async def ps(remote, output_format, extend, all=False, tags=[], use_ssl=False):
"Show runs in progress, or every tracked run (--all), or with a particular tag (--tag)."
with server(remote, use_ssl) as serv:
with output_format(extend) as formatter:
resp = await serv.GetRuns(RunListRequest(all=all, tags=tags))
for run in resp.runs.runs:
formatter(run)
async def load(remote, samplesheet, run_id=None, use_ssl=False):
"Load a sample sheet to be attached to a run, or to the next run that is started."
try:
if '.csv' in samplesheet:
with open(samplesheet, 'r') as file:
ss = load_from_csv(file)
elif '.tsv' in samplesheet or '.txt' in samplesheet:
with open(samplesheet, 'r') as file:
ss = load_from_csv(file, delimiter='\t')
elif '.xls' in samplesheet:
with open(samplesheet, 'rb') as file:
ss = load_from_excel(file)
except FileNotFoundError:
click.echo(f"File '{samplesheet}' not found.")
return 2
except ValueError as e:
click.echo(e, err=True)
except ImportError:
click.echo(f"ERROR: OpenPyXL not installed; Excel files ({samplesheet}) can't be read. Use pip to install OpenPyXL.", err=True)
else:
with server(*remote) as serv:
req = RunAttachRequest(sheet=ss)
if isinstance(run_id, int):
req.id = run_id
elif run_id:
req.name = run_id
resp = await serv.AttachSheetToRun(req)
if resp.error:
click.echo(resp.error.err_message, err=True)
return 1
else:
click.echo(f"{samplesheet} loaded successfully.")
async def tag_runner(remote, run_id, tags=[], untag=False, use_ssl=False):
with server(remote, use_ssl) as serv:
req = RunRequest()
if isinstance(run_id, str):
req.name = run_id
else:
req.id = run_id
resp = await serv.GetRunInfo(req)
if resp.HasField('error'):
click.echo(f"ERROR: {resp.error.err_message}", err=True)
quit(1)
else:
run_id = resp.run.id
return await serv.Tag(TagRequest(id=run_id, tags=tags, untag=untag))
async def info(remote, output_format, run_id, use_ssl=False):
"Return information about a run, historical or in progress."
with server(remote, use_ssl) as serv:
with output_format(extend=True) as formatter:
req = RunRequest()
if isinstance(run_id, str):
req.name = run_id
else:
req.id = run_id
resp = await serv.GetRunInfo(req)
if resp.HasField('error'):
click.echo(f"ERROR: {resp.error.err_message}", err=True)
quit(1)
else:
formatter(resp.run)
async def list_run_runner(all, tags):
with server(current_app.config['config_file']) as serv:
return await serv.GetRuns(RunListRequest(all=True, tags=tags))
async def run_getter(run_id):
with server(current_app.config['config_file']) as serv:
return await serv.GetRunInfo(RunRequest(id=run_id))
async def attach_runner(run_id, message):
with server(current_app.config['config_file']) as serv:
return await serv.AttachSheetToRun(
RunAttachRequest(name=run_id, sheet=message))
async def get_run(run_id):
config = current_app.config['config_file']
with server(config) as serv:
return await serv.GetRunInfo(RunRequest(id=run_id))
async def list_run_runner():
config = current_app.config['config_file']
with server(config) as serv:
return await serv.GetRuns(RunListRequest(all=True))
def test_server(self, mock_conf, mock_chan):
from porerefiner.protocols.porerefiner.rpc.porerefiner_grpc import PoreRefinerStub
with cli_utils.server() as serv:
self.assertIsInstance(serv, PoreRefinerStub)
mock_chan.assert_called()
mock_chan.closed.assert_called()