From b9fefbd8d0e09b329b86aecd72af9df7dab6ed2b Mon Sep 17 00:00:00 2001 From: davelopez <46503462+davelopez@users.noreply.github.com> Date: Wed, 17 Apr 2024 15:30:13 +0200 Subject: [PATCH 01/11] Add Invenio scheme Replaces the `gxfiles` scheme with `invenio` and provides backwards compatibility with existing uris. --- client/src/utils/upload-payload.js | 1 + lib/galaxy/files/sources/_rdm.py | 2 +- lib/galaxy/files/sources/invenio.py | 24 ++++++++++++++++++++++++ lib/galaxy/tools/parameters/grouping.py | 14 +++++++++++++- 4 files changed, 39 insertions(+), 2 deletions(-) diff --git a/client/src/utils/upload-payload.js b/client/src/utils/upload-payload.js index 31a0306180e3..52c8df06692e 100644 --- a/client/src/utils/upload-payload.js +++ b/client/src/utils/upload-payload.js @@ -9,6 +9,7 @@ export const URI_PREFIXES = [ "gxuserimport://", "gxftp://", "drs://", + "invenio://", ]; export function isUrl(content) { diff --git a/lib/galaxy/files/sources/_rdm.py b/lib/galaxy/files/sources/_rdm.py index 14f7e9e1daa0..8cd6d8523e26 100644 --- a/lib/galaxy/files/sources/_rdm.py +++ b/lib/galaxy/files/sources/_rdm.py @@ -138,7 +138,7 @@ class RDMFilesSource(BaseFilesSource): plugin_kind = PluginKind.rdm - def __init__(self, **kwd: Unpack[FilesSourceProperties]): + def __init__(self, **kwd: Unpack[RDMFilesSourceProperties]): props = self._parse_common_config_opts(kwd) base_url = props.get("url") if not base_url: diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py index 6edc46dfe78c..8b237960878c 100644 --- a/lib/galaxy/files/sources/invenio.py +++ b/lib/galaxy/files/sources/invenio.py @@ -1,5 +1,6 @@ import datetime import json +import re import urllib.request from typing import ( Any, @@ -13,9 +14,11 @@ from typing_extensions import ( Literal, TypedDict, + Unpack, ) from galaxy.files.sources import ( + DEFAULT_SCHEME, Entry, EntryData, FilesSourceOptions, @@ -25,6 +28,7 @@ from galaxy.files.sources._rdm import ( OptionalUserContext, RDMFilesSource, + RDMFilesSourceProperties, RDMRepositoryInteractor, ) from galaxy.util import ( @@ -112,6 +116,26 @@ class InvenioRDMFilesSource(RDMFilesSource): plugin_type = "inveniordm" + def __init__(self, **kwd: Unpack[RDMFilesSourceProperties]): + super().__init__(**kwd) + self._scheme_regex = re.compile(rf"^{self.get_scheme()}?://{self.id}|^{DEFAULT_SCHEME}://{self.id}") + + def get_scheme(self) -> str: + return "invenio" + + def score_url_match(self, url: str): + if match := self._scheme_regex.match(url): + return match.span()[1] + else: + return 0 + + def to_relative_path(self, url: str) -> str: + legacy_uri_root = f"{DEFAULT_SCHEME}://{self.id}" + if url.startswith(legacy_uri_root): + return url[len(legacy_uri_root) :] + else: + return super().to_relative_path(url) + def get_repository_interactor(self, repository_url: str) -> RDMRepositoryInteractor: return InvenioRepositoryInteractor(repository_url, self) diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py index e49ba3de3f4d..910ad6ac15e8 100644 --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -38,7 +38,19 @@ log = logging.getLogger(__name__) URI_PREFIXES = [ - f"{x}://" for x in ["http", "https", "ftp", "file", "gxfiles", "gximport", "gxuserimport", "gxftp", "drs"] + f"{x}://" + for x in [ + "http", + "https", + "ftp", + "file", + "gxfiles", + "gximport", + "gxuserimport", + "gxftp", + "drs", + "invenio", + ] ] From 44d8dc7e304b9f409e785f7a6b7e0024928acc26 Mon Sep 17 00:00:00 2001 From: davelopez <46503462+davelopez@users.noreply.github.com> Date: Thu, 18 Apr 2024 11:36:24 +0200 Subject: [PATCH 02/11] Add Zenodo as a standalone plugin --- client/src/utils/upload-payload.js | 1 + .../sample/file_sources_conf.yml.sample | 18 +++++++++++++ .../user_preferences_extra_conf.yml.sample | 26 +++++++++++++++++++ lib/galaxy/files/sources/zenodo.py | 21 +++++++++++++++ lib/galaxy/tools/parameters/grouping.py | 1 + 5 files changed, 67 insertions(+) create mode 100644 lib/galaxy/files/sources/zenodo.py diff --git a/client/src/utils/upload-payload.js b/client/src/utils/upload-payload.js index 52c8df06692e..2ff3395828e3 100644 --- a/client/src/utils/upload-payload.js +++ b/client/src/utils/upload-payload.js @@ -10,6 +10,7 @@ export const URI_PREFIXES = [ "gxftp://", "drs://", "invenio://", + "zenodo://", ]; export function isUrl(content) { diff --git a/lib/galaxy/config/sample/file_sources_conf.yml.sample b/lib/galaxy/config/sample/file_sources_conf.yml.sample index e810770d0f31..1295f05f53d7 100644 --- a/lib/galaxy/config/sample/file_sources_conf.yml.sample +++ b/lib/galaxy/config/sample/file_sources_conf.yml.sample @@ -211,6 +211,24 @@ public_name: ${user.preferences['invenio_sandbox|public_name']} writable: true +- type: zenodo + id: zenodo + doc: Zenodo is a general-purpose open-access repository developed under the European OpenAIRE program and operated by CERN. It allows researchers to deposit data sets, research software, reports, and any other research-related digital artifacts. For each submission, a persistent digital object identifier (DOI) is minted, which makes the stored items easily citeable. + label: Zenodo + url: https://zenodo.org + token: ${user.user_vault.read_secret('preferences/zenodo/token')} + public_name: ${user.preferences['zenodo|public_name']} + writable: true + +- type: zenodo + id: zenodo_sandbox + doc: This is the Sandbox instance of Zenodo. It is used for testing purposes only, content is NOT preserved. DOIs created in this instance are not real and will not resolve. + label: Zenodo Sandbox (TESTING ONLY) + url: https://sandbox.zenodo.org + token: ${user.user_vault.read_secret('preferences/zenodo_sandbox/token')} + public_name: ${user.preferences['zenodo_sandbox|public_name']} + writable: true + - type: onedata id: onedata1 label: Onedata diff --git a/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample b/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample index f37f30165132..511cb6f13434 100644 --- a/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample +++ b/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample @@ -110,6 +110,32 @@ preferences: type: text required: False + zenodo: + description: Your Zenodo Integration Settings + inputs: + - name: token + label: Personal Access Token used to create draft records and to upload files. You can manage your tokens at https://zenodo.org/account/settings/applications/ + type: secret + store: vault # Requires setting up vault_config_file in your galaxy.yml + required: False + - name: public_name + label: Creator name to associate with new records (formatted as "Last name, First name"). If left blank "Anonymous Galaxy User" will be used. You can always change this by editing your record directly. + type: text + required: False + + zenodo_sandbox: + description: Your Zenodo Sandbox Integration Settings (TESTING ONLY) + inputs: + - name: token + label: Personal Access Token used to create draft records and to upload files. You can manage your tokens at https://sandbox.zenodo.org/account/settings/applications/ + type: secret + store: vault # Requires setting up vault_config_file in your galaxy.yml + required: False + - name: public_name + label: Creator name to associate with new records (formatted as "Last name, First name"). If left blank "Anonymous Galaxy User" will be used. You can always change this by editing your record directly. + type: text + required: False + # Used in file_sources_conf.yml onedata: description: Your Onedata account diff --git a/lib/galaxy/files/sources/zenodo.py b/lib/galaxy/files/sources/zenodo.py new file mode 100644 index 000000000000..01385c4650d1 --- /dev/null +++ b/lib/galaxy/files/sources/zenodo.py @@ -0,0 +1,21 @@ +from galaxy.files.sources.invenio import InvenioRDMFilesSource + + +class ZenodoRDMFilesSource(InvenioRDMFilesSource): + """A files source for Zenodo repositories. + + Zenodo is an open science platform developed by CERN. It allows researchers + to deposit data, software, and other research outputs for long-term + preservation and sharing. + + Zenodo repositories are based on InvenioRDM, so this class is a subclass of + InvenioRDMFilesSource with the appropriate plugin type. + """ + + plugin_type = "zenodo" + + def get_scheme(self) -> str: + return "zenodo" + + +__all__ = ("ZenodoRDMFilesSource",) diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py index 910ad6ac15e8..ebf64542dd2e 100644 --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -50,6 +50,7 @@ "gxftp", "drs", "invenio", + "zenodo", ] ] From a9eeca84cba665ed0bd472a26022e72431d37233 Mon Sep 17 00:00:00 2001 From: davelopez <46503462+davelopez@users.noreply.github.com> Date: Thu, 18 Apr 2024 12:08:58 +0200 Subject: [PATCH 03/11] Add getFileSourceById to fileSources composable --- client/src/composables/fileSources.ts | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/client/src/composables/fileSources.ts b/client/src/composables/fileSources.ts index 8f9790f1e5b8..ab6a89e20b9b 100644 --- a/client/src/composables/fileSources.ts +++ b/client/src/composables/fileSources.ts @@ -18,6 +18,10 @@ export function useFileSources(options: FilterFileSourcesOptions = {}) { isLoading.value = false; }); + function getFileSourceById(id: string) { + return fileSources.value.find((fs) => fs.id === id); + } + return { /** * The list of available file sources from the server. @@ -31,5 +35,12 @@ export function useFileSources(options: FilterFileSourcesOptions = {}) { * Whether the user can write files to any of the available file sources. */ hasWritable: readonly(hasWritable), + /** + * Get the file source with the given ID. + * + * @param id - The ID of the file source to get. + * @returns The file source with the given ID, if found. + */ + getFileSourceById, }; } From 93e102ef21e10f15a012e17e81edcacd3ed984ef Mon Sep 17 00:00:00 2001 From: davelopez <46503462+davelopez@users.noreply.github.com> Date: Thu, 18 Apr 2024 15:13:33 +0200 Subject: [PATCH 04/11] Add optional selected item to FilesDialog It allows to set an initial item (file source) to browse from. --- client/src/components/FilesDialog/FilesDialog.vue | 5 ++++- client/src/components/FilesDialog/FilesInput.vue | 5 +++++ 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/client/src/components/FilesDialog/FilesDialog.vue b/client/src/components/FilesDialog/FilesDialog.vue index 201b14f887cc..f27f9c20fc71 100644 --- a/client/src/components/FilesDialog/FilesDialog.vue +++ b/client/src/components/FilesDialog/FilesDialog.vue @@ -33,6 +33,8 @@ interface FilesDialogProps { multiple?: boolean; /** Whether to show only writable sources */ requireWritable?: boolean; + /** Optional selected item to start browsing from */ + selectedItem?: SelectionItem; } const props = withDefaults(defineProps(), { @@ -42,6 +44,7 @@ const props = withDefaults(defineProps(), { mode: "file", multiple: false, requireWritable: false, + selectedItem: undefined, }); const { config, isConfigLoaded } = useConfig(); @@ -343,7 +346,7 @@ function onOk() { } onMounted(() => { - load(); + load(props.selectedItem); }); diff --git a/client/src/components/FilesDialog/FilesInput.vue b/client/src/components/FilesDialog/FilesInput.vue index f72af2387ad5..b1e7390a3483 100644 --- a/client/src/components/FilesDialog/FilesInput.vue +++ b/client/src/components/FilesDialog/FilesInput.vue @@ -5,11 +5,14 @@ import { computed } from "vue"; import { FileSourceBrowsingMode, FilterFileSourcesOptions } from "@/api/remoteFiles"; import { filesDialog } from "@/utils/data"; +import { SelectionItem } from "../SelectionDialog/selectionTypes"; + interface Props { value: string; mode?: FileSourceBrowsingMode; requireWritable?: boolean; filterOptions?: FilterFileSourcesOptions; + selectedItem?: SelectionItem; } interface SelectableFile { @@ -20,6 +23,7 @@ const props = withDefaults(defineProps(), { mode: "file", requireWritable: false, filterOptions: undefined, + selectedItem: undefined, }); const emit = defineEmits<{ @@ -40,6 +44,7 @@ const selectFile = () => { mode: props.mode, requireWritable: props.requireWritable, filterOptions: props.filterOptions, + selectedItem: props.selectedItem, }; filesDialog((selected: SelectableFile) => { currentValue.value = selected?.url; From 90aed7aa0596b26c7b9c6e1e41ced5bee2bb01ad Mon Sep 17 00:00:00 2001 From: davelopez <46503462+davelopez@users.noreply.github.com> Date: Thu, 18 Apr 2024 18:19:34 +0200 Subject: [PATCH 05/11] Refactor move files dialog's conversion function to utils --- .../src/components/FilesDialog/FilesDialog.vue | 16 ++-------------- client/src/components/FilesDialog/utilities.ts | 15 +++++++++++++++ 2 files changed, 17 insertions(+), 14 deletions(-) diff --git a/client/src/components/FilesDialog/FilesDialog.vue b/client/src/components/FilesDialog/FilesDialog.vue index f27f9c20fc71..aafcd559aac2 100644 --- a/client/src/components/FilesDialog/FilesDialog.vue +++ b/client/src/components/FilesDialog/FilesDialog.vue @@ -3,7 +3,6 @@ import { BAlert } from "bootstrap-vue"; import Vue, { computed, onMounted, ref } from "vue"; import { - BrowsableFilesSourcePlugin, browseRemoteFiles, FileSourceBrowsingMode, FilterFileSourcesOptions, @@ -11,7 +10,7 @@ import { RemoteEntry, } from "@/api/remoteFiles"; import { UrlTracker } from "@/components/DataDialog/utilities"; -import { isSubPath } from "@/components/FilesDialog/utilities"; +import { fileSourcePluginToItem, isSubPath } from "@/components/FilesDialog/utilities"; import { SELECTION_STATES, type SelectionItem } from "@/components/SelectionDialog/selectionTypes"; import { useConfig } from "@/composables/config"; import { errorMessageAsString } from "@/utils/simple-error"; @@ -236,7 +235,7 @@ function load(record?: SelectionItem) { .then((results) => { const convertedItems = results .filter((item) => !props.requireWritable || item.writable) - .map(fileSourcePluginToRecord); + .map(fileSourcePluginToItem); items.value = convertedItems; formatRows(); optionsShow.value = true; @@ -293,17 +292,6 @@ function entryToRecord(entry: RemoteEntry): SelectionItem { return result; } -function fileSourcePluginToRecord(plugin: BrowsableFilesSourcePlugin): SelectionItem { - const result = { - id: plugin.id, - label: plugin.label, - details: plugin.doc, - isLeaf: false, - url: plugin.uri_root, - }; - return result; -} - /** select all files in current folder**/ function onSelectAll() { if (!currentDirectory.value) { diff --git a/client/src/components/FilesDialog/utilities.ts b/client/src/components/FilesDialog/utilities.ts index 2e4067fbc668..21aff76122a0 100644 --- a/client/src/components/FilesDialog/utilities.ts +++ b/client/src/components/FilesDialog/utilities.ts @@ -1,3 +1,7 @@ +import type { BrowsableFilesSourcePlugin } from "@/api/remoteFiles"; + +import type { SelectionItem } from "../SelectionDialog/selectionTypes"; + export const isSubPath = (originPath: string, destinationPath: string) => { return subPathCondition(ensureTrailingSlash(originPath), ensureTrailingSlash(destinationPath)); }; @@ -9,3 +13,14 @@ function ensureTrailingSlash(path: string) { function subPathCondition(originPath: string, destinationPath: string) { return originPath !== destinationPath && destinationPath.startsWith(originPath); } + +export function fileSourcePluginToItem(plugin: BrowsableFilesSourcePlugin): SelectionItem { + const result = { + id: plugin.id, + label: plugin.label, + details: plugin.doc, + isLeaf: false, + url: plugin.uri_root, + }; + return result; +} From 0183725c5bbd8162524dccc6a1896c12a08515c8 Mon Sep 17 00:00:00 2001 From: davelopez <46503462+davelopez@users.noreply.github.com> Date: Thu, 18 Apr 2024 18:39:32 +0200 Subject: [PATCH 06/11] Support preselecting a file source in RDM export --- .../src/components/Common/ExportRDMForm.vue | 37 ++++++++++++++++--- .../History/Export/HistoryExport.vue | 25 ++++++------- .../History/Export/RDMCredentialsInfo.vue | 23 ++++++++++++ 3 files changed, 65 insertions(+), 20 deletions(-) create mode 100644 client/src/components/History/Export/RDMCredentialsInfo.vue diff --git a/client/src/components/Common/ExportRDMForm.vue b/client/src/components/Common/ExportRDMForm.vue index ee7411a70e61..f99510a59907 100644 --- a/client/src/components/Common/ExportRDMForm.vue +++ b/client/src/components/Common/ExportRDMForm.vue @@ -2,11 +2,18 @@ import { BButton, BCard, BFormGroup, BFormInput, BFormRadio, BFormRadioGroup } from "bootstrap-vue"; import { computed, ref } from "vue"; -import { CreatedEntry, createRemoteEntry, FilterFileSourcesOptions } from "@/api/remoteFiles"; +import { + BrowsableFilesSourcePlugin, + CreatedEntry, + createRemoteEntry, + FilterFileSourcesOptions, +} from "@/api/remoteFiles"; import { useToast } from "@/composables/toast"; import localize from "@/utils/localization"; import { errorMessageAsString } from "@/utils/simple-error"; +import { fileSourcePluginToItem } from "../FilesDialog/utilities"; + import ExternalLink from "@/components/ExternalLink.vue"; import FilesInput from "@/components/FilesDialog/FilesInput.vue"; @@ -17,6 +24,11 @@ interface Props { clearInputAfterExport?: boolean; defaultRecordName?: string; defaultFilename?: string; + /** + * If undefined, the user will need to select a repository to export to, + * otherwise this file source will be pre-selected. + */ + fileSource?: BrowsableFilesSourcePlugin; } const props = withDefaults(defineProps(), { @@ -24,6 +36,7 @@ const props = withDefaults(defineProps(), { clearInputAfterExport: false, defaultRecordName: "", defaultFilename: "", + fileSource: undefined, }); const emit = defineEmits<{ @@ -35,7 +48,7 @@ type ExportChoice = "existing" | "new"; const includeOnlyRDMCompatible: FilterFileSourcesOptions = { include: ["rdm"] }; const recordUri = ref(""); -const sourceUri = ref(""); +const sourceUri = ref(props.fileSource?.uri_root ?? ""); const fileName = ref(props.defaultFilename); const exportChoice = ref("new"); const recordName = ref(props.defaultRecordName); @@ -53,6 +66,9 @@ const recordNameDescription = computed(() => localize("Give the new record a nam const namePlaceholder = computed(() => localize("File name")); const recordNamePlaceholder = computed(() => localize("Record name")); +const uniqueSourceId = computed(() => props.fileSource?.id ?? "any"); +const fileSourceAsItem = computed(() => (props.fileSource ? fileSourcePluginToItem(props.fileSource) : undefined)); + function doExport() { emit("export", recordUri.value, fileName.value); @@ -72,7 +88,7 @@ async function doCreateRecord() { function clearInputs() { recordUri.value = ""; - sourceUri.value = ""; + sourceUri.value = props.fileSource?.uri_root ?? ""; fileName.value = ""; newEntry.value = undefined; } @@ -84,10 +100,17 @@ function clearInputs() { +

+ Your {{ what }} needs to be uploaded to an existing draft record. You will need to create a + new record or select an existing draft record and then export your {{ what }} to it. +

+ - Export to new record + + Export to new record + - + Export to existing draft record @@ -123,6 +146,7 @@ function clearInputs() {
+ :filter-options="fileSource ? undefined : includeOnlyRDMCompatible" + :selected-item="fileSourceAsItem" /> ([]); const historyName = computed(() => history.value?.name ?? props.historyId); +const defaultFileName = computed(() => `(Galaxy History) ${historyName.value}`); const latestExportRecord = computed(() => (exportRecords.value?.length ? exportRecords.value.at(0) : null)); const isLatestExportRecordReadyToDownload = computed( () => @@ -203,11 +205,13 @@ function updateExportParams(newParams: ExportParams) { Here you can generate a temporal download for your history. When your download link expires or your history changes you can re-generate it again.

+ History archive downloads can expire and are removed at regular intervals. For permanent storage, export to a remote file or download and then import the archive on another Galaxy server. + Generate direct download + @@ -233,6 +238,7 @@ function updateExportParams(newParams: ExportParams) { one of the available remote file sources here. You will be able to re-import it later as long as it remains available on the remote server.

+

You can upload your history to one of the available RDM repositories here.

-

- Your history export archive needs to be uploaded to an existing draft record. You will - need to create a new record on the repository or select an existing - draft record and then export your history to it. -

- - You may need to setup your credentials for the selected repository in your - settings page to be able to - export. You can also define some default options for the export in those settings, like the - public name you want to associate with your records or whether you want to publish them - immediately or keep them as drafts after export. - + + + diff --git a/client/src/components/History/Export/RDMCredentialsInfo.vue b/client/src/components/History/Export/RDMCredentialsInfo.vue new file mode 100644 index 000000000000..7a04b472d93f --- /dev/null +++ b/client/src/components/History/Export/RDMCredentialsInfo.vue @@ -0,0 +1,23 @@ + + + From c3618d09cfb3489fb989ccd0ac6eefb7559809bc Mon Sep 17 00:00:00 2001 From: davelopez <46503462+davelopez@users.noreply.github.com> Date: Thu, 18 Apr 2024 18:41:59 +0200 Subject: [PATCH 07/11] Add Zenodo as export for histories If the plugin is setup it will show up as a first class option when exporting a history. --- .../History/Export/HistoryExport.vue | 42 ++++++++++++++++++- 1 file changed, 41 insertions(+), 1 deletion(-) diff --git a/client/src/components/History/Export/HistoryExport.vue b/client/src/components/History/Export/HistoryExport.vue index 15b6d3a36e78..746b8c8b4122 100644 --- a/client/src/components/History/Export/HistoryExport.vue +++ b/client/src/components/History/Export/HistoryExport.vue @@ -38,7 +38,7 @@ const { } = useTaskMonitor(); const { hasWritable: hasWritableFileSources } = useFileSources({ exclude: ["rdm"] }); -const { hasWritable: hasWritableRDMFileSources } = useFileSources({ include: ["rdm"] }); +const { hasWritable: hasWritableRDMFileSources, getFileSourceById } = useFileSources({ include: ["rdm"] }); const { isPreparing: isPreparingDownload, @@ -92,6 +92,7 @@ const history = computed(() => { const errorMessage = ref(undefined); const actionMessage = ref(undefined); const actionMessageVariant = ref(undefined); +const zenodoSource = computed(() => getFileSourceById("zenodo")); onMounted(async () => { updateExports(); @@ -260,6 +261,37 @@ function updateExportParams(newParams: ExportParams) { :clear-input-after-export="true" @export="doExportToFileSource" /> + +
+ ZENODO Logo +

+ Zenodo is a general-purpose + open repository developed under the + European OpenAIRE program and + operated by CERN. It allows + researchers to deposit research papers, data sets, research software, reports, and any other + research related digital artefacts. For each submission, a persistent + digital object identifier (DOI) is minted, which makes the stored items easily + citeable. +

+
+ + + + + @@ -292,3 +324,11 @@ function updateExportParams(newParams: ExportParams) { @onReimport="reimportFromRecord" /> + + From 1ec61fca56354673a24053e3e2eafd5e4a8c06f7 Mon Sep 17 00:00:00 2001 From: davelopez <46503462+davelopez@users.noreply.github.com> Date: Fri, 19 Apr 2024 09:56:41 +0200 Subject: [PATCH 08/11] Adapt choice selector in unit tests --- client/src/components/Common/ExportRDMForm.test.ts | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/client/src/components/Common/ExportRDMForm.test.ts b/client/src/components/Common/ExportRDMForm.test.ts index 116b1d84d932..6c38958e6257 100644 --- a/client/src/components/Common/ExportRDMForm.test.ts +++ b/client/src/components/Common/ExportRDMForm.test.ts @@ -100,8 +100,9 @@ describe("ExportRDMForm", () => { }); }); - async function selectExportChoice(choice: string) { - const exportChoice = wrapper.find(`#radio-${choice}`); + async function selectExportChoice(choice: string, fileSourceId?: string) { + const suffix = fileSourceId ? `${fileSourceId}` : "any"; + const exportChoice = wrapper.find(`#radio-${choice}-${suffix}`); await exportChoice.setChecked(true); } From be46445382288f524b19560cf597fea8750c6bcd Mon Sep 17 00:00:00 2001 From: davelopez <46503462+davelopez@users.noreply.github.com> Date: Fri, 19 Apr 2024 11:07:09 +0200 Subject: [PATCH 09/11] Add unit tests for selecting specific file source --- .../components/Common/ExportRDMForm.test.ts | 54 +++++++++++++++++-- 1 file changed, 50 insertions(+), 4 deletions(-) diff --git a/client/src/components/Common/ExportRDMForm.test.ts b/client/src/components/Common/ExportRDMForm.test.ts index 6c38958e6257..1f53d7cc1a99 100644 --- a/client/src/components/Common/ExportRDMForm.test.ts +++ b/client/src/components/Common/ExportRDMForm.test.ts @@ -2,7 +2,7 @@ import { getLocalVue } from "@tests/jest/helpers"; import { mount, Wrapper } from "@vue/test-utils"; import flushPromises from "flush-promises"; -import { CreatedEntry } from "@/api/remoteFiles"; +import { type BrowsableFilesSourcePlugin, CreatedEntry } from "@/api/remoteFiles"; import { mockFetcher } from "@/api/schema/__mocks__"; import ExportRDMForm from "./ExportRDMForm.vue"; @@ -25,11 +25,13 @@ const FAKE_ENTRY: CreatedEntry = { external_link: "http://example.com", }; -async function initWrapper() { +async function initWrapper(fileSource?: BrowsableFilesSourcePlugin) { mockFetcher.path("/api/remote_files").method("post").mock({ data: FAKE_ENTRY }); - const wrapper = mount(ExportRDMForm, { - propsData: {}, + const wrapper = mount(ExportRDMForm as object, { + propsData: { + fileSource, + }, localVue, }); await flushPromises(); @@ -100,6 +102,50 @@ describe("ExportRDMForm", () => { }); }); + describe("Pre-select specific File Source", () => { + beforeEach(async () => { + const specificFileSource: BrowsableFilesSourcePlugin = { + id: "test-file-source", + label: "Test File Source", + doc: "Test File Source Description", + uri_root: "gxfiles://test-file-source", + writable: true, + browsable: true, + type: "rdm", + }; + wrapper = await initWrapper(specificFileSource); + }); + + it("enables the create new record button only by setting the record name", async () => { + await selectExportChoice("new", "test-file-source"); + expect(wrapper.find(CREATE_RECORD_BTN).attributes("disabled")).toBeTruthy(); + + await setRecordNameInput(FAKE_RECORD_NAME); + + expect(wrapper.find(CREATE_RECORD_BTN).attributes("disabled")).toBeFalsy(); + }); + + it("displays the export to this record button when the create new record button is clicked", async () => { + await selectExportChoice("new", "test-file-source"); + expect(wrapper.find(EXPORT_TO_NEW_RECORD_BTN).exists()).toBeFalsy(); + + await setRecordNameInput(FAKE_RECORD_NAME); + await clickCreateNewRecordButton(); + + expect(wrapper.find(EXPORT_TO_NEW_RECORD_BTN).exists()).toBeTruthy(); + }); + + it("emits an export event when the export to new record button is clicked", async () => { + await selectExportChoice("new", "test-file-source"); + await setFileNameInput("test file name"); + await setRecordNameInput(FAKE_RECORD_NAME); + await clickCreateNewRecordButton(); + + await wrapper.find(EXPORT_TO_NEW_RECORD_BTN).trigger("click"); + expect(wrapper.emitted("export")).toBeTruthy(); + }); + }); + async function selectExportChoice(choice: string, fileSourceId?: string) { const suffix = fileSourceId ? `${fileSourceId}` : "any"; const exportChoice = wrapper.find(`#radio-${choice}-${suffix}`); From c0c893dc621542644bb24647d077e98cf30416de Mon Sep 17 00:00:00 2001 From: davelopez <46503462+davelopez@users.noreply.github.com> Date: Fri, 19 Apr 2024 11:26:23 +0200 Subject: [PATCH 10/11] Add unit test for displaying the Zenodo tab --- client/src/api/remoteFiles.ts | 1 + .../History/Export/HistoryExport.test.ts | 25 ++++++++++++++++--- 2 files changed, 22 insertions(+), 4 deletions(-) diff --git a/client/src/api/remoteFiles.ts b/client/src/api/remoteFiles.ts index 95ae19c1dd2a..ae9a86cd3ffe 100644 --- a/client/src/api/remoteFiles.ts +++ b/client/src/api/remoteFiles.ts @@ -7,6 +7,7 @@ import { fetcher } from "@/api/schema/fetcher"; * - `source` - allows to select a source plugin root and doesn't list its contents */ export type FileSourceBrowsingMode = "file" | "directory" | "source"; +export type FilesSourcePlugin = components["schemas"]["FilesSourcePlugin"]; export type BrowsableFilesSourcePlugin = components["schemas"]["BrowsableFilesSourcePlugin"]; export type RemoteFile = components["schemas"]["RemoteFile"]; export type RemoteDirectory = components["schemas"]["RemoteDirectory"]; diff --git a/client/src/components/History/Export/HistoryExport.test.ts b/client/src/components/History/Export/HistoryExport.test.ts index 13668295cffa..20a270927acb 100644 --- a/client/src/components/History/Export/HistoryExport.test.ts +++ b/client/src/components/History/Export/HistoryExport.test.ts @@ -6,7 +6,7 @@ import { setActivePinia } from "pinia"; import type { HistorySummary } from "@/api"; import { fetchHistoryExportRecords } from "@/api/histories.export"; -import type { components } from "@/api/schema"; +import type { FilesSourcePlugin } from "@/api/remoteFiles"; import { mockFetcher } from "@/api/schema/__mocks__"; import { EXPIRED_STS_DOWNLOAD_RECORD, @@ -32,8 +32,7 @@ const FAKE_HISTORY = { const REMOTE_FILES_API_ENDPOINT = new RegExp("/api/remote_files/plugins"); -type FilesSourcePluginList = components["schemas"]["FilesSourcePlugin"][]; -const REMOTE_FILES_API_RESPONSE: FilesSourcePluginList = [ +const REMOTE_FILES_API_RESPONSE: FilesSourcePlugin[] = [ { id: "test-posix-source", type: "posix", @@ -57,7 +56,7 @@ async function mountHistoryExport() { (_history_id: string) => FAKE_HISTORY as HistorySummary ); - const wrapper = shallowMount(HistoryExport, { + const wrapper = shallowMount(HistoryExport as object, { propsData: { historyId: FAKE_HISTORY_ID }, localVue, pinia, @@ -121,4 +120,22 @@ describe("HistoryExport.vue", () => { expect(wrapper.find("#direct-download-tab").exists()).toBe(true); expect(wrapper.find("#file-source-tab").exists()).toBe(false); }); + + it("should display the ZENODO tab if the Zenodo plugin is available", async () => { + const zenodoPlugin: FilesSourcePlugin = { + id: "zenodo", + type: "rdm", + label: "Zenodo", + doc: "For testing", + writable: true, + browsable: true, + }; + mockFetcher + .path(REMOTE_FILES_API_ENDPOINT) + .method("get") + .mock({ data: [zenodoPlugin] }); + const wrapper = await mountHistoryExport(); + + expect(wrapper.find("#zenodo-file-source-tab").exists()).toBe(true); + }); }); From 0ba0a6fd0853beb98b652a4dff00d4a886d9a543 Mon Sep 17 00:00:00 2001 From: davelopez <46503462+davelopez@users.noreply.github.com> Date: Mon, 22 Apr 2024 12:21:49 +0200 Subject: [PATCH 11/11] Remove info about auto-publishing This is more accurate as the auto-publish option is not available anymore. The publishing must be done through the Zenodo website for extra security. --- client/src/components/History/Export/RDMCredentialsInfo.vue | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/src/components/History/Export/RDMCredentialsInfo.vue b/client/src/components/History/Export/RDMCredentialsInfo.vue index 7a04b472d93f..306944e64d80 100644 --- a/client/src/components/History/Export/RDMCredentialsInfo.vue +++ b/client/src/components/History/Export/RDMCredentialsInfo.vue @@ -18,6 +18,6 @@ withDefaults(defineProps(), { You may need to setup your credentials for {{ selectedRepository }} in your preferences page to be able to export. You can also define some default options for the export in those settings, like the public name you want to associate - with your records or whether you want to publish them immediately or keep them as drafts after export. + with your records.