Source code for galaxy.webapps.galaxy.api.histories

"""
API operations on a history.

.. seealso:: :class:`galaxy.model.History`
"""
import glob
import logging
import os

from sqlalchemy import (
    false,
    true
)

from galaxy import (
    exceptions,
    model,
    util
)
from galaxy.managers import (
    citations,
    histories,
    users,
    workflows,
)
from galaxy.util import (
    restore_text,
    string_as_bool
)
from galaxy.web import (
    _future_expose_api as expose_api,
    _future_expose_api_anonymous as expose_api_anonymous,
    _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless,
    _future_expose_api_raw as expose_api_raw,
    url_for
)
from galaxy.web.base.controller import (
    BaseAPIController,
    ExportsHistoryMixin,
    ImportsHistoryMixin,
    SharableMixin
)

log = logging.getLogger(__name__)


[docs]class HistoriesController(BaseAPIController, ExportsHistoryMixin, ImportsHistoryMixin, SharableMixin):
[docs] def __init__(self, app): super(HistoriesController, self).__init__(app) self.citations_manager = citations.CitationsManager(app) self.user_manager = users.UserManager(app) self.workflow_manager = workflows.WorkflowsManager(app) self.manager = histories.HistoryManager(app) self.serializer = histories.HistorySerializer(app) self.deserializer = histories.HistoryDeserializer(app) self.filters = histories.HistoryFilters(app)
[docs] @expose_api_anonymous def index(self, trans, deleted='False', **kwd): """ index( trans, deleted='False' ) * GET /api/histories: return undeleted histories for the current user * GET /api/histories/deleted: return deleted histories for the current user .. note:: Anonymous users are allowed to get their current history :type deleted: boolean :param deleted: if True, show only deleted histories, if False, non-deleted :rtype: list :returns: list of dictionaries containing summary history information The following are optional parameters: view: string, one of ('summary','detailed'), defaults to 'summary' controls which set of properties to return keys: comma separated strings, unused by default keys/names of individual properties to return If neither keys or views are sent, the default view (set of keys) is returned. If both a view and keys are sent, the key list and the view's keys are combined. If keys are send and no view, only those properties in keys are returned. For which properties are available see: galaxy/managers/histories/HistorySerializer The list returned can be filtered by using two optional parameters: q: string, generally a property name to filter by followed by an (often optional) hyphen and operator string. qv: string, the value to filter by ..example: To filter the list to only those created after 2015-01-29, the query string would look like: '?q=create_time-gt&qv=2015-01-29' Multiple filters can be sent in using multiple q/qv pairs: '?q=create_time-gt&qv=2015-01-29&q=tag-has&qv=experiment-1' The list returned can be paginated using two optional parameters: limit: integer, defaults to no value and no limit (return all) how many items to return offset: integer, defaults to 0 and starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item ..example: limit and offset can be combined. Skip the first two and return five: '?limit=5&offset=3' The list returned can be ordered using the optional parameter: order: string containing one of the valid ordering attributes followed (optionally) by '-asc' or '-dsc' for ascending and descending order respectively. Orders can be stacked as a comma- separated list of values. ..example: To sort by name descending then create time descending: '?order=name-dsc,create_time' The ordering attributes and their default orders are: create_time defaults to 'create_time-dsc' update_time defaults to 'update_time-dsc' name defaults to 'name-asc' 'order' defaults to 'create_time-dsc' """ serialization_params = self._parse_serialization_params(kwd, 'summary') limit, offset = self.parse_limit_offset(kwd) filter_params = self.parse_filter_params(kwd) # bail early with current history if user is anonymous current_user = self.user_manager.current_user(trans) if self.user_manager.is_anonymous(current_user): current_history = self.manager.get_current(trans) if not current_history: return [] # note: ignores filters, limit, offset return [self.serializer.serialize_to_view(current_history, user=current_user, trans=trans, **serialization_params)] filters = [] # support the old default of not-returning/filtering-out deleted histories filters += self._get_deleted_filter(deleted, filter_params) # users are limited to requesting only their own histories (here) filters += [self.app.model.History.user == current_user] # and any sent in from the query string filters += self.filters.parse_filters(filter_params) order_by = self._parse_order_by(kwd.get('order', 'create_time-dsc')) histories = self.manager.list(filters=filters, order_by=order_by, limit=limit, offset=offset) rval = [] for history in histories: history_dict = self.serializer.serialize_to_view(history, user=trans.user, trans=trans, **serialization_params) rval.append(history_dict) return rval
def _get_deleted_filter(self, deleted, filter_params): # TODO: this should all be removed (along with the default) in v2 # support the old default of not-returning/filtering-out deleted histories try: # the consumer must explicitly ask for both deleted and non-deleted # but pull it from the parsed params (as the filter system will error on None) deleted_filter_index = filter_params.index(('deleted', 'eq', 'None')) filter_params.pop(deleted_filter_index) return [] except ValueError: pass # the deleted string bool was also used as an 'include deleted' flag if deleted in ('True', 'true'): return [self.app.model.History.deleted == true()] # the third option not handled here is 'return only deleted' # if this is passed in (in the form below), simply return and let the filter system handle it if ('deleted', 'eq', 'True') in filter_params: return [] # otherwise, do the default filter of removing the deleted histories return [self.app.model.History.deleted == false()] def _parse_order_by(self, order_by_string): ORDER_BY_SEP_CHAR = ',' manager = self.manager if ORDER_BY_SEP_CHAR in order_by_string: return [manager.parse_order_by(o) for o in order_by_string.split(ORDER_BY_SEP_CHAR)] return manager.parse_order_by(order_by_string)
[docs] @expose_api_anonymous def show(self, trans, id, deleted='False', **kwd): """ show( trans, id, deleted='False' ) * GET /api/histories/{id}: return the history with ``id`` * GET /api/histories/deleted/{id}: return the deleted history with ``id`` * GET /api/histories/most_recently_used: return the most recently used history :type id: an encoded id string :param id: the encoded id of the history to query or the string 'most_recently_used' :type deleted: boolean :param deleted: if True, allow information on a deleted history to be shown. :param keys: same as the use of `keys` in the `index` function above :param view: same as the use of `view` in the `index` function above :rtype: dictionary :returns: detailed history information """ history_id = id deleted = string_as_bool(deleted) if history_id == "most_recently_used": history = self.manager.most_recent(trans.user, filters=(self.app.model.History.deleted == false()), current_history=trans.history) else: history = self.manager.get_accessible(self.decode_id(history_id), trans.user, current_history=trans.history) return self.serializer.serialize_to_view(history, user=trans.user, trans=trans, **self._parse_serialization_params(kwd, 'detailed'))
[docs] @expose_api_anonymous def citations(self, trans, history_id, **kwd): """ """ history = self.manager.get_accessible(self.decode_id(history_id), trans.user, current_history=trans.history) tool_ids = set([]) for dataset in history.datasets: job = dataset.creating_job if not job: continue tool_id = job.tool_id if not tool_id: continue tool_ids.add(tool_id) return [citation.to_dict("bibtex") for citation in self.citations_manager.citations_for_tool_ids(tool_ids)]
[docs] @expose_api_anonymous_and_sessionless def published(self, trans, **kwd): """ published( self, trans, **kwd ): * GET /api/histories/published: return all histories that are published :rtype: list :returns: list of dictionaries containing summary history information Follows the same filtering logic as the index() method above. """ limit, offset = self.parse_limit_offset(kwd) filter_params = self.parse_filter_params(kwd) filters = self.filters.parse_filters(filter_params) order_by = self._parse_order_by(kwd.get('order', 'create_time-dsc')) histories = self.manager.list_published(filters=filters, order_by=order_by, limit=limit, offset=offset) rval = [] for history in histories: history_dict = self.serializer.serialize_to_view(history, user=trans.user, trans=trans, **self._parse_serialization_params(kwd, 'summary')) rval.append(history_dict) return rval
# TODO: does this need to be anonymous_and_sessionless? Not just expose_api?
[docs] @expose_api_anonymous_and_sessionless def shared_with_me(self, trans, **kwd): """ shared_with_me( self, trans, **kwd ) * GET /api/histories/shared_with_me: return all histories that are shared with the current user :rtype: list :returns: list of dictionaries containing summary history information Follows the same filtering logic as the index() method above. """ current_user = trans.user limit, offset = self.parse_limit_offset(kwd) filter_params = self.parse_filter_params(kwd) filters = self.filters.parse_filters(filter_params) order_by = self._parse_order_by(kwd.get('order', 'create_time-dsc')) histories = self.manager.list_shared_with(current_user, filters=filters, order_by=order_by, limit=limit, offset=offset) rval = [] for history in histories: history_dict = self.serializer.serialize_to_view(history, user=current_user, trans=trans, **self._parse_serialization_params(kwd, 'summary')) rval.append(history_dict) return rval
[docs] @expose_api_anonymous def create(self, trans, payload, **kwd): """ create( trans, payload ) * POST /api/histories: create a new history :type payload: dict :param payload: (optional) dictionary structure containing: * name: the new history's name * history_id: the id of the history to copy * all_datasets: copy deleted hdas/hdcas? 'True' or 'False', defaults to True * archive_source: the url that will generate the archive to import * archive_type: 'url' (default) :param keys: same as the use of `keys` in the `index` function above :param view: same as the use of `view` in the `index` function above :rtype: dict :returns: element view of new history """ hist_name = None if payload.get('name', None): hist_name = restore_text(payload['name']) copy_this_history_id = payload.get('history_id', None) all_datasets = util.string_as_bool(payload.get('all_datasets', True)) if "archive_source" in payload: archive_source = payload["archive_source"] archive_file = payload.get("archive_file") if archive_source: archive_type = payload.get("archive_type", "url") elif hasattr(archive_file, "file"): # archive_file.file is a TemporaryFile and will be deleted once it is closed. # We prevent this by setting `delete` to `False`. archive_file.file.delete = False archive_source = payload["archive_file"].file.name archive_type = "file" else: raise exceptions.MessageException("Please provide a url or file.") self.queue_history_import(trans, archive_type=archive_type, archive_source=archive_source) return {"message": "Importing history from source '%s'. This history will be visible when the import is complete." % archive_source} new_history = None # if a history id was passed, copy that history if copy_this_history_id: decoded_id = self.decode_id(copy_this_history_id) original_history = self.manager.get_accessible(decoded_id, trans.user, current_history=trans.history) hist_name = hist_name or ("Copy of '%s'" % original_history.name) new_history = original_history.copy(name=hist_name, target_user=trans.user, all_datasets=all_datasets) # otherwise, create a new empty history else: new_history = self.manager.create(user=trans.user, name=hist_name) trans.sa_session.add(new_history) trans.sa_session.flush() # an anonymous user can only have one history if self.user_manager.is_anonymous(trans.user): self.manager.set_current(trans, new_history) return self.serializer.serialize_to_view(new_history, user=trans.user, trans=trans, **self._parse_serialization_params(kwd, 'detailed'))
[docs] @expose_api def delete(self, trans, id, **kwd): """ delete( self, trans, id, **kwd ) * DELETE /api/histories/{id} delete the history with the given ``id`` .. note:: Stops all active jobs in the history if purge is set. :type id: str :param id: the encoded id of the history to delete :type kwd: dict :param kwd: (optional) dictionary structure containing extra parameters You can purge a history, removing all it's datasets from disk (if unshared), by passing in ``purge=True`` in the url. :param keys: same as the use of `keys` in the `index` function above :param view: same as the use of `view` in the `index` function above :rtype: dict :returns: the deleted or purged history """ history_id = id # a request body is optional here purge = string_as_bool(kwd.get('purge', False)) # for backwards compat, keep the payload sub-dictionary if kwd.get('payload', None): purge = string_as_bool(kwd['payload'].get('purge', purge)) history = self.manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history) if purge: self.manager.purge(history) else: self.manager.delete(history) return self.serializer.serialize_to_view(history, user=trans.user, trans=trans, **self._parse_serialization_params(kwd, 'detailed'))
[docs] @expose_api def undelete(self, trans, id, **kwd): """ undelete( self, trans, id, **kwd ) * POST /api/histories/deleted/{id}/undelete: undelete history (that hasn't been purged) with the given ``id`` :type id: str :param id: the encoded id of the history to undelete :param keys: same as the use of `keys` in the `index` function above :param view: same as the use of `view` in the `index` function above :rtype: str :returns: 'OK' if the history was undeleted """ # TODO: remove at v2 history_id = id history = self.manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history) self.manager.undelete(history) return self.serializer.serialize_to_view(history, user=trans.user, trans=trans, **self._parse_serialization_params(kwd, 'detailed'))
[docs] @expose_api def update(self, trans, id, payload, **kwd): """ update( self, trans, id, payload, **kwd ) * PUT /api/histories/{id} updates the values for the history with the given ``id`` :type id: str :param id: the encoded id of the history to update :type payload: dict :param payload: a dictionary containing any or all the fields in :func:`galaxy.model.History.to_dict` and/or the following: * annotation: an annotation for the history :param keys: same as the use of `keys` in the `index` function above :param view: same as the use of `view` in the `index` function above :rtype: dict :returns: an error object if an error occurred or a dictionary containing any values that were different from the original and, therefore, updated """ # TODO: PUT /api/histories/{encoded_history_id} payload = { rating: rating } (w/ no security checks) history = self.manager.get_owned(self.decode_id(id), trans.user, current_history=trans.history) self.deserializer.deserialize(history, payload, user=trans.user, trans=trans) return self.serializer.serialize_to_view(history, user=trans.user, trans=trans, **self._parse_serialization_params(kwd, 'detailed'))
[docs] @expose_api def archive_export(self, trans, id, **kwds): """ export_archive( self, trans, id, payload ) * PUT /api/histories/{id}/exports: start job (if needed) to create history export for corresponding history. :type id: str :param id: the encoded id of the history to export :rtype: dict :returns: object containing url to fetch export from. """ # PUT instead of POST because multiple requests should just result # in one object being created. history = self.manager.get_accessible(self.decode_id(id), trans.user, current_history=trans.history) jeha = history.latest_export up_to_date = jeha and jeha.up_to_date if 'force' in kwds: up_to_date = False # Temp hack to force rebuild everytime during dev if not up_to_date: # Need to create new JEHA + job. gzip = kwds.get("gzip", True) include_hidden = kwds.get("include_hidden", False) include_deleted = kwds.get("include_deleted", False) self.queue_history_export(trans, history, gzip=gzip, include_hidden=include_hidden, include_deleted=include_deleted) if up_to_date and jeha.ready: jeha_id = trans.security.encode_id(jeha.id) return dict(download_url=url_for("history_archive_download", id=id, jeha_id=jeha_id)) else: # Valid request, just resource is not ready yet. trans.response.status = "202 Accepted" return ''
[docs] @expose_api_raw def archive_download(self, trans, id, jeha_id, **kwds): """ export_download( self, trans, id, jeha_id ) * GET /api/histories/{id}/exports/{jeha_id}: If ready and available, return raw contents of exported history. Use/poll "PUT /api/histories/{id}/exports" to initiate the creation of such an export - when ready that route will return 200 status code (instead of 202) with a JSON dictionary containing a `download_url`. """ # Seems silly to put jeha_id in here, but want GET to be immuatable? # and this is being accomplished this way. history = self.manager.get_accessible(self.decode_id(id), trans.user, current_history=trans.history) matching_exports = [e for e in history.exports if trans.security.encode_id(e.id) == jeha_id] if not matching_exports: raise exceptions.ObjectNotFound() jeha = matching_exports[0] if not jeha.ready: # User should not have been given this URL, PUT export should have # return a 202. raise exceptions.MessageException("Export not available or not yet ready.") return self.serve_ready_history_export(trans, jeha)
[docs] @expose_api def get_custom_builds_metadata(self, trans, id, payload=None, **kwd): """ GET /api/histories/{id}/custom_builds_metadata Returns meta data for custom builds. :param id: the encoded history id :type id: str """ if payload is None: payload = {} history = self.manager.get_accessible(self.decode_id(id), trans.user, current_history=trans.history) installed_builds = [] for build in glob.glob(os.path.join(trans.app.config.len_file_path, "*.len")): installed_builds.append(os.path.basename(build).split(".len")[0]) fasta_hdas = trans.sa_session.query(model.HistoryDatasetAssociation) \ .filter_by(history=history, extension="fasta", deleted=False) \ .order_by(model.HistoryDatasetAssociation.hid.desc()) return { 'installed_builds' : [{'label' : ins, 'value' : ins} for ins in installed_builds], 'fasta_hdas' : [{'label' : '%s: %s' % (hda.hid, hda.name), 'value' : trans.security.encode_id(hda.id)} for hda in fasta_hdas], }