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_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_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 create(self,
trans,
visualization_title="",
visualization_slug="",
visualization_annotation="",
visualization_dbkey=""):
"""
Create a new visualization
"""
user = trans.get_user()
visualization_title_err = visualization_slug_err = visualization_annotation_err = ""
if trans.request.method == "POST":
if not visualization_title:
visualization_title_err = "visualization name is required"
elif not visualization_slug:
visualization_slug_err = "visualization id is required"
elif not VALID_SLUG_RE.match(visualization_slug):
visualization_slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character"
elif trans.sa_session.query(model.Visualization).filter_by(
user=user, slug=visualization_slug, deleted=False).first():
visualization_slug_err = "visualization id must be unique"
else:
# Create the new stored visualization
visualization = model.Visualization()
visualization.title = visualization_title
visualization.slug = visualization_slug
visualization.dbkey = visualization_dbkey
visualization.type = 'trackster' # HACK: set visualization type to trackster since it's the only viz
visualization_annotation = sanitize_html(
visualization_annotation, 'utf-8', 'text/html')
self.add_item_annotation(trans.sa_session, trans.get_user(),
visualization,
visualization_annotation)
visualization.user = user
# And the first (empty) visualization revision
visualization_revision = model.VisualizationRevision()
visualization_revision.title = visualization_title
visualization_revision.config = {}
visualization_revision.dbkey = visualization_dbkey
visualization_revision.visualization = visualization
visualization.latest_revision = visualization_revision
# Persist
session = trans.sa_session
session.add(visualization)
session.add(visualization_revision)
session.flush()
return trans.response.send_redirect(web.url_for(action='list'))
return trans.show_form(web.FormBuilder(
web.url_for(), "Create new visualization", submit_text="Submit"
).add_text(
"visualization_title",
"Visualization title",
value=visualization_title,
error=visualization_title_err
).add_text(
"visualization_slug",
"Visualization identifier",
value=visualization_slug,
error=visualization_slug_err,
help="""A unique identifier that will be used for
public links to this visualization. A default is generated
from the visualization title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character."""
).add_select(
"visualization_dbkey",
"Visualization DbKey/Build",
value=visualization_dbkey,
options=self
._get_dbkeys(
trans),
error=None
).add_text(
"visualization_annotation",
"Visualization annotation",
value=visualization_annotation,
error=visualization_annotation_err,
help
="A description of the visualization; annotation is shown alongside published visualizations."
),
template="visualization/create.mako")
