WIP: modern tool shed frontend

.github/workflows/toolshed.yaml

@@ -20,14 +20,23 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
-        test-install-client: ['standalone', 'galaxy_api']
-        # v1 is mostly working...
-        shed-api: ['v1']
-        # lets get twill working with twill then try to
-        # make progress on the playwright
-        # shed-browser: ['twill', 'playwright']
-        shed-browser: ['playwright']
+        include:
+        - test-install-client: 'galaxy_api'
+          python-version: '3.7'
+          shed-api: 'v1'
+          shed-browser: 'twill'
+        - test-install-client: 'standalone'
+          python-version: '3.8'
+          shed-api: 'v1'
+          shed-browser: 'twill'
+        - test-install-client: 'galaxy_api'
+          python-version: '3.9'
+          shed-api: 'v2'
+          shed-browser: 'playwright'
+        - test-install-client: 'standalone'
+          python-version: '3.10'
+          shed-api: 'v2'
+          shed-browser: 'playwright'
     services:
       postgres:
         image: postgres:13

.vscode/shed.code-snippets

@@ -0,0 +1,41 @@
+{
+    "shedcomp": {
+        "prefix": "shed_component",
+        "body": [
+            "<script setup lang=\"ts\">",
+            "\t$0",
+            "</script>",
+            "<template>",
+            "</template>"
+        ],
+       "description": "outline of a tool shed component"
+    },
+    "shedpage": {
+        "prefix": "shed_page",
+        "body": [
+            "<script setup lang=\"ts\">",
+            "import PageContainer from \"@/components/PageContainer.vue\"",
+            "</script>",
+            "<template>",
+            "    <page-container>",
+            "        $0",
+            "    </page-container>",
+            "</template>"
+        ],
+       "description": "outline of a tool shed page"
+    },
+    "shedfetcher": {
+        "prefix": "shed_fetcher",
+        "body": [
+            "import { fetcher } from \"@/schema\"",
+            "const fetcher = fetcher.path(\"$1\").method(\"get\").create()"
+        ],
+        "description": "Import shed fetcher and instantiate with a path"
+    },
+    "shedrouter": {
+        "prefix": "shed_router",
+        "body": [
+            "import router from \"@/router\""
+        ]
+    }
+}

Makefile

@@ -190,6 +190,7 @@ remove-api-schema:
 
 update-client-api-schema: client-node-deps build-api-schema
 	$(IN_VENV) cd client && node openapi_to_schema.mjs ../_schema.yaml > src/schema/schema.ts && npx prettier --write src/schema/schema.ts
+	$(IN_VENV) cd client && node openapi_to_schema.mjs ../_shed_schema.yaml > ../lib/tool_shed/webapp/frontend/src/schema/schema.ts && npx prettier --write ../lib/tool_shed/webapp/frontend/src/schema/schema.ts
 	$(MAKE) remove-api-schema
 
 lint-api-schema: build-api-schema

lib/galaxy/dependencies/pinned-requirements.txt

@@ -73,6 +73,7 @@ fsspec==2023.1.0 ; python_version >= "3.7" and python_version < "3.12"
 future==0.18.3 ; python_version >= "3.7" and python_version < "3.12"
 galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.12"
 galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.12"
+graphene-sqlalchemy==3.0.0b3 ; python_version >= "3.7" and python_version < "3.12"
 gravity==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
 greenlet==2.0.2 ; python_version >= "3.7" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version < "3.12"
 gunicorn==21.2.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -179,6 +180,7 @@ sqlalchemy==1.4.49 ; python_version >= "3.7" and python_version < "3.12"
 sqlitedict==2.1.0 ; python_version >= "3.7" and python_version < "3.12"
 sqlparse==0.4.4 ; python_version >= "3.7" and python_version < "3.12"
 starlette-context==0.3.5 ; python_version >= "3.7" and python_version < "3.12"
+starlette_graphene3==0.6.0 ; python_version >= "3.7" and python_version < "3.12"
 starlette==0.27.0 ; python_version >= "3.7" and python_version < "3.12"
 supervisor==4.2.5 ; python_version >= "3.7" and python_version < "3.12"
 svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/managers/api_keys.py

@@ -3,19 +3,24 @@
     TYPE_CHECKING,
 )
 
-from galaxy.model import User
+from typing_extensions import Protocol
+
 from galaxy.model.base import transaction
 from galaxy.structured_app import BasicSharedApp
 
 if TYPE_CHECKING:
     from galaxy.model import APIKeys
 
 
+class IsUserModel(Protocol):
+    id: str
+
+
 class ApiKeyManager:
     def __init__(self, app: BasicSharedApp):
         self.app = app
 
-    def get_api_key(self, user: User) -> Optional["APIKeys"]:
+    def get_api_key(self, user: IsUserModel) -> Optional["APIKeys"]:
         sa_session = self.app.model.context
         api_key = (
             sa_session.query(self.app.model.APIKeys)
@@ -25,7 +30,7 @@ def get_api_key(self, user: User) -> Optional["APIKeys"]:
         )
         return api_key
 
-    def create_api_key(self, user: User) -> "APIKeys":
+    def create_api_key(self, user: IsUserModel) -> "APIKeys":
         guid = self.app.security.get_new_guid()
         new_key = self.app.model.APIKeys()
         new_key.user_id = user.id
@@ -36,15 +41,15 @@ def create_api_key(self, user: User) -> "APIKeys":
             sa_session.commit()
         return new_key
 
-    def get_or_create_api_key(self, user: User) -> str:
+    def get_or_create_api_key(self, user: IsUserModel) -> str:
         # Logic Galaxy has always used - but it would appear to have a race
         # condition. Worth fixing? Would kind of need a message queue to fix
         # in multiple process mode.
         api_key = self.get_api_key(user)
         key = api_key.key if api_key else self.create_api_key(user).key
         return key
 
-    def delete_api_key(self, user: User) -> None:
+    def delete_api_key(self, user: IsUserModel) -> None:
         """Marks the current user API key as deleted."""
         sa_session = self.app.model.context
         # Before it was possible to create multiple API keys for the same user although they were not considered valid

lib/galaxy/managers/users.py

@@ -451,7 +451,9 @@ def change_password(self, trans, password=None, confirm=None, token=None, id=Non
             trans.sa_session.add(token_result)
             return user, "Password has been changed. Token has been invalidated."
         else:
-            user = self.by_id(self.app.security.decode_id(id))
+            if not isinstance(id, int):
+                id = self.app.security.decode_id(id)
+            user = self.by_id(id)
             if user:
                 message = self.app.auth_manager.check_change_password(user, current, trans.request)
                 if message:

lib/galaxy/webapps/base/webapp.py

@@ -735,21 +735,9 @@ def __create_new_session(self, prev_galaxy_session=None, user_for_new_session=No
 
         Caller is responsible for flushing the returned session.
         """
-        session_key = self.security.get_new_guid()
-        galaxy_session = self.app.model.GalaxySession(
-            session_key=session_key,
-            is_valid=True,
-            remote_host=self.request.remote_host,
-            remote_addr=self.request.remote_addr,
-            referer=self.request.headers.get("Referer", None),
+        return create_new_session(
+            self, prev_galaxy_session=prev_galaxy_session, user_for_new_session=user_for_new_session
         )
-        if prev_galaxy_session:
-            # Invalidated an existing session for some reason, keep track
-            galaxy_session.prev_session_id = prev_galaxy_session.id
-        if user_for_new_session:
-            # The new session should be associated with the user
-            galaxy_session.user = user_for_new_session
-        return galaxy_session
 
     @property
     def cookie_path(self):
@@ -1106,6 +1094,31 @@ def qualified_url_for_path(self, path):
         return url_for(path, qualified=True)
 
 
+def create_new_session(trans, prev_galaxy_session=None, user_for_new_session=None):
+    """
+    Create a new GalaxySession for this request, possibly with a connection
+    to a previous session (in `prev_galaxy_session`) and an existing user
+    (in `user_for_new_session`).
+
+    Caller is responsible for flushing the returned session.
+    """
+    session_key = trans.security.get_new_guid()
+    galaxy_session = trans.app.model.GalaxySession(
+        session_key=session_key,
+        is_valid=True,
+        remote_host=trans.request.remote_host,
+        remote_addr=trans.request.remote_addr,
+        referer=trans.request.headers.get("Referer", None),
+    )
+    if prev_galaxy_session:
+        # Invalidated an existing session for some reason, keep track
+        galaxy_session.prev_session_id = prev_galaxy_session.id
+    if user_for_new_session:
+        # The new session should be associated with the user
+        galaxy_session.user = user_for_new_session
+    return galaxy_session
+
+
 def default_url_path(path):
     return os.path.abspath(os.path.join(os.path.dirname(__file__), path))
 

lib/galaxy/webapps/galaxy/api/__init__.py

@@ -47,6 +47,7 @@
     NoMatchFound,
 )
 from starlette.types import Scope
+from typing_extensions import Literal
 
 try:
     from starlette_context import context as request_context
@@ -200,6 +201,8 @@ class GalaxyASGIRequest(GalaxyAbstractRequest):
     Implements the GalaxyAbstractRequest interface to provide access to some properties
     of the request commonly used."""
 
+    __request: Request
+
     def __init__(self, request: Request):
         self.__request = request
         self.__environ: Optional[MutableMapping[str, Any]] = None
@@ -232,6 +235,28 @@ def environ(self) -> MutableMapping[str, Any]:
             self.__environ = build_environ(self.__request.scope, None)  # type: ignore[arg-type]
         return self.__environ
 
+    @property
+    def headers(self):
+        return self.__request.headers
+
+    @property
+    def remote_host(self) -> str:
+        # was available in wsgi and is used create_new_session
+        return self.host
+
+    @property
+    def remote_addr(self) -> Optional[str]:
+        # was available in wsgi and is used create_new_session
+        # not sure what to do here...
+        return None
+
+    @property
+    def is_secure(self) -> bool:
+        return self.__request.url.scheme == "https"
+
+    def get_cookie(self, name):
+        return self.__request.cookies.get(name)
+
 
 class GalaxyASGIResponse(GalaxyAbstractResponse):
     """Wrapper around Starlette/FastAPI Response object.
@@ -246,6 +271,31 @@ def __init__(self, response: Response):
     def headers(self):
         return self.__response.headers
 
+    def set_cookie(
+        self,
+        key: str,
+        value: str = "",
+        max_age: Optional[int] = None,
+        expires: Optional[int] = None,
+        path: str = "/",
+        domain: Optional[str] = None,
+        secure: bool = False,
+        httponly: bool = False,
+        samesite: Optional[Literal["lax", "strict", "none"]] = "lax",
+    ) -> None:
+        """Set a cookie."""
+        self.__response.set_cookie(
+            key,
+            value,
+            max_age=max_age,
+            expires=expires,
+            path=path,
+            domain=domain,
+            secure=secure,
+            httponly=httponly,
+            samesite=samesite,
+        )
+
 
 DependsOnUser = cast(Optional[User], Depends(get_user))
 

lib/galaxy/webapps/galaxy/controllers/user.py

@@ -188,7 +188,7 @@ def __validate_login(self, trans, payload=None, **kwd):
                 message, status = self.resend_activation_email(trans, user.email, user.username)
                 return self.message_exception(trans, message, sanitize=False)
         else:  # activation is OFF
-            pw_expires = trans.app.config.password_expiration_period
+            pw_expires = getattr(trans.app.config, "password_expiration_period", None)
             if pw_expires and user.last_password_change < datetime.today() - pw_expires:
                 # Password is expired, we don't log them in.
                 return {

lib/galaxy/work/context.py

@@ -4,6 +4,8 @@
     Optional,
 )
 
+from typing_extensions import Literal
+
 from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.model import (
     GalaxySession,
@@ -85,6 +87,14 @@ def base(self) -> str:
     def host(self) -> str:
         """The host address."""
 
+    @abc.abstractproperty
+    def is_secure(self) -> bool:
+        """Was this a secure (https) request."""
+
+    @abc.abstractmethod
+    def get_cookie(self, name):
+        """Return cookie."""
+
 
 class GalaxyAbstractResponse:
     """Abstract interface to provide access to some response utilities."""
@@ -102,6 +112,21 @@ def set_content_type(self, content_type: str):
     def get_content_type(self):
         return self.headers.get("content-type", None)
 
+    @abc.abstractmethod
+    def set_cookie(
+        self,
+        key: str,
+        value: str = "",
+        max_age: Optional[int] = None,
+        expires: Optional[int] = None,
+        path: str = "/",
+        domain: Optional[str] = None,
+        secure: bool = False,
+        httponly: bool = False,
+        samesite: Optional[Literal["lax", "strict", "none"]] = "lax",
+    ) -> None:
+        """Set a cookie."""
+
 
 class SessionRequestContext(WorkRequestContext):
     """Like WorkRequestContext, but provides access to request."""