def suggest_for_files(gear, files, context=None):
invocation_schema = get_invocation_schema(gear)
schemas = {}
suggested_inputs = {}
for x in gear['gear']['inputs']:
input_ = gear['gear']['inputs'][x]
if input_.get('base') == 'context':
if x in context:
suggested_inputs[x] = [{
'base': 'context',
'found': True,
'value': context[x]['value']
}]
else:
suggested_inputs[x] = [{'base': 'context', 'found': False}]
elif input_.get('base') == 'file':
schema = gear_tools.isolate_file_invocation(invocation_schema, x)
schemas[x] = Draft4Validator(schema)
for input_name, schema in schemas.iteritems():
suggested_inputs[input_name] = []
for f in files:
if schema.is_valid(f):
suggested_inputs[input_name].append({
'base': 'file',
'name': f.get('name')
})
return suggested_inputs
def suggest_container(gear, cont_name, cid):
"""
Given a container reference, suggest files that would work well for each input on a gear.
"""
root = ContainerStorage.factory(cont_name).get_container(
cid, projection={'permissions': 0}, get_children=True)
root['analyses'] = ContainerStorage.factory('analyses').get_analyses(
cont_name, cid, False)
invocation_schema = get_invocation_schema(gear)
schemas = {}
for x in gear['gear']['inputs']:
schema = gear_tools.isolate_file_invocation(invocation_schema, x)
schemas[x] = Draft4Validator(schema)
# It would be nice to have use a visitor here instead of manual key loops.
for acq in root.get('acquisitions', []):
for f in acq.get('files', []):
f['suggested'] = {}
for x in schemas:
f['suggested'][x] = schemas[x].is_valid(f)
for analysis in root.get('analyses', []):
files = analysis.get('files', [])
files[:] = [x for x in files if x.get('output')]
for f in files:
f['suggested'] = {}
for x in schemas:
f['suggested'][x] = schemas[x].is_valid(f)
analysis['files'] = files
return root
def suggest_for_files(gear, files):
invocation_schema = get_invocation_schema(gear)
schemas = {}
for x in gear['gear']['inputs']:
schema = gear_tools.isolate_file_invocation(invocation_schema, x)
schemas[x] = Draft4Validator(schema)
suggested_files = {}
for input_name, schema in schemas.iteritems():
suggested_files[input_name] = []
for f in files:
if schema.is_valid(f):
suggested_files[input_name].append(f.get('name'))
return suggested_files
def suggest_for_files(gear, files):
invocation_schema = get_invocation_schema(gear)
schemas = {}
for x in gear['gear']['inputs']:
schema = gear_tools.isolate_file_invocation(invocation_schema, x)
schemas[x] = Draft4Validator(schema)
suggested_files = {}
log.debug(schemas)
for input_name, schema in schemas.iteritems():
suggested_files[input_name] = []
for f in files:
if schema.is_valid(f):
suggested_files[input_name].append(f.get('name'))
return suggested_files
def add_suggest_info_to_files(gear, files):
"""
Given a list of files, add information to each file that details those that would work well for each input on a gear.
"""
invocation_schema = get_invocation_schema(gear)
schemas = {}
for x in gear['gear']['inputs']:
schema = gear_tools.isolate_file_invocation(invocation_schema, x)
schemas[x] = Draft4Validator(schema)
for f in files:
f['suggested'] = {}
for x in schemas:
f['suggested'][x] = schemas[x].is_valid(f)
return files
def add_suggest_info_to_files(gear, files):
"""
Given a list of files, add information to each file that details those that would work well for each input on a gear.
"""
invocation_schema = get_invocation_schema(gear)
schemas = {}
for x in gear['gear']['inputs']:
input_ = gear['gear']['inputs'][x]
if input_.get('base') == 'file':
schema = gear_tools.isolate_file_invocation(invocation_schema, x)
schemas[x] = Draft4Validator(schema)
for f in files:
f['suggested'] = {}
for x in schemas:
f['suggested'][x] = schemas[x].is_valid(f)
return files