Re: [galaxy-dev] Nothing being tested on Test and main Tool Shed?
Thanks John, Fingers crossed we'll get some more detailed logs in a day or two :) Peter On Wed, Nov 19, 2014 at 5:48 PM, John Chilton wrote: > Hey Peter, > > Dave is out this week - so I have tried to fumble around and see if I > could make some progress on this. I found some bugs in a recent commit > and fixed them - that might help > (https://bitbucket.org/galaxy/galaxy-central/commits/b81798f94dc0fd14de1d585ed7e57f820f998fae). > I also have enabled more verbose logging that might help those > "History in error state" exceptions > (https://bitbucket.org/galaxy/galaxy-central/commits/a799879a82c54c2d1afec6e33d8918479bbf2373) > but I am not sure it will propagate through to the tool shed API - we > will see I guess. > > If the install and test framework just picks up the latest central - > these fixes will hopefully be reflected in the next run. > > -John > > > On Wed, Nov 19, 2014 at 4:48 AM, Peter Cock wrote: >> >> Hi Dave, >> >> Any progress? All the following seem to have been tested >> in the last few days on the TestToolShed, but failed with >> "Exception: History in error state." >> >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id >> >> That's about half of my TestToolShed repositories - most >> of the others report their tests passed :) >> >> I am also seeing unexpected problems with packages, e.g. >> >> https://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_29 >> >> Error getting revision e78bbab7933d of repository >> package_blast_plus_2_2_29 owned by iuc: An entry for the repository >> was not found in the database. >> >> 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] Nothing being tested on Test and main Tool Shed?
Hey Peter, Dave is out this week - so I have tried to fumble around and see if I could make some progress on this. I found some bugs in a recent commit and fixed them - that might help (https://bitbucket.org/galaxy/galaxy-central/commits/b81798f94dc0fd14de1d585ed7e57f820f998fae). I also have enabled more verbose logging that might help those "History in error state" exceptions (https://bitbucket.org/galaxy/galaxy-central/commits/a799879a82c54c2d1afec6e33d8918479bbf2373) but I am not sure it will propagate through to the tool shed API - we will see I guess. If the install and test framework just picks up the latest central - these fixes will hopefully be reflected in the next run. -John On Wed, Nov 19, 2014 at 4:48 AM, Peter Cock wrote: > On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock wrote: >> Thanks Dave, >> >> The good news is yes, the tests are running again on the >> Test Tool Shed (although not the main Tool Shed yet), and >> many of my tools now have successful test results from >> last night. >> >> e.g. My new basic mummer tool which now has a full set >> of dependency packages thanks to Bjoern: >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer >> >> The bad news is there are many unexpected failures with: >> "Exception: History in error state." >> >> I'm sure you'll learn more once you look over the logs, >> >> Thank you, >> >> Peter > > Hi Dave, > > Any progress? All the following seem to have been tested > in the last few days on the TestToolShed, but failed with > "Exception: History in error state." > > https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go > https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr > https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod > https://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired > https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss > https://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler > https://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus > https://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus > https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id > https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip > https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename > https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id > > That's about half of my TestToolShed repositories - most > of the others report their tests passed :) > > I am also seeing unexpected problems with packages, e.g. > > https://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_29 > > Error getting revision e78bbab7933d of repository > package_blast_plus_2_2_29 owned by iuc: An entry for the repository > was not found in the database. > > 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/ ___ 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] Nothing being tested on Test and main Tool Shed?
On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock wrote: > Thanks Dave, > > The good news is yes, the tests are running again on the > Test Tool Shed (although not the main Tool Shed yet), and > many of my tools now have successful test results from > last night. > > e.g. My new basic mummer tool which now has a full set > of dependency packages thanks to Bjoern: > https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer > > The bad news is there are many unexpected failures with: > "Exception: History in error state." > > I'm sure you'll learn more once you look over the logs, > > Thank you, > > Peter Hi Dave, Any progress? All the following seem to have been tested in the last few days on the TestToolShed, but failed with "Exception: History in error state." https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod https://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss https://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler https://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus https://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id That's about half of my TestToolShed repositories - most of the others report their tests passed :) I am also seeing unexpected problems with packages, e.g. https://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_29 Error getting revision e78bbab7933d of repository package_blast_plus_2_2_29 owned by iuc: An entry for the repository was not found in the database. 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] Nothing being tested on Test and main Tool Shed?
Thanks Dave, The good news is yes, the tests are running again on the Test Tool Shed (although not the main Tool Shed yet), and many of my tools now have successful test results from last night. e.g. My new basic mummer tool which now has a full set of dependency packages thanks to Bjoern: https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer The bad news is there are many unexpected failures with: "Exception: History in error state." I'm sure you'll learn more once you look over the logs, Thank you, Peter On Wed, Nov 5, 2014 at 6:21 PM, Dave Bouvier wrote: > Peter, > > This was due to a number of issues with the testing framework, the last of > which appears to have been resolved, and I see tools being tested in the > framework log. I'll check again in the morning to see if any of the tools > you listed below were still not tested. > >--Dave B. > > > On 11/03/2014 05:51 AM, Peter Cock wrote: >> >> Hello all, >> >> I am currently hoping to review the automated test results for >> some repositories which I have recently updated, in one case >> for dependency handling, the other functional changes: >> >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus >> >> These have not yet been tested. On further investigation >> of a sample of my other tools, it appears none of them have >> been tested on the Test Tool Shed since 2014-09-15, e.g. >> >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3 >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod >> >> Similarly, some of my tools on the Main Tool Shed appear >> not to have been tested since 2014-09-21, e.g. >> >> https://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename >> https://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3 >> https://toolshed.g2.bx.psu.edu/view/peterjc/clinod >> >> or 2014-10-27, >> >> https://toolshed.g2.bx.psu.edu/view/peterjc/sample_seqs >> https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats >> >> Is there a known problem with the automated tool testing >> (previously every second night) on the Tool Sheds? >> Or have you had to further reduce the testing cycle? >> >> Testing less frequently seems fine, say fortnightly, if this can >> be supplemented by testing updated tools everynight. That >> would give Tool Authors prompt feedback on their updates, >> but also catch regressions where changes in Galaxy break >> a previously working tool. >> >> Regards, >> >> 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/ >> > ___ 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] Nothing being tested on Test and main Tool Shed?
Peter, This was due to a number of issues with the testing framework, the last of which appears to have been resolved, and I see tools being tested in the framework log. I'll check again in the morning to see if any of the tools you listed below were still not tested. --Dave B. On 11/03/2014 05:51 AM, Peter Cock wrote: Hello all, I am currently hoping to review the automated test results for some repositories which I have recently updated, in one case for dependency handling, the other functional changes: https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer https://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus These have not yet been tested. On further investigation of a sample of my other tools, it appears none of them have been tested on the Test Tool Shed since 2014-09-15, e.g. https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats https://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3 https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod Similarly, some of my tools on the Main Tool Shed appear not to have been tested since 2014-09-21, e.g. https://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename https://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3 https://toolshed.g2.bx.psu.edu/view/peterjc/clinod or 2014-10-27, https://toolshed.g2.bx.psu.edu/view/peterjc/sample_seqs https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats Is there a known problem with the automated tool testing (previously every second night) on the Tool Sheds? Or have you had to further reduce the testing cycle? Testing less frequently seems fine, say fortnightly, if this can be supplemented by testing updated tools everynight. That would give Tool Authors prompt feedback on their updates, but also catch regressions where changes in Galaxy break a previously working tool. Regards, 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/ ___ 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/
[galaxy-dev] Nothing being tested on Test and main Tool Shed?
Hello all, I am currently hoping to review the automated test results for some repositories which I have recently updated, in one case for dependency handling, the other functional changes: https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer https://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus These have not yet been tested. On further investigation of a sample of my other tools, it appears none of them have been tested on the Test Tool Shed since 2014-09-15, e.g. https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats https://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3 https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod Similarly, some of my tools on the Main Tool Shed appear not to have been tested since 2014-09-21, e.g. https://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename https://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3 https://toolshed.g2.bx.psu.edu/view/peterjc/clinod or 2014-10-27, https://toolshed.g2.bx.psu.edu/view/peterjc/sample_seqs https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats Is there a known problem with the automated tool testing (previously every second night) on the Tool Sheds? Or have you had to further reduce the testing cycle? Testing less frequently seems fine, say fortnightly, if this can be supplemented by testing updated tools everynight. That would give Tool Authors prompt feedback on their updates, but also catch regressions where changes in Galaxy break a previously working tool. Regards, 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/
