Hi all,
I was testing a new workflow which I developed on the current stable release, Galaxy 15.03, and uploaded to the Tool Shed yesterday:
https://github.com/peterjc/galaxy_blast/tree/master/workflows/blast_top_hit_... http://toolshed.g2.bx.psu.edu/view/peterjc/blast_top_hit_species
I then switched to my development instance running the dev branch from github,
1. Log in as an Admin 2. Install http://toolshed.g2.bx.psu.edu/view/peterjc/blast_top_hit_species 3. Upload suggested test dataset (in workflow README file): http://nematode.net/Data/nacobbus_aberrans_transcript_assembly/N.abberans_re... 4. Click on "All Workflows" (bottom of left pane tool list) 5. Click on "Species of top BLAST hits (imported from uploaded file)" 6. On preview screen, examine step 3, blastx 7. Notice it will run against Protein BLAST database "nr" 8. Click "Run workflow"
As noted in the README file, this workflow assumes the local blastdb_p.loc file includes an entry "nr" for a current/recent mirror of the NCBI "non-redundant" protein BLAST database.
Initially my development galaxy had an empty blastdb_p.loc file, so I expected the workflow to spot this problem at the preview step (before ever clicking "run workflow").
Instead it proceeds and attempted to run BLASTX without no database (which of course failed):
blastx -query "/mnt/galaxy/repositories/galaxy/database/files/000/dataset_81.dat" -db "" -query_gencode 1 -evalue 0.001 -out "/mnt/galaxy/repositories/galaxy/database/files/000/dataset_82.dat" -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sscinames scomnames sblastnames sskingdoms" -num_threads "${GALAXY_SLOTS:-8}" -strand both -matrix BLOSUM62 -seg yes -max_target_seqs 1
That's the bad news: It fails, but it fails with a reasonably clear error:
Fatal error: Exit code 2 () BLAST Database error: Database name is required.
Good news: If I update blastdb_p.loc to add the "nr" database it works.
Very bad news: If I update blastdb_p.loc to add other databases (but not an entry for "nr"), the workflow defaults to the first database in blastdb_p.loc
Summary: Workflow requesting key entry "xxx" from example.loc (a) example.loc empty, gets empty path, fails cleanly. (b) example.loc contains xxx, gets correct path, works. (c) example.loc non empty but lacks xxx, runs with WRONG path.
Peter
On Tue, Mar 31, 2015 at 11:31 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
...
Summary: Workflow requesting key entry "xxx" from example.loc (a) example.loc empty, gets empty path, fails cleanly. (b) example.loc contains xxx, gets correct path, works. (c) example.loc non empty but lacks xxx, runs with WRONG path.
Peter
That was running:
commit 1bfb977c7293744cf3e277e4b887bf79cacceddf Author: John Chilton jmchilton@gmail.com Date: Thu Mar 19 09:19:16 2015 -0400
Confirmed with the very latest dev branch commit,
commit b448ccb93bf432fa929fcdf520c9508fb6e5c525 Merge: db86fc4 080a5d0 Author: John Chilton jmchilton@gmail.com Date: Mon Mar 30 20:33:33 2015 -0500
Problem persists on this instance after switching to the release_15.03 tag (which ought to be the same code on github and bitbucket - thankfully the dev branch has not yet changed the schema, so this switchover worked):
commit a6256b547115292fb5a9270ddabd542bced182f3 Merge: a812633 65a42e9 Author: Dannon Baker dannon.baker@gmail.com
Regards,
Peter
On Tue, Mar 31, 2015 at 12:04 PM, Peter Cock p.j.a.cock@googlemail.com wrote:
On Tue, Mar 31, 2015 at 11:31 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
...
Summary: Workflow requesting key entry "xxx" from example.loc (a) example.loc empty, gets empty path, fails cleanly. (b) example.loc contains xxx, gets correct path, works. (c) example.loc non empty but lacks xxx, runs with WRONG path.
Peter
I've started adding debug logging to traces this, focusing on lib/galaxy/tools/parameters/dynamic_options.py
At the "workflow preview", the BLAST database is still "nr" (and has not yet been validated). At this point class DynamicOptions method get_fields and get_options have been called, so the mismatch could be spotted...
After clicking "run workflow", by the time the DynamicOptions methods get_fields_by_value and get_field_by_name_for_value are called "nr" has been replaced with the first entry in the loc file.
I might need a few more clues to make any headway here. The code in lib/galaxy/workflow/run.py is not yet clear to me...
Peter
Hi Peter,
I just wanted to chime in and say that I have been able to reproduce this issue locally (on a different tool), and I’d consider it a pretty significant bug for reproducibility, etc.
Thanks,
Dan
On Mar 31, 2015, at 12:33 PM, Peter Cock p.j.a.cock@googlemail.com wrote:
On Tue, Mar 31, 2015 at 12:04 PM, Peter Cock p.j.a.cock@googlemail.com wrote:
On Tue, Mar 31, 2015 at 11:31 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
...
Summary: Workflow requesting key entry "xxx" from example.loc (a) example.loc empty, gets empty path, fails cleanly. (b) example.loc contains xxx, gets correct path, works. (c) example.loc non empty but lacks xxx, runs with WRONG path.
Peter
I've started adding debug logging to traces this, focusing on lib/galaxy/tools/parameters/dynamic_options.py
At the "workflow preview", the BLAST database is still "nr" (and has not yet been validated). At this point class DynamicOptions method get_fields and get_options have been called, so the mismatch could be spotted...
After clicking "run workflow", by the time the DynamicOptions methods get_fields_by_value and get_field_by_name_for_value are called "nr" has been replaced with the first entry in the loc file.
I might need a few more clues to make any headway here. The code in lib/galaxy/workflow/run.py is not yet clear to me...
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: https://lists.galaxyproject.org/
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Thanks Dan,
That's very reassuring - will you file a Trello issue, or should I?
Peter
On Tue, Mar 31, 2015 at 5:56 PM, Daniel Blankenberg dan@bx.psu.edu wrote:
Hi Peter,
I just wanted to chime in and say that I have been able to reproduce this issue locally (on a different tool), and I’d consider it a pretty significant bug for reproducibility, etc.
Thanks,
Dan
On Tue, Mar 31, 2015 at 11:31 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
...
Summary: Workflow requesting key entry "xxx" from example.loc (a) example.loc empty, gets empty path, fails cleanly. (b) example.loc contains xxx, gets correct path, works. (c) example.loc non empty but lacks xxx, runs with WRONG path.
Peter
I think it is probably a pair of bugs you are seeing:
The wrong database being selected is probably this: https://trello.com/c/72WuZ8mu. It would be interesting to know if reverting this pull request https://bitbucket.org/galaxy/galaxy-central/pull-request/433/fix-allow-editi... fixes it - that would be a good indication this is the problem.
The tool running even though no valid inputs are found - is a sort of known-ish issue but I cannot find any Trello card on it. I know I have some WIP on a fix here: https://github.com/jmchilton/galaxy/commit/900b7bbbf7f0084a86da9b737967fd8eb...
... and a related failing test case here. https://github.com/galaxyproject/galaxy/blob/dev/test/api/test_tools.py#L223
The fix unfortunately is messy and will likely break stuff.
-John
On Tue, Mar 31, 2015 at 1:03 PM, Peter Cock p.j.a.cock@googlemail.com wrote:
Thanks Dan,
That's very reassuring - will you file a Trello issue, or should I?
Peter
On Tue, Mar 31, 2015 at 5:56 PM, Daniel Blankenberg dan@bx.psu.edu wrote:
Hi Peter,
I just wanted to chime in and say that I have been able to reproduce this issue locally (on a different tool), and I’d consider it a pretty significant bug for reproducibility, etc.
Thanks,
Dan
On Tue, Mar 31, 2015 at 11:31 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
...
Summary: Workflow requesting key entry "xxx" from example.loc (a) example.loc empty, gets empty path, fails cleanly. (b) example.loc contains xxx, gets correct path, works. (c) example.loc non empty but lacks xxx, runs with WRONG path.
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
On Tue, Mar 31, 2015 at 6:12 PM, John Chilton jmchilton@gmail.com wrote:
I think it is probably a pair of bugs you are seeing:
Having tried the revert, yes, I think so too.
The wrong database being selected is probably this: https://trello.com/c/72WuZ8mu. It would be interesting to know if reverting this pull request https://bitbucket.org/galaxy/galaxy-central/pull-request/433/fix-allow-editi... fixes it - that would be a good indication this is the problem.
Looking at your comments on BitBucket, it was this commit in particular: https://bitbucket.org/galaxy/galaxy-central/commits/757412c63654ff16f6cd6a0b...
i.e. The commit also known as: https://github.com/galaxyproject/galaxy/commit/667c04844e35e76a698161fff6c88...
Unfortunately a clean revert is not possible,
$ git revert -n 667c04844e35e76a698161fff6c88cb03be8396a warning: too many files (created: 778 deleted: 393), skipping inexact rename detection Automatic revert failed. After resolving the conflicts, mark the corrected paths with 'git add <paths>' or 'git rm <paths>' and commit the result.
This seems to work (after resetting the symlink static/scripts/packed which seemed to have been a recent change):
https://github.com/peterjc/galaxy/commit/d6a2ded29c2bc404a0375fe4f6111311eea...
i.e. With this change, my workflow trying to use "nr" no longer defaults to the first entry in blastdb_p.loc if "nr" was missing.
Instead, as with an empty blastdb_p.loc, the workflow runs with an empty path for the database (and blastx fails cleanly).
This is MUCH better, since the workflow now fails rather than runs and gives misleading data.
The tool running even though no valid inputs are found - is a sort of known-ish issue but I cannot find any Trello card on it. I know I have some WIP on a fix here: https://github.com/jmchilton/galaxy/commit/900b7bbbf7f0084a86da9b737967fd8eb...
... and a related failing test case here. https://github.com/galaxyproject/galaxy/blob/dev/test/api/test_tools.py#L223
The fix unfortunately is messy and will likely break stuff.
-John
Running tools anyway where the expected example.loc entry is missing is bad, but most tools would fail cleanly when given an empty path - so this is less critical than the first half of the bug.
i.e. Can we address the side effects of Saket's commit?:
https://github.com/galaxyproject/galaxy/commit/667c04844e35e76a698161fff6c88... https://bitbucket.org/galaxy/galaxy-central/commits/757412c63654ff16f6cd6a0b...
Peter
On 1 April 2015 at 02:06, Peter Cock p.j.a.cock@googlemail.com wrote:
On Tue, Mar 31, 2015 at 6:12 PM, John Chilton jmchilton@gmail.com wrote:
I think it is probably a pair of bugs you are seeing:
Having tried the revert, yes, I think so too.
The wrong database being selected is probably this: https://trello.com/c/72WuZ8mu. It would be interesting to know if reverting this pull request https://bitbucket.org/galaxy/galaxy-central/pull-request/433/fix-allow-editi... fixes it - that would be a good indication this is the problem.
Looking at your comments on BitBucket, it was this commit in particular: https://bitbucket.org/galaxy/galaxy-central/commits/757412c63654ff16f6cd6a0b...
i.e. The commit also known as: https://github.com/galaxyproject/galaxy/commit/667c04844e35e76a698161fff6c88...
Unfortunately a clean revert is not possible,
$ git revert -n 667c04844e35e76a698161fff6c88cb03be8396a warning: too many files (created: 778 deleted: 393), skipping inexact rename detection Automatic revert failed. After resolving the conflicts, mark the corrected paths with 'git add <paths>' or 'git rm <paths>' and commit the result.
This seems to work (after resetting the symlink static/scripts/packed which seemed to have been a recent change):
https://github.com/peterjc/galaxy/commit/d6a2ded29c2bc404a0375fe4f6111311eea...
i.e. With this change, my workflow trying to use "nr" no longer defaults to the first entry in blastdb_p.loc if "nr" was missing.
Instead, as with an empty blastdb_p.loc, the workflow runs with an empty path for the database (and blastx fails cleanly).
This is MUCH better, since the workflow now fails rather than runs and gives misleading data.
The tool running even though no valid inputs are found - is a sort of known-ish issue but I cannot find any Trello card on it. I know I have some WIP on a fix here: https://github.com/jmchilton/galaxy/commit/900b7bbbf7f0084a86da9b737967fd8eb...
... and a related failing test case here. https://github.com/galaxyproject/galaxy/blob/dev/test/api/test_tools.py#L223
The fix unfortunately is messy and will likely break stuff.
-John
Running tools anyway where the expected example.loc entry is missing is bad, but most tools would fail cleanly when given an empty path - so this is less critical than the first half of the bug.
i.e. Can we address the side effects of Saket's commit?:
https://github.com/galaxyproject/galaxy/commit/667c04844e35e76a698161fff6c88... https://bitbucket.org/galaxy/galaxy-central/commits/757412c63654ff16f6cd6a0b...
Hi Peter,
Sorry, this really is a major bug. I agree this was pushed without much testing. In fact, I did not at all consider the use case you just pointed out. I can send a PR that simply reverts the change, since I am not sure I will have enough time to look into it deeper.
Looks like I have broken more things than what I have contributed.
Saket
Peter
On Wed, Apr 1, 2015 at 11:29 AM, Saket Choudhary saketkc@gmail.com wrote:
On 1 April 2015 at 02:06, Peter Cock p.j.a.cock@googlemail.com wrote:
On Tue, Mar 31, 2015 at 6:12 PM, John Chilton jmchilton@gmail.com wrote:
I think it is probably a pair of bugs you are seeing:
...
The fix unfortunately is messy and will likely break stuff.
-John
Running tools anyway where the expected example.loc entry is missing is bad, but most tools would fail cleanly when given an empty path - so this is less critical than the first half of the bug.
i.e. Can we address the side effects of Saket's commit?:
https://github.com/galaxyproject/galaxy/commit/667c04844e35e76a698161fff6c88... https://bitbucket.org/galaxy/galaxy-central/commits/757412c63654ff16f6cd6a0b...
Hi Peter,
Sorry, this really is a major bug. I agree this was pushed without much testing. In fact, I did not at all consider the use case you just pointed out. I can send a PR that simply reverts the change, since I am not sure I will have enough time to look into it deeper.
Looks like I have broken more things than what I have contributed.
Saket
Thanks Saket,
I didn't mean to criticize - only to ensure you were aware of this (in case you had any insight about how to fix it). Galaxy is amazingly complicated, so subtle side-effects like this can be hard to avoid - especially on the interactive side where testing is harder.
[We don't yet have a proper test framework for workflows - although John has been working on that.]
I don't understand this area of Galaxy at all (mako templates etc), so I think we'll need to defer to the full time developers who know this bit best.
Regards,
Peter
On Wed, Apr 1, 2015 at 6:50 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
On Wed, Apr 1, 2015 at 11:29 AM, Saket Choudhary saketkc@gmail.com wrote:
On 1 April 2015 at 02:06, Peter Cock p.j.a.cock@googlemail.com wrote:
On Tue, Mar 31, 2015 at 6:12 PM, John Chilton jmchilton@gmail.com wrote:
I think it is probably a pair of bugs you are seeing:
...
The fix unfortunately is messy and will likely break stuff.
-John
Running tools anyway where the expected example.loc entry is missing is bad, but most tools would fail cleanly when given an empty path - so this is less critical than the first half of the bug.
i.e. Can we address the side effects of Saket's commit?:
https://github.com/galaxyproject/galaxy/commit/667c04844e35e76a698161fff6c88... https://bitbucket.org/galaxy/galaxy-central/commits/757412c63654ff16f6cd6a0b...
Hi Peter,
Sorry, this really is a major bug. I agree this was pushed without much testing. In fact, I did not at all consider the use case you just pointed out. I can send a PR that simply reverts the change, since I am not sure I will have enough time to look into it deeper.
Looks like I have broken more things than what I have contributed.
Saket
Thanks Saket,
I didn't mean to criticize - only to ensure you were aware of this (in case you had any insight about how to fix it). Galaxy is amazingly complicated, so subtle side-effects like this can be hard to avoid - especially on the interactive side where testing is harder.
[We don't yet have a proper test framework for workflows - although John has been working on that.]
I don't understand this area of Galaxy at all (mako templates etc), so I think we'll need to defer to the full time developers who know this bit best.
Definitely - I will definitely take a crack at fixing it - though I cannot do it this week. Monday I will set aside some to try to tweak it so the fix for radio buttons will still work without actually resubmitting every workflow parameter - if I cannot fix it I will revert the commit.
-John
P.S.
I am with Peter on this Saket - I wouldn't feel bad - this is a really subtle bug. I do know that feeling of being worried the bugs I have added to Galaxy greatly out number the features though. I know that you have not actually done this - but I have added so many more bugs than you that I am less sure about myself.
Regards,
Peter
John,
I've filed a Trello card for this (please edit as you see fit):
https://trello.com/c/lkYlW14W/2615-workflows-break-when-select-parameter-loc...
Peter
On Thu, Apr 2, 2015 at 2:11 PM, John Chilton jmchilton@gmail.com wrote:
Definitely - I will definitely take a crack at fixing it - though I cannot do it this week. Monday I will set aside some to try to tweak it so the fix for radio buttons will still work without actually resubmitting every workflow parameter - if I cannot fix it I will revert the commit.
-John
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