Source code for galaxy.webapps.galaxy.controllers.data_manager

import logging
from json import loads

import paste.httpexceptions
from markupsafe import escape
from six import string_types

import galaxy.queue_worker
from galaxy import web
from galaxy.web.base.controller import BaseUIController

log = logging.getLogger(__name__)


[docs]class DataManager(BaseUIController):

[docs]    @web.expose
    def index(self, trans, **kwd):
        not_is_admin = not trans.user_is_admin()
        if not_is_admin and not trans.app.config.enable_data_manager_user_view:
            raise paste.httpexceptions.HTTPUnauthorized("This Galaxy instance is not configured to allow non-admins to view the data manager.")
        message = escape(kwd.get('message', ''))
        status = escape(kwd.get('status', 'info'))
        return trans.fill_template("data_manager/index.mako", data_managers=trans.app.data_managers, tool_data_tables=trans.app.tool_data_tables, view_only=not_is_admin, message=message, status=status)

[docs]    @web.expose
    def manage_data_manager(self, trans, **kwd):
        not_is_admin = not trans.user_is_admin()
        if not_is_admin and not trans.app.config.enable_data_manager_user_view:
            raise paste.httpexceptions.HTTPUnauthorized("This Galaxy instance is not configured to allow non-admins to view the data manager.")
        message = escape(kwd.get('message', ''))
        status = escape(kwd.get('status', 'info'))
        data_manager_id = kwd.get('id', None)
        data_manager = trans.app.data_managers.get_manager(data_manager_id)
        if data_manager is None:
            return trans.response.send_redirect(web.url_for(controller="data_manager", action="index", message="Invalid Data Manager (%s) was requested" % data_manager_id, status="error"))
        jobs = list(reversed([assoc.job for assoc in trans.sa_session.query(trans.app.model.DataManagerJobAssociation).filter_by(data_manager_id=data_manager_id)]))
        return trans.fill_template("data_manager/manage_data_manager.mako", data_manager=data_manager, jobs=jobs, view_only=not_is_admin, message=message, status=status)

[docs]    @web.expose
    def view_job(self, trans, **kwd):
        not_is_admin = not trans.user_is_admin()
        if not_is_admin and not trans.app.config.enable_data_manager_user_view:
            raise paste.httpexceptions.HTTPUnauthorized("This Galaxy instance is not configured to allow non-admins to view the data manager.")
        message = escape(kwd.get('message', ''))
        status = escape(kwd.get('status', 'info'))
        job_id = kwd.get('id', None)
        try:
            job_id = trans.security.decode_id(job_id)
            job = trans.sa_session.query(trans.app.model.Job).get(job_id)
        except Exception as e:
            job = None
            log.error("Bad job id (%s) passed to view_job: %s" % (job_id, e))
        if not job:
            return trans.response.send_redirect(web.url_for(controller="data_manager", action="index", message="Invalid job (%s) was requested" % job_id, status="error"))
        data_manager_id = job.data_manager_association.data_manager_id
        data_manager = trans.app.data_managers.get_manager(data_manager_id)
        hdas = [assoc.dataset for assoc in job.get_output_datasets()]
        data_manager_output = []
        error_messages = []
        for hda in hdas:
            try:
                data_manager_json = loads(open(hda.get_file_name()).read())
            except Exception as e:
                data_manager_json = {}
                error_messages.append(escape("Unable to obtain data_table info for hda (%s): %s" % (hda.id, e)))
            values = []
            for key, value in data_manager_json.get('data_tables', {}).items():
                values.append((key, value))
            data_manager_output.append(values)
        return trans.fill_template("data_manager/view_job.mako", data_manager=data_manager, job=job, view_only=not_is_admin, hdas=hdas, data_manager_output=data_manager_output, message=message, status=status, error_messages=error_messages)

[docs]    @web.expose
    def manage_data_table(self, trans, **kwd):
        not_is_admin = not trans.user_is_admin()
        if not_is_admin and not trans.app.config.enable_data_manager_user_view:
            raise paste.httpexceptions.HTTPUnauthorized("This Galaxy instance is not configured to allow non-admins to view the data manager.")
        message = escape(kwd.get('message', ''))
        status = escape(kwd.get('status', 'info'))
        data_table_name = kwd.get('table_name', None)
        if not data_table_name:
            return trans.response.send_redirect(web.url_for(controller="data_manager", action="index"))
        data_table = trans.app.tool_data_tables.get(data_table_name, None)
        if data_table is None:
            return trans.response.send_redirect(web.url_for(controller="data_manager", action="index", message="Invalid Data table (%s) was requested" % data_table_name, status="error"))
        return trans.fill_template("data_manager/manage_data_table.mako", data_table=data_table, view_only=not_is_admin, message=message, status=status)

[docs]    @web.expose
    @web.require_admin
    def reload_tool_data_tables(self, trans, table_name=None, **kwd):
        if table_name and isinstance(table_name, string_types):
            table_name = table_name.split(",")
        # Reload the tool data tables
        table_names = self.app.tool_data_tables.reload_tables(table_names=table_name)
        galaxy.queue_worker.send_control_task(trans.app, 'reload_tool_data_tables',
                                              noop_self=True,
                                              kwargs={'table_name': table_name})
        redirect_url = None
        if table_names:
            status = 'done'
            if len(table_names) == 1:
                message = "The data table '%s' has been reloaded." % table_names[0]
                redirect_url = web.url_for(controller='data_manager',
                                           action='manage_data_table',
                                           table_name=table_names[0],
                                           message=message,
                                           status=status)
            else:
                message = "The data tables '%s' have been reloaded." % ', '.join(table_names)
        else:
            message = "No data tables have been reloaded."
            status = 'error'
        if redirect_url is None:
            redirect_url = web.url_for(controller='admin',
                                       action='view_tool_data_tables',
                                       message=message,
                                       status=status)
        return trans.response.send_redirect(redirect_url)

[docs]    @web.expose
    @web.json
    @web.require_admin
    def tool_data_table_items(self, trans, **kwd):
        data = {'columns': [], 'items': []}
        message = kwd.get('message', '')
        status = kwd.get('status', 'info')
        table_name = kwd.get('table_name', None)

        if not table_name:
            return {
                'data': data,
                'message': 'No Data table name provided.',
                'status': 'warning',
            }

        data_table = trans.app.tool_data_tables.get(table_name, None)

        if data_table is None:
            return {
                'data': data,
                'message': 'Invalid Data table (%s) was requested' % table_name,
                'status': 'error'
            }

        columns = data_table.get_column_name_list()
        rows = [dict(zip(columns, table_row)) for table_row in data_table.data]
        data['columns'] = columns
        data['items'] = rows

        return {'data': data, 'message': message, 'status': status}

[docs]    @web.expose
    @web.json
    @web.require_admin
    def reload_tool_data_table(self, trans, **kwd):
        table_name = kwd.get('table_name', None)

        if not table_name:
            return {
                'message': 'No data table has been reloaded.',
                'status': 'error',
            }

        redirect_url = web.url_for(
            controller='data_manager',
            action='tool_data_table_items',
            table_name=table_name,
            message='The data table "%s" has been reloaded.' % table_name,
            status='done',
        )

        return trans.response.send_redirect(redirect_url)