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Bulk delete and hide operations.

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This commit is contained in:
John Chilton
2019-04-10 20:59:33 -04:00
parent 8d5b155f1a
commit d89749bad7
5 changed files with 147 additions and 33 deletions
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client/galaxy/scripts/mvc/history/history-view-edit.js
+50 -9
View File
@@ -247,35 +247,76 @@ var HistoryViewEdit = _super.extend(
* ajax calls made for multiple datasets are queued
*/
multiselectActions: function() {
var Galaxy = getGalaxyInstance();
var panel = this;
const batchUpdate = (key, value) => {
const actionModels = {};
const items = panel
.getSelectedModels()
.filter(model => {
console.log(model.attributes[key]);
return model.attributes[key] != value;
})
.map(model => {
const res = {
history_content_type: model.attributes.history_content_type,
id: model.attributes.id
};
actionModels[model.id] = model;
// Tried "optimistically" deleting the dataset - but it didn't quite work -
// maybe history polling restored the previous state?
return res;
});
if (items.length == 0) {
return;
}
const options = {};
options.url = `${Galaxy.root}api/histories/${this.model.id}/contents`;
options.type = "PUT";
const requestData = { items: items };
requestData[key] = value;
options.data = JSON.stringify(requestData);
options.contentType = "application/json";
var xhr = jQuery.ajax(options);
xhr.done((message, status, responseObj) => {
for (let updated of message) {
const typeId = updated.history_content_type + "-" + updated.id;
actionModels[typeId].set(updated);
}
});
xhr.fail((xhr, status, message) => {
console.error(message);
});
return xhr;
};
var actions = [
{
html: _l("Hide datasets"),
func: function() {
var action = HDA_MODEL.HistoryDatasetAssociation.prototype.hide;
panel.getSelectedModels().ajaxQueue(action);
batchUpdate("visible", false);
}
},
{
html: _l("Unhide datasets"),
func: function() {
var action = HDA_MODEL.HistoryDatasetAssociation.prototype.unhide;
panel.getSelectedModels().ajaxQueue(action);
batchUpdate("visible", true);
}
},
{
html: _l("Delete datasets"),
func: function() {
var action = HDA_MODEL.HistoryDatasetAssociation.prototype["delete"];
panel.getSelectedModels().ajaxQueue(action);
func: () => {
batchUpdate("deleted", true);
}
},
{
html: _l("Undelete datasets"),
func: function() {
var action = HDA_MODEL.HistoryDatasetAssociation.prototype.undelete;
panel.getSelectedModels().ajaxQueue(action);
batchUpdate("deleted", false);
}
}
];
lib/galaxy/managers/hdas.py
+7
View File
@@ -47,6 +47,13 @@ class HDAManager(datasets.DatasetAssociationManager,
super(HDAManager, self).__init__(app)
self.user_manager = users.UserManager(app)
def get_owned_ids(self, object_ids, history=None):
"""Get owned IDs.
"""
log.info("object_ids are %s" % object_ids)
filters = [self.model_class.id.in_(object_ids), self.model_class.history_id == history.id]
return self.list(filters=filters)
# .... security and permissions
def is_accessible(self, hda, user, **kwargs):
"""
lib/galaxy/webapps/galaxy/api/history_contents.py
+72 -24
View File
@@ -600,15 +600,60 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
self.hda_manager.update_permissions(trans, hda, **kwd)
return self.hda_manager.serialize_dataset_association_roles(trans, hda)
@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
# aggregate by ids.
# hdas_manager.by_ids() with history or user.
# dataset_collection_service.by_ids() with history or user.
@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``
updates the values for the history content item with the given ``id``
:type history_id: str
:param history_id: encoded id string of the HDA's History
:param history_id: encoded id string of the items's History
:type id: str
:param id: the encoded id of the history to update
:type payload: dict
@@ -634,13 +679,20 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
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:
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']
@@ -648,25 +700,21 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
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)
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:
# 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)
# 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 hdas
return {}
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)
@@ -700,8 +748,8 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
: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
* 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":
lib/galaxy/webapps/galaxy/buildapp.py
+5
View File
@@ -216,6 +216,11 @@ def populate_api_routes(webapp, app):
name_prefix='history_',
path_prefix='/api/histories/{history_id}',
parent_resources=dict(member_name='history', collection_name='histories'))
webapp.mapper.connect("history_contents_batch_update",
"/api/histories/{history_id}/contents",
controller="history_contents",
action="update_batch",
conditions=dict(method=["PUT"]))
webapp.mapper.connect("history_contents_display",
"/api/histories/{history_id}/contents/{history_content_id}/display",
controller="datasets",
test/api/test_history_contents.py
+13
View File
@@ -218,6 +218,14 @@ class HistoryContentsApiTestCase(api.ApiTestCase, TestsDatasets):
# and this is an invalid ID.
assert update_response.status_code == 400, update_response.content
def test_update_batch(self):
hda1 = self._wait_for_new_hda()
assert str(hda1["deleted"]).lower() == "false"
payload = dict(items=[{"history_content_type": "dataset", "id": hda1["id"]}], deleted=True)
update_response = self._raw_update_batch(payload)
objects = update_response.json()
assert objects[0]["deleted"]
def test_update_type_failures(self):
hda1 = self._wait_for_new_hda()
update_response = self._raw_update(hda1["id"], dict(deleted='not valid'))
@@ -246,6 +254,11 @@ class HistoryContentsApiTestCase(api.ApiTestCase, TestsDatasets):
update_response = put(update_url, json=data)
return update_response
def _raw_update_batch(self, data):
update_url = self._api_url("histories/%s/contents" % (self.history_id), use_key=True)
update_response = put(update_url, json=data)
return update_response
def test_delete(self):
hda1 = self._new_dataset(self.history_id)
self._wait_for_history(self.history_id)