def list_workspaces():
try:
return sorted([
{
'accessLevel': workspace['accessLevel'],
'public': workspace['public'],
'namespace': workspace['workspace']['namespace'],
'name': workspace['workspace']['name'],
'bucket': workspace['workspace']['bucketName'],
'id': workspace['workspace']['workspaceId']
} for workspace in fc.list_workspaces().json()
], key=lambda x:(x['namespace'], x['name'])), 200
except:
print(traceback.format_exc())
all_workspaces = readvar(current_app.config, 'storage', 'cache', 'all_workspaces')
if all_workspaces is not None:
workspace_data = []
for ns, ws, in all_workspaces:
workspace = get_workspace_object(ns, ws).get_workspace_metadata()
workspace_data.append({
'accessLevel': workspace['accessLevel'],
'public': False,
'namespace': ns,
'name': ws,
'bucket': workspace['workspace']['bucketName'],
'id': workspace['workspace']['workspaceId']
})
return sorted(workspace_data, key=lambda x:(x['namespace'], x['name'])), 200
return {
'failed': True,
'reason': "The Firecloud api is currently offline, and there are no workspaces in the cache"
}, 500
def get_projects(namespaces=None, project_pattern=None):
"""Filter terra workspaces by namespaces and project_pattern.
Args:
namespaces ([str]): Optional, list of workspace `namespace` to match ex: 'anvil-datastorage'.
project_pattern (str): Optional, regexp to match workspace `name` ex: 'AnVIL_CCDG.*'.
Returns:
dict: keys ['accessLevel', 'public', 'workspace', 'workspaceSubmissionStats']
"""
workspaces = FAPI.list_workspaces()
workspaces = workspaces.json()
if namespaces:
workspaces = [
AttrDict(w) for w in workspaces
if w['workspace']['namespace'] in namespaces
]
if project_pattern:
workspaces = [
AttrDict(w) for w in workspaces
if re.match(project_pattern, w['workspace']['name'], re.IGNORECASE)
]
# normalize fields
for w in workspaces:
if 'project_files' not in w.workspace:
w.workspace.project_files = []
return workspaces
def test_list_workspaces(self):
"""Test list_workspaces()."""
r = fapi.list_workspaces()
print(r.status_code, r.content)
self.assertEqual(r.status_code, 200)
workspace_names = [w['workspace']['name'] for w in r.json()]
self.assertIn(self.workspace, workspace_names)
def get_workspaces(namespace):
# This is based on the fiss list_spaces function but only workspaces are returned
workspaces = api.list_workspaces()
api._check_response_code(workspaces, 200)
for space in workspaces.json():
if namespace == space['workspace']['namespace']:
yield space['workspace']['name']
def __init__(self):
self.user = os.getenv('OWNER_EMAIL')
self.terra_workspaces = fapi.list_workspaces().json()
if self.user.endswith(self.AOU_DOMAIN):
aou_api = os.getenv('RW_API_BASE_URL')
if not aou_api:
aou_api = self.AOU_PROD_API
# Use the All of Us API to get the human-readable workspace names. For All of Us workspaces,
# the Terra workspace metadata the workspace names are actually the AoU workspace ids.
aou_response = get_ipython().getoutput(f'''curl -H "Content-Type: application/json" \
-H "Authorization: Bearer $(gcloud auth print-access-token)" \
"{aou_api}" 2>/dev/null | jq .''')
self.aou_workspaces = json.loads(''.join(aou_response))['items']
else:
self.aou_workspaces = None
def export_workspaces(project, get_cost):
# call list workspaces
response = fapi.list_workspaces(
fields=
"workspace.namespace,workspace.name,workspace.createdBy,workspace.createdDate"
)
fapi._check_response_code(response, 200)
all_workspaces = response.json()
# limit the workspaces to the desired project
workspaces = [
ws['workspace'] for ws in all_workspaces
if ws['workspace']['namespace'] == project
]
print(f"Found {len(workspaces)} workspaces in Terra project {project}")
if get_cost:
print(f"Retrieving workspace bucket cost estimates")
ws_costs = {}
for ws in workspaces:
ws_costs[ws['name']] = get_storage_cost_estimate(
ws['name'], project, get_access_token())
# write to csv
csv_name = f"Terra_workspaces_{project}.csv"
with open(csv_name, "w") as csvout:
if get_cost:
# add header with attribute values to csv
csvout.write(
"workspace,created by,storage cost estimate,date created,link\n"
)
for ws in workspaces:
name_for_link = ws['name'].replace(" ", "%20")
csvout.write(
f"{ws['name']},{ws['createdBy']},{ws_costs[ws['name']]},{ws['createdDate']},https://app.terra.bio/#workspaces/{project}/{name_for_link}\n"
)
else:
# add header with attribute values to csv
csvout.write("workspace,created by,date created,link\n")
for ws in workspaces:
name_for_link = ws['name'].replace(" ", "%20")
csvout.write(
f"{ws['name']},{ws['createdBy']},{ws['createdDate']},https://app.terra.bio/#workspaces/{project}/{name_for_link}\n"
)
def create_workspaces_attributes_csv(workspace_project, verbose=False):
"""Getting all the workspaces attributes."""
# Assigning dictionary containing all workspaces
dict_of_all_workspaces = {}
# Assigning list that will combine keys from all attributes
csv_columns = []
# Getting List of workspaces json
response = fapi.list_workspaces(
fields="workspace.name, workspace.namespace, workspace.attributes")
workspaces = response.json()
# Looping through all workspaces
for workspace_json in workspaces:
# Getting attributes from workspaces in a certain project
if workspace_json["workspace"]["namespace"] == workspace_project:
workspace_name = workspace_json["workspace"]["name"]
attributes = get_attributes(workspace_json, workspace_name)
dict_of_all_workspaces[workspace_name] = attributes
# Adding keys to make a master attributes list
for key in attributes.keys():
if key not in csv_columns:
csv_columns.append(key)
# Looping through all attributes_values
for attributes_values in dict_of_all_workspaces.values():
attributes_list = list(attributes_values.keys())
# Finding which keys are not in the combine/master keys list
extra_columns = [
i for i in csv_columns + attributes_list
if i not in csv_columns or i not in attributes_list
]
# Looping through extra Keys and adding them as None Value to the attributes List
for extra_key in extra_columns:
attributes_values[extra_key] = None
# Assigning csv variable name
csv_filename = "attributes_for_AnVIL_workspaces.csv"
# Creating csv
create_csv(dict_of_all_workspaces, csv_filename, csv_columns)
def main(argv):
parser = argparse.ArgumentParser(
description=
'Export workspace storage cost estimates associated with the user to TSV'
)
parser.add_argument('--output', help='Output TSV path', required=True)
parser.add_argument('--access',
help='Workspace access levels',
choices=['owner', 'reader', 'writer'],
action='append')
args = parser.parse_args(argv)
workspaces = fapi.list_workspaces().json()
access = args.access
if access is None:
access = []
output = args.output
access_filter = set()
if 'reader' in access:
access_filter.add('READER')
if 'writer' in access:
access_filter.add('WRITER')
if 'owner' in access or len(access) == 0:
access_filter.add('PROJECT_OWNER')
with open(output, 'wt') as out:
out.write('namespace\tname\testimate\n')
for w in workspaces:
if w['accessLevel'] in access_filter:
namespace = w['workspace']['namespace']
name = w['workspace']['name']
headers = fapi._fiss_agent_header()
root_url = fapi.fcconfig.root_url
r = fapi.__SESSION.get(urljoin(
root_url,
f'workspaces/{namespace}/{name}/storageCostEstimate'),
headers=headers).json()
estimate = r['estimate']
out.write(f'{namespace}\t{name}\t{estimate}\n')
import firecloud.api as FAPI import logging import re from attrdict import AttrDict from dotenv import load_dotenv load_dotenv() print(FAPI.list_workspaces().json())
import firecloud.api as fapi
import re
from datetime import date
def sizeof_fmt(num, suffix='B'):
for unit in ['', 'Ki', 'Mi', 'Gi', 'Ti', 'Pi', 'Ei', 'Zi']:
if abs(num) < 1024.0:
return "%3.1f%s%s" % (num, unit, suffix)
num /= 1024.0
return "%.1f%s%s" % (num, 'Yi', suffix)
r = fapi.list_workspaces()
workspaceList = []
for workspace in r.json():
try:
thedate = (re.sub(
"-", ",", workspace['workspaceSubmissionStats']
['lastSuccessDate']).split("T")[0]).split(",")
if date(int(thedate[0]), int(thedate[1]), int(thedate[2])) < date(
2018, 8, 30):
continue
except KeyError:
continue
if workspace["public"] == False and workspace["workspace"][
"namespace"] == "broadtagteam" and (
workspace["accessLevel"] == "OWNER"
or workspace["accessLevel"] == "PROJECT_OWNER"):
workspaceList.append(workspace["workspace"]["name"])