diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/conftest.py | 13 | ||||
| -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/__init__.py | 1 | ||||
| -rw-r--r-- | tests/uploader/phenotypes/test_misc.py | 387 | ||||
| -rw-r--r-- | tests/uploader/publications/__init__.py | 1 | ||||
| -rw-r--r-- | tests/uploader/publications/test_misc.py | 68 | ||||
| -rw-r--r-- | tests/uploader/test_parse.py | 5 |
8 files changed, 471 insertions, 7 deletions
diff --git a/tests/conftest.py b/tests/conftest.py index 9012221..2009aab 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -2,6 +2,8 @@ import io import os import uuid +import shutil +from pathlib import Path from hashlib import sha256 import redis @@ -46,17 +48,20 @@ def cleanup_redis(redisuri: str, prefix: str): @pytest.fixture(scope="module") def client(): "Fixture for test client" - app = create_app() test_prefix = sha256(f"test:{uuid.uuid4()}".encode("utf8")).hexdigest() - app.config.update({ + tests_work_dir = Path("/tmp/{test_prefix}") + tests_work_dir.mkdir(exist_ok=True) + app = create_app({ "TESTING": True, "GNQC_REDIS_PREFIX": f"{test_prefix}:GNQC", - "JOBS_TTL_SECONDS": 2 * 60 * 60# 2 hours + "JOBS_TTL_SECONDS": 2 * 60 * 60,# 2 hours + "ASYNCHRONOUS_JOBS_SQLITE_DB": f"{tests_work_dir}/jobs.db" }) with app.app_context(): yield app.test_client() cleanup_redis(app.config["REDIS_URL"], test_prefix) + shutil.rmtree(tests_work_dir, ignore_errors=True) @pytest.fixture(scope="module") def db_url(client):#pylint: disable=[redefined-outer-name] @@ -178,7 +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/__init__.py b/tests/uploader/phenotypes/__init__.py new file mode 100644 index 0000000..1e0a932 --- /dev/null +++ b/tests/uploader/phenotypes/__init__.py @@ -0,0 +1 @@ +"""phenotypes tests""" diff --git a/tests/uploader/phenotypes/test_misc.py b/tests/uploader/phenotypes/test_misc.py new file mode 100644 index 0000000..cf475ad --- /dev/null +++ b/tests/uploader/phenotypes/test_misc.py @@ -0,0 +1,387 @@ +"""Test miscellaneous phenotypes functions.""" + +import pytest + +from uploader.phenotypes.misc import phenotypes_data_differences + +__sample_db_phenotypes_data__ = ( + { + "PhenotypeId": 4, + "xref_id": 10001, + "DataId": 8967043, + "data": { + "B6D2F1": {"StrainId": 1, "value": None}, + "C57BL/6J": {"StrainId": 2, "value": None}, + "DBA/2J": {"StrainId": 3, "value": None}, + "BXD1": {"StrainId": 4, "value": 61.4}, + "BXD2": {"StrainId": 5, "value": 49}, + "BXD5": {"StrainId": 6, "value": 62.5}, + "BXD6": {"StrainId": 7, "value": 53.1} + } + }, + { + "PhenotypeId": 10, + "xref_id": 10002, + "DataId": 8967044, + "data": { + "B6D2F1": {"StrainId": 1, "value": None}, + "C57BL/6J": {"StrainId": 2, "value": None}, + "DBA/2J": {"StrainId": 3, "value": None}, + "BXD1": {"StrainId": 4, "value": 54.1}, + "BXD2": {"StrainId": 5, "value": 50.1}, + "BXD5": {"StrainId": 6, "value": 53.3}, + "BXD6": {"StrainId": 7, "value": 55.1} + } + }, + { + "PhenotypeId": 15, + "xref_id": 10003, + "DataId": 8967045, + "data": { + "B6D2F1": {"StrainId": 1, "value": None}, + "C57BL/6J": {"StrainId": 2, "value": None}, + "DBA/2J": {"StrainId": 3, "value": None}, + "BXD1": {"StrainId": 4, "value": 483}, + "BXD2": {"StrainId": 5, "value": 403}, + "BXD5": {"StrainId": 6, "value": 501}, + "BXD6": {"StrainId": 7, "value": 403} + } + }, + { + "PhenotypeId": 20, + "xref_id": 10004, + "DataId": 8967046, + "data": { + "B6D2F1": {"StrainId": 1, "value": None}, + "C57BL/6J": {"StrainId": 2, "value": None}, + "DBA/2J": {"StrainId": 3, "value": None}, + "BXD1": {"StrainId": 4, "value": 49.8}, + "BXD2": {"StrainId": 5, "value": 45.5}, + "BXD5": {"StrainId": 6, "value": 62.9}, + "BXD6": {"StrainId": 7, "value": None} + } + }, + { + "PhenotypeId": 25, + "xref_id": 10005, + "DataId": 8967047, + "data": { + "B6D2F1": {"StrainId": 1, "value": None}, + "C57BL/6J": {"StrainId": 2, "value": None}, + "DBA/2J": {"StrainId": 3, "value": None}, + "BXD1": {"StrainId": 4, "value": 46}, + "BXD2": {"StrainId": 5, "value": 44.9}, + "BXD5": {"StrainId": 6, "value": 52.5}, + "BXD6": {"StrainId": 7, "value": None} + } + }) + + +@pytest.mark.unit_test +@pytest.mark.parametrize( + "filedata,dbdata,expected", + ((tuple(), tuple(), tuple()), # No data + + # No data difference + (({ + "phenotype_id": 4, + "xref_id": 10001, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": None, + "BXD1": 61.4, + "BXD2": 49, + "BXD5":62.5, + "BXD6": 53.1 + } + }, + { + "phenotype_id": 10, + "xref_id": 10002, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": None, + "BXD1": 54.1, + "BXD2": 50.1, + "BXD5": 53.3, + "BXD6": 55.1 + } + }, + { + "phenotype_id": 15, + "xref_id": 10003, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": None, + "BXD1": 483, + "BXD2": 403, + "BXD5": 501, + "BXD6": 403 + } + }, + { + "phenotype_id": 20, + "xref_id": 10004, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": None, + "BXD1": 49.8, + "BXD2": 45.5, + "BXD5": 62.9, + "BXD6": None + } + }, + { + "phenotype_id": 25, + "xref_id": 10005, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": None, + "BXD1": 46, + "BXD2": 44.9, + "BXD5": 52.5, + "BXD6": None + } + }), + __sample_db_phenotypes_data__, + tuple()), + + # Change values: No deletions + (({ + "phenotype_id": 4, + "xref_id": 10001, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": None, + "BXD1": 77.2, + "BXD2": 49, + "BXD5":62.5, + "BXD6": 53.1 + } + }, + { + "phenotype_id": 10, + "xref_id": 10002, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": None, + "BXD1": 54.1, + "BXD2": 50.1, + "BXD5": 53.3, + "BXD6": 55.1 + } + }, + { + "phenotype_id": 15, + "xref_id": 10003, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": None, + "BXD1": 483, + "BXD2": 403, + "BXD5": 503, + "BXD6": 903 + } + }, + { + "phenotype_id": 20, + "xref_id": 10004, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": 1, + "BXD1": 8, + "BXD2": 9, + "BXD5": 62.9, + "BXD6": None + } + }, + { + "phenotype_id": 25, + "xref_id": 10005, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": None, + "BXD1": 46, + "BXD2": 44.9, + "BXD5": 52.5, + "BXD6": None + } + }), + __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 + })), + + # Changes — with deletions + (({ + "phenotype_id": 4, + "xref_id": 10001, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": None, + "BXD1": None, + "BXD2": 49, + "BXD5":62.5, + "BXD6": 53.1 + } + }, + { + "phenotype_id": 10, + "xref_id": 10002, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": None, + "BXD1": 54.1, + "BXD2": 50.1, + "BXD5": 53.3, + "BXD6": 55.1 + } + }, + { + "phenotype_id": 15, + "xref_id": 10003, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": None, + "BXD1": 483, + "BXD2": 403, + "BXD5": None, + "BXD6": None + } + }, + { + "phenotype_id": 20, + "xref_id": 10004, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": 15, + "BXD1": None, + "BXD2": 24, + "BXD5": 62.9, + "BXD6": None + } + }, + { + "phenotype_id": 25, + "xref_id": 10005, + "data": { + "B6D2F1": None, + "C57BL/6J": None, + "DBA/2J": None, + "BXD1": 46, + "BXD2": 44.9, + "BXD5": 52.5, + "BXD6": None + } + }), + __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 + })))) +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/__init__.py b/tests/uploader/publications/__init__.py new file mode 100644 index 0000000..de15e08 --- /dev/null +++ b/tests/uploader/publications/__init__.py @@ -0,0 +1 @@ +"""publications tests""" diff --git a/tests/uploader/publications/test_misc.py b/tests/uploader/publications/test_misc.py new file mode 100644 index 0000000..8c7e567 --- /dev/null +++ b/tests/uploader/publications/test_misc.py @@ -0,0 +1,68 @@ +"""Tests for functions used for bulk editing.""" +import pytest + +from uploader.publications.misc import publications_differences + + +@pytest.mark.unit_test +@pytest.mark.parametrize( + "filedata,dbdata,pubmed2pubidmap,expected", + (((), (), {}, tuple()), # no data + + # Same Data + (({"phenotype_id": 1, "xref_id": 10001, "PubMed_ID": 9999999999999}, + {"phenotype_id": 1, "xref_id": 10002, "PubMed_ID": 9999999999999}, + {"phenotype_id": 1, "xref_id": 10003, "PubMed_ID": 9999999999999}, + {"phenotype_id": 1, "xref_id": 10005, "PubMed_ID": 9999999999999}), + ({"PhenotypeId": 1, "xref_id": 10001, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10002, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10003, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": 15, + "PubMed_ID": 9999999999999}), + {9999999999999: 15}, + tuple()), + + # Differences: no new pubmeds (all pubmeds in db) + (({"phenotype_id": 1, "xref_id": 10001, "PubMed_ID": 9999999999999}, + {"phenotype_id": 1, "xref_id": 10002, "PubMed_ID": 9999999999998}, + {"phenotype_id": 1, "xref_id": 10003, "PubMed_ID": 9999999999999}, + {"phenotype_id": 1, "xref_id": 10004, "PubMed_ID": 9999999999997}), + ({"PhenotypeId": 1, "xref_id": 10001, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10002, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10003, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": 15, + "PubMed_ID": None}), + {9999999999999: 15, 9999999999998: 18, 9999999999997: 12}, + ({"PhenotypeId": 1, "xref_id": 10002, "PublicationId": 18, + "PubMed_ID": 9999999999998}, + {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": 12, + "PubMed_ID": 9999999999997})), + + # Differences: Deletions of pubmeds + (({"phenotype_id": 1, "xref_id": 10001, "PubMed_ID": 9999999999999}, + {"phenotype_id": 1, "xref_id": 10002, "PubMed_ID": None}, + {"phenotype_id": 1, "xref_id": 10003, "PubMed_ID": 9999999999999}, + {"phenotype_id": 1, "xref_id": 10004, "PubMed_ID": None}), + ({"PhenotypeId": 1, "xref_id": 10001, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10002, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10003, "PublicationId": 15, + "PubMed_ID": 9999999999999}, + {"PhenotypeId": 1, "xref_id": 10004, "PublicationId": 15, + "PubMed_ID": 9999999999999}), + {9999999999999: 15, 9999999999998: 18, 9999999999997: 12}, + ({"PhenotypeId": 1, "xref_id": 10002, "PublicationId": None, + "PubMed_ID": None}, + {"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", |