Re: [galaxy-dev] my.galaxy/toolshed bioblend or install_tool_shed_tools swallows toolshed
It only works when specifying the url like this (http + trailing slash) otherwise urljoin removes the subdir: 'http://server/subdir/' and I use ephemeris thank you very much, ido
On 30 Aug 2016, at 17:55, Marius van den Beek <m.vandenbeek@gmail.com> wrote:
Hi Ido,
please use ephemeris, it’s as easy as it gets: pip install ephemeris shed-install -g <galaxy_url> -a <admin_key> -t <tool_list_file>. The install_tool_shed_tools.py is deprecated and will not work anymore. That said, we haven’t tested installing from toolshed on subdirectories, it’s entirely possible that there is a problem. I will have a look and let you know.
Best, Marius
On 30 August 2016 at 17:14, Tamir,Ido <Ido.Tamir@vbcf.ac.at> wrote: Hi,
a) short version: instead of: http://gecko.imp.univie.ac.at/galtools/api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw
the tool makes a request to: http://gecko.imp.univie.ac.at/api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw
(i.e. galtools is missing)
b) long version:
my toolshed is running behind a proxy under: my.server/galtools
I use the script install_tool_shed_tools.py via galaxy-ansible-playbook (I know of ephemeris but don’t know how to use it yet).
Installing tools from the default toolshed works, but when I try to access my own tools I see in nxginx logs that the request from the script swallowed the “galtools” part.
But the url is stored correctly in json, and I can get the appropriate response when I specify the url in a browser:
=>
["f663fded0c69", "4aeaa49154f8"]
thank you very much for your input, ido
ansible log: ok: [localhost] => (item={u'owner': u'itme', u'tool_shed_url': u'gecko.imp.univie.ac.at/galtools', u'tool_panel_section_id': u'ngs_rna', u'name': u'shrnaseqw'}) => {"changed": false, "cmd": ["/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/bin/python", "install_tool_shed_tools.py", "-y", "name: shrnaseqw\nowner: itme\ntool_panel_section_id: ngs_rna\ntool_shed_url: gecko.imp.univie.ac.at/galtools\n", "-a", "7e7c8ec27a0a99acee883d2beea8a60b", "-g", "http://127.0.0.1:9098/"], "delta": "0:00:00.820941", "end": "2016-08-30 16:55:58.869977", "failed": false, "failed_when_result": false, "invocation": {"module_args": {"_raw_params": "/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/bin/python install_tool_shed_tools.py -y \"name: shrnaseqw\nowner: itme\ntool_panel_section_id: ngs_rna\ntool_shed_url: gecko.imp.univie.ac.at/galtools\n\" -a 7e7c8ec27a0a99acee883d2beea8a60b -g http://127.0.0.1:9098/", "_uses_shell": false, "chdir": "/groups/vbcf-ngs/wfsys/galaxy/galaxy", "creates": null, "executable": null, "removes": null, "warn": true}, "module_name": "command"}, "item": {"name": "shrnaseqw", "owner": "itme", "tool_panel_section_id": "ngs_rna", "tool_shed_url": "gecko.imp.univie.ac.at/galtools"}, "rc": 1, "start": "2016-08-30 16:55:58.049036", "stderr": "Traceback (most recent call last):\n File \"install_tool_shed_tools.py\", line 652, in <module>\n install_tools(options)\n File \"install_tool_shed_tools.py\", line 590, in install_tools\n (tool['name'], tool['owner'])[-1])\n File \"/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/lib/python2.7/site-packages/bioblend/toolshed/repositories/__init__.py\", line 147, in get_ordered_installable_revisions\n r = Client._get(self, url=url, params=params)\n File \"/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/client.py\", line 147, in _get\n raise ConnectionError(msg)\nbioblend.galaxy.client.ConnectionError: GET: error 404: '<html>\\r\\n<head><title>404 Not Found</title></head>\\r\\n<body bgcolor=\"white\">\\r\\n<center><h1>404 Not Found</h1></center>\\r\\n<hr><center>nginx/1.2.1</center>\\r\\n</body>\\r\\n</html>\\r\\n', 0 attempts left: None", "stdout": "", "stdout_lines": [], "warnings": []}
nginx: ==> error.log <== 2016/08/30 16:47:54 [error] 833#0: *442173 open() "/etc/nginx/html/api/repositories/get_ordered_installable_revisions" failed (2: No such file or directory), client: 10.42.160.35, server: gecko, request: "GET /api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw HTTP/1.1", host: "gecko.imp.univie.ac.at"
==> access.log <== 10.42.160.35 - - [30/Aug/2016:16:47:54 +0200] "GET /api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw HTTP/1.1" 404 142 "-" "python-requests/2.8.1”
… this is how it should be:
10.42.160.51 - - [30/Aug/2016:16:52:54 +0200] "GET /galtools/api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw HTTP/1.1" 200 43 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:48.0) Gecko/20100101 Firefox/48.0"
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Hi Ido, your analysis is correct, this is what the BioBlend documentation prescribes: https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html#bioblend.... Cheers, Nicola ---- Tamir,Ido ha scritto ----
It only works when specifying the url like this (http + trailing slash) otherwise urljoin removes the subdir: 'http://server/subdir/'
and I use ephemeris
thank you very much, ido
On 30 Aug 2016, at 17:55, Marius van den Beek <m.vandenbeek@gmail.com> wrote:
Hi Ido,
please use ephemeris, it’s as easy as it gets: pip install ephemeris shed-install -g <galaxy_url> -a <admin_key> -t <tool_list_file>. The install_tool_shed_tools.py is deprecated and will not work anymore. That said, we haven’t tested installing from toolshed on subdirectories, it’s entirely possible that there is a problem. I will have a look and let you know.
Best, Marius
On 30 August 2016 at 17:14, Tamir,Ido <Ido.Tamir@vbcf.ac.at> wrote: Hi,
a) short version: instead of: http://gecko.imp.univie.ac.at/galtools/api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw
the tool makes a request to: http://gecko.imp.univie.ac.at/api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw
(i.e. galtools is missing)
b) long version:
my toolshed is running behind a proxy under: my.server/galtools
I use the script install_tool_shed_tools.py via galaxy-ansible-playbook (I know of ephemeris but don’t know how to use it yet).
Installing tools from the default toolshed works, but when I try to access my own tools I see in nxginx logs that the request from the script swallowed the “galtools” part.
But the url is stored correctly in json, and I can get the appropriate response when I specify the url in a browser:
=>
["f663fded0c69", "4aeaa49154f8"]
thank you very much for your input, ido
ansible log: ok: [localhost] => (item={u'owner': u'itme', u'tool_shed_url': u'gecko.imp.univie.ac.at/galtools', u'tool_panel_section_id': u'ngs_rna', u'name': u'shrnaseqw'}) => {"changed": false, "cmd": ["/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/bin/python", "install_tool_shed_tools.py", "-y", "name: shrnaseqw\nowner: itme\ntool_panel_section_id: ngs_rna\ntool_shed_url: gecko.imp.univie.ac.at/galtools\n", "-a", "7e7c8ec27a0a99acee883d2beea8a60b", "-g", "http://127.0.0.1:9098/"], "delta": "0:00:00.820941", "end": "2016-08-30 16:55:58.869977", "failed": false, "failed_when_result": false, "invocation": {"module_args": {"_raw_params": "/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/bin/python install_tool_shed_tools.py -y \"name: shrnaseqw\nowner: itme\ntool_panel_section_id: ngs_rna\ntool_shed_url: gecko.imp.univie.ac.at/galtools\n\" -a 7e7c8ec27a0a99acee883d2beea8a60b -g http://127.0.0.1:9098/", "_uses_shell": false, "chdir": "/groups/vbcf-ngs/wfsys/galaxy/galaxy", "creates": null, "executable": null, "removes": null, "warn": true}, "module_name": "command"}, "item": {"name": "shrnaseqw", "owner": "itme", "tool_panel_section_id": "ngs_rna", "tool_shed_url": "gecko.imp.univie.ac.at/galtools"}, "rc": 1, "start": "2016-08-30 16:55:58.049036", "stderr": "Traceback (most recent call last):\n File \"install_tool_shed_tools.py\", line 652, in <module>\n install_tools(options)\n File \"install_tool_shed_tools.py\", line 590, in install_tools\n (tool['name'], tool['owner'])[-1])\n File \"/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/lib/python2.7/site-packages/bioblend/toolshed/repositories/__init__.py\", line 147, in get_ordered_installable_revisions\n r = Client._get(self, url=url, params=params)\n File \"/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/lib/python2.7/site-packages/bioblend/galaxy/client.py\", line 147, in _get\n raise ConnectionError(msg)\nbioblend.galaxy.client.ConnectionError: GET: error 404: '<html>\\r\\n<head><title>404 Not Found</title></head>\\r\\n<body bgcolor=\"white\">\\r\\n<center><h1>404 Not Found</h1></center>\\r\\n<hr><center>nginx/1.2.1</center>\\r\\n</body>\\r\\n</html>\\r\\n', 0 attempts left: None", "stdout": "", "stdout_lines": [], "warnings": []}
nginx: ==> error.log <== 2016/08/30 16:47:54 [error] 833#0: *442173 open() "/etc/nginx/html/api/repositories/get_ordered_installable_revisions" failed (2: No such file or directory), client: 10.42.160.35, server: gecko, request: "GET /api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw HTTP/1.1", host: "gecko.imp.univie.ac.at"
==> access.log <== 10.42.160.35 - - [30/Aug/2016:16:47:54 +0200] "GET /api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw HTTP/1.1" 404 142 "-" "python-requests/2.8.1”
… this is how it should be:
10.42.160.51 - - [30/Aug/2016:16:52:54 +0200] "GET /galtools/api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw HTTP/1.1" 200 43 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:48.0) Gecko/20100101 Firefox/48.0"
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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I have also added the addition of a trailing slash to ephemeris. Thanks for reporting this. On Aug 31, 2016 7:43 PM, "Nicola Soranzo" <nsoranzo@tiscali.it> wrote:
Hi Ido, your analysis is correct, this is what the BioBlend documentation prescribes:
https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/ all.html#bioblend.galaxy.GalaxyInstance
Cheers, Nicola
---- Tamir,Ido ha scritto ----
It only works when specifying the url like this (http + trailing slash) otherwise urljoin removes the subdir: 'http://server/subdir/'
and I use ephemeris
thank you very much, ido
On 30 Aug 2016, at 17:55, Marius van den Beek <m.vandenbeek@gmail.com> wrote:
Hi Ido,
please use ephemeris, it’s as easy as it gets: pip install ephemeris shed-install -g <galaxy_url> -a <admin_key> -t <tool_list_file>. The install_tool_shed_tools.py is deprecated and will not work anymore. That said, we haven’t tested installing from toolshed on subdirectories, it’s entirely possible that there is a problem. I will have a look and let you know.
Best, Marius
On 30 August 2016 at 17:14, Tamir,Ido <Ido.Tamir@vbcf.ac.at> wrote: Hi,
a) short version: instead of: http://gecko.imp.univie.ac.at/galtools/api/repositories/get_ ordered_installable_revisions?owner=itme&name=shrnaseqw
the tool makes a request to: http://gecko.imp.univie.ac.at/api/repositories/get_ordered_ installable_revisions?owner=itme&name=shrnaseqw
(i.e. galtools is missing)
b) long version:
my toolshed is running behind a proxy under: my.server/galtools
I use the script install_tool_shed_tools.py via galaxy-ansible-playbook (I know of ephemeris but don’t know how to use it yet).
Installing tools from the default toolshed works, but when I try to access my own tools I see in nxginx logs that the request from the script swallowed the “galtools” part.
But the url is stored correctly in json, and I can get the appropriate response when I specify the url in a browser:
http://gecko.imp.univie.ac.at/galtools/api/repositories/get_ ordered_installable_revisions?owner=itme&name=shrnaseqw
=>
["f663fded0c69", "4aeaa49154f8"]
thank you very much for your input, ido
ansible log: ok: [localhost] => (item={u'owner': u'itme', u'tool_shed_url': u' gecko.imp.univie.ac.at/galtools', u'tool_panel_section_id': u'ngs_rna', u'name': u'shrnaseqw'}) => {"changed": false, "cmd": ["/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/bin/python", "install_tool_shed_tools.py", "-y", "name: shrnaseqw\nowner: itme\ntool_panel_section_id: ngs_rna\ntool_shed_url: gecko.imp.univie.ac.at/galtools\n", "-a", "7e7c8ec27a0a99acee883d2beea8a60b", "-g", "http://127.0.0.1:9098/"], "delta": "0:00:00.820941", "end": "2016-08-30 16:55:58.869977", "failed": false, "failed_when_result": false, "invocation": {"module_args": {"_raw_params": "/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/bin/python install_tool_shed_tools.py -y \"name: shrnaseqw\nowner: itme\ntool_panel_section_id: ngs_rna\ntool_shed_url: gecko.imp.univie.ac.at/galtools\n\" -a 7e7c8ec27a0a99acee883d2beea8a60b -g http://127.0.0.1:9098/", "_uses_shell": false, "chdir": "/groups/vbcf-ngs/wfsys/galaxy/galaxy", "creates": null, "executable": null, "removes": null, "warn": true}, "module_name": "command"}, "item": {"name": "shrnaseqw", "owner": "itme", "tool_panel_section_id": "ngs_rna", "tool_shed_url": "gecko.imp.univie.ac.at/galtools"}, "rc": 1, "start": "2016-08-30 16:55:58.049036", "stderr": "Traceback (most recent call last):\n File \"install_tool_shed_tools.py\", line 652, in <module>\n install_tools(options)\n File \"install_tool_shed_tools.py\", line 590, in install_tools\n (tool['name'], tool['owner'])[-1])\n File \"/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/lib/python2.7/site-packages/ bioblend/toolshed/repositories/__init__.py\", line 147, in get_ordered_installable_revisions\n r = Client._get(self, url=url, params=params)\n File \"/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/lib/ python2.7/site-packages/bioblend/galaxy/client.py\", line 147, in _get\n raise ConnectionError(msg)\nbioblend.galaxy.client.ConnectionError: GET: error 404: '<html>\\r\\n<head><title>404 Not Found</title></head>\\r\\n<body bgcolor=\"white\">\\r\\n<center><h1>404 Not Found</h1></center>\\r\\n<hr><center>nginx/1.2.1</center>\\ r\\n</body>\\r\\n</html>\\r\\n', 0 attempts left: None", "stdout": "", "stdout_lines": [], "warnings": []}
nginx: ==> error.log <== 2016/08/30 16:47:54 [error] 833#0: *442173 open() "/etc/nginx/html/api/ repositories/get_ordered_installable_revisions" failed (2: No such file or directory), client: 10.42.160.35, server: gecko, request: "GET /api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw HTTP/1.1", host: "gecko.imp.univie.ac.at"
==> access.log <== 10.42.160.35 - - [30/Aug/2016:16:47:54 +0200] "GET /api/repositories/get_ordered_installable_revisions?owner=itme&name=shrnaseqw HTTP/1.1" 404 142 "-" "python-requests/2.8.1”
… this is how it should be:
10.42.160.51 - - [30/Aug/2016:16:52:54 +0200] "GET /galtools/api/repositories/get_ordered_installable_ revisions?owner=itme&name=shrnaseqw HTTP/1.1" 200 43 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:48.0) Gecko/20100101 Firefox/48.0"
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
-
Marius van den Beek -
Nicola Soranzo -
Tamir,Ido