mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 05:45:37 +08:00
Merge branch 'release_23.2' into 'release_23.3'
This commit is contained in:
John Davis
@@ -36,7 +36,7 @@ const defaultOptions = {
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{ id: "hda1", hid: 1, name: "hdaName1", src: "hda", tags: ["tag1"] },
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{ id: "hda2", hid: 2, name: "hdaName2", src: "hda", tags: ["tag1", "tag2"] },
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{ id: "hda3", hid: 3, name: "hdaName3", src: "hda", tags: ["tag2", "tag3"] },
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{ id: "hda3", hid: 4, name: "hdaName4", src: "hda" },
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{ id: "hda4", hid: 4, name: "hdaName4", src: "hda" },
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],
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hdca: [
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{ id: "hdca5", hid: 5, name: "hdcaName5", src: "hdca" },
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@@ -61,7 +61,7 @@ describe("FormData", () => {
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const value_1 = {
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batch: false,
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product: false,
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values: [{ id: "hda3", src: "hda", map_over_type: null }],
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values: [{ id: "hda4", src: "hda", map_over_type: null }],
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};
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const options = wrapper.find(".btn-group").findAll("button");
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expect(options.length).toBe(4);
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@@ -122,7 +122,7 @@ describe("FormData", () => {
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expect(wrapper.emitted().input.length).toEqual(1);
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const selectedValues = wrapper.findAll(SELECTED_VALUE);
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expect(selectedValues.length).toBe(2);
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expect(selectedValues.at(0).text()).toBe("4: hdaName4");
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expect(selectedValues.at(0).text()).toBe("3: hdaName3");
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expect(selectedValues.at(1).text()).toBe("2: hdaName2");
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const value_0 = {
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batch: false,
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@@ -153,6 +153,39 @@ describe("FormData", () => {
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expect(wrapper.emitted().input[2][0]).toEqual(null);
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});
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it("properly sorts multiple datasets", async () => {
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const wrapper = createTarget({
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value: {
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// the order of values does not matter here
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values: [
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{ id: "hda2", src: "hda" },
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{ id: "hda3", src: "hda" },
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{ id: "hda1", src: "hda" },
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],
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},
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multiple: true,
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optional: true,
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options: defaultOptions,
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});
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const selectedValues = wrapper.findAll(SELECTED_VALUE);
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expect(selectedValues.length).toBe(3);
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// the values in the multiselect are sorted by hid DESC
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expect(selectedValues.at(0).text()).toBe("3: hdaName3");
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expect(selectedValues.at(1).text()).toBe("2: hdaName2");
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expect(selectedValues.at(2).text()).toBe("1: hdaName1");
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await selectedValues.at(0).trigger("click");
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const value_sorted = {
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batch: false,
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product: false,
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values: [
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// the values in the emitted input are sorted by hid ASC
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{ id: "hda1", map_over_type: null, src: "hda" },
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{ id: "hda2", map_over_type: null, src: "hda" },
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],
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};
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expect(wrapper.emitted().input[1][0]).toEqual(value_sorted);
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});
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it("dataset collection as hda", async () => {
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const wrapper = createTarget({
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value: { values: [{ id: "dce1", src: "dce" }] },
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@@ -111,6 +111,17 @@ const currentValue = computed({
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return undefined;
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},
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set: (val) => {
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if (val && Array.isArray(val) && val.length > 0) {
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val.sort((a, b) => {
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const aHid = a.hid;
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const bHid = b.hid;
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if (aHid && bHid) {
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return aHid - bHid;
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} else {
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return 0;
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}
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});
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}
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$emit("input", createValue(val));
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},
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});
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@@ -1,6 +1,6 @@
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===========================================================
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2023 Galaxy Release (v 23.0)
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23.0 Galaxy Release (April 2023)
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===========================================================
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.. include:: _header.rst
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@@ -1,6 +1,6 @@
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===========================================================
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2023 Galaxy Release (v 23.0)
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23.0 Galaxy Release (April 2023)
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===========================================================
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.. include:: _header.rst
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@@ -1,6 +1,6 @@
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===========================================================
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Mid 2023 Galaxy Release (v 23.1)
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23.1 Galaxy Release (June 2023)
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===========================================================
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.. include:: _header.rst
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@@ -1,6 +1,6 @@
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===========================================================
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June 2023 Galaxy Release (v 23.1)
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23.1 Galaxy Release (June 2023)
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===========================================================
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.. include:: _header.rst
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@@ -160,6 +160,12 @@ Enhancements
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`Pull Request 17178`_
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.. enhancement
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* Make release titles consistent
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(thanks to `@martenson <https://github.com/martenson>`__).
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`Pull Request 17341`_
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* Use python-isal for fast zip deflate compression in rocrate export
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(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
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`Pull Request 17342`_
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* Improve embed performance
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(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
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`Pull Request 17326`_
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@@ -378,6 +384,9 @@ Enhancements
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`Pull Request 17182`_
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.. small_enhancement
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* Ensure release notes include all PRs added during the freeze by re-running the release note bootstrapping
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(thanks to `@jdavcs <https://github.com/jdavcs>`__).
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`Pull Request 17344`_
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* Tool Shed client build separation
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(thanks to `@dannon <https://github.com/dannon>`__).
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`Pull Request 15000`_
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@@ -687,6 +696,12 @@ Fixes
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`Pull Request 17055`_
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.. bug
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* Write to a temp filename in posix file source plugin
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(thanks to `@natefoo <https://github.com/natefoo>`__).
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`Pull Request 17350`_
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* Always store multi select data input values in fixed order
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(thanks to `@guerler <https://github.com/guerler>`__).
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`Pull Request 17352`_
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* Remove duplicates when copying sections for tool panel view
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(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
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`Pull Request 17117`_
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@@ -1,6 +1,6 @@
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===========================================================
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Late 2023 Galaxy Release (v 23.2)
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23.2 Galaxy Release (January 2024)
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===========================================================
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.. include:: _header.rst
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@@ -12,7 +12,7 @@ Highlights
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**InvenioRDM** has been integrated into Galaxy. Users can now import files directly from InvenioRDM repositories into Galaxy, and publish records containing artifacts (Histories, datasets, etc.) from Galaxy to InvenioRDM.
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**Miscellaneous improvements.** There have been numerous updates to the UI, including Galaxy Help forum integration, improved navigation and styling, helpful warnings, improvements to search, etc. Check out the `23.2 user release notes <23.2_announce_user.html>`__ for all the details.
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**Miscellaneous improvements.** There have been numerous updates to the UI, including Galaxy Help forum integration, improved navigation and styling, helpful warnings, improvements to search, etc. Check out the `23.2 user release notes <23.2_announce_user.html>`__ for all the details.
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Are you an admin? See the Administration Notes below, and check out `some admin relevant PRs <https://github.com/galaxyproject/galaxy/pulls?q=label%3Ahighlight%2Fadmin+milestone%3A23.2+is%3Aclosed+is%3Apr>`__.
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@@ -1,6 +1,6 @@
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===========================================================
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Late 2023 Galaxy Release (v 23.2)
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23.2 Galaxy Release (January 2024)
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===========================================================
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.. include:: _header.rst
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@@ -1,5 +1,11 @@
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.. github_links
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.. _Pull Request 17341: https://github.com/galaxyproject/galaxy/pull/17341
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.. _Pull Request 17342: https://github.com/galaxyproject/galaxy/pull/17342
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.. _Pull Request 17343: https://github.com/galaxyproject/galaxy/pull/17343
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.. _Pull Request 17344: https://github.com/galaxyproject/galaxy/pull/17344
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.. _Pull Request 17350: https://github.com/galaxyproject/galaxy/pull/17350
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.. _Pull Request 17352: https://github.com/galaxyproject/galaxy/pull/17352
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.. _Pull Request 15238: https://github.com/galaxyproject/galaxy/pull/15238
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.. _Pull Request 16883: https://github.com/galaxyproject/galaxy/pull/16883
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.. _Pull Request 17117: https://github.com/galaxyproject/galaxy/pull/17117
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@@ -2,7 +2,7 @@
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:orphan:
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===========================================================
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February 2024 Galaxy Release (v 24.0)
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24.0 Galaxy Release (Early 2024)
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===========================================================
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@@ -105,14 +105,18 @@ class PosixFilesSource(BaseFilesSource):
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target_native_path = os.path.normpath(target_native_path)
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assert target_native_path.startswith(os.path.normpath(effective_root))
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target_native_path_parent = os.path.dirname(target_native_path)
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target_native_path_parent, target_native_path_name = os.path.split(target_native_path)
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if not os.path.exists(target_native_path_parent):
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if self.allow_subdir_creation:
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os.makedirs(target_native_path_parent)
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else:
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raise Exception("Parent directory does not exist.")
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shutil.copyfile(native_path, target_native_path)
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# Use a temporary name while writing so anything that consumes written files can detect when they've completed,
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# and identify interrupted writes
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target_native_path_part = os.path.join(target_native_path_parent, f"_{target_native_path_name}.part")
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shutil.copyfile(native_path, target_native_path_part)
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os.rename(target_native_path_part, target_native_path)
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def _to_native_path(self, source_path: str, user_context=None):
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source_path = os.path.normpath(source_path)
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@@ -912,7 +912,8 @@ class PurgeHistorylessHDAs(PurgesHDAs, RemovesMetadataFiles, RequiresDiskUsageRe
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FROM dataset
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WHERE history_id IS NULL{force_retry_sql}{object_store_id_sql}
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AND history_dataset_association.update_time < (NOW() AT TIME ZONE 'utc' - interval '%(days)s days')
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RETURNING id),
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RETURNING history_dataset_association.id as id,
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history_dataset_association.history_id as history_id),
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hda_events
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AS (INSERT INTO cleanup_event_hda_association
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(create_time, cleanup_event_id, hda_id)
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@@ -920,12 +921,15 @@ class PurgeHistorylessHDAs(PurgesHDAs, RemovesMetadataFiles, RequiresDiskUsageRe
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FROM purged_hda_ids),
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{purge_hda_dependencies_sql}
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SELECT purged_hda_ids.id AS purged_hda_id,
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history.user_id AS recalculate_disk_usage_user_id,
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deleted_metadata_file_ids.id AS deleted_metadata_file_id,
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deleted_metadata_file_ids.uuid AS deleted_metadata_file_uuid,
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deleted_metadata_file_ids.object_store_id AS object_store_id,
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deleted_icda_ids.id AS deleted_icda_id,
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deleted_icda_ids.hda_id AS deleted_icda_hda_id
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FROM purged_hda_ids
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LEFT OUTER JOIN history
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ON purged_hda_ids.history_id = history.id
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LEFT OUTER JOIN deleted_metadata_file_ids
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ON deleted_metadata_file_ids.hda_id = purged_hda_ids.id
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LEFT OUTER JOIN deleted_icda_ids
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