-
Notifications
You must be signed in to change notification settings - Fork 992
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Implement simple history copy unit tests.
- Loading branch information
Showing
1 changed file
with
134 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,134 @@ | ||
import contextlib | ||
import os | ||
import threading | ||
|
||
import galaxy.datatypes.registry | ||
import galaxy.model | ||
import galaxy.model.mapping as mapping | ||
from galaxy.model.metadata import MetadataTempFile | ||
from galaxy.util import ExecutionTimer | ||
from .test_objectstore import DISK_TEST_CONFIG, TestConfig | ||
|
||
|
||
datatypes_registry = galaxy.datatypes.registry.Registry() | ||
datatypes_registry.load_datatypes() | ||
galaxy.model.set_datatypes_registry(datatypes_registry) | ||
|
||
NUM_DATASETS = 3 | ||
NUM_COLLECTIONS = 1 | ||
SLOW_QUERY_LOG_THRESHOLD = 1000 | ||
INCLUDE_METADATA_FILE = True | ||
THREAD_LOCAL_LOG = threading.local() | ||
|
||
|
||
def test_history_dataset_copy(num_datasets=NUM_DATASETS, include_metadata_file=INCLUDE_METADATA_FILE): | ||
with _setup_mapping_and_user() as (test_config, object_store, model, old_history): | ||
for i in range(num_datasets): | ||
hda_path = test_config.write("moo", "test_metadata_original_%d" % i) | ||
_create_hda(model, object_store, old_history, hda_path, include_metadata_file=include_metadata_file) | ||
|
||
model.context.flush() | ||
|
||
history_copy_timer = ExecutionTimer() | ||
new_history = old_history.copy(target_user=old_history.user) | ||
print("history copied %s" % history_copy_timer) | ||
assert new_history.name == "HistoryCopyHistory1" | ||
assert new_history.user == old_history.user | ||
for i, hda in enumerate(new_history.active_datasets): | ||
assert hda.get_size() == 3 | ||
if include_metadata_file: | ||
_check_metadata_file(hda) | ||
annotation_str = hda.get_item_annotation_str(model.context, old_history.user, hda) | ||
assert annotation_str == "annotation #%d" % hda.hid, annotation_str | ||
|
||
|
||
def test_history_collection_copy(list_size=NUM_DATASETS): | ||
with _setup_mapping_and_user() as (test_config, object_store, model, old_history): | ||
for i in range(NUM_COLLECTIONS): | ||
hdas = [] | ||
for i in range(list_size * 2): | ||
hda_path = test_config.write("moo", "test_metadata_original_%d" % i) | ||
hda = _create_hda(model, object_store, old_history, hda_path, visible=False, include_metadata_file=False) | ||
hdas.append(hda) | ||
|
||
list_elements = [] | ||
list_collection = model.DatasetCollection(collection_type="list:paired") | ||
for j in range(list_size): | ||
paired_collection = model.DatasetCollection(collection_type="paired") | ||
forward_dce = model.DatasetCollectionElement(collection=paired_collection, element=hdas[j * 2]) | ||
reverse_dce = model.DatasetCollectionElement(collection=paired_collection, element=hdas[j * 2 + 1]) | ||
paired_collection.elements = [forward_dce, reverse_dce] | ||
paired_collection_element = model.DatasetCollectionElement(collection=list_collection, element=paired_collection) | ||
list_elements.append(paired_collection_element) | ||
model.context.add_all([forward_dce, reverse_dce, paired_collection_element]) | ||
list_collection.elements = list_elements | ||
history_dataset_collection = model.HistoryDatasetCollectionAssociation(collection=list_collection) | ||
history_dataset_collection.user = old_history.user | ||
model.context.add(history_dataset_collection) | ||
|
||
model.context.flush() | ||
old_history.add_dataset_collection(history_dataset_collection) | ||
history_dataset_collection.add_item_annotation(model.context, old_history.user, history_dataset_collection, "annotation #%d" % history_dataset_collection.hid) | ||
|
||
model.context.flush() | ||
annotation_str = history_dataset_collection.get_item_annotation_str(model.context, old_history.user, history_dataset_collection) | ||
|
||
# Saving magic SA invocations for detecting full flushes that may harm performance. | ||
# from sqlalchemy import event | ||
# @event.listens_for(model.context, "before_flush") | ||
# def track_instances_before_flush(session, context, instances): | ||
# if not instances: | ||
# print("FULL FLUSH...") | ||
# else: | ||
# print("Flushing just %s" % instances) | ||
|
||
history_copy_timer = ExecutionTimer() | ||
new_history = old_history.copy(target_user=old_history.user) | ||
print("history copied %s" % history_copy_timer) | ||
|
||
for i, hda in enumerate(new_history.active_datasets): | ||
assert hda.get_size() == 3 | ||
annotation_str = hda.get_item_annotation_str(model.context, old_history.user, hda) | ||
assert annotation_str == "annotation #%d" % hda.hid, annotation_str | ||
|
||
assert len(new_history.active_dataset_collections) == NUM_COLLECTIONS | ||
for hdca in new_history.active_dataset_collections: | ||
annotation_str = hdca.get_item_annotation_str(model.context, old_history.user, hdca) | ||
assert annotation_str == "annotation #%d" % hdca.hid, annotation_str | ||
|
||
|
||
@contextlib.contextmanager | ||
def _setup_mapping_and_user(): | ||
with TestConfig(DISK_TEST_CONFIG) as (test_config, object_store): | ||
# Start the database and connect the mapping | ||
model = mapping.init("/tmp", "sqlite:///:memory:", create_tables=True, object_store=object_store, slow_query_log_threshold=SLOW_QUERY_LOG_THRESHOLD, thread_local_log=THREAD_LOCAL_LOG) | ||
|
||
u = model.User(email="historycopy@example.com", password="password") | ||
h1 = model.History(name="HistoryCopyHistory1", user=u) | ||
model.context.add_all([u, h1]) | ||
model.context.flush() | ||
yield test_config, object_store, model, h1 | ||
|
||
|
||
def _create_hda(model, object_store, history, path, visible=True, include_metadata_file=False): | ||
hda = model.HistoryDatasetAssociation(extension="bam", create_dataset=True, sa_session=model.context) | ||
hda.visible = visible | ||
model.context.add(hda) | ||
model.context.flush([hda]) | ||
object_store.update_from_file(hda, file_name=path, create=True) | ||
if include_metadata_file: | ||
hda.metadata.from_JSON_dict(json_dict={"bam_index": MetadataTempFile.from_JSON({"kwds": {}, "filename": path})}) | ||
_check_metadata_file(hda) | ||
hda.set_size() | ||
history.add_dataset(hda) | ||
hda.add_item_annotation(model.context, history.user, hda, "annotation #%d" % hda.hid) | ||
return hda | ||
|
||
|
||
def _check_metadata_file(hda): | ||
assert hda.metadata.bam_index.id | ||
copied_index = hda.metadata.bam_index.file_name | ||
assert os.path.exists(copied_index) | ||
with open(copied_index, "r") as f: | ||
assert f.read() == "moo" | ||
assert copied_index.endswith("metadata_%d.dat" % hda.id) |