diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/conftest.py | 2 | ||||
| -rw-r--r-- | tests/r_qtl/test_r_qtl2_control_file.py | 1 | ||||
| -rw-r--r-- | tests/test_instance_dir/config.py | 2 | ||||
| -rw-r--r-- | tests/uploader/phenotypes/test_misc.py | 108 | ||||
| -rw-r--r-- | tests/uploader/publications/test_misc.py | 1 | ||||
| -rw-r--r-- | tests/uploader/test_parse.py | 5 |
6 files changed, 103 insertions, 16 deletions
diff --git a/tests/conftest.py b/tests/conftest.py index a716c52..2009aab 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -183,7 +183,7 @@ def redis_conn_with_completed_job_some_errors(redis_url, redis_ttl, jobs_prefix, def uploads_dir(client): # pylint: disable=[redefined-outer-name] """Returns the configured, uploads directory, creating it if it does not exist.""" - the_dir = client.application.config["UPLOAD_FOLDER"] + the_dir = client.application.config["UPLOADS_DIRECTORY"] if not os.path.exists(the_dir): os.mkdir(the_dir) diff --git a/tests/r_qtl/test_r_qtl2_control_file.py b/tests/r_qtl/test_r_qtl2_control_file.py index 316307d..5b9fef6 100644 --- a/tests/r_qtl/test_r_qtl2_control_file.py +++ b/tests/r_qtl/test_r_qtl2_control_file.py @@ -16,6 +16,7 @@ __DEFAULTS__ = { "pheno_transposed": False, "covar_transposed": False, "phenocovar_transposed": False, + "phenonum_transposed": False, "gmap_transposed": False, "pmap_transposed": False, "phenose_transposed": False diff --git a/tests/test_instance_dir/config.py b/tests/test_instance_dir/config.py index 2ee569b..f04b3df 100644 --- a/tests/test_instance_dir/config.py +++ b/tests/test_instance_dir/config.py @@ -6,6 +6,6 @@ import os LOG_LEVEL = os.getenv("LOG_LEVEL", "WARNING") SECRET_KEY = b"<Please! Please! Please! Change This!>" -UPLOAD_FOLDER = "/tmp/qc_app_files" +UPLOADS_DIRECTORY = "/tmp/qc_app_files" REDIS_URL = "redis://" JOBS_TTL_SECONDS = 600 # 10 minutes diff --git a/tests/uploader/phenotypes/test_misc.py b/tests/uploader/phenotypes/test_misc.py index c0261aa..cf475ad 100644 --- a/tests/uploader/phenotypes/test_misc.py +++ b/tests/uploader/phenotypes/test_misc.py @@ -218,12 +218,54 @@ __sample_db_phenotypes_data__ = ( } }), __sample_db_phenotypes_data__, - ({"PhenotypeId": 4, "xref_id": 10001, "DataId": 8967043, "StrainId": 4, "StrainName": "BXD1", "value": 77.2}, - {"PhenotypeId": 15, "xref_id": 10003, "DataId": 8967045, "StrainId": 6, "StrainName": "BXD5", "value": 503}, - {"PhenotypeId": 15, "xref_id": 10003, "DataId": 8967045, "StrainId": 7, "StrainName": "BXD6", "value": 903}, - {"PhenotypeId": 20, "xref_id": 10004, "DataId": 8967046, "StrainId": 3, "StrainName": "DBA/2J", "value": 1}, - {"PhenotypeId": 20, "xref_id": 10004, "DataId": 8967046, "StrainId": 4, "StrainName": "BXD1", "value": 8}, - {"PhenotypeId": 20, "xref_id": 10004, "DataId": 8967046, "StrainId": 5, "StrainName": "BXD2", "value": 9})), + ({ + "PhenotypeId": 4, + "xref_id": 10001, + "DataId": 8967043, + "StrainId": 4, + "StrainName": "BXD1", + "value": 77.2 + }, + { + "PhenotypeId": 15, + "xref_id": 10003, + "DataId": 8967045, + "StrainId": 6, + "StrainName": "BXD5", + "value": 503 + }, + { + "PhenotypeId": 15, + "xref_id": 10003, + "DataId": 8967045, + "StrainId": 7, + "StrainName": "BXD6", + "value": 903 + }, + { + "PhenotypeId": 20, + "xref_id": 10004, + "DataId": 8967046, + "StrainId": 3, + "StrainName": "DBA/2J", + "value": 1 + }, + { + "PhenotypeId": 20, + "xref_id": 10004, + "DataId": 8967046, + "StrainId": 4, + "StrainName": "BXD1", + "value": 8 + }, + { + "PhenotypeId": 20, + "xref_id": 10004, + "DataId": 8967046, + "StrainId": 5, + "StrainName": "BXD2", + "value": 9 + })), # Changes — with deletions (({ @@ -292,12 +334,54 @@ __sample_db_phenotypes_data__ = ( } }), __sample_db_phenotypes_data__, - ({"PhenotypeId": 4, "xref_id": 10001, "DataId": 8967043, "StrainId": 4, "StrainName": "BXD1", "value": None}, - {"PhenotypeId": 15, "xref_id": 10003, "DataId": 8967045, "StrainId": 6, "StrainName": "BXD5", "value": None}, - {"PhenotypeId": 15, "xref_id": 10003, "DataId": 8967045, "StrainId": 7, "StrainName": "BXD6", "value": None}, - {"PhenotypeId": 20, "xref_id": 10004, "DataId": 8967046, "StrainId": 3, "StrainName": "DBA/2J", "value": 15}, - {"PhenotypeId": 20, "xref_id": 10004, "DataId": 8967046, "StrainId": 4, "StrainName": "BXD1", "value": None}, - {"PhenotypeId": 20, "xref_id": 10004, "DataId": 8967046, "StrainId": 5, "StrainName": "BXD2", "value": 24})))) + ({ + "PhenotypeId": 4, + "xref_id": 10001, + "DataId": 8967043, + "StrainId": 4, + "StrainName": "BXD1", + "value": None + }, + { + "PhenotypeId": 15, + "xref_id": 10003, + "DataId": 8967045, + "StrainId": 6, + "StrainName": "BXD5", + "value": None + }, + { + "PhenotypeId": 15, + "xref_id": 10003, + "DataId": 8967045, + "StrainId": 7, + "StrainName": "BXD6", + "value": None + }, + { + "PhenotypeId": 20, + "xref_id": 10004, + "DataId": 8967046, + "StrainId": 3, + "StrainName": "DBA/2J", + "value": 15 + }, + { + "PhenotypeId": 20, + "xref_id": 10004, + "DataId": 8967046, + "StrainId": 4, + "StrainName": "BXD1", + "value": None + }, + { + "PhenotypeId": 20, + "xref_id": 10004, + "DataId": 8967046, + "StrainId": 5, + "StrainName": "BXD2", + "value": 24 + })))) def test_phenotypes_data_differences(filedata, dbdata, expected): """Test differences are computed correctly.""" assert phenotypes_data_differences(filedata, dbdata) == expected diff --git a/tests/uploader/publications/test_misc.py b/tests/uploader/publications/test_misc.py index 7a52941..8c7e567 100644 --- a/tests/uploader/publications/test_misc.py +++ b/tests/uploader/publications/test_misc.py @@ -63,5 +63,6 @@ from uploader.publications.misc import publications_differences {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": None, "PubMed_ID": None})))) def test_publications_differences(filedata, dbdata, pubmed2pubidmap, expected): + """Test publication differences — flesh out description…""" assert publications_differences( filedata, dbdata, pubmed2pubidmap) == expected diff --git a/tests/uploader/test_parse.py b/tests/uploader/test_parse.py index 076c47c..56e1b41 100644 --- a/tests/uploader/test_parse.py +++ b/tests/uploader/test_parse.py @@ -8,7 +8,8 @@ from uploader.jobs import job, jobsnamespace from tests.conftest import uploadable_file_object -def test_parse_with_existing_uploaded_file(#pylint: disable=[too-many-arguments] +def test_parse_with_existing_uploaded_file( + #pylint: disable=[too-many-arguments,too-many-positional-arguments] client, db_url, redis_url, @@ -49,7 +50,7 @@ def test_parse_with_existing_uploaded_file(#pylint: disable=[too-many-arguments] assert the_job["command"] == " ".join([ sys.executable, "-m", "scripts.validate_file", db_url, redis_url, jobs_prefix, job_id, "--redisexpiry", str(redis_ttl), str(speciesid), - filetype, f"{client.application.config['UPLOAD_FOLDER']}/{filename}"]) + filetype, f"{client.application.config['UPLOADS_DIRECTORY']}/{filename}"]) @pytest.mark.parametrize( "filename,uri,error_msgs", |