How to use the bioblend.galaxy.GalaxyInstance function in bioblend

To help you get started, we’ve selected a few bioblend examples, based on popular ways it is used in public projects.

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github ARTbio / tools-artbio / helper_scripts / test_upload.py View on Github external
def main():
    args = parse_args()
    web_protocol, fqdn, ftp_protocol, port, api_key = \
    args.protocol, args.fqdn, args.ftp_protocol, args.port, args.api_key
    if args.http_auth_username:
        GalaxyInstance.make_delete_request = inject_auth(make_delete_request, args.http_auth_username, args.http_auth_password)
        GalaxyInstance.make_post_request = inject_auth(make_post_request, args.http_auth_username, args.http_auth_password)
        GalaxyInstance.make_put_request = inject_auth(make_put_request, args.http_auth_username, args.http_auth_password)
        GalaxyInstance.make_get_request = inject_auth(GalaxyInstance.make_get_request, args.http_auth_username, args.http_auth_password)
    url = web_protocol + "://" + fqdn
    new_api_key, user_email, password = create_user(url, api_key)
    tmpfile = NamedTemporaryFile()
    tmpfile.write("1\n2\n3\n")
    if ftp_protocol == "ftp":
        ftp_upload_file(fqdn, user_email, password, port, tmpfile.name)
    else:
        sftp_upload_file(fqdn, user_email, password, port, tmpfile.name)
    if not successfull_upload(url, new_api_key, tmpfile.name):
        sys.exit("{ftp_protocol} upload to galaxy server {fqdn} failed.".format(ftp_protocol = ftp_protocol, fqdn = fqdn))
github galaxyproject / galaxy / test / manual / workflows_scaling.py View on Github external
def _gi(args):
    gi = galaxy.GalaxyInstance(args.host, key=args.api_key)
    name = "wftest-user-%d" % random.randint(0, 1000000)

    user = gi.users.create_local_user(name, "%s@galaxytesting.dev" % name, "pass123")
    user_id = user["id"]
    api_key = gi.users.create_user_apikey(user_id)
    user_gi = galaxy.GalaxyInstance(args.host, api_key)
    return user_gi
github galaxyproject / bioblend / docs / examples / create_user_get_api_key.py View on Github external
Usage: python3 create_user_get_api_key.py     
"""
from __future__ import print_function

import sys

import bioblend.galaxy

if len(sys.argv) != 6:
    print("Usage: python3 create_user_get_api_key.py     ")
    sys.exit(1)
galaxy_url = sys.argv[1]
galaxy_api_key = sys.argv[2]

# Initiating Galaxy connection
gi = bioblend.galaxy.GalaxyInstance(galaxy_url, galaxy_api_key)

# Create a new user and get a new API key for her
new_user = gi.users.create_local_user(sys.argv[3], sys.argv[4], sys.argv[5])
new_api_key = gi.users.create_user_apikey(new_user['id'])
print(new_api_key)
github SGBC / galaksio / server / servlets / GalaxyAPI.py View on Github external
def generateWorkflowReport(request, settings):
    # Get the invocation and workflow data
    invocation = request.json.get("invocation")
    workflow = request.json.get("workflow")

    # Open a new connection with bioblend
    galaxy_key = request.values.get("key")
    gi = GalaxyInstance(settings.GALAXY_SERVER, galaxy_key)

    workflow_steps = {}
    for step in workflow.get("steps"):
        workflow_steps[step.get("uuid")] = step

    for step in invocation.get("steps"):
        workflow_step = workflow_steps[step.get("workflow_step_uuid")]
        workflow_step["state"] = step.get("state")
        workflow_step["job_id"] = step.get("job_id")
        workflow_step["job"] = gi.jobs.show_job(step.get("job_id"))

    # GENERATE THE HTML
    html_code = ""
    to_close_tags = []

    html_code += addTag("h2", "Workflow details", "font-size: 30px; color:red")
github ARTbio / GalaxyKickStart / extra-files / get_tool_yml_from_gi.py View on Github external
def get_instance(self):
        return bioblend.galaxy.GalaxyInstance(url=self.url, key=self.api_key)
github gvlproject / gvl_commandline_utilities / roles / gvl.commandline-utilities / files / galaxy-fuse.py View on Github external
def __init__(self, api_key):
        self.gi = galaxy.GalaxyInstance(url='http://127.0.0.1:80/galaxy/', key=api_key)
        self.datasets_cache = {}
        self.histories_cache = {'time':None, 'contents':None}
github galaxyproject / ansible-galaxy-tools / files / install_tool_shed_tools.py View on Github external
def galaxy_instance(url=None, api_key=None):
    """
    Get an instance of the `GalaxyInstance` object. If the arguments are not
    provided, load the default values using `load_input_file` method.
    """
    if not (url and api_key):
        tl = load_input_file()
        url = tl['galaxy_instance']
        api_key = tl['api_key']
    return GalaxyInstance(url, api_key)
github ARTbio / GalaxyKickStart / roles / artimed_extras / files / galaxy_data_managers.py View on Github external
def galaxy_instance(url=None, api_key=None):
    """
    Get an instance of the `GalaxyInstance` object. If the arguments are not
    provided, load the default values using `load_input_file` method.
    """
    if not (url and api_key):
        tl = load_input_file()
        url = tl['galaxy_instance']
        api_key = tl['api_key']
    return GalaxyInstance(url, api_key)