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

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

---

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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/