def upload_collection(user: User, filename: str, new_data: Dict[str, Any], remove_file=True) -> Collection:
"""
From an uploaded HDF5 file, create a new collection. Metadata will be set from new_data
:param user:
:param filename:
:param new_data:
:return:
"""
if validate_file(filename):
parent_id = new_data['parent_id'] if 'parent_id' in new_data else None
analysis_id = new_data['analysis_id'] if 'analysis_id' in new_data else None
analyses = [get_analysis(user, analysis_id)] if analysis_id is not None else []
new_collection = Collection(owner=user, creator=user, last_editor=user, name=new_data['name'], parent_id=parent_id, analyses=analyses)
db.session.add(new_collection)
db.session.commit()
new_collection.filename = f'{DATADIR}/collections/{new_collection.id}.h5'
shutil.copy(filename, new_collection.filename)
if remove_file:
os.remove(filename)
new_data['creator_id'] = user.id if 'creator_id' not in new_data else new_data['creator_id']
new_data['owner_id'] = user.id if 'owner_id' not in new_data else new_data['owner_id']
update_collection(user, new_collection, new_data) # apply metadata
db.session.commit()
return new_collection
raise Exception('File not valid.')
def render_analysis(analysis_id=None):
try:
current_user = get_current_user()
return render_template('pages/analysis_entry.html',
page_data=AnalysisPageData(current_user, get_analysis(current_user, analysis_id)))
except Exception as e:
return handle_exception_browser(e)
def update_workflow(user: User,
workflow: Workflow,
new_data: Dict[str, Any],
filename: str = None) -> Workflow:
"""
Update workflow metadata.
:param user:
:param workflow:
:param new_data:
:parma filename:
:return:
"""
if is_write_permitted(user, workflow):
if 'id' in new_data:
if workflow.id != int(new_data['id']) and Workflow.query.filter_by(
id=new_data['id']) is not None:
raise ValueError(
f'Workflow with id {new_data["id"]} already exists!')
if 'analysis_ids' in new_data:
new_analyses = [
get_analysis(user, analysis_id)
for analysis_id in new_data['analysis_ids']
]
remove_analyses = [
analysis for analysis in workflow.analyses
if analysis.id not in new_data['analysis_ids']
]
for analysis in new_analyses:
if not is_write_permitted(user, analysis):
raise AuthException(
f'User {user.email} is not permitted to attach workflow {workflow.id} to analysis {analysis.id}'
)
for analysis in remove_analyses:
if not is_write_permitted(user, analysis):
raise AuthException(
f'User {user.email} is not permitted to detach workflow {workflow.id} from analysis {analysis.id}'
)
workflow.analyses = new_analyses
workflow.update(new_data)
if 'workflow_definition' in new_data:
if workflow.file_type == 'json':
json.dump(new_data['workflow_definition'],
open(workflow.filename, 'w+'))
elif workflow.file_type == 'yaml':
yaml.dump(new_data['workflow_definition'],
open(workflow.filename, 'w+'))
else:
open(workflow.filename,
'w+').write(new_data['workflow_definition'])
if filename is not None:
os.remove(workflow.filename)
shutil.copy(filename, workflow.filename)
os.remove(filename)
db.session.commit()
return workflow
raise AuthException(
f'User {user.email} is not permitted to modify workflow {workflow.id}')
def update_external_file(user: User,
external_file: ExternalFile,
new_data: Dict[str, Any],
move_file: bool = False,
filename: str = None) -> ExternalFile:
"""
Update the data in the external file record
:param user:
:param external_file:
:param new_data:
:param move_file:
:param filename:
:return:
"""
if is_write_permitted(user, external_file):
if 'id' in new_data:
if external_file.id != int(
new_data['id']) and ExternalFile.query.filter_by(
id=new_data['id']) is not None:
raise ValueError(
f'External file with id {new_data["id"]} already exists!')
if 'analysis_ids' in new_data:
new_analyses = [
get_analysis(user, analysis_id)
for analysis_id in new_data['analysis_ids']
]
remove_analyses = [
analysis for analysis in external_file.analyses
if analysis.id not in new_data['analysis_ids']
]
for analysis in new_analyses:
if not is_write_permitted(user, analysis):
raise AuthException(
f'User {user.email} is not permitted to attach external file {external_file.id} to analysis {analysis.id}'
)
for analysis in remove_analyses:
if not is_write_permitted(user, analysis):
raise AuthException(
f'User {user.email} is not permitted to detach external file {external_file.id} from analysis {analysis.id}'
)
external_file.analyses = new_analyses
if move_file and 'filename' in new_data:
original_filename = external_file.filename
shutil.copy(original_filename, new_data['filename'])
os.remove(original_filename)
if filename is not None:
os.remove(external_file.filename)
shutil.copy(filename, external_file.filename)
os.remove(filename)
external_file.update(new_data)
external_file.last_editor = user
db.session.commit()
return external_file
raise AuthException(
f'User {user.id} is not permitted to modify external file record {external_file.id}'
)
def update_collection(user: User, collection: Collection, new_data: Dict[str, Any], filename: str = None) -> Collection:
"""
Update collection attributes
:param user:
:param collection:
:param new_data:
:return:
"""
if is_write_permitted(user, collection):
# file attributes and database attributes should be separated
if 'id' in new_data:
if collection.id != int(new_data['id']) and Collection.query.filter_by(id=new_data['id']) is not None:
raise ValueError(f'Collection with id {new_data["id"]} already exists!')
# verify write permissions on analyses to attach to or detach from
if 'analysis_ids' in new_data:
new_analyses = [get_analysis(user, analysis_id) for analysis_id in new_data['analysis_ids']]
remove_analyses = [analysis for analysis in collection.analyses
if analysis.id not in new_data['analysis_ids']]
for analysis in new_analyses:
if not is_write_permitted(user, analysis):
raise AuthException(f'User {user.email} is not permitted to attach collection {collection.id} '
f'to analysis {analysis.id}')
for analysis in remove_analyses:
if not is_write_permitted(user, analysis):
raise AuthException(f'User {user.email} is not permitted to detach collection {collection.id} '
f'from analysis {analysis.id}')
collection.analyses = new_analyses
collection.update(new_data)
if filename is not None:
os.remove(collection.filename)
shutil.copy(filename, collection.filename)
os.remove(filename)
if 'file_info' in new_data:
mdt.update_metadata(collection.filename,
{key: value for key, value in new_data['file_info'].items()})
collection.last_editor = user
db.session.commit()
return collection
raise AuthException(f'User {user.email} is not permitted to modify collection {collection.id}')