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Merge branch 'release_23.2' into release-titles

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This commit is contained in:
Martin Cech
2024-01-23 17:58:54 +01:00
committed by GitHub
parent cdfc8eb841 77d57ec98d
commit e9a7bdddca
12 changed files with 186 additions and 37 deletions
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client/src/components/Page/PageList.test.js
+20 -34
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@@ -5,6 +5,7 @@ import MockAdapter from "axios-mock-adapter";
import { formatDistanceToNow, parseISO } from "date-fns";
import flushPromises from "flush-promises";
import { PiniaVuePlugin } from "pinia";
import { useUserStore } from "stores/userStore";
import { getLocalVue, wait } from "tests/jest/helpers";
import PageList from "./PageList.vue";
@@ -98,16 +99,29 @@ describe("PgeList.vue", () => {
const mockPublishedPageData = [publishedPage];
const mockTwoPageData = [privatePage, pageA];
function mountPersonalGrid() {
function mountGrid(propsData) {
const pinia = createTestingPinia();
const userStore = useUserStore();
userStore.currentUser = { username: "jimmyPage", tags_used: [] };
wrapper = mount(PageList, {
propsData: propsDataPersonalGrid,
propsData,
localVue,
pinia,
stubs: {
icon: { template: "<div></div>" },
},
});
}
function mountPersonalGrid() {
mountGrid(propsDataPersonalGrid);
}
function mountPublishedGrid() {
mountGrid(propsDataPublishedGrid);
}
describe(" with empty page list", () => {
beforeEach(async () => {
axiosMock.onAny().reply(200, [], { total_matches: "0" });
@@ -145,14 +159,7 @@ describe("PgeList.vue", () => {
jest.spyOn(PageList.methods, "decorateData").mockImplementation((page) => {
page.shared = false;
});
wrapper = mount(PageList, {
propsData: propsDataPersonalGrid,
localVue,
pinia: createTestingPinia(),
stubs: {
icon: { template: "<div></div>" },
},
});
mountPersonalGrid();
await flushPromises();
});
@@ -215,14 +222,7 @@ describe("PgeList.vue", () => {
jest.spyOn(PageList.methods, "decorateData").mockImplementation((page) => {
page.shared = true;
});
wrapper = mount(PageList, {
propsData: propsDataPersonalGrid,
localVue,
pinia: createTestingPinia(),
stubs: {
icon: { template: "<div></div>" },
},
});
mountPersonalGrid();
await flushPromises();
});
it("updates filter when published icon is clicked", async () => {
@@ -257,14 +257,7 @@ describe("PgeList.vue", () => {
jest.spyOn(PageList.methods, "decorateData").mockImplementation((page) => {
page.shared = false;
});
wrapper = mount(PageList, {
propsData: propsDataPublishedGrid,
localVue,
pinia: createTestingPinia(),
stubs: {
icon: { template: "<div></div>" },
},
});
mountPublishedGrid();
await flushPromises();
});
@@ -301,14 +294,7 @@ describe("PgeList.vue", () => {
jest.spyOn(PageList.methods, "decorateData").mockImplementation((page) => {
page.shared = false;
});
wrapper = mount(PageList, {
propsData: propsDataPublishedGrid,
localVue,
pinia: createTestingPinia(),
stubs: {
icon: { template: "<div></div>" },
},
});
mountPublishedGrid();
await flushPromises();
});
client/src/components/Page/PageList.vue
+8 -1
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@@ -50,7 +50,7 @@
clickable
:value="row.item.tags"
:index="row.index"
:disabled="published"
:disabled="published || !currentUserOwnsItem(row.item)"
@input="(tags) => onTags(tags, row.index)"
@tag-click="(tag) => applyFilter('tag', tag, true)" />
</template>
@@ -100,11 +100,13 @@ import StatelessTags from "components/TagsMultiselect/StatelessTags";
import UtcDate from "components/UtcDate";
import paginationMixin from "components/Workflow/paginationMixin";
import { getAppRoot } from "onload/loadConfig";
import { storeToRefs } from "pinia";
import Filtering, { contains, equals, expandNameTag, toBool } from "utils/filtering";
import _l from "utils/localization";
import { useRouter } from "vue-router/composables";
import { updateTags } from "@/api/tags";
import { useUserStore } from "@/stores/userStore";
import { absPath } from "@/utils/redirect";
import PageDropdown from "./PageDropdown";
@@ -224,8 +226,10 @@ export default {
},
setup() {
const router = useRouter();
const { currentUser } = storeToRefs(useUserStore());
return {
router,
currentUser,
};
},
data() {
@@ -304,6 +308,9 @@ export default {
shareLink: function (item) {
this.router.push(`sharing?id=${item.id}`);
},
currentUserOwnsItem: function (item) {
return item.username === this.currentUser.username;
},
decorateData(page) {
const Galaxy = getGalaxyInstance();
page.shared = page.username !== Galaxy.user.attributes.username;
doc/source/releases/23.2.rst
+45
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@@ -14,6 +14,9 @@ Enhancements
.. feature
* Initial release notes for 23.2
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 17259`_
* Make form repeat blocks reorderable
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
`Pull Request 14892`_
@@ -135,6 +138,9 @@ Enhancements
`Pull Request 16345`_
.. enhancement_tag_jobs
* Enable job resubmissions in k8s runner
(thanks to `@pcm32 <https://github.com/pcm32>`__).
`Pull Request 15238`_
* Towards SQLAlchemy 2.0 (upgrades to SQLAlchemy Core usage)
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 16264`_
@@ -154,6 +160,9 @@ Enhancements
`Pull Request 17178`_
.. enhancement
* Improve embed performance
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
`Pull Request 17326`_
* Add parameter name to validation errors
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 15440`_
@@ -554,6 +563,9 @@ Fixes
`Pull Request 17233`_
.. bug_tag_tools
* Add back 1.1.0 version of Filtering1 tool
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16883`_
* Add missing requirements to perl tools
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16763`_
@@ -571,6 +583,9 @@ Fixes
`Pull Request 17036`_
.. bug_tag_workflows
* Fix ``to_cwl`` for nested collections
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 17276`_
* Fix workflow output display without label
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16749`_
@@ -629,6 +644,12 @@ Fixes
`Pull Request 17104`_
.. bug_tag_jobs
* Rollback invalidated transaction
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 17280`_
* Rollback invalidated transaction: catch them earlier
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 17312`_
* Ensure Job belongs to current SQLAlchemy session
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 16647`_
@@ -666,6 +687,30 @@ Fixes
`Pull Request 17055`_
.. bug
* Remove duplicates when copying sections for tool panel view
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 17117`_
* Tagging component performance improvements
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
`Pull Request 17253`_
* Always copy datasets in collection builder modals
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 17268`_
* Install newer celery on python 3.8+
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 17309`_
* Backport Rollback invalidated transaction: catch them earlier
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 17315`_
* Discard SQLAlchemy session after task completion
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 17317`_
* Scope session for job runner monitor loop
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 17319`_
* Fix subworkflow edit button
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
`Pull Request 17330`_
* Disable verbose parso logging in db_shell.py
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16410`_
doc/source/releases/23.2_announce_user.rst
+3
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@@ -172,6 +172,9 @@ Builtin Tool Updates
===========================================================
.. tools
* Add back 1.1.0 version of Filtering1 tool
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16883`_
* Update cellxgene interactive tool to 1.1.1
(thanks to `@pcm32 <https://github.com/pcm32>`__).
`Pull Request 15313`_
doc/source/releases/23.2_prs.rst
+16
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@@ -1,5 +1,21 @@
.. github_links
.. _Pull Request 15238: https://github.com/galaxyproject/galaxy/pull/15238
.. _Pull Request 16883: https://github.com/galaxyproject/galaxy/pull/16883
.. _Pull Request 17117: https://github.com/galaxyproject/galaxy/pull/17117
.. _Pull Request 17253: https://github.com/galaxyproject/galaxy/pull/17253
.. _Pull Request 17259: https://github.com/galaxyproject/galaxy/pull/17259
.. _Pull Request 17268: https://github.com/galaxyproject/galaxy/pull/17268
.. _Pull Request 17276: https://github.com/galaxyproject/galaxy/pull/17276
.. _Pull Request 17280: https://github.com/galaxyproject/galaxy/pull/17280
.. _Pull Request 17309: https://github.com/galaxyproject/galaxy/pull/17309
.. _Pull Request 17312: https://github.com/galaxyproject/galaxy/pull/17312
.. _Pull Request 17315: https://github.com/galaxyproject/galaxy/pull/17315
.. _Pull Request 17317: https://github.com/galaxyproject/galaxy/pull/17317
.. _Pull Request 17319: https://github.com/galaxyproject/galaxy/pull/17319
.. _Pull Request 17323: https://github.com/galaxyproject/galaxy/pull/17323
.. _Pull Request 17326: https://github.com/galaxyproject/galaxy/pull/17326
.. _Pull Request 17330: https://github.com/galaxyproject/galaxy/pull/17330
.. _Pull Request 14892: https://github.com/galaxyproject/galaxy/pull/14892
.. _Pull Request 14955: https://github.com/galaxyproject/galaxy/pull/14955
.. _Pull Request 15000: https://github.com/galaxyproject/galaxy/pull/15000
doc/source/releases/24.0_announce.rst
+1 -1
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@@ -2,7 +2,7 @@
:orphan:
===========================================================
24.0 Galaxy Release
24.0 Galaxy Release (Early 2024)
===========================================================
lib/galaxy/dependencies/pinned-requirements.txt
+1
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@@ -92,6 +92,7 @@ idna==3.5 ; python_version >= "3.7" and python_version < "3.12"
importlib-metadata==4.13.0 ; python_version >= "3.7" and python_version < "3.12"
importlib-resources==5.12.0 ; python_version >= "3.7" and python_version < "3.12"
isa-rwval==0.10.10 ; python_version >= "3.7" and python_version < "3.12"
isal==1.3.0 ; python_version >= "3.7" and python_version < "3.12"
isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.12"
jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.12"
jmespath==1.0.1 ; python_version >= "3.7" and python_version < "3.12"
lib/galaxy/model/store/__init__.py
+1 -1
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@@ -2753,7 +2753,7 @@ class ROCrateArchiveModelExportStore(DirectoryModelExportStore, WriteCrates):
out_file = out_file_name[: -len(".zip")]
else:
out_file = out_file_name
rval = shutil.make_archive(out_file, "zip", self.export_directory)
rval = shutil.make_archive(out_file, "fastzip", self.export_directory)
if not self.file_source_uri:
shutil.move(rval, self.out_file)
else:
lib/galaxy/util/compression_utils.py
+88
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@@ -3,6 +3,7 @@ import gzip
import io
import logging
import os
import shutil
import tarfile
import tempfile
import zipfile
@@ -30,6 +31,12 @@ from .checkers import (
is_gzip,
)
try:
from isal import isal_zlib
except ImportError:
isal_zlib = None # type: ignore[assignment,unused-ignore]
log = logging.getLogger(__name__)
FileObjTypeStr = Union[IO[str], io.TextIOWrapper]
@@ -345,3 +352,84 @@ class CompressedFile:
if not member_path.startswith(basename):
return False
return True
class FastZipFile(zipfile.ZipFile):
"""
Simple wrapper around ZipFile that uses the default compression strategy of ISA-L
to write zip files. Ignores compresslevel and compresstype arguments, and is
3 to 4 times faster than the zlib implementation at the default compression level.
"""
def _open_to_write(self, *args, **kwargs): # type: ignore[no-untyped-def]
zwf = super()._open_to_write(*args, **kwargs) # type: ignore[misc]
if isal_zlib and self.compression == zipfile.ZIP_DEFLATED:
zwf._compressor = isal_zlib.compressobj(isal_zlib.ISAL_DEFAULT_COMPRESSION, isal_zlib.DEFLATED, -15, 9)
return zwf
# modified from shutil._make_zipfile
def make_fast_zipfile(
base_name: str,
base_dir: str,
verbose: int = 0,
dry_run: int = 0,
logger: Optional[logging.Logger] = None,
owner: Optional[str] = None,
group: Optional[str] = None,
root_dir: Optional[str] = None,
) -> str:
"""Create a zip file from all the files under 'base_dir'.
The output zip file will be named 'base_name' + ".zip". Returns the
name of the output zip file.
"""
zip_filename = base_name + ".zip"
archive_dir = os.path.dirname(base_name)
if archive_dir and not os.path.exists(archive_dir):
if logger is not None:
logger.info("creating %s", archive_dir)
if not dry_run:
os.makedirs(archive_dir)
if logger is not None:
logger.info("creating '%s' and adding '%s' to it", zip_filename, base_dir)
if not dry_run:
with FastZipFile(zip_filename, mode="w", compression=zipfile.ZIP_DEFLATED) as zf:
arcname = os.path.normpath(base_dir)
if root_dir is not None:
base_dir = os.path.join(root_dir, base_dir)
base_dir = os.path.normpath(base_dir)
if arcname != os.curdir:
zf.write(base_dir, arcname)
if logger is not None:
logger.info("adding '%s'", base_dir)
for dirpath, dirnames, filenames in os.walk(base_dir):
arcdirpath = dirpath
if root_dir is not None:
arcdirpath = os.path.relpath(arcdirpath, root_dir)
arcdirpath = os.path.normpath(arcdirpath)
for name in sorted(dirnames):
path = os.path.join(dirpath, name)
arcname = os.path.join(arcdirpath, name)
zf.write(path, arcname)
if logger is not None:
logger.info("adding '%s'", path)
for name in filenames:
path = os.path.join(dirpath, name)
path = os.path.normpath(path)
if os.path.isfile(path):
arcname = os.path.join(arcdirpath, name)
zf.write(path, arcname)
if logger is not None:
logger.info("adding '%s'", path)
if root_dir is not None:
zip_filename = os.path.abspath(zip_filename)
return zip_filename
shutil.register_archive_format("fastzip", make_fast_zipfile)
packages/data/setup.cfg
+1
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@@ -44,6 +44,7 @@ install_requires =
h5grove
h5py
isa-rwval
isal
MarkupSafe
msal
mrcfile
packages/files/setup.cfg
+1
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@@ -34,6 +34,7 @@ include_package_data = True
install_requires =
galaxy-util
fs
isal
typing-extensions
packages = find:
python_requires = >=3.7
pyproject.toml
+1
View File
@@ -71,6 +71,7 @@ h5py = "*"
importlib-metadata = "<5" # Work around https://github.com/celery/kombu/issues/1600
importlib-resources = "*"
isa-rwval = ">=0.10.10"
isal = "*"
kombu = "*"
lagom = "*"
Mako = "*"