Re: [galaxy-dev] Job submission failed
Hi Martin, I am in a debug mode and happy to share the config and logs file private more. thanks, Vipin On Mon, May 4, 2015 at 4:53 PM, Martin Čech wrote: > Hello Vipin, > > the request goes to index() method at > galaxy/lib/galaxy/webapps/galaxy/api/tools.py > > I also see in console the 403 Forbidden > https://galaxy.cbio.mskcc.org/api/tools/ when trying to upload. This is > probably connected with the upload problems some users were having with > your Oqtans instance (some files >50MB getting reliably stuck with the > "user not logged in" error - > https://www.dropbox.com/s/o072cludvcxg9qv/Screenshot%202015-05-04%2015.12.18.png?dl=0 > ). > > I tried multiple revisions of 15.03 including the latest but did not > succeed in reproducing this localy. > > Could you please show us the config and/or server log output. (you can do > so privately at galaxy-b...@bx.psu.edu or mar...@bx.psu.edu) > > Thanks > > Martin > > > On Mon, Apr 27, 2015 at 2:54 PM Vipin TS wrote: > >> Hi John, >> >> Still the problem exist. The codebase is in latest_15.03 revision. >> >> my instance is not behind a proxy server, I m confused about the 403 >> Forbidden error message with https://galaxy.cbio.mskcc.org/api/tools/ >> where is this request goes? >> >> Vipin >> >> >> On Fri, Apr 24, 2015 at 9:04 AM, John Chilton >> wrote: >> >>> I am pretty stumped by this - my next actions would be to upgrade to >>> the newest latest_15.03 in case this has been fixed. >>> >>> If that doesn't fix it I might look at your proxy configuration - is >>> there a proxy server sitting in front of Galaxy? It looks like upload >>> works on this server and I believe that is using the same endpoint >>> POST /api/tools. I don't know why upload would work but all other >>> tools fail - but one possibility is the proxy is blocking the request >>> if it doesn't look like an upload. >>> >>> -John >>> >>> On Tue, Apr 21, 2015 at 10:11 PM, Vipin TS wrote: >>> > Hi John, >>> > >>> > I am seeing an error in browser console when click on a tool link: >>> > POST https://galaxy.cbio.mskcc.org/api/tools 403 (Forbidden) >>> > >>> > " >>> > >>> > 403 Forbidden >>> > >>> > Forbidden >>> > You don't have permission to access /api/tools >>> > on this server. >>> > >>> > >>> > which points to the tool-jobs.js line #65, which is the error part of >>> the >>> > Utils.request function. >>> > Something related with authentication? >>> > >>> > Vipin >>> > >>> > On Tue, Apr 21, 2015 at 9:05 AM, John Chilton >>> wrote: >>> >> >>> >> Another question is are there any logs indicating issues on the server >>> >> side and can you open your web console and let us know if there are >>> >> any errors reported there on the client side (e.g. >>> >> https://developer.mozilla.org/en-US/docs/Tools/Web_Console). >>> >> >>> >> -John >>> >> >>> >> On Tue, Apr 21, 2015 at 3:45 AM, Hans-Rudolf Hotz wrote: >>> >> > Hi Vipin >>> >> > >>> >> > Is this a new problem you encounter since you have done the upgrade >>> to >>> >> > "latest_15.03"? If so, did you experience any troubles during the >>> >> > database >>> >> > schema upgrade to '128'? >>> >> > >>> >> > >>> >> > Regards, Hans-Rudolf >>> >> > >>> >> > >>> >> > On 04/20/2015 08:44 PM, Vipin TS wrote: >>> >> >> >>> >> >> Hi dev-team, >>> >> >> >>> >> >> >>> >> >> I am experiencing an issue with my production instance in >>> dispatching >>> >> >> the jobs. When I click on execute button, each tool page shows the >>> >> >> popup >>> >> >> error message as here: >>> >> >> Inline image 1 >>> >> >> I am not sure what is happening, not getting any single line of >>> error >>> >> >> message in log file. >>> >> >> >>> >> >> Here is the version I am using: >>> >> >> changeset: 17051:28113212 >>> >> >> branch: stable >>> >> >> date:Mon Mar 16 22:38:27 2015 -0400 >>> >> >> summary: Update tag latest_15.03 for changeset 9f40ff3e3fe1 >>> >> >> >>> >> >> any suggestions, Thank you! >>> >> >> >>> >> >> Vipin | Rätsch Lab >>> >> >> >>> >> >> >>> >> >> ___ >>> >> >> 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/ >>> > >>> > >>> >> >> ___ >> Please keep all
Re: [galaxy-dev] Job submission failed
Hello Vipin, the request goes to index() method at galaxy/lib/galaxy/webapps/galaxy/api/tools.py I also see in console the 403 Forbidden https://galaxy.cbio.mskcc.org/api/tools/ when trying to upload. This is probably connected with the upload problems some users were having with your Oqtans instance (some files >50MB getting reliably stuck with the "user not logged in" error - https://www.dropbox.com/s/o072cludvcxg9qv/Screenshot%202015-05-04%2015.12.18.png?dl=0 ). I tried multiple revisions of 15.03 including the latest but did not succeed in reproducing this localy. Could you please show us the config and/or server log output. (you can do so privately at galaxy-b...@bx.psu.edu or mar...@bx.psu.edu) Thanks Martin On Mon, Apr 27, 2015 at 2:54 PM Vipin TS wrote: > Hi John, > > Still the problem exist. The codebase is in latest_15.03 revision. > > my instance is not behind a proxy server, I m confused about the 403 > Forbidden error message with https://galaxy.cbio.mskcc.org/api/tools/ > where is this request goes? > > Vipin > > > On Fri, Apr 24, 2015 at 9:04 AM, John Chilton wrote: > >> I am pretty stumped by this - my next actions would be to upgrade to >> the newest latest_15.03 in case this has been fixed. >> >> If that doesn't fix it I might look at your proxy configuration - is >> there a proxy server sitting in front of Galaxy? It looks like upload >> works on this server and I believe that is using the same endpoint >> POST /api/tools. I don't know why upload would work but all other >> tools fail - but one possibility is the proxy is blocking the request >> if it doesn't look like an upload. >> >> -John >> >> On Tue, Apr 21, 2015 at 10:11 PM, Vipin TS wrote: >> > Hi John, >> > >> > I am seeing an error in browser console when click on a tool link: >> > POST https://galaxy.cbio.mskcc.org/api/tools 403 (Forbidden) >> > >> > " >> > >> > 403 Forbidden >> > >> > Forbidden >> > You don't have permission to access /api/tools >> > on this server. >> > >> > >> > which points to the tool-jobs.js line #65, which is the error part of >> the >> > Utils.request function. >> > Something related with authentication? >> > >> > Vipin >> > >> > On Tue, Apr 21, 2015 at 9:05 AM, John Chilton >> wrote: >> >> >> >> Another question is are there any logs indicating issues on the server >> >> side and can you open your web console and let us know if there are >> >> any errors reported there on the client side (e.g. >> >> https://developer.mozilla.org/en-US/docs/Tools/Web_Console). >> >> >> >> -John >> >> >> >> On Tue, Apr 21, 2015 at 3:45 AM, Hans-Rudolf Hotz wrote: >> >> > Hi Vipin >> >> > >> >> > Is this a new problem you encounter since you have done the upgrade >> to >> >> > "latest_15.03"? If so, did you experience any troubles during the >> >> > database >> >> > schema upgrade to '128'? >> >> > >> >> > >> >> > Regards, Hans-Rudolf >> >> > >> >> > >> >> > On 04/20/2015 08:44 PM, Vipin TS wrote: >> >> >> >> >> >> Hi dev-team, >> >> >> >> >> >> >> >> >> I am experiencing an issue with my production instance in >> dispatching >> >> >> the jobs. When I click on execute button, each tool page shows the >> >> >> popup >> >> >> error message as here: >> >> >> Inline image 1 >> >> >> I am not sure what is happening, not getting any single line of >> error >> >> >> message in log file. >> >> >> >> >> >> Here is the version I am using: >> >> >> changeset: 17051:28113212 >> >> >> branch: stable >> >> >> date:Mon Mar 16 22:38:27 2015 -0400 >> >> >> summary: Update tag latest_15.03 for changeset 9f40ff3e3fe1 >> >> >> >> >> >> any suggestions, Thank you! >> >> >> >> >> >> Vipin | Rätsch Lab >> >> >> >> >> >> >> >> >> ___ >> >> >> 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/ >> > >> > >> > > ___ > 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/ __
Re: [galaxy-dev] Job submission failed
Hi John, Still the problem exist. The codebase is in latest_15.03 revision. my instance is not behind a proxy server, I m confused about the 403 Forbidden error message with https://galaxy.cbio.mskcc.org/api/tools/ where is this request goes? Vipin On Fri, Apr 24, 2015 at 9:04 AM, John Chilton wrote: > I am pretty stumped by this - my next actions would be to upgrade to > the newest latest_15.03 in case this has been fixed. > > If that doesn't fix it I might look at your proxy configuration - is > there a proxy server sitting in front of Galaxy? It looks like upload > works on this server and I believe that is using the same endpoint > POST /api/tools. I don't know why upload would work but all other > tools fail - but one possibility is the proxy is blocking the request > if it doesn't look like an upload. > > -John > > On Tue, Apr 21, 2015 at 10:11 PM, Vipin TS wrote: > > Hi John, > > > > I am seeing an error in browser console when click on a tool link: > > POST https://galaxy.cbio.mskcc.org/api/tools 403 (Forbidden) > > > > " > > > > 403 Forbidden > > > > Forbidden > > You don't have permission to access /api/tools > > on this server. > > > > > > which points to the tool-jobs.js line #65, which is the error part of the > > Utils.request function. > > Something related with authentication? > > > > Vipin > > > > On Tue, Apr 21, 2015 at 9:05 AM, John Chilton > wrote: > >> > >> Another question is are there any logs indicating issues on the server > >> side and can you open your web console and let us know if there are > >> any errors reported there on the client side (e.g. > >> https://developer.mozilla.org/en-US/docs/Tools/Web_Console). > >> > >> -John > >> > >> On Tue, Apr 21, 2015 at 3:45 AM, Hans-Rudolf Hotz wrote: > >> > Hi Vipin > >> > > >> > Is this a new problem you encounter since you have done the upgrade to > >> > "latest_15.03"? If so, did you experience any troubles during the > >> > database > >> > schema upgrade to '128'? > >> > > >> > > >> > Regards, Hans-Rudolf > >> > > >> > > >> > On 04/20/2015 08:44 PM, Vipin TS wrote: > >> >> > >> >> Hi dev-team, > >> >> > >> >> > >> >> I am experiencing an issue with my production instance in dispatching > >> >> the jobs. When I click on execute button, each tool page shows the > >> >> popup > >> >> error message as here: > >> >> Inline image 1 > >> >> I am not sure what is happening, not getting any single line of error > >> >> message in log file. > >> >> > >> >> Here is the version I am using: > >> >> changeset: 17051:28113212 > >> >> branch: stable > >> >> date:Mon Mar 16 22:38:27 2015 -0400 > >> >> summary: Update tag latest_15.03 for changeset 9f40ff3e3fe1 > >> >> > >> >> any suggestions, Thank you! > >> >> > >> >> Vipin | Rätsch Lab > >> >> > >> >> > >> >> ___ > >> >> 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/ > > > > > ___ 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/
Re: [galaxy-dev] Job submission failed
I am pretty stumped by this - my next actions would be to upgrade to the newest latest_15.03 in case this has been fixed. If that doesn't fix it I might look at your proxy configuration - is there a proxy server sitting in front of Galaxy? It looks like upload works on this server and I believe that is using the same endpoint POST /api/tools. I don't know why upload would work but all other tools fail - but one possibility is the proxy is blocking the request if it doesn't look like an upload. -John On Tue, Apr 21, 2015 at 10:11 PM, Vipin TS wrote: > Hi John, > > I am seeing an error in browser console when click on a tool link: > POST https://galaxy.cbio.mskcc.org/api/tools 403 (Forbidden) > > " > > 403 Forbidden > > Forbidden > You don't have permission to access /api/tools > on this server. > > > which points to the tool-jobs.js line #65, which is the error part of the > Utils.request function. > Something related with authentication? > > Vipin > > On Tue, Apr 21, 2015 at 9:05 AM, John Chilton wrote: >> >> Another question is are there any logs indicating issues on the server >> side and can you open your web console and let us know if there are >> any errors reported there on the client side (e.g. >> https://developer.mozilla.org/en-US/docs/Tools/Web_Console). >> >> -John >> >> On Tue, Apr 21, 2015 at 3:45 AM, Hans-Rudolf Hotz wrote: >> > Hi Vipin >> > >> > Is this a new problem you encounter since you have done the upgrade to >> > "latest_15.03"? If so, did you experience any troubles during the >> > database >> > schema upgrade to '128'? >> > >> > >> > Regards, Hans-Rudolf >> > >> > >> > On 04/20/2015 08:44 PM, Vipin TS wrote: >> >> >> >> Hi dev-team, >> >> >> >> >> >> I am experiencing an issue with my production instance in dispatching >> >> the jobs. When I click on execute button, each tool page shows the >> >> popup >> >> error message as here: >> >> Inline image 1 >> >> I am not sure what is happening, not getting any single line of error >> >> message in log file. >> >> >> >> Here is the version I am using: >> >> changeset: 17051:28113212 >> >> branch: stable >> >> date:Mon Mar 16 22:38:27 2015 -0400 >> >> summary: Update tag latest_15.03 for changeset 9f40ff3e3fe1 >> >> >> >> any suggestions, Thank you! >> >> >> >> Vipin | Rätsch Lab >> >> >> >> >> >> ___ >> >> 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/ > > ___ 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/
Re: [galaxy-dev] Job submission failed
Hi John, I am seeing an error in browser console when click on a tool link: POST https://galaxy.cbio.mskcc.org/api/tools 403 (Forbidden) " 403 Forbidden Forbidden You don't have permission to access /api/tools on this server. which points to the tool-jobs.js line #65, which is the error part of the Utils.request function. Something related with authentication? Vipin On Tue, Apr 21, 2015 at 9:05 AM, John Chilton wrote: > Another question is are there any logs indicating issues on the server > side and can you open your web console and let us know if there are > any errors reported there on the client side (e.g. > https://developer.mozilla.org/en-US/docs/Tools/Web_Console). > > -John > > On Tue, Apr 21, 2015 at 3:45 AM, Hans-Rudolf Hotz wrote: > > Hi Vipin > > > > Is this a new problem you encounter since you have done the upgrade to > > "latest_15.03"? If so, did you experience any troubles during the > database > > schema upgrade to '128'? > > > > > > Regards, Hans-Rudolf > > > > > > On 04/20/2015 08:44 PM, Vipin TS wrote: > >> > >> Hi dev-team, > >> > >> > >> I am experiencing an issue with my production instance in dispatching > >> the jobs. When I click on execute button, each tool page shows the popup > >> error message as here: > >> Inline image 1 > >> I am not sure what is happening, not getting any single line of error > >> message in log file. > >> > >> Here is the version I am using: > >> changeset: 17051:28113212 > >> branch: stable > >> date:Mon Mar 16 22:38:27 2015 -0400 > >> summary: Update tag latest_15.03 for changeset 9f40ff3e3fe1 > >> > >> any suggestions, Thank you! > >> > >> Vipin | Rätsch Lab > >> > >> > >> ___ > >> 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/ > ___ 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/
Re: [galaxy-dev] Job submission failed
Hi Hans, Yes, this happened after upgrading to the version latest_15.03. The db upgrade was fine, didn't throw any error message to me. Thanks, Vipin On Tue, Apr 21, 2015 at 3:45 AM, Hans-Rudolf Hotz wrote: > Hi Vipin > > Is this a new problem you encounter since you have done the upgrade to > "latest_15.03"? If so, did you experience any troubles during the database > schema upgrade to '128'? > > > Regards, Hans-Rudolf > > > On 04/20/2015 08:44 PM, Vipin TS wrote: > >> Hi dev-team, >> >> >> I am experiencing an issue with my production instance in dispatching >> the jobs. When I click on execute button, each tool page shows the popup >> error message as here: >> Inline image 1 >> I am not sure what is happening, not getting any single line of error >> message in log file. >> >> Here is the version I am using: >> changeset: 17051:28113212 >> branch: stable >> date:Mon Mar 16 22:38:27 2015 -0400 >> summary: Update tag latest_15.03 for changeset 9f40ff3e3fe1 >> >> any suggestions, Thank you! >> >> Vipin | Rätsch Lab >> >> >> ___ >> 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/
Re: [galaxy-dev] Job submission failed
Another question is are there any logs indicating issues on the server side and can you open your web console and let us know if there are any errors reported there on the client side (e.g. https://developer.mozilla.org/en-US/docs/Tools/Web_Console). -John On Tue, Apr 21, 2015 at 3:45 AM, Hans-Rudolf Hotz wrote: > Hi Vipin > > Is this a new problem you encounter since you have done the upgrade to > "latest_15.03"? If so, did you experience any troubles during the database > schema upgrade to '128'? > > > Regards, Hans-Rudolf > > > On 04/20/2015 08:44 PM, Vipin TS wrote: >> >> Hi dev-team, >> >> >> I am experiencing an issue with my production instance in dispatching >> the jobs. When I click on execute button, each tool page shows the popup >> error message as here: >> Inline image 1 >> I am not sure what is happening, not getting any single line of error >> message in log file. >> >> Here is the version I am using: >> changeset: 17051:28113212 >> branch: stable >> date:Mon Mar 16 22:38:27 2015 -0400 >> summary: Update tag latest_15.03 for changeset 9f40ff3e3fe1 >> >> any suggestions, Thank you! >> >> Vipin | Rätsch Lab >> >> >> ___ >> 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/ ___ 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/
Re: [galaxy-dev] Job submission failed
Hi Vipin Is this a new problem you encounter since you have done the upgrade to "latest_15.03"? If so, did you experience any troubles during the database schema upgrade to '128'? Regards, Hans-Rudolf On 04/20/2015 08:44 PM, Vipin TS wrote: Hi dev-team, I am experiencing an issue with my production instance in dispatching the jobs. When I click on execute button, each tool page shows the popup error message as here: Inline image 1 I am not sure what is happening, not getting any single line of error message in log file. Here is the version I am using: changeset: 17051:28113212 branch: stable date:Mon Mar 16 22:38:27 2015 -0400 summary: Update tag latest_15.03 for changeset 9f40ff3e3fe1 any suggestions, Thank you! Vipin | Rätsch Lab ___ 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/
