% gpas download --environment dev --rename --mapping-csv E-39dc5633.mapping.csv --out-dir ~/Desktop/oot --file-types fasta tests/test-data/token.json
Querying status for 4 sample(s): 100%|█████████████████████████████████████| 4/4
INFO: Fetching file types ['fasta']
Downloading 4 files for 4 sample(s): 0%| | 0/4Traceback (most recent call last):
File "/Users/bede/Research/Git/gpas-cli/src/gpas/lib.py", line 246, in download_async
return [
File "/Users/bede/Research/Git/gpas-cli/src/gpas/lib.py", line 247, in <listcomp>
await f
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/asyncio/tasks.py", line 571, in _wait_for_one
return f.result() # May raise f.exception().
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/site-packages/tenacity/_asyncio.py", line 86, in async_wrapped
return await fn(*args, **kwargs)
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/site-packages/tenacity/_asyncio.py", line 48, in __call__
do = self.iter(retry_state=retry_state)
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/site-packages/tenacity/__init__.py", line 351, in iter
return fut.result()
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/concurrent/futures/_base.py", line 451, in result
return self.__get_result()
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
raise self._exception
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/site-packages/tenacity/_asyncio.py", line 51, in __call__
result = await fn(*args, **kwargs)
File "/Users/bede/Research/Git/gpas-cli/src/gpas/lib.py", line 284, in download_single_async
update_fasta_header(
File "/Users/bede/Research/Git/gpas-cli/src/gpas/lib.py", line 116, in update_fasta_header
with gzip.open(path, "rt") as fh:
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/gzip.py", line 174, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '00c5bc2d-c95e-1b19-4053-0ae49b5d69a0.fasta.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/bede/miniconda3/envs/gpas-cli-dev/bin/gpas", line 8, in <module>
sys.exit(main())
File "/Users/bede/Research/Git/gpas-cli/src/gpas/cli.py", line 271, in main
defopt.run(
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/site-packages/defopt.py", line 356, in run
return call()
File "/Users/bede/Research/Git/gpas-cli/src/gpas/cli.py", line 259, in download
asyncio.run(
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/asyncio/runners.py", line 44, in run
return loop.run_until_complete(main)
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/asyncio/base_events.py", line 649, in run_until_complete
return future.result()
File "/Users/bede/Research/Git/gpas-cli/src/gpas/lib.py", line 229, in download_async
async with httpx.AsyncClient(transport=transport, timeout=120) as client:
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/site-packages/httpx/_client.py", line 2003, in __aexit__
await self._transport.__aexit__(exc_type, exc_value, traceback)
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/site-packages/httpx/_transports/default.py", line 332, in __aexit__
await self._pool.__aexit__(exc_type, exc_value, traceback)
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/site-packages/httpcore/_async/connection_pool.py", line 326, in __aexit__
await self.aclose()
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/site-packages/httpcore/_async/connection_pool.py", line 312, in aclose
raise RuntimeError(
RuntimeError: The connection pool was closed while 2 HTTP requests/responses were still in-flight.
Downloading 4 files for 4 sample(s): 0%| | 0/4
ERROR: Task exception was never retrieved
future: <Task finished name='Task-16' coro=<download_single_async() done, defined at /Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/site-packages/tenacity/_asyncio.py:84> exception=FileNotFoundError(2, 'No such file or directory')>
Traceback (most recent call last):
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/site-packages/tenacity/_asyncio.py", line 86, in async_wrapped
return await fn(*args, **kwargs)
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/site-packages/tenacity/_asyncio.py", line 48, in __call__
do = self.iter(retry_state=retry_state)
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/site-packages/tenacity/__init__.py", line 351, in iter
return fut.result()
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/concurrent/futures/_base.py", line 451, in result
return self.__get_result()
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
raise self._exception
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/site-packages/tenacity/_asyncio.py", line 51, in __call__
result = await fn(*args, **kwargs)
File "/Users/bede/Research/Git/gpas-cli/src/gpas/lib.py", line 284, in download_single_async
update_fasta_header(
File "/Users/bede/Research/Git/gpas-cli/src/gpas/lib.py", line 116, in update_fasta_header
with gzip.open(path, "rt") as fh:
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/Users/bede/miniconda3/envs/gpas-cli-dev/lib/python3.10/gzip.py", line 174, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '0537ce51-866e-a6b9-0601-9c775fd74fb3.fasta.gz'
(gpas-cli-dev) bede@zizzle gpas-cli %
bede
commented
1 year ago