Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

2013-03-20 Thread Nicola Soranzo
Il giorno mar, 19/03/2013 alle 15.20 -0400, Raj Ayyampalayam ha
scritto: 
 One of the first few tools I tested was the ncbi makebkastdb tool. When 
 I try to run it the history for that particular job is immediately shown 
 as follows:
 
 0: (unnamed dataset)
 Failed to retrieve dataset information.
 An error occurred with this dataset:/hasattr(): attribute name must be 
 string/

Hi Raj,
this error in the history should be fixed by this patch:

https://bitbucket.org/nsoranzo/peterjc-galaxy-central-tools2/commits/35163cbc6c694f598ed1a1875353c58b275e2423

I have sent a pull request to Peter (the maintainer), hopefully he will
release soon a new version of blast_datatypes with this fix.

Best,
Nicola


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Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

2013-03-20 Thread Peter Cock
On Wed, Mar 20, 2013 at 10:08 AM, Nicola Soranzo sora...@crs4.it wrote:
 Il giorno mar, 19/03/2013 alle 15.20 -0400, Raj Ayyampalayam ha
 scritto:
 One of the first few tools I tested was the ncbi makebkastdb tool. When
 I try to run it the history for that particular job is immediately shown
 as follows:

 0: (unnamed dataset)
 Failed to retrieve dataset information.
 An error occurred with this dataset:/hasattr(): attribute name must be
 string/

 Hi Raj,
 this error in the history should be fixed by this patch:

 https://bitbucket.org/nsoranzo/peterjc-galaxy-central-tools2/commits/35163cbc6c694f598ed1a1875353c58b275e2423

 I have sent a pull request to Peter (the maintainer), hopefully he will
 release soon a new version of blast_datatypes with this fix.

 Best,
 Nicola

The patch just removes the MetadataElement call - is that wise?

Looking at the code, I don't see a recent API change regarding
the name:

https://bitbucket.org/galaxy/galaxy-central/history-node/default/lib/galaxy/datatypes/metadata.py?at=default

Is there perhaps a universe_wsgi.ini setting which might be involved,
since I've not seen this error locally?

Peter
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Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

2013-03-20 Thread Nicola Soranzo
Il giorno mer, 20/03/2013 alle 12.41 +, Peter Cock ha scritto: 
 On Wed, Mar 20, 2013 at 10:08 AM, Nicola Soranzo sora...@crs4.it wrote:
  Il giorno mar, 19/03/2013 alle 15.20 -0400, Raj Ayyampalayam ha
  scritto:
  One of the first few tools I tested was the ncbi makebkastdb tool. When
  I try to run it the history for that particular job is immediately shown
  as follows:
 
  0: (unnamed dataset)
  Failed to retrieve dataset information.
  An error occurred with this dataset:/hasattr(): attribute name must be
  string/
 
  Hi Raj,
  this error in the history should be fixed by this patch:
 
  https://bitbucket.org/nsoranzo/peterjc-galaxy-central-tools2/commits/35163cbc6c694f598ed1a1875353c58b275e2423
 
  I have sent a pull request to Peter (the maintainer), hopefully he will
  release soon a new version of blast_datatypes with this fix.
 
  Best,
  Nicola
 
 The patch just removes the MetadataElement call - is that wise?

Hi Peter,
my question instead is, what are they for? With 'name' they have no
meaning.

 Looking at the code, I don't see a recent API change regarding
 the name:
 
 https://bitbucket.org/galaxy/galaxy-central/history-node/default/lib/galaxy/datatypes/metadata.py?at=default
 
 Is there perhaps a universe_wsgi.ini setting which might be involved,
 since I've not seen this error locally?

$ cd lib/galaxy/datatypes/
$ grep 'MetadataElement(' *.py|grep -v name

returns nothing, so the 'name' parameter is really mandatory.

Best,
Nicola

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Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

2013-03-20 Thread Peter Cock
On Wed, Mar 20, 2013 at 1:55 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
 On Wed, Mar 20, 2013 at 1:52 PM, Nicola Soranzo sora...@crs4.it wrote:
 Il giorno mer, 20/03/2013 alle 12.41 +, Peter Cock ha scritto:

 The patch just removes the MetadataElement call - is that wise?

 Hi Peter,
 my question instead is, what are they for? With 'name' they have no
 meaning.

 Looking at the code, I don't see a recent API change regarding
 the name:

 https://bitbucket.org/galaxy/galaxy-central/history-node/default/lib/galaxy/datatypes/metadata.py?at=default

 Is there perhaps a universe_wsgi.ini setting which might be involved,
 since I've not seen this error locally?

 $ cd lib/galaxy/datatypes/
 $ grep 'MetadataElement(' *.py|grep -v name

 returns nothing, so the 'name' parameter is really mandatory.

 Best,
 Nicola


 Good question - I'd have to ask Edward what he thought this did,
 but you seem to be right that as the code stands this metadata
 element is rather pointless.

 (I'm still puzzled why we don't see the error here though).

 I'll apply your patch and test it locally...

 Peter

Nicola - It looks good here, uploaded to the ToolShed as v0.0.15
http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes

Raj - Could you apply the update from the ToolShed and
confirm if that fixes the problem for you?

Edward - have you received my direct email off list?

Thanks,

Peter
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Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

2013-03-20 Thread Raj Ayyampalayam

Hi Guys,

Thanks for the quick response. I installed the latest blast datatypes 
from the toolshed and that fixed the issue.


Peter, can you also fix the  $outfile.extra_files_path to 
$outfile.files_path on line 5 in the makedb wrapper xml file.


Thanks,
-Raj



On Wednesday, March 20, 2013 10:42:43 AM, Peter Cock wrote:

On Wed, Mar 20, 2013 at 1:55 PM, Peter Cock p.j.a.c...@googlemail.com wrote:

On Wed, Mar 20, 2013 at 1:52 PM, Nicola Soranzo sora...@crs4.it wrote:

Il giorno mer, 20/03/2013 alle 12.41 +, Peter Cock ha scritto:


The patch just removes the MetadataElement call - is that wise?


Hi Peter,
my question instead is, what are they for? With 'name' they have no
meaning.


Looking at the code, I don't see a recent API change regarding
the name:

https://bitbucket.org/galaxy/galaxy-central/history-node/default/lib/galaxy/datatypes/metadata.py?at=default

Is there perhaps a universe_wsgi.ini setting which might be involved,
since I've not seen this error locally?


$ cd lib/galaxy/datatypes/
$ grep 'MetadataElement(' *.py|grep -v name

returns nothing, so the 'name' parameter is really mandatory.

Best,
Nicola



Good question - I'd have to ask Edward what he thought this did,
but you seem to be right that as the code stands this metadata
element is rather pointless.

(I'm still puzzled why we don't see the error here though).

I'll apply your patch and test it locally...

Peter


Nicola - It looks good here, uploaded to the ToolShed as v0.0.15
http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes

Raj - Could you apply the update from the ToolShed and
confirm if that fixes the problem for you?

Edward - have you received my direct email off list?

Thanks,

Peter



--
Bio-informatics consultant
QBCG (http://qbcg.uga.edu)
706-542-6092
706-583-0442

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Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

2013-03-20 Thread Peter Cock
On Wed, Mar 20, 2013 at 3:43 PM, Raj Ayyampalayam ra...@uga.edu wrote:
 Hi Guys,

 Thanks for the quick response. I installed the latest blast datatypes from
 the toolshed and that fixed the issue.

Great - thanks for letting us know so promptly.

 Peter, can you also fix the  $outfile.extra_files_path to
 $outfile.files_path on line 5 in the makedb wrapper xml file.

What do you mean 'fix' it? It should be using extra_files_path
shouldn't it? This is a composite datatype in Galaxy.

Peter
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Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

2013-03-20 Thread Peter Cock
On Wed, Mar 20, 2013 at 3:47 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
 On Wed, Mar 20, 2013 at 3:43 PM, Raj Ayyampalayam ra...@uga.edu wrote:
 Hi Guys,

 Thanks for the quick response. I installed the latest blast datatypes from
 the toolshed and that fixed the issue.

 Great - thanks for letting us know so promptly.

 Peter, can you also fix the  $outfile.extra_files_path to
 $outfile.files_path on line 5 in the makedb wrapper xml file.

 What do you mean 'fix' it? It should be using extra_files_path
 shouldn't it? This is a composite datatype in Galaxy.

Are you perhaps running jobs as real user? That might explain
when this difference is important:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-April/009579.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-March/013889.html

Thanks,

Peter
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