def _save_samples(samples, acls, sample_url, token):
""""""
saved_samples = []
for data in samples:
sample = data['sample']
prev_sample = data['prev_sample']
name = data['name']
sample_id, sample_ver = save_sample(sample,
sample_url,
token,
previous_version=prev_sample)
saved_samples.append({
"id": sample_id,
"name": name,
"version": sample_ver
})
# check input for any reason to update access control list
# should have a "write", "read", "admin" entry
writer = data.get('write')
reader = data.get('read')
admin = data.get('admin')
if writer or reader or admin:
acls["read"] += [r for r in reader]
acls["write"] += [w for w in writer]
acls["admin"] += [a for a in admin]
if len(acls["read"]) > 0 or len(acls['write']) > 0 or len(
acls['admin']) > 0:
_ = update_acls(sample_url, sample_id, acls, token)
return saved_samples
def update_sample_set_acls(self, ctx, params):
"""
:param params: instance of type "update_sample_set_acls_params" ->
structure: parameter "workspace_name" of String, parameter
"workspace_id" of Long, parameter "sample_set_ref" of String,
parameter "new_users" of list of String, parameter "is_reader" of
Long, parameter "is_writer" of Long, parameter "is_admin" of Long,
parameter "share_within_workspace" of Long
:returns: instance of type "update_sample_set_acls_output" ->
structure: parameter "status" of String
"""
# ctx is the context object
# return variables are: output
#BEGIN update_sample_set_acls
# first get sample_set object
sample_set_ref = params.get('sample_set_ref')
ret = self.dfu.get_objects({'object_refs':
[sample_set_ref]})['data'][0]
sample_set = ret['data']
sample_url = get_sample_service_url(self.sw_url)
acls = {'read': [], 'write': [], 'admin': []}
if params.get('share_within_workspace'):
acls = get_workspace_user_perms(self.workspace_url,
params.get('workspace_id'),
ctx['token'], ctx['user_id'], acls)
for new_user in params.get('new_users'):
if params.get('is_admin'):
acls['admin'].append(new_user)
elif params.get('is_writer'):
acls['write'].append(new_user)
elif params.get('is_reader'):
acls['read'].append(new_user)
for sample in sample_set['samples']:
sample_id = sample['id']
status = update_acls(sample_url, sample_id, acls, ctx['token'])
output = {"status": status}
#END update_sample_set_acls
# At some point might do deeper type checking...
if not isinstance(output, dict):
raise ValueError('Method update_sample_set_acls return value ' +
'output is not type dict as required.')
# return the results
return [output]
def produce_samples(
df,
cols,
column_groups,
column_unit_regex,
sample_url,
token,
existing_samples,
columns_to_input_names,
acls
):
""""""
samples = []
existing_sample_names = {sample['name']: sample for sample in existing_samples}
for idx, row in df.iterrows():
if row.get('id'):
# first we check if a 'kbase_sample_id' column is specified
kbase_sample_id = None
if row.get('kbase_sample_id'):
kbase_sample_id = str(row.pop('kbase_sample_id'))
if 'kbase_sample_id' in cols:
cols.pop(cols.index('kbase_sample_id'))
# use name field as name, if there is non-reuse id.
if row.get('name'):
name = str(row['name'])
else:
name = str(row['id'])
if row.get('parent_id'):
parent = str(row.pop('parent_id'))
if 'parent_id' in cols:
cols.pop(cols.index('parent_id'))
if 'id' in cols:
cols.pop(cols.index('id'))
if 'name' in cols:
cols.pop(cols.index('name'))
controlled_metadata = generate_controlled_metadata(
row,
column_groups
)
user_metadata = generate_user_metadata(
row,
cols,
column_groups,
column_unit_regex
)
source_meta = generate_source_meta(
row,
controlled_metadata.keys(),
columns_to_input_names
)
sample = {
'node_tree': [{
"id": str(row['id']),
"parent": None,
"type": "BioReplicate",
"meta_controlled": controlled_metadata,
"meta_user": user_metadata,
'source_meta': source_meta
}],
'name': name,
}
prev_sample = None
if kbase_sample_id:
prev_sample = get_sample({"id": kbase_sample_id}, sample_url, token)
if name in existing_sample_names and prev_sample['name'] == name:
# now we check if the sample 'id' and 'name' are the same
if existing_sample_names[name]['id'] != prev_sample['id']:
raise ValueError(f"'kbase_sample_id' and input sample set have different ID's for sample: {name}")
elif name in existing_sample_names and name != prev_sample['name']:
# not sure if this is an error case
raise ValueError(f"Cannot rename existing sample from {prev_sample['name']} to {name}")
elif name in existing_sample_names:
prev_sample = get_sample(existing_sample_names[name], sample_url, token)
if compare_samples(sample, prev_sample):
if sample.get('name') not in existing_sample_names:
existing_sample_names[sample['name']] = prev_sample
continue
elif name in existing_sample_names:
existing_sample_names.pop(name)
sample_id, sample_ver = save_sample(sample, sample_url, token, previous_version=prev_sample)
samples.append({
"id": sample_id,
"name": name,
"version": sample_ver
})
# check input for any reason to update access control list
# should have a "write", "read", "admin" entry
writer = row.get('write')
reader = row.get('read')
admin = row.get('admin')
if writer or reader or admin:
acls["read"] += [r for r in reader]
acls["write"] += [w for w in writer]
acls["admin"] += [a for a in admin]
if len(acls["read"]) > 0 or len(acls['write']) > 0 or len(acls['admin']) > 0:
resp = update_acls(sample_url, sample_id, acls, token)
else:
raise RuntimeError(f"{row.get('id')} evaluates as false - {row.keys()}")
# add the missing samples from existing_sample_names
samples += [existing_sample_names[key] for key in existing_sample_names]
return samples