def __walk_step_dicts(self, data):
""" Walk over the supplid step dictionaries and return them in a way designed
to preserve step order when possible.
"""
supplied_steps = data['steps']
# Try to iterate through imported workflow in such a way as to
# preserve step order.
step_indices = list(supplied_steps.keys())
try:
step_indices = sorted(step_indices, key=int)
except ValueError:
# to defensive, were these ever or will they ever not be integers?
pass
discovered_labels = set()
discovered_uuids = set()
discovered_output_labels = set()
discovered_output_uuids = set()
# First pass to build step objects and populate basic values
for step_index in step_indices:
step_dict = supplied_steps[step_index]
uuid = step_dict.get("uuid", None)
if uuid and uuid != "None":
if uuid in discovered_uuids:
raise exceptions.DuplicatedIdentifierException(
"Duplicate step UUID in request.")
discovered_uuids.add(uuid)
label = step_dict.get("label", None)
if label:
if label in discovered_labels:
raise exceptions.DuplicatedIdentifierException(
"Duplicated step label in request.")
discovered_labels.add(label)
if 'workflow_outputs' in step_dict:
outputs = step_dict['workflow_outputs']
# outputs may be list of name (deprecated legacy behavior)
# or dictionary of names to {uuid: <uuid>, label: <label>}
if isinstance(outputs, dict):
for output_name in outputs:
output_dict = outputs[output_name]
output_label = output_dict.get("label", None)
if output_label:
if label in discovered_output_labels:
raise exceptions.DuplicatedIdentifierException(
"Duplicated workflow output label in request."
)
discovered_output_labels.add(label)
output_uuid = step_dict.get("output_uuid", None)
if output_uuid:
if output_uuid in discovered_output_uuids:
raise exceptions.DuplicatedIdentifierException(
"Duplicate workflow output UUID in request."
)
discovered_output_uuids.add(uuid)
yield step_dict
def __walk_step_dicts(self, data):
""" Walk over the supplid step dictionaries and return them in a way designed
to preserve step order when possible.
"""
supplied_steps = data['steps']
# Try to iterate through imported workflow in such a way as to
# preserve step order.
step_indices = supplied_steps.keys()
try:
step_indices = sorted(step_indices, key=int)
except ValueError:
# to defensive, were these ever or will they ever not be integers?
pass
discovered_labels = set()
discovered_uuids = set()
# First pass to build step objects and populate basic values
for step_index in step_indices:
step_dict = supplied_steps[step_index]
uuid = step_dict.get("uuid", None)
if uuid and uuid != "None":
if uuid in discovered_uuids:
raise exceptions.DuplicatedIdentifierException(
"Duplicate step UUID in request.")
discovered_uuids.add(uuid)
label = step_dict.get("label", None)
if label:
if label in discovered_labels:
raise exceptions.DuplicatedIdentifierException(
"Duplicated step label in request.")
discovered_labels.add(label)
yield step_dict
def add_custom_builds(self, trans, id, key, payload={}, **kwd):
"""
PUT /api/users/{id}/custom_builds/{key}
Add new custom build.
:param id: the encoded id of the user
:type id: str
:param id: custom build key
:type id: str
:param payload: data with new build details
:type payload: dict
"""
user = self._get_user(trans, id)
dbkeys = json.loads(user.preferences['dbkeys']
) if 'dbkeys' in user.preferences else {}
name = payload.get('name')
len_type = payload.get('len|type')
len_value = payload.get('len|value')
if len_type not in ['file', 'fasta', 'text'] or not len_value:
raise exceptions.RequestParameterInvalidException(
'Please specify a valid data source type.')
if not name or not key:
raise exceptions.RequestParameterMissingException(
'You must specify values for all the fields.')
elif key in dbkeys:
raise exceptions.DuplicatedIdentifierException(
'There is already a custom build with that key. Delete it first if you want to replace it.'
)
else:
# Have everything needed; create new build.
build_dict = {'name': name}
if len_type in ['text', 'file']:
# Create new len file
new_len = trans.app.model.HistoryDatasetAssociation(
extension='len',
create_dataset=True,
sa_session=trans.sa_session)
trans.sa_session.add(new_len)
new_len.name = name
new_len.visible = False
new_len.state = trans.app.model.Job.states.OK
new_len.info = 'custom build .len file'
try:
trans.app.object_store.create(new_len.dataset)
except ObjectInvalid:
raise exceptions.InternalServerError(
'Unable to create output dataset: object store is full.'
)
trans.sa_session.flush()
counter = 0
lines_skipped = 0
with open(new_len.file_name, 'w') as f:
# LEN files have format:
# <chrom_name><tab><chrom_length>
for line in len_value.split('\n'):
# Splits at the last whitespace in the line
lst = line.strip().rsplit(None, 1)
if not lst or len(lst) < 2:
lines_skipped += 1
continue
chrom, length = lst[0], lst[1]
try:
length = int(length)
except ValueError:
lines_skipped += 1
continue
if chrom != escape(chrom):
build_dict[
'message'] = 'Invalid chromosome(s) with HTML detected and skipped.'
lines_skipped += 1
continue
counter += 1
f.write('{}\t{}\n'.format(chrom, length))
build_dict['len'] = new_len.id
build_dict['count'] = counter
else:
build_dict['fasta'] = trans.security.decode_id(len_value)
dataset = trans.sa_session.query(
trans.app.model.HistoryDatasetAssociation).get(
build_dict['fasta'])
try:
new_len = dataset.get_converted_dataset(trans, 'len')
new_linecount = new_len.get_converted_dataset(
trans, 'linecount')
build_dict['len'] = new_len.id
build_dict['linecount'] = new_linecount.id
except Exception:
raise exceptions.ToolExecutionError(
'Failed to convert dataset.')
dbkeys[key] = build_dict
user.preferences['dbkeys'] = json.dumps(dbkeys)
trans.sa_session.flush()
return build_dict
