Uploads with embedded citations causing red error on Tool Shed
Hi John, Following the work at the BOSC 2014 CodeFest to support embedded citations within Galaxy Tool XML files [1], and your work adding this to the BLAST tools as an example [2], I tried uploading a minor tool using this to the Tool Shed. The upload seems to have worked, but there was a scary red error message about metadata... see below (both main and test toolsheds affected). Regards, Peter [1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/ [2] https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b9... -- Uploading on the Test Tool Shed, red error: Metadata may have been defined for some items in revision '796dc2ff8e8e'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager' https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr -- Uploading on the Tool Shed, red error: Metadata may have been defined for some items in revision 'fe1ed74793c9'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager' https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
Hey Peter, Opps sorry about that and thanks for the bug report. The tool shed code should be fixed with https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5be65b3b743fc0... - it is in next-stable so I think the tool shed should pick up that fix at next tool shed update. -John On Wed, Jul 30, 2014 at 5:43 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi John,
Following the work at the BOSC 2014 CodeFest to support embedded citations within Galaxy Tool XML files [1], and your work adding this to the BLAST tools as an example [2], I tried uploading a minor tool using this to the Tool Shed.
The upload seems to have worked, but there was a scary red error message about metadata... see below (both main and test toolsheds affected).
Regards,
Peter
[1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/
[2] https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b9...
--
Uploading on the Test Tool Shed, red error:
Metadata may have been defined for some items in revision '796dc2ff8e8e'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager'
https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
--
Uploading on the Tool Shed, red error:
Metadata may have been defined for some items in revision 'fe1ed74793c9'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager'
https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
Thanks John - is there any point/benefit to re-uploading my tool once the fix is live on the Tool Shed? i.e. Was it a harmless warning? Peter On Wed, Jul 30, 2014 at 12:12 PM, John Chilton <jmchilton@gmail.com> wrote:
Hey Peter,
Opps sorry about that and thanks for the bug report. The tool shed code should be fixed with https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5be65b3b743fc0... - it is in next-stable so I think the tool shed should pick up that fix at next tool shed update.
-John
On Wed, Jul 30, 2014 at 5:43 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi John,
Following the work at the BOSC 2014 CodeFest to support embedded citations within Galaxy Tool XML files [1], and your work adding this to the BLAST tools as an example [2], I tried uploading a minor tool using this to the Tool Shed.
The upload seems to have worked, but there was a scary red error message about metadata... see below (both main and test toolsheds affected).
Regards,
Peter
[1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/
[2] https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b9...
--
Uploading on the Test Tool Shed, red error:
Metadata may have been defined for some items in revision '796dc2ff8e8e'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager'
https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
--
Uploading on the Tool Shed, red error:
Metadata may have been defined for some items in revision 'fe1ed74793c9'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager'
https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
... that might be a Greg question. The tool shed isn't going to use the citation information in anyway at this time (https://trello.com/c/R8vKH4PQ) - so you won't gain anything from a citation-y perspective by re-uploading. That bug might have interfered with the tool shed metadata generation process though(?) so it might be worth regenerating that when the tool shed is updated(?). That is just a guess though - maybe Greg will weigh in on whether that makes sense. -John On Wed, Jul 30, 2014 at 7:14 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Thanks John - is there any point/benefit to re-uploading my tool once the fix is live on the Tool Shed?
i.e. Was it a harmless warning?
Peter
On Wed, Jul 30, 2014 at 12:12 PM, John Chilton <jmchilton@gmail.com> wrote:
Hey Peter,
Opps sorry about that and thanks for the bug report. The tool shed code should be fixed with https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5be65b3b743fc0... - it is in next-stable so I think the tool shed should pick up that fix at next tool shed update.
-John
On Wed, Jul 30, 2014 at 5:43 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi John,
Following the work at the BOSC 2014 CodeFest to support embedded citations within Galaxy Tool XML files [1], and your work adding this to the BLAST tools as an example [2], I tried uploading a minor tool using this to the Tool Shed.
The upload seems to have worked, but there was a scary red error message about metadata... see below (both main and test toolsheds affected).
Regards,
Peter
[1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/
[2] https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b9...
--
Uploading on the Test Tool Shed, red error:
Metadata may have been defined for some items in revision '796dc2ff8e8e'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager'
https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
--
Uploading on the Tool Shed, red error:
Metadata may have been defined for some items in revision 'fe1ed74793c9'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager'
https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
Yes, it looks like metadata just needs to be regenerated on the affected repositories. Let me know if doing so uncovers something else. Greg On Jul 30, 2014, at 7:20 AM, John Chilton <jmchilton@gmail.com> wrote:
... that might be a Greg question. The tool shed isn't going to use the citation information in anyway at this time (https://trello.com/c/R8vKH4PQ) - so you won't gain anything from a citation-y perspective by re-uploading. That bug might have interfered with the tool shed metadata generation process though(?) so it might be worth regenerating that when the tool shed is updated(?). That is just a guess though - maybe Greg will weigh in on whether that makes sense.
-John
On Wed, Jul 30, 2014 at 7:14 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Thanks John - is there any point/benefit to re-uploading my tool once the fix is live on the Tool Shed?
i.e. Was it a harmless warning?
Peter
On Wed, Jul 30, 2014 at 12:12 PM, John Chilton <jmchilton@gmail.com> wrote:
Hey Peter,
Opps sorry about that and thanks for the bug report. The tool shed code should be fixed with https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5be65b3b743fc0... - it is in next-stable so I think the tool shed should pick up that fix at next tool shed update.
-John
On Wed, Jul 30, 2014 at 5:43 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi John,
Following the work at the BOSC 2014 CodeFest to support embedded citations within Galaxy Tool XML files [1], and your work adding this to the BLAST tools as an example [2], I tried uploading a minor tool using this to the Tool Shed.
The upload seems to have worked, but there was a scary red error message about metadata... see below (both main and test toolsheds affected).
Regards,
Peter
[1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/
[2] https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b9...
--
Uploading on the Test Tool Shed, red error:
Metadata may have been defined for some items in revision '796dc2ff8e8e'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager'
https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
--
Uploading on the Tool Shed, red error:
Metadata may have been defined for some items in revision 'fe1ed74793c9'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager'
https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
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/
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OK - I ran the "Reset all repository metadata" action on both Tool Sheds - no errors reported. Thanks, Peter On Wed, Jul 30, 2014 at 12:23 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Yes, it looks like metadata just needs to be regenerated on the affected repositories. Let me know if doing so uncovers something else.
Greg
On Jul 30, 2014, at 7:20 AM, John Chilton <jmchilton@gmail.com> wrote:
... that might be a Greg question. The tool shed isn't going to use the citation information in anyway at this time (https://trello.com/c/R8vKH4PQ) - so you won't gain anything from a citation-y perspective by re-uploading. That bug might have interfered with the tool shed metadata generation process though(?) so it might be worth regenerating that when the tool shed is updated(?). That is just a guess though - maybe Greg will weigh in on whether that makes sense.
-John
On Wed, Jul 30, 2014 at 7:14 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Thanks John - is there any point/benefit to re-uploading my tool once the fix is live on the Tool Shed?
i.e. Was it a harmless warning?
Peter
On Wed, Jul 30, 2014 at 12:12 PM, John Chilton <jmchilton@gmail.com> wrote:
Hey Peter,
Opps sorry about that and thanks for the bug report. The tool shed code should be fixed with https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5be65b3b743fc0... - it is in next-stable so I think the tool shed should pick up that fix at next tool shed update.
-John
On Wed, Jul 30, 2014 at 5:43 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi John,
Following the work at the BOSC 2014 CodeFest to support embedded citations within Galaxy Tool XML files [1], and your work adding this to the BLAST tools as an example [2], I tried uploading a minor tool using this to the Tool Shed.
The upload seems to have worked, but there was a scary red error message about metadata... see below (both main and test toolsheds affected).
Regards,
Peter
[1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/
[2] https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b9...
--
Uploading on the Test Tool Shed, red error:
Metadata may have been defined for some items in revision '796dc2ff8e8e'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager'
https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
--
Uploading on the Tool Shed, red error:
Metadata may have been defined for some items in revision 'fe1ed74793c9'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager'
https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
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/
Both Galaxy Tool Sheds have been updated with this fix. Greg On Jul 30, 2014, at 7:14 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Thanks John - is there any point/benefit to re-uploading my tool once the fix is live on the Tool Shed?
i.e. Was it a harmless warning?
Peter
On Wed, Jul 30, 2014 at 12:12 PM, John Chilton <jmchilton@gmail.com> wrote:
Hey Peter,
Opps sorry about that and thanks for the bug report. The tool shed code should be fixed with https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5be65b3b743fc0... - it is in next-stable so I think the tool shed should pick up that fix at next tool shed update.
-John
On Wed, Jul 30, 2014 at 5:43 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi John,
Following the work at the BOSC 2014 CodeFest to support embedded citations within Galaxy Tool XML files [1], and your work adding this to the BLAST tools as an example [2], I tried uploading a minor tool using this to the Tool Shed.
The upload seems to have worked, but there was a scary red error message about metadata... see below (both main and test toolsheds affected).
Regards,
Peter
[1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/
[2] https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b9...
--
Uploading on the Test Tool Shed, red error:
Metadata may have been defined for some items in revision '796dc2ff8e8e'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager'
https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
--
Uploading on the Tool Shed, red error:
Metadata may have been defined for some items in revision 'fe1ed74793c9'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager'
https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
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/
participants (3)
-
Greg Von Kuster -
John Chilton -
Peter Cock