[25.1] Assorted workbook upload fixes.

client/src/components/Collections/BuildFileSetWizard.vue

@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { BCardGroup } from "bootstrap-vue";
+import { BAlert, BCardGroup } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
 import { GalaxyApi } from "@/api";
@@ -11,6 +11,7 @@ import { forBuilder, type ForBuilderResponse } from "@/components/Collections/wi
 import { useWizard } from "@/components/Common/Wizard/useWizard";
 import { useToolRouting } from "@/composables/route";
 import localize from "@/utils/localization";
+import { errorMessageAsString } from "@/utils/simple-error";
 
 import type {
     ParsedFetchWorkbook,
@@ -112,7 +113,7 @@ const wizard = useWizard({
     },
     "upload-workbook": {
         label: "Upload workbook",
-        instructions: "Upload a workbook containing with URIs and metadata",
+        instructions: "Upload a workbook containing URIs with metadata",
         isValid: () => sourceFrom.value === "workbook" && workbookCompleted.value,
         isSkippable: () => sourceFrom.value !== "workbook",
     },
@@ -239,7 +240,7 @@ async function handleWorkbook(base64Content: string) {
         handleUploadedData(data);
     } else {
         console.log(error);
-        uploadErrorMessage.value = "There was an error processing the file.";
+        uploadErrorMessage.value = "There was an error processing the file. " + errorMessageAsString(error);
     }
 }
 
@@ -260,17 +261,26 @@ const {
 <template>
     <GenericWizard :use="wizard" :submit-button-label="importButtonLabel" :title="title" @submit="submit">
         <template v-slot:header>
+            <BAlert
+                :show="!!uploadErrorMessage"
+                variant="danger"
+                class="my-2"
+                dismissible
+                @dismissed="uploadErrorMessage = ''">
+                {{ uploadErrorMessage }}
+            </BAlert>
             <h2 data-galaxy-file-drop-target>
                 {{ title }}
-                <FontAwesomeIcon
-                    class="workbook-upload-helper mr-1"
-                    :class="dropZoneClasses"
-                    :title="dropWorkbookTitle"
-                    :icon="faUpload"
-                    @click.prevent="browseFiles"
-                    @drop.prevent="handleDrop"
-                    @dragover.prevent="isDragging = true"
-                    @dragleave.prevent="isDragging = false" />
+                <a v-b-tooltip.hover aria-label="Upload Completed Workbook" :title="dropWorkbookTitle" href="#">
+                    <FontAwesomeIcon
+                        class="workbook-upload-helper mr-1"
+                        :class="dropZoneClasses"
+                        :icon="faUpload"
+                        @click.prevent="browseFiles"
+                        @drop.prevent="handleDrop"
+                        @dragover.prevent="isDragging = true"
+                        @dragleave.prevent="isDragging = false" />
+                </a>
                 <HiddenWorkbookUploadInput ref="uploadRef" @onFileUpload="onFileUpload" />
             </h2>
         </template>
@@ -337,5 +347,8 @@ const {
 // modeled a bit after upload-helper in the upload component...
 .workbook-upload-helper {
     color: $border-color;
+    &:hover {
+        color: $brand-primary;
+    }
 }
 </style>

client/src/components/Collections/wizard/CardDownloadWorkbook.vue

@@ -3,6 +3,16 @@ import { faDownload } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BCard, BCardTitle, BLink } from "bootstrap-vue";
 
+// We use this in two capacities - one where we have to do a post and do complex things
+// to generate the workbook and one where we just have an easy link. Support both.
+interface Props {
+    generateWorkbookLink?: string;
+}
+
+withDefaults(defineProps<Props>(), {
+    generateWorkbookLink: undefined,
+});
+
 const emit = defineEmits(["download"]);
 </script>
 
@@ -11,6 +21,8 @@ const emit = defineEmits(["download"]);
         <BCardTitle>
             <b>Step 1: Download</b>
         </BCardTitle>
-        <BLink @click="emit('download')"><FontAwesomeIcon size="xl" :icon="faDownload" /> Download workbook.</BLink>
+        <BLink :href="generateWorkbookLink" @click="emit('download')"
+            ><FontAwesomeIcon size="xl" :icon="faDownload" /> Download workbook.</BLink
+        >
     </BCard>
 </template>

client/src/components/Collections/wizard/HiddenWorkbookUploadInput.vue

@@ -19,6 +19,6 @@ defineExpose({
 
 <template>
     <label style="display: none">
-        <input ref="fileInputRef" type="file" accept=".xlsx" @change="onFileUpload" />
+        <input ref="fileInputRef" type="file" accept=".xlsx,.xls,.tsv,.csv,.tabular" @change="onFileUpload" />
     </label>
 </template>

client/src/components/Collections/wizard/fetchWorkbooks.ts

@@ -88,7 +88,9 @@ const COLUMN_TITLE_PREFIXES: Record<string, ColumnMappingType> = {
     deferredurl: "url_deferred",
     genome: "dbkey",
     dbkey: "dbkey",
+    build: "dbkey",
     filetype: "file_type",
+    type: "file_type",
     extension: "file_type",
     info: "info",
     tag: "tags",

lib/galaxy/model/dataset_collections/rule_target_column_specification.yml

@@ -48,13 +48,20 @@
 - doc: "dbkey maps to the dbkey target type"
   column_header: "dbkey"
   maps_to: "dbkey"
+- doc: "build maps to the dbkey target type"
+  column_header: "build"
+  maps_to: "dbkey"
+
 
 - doc: "filetype maps to the file_type target type"
   column_header: "file type"
   maps_to: "file_type"
 - doc: "extension maps to the file_type target type"
   column_header: "extension"
   maps_to: "file_type"
+- doc: "Type maps to the file_type target type"
+  column_header: "Type"
+  maps_to: "file_type"
 
 - doc: "info maps to the info target type"
   column_header: "info"

lib/galaxy/model/dataset_collections/rule_target_columns.py

@@ -23,9 +23,11 @@
     "genome": "dbkey",
     "dbkey": "dbkey",
     "genomebuild": "dbkey",
+    "build": "dbkey",
     "filetype": "file_type",
     "extension": "file_type",
     "fileextension": "file_type",
+    "type": "file_type",
     "info": "info",
     "tag": "tags",
     "grouptag": "group_tags",

lib/galaxy/model/dataset_collections/workbook_util.py

@@ -235,17 +235,24 @@ def load_workbook_from_base64(content: str) -> ReadOnlyWorkbook:
     is_excel = file_like.read(4) == b"\x50\x4b\x03\x04"
     workbook: ReadOnlyWorkbook
     file_like.seek(0)
-    try:
-        if is_excel:
+    if is_excel:
+        try:
             workbook = ExcelReadOnlyWorkbook(load_workbook(file_like, data_only=True))
-        else:
+        except Exception as e:
+            extra_message = str(e)
+            raise RequestParameterInvalidException(
+                f"The provided content is not a valid Excel file (or at least not one Galaxy knows how to parse). Please check the content and try again. The underlying error was [{extra_message}]"
+            )
+    else:
+        try:
             tabular = decoded_content.decode("utf-8")
             file_like_as_utf8 = StringIO(tabular)
             workbook = CsvReaderReadOnlyWorkbook(file_like_as_utf8)
-    except Exception:
-        raise RequestParameterInvalidException(
-            "The provided content is not a valid Excel file. Please check the content and try again."
-        )
+        except Exception as e:
+            extra_message = str(e)
+            raise RequestParameterInvalidException(
+                f"The provided content is not a parsable as a valid CSV or TSV (or at least not one Galaxy knows how to parse). Please check the content and try again. The underlying error was [{extra_message}]"
+            )
     return workbook
 
 

test/unit/data/dataset_collections/test_workbook_util.py

@@ -1,4 +1,10 @@
-from galaxy.model.dataset_collections.workbook_util import index_to_excel_column
+import base64
+
+from galaxy.model.dataset_collections.workbook_util import (
+    index_to_excel_column,
+    load_workbook_from_base64,
+)
+from galaxy.util.resources import resource_path
 
 
 def test_index_to_excel_column():
@@ -8,3 +14,18 @@ def test_index_to_excel_column():
     assert index_to_excel_column(700) == "ZY"
     assert index_to_excel_column(701) == "ZZ"
     assert index_to_excel_column(702) == "AAA"
+
+
+def test_load_workbook_from_base64():
+    workbook_base64 = resource_path_to_base64("filled_in_workbook_1.xlsx")
+    workbook = load_workbook_from_base64(workbook_base64)
+    assert workbook is not None
+
+    workbook_base64 = resource_path_to_base64("filled_in_workbook_1.tsv")
+    workbook = load_workbook_from_base64(workbook_base64)
+    assert workbook is not None
+
+
+def resource_path_to_base64(resource_name: str) -> str:
+    resource_bytes = resource_path("galaxy.model.unittest_utils", resource_name).read_bytes()
+    return base64.b64encode(resource_bytes).decode("utf-8")