```
/Users/joeflack4/virtualenvs/mondo-ingest/bin/python /Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/[pydevd.py](http://pydevd.py/) --multiprocess --qt-support=auto --client 127.0.0.1 --port 55914 --file /Applications/PyCharm.app/Contents/plugins/python/helpers/pycharm/_jb_pytest_runner.py --path /Users/joeflack4/projects/mondo-ingest/tests/[test_sync_synonym.py](http://test_sync_synonym.py/)
Testing started at 4:09 PM ...
Connected to pydev debugger (build 233.15325.20)
Launching pytest with arguments /Users/joeflack4/projects/mondo-ingest/tests/[test_sync_synonym.py](http://test_sync_synonym.py/) --no-header --no-summary -q in /Users/joeflack4/projects/mondo-ingest/tests
============================= test session starts ==============================
collecting ... collected 4 items
[test_sync_synonym.py](http://test_sync_synonym.py/)::TestSyncSynonyms::test_added
[test_sync_synonym.py](http://test_sync_synonym.py/)::TestSyncSynonyms::test_confirmed
[test_sync_synonym.py](http://test_sync_synonym.py/)::TestSyncSynonyms::test_deleted
[test_sync_synonym.py](http://test_sync_synonym.py/)::TestSyncSynonyms::test_updated
======================== 3 warnings, 4 errors in 3.44s =========================
ERROR [ 25%]
test setup failed
cls =
@classmethod
def setUpClass(cls):
"""Set up"""
# todo: #1 run pipeline / prereqs - dependent on fixing _run_make_goal()
# if not os.path.exists(INPUT_SOURCE_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/omim.db')
# if not os.path.exists(INPUT_MONDO_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo.db')
# if not os.path.exists(INPUT_MONDO_SYNONYMS):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
> sync_synonyms(
ontology_db_path=INPUT_SOURCE_DB,
mondo_synonyms_path=INPUT_MONDO_SYNONYMS,
mondo_exclusion_configs=INPUT_EXCLUDED_SYNONYMS,
mondo_mappings_path=INPUT_MAPPINGS,
onto_synonym_types_path=INPUT_ONTO_SYNONYMS,
onto_config_path=INPUT_SOURCE_METADATA,
outpath_added=OUTPUT_ADDED,
outpath_confirmed=OUTPUT_CONFIRMED,
# outpath_deleted=OUTPUT_DELETED,
outpath_updated=OUTPUT_UPDATED,
combined_outpath_template_str=None
)
[test_sync_synonym.py](http://test_sync_synonym.py/):77:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
ontology_db_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_omim.db')
mondo_synonyms_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
mondo_exclusion_configs = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml')
onto_synonym_types_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/omim-synonyms-scope-type-xref.tsv')
mondo_mappings_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_mondo.sssom.tsv')
onto_config_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/metadata/omim.yml')
outpath_added = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.added.robot.tsv')
outpath_confirmed = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.confirmed.robot.tsv')
outpath_updated = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.updated.robot.tsv')
outpath_deleted = None, combined_outpath_template_str = None
def sync_synonyms(
ontology_db_path: Union[Path, str], mondo_synonyms_path: Union[Path, str],
mondo_exclusion_configs: Union[Path, str], onto_synonym_types_path: Union[Path, str],
mondo_mappings_path: Union[Path, str], onto_config_path: Union[Path, str], outpath_added: Union[Path, str],
outpath_confirmed: Union[Path, str], outpath_updated: Union[Path, str], outpath_deleted: Union[Path, str] = None,
combined_outpath_template_str='tmp/synonym_sync_combined_cases_{}.tsv'
):
"""Create outputs for syncing synonyms between Mondo and its sources.
todo: update when -deleted is reactivated
:param outpath_deleted: Optional. This case isn't fully fleshed out yet.
todo: if we decided that this param should stay, set as required CLI/functional param w/ no default value.
:param combined_outpath_template_str: Creates an additional file concatenating all case files.
todo: possible refactor: labels: Maybe could be done more cleanly and consistently. At first, wanted to add to both
source_df and mondo_df, but this caused _x and _y cols during joins, or I would have to join on those cols as well.
So I arbitrarily chose mondo_df. This is fine in all cases but -added, where they're added in a custom way.
"""
# Read configurations
> with open(mondo_exclusion_configs, 'r') as stream:
E FileNotFoundError: [Errno 2] No such file or directory: '/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml'
../src/scripts/[sync_synonym.py](http://sync_synonym.py/):223: FileNotFoundError
ERROR [ 50%]
test setup failed
cls =
@classmethod
def setUpClass(cls):
"""Set up"""
# todo: #1 run pipeline / prereqs - dependent on fixing _run_make_goal()
# if not os.path.exists(INPUT_SOURCE_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/omim.db')
# if not os.path.exists(INPUT_MONDO_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo.db')
# if not os.path.exists(INPUT_MONDO_SYNONYMS):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
> sync_synonyms(
ontology_db_path=INPUT_SOURCE_DB,
mondo_synonyms_path=INPUT_MONDO_SYNONYMS,
mondo_exclusion_configs=INPUT_EXCLUDED_SYNONYMS,
mondo_mappings_path=INPUT_MAPPINGS,
onto_synonym_types_path=INPUT_ONTO_SYNONYMS,
onto_config_path=INPUT_SOURCE_METADATA,
outpath_added=OUTPUT_ADDED,
outpath_confirmed=OUTPUT_CONFIRMED,
# outpath_deleted=OUTPUT_DELETED,
outpath_updated=OUTPUT_UPDATED,
combined_outpath_template_str=None
)
[test_sync_synonym.py](http://test_sync_synonym.py/):77:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
ontology_db_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_omim.db')
mondo_synonyms_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
mondo_exclusion_configs = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml')
onto_synonym_types_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/omim-synonyms-scope-type-xref.tsv')
mondo_mappings_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_mondo.sssom.tsv')
onto_config_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/metadata/omim.yml')
outpath_added = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.added.robot.tsv')
outpath_confirmed = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.confirmed.robot.tsv')
outpath_updated = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.updated.robot.tsv')
outpath_deleted = None, combined_outpath_template_str = None
def sync_synonyms(
ontology_db_path: Union[Path, str], mondo_synonyms_path: Union[Path, str],
mondo_exclusion_configs: Union[Path, str], onto_synonym_types_path: Union[Path, str],
mondo_mappings_path: Union[Path, str], onto_config_path: Union[Path, str], outpath_added: Union[Path, str],
outpath_confirmed: Union[Path, str], outpath_updated: Union[Path, str], outpath_deleted: Union[Path, str] = None,
combined_outpath_template_str='tmp/synonym_sync_combined_cases_{}.tsv'
):
"""Create outputs for syncing synonyms between Mondo and its sources.
todo: update when -deleted is reactivated
:param outpath_deleted: Optional. This case isn't fully fleshed out yet.
todo: if we decided that this param should stay, set as required CLI/functional param w/ no default value.
:param combined_outpath_template_str: Creates an additional file concatenating all case files.
todo: possible refactor: labels: Maybe could be done more cleanly and consistently. At first, wanted to add to both
source_df and mondo_df, but this caused _x and _y cols during joins, or I would have to join on those cols as well.
So I arbitrarily chose mondo_df. This is fine in all cases but -added, where they're added in a custom way.
"""
# Read configurations
> with open(mondo_exclusion_configs, 'r') as stream:
E FileNotFoundError: [Errno 2] No such file or directory: '/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml'
../src/scripts/[sync_synonym.py](http://sync_synonym.py/):223: FileNotFoundError
ERROR [ 75%]
test setup failed
cls =
@classmethod
def setUpClass(cls):
"""Set up"""
# todo: #1 run pipeline / prereqs - dependent on fixing _run_make_goal()
# if not os.path.exists(INPUT_SOURCE_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/omim.db')
# if not os.path.exists(INPUT_MONDO_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo.db')
# if not os.path.exists(INPUT_MONDO_SYNONYMS):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
> sync_synonyms(
ontology_db_path=INPUT_SOURCE_DB,
mondo_synonyms_path=INPUT_MONDO_SYNONYMS,
mondo_exclusion_configs=INPUT_EXCLUDED_SYNONYMS,
mondo_mappings_path=INPUT_MAPPINGS,
onto_synonym_types_path=INPUT_ONTO_SYNONYMS,
onto_config_path=INPUT_SOURCE_METADATA,
outpath_added=OUTPUT_ADDED,
outpath_confirmed=OUTPUT_CONFIRMED,
# outpath_deleted=OUTPUT_DELETED,
outpath_updated=OUTPUT_UPDATED,
combined_outpath_template_str=None
)
[test_sync_synonym.py](http://test_sync_synonym.py/):77:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
ontology_db_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_omim.db')
mondo_synonyms_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
mondo_exclusion_configs = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml')
onto_synonym_types_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/omim-synonyms-scope-type-xref.tsv')
mondo_mappings_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_mondo.sssom.tsv')
onto_config_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/metadata/omim.yml')
outpath_added = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.added.robot.tsv')
outpath_confirmed = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.confirmed.robot.tsv')
outpath_updated = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.updated.robot.tsv')
outpath_deleted = None, combined_outpath_template_str = None
def sync_synonyms(
ontology_db_path: Union[Path, str], mondo_synonyms_path: Union[Path, str],
mondo_exclusion_configs: Union[Path, str], onto_synonym_types_path: Union[Path, str],
mondo_mappings_path: Union[Path, str], onto_config_path: Union[Path, str], outpath_added: Union[Path, str],
outpath_confirmed: Union[Path, str], outpath_updated: Union[Path, str], outpath_deleted: Union[Path, str] = None,
combined_outpath_template_str='tmp/synonym_sync_combined_cases_{}.tsv'
):
"""Create outputs for syncing synonyms between Mondo and its sources.
todo: update when -deleted is reactivated
:param outpath_deleted: Optional. This case isn't fully fleshed out yet.
todo: if we decided that this param should stay, set as required CLI/functional param w/ no default value.
:param combined_outpath_template_str: Creates an additional file concatenating all case files.
todo: possible refactor: labels: Maybe could be done more cleanly and consistently. At first, wanted to add to both
source_df and mondo_df, but this caused _x and _y cols during joins, or I would have to join on those cols as well.
So I arbitrarily chose mondo_df. This is fine in all cases but -added, where they're added in a custom way.
"""
# Read configurations
> with open(mondo_exclusion_configs, 'r') as stream:
E FileNotFoundError: [Errno 2] No such file or directory: '/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml'
../src/scripts/[sync_synonym.py](http://sync_synonym.py/):223: FileNotFoundError
ERROR [100%]
test setup failed
cls =
@classmethod
def setUpClass(cls):
"""Set up"""
# todo: #1 run pipeline / prereqs - dependent on fixing _run_make_goal()
# if not os.path.exists(INPUT_SOURCE_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/omim.db')
# if not os.path.exists(INPUT_MONDO_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo.db')
# if not os.path.exists(INPUT_MONDO_SYNONYMS):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
> sync_synonyms(
ontology_db_path=INPUT_SOURCE_DB,
mondo_synonyms_path=INPUT_MONDO_SYNONYMS,
mondo_exclusion_configs=INPUT_EXCLUDED_SYNONYMS,
mondo_mappings_path=INPUT_MAPPINGS,
onto_synonym_types_path=INPUT_ONTO_SYNONYMS,
onto_config_path=INPUT_SOURCE_METADATA,
outpath_added=OUTPUT_ADDED,
outpath_confirmed=OUTPUT_CONFIRMED,
# outpath_deleted=OUTPUT_DELETED,
outpath_updated=OUTPUT_UPDATED,
combined_outpath_template_str=None
)
[test_sync_synonym.py](http://test_sync_synonym.py/):77:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
ontology_db_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_omim.db')
mondo_synonyms_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
mondo_exclusion_configs = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml')
onto_synonym_types_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/omim-synonyms-scope-type-xref.tsv')
mondo_mappings_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_mondo.sssom.tsv')
onto_config_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/metadata/omim.yml')
outpath_added = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.added.robot.tsv')
outpath_confirmed = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.confirmed.robot.tsv')
outpath_updated = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.updated.robot.tsv')
outpath_deleted = None, combined_outpath_template_str = None
def sync_synonyms(
ontology_db_path: Union[Path, str], mondo_synonyms_path: Union[Path, str],
mondo_exclusion_configs: Union[Path, str], onto_synonym_types_path: Union[Path, str],
mondo_mappings_path: Union[Path, str], onto_config_path: Union[Path, str], outpath_added: Union[Path, str],
outpath_confirmed: Union[Path, str], outpath_updated: Union[Path, str], outpath_deleted: Union[Path, str] = None,
combined_outpath_template_str='tmp/synonym_sync_combined_cases_{}.tsv'
):
"""Create outputs for syncing synonyms between Mondo and its sources.
todo: update when -deleted is reactivated
:param outpath_deleted: Optional. This case isn't fully fleshed out yet.
todo: if we decided that this param should stay, set as required CLI/functional param w/ no default value.
:param combined_outpath_template_str: Creates an additional file concatenating all case files.
todo: possible refactor: labels: Maybe could be done more cleanly and consistently. At first, wanted to add to both
source_df and mondo_df, but this caused _x and _y cols during joins, or I would have to join on those cols as well.
So I arbitrarily chose mondo_df. This is fine in all cases but -added, where they're added in a custom way.
"""
# Read configurations
> with open(mondo_exclusion_configs, 'r') as stream:
E FileNotFoundError: [Errno 2] No such file or directory: '/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml'
../src/scripts/[sync_synonym.py](http://sync_synonym.py/):223: FileNotFoundError
Process finished with exit code 1
```
Overview
Due to some refactoring these tests are failing.
Details
``` /Users/joeflack4/virtualenvs/mondo-ingest/bin/python /Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/[pydevd.py](http://pydevd.py/) --multiprocess --qt-support=auto --client 127.0.0.1 --port 55914 --file /Applications/PyCharm.app/Contents/plugins/python/helpers/pycharm/_jb_pytest_runner.py --path /Users/joeflack4/projects/mondo-ingest/tests/[test_sync_synonym.py](http://test_sync_synonym.py/) Testing started at 4:09 PM ... Connected to pydev debugger (build 233.15325.20) Launching pytest with arguments /Users/joeflack4/projects/mondo-ingest/tests/[test_sync_synonym.py](http://test_sync_synonym.py/) --no-header --no-summary -q in /Users/joeflack4/projects/mondo-ingest/tests ============================= test session starts ============================== collecting ... collected 4 items [test_sync_synonym.py](http://test_sync_synonym.py/)::TestSyncSynonyms::test_added [test_sync_synonym.py](http://test_sync_synonym.py/)::TestSyncSynonyms::test_confirmed [test_sync_synonym.py](http://test_sync_synonym.py/)::TestSyncSynonyms::test_deleted [test_sync_synonym.py](http://test_sync_synonym.py/)::TestSyncSynonyms::test_updated ======================== 3 warnings, 4 errors in 3.44s ========================= ERROR [ 25%] test setup failed cls =
@classmethod
def setUpClass(cls):
"""Set up"""
# todo: #1 run pipeline / prereqs - dependent on fixing _run_make_goal()
# if not os.path.exists(INPUT_SOURCE_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/omim.db')
# if not os.path.exists(INPUT_MONDO_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo.db')
# if not os.path.exists(INPUT_MONDO_SYNONYMS):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
> sync_synonyms(
ontology_db_path=INPUT_SOURCE_DB,
mondo_synonyms_path=INPUT_MONDO_SYNONYMS,
mondo_exclusion_configs=INPUT_EXCLUDED_SYNONYMS,
mondo_mappings_path=INPUT_MAPPINGS,
onto_synonym_types_path=INPUT_ONTO_SYNONYMS,
onto_config_path=INPUT_SOURCE_METADATA,
outpath_added=OUTPUT_ADDED,
outpath_confirmed=OUTPUT_CONFIRMED,
# outpath_deleted=OUTPUT_DELETED,
outpath_updated=OUTPUT_UPDATED,
combined_outpath_template_str=None
)
[test_sync_synonym.py](http://test_sync_synonym.py/):77:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
ontology_db_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_omim.db')
mondo_synonyms_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
mondo_exclusion_configs = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml')
onto_synonym_types_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/omim-synonyms-scope-type-xref.tsv')
mondo_mappings_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_mondo.sssom.tsv')
onto_config_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/metadata/omim.yml')
outpath_added = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.added.robot.tsv')
outpath_confirmed = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.confirmed.robot.tsv')
outpath_updated = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.updated.robot.tsv')
outpath_deleted = None, combined_outpath_template_str = None
def sync_synonyms(
ontology_db_path: Union[Path, str], mondo_synonyms_path: Union[Path, str],
mondo_exclusion_configs: Union[Path, str], onto_synonym_types_path: Union[Path, str],
mondo_mappings_path: Union[Path, str], onto_config_path: Union[Path, str], outpath_added: Union[Path, str],
outpath_confirmed: Union[Path, str], outpath_updated: Union[Path, str], outpath_deleted: Union[Path, str] = None,
combined_outpath_template_str='tmp/synonym_sync_combined_cases_{}.tsv'
):
"""Create outputs for syncing synonyms between Mondo and its sources.
todo: update when -deleted is reactivated
:param outpath_deleted: Optional. This case isn't fully fleshed out yet.
todo: if we decided that this param should stay, set as required CLI/functional param w/ no default value.
:param combined_outpath_template_str: Creates an additional file concatenating all case files.
todo: possible refactor: labels: Maybe could be done more cleanly and consistently. At first, wanted to add to both
source_df and mondo_df, but this caused _x and _y cols during joins, or I would have to join on those cols as well.
So I arbitrarily chose mondo_df. This is fine in all cases but -added, where they're added in a custom way.
"""
# Read configurations
> with open(mondo_exclusion_configs, 'r') as stream:
E FileNotFoundError: [Errno 2] No such file or directory: '/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml'
../src/scripts/[sync_synonym.py](http://sync_synonym.py/):223: FileNotFoundError
ERROR [ 50%]
test setup failed
cls =
@classmethod
def setUpClass(cls):
"""Set up"""
# todo: #1 run pipeline / prereqs - dependent on fixing _run_make_goal()
# if not os.path.exists(INPUT_SOURCE_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/omim.db')
# if not os.path.exists(INPUT_MONDO_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo.db')
# if not os.path.exists(INPUT_MONDO_SYNONYMS):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
> sync_synonyms(
ontology_db_path=INPUT_SOURCE_DB,
mondo_synonyms_path=INPUT_MONDO_SYNONYMS,
mondo_exclusion_configs=INPUT_EXCLUDED_SYNONYMS,
mondo_mappings_path=INPUT_MAPPINGS,
onto_synonym_types_path=INPUT_ONTO_SYNONYMS,
onto_config_path=INPUT_SOURCE_METADATA,
outpath_added=OUTPUT_ADDED,
outpath_confirmed=OUTPUT_CONFIRMED,
# outpath_deleted=OUTPUT_DELETED,
outpath_updated=OUTPUT_UPDATED,
combined_outpath_template_str=None
)
[test_sync_synonym.py](http://test_sync_synonym.py/):77:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
ontology_db_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_omim.db')
mondo_synonyms_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
mondo_exclusion_configs = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml')
onto_synonym_types_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/omim-synonyms-scope-type-xref.tsv')
mondo_mappings_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_mondo.sssom.tsv')
onto_config_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/metadata/omim.yml')
outpath_added = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.added.robot.tsv')
outpath_confirmed = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.confirmed.robot.tsv')
outpath_updated = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.updated.robot.tsv')
outpath_deleted = None, combined_outpath_template_str = None
def sync_synonyms(
ontology_db_path: Union[Path, str], mondo_synonyms_path: Union[Path, str],
mondo_exclusion_configs: Union[Path, str], onto_synonym_types_path: Union[Path, str],
mondo_mappings_path: Union[Path, str], onto_config_path: Union[Path, str], outpath_added: Union[Path, str],
outpath_confirmed: Union[Path, str], outpath_updated: Union[Path, str], outpath_deleted: Union[Path, str] = None,
combined_outpath_template_str='tmp/synonym_sync_combined_cases_{}.tsv'
):
"""Create outputs for syncing synonyms between Mondo and its sources.
todo: update when -deleted is reactivated
:param outpath_deleted: Optional. This case isn't fully fleshed out yet.
todo: if we decided that this param should stay, set as required CLI/functional param w/ no default value.
:param combined_outpath_template_str: Creates an additional file concatenating all case files.
todo: possible refactor: labels: Maybe could be done more cleanly and consistently. At first, wanted to add to both
source_df and mondo_df, but this caused _x and _y cols during joins, or I would have to join on those cols as well.
So I arbitrarily chose mondo_df. This is fine in all cases but -added, where they're added in a custom way.
"""
# Read configurations
> with open(mondo_exclusion_configs, 'r') as stream:
E FileNotFoundError: [Errno 2] No such file or directory: '/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml'
../src/scripts/[sync_synonym.py](http://sync_synonym.py/):223: FileNotFoundError
ERROR [ 75%]
test setup failed
cls =
@classmethod
def setUpClass(cls):
"""Set up"""
# todo: #1 run pipeline / prereqs - dependent on fixing _run_make_goal()
# if not os.path.exists(INPUT_SOURCE_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/omim.db')
# if not os.path.exists(INPUT_MONDO_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo.db')
# if not os.path.exists(INPUT_MONDO_SYNONYMS):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
> sync_synonyms(
ontology_db_path=INPUT_SOURCE_DB,
mondo_synonyms_path=INPUT_MONDO_SYNONYMS,
mondo_exclusion_configs=INPUT_EXCLUDED_SYNONYMS,
mondo_mappings_path=INPUT_MAPPINGS,
onto_synonym_types_path=INPUT_ONTO_SYNONYMS,
onto_config_path=INPUT_SOURCE_METADATA,
outpath_added=OUTPUT_ADDED,
outpath_confirmed=OUTPUT_CONFIRMED,
# outpath_deleted=OUTPUT_DELETED,
outpath_updated=OUTPUT_UPDATED,
combined_outpath_template_str=None
)
[test_sync_synonym.py](http://test_sync_synonym.py/):77:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
ontology_db_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_omim.db')
mondo_synonyms_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
mondo_exclusion_configs = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml')
onto_synonym_types_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/omim-synonyms-scope-type-xref.tsv')
mondo_mappings_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_mondo.sssom.tsv')
onto_config_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/metadata/omim.yml')
outpath_added = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.added.robot.tsv')
outpath_confirmed = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.confirmed.robot.tsv')
outpath_updated = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.updated.robot.tsv')
outpath_deleted = None, combined_outpath_template_str = None
def sync_synonyms(
ontology_db_path: Union[Path, str], mondo_synonyms_path: Union[Path, str],
mondo_exclusion_configs: Union[Path, str], onto_synonym_types_path: Union[Path, str],
mondo_mappings_path: Union[Path, str], onto_config_path: Union[Path, str], outpath_added: Union[Path, str],
outpath_confirmed: Union[Path, str], outpath_updated: Union[Path, str], outpath_deleted: Union[Path, str] = None,
combined_outpath_template_str='tmp/synonym_sync_combined_cases_{}.tsv'
):
"""Create outputs for syncing synonyms between Mondo and its sources.
todo: update when -deleted is reactivated
:param outpath_deleted: Optional. This case isn't fully fleshed out yet.
todo: if we decided that this param should stay, set as required CLI/functional param w/ no default value.
:param combined_outpath_template_str: Creates an additional file concatenating all case files.
todo: possible refactor: labels: Maybe could be done more cleanly and consistently. At first, wanted to add to both
source_df and mondo_df, but this caused _x and _y cols during joins, or I would have to join on those cols as well.
So I arbitrarily chose mondo_df. This is fine in all cases but -added, where they're added in a custom way.
"""
# Read configurations
> with open(mondo_exclusion_configs, 'r') as stream:
E FileNotFoundError: [Errno 2] No such file or directory: '/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml'
../src/scripts/[sync_synonym.py](http://sync_synonym.py/):223: FileNotFoundError
ERROR [100%]
test setup failed
cls =
@classmethod
def setUpClass(cls):
"""Set up"""
# todo: #1 run pipeline / prereqs - dependent on fixing _run_make_goal()
# if not os.path.exists(INPUT_SOURCE_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/omim.db')
# if not os.path.exists(INPUT_MONDO_DB):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo.db')
# if not os.path.exists(INPUT_MONDO_SYNONYMS):
# cls._run_make_goal('../../tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
> sync_synonyms(
ontology_db_path=INPUT_SOURCE_DB,
mondo_synonyms_path=INPUT_MONDO_SYNONYMS,
mondo_exclusion_configs=INPUT_EXCLUDED_SYNONYMS,
mondo_mappings_path=INPUT_MAPPINGS,
onto_synonym_types_path=INPUT_ONTO_SYNONYMS,
onto_config_path=INPUT_SOURCE_METADATA,
outpath_added=OUTPUT_ADDED,
outpath_confirmed=OUTPUT_CONFIRMED,
# outpath_deleted=OUTPUT_DELETED,
outpath_updated=OUTPUT_UPDATED,
combined_outpath_template_str=None
)
[test_sync_synonym.py](http://test_sync_synonym.py/):77:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
ontology_db_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_omim.db')
mondo_synonyms_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
mondo_exclusion_configs = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml')
onto_synonym_types_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/omim-synonyms-scope-type-xref.tsv')
mondo_mappings_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_mondo.sssom.tsv')
onto_config_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/metadata/omim.yml')
outpath_added = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.added.robot.tsv')
outpath_confirmed = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.confirmed.robot.tsv')
outpath_updated = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.updated.robot.tsv')
outpath_deleted = None, combined_outpath_template_str = None
def sync_synonyms(
ontology_db_path: Union[Path, str], mondo_synonyms_path: Union[Path, str],
mondo_exclusion_configs: Union[Path, str], onto_synonym_types_path: Union[Path, str],
mondo_mappings_path: Union[Path, str], onto_config_path: Union[Path, str], outpath_added: Union[Path, str],
outpath_confirmed: Union[Path, str], outpath_updated: Union[Path, str], outpath_deleted: Union[Path, str] = None,
combined_outpath_template_str='tmp/synonym_sync_combined_cases_{}.tsv'
):
"""Create outputs for syncing synonyms between Mondo and its sources.
todo: update when -deleted is reactivated
:param outpath_deleted: Optional. This case isn't fully fleshed out yet.
todo: if we decided that this param should stay, set as required CLI/functional param w/ no default value.
:param combined_outpath_template_str: Creates an additional file concatenating all case files.
todo: possible refactor: labels: Maybe could be done more cleanly and consistently. At first, wanted to add to both
source_df and mondo_df, but this caused _x and _y cols during joins, or I would have to join on those cols as well.
So I arbitrarily chose mondo_df. This is fine in all cases but -added, where they're added in a custom way.
"""
# Read configurations
> with open(mondo_exclusion_configs, 'r') as stream:
E FileNotFoundError: [Errno 2] No such file or directory: '/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml'
../src/scripts/[sync_synonym.py](http://sync_synonym.py/):223: FileNotFoundError
Process finished with exit code 1
```