Re: [galaxy-dev] Workflow import is not working, KeyError: 'header_lines'
n Wed, Aug 21, 2013 at 2:59 PM, Dannon Baker wrote: > Hey Peter, > > The reason it's actually failing has to do with the tool Filter1, and your > particular version of the filter tool not having the header lines parameter. > This was added in 8678:a14006775b08. In this instance, we should have just > used the default value. Yes - I realised later that the header_lines was from the Filter1 tool, http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016224.html > Once all tools and versions are in the toolshed, this sort of thing > shouldn't crop up because you'll have the correct version available. I was under the impression at GCC2013 that Galaxy would continue to keep a set of 'core' tools with no dependencies (like Filter1), but perhaps the goal is more a set of tools installed from the Tool Shed by default? > I've committed a temporary fix in 10423:3c60f6a7dedc. > Thanks, Peter ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Workflow import is not working, KeyError: 'header_lines'
Hey Peter, The reason it's actually failing has to do with the tool Filter1, and your particular version of the filter tool not having the header lines parameter. This was added in 8678:a14006775b08. In this instance, we should have just used the default value. Once all tools and versions are in the toolshed, this sort of thing shouldn't crop up because you'll have the correct version available. I've committed a temporary fix in 10423:3c60f6a7dedc. On Wed, Aug 21, 2013 at 9:14 AM, Dannon Baker wrote: > On Wed, Aug 21, 2013 at 9:10 AM, Peter Cock wrote: > >> Via the Tool Shed I couldn't see the import workflow action... from >> memory it was on the broken SVG page? >> > > Yep, that's where it was. > > These are not tweaked - it is an old workflow created with manually >> installed tools which therefore have the short form identifiers. This >> is something Galaxy may need to continue to support for backwards >> compatibility with old workflows supplied as supplementary files etc. >> >> I'm attempting to update the workflow to use the new long-form >> toolshed identifiers (although this has the minor downside of no >> longer being portable between different Tool Sheds). > > > Ok, thanks for the extra info, just wanted to make sure I knew what I was > dealing with :) > ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Workflow import is not working, KeyError: 'header_lines'
On Wed, Aug 21, 2013 at 9:10 AM, Peter Cock wrote: > Via the Tool Shed I couldn't see the import workflow action... from > memory it was on the broken SVG page? > Yep, that's where it was. These are not tweaked - it is an old workflow created with manually > installed tools which therefore have the short form identifiers. This > is something Galaxy may need to continue to support for backwards > compatibility with old workflows supplied as supplementary files etc. > > I'm attempting to update the workflow to use the new long-form > toolshed identifiers (although this has the minor downside of no > longer being portable between different Tool Sheds). Ok, thanks for the extra info, just wanted to make sure I knew what I was dealing with :) ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Workflow import is not working, KeyError: 'header_lines'
> On Wed, Aug 21, 2013 at 8:25 AM, Dannon Baker > wrote: >> >> Hey Peter, >> >> I've reproduced this here, thanks. Unfortunately this got missed >> previously, once we had the import itself working. To be clear, though, the >> workflow itself is still completely functional, imports and runs, and the >> only issue is the inability to view the svg? Via the Tool Shed I couldn't see the import workflow action... from memory it was on the broken SVG page? I could manually import the workflow from the *.ga file on disk, and it runs OK. >> I think what's causing this is that generate_workflow_image uses >> completely separate workflow modules which didn't have my previous fixes >> applied. This should be refactored so we don't have duplicated code sitting >> around, but I'll go ahead and patch it to get it working again shortly. Sounds good. On Wed, Aug 21, 2013 at 1:47 PM, Dannon Baker wrote: > Quick followup on this one -- had you manually tweaked this workflow prior > to upload? I see all of the tool identifiers are the short form 'signalp3' > and not the long-form toolshed included versions. These are not tweaked - it is an old workflow created with manually installed tools which therefore have the short form identifiers. This is something Galaxy may need to continue to support for backwards compatibility with old workflows supplied as supplementary files etc. I'm attempting to update the workflow to use the new long-form toolshed identifiers (although this has the minor downside of no longer being portable between different Tool Sheds). Peter ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Workflow import is not working, KeyError: 'header_lines'
Quick followup on this one -- had you manually tweaked this workflow prior to upload? I see all of the tool identifiers are the short form 'signalp3' and not the long-form toolshed included versions. On Wed, Aug 21, 2013 at 8:25 AM, Dannon Baker wrote: > Hey Peter, > > I've reproduced this here, thanks. Unfortunately this got missed > previously, once we had the import itself working. To be clear, though, > the workflow itself is still completely functional, imports and runs, and > the only issue is the inability to view the svg? > > I think what's causing this is that generate_workflow_image uses > completely separate workflow modules which didn't have my previous fixes > applied. This should be refactored so we don't have duplicated code > sitting around, but I'll go ahead and patch it to get it working again > shortly. > > > On Wed, Aug 21, 2013 at 6:45 AM, Peter Cock wrote: > >> Hi Dannon, >> >> I'm seeing a problem which seems very similar to the one Bjoern >> had back in June with the same workflow (which appeared to have >> been fixed according to the old IUC thread "Workflow import is not >> working"). >> >> This server is running the current galaxy-dist release, >> >> $ sudo -u galaxy hg head >> changeset: 10411:c42567f43aa7 >> tag: tip >> user:greg >> date:Mon Aug 19 13:19:56 2013 -0400 >> summary: Filter invalid objects when generating the list of >> repository_dependencies objects that are associated with a tool shed >> repository installed into Galaxy. >> >> changeset: 10408:6822f41bc9bb >> branch: stable >> parent: 10393:d05bf67aefa6 >> user:Dave Bouvier >> date:Mon Aug 19 13:06:17 2013 -0400 >> summary: Fix for case where running functional tests might >> overwrite certain files in database/files. >> >> I have just installed this workflow repository with its dependencies >> (some of where I had previously installed via the Tool Shed). Most >> of the tools were actually already manually installed but have been >> commented out in my tool_conf.xml file: >> >> >> http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow/606da4e1d925 >> >> Installation appeared to be successful, so I wanted to import the >> workflow into Galaxy. I clicked on the workflow and expected to >> see an SVG of the workflow and the import action to be available. >> In the browser I saw: >> >> >> Find secreted proteins with TMHMM and SignalP >> (this page displays SVG graphics) >> >> Internal Server Error >> Galaxy was unable to sucessfully complete your request >> >> An error occurred. >> This may be an intermittent problem due to load or other unpredictable >> factors, reloading the page may address the problem. >> >> The error has been logged to our team. >> >> >> On the terminal I have: >> >> 143.234.97.120 - - [21/Aug/2013:11:14:18 +0100] "GET >> /galaxy/admin_toolshed/browse_repositories HTTP/1.1" 200 - >> "http://ppcollab/galaxy/admin"; "Mozilla/5.0 (Macintosh; Intel Mac OS X >> 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" >> 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] "GET >> >> /galaxy/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=false&operation=manage_repository&id=eede92f8a72bf85d&f-deleted=False >> HTTP/1.1" 302 - >> "http://ppcollab/galaxy/admin_toolshed/browse_repositories"; >> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 >> Firefox/22.0" >> 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] "GET >> >> /galaxy/admin_toolshed/manage_repository?sort=name&f-deleted=False&async=false&show_item_checkboxes=false&id=eede92f8a72bf85d&page=1 >> HTTP/1.1" 200 - >> "http://ppcollab/galaxy/admin_toolshed/browse_repositories"; >> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 >> Firefox/22.0" >> 143.234.97.120 - - [21/Aug/2013:11:14:40 +0100] "GET >> >> /galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 >> HTTP/1.1" 200 - >> " >> http://ppcollab/galaxy/admin_toolshed/manage_repository?sort=name&f-deleted=False&async=false&show_item_checkboxes=false&id=eede92f8a72bf85d&page=1 >> " >> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 >> Firefox/22.0" >> 143.234.97.120 - - [21/Aug/2013:11:14:41 +0100] "GET >> >> /galaxy/admin_toolshed/generate_workflow_image?repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 >> HTTP/1.1" 500 - >> " >> http://ppcollab/galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 >> " >> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 >> Firefox
Re: [galaxy-dev] Workflow import is not working, KeyError: 'header_lines'
Hey Peter, I've reproduced this here, thanks. Unfortunately this got missed previously, once we had the import itself working. To be clear, though, the workflow itself is still completely functional, imports and runs, and the only issue is the inability to view the svg? I think what's causing this is that generate_workflow_image uses completely separate workflow modules which didn't have my previous fixes applied. This should be refactored so we don't have duplicated code sitting around, but I'll go ahead and patch it to get it working again shortly. On Wed, Aug 21, 2013 at 6:45 AM, Peter Cock wrote: > Hi Dannon, > > I'm seeing a problem which seems very similar to the one Bjoern > had back in June with the same workflow (which appeared to have > been fixed according to the old IUC thread "Workflow import is not > working"). > > This server is running the current galaxy-dist release, > > $ sudo -u galaxy hg head > changeset: 10411:c42567f43aa7 > tag: tip > user:greg > date:Mon Aug 19 13:19:56 2013 -0400 > summary: Filter invalid objects when generating the list of > repository_dependencies objects that are associated with a tool shed > repository installed into Galaxy. > > changeset: 10408:6822f41bc9bb > branch: stable > parent: 10393:d05bf67aefa6 > user:Dave Bouvier > date:Mon Aug 19 13:06:17 2013 -0400 > summary: Fix for case where running functional tests might > overwrite certain files in database/files. > > I have just installed this workflow repository with its dependencies > (some of where I had previously installed via the Tool Shed). Most > of the tools were actually already manually installed but have been > commented out in my tool_conf.xml file: > > > http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow/606da4e1d925 > > Installation appeared to be successful, so I wanted to import the > workflow into Galaxy. I clicked on the workflow and expected to > see an SVG of the workflow and the import action to be available. > In the browser I saw: > > > Find secreted proteins with TMHMM and SignalP > (this page displays SVG graphics) > > Internal Server Error > Galaxy was unable to sucessfully complete your request > > An error occurred. > This may be an intermittent problem due to load or other unpredictable > factors, reloading the page may address the problem. > > The error has been logged to our team. > > > On the terminal I have: > > 143.234.97.120 - - [21/Aug/2013:11:14:18 +0100] "GET > /galaxy/admin_toolshed/browse_repositories HTTP/1.1" 200 - > "http://ppcollab/galaxy/admin"; "Mozilla/5.0 (Macintosh; Intel Mac OS X > 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" > 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] "GET > > /galaxy/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=false&operation=manage_repository&id=eede92f8a72bf85d&f-deleted=False > HTTP/1.1" 302 - > "http://ppcollab/galaxy/admin_toolshed/browse_repositories"; > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 > Firefox/22.0" > 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] "GET > > /galaxy/admin_toolshed/manage_repository?sort=name&f-deleted=False&async=false&show_item_checkboxes=false&id=eede92f8a72bf85d&page=1 > HTTP/1.1" 200 - > "http://ppcollab/galaxy/admin_toolshed/browse_repositories"; > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 > Firefox/22.0" > 143.234.97.120 - - [21/Aug/2013:11:14:40 +0100] "GET > > /galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 > HTTP/1.1" 200 - > " > http://ppcollab/galaxy/admin_toolshed/manage_repository?sort=name&f-deleted=False&async=false&show_item_checkboxes=false&id=eede92f8a72bf85d&page=1 > " > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 > Firefox/22.0" > 143.234.97.120 - - [21/Aug/2013:11:14:41 +0100] "GET > > /galaxy/admin_toolshed/generate_workflow_image?repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 > HTTP/1.1" 500 - > " > http://ppcollab/galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 > " > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 > Firefox/22.0" > Error - : 'header_lines' > URL: > http://ppcollab/galaxy/admin_toolshed/generate_workflow_image?repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 > File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', > line 149 in __cal
