Empower Developers to Build Rich, Automated Tutorials

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/HiddenWorkbookUploadInput.vue

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

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:
@@ -1380,6 +1386,13 @@ 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"
+
+
 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

@@ -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/selenium/cli.py

@@ -6,17 +6,24 @@
 HEADLESS_DESCRIPTION = "Use local selenium headlessly (native in chrome, otherwise this requires pyvirtualdisplay)."
 BACKEND_DESCRIPTION = "Browser automation backend to use (selenium or playwright)."
 
-from typing import Literal
+import os
+from typing import (
+    Literal,
+    Optional,
+)
 from urllib.parse import urljoin
 
 from .driver_factory import (
     ConfiguredDriver,
     virtual_display_if_enabled,
 )
-from .navigates_galaxy import (
-    galaxy_timeout_handler,
-    NavigatesGalaxy,
+from .navigates_galaxy import galaxy_timeout_handler
+from .stories import (
+    NoopStory,
+    Story,
+    StoryProtocol,
 )
+from .stories.data.upload import UploadStoriesMixin
 
 
 def add_selenium_arguments(parser):
@@ -60,11 +67,41 @@ def add_selenium_arguments(parser):
         choices=["selenium", "playwright"],
         help=BACKEND_DESCRIPTION,
     )
+    parser.add_argument(
+        "--timeout-multiplier",
+        type=float,
+        default=1.0,
+        help="Multiplier to apply to all timeout values (for slower environments).",
+    )
+    return parser
+
+
+def add_story_arguments(parser):
+    """Add story generation arguments for CLI scripts.
+
+    All the browser automation arguments (add_selenium_arguments) are also added.
+    """
+    add_selenium_arguments(parser)
+    parser.add_argument(
+        "--story-output",
+        default=None,
+        help="Directory to generate story documentation (markdown, HTML, PDF)",
+    )
+    parser.add_argument(
+        "--story-title",
+        default=None,
+        help="Title for the generated story",
+    )
+    parser.add_argument(
+        "--story-description",
+        default=None,
+        help="Description for the generated story",
+    )
 
     return parser
 
 
-class DriverWrapper(NavigatesGalaxy):
+class DriverWrapper(UploadStoriesMixin):
     """Adapt argparse command-line options to a browser automation driver."""
 
     def __init__(self, args):
@@ -81,9 +118,8 @@ def __init__(self, args):
             self.display = virtual_display_if_enabled(args.selenium_headless)
 
         # Create configured driver with the specified backend
-        # TODO: parameterize timeout multiplier
         self.configured_driver = ConfiguredDriver(
-            galaxy_timeout_handler(1.0),
+            galaxy_timeout_handler(args.timeout_multiplier),
             browser=browser,
             remote=args.selenium_remote,
             remote_host=args.selenium_remote_host,
@@ -93,6 +129,18 @@ def __init__(self, args):
         )
         self.target_url = args.galaxy_url
 
+        # Initialize story (real or noop)
+        # Scripts opt-in by calling add_story_arguments()
+        if hasattr(args, "story_output") and args.story_output:
+            if not os.path.exists(args.story_output):
+                os.makedirs(args.story_output)
+
+            title = args.story_title or "Galaxy Tutorial"
+            description = args.story_description or ""
+            self.story: StoryProtocol = Story(title, description, args.story_output)
+        else:
+            self.story = NoopStory()
+
     @property
     def _driver_impl(self):
         """Provide driver implementation from configured_driver."""
@@ -101,11 +149,23 @@ def _driver_impl(self):
     def build_url(self, url="", for_selenium: bool = True):
         return urljoin(self.target_url, url)
 
-    def screenshot(self, label: str) -> None:
-        """No-op in this context, not saving debugging/testing screenshots.
+    def screenshot(self, label: str, caption: Optional[str] = None) -> None:
+        """Save screenshot if story tracking is enabled.
 
-        Consider a verbose or debug option for saving these.
+        Args:
+            label: Base filename for screenshot
+            caption: Optional caption for the screenshot in the story
         """
+        if self.story.enabled:
+            # Generate screenshot path with sequential numbering
+            target = os.path.join(self.story.output_directory, f"{self.story.screenshot_counter:03d}_{label}.png")
+            self.story.screenshot_counter += 1
+
+            # Save screenshot
+            self.save_screenshot(target)
+
+            # Add to story
+            self.story.add_screenshot(target, caption or label)
 
     @property
     def default_timeout(self):
@@ -130,3 +190,6 @@ def finish(self):
 
         if exception is not None:
             raise exception
+
+    def _screenshot_path(self, label: str, extension: str = ".png") -> Optional[str]:
+        return None