Empower Developers to Build Rich, Automated Tutorials

client/src/api/schema/schema.ts

@@ -14887,7 +14887,19 @@ export interface components {
             /** Message */
             message: string;
         };
-        /** InferredColumnMapping */
+        /**
+         * InferredColumnMapping
+         * @description Records that a column at a specific index was successfully parsed and mapped.
+         *
+         *     Used in parse logs to show users which columns were recognized and how they were interpreted.
+         *
+         *     Example log entry:
+         *         InferredColumnMapping(
+         *             column_index=2,
+         *             column_title="MD5 Sum",
+         *             parsed_column=ParsedColumn(type="hash_md5", type_index=0, title="MD5 Sum")
+         *         )
+         */
         InferredColumnMapping: {
             /** Column Index */
             column_index: number;
@@ -18660,7 +18672,12 @@ export interface components {
              */
             content: string;
         };
-        /** ParsedColumn */
+        /**
+         * ParsedColumn
+         * @description Serializable representation of a parsed column (Pydantic model version of HeaderColumn).
+         *
+         *     Used in API responses and logging to communicate which columns were recognized.
+         */
         ParsedColumn: {
             /** Title */
             title: string;

client/src/components/ActivityBar/ActivitySettings.vue

@@ -88,6 +88,8 @@ function executeActivity(activity: Activity) {
                 v-for="activity in filteredActivities"
                 :key="activity.id"
                 class="activity-settings-item p-2 cursor-pointer"
+                :data-activity-id="activity.id"
+                :data-activity-visible="!!activity.visible"
                 @click="executeActivity(activity)">
                 <div class="d-flex justify-content-between align-items-start">
                     <span class="d-flex justify-content-between w-100">

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

@@ -21,7 +21,7 @@ const emit = defineEmits(["download"]);
         <BCardTitle>
             <b>Step 1: Download</b>
         </BCardTitle>
-        <BLink :href="generateWorkbookLink" @click="emit('download')"
+        <BLink data-description="workbook download link" :href="generateWorkbookLink" @click="emit('download')"
             ><FontAwesomeIcon size="xl" :icon="faDownload" /> Download workbook.</BLink
         >
     </BCard>

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

@@ -24,6 +24,7 @@ const emit = defineEmits(["workbookContents"]);
 </script>
 <template>
     <BCard
+        data-description="workbook upload card"
         data-galaxy-file-drop-target
         :class="dropZoneClasses"
         @drop.prevent="handleDrop"
@@ -38,7 +39,7 @@ const emit = defineEmits(["workbookContents"]);
             </BAlert>
         </div>
         <div>
-            <BLink href="#" @click.prevent="browseFiles">
+            <BLink data-description="workbook upload link" href="#" @click.prevent="browseFiles">
                 <FontAwesomeIcon size="xl" :icon="faUpload" />
                 Drop completed workbook here or click to upload.
             </BLink>

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

@@ -19,6 +19,11 @@ defineExpose({
 
 <template>
     <label style="display: none">
-        <input ref="fileInputRef" type="file" accept=".xlsx,.xls,.tsv,.csv,.tabular" @change="onFileUpload" />
+        <input
+            ref="fileInputRef"
+            data-description="workbook-file-input"
+            type="file"
+            accept=".xlsx,.xls,.tsv,.csv,.tabular"
+            @change="onFileUpload" />
     </label>
 </template>

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

@@ -2,6 +2,8 @@
 import { BCardGroup } from "bootstrap-vue";
 import { computed } from "vue";
 
+import { withPrefix } from "@/utils/redirect";
+
 import type { ParsedFetchWorkbookForCollectionCollectionType, RulesCreatingWhat } from "./types";
 
 import CardDownloadWorkbook from "./CardDownloadWorkbook.vue";
@@ -25,7 +27,7 @@ const emit = defineEmits(["workbookContents"]);
 const generateWorkbookHref = computed(() => {
     let type;
     if (props.creatingWhat === "datasets") {
-        type = "dataset";
+        type = "datasets";
     } else if (props.includeCollectionName) {
         type = "collections";
     } else {
@@ -36,7 +38,7 @@ const generateWorkbookHref = computed(() => {
     if (type === "collection" || type === "collections") {
         url = `${url}&collection_type=${props.collectionType}`;
     }
-    return url;
+    return withPrefix(url);
 });
 </script>
 

client/src/utils/navigation/navigation.yml

@@ -170,6 +170,12 @@ dataset_display:
     container: .dataset-display
     content: body
 
+activity_bar:
+  selectors:
+    settings: "#activity-settings"
+    show_activity: "button[data-activity-id='${activity_id}'] button"
+    additional_activities: '[data-description="Additional Activities"]'
+
 history_panel:
   menu:
     labels:
@@ -1386,6 +1392,17 @@ rule_builder:
     table: '#rules-ag-grid .ag-root'
     extension_select: '.rule-footer-extension-group .extension-select'
 
+    activity: '#activity-rules'
+    workbook_upload_button: '.workbook-upload-helper'
+    workbook_upload_file_input: '[data-description="workbook-file-input"]'
+    create_collections: '[data-creating-what="collections"]'
+    wizard_import: ".wizard-actions .btn-primary"
+    wizard_next: ".wizard-actions .go-next-btn"
+    data_import_source_from: '[data-import-source-from="${source}"]'
+    workbook_download_link: '[data-description="workbook download link"]'
+    workbook_upload_link: '[data-description="workbook upload card"] [data-description="workbook upload link"]'
+    workbook_upload_file_input_explicit: '[data-description="workbook upload card"] [data-description="workbook-file-input"]'
+
 charts:
   selectors:
     visualize_button: '.ui-portlet .button i.fa-line-chart'  # without icon - it waits on other buttons that aren't visible, need more specific class

lib/galaxy/managers/configuration.py

@@ -13,9 +13,9 @@
 
 from galaxy.managers import base
 from galaxy.managers.context import ProvidesUserContext
-from galaxy.managers.markdown_util import weasyprint_available
 from galaxy.schema import SerializationParams
 from galaxy.structured_app import StructuredApp
+from galaxy.util.markdown import weasyprint_available
 
 log = logging.getLogger(__name__)
 

lib/galaxy/managers/markdown_util.py

@@ -16,22 +16,13 @@
 import logging
 import os
 import re
-import shutil
-import tempfile
 from datetime import datetime
 from re import Match
 from typing import (
     Any,
     Optional,
 )
 
-import markdown
-
-try:
-    import weasyprint
-except Exception:
-    weasyprint = None
-
 from galaxy.config import GalaxyAppConfiguration
 from galaxy.exceptions import (
     MalformedContents,
@@ -54,9 +45,11 @@
     ShortTermStorageMonitor,
     storage_context,
 )
-from galaxy.util.markdown import literal_via_fence
-from galaxy.util.resources import resource_string
-from galaxy.util.sanitize_html import sanitize_html
+from galaxy.util.markdown import (
+    literal_via_fence,
+    to_pdf_raw,
+    weasyprint_available,
+)
 from .markdown_parse import (
     EMBED_DIRECTIVE_REGEX,
     GALAXY_MARKDOWN_FUNCTION_CALL_LINE,
@@ -915,38 +908,6 @@ def to_basic_markdown(trans, internal_galaxy_markdown: str) -> str:
     return plain_markdown
 
 
-def to_html(basic_markdown: str) -> str:
-    # Allow data: urls so we can embed images.
-    html = sanitize_html(markdown.markdown(basic_markdown, extensions=["tables"]), allow_data_urls=True)
-    return html
-
-
-def to_pdf_raw(basic_markdown: str, css_paths: Optional[list[str]] = None) -> bytes:
-    """Convert RAW markdown with specified CSS paths into bytes of a PDF."""
-    css_paths = css_paths or []
-    as_html = to_html(basic_markdown)
-    directory = tempfile.mkdtemp("gxmarkdown")
-    index = os.path.join(directory, "index.html")
-    try:
-        output_file = open(index, "w", encoding="utf-8", errors="xmlcharrefreplace")
-        output_file.write(as_html)
-        output_file.close()
-        html = weasyprint.HTML(filename=index)
-        stylesheets = [weasyprint.CSS(string=resource_string(__name__, "markdown_export_base.css"))]
-        for css_path in css_paths:
-            with open(css_path) as f:
-                css_content = f.read()
-            css = weasyprint.CSS(string=css_content)
-            stylesheets.append(css)
-        return html.write_pdf(stylesheets=stylesheets)
-    finally:
-        shutil.rmtree(directory)
-
-
-def weasyprint_available() -> bool:
-    return weasyprint is not None
-
-
 def _check_can_convert_to_pdf_or_raise():
     """Checks if the HTML to PDF converter is available."""
     if not weasyprint_available():

lib/galaxy/managers/notification.py

@@ -36,7 +36,6 @@
     ConfigDoesNotAllowException,
     ObjectNotFound,
 )
-from galaxy.managers.markdown_util import to_html
 from galaxy.model import (
     GroupRoleAssociation,
     Notification,
@@ -64,6 +63,7 @@
     UserNotificationPreferences,
     UserNotificationUpdateRequest,
 )
+from galaxy.util.markdown import to_html
 
 log = logging.getLogger(__name__)
 

lib/galaxy/model/dataset_collections/rule_target_column_specification.yml

@@ -1,8 +1,32 @@
-# The idea that we reserve some column names for reserved purposes in Galaxy
-# is going to span fetch workbooks and sample sheet workbooks - and we need
-# to validate it both on the backend and the frontend. So having a set of tests
-# that validate what are reserved column names that we can run across both languages
-# utilities for doing this is valuable.
+# Test Specification: Column Header to Target Type Mappings
+#
+# This file defines test cases for Galaxy's flexible column header parsing system.
+# Each test case specifies:
+#   - doc: Human-readable description
+#   - column_header: The user-provided column header (as it appears in workbook)
+#   - maps_to: The expected internal target type key
+#
+# Purpose:
+#   Galaxy needs to recognize column headers in workbooks (Excel/CSV) across different
+#   naming conventions and formats. This specification serves as:
+#   1. Test cases for backend Python parsing (column_title_to_target_type)
+#   2. Test cases for frontend TypeScript parsing (when implemented)
+#   3. Documentation of supported column header variations
+#
+# The parsing is case-insensitive and ignores:
+#   - Whitespace
+#   - Special characters: ( ) - _
+#   - The word "optional"
+#
+# Examples of flexible parsing:
+#   "Name", "name", "NAME"                     -> "name"
+#   "MD5 Sum", "MD5", "Hash MD5", "md5sum"     -> "hash_md5"
+#   "URI 1 (Forward)", "url", "URL"            -> "url"
+#   "Genome Build", "DBKey", "genome"          -> "dbkey"
+#
+# Test Execution:
+#   Python: test/unit/data/dataset_collections/test_column_to_target_mapping.py
+#   TypeScript: (future implementation)
 
 - doc: "Name (with uppercase) maps directly to the name target type"
   column_header: "Name"