Merge branch 'release_23.1' into dev

bgruening · Jul 26, 2023 · 9b0c3c9 · 9b0c3c9
2 parents 43c1ea6 + 2900691
commit 9b0c3c9
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Showing 5 changed files with 22 additions and 14 deletions.
diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
@@ -58,9 +58,9 @@
                         v-for="(resultMessage, index) in resultMessages"
                         :key="index"
                         :variant="resultMessage[1]"
-                        show
-                        >{{ resultMessage[0] }}</b-alert
-                    >
+                        show>
+                        <span v-html="renderMarkdown(resultMessage[0])"></span>
+                    </b-alert>
                     <div v-if="showForm" id="fieldsAndButton">
                         <span class="mr-2 font-weight-bold">{{ emailTitle }}</span>
                         <span v-if="!!currentUser?.email">{{ currentUser?.email }}</span>
@@ -93,6 +93,7 @@ import { DatasetProvider } from "components/providers";
 import { JobDetailsProvider, JobProblemProvider } from "components/providers/JobProvider";
 import { mapState } from "pinia";
 
+import { useMarkdown } from "@/composables/markdown";
 import { useUserStore } from "@/stores/userStore";
 
 import DatasetErrorDetails from "./DatasetErrorDetails";
@@ -115,6 +116,10 @@ export default {
             required: true,
         },
     },
+    setup() {
+        const { renderMarkdown } = useMarkdown({ openLinksInNewPage: true });
+        return { renderMarkdown };
+    },
     data() {
         return {
             message: null,

diff --git a/client/src/components/User/UserPreferences.vue b/client/src/components/User/UserPreferences.vue
@@ -179,7 +179,10 @@ export default {
     computed: {
         ...mapState(useUserStore, ["currentUser"]),
         activePreferences() {
-            const enabledPreferences = Object.entries(getUserPreferencesModel()).filter((f) => !f.disabled);
+            const userPreferencesEntries = Object.entries(getUserPreferencesModel());
+            // Object.entries returns an array of arrays, where the first element
+            // is the key (string) and the second is the value (object)
+            const enabledPreferences = userPreferencesEntries.filter((f) => !f[1].disabled);
             return Object.fromEntries(enabledPreferences);
         },
         hasLogout() {

diff --git a/lib/galaxy/tool_util/biotools/interface.py b/lib/galaxy/tool_util/biotools/interface.py
@@ -28,8 +28,8 @@ class BiotoolsEntry:
     def from_json(from_json: Dict[str, Any]) -> "BiotoolsEntry":
         entry = BiotoolsEntry()
         entry.biotoolsID = from_json["biotoolsID"]
-        entry.topic = from_json["topic"]
-        entry.function = from_json["function"]
+        entry.topic = from_json.get("topic", [])
+        entry.function = from_json.get("function", [])
         return entry
 
     @property

diff --git a/lib/galaxy/tools/error_reports/plugins/github.py b/lib/galaxy/tools/error_reports/plugins/github.py
@@ -99,12 +99,12 @@ def submit_report(self, dataset, job, tool, **kwargs):
             else:
                 self._append_issue(issue_cache_key, error_title, error_message)
             return (
-                'Submitted error report to GitHub. Your issue number is <a href="{}/{}/issues/{}" '
-                'target="_blank">#{}</a>.'.format(
+                "Submitted error report to GitHub. Your issue number is [#%s](%s/%s/issues/%s)"
+                % (
+                    self.issue_cache[issue_cache_key][error_title].number,
                     self.github_base_url,
                     github_projecturl,
                     self.issue_cache[issue_cache_key][error_title].number,
-                    self.issue_cache[issue_cache_key][error_title].number,
                 ),
                 "success",
             )

diff --git a/lib/galaxy/tools/error_reports/plugins/gitlab.py b/lib/galaxy/tools/error_reports/plugins/gitlab.py
@@ -185,12 +185,12 @@ def submit_report(self, dataset, job, tool, **kwargs):
                         )
 
                 return (
-                    'Submitted error report to GitLab. Your issue number is <a href="{}/{}/issues/{}" '
-                    'target="_blank">#{}</a>.'.format(
+                    "Submitted error report to GitLab. Your Issue number is [#%s](%s/%s/issues/%s)"
+                    % (
+                        self.issue_cache[issue_cache_key][error_title],
                         self.gitlab_base_url,
                         gitlab_projecturl,
                         self.issue_cache[issue_cache_key][error_title],
-                        self.issue_cache[issue_cache_key][error_title],
                     ),
                     "success",
                 )
@@ -275,7 +275,7 @@ def _append_issue(self, issue_cache_key, error_title, error_message, **kwargs):
                 "api",
                 "v4",
                 "projects",
-                kwargs.get("gitlab_projecturl"),
+                urllib.parse.quote(kwargs.get("gitlab_projecturl"), safe=""),
                 "issues",
                 str(self.issue_cache[issue_cache_key][error_title]),
                 "notes",
@@ -287,7 +287,7 @@ def _fill_issue_cache(self, git_project, issue_cache_key):
         self.issue_cache[issue_cache_key] = {}
         # Loop over all open issues and add the issue iid to the cache
         for issue in git_project.issues.list():
-            if issue.state != "closed":
+            if issue.state != "closed" or not self.gitlab_new_issue_on_closed:
                 log.info("GitLab error reporting - Repo issue: %s", str(issue.iid))
                 self.issue_cache[issue_cache_key][issue.title] = issue.iid