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

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github galaxyproject / planemo / planemo / training / tutorial.py View on Github external
def export_workflow_file(self):
        """Copy or extract workflow file and add it to the tutorial directory."""
        if not os.path.exists(self.wf_dir):
            os.makedirs(self.wf_dir)
        if not os.path.exists(os.path.join(self.wf_dir, 'index.md')):
            with open(os.path.join(self.wf_dir, 'index.md'), 'w') as handle:
                handle.write('---\nlayout: workflow-list\n---\n')
        if self.init_wf_fp:
            shutil.copy(self.init_wf_fp, self.wf_fp)
        elif self.init_wf_id:
            gi = galaxy.GalaxyInstance(self.training.galaxy_url, key=self.training.galaxy_api_key)
            gi.workflows.export_workflow_to_local_path(
                self.init_wf_id,
                self.wf_fp,
                use_default_filename=False)
github galaxyproject / planemo / planemo / galaxy / api.py View on Github external
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_MASTER_API_KEY
    if port is None:
        url = url
    else:
        url = "http://localhost:%d" % int(port)

    return galaxy.GalaxyInstance(
        url=url,
        key=key
    )
github galaxyproject / planemo / planemo / training.py View on Github external
def get_wf_tools_from_running_galaxy(kwds):
    """Get the workflow dictionary from a running Galaxy instance with the workflow installed there"""
    gi = galaxy.GalaxyInstance(kwds['galaxy_url'], key=kwds['galaxy_api_key'])
    wf = gi.workflows.export_workflow_dict(kwds['workflow_id'])
    tools = get_wf_tool_description(wf, gi)
    return wf, tools
github galaxyproject / planemo / planemo / training / tutorial.py View on Github external
def get_hands_on_boxes_from_running_galaxy(wf_id, galaxy_url, galaxy_api_key):
    """Get the workflow dictionary from a running Galaxy instance with the workflow installed on it."""
    gi = galaxy.GalaxyInstance(galaxy_url, key=galaxy_api_key)
    wf = gi.workflows.export_workflow_dict(wf_id)
    tuto_body = format_wf_steps(wf, gi)
    return tuto_body
github galaxyproject / planemo / planemo / training.py View on Github external
def add_workflow_file(kwds, tuto_dir):
    """Copy or extract workflow file and add it to the tutorial directory"""
    wf_dir = os.path.join(tuto_dir, "workflows")
    # copy / extract workflow
    wf_filepath = os.path.join(wf_dir, "init_workflow.ga")
    if kwds["workflow"]:
        shutil.copy(kwds["workflow"], wf_filepath)
    else:
        gi = galaxy.GalaxyInstance(kwds['galaxy_url'], key=kwds['galaxy_api_key'])
        gi.workflows.export_workflow_to_local_path(kwds['workflow_id'],
                                                   wf_filepath,
                                                   use_default_filename=False)
    # remove empty workflow file if there
    empty_wf_filepath = os.path.join(wf_dir, "empty_workflow.ga")
    if os.path.exists(empty_wf_filepath):
        os.remove(empty_wf_filepath)