Re: [galaxy-dev] bioblend problem trying to use run_tool function
Hello John,
Sorry to bother you again with this. I saw the many improvments added
but I still can't run my tool using bioblend.
The inputs names are 'input' and 'prefix' and the tool is very simple.
The problem is still a mapping issue. Parameters are not assigned
correctly in the command line. options are there but no values are there.
Could you give me a use case, so I can mime it to my project ?
Thanks in advance,
--
Olivia Doppelt-Azeroual
CIB, Institut Pasteur, Paris
Le 27/02/14 14:46, John Chilton a écrit :
I think you are right, and I am right, but you more so :). I bet the
inputs need to be dumped to json if files are being attached (i.e.
upload is being used) but should not be otherwise (because
content-type will be different). I wrote the client just to test
uploads - so this is probably the problem.
I have created a Trello card (https://trello.com/c/67HsrgVm) to fix
bioblend to handle these details transparently and (per your other
email) to test and provide examples of using a repeat with data
parameters. I am certain the Galaxy API allows this - I am not sure
the bioblend tool client is quite there yet - it shouldn't be hard to
update it or provide examples - but I will need to find some time
which can be difficult.
-John
On Tue, Feb 25, 2014 at 4:41 AM, Olivia Doppelt-Azeroual
olivia.dopp...@pasteur.fr wrote:
Dear John,
I am doing tests on a local version of the last galaxy-dist version before
updating our Galaxy server. And I have a question concernant the second
remark you made in your last email.
I've written a small script to test the run_tool function. When i put back
the dumps(inputs_dict), the script fails whereas the type of my input_dict
is a dictionnary.
The script is the following:
--
from bioblend.galaxy import GalaxyInstance
giLocal=GalaxyInstance('http://127.0.0.1:8080/',
key='43359c833b8977b01d6237d9b839dc27')
tool_inputs_loc={'input':'f597429621d6eb2b','name':data}
print type(tool_inputs_loc)
giLocal.tools.run_tool(history_id='1cd8e2f6b131e891',tool_id='export',tool_inputs=tool_inputs_loc)
---
when i print the payload it is:
{'tool_id': 'export', 'history_id': '1cd8e2f6b131e891', 'inputs': '{input:
f597429621d6eb2b, name: data}'}
On the server side, the error is the following:
--
galaxy.web.framework ERROR 2014-02-25 11:35:34,865 Uncaught exception in
exposed API method:
Traceback (most recent call last):
File
/home/odoppelt/localStuff_VM/tools/new_galaxy_disr/galaxy-dist/lib/galaxy/web/framework/__init__.py,
line 200, in decorator
rval = func( self, trans, *args, **kwargs)
File
/home/odoppelt/localStuff_VM/tools/new_galaxy_disr/galaxy-dist/lib/galaxy/webapps/galaxy/api/tools.py,
line 104, in create
for k, v in inputs.iteritems():
AttributeError: 'unicode' object has no attribute 'iteritems'
Do you have an idea ?
Have a nice day,
Thank you for your help,
--
Olivia
Le 24/02/14 16:18, John Chilton a écrit :
Yes, the get_intial_value bug was a bug that has been fixed in a
recent Galaxy release (I think the most recent one, but maybe the
previous one). Unfortunately though, I fixed other bugs related to
running more sophisticated tools through the API at the same time - so
I would again strongly recommend upgrading before proceeding or you
going to find all the same bugs I did. The tool running API has
significantly improved over the last couple releases.
As for removing the dumps statement in bioblend - I think (though am
not certain) that is the wrong thing to do. I think you are likely
somehow doing this at a level above the client call and shouldn't be -
i.e. my guess is you are passing in a string instead of a dictionary
and the result is that dumps it dumping an escaped string - instead of
jsonifing a dictionary.
For instance, the API driven test framework runs by calling this API
and does almost this exact dumps.
https://bitbucket.org/galaxy/galaxy-central/src/f573461f3667e8f120dc05bbd11a019d5fae1960/test/base/interactor.py?at=default#cl-251
Hope this helps.
-John
On Mon, Feb 24, 2014 at 8:51 AM, Olivia Doppelt-Azeroual
olivia.dopp...@pasteur.fr wrote:
I detected another problem which enables me to go further, however
doesn't
resolve the whole problem yet.
the function get_initial value didn't use the history in the recursive
call,
which led to an empty history. I changed it juste adding history to the
input.get_initial_value
def get_initial_value( self, trans, context, history=None ):
rval = []
for i in range( self.default ):
rval_dict = { '__index__': i}
for input in self.inputs.itervalues():
rval_dict[ input.name ] = input.get_initial_value(
trans,
context, history )
rval.append( rval_dict )
return rval
There is another problem though.
On the bioblend side:
_
Traceback (most recent call last):
File
Re: [galaxy-dev] workflow_execute_parameters.py
Dear Dannon,
when the parameter (that I need to fix) is 'set at runtime', the value
that it gets is: __lt__galaxy.tools.parameters.basic.RuntimeValue
python workflow_execute_parameters.py 43359c833b8977b01d6237d9b839dc27
http://127.0.0.1:8080/api/workflows f2db41e1fa331b3e a799d38679e985db
'14=hda=52ea4fd71e9f7c3f' 'param=export_sbw=prefix=test'
the parameter prefix needs to be set at the value test (I tried
without the quotes also)
---
Here is what you asked for:
{
id: f2db41e1fa331b3e,
inputs: {
14: {
label: input Dataset,
value:
}
},
model_class: StoredWorkflow,
name: export_WF,
published: false,
steps: {
14: {
id: 14,
input_steps: {},
tool_id: null,
type: data_input
},
15: {
id: 15,
input_steps: {
inputs_0|input: {
source_step: 14,
step_output: output
}
},
tool_id: export_sbw,
type: tool
}
},
tags: [],
url: /api/workflows/f2db41e1fa331b3e
}
as you can see, the parameter called prefix, is not there.
Thank you for your help
--
Olivia
Le 25/04/14 19:49, Dannon Baker a écrit :
Olivia,
Is the parameter set to 'set at runtime' when you view the workflow in
the editor? Could you send me the workflow json (just the
http://127.0.0.1:8080/api/workflows/workflow_id/ bit)?
-Dannon
On Fri, Apr 25, 2014 at 5:26 AM, Olivia Doppelt-Azeroual
olivia.dopp...@pasteur.fr mailto:olivia.dopp...@pasteur.fr wrote:
Dear Dannon,
Thank you for your answer, it works better now that I know the
steps ID for my workflow.
I have another question though.
The second step of my WF uses a parameter input named prefix. I
really need to specify it when I launch the WF using the API.
When i display the WF using the url you gave me, the parameters
prefix, is not there and when I use this in my command line, the
specified Value is not read by Galaxy.
python workflow_execute_parameters.py
43359c833b8977b01d6237d9b839dc27
http://127.0.0.1:8080/api/workflows f2db41e1fa331b3e
a799d38679e985db '10=hda=52ea4fd71e9f7c3f'
'param=export_sbw=prefix=test'
Could you help me on that ? How do I give a value to a parameter
if it does not appear in the WF description ??
Thanks in advance,
--
Olivia
Le 23/04/14 18:40, Dannon Baker a écrit :
Hi Olivia!
It's probably talking about the workflowstep object with
identifier 8. If you request the description of this workflow
via the API (http://yourgalaxyinstance.org/api/workflows/the id
of this workflow), you'll be given the exact step identifiers
to use. In other words, unless this is the first workflow ever
created on a brand new galaxy instance, your step ids will not be
0 and 1.
-Dannon
On Wed, Apr 23, 2014 at 12:30 PM, Olivia Doppelt-Azeroual
olivia.dopp...@pasteur.fr mailto:olivia.dopp...@pasteur.fr wrote:
Dear developpers,
I'm trying to launch a small workflow using the api script
workflow_execute_parameters.py
I have 2 steps: the input data step and a second step which
needs a parameter called prefix.
The workflow is attached to this email.
I get an error on the parameters inputs which asks me to
specify information about an 8th step (which does not exist)
Is there a test case available to use this script ?
Please keep me informed on that.
Have a nice day,
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
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--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
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Re: [galaxy-dev] workflow_execute_parameters.py
Dear Dannon, Thank you for your answer, it works better now that I know the steps ID for my workflow. I have another question though. The second step of my WF uses a parameter input named prefix. I really need to specify it when I launch the WF using the API. When i display the WF using the url you gave me, the parameters prefix, is not there and when I use this in my command line, the specified Value is not read by Galaxy. python workflow_execute_parameters.py 43359c833b8977b01d6237d9b839dc27 http://127.0.0.1:8080/api/workflows f2db41e1fa331b3e a799d38679e985db '10=hda=52ea4fd71e9f7c3f' 'param=export_sbw=prefix=test' Could you help me on that ? How do I give a value to a parameter if it does not appear in the WF description ?? Thanks in advance, -- Olivia Le 23/04/14 18:40, Dannon Baker a écrit : Hi Olivia! It's probably talking about the workflowstep object with identifier 8. If you request the description of this workflow via the API (http://yourgalaxyinstance.org/api/workflows/the id of this workflow), you'll be given the exact step identifiers to use. In other words, unless this is the first workflow ever created on a brand new galaxy instance, your step ids will not be 0 and 1. -Dannon On Wed, Apr 23, 2014 at 12:30 PM, Olivia Doppelt-Azeroual olivia.dopp...@pasteur.fr mailto:olivia.dopp...@pasteur.fr wrote: Dear developpers, I'm trying to launch a small workflow using the api script workflow_execute_parameters.py I have 2 steps: the input data step and a second step which needs a parameter called prefix. The workflow is attached to this email. I get an error on the parameters inputs which asks me to specify information about an 8th step (which does not exist) Is there a test case available to use this script ? Please keep me informed on that. Have a nice day, -- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur ___ 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/ -- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur ___ 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] workflow_execute_parameters.py
Dear developpers,
I'm trying to launch a small workflow using the api script
workflow_execute_parameters.py
I have 2 steps: the input data step and a second step which needs a
parameter called prefix.
The workflow is attached to this email.
I get an error on the parameters inputs which asks me to specify
information about an 8th step (which does not exist)
Is there a test case available to use this script ?
Please keep me informed on that.
Have a nice day,
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
{
a_galaxy_workflow: true,
annotation: ,
format-version: 0.1,
name: export_WF,
steps: {
0: {
annotation: ,
id: 0,
input_connections: {},
inputs: [
{
description: ,
name: input Dataset
}
],
name: Input dataset,
outputs: [],
position: {
left: 289.8824539185,
top: 449.500984192
},
tool_errors: null,
tool_id: null,
tool_state: {\name\: \input Dataset\},
tool_version: null,
type: data_input,
user_outputs: []
},
1: {
annotation: ,
id: 1,
input_connections: {
inputs_0|input: {
id: 0,
output_name: output
}
},
inputs: [],
name: export data for SynBioWatch,
outputs: [
{
name: output,
type: text
}
],
position: {
left: 569.882453918,
top: 369.806159973
},
post_job_actions: {},
tool_errors: null,
tool_id: export_sbw,
tool_state: {\inputs\: \[{\\\__index__\\\: 0,
\\\prefix\\\: {\\\__class__\\\: \\\RuntimeValue\\\}, \\\input\\\:
null}]\, \__rerun_remap_job_id__\: null, \__page__\: 0},
tool_version: 1.0,
type: tool,
user_outputs: []
}
}
}___
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[galaxy-dev] launching openmpi tool with Galaxy
Dear developers, I'm trying to launch a mpi version of test tool. To do so, I have a test xml called sleep.xml but all he does is write the hostname of the machine in an output file. (command: /usr/lib64/openmpi/bin/mpirun hostname $output) When I launch this tool as a local job (we use son of grid engine as the job scheduler), everything is ok. When i specify the following line in the universe_wsgi.xml: sleep = drmaa://-q galaxy -pe openmpi 8/ The program is launched but it is lost somewhere and juste doesn't do anything. It is just running and never ends. Does someone has an explanation for that ? Thanks in advance, -- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur ___ 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] bioblend run_tool function used with a tool containing repeats for inputs in its XML
Dear Developpers, I'm still trying to use the bioblend function run_tool and now that I've uptdated my version of galaxy, the problem comes from the input_dict used to define the inputs. The command line generated is right except for the inputs information, it is either None are sometimes, nothing is just written there. I'm starting to think that it is due to the fact that in my xml tool, there is a way to add as many inputs as needed using the repeats tag. This maybe confuses the link between bioblend and galaxy as the variables are named differently in the cheetah command line. Is there an example of a run_tool utilisation ? somewhere ? Thanks in advance for your help. Have a nice day, -- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur ___ 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] bioblend problem trying to use run_tool function
Hello John,
Yes it helps a little but I still have the following error:
___
Traceback (most recent call last):
File script_testBioblend_distant.py, line 16, in module
giLocal.tools.run_tool(history_id='0a248a1f62a0cc04',tool_id='export',tool_inputs=tool_inputs_loc)
File
/home/odoppelt/localStuff_VM/galaxy_work/SBW_project/bioblend/bioblend/galaxy/tools/__init__.py,
line 26, in run_tool
return Client._post(self, payload)
File
/home/odoppelt/localStuff_VM/galaxy_work/SBW_project/bioblend/bioblend/galaxy/client.py,
line 181, in _post
r = self.gi.make_post_request(url, payload=payload,
files_attached=files_attached)
File
/home/odoppelt/localStuff_VM/galaxy_work/SBW_project/bioblend/bioblend/galaxyclient.py,
line 94, in make_post_request
r.status_code, body=r.text) # @see self.body for HTTP response body
bioblend.galaxy.client.ConnectionError: Unexpected response from galaxy:
500: html
headtitleInternal Server Error/title/head
body
h1Internal Server Error/h1
pThe server has either erred or is incapable of performing
the requested operation.
br/
!-- --/p
hr noshade
div align=rightWSGI Server/div
/body
/html
___
I'm currently trying to understand this error. Please tell me if you
know anything about this error.
Have a nice day,
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
Le 21/02/14 15:49, John Chilton a écrit :
I copied the HTML into a new document, opened it, and copied the
stacktrace produced by Galaxy - it looks like this:
Internal Server Error
Galaxy was unable to successfully complete your request
URL: http://galaxy.web.pasteur.fr/api/tools?key=c23d8cb98671911813305051710d4ae1
Module galaxy.web.framework.middleware.error:149 in __call__
app_iter = self.application(environ, sr_checker)
Module paste.recursive:84 in __call__
return self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:96 in __call__
return self.app( environ, start_response )
Module paste.httpexceptions:633 in __call__
return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
body = method( trans, **kwargs )
Module galaxy.web.framework:201 in decorator
log.exception( 'Uncaught exception in exposed API method:'+
str(err),exc_info=True)
TypeError: exception() got an unexpected keyword argument 'exc_info'
So what is happening here is and error is occurring when Galaxy is
trying to log another error - causing the API to break down. I don't
think the newest release of Galaxy has this line:
log.exception( 'Uncaught exception in exposed API method:'+
str(err),exc_info=True)
I am not sure what exc_info is - but it looks like it shouldn't be
there. You may want to remove that and see if you get a cleaner error
message that is easier to interpret.
Hope this helps.
-John
On Fri, Feb 21, 2014 at 3:50 AM, Olivia Doppelt
olivia.dopp...@pasteur.fr wrote:
Dear Developers,
I would like to use bioblend to export the result of a galaxy workflow.
To do that, we want to use an implemented tool called export_data; which
enables the copy of a result file from galaxy arborescence to a local
directory which belong to the user making the analysis and the export.
We tried to launch this tool using the run_tool function but it doesn't
work.
giOlivia.tools.run_tool(history_id='xxx',tool_id='/export_data/export/2.2',tool_inputs={'input':'id_data','name':data})
I get an error message which is very long and attached to this email.
Please help me on that it is the final step of several ones using bioblend.
Have a nice day,
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
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___
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Re: [galaxy-dev] bioblend problem trying to use run_tool function
I detected another problem which enables me to go further, however
doesn't resolve the whole problem yet.
the function get_initial value didn't use the history in the recursive
call, which led to an empty history. I changed it juste adding *history*
to the input.get_initial_value
def get_initial_value( self, trans, context, history=None ):
rval = []
for i in range( self.default ):
rval_dict = { '__index__': i}
for input in self.inputs.itervalues():
rval_dict[ input.name ] = input.get_initial_value(
trans, context, *history* )
rval.append( rval_dict )
return rval
There is another problem though.
On the bioblend side:
_
Traceback (most recent call last):
File script_testBioblend_distant.py, line 16, in module
giLocal.tools.run_tool(history_id='0a248a1f62a0cc04',tool_id='export',tool_inputs={'input':'8ad39366bdad8699','name':data})
File
/home/odoppelt/localStuff_VM/galaxy_work/SBW_project/bioblend/bioblend/galaxy/tools/__init__.py,
line 26, in run_tool
return Client._post(self, payload)
File
/home/odoppelt/localStuff_VM/galaxy_work/SBW_project/bioblend/bioblend/galaxy/client.py,
line 181, in _post
r = self.gi.make_post_request(url, payload=payload,
files_attached=files_attached)
File
/home/odoppelt/localStuff_VM/galaxy_work/SBW_project/bioblend/bioblend/galaxyclient.py,
line 94, in make_post_request
r.status_code, body=r.text) # @see self.body for HTTP response body
bioblend.galaxy.client.ConnectionError: Unexpected response from galaxy:
400: {
message: {
data: {
inputs: [
{
input: History does not include a dataset of the
required format / build
}
]
},
type: error
}
}
On the galaxy side, there is no error message.
Sorry for the many mails but I prefer to keep you updated so you dont
waste time.
--
Olivia
Le 24/02/14 15:29, Olivia Doppelt-Azeroual a écrit :
Yes, indeed,
the log from galaxy are the following:
The first error was due to the fact that bioblend function run_tools;
gave galaxy a dump of the input_dicts which type is string where
galaxy was waiting for an item structure.
I removed the dump:
payload[inputs] = tool_inputs
instead of
payload[inputs] = dumps(tool_inputs)
However, there is another error afterwards which is:
___
/home/odoppelt/localStuff_VM/tools/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/types.py:215:
SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects
natively, and SQLAlchemy must convert from floating point - rounding
errors and other issues may occur. Please consider storing Decimal
numbers as strings or integers on this platform for lossless storage.
galaxy.web.framework ERROR 2014-02-24 15:15:15,374 Uncaught exception
in exposed API method:
Traceback (most recent call last):
File
/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/web/framework/__init__.py,
line 203, in decorator
rval = func( self, trans, *args, **kwargs)
File
/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/webapps/galaxy/api/tools.py,
line 123, in create
template, vars = tool.handle_input( trans, params.__dict__,
history=target_history )
File
/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/tools/__init__.py,
line 1921, in handle_input
state = self.new_state( trans, history=history )
File
/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/tools/__init__.py,
line 1846, in new_state
self.fill_in_new_state( trans, inputs, state.inputs,
history=history )
File
/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/tools/__init__.py,
line 1855, in fill_in_new_state
state[ input.name ] = input.get_initial_value( trans, context,
history=history )
File
/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/tools/parameters/grouping.py,
line 116, in get_initial_value
rval_dict[ input.name ] = input.get_initial_value( trans, context )
File
/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/tools/parameters/basic.py,
line 1657, in get_initial_value
return self.get_initial_value_from_history_prevent_repeats(trans,
context, None, history=history);
File
/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/tools/parameters/basic.py,
line 1670, in get_initial_value_from_history_prevent_repeats
assert history is not None, DataToolParameter requires a history
AssertionError: DataToolParameter requires a history
127.0.0.1 - - [24/Feb/2014:15:15:15 +0200] POST
/api/tools?key=cd065330048989af4ae266cf94685e6b HTTP/1.1 500 - -
python-requests/2.0.1 CPython/2.7.5+ Linux/3.11.0-15-generic
___
Thanks for your help,
Olivia
