Merge branch '1-demo-of-calling-a-galaxy-tool-from-a-python-script' into 'main'

.idea

.pyc

#### To run examples:

- install python _bioblend_ package

- set _GALAXY_URL_ to _https://calvera.ornl.gov_

- on Calvera web site - go to _User->Preferences->Manage API Key_ and 

set _GALAXY_API_KEY_

#### Documentation

some documentation for Bioblend can be found here:

https://bioblend.readthedocs.io/en/latest

you may also want to go through tutorial:

https://training.galaxyproject.org/training-material/topics/dev/tutorials/bioblend-api/tutorial.html

#### Description

This is a simple script to demonstrate how one can execute a Galaxy tool from Python.

It uploads `test.json` file from a local filesystem, runs a tool called _Line/Word/Character count_

(which has an id `wc_gnu` set in tool's xml file), waits until output dataset is ready and

export the result (outputs the amount of words and lines in `test.json` to the screen in this demo)

#### To run it:

see README in a root folder

import os

from bioblend import galaxy

from bioblend.galaxy.tools.inputs import inputs

galaxy_url = os.getenv("GALAXY_URL")

galaxy_user_api_key = os.getenv("GALAXY_API_KEY")

# connect to a Galaxy instance, create dataset client

galaxy_instance = galaxy.GalaxyInstance(url=galaxy_url, key=galaxy_user_api_key)

dataset_client = galaxy.datasets.DatasetClient(galaxy_instance)

# get active history id

history_id = galaxy_instance.histories.get_histories()[0]["id"]

# or create a new one

# history_id = gi.histories.create_history(name="New history")["id"]

# upload a file and wait until upload is finished

uploaded_dataset_id = galaxy_instance.tools.upload_file('test.json', history_id)['outputs'][0]['id']

dataset_client.wait_for_dataset(uploaded_dataset_id)

# set tool inputs, run tool and wait it finishes

# wc_gnu - id of the Galaxy's Line/Word/Character count tool

# so one needs to know tool id and tool inputs and outputs. This tool takes an input file and options for what to count

# and returns a single output file (hence ['outputs'][0]['id'])

tool_inputs = inputs().set("options", ["lines", "words"]).set("input", uploaded_dataset_id)

result_dataset_id = galaxy_instance.tools.run_tool(history_id, 'wc_gnu', tool_inputs)['outputs'][0]['id']

dataset_client.wait_for_dataset(result_dataset_id)

# export results

exported_data = dataset_client.download_dataset(dataset_id=result_dataset_id,

                                                file_path=None,  # set file_path to output to file

                                                use_default_filename=False)

print(exported_data)

# uncomment to delete datasets

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

# galaxy_instance.histories.delete_dataset(history_id, result_dataset_id, 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)

{

  "hello": "world"

}

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