Merge branch 'dev' into job_files_fastapi_migration

Author: kysrpex

.gitignore

@@ -165,6 +165,7 @@ client/webpack-stats.json
 packages/*/build
 packages/*/dist
 packages/*/*.egg-info
+packages/meta/requirements.txt
 
 # Standalone script + main, or build into dist
 config/plugins/**/static/dist

.pre-commit-config.yaml.sample

@@ -8,13 +8,14 @@ repos:
     hooks:
     - id: flake8
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.7.1 # Use the sha or tag you want to point at
+    rev: v3.1.0
     hooks:
-      - id: prettier
-        types: [file]
-        types_or: [javascript, jsx, ts, tsx, vue]
-        additional_dependencies:
-          - [email protected] # Workaround. See https://github.com/pre-commit/mirrors-prettier/issues/29
+    - id: prettier
+      additional_dependencies:
+        - [email protected] # SEE: https://github.com/pre-commit/pre-commit/issues/3133
+      exclude_types:  # .prettierignore ignored apparently ...
+        - yaml
+        - json
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0  # Use the ref you want to point at
     hooks:

Makefile

@@ -30,10 +30,10 @@ SPACE := $() $()
 NEVER_PYUPGRADE_PATHS := .venv/ .tox/ lib/galaxy/schema/bco/ \
 	lib/galaxy/schema/drs/ lib/tool_shed_client/schema/trs \
 	scripts/check_python.py tools/ test/functional/tools/cwl_tools/
-PY37_PYUPGRADE_PATHS := lib/galaxy/exceptions/ lib/galaxy/job_metrics/ \
-	lib/galaxy/objectstore/ lib/galaxy/tool_util/ lib/galaxy/util/ \
-	test/unit/job_metrics/ test/unit/objectstore/ test/unit/tool_util/ \
-	test/unit/util/
+PY38_PYUPGRADE_PATHS := lib/galaxy/exceptions/ lib/galaxy/job_metrics/ \
+	lib/galaxy/objectstore/ lib/galaxy/tool_util/ lib/galaxy/tool_util_models/ \
+	lib/galaxy/util/ test/unit/job_metrics/ test/unit/objectstore/ \
+	test/unit/tool_util/ test/unit/tool_util_models/ test/unit/util/
 
 all: help
 	@echo "This makefile is used for building Galaxy's JS client, documentation, and drive the release process. A sensible all target is not implemented."
@@ -62,10 +62,10 @@ format:  ## Format Python code base
 remove-unused-imports:  ## Remove unused imports in Python code base
 	$(IN_VENV) autoflake --in-place --remove-all-unused-imports --recursive --verbose lib/ test/
 
-pyupgrade:  ## Convert older code patterns to Python 3.7/3.9 idiomatic ones
-	ack --type=python -f | grep -v '^$(subst $(SPACE),\|^,$(NEVER_PYUPGRADE_PATHS) $(PY37_PYUPGRADE_PATHS))' | xargs pyupgrade --py39-plus
-	ack --type=python -f | grep -v '^$(subst $(SPACE),\|^,$(NEVER_PYUPGRADE_PATHS) $(PY37_PYUPGRADE_PATHS))' | xargs auto-walrus
-	ack --type=python -f $(PY37_PYUPGRADE_PATHS) | xargs pyupgrade --py37-plus
+pyupgrade:  ## Convert older code patterns to Python 3.8/3.9 idiomatic ones
+	ack --type=python -f | grep -v '^$(subst $(SPACE),\|^,$(NEVER_PYUPGRADE_PATHS) $(PY38_PYUPGRADE_PATHS))' | xargs pyupgrade --py39-plus
+	ack --type=python -f | grep -v '^$(subst $(SPACE),\|^,$(NEVER_PYUPGRADE_PATHS) $(PY38_PYUPGRADE_PATHS))' | xargs auto-walrus
+	ack --type=python -f $(PY38_PYUPGRADE_PATHS) | xargs pyupgrade --py38-plus
 
 docs-slides-ready:
 	test -f plantuml.jar ||  wget http://jaist.dl.sourceforge.net/project/plantuml/plantuml.jar
@@ -262,6 +262,12 @@ client-test-watch: client ## Watch and run all client unit tests on changes
 serve-selenium-notebooks: ## Serve testing notebooks for Jupyter
 	cd lib && export PYTHONPATH=`pwd`; jupyter notebook --notebook-dir=galaxy_test/selenium/jupyter
 
+files-sources-lint: ## Validate file sources configuration
+	$(IN_VENV) cd lib && PYTHONPATH=`pwd` python galaxy/files/validate/script.py
+
+files-sources-lint-verbose: ## Validate file sources configuration (verbose)
+	$(IN_VENV) cd lib && PYTHONPATH=`pwd` python galaxy/files/validate/script.py --verbose
+
 # Release Targets
 release-create-rc: ## Create a release-candidate branch or new release-candidate version
 	$(IN_VENV) ./scripts/release.sh -c

client-api/tsconfig.json

@@ -1,7 +1,7 @@
 {
     "compilerOptions": {
-        "target": "es2020",
-        "module": "es2020",
+        "target": "es2022",
+        "module": "es2022",
         "moduleResolution": "node",
 
         "verbatimModuleSyntax": true,

client-api/tsup.config.ts

@@ -8,7 +8,7 @@ export default defineConfig({
   clean: true,
   treeshake: true,
   minify: false,
-  target: 'es2020',
+  target: 'es2022',
   esbuildOptions(options) {
     options.external = [
       ...options.external || [],

client/docs/avoid-using-global-Galaxy.md

@@ -14,8 +14,8 @@ There are definitely use-cases where the Backbone models update over time and we
 value inside Vue. Instead of importing backbone models directly into Vue components, try building a
 backbone event listener that updates some relevant Vuex store.
 
--   [Keeping Vuex in Sync with
-    Galaxy](https://github.com/galaxyproject/galaxy/blob/dev/client/src/store/syncVuexToGalaxy.js)
+- [Keeping Vuex in Sync with
+  Galaxy](https://github.com/galaxyproject/galaxy/blob/dev/client/src/store/syncVuexToGalaxy.js)
 
 These issues should disappear over time as the all of the old client is rebuilt in the new
 ecosystem.

client/docs/composables.md

@@ -6,9 +6,9 @@ Using them effectively can make your code more reusable, decoupled, and easier t
 
 **More about Composables:**
 
--   [Composables Overview](https://vuejs.org/guide/reusability/composables.html)
--   [Composition API](https://vuejs.org/api/composition-api-setup.html)
--   [\<script setup\>](https://vuejs.org/api/sfc-script-setup.html)
+- [Composables Overview](https://vuejs.org/guide/reusability/composables.html)
+- [Composition API](https://vuejs.org/api/composition-api-setup.html)
+- [\<script setup\>](https://vuejs.org/api/sfc-script-setup.html)
 
 ## Using Composables in the Composition API
 

client/docs/headings.md

@@ -6,23 +6,23 @@ Heading Levels are used by screen readers, and other software, to get a rough id
 
 ## Heading Level best practices
 
--   Make sure every route has exactly one `<h1>` element, which best describes the content of the current page.
+- Make sure every route has exactly one `<h1>` element, which best describes the content of the current page.
 
--   When increasing a heading level, do not skip Levels.
+- When increasing a heading level, do not skip Levels.
 
--   Do not use a headings level to determine it's size. Use one of the heading utility classes (e.g. `h-lg`) instead.
+- Do not use a headings level to determine it's size. Use one of the heading utility classes (e.g. `h-lg`) instead.
 
--   Do not use a heading tag to make a non-heading text large. Use a heading utility class on a `<span>` instead.
+- Do not use a heading tag to make a non-heading text large. Use a heading utility class on a `<span>` instead.
 
 ## Sizing Headings
 
 There are several utility classes which size headings:
 
--   `h-xl` - Extra large headings
--   `h-lg` - Large headings (most main headings should have this size)
--   `h-md` - Medium headings
--   `h-sm` - Small headings (many sub-headings have this size)
--   `h-text` - Text sized headings
+- `h-xl` - Extra large headings
+- `h-lg` - Large headings (most main headings should have this size)
+- `h-md` - Medium headings
+- `h-sm` - Small headings (many sub-headings have this size)
+- `h-text` - Text sized headings
 
 Galaxy uses `h-lg` for most top-level (`<h1>`) headings.
 
@@ -45,8 +45,8 @@ Set the headings level, by setting aa `h1 ... h6` prop:
 
 Following properties allow for further styling the component:
 
--   `size=["xl", "lg", "md", "sm", "text"]` - sets the headings size class
--   `bold` - makes a heading bold
--   `inline` - displays the heading inline
--   `separator` - draws a separating line, to better distinguish sections
--   `icon="..."` - adds a font-awesome icon decoration to the left of the heading. Make sure to also load the icon with `library.add(...)`.
+- `size=["xl", "lg", "md", "sm", "text"]` - sets the headings size class
+- `bold` - makes a heading bold
+- `inline` - displays the heading inline
+- `separator` - draws a separating line, to better distinguish sections
+- `icon="..."` - adds a font-awesome icon decoration to the left of the heading. Make sure to also load the icon with `library.add(...)`.

client/docs/never-use-jquery.md

@@ -15,5 +15,5 @@ from our source, along with all its invasive plugins.
 
 ### References
 
--   [You Don't Need jQuery](https://github.com/nefe/You-Dont-Need-jQuery)
--   [document.querySelector](https://developer.mozilla.org/en-US/docs/Web/API/Document/querySelector)
+- [You Don't Need jQuery](https://github.com/nefe/You-Dont-Need-jQuery)
+- [document.querySelector](https://developer.mozilla.org/en-US/docs/Web/API/Document/querySelector)

client/docs/querying-the-api.md

@@ -10,25 +10,25 @@ When querying APIs in Vue components, consider the following approaches and thei
 
 ### Composables
 
--   **What Are Composables?**: please read the official Vue documentation on composables [here](https://vuejs.org/guide/reusability/composables.html).
+- **What Are Composables?**: please read the official Vue documentation on composables [here](https://vuejs.org/guide/reusability/composables.html).
 
 If there is already a composable that takes care of the logic you need for accessing a particular resource in the API please use it or consider writing a new one. They provide a type-safe interface and a higher level of abstraction than the related Store or the API itself. They might rely on one or more Stores for caching and reactivity.
 
 ### Stores
 
--   **Stores Explained**: Please read the official Vue documentation on State Management [here](https://vuejs.org/guide/scaling-up/state-management.html).
+- **Stores Explained**: Please read the official Vue documentation on State Management [here](https://vuejs.org/guide/scaling-up/state-management.html).
 
 If there is no Composable for the API endpoint you are using, try using a (Pinia) Store instead. Stores are type-safe and provide a reactive interface to the API. They can also be used to cache data, ensuring a single source of truth.
 
--   **Use Pinia Stores**: If you need to create a new Store, make sure to create a Pinia Store, and not a Vuex Store as Pinia will be the replacement for Vuex. Also, use [Composition API syntax over the Options API](https://vuejs.org/guide/extras/composition-api-faq.html) for increased readability, code organization, type inference, etc.
+- **Use Pinia Stores**: If you need to create a new Store, make sure to create a Pinia Store, and not a Vuex Store as Pinia will be the replacement for Vuex. Also, use [Composition API syntax over the Options API](https://vuejs.org/guide/extras/composition-api-faq.html) for increased readability, code organization, type inference, etc.
 
 ### Direct API Calls
 
--   If the type of data you are querying should not be cached, or you just need to update or create new data, you can use the API directly. Make sure to use the **GalaxyApi client** (see below) instead of Axios, as it provides a type-safe interface to the API along with some extra benefits.
+- If the type of data you are querying should not be cached, or you just need to update or create new data, you can use the API directly. Make sure to use the **GalaxyApi client** (see below) instead of Axios, as it provides a type-safe interface to the API along with some extra benefits.
 
 ## 2. Prefer **GalaxyApi client** over Axios (when possible)
 
--   **Use **GalaxyApi client** with OpenAPI Specs**: If there is an OpenAPI spec for the API endpoint you are using (in other words, there is a FastAPI route defined in Galaxy), always use the GalaxyApi client. It will provide you with a type-safe interface to the API.
+- **Use **GalaxyApi client** with OpenAPI Specs**: If there is an OpenAPI spec for the API endpoint you are using (in other words, there is a FastAPI route defined in Galaxy), always use the GalaxyApi client. It will provide you with a type-safe interface to the API.
 
 **Do**
 
@@ -142,6 +142,6 @@ If so, you should consider putting it under src/api/<resource>.ts and exporting
 
 ### Should I use the `GalaxyApi client` directly or should I write a wrapper function?
 
--   If you **don't need to do any additional processing** of the data, you **should** use the `GalaxyApi client` directly.
--   If you **need to do some additional processing**, then consider writing a wrapper function. Additional processing can be anything from transforming the data to adding extra parameters to the query, providing useful defaults, handling conditional types in response data, etc.
--   In any case, please try to avoid modeling your own types if you can use the ones defined in the OpenAPI spec (client/src/api/schema/schema.ts). This will help to keep the codebase consistent and avoid duplication of types or API specification drifting.
+- If you **don't need to do any additional processing** of the data, you **should** use the `GalaxyApi client` directly.
+- If you **need to do some additional processing**, then consider writing a wrapper function. Additional processing can be anything from transforming the data to adding extra parameters to the query, providing useful defaults, handling conditional types in response data, etc.
+- In any case, please try to avoid modeling your own types if you can use the ones defined in the OpenAPI spec (client/src/api/schema/schema.ts). This will help to keep the codebase consistent and avoid duplication of types or API specification drifting.