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Source code for galaxy.webapps.galaxy.api.history_contents
"""
API operations on the contents of a history.
"""
import logging
import os
import re
from galaxy import (
exceptions,
util
)
from galaxy.managers import (
folders,
hdas,
hdcas,
histories,
history_contents
)
from galaxy.managers.collections_util import (
api_payload_to_create_params,
dictify_dataset_collection_instance,
get_hda_and_element_identifiers
)
from galaxy.managers.jobs import fetch_job_states, summarize_jobs_to_dict
from galaxy.util.json import safe_dumps
from galaxy.util.streamball import StreamBall
from galaxy.web import (
expose_api,
expose_api_anonymous,
expose_api_raw,
expose_api_raw_anonymous
)
from galaxy.webapps.base.controller import (
BaseAPIController,
UsesLibraryMixin,
UsesLibraryMixinItems,
UsesTagsMixin
)
log = logging.getLogger(__name__)
[docs]class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, UsesTagsMixin):
[docs] def __init__(self, app):
super(HistoryContentsController, self).__init__(app)
self.hda_manager = hdas.HDAManager(app)
self.history_manager = histories.HistoryManager(app)
self.history_contents_manager = history_contents.HistoryContentsManager(app)
self.folder_manager = folders.FolderManager()
self.hda_serializer = hdas.HDASerializer(app)
self.hda_deserializer = hdas.HDADeserializer(app)
self.hdca_serializer = hdcas.HDCASerializer(app)
self.history_contents_filters = history_contents.HistoryContentsFilters(app)
[docs] @expose_api_anonymous
def index(self, trans, history_id, ids=None, v=None, **kwd):
"""
index( self, trans, history_id, ids=None, **kwd )
* GET /api/histories/{history_id}/contents
return a list of HDA data for the history with the given ``id``
.. note:: Anonymous users are allowed to get their current history contents
If Ids is not given, index returns a list of *summary* objects for
every HDA associated with the given `history_id`.
If ids is given, index returns a *more complete* json object for each
HDA in the ids list.
:type history_id: str
:param history_id: encoded id string of the HDA's History
:type ids: str
:param ids: (optional) a comma separated list of encoded `HDA` ids
:param types: (optional) kinds of contents to index (currently just
dataset, but dataset_collection will be added shortly).
:type types: str
:rtype: list
:returns: dictionaries containing summary or detailed HDA information
"""
if v == 'dev':
return self.__index_v2(trans, history_id, **kwd)
rval = []
history = self.history_manager.get_accessible(self.decode_id(history_id), trans.user, current_history=trans.history)
# Allow passing in type or types - for continuity rest of methods
# take in type - but this one can be passed multiple types and
# type=dataset,dataset_collection is a bit silly.
types = kwd.get('type', kwd.get('types', None)) or []
if types:
types = util.listify(types)
else:
types = ['dataset', "dataset_collection"]
contents_kwds = {'types': types}
if ids:
ids = [self.decode_id(id) for id in ids.split(',')]
contents_kwds['ids'] = ids
# If explicit ids given, always used detailed result.
details = 'all'
else:
contents_kwds['deleted'] = kwd.get('deleted', None)
contents_kwds['visible'] = kwd.get('visible', None)
# details param allows a mixed set of summary and detailed hdas
# Ever more convoluted due to backwards compat..., details
# should be considered deprecated in favor of more specific
# dataset_details (and to be implemented dataset_collection_details).
details = kwd.get('details', None) or kwd.get('dataset_details', None) or []
if details and details != 'all':
details = util.listify(details)
for content in history.contents_iter(**contents_kwds):
encoded_content_id = trans.security.encode_id(content.id)
detailed = details == 'all' or (encoded_content_id in details)
if isinstance(content, trans.app.model.HistoryDatasetAssociation):
view = 'detailed' if detailed else 'summary'
hda_dict = self.hda_serializer.serialize_to_view(content, view=view, user=trans.user, trans=trans)
rval.append(hda_dict)
elif isinstance(content, trans.app.model.HistoryDatasetCollectionAssociation):
view = 'element' if detailed else 'collection'
collection_dict = self.__collection_dict(trans, content, view=view)
rval.append(collection_dict)
return rval
def __collection_dict(self, trans, dataset_collection_instance, **kwds):
return dictify_dataset_collection_instance(dataset_collection_instance,
security=trans.security, parent=dataset_collection_instance.history, **kwds)
[docs] @expose_api_anonymous
def show(self, trans, id, history_id, **kwd):
"""
* GET /api/histories/{history_id}/contents/{id}
* GET /api/histories/{history_id}/contents/{type}/{id}
return detailed information about an HDA or HDCA within a history
.. note:: Anonymous users are allowed to get their current history contents
:type id: str
:param id: the encoded id of the HDA or HDCA to return
:type type: str
:param id: 'dataset' or 'dataset_collection'
:type history_id: str
:param history_id: encoded id string of the HDA's or HDCA's History
:type view: str
:param view: if fetching a dataset collection - the view style of
the dataset collection to produce.
'collection' returns no element information, 'element'
returns detailed element information for all datasets,
'element-reference' returns a minimal set of information
about datasets (for instance id, type, and state but not
metadata, peek, info, or name). The default is 'element'.
:type fuzzy_count: int
:param fuzzy_count: this value can be used to broadly restrict the magnitude
of the number of elements returned via the API for large
collections. The number of actual elements returned may
be "a bit" more than this number or "a lot" less - varying
on the depth of nesting, balance of nesting at each level,
and size of target collection. The consumer of this API should
not expect a stable number or pre-calculable number of
elements to be produced given this parameter - the only
promise is that this API will not respond with an order
of magnitude more elements estimated with this value.
The UI uses this parameter to fetch a "balanced" concept of
the "start" of large collections at every depth of the
collection.
:rtype: dict
:returns: dictionary containing detailed HDA or HDCA information
"""
contents_type = self.__get_contents_type(trans, kwd)
if contents_type == 'dataset':
return self.__show_dataset(trans, id, **kwd)
elif contents_type == 'dataset_collection':
return self.__show_dataset_collection(trans, id, history_id, **kwd)
[docs] @expose_api_anonymous
def index_jobs_summary(self, trans, history_id, **kwd):
"""
* GET /api/histories/{history_id}/jobs_summary
return job state summary info for jobs, implicit groups jobs for collections or workflow invocations
Warning: We allow anyone to fetch job state information about any object they
can guess an encoded ID for - it isn't considered protected data. This keeps
polling IDs as part of state calculation for large histories and collections as
efficient as possible.
:type history_id: str
:param history_id: encoded id string of the target history
:type ids: str[]
:param ids: the encoded ids of job summary objects to return - if ids
is specified types must also be specified and have same length.
:type types: str[]
:param types: type of object represented by elements in the ids array - any of
Job, ImplicitCollectionJob, or WorkflowInvocation.
:rtype: dict[]
:returns: an array of job summary object dictionaries.
"""
ids = kwd.get("ids", None)
types = kwd.get("types", None)
if ids is None:
assert types is None
# TODO: ...
pass
else:
ids = [self.app.security.decode_id(i) for i in util.listify(ids)]
types = util.listify(types)
return [self.encode_all_ids(trans, s) for s in fetch_job_states(trans.sa_session, ids, types)]
[docs] @expose_api_anonymous
def show_jobs_summary(self, trans, id, history_id, **kwd):
"""
* GET /api/histories/{history_id}/contents/{type}/{id}/jobs_summary
return detailed information about an HDA or HDCAs jobs
Warning: We allow anyone to fetch job state information about any object they
can guess an encoded ID for - it isn't considered protected data. This keeps
polling IDs as part of state calculation for large histories and collections as
efficient as possible.
:type id: str
:param id: the encoded id of the HDA to return
:type history_id: str
:param history_id: encoded id string of the HDA's or the HDCA's History
:rtype: dict
:returns: dictionary containing jobs summary object
"""
contents_type = self.__get_contents_type(trans, kwd)
# At most one of job or implicit_collection_jobs should be found.
job = None
implicit_collection_jobs = None
if contents_type == 'dataset':
hda = self.hda_manager.get_accessible(self.decode_id(id), trans.user)
job = hda.creating_job
elif contents_type == 'dataset_collection':
dataset_collection_instance = self.__get_accessible_collection(trans, id, history_id)
job_source_type = dataset_collection_instance.job_source_type
if job_source_type == "Job":
job = dataset_collection_instance.job
elif job_source_type == "ImplicitCollectionJobs":
implicit_collection_jobs = dataset_collection_instance.implicit_collection_jobs
assert job is None or implicit_collection_jobs is None
return self.encode_all_ids(trans, summarize_jobs_to_dict(trans.sa_session, job or implicit_collection_jobs))
def __get_contents_type(self, trans, kwd):
contents_type = kwd.get('type', 'dataset')
if contents_type not in ['dataset', 'dataset_collection']:
self.__handle_unknown_contents_type(trans, contents_type)
return contents_type
def __show_dataset(self, trans, id, **kwd):
hda = self.hda_manager.get_accessible(self.decode_id(id), trans.user)
return self.hda_serializer.serialize_to_view(hda,
user=trans.user,
trans=trans,
**self._parse_serialization_params(kwd, 'detailed'))
def __show_dataset_collection(self, trans, id, history_id, **kwd):
dataset_collection_instance = self.__get_accessible_collection(trans, id, history_id)
view = kwd.get("view", "element")
fuzzy_count = kwd.get("fuzzy_count", None)
if fuzzy_count:
fuzzy_count = int(fuzzy_count)
return self.__collection_dict(trans, dataset_collection_instance, view=view, fuzzy_count=fuzzy_count)
def __get_accessible_collection(self, trans, id, history_id):
return trans.app.dataset_collections_service.get_dataset_collection_instance(
trans=trans,
instance_type="history",
id=id
)
[docs] @expose_api_raw_anonymous
def download_dataset_collection(self, trans, id, history_id=None, **kwd):
"""
* GET /api/histories/{history_id}/contents/{id}/download
* GET /api/dataset_collection/{id}/download
Download the content of a HistoryDatasetCollection as a tgz archive
while maintaining approximate collection structure.
:param id: encoded HistoryDatasetCollectionAssociation (HDCA) id
:param history_id: encoded id string of the HDCA's History
"""
try:
dataset_collection_instance = self.__get_accessible_collection(trans, id, history_id)
return self.__stream_dataset_collection(trans, dataset_collection_instance)
except Exception as e:
log.exception("Error in API while creating dataset collection archive")
trans.response.status = 500
return {'error': util.unicodify(e)}
def __stream_dataset_collection(self, trans, dataset_collection_instance):
archive_type_string = 'w|gz'
archive_ext = 'tgz'
if self.app.config.upstream_gzip:
archive_type_string = 'w|'
archive_ext = 'tar'
archive = StreamBall(mode=archive_type_string)
names, hdas = get_hda_and_element_identifiers(dataset_collection_instance)
for name, hda in zip(names, hdas):
if hda.state != hda.states.OK:
continue
for file_path, relpath in hda.datatype.to_archive(trans=trans, dataset=hda, name=name):
archive.add(file=file_path, relpath=relpath)
archive_name = "%s: %s.%s" % (dataset_collection_instance.hid, dataset_collection_instance.name, archive_ext)
trans.response.set_content_type("application/x-tar")
trans.response.headers["Content-Disposition"] = 'attachment; filename="{}"'.format(archive_name)
archive.wsgi_status = trans.response.wsgi_status()
archive.wsgi_headeritems = trans.response.wsgi_headeritems()
return archive.stream
[docs] @expose_api_anonymous
def create(self, trans, history_id, payload, **kwd):
"""
create( self, trans, history_id, payload, **kwd )
* POST /api/histories/{history_id}/contents/{type}s
* POST /api/histories/{history_id}/contents
create a new HDA or HDCA
:type history_id: str
:param history_id: encoded id string of the new HDA's History
:type type: str
:param type: Type of history content - 'dataset' (default) or
'dataset_collection'. This can be passed in via payload
or parsed from the route.
:type payload: dict
:param payload: dictionary structure containing::
copy from library (for type 'dataset'):
'source' = 'library'
'content' = [the encoded id from the library dataset]
copy from library folder
'source' = 'library_folder'
'content' = [the encoded id from the library folder]
copy from history dataset (for type 'dataset'):
'source' = 'hda'
'content' = [the encoded id from the HDA]
copy from history dataset collection (for type 'dataset_collection')
'source' = 'hdca'
'content' = [the encoded id from the HDCA]
'copy_elements' = Copy child HDAs into the target history as well,
defaults to False but this is less than ideal and may
be changed in future releases.
create new history dataset collection (for type 'dataset_collection')
'source' = 'new_collection' (default 'source' if type is
'dataset_collection' - no need to specify this)
'collection_type' = For example, "list", "paired", "list:paired".
'copy_elements' = Copy child HDAs when creating new collection,
defaults to False in the API but is set to True in the UI,
so that we can modify HDAs with tags when creating collections.
'name' = Name of new dataset collection.
'element_identifiers' = Recursive list structure defining collection.
Each element must have 'src' which can be
'hda', 'ldda', 'hdca', or 'new_collection',
as well as a 'name' which is the name of
element (e.g. "forward" or "reverse" for
paired datasets, or arbitrary sample names
for instance for lists). For all src's except
'new_collection' - a encoded 'id' attribute
must be included wiht element as well.
'new_collection' sources must defined a
'collection_type' and their own list of
(potentially) nested 'element_identifiers'.
..note:
Currently, a user can only copy an HDA from a history that the user owns.
:rtype: dict
:returns: dictionary containing detailed information for the new HDA
"""
# TODO: Flush out create new collection documentation above, need some
# examples. See also bioblend and API tests for specific examples.
history = self.history_manager.get_owned(self.decode_id(history_id), trans.user,
current_history=trans.history)
type = payload.get('type', 'dataset')
if type == 'dataset':
source = payload.get('source', None)
if source == 'library_folder':
return self.__create_datasets_from_library_folder(trans, history, payload, **kwd)
else:
return self.__create_dataset(trans, history, payload, **kwd)
elif type == 'dataset_collection':
return self.__create_dataset_collection(trans, history, payload, **kwd)
else:
return self.__handle_unknown_contents_type(trans, type)
def __create_dataset(self, trans, history, payload, **kwd):
source = payload.get('source', None)
if source not in ('library', 'hda'):
raise exceptions.RequestParameterInvalidException(
"'source' must be either 'library' or 'hda': %s" % (source))
content = payload.get('content', None)
if content is None:
raise exceptions.RequestParameterMissingException("'content' id of lda or hda is missing")
# copy from library dataset
hda = None
if source == 'library':
hda = self.__create_hda_from_ldda(trans, content, history)
# copy an existing, accessible hda
elif source == 'hda':
unencoded_hda_id = self.decode_id(content)
original = self.hda_manager.get_accessible(unencoded_hda_id, trans.user)
# check for access on history that contains the original hda as well
self.history_manager.error_unless_accessible(original.history, trans.user, current_history=trans.history)
hda = self.hda_manager.copy(original, history=history)
trans.sa_session.flush()
if not hda:
return None
return self.hda_serializer.serialize_to_view(hda,
user=trans.user, trans=trans, **self._parse_serialization_params(kwd, 'detailed'))
def __create_hda_from_ldda(self, trans, content, history):
ld = self.get_library_dataset(trans, content)
if type(ld) is not trans.app.model.LibraryDataset:
raise exceptions.RequestParameterInvalidException(
"Library content id ( %s ) is not a dataset" % content)
hda = ld.library_dataset_dataset_association.to_history_dataset_association(history, add_to_history=True)
return hda
def __create_datasets_from_library_folder(self, trans, history, payload, **kwd):
rval = []
source = payload.get('source', None)
if source == 'library_folder':
content = payload.get('content', None)
if content is None:
raise exceptions.RequestParameterMissingException("'content' id of lda or hda is missing")
folder_id = self.folder_manager.cut_and_decode(trans, content)
folder = self.folder_manager.get(trans, folder_id)
current_user_roles = trans.get_current_user_roles()
def traverse(folder):
admin = trans.user_is_admin
rval = []
for subfolder in folder.active_folders:
if not admin:
can_access, folder_ids = trans.app.security_agent.check_folder_contents(trans.user, current_user_roles, subfolder)
if (admin or can_access) and not subfolder.deleted:
rval.extend(traverse(subfolder))
for ld in folder.datasets:
if not admin:
can_access = trans.app.security_agent.can_access_dataset(
current_user_roles,
ld.library_dataset_dataset_association.dataset
)
if (admin or can_access) and not ld.deleted:
rval.append(ld)
return rval
for ld in traverse(folder):
hda = ld.library_dataset_dataset_association.to_history_dataset_association(history, add_to_history=True)
hda_dict = self.hda_serializer.serialize_to_view(hda,
user=trans.user, trans=trans, **self._parse_serialization_params(kwd, 'detailed'))
rval.append(hda_dict)
else:
message = "Invalid 'source' parameter in request %s" % source
raise exceptions.RequestParameterInvalidException(message)
trans.sa_session.flush()
return rval
def __create_dataset_collection(self, trans, history, payload, **kwd):
"""Create hdca in a history from the list of element identifiers
:param history: history the new hdca should be added to
:type history: History
:param source: whether to create a new collection or copy existing one
:type source: str
:param payload: dictionary structure containing:
:param collection_type: type (and depth) of the new collection
:type name: str
:param element_identifiers: list of elements that should be in the new collection
:param element: one member of the collection
:param name: name of the element
:type name: str
:param src: source of the element (hda/ldda)
:type src: str
:param id: identifier
:type id: str
:param id: tags
:type id: list
:type element: dict
:type name: list
:param name: name of the collection
:type name: str
:param hide_source_items: whether to mark the original hdas as hidden
:type name: bool
:param copy_elements: whether to copy HDAs when creating collection
:type name: bool
:type payload: dict
.. note:: Elements may be nested depending on the collection_type
:returns: dataset collection information
:rtype: dict
:raises: RequestParameterInvalidException, RequestParameterMissingException
"""
source = kwd.get("source", payload.get("source", "new_collection"))
service = trans.app.dataset_collections_service
if source == "new_collection":
create_params = api_payload_to_create_params(payload)
dataset_collection_instance = service.create(
trans,
parent=history,
**create_params
)
elif source == "hdca":
content = payload.get('content', None)
if content is None:
raise exceptions.RequestParameterMissingException("'content' id of target to copy is missing")
copy_elements = payload.get('copy_elements', False)
dataset_collection_instance = service.copy(
trans=trans,
parent=history,
source="hdca",
encoded_source_id=content,
copy_elements=copy_elements,
)
else:
message = "Invalid 'source' parameter in request %s" % source
raise exceptions.RequestParameterInvalidException(message)
# if the consumer specified keys or view, use the secondary serializer
if 'view' in kwd or 'keys' in kwd:
return self.hdca_serializer.serialize_to_view(dataset_collection_instance,
user=trans.user, trans=trans, **self._parse_serialization_params(kwd, 'detailed'))
return self.__collection_dict(trans, dataset_collection_instance, view="element")
[docs] @expose_api
def show_roles(self, trans, encoded_dataset_id, **kwd):
"""
Display information about current or available roles for a given dataset permission.
* GET /api/histories/{history_id}/contents/datasets/{encoded_dataset_id}/permissions
:param encoded_dataset_id: the encoded id of the dataset to query
:type encoded_dataset_id: an encoded id string
:returns: either dict of current roles for all permission types
or dict of available roles to choose from (is the same for any permission type)
:rtype: dictionary
:raises: InsufficientPermissionsException
"""
hda = self.hda_manager.get_owned(self.decode_id(encoded_dataset_id), trans.user, current_history=trans.history, trans=trans)
return self.hda_manager.serialize_dataset_association_roles(trans, hda)
[docs] @expose_api
def update_permissions(self, trans, history_id, history_content_id, payload=None, **kwd):
"""
Set permissions of the given library dataset to the given role ids.
* PUT /api/histories/{history_id}/contents/datasets/{encoded_dataset_id}/permissions
:param encoded_dataset_id: the encoded id of the dataset to update permissions of
:type encoded_dataset_id: an encoded id string
:param payload: dictionary structure containing:
:param action: (required) describes what action should be performed
available actions: make_private, remove_restrictions, set_permissions
:type action: string
:param access_ids[]: list of Role.id defining roles that should have access permission on the dataset
:type access_ids[]: string or list
:param manage_ids[]: list of Role.id defining roles that should have manage permission on the dataset
:type manage_ids[]: string or list
:param modify_ids[]: list of Role.id defining roles that should have modify permission on the library dataset item
:type modify_ids[]: string or list
:type: dictionary
:returns: dict of current roles for all available permission types
:rtype: dictionary
:raises: RequestParameterInvalidException, ObjectNotFound, InsufficientPermissionsException, InternalServerError
RequestParameterMissingException
"""
if payload:
kwd.update(payload)
hda = self.hda_manager.get_owned(self.decode_id(history_content_id), trans.user, current_history=trans.history, trans=trans)
assert hda is not None
self.hda_manager.update_permissions(trans, hda, **kwd)
return self.hda_manager.serialize_dataset_association_roles(trans, hda)
[docs] @expose_api_anonymous
def update_batch(self, trans, history_id, payload, **kwd):
"""
update( self, trans, history_id, id, payload, **kwd )
* PUT /api/histories/{history_id}/contents
:type history_id: str
:param history_id: encoded id string of the history containing supplied items
: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
: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
"""
items = payload.get("items")
hda_ids = []
hdca_ids = []
for item in items:
contents_type = item["history_content_type"]
if contents_type == "dataset":
decoded_id = self.decode_id(item["id"])
hda_ids.append(decoded_id)
else:
hdca_ids.append(item["id"])
history = self.history_manager.get_owned(self.decode_id(history_id), trans.user,
current_history=trans.history)
hdas = self.__datasets_for_update(trans, history, hda_ids, payload)
rval = []
for hda in hdas:
self.__deserialize_dataset(hda, payload, trans)
rval.append(self.hda_serializer.serialize_to_view(hda,
user=trans.user, trans=trans, **self._parse_serialization_params(kwd, 'summary')))
for hdca_id in hdca_ids:
self.__update_dataset_collection(trans, history_id, hdca_id, payload, **kwd)
dataset_collection_instance = self.__get_accessible_collection(trans, hdca_id, history_id)
rval.append(self.__collection_dict(trans, dataset_collection_instance, view="summary"))
return rval
[docs] @expose_api_anonymous
def update(self, trans, history_id, id, payload, **kwd):
"""
update( self, trans, history_id, id, payload, **kwd )
* PUT /api/histories/{history_id}/contents/{id}
updates the values for the history content item with the given ``id``
:type history_id: str
:param history_id: encoded id string of the items's History
:type id: str
:param id: the encoded id of the history item to update
:type payload: dict
:param payload: a dictionary containing any or all the
fields in :func:`galaxy.model.HistoryDatasetAssociation.to_dict`
and/or the following:
* annotation: an annotation for the HDA
: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)
contents_type = kwd.get('type', 'dataset')
if contents_type == "dataset":
return self.__update_dataset(trans, history_id, id, payload, **kwd)
elif contents_type == "dataset_collection":
return self.__update_dataset_collection(trans, history_id, id, payload, **kwd)
else:
return self.__handle_unknown_contents_type(trans, contents_type)
[docs] @expose_api_anonymous
def validate(self, trans, history_id, history_content_id, payload=None, **kwd):
"""
update( self, trans, history_id, id, payload, **kwd )
* PUT /api/histories/{history_id}/contents/{id}/validate
updates the values for the history content item with the given ``id``
:type history_id: str
:param history_id: encoded id string of the items's History
:type id: str
:param id: the encoded id of the history item to validate
:rtype: dict
:returns: TODO
"""
decoded_id = self.decode_id(history_content_id)
history = self.history_manager.get_owned(self.decode_id(history_id), trans.user,
current_history=trans.history)
hda = self.hda_manager.get_owned_ids([decoded_id], history=history)[0]
if hda:
self.hda_manager.set_metadata(trans, hda, overwrite=True, validate=True)
return {}
def __update_dataset(self, trans, history_id, id, payload, **kwd):
# anon user: ensure that history ids match up and the history is the current,
# check for uploading, and use only the subset of attribute keys manipulatable by anon users
decoded_id = self.decode_id(id)
history = self.history_manager.get_owned(self.decode_id(history_id), trans.user,
current_history=trans.history)
hda = self.__datasets_for_update(trans, history, [decoded_id], payload)[0]
if hda:
self.__deserialize_dataset(hda, payload, trans)
return self.hda_serializer.serialize_to_view(hda,
user=trans.user, trans=trans, **self._parse_serialization_params(kwd, 'detailed'))
return {}
def __datasets_for_update(self, trans, history, hda_ids, payload):
anonymous_user = not trans.user_is_admin and trans.user is None
if anonymous_user:
anon_allowed_payload = {}
if 'deleted' in payload:
anon_allowed_payload['deleted'] = payload['deleted']
if 'visible' in payload:
anon_allowed_payload['visible'] = payload['visible']
payload = anon_allowed_payload
hdas = self.hda_manager.get_owned_ids(hda_ids, history=history)
# only check_state if not deleting, otherwise cannot delete uploading files
check_state = not payload.get('deleted', False)
if check_state:
for hda in hdas:
hda = self.hda_manager.error_if_uploading(hda)
return hdas
def __deserialize_dataset(self, hda, payload, trans):
self.hda_deserializer.deserialize(hda, payload, user=trans.user, trans=trans)
# TODO: this should be an effect of deleting the hda
if payload.get('deleted', False):
self.hda_manager.stop_creating_job(hda)
def __update_dataset_collection(self, trans, history_id, id, payload, **kwd):
return trans.app.dataset_collections_service.update(trans, "history", id, payload)
# TODO: allow anonymous del/purge and test security on this
[docs] @expose_api
def delete(self, trans, history_id, id, purge=False, recursive=False, **kwd):
"""
delete( self, trans, history_id, id, **kwd )
* DELETE /api/histories/{history_id}/contents/{id}
* DELETE /api/histories/{history_id}/contents/{type}s/{id}
delete the history content with the given ``id`` and specified type (defaults to dataset)
.. note:: Currently does not stop any active jobs for which this dataset is an output.
:type id: str
:param id: the encoded id of the history to delete
:type recursive: bool
:param recursive: if True, and deleted an HDCA also delete containing HDAs
:type purge: bool
:param purge: if True, purge the target HDA or child HDAs of the target HDCA
:type kwd: dict
:param kwd: (optional) dictionary structure containing:
* payload: a dictionary itself containing:
* purge: if True, purge the HDA
* recursive: if True, see above.
.. note:: that payload optionally can be placed in the query string of the request.
This allows clients that strip the request body to still purge the dataset.
:rtype: dict
:returns: an error object if an error occurred or a dictionary containing:
* id: the encoded id of the history,
* deleted: if the history content was marked as deleted,
* purged: if the history content was purged
"""
contents_type = kwd.get('type', 'dataset')
if contents_type == "dataset":
return self.__delete_dataset(trans, history_id, id, purge=purge, **kwd)
elif contents_type == "dataset_collection":
purge = util.string_as_bool(purge)
recursive = util.string_as_bool(recursive)
if kwd.get('payload', None):
# payload takes priority
purge = util.string_as_bool(kwd['payload'].get('purge', purge))
recursive = util.string_as_bool(kwd['payload'].get('recursive', recursive))
trans.app.dataset_collections_service.delete(trans, "history", id, recursive=recursive, purge=purge)
return {'id' : id, "deleted": True}
else:
return self.__handle_unknown_contents_type(trans, contents_type)
def __delete_dataset(self, trans, history_id, id, purge, **kwd):
# get purge from the query or from the request body payload (a request body is optional here)
purge = util.string_as_bool(purge)
if kwd.get('payload', None):
# payload takes priority
purge = util.string_as_bool(kwd['payload'].get('purge', purge))
hda = self.hda_manager.get_owned(self.decode_id(id), trans.user, current_history=trans.history)
self.hda_manager.error_if_uploading(hda)
if purge:
self.hda_manager.purge(hda)
else:
self.hda_manager.delete(hda)
return self.hda_serializer.serialize_to_view(hda,
user=trans.user, trans=trans, **self._parse_serialization_params(kwd, 'detailed'))
def __handle_unknown_contents_type(self, trans, contents_type):
raise exceptions.UnknownContentsType('Unknown contents type: %s' % type)
def __index_v2(self, trans, history_id, **kwd):
"""
index( self, trans, history_id, **kwd )
* GET /api/histories/{history_id}/contents
return a list of HDA data for the history with the given ``id``
.. note:: Anonymous users are allowed to get their current history contents
If ids is given, index returns a *more complete* json object for each
HDA in the ids list.
:type history_id: str
:param history_id: encoded id string of the HDA's History
:rtype: list
:returns: dictionaries containing summary or detailed HDA 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 sent and no view, only those properties in keys are returned.
For which properties are available see:
galaxy/managers/hdas/HDASerializer
and:
galaxy/managers/collection_util
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=name-contains&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:
hid defaults to 'hid-asc'
create_time defaults to 'create_time-dsc'
update_time defaults to 'update_time-dsc'
name defaults to 'name-asc'
'order' defaults to 'hid-asc'
"""
rval = []
history = self.history_manager.get_accessible(self.decode_id(history_id), trans.user,
current_history=trans.history)
filter_params = self.parse_filter_params(kwd)
filters = self.history_contents_filters.parse_filters(filter_params)
limit, offset = self.parse_limit_offset(kwd)
order_by = self._parse_order_by(manager=self.history_contents_manager, order_by_string=kwd.get('order', 'hid-asc'))
serialization_params = self._parse_serialization_params(kwd, 'summary')
# TODO: > 16.04: remove these
# TODO: remove 'dataset_details' and the following section when the UI doesn't need it
# details param allows a mixed set of summary and detailed hdas
# Ever more convoluted due to backwards compat..., details
# should be considered deprecated in favor of more specific
# dataset_details (and to be implemented dataset_collection_details).
details = kwd.get('details', [])
if details and details != 'all':
details = util.listify(details)
view = serialization_params.pop('view')
contents = self.history_contents_manager.contents(history,
filters=filters, limit=limit, offset=offset, order_by=order_by)
for content in contents:
# TODO: remove split
if isinstance(content, trans.app.model.HistoryDatasetAssociation):
# TODO: remove split
if details == 'all' or trans.security.encode_id(content.id) in details:
rval.append(self.hda_serializer.serialize_to_view(content,
user=trans.user, trans=trans, view='detailed', **serialization_params))
else:
rval.append(self.hda_serializer.serialize_to_view(content,
user=trans.user, trans=trans, view=view, **serialization_params))
elif isinstance(content, trans.app.model.HistoryDatasetCollectionAssociation):
collection = self.hdca_serializer.serialize_to_view(content,
user=trans.user, trans=trans, view=view, **serialization_params)
rval.append(collection)
return rval
[docs] def encode_type_id(self, type_id):
TYPE_ID_SEP = '-'
split = type_id.split(TYPE_ID_SEP, 1)
return TYPE_ID_SEP.join([split[0], self.app.security.encode_id(split[1])])
[docs] @expose_api_raw
def archive(self, trans, history_id, filename='', format='tgz', dry_run=True, **kwd):
"""
archive( self, trans, history_id, filename='', format='tgz', dry_run=True, **kwd )
* GET /api/histories/{history_id}/contents/archive/{id}
* GET /api/histories/{history_id}/contents/archive/{filename}.{format}
build and return a compressed archive of the selected history contents
:type filename: string
:param filename: (optional) archive name (defaults to history name)
:type dry_run: boolean
:param dry_run: (optional) if True, return the archive and file paths only
as json and not an archive file
:returns: archive file for download
.. note:: this is a volatile endpoint and settings and behavior may change.
"""
# roughly from: http://stackoverflow.com/a/31976060 (windows, linux)
invalid_filename_char_regex = re.compile(r'[:<>|\\\/\?\* "]')
# path format string - dot separator between id and name
id_name_format = u'{}.{}'
def name_to_filename(name, max_length=150, replace_with=u'_'):
# TODO: seems like shortening unicode with [:] would cause unpredictable display strings
return invalid_filename_char_regex.sub(replace_with, name)[0:max_length]
# given a set of parents for a dataset (HDCAs, DC, DCEs, etc.) - build a directory structure that
# (roughly) recreates the nesting in the contents using the parent names and ids
def build_path_from_parents(parents):
parent_names = []
for parent in parents:
# an HDCA
if hasattr(parent, 'hid'):
name = name_to_filename(parent.name)
parent_names.append(id_name_format.format(parent.hid, name))
# a DCE
elif hasattr(parent, 'element_index'):
name = name_to_filename(parent.element_identifier)
parent_names.append(id_name_format.format(parent.element_index, name))
# NOTE: DCs are skipped and use the wrapping DCE info instead
return parent_names
# get the history used for the contents query and check for accessibility
history = self.history_manager.get_accessible(trans.security.decode_id(history_id), trans.user)
archive_base_name = filename or name_to_filename(history.name)
# this is the fn applied to each dataset contained in the query
paths_and_files = []
def build_archive_files_and_paths(content, *parents):
archive_path = archive_base_name
if not self.hda_manager.is_accessible(content, trans.user):
# if the underlying dataset is not accessible, skip it silently
return
content_container_id = content.hid
content_name = name_to_filename(content.name)
if parents:
if hasattr(parents[0], 'element_index'):
# if content is directly wrapped in a DCE, strip it from parents (and the resulting path)
# and instead replace the content id and name with the DCE index and identifier
parent_dce, parents = parents[0], parents[1:]
content_container_id = parent_dce.element_index
content_name = name_to_filename(parent_dce.element_identifier)
# reverse for path from parents: oldest parent first
archive_path = os.path.join(archive_path, *build_path_from_parents(parents)[::-1])
# TODO: this is brute force - building the path each time instead of re-using it
# possibly cache
# add the name as the last element in the archive path
content_id_and_name = id_name_format.format(content_container_id, content_name)
archive_path = os.path.join(archive_path, content_id_and_name)
# ---- for composite files, we use id and name for a directory and, inside that, ...
if self.hda_manager.is_composite(content):
# ...save the 'main' composite file (gen. html)
paths_and_files.append((content.file_name, os.path.join(archive_path, content.name + '.html')))
for extra_file in self.hda_manager.extra_files(content):
extra_file_basename = os.path.basename(extra_file)
archive_extra_file_path = os.path.join(archive_path, extra_file_basename)
# ...and one for each file in the composite
paths_and_files.append((extra_file, archive_extra_file_path))
# ---- for single files, we add the true extension to id and name and store that single filename
else:
# some dataset names can contain their original file extensions, don't repeat
if not archive_path.endswith('.' + content.extension):
archive_path += '.' + content.extension
paths_and_files.append((content.file_name, archive_path))
# filter the contents that contain datasets using any filters possible from index above and map the datasets
filter_params = self.parse_filter_params(kwd)
filters = self.history_contents_filters.parse_filters(filter_params)
self.history_contents_manager.map_datasets(history, build_archive_files_and_paths, filters=filters)
# if dry_run, return the structure as json for debugging
if dry_run == 'True':
trans.response.headers['Content-Type'] = 'application/json'
return safe_dumps(paths_and_files)
# create the archive, add the dataset files, then stream the archive as a download
archive_type_string = 'w|gz'
archive_ext = 'tgz'
if self.app.config.upstream_gzip:
archive_type_string = 'w|'
archive_ext = 'tar'
archive = StreamBall(archive_type_string)
for file_path, archive_path in paths_and_files:
archive.add(file_path, archive_path)
archive_name = '.'.join([archive_base_name, archive_ext])
trans.response.set_content_type("application/x-tar")
trans.response.headers["Content-Disposition"] = 'attachment; filename="{}"'.format(archive_name)
archive.wsgi_status = trans.response.wsgi_status()
archive.wsgi_headeritems = trans.response.wsgi_headeritems()
return archive.stream