def update_metadata(namespace, workspace, vcf_lists):
fpath = 'gs://{0}/other_vcf_lists/{1}'
bucket_name = get_bucket_name(namespace, workspace)
for batch, pesr_vcflist, depth_vcflist in vcf_lists:
list_path = fpath.format(bucket_name, pesr_vcflist)
update = fapi._attr_set('other_batches_filtered_pesr_vcf_list', list_path)
r = fapi.update_entity(namespace, workspace, 'sample_set', batch, [update])
fapi._check_response_code(r, 200)
list_path = fpath.format(bucket_name, depth_vcflist)
update = fapi._attr_set('other_batches_filtered_depth_vcf_list', list_path)
r = fapi.update_entity(namespace, workspace, 'sample_set', batch, [update])
fapi._check_response_code(r, 200)
def update_metadata(namespace, workspace, cohort_batch_id, pesr_vcflist,
depth_vcflist):
fpath = 'gs://{0}/cohort_vcf_lists/{1}'
bucket_name = get_bucket_name(namespace, workspace)
list_path = fpath.format(bucket_name, pesr_vcflist)
update = fapi._attr_set('cohort_filtered_pesr_vcf_list', list_path)
r = fapi.update_entity(namespace, workspace, 'sample_set', cohort_batch_id,
[update])
fapi._check_response_code(r, 200)
list_path = fpath.format(bucket_name, depth_vcflist)
update = fapi._attr_set('cohort_filtered_depth_vcf_list', list_path)
r = fapi.update_entity(namespace, workspace, 'sample_set', cohort_batch_id,
[update])
fapi._check_response_code(r, 200)
def test_update_workspace_attributes(self):
"""Test update_workspace_attributes()."""
updates = [fapi._attr_set("key1", "value1")]
r = fapi.update_workspace_attributes(self.project, self.workspace,
updates)
print(r.status_code, r.content)
self.assertEqual(r.status_code, 200)
def update_entity_data_paths(workspace_name, workspace_project, bucket_list):
print("Listing all gs:// paths in DATA ENTITIES for " + workspace_name)
# get data attributes
response = call_fiss(fapi.get_entities_with_type, 200, workspace_project,
workspace_name)
entities = response
paths_without_replacements = {
} # where we store paths for which we don't have a replacement
replacements_made = 0
for ent in entities:
ent_name = ent['name']
ent_type = ent['entityType']
ent_attrs = ent['attributes']
gs_paths = {}
attrs_list = []
for attr in ent_attrs.keys():
if is_gs_path(attr, ent_attrs[attr]): # this is a gs:// path
original_path = ent_attrs[attr]
if is_in_bucket_list(
original_path, bucket_list
): # this is a path we think we want to update
new_path = get_replacement_path(original_path)
gs_paths[attr] = original_path
if new_path:
# format the update
updated_attr = fapi._attr_set(attr, new_path)
attrs_list.append(
updated_attr) # what we have replacements for
replacements_made += 1
else:
paths_without_replacements[
attr] = original_path # what we don't have replacements for
if len(gs_paths) > 0:
print(f'Found the following paths to update in {ent_name}:')
for item in gs_paths.keys():
print(' ' + item + ' : ' + gs_paths[item])
if len(attrs_list) > 0:
response = fapi.update_entity(workspace_project, workspace_name,
ent_type, ent_name, attrs_list)
if response.status_code == 200:
print(f'\nUpdated entities in {ent_name}:')
for attr in attrs_list:
print(' ' + attr['attributeName'] + ' : ' +
attr['addUpdateAttribute'])
if replacements_made == 0:
print('\nNo paths were updated!')
if len(paths_without_replacements) > 0:
print('\nWe could not find replacements for the following paths: ')
for item in paths_without_replacements.keys():
print(' ' + item + ' : ' + paths_without_replacements[item])
def update_metadata(namespace, workspace, sample_set, data):
fpath = 'gs://{0}/cohort_lists/{1}'
bucket_name = get_bucket_name(namespace, workspace)
for attr, fname in data:
list_path = fpath.format(bucket_name, fname)
update = fapi._attr_set(attr, list_path)
try:
r = fapi.update_entity(namespace, workspace, 'sample_set',
sample_set, [update])
fapi._check_response_code(r, 200)
except ferrors.FireCloudServerError:
pass
def find_and_replace(attr, value, replace_this, with_this):
"""Replace an attribute in a data table row."""
updated_attr = None
if isinstance(value, str): # if value is just a string
if replace_this in value:
new_value = value.replace(replace_this, with_this)
updated_attr = fapi._attr_set(attr, new_value)
elif isinstance(value, dict):
if replace_this in str(value):
value_str = str(value)
value_str_new = value_str.replace(replace_this, with_this)
value_new = ast.literal_eval(value_str_new)
updated_attr = fapi._attr_set(attr, value_new)
elif isinstance(value, (bool, int, float, complex)):
pass
elif value is None:
pass
else: # some other type, hopefully this doesn't exist
print('unknown type of attribute')
print('attr: ' + attr)
print('value: ' + str(value))
return updated_attr
def update_entity_data_paths_deprecated(workspace_name,
workspace_project,
mapping_tsv,
do_replacement=True):
if do_replacement:
print(
f'Updating paths in {workspace_name}\n\nNOTE: THIS STEP MAY TAKE A FEW MINUTES. As long as you see `In [*]:` to the left of this cell, it\'s still working!'
)
else:
print(f'Listing paths to update in {workspace_name}')
# load path mapping
mapping = load_mapping(mapping_tsv)
# set up dataframe to track all paths
columns = [
'entity_name', 'entity_type', 'attribute', 'original_path', 'new_path',
'map_key', 'fail_reason', 'file_type', 'update_status'
]
df_paths = pd.DataFrame(columns=columns)
# get data attributes
entities = call_fiss(fapi.get_entities_with_type, 200, workspace_project,
workspace_name)
for ent in entities:
ent_name = ent['name']
ent_type = ent['entityType']
ent_attrs = ent['attributes']
gs_paths = {}
attrs_list = []
inds = [] # to keep track of rows to update with API call status
for attr in ent_attrs.keys():
if is_gs_path(attr, ent_attrs[attr]) and is_migratable_extension(
attr, ent_attrs[attr]): # this is a gs:// path
original_path = ent_attrs[attr]
if is_in_bucket_list(
original_path, bucket_list=None
): # this is a path we think we want to update
new_path, map_key, fail_reason = get_replacement_path(
original_path, mapping)
gs_paths[attr] = original_path
if new_path:
updated_attr = fapi._attr_set(
attr, new_path) # format the update
attrs_list.append(
updated_attr) # what we have replacements for
inds.append(len(df_paths))
df_paths = df_paths.append(
{
'entity_name': ent_name,
'entity_type': ent_type,
'attribute': attr,
'original_path': original_path,
'new_path': new_path,
'map_key': map_key,
'fail_reason': fail_reason,
'file_type': original_path.split('.')[-1]
},
ignore_index=True)
if len(attrs_list) > 0:
if do_replacement:
# DO THE REPLACEMENT
response = fapi.update_entity(workspace_project,
workspace_name, ent_type,
ent_name, attrs_list)
status_code = response.status_code
if status_code != 200:
print(
f'ERROR {status_code} updating {ent_name} with {str(attrs_list)} - {response.text}'
)
else:
status_code = 0
df_paths.loc[inds, 'update_status'] = status_code
summarize_results(df_paths)
return df_paths
