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adding all wc_sim fixtures to migration list
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@jonrkarr
jonrkarr committed Mar 15, 2020
1 parent cee25c3 commit a46b3f9
Showing 1 changed file with 75 additions and 8 deletions.
83 changes: 75 additions & 8 deletions migrations/run_custom_migration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,8 @@
{'path': 'wc_sim/tests/fixtures/test_dry_model_with_mass_computation.xlsx',
'ignore_extra_models': True},
{'path': 'wc_sim/tests/fixtures/test_dynamic_expressions.xlsx'},
{'path': 'wc_sim/tests/fixtures/test_model.xlsx'},
{'path': 'wc_sim/tests/fixtures/test_model.xlsx',
'ignore_extra_models': True},
{'path': 'wc_sim/tests/fixtures/test_model_for_access_species_populations.xlsx'},
{'path': 'wc_sim/tests/fixtures/test_model_for_access_species_populations_steady_state.xlsx'},
{'path': 'wc_sim/tests/fixtures/test_new_features_model.xlsx'},
Expand All @@ -54,6 +55,69 @@
'ignore_extra_models': True},
{'path': 'wc_sim/tests/submodels/fixtures/test_submodel.xlsx'},
{'path': 'wc_sim/tests/submodels/fixtures/test_submodel_no_shared_species.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/multialgorithmic/00001/00001-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/multialgorithmic/00003/00003-wc_lang_1_submodel.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/multialgorithmic/00003/00003-wc_lang_2_submodels.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/multialgorithmic/00003/00003-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/multialgorithmic/00007/00007-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/multialgorithmic/00020/00020-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/multialgorithmic/00021/00021-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/multialgorithmic/00030/00007-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/multialgorithmic/00030/00030-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00001/00001-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00002/00002-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00003/00003-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00004/00004-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00005/00005-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00006/00006-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00010/00010-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00014/00014-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00015/00015-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00017/00017-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00018/00018-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00019/00019-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00020/00020-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00021/00021-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00022/00022-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00028/00028-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/semantic/00054/00054-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/stochastic/00001/00001-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/stochastic/00003/00003-wc_lang_1_submodel.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/stochastic/00003/00003-wc_lang_2_submodels.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/stochastic/00003/00003-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/stochastic/00004/00004-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/stochastic/00007/00007-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/stochastic/00007_hybrid/00007_hybrid-wc_lang_old.xlsx',
'validate': False},
{'path': 'wc_sim/tests/fixtures/verification/cases/stochastic/00007_hybrid/00007_hybrid-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/stochastic/00012/00012-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/stochastic/00020/00020-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/stochastic/00021/00021-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/stochastic/00030/00030-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/stochastic/00037/00037-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/cases/stochastic/transcription_translation/transcription_translation-wc_lang.xlsx',
'validate': False},
{'path': 'wc_sim/tests/fixtures/verification/testing/hybrid/transcription_translation/transcription_translation_correct_ssa.xlsx',
'validate': False},
{'path': 'wc_sim/tests/fixtures/verification/testing/hybrid/transcription_translation/transcription_translation_hybrid.xlsx',
'validate': False},
{'path': 'wc_sim/tests/fixtures/verification/testing/hybrid/transcription_translation/transcription_translation-wc_lang_JK.xlsx',
'validate': False},
{'path': 'wc_sim/tests/fixtures/verification/testing/hybrid/translation_metabolism/translation_metabolism_correct_ssa.xlsx',
'validate': False},
{'path': 'wc_sim/tests/fixtures/verification/testing/hybrid/translation_metabolism/translation_metabolism_hybrid.xlsx',
'validate': False},
{'path': 'wc_sim/tests/fixtures/verification/testing/multialgorithmic/00007/00007-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/testing/semantic/00001/00001-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/testing/semantic/00004/00004-wc_lang.xlsx',
'validate': False},
{'path': 'wc_sim/tests/fixtures/verification/testing/semantic/00054/00054-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/testing/stochastic/00001/00001-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/testing/stochastic/00006/00006-wc_lang.xlsx'},
{'path': 'wc_sim/tests/fixtures/verification/testing_ValidationSuite_run/stochastic/00001/00001-wc_lang.xlsx',
'validate': False},
{'path': 'wc_sim/tests/fixtures/verification/testing_ValidationSuite_run/stochastic/00006/00006-wc_lang.xlsx',
'validate': False},

# wc_test
{'path': 'wc_test/tests/fixtures/min_model.xlsx'},
Expand Down Expand Up @@ -85,12 +149,15 @@
abs_path = os.path.join(base_dir, path['path'])

# migrate
migration.transform(abs_path)
# migration.transform(abs_path)

# validate
kwargs = copy.copy(path)
kwargs.pop('path')
try:
wc_lang.io.Reader().run(abs_path, **kwargs)
except ValueError as err:
warnings.warn('{} is invalid: {}'.format(path['path'], str(err)))
if path.get('validate', True):
kwargs = copy.copy(path)
kwargs.pop('path')
if 'validate' in kwards:
kwargs.pop('validate')
try:
wc_lang.io.Reader().run(abs_path, **kwargs)
except ValueError as err:
warnings.warn('{} is invalid: {}'.format(path['path'], str(err)))

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