def show_workflow( workflow_id ):
# http://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController.show
# lib/galaxy/webapps/galaxy/api/workflows.py, def import
#EXERCISE: return...
# -----------------------------------------------------------------------------
if __name__ == '__main__':
response = show_workflow( sys.argv[1] )
output.output_response( response )
def list_workflows():
# http://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController.index
# lib/galaxy/webapps/galaxy/api/workflows.py, def index
#EXERCISE: GET/index available workflows
# -----------------------------------------------------------------------------
if __name__ == '__main__':
response = list_workflows()
output.output_response( response )
def show_tool( tool_id ):
#EXERCISE: build params, including 'io_details' : True, and request
# -----------------------------------------------------------------------------
if __name__ == '__main__':
response = None
# if passed an id, show details for that; if no id: return info for all tools
if len( sys.argv ) == 1:
response = list_tools()
else:
response = show_tool( sys.argv[1] )
output.output_response( response )
'file_type' : 'auto',
}
data = {
# like any post, the api key can go directly into the data
'key' : open( '.api-key' ).readline().strip(),
# the id of the upload tool - tool ids are more human readable but don't
# always correspond to the name in the tool panel; use api/tools to get more info
'tool_id' : 'upload1',
# to which history are we uploading?
'history_id' : history_id,
# for many tools the inputs need to be sent as a json encoded string
'inputs' : json.dumps( inputs )
}
# for upload, we're using a special post parameter named 'files' which allows
# us to attach the file data to the request
# requests makes this much easier than urllib or other libraries
response = None
with open( filepath, 'rb' ) as file_to_upload:
files = { 'files_0|file_data' : file_to_upload }
response = requests.post( full_url, data=data, files=files )
return response
# -----------------------------------------------------------------------------
if __name__ == '__main__':
history_id, filepath = sys.argv[1:3]
response = upload_file( history_id, filepath )
output.output_response( response )
#!/usr/bin/env python
import sys
import json
import output
import requests
BASE_URL = 'http://localhost:8080'
# -----------------------------------------------------------------------------
# http://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#galaxy.webapps.galaxy.api.history_contents.HistoryContentsController.show
# lib/galaxy/webapps/galaxy/api/history_contents.py, def index
def show_history_contents( history_id, contents_id ):
# even further specify a resource by using the URL - this time telling the
# API to look for a specific element (contents_id) in a specific history
full_url = #...
# -----------------------------------------------------------------------------
if __name__ == '__main__':
history_id, contents_id = sys.argv[1:3]
response = show_history_contents( history_id, contents_id )
output.output_response( response )
