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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 (
expose_api,
expose_api_anonymous,
expose_api_anonymous_and_sessionless,
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(manager=self.manager, order_by_string=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()]
[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(manager=self.manager, order_by_string=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
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],
}