From Ido.Tamir@vbcf.ac.at Tue Aug 30 11:14:49 2016 From: "Tamir,Ido" To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] my.galaxy/toolshed bioblend or install_tool_shed_tools swallows toolshed Date: Tue, 30 Aug 2016 15:14:27 +0000 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============3354078357107104404==" --===============3354078357107104404== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi, a) short version: instead of: http://gecko.imp.univie.ac.at/galtools/api/repositories/get_ordered_installab= le_revisions?owner=3Ditme&name=3Dshrnaseqw the tool makes a request to: http://gecko.imp.univie.ac.at/api/repositories/get_ordered_installable_revisi= ons?owner=3Ditme&name=3Dshrnaseqw (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 kn= ow of ephemeris but don=E2=80=99t 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 =E2=80=9Cgaltools=E2=80=9D par= t. But the url is stored correctly in json, and I can get the appropriate respon= se when I specify the url in a browser: http://gecko.imp.univie.ac.at/galtools/api/repositories/get_ordered_installab= le_revisions?owner=3Ditme&name=3Dshrnaseqw =3D> ["f663fded0c69", "4aeaa49154f8"] thank you very much for your input, ido ansible log: ok: [localhost] =3D> (item=3D{u'owner': u'itme', u'tool_shed_url': u'gecko.im= p.univie.ac.at/galtools', u'tool_panel_section_id': u'ngs_rna', u'name': u'sh= rnaseqw'}) =3D> {"changed": false, "cmd": ["/groups/vbcf-ngs/wfsys/galaxy/gal= axy/.venv/bin/python", "install_tool_shed_tools.py", "-y", "name: shrnaseqw\n= owner: itme\ntool_panel_section_id: ngs_rna\ntool_shed_url: gecko.imp.univie.= ac.at/galtools\n", "-a", "7e7c8ec27a0a99acee883d2beea8a60b", "-g", "http://12= 7.0.0.1:9098/"], "delta": "0:00:00.820941", "end": "2016-08-30 16:55:58.86997= 7", "failed": false, "failed_when_result": false, "invocation": {"module_args= ": {"_raw_params": "/groups/vbcf-ngs/wfsys/galaxy/galaxy/.venv/bin/python ins= tall_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 7e7c8ec27= a0a99acee883d2beea8a60b -g http://127.0.0.1:9098/", "_uses_shell": false, "ch= dir": "/groups/vbcf-ngs/wfsys/galaxy/galaxy", "creates": null, "executable": = null, "removes": null, "warn": true}, "module_name": "command"}, "item": {"na= me": "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 \"ins= tall_tool_shed_tools.py\", line 652, in \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 =3D Client._get(self= , url=3Durl, params=3Dparams)\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: '\\r\\n404 Not Found\\r\\n<= body bgcolor=3D\"white\">\\r\\n

404 Not Found

\\r\\n<= hr>
nginx/1.2.1
\\r\\n\\r\\n\\r\\n', 0 attempts = left: None", "stdout": "", "stdout_lines": [], "warnings": []} nginx: =3D=3D> error.log <=3D=3D 2016/08/30 16:47:54 [error] 833#0: *442173 open() "/etc/nginx/html/api/reposi= tories/get_ordered_installable_revisions" failed (2: No such file or director= y), client: 10.42.160.35, server: gecko, request: "GET /api/repositories/get_= ordered_installable_revisions?owner=3Ditme&name=3Dshrnaseqw HTTP/1.1", host: = "gecko.imp.univie.ac.at" =3D=3D> access.log <=3D=3D 10.42.160.35 - - [30/Aug/2016:16:47:54 +0200] "GET /api/repositories/get_orde= red_installable_revisions?owner=3Ditme&name=3Dshrnaseqw HTTP/1.1" 404 142 "-"= "python-requests/2.8.1=E2=80=9D =E2=80=A6 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=3Ditme&name=3Dshrnaseqw HTTP/1.1" 20= 0 43 "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:48.0) Gecko/201001= 01 Firefox/48.0" --===============3354078357107104404==--