Merge branch 'release_24.1' into dev

client/src/components/Upload/UploadContainer.vue

@@ -74,13 +74,15 @@ const props = defineProps({
     },
 });
 
+const collectionTabActive = ref(null);
 const extensionsSet = ref(false);
 const datatypesMapper = ref(null);
 const datatypesMapperReady = ref(false);
 const dbKeysSet = ref(false);
 const listExtensions = ref([]);
 const listDbKeys = ref([]);
 const regular = ref(null);
+const regularTabActive = ref(null);
 
 const { percentage, status } = storeToRefs(useUploadStore());
 
@@ -112,12 +114,15 @@ const ready = computed(
 );
 const canUploadToHistory = computed(() => currentHistory.value && canMutateHistory(currentHistory.value));
 const showCollection = computed(() => !props.formats && props.multiple);
-const showComposite = computed(() => !props.formats || hasCompositeExtension);
-const showRegular = computed(() => !props.formats || hasRegularExtension);
+const showComposite = computed(() => !props.formats || hasCompositeExtension.value);
+const showRegular = computed(() => !props.formats || hasRegularExtension.value);
 const showRules = computed(() => !props.formats || props.multiple);
 
 function immediateUpload(files) {
-    regular.value?.addFiles(files, true);
+    if (showRegular.value) {
+        regularTabActive.value = true;
+        regular.value?.addFiles(files, true);
+    }
 }
 
 function toData(items, history_id, composite = false) {
@@ -172,21 +177,7 @@ defineExpose({
         </span>
     </BAlert>
     <BTabs v-else-if="ready">
-        <BTab v-if="showRegular" id="regular" title="Regular" button-id="tab-title-link-regular">
-            <DefaultBox
-                ref="regular"
-                :chunk-upload-size="chunkUploadSize"
-                :default-db-key="defaultDbKey"
-                :default-extension="defaultExtension"
-                :effective-extensions="effectiveExtensions"
-                :file-sources-configured="fileSourcesConfigured"
-                :ftp-upload-site="currentUserId && ftpUploadSite"
-                :has-callback="hasCallback"
-                :history-id="currentHistoryId"
-                :list-db-keys="listDbKeys"
-                :multiple="multiple"
-                @progress="progress"
-                v-on="$listeners" />
+        <BTab v-if="showRegular" title="Regular" button-id="tab-title-link-regular" :active.sync="regularTabActive">
         </BTab>
         <BTab v-if="showComposite" id="composite" title="Composite" button-id="tab-title-link-composite">
             <CompositeBox
@@ -199,19 +190,11 @@ defineExpose({
                 :list-db-keys="listDbKeys"
                 v-on="$listeners" />
         </BTab>
-        <BTab v-if="showCollection" id="collection" title="Collection" button-id="tab-title-link-collection">
-            <DefaultBox
-                :chunk-upload-size="chunkUploadSize"
-                :default-db-key="defaultDbKey"
-                :default-extension="defaultExtension"
-                :effective-extensions="effectiveExtensions"
-                :file-sources-configured="fileSourcesConfigured"
-                :ftp-upload-site="currentUserId && ftpUploadSite"
-                :has-callback="hasCallback"
-                :history-id="currentHistoryId"
-                :is-collection="true"
-                :list-db-keys="listDbKeys"
-                v-on="$listeners" />
+        <BTab
+            v-if="showCollection"
+            title="Collection"
+            button-id="tab-title-link-collection"
+            :active.sync="collectionTabActive">
         </BTab>
         <BTab v-if="showRules" id="rule-based" title="Rule-based" button-id="tab-title-link-rule-based">
             <RulesInput
@@ -221,6 +204,24 @@ defineExpose({
                 :history-id="currentHistoryId"
                 v-on="$listeners" />
         </BTab>
+        <DefaultBox
+            v-if="showRegular || showCollection"
+            v-show="regularTabActive || collectionTabActive"
+            :id="collectionTabActive ? 'collection' : 'regular'"
+            ref="regular"
+            :chunk-upload-size="chunkUploadSize"
+            :default-db-key="defaultDbKey"
+            :default-extension="defaultExtension"
+            :effective-extensions="effectiveExtensions"
+            :file-sources-configured="fileSourcesConfigured"
+            :ftp-upload-site="currentUserId && ftpUploadSite"
+            :has-callback="hasCallback"
+            :history-id="currentHistoryId"
+            :list-db-keys="listDbKeys"
+            :multiple="regularTabActive ? multiple : undefined"
+            :is-collection="collectionTabActive"
+            @progress="progress"
+            v-on="$listeners" />
     </BTabs>
     <div v-else>
         <LoadingSpan message="Loading required information from Galaxy server." />

client/src/utils/navigation/navigation.yml

@@ -1139,7 +1139,7 @@ upload:
     setting_space_to_tab: '.upload-space-to-tab'
     source_button: '#upload-row-${n} .upload-source'
     start: '#activity-upload'
-    start_button: '#btn-start'
+    start_button: '#regular #btn-start'
     local_button: '#btn-local'
 
 new_user_welcome:

config/plugins/tours/core.history.yaml

@@ -28,11 +28,11 @@ steps:
         https://raw.githubusercontent.com/bgruening/galaxytools/adf077b912ddebd97b07b947b855cdd2862ed8ef/tools/statistics/test-data/anderson.tabular
 
     - title: "Start the upload"
-      element: "#btn-start"
+      element: "#regular #btn-start"
       intro: "Upload the data into your Galaxy <b>History</b>."
       postclick:
-        - "#btn-start"
-        - "#btn-close"
+        - "#regular #btn-start"
+        - "#regular #btn-close"
 
     - title: "History"
       element: "#current-history-panel"

lib/galaxy/datatypes/registry.py

@@ -891,7 +891,16 @@ def find_conversion_destination_for_dataset_by_extensions(
         if datatype and datatype.matches_any(accepted_datatypes):
             return True, None, None
 
-        for convert_ext in self.get_converters_by_datatype(ext):
+        converter_extensions = self.get_converters_by_datatype(ext)
+        uncompressed_instance = getattr(datatype, "uncompressed_datatype_instance", None)
+        if uncompressed_instance and uncompressed_instance.file_ext in converter_extensions:
+            # sort uncompressed instance ahead of other possible conversions
+            converter_extensions = [
+                uncompressed_instance.file_ext,
+                *(ext for ext in converter_extensions if ext != uncompressed_instance.file_ext),
+            ]
+
+        for convert_ext in converter_extensions:
             convert_ext_datatype = self.get_datatype_by_extension(convert_ext)
             if convert_ext_datatype is None:
                 self.log.warning(

lib/galaxy/jobs/handler.py

@@ -1269,7 +1269,8 @@ def stop(self, job, job_wrapper):
             runner_name = job_runner_name.split(":", 1)[0]
             log.debug(f"Stopping job {job_wrapper.get_id_tag()} in {runner_name} runner")
             try:
-                self.job_runners[runner_name].stop_job(job_wrapper)
+                if job.state != model.Job.states.NEW:
+                    self.job_runners[runner_name].stop_job(job_wrapper)
             except KeyError:
                 log.error(f"stop(): ({job_wrapper.get_id_tag()}) Invalid job runner: {runner_name}")
                 # Job and output dataset states have already been updated, so nothing is done here.

lib/galaxy/jobs/runners/__init__.py

@@ -589,7 +589,8 @@ def _handle_runner_state(self, runner_state, job_state: "JobState"):
             log.exception("Caught exception in runner state handler")
 
     def fail_job(self, job_state: "JobState", exception=False, message="Job failed", full_status=None):
-        if getattr(job_state, "stop_job", True):
+        job = job_state.job_wrapper.get_job()
+        if getattr(job_state, "stop_job", True) and job.state != model.Job.states.NEW:
             self.stop_job(job_state.job_wrapper)
         job_state.job_wrapper.reclaim_ownership()
         self._handle_runner_state("failure", job_state)

lib/galaxy/jobs/runners/aws.py

@@ -420,7 +420,8 @@ def recover(self, job, job_wrapper):
             self.monitor_queue.put(ajs)
 
     def fail_job(self, job_state: JobState, exception=False, message="Job failed", full_status=None):
-        if getattr(job_state, "stop_job", True):
+        job = job_state.job_wrapper.get_job()
+        if getattr(job_state, "stop_job", True) and job.state != model.Job.states.NEW:
             self.stop_job(job_state.job_wrapper)
         job_state.job_wrapper.reclaim_ownership()
         self._handle_runner_state("failure", job_state)

lib/galaxy/selenium/navigates_galaxy.py

@@ -876,7 +876,7 @@ def _perform_upload(
 
         self.upload_start()
 
-        self.wait_for_and_click_selector("button#btn-close")
+        self.components.upload.close_button.wait_for_and_click()
 
     def perform_upload_of_composite_dataset_pasted_data(self, ext, paste_content):
         self.home()

lib/galaxy_test/selenium/test_uploads.py

@@ -182,7 +182,7 @@ def test_upload_modal_retains_content(self):
         self.upload_start_click()
         self.upload_queue_local_file(self.get_filename("1.sam"))
         self.upload_paste_data("some pasted data")
-        self.wait_for_and_click_selector("button#btn-close")
+        self.components.upload.close_button.wait_for_and_click()
 
         # reopen modal and check that the files are still there
         self.upload_start_click()
@@ -191,12 +191,12 @@ def test_upload_modal_retains_content(self):
 
         # perform upload and close modal
         self.upload_start()
-        self.wait_for_and_click_selector("button#btn-close")
+        self.components.upload.close_button.wait_for_and_click()
 
         # add another pasted file, but don't upload it
         self.upload_start_click()
         self.upload_paste_data("some more pasted data")
-        self.wait_for_and_click_selector("button#btn-close")
+        self.components.upload.close_button.wait_for_and_click()
 
         # reopen modal and see 2 uploaded, 1 yet to upload
         self.upload_start_click()

test/functional/tools/implicit_conversion_format_input.xml

@@ -3,7 +3,7 @@
     cut -f 1 '$input1' > '$output1'
   </command>
   <inputs>
-    <param type="data" format="fasta" name="input1" label="Input 1" />
+    <param type="data" format="txt" name="input1" label="Input 1" />
   </inputs>
   <outputs>
     <data name="output1" format="input" />