Commit 2d89f1a1 authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

add model and constraint function to script

parent 2f7b69a7

examples/3_run_qclimax/CaCl_H2O_MCM_293K.dat

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examples/3_run_qclimax/CaCl_H2O_MCM_303K.dat

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examples/3_run_qclimax/FirstOrderSphericalBessel.py

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def FirstOrderSphericalBessel(symtable, X, sin, cos):

from math import sin,cos



def FirstOrderSphericalBessel(symtable, X):

    """Performs the first order spherical bessel function on the given variable.

    """

    return (sin * X / (X**2)) - (cos * X / X)
 
    return (sin(X) / (X**2)) - (cos(X) / X)

examples/3_run_qclimax/qclimax.ini

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      -data-dir /input/

      -select-qs 00,01,02,03,04,05,06,07,08,09,10

      -export-params

      -method leastsq

      -instrument Instrument

      -resolution res.dat

	  -data data0.dat

              -function Linear:intercept,value=1e-08:slope,value=1e-08

              -function DeltaCustom:amp,value=1.0,min=0.0:cen,value=0.0001,max=100.0,min=-100.0

          -run

          -constraint DeltaCustom1_amp FirstOrderSphericalBessel(1)

examples/3_run_qclimax/run_qclimax.py

+16 −8
Original line number Diff line number Diff line
@@ -18,29 +18,36 @@ history_id = galaxy_instance.histories.get_histories()[0]["id"] 
# history_id = gi.histories.create_history(name="New history")["id"]



# upload files and wait until upload is finished

# use real filenames here (e.g. from comamnd args)

uploaded_resolution_id = galaxy_instance.tools.upload_file('res.dat', history_id)['outputs'][0]['id']

uploaded_data_id = galaxy_instance.tools.upload_file('data.dat', history_id)['outputs'][0]['id']

uploaded_ini_id = galaxy_instance.tools.upload_file('ini.csv', history_id)['outputs'][0]['id']

uploaded_resolution_id = galaxy_instance.tools.upload_file('CaCl_H2O_MCM_293K.dat', history_id)['outputs'][0]['id']

uploaded_data_id = galaxy_instance.tools.upload_file('CaCl_H2O_MCM_303K.dat', history_id)['outputs'][0]['id']

uploaded_ini_id = galaxy_instance.tools.upload_file('qclimax.ini', history_id)['outputs'][0]['id']

uploaded_model_id = galaxy_instance.tools.upload_file('DeltaCustom.py', history_id)['outputs'][0]['id']

uploaded_constraint_id = galaxy_instance.tools.upload_file('FirstOrderSphericalBessel.py', history_id)['outputs'][0]['id']

dataset_client.wait_for_dataset(uploaded_resolution_id)

dataset_client.wait_for_dataset(uploaded_data_id)

dataset_client.wait_for_dataset(uploaded_ini_id)

dataset_client.wait_for_dataset(uploaded_model_id)

dataset_client.wait_for_dataset(uploaded_constraint_id)



# set tool inputs

tool_inputs = inputs()\

                .set_dataset_param("resolutionFile", uploaded_resolution_id)\

                .set_dataset_param("ini_file", uploaded_ini_id)\

                .set_dataset_param("dataFiles_0|Datafile", [uploaded_data_id])

                .set_dataset_param("dataFiles_0|dataFile", uploaded_data_id)\

                .set_dataset_param("constraintFunctions_0|constraintFunction", uploaded_constraint_id)\

                .set_dataset_param("modelFunctions_0|modelFunction", uploaded_model_id)



# this helps to check if input is constructed correctly, set inputs=None to see expected input

#print (galaxy_instance.tools.build('neutrons_qclimax',inputs=tool_inputs.to_dict(),history_id=history_id)["state_inputs"])



# run a tool,  get result ids

res = galaxy_instance.tools.run_tool(history_id, 'neutrons_qclimax', tool_inputs)

result_collection_id = res['output_collections'][0]['id']

result_dataset_id = res['outputs'][0]['id']



#wait until tool has finised

#wait until tool has finised (actually, wait until output dataset is ready, which indicates the tool is finished)

dataset_client.wait_for_dataset(result_dataset_id)





# if you need a dataset from output collection

#col = dataset_collections_client.show_dataset_collection(result_collection_id)

#dataset_in_collection_0=col['elements'][0]['object']['id']
@@ -58,9 +65,10 @@ print(exported_data.decode("utf-8")) 
# galaxy_instance.histories.delete_dataset(history_id, uploaded_resolution_id, purge=True)

# galaxy_instance.histories.delete_dataset(history_id, uploaded_data_id, purge=True)

# galaxy_instance.histories.delete_dataset(history_id, uploaded_ini_id, purge=True)

# galaxy_instance.histories.delete_dataset(history_id, uploaded_model_id, purge=True)

# galaxy_instance.histories.delete_dataset(history_id, uploaded_constraint_id, purge=True)

# galaxy_instance.histories.delete_dataset(history_id, result_dataset_id, purge=True)

# galaxy_instance.histories.delete_dataset(history_id, dataset_in_collection_0, purge=True)



# uncomment to delete history and all data, purge=True might be not allowed by Galaxy admin

# galaxy_instance.histories.delete_history(history_id, purge=True)