Re: [galaxy-dev] bioblend problem trying to use run_tool function
Hmm... the random_lines1 test case distributed with bioblend is kind
of like this but a little more complex because it includes a
conditional also:
https://github.com/jmchilton/bioblend/blob/master/tests/TestGalaxyTools.py#L68
Just using random_lines1 without specifying anything in the
conditional (so just a numeric property and dataset input) the
following snippet works for me:
from bioblend import galaxy
gi = galaxy.GalaxyInstance(localhost:8080, 1957431058be3aa3c57ca312f4a05521)
history = gi.histories.create_history(name=TestRandomLines)
dataset_id = gi.tools.paste_content(1\n2\n3,
history[id])['outputs'][0][id]
from bioblend.galaxy.tools.inputs import inputs, dataset
random_lines_inputs = inputs().set(num_lines, 1).set(input,
dataset(dataset_id))
tool_outputs = gi.tools.run_tool(history_id=history[id],
tool_id=random_lines1, tool_inputs=random_lines_inputs)
This seems very comparable to the two input tool execution you are describing.
Cleaner version of above script @
https://gist.github.com/jmchilton/38c33d365e116c750c21.
If this is not working, please make sure you are using a relatively
recent version of Galaxy (probably either of the last two releases
should work - one before that might as well) and the latest
development version of bioblend (right from github - don't know if a
full version has been released since I added tool inputs helpers).
If none of that works - please make sure the tool works through the
GUI and if it does can you share the tool XML with me?
Thanks,
-John
On Mon, Jun 30, 2014 at 9:49 AM, Olivia Doppelt-Azeroual
olivia.dopp...@pasteur.fr wrote:
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
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] bioblend problem trying to use run_tool function
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 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 =
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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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
Re: [galaxy-dev] bioblend problem trying to use run_tool function
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 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,
Re: [galaxy-dev] bioblend problem trying to use run_tool function
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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