galaxy

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Files

T

mvdbeek 64e74b8b48 Tighten TRS url check

Fixes
https://sentry.galaxyproject.org/share/issue/5b8d495edd6545278d4d93d0ed69ac3a/:
```
Message
Uncaught exception in exposed API method:
Stack Trace

Newest

gaierror: [Errno -2] Name or service not known
  File "urllib3/connection.py", line 174, in _new_conn
    conn = connection.create_connection(
  File "urllib3/util/connection.py", line 72, in create_connection
    for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
  File "socket.py", line 962, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7f8e35406450>: Failed to establish a new connection: [Errno -2] Name or service not known
  File "urllib3/connectionpool.py", line 715, in urlopen
    httplib_response = self._make_request(
  File "urllib3/connectionpool.py", line 416, in _make_request
    conn.request(method, url, **httplib_request_kw)
  File "urllib3/connection.py", line 244, in request
    super(HTTPConnection, self).request(method, url, body=body, headers=headers)
  File "http/client.py", line 1286, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "http/client.py", line 1332, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "http/client.py", line 1281, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "http/client.py", line 1041, in _send_output
    self.send(msg)
  File "http/client.py", line 979, in send
    self.connect()
  File "urllib3/connection.py", line 205, in connect
    conn = self._new_conn()
  File "urllib3/connection.py", line 186, in _new_conn
    raise NewConnectionError(
MaxRetryError: HTTPConnectionPool(host='https', port=80): Max retries exceeded with url: //training.galaxyproject.org/training-material//api/ga4gh/trs/v2/tools/variant-analysis-microbial-variants/versions/microbial_variant_calling/GALAXY/descriptor (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f8e35406450>: Failed to establish a new connection: [Errno -2] Name or service not known'))
  File "requests/adapters.py", line 486, in send
    resp = conn.urlopen(
  File "urllib3/connectionpool.py", line 799, in urlopen
    retries = retries.increment(
  File "urllib3/util/retry.py", line 592, in increment
    raise MaxRetryError(_pool, url, error or ResponseError(cause))
ConnectionError: HTTPConnectionPool(host='https', port=80): Max retries exceeded with url: //training.galaxyproject.org/training-material//api/ga4gh/trs/v2/tools/variant-analysis-microbial-variants/versions/microbial_variant_calling/GALAXY/descriptor (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f8e35406450>: Failed to establish a new connection: [Errno -2] Name or service not known'))
  File "galaxy/web/framework/decorators.py", line 346, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/api/workflows.py", line 261, in create
    archive_data = server.get_version_descriptor(trs_tool_id, trs_version_id)
  File "galaxy/workflow/trs_proxy.py", line 115, in get_version_descriptor
    return self._get(trs_api_url)["content"]
  File "galaxy/workflow/trs_proxy.py", line 126, in _get
    response = requests.get(url, params=params, timeout=DEFAULT_SOCKET_TIMEOUT)
  File "galaxy/util/requests.py", line 29, in wrapper
    rval = f(*args, **kwargs)
  File "requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "requests/sessions.py", line 589, in request
    resp = self.send(prep, **send_kwargs)
  File "requests/sessions.py", line 703, in send
    r = adapter.send(request, **kwargs)
  File "requests/adapters.py", line 519, in send
    raise ConnectionError(e, request=request)
```
which happened for https://usegalaxy.org/workflows/trs_import?run_form=true&trs_url=http%3A%2F%2Flocalhost%3A4000%2F%2Ftraining-material%2F%2Fapi%2Fga4gh%2Ftrs%2Fv2%2Ftools%2Fvariant-analysis-microbial-variants%2Fversions%2Fmicrobial_variant_calling"

2024-09-18 10:31:23 +02:00

__init__.py

Implement workflow scheduling 'plugin' framework.

2014-11-13 13:47:38 -05:00

test_extract_summary.py

Replace `unittest.TestCase` with pytest-based partial re-implementation

2022-09-27 03:34:58 +01:00

test_modules.py

Allow DCE as outer input to to_cwl

2024-06-07 17:29:07 +02:00

test_refactor_models.py

.dict() -> .model_dump()