Tool Shed 2.0 #15639

jmchilton · 2023-02-23T16:25:55Z

Goals

The goal here is to introduce a new tool shed that breaks nothing but cuts all sorts of ties to old technologies and old concepts that we’re no longer interested in supporting.

Not a single line of mako, jQuery, or untyped JavaScript is used in the modern tool shed interface. The frontend is built on Typescript, Vue 3.2, Vite, Pinia, and Quasar.
Not a single old controller (web or API) is needed - the entire API is FastAPI based.
No Twill is needed to run the remaining and new test cases - everything can (and in some cases must) be run in Playwright.
A GraphQL engine and client is used to power a lot of the frontend and backend.
Planemo and Ephemeris are heavily featured in UX for the new frontend - the best practice is now supported more strongly and other paths that are not longer used are no longer supported.
The new tool shed implements the GA4GH TRS API (to some degree)

Technology Choices

At its core, these technologies mirror the directions Galaxy has moved over the last decade but in some cases there is small divergence. The long term goal of stripping the tool shed out of the Galaxy code base remains firmly intact. The tool shed now has its own client build process and such and doesn’t depend on any shared mako or Javascript glue with Galaxy client - and I hope this allows for that freedom to make some small different choices at the top of the client stack. In particular, the tool shed is very small (especially now) compared Galaxy so the freedom and flexibility and configurability of say Bootstrap and WebPack that are important for large projects with significant legacy features are probably not as important as the rapid prototyping and more on the rails experience (both visually and in terms of developer workflow) of say Quasar, Material, and Vite.

GraphQL remains an interesting experiment to my mind. I’ve done the hard work here of figuring out how to integrate it with a Galaxy-like app (both in terms of the backend and frontend). I don’t think it should be thrown out and I think it should remain in the tool shed - I’m somewhat more ambivalent about whether I’d use it in Galaxy or if I would keep in a second cleanroom rewrite of the Tool Shed. What is here is a good and successful experiment though I think and remains valuable data.

A Non-exhaustive List of Things I’ve Removed from the Frontend

Workflows
Datatypes
Repository Dependencies
Tool Dependencies
Visual Clues about repository “type” (there is only one best practice type)
Upload to the repository (everyone should be using Planemo)
Navigating repository contents (these are firmly packages - there is zero indication anymore that these are development repositories - we’re not competing against Github)
Pagination (everything is infinite scroll)

Developing the Tool Shed

The TypeScript GraphQL development tools require a GraphQL server to query for typing details and such. So the backend of the tool shed must be running before the frontend development tools can be launched (at least the GraphQL ones).

Backend Runtime

The backend (along with a GraphQL console) can be started with the following command:

TOOL_SHED_CONFIG_OVERRIDE_BOOTSTRAP_ADMIN_API_KEY=tsadminkey TOOL_SHED_CONFIG_CONFIG_HG_FOR_DEV=1 TOOL_SHED_VITE_PORT=4040 TOOL_SHED_API_VERSION=v2 ./run_tool_shed.sh

If that API key is set as that, the following script will bootstrap the new tool shed against the main tool shed to have some things to play with.

. .venv/bin/activate; python scripts/bootstrap_test_shed.py

Frontend Runtime:

make dev (from the frontend directory) or yarn dev-all from that same directory will run a Vite development server for the frontend (kind of the equivalent of webpack watch) and it will monitor the frontend code for GraphQL queries and generated typed TypeScript artifacts against the the backend server.

The one thing that isn’t covered by that - is TypeScript fetcher stuff for the API. I’ve piggy-backed on the Galaxy Makefile task for this - so make update-client-api-schema from Galaxy’s Makefile will generate these.

Production:

Run make client from the frontend script to build artifacts needed to for deploying the frontend.

Frontend Linting:

yarn and Makefile targets for linting and running prettier are included. make lint will check both of those as well as type checking. "make format” will format the code.

How to test the changes?

(Select all options that apply)

I've included appropriate automated tests.
Instructions for manual testing are as follows:
1. See above under developing the tool shed.

License

I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

This is a piece that is needed to create a schema package - which I would really like to have around for galaxyproject#15639 and to in general write higher-level API tests.

ElectronicBlueberry

Following the instructions outlined in the PR description, I ran into two errors which prevented me from running the toolshed locally:

The frontend threw an error which I detailed in the review comment for [...]/frontend/package.json

The backend threw the following error, causing a worker to be stuck in a restart loop:

Traceback (most recent call last):
  File "/home/lailalos/Projects/galaxy/lib/tool_shed/webapp/buildapp.py", line 91, in app_pair
    app = tool_shed.webapp.app.UniverseApplication(global_conf=global_conf, **kwargs)
  File "/home/lailalos/Projects/galaxy/lib/tool_shed/webapp/app.py", line 56, in __init__
    self.config: Any = config.Configuration(**kwd)
  File "/home/lailalos/Projects/galaxy/lib/tool_shed/webapp/config.py", line 41, in __init__
    self._process_config(kwargs)
  File "/home/lailalos/Projects/galaxy/lib/tool_shed/webapp/config.py", line 136, in _process_config
    self.password_expiration_period = timedelta(days=int(self.password_expiration_period))
AttributeError: 'ToolShedAppConfiguration' object has no attribute 'password_expiration_period'

I tried creating a tool_shed.yml from the provided sample and setting password_expiration_period to 0, which did not fix the issue.

ElectronicBlueberry · 2023-09-04T08:44:41Z

lib/tool_shed/webapp/frontend/package.json

+  "scripts": {
+    "dev": "vite --port 4040 --strict-port",
+    "build": "vue-tsc --noEmit && vite build",
+    "graphql": "graphql-codegen --watch",


Running this either directly, or through dev all, throws the following error:

Failed to load schema from http://localhost:9009/graphql/: connect ECONNREFUSED ::1:9009 Error: connect ECONNREFUSED ::1:9009 at TCPConnectWrap.afterConnect [as oncomplete] (node:net:1494:16) GraphQL Code Generator supports: - ES Modules and CommonJS exports (export as default or named export "schema") - Introspection JSON File - URL of GraphQL endpoint - Multiple files with type definitions (glob expression) - String in config file Try to use one of above options and run codegen again.

Steps from clean slate:

dependencies installed with yarn

ran make dev

jmchilton · 2023-09-26T17:39:49Z

The toolshed backend error was caused by a messed up rebase and I think I've fixed it now. The backend serves as the GraphQL server the frontend needs to generate code... so that is why dev code doesn't work... it needs a GraphQL server to monitor for model changes. Maybe it is worth exploring if a vite server without the model watching for GraphQL is viable... it wouldn't be as full reactive to dev changes but it would be sufficient for all sorts of development.

jdavcs · 2023-09-26T17:43:01Z

lib/galaxy/app_unittest_utils/toolbox_support.py

+        self._repo_install(changeset="1")
+        version1 = tool_shed_install.ToolVersion()
+        version1.tool_id = "github.com/galaxyproject/example/test_tool/0.1"
+        self.app.install_model.context.add(version1)


I think the context for backward compatibility? Given that context here is the session, do you want to switch to calling it session (or sa_session, etc.) for consistency? (i.e., self.app.install_model.session)

I think that comment meant context.current was the backward compatible thing. I'm fine with install_model.session but it hasn't been my go to for tens of thousands of lines of code since that comment 😅. We should document a best practice here maybe.

I like session (or sa_sesssion). I think session is a slightly more accurate term for what the object is; even with the occasional presence of galaxy_session, I think context is more generic and may be harder to immediately recognize as the identifier for SQLAlchemy's session. But I'm +100 on documenting best practices (naming key objects like Session, as well as how to handle typical db access tasks, etc.)

jdavcs · 2023-09-26T17:46:46Z

lib/tool_shed/managers/categories.py

+        if deleted and not trans.user_is_admin:
+            raise exceptions.AdminRequiredException("Only administrators can query deleted categories.")
+        for category in (
+            trans.sa_session.query(Category).filter(Category.table.c.deleted == deleted).order_by(Category.table.c.name)


Suggested change

trans.sa_session.query(Category).filter(Category.table.c.deleted == deleted).order_by(Category.table.c.name)

trans.sa_session.scalars(select(Category).where(Category.deleted == deleted).order_by(Category.name))

…nal changes

…tions... ... so we can get the typing right and not depend on app.name.

…ions. Stronger typing and flatter functions

…plementations.

…ations.

…d ts versions. Avoid all the big conditionals in the middle - again for stronger typing and flatter functions.

Goals: - Replace direct database access with pydantic typed API requests. - Replace Twill with playwright. - Eliminate access to the Galaxy UI in the tests - the tests should assume API access from the installing party. pytest-playwright requires small bits of galaxyproject#13909. This is a worthy project that could let us remove a bunch of deprecated stuff from the Galaxy admin controllers and a bunch of mako stuff that is unused and could be used to test PRs like galaxyproject#14609 (which prompted me to do this) but I'm anxious about growing emotionally attached to code I want to remove and I'm worried about losing track of which helpers are required for Planemo/Emphemeris/Galaxy and which helpers are just being used to test the tool shed.

jdavcs · 2023-09-26T17:48:46Z

lib/tool_shed/managers/repositories.py

+            app.model.Repository.table.c.user_id == app.model.User.table.c.id,
+        )
+    ]
+    repository = app.model.context.query(app.model.Repository).filter(*clause_list).first()


Suggested change

repository = app.model.context.query(app.model.Repository).filter(*clause_list).first()

repository = app.model.context.scalars(select(app.model.Repository).where(*clause_list).limit(1)).first()

jdavcs · 2023-09-26T17:50:06Z

lib/tool_shed/managers/repositories.py

+            app.model.Repository.table.c.deprecated == false(),
+            app.model.Repository.table.c.deleted == false(),
+            app.model.Repository.table.c.name == name,
+            app.model.User.table.c.username == owner,


Suggested change

app.model.Repository.table.c.deprecated == false(),

app.model.Repository.table.c.deleted == false(),

app.model.Repository.table.c.name == name,

app.model.User.table.c.username == owner,

app.model.Repository.deprecated == false(),

app.model.Repository.deleted == false(),

app.model.Repository.name == name,

app.model.User.username == owner,

jdavcs · 2023-09-26T17:50:45Z

lib/tool_shed/managers/repositories.py

+            app.model.Repository.table.c.deleted == false(),
+            app.model.Repository.table.c.name == name,
+            app.model.User.table.c.username == owner,
+            app.model.Repository.table.c.user_id == app.model.User.table.c.id,


Suggested change

app.model.Repository.table.c.user_id == app.model.User.table.c.id,

app.model.Repository.user_id == app.model.User.id,

jdavcs · 2023-09-26T17:53:58Z

I'll wait to go over the SQLAlchemy syntax until you move it out of review.

jmchilton · 2023-09-26T18:02:20Z

I'll wait to go over the SQLAlchemy syntax until you move it out of review.

Such a chicken and egg thing here... they will be further divergent from the other code that you also wanted to update that brought you here. I'll collect your suggestion into a commit though! I appreciate the feedback. A fun winter break project becoming the whole project's chore is just such a John thing 😆 - looking at you planemo and pulsar.

jdavcs · 2023-09-26T18:06:45Z

I'll wait to go over the SQLAlchemy syntax until you move it out of review.

Such a chicken and egg thing here... they will be further divergent from the other code that you also wanted to update that brought you here. I'll collect your suggestion into a commit though! I appreciate the feedback. A fun winter break project becoming the whole project's chore is just such a John thing 😆 - looking at you planemo and pulsar.

LOL :) Only reason: I thought you were force-pushing stuff - I was afraid my suggestions would be immediately outdated. I'll go over it today.

jdavcs · 2023-09-26T21:41:06Z

It'll be easier to fix all syntax issues in a follow-up PR: too much of the same cut and paste, and my browser is literally stalling (I suspect it's the 23K-lines editable change set it's trying to display). It's all under lib/tool_shed and test/ - I won't touch those until this is merged (I suppose we'll be merging this soon).

jdavcs · 2023-09-26T18:03:01Z

lib/galaxy/app_unittest_utils/toolbox_support.py

+        self._repo_install(changeset="1")
+        version1 = tool_shed_install.ToolVersion()
+        version1.tool_id = "github.com/galaxyproject/example/test_tool/0.1"
+        self.app.install_model.context.add(version1)


I like session (or sa_sesssion). I think session is a slightly more accurate term for what the object is; even with the occasional presence of galaxy_session, I think context is more generic and may be harder to immediately recognize as the identifier for SQLAlchemy's session. But I'm +100 on documenting best practices (naming key objects like Session, as well as how to handle typical db access tasks, etc.)

jdavcs · 2023-09-26T21:10:59Z

lib/tool_shed/managers/repositories.py

+                app.model.Repository.table.c.deprecated == false(),
+                app.model.Repository.table.c.deleted == false(),
+                app.model.Repository.table.c.name == name,
+                app.model.User.table.c.username == owner,
+                app.model.Repository.table.c.user_id == app.model.User.table.c.id,


Same as above: app.model.Foo.table.c.bar >> app.model.Foo.bar

jdavcs · 2023-09-26T21:15:11Z

lib/tool_shed/managers/repositories.py

+                app.model.Repository.table.c.user_id == app.model.User.table.c.id,
+            )
+        ]
+        repository = app.model.context.current.sa_session.query(app.model.Repository).filter(*clause_list).first()


Suggested change

repository = app.model.context.current.sa_session.query(app.model.Repository).filter(*clause_list).first()

repository = app.model.context.current.sa_session.scalars(app.model.Repository).where(*clause_list).limit(1)).first()

jdavcs · 2023-09-26T21:15:50Z

lib/tool_shed/managers/repositories.py

+            app.model.Repository.table.c.deprecated == false(),
+            app.model.Repository.table.c.deleted == deleted,
+        )


same as above: drop table.c.

jdavcs · 2023-09-26T21:16:16Z

lib/tool_shed/managers/repositories.py

+                app.model.User.table.c.username == owner,
+                app.model.Repository.table.c.user_id == app.model.User.table.c.id,
+            )


same: table.c.

jdavcs · 2023-09-26T21:23:32Z

lib/tool_shed/metadata/repository_metadata_manager.py

+                repository = (
+                    self.sa_session.query(self.app.model.Repository)
+                    .filter(
+                        and_(
+                            self.app.model.Repository.table.c.name == name,
+                            self.app.model.Repository.table.c.user_id == user.id,
+                        )
+                    )
+                    .one()
+                )


Suggested change

repository = (

self.sa_session.query(self.app.model.Repository)

.filter(

and_(

self.app.model.Repository.table.c.name == name,

self.app.model.Repository.table.c.user_id == user.id,

)

)

.one()

)

repository = (

self.sa_session.execute(select(self.app.model.Repository)

.where(

and_(

self.app.model.Repository.name == name,

self.app.model.Repository.user_id == user.id,

)

)

).scalar_one()

)

formatting will be off here (my browser is barely handling this inline editing..)

jdavcs · 2023-09-26T21:30:51Z

lib/tool_shed/test/base/test_db_util.py

+        session.query(galaxy.model.tool_shed_install.ToolShedRepository)
+        .filter(
+            and_(
+                galaxy.model.tool_shed_install.ToolShedRepository.table.c.deleted == false(),
+                galaxy.model.tool_shed_install.ToolShedRepository.table.c.uninstalled == false(),
+                galaxy.model.tool_shed_install.ToolShedRepository.table.c.status
+                == galaxy.model.tool_shed_install.ToolShedRepository.installation_status.INSTALLED,
            )
-            .all()
        )
-    else:
-        return install_session().query(galaxy.model.tool_shed_install.ToolShedRepository).all()
+        .all()
+    )


stmt = select(ToolShedRepository).where(and_(ToolShedRepository.deleted == false(), ToolShedRepository.uninstalled == false(), ToolShedRepository.stats == ToolShedRepository.installation_status.INSTALLED) return session.scalars(stmt).all()

Also, no need to call list(): all() produces a list.

jdavcs · 2023-09-26T21:33:06Z

lib/tool_shed/test/base/test_db_util.py

+def get_installed_repository_by_name_owner(repository_name, owner, return_multiple=False, session=None):
+    if session is None:
+        session = install_session()
+    query = session.query(galaxy.model.tool_shed_install.ToolShedRepository).filter(


convert to select construct? Then, in the return clause, just session.scalars(stmt).all() for multiple and
session.scalars(stmt.limit(1)).first() for one (note the limit clause).

jdavcs · 2023-09-26T21:33:29Z

lib/tool_shed/test/base/test_db_util.py

+        session = install_session()
+    query = session.query(galaxy.model.tool_shed_install.ToolShedRepository).filter(
+        and_(
+            galaxy.model.tool_shed_install.ToolShedRepository.table.c.name == repository_name,


table.c. (same as above)

jdavcs · 2023-09-26T21:36:10Z

lib/tool_shed/test/base/twilltestcase.py

+    ) -> Optional[Dict[str, Any]]:
+        clause_list = []
+        if name is not None:
+            clause_list.append(galaxy_model.ToolShedRepository.table.c.name == name)


The test ToolShed https://testtoolshed.g2.bx.psu.edu/ has been updated after galaxyproject/galaxy#15639 was merged.

jmchilton added kind/feature area/toolshed labels Feb 23, 2023

jmchilton changed the title ~~Tool shed 2~~ Tool Shed 2.0 Feb 23, 2023

jmchilton force-pushed the tool_shed_2 branch from b69d768 to ad7b6b0 Compare February 23, 2023 16:58

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jmchilton mentioned this pull request May 12, 2023

Refactor models enums to eliminate schema dependency on model layer. #16080

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ElectronicBlueberry reviewed Sep 4, 2023

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jdavcs mentioned this pull request Sep 26, 2023

SQLAlchemy 2.0 upgrades (part 2) #16724

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jmchilton added 9 commits September 26, 2023 13:46

Cleanup method signature for uninstall_repository in twilltestcase.

d4dec27

metadata_generator: initial typing for metadata_generator, no functio…

42b0d30

…nal changes

metadata_generator: populate initial dict with helper (to split later)

338dfe9

metadata_generator: Spit into Base and Galaxy and ToolShed implementa…

f000b83

…tions... ... so we can get the typing right and not depend on app.name.

metadata_generator: simplify NOT_TOOL_CONFIG handling

3ba9888

metadata_generator: split constructors into Galaxy and tool shed vers…

f338fc7

…ions. Stronger typing and flatter functions

metadata_generator: split initial_metadata_dict into Galaxy and TS im…

cb8a7f4

…plementations.

metadata_generator: split set_repository into Galaxy and TS implement…

ea74b1f

…ations.

metadata_generator: Split handle_repo_elem implementations into gx an…

d22eb01

…d ts versions. Avoid all the big conditionals in the middle - again for stronger typing and flatter functions.

jmchilton added 7 commits September 26, 2023 13:46

Implement the GA4GH TRS API in the new tool shed.

dd58bfc

Category test stuff...

b5fb7c0

Category reworking..

c98fa8c

bismark populator improvement...

0d42ad7

Option config_hg_for_dev...

04e7563

DEBUG lint openapi CI

e2e0d44

jdavcs reviewed Sep 26, 2023

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jdavcs reviewed Sep 26, 2023

View reviewed changes

jmchilton added 4 commits September 27, 2023 14:30

WIP: modern tool shed frontend

7dc0b13

More typing?

990f3dc

Remove incorrect auto-generated readme for frontend.

bb45581

Fixes...

ec6d8fd

jmchilton force-pushed the tool_shed_2 branch from d3b434c to ec6d8fd Compare September 27, 2023 18:30

jmchilton marked this pull request as ready for review October 3, 2023 19:36

github-actions bot added this to the 23.2 milestone Oct 3, 2023

mvdbeek merged commit cc6f437 into galaxyproject:dev Oct 3, 2023
37 of 42 checks passed

nsoranzo added a commit to nsoranzo/bioblend that referenced this pull request Oct 18, 2023

Update tests for ToolShed 2.0

9fb9a48

The test ToolShed https://testtoolshed.g2.bx.psu.edu/ has been updated after galaxyproject/galaxy#15639 was merged.

nsoranzo added a commit to nsoranzo/bioblend that referenced this pull request Oct 18, 2023

Update tests for ToolShed 2.0

22fc538

The test ToolShed https://testtoolshed.g2.bx.psu.edu/ has been updated after galaxyproject/galaxy#15639 was merged.

nsoranzo added a commit to nsoranzo/bioblend that referenced this pull request Oct 18, 2023

Update tests for ToolShed 2.0

933b910

The test ToolShed https://testtoolshed.g2.bx.psu.edu/ has been updated after galaxyproject/galaxy#15639 was merged.

jdavcs mentioned this pull request Dec 18, 2023

RFC: Dependency conflict: fastapi-utils prevents upgrade to sqlachemy 2.0 #17185

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Tool Shed 2.0 #15639

Tool Shed 2.0 #15639

jmchilton commented Feb 23, 2023 •

edited

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	trans.sa_session.query(Category).filter(Category.table.c.deleted == deleted).order_by(Category.table.c.name)
	trans.sa_session.scalars(select(Category).where(Category.deleted == deleted).order_by(Category.name))

	repository = app.model.context.query(app.model.Repository).filter(*clause_list).first()
	repository = app.model.context.scalars(select(app.model.Repository).where(*clause_list).limit(1)).first()

	app.model.Repository.table.c.user_id == app.model.User.table.c.id,
	app.model.Repository.user_id == app.model.User.id,

	repository = app.model.context.current.sa_session.query(app.model.Repository).filter(*clause_list).first()
	repository = app.model.context.current.sa_session.scalars(app.model.Repository).where(*clause_list).limit(1)).first()

Tool Shed 2.0 #15639

Tool Shed 2.0 #15639

Conversation

jmchilton commented Feb 23, 2023 • edited Loading

Goals

Technology Choices

A Non-exhaustive List of Things I’ve Removed from the Frontend

Developing the Tool Shed

Backend Runtime

Frontend Runtime:

Production:

Frontend Linting:

How to test the changes?

License

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jdavcs commented Sep 26, 2023

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jmchilton commented Feb 23, 2023 •

edited

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