Merge branch '2-demo-of-running-galaxy-workflows-from-a-python-script' into 'main'

#### Description

this examples imports `test.json` file and `test_workflow.ga` 

from a local filesystem to Galaxy, runs this workflow and prints the output.

The workflow is quite simple - it counts lines and words (like in example 1)

and as a second step returns the last line of the result (removes header). 

The workflow was prepared in advance in Galaxy Web interface and exported to a file.  

#### To run it:

see README in a root folder

# this examples imports test.json file and test_workflow.ga to Galaxy, runs this workflow and prints output

# the workflow is quite simple - it counts lines and words (like in example 1)

# and as a second step returns last line of the result (removes header)

import os

from bioblend import galaxy

galaxy_url = os.getenv("GALAXY_URL")

galaxy_user_api_key = os.getenv("GALAXY_API_KEY")

# connect to a Galaxy instance, create clients

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

dataset_client = galaxy.datasets.DatasetClient(galaxy_instance)

invocations_client = galaxy.invocations.InvocationClient(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 input 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)

# import workflow

workflow = galaxy_instance.workflows.import_workflow_from_local_path('test_workflow.ga')

workflow_id = workflow["id"]

# alteratively - use existing workflow

#workflows = galaxy_instance.workflows.get_workflows(workflow_id=None, name="test", published=False)

#workflow_id=workflows[0]["id"]

# prepare workflow input map, in our case - assign input to uploaded dataset id

inputs = galaxy_instance.workflows.get_workflow_inputs(workflow_id,label="input")

datamap = {

    inputs[0]: {"src": "hda", "id": uploaded_dataset_id},

}

# invoke workflow

invocation_id = galaxy_instance.workflows.invoke_workflow(

    workflow_id, inputs=datamap, history_id=history_id, import_inputs_to_history=False

)["id"]

# wait until workflow schedulled so that we could get last workflow step id

scheduled_invocation = invocations_client.wait_for_invocation(invocation_id)

last_step_id=scheduled_invocation["steps"][-1]["id"]

# from that id - get output dataset id

result_dataset_id = invocations_client.show_invocation_step(invocation_id,last_step_id)["outputs"]["out_file1"]["id"]

# wait for this dataset is ready

dataset_client.wait_for_dataset(result_dataset_id)

# download this dataset from Galaxy

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 workflow

#galaxy_instance.workflows.delete_workflow(workflow_id)

# 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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{

    "a_galaxy_workflow": "true",

    "annotation": "",

    "format-version": "0.1",

    "name": "test",

    "steps": {

        "0": {

            "annotation": "",

            "content_id": null,

            "errors": null,

            "id": 0,

            "input_connections": {},

            "inputs": [

                {

                    "description": "",

                    "name": "input"

                }

            ],

            "label": "input",

            "name": "Input dataset",

            "outputs": [],

            "position": {

                "left": 0.0,

                "top": 1.953125

            },

            "tool_id": null,

            "tool_state": "{\"optional\": false, \"tag\": \"\"}",

            "tool_version": null,

            "type": "data_input",

            "uuid": "cc9eaf78-dd54-488e-a591-6ef7bfc7fc28",

            "workflow_outputs": [

                {

                    "label": null,

                    "output_name": "output",

                    "uuid": "a30e6c01-829d-4cca-8b60-8e28c5e69e4f"

                }

            ]

        },

        "1": {

            "annotation": "",

            "content_id": "wc_gnu",

            "errors": null,

            "id": 1,

            "input_connections": {

                "input1": {

                    "id": 0,

                    "output_name": "output"

                }

            },

            "inputs": [

                {

                    "description": "runtime parameter for tool Line/Word/Character count",

                    "name": "input1"

                }

            ],

            "label": null,

            "name": "Line/Word/Character count",

            "outputs": [

                {

                    "name": "out_file1",

                    "type": "tabular"

                }

            ],

            "position": {

                "left": 242.03123827980772,

                "top": 0.0

            },

            "post_job_actions": {},

            "tool_id": "wc_gnu",

            "tool_state": "{\"include_header\": \"true\", \"input1\": {\"__class__\": \"RuntimeValue\"}, \"options\": [\"lines\", \"words\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",

            "tool_version": "1.0.0",

            "type": "tool",

            "uuid": "ff48f34b-c6de-4947-b893-7fa2d0b74460",

            "workflow_outputs": [

                {

                    "label": null,

                    "output_name": "out_file1",

                    "uuid": "4e7752e9-05bc-46f7-a618-505df57baa15"

                }

            ]

        },

        "2": {

            "annotation": "",

            "content_id": "Show tail1",

            "errors": null,

            "id": 2,

            "input_connections": {

                "input": {

                    "id": 1,

                    "output_name": "out_file1"

                }

            },

            "inputs": [

                {

                    "description": "runtime parameter for tool Select last",

                    "name": "input"

                }

            ],

            "label": null,

            "name": "Select last",

            "outputs": [

                {

                    "name": "out_file1",

                    "type": "input"

                }

            ],

            "position": {

                "left": 510.2968878020569,

                "top": 31.03124936891274

            },

            "post_job_actions": {},

            "tool_id": "Show tail1",

            "tool_state": "{\"header\": \"false\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineNum\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",

            "tool_version": "1.0.1",

            "type": "tool",

            "uuid": "c51df68e-6513-423d-9cbd-cc462c403d46",

            "workflow_outputs": [

                {

                    "label": null,

                    "output_name": "out_file1",

                    "uuid": "83d29c39-aa7a-435a-bdf0-072192f58b4d"

                }

            ]

        }

    },

    "tags": [],

    "uuid": "e11bc06e-7b1b-4f9e-96c8-99d71d6ef030",

    "version": 1

}

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