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Source code for galaxy.managers.interactivetool

import logging
import sqlite3

from sqlalchemy import or_

from galaxy import (
from galaxy.util.filelock import FileLock

log = logging.getLogger(__name__)


[docs]class InteractiveToolSqlite:
[docs] def __init__(self, sqlite_filename, encode_id): self.sqlite_filename = sqlite_filename self.encode_id = encode_id
[docs] def get(self, key, key_type): with FileLock(self.sqlite_filename): conn = sqlite3.connect(self.sqlite_filename) try: c = conn.cursor() select = '''SELECT token, host, port, info FROM %s WHERE key=? and key_type=?''' % (DATABASE_TABLE_NAME) c.execute(select, (key, key_type,)) try: token, host, port, info = c.fetchone() except TypeError: log.warning('get(): invalid key: %s key_type %s', key, key_type) return None return dict( key=key, key_type=key_type, token=token, host=host, port=port, info=info) finally: conn.close()
[docs] def save(self, key, key_type, token, host, port, info=None): """ Writeout a key, key_type, token, value store that is can be used for coordinating with external resources. """ assert key, ValueError("A non-zero length key is required.") assert key_type, ValueError("A non-zero length key_type is required.") assert token, ValueError("A non-zero length token is required.") with FileLock(self.sqlite_filename): conn = sqlite3.connect(self.sqlite_filename) try: c = conn.cursor() try: # Create table c.execute('''CREATE TABLE %s (key text, key_type text, token text, host text, port integer, info text, PRIMARY KEY (key, key_type) )''' % (DATABASE_TABLE_NAME)) except Exception: pass delete = '''DELETE FROM %s WHERE key=? and key_type=?''' % (DATABASE_TABLE_NAME) c.execute(delete, (key, key_type,)) insert = '''INSERT INTO %s (key, key_type, token, host, port, info) VALUES (?, ?, ?, ?, ?, ?)''' % (DATABASE_TABLE_NAME) c.execute(insert, (key, key_type, token, host, port, info, )) conn.commit() finally: conn.close()
[docs] def remove(self, **kwd): """ Remove entry from a key, key_type, token, value store that is can be used for coordinating with external resources. Remove entries that match all provided key=values """ assert kwd, ValueError("You must provide some values to key upon") delete = 'DELETE FROM %s WHERE' % (DATABASE_TABLE_NAME) value_list = [] for i, (key, value) in enumerate(kwd.items()): if i != 0: delete += ' and' delete += ' %s=?' % (key) value_list.append(value) with FileLock(self.sqlite_filename): conn = sqlite3.connect(self.sqlite_filename) try: c = conn.cursor() try: # Delete entry # NB: This does not invalidate in-memory caches used by uwsgi (if any) c.execute(delete, tuple(value_list)) except Exception as e: log.debug('Error removing entry (%s): %s', delete, e) conn.commit() finally: conn.close()
[docs] def save_entry_point(self, entry_point): """Convenience method to easily save an entry_point. """ return self.save(self.encode_id(entry_point.id), entry_point.__class__.__name__.lower(), entry_point.token, entry_point.host, entry_point.port, None)
[docs] def remove_entry_point(self, entry_point): """Convenience method to easily remove an entry_point. """ return self.remove(key=self.encode_id(entry_point.id), key_type=entry_point.__class__.__name__.lower())
[docs]class InteractiveToolManager: """ Manager for dealing with InteractiveTools """
[docs] def __init__(self, app): self.app = app self.model = app.model self.security = app.security self.sa_session = app.model.context self.job_manager = app.job_manager self.propagator = InteractiveToolSqlite(app.config.interactivetools_map, app.security.encode_id)
[docs] def create_entry_points(self, job, tool, entry_points=None, flush=True): entry_points = entry_points or tool.ports for entry in entry_points: ep = self.model.InteractiveToolEntryPoint(job=job, tool_port=entry['port'], entry_url=entry['url'], name=entry['name']) self.sa_session.add(ep) if flush: self.sa_session.flush()
[docs] def configure_entry_point(self, job, tool_port=None, host=None, port=None, protocol=None): return self.configure_entry_points(job, {tool_port: dict(tool_port=tool_port, host=host, port=port, protocol=protocol)})
[docs] def configure_entry_points(self, job, ports_dict): # There can be multiple entry points that reference the same tool port (could have different entry URLs) configured = [] not_configured = [] for ep in job.interactivetool_entry_points: port_dict = ports_dict.get(str(ep.tool_port), None) if port_dict is None: log.error("Did not find port to assign to InteractiveToolEntryPoint by tool port: %s.", ep.tool_port) not_configured.append(ep) else: ep.host = port_dict['host'] ep.port = port_dict['port'] ep.protocol = port_dict['protocol'] ep.configured = True self.sa_session.add(ep) self.save_entry_point(ep) configured.append(ep) if configured: self.sa_session.flush() return dict(not_configured=not_configured, configured=configured)
[docs] def save_entry_point(self, entry_point): """ Writeout a key, key_type, token, value store that is used validating access """ self.propagator.save_entry_point(entry_point)
[docs] def create_interactivetool(self, job, tool, entry_points): # create from initial job if job and tool: self.create_entry_points(job, tool, entry_points) else: log.warning('Called InteractiveToolManager.create_interactivetool, but job (%s) or tool (%s) is None', job, tool)
[docs] def get_nonterminal_for_user_by_trans(self, trans): if trans.user: jobs = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.user == trans.user) else: jobs = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.session_id == trans.get_galaxy_session().id) def build_and_apply_filters(query, objects, filter_func): if objects is not None: if isinstance(objects, str): query = query.filter(filter_func(objects)) elif isinstance(objects, list): t = [] for obj in objects: t.append(filter_func(obj)) query = query.filter(or_(*t)) return query jobs = build_and_apply_filters(jobs, trans.app.model.Job.non_ready_states, lambda s: trans.app.model.Job.state == s) return trans.sa_session.query(trans.app.model.InteractiveToolEntryPoint).filter(trans.app.model.InteractiveToolEntryPoint.job_id.in_([job.id for job in jobs]))
[docs] def can_access_job(self, trans, job): if job: if trans.user is None: galaxy_session = trans.get_galaxy_session() if galaxy_session is None or job.session_id != galaxy_session.id: return False elif job.user != trans.user: return False else: return False return True
[docs] def can_access_entry_point(self, trans, entry_point): if entry_point: return self.can_access_job(trans, entry_point.job) return False
[docs] def can_access_entry_points(self, trans, entry_points): for ep in entry_points: if not self.can_access_entry_point(trans, ep): return False return True
[docs] def stop(self, trans, entry_point): try: self.remove_entry_point(entry_point) job = entry_point.job if not job.finished: log.debug('Stopping Job: %s for InteractiveToolEntryPoint: %s', job, entry_point) job.mark_deleted(trans.app.config.track_jobs_in_database) # This self.job_manager.stop(job) does nothing without changing job.state, manually or e.g. with .mark_deleted() self.job_manager.stop(job) trans.sa_session.add(job) trans.sa_session.flush() except Exception as e: log.debug('Unable to stop job for InteractiveToolEntryPoint (%s): %s', entry_point, e) return False return True
[docs] def remove_entry_points(self, entry_points): if entry_points: for entry_point in entry_points: self.remove_entry_point(entry_point, flush=False) self.sa_session.flush()
[docs] def remove_entry_point(self, entry_point, flush=True): entry_point.deleted = True self.sa_session.add(entry_point) if flush: self.sa_session.flush() self.propagator.remove_entry_point(entry_point)
[docs] def target_if_active(self, trans, entry_point): if entry_point.active and not entry_point.deleted: request_host = trans.request.host protocol = trans.request.host_url.split('//', 1)[0] entry_point_encoded_id = trans.security.encode_id(entry_point.id) entry_point_class = entry_point.__class__.__name__.lower() entry_point_prefix = self.app.config.interactivetools_prefix interactivetools_proxy_host = self.app.config.interactivetools_proxy_host or request_host rval = '{}//{}-{}.{}.{}.{}/'.format(protocol, entry_point_encoded_id, entry_point.token, entry_point_class, entry_point_prefix, interactivetools_proxy_host) if entry_point.entry_url: rval = '{}/{}'.format(rval.rstrip('/'), entry_point.entry_url.lstrip('/')) return rval
[docs] def access_entry_point_target(self, trans, entry_point_id): entry_point = trans.sa_session.query(model.InteractiveToolEntryPoint).get(entry_point_id) if self.app.interactivetool_manager.can_access_entry_point(trans, entry_point): if entry_point.active: return self.target_if_active(trans, entry_point) elif entry_point.deleted: raise exceptions.MessageException('InteractiveTool has ended. You will have to start a new one.') else: raise exceptions.MessageException('InteractiveTool is not active. If you recently launched this tool it may not be ready yet, please wait a moment and refresh this page.') raise exceptions.ItemAccessibilityException("You do not have access to this InteractiveTool entry point.")