ct.MISSING_FASTAS_EXCEPTION), + (ta.ALLELECALL_TEST_ZERO_BYTES, ct.MISSING_FASTAS_EXCEPTION), + (ta.ALLELECALL_TEST_FAKE_PATH, ct.INVALID_INPUT_PATH) ], indirect=True ) @@ -106,14 +107,14 @@ def test_allelecall_invalid_input(monkeypatch, args_fixture): @pytest.mark.parametrize( "args_fixture", [ - (ct.ALLELECALL_TEST_DEFAULT+['--bsr', '-1'], ct.INVALID_BSR), - (ct.ALLELECALL_TEST_DEFAULT+['--bsr', '1.1'], ct.INVALID_BSR), - (ct.ALLELECALL_TEST_DEFAULT+['--bsr', 'sus'], ct.INVALID_BSR_TYPE.format('sus')), - (ct.ALLELECALL_TEST_DEFAULT+['--l', '-1'], ct.INVALID_MINLEN), - (ct.ALLELECALL_TEST_DEFAULT+['--l', 'sus'], ct.INVALID_MINLEN_TYPE), - (ct.ALLELECALL_TEST_DEFAULT+['--st', '-1'], ct.INVALID_ST), - (ct.ALLELECALL_TEST_DEFAULT+['--st', '1.1'], ct.INVALID_ST), - (ct.ALLELECALL_TEST_DEFAULT+['--st', 'sus'], ct.INVALID_ST_TYPE) + (ta.ALLELECALL_TEST_DEFAULT+['--bsr', '-1'], ct.INVALID_BSR), + (ta.ALLELECALL_TEST_DEFAULT+['--bsr', '1.1'], ct.INVALID_BSR), + (ta.ALLELECALL_TEST_DEFAULT+['--bsr', 'sus'], ct.INVALID_BSR_TYPE.format('sus')), + (ta.ALLELECALL_TEST_DEFAULT+['--l', '-1'], ct.INVALID_MINLEN), + (ta.ALLELECALL_TEST_DEFAULT+['--l', 'sus'], ct.INVALID_MINLEN_TYPE), + (ta.ALLELECALL_TEST_DEFAULT+['--st', '-1'], ct.INVALID_ST), + (ta.ALLELECALL_TEST_DEFAULT+['--st', '1.1'], ct.INVALID_ST), + (ta.ALLELECALL_TEST_DEFAULT+['--st', 'sus'], ct.INVALID_ST_TYPE) ], indirect=True ) diff --git a/CHEWBBACA/tests/test_allelecall_evaluator.py b/CHEWBBACA/tests/test_allelecall_evaluator.py index 9bbe6e09..f1e8d3b9 100644 --- a/CHEWBBACA/tests/test_allelecall_evaluator.py +++ b/CHEWBBACA/tests/test_allelecall_evaluator.py @@ -10,6 +10,7 @@ from CHEWBBACA import chewBBACA from CHEWBBACA.utils import constants as ct +from CHEWBBACA.tests import test_arguments as ta # Use the tmp_path fixture to create a tmp directory for each test @@ -26,7 +27,7 @@ def args_fixture(request, tmp_path): @pytest.mark.parametrize( "args_fixture", [ - (ct.ALLELECALL_EVALUATOR_VALID, 'data/allelecallevaluator_data/expected_results'), + (ta.ALLELECALL_EVALUATOR_VALID, 'data/allelecallevaluator_data/expected_results'), ], indirect=True ) @@ -64,7 +65,7 @@ def test_allelecallevaluator_valid_input(monkeypatch, args_fixture): @pytest.mark.parametrize( "args_fixture", [ - (ct.ALLELECALL_EVALUATOR_INVALID_PATH, ct.MISSING_INPUT_ARG), + (ta.ALLELECALL_EVALUATOR_INVALID_PATH, ct.MISSING_INPUT_ARG), ], indirect=True ) diff --git a/CHEWBBACA/tests/test_arguments.py b/CHEWBBACA/tests/test_arguments.py new file mode 100644 index 00000000..0b1bfd00 --- /dev/null +++ b/CHEWBBACA/tests/test_arguments.py @@ -0,0 +1,215 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +""" +Purpose +------- + +This module contains variables used to test chewBBACA modules with pytest. + +Code documentation +------------------ +""" + +# Test variables used by pytest +# AlleleCall default test command +ALLELECALL_TEST_GENOME_TEMPLATE = ['chewBBACA.py', 'AlleleCall', + '-i', 'data/allelecall_data/test_genome', + '-g', 'data/allelecall_data/sagalactiae_schema', + '-o', 'allelecall_results'] + +ALLELECALL_TEST_DEFAULT = ALLELECALL_TEST_GENOME_TEMPLATE[:] +ALLELECALL_TEST_MODE1 = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--mode', '1'] +ALLELECALL_TEST_MODE2 = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--mode', '2'] +ALLELECALL_TEST_MODE3 = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--mode', '3'] +ALLELECALL_TEST_MODE4 = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--mode', '4'] + +ALLELECALL_TEST_CDS_TEMPLATE = ['chewBBACA.py', 'AlleleCall', + '-i', 'data/allelecall_data/test_cds_input', + '-g', 'data/allelecall_data/sagalactiae_schema', + '-o', 'allelecall_results', + '--cds-input'] + +ALLELECALL_TEST_CDS_DEFAULT = ALLELECALL_TEST_CDS_TEMPLATE[:] +ALLELECALL_TEST_CDS_MODE1 = ALLELECALL_TEST_CDS_TEMPLATE[:]+['--mode', '1'] +ALLELECALL_TEST_CDS_MODE2 = ALLELECALL_TEST_CDS_TEMPLATE[:]+['--mode', '2'] +ALLELECALL_TEST_CDS_MODE3 = ALLELECALL_TEST_CDS_TEMPLATE[:]+['--mode', '3'] +ALLELECALL_TEST_CDS_MODE4 = ALLELECALL_TEST_CDS_TEMPLATE[:]+['--mode', '4'] + +ALLELECALL_TEST_GENOME_LIST = ['chewBBACA.py', 'AlleleCall', + '-i', 'data/allelecall_data/test_genomes_list/test_genomes.txt', + '-g', 'data/allelecall_data/sagalactiae_schema', + '-o', 'allelecall_results'] + +ALLELECALL_TEST_LOCI_IDS_EXTENSION = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--gl', 'data/allelecall_data/test_genes_list/test_genes_extension.txt'] +ALLELECALL_TEST_LOCI_IDS_NOEXTENSION = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--gl', 'data/allelecall_data/test_genes_list/test_genes_no_extension.txt'] +ALLELECALL_TEST_LOCI_PATHS = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--gl', 'data/allelecall_data/test_genes_list/test_genes_path.txt'] + +ALLELECALL_TEST_EMPTY_DIR = ['chewBBACA.py', 'AlleleCall', + '-i', 'empty_dir', + '-g', 'data/allelecall_data/sagalactiae_schema', + '-o', 'allelecall_results'] + +ALLELECALL_TEST_EMPTY_FILES = ['chewBBACA.py', 'AlleleCall', + '-i', 'data/createschema_data/genome_dir_with_empty_genomes', + '-g', 'data/allelecall_data/sagalactiae_schema', + '-o', 'allelecall_results'] + +ALLELECALL_TEST_ZERO_BYTES = ['chewBBACA.py', 'AlleleCall', + '-i', 'data/createschema_data/zero_bytes_pair', + '-g', 'data/allelecall_data/sagalactiae_schema', + '-o', 'allelecall_results'] + +ALLELECALL_TEST_FAKE_PATH = ['chewBBACA.py', 'AlleleCall', + '-i', 'this/path/aint/real', + '-g', 'data/allelecall_data/sagalactiae_schema', + '-o', 'allelecall_results'] + +CREATESCHEMA_TEST_GENOME_TEMPLATE = ['chewBBACA.py', 'CreateSchema', + '-i', 'data/createschema_data/mock_genome_dir', + '-o', 'createschema_results', + '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] + +CREATESCHEMA_TEST_GENOME_LIST = ['chewBBACA.py', 'CreateSchema', + '-i', 'data/createschema_data/mock_genome_list/mock_genomes.txt', + '-o', 'createschema_results', + '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] + +CREATESCHEMA_TEST_CDS = ['chewBBACA.py', 'CreateSchema', + '-i', 'data/createschema_data/mock_cds_dir', + '-o', 'createschema_results', + '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn', + '--cds-input'] + +CREATESCHEMA_TEST_EMPTY_FILES = ['chewBBACA.py', 'CreateSchema', + '-i', 'data/createschema_data/genome_dir_with_empty_genomes', + '-o', 'createschema_results', + '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] + +CREATESCHEMA_TEST_ZERO_BYTES = ['chewBBACA.py', 'CreateSchema', + '-i', 'data/createschema_data/zero_bytes_pair', + '-o', 'createschema_results', + '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] + +CREATESCHEMA_INVALID_PTF_PATH = ['chewBBACA.py', 'CreateSchema', + '-i', 'data/createschema_data/mock_schema_dir', + '-o', 'createschema_results', + '--ptf', 'path/does/not/exist'] + +CREATESCHEMA_TEST_HEADER_ONLY = ['chewBBACA.py', 'CreateSchema', + '-i', 'data/createschema_data/genome_dir_with_header_fasta_only', + '-o', 'createschema_results', + '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] + +CREATESCHEMA_TEST_INVALID_GENOME = ['chewBBACA.py', 'CreateSchema', + '-i', 'data/createschema_data/invalid_genome_dir', + '-o', 'createschema_results', + '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] + +ALLELECALL_EVALUATOR_INVALID_PATH = ['chewBBACA.py', 'AlleleCallEvaluator', + '-i', 'data/allelecall_data/fake_results', + '-g', 'data/allelecall_data/sagalactiae_schema', + '-o', 'results_report'] + +ALLELECALL_EVALUATOR_VALID = ['chewBBACA.py', 'AlleleCallEvaluator', + '-i', 'data/allelecall_data/test_results/mode4', + '-g', 'data/allelecall_data/sagalactiae_schema', + '-o', 'results_report'] + + +CHEWIE_TEST_H = ['chewBBACA.py', '-h'] +CHEWIE_TEST_HELP = ['chewBBACA.py', '--help'] +CHEWIE_TEST_V = ['chewBBACA.py', '-v'] +CHEWIE_TEST_VERSION = ['chewBBACA.py', '--version'] +CREATESCHEMA_TEST_H = ['chewBBACA.py', 'CreateSchema', '-h'] +CREATESCHEMA_TEST_HELP = ['chewBBACA.py', 'CreateSchema', '--help'] +ALLELECALL_TEST_H = ['chewBBACA.py', 'AlleleCall', '-h'] +ALLELECALL_TEST_HELP = ['chewBBACA.py', 'AlleleCall', '--help'] +SCHEMAEVALUATOR_TEST_H = ['chewBBACA.py', 'SchemaEvaluator', '-h'] +SCHEMAEVALUATOR_TEST_HELP = ['chewBBACA.py', 'SchemaEvaluator', '--help'] +ALLELECALL_EVALUATOR_TEST_H = ['chewBBACA.py', 'AlleleCallEvaluator', '-h'] +ALLELECALL_EVALUATOR_TEST_HELP = ['chewBBACA.py', 'AlleleCallEvaluator', '--help'] +EXTRACTCGMLST_TEST_H = ['chewBBACA.py', 'ExtractCgMLST', '-h'] +EXTRACTCGMLST_TEST_HELP = ['chewBBACA.py', 'ExtractCgMLST', '--help'] +REMOVEGENES_TEST_H = ['chewBBACA.py', 'RemoveGenes', '-h'] +REMOVEGENES_TEST_HELP = ['chewBBACA.py', 'RemoveGenes', '--help'] +PREPEXTERNALSCHEMA_TEST_H = ['chewBBACA.py', 'PrepExternalSchema', '-h'] +PREPEXTERNALSCHEMA_TEST_HELP = ['chewBBACA.py', 'PrepExternalSchema', '--help'] +JOINPROFILES_TEST_H = ['chewBBACA.py', 'JoinProfiles', '-h'] +JOINPROFILES_TEST_HELP = ['chewBBACA.py', 'JoinProfiles', '--help'] +UNIPROTFINDER_TEST_H = ['chewBBACA.py', 'UniprotFinder', '-h'] +UNIPROTFINDER_TEST_HELP = ['chewBBACA.py', 'UniprotFinder', '--help'] +DOWNLOADSCHEMA_TEST_H = ['chewBBACA.py', 'DownloadSchema', '-h'] +DOWNLOADSCHEMA_TEST_HELP = ['chewBBACA.py', 'DownloadSchema', '--help'] +LOADSCHEMA_TEST_H = ['chewBBACA.py', 'LoadSchema', '-h'] +LOADSCHEMA_TEST_HELP = ['chewBBACA.py', 'LoadSchema', '--help'] +SYNCSCHEMA_TEST_H = ['chewBBACA.py', 'SyncSchema', '-h'] +SYNCSCHEMA_TEST_HELP = ['chewBBACA.py', 'SyncSchema', '--help'] +NSSTATS_TEST_H = ['chewBBACA.py', 'NSStats', '-h'] +NSSTATS_TEST_HELP = ['chewBBACA.py', 'NSStats', '--help'] +FAKEMODULE_TEST_H = ['chewBBACA.py', 'FakeModule', '-h'] +FAKEMODULE_TEST_HELP = ['chewBBACA.py', 'FakeModule', '--help'] + +PREPEXTERNALSCHEMA_TEST_EMPTY_DIR = ['chewBBACA.py', 'PrepExternalSchema', + '-g', 'empty_dir', + '-o', 'adapted_schema'] + +PREPEXTERNALSCHEMA_TEST_EMPTY_FILES = ['chewBBACA.py', 'PrepExternalSchema', + '-g', 'data/prep_data/empty_files', + '-o', 'adapted_schema'] + +PREPEXTERNALSCHEMA_TEST_ZERO_BYTES = ['chewBBACA.py', 'PrepExternalSchema', + '-g', 'data/prep_data/zero_bytes_pair', + '-o', 'adapted_schema'] + +PREPEXTERNALSCHEMA_TEST_INVALID_PATH = ['chewBBACA.py', 'PrepExternalSchema', + '-g', 'this/path/aint/real', + '-o', 'adapted_schema'] + +PREPEXTERNALSCHEMA_TEST_VALID_INPUT = ['chewBBACA.py', 'PrepExternalSchema', + '-g', 'data/prep_data/valid_input', + '-o', 'preped_schema'] + +PREPEXTERNALSCHEMA_TEST_EXTENSIONS = ['chewBBACA.py', 'PrepExternalSchema', + '-g', 'data/prep_data/file_extensions', + '-o', 'preped_schema'] + +PREPEXTERNALSCHEMA_TEST_GENE_LIST = ['chewBBACA.py', 'PrepExternalSchema', + '-g', 'data/prep_data/file_extensions', + '-o', 'preped_schema', + '--gl', 'data/prep_data/test_genes_list/test_genes_extension.txt'] + +SCHEMAEVALUATOR_TEST_EMPTY_FILES = ['chewBBACA.py', 'SchemaEvaluator', + '-g', 'data/schemaevaluator_data/empty_files', + '-o', 'schema_report'] + +SCHEMAEVALUATOR_TEST_ZERO_BYTES = ['chewBBACA.py', 'SchemaEvaluator', + '-g', 'data/schemaevaluator_data/zero_bytes_pair', + '-o', 'schema_report'] + +SCHEMAEVALUATOR_TEST_FAKE_PATH = ['chewBBACA.py', 'SchemaEvaluator', + '-g', 'this/path/aint/real', + '-o', 'schema_report'] + +SCHEMAEVALUATOR_TEST_VALID_INPUT = ['chewBBACA.py', 'SchemaEvaluator', + '-g', 'data/schemaevaluator_data/test_schema', + '-o', 'schema_report', + '--loci-reports', '--add-sequences'] + +SCHEMAEVALUATOR_TEST_SINGLE_ALLELE = ['chewBBACA.py', 'SchemaEvaluator', + '-g', 'data/schemaevaluator_data/single_allele', + '-o', 'schema_report', + '--loci-reports', '--add-sequences'] + +SCHEMAEVALUATOR_TEST_SINGLE_INVALID_ALLELE = ['chewBBACA.py', 'SchemaEvaluator', + '-g', 'data/schemaevaluator_data/single_invalid_allele', + '-o', 'schema_report', + '--loci-reports', '--add-sequences'] + +SCHEMAEVALUATOR_TEST_SEVERAL_INVALID_ALLELES = ['chewBBACA.py', 'SchemaEvaluator', + '-g', 'data/schemaevaluator_data/several_invalid_alleles', + '-o', 'schema_report', + '--loci-reports', '--add-sequences'] + + + + diff --git a/CHEWBBACA/tests/test_basic_messages.py b/CHEWBBACA/tests/test_basic_messages.py index b444d3ef..3ff1cc8a 100644 --- a/CHEWBBACA/tests/test_basic_messages.py +++ b/CHEWBBACA/tests/test_basic_messages.py @@ -11,7 +11,7 @@ import filecmp from CHEWBBACA import chewBBACA -from CHEWBBACA.utils import constants as ct +from CHEWBBACA.tests import test_arguments as ta # Use the tmp_path fixture to create a tmp directory for each test @@ -27,38 +27,38 @@ def args_fixture(request, tmp_path): @pytest.mark.parametrize( "args_fixture", [ - (ct.CHEWIE_TEST_V, 0), - (ct.CHEWIE_TEST_VERSION, 0), - (ct.CHEWIE_TEST_H, 0), - (ct.CHEWIE_TEST_HELP, 0), - (ct.CREATESCHEMA_TEST_H, 0), - (ct.CREATESCHEMA_TEST_HELP, 0), - (ct.ALLELECALL_TEST_H, 0), - (ct.ALLELECALL_TEST_HELP, 0), - (ct.SCHEMAEVALUATOR_TEST_H, 0), - (ct.SCHEMAEVALUATOR_TEST_HELP, 0), - (ct.ALLELECALL_EVALUATOR_TEST_H, 0), - (ct.ALLELECALL_EVALUATOR_TEST_HELP, 0), - (ct.EXTRACTCGMLST_TEST_H, 0), - (ct.EXTRACTCGMLST_TEST_HELP, 0), - (ct.REMOVEGENES_TEST_H, 0), - (ct.REMOVEGENES_TEST_HELP, 0), - (ct.PREPEXTERNALSCHEMA_TEST_H, 0), - (ct.PREPEXTERNALSCHEMA_TEST_HELP, 0), - (ct.JOINPROFILES_TEST_H, 0), - (ct.JOINPROFILES_TEST_HELP, 0), - (ct.UNIPROTFINDER_TEST_H, 0), - (ct.UNIPROTFINDER_TEST_HELP, 0), - (ct.DOWNLOADSCHEMA_TEST_H, 0), - (ct.DOWNLOADSCHEMA_TEST_HELP, 0), - (ct.LOADSCHEMA_TEST_H, 0), - (ct.LOADSCHEMA_TEST_HELP, 0), - (ct.SYNCSCHEMA_TEST_H, 0), - (ct.SYNCSCHEMA_TEST_HELP, 0), - (ct.NSSTATS_TEST_H, 0), - (ct.NSSTATS_TEST_HELP, 0), - (ct.FAKEMODULE_TEST_H, 1), # Test with module that does not exist - (ct.FAKEMODULE_TEST_HELP, 1) + (ta.CHEWIE_TEST_V, 0), + (ta.CHEWIE_TEST_VERSION, 0), + (ta.CHEWIE_TEST_H, 0), + (ta.CHEWIE_TEST_HELP, 0), + (ta.CREATESCHEMA_TEST_H, 0), + (ta.CREATESCHEMA_TEST_HELP, 0), + (ta.ALLELECALL_TEST_H, 0), + (ta.ALLELECALL_TEST_HELP, 0), + (ta.SCHEMAEVALUATOR_TEST_H, 0), + (ta.SCHEMAEVALUATOR_TEST_HELP, 0), + (ta.ALLELECALL_EVALUATOR_TEST_H, 0), + (ta.ALLELECALL_EVALUATOR_TEST_HELP, 0), + (ta.EXTRACTCGMLST_TEST_H, 0), + (ta.EXTRACTCGMLST_TEST_HELP, 0), + (ta.REMOVEGENES_TEST_H, 0), + (ta.REMOVEGENES_TEST_HELP, 0), + (ta.PREPEXTERNALSCHEMA_TEST_H, 0), + (ta.PREPEXTERNALSCHEMA_TEST_HELP, 0), + (ta.JOINPROFILES_TEST_H, 0), + (ta.JOINPROFILES_TEST_HELP, 0), + (ta.UNIPROTFINDER_TEST_H, 0), + (ta.UNIPROTFINDER_TEST_HELP, 0), + (ta.DOWNLOADSCHEMA_TEST_H, 0), + (ta.DOWNLOADSCHEMA_TEST_HELP, 0), + (ta.LOADSCHEMA_TEST_H, 0), + (ta.LOADSCHEMA_TEST_HELP, 0), + (ta.SYNCSCHEMA_TEST_H, 0), + (ta.SYNCSCHEMA_TEST_HELP, 0), + (ta.NSSTATS_TEST_H, 0), + (ta.NSSTATS_TEST_HELP, 0), + (ta.FAKEMODULE_TEST_H, 1), # Test with module that does not exist + (ta.FAKEMODULE_TEST_HELP, 1) ], indirect=True ) diff --git a/CHEWBBACA/tests/test_createschema.py b/CHEWBBACA/tests/test_createschema.py index af408c11..5424dc63 100644 --- a/CHEWBBACA/tests/test_createschema.py +++ b/CHEWBBACA/tests/test_createschema.py @@ -13,6 +13,7 @@ from CHEWBBACA import chewBBACA from CHEWBBACA.utils import constants as ct +from CHEWBBACA.tests import test_arguments as ta from CHEWBBACA.utils import file_operations as fo @@ -33,9 +34,9 @@ def args_fixture(request, tmp_path): @pytest.mark.parametrize( "args_fixture", [ - (ct.CREATESCHEMA_TEST_GENOME_TEMPLATE, 'data/createschema_data/expected_results'), - (ct.CREATESCHEMA_TEST_GENOME_LIST, 'data/createschema_data/expected_results'), - (ct.CREATESCHEMA_TEST_CDS, 'data/createschema_data/expected_results'), + (ta.CREATESCHEMA_TEST_GENOME_TEMPLATE, 'data/createschema_data/expected_results'), + (ta.CREATESCHEMA_TEST_GENOME_LIST, 'data/createschema_data/expected_results'), + (ta.CREATESCHEMA_TEST_CDS, 'data/createschema_data/expected_results'), ], indirect=True ) @@ -89,11 +90,11 @@ def test_createschema_valid_input(monkeypatch, args_fixture): @pytest.mark.parametrize( "args_fixture", [ - (ct.CREATESCHEMA_TEST_EMPTY_FILES, ct.MISSING_FASTAS_EXCEPTION), - (ct.CREATESCHEMA_TEST_ZERO_BYTES, ct.MISSING_FASTAS_EXCEPTION), - (ct.CREATESCHEMA_INVALID_PTF_PATH, ct.INVALID_PTF_PATH), - (ct.CREATESCHEMA_TEST_HEADER_ONLY, ct.CANNOT_PREDICT), - (ct.CREATESCHEMA_TEST_INVALID_GENOME, ct.CANNOT_PREDICT) + (ta.CREATESCHEMA_TEST_EMPTY_FILES, ct.MISSING_FASTAS_EXCEPTION), + (ta.CREATESCHEMA_TEST_ZERO_BYTES, ct.MISSING_FASTAS_EXCEPTION), + (ta.CREATESCHEMA_INVALID_PTF_PATH, ct.INVALID_PTF_PATH), + (ta.CREATESCHEMA_TEST_HEADER_ONLY, ct.CANNOT_PREDICT), + (ta.CREATESCHEMA_TEST_INVALID_GENOME, ct.CANNOT_PREDICT) ], indirect=True ) diff --git a/CHEWBBACA/tests/test_prepexternalschema.py b/CHEWBBACA/tests/test_prepexternalschema.py index 869bf4ff..5f5a64e4 100644 --- a/CHEWBBACA/tests/test_prepexternalschema.py +++ b/CHEWBBACA/tests/test_prepexternalschema.py @@ -13,6 +13,7 @@ from CHEWBBACA import chewBBACA from CHEWBBACA.utils import constants as ct +from CHEWBBACA.tests import test_arguments as ta from CHEWBBACA.utils import file_operations as fo @@ -30,9 +31,9 @@ def args_fixture(request, tmp_path): @pytest.mark.parametrize( "args_fixture", [ - (ct.PREPEXTERNALSCHEMA_TEST_VALID_INPUT, 'data/prep_data/expected_results_valid'), - (ct.PREPEXTERNALSCHEMA_TEST_EXTENSIONS, 'data/prep_data/expected_results_extension'), - (ct.PREPEXTERNALSCHEMA_TEST_GENE_LIST, 'data/prep_data/expected_results_extension') + (ta.PREPEXTERNALSCHEMA_TEST_VALID_INPUT, 'data/prep_data/expected_results_valid'), + (ta.PREPEXTERNALSCHEMA_TEST_EXTENSIONS, 'data/prep_data/expected_results_extension'), + (ta.PREPEXTERNALSCHEMA_TEST_GENE_LIST, 'data/prep_data/expected_results_extension') ], indirect=True ) @@ -85,10 +86,10 @@ def test_prep_valid_input(monkeypatch, args_fixture): @pytest.mark.parametrize( "args_fixture", [ - (ct.PREPEXTERNALSCHEMA_TEST_EMPTY_DIR, ct.MISSING_FASTAS_EXCEPTION), - (ct.PREPEXTERNALSCHEMA_TEST_EMPTY_FILES, ct.MISSING_FASTAS_EXCEPTION), - (ct.PREPEXTERNALSCHEMA_TEST_ZERO_BYTES, ct.MISSING_FASTAS_EXCEPTION), - (ct.PREPEXTERNALSCHEMA_TEST_INVALID_PATH, ct.INVALID_INPUT_PATH) + (ta.PREPEXTERNALSCHEMA_TEST_EMPTY_DIR, ct.MISSING_FASTAS_EXCEPTION), + (ta.PREPEXTERNALSCHEMA_TEST_EMPTY_FILES, ct.MISSING_FASTAS_EXCEPTION), + (ta.PREPEXTERNALSCHEMA_TEST_ZERO_BYTES, ct.MISSING_FASTAS_EXCEPTION), + (ta.PREPEXTERNALSCHEMA_TEST_INVALID_PATH, ct.INVALID_INPUT_PATH) ], indirect=True ) diff --git a/CHEWBBACA/tests/test_schema_evaluator.py b/CHEWBBACA/tests/test_schema_evaluator.py index d940c69e..adc33495 100644 --- a/CHEWBBACA/tests/test_schema_evaluator.py +++ b/CHEWBBACA/tests/test_schema_evaluator.py @@ -10,6 +10,7 @@ from CHEWBBACA import chewBBACA from CHEWBBACA.utils import constants as ct +from CHEWBBACA.tests import test_arguments as ta # Use the tmp_path fixture to create a tmp directory for each test @@ -26,10 +27,10 @@ def args_fixture(request, tmp_path): @pytest.mark.parametrize( "args_fixture", [ - (ct.SCHEMAEVALUATOR_TEST_VALID_INPUT, 'data/schemaevaluator_data/expected_results/valid'), - (ct.SCHEMAEVALUATOR_TEST_SINGLE_ALLELE, 'data/schemaevaluator_data/expected_results/single_allele'), - (ct.SCHEMAEVALUATOR_TEST_SINGLE_INVALID_ALLELE, 'data/schemaevaluator_data/expected_results/single_invalid_allele'), - (ct.SCHEMAEVALUATOR_TEST_SEVERAL_INVALID_ALLELES, 'data/schemaevaluator_data/expected_results/several_invalid_alleles'), + (ta.SCHEMAEVALUATOR_TEST_VALID_INPUT, 'data/schemaevaluator_data/expected_results/valid'), + (ta.SCHEMAEVALUATOR_TEST_SINGLE_ALLELE, 'data/schemaevaluator_data/expected_results/single_allele'), + (ta.SCHEMAEVALUATOR_TEST_SINGLE_INVALID_ALLELE, 'data/schemaevaluator_data/expected_results/single_invalid_allele'), + (ta.SCHEMAEVALUATOR_TEST_SEVERAL_INVALID_ALLELES, 'data/schemaevaluator_data/expected_results/several_invalid_alleles'), ], indirect=True ) @@ -67,9 +68,9 @@ def test_schemaEvaluator_valid_input(monkeypatch, args_fixture): @pytest.mark.parametrize( "args_fixture", [ - (ct.SCHEMAEVALUATOR_TEST_EMPTY_FILES, 'Could not get input files.'), - (ct.SCHEMAEVALUATOR_TEST_ZERO_BYTES, 'Could not get input files.'), - (ct.SCHEMAEVALUATOR_TEST_FAKE_PATH, 'Path to input schema does not exist. Please provide a valid path.') + (ta.SCHEMAEVALUATOR_TEST_EMPTY_FILES, 'Could not get input files.'), + (ta.SCHEMAEVALUATOR_TEST_ZERO_BYTES, 'Could not get input files.'), + (ta.SCHEMAEVALUATOR_TEST_FAKE_PATH, 'Path to input schema does not exist. Please provide a valid path.') ], indirect=True ) diff --git a/CHEWBBACA/utils/constants.py b/CHEWBBACA/utils/constants.py index ea27e2f3..0ed98ca5 100755 --- a/CHEWBBACA/utils/constants.py +++ b/CHEWBBACA/utils/constants.py @@ -507,60 +507,6 @@ CANNOT_PREDICT = ('Could not predict CDSs from any of the input files.' '\nPlease provide input files in the accepted FASTA format.') -# Test variables used by pytest -# AlleleCall default test command -ALLELECALL_TEST_GENOME_TEMPLATE = ['chewBBACA.py', 'AlleleCall', - '-i', 'data/allelecall_data/test_genome', - '-g', 'data/allelecall_data/sagalactiae_schema', - '-o', 'allelecall_results'] - -ALLELECALL_TEST_DEFAULT = ALLELECALL_TEST_GENOME_TEMPLATE[:] -ALLELECALL_TEST_MODE1 = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--mode', '1'] -ALLELECALL_TEST_MODE2 = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--mode', '2'] -ALLELECALL_TEST_MODE3 = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--mode', '3'] -ALLELECALL_TEST_MODE4 = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--mode', '4'] - -ALLELECALL_TEST_CDS_TEMPLATE = ['chewBBACA.py', 'AlleleCall', - '-i', 'data/allelecall_data/test_cds_input', - '-g', 'data/allelecall_data/sagalactiae_schema', - '-o', 'allelecall_results', - '--cds-input'] - -ALLELECALL_TEST_CDS_DEFAULT = ALLELECALL_TEST_CDS_TEMPLATE[:] -ALLELECALL_TEST_CDS_MODE1 = ALLELECALL_TEST_CDS_TEMPLATE[:]+['--mode', '1'] -ALLELECALL_TEST_CDS_MODE2 = ALLELECALL_TEST_CDS_TEMPLATE[:]+['--mode', '2'] -ALLELECALL_TEST_CDS_MODE3 = ALLELECALL_TEST_CDS_TEMPLATE[:]+['--mode', '3'] -ALLELECALL_TEST_CDS_MODE4 = ALLELECALL_TEST_CDS_TEMPLATE[:]+['--mode', '4'] - -ALLELECALL_TEST_GENOME_LIST = ['chewBBACA.py', 'AlleleCall', - '-i', 'data/allelecall_data/test_genomes_list/test_genomes.txt', - '-g', 'data/allelecall_data/sagalactiae_schema', - '-o', 'allelecall_results'] - -ALLELECALL_TEST_LOCI_IDS_EXTENSION = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--gl', 'data/allelecall_data/test_genes_list/test_genes_extension.txt'] -ALLELECALL_TEST_LOCI_IDS_NOEXTENSION = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--gl', 'data/allelecall_data/test_genes_list/test_genes_no_extension.txt'] -ALLELECALL_TEST_LOCI_PATHS = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--gl', 'data/allelecall_data/test_genes_list/test_genes_path.txt'] - -ALLELECALL_TEST_EMPTY_DIR = ['chewBBACA.py', 'AlleleCall', - '-i', 'empty_dir', - '-g', 'data/allelecall_data/sagalactiae_schema', - '-o', 'allelecall_results'] - -ALLELECALL_TEST_EMPTY_FILES = ['chewBBACA.py', 'AlleleCall', - '-i', 'data/createschema_data/genome_dir_with_empty_genomes', - '-g', 'data/allelecall_data/sagalactiae_schema', - '-o', 'allelecall_results'] - -ALLELECALL_TEST_ZERO_BYTES = ['chewBBACA.py', 'AlleleCall', - '-i', 'data/createschema_data/zero_bytes_pair', - '-g', 'data/allelecall_data/sagalactiae_schema', - '-o', 'allelecall_results'] - -ALLELECALL_TEST_FAKE_PATH = ['chewBBACA.py', 'AlleleCall', - '-i', 'this/path/aint/real', - '-g', 'data/allelecall_data/sagalactiae_schema', - '-o', 'allelecall_results'] - INVALID_BSR = ('\nBSR value is not contained in the [0.0, 1.0] interval.') INVALID_BSR_TYPE = ('\nInvalid BSR value of {0}. BSR value must be contained in the [0.0, 1.0] interval.') @@ -660,149 +606,4 @@ '30 characters:\n{0}\nPlease make sure that input ' 'files have a shorter and unique prefix.') -CREATESCHEMA_TEST_GENOME_TEMPLATE = ['chewBBACA.py', 'CreateSchema', - '-i', 'data/createschema_data/mock_genome_dir', - '-o', 'createschema_results', - '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] - -CREATESCHEMA_TEST_GENOME_LIST = ['chewBBACA.py', 'CreateSchema', - '-i', 'data/createschema_data/mock_genome_list/mock_genomes.txt', - '-o', 'createschema_results', - '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] - -CREATESCHEMA_TEST_CDS = ['chewBBACA.py', 'CreateSchema', - '-i', 'data/createschema_data/mock_cds_dir', - '-o', 'createschema_results', - '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn', - '--cds-input'] - -CREATESCHEMA_TEST_EMPTY_FILES = ['chewBBACA.py', 'CreateSchema', - '-i', 'data/createschema_data/genome_dir_with_empty_genomes', - '-o', 'createschema_results', - '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] - -CREATESCHEMA_TEST_ZERO_BYTES = ['chewBBACA.py', 'CreateSchema', - '-i', 'data/createschema_data/zero_bytes_pair', - '-o', 'createschema_results', - '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] - -CREATESCHEMA_INVALID_PTF_PATH = ['chewBBACA.py', 'CreateSchema', - '-i', 'data/createschema_data/mock_schema_dir', - '-o', 'createschema_results', - '--ptf', 'path/does/not/exist'] - -CREATESCHEMA_TEST_HEADER_ONLY = ['chewBBACA.py', 'CreateSchema', - '-i', 'data/createschema_data/genome_dir_with_header_fasta_only', - '-o', 'createschema_results', - '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] - -CREATESCHEMA_TEST_INVALID_GENOME = ['chewBBACA.py', 'CreateSchema', - '-i', 'data/createschema_data/invalid_genome_dir', - '-o', 'createschema_results', - '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] - -ALLELECALL_EVALUATOR_INVALID_PATH = ['chewBBACA.py', 'AlleleCallEvaluator', - '-i', 'data/allelecall_data/fake_results', - '-g', 'data/allelecall_data/sagalactiae_schema', - '-o', 'results_report'] - -ALLELECALL_EVALUATOR_VALID = ['chewBBACA.py', 'AlleleCallEvaluator', - '-i', 'data/allelecall_data/test_results/mode4', - '-g', 'data/allelecall_data/sagalactiae_schema', - '-o', 'results_report'] - MISSING_INPUT_ARG = ('Path to input files does not exist. Please provide a valid path.') - -CHEWIE_TEST_H = ['chewBBACA.py', '-h'] -CHEWIE_TEST_HELP = ['chewBBACA.py', '--help'] -CHEWIE_TEST_V = ['chewBBACA.py', '-v'] -CHEWIE_TEST_VERSION = ['chewBBACA.py', '--version'] -CREATESCHEMA_TEST_H = ['chewBBACA.py', 'CreateSchema', '-h'] -CREATESCHEMA_TEST_HELP = ['chewBBACA.py', 'CreateSchema', '--help'] -ALLELECALL_TEST_H = ['chewBBACA.py', 'AlleleCall', '-h'] -ALLELECALL_TEST_HELP = ['chewBBACA.py', 'AlleleCall', '--help'] -SCHEMAEVALUATOR_TEST_H = ['chewBBACA.py', 'SchemaEvaluator', '-h'] -SCHEMAEVALUATOR_TEST_HELP = ['chewBBACA.py', 'SchemaEvaluator', '--help'] -ALLELECALL_EVALUATOR_TEST_H = ['chewBBACA.py', 'AlleleCallEvaluator', '-h'] -ALLELECALL_EVALUATOR_TEST_HELP = ['chewBBACA.py', 'AlleleCallEvaluator', '--help'] -EXTRACTCGMLST_TEST_H = ['chewBBACA.py', 'ExtractCgMLST', '-h'] -EXTRACTCGMLST_TEST_HELP = ['chewBBACA.py', 'ExtractCgMLST', '--help'] -REMOVEGENES_TEST_H = ['chewBBACA.py', 'RemoveGenes', '-h'] -REMOVEGENES_TEST_HELP = ['chewBBACA.py', 'RemoveGenes', '--help'] -PREPEXTERNALSCHEMA_TEST_H = ['chewBBACA.py', 'PrepExternalSchema', '-h'] -PREPEXTERNALSCHEMA_TEST_HELP = ['chewBBACA.py', 'PrepExternalSchema', '--help'] -JOINPROFILES_TEST_H = ['chewBBACA.py', 'JoinProfiles', '-h'] -JOINPROFILES_TEST_HELP = ['chewBBACA.py', 'JoinProfiles', '--help'] -UNIPROTFINDER_TEST_H = ['chewBBACA.py', 'UniprotFinder', '-h'] -UNIPROTFINDER_TEST_HELP = ['chewBBACA.py', 'UniprotFinder', '--help'] -DOWNLOADSCHEMA_TEST_H = ['chewBBACA.py', 'DownloadSchema', '-h'] -DOWNLOADSCHEMA_TEST_HELP = ['chewBBACA.py', 'DownloadSchema', '--help'] -LOADSCHEMA_TEST_H = ['chewBBACA.py', 'LoadSchema', '-h'] -LOADSCHEMA_TEST_HELP = ['chewBBACA.py', 'LoadSchema', '--help'] -SYNCSCHEMA_TEST_H = ['chewBBACA.py', 'SyncSchema', '-h'] -SYNCSCHEMA_TEST_HELP = ['chewBBACA.py', 'SyncSchema', '--help'] -NSSTATS_TEST_H = ['chewBBACA.py', 'NSStats', '-h'] -NSSTATS_TEST_HELP = ['chewBBACA.py', 'NSStats', '--help'] -FAKEMODULE_TEST_H = ['chewBBACA.py', 'FakeModule', '-h'] -FAKEMODULE_TEST_HELP = ['chewBBACA.py', 'FakeModule', '--help'] - -PREPEXTERNALSCHEMA_TEST_EMPTY_DIR = ['chewBBACA.py', 'PrepExternalSchema', - '-g', 'empty_dir', - '-o', 'adapted_schema'] - -PREPEXTERNALSCHEMA_TEST_EMPTY_FILES = ['chewBBACA.py', 'PrepExternalSchema', - '-g', 'data/prep_data/empty_files', - '-o', 'adapted_schema'] - -PREPEXTERNALSCHEMA_TEST_ZERO_BYTES = ['chewBBACA.py', 'PrepExternalSchema', - '-g', 'data/prep_data/zero_bytes_pair', - '-o', 'adapted_schema'] - -PREPEXTERNALSCHEMA_TEST_INVALID_PATH = ['chewBBACA.py', 'PrepExternalSchema', - '-g', 'this/path/aint/real', - '-o', 'adapted_schema'] - -PREPEXTERNALSCHEMA_TEST_VALID_INPUT = ['chewBBACA.py', 'PrepExternalSchema', - '-g', 'data/prep_data/valid_input', - '-o', 'preped_schema'] - -PREPEXTERNALSCHEMA_TEST_EXTENSIONS = ['chewBBACA.py', 'PrepExternalSchema', - '-g', 'data/prep_data/file_extensions', - '-o', 'preped_schema'] - -PREPEXTERNALSCHEMA_TEST_GENE_LIST = ['chewBBACA.py', 'PrepExternalSchema', - '-g', 'data/prep_data/file_extensions', - '-o', 'preped_schema', - '--gl', 'data/prep_data/test_genes_list/test_genes_extension.txt'] - -SCHEMAEVALUATOR_TEST_EMPTY_FILES = ['chewBBACA.py', 'SchemaEvaluator', - '-g', 'data/schemaevaluator_data/empty_files', - '-o', 'schema_report'] - -SCHEMAEVALUATOR_TEST_ZERO_BYTES = ['chewBBACA.py', 'SchemaEvaluator', - '-g', 'data/schemaevaluator_data/zero_bytes_pair', - '-o', 'schema_report'] - -SCHEMAEVALUATOR_TEST_FAKE_PATH = ['chewBBACA.py', 'SchemaEvaluator', - '-g', 'this/path/aint/real', - '-o', 'schema_report'] - -SCHEMAEVALUATOR_TEST_VALID_INPUT = ['chewBBACA.py', 'SchemaEvaluator', - '-g', 'data/schemaevaluator_data/test_schema', - '-o', 'schema_report', - '--loci-reports', '--add-sequences'] - -SCHEMAEVALUATOR_TEST_SINGLE_ALLELE = ['chewBBACA.py', 'SchemaEvaluator', - '-g', 'data/schemaevaluator_data/single_allele', - '-o', 'schema_report', - '--loci-reports', '--add-sequences'] - -SCHEMAEVALUATOR_TEST_SINGLE_INVALID_ALLELE = ['chewBBACA.py', 'SchemaEvaluator', - '-g', 'data/schemaevaluator_data/single_invalid_allele', - '-o', 'schema_report', - '--loci-reports', '--add-sequences'] - -SCHEMAEVALUATOR_TEST_SEVERAL_INVALID_ALLELES = ['chewBBACA.py', 'SchemaEvaluator', - '-g', 'data/schemaevaluator_data/several_invalid_alleles', - '-o', 'schema_report', - '--loci-reports', '--add-sequences']