def test_export_copied_collection():
app, sa_session, h = _setup_history_for_export("Collection History with copied collection")
d1, d2 = _create_datasets(sa_session, h, 2)
c1 = model.DatasetCollection(collection_type="paired")
hc1 = model.HistoryDatasetCollectionAssociation(history=h, hid=3, collection=c1, name="HistoryCollectionTest1")
h.hid_counter = 4
dce1 = model.DatasetCollectionElement(collection=c1, element=d1, element_identifier="forward", element_index=0)
dce2 = model.DatasetCollectionElement(collection=c1, element=d2, element_identifier="reverse", element_index=1)
sa_session.add_all((dce1, dce2, d1, d2, hc1))
sa_session.flush()
hc2 = hc1.copy(element_destination=h)
h.add_pending_items()
assert h.hid_counter == 7
sa_session.add(hc2)
sa_session.flush()
assert hc2.copied_from_history_dataset_collection_association == hc1
imported_history = _import_export(app, h)
assert imported_history.hid_counter == 7
assert len(imported_history.dataset_collections) == 2
assert len(imported_history.datasets) == 4
_assert_distinct_hids(imported_history)
imported_by_hid = _hid_dict(imported_history)
assert imported_by_hid[4].copied_from_history_dataset_association == imported_by_hid[1]
assert imported_by_hid[5].copied_from_history_dataset_association == imported_by_hid[2]
assert imported_by_hid[6].copied_from_history_dataset_collection_association == imported_by_hid[3]
def __assert_output_format_is(expected, output, input_extensions=[], param_context=[], add_collection=False):
inputs = {}
last_ext = "data"
i = 1
for name, ext in input_extensions:
hda = model.HistoryDatasetAssociation(extension=ext)
hda.metadata.random_field = str(i) # Populate a random metadata field for testing
inputs[name] = hda
last_ext = ext
i += 1
input_collections = {}
if add_collection:
hda_forward = model.HistoryDatasetAssociation(extension="txt")
hda_reverse = model.HistoryDatasetAssociation(extension="txt")
c1 = model.DatasetCollection(collection_type="pair")
hc1 = model.HistoryDatasetCollectionAssociation(collection=c1, name="HistoryCollectionTest1")
dce1 = model.DatasetCollectionElement(collection=c1, element=hda_forward, element_identifier="forward", element_index=0)
dce2 = model.DatasetCollectionElement(collection=c1, element=hda_reverse, element_identifier="reverse", element_index=1)
c1.elements = [dce1, dce2]
input_collections["hdcai"] = [(hc1, False)]
actual_format = determine_output_format(output, param_context, inputs, input_collections, last_ext)
assert actual_format == expected, "Actual format %s, does not match expected %s" % (actual_format, expected)
def test_export_collection_hids():
app, sa_session, h = _setup_history_for_export("Collection History with dataset from this history")
d1, d2 = _create_datasets(sa_session, h, 2)
c1 = model.DatasetCollection(collection_type="paired")
hc1 = model.HistoryDatasetCollectionAssociation(history=h, hid=3, collection=c1, name="HistoryCollectionTest1")
h.hid_counter = 4
dce1 = model.DatasetCollectionElement(collection=c1, element=d1, element_identifier="forward", element_index=0)
dce2 = model.DatasetCollectionElement(collection=c1, element=d2, element_identifier="reverse", element_index=1)
sa_session.add(dce1)
sa_session.add(dce2)
sa_session.add(d1)
sa_session.add(d2)
sa_session.add(hc1)
sa_session.flush()
imported_history = _import_export(app, h)
assert imported_history.hid_counter == 4, imported_history.hid_counter
assert len(imported_history.dataset_collections) == 1
assert len(imported_history.datasets) == 2
for hdca in imported_history.dataset_collections:
assert hdca.hid == 3, hdca.hid
for hda in imported_history.datasets:
assert hda.hid in [1, 2], hda.hid
_assert_distinct_hids(imported_history)
def test_export_collection_with_copied_datasets_and_overlapping_hids():
app, sa_session, h = _setup_history_for_export("Collection History with dataset from other history")
dataset_history = model.History(name="Dataset History", user=h.user)
d1, d2 = _create_datasets(sa_session, dataset_history, 2)
sa_session.add(d1)
sa_session.add(d2)
sa_session.add(dataset_history)
sa_session.flush()
app.object_store.update_from_file(d1, file_name="test-data/1.txt", create=True)
app.object_store.update_from_file(d2, file_name="test-data/2.bed", create=True)
d1_copy = d1.copy()
d2_copy = d2.copy()
d1_copy.history = h
d2_copy.history = h
c1 = model.DatasetCollection(collection_type="paired")
hc1 = model.HistoryDatasetCollectionAssociation(history=h, hid=3, collection=c1, name="HistoryCollectionTest1")
h.hid_counter = 5
dce1 = model.DatasetCollectionElement(collection=c1, element=d1, element_identifier="forward", element_index=0)
dce2 = model.DatasetCollectionElement(collection=c1, element=d2, element_identifier="reverse", element_index=1)
sa_session.add(dce1)
sa_session.add(dce2)
sa_session.add(d1_copy)
sa_session.add(d2_copy)
sa_session.add(hc1)
sa_session.flush()
_import_export(app, h)
def test_collections_in_histories(self):
model = self.model
u = model.User(email="*****@*****.**", password="******")
h1 = model.History(name="History 1", user=u)
d1 = model.HistoryDatasetAssociation(extension="txt",
history=h1,
create_dataset=True,
sa_session=model.session)
d2 = model.HistoryDatasetAssociation(extension="txt",
history=h1,
create_dataset=True,
sa_session=model.session)
c1 = model.DatasetCollection(collection_type="pair")
hc1 = model.HistoryDatasetCollectionAssociation(
history=h1, collection=c1, name="HistoryCollectionTest1")
dce1 = model.DatasetCollectionElement(collection=c1,
element=d1,
element_identifier="left")
dce2 = model.DatasetCollectionElement(collection=c1,
element=d2,
element_identifier="right")
self.persist(u, h1, d1, d2, c1, hc1, dce1, dce2)
loaded_dataset_collection = self.query(
model.HistoryDatasetCollectionAssociation).filter(
model.HistoryDatasetCollectionAssociation.name ==
"HistoryCollectionTest1").first().collection
self.assertEqual(len(loaded_dataset_collection.elements), 2)
assert loaded_dataset_collection.collection_type == "pair"
assert loaded_dataset_collection["left"] == dce1
assert loaded_dataset_collection["right"] == dce2
def _create_output_dataset_collection(self, **kwd):
output_dataset_collection = model.HistoryDatasetCollectionAssociation(
**kwd)
self.history.add_dataset_collection(output_dataset_collection)
assert output_dataset_collection.collection
self.app.model.session.add(output_dataset_collection)
self.app.model.session.flush()
return output_dataset_collection
def test_annotations(self):
model = self.model
u = model.User(email="*****@*****.**", password="******")
self.persist(u)
def persist_and_check_annotation(annotation_class, **kwds):
annotated_association = annotation_class()
annotated_association.annotation = "Test Annotation"
annotated_association.user = u
for key, value in kwds.items():
setattr(annotated_association, key, value)
self.persist(annotated_association)
self.expunge()
stored_annotation = self.query(annotation_class).all()[0]
assert stored_annotation.annotation == "Test Annotation"
assert stored_annotation.user.email == "*****@*****.**"
sw = model.StoredWorkflow()
sw.user = u
self.persist(sw)
persist_and_check_annotation(model.StoredWorkflowAnnotationAssociation, stored_workflow=sw)
workflow = model.Workflow()
workflow.stored_workflow = sw
self.persist(workflow)
ws = model.WorkflowStep()
ws.workflow = workflow
self.persist(ws)
persist_and_check_annotation(model.WorkflowStepAnnotationAssociation, workflow_step=ws)
h = model.History(name="History for Annotation", user=u)
self.persist(h)
persist_and_check_annotation(model.HistoryAnnotationAssociation, history=h)
d1 = model.HistoryDatasetAssociation(extension="txt", history=h, create_dataset=True, sa_session=model.session)
self.persist(d1)
persist_and_check_annotation(model.HistoryDatasetAssociationAnnotationAssociation, hda=d1)
page = model.Page()
page.user = u
self.persist(page)
persist_and_check_annotation(model.PageAnnotationAssociation, page=page)
visualization = model.Visualization()
visualization.user = u
self.persist(visualization)
persist_and_check_annotation(model.VisualizationAnnotationAssociation, visualization=visualization)
dataset_collection = model.DatasetCollection(collection_type="paired")
history_dataset_collection = model.HistoryDatasetCollectionAssociation(collection=dataset_collection)
self.persist(history_dataset_collection)
persist_and_check_annotation(model.HistoryDatasetCollectionAssociationAnnotationAssociation, history_dataset_collection=history_dataset_collection)
library_dataset_collection = model.LibraryDatasetCollectionAssociation(collection=dataset_collection)
self.persist(library_dataset_collection)
persist_and_check_annotation(model.LibraryDatasetCollectionAnnotationAssociation, library_dataset_collection=library_dataset_collection)
def test_export_copied_objects_copied_outside_history():
app, sa_session, h = _setup_history_for_export("Collection History with copied objects")
d1, d2 = _create_datasets(sa_session, h, 2)
c1 = model.DatasetCollection(collection_type="paired")
hc1 = model.HistoryDatasetCollectionAssociation(history=h, hid=3, collection=c1, name="HistoryCollectionTest1")
h.hid_counter = 4
dce1 = model.DatasetCollectionElement(collection=c1, element=d1, element_identifier="forward", element_index=0)
dce2 = model.DatasetCollectionElement(collection=c1, element=d2, element_identifier="reverse", element_index=1)
sa_session.add_all((dce1, dce2, d1, d2, hc1))
sa_session.flush()
hc2 = hc1.copy(element_destination=h)
h.add_dataset_collection(hc2)
sa_session.add(hc2)
other_h = model.History(name=h.name + "-other", user=h.user)
sa_session.add(other_h)
hc3 = hc2.copy(element_destination=other_h)
other_h.add_dataset_collection(hc3)
sa_session.add(hc3)
sa_session.flush()
hc4 = hc3.copy(element_destination=h)
h.add_dataset_collection(hc4)
sa_session.add(hc4)
sa_session.flush()
assert h.hid_counter == 10
original_by_hid = _hid_dict(h)
assert original_by_hid[7].copied_from_history_dataset_association != original_by_hid[4]
assert original_by_hid[8].copied_from_history_dataset_association != original_by_hid[5]
assert original_by_hid[9].copied_from_history_dataset_collection_association != original_by_hid[6]
imported_history = _import_export(app, h)
assert imported_history.hid_counter == 10
assert len(imported_history.dataset_collections) == 3
assert len(imported_history.datasets) == 6
_assert_distinct_hids(imported_history)
imported_by_hid = _hid_dict(imported_history)
assert imported_by_hid[4].copied_from_history_dataset_association == imported_by_hid[1]
assert imported_by_hid[5].copied_from_history_dataset_association == imported_by_hid[2]
assert imported_by_hid[6].copied_from_history_dataset_collection_association == imported_by_hid[3]
assert imported_by_hid[7].copied_from_history_dataset_association == imported_by_hid[4]
assert imported_by_hid[8].copied_from_history_dataset_association == imported_by_hid[5]
assert imported_by_hid[9].copied_from_history_dataset_collection_association == imported_by_hid[6]
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
def _create_instance_for_collection(self,
trans,
parent,
name,
dataset_collection,
implicit_output_name=None,
implicit_inputs=None,
tags=None,
set_hid=True,
flush=True):
if isinstance(parent, model.History):
dataset_collection_instance = model.HistoryDatasetCollectionAssociation(
collection=dataset_collection,
name=name,
)
if implicit_inputs:
for input_name, input_collection in implicit_inputs:
dataset_collection_instance.add_implicit_input_collection(
input_name, input_collection)
if implicit_output_name:
dataset_collection_instance.implicit_output_name = implicit_output_name
log.debug("Created collection with %d elements" %
(len(dataset_collection_instance.collection.elements)))
if set_hid:
parent.add_dataset_collection(dataset_collection_instance)
elif isinstance(parent, model.LibraryFolder):
dataset_collection_instance = model.LibraryDatasetCollectionAssociation(
collection=dataset_collection,
folder=parent,
name=name,
)
else:
message = "Internal logic error - create called with unknown parent type %s" % type(
parent)
log.exception(message)
raise MessageException(message)
# Tags may be coming in as a dictionary of tag model objects if copying them from other
# existing Galaxy objects or as a list of strings if the tags are coming from user supplied
# values.
if isinstance(tags, list):
assert implicit_inputs is None, implicit_inputs
tags = self.tag_handler.add_tags_from_list(
trans.user, dataset_collection_instance, tags)
else:
tags = self._append_tags(dataset_collection_instance,
implicit_inputs, tags)
return self.__persist(dataset_collection_instance, flush=flush)
def test_dataset_dbkeys_and_extensions_summary(self):
model = self.model
u = model.User(email="*****@*****.**", password="******")
h1 = model.History(name="History 1", user=u)
d1 = model.HistoryDatasetAssociation(extension="bam", dbkey="hg19", history=h1, create_dataset=True, sa_session=model.session)
d2 = model.HistoryDatasetAssociation(extension="txt", dbkey="hg19", history=h1, create_dataset=True, sa_session=model.session)
c1 = model.DatasetCollection(collection_type='paired')
dce1 = model.DatasetCollectionElement(collection=c1, element=d1, element_identifier="forward", element_index=0)
dce2 = model.DatasetCollectionElement(collection=c1, element=d2, element_identifier="reverse", element_index=1)
hdca = model.HistoryDatasetCollectionAssociation(collection=c1, history=h1)
model.session.add_all([d1, d2, c1, dce1, dce2, hdca])
model.session.flush()
assert hdca.dataset_dbkeys_and_extensions_summary[0] == {"hg19"}
assert hdca.dataset_dbkeys_and_extensions_summary[1] == {"bam", "txt"}
def test_ratings(self):
model = self.model
u = model.User(email="*****@*****.**", password="******")
self.persist(u)
def persist_and_check_rating(rating_class, **kwds):
rating_association = rating_class()
rating_association.rating = 5
rating_association.user = u
for key, value in kwds.items():
setattr(rating_association, key, value)
self.persist(rating_association)
self.expunge()
stored_annotation = self.query(rating_class).all()[0]
assert stored_annotation.rating == 5
assert stored_annotation.user.email == "*****@*****.**"
sw = model.StoredWorkflow()
sw.user = u
self.persist(sw)
persist_and_check_rating(model.StoredWorkflowRatingAssociation, stored_workflow=sw)
h = model.History(name="History for Rating", user=u)
self.persist(h)
persist_and_check_rating(model.HistoryRatingAssociation, history=h)
d1 = model.HistoryDatasetAssociation(extension="txt", history=h, create_dataset=True, sa_session=model.session)
self.persist(d1)
persist_and_check_rating(model.HistoryDatasetAssociationRatingAssociation, hda=d1)
page = model.Page()
page.user = u
self.persist(page)
persist_and_check_rating(model.PageRatingAssociation, page=page)
visualization = model.Visualization()
visualization.user = u
self.persist(visualization)
persist_and_check_rating(model.VisualizationRatingAssociation, visualization=visualization)
dataset_collection = model.DatasetCollection(collection_type="paired")
history_dataset_collection = model.HistoryDatasetCollectionAssociation(collection=dataset_collection)
self.persist(history_dataset_collection)
persist_and_check_rating(model.HistoryDatasetCollectionRatingAssociation, history_dataset_collection=history_dataset_collection)
library_dataset_collection = model.LibraryDatasetCollectionAssociation(collection=dataset_collection)
self.persist(library_dataset_collection)
persist_and_check_rating(model.LibraryDatasetCollectionRatingAssociation, library_dataset_collection=library_dataset_collection)
def test_ratings(self):
model = self.model
user_email = "*****@*****.**"
u = model.User(email=user_email, password="******")
self.persist(u)
def persist_and_check_rating(rating_class, item):
rating = 5
rating_association = rating_class(u, item, rating)
self.persist(rating_association)
self.expunge()
stored_rating = self.query(rating_class).all()[0]
assert stored_rating.rating == rating
assert stored_rating.user.email == user_email
sw = model.StoredWorkflow()
sw.user = u
self.persist(sw)
persist_and_check_rating(model.StoredWorkflowRatingAssociation, sw)
h = model.History(name="History for Rating", user=u)
self.persist(h)
persist_and_check_rating(model.HistoryRatingAssociation, h)
d1 = model.HistoryDatasetAssociation(extension="txt", history=h, create_dataset=True, sa_session=model.session)
self.persist(d1)
persist_and_check_rating(model.HistoryDatasetAssociationRatingAssociation, d1)
page = model.Page()
page.user = u
self.persist(page)
persist_and_check_rating(model.PageRatingAssociation, page)
visualization = model.Visualization()
visualization.user = u
self.persist(visualization)
persist_and_check_rating(model.VisualizationRatingAssociation, visualization)
dataset_collection = model.DatasetCollection(collection_type="paired")
history_dataset_collection = model.HistoryDatasetCollectionAssociation(collection=dataset_collection)
self.persist(history_dataset_collection)
persist_and_check_rating(model.HistoryDatasetCollectionRatingAssociation, history_dataset_collection)
library_dataset_collection = model.LibraryDatasetCollectionAssociation(collection=dataset_collection)
self.persist(library_dataset_collection)
persist_and_check_rating(model.LibraryDatasetCollectionRatingAssociation, library_dataset_collection)
def test_history_collection_paired(self):
hdca = model.HistoryDatasetCollectionAssociation()
hdca.name = "cool name"
hdca.collection = self._new_pair_collection()
hdca.id = 1
self.trans.app.dataset_collections_service.get_dataset_collection_instance.return_value = hdca
example = """# Example
```galaxy
history_dataset_collection_display(history_dataset_collection_id=1)
```
"""
result = self._to_basic(example)
assert "**Dataset Collection:** cool name\n" in result
assert "**Element:** forward" in result, result
assert "**Element Contents:**\n" in result
assert "\n Forward dataset.\n" in result
assert "**Element:** reverse" in result, result
assert "\n Reverse dataset.\n" in result
def test_export_dataset_collection_paired(self):
hdca = model.HistoryDatasetCollectionAssociation()
hdca.name = "cool name"
hdca.collection = self._new_pair_collection()
hdca.id = 1
hdca.history_id = 1
hdca.collection_id = hdca.collection.id
self.trans.app.dataset_collections_service.get_dataset_collection_instance.return_value = hdca
example = """# Example
```galaxy
history_dataset_collection_display(history_dataset_collection_id=1)
```
"""
# Patch out url_for since we haven't initialized an app.
from galaxy.managers.hdcas import HDCASerializer
with mock.patch.object(HDCASerializer, 'url_for', return_value="http://google.com"):
export, extra_data = self._ready_export(example)
assert "history_dataset_collections" in extra_data
assert len(extra_data.get("history_dataset_collections")) == 1
def test_tags(self):
model = self.model
my_tag = model.Tag(name="Test Tag")
u = model.User(email="*****@*****.**", password="******")
self.persist(my_tag, u)
def tag_and_test(taggable_object, tag_association_class, backref_name):
assert len(getattr(self.query(model.Tag).filter(model.Tag.name == "Test Tag").all()[0], backref_name)) == 0
tag_association = tag_association_class()
tag_association.tag = my_tag
taggable_object.tags = [tag_association]
self.persist(tag_association, taggable_object)
assert len(getattr(self.query(model.Tag).filter(model.Tag.name == "Test Tag").all()[0], backref_name)) == 1
sw = model.StoredWorkflow()
sw.user = u
tag_and_test(sw, model.StoredWorkflowTagAssociation, "tagged_workflows")
h = model.History(name="History for Tagging", user=u)
tag_and_test(h, model.HistoryTagAssociation, "tagged_histories")
d1 = model.HistoryDatasetAssociation(extension="txt", history=h, create_dataset=True, sa_session=model.session)
tag_and_test(d1, model.HistoryDatasetAssociationTagAssociation, "tagged_history_dataset_associations")
page = model.Page()
page.user = u
tag_and_test(page, model.PageTagAssociation, "tagged_pages")
visualization = model.Visualization()
visualization.user = u
tag_and_test(visualization, model.VisualizationTagAssociation, "tagged_visualizations")
dataset_collection = model.DatasetCollection(collection_type="paired")
history_dataset_collection = model.HistoryDatasetCollectionAssociation(collection=dataset_collection)
tag_and_test(history_dataset_collection, model.HistoryDatasetCollectionTagAssociation, "tagged_history_dataset_collections")
library_dataset_collection = model.LibraryDatasetCollectionAssociation(collection=dataset_collection)
tag_and_test(library_dataset_collection, model.LibraryDatasetCollectionTagAssociation, "tagged_library_dataset_collections")
def test_export_collection_history():
app, sa_session, h = _setup_history_for_export("Collection History")
d1, d2, d3, d4 = _create_datasets(sa_session, h, 4)
c1 = model.DatasetCollection(collection_type="paired")
hc1 = model.HistoryDatasetCollectionAssociation(
history=h, hid=1, collection=c1, name="HistoryCollectionTest1")
dce1 = model.DatasetCollectionElement(collection=c1,
element=d1,
element_identifier="forward",
element_index=0)
dce2 = model.DatasetCollectionElement(collection=c1,
element=d2,
element_identifier="reverse",
element_index=1)
c2 = model.DatasetCollection(collection_type="list:paired")
hc2 = model.HistoryDatasetCollectionAssociation(
history=h, hid=2, collection=c2, name="HistoryCollectionTest2")
cleaf = model.DatasetCollection(collection_type="paired")
dce2leaf1 = model.DatasetCollectionElement(collection=cleaf,
element=d3,
element_identifier="forward",
element_index=0)
dce2leaf2 = model.DatasetCollectionElement(collection=cleaf,
element=d4,
element_identifier="reverse",
element_index=1)
dce21 = model.DatasetCollectionElement(collection=c2,
element=cleaf,
element_identifier="listel",
element_index=0)
j = model.Job()
j.user = h.user
j.tool_id = "cat1"
j.add_input_dataset_collection("input1_collect", hc1)
j.add_output_dataset_collection("output_collect", hc2)
sa_session.add(dce1)
sa_session.add(dce2)
sa_session.add(dce21)
sa_session.add(dce2leaf1)
sa_session.add(dce2leaf2)
sa_session.add(hc1)
sa_session.add(hc2)
sa_session.add(j)
sa_session.flush()
imported_history = _import_export(app, h)
datasets = imported_history.datasets
assert len(datasets) == 4
dataset_collections = list(
imported_history.contents_iter(types=["dataset_collection"]))
assert len(dataset_collections) == 2
imported_hdca1 = dataset_collections[0]
imported_hdca2 = dataset_collections[1]
imported_collection_2 = imported_hdca2.collection
assert imported_hdca1.collection.collection_type == "paired"
assert imported_collection_2.collection_type == "list:paired"
assert len(imported_collection_2.elements) == 1
imported_top_level_element = imported_collection_2.elements[0]
assert imported_top_level_element.element_identifier == "listel", imported_top_level_element.element_identifier
assert imported_top_level_element.element_index == 0, imported_top_level_element.element_index
imported_nested_collection = imported_top_level_element.child_collection
assert len(imported_nested_collection.elements) == 2
assert imported_nested_collection.collection_type == "paired", imported_nested_collection.collection_type
assert len(imported_history.jobs) == 1
imported_job = imported_history.jobs[0]
assert imported_job
assert len(imported_job.input_dataset_collections) == 1, len(
imported_job.input_dataset_collections)
assert len(imported_job.output_dataset_collection_instances) == 1
assert imported_job.id != j.id
def test_import_export_edit_collection():
"""Test modifying existing collections with imports."""
app = _mock_app()
sa_session = app.model.context
u = model.User(email="*****@*****.**", password="******")
h = model.History(name="Test History", user=u)
c1 = model.DatasetCollection(collection_type="list", populated=False)
hc1 = model.HistoryDatasetCollectionAssociation(
history=h, hid=1, collection=c1, name="HistoryCollectionTest1")
sa_session.add(hc1)
sa_session.add(h)
sa_session.flush()
import_history = model.History(name="Test History for Import", user=u)
sa_session.add(import_history)
temp_directory = mkdtemp()
with store.DirectoryModelExportStore(temp_directory,
app=app,
for_edit=True) as export_store:
export_store.add_dataset_collection(hc1)
# Fabric editing metadata for collection...
collections_metadata_path = os.path.join(temp_directory,
store.ATTRS_FILENAME_COLLECTIONS)
datasets_metadata_path = os.path.join(temp_directory,
store.ATTRS_FILENAME_DATASETS)
with open(collections_metadata_path, "r") as f:
hdcas_metadata = json.load(f)
assert len(hdcas_metadata) == 1
hdca_metadata = hdcas_metadata[0]
assert hdca_metadata
assert "id" in hdca_metadata
assert "collection" in hdca_metadata
collection_metadata = hdca_metadata["collection"]
assert "populated_state" in collection_metadata
assert collection_metadata[
"populated_state"] == model.DatasetCollection.populated_states.NEW
collection_metadata[
"populated_state"] = model.DatasetCollection.populated_states.OK
d1 = model.HistoryDatasetAssociation(extension="txt",
create_dataset=True,
flush=False)
d1.hid = 1
d2 = model.HistoryDatasetAssociation(extension="txt",
create_dataset=True,
flush=False)
d2.hid = 2
serialization_options = model.SerializationOptions(for_edit=True)
dataset_list = [
d1.serialize(app.security, serialization_options),
d2.serialize(app.security, serialization_options)
]
dc = model.DatasetCollection(
id=collection_metadata["id"],
collection_type="list",
element_count=2,
)
dc.populated_state = model.DatasetCollection.populated_states.OK
dce1 = model.DatasetCollectionElement(
element=d1,
element_index=0,
element_identifier="first",
)
dce2 = model.DatasetCollectionElement(
element=d2,
element_index=1,
element_identifier="second",
)
dc.elements = [dce1, dce2]
with open(datasets_metadata_path, "w") as datasets_f:
json.dump(dataset_list, datasets_f)
hdca_metadata["collection"] = dc.serialize(app.security,
serialization_options)
with open(collections_metadata_path, "w") as collections_f:
json.dump(hdcas_metadata, collections_f)
_perform_import_from_directory(temp_directory, app, u, import_history,
store.ImportOptions(allow_edit=True))
sa_session.refresh(c1)
assert c1.populated_state == model.DatasetCollection.populated_states.OK, c1.populated_state
assert len(c1.elements) == 2
def test_export_collection_with_mapping_history():
app, sa_session, h = _setup_history_for_export(
"Collection Mapping History")
d1, d2, d3, d4 = _create_datasets(sa_session, h, 4)
c1 = model.DatasetCollection(collection_type="list")
hc1 = model.HistoryDatasetCollectionAssociation(
history=h, hid=1, collection=c1, name="HistoryCollectionTest1")
dce1 = model.DatasetCollectionElement(collection=c1,
element=d1,
element_identifier="el1",
element_index=0)
dce2 = model.DatasetCollectionElement(collection=c1,
element=d2,
element_identifier="el2",
element_index=1)
c2 = model.DatasetCollection(collection_type="list")
hc2 = model.HistoryDatasetCollectionAssociation(
history=h, hid=2, collection=c2, name="HistoryCollectionTest2")
dce3 = model.DatasetCollectionElement(collection=c2,
element=d3,
element_identifier="el1",
element_index=0)
dce4 = model.DatasetCollectionElement(collection=c2,
element=d4,
element_identifier="el2",
element_index=1)
hc2.add_implicit_input_collection("input1", hc1)
j1 = model.Job()
j1.user = h.user
j1.tool_id = "cat1"
j1.add_input_dataset("input1", d1)
j1.add_output_dataset("out_file1", d3)
j2 = model.Job()
j2.user = h.user
j2.tool_id = "cat1"
j2.add_input_dataset("input1", d2)
j2.add_output_dataset("out_file1", d4)
sa_session.add(dce1)
sa_session.add(dce2)
sa_session.add(dce3)
sa_session.add(dce4)
sa_session.add(hc1)
sa_session.add(hc2)
sa_session.add(j1)
sa_session.add(j2)
sa_session.flush()
implicit_collection_jobs = model.ImplicitCollectionJobs()
j1.add_output_dataset_collection("out_file1", hc2) # really?
ija1 = model.ImplicitCollectionJobsJobAssociation()
ija1.order_index = 0
ija1.implicit_collection_jobs = implicit_collection_jobs
ija1.job = j1
j2.add_output_dataset_collection("out_file1", hc2) # really?
ija2 = model.ImplicitCollectionJobsJobAssociation()
ija2.order_index = 1
ija2.implicit_collection_jobs = implicit_collection_jobs
ija2.job = j2
sa_session.add(implicit_collection_jobs)
sa_session.add(ija1)
sa_session.add(ija2)
sa_session.flush()
imported_history = _import_export(app, h)
assert len(imported_history.jobs) == 2
imported_job0 = imported_history.jobs[0]
imported_icj = imported_job0.implicit_collection_jobs_association.implicit_collection_jobs
assert imported_icj
assert len(imported_icj.jobs) == 2, len(imported_icj.jobs)
