Comments (27)
maikknebel
commented on August 14, 2024
1
That worked so far. I'm going to prepare a clean installation to check if thats working too, might take a bit, i will post the result.
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bernt-matthias
commented on August 14, 2024
I observe the same here. When installing via the UI I often observe timeouts from the proxy. We are currently planning to increase the timeout.
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maikknebel
commented on August 14, 2024
After a few more tries... the error appears exactly after 60 seconds in the given task-step. The error message above shows that as well.
"start": "2019-05-28 09:30:47.820653"
"end": "2019-05-28 09:31:49.159597",
The gui installation runs fine for me - is requesting the status every few seconds from the api. Just the shed-install seems to get a timeout somewhere when using the ansible role.
Edit:
The error also occurres from the terminal, when i manually activate the virtualenv and call shed-install directly.
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mvdbeek
commented on August 14, 2024
Try bumping up the ephemeris version. 0.9.0 should contain galaxyproject/ephemeris@2499ba5
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bernt-matthias
commented on August 14, 2024
@maikknebel can you try to change this here:
ansible-galaxy-tools/tasks/tools.yml
Line 6 in 935fc8b
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bernt-matthias
commented on August 14, 2024
Hmm. In my case its actually a 502 Proxy Error.
The proxy server could not handle the request <em><a href=\"/api/tool_shed_repositories/new/install_repository_revision\">POST /api/tool_shed_repositories/new/install_repository_revision</a>
...
Reason: <strong>Error reading from remote server
Since the runtime in 0:01:01.485219 I guess this is apache's way to signal a timeout..? But might also be a misconfiguration of the Apache.
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maikknebel
commented on August 14, 2024
I tried version 0.8.0 and 0.9.0 both give me the following error:
fatal: [172.18.1.32]: FAILED! => {
"msg": "The conditional check ''installed successfully' in install_result.stderr' failed. The error was: error while evaluating conditional ('installed successfully' in install_result.stderr): Unable to look up a name or access an attribute in template string ({% if 'installed successfully' in install_result.stderr %} True {% else %} False {% endif %}).\nMake sure your variable name does not contain invalid characters like '-': argument of type 'StrictUndefined' is not iterable"
}
Coming from this block in tasks/instal_tool_lists.yml
- name: Install Tool Shed tools
command: '{{ galaxy_tools_base_dir }}/venv/bin/shed-install -y "{{ item | to_nice_yaml }}" -a "{{ galaxy_tools_api_key
}}" -g "{{ galaxy_tools_galaxy_instance_url }}"'
register: install_result
changed_when: "'installed successfully' in install_result.stderr"
failed_when: ('Error installing' in install_result.stderr) or ('Missing required' in install_result.stderr) or (instal
l_result.rc != 0)
ignore_errors: "{{ galaxy_tools_ignore_errors }}"
notify:
- restart galaxy
with_items:
- "{{ tools }}"
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maikknebel
commented on August 14, 2024
I had to replace the command, since it has changed from 0.4.0 to 0.8.0/0.9.0
command: '{{ galaxy_tools_base_dir }}/venv/bin/shed-install -y "{{ item | to_nice_yaml }}" -a "{{ galaxy_tools_api_key }}" -g "{{ galaxy_tools_galaxy_instance_url }}"'
with
command: '{{ galaxy_tools_base_dir }}/venv/bin/shed-tools install -y "{{ item | to_nice_yaml }}" -a "{{ galaxy_tools_api_key }}" -g "{{ galaxy_tools_galaxy_instance_url }}"'
The error stays the same. The role terminates after 60 seconds but the installation continiues.
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mvdbeek
commented on August 14, 2024
Is it really the exact same traceback ?
This
requests.exceptions.ConnectionError: ('Connection aborted.', BadStatusLine(\"''\",))
should really not appear anymore in 0.9.0
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maikknebel
commented on August 14, 2024
Most likely, some of the scripts in the trace have changed but i guess thats ok due to the changes in ephemeris. The error message and the last calls in the trace are the same.
failed: [172.18.1.32] (item={u'owner': u'devteam', u'tool_panel_section_label': u'BLAST', u'name': u'ncbi_blast_plus'}) => {
"changed": false,
"cmd": [
"/srv/galaxy/var/tmp//venv/bin/shed-tools",
"install",
"-y",
"name: ncbi_blast_plus\nowner: devteam\ntool_panel_section_label: BLAST\n",
"-a",
"1111111",
"-g",
"http://127.0.0.1:8080/"
],
"delta": "0:01:01.789697",
"end": "2019-05-28 14:33:59.683804",
"failed_when_result": true,
"invocation": {
"module_args": {
"_raw_params": "/srv/galaxy/var/tmp//venv/bin/shed-tools install -y \"name: ncbi_blast_plus\nowner: devteam\ntool_panel_section_label: BLAST\n\" -a \"11111111\" -g \"http://127.0.0.1:8080/\"",
"_uses_shell": false,
"argv": null,
"chdir": null,
"creates": null,
"executable": null,
"removes": null,
"stdin": null,
"warn": true
}
},
"item": {
"name": "ncbi_blast_plus",
"owner": "devteam",
"tool_panel_section_label": "BLAST"
},
"msg": "non-zero return code",
"rc": 1,
"start": "2019-05-28 14:32:57.894107",
"stderr": "Storing log file in: /tmp/ephemeris_tniPFt\r\n(1/1) Installing repository ncbi_blast_plus from devteam to section \"BLAST\" at revision e25d3acf6e68 (TRT: 0:00:00.669282)\r\nTraceback (most recent call last):\n File \"/srv/galaxy/var/tmp//venv/bin/shed-tools\", line 10, in <module>\n sys.exit(main())\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 937, in main\n install_tool_manager.install_repositories()\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 716, in install_repositories\n install_repository_revision(repository, self.tsc)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 517, in install_repository_revision\n response = tool_shed_client.install_repository_revision(**repository)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/bioblend/galaxy/toolshed/__init__.py\", line 146, in install_repository_revision\n return self._post(url=url, payload=payload)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/bioblend/galaxy/client.py\", line 152, in _post\n files_attached=files_attached)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/bioblend/galaxyclient.py\", line 137, in make_post_request\n timeout=self.timeout)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/api.py\", line 116, in post\n return request('post', url, data=data, json=json, **kwargs)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/api.py\", line 60, in request\n return session.request(method=method, url=url, **kwargs)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/sessions.py\", line 533, in request\n resp = self.send(prep, **send_kwargs)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/sessions.py\", line 646, in send\n r = adapter.send(request, **kwargs)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/adapters.py\", line 498, in send\n raise ConnectionError(err, request=request)\nrequests.exceptions.ConnectionError: ('Connection aborted.', BadStatusLine(\"''\",))",
"stderr_lines": [
"Storing log file in: /tmp/ephemeris_tniPFt",
"(1/1) Installing repository ncbi_blast_plus from devteam to section \"BLAST\" at revision e25d3acf6e68 (TRT: 0:00:00.669282)",
"Traceback (most recent call last):",
" File \"/srv/galaxy/var/tmp//venv/bin/shed-tools\", line 10, in <module>",
" sys.exit(main())",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 937, in main",
" install_tool_manager.install_repositories()",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 716, in install_repositories",
" install_repository_revision(repository, self.tsc)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 517, in install_repository_revision",
" response = tool_shed_client.install_repository_revision(**repository)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/bioblend/galaxy/toolshed/__init__.py\", line 146, in install_repository_revision",
" return self._post(url=url, payload=payload)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/bioblend/galaxy/client.py\", line 152, in _post",
" files_attached=files_attached)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/bioblend/galaxyclient.py\", line 137, in make_post_request",
" timeout=self.timeout)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/api.py\", line 116, in post",
" return request('post', url, data=data, json=json, **kwargs)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/api.py\", line 60, in request",
" return session.request(method=method, url=url, **kwargs)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/sessions.py\", line 533, in request",
" resp = self.send(prep, **send_kwargs)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/sessions.py\", line 646, in send",
" r = adapter.send(request, **kwargs)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/adapters.py\", line 498, in send",
" raise ConnectionError(err, request=request)",
"requests.exceptions.ConnectionError: ('Connection aborted.', BadStatusLine(\"''\",))"
],
"stdout": "",
"stdout_lines": []
}
...ignoring
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mvdbeek
commented on August 14, 2024
galaxyproject/ephemeris@0.9.0...master ... we released 0.9.0 not so long ago, but we need another release to get that commit ...
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mvdbeek
commented on August 14, 2024
There's a new package on pypi now, 0.10.0, that should hopefully work
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maikknebel
commented on August 14, 2024
With 0.10.0 its working. Thank you.
Should the playbook in ansible galaxy be updated or the admintraining to directly pull the playbook from git? To reflect the version change.
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bernt-matthias
commented on August 14, 2024
I guess so. Maybe just open a PR?
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maikknebel
commented on August 14, 2024
I just made a clean install to test everything again... not working :( After 60 seconds in TASK [galaxyproject.galaxy-tools : Install Tool Shed tools], the script fails with the BadStatusLine-Error. My guess is, that it has worked before, because conda has cached the dependency package in the previous tries.
While this error appears, htop shows the following line that with conda installing the dependencies of the package. In the admin interface it says "installing dependencies". The Installation Monitor says, dependency not installed and no error. The dependency overview says that blast is installed. After a few minutes, the conda-task is gone from htop and nothing changed. After a restart of galaxy, the conda task appears again with the same command but taking far longer (10-15 min) than before. Another conda task appeared after that is still running... not sure if thats ok but nothing changed in the installation status. There have been no errors in the galaxy console so far.
Update: After 25 minutes, the second conda task finished and "manage dependencies" lists blast with a red cross, dependency not installed. Manage tools says installed for the first, and installed but missing dependencies for the second and third.
First conda task
12398 galaxy 20 0 613M 505M 12500 D 17.2 8.5 0:58.31 /srv/galaxy/var/dependencies/_conda/bin/python /srv/galaxy/var/dependencies/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name [email protected] blast=2.7.1
Second conda task
12746 galaxy 21 1 577M 469M 12428 R 9.0 7.9 0:43.84 /srv/galaxy/var/dependencies/_conda/bin/python /srv/galaxy/var/dependencies/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __blast@_uv_ blast
TASK [galaxyproject.galaxy-tools : Install Tool Shed tools]
failed: [172.18.1.32] (item={u'owner': u'devteam', u'tool_panel_section_label': u'BLAST', u'name': u'ncbi_blast_plus'}) => {
"changed": false,
"cmd": [
"/srv/galaxy/var/tmp//venv/bin/shed-tools",
"install",
"-y",
"name: ncbi_blast_plus\nowner: devteam\ntool_panel_section_label: BLAST\n",
"-a",
"1111111111111111",
"-g",
"http://127.0.0.1:8080/"
],
"delta": "0:01:02.685348",
"end": "2019-06-04 05:45:55.272057",
"failed_when_result": true,
"invocation": {
"module_args": {
"_raw_params": "/srv/galaxy/var/tmp//venv/bin/shed-tools install -y \"name: ncbi_blast_plus\nowner: devteam\ntool_panel_section_label: BLAST\n\" -a \"11111111111111111111111\" -g \"http://127.0.0.1:8080/\"",
"_uses_shell": false,
"argv": null,
"chdir": null,
"creates": null,
"executable": null,
"removes": null,
"stdin": null,
"warn": true
}
},
"item": {
"name": "ncbi_blast_plus",
"owner": "devteam",
"tool_panel_section_label": "BLAST"
},
"msg": "non-zero return code",
"rc": 1,
"start": "2019-06-04 05:44:52.586709",
"stderr": "Storing log file in: /tmp/ephemeris_zAoFxM\r\n(1/1) Installing repository ncbi_blast_plus from devteam to section \"BLAST\" at revision e25d3acf6e68 (TRT: 0:00:01.542898)\r\nTraceback (most recent call last):\n File \"/srv/galaxy/var/tmp//venv/bin/shed-tools\", line 10, in <module>\n sys.exit(main())\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 546, in main\n **kwargs)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 160, in install_repositories\n result = self.install_repository_revision(repository, log)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 355, in install_repository_revision\n response = self.tool_shed_client.install_repository_revision(**repository)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/bioblend/galaxy/toolshed/__init__.py\", line 146, in install_repository_revision\n return self._post(url=url, payload=payload)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/bioblend/galaxy/client.py\", line 160, in _post\n files_attached=files_attached)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/bioblend/galaxyclient.py\", line 137, in make_post_request\n timeout=self.timeout)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/api.py\", line 116, in post\n return request('post', url, data=data, json=json, **kwargs)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/api.py\", line 60, in request\n return session.request(method=method, url=url, **kwargs)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/sessions.py\", line 533, in request\n resp = self.send(prep, **send_kwargs)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/sessions.py\", line 646, in send\n r = adapter.send(request, **kwargs)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/adapters.py\", line 498, in send\n raise ConnectionError(err, request=request)\nrequests.exceptions.ConnectionError: ('Connection aborted.', BadStatusLine(\"''\",))",
"stderr_lines": [
"Storing log file in: /tmp/ephemeris_zAoFxM",
"(1/1) Installing repository ncbi_blast_plus from devteam to section \"BLAST\" at revision e25d3acf6e68 (TRT: 0:00:01.542898)",
"Traceback (most recent call last):",
" File \"/srv/galaxy/var/tmp//venv/bin/shed-tools\", line 10, in <module>",
" sys.exit(main())",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 546, in main",
" **kwargs)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 160, in install_repositories",
" result = self.install_repository_revision(repository, log)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 355, in install_repository_revision",
" response = self.tool_shed_client.install_repository_revision(**repository)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/bioblend/galaxy/toolshed/__init__.py\", line 146, in install_repository_revision",
" return self._post(url=url, payload=payload)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/bioblend/galaxy/client.py\", line 160, in _post",
" files_attached=files_attached)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/bioblend/galaxyclient.py\", line 137, in make_post_request",
" timeout=self.timeout)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/api.py\", line 116, in post",
" return request('post', url, data=data, json=json, **kwargs)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/api.py\", line 60, in request",
" return session.request(method=method, url=url, **kwargs)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/sessions.py\", line 533, in request",
" resp = self.send(prep, **send_kwargs)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/sessions.py\", line 646, in send",
" r = adapter.send(request, **kwargs)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/requests/adapters.py\", line 498, in send",
" raise ConnectionError(err, request=request)",
"requests.exceptions.ConnectionError: ('Connection aborted.', BadStatusLine(\"''\",))"
],
"stdout": "",
"stdout_lines": []
}
...ignoring
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mvdbeek
commented on August 14, 2024
This is very strange, the line numbers in the traceback match 0.10.0, but the exception is explicitly wrapped in
try:
response = self.tool_shed_client.install_repository_revision(**repository)
...
except ConnectionError as e:
...
elif "504" in str(e) or 'Connection aborted' in str(e):
success = self.wait_for_install(repository=repository, log=log, timeout=3600)
that condition really should evaluate to true in your traceback.
Can you print out the ephemeris version before the install and provide an explicit log file with --log_file ? (/dev/stdout should work to get the log reported in ansible)
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mvdbeek
commented on August 14, 2024
ahhhhh! Wrong ConnectionError, it's the vanilla requests.exceptions.ConnectionError that bubbles up.
>>> import requests
>>> from bioblend.galaxy.client import ConnectionError
>>>
>>> try:
... raise requests.exceptions.ConnectionError('bla')
... except ConnectionError as e:
... print(str(e))
...
Traceback (most recent call last):
File "<stdin>", line 2, in <module>
requests.exceptions.ConnectionError: bla
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maikknebel
commented on August 14, 2024
This is printed by the playbook when the virtualenv is setup for the installation. Does that help? If not i will try to figure out how i can print the version of the packages in the virtualenv that is created/used by the playbook.
"Installing collected packages: six, urllib3, certifi, chardet, idna, requests, requests-toolbelt, PyYAML, boto, bioblend, futures, MarkupSafe, Jinja2, boltons, docutils, pyparsing, packaging, galaxy-lib, ephemeris",
"Successfully installed Jinja2-2.10.1 MarkupSafe-1.1.1 PyYAML-5.1 bioblend-0.10.0 boltons-19.1.0 boto-2.49.0 certifi-2019.3.9 chardet-3.0.4 docutils-0.14 ephemeris-0.10.0 futures-3.2.0 galaxy-lib-19.5.2 idna-2.8 packaging-19.0 pyparsing-2.4.0 requests-2.22.0 requests-toolbelt-0.9.1 six-1.12.0 urllib3-1.25.3"
],
"version": null,
"virtualenv": "/srv/galaxy/var/tmp//venv"
I pulled the role from git and changed the emphemeris version from 0.4.0 to 0.10.0 manually. Should i change the bioblend versions to the current release as well? Bioblend doesnt list19.01 as supported version yet.
Logfile shows only this line:
Storing log file in: /srv/galaxy/var/tmp//install.log
(1/1) Installing repository ncbi_blast_plus from devteam to section "BLAST" at revision e25d3acf6e68 (TRT: 0:00:00.974527)
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mvdbeek
commented on August 14, 2024
No that's not necessary, galaxyproject/ephemeris#134 will fix it.
fwiw, bioblend always supports all versions of Galaxy, it uses the API and the API should never change.
It's just that some functions or parameters may be missing.
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mvdbeek
commented on August 14, 2024
@maikknebel 0.10.1 is out that should work now.
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maikknebel
commented on August 14, 2024
The error has changed now, but is still there.
Installed versions in the virtualenv:
"Successfully installed Jinja2-2.10.1 MarkupSafe-1.1.1 PyYAML-5.1 bioblend-0.10.0 boltons-19.1.0 boto-2.49.0 certifi-2019.3.9 chardet-3.0.4 docutils-0.14 ephemeris-0.10.1 futures-3.2.0 galaxy-lib-19.5.2 idna-2.8 packaging-19.0 pyparsing-2.4.0 requests-2.22.0 requests-toolbelt-0.9.1 six-1.12.0 urllib3-1.25.3"
],
"version": null,
"virtualenv": "/srv/galaxy/var/tmp/venv"
Error-Message
failed: [172.18.1.32] (item={u'owner': u'devteam', u'tool_panel_section_label': u'BLAST', u'name': u'ncbi_blast_plus'}) => {
"changed": false,
"cmd": [
"/srv/galaxy/var/tmp/venv/bin/shed-tools",
"install",
"-y",
"name: ncbi_blast_plus\nowner: devteam\ntool_panel_section_label: BLAST\n",
"-a",
"11111111",
"-g",
"http://127.0.0.1:8080/"
],
"delta": "0:01:02.507261",
"end": "2019-06-04 10:58:06.309762",
"failed_when_result": true,
"invocation": {
"module_args": {
"_raw_params": "/srv/galaxy/var/tmp/venv/bin/shed-tools install -y \"name: ncbi_blast_plus\nowner: devteam\ntool_panel_section_label: BLAST\n\" -a \"11111111\" -g \"http://127.0.0.1:8080/\"",
"_uses_shell": false,
"argv": null,
"chdir": null,
"creates": null,
"executable": null,
"removes": null,
"stdin": null,
"warn": true
}
},
"item": {
"name": "ncbi_blast_plus",
"owner": "devteam",
"tool_panel_section_label": "BLAST"
},
"msg": "non-zero return code",
"rc": 1,
"start": "2019-06-04 10:57:03.802501",
"stderr": "Storing log file in: /tmp/ephemeris_dwhewP\r\n(1/1) Installing repository ncbi_blast_plus from devteam to section \"BLAST\" at revision e25d3acf6e68 (TRT: 0:00:01.304021)\r\nTraceback (most recent call last):\n File \"/srv/galaxy/var/tmp/venv/bin/shed-tools\", line 10, in <module>\n sys.exit(main())\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 547, in main\n **kwargs)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 161, in install_repositories\n result = self.install_repository_revision(repository, log)\n File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 373, in install_repository_revision\n if default_err_msg in e.body:\nAttributeError: 'ConnectionError' object has no attribute 'body'",
"stderr_lines": [
"Storing log file in: /tmp/ephemeris_dwhewP",
"(1/1) Installing repository ncbi_blast_plus from devteam to section \"BLAST\" at revision e25d3acf6e68 (TRT: 0:00:01.304021)",
"Traceback (most recent call last):",
" File \"/srv/galaxy/var/tmp/venv/bin/shed-tools\", line 10, in <module>",
" sys.exit(main())",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 547, in main",
" **kwargs)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 161, in install_repositories",
" result = self.install_repository_revision(repository, log)",
" File \"/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py\", line 373, in install_repository_revision",
" if default_err_msg in e.body:",
"AttributeError: 'ConnectionError' object has no attribute 'body'"
],
"stdout": "",
"stdout_lines": []
}
...ignoring
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mvdbeek
commented on August 14, 2024
arg ... could you just manually change
/srv/galaxy/var/tmp/venv/local/lib/python2.7/site-packages/ephemeris/shed_tools.py
on line 373 from if default_err_msg in e.body to if default_err_msg in str(e): and check that it work ?
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mvdbeek
commented on August 14, 2024
Alright, if that works I'll push out a new version.
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maikknebel
commented on August 14, 2024
Its working, thanks.
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mvdbeek
commented on August 14, 2024
0.10.2 is out, so I guess we can close this ?
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bernt-matthias
commented on August 14, 2024
Wondering if it would be an option to check for error 502 as well. This seems to be the error raised for time outs if apache is used as proxy.
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mvdbeek
commented on August 14, 2024
Feel free to add it to https://github.com/galaxyproject/ephemeris/blob/master/src/ephemeris/shed_tools.py#L379 -- we actually don't care about this too much, we should probably just start the install in a thread, we don't care about the return value.
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Related Issues (20)
- tool_panel_section_label isn't working, nor is tool_panel_section_id HOT 6
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- install_tool_shed_tools.py HOT 15
- manage_bootstrap_user.py command line parsing HOT 1
- tool_list file loading
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- dynamic and static include in restart_galaxy.yml handler HOT 1
- Tool labels
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