Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Remove copy dataset mako #17507

Draft
wants to merge 4 commits into
base: dev
Choose a base branch
from
+1 −323
Draft

Remove copy dataset mako #17507

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
c95c601
Remove copy dataset interface, datasets can already be copied across …
guerler Apr 2, 2024
b27f736
Remove legacy copy dataset mako
guerler Feb 20, 2024
7b30d12
Remove copy dataset mako associated controller endpoint
guerler Feb 20, 2024
997d1b5
Remove unused import from dataseet controller
guerler Feb 20, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 0 additions & 9 deletions client/src/components/History/CurrentHistory/HistoryOperations/DefaultOperations.vue
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,6 @@ import {
purgeAllDeletedContent,
unhideAllHiddenContent,
} from "@/components/History/model/crud";
import { iframeRedirect } from "@/components/plugins/legacyNavigation";
import { useHistoryContentStats } from "@/composables/historyContentStats";

library.add(faCog);
Expand All @@ -26,10 +25,6 @@ const emit = defineEmits(["update:operation-running"]);

const { numItemsDeleted, numItemsHidden } = useHistoryContentStats(toRef(props, "history"));

function onCopy() {
iframeRedirect("/dataset/copy_datasets");
}

function unhideAll() {
runOperation(() => unhideAllHiddenContent(props.history));
}
Expand Down Expand Up @@ -68,10 +63,6 @@ async function runOperation(operation: () => Promise<HistorySummary>) {
<span v-localize>With entire history...</span>
</BDropdownText>

<BDropdownItem data-description="copy datasets" @click="onCopy">
<span v-localize>Copy Datasets</span>
</BDropdownItem>

<BDropdownItem v-if="numItemsHidden" v-b-modal:show-all-hidden-content>
<span v-localize>Unhide All Hidden Content</span>
</BDropdownItem>
Expand Down
151 changes: 1 addition & 150 deletions lib/galaxy/webapps/galaxy/controllers/dataset.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,10 +32,7 @@
UsesItemRatings,
)
from galaxy.structured_app import StructuredApp
from galaxy.util import (
inflector,
sanitize_text,
)
from galaxy.util import sanitize_text
from galaxy.util.sanitize_html import sanitize_html
from galaxy.util.zipstream import ZipstreamWrapper
from galaxy.web import form_builder
Expand Down Expand Up @@ -892,152 +889,6 @@ def purge_async(self, trans, dataset_id, filename):
else:
raise Exception(message)

@web.expose
def copy_datasets(
self,
trans,
source_history=None,
source_content_ids="",
target_history_id=None,
target_history_ids="",
new_history_name="",
do_copy=False,
**kwd,
):
user = trans.get_user()
if source_history is not None:
decoded_source_history_id = self.decode_id(source_history)
history = self.history_manager.get_owned(
decoded_source_history_id, trans.user, current_history=trans.history
)
current_history = trans.get_history()
else:
history = current_history = trans.get_history()
refresh_frames = []
if source_content_ids:
if not isinstance(source_content_ids, list):
source_content_ids = source_content_ids.split(",")
encoded_dataset_collection_ids = [
s[len("dataset_collection|") :] for s in source_content_ids if s.startswith("dataset_collection|")
]
encoded_dataset_ids = [s[len("dataset|") :] for s in source_content_ids if s.startswith("dataset|")]
decoded_dataset_collection_ids = set(map(self.decode_id, encoded_dataset_collection_ids))
decoded_dataset_ids = set(map(self.decode_id, encoded_dataset_ids))
else:
decoded_dataset_collection_ids = []
decoded_dataset_ids = []
if new_history_name:
target_history_ids = []
else:
if target_history_id:
target_history_ids = [self.decode_id(target_history_id)]
elif target_history_ids:
if not isinstance(target_history_ids, list):
target_history_ids = target_history_ids.split(",")
target_history_ids = list({self.decode_id(h) for h in target_history_ids if h})
else:
target_history_ids = []
done_msg = error_msg = ""
new_history = None
if do_copy:
invalid_contents = 0
if not (decoded_dataset_ids or decoded_dataset_collection_ids) or not (
target_history_ids or new_history_name
):
error_msg = "You must provide both source datasets and target histories. "
else:
if new_history_name:
new_history = trans.app.model.History()
new_history.name = new_history_name
new_history.user = user
trans.sa_session.add(new_history)
with transaction(trans.sa_session):
trans.sa_session.commit()
target_history_ids.append(new_history.id)
if user:
target_histories = [
hist
for hist in map(trans.sa_session.query(trans.app.model.History).get, target_history_ids)
if hist is not None and hist.user == user
]
else:
target_histories = [history]
if len(target_histories) != len(target_history_ids):
error_msg = (
error_msg
+ "You do not have permission to add datasets to %i requested histories. "
% (len(target_history_ids) - len(target_histories))
)
source_contents = list(
map(trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get, decoded_dataset_ids)
)
source_contents.extend(
map(
trans.sa_session.query(trans.app.model.HistoryDatasetCollectionAssociation).get,
decoded_dataset_collection_ids,
)
)
source_contents.sort(key=lambda content: content.hid)
for content in source_contents:
if content is None:
error_msg = f"{error_msg}You tried to copy a dataset that does not exist. "
invalid_contents += 1
elif content.history != history:
error_msg = f"{error_msg}You tried to copy a dataset which is not in your current history. "
invalid_contents += 1
else:
for hist in target_histories:
if content.history_content_type == "dataset":
copy = content.copy(flush=False)
hist.stage_addition(copy)
else:
copy = content.copy(element_destination=hist)
if user:
copy.copy_tags_from(user, content)
for hist in target_histories:
hist.add_pending_items()
with transaction(trans.sa_session):
trans.sa_session.commit()
if current_history in target_histories:
refresh_frames = ["history"]
hist_names_str = ", ".join(
'<a href="{}" target="_top">{}</a>'.format(
url_for(
controller="history", action="switch_to_history", hist_id=trans.security.encode_id(hist.id)
),
escape(hist.name),
)
for hist in target_histories
)
num_source = len(source_content_ids) - invalid_contents
num_target = len(target_histories)
done_msg = "%i %s copied to %i %s: %s." % (
num_source,
inflector.cond_plural(num_source, "dataset"),
num_target,
inflector.cond_plural(num_target, "history"),
hist_names_str,
)
trans.sa_session.refresh(history)
source_contents = history.active_contents
target_histories = [history]
if user:
target_histories = user.active_histories
return trans.fill_template(
"/dataset/copy_view.mako",
source_history=history,
current_history=current_history,
source_content_ids=source_content_ids,
target_history_id=target_history_id,
target_history_ids=target_history_ids,
source_contents=source_contents,
target_histories=target_histories,
new_history_name=new_history_name,
done_msg=done_msg,
error_msg=error_msg,
refresh_frames=refresh_frames,
)

def _copy_datasets(self, trans, dataset_ids, target_histories, imported=False):
"""Helper method for copying datasets."""
user = trans.get_user()
Expand Down
164 changes: 0 additions & 164 deletions templates/webapps/galaxy/dataset/copy_view.mako
View file
Open in desktop

This file was deleted.

Loading