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#L... 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.doppelt@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.doppelt@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/f573461f3667e8f120dc05bbd11a...
Hope this helps.
-John
On Mon, Feb 24, 2014 at 8:51 AM, Olivia Doppelt-Azeroual <olivia.doppelt@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 don"t 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 Doppelt-Azeroual
Le 24/02/14 15:21, John Chilton a écrit :
Hard to infer much from this, usually when I get this error there is a full stack trace for this error in the Galaxy logs giving some indication what went wrong.
-John
On Mon, Feb 24, 2014 at 4:36 AM, Olivia Doppelt-Azeroual <olivia.doppelt@pasteur.fr> wrote:
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> <head><title>Internal Server Error</title></head> <body> <h1>Internal Server Error</h1> <p>The server has either erred or is incapable of performing the requested operation.
<br/> <!-- --></p> <hr noshade> <div align="right">WSGI 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.doppelt@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='xxxxxxxxxxx',tool_id='yyyyyyyy/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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-- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur
-- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur
-- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur