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 "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.dopp...@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.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='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

___________________________________________________________
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/

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