diff --git a/tests/app/test_optimade.py b/tests/app/test_optimade.py
index 77933d55c2d1c473efa88c335af9e1319241d920..0cbe4a4e513d970ac73d15b0b807957d614a3122 100644
--- a/tests/app/test_optimade.py
+++ b/tests/app/test_optimade.py
@@ -39,7 +39,7 @@ def test_get_entry(published: Upload):
assert 'optimade.chemical_formula_hill' in utils.flatten_dict(search_result)
-def test_no_optimade(mongo, elastic, raw_files_function, client, test_user):
+def test_no_optimade(mongo_function, elastic, raw_files_function, client, test_user):
example_data = ExampleData(main_author=test_user)
example_data.create_upload(
upload_id='test_upload', published=True, embargo_length=0
diff --git a/tests/app/test_resources.py b/tests/app/test_resources.py
index 9bf3b0814f413c6b724ad4375955f9db434a513e..17172f73faa5987b5662d8dd7ea25a031cce59eb 100644
--- a/tests/app/test_resources.py
+++ b/tests/app/test_resources.py
@@ -92,7 +92,7 @@ def patched_download(monkeypatch):
@pytest.fixture(scope='function')
-def resources(mongo, monkeypatch):
+def resources(mongo_function, monkeypatch):
monkeypatch.setattr('nomad.config.resources.enabled', True)
monkeypatch.setattr('nomad.config.resources.db_name', 'test_db_resources')
remove_mongo()
diff --git a/tests/app/v1/routers/test_datasets.py b/tests/app/v1/routers/test_datasets.py
index 9ae58c840115893b30126ace7368651bea119eb1..edf77153072e66702a211d8bf34a304edce78658 100644
--- a/tests/app/v1/routers/test_datasets.py
+++ b/tests/app/v1/routers/test_datasets.py
@@ -54,7 +54,7 @@ def create_dataset(**kwargs):
@pytest.fixture(scope='function')
-def data(elastic, raw_files_function, mongo, test_user, other_test_user):
+def data(elastic, raw_files_function, mongo_function, test_user, other_test_user):
data = ExampleData(main_author=test_user)
data.create_upload(upload_id='upload_1', published=True)
data.create_entry(
diff --git a/tests/app/v1/routers/test_entries_edit.py b/tests/app/v1/routers/test_entries_edit.py
index 19785d725d58b9e653f6ca14f6d263ccf46492dd..56cd1d63530e841a2ca86f3eb790e0c28259f9bd 100644
--- a/tests/app/v1/routers/test_entries_edit.py
+++ b/tests/app/v1/routers/test_entries_edit.py
@@ -40,11 +40,11 @@ class TestEditRepo:
return {'upload_id:any': uploads}
@pytest.fixture(autouse=True)
- def set_api(self, client, elastic, mongo):
+ def set_api(self, client, elastic, mongo_function):
self.api = client
@pytest.fixture(autouse=True)
- def example_datasets(self, test_user, other_test_user, mongo):
+ def example_datasets(self, test_user, other_test_user, mongo_function):
self.example_dataset = Dataset(
dataset_id='example_ds',
dataset_name='example_ds',
@@ -61,7 +61,7 @@ class TestEditRepo:
@pytest.fixture(autouse=True)
def example_data(
- self, test_user, other_test_user, raw_files_function, elastic, mongo
+ self, test_user, other_test_user, raw_files_function, elastic, mongo_function
):
# TODO
example_data = ExampleData()
diff --git a/tests/app/v1/routers/test_uploads.py b/tests/app/v1/routers/test_uploads.py
index e95a5936583e3c443f5b20cfe019aac291d2b7db..e8cfd1d6f546f723f6102b4a356e8c417083a01d 100644
--- a/tests/app/v1/routers/test_uploads.py
+++ b/tests/app/v1/routers/test_uploads.py
@@ -3135,7 +3135,7 @@ def test_post_upload_edit(
)
def test_post_upload(
client,
- mongo,
+ mongo_function,
proc_infra,
monkeypatch,
test_auth_dict,
@@ -3394,7 +3394,7 @@ def test_post_upload_action_publish_to_central_nomad(
)
def test_post_upload_action_process(
client,
- mongo,
+ mongo_function,
proc_infra,
monkeypatch,
example_data_writeable,
@@ -3503,7 +3503,7 @@ def test_post_upload_action_process(
)
def test_post_upload_action_delete_entry_files(
client,
- mongo,
+ mongo_function,
proc_infra,
example_data_writeable,
test_auth_dict,
diff --git a/tests/archive/test_archive.py b/tests/archive/test_archive.py
index 3865d51ba2c7e8800882cd323c0f39057264cc42..e55b4cca7e411e31c9d96dc28b027b24f4479398 100644
--- a/tests/archive/test_archive.py
+++ b/tests/archive/test_archive.py
@@ -813,7 +813,7 @@ def all_archive():
],
)
def test_required_reader(
- archive, required, inplace_result, root_result, resolve_inplace, mongo
+ archive, required, inplace_result, root_result, resolve_inplace, mongo_function
):
f = BytesIO()
write_archive(f, 1, [('entry_id', archive.m_to_dict())], entry_toc_depth=2)
@@ -1243,12 +1243,12 @@ def test_partial_archive(archive):
assert_partial_archive(partial_archive)
-def test_partial_archive_read_write(archive, mongo):
+def test_partial_archive_read_write(archive, mongo_function):
write_partial_archive_to_mongo(archive)
assert_partial_archive(read_partial_archive_from_mongo('test_id'))
-def test_partial_archive_re_write(archive, mongo):
+def test_partial_archive_re_write(archive, mongo_function):
write_partial_archive_to_mongo(archive)
archive.metadata.comment = 'changed'
write_partial_archive_to_mongo(archive)
@@ -1256,7 +1256,7 @@ def test_partial_archive_re_write(archive, mongo):
assert archive.metadata.comment == 'changed'
-def test_read_partial_archives(archive, mongo):
+def test_read_partial_archives(archive, mongo_function):
write_partial_archive_to_mongo(archive)
assert_partial_archive(read_partial_archives_from_mongo(['test_id'])['test_id'])
diff --git a/tests/conftest.py b/tests/conftest.py
index be68effeafe507d6213d52c5e662518fce9a53d4..c531032542b5b018871162f04b62e04edcbe17ad 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -193,7 +193,7 @@ def celery_inspect(purged_app):
# It might be necessary to make this a function scoped fixture, if old tasks keep
# 'bleeding' into successive tests.
@pytest.fixture(scope='function')
-def worker(mongo, celery_session_worker, celery_inspect):
+def worker(mongo_function, celery_session_worker, celery_inspect):
"""Provides a clean worker (no old tasks) per function. Waits for all tasks to be completed."""
yield
@@ -242,12 +242,6 @@ def mongo_function(mongo_infra):
return clear_mongo(mongo_infra)
-@pytest.fixture(scope='function')
-def mongo(mongo_infra):
- """Provides a cleaned mocked mongo per function."""
- return clear_mongo(mongo_infra)
-
-
@pytest.fixture(scope='session')
def elastic_infra(monkeysession):
"""Provides elastic infrastructure to the session"""
@@ -444,7 +438,7 @@ def keycloak(monkeypatch):
@pytest.fixture(scope='function')
-def proc_infra(worker, elastic, mongo, raw_files_function):
+def proc_infra(worker, elastic, mongo_function, raw_files_function):
"""Combines all fixtures necessary for processing (elastic, worker, files, mongo)"""
return dict(elastic=elastic)
@@ -1208,7 +1202,7 @@ def plugin_schema():
@pytest.fixture(scope='function')
-def example_data_writeable(mongo, test_user, normalized):
+def example_data_writeable(mongo_function, test_user, normalized):
data = ExampleData(main_author=test_user)
# one upload with one entry, published
@@ -1246,7 +1240,7 @@ def example_data_writeable(mongo, test_user, normalized):
@pytest.fixture(scope='function')
-def example_datasets(mongo, test_user, other_test_user):
+def example_datasets(mongo_function, test_user, other_test_user):
dataset_specs = (
('test_dataset_1', test_user, None),
('test_dataset_2', test_user, 'test_doi_2'),
@@ -1283,7 +1277,7 @@ def reset_config():
@pytest.fixture
-def reset_infra(mongo, elastic):
+def reset_infra(mongo_function, elastic):
"""Fixture that resets infrastructure after deleting db or search index."""
yield None
diff --git a/tests/data/test_examples.py b/tests/data/test_examples.py
index 3d1068e8a70ee070b060676211e9e48cdb53159c..2255a563cab64c7ef9176b8a3a484a99b86a7b90 100644
--- a/tests/data/test_examples.py
+++ b/tests/data/test_examples.py
@@ -86,7 +86,7 @@ def test_sample_tabular(mainfile, assert_xpaths, raw_files_function, no_warn):
],
)
def test_sample_entry_mode(
- mongo,
+ mongo_function,
test_user,
raw_files_function,
monkeypatch,
@@ -212,7 +212,13 @@ def test_sample_entry_mode(
],
)
def test_tabular_doc_examples(
- mongo, test_user, raw_files_function, monkeypatch, proc_infra, test_files, status
+ mongo_function,
+ test_user,
+ raw_files_function,
+ monkeypatch,
+ proc_infra,
+ test_files,
+ status,
):
upload = create_upload('test_upload_id', test_user.user_id, test_files)
assert upload is not None
diff --git a/tests/datamodel/metainfo/eln/test_labfolder.py b/tests/datamodel/metainfo/eln/test_labfolder.py
index 6fe92979016bad51735b910901102e826ab23e6d..22b4be109d52c0a13f68084cef113f8f02dab34d 100644
--- a/tests/datamodel/metainfo/eln/test_labfolder.py
+++ b/tests/datamodel/metainfo/eln/test_labfolder.py
@@ -33,7 +33,7 @@ from nomad.utils.exampledata import ExampleData
from tests.test_files import example_mainfile_contents, append_raw_files # pylint: disable=unused-import
-def test_labfolder_integration(mongo, monkeypatch, test_user):
+def test_labfolder_integration(mongo_function, monkeypatch, test_user):
directory = 'tests/data/datamodel/metainfo/eln/material_library'
mainfile = 'example-labfolder.archive.json'
@@ -187,7 +187,7 @@ def test_labfolder_integration(mongo, monkeypatch, test_user):
],
)
def test_labfolder_detailed(
- mongo,
+ mongo_function,
monkeypatch,
test_user,
status_code,
diff --git a/tests/datamodel/metainfo/eln/test_openbis.py b/tests/datamodel/metainfo/eln/test_openbis.py
index f2c270d03e9188faf802e711f98de8607671f8e1..1da5bfdde3df538f3b59fb00a0e529a9f2caf870 100644
--- a/tests/datamodel/metainfo/eln/test_openbis.py
+++ b/tests/datamodel/metainfo/eln/test_openbis.py
@@ -92,7 +92,7 @@ def mocked_login(url):
],
)
def test_openbis(
- mongo,
+ mongo_function,
monkeypatch,
test_user,
status_code,
diff --git a/tests/datamodel/metainfo/eln/test_perovskite_database.py b/tests/datamodel/metainfo/eln/test_perovskite_database.py
index b1193c2b0682c0c0d6d64c415e2fbb3ce4cb87ee..7391c86e50ab702d9b757f57a66deab768c1cee6 100644
--- a/tests/datamodel/metainfo/eln/test_perovskite_database.py
+++ b/tests/datamodel/metainfo/eln/test_perovskite_database.py
@@ -22,7 +22,7 @@ from nomad.datamodel.context import ClientContext
from nomad.utils.exampledata import ExampleData
-def test_processing(raw_files_function, no_warn, test_user, mongo):
+def test_processing(raw_files_function, no_warn, test_user, mongo_function):
directory = 'tests/data/datamodel/metainfo/eln/perovskite_database'
mainfile = 'example.archive.json'
upload_id = 'test_upload_id'
diff --git a/tests/datamodel/metainfo/eln/test_system.py b/tests/datamodel/metainfo/eln/test_system.py
index 081739850632e9afc8f2196a9ed6146412b4c2b6..ff025eff8e6d11b74b97715497a96cc3ed9aff9c 100644
--- a/tests/datamodel/metainfo/eln/test_system.py
+++ b/tests/datamodel/metainfo/eln/test_system.py
@@ -28,7 +28,7 @@ from tests.normalizing.conftest import run_processing, run_normalize
from nomad.datamodel.data import User
-def test_substance(raw_files_function, test_user, mongo):
+def test_substance(raw_files_function, test_user, mongo_function):
directory = 'tests/data/datamodel/metainfo/eln'
mainfile = 'test_substance.archive.yaml'
upload_id = 'test_upload_id'
@@ -53,7 +53,7 @@ def test_substance(raw_files_function, test_user, mongo):
assert 'Pb' in test_archive.results.material.elements
-def test_ensemble(raw_files_function, test_user, mongo):
+def test_ensemble(raw_files_function, test_user, mongo_function):
directory = 'tests/data/datamodel/metainfo/eln'
mainfile = 'test_ensemble.archive.yaml'
upload_id = 'test_upload_id'
diff --git a/tests/examples/test_archive_query.py b/tests/examples/test_archive_query.py
index 5170f49cbfc99165457c74d512bc3fd44f2168c9..3a9a02874643c7bf1a7148913d18094b81f539c2 100644
--- a/tests/examples/test_archive_query.py
+++ b/tests/examples/test_archive_query.py
@@ -28,7 +28,7 @@ from tests.test_client import async_api_v1
def test_archive_query(
- async_api_v1, elastic, raw_files_function, mongo, test_user, capsys
+ async_api_v1, elastic, raw_files_function, mongo_function, test_user, capsys
):
mainfile = os.path.join(
__file__, '..', '..', 'data', 'examples', 'archive_query_vasprun.xml.gz'
diff --git a/tests/metainfo/test_mongodb_extension.py b/tests/metainfo/test_mongodb_extension.py
index 61911d1d14a5ce4272b0decad3cce3d7bc6010b6..3f03c65a6dc97bb47f92e9532971d2e31d38b5f3 100644
--- a/tests/metainfo/test_mongodb_extension.py
+++ b/tests/metainfo/test_mongodb_extension.py
@@ -51,7 +51,7 @@ class A(MSection):
d = SubSection(sub_section=D.m_def)
-def test_create_new(mongo):
+def test_create_new(mongo_function):
a = A()
a.primary_id = '123'
a.not_in_mongo = 'not_in_mongo'
@@ -119,7 +119,7 @@ def test_update_self():
assert a_from_db.value2 == 3
-def test_annotations(mongo):
+def test_annotations(mongo_function):
"""Test that non-annotated quantities and sections are not stored."""
a = A()
a.primary_id = '123'
diff --git a/tests/parsing/test_tabular.py b/tests/parsing/test_tabular.py
index d37ef3f9dca9b508341488f259f993a683dd44d2..29032ba2a75160b2223c420d7662cdbff2dac6dd 100644
--- a/tests/parsing/test_tabular.py
+++ b/tests/parsing/test_tabular.py
@@ -339,7 +339,7 @@ def test_tabular_complex_schema(raw_files_function, monkeypatch, schema):
def test_tabular_entry_mode(
- mongo, test_user, raw_files_function, monkeypatch, proc_infra
+ mongo_function, test_user, raw_files_function, monkeypatch, proc_infra
):
upload = Upload(upload_id='test_upload_id', main_author=test_user.user_id)
upload.save()
diff --git a/tests/plugins/perovskite_solar_cell_database/test_perovskite_database.py b/tests/plugins/perovskite_solar_cell_database/test_perovskite_database.py
index 23a4dd81e7de75290e410edad6eb23d54c2b497b..93b7b7265d6fd74a270db34441cdd5fe999da131 100644
--- a/tests/plugins/perovskite_solar_cell_database/test_perovskite_database.py
+++ b/tests/plugins/perovskite_solar_cell_database/test_perovskite_database.py
@@ -23,7 +23,7 @@ from nomad.utils.exampledata import ExampleData
def test_perovskite_solar_cell_plugin_processing(
- raw_files_function, no_warn, test_user, mongo
+ raw_files_function, no_warn, test_user, mongo_function
):
directory = 'tests/data/plugins/perovskite_solar_cell_database'
mainfile = 'example.archive.json'
diff --git a/tests/processing/test_base.py b/tests/processing/test_base.py
index c327a41b119093726e35ee3f57dff9a18373bea9..664845942043ea7ae64cac96e2d59a5bfc1d5cac 100644
--- a/tests/processing/test_base.py
+++ b/tests/processing/test_base.py
@@ -101,7 +101,7 @@ class SimpleProc(Proc):
@pytest.mark.parametrize(
'with_args', [pytest.param(False, id='no-args'), pytest.param(True, id='with-args')]
)
-def test_simple_process(worker, mongo, no_warn, with_args):
+def test_simple_process(worker, mongo_function, no_warn, with_args):
p = SimpleProc.create()
if with_args:
process = 'a_process_with_arguments'
@@ -128,7 +128,7 @@ class FailingProc(Proc):
_ = 1 / 0
-def test_failing_process(worker, mongo, with_error):
+def test_failing_process(worker, mongo_function, with_error):
p = FailingProc.create()
event = 'process failed with exception'
@@ -151,7 +151,7 @@ class ProcTwice(Proc):
pass
-def test_process_twice(worker, mongo, no_warn):
+def test_process_twice(worker, mongo_function, no_warn):
p = ProcTwice.create()
p.process()
p.block_until_complete()
@@ -382,7 +382,9 @@ class ParentProc(Proc):
),
],
)
-def test_parent_child(worker, mongo, reset_events, spawn_kwargs, expected_events):
+def test_parent_child(
+ worker, mongo_function, reset_events, spawn_kwargs, expected_events
+):
child_args = spawn_kwargs.get('child_args', [])
join_args = spawn_kwargs.get('join_args', [])
fail_spawn = spawn_kwargs.get('fail_spawn', False)
@@ -418,7 +420,7 @@ def test_parent_child(worker, mongo, reset_events, spawn_kwargs, expected_events
assert_events(expected_events)
-def test_queueing(worker, mongo, reset_events):
+def test_queueing(worker, mongo_function, reset_events):
p = ParentProc.create(parent_id='p')
expected_events = []
# Schedule 20 calls
@@ -438,7 +440,7 @@ def test_queueing(worker, mongo, reset_events):
assert_events(expected_events)
-def test_queueing_failure(worker, mongo, reset_events):
+def test_queueing_failure(worker, mongo_function, reset_events):
p = ParentProc.create(parent_id='p')
# Schedule 20 calls, the second should fail
for i in range(20):
@@ -464,7 +466,7 @@ def test_queueing_failure(worker, mongo, reset_events):
)
-def test_non_blocking_then_blocking(worker, mongo, reset_events):
+def test_non_blocking_then_blocking(worker, mongo_function, reset_events):
p = ParentProc.create(parent_id='p')
p.spawn(delay=1.0)
p.blocking()
@@ -482,7 +484,7 @@ def test_non_blocking_then_blocking(worker, mongo, reset_events):
)
-def test_blocking_then_non_blocking(worker, mongo, reset_events):
+def test_blocking_then_non_blocking(worker, mongo_function, reset_events):
p = ParentProc.create(parent_id='p')
p.blocking(delay=1.0)
with pytest.raises(ProcessAlreadyRunning):
@@ -492,7 +494,7 @@ def test_blocking_then_non_blocking(worker, mongo, reset_events):
assert_events(['p:blocking:start', 'p:blocking:succ'])
-def test_local_blocked(worker, mongo, reset_events):
+def test_local_blocked(worker, mongo_function, reset_events):
p = ParentProc.create(parent_id='p')
def other_call():
@@ -512,7 +514,7 @@ def test_local_blocked(worker, mongo, reset_events):
assert_events(['p:non_blocking:start', 'other_call:blocked', 'p:non_blocking:succ'])
-def test_local_blocking(worker, mongo, reset_events):
+def test_local_blocking(worker, mongo_function, reset_events):
p = ParentProc.create(parent_id='p')
def other_call():
@@ -542,7 +544,7 @@ def test_local_blocking(worker, mongo, reset_events):
)
-def test_local_failed(worker, mongo, reset_events):
+def test_local_failed(worker, mongo_function, reset_events):
p = ParentProc.create(parent_id='p')
try:
p.local_process(fail=True)
diff --git a/tests/processing/test_data.py b/tests/processing/test_data.py
index 8506f5c0d00cf1319cf84d618023d1e9b56c9ef7..1be228edaa47ca8aa5cf623165edfbda033766f8 100644
--- a/tests/processing/test_data.py
+++ b/tests/processing/test_data.py
@@ -118,7 +118,7 @@ def test_send_mail(mails, monkeypatch):
@pytest.fixture(scope='function', autouse=True)
-def mongo_forall(mongo):
+def mongo_forall(mongo_function):
pass
@@ -1179,7 +1179,7 @@ def test_skip_matching(proc_infra, test_user):
],
)
def test_upload_context(
- raw_files_function, mongo, test_user, url, normalized_url, monkeypatch
+ raw_files_function, mongo_function, test_user, url, normalized_url, monkeypatch
):
monkeypatch.setattr(
'nomad.utils.generate_entry_id', lambda *args, **kwargs: 'test_id'
diff --git a/tests/test_cli.py b/tests/test_cli.py
index dfd6c58d18c1f96c59c4fb9efe9e87a609b8a158..9e0cc7f7edb4be8a52283a8ced239cd45a4582d0 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -353,7 +353,7 @@ class TestAdminUploads:
assert entry.process_status == expected_state
@pytest.mark.parametrize('indexed', [True, False])
- def test_integrity_entry_index(self, test_user, mongo, elastic, indexed):
+ def test_integrity_entry_index(self, test_user, mongo_function, elastic, indexed):
data = ExampleData(main_author=test_user)
data.create_upload(upload_id='test_upload')
data.create_entry(upload_id='test_upload')
diff --git a/tests/test_doi.py b/tests/test_doi.py
index 94156d084d933bd8c1a5dbe6f76863d881820e28..a102cf664c2c8e8d5aa1ea3f58c617e1a56e1d17 100644
--- a/tests/test_doi.py
+++ b/tests/test_doi.py
@@ -21,20 +21,20 @@ import pytest
from unittest.mock import MagicMock
-def test_create(mongo, test_user, no_warn):
+def test_create(mongo_function, test_user, no_warn):
doi = DOI.create('the_title', test_user)
assert DOI.objects(doi=doi.doi).first() is not None
assert doi.metadata_xml is not None
-def test_create_doi_counter(mongo, test_user, no_warn):
+def test_create_doi_counter(mongo_function, test_user, no_warn):
DOI.create('the_title', test_user)
doi = DOI.create('the_title', test_user)
assert doi.doi.endswith('-2')
-def test_create_draft_doi(mongo, test_user, no_warn):
+def test_create_draft_doi(mongo_function, test_user, no_warn):
if config.datacite.enabled:
doi = DOI.create('the_title', test_user)
doi.create_draft()
@@ -52,7 +52,7 @@ def test_create_draft_doi(mongo, test_user, no_warn):
],
)
def test_datacite_requests(
- mongo, monkeypatch, test_user, status_code, response_ok, is_findable, text
+ mongo_function, monkeypatch, test_user, status_code, response_ok, is_findable, text
):
if config.datacite.enabled: