Python ensure_module Examples

Example #1

def tool_shed_instance(url, key, email, password):
    ensure_module()
    tsi = toolshed.ToolShedInstance(url=url,
                                    key=key,
                                    email=email,
                                    password=password)
    return tsi

Example #2

def user_api_key(admin_gi):
    """Use an admin authenticated account to generate a user API key."""
    ensure_module()
    # TODO: thread-safe
    users = admin_gi.users
    all_users = users.get_users()

    user_id = None
    for user in all_users:
        if user["email"] == "*****@*****.**":
            user_id = user["id"]

    if user_id is None:
        # TODO: Allow override with --user_api_key.
        galaxy_config = admin_gi.config.get_config()
        use_remote_user = bool(galaxy_config["use_remote_user"])
        if not use_remote_user:
            user_response = users.create_local_user(
                "planemo",
                "*****@*****.**",
                "planemo",
            )
            user_id = user_response["id"]
        else:
            user_response = users.create_remote_user(
                "*****@*****.**", )
            user_id = user_response["id"]
    return users.create_user_apikey(user_id)

Example #3

File: api.py Project: galaxyproject/planemo

def user_api_key(admin_gi):
    """Use an admin authenticated account to generate a user API key."""
    ensure_module()
    # TODO: thread-safe
    users = admin_gi.users
    all_users = users.get_users()

    user_id = None
    for user in all_users:
        if user["email"] == "*****@*****.**":
            user_id = user["id"]

    if user_id is None:
        # TODO: Allow override with --user_api_key.
        galaxy_config = admin_gi.config.get_config()
        use_remote_user = bool(galaxy_config["use_remote_user"])
        if not use_remote_user:
            user_response = users.create_local_user(
                "planemo",
                "*****@*****.**",
                "planemo",
            )
            user_id = user_response["id"]
        else:
            user_response = users.create_remote_user(
                "*****@*****.**",
            )
            user_id = user_response["id"]
    return users.create_user_apikey(user_id)

Example #4

def gi(port, key=None):
    """Return a bioblend ``GalaxyInstance`` for Galaxy on this port."""
    ensure_module()
    if key is None:
        key = DEFAULT_MASTER_API_KEY
    return galaxy.GalaxyInstance(url="http://localhost:%d" % int(port),
                                 key=key)

Example #5

File: interface.py Project: galaxyproject/planemo

def tool_shed_instance(url, key, email, password):
    ensure_module()
    tsi = toolshed.ToolShedInstance(
        url=url,
        key=key,
        email=email,
        password=password
    )
    return tsi

Example #6

File: api.py Project: natefoo/planemo

def gi(port, key=None):
    """Return a bioblend ``GalaxyInstance`` for Galaxy on this port."""
    ensure_module()
    if key is None:
        key = DEFAULT_MASTER_API_KEY
    return galaxy.GalaxyInstance(
        url="http://localhost:%d" % int(port),
        key=key
    )

Example #7

def gi(port=None, url=None, key=None):
    """Return a bioblend ``GalaxyInstance`` for Galaxy on this port."""
    ensure_module()
    if key is None:
        key = DEFAULT_ADMIN_API_KEY
    if port is None:
        url = url
    else:
        url = "http://localhost:%d" % int(port)

    return galaxy.GalaxyInstance(url=url, key=key)

Example #8

File: api.py Project: lecorguille/planemo

def user_api_key(admin_gi):
    """Use an admin authenticated account to generate a user API key."""
    ensure_module()
    # TODO: thread-safe
    users = admin_gi.users
    # Allow override with --user_api_key.
    user_response = users.create_local_user(
        "planemo",
        "*****@*****.**",
        "planemo",
    )
    user_id = user_response["id"]

    return users.create_user_apikey(user_id)

Example #9

File: galaxy_config.py Project: nebiolabs/planemo

 def gi(self):
     ensure_module(galaxy)
     return galaxy.GalaxyInstance(
         url="http://localhost:%d" % self.port,
         key=self.master_api_key
     )

Example #10

File: galaxy_config.py Project: einon/planemo

 def _gi_for_key(self, key):
     ensure_module(galaxy)
     return galaxy.GalaxyInstance(
         url="http://localhost:%d" % self.port,
         key=key
     )

Example #11

File: galaxy_config.py Project: chambm/planemo

 def gi(self):
     ensure_module(galaxy)
     return galaxy.GalaxyInstance(url="http://localhost:%d" % self.port,
                                  key=self.master_api_key)