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Merge pull request #15695 from mvdbeek/dont_process_dataset_param

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[23.0] Do not pass dataset keyword parameter into datatype.display_data
This commit is contained in:
Dannon
2023-03-06 07:52:11 -05:00
committed by GitHub
parent c91e4c49f4 d97adf6359
commit 4f52b74549
14 changed files with 32 additions and 30 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/actions/library.py
+1 -1
View File
@@ -333,7 +333,7 @@ class LibraryActions:
raise ObjectNotFound(message)
elif (
not trans.app.security_agent.can_access_dataset(current_user_roles, item.dataset)
and item.history.user == trans.user
and item.user == trans.user
):
message = f"You do not have permission to access the history dataset with id ({str(item.id)})."
raise ItemAccessibilityException(message)
lib/galaxy/managers/hdas.py
+2 -2
View File
@@ -182,7 +182,7 @@ class HDAManager(
copy.set_size()
original_annotation = self.annotation(hda)
self.annotate(copy, original_annotation, user=hda.history.user, flush=False)
self.annotate(copy, original_annotation, user=hda.user, flush=False)
if flush:
if history:
history.add_pending_items()
@@ -292,7 +292,7 @@ class HDAManager(
# .... annotatable
def annotation(self, hda):
# override to scope to history owner
return self._user_annotation(hda, hda.history.user)
return self._user_annotation(hda, hda.user)
def _set_permissions(self, trans, hda, role_ids_dict):
# The user associated the DATASET_ACCESS permission on the dataset with 1 or more roles. We
lib/galaxy/model/__init__.py
+7 -2
View File
@@ -4492,6 +4492,11 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
self.copied_from_history_dataset_association = copied_from_history_dataset_association
self.copied_from_library_dataset_dataset_association = copied_from_library_dataset_dataset_association
@property
def user(self):
if self.history:
return self.history.user
def __create_version__(self, session):
state = inspect(self)
changes = {}
@@ -4539,7 +4544,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
self.validated_state = other_hda.validated_state
self.validated_state_message = other_hda.validated_state_message
if include_tags and self.history:
self.copy_tags_from(self.history.user, other_hda)
self.copy_tags_from(self.user, other_hda)
self.dataset = new_dataset or other_hda.dataset
if old_dataset:
old_dataset.full_delete()
@@ -4687,7 +4692,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
for hda in self.dataset.history_associations:
if hda.id == self.id:
continue
if not hda.purged and hda.history and hda.history.user and hda.history.user == user:
if not hda.purged and hda.history and hda.user and hda.user == user:
break
else:
rval += self.get_total_size()
lib/galaxy/tools/__init__.py
+2 -2
View File
@@ -2152,8 +2152,8 @@ class Tool(Dictifiable):
for p_name in rup_dict:
redirect_url += f"&{p_name}={rup_dict[p_name]}"
# Add the current user email to redirect_url
if data.history.user:
USERNAME = str(data.history.user.email)
if data.user:
USERNAME = str(data.user.email)
else:
USERNAME = "Anonymous"
redirect_url += f"&USERNAME={USERNAME}"
lib/galaxy/webapps/base/controller.py
+1 -1
View File
@@ -1077,7 +1077,7 @@ class UsesVisualizationMixin(UsesLibraryMixinItems):
user = trans.get_user()
if not user:
error("Must be logged in to manage Galaxy items")
if data.history.user != user:
if data.user != user:
error(f"{data.__class__.__name__} is not owned by current user")
if check_accessible:
lib/galaxy/webapps/galaxy/api/datasets.py
+3 -1
View File
@@ -258,7 +258,9 @@ class FastAPIDatasets:
),
):
"""Streams the dataset for download or the contents preview to be displayed in a browser."""
extra_params = get_query_parameters_from_request_excluding(request, {"preview", "filename", "to_ext", "raw"})
extra_params = get_query_parameters_from_request_excluding(
request, {"preview", "filename", "to_ext", "raw", "dataset"}
)
display_data, headers = self.service.display(
trans, history_content_id, preview=preview, filename=filename, to_ext=to_ext, raw=raw, **extra_params
)
lib/galaxy/webapps/galaxy/controllers/dataset.py
+6 -6
View File
@@ -153,7 +153,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
return trans.show_error_message("You are not allowed to access this dataset")
if data.purged or data.dataset.purged:
return trans.show_error_message("The dataset you are attempting to view has been purged.")
elif data.deleted and not (trans.user_is_admin or (data.history and trans.get_user() == data.history.user)):
elif data.deleted and not (trans.user_is_admin or (data.history and trans.get_user() == data.user)):
return trans.show_error_message("The dataset you are attempting to view has been deleted.")
elif data.state == Dataset.states.UPLOAD:
return trans.show_error_message(
@@ -210,6 +210,8 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
# Ensure ck_size is an integer before passing through to datatypes.
if ck_size:
ck_size = int(ck_size)
kwd.pop("dataset", None)
# `dataset` in kwd would interfere with positional dataset argument of `display_data` method.
display_data, headers = data.datatype.display_data(
trans, data, preview, filename, to_ext, offset=offset, ck_size=ck_size, **kwd
)
@@ -488,7 +490,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
if data is None:
trans.log_event(f"Problem retrieving dataset id ({dataset_id}).")
return None, self.message_exception(trans, "The dataset id is invalid.")
if dataset_id is not None and data.history.user is not None and data.history.user != trans.user:
if dataset_id is not None and data.user and data.user != trans.user:
trans.log_event(f"User attempted to edit a dataset they do not own (encoded: {dataset_id}, decoded: {id}).")
return None, self.message_exception(trans, "The dataset id is invalid.")
if data.history.user and not data.dataset.has_manage_permissions_roles(trans.app.security_agent):
@@ -498,9 +500,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
manage_permissions_action = trans.app.security_agent.get_action(
trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action
)
permissions = {
manage_permissions_action: [trans.app.security_agent.get_private_user_role(data.history.user)]
}
permissions = {manage_permissions_action: [trans.app.security_agent.get_private_user_role(data.user)]}
trans.app.security_agent.set_dataset_permission(data.dataset, permissions)
return data, None
@@ -571,7 +571,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
return self.display(trans, dataset_id=slug, filename=filename)
truncated, dataset_data = self.hda_manager.text_data(dataset, preview)
dataset.annotation = self.get_item_annotation_str(trans.sa_session, dataset.history.user, dataset)
dataset.annotation = self.get_item_annotation_str(trans.sa_session, dataset.user, dataset)
# If dataset is chunkable, get first chunk.
first_chunk = None
lib/galaxy/webapps/galaxy/services/datasets.py
+1 -1
View File
@@ -573,7 +573,7 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin):
item_url = web.url_for(
controller="dataset",
action="display_by_username_and_slug",
username=hda.history.user.username,
username=hda.user and hda.user.username,
slug=self.encode_id(hda.id),
preview=False,
)
scripts/cleanup_datasets/cleanup_datasets.py
+1 -1
View File
@@ -624,7 +624,7 @@ def _purge_dataset(app, dataset, remove_from_disk, info_only=False):
for hda in dataset.history_associations:
if not hda.purged:
hda.purged = True
if hda.history.user is not None and hda.history.user not in usage_users:
if hda.user and hda.user not in usage_users:
usage_users.append(hda.history.user)
for user in usage_users:
user.adjust_total_disk_usage(-dataset.get_total_size())
templates/display_base.mako
+2 -4
View File
@@ -101,8 +101,7 @@
modern_route = modern_route_for_controller(get_controller_name(item))
item_plural = get_item_plural( item )
href_to_all_items = h.url_for( controller='/' + modern_route, action='list_published')
href_to_user_items = h.url_for( controller='/' + modern_route, action='list_published', xxx=item.user.username)
href_to_user_items = href_to_user_items.replace( 'xxx', 'f-username')
href_to_user_items = h.url_for( controller='/' + modern_route, action='list_published', **{"f-username": item.user and item.user.username})
%>
<div class="page-body p-3">
<div class="page-item-header">
@@ -118,8 +117,7 @@
modern_route = modern_route_for_controller(get_controller_name(item))
item_plural = get_item_plural( item )
href_to_all_items = h.url_for( controller='/' + modern_route , action='list_published')
href_to_user_items = h.url_for( controller='/' + modern_route, action='list_published', xxx=item.user.username)
href_to_user_items = href_to_user_items.replace( 'xxx', 'f-username')
href_to_user_items = h.url_for( controller='/' + modern_route, action='list_published', **{"f-username": item.user and item.user.username})
%>
<div class="unified-panel-header" unselectable="on">
<div class="unified-panel-header-inner">
templates/display_common.mako
+1 -4
View File
@@ -125,10 +125,7 @@
<%def name="get_item_user( item )">
<%
# Exceptions first, default last.
if isinstance( item, model.HistoryDatasetAssociation ):
return item.history.user
else:
return item.user
return item.user
%>
</%def>
templates/webapps/galaxy/dataset/display.mako
+3 -3
View File
@@ -66,7 +66,7 @@
%if truncated:
<div class="warningmessagelarge">
This dataset is large and only the first megabyte is shown below. |
<a href="${h.url_for( controller='dataset', action='display_by_username_and_slug', username=data.history.user.username, slug=trans.security.encode_id( data.id ), preview=False )}">Show all</a>
<a href="${h.url_for( controller='dataset', action='display_by_username_and_slug', username=data.user.username, slug=trans.security.encode_id( data.id ), preview=False )}">Show all</a>
</div>
%endif
## TODO: why is the default font size so small?
@@ -126,9 +126,9 @@
<div style="padding: 10px;">
<h4>Author</h4>
<p>${item.history.user.username | h}</p>
<p>${item.user.username | h}</p>
<div><img src="https://secure.gravatar.com/avatar/${h.md5(item.history.user.email)}?d=identicon&s=150"></div>
<div><img src="https://secure.gravatar.com/avatar/${h.md5(item.user.email)}?d=identicon&s=150"></div>
## Page meta.
templates/webapps/reports/dataset_info.mako
+1 -1
View File
@@ -61,7 +61,7 @@
<td>${time_ago( hda.update_time )}</td>
<td>
%if hda.history and hda.history.user:
${hda.history.user.email}
${hda.user.email}
%else:
anonymous
%endif
test/unit/app/managers/test_HDAManager.py
+1 -1
View File
@@ -480,7 +480,7 @@ class TestHDASerializer(HDATestCase):
def test_file_name_serializers(self):
hda = self._create_vanilla_hda()
owner = hda.history.user
owner = hda.user
keys = ["file_name"]
self.log("file_name should be included if app configured to do so")