date:20160308

Re: [galaxy-dev] iRODS

2016-03-08 Thread Kandalaft, Iyad

We were considering implementing data pull/push tools for Galaxy-iRODS 
integration but we haven't started work on that.
I recall that the Galaxy team looked at backing Galaxy with iRODS but moved 
away from the idea.  There was a trello card with that information.

Iyad Kandalaft
Bioinformatics Systems Developer
Microbial Biodiversity Bioinformatics
Science & Technology Branch
Agriculture & Agri-Food Canada
iyad.kandal...@agr.gc.ca | (613) 759-1228

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
James Taylor [ja...@bx.psu.edu]
Sent: March 8, 2016 10:09 AM
To: Mohamed Kassam
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] iRODS

Mohamed,

We implemented but never deployed the iRODS object store, so I suspect
it has not been tested much. If anyone out there is using it please
let us know.

On Mon, Mar 7, 2016 at 10:30 AM, Mohamed Kassam  wrote:
> Dear all,
> I would like to use our interlan iRODs to pull data.
> I searched and i find that there is an object store for that.
> How it works ? DO  I need to configure something else ?
>
> Thanks in advance,
>
>
> Mohamed
>
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Re: [galaxy-dev] quota api error

2016-03-08 Thread Fabien Mareuil


Hi Dannon,

I got this error with a detail view (/api/quotas/f597429621d6eb2b) when 
the quota has associated users with a disk usage different of 0, 
total_disk_usage in the user dictionary is a Decimal object and is not 
serializable.
I worked on it this afternoon, it's possible to correct it just by 
adding the key 'total_disk_usage' in the value_mapper of the show method 
of QuotaAPIController class like the show method of UserAPIController class.

I join a patch for the quota.py file with this email
I can propose a pull request if you want.


Best,

--
Fabien Mareuil | Centre d'Informatique pour la Biologie
fabien.mare...@pasteur.fr  | Institut 
Pasteur

25,28 rue du Docteur Roux 75015 Paris, France



Le 08/03/2016 16:24, Dannon Baker a écrit :

Hi Fabien,

I'm having trouble reproducing this error on my side.  In the trace it 
looks like the error is being thrown at the collection view 
(/api/quotas) and not the detail view (/api/quotas/f597429621d6eb2b or 
the like).  Is that true?


Can you show me the exact configuration of this quota in the admin panel?

On Tue, Mar 8, 2016 at 8:10 AM, Fabien Mareuil > wrote:


Hi,

We got an error when we used API to see a quota detail, we get the
following traceback:

157.99.60.167 - - [08/Mar/2016:10:13:58 +0200] "GET /api/quotas
HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:44.0) Gecko/20100101 Firefox/44.0"
galaxy.web.framework.decorators ERROR 2016-03-08 10:14:10,273
Uncaught exception in exposed API method:
Traceback (most recent call last):
  File ".../lib/galaxy/web/framework/decorators.py", line 142, in
decorator
rval = dumps( rval, indent=4, sort_keys=True )
  File ".../lib/galaxy/util/json.py", line 65, in safe_dumps
dumped = json.dumps( *args, allow_nan=False, **kwargs )
  File "/usr/lib64/python2.6/json/__init__.py", line 237, in dumps
**kw).encode(obj)
  File "/usr/lib64/python2.6/json/encoder.py", line 367, in encode
chunks = list(self.iterencode(o))
  File "/usr/lib64/python2.6/json/encoder.py", line 309, in
_iterencode
for chunk in self._iterencode_dict(o, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 275, in
_iterencode_dict
for chunk in self._iterencode(value, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 306, in
_iterencode
for chunk in self._iterencode_list(o, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 204, in
_iterencode_list
for chunk in self._iterencode(value, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 309, in
_iterencode
for chunk in self._iterencode_dict(o, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 275, in
_iterencode_dict
for chunk in self._iterencode(value, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 309, in
_iterencode
for chunk in self._iterencode_dict(o, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 275, in
_iterencode_dict
for chunk in self._iterencode(value, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 317, in
_iterencode
for chunk in self._iterencode_default(o, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 323, in
_iterencode_default
newobj = self.default(o)
  File "/usr/lib64/python2.6/json/encoder.py", line 344, in default
raise TypeError(repr(o) + " is not JSON serializable")
TypeError: Decimal('856488698767') is not JSON serializable

json can't serialize Decimal object.
I tested it with simplejson and it works.
An other solution is to convert the Decimal object to a float
before the dumps.

Thanks a lot for your help
Best regards,

-- 
Fabien Mareuil | Centre d'Informatique pour la Biologie

fabien.mare...@pasteur.fr  |
Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France


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--- lib/galaxy/webapps/galaxy/api/quotas_orig.py	2016-03-08 17:27:03.235186824 +0100
+++ lib/galaxy/webapps/galaxy/api/quotas.py	2016-03-08 17:27:53.339187785 +0100
@@ -50,7 +50,7 @@
 Displays information about a quota.
 """
 quota = self.get_quota( trans, id, deleted=util.string_as_bool( deleted ) )
-return quota.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } )
+return quota.to_dict( view='element', value_mapper={ 'id

Re: [galaxy-dev] quota api error

2016-03-08 Thread Dannon Baker

Hi Fabien,

I'm having trouble reproducing this error on my side.  In the trace it
looks like the error is being thrown at the collection view (/api/quotas)
and not the detail view (/api/quotas/f597429621d6eb2b or the like).  Is
that true?

Can you show me the exact configuration of this quota in the admin panel?

On Tue, Mar 8, 2016 at 8:10 AM, Fabien Mareuil  wrote:

> Hi,
>
> We got an error when we used API to see a quota detail, we get the
> following traceback:
>
> 157.99.60.167 - - [08/Mar/2016:10:13:58 +0200] "GET /api/quotas HTTP/1.1"
> 200 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:44.0) Gecko/20100101
> Firefox/44.0"
> galaxy.web.framework.decorators ERROR 2016-03-08 10:14:10,273 Uncaught
> exception in exposed API method:
> Traceback (most recent call last):
>   File ".../lib/galaxy/web/framework/decorators.py", line 142, in decorator
> rval = dumps( rval, indent=4, sort_keys=True )
>   File ".../lib/galaxy/util/json.py", line 65, in safe_dumps
> dumped = json.dumps( *args, allow_nan=False, **kwargs )
>   File "/usr/lib64/python2.6/json/__init__.py", line 237, in dumps
> **kw).encode(obj)
>   File "/usr/lib64/python2.6/json/encoder.py", line 367, in encode
> chunks = list(self.iterencode(o))
>   File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
> for chunk in self._iterencode_dict(o, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 275, in
> _iterencode_dict
> for chunk in self._iterencode(value, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 306, in _iterencode
> for chunk in self._iterencode_list(o, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 204, in
> _iterencode_list
> for chunk in self._iterencode(value, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
> for chunk in self._iterencode_dict(o, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 275, in
> _iterencode_dict
> for chunk in self._iterencode(value, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
> for chunk in self._iterencode_dict(o, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 275, in
> _iterencode_dict
> for chunk in self._iterencode(value, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 317, in _iterencode
> for chunk in self._iterencode_default(o, markers):
>   File "/usr/lib64/python2.6/json/encoder.py", line 323, in
> _iterencode_default
> newobj = self.default(o)
>   File "/usr/lib64/python2.6/json/encoder.py", line 344, in default
> raise TypeError(repr(o) + " is not JSON serializable")
> TypeError: Decimal('856488698767') is not JSON serializable
>
> json can't serialize Decimal object.
> I tested it with simplejson and it works.
> An other solution is to convert the Decimal object to a float before the
> dumps.
>
> Thanks a lot for your help
> Best regards,
>
> --
> Fabien Mareuil | Centre d'Informatique pour la Biologie
> fabien.mare...@pasteur.fr | Institut Pasteur
> 25,28 rue du Docteur Roux 75015 Paris, France
>
>
> ___
> 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/
>
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in your mail client.  To manage your subscriptions to this
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Re: [galaxy-dev] iRODS

2016-03-08 Thread James Taylor

Mohamed,

We implemented but never deployed the iRODS object store, so I suspect
it has not been tested much. If anyone out there is using it please
let us know.

On Mon, Mar 7, 2016 at 10:30 AM, Mohamed Kassam  wrote:
> Dear all,
> I would like to use our interlan iRODs to pull data.
> I searched and i find that there is an object store for that.
> How it works ? DO  I need to configure something else ?
>
> Thanks in advance,
>
>
> Mohamed
>
> ___
> 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/
___
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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[galaxy-dev] quota api error

2016-03-08 Thread Fabien Mareuil


Hi,

We got an error when we used API to see a quota detail, we get the 
following traceback:


157.99.60.167 - - [08/Mar/2016:10:13:58 +0200] "GET /api/quotas 
HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:44.0) 
Gecko/20100101 Firefox/44.0"
galaxy.web.framework.decorators ERROR 2016-03-08 10:14:10,273 Uncaught 
exception in exposed API method:

Traceback (most recent call last):
  File ".../lib/galaxy/web/framework/decorators.py", line 142, in decorator
rval = dumps( rval, indent=4, sort_keys=True )
  File ".../lib/galaxy/util/json.py", line 65, in safe_dumps
dumped = json.dumps( *args, allow_nan=False, **kwargs )
  File "/usr/lib64/python2.6/json/__init__.py", line 237, in dumps
**kw).encode(obj)
  File "/usr/lib64/python2.6/json/encoder.py", line 367, in encode
chunks = list(self.iterencode(o))
  File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
for chunk in self._iterencode_dict(o, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 275, in 
_iterencode_dict

for chunk in self._iterencode(value, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 306, in _iterencode
for chunk in self._iterencode_list(o, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 204, in 
_iterencode_list

for chunk in self._iterencode(value, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
for chunk in self._iterencode_dict(o, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 275, in 
_iterencode_dict

for chunk in self._iterencode(value, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
for chunk in self._iterencode_dict(o, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 275, in 
_iterencode_dict

for chunk in self._iterencode(value, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 317, in _iterencode
for chunk in self._iterencode_default(o, markers):
  File "/usr/lib64/python2.6/json/encoder.py", line 323, in 
_iterencode_default

newobj = self.default(o)
  File "/usr/lib64/python2.6/json/encoder.py", line 344, in default
raise TypeError(repr(o) + " is not JSON serializable")
TypeError: Decimal('856488698767') is not JSON serializable

json can't serialize Decimal object.
I tested it with simplejson and it works.
An other solution is to convert the Decimal object to a float before the 
dumps.


Thanks a lot for your help
Best regards,

--
Fabien Mareuil | Centre d'Informatique pour la Biologie
fabien.mare...@pasteur.fr  | Institut 
Pasteur

25,28 rue du Docteur Roux 75015 Paris, France

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[galaxy-dev] Setting job_working_directory on per-tool basis? (cuffdiff/cummerbund SQLite db error)

2016-03-08 Thread Peter Briggs


Hello

I've encountered an issue with running the cuffdiff tool on our local 
production Galaxy instance.


Specifically when a cummerbund SQLite database is requested as output 
then the tool fails with an error:


Creating database ./cummeRbund.sqlite
Error in sqliteSendQuery(con, statement, bind.data) :
  error in statement: disk I/O error
Error in sqliteSendQuery(con, statement, bind.data) :
  error in statement: disk I/O error
Calls: readCufflinks ... .local -> sqliteGetQuery -> sqliteSendQuery -> 
.Call

Execution halted

Our Galaxy is configured to use a LustreFS scratch directory for the 
'job_working_directory', which I understand is where each job will have 
its own working directory created, and I'm wondering if the SQLite error 
above is a manifestation of a general problem with SQLite on LustreFS 
(see e.g. the answer to this BioStars question 
https://www.biostars.org/p/115452/).


The obvious workaround is to change 'job_working_directory', preferably 
just for the cuffdiff tool. Does anyone know if it's possible to do this 
i.e. set 'job_working_directory' on a per-tool basis?


(Also, has anyone else seen this specific problem with 
cuffdiff/cummerbund/SQLite on their local Galaxy instances?)


Thanks for your help - any suggestions greatly appreciated,

Best wishes

Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: [galaxy-dev] iRODS

Re: [galaxy-dev] quota api error

Re: [galaxy-dev] quota api error

Re: [galaxy-dev] iRODS

[galaxy-dev] quota api error

[galaxy-dev] Setting job_working_directory on per-tool basis? (cuffdiff/cummerbund SQLite db error)

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