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 (
    _future_expose_api as expose_api,
    _future_expose_api_anonymous as expose_api_anonymous,
    _future_expose_api_raw as expose_api_raw,
    _future_expose_api_raw_anonymous as expose_api_raw_anonymous
)
from galaxy.web.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 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 history_id: str :param history_id: encoded id string of the HDA's or the HDCA's 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 - either Job or ImplicitCollectionJob. :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 = util.listify(ids) types = util.listify(types) return [self.encode_all_ids(trans, s) for s in fetch_job_states(self.app, 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': str(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(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 HDA with the given ``id`` :type history_id: str :param history_id: encoded id string of the HDA's History :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.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)
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 anonymous_user = not trans.user_is_admin and trans.user is None if anonymous_user: hda = self.hda_manager.by_id(self.decode_id(id)) if hda.history != trans.history: raise exceptions.AuthenticationRequired('API authentication required for this request') hda = self.hda_manager.error_if_uploading(hda) 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 # logged in user: use full payload, check state if deleting, and make sure the history is theirs else: hda = self.hda_manager.get_owned(self.decode_id(id), trans.user, current_history=trans.history, trans=trans) # only check_state if not deleting, otherwise cannot delete uploading files check_state = not payload.get('deleted', False) if check_state: hda = self.hda_manager.error_if_uploading(hda) # make the actual changes if hda: 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) return self.hda_serializer.serialize_to_view(hda, user=trans.user, trans=trans, **self._parse_serialization_params(kwd, 'detailed')) return {} 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 was marked as deleted, * purged: if the history 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(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])])
def _parse_order_by(self, order_by_string): ORDER_BY_SEP_CHAR = ',' manager = self.history_contents_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_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