def logout():
pc = PilotClient()
if pc.is_logged_in():
pc.logout()
click.echo('You have been logged out.')
else:
click.echo('No user logged in, no logout necessary.')
def login(refresh_tokens, force, local_server, browser):
pc = PilotClient()
is_logged_in = pc.is_logged_in()
if is_logged_in and not force:
click.echo('You are already logged in.')
return
elif is_logged_in and force:
pc.logout()
pc.login(refresh_tokens=refresh_tokens,
no_local_server=not local_server,
no_browser=not browser,
force=force)
click.echo('You have been logged in.')
def list_command(test, output_json, limit):
# Should require login if there are publicly visible records
pc = PilotClient()
if not pc.is_logged_in():
click.echo('You are not logged in.')
return
search_authorizer = pc.get_authorizers()['search.api.globus.org']
sc = globus_sdk.SearchClient(authorizer=search_authorizer)
# TO DO: iterate instead of upping limit
search_results = sc.search(index_id=pc.get_index(test), q='*', limit=limit)
if output_json:
click.echo(json.dumps(search_results.data, indent=4))
return
fmt = '{:21.20}{:11.10}{:10.9}{:7.6}{:7.6}{:7.6}{}'
columns = [
('Title', lambda r: r['dc']['titles'][0]['title']),
('Data', lambda r: r['ncipilot']['data_type']),
('Dataframe', lambda r: r['ncipilot']['dataframe_type']),
('Rows', lambda r: str(r['field_metadata']['numrows'])),
('Cols', lambda r: str(r['field_metadata']['numcols'])),
('Size', get_size),
('Filename', get_identifier),
]
# Build row data
rows = []
for result in search_results['gmeta']:
content = result['content'][0]
if content.get('testing'):
content = content['testing']
row = []
for _, function in columns:
try:
row.append(function(content))
except Exception:
row.append('')
# raise
rows.append(row)
formatted_rows = [fmt.format(*r) for r in rows]
header = fmt.format(*[c[0] for c in columns])
output = '{}\n{}'.format(header, '\n'.join(formatted_rows))
click.echo(output)
def describe(path, test, output_json):
pc = PilotClient()
if not pc.is_logged_in():
click.echo('You are not logged in.')
return
old_entry = False
fname, dirname = os.path.basename(path), os.path.dirname(path)
entry = pc.get_search_entry(fname, dirname, test)
if not entry:
old_entry = True
entry = pc.get_search_entry(fname, dirname, old=True)
if not entry:
click.echo('Unable to find entry')
return
if output_json:
click.echo(json.dumps(entry, indent=4))
return
general_fmt = '{:21.20}{}'
general_columns = [
('Title', lambda r: r['dc']['titles'][0]['title']),
('Authors', lambda r: [c['creatorName'] for c in r['dc']['creators']]),
('Publisher', lambda r: r['dc']['publisher']),
('Subjects', lambda r: [s['subject'] for s in r['dc']['subjects']]),
('Dates', get_dates),
('Data', lambda r: r['ncipilot']['data_type']),
('Dataframe', lambda r: r['ncipilot']['dataframe_type']),
('Rows', lambda r: str(r['field_metadata']['numrows'])),
('Columns', lambda r: str(r['field_metadata']['numcols'])),
('Formats', lambda r: r['dc']['formats']),
('Version', lambda r: r['dc']['version']),
('Size', get_size),
('Filename', get_identifier),
('Description', lambda r: r['dc']['descriptions'][0]['description']),
]
def format_list(name, content):
return [general_fmt.format(name, content[0])] + \
[general_fmt.format('', item) for item in content[1:]]
def format_entry(name, content):
return [general_fmt.format(name, content)]
output = fetch_format(general_columns, entry, format_entry, format_list)
fmt = ('{:21.20}'
'{:8.7}{:7.6}{:5.4}{:12.11}{:7.6}'
'{:7.6}{:7.6}{:7.6}{:7.6}'
'{:8.7}{:8.7}{:8.7}'
)
field_metadata = [
('Column Name', 'name'),
('Type', 'type'),
('Count', 'count'),
('Freq', 'frequency'),
('Top', 'top'),
('Unique', 'unique'),
('Min', 'min'),
('Max', 'max'),
('Mean', 'mean'),
('Std', 'std'),
('25-PCTL', '25'),
('50-PCTL', '50'),
('75-PCTL', '75'),
]
names = [n for n, f in field_metadata]
keys = [f for n, f in field_metadata]
fm_output = []
try:
for field in entry['field_metadata']['field_definitions']:
f_metadata = [str(field.get(key, '')) for key in keys]
fm_output.append(fmt.format(*f_metadata))
field_metadata_names = fmt.format(*names)
output = '{}\n\nField Metadata\n{}\n{}'.format(output,
field_metadata_names,
'\n'.join(fm_output))
except KeyError:
output = '{}\n\nField Metadata\nNo Field Metadata'.format(output)
if not test:
sub = pc.get_subject_url(fname, dirname, test, old=old_entry)
qsub = urllib.parse.quote_plus(urllib.parse.quote_plus(sub))
portal_url = '{}{}'.format(PORTAL_DETAIL_PAGE_PREFIX, qsub)
other_data = [general_fmt.format('Subject', sub),
general_fmt.format(path, portal_url)]
output = '{}\n\nOther Data\n{}'.format(output, '\n'.join(other_data))
click.echo(output)