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EGA-archive / ega-download-client

A Python-based EGA download client
Apache License 2.0
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Cannot connect to server #204

Closed clai725 closed 1 year ago

clai725 commented 1 year ago

Unable to connect to server to download dataset

I am using a university computing cluster and university storage space to download the dataset I've been granted. After I install pip3 in the computing cluster space I am unable to connect to the server using the command pyega3 -cf CREDENTIALSFILE datasets. My university computing cluster should be able to connect to any server abroad. I work in the States

Used python3

Code after $ pyega3 -cf CREDENTIALSFILE datasets Traceback (most recent call last): File "/home/users/clai725/.local/lib/python3.6/site-packages/requests/adapters.py", line 450, in send timeout=timeout File "/home/users/clai725/.local/lib/python3.6/site-packages/urllib3/connectionpool.py", line 799, in urlopen method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2] File "/home/users/clai725/.local/lib/python3.6/site-packages/urllib3/util/retry.py", line 592, in increment raise MaxRetryError(_pool, url, error or ResponseError(cause)) urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='ega.ebi.ac.uk', port=8052): Max retries exceeded with url: /elixir/data/metadata/datasets (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f7c458fc9b0>: Failed to establish a new connection: [Errno 111] Connection refused',))

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/users/clai725/.local/bin/pyega3", line 8, in sys.exit(main()) File "/home/users/clai725/.local/lib/python3.6/site-packages/pyega3/pyega3.py", line 647, in main reply = api_list_authorized_datasets(token) File "/home/users/clai725/.local/lib/python3.6/site-packages/pyega3/pyega3.py", line 162, in api_list_authorized_datasets r = requests.get(url, headers=headers) File "/home/users/clai725/.local/lib/python3.6/site-packages/requests/api.py", line 75, in get return request('get', url, params=params, kwargs) File "/home/users/clai725/.local/lib/python3.6/site-packages/requests/api.py", line 61, in request return session.request(method=method, url=url, kwargs) File "/home/users/clai725/.local/lib/python3.6/site-packages/requests/sessions.py", line 529, in request resp = self.send(prep, send_kwargs) File "/home/users/clai725/.local/lib/python3.6/site-packages/requests/sessions.py", line 645, in send r = adapter.send(request, kwargs) File "/home/users/clai725/.local/lib/python3.6/site-packages/requests/adapters.py", line 519, in send raise ConnectionError(e, request=request) requests.exceptions.ConnectionError: HTTPSConnectionPool(host='ega.ebi.ac.uk', port=8052): Max retries exceeded with url: /elixir/data/metadata/datasets (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f7c458fc9b0>: Failed to establish a new connection: [Errno 111] Connection refused',)

sjparsa commented 1 year ago

I am also experiencing this issue has any solution been found?

CsabaHalmagyi commented 1 year ago

Hi @clai725, Thank you for contacting us. You are using an older version of the pyega3 client that is trying to connect to our old data api (which was retired in March this year). If you upgrade the client this issue should be solved. Regards, Csaba

clai725 commented 1 year ago

How do I upgrade the client?

Sent from my iPhone

On Aug 24, 2023, at 6:28 AM, Csaba Halmagyi @.***> wrote:



Hi @clai725https://github.com/clai725, Thank you for contacting us. You are using an older version of the pyega3 client that is trying to connect to our old data api (which was retired in March this year). If you upgrade the client this issue should be solved. Regards, Csaba

— Reply to this email directly, view it on GitHubhttps://github.com/EGA-archive/ega-download-client/issues/204#issuecomment-1691677548, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BB5U2U7NLXWNFP2F7PM7L63XW5JHJANCNFSM6AAAAAA3QXMMR4. You are receiving this because you were mentioned.Message ID: @.***>

clai725 commented 1 year ago

pip3 install pyega3==5.0.2

Defaulting to user installation because normal site-packages is not writeable

Collecting pyega3==5.0.2

Using cached pyega3-5.0.2.tar.gz (42 kB)

Preparing metadata (setup.py) ... done

Collecting requests==2.26.0

Using cached requests-2.26.0-py2.py3-none-any.whl (62 kB)

Collecting tqdm==4.19.6

Using cached tqdm-4.19.6-py2.py3-none-any.whl (52 kB)

Collecting htsget==0.2.5

Using cached htsget-0.2.5.tar.gz (29 kB)

Preparing metadata (setup.py) ... error

ERROR: Command errored out with exit status 1:

command: /share/software/user/open/python/3.6.1/bin/python3.6 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-8odvahxb/htsget_f5c9dc82faf34574afc64f5bd2df459e/setup.py'"'"'; file='"'"'/tmp/pip-install-8odvahxb/htsget_f5c9dc82faf34574afc64f5bd2df459e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-v0j5hwfn

   cwd: /tmp/pip-install-8odvahxb/htsget_f5c9dc82faf34574afc64f5bd2df459e/

Complete output (22 lines):

Traceback (most recent call last):

File "<string>", line 1, in <module>

File "/tmp/pip-install-8odvahxb/htsget_f5c9dc82faf34574afc64f5bd2df459e/setup.py", line 43, in <module>

  use_scm_version={"write_to": "htsget/_version.py"},

File "/share/software/user/open/python/3.6.1/lib/python3.6/site-packages/setuptools/__init__.py", line 129, in setup

  return distutils.core.setup(**attrs)

File "/share/software/user/open/python/3.6.1/lib/python3.6/distutils/core.py", line 108, in setup

  _setup_distribution = dist = klass(attrs)

File "/share/software/user/open/python/3.6.1/lib/python3.6/site-packages/setuptools/dist.py", line 370, in __init__

  k: v for k, v in attrs.items()

File "/share/software/user/open/python/3.6.1/lib/python3.6/distutils/dist.py", line 281, in __init__

  self.finalize_options()

File "/share/software/user/open/python/3.6.1/lib/python3.6/site-packages/setuptools/dist.py", line 529, in finalize_options

  ep.load()(self, ep.name, value)

File "/share/software/user/open/python/3.6.1/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2318, in load

  return self.resolve()

File "/share/software/user/open/python/3.6.1/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2324, in resolve

  module = __import__(self.module_name, fromlist=['__name__'], level=0)

File "/tmp/pip-install-8odvahxb/htsget_f5c9dc82faf34574afc64f5bd2df459e/.eggs/setuptools_scm-7.1.0-py3.6.egg/setuptools_scm/__init__.py", line 5

  from __future__ import annotations

  ^

SyntaxError: future feature annotations is not defined

WARNING: Discarding https://files.pythonhosted.org/packages/99/23/dedd2de16464cff36870019c7894cdbae83f121ab479121ababbef2add48/htsget-0.2.5.tar.gz#sha256=d383dc36f699bd921f760f5500c8ed251e5f8358a7cc219c6c89c35d103e8045 (from https://pypi.org/simple/htsget/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

ERROR: Could not find a version that satisfies the requirement htsget==0.2.5 (from pyega3) (from versions: 0.1.0a1, 0.1.0a2, 0.1.0a3, 0.1.0a4, 0.1.0a5, 0.1.0, 0.1.1, 0.1.2, 0.2.0, 0.2.1, 0.2.2, 0.2.3, 0.2.4, 0.2.5, 0.2.6)

ERROR: No matching distribution found for htsget==0.2.5

From: Christine Shyrue Lai Sent: Thursday, August 24, 2023 8:54 AM To: EGA-archive/ega-download-client @.***> Subject: Re: [EGA-archive/ega-download-client] Cannot connect to server (Issue #204)

How do I upgrade the client?

Sent from my iPhone

On Aug 24, 2023, at 6:28 AM, Csaba Halmagyi @.***> wrote:



Hi @clai725https://github.com/clai725, Thank you for contacting us. You are using an older version of the pyega3 client that is trying to connect to our old data api (which was retired in March this year). If you upgrade the client this issue should be solved. Regards, Csaba

— Reply to this email directly, view it on GitHubhttps://github.com/EGA-archive/ega-download-client/issues/204#issuecomment-1691677548, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BB5U2U7NLXWNFP2F7PM7L63XW5JHJANCNFSM6AAAAAA3QXMMR4. You are receiving this because you were mentioned.Message ID: @.***>