Composition API Migration for moving towards real-time collaboration (#…

…186)

* First steps of work in progress to migrate towards using the composition API and applying a store to manage the view.

* work in progress for revising tests for composition API and first pass for composition api with an analysisStore and view

* Fixed issues discovered during system testing with the first pass of the store migration

* first draft of testing done; cut time down in half but its still taking too long at around 300 something ms

* Finished cleaning up unit tests for the migrated toast code, and updated VueJS' version to be able to use useTempalteRef

* Renaming the RosalutionToast to ToastDialog to correspond with the other dialog components

* Secured the specific endpoints by requiring an authenticated user to access them

* Updated system test to force click in the situation the menu visibility isn't opened correctly by the test

* Fixed the 'AS' characters for the dockerfiles and fixing the accidental change as an option

* Fixed issue Rabab found in review; where the store was not switching to representing a different analysis when loading a different analysis.

backend/Dockerfile

@@ -1,13 +1,13 @@
 # Local Development Stage
-FROM python:3.11-slim-bookworm as development-stage
+FROM python:3.11-slim-bookworm AS development-stage
 WORKDIR /app
 COPY requirements.txt /app/requirements.txt
 RUN pip install --no-cache-dir --upgrade -r /app/requirements.txt
 COPY ./src /app/src
 ENTRYPOINT ["/bin/sh", "-c", "uvicorn src.main:app --host 0.0.0.0 --port 8000 --log-level info --reload"]
 
 # Production Build Stage
-FROM python:3.11-slim-bookworm as production-stage
+FROM python:3.11-slim-bookworm AS production-stage
 WORKDIR /app
 COPY logging.conf /app/logging.conf
 COPY requirements.txt /app/requirements.txt

backend/src/routers/analysis_discussion_router.py

@@ -13,7 +13,11 @@
 
 
 @router.get("/{analysis_name}/discussions")
-def get_analysis_discussions(analysis_name: str, repositories=Depends(database)):
+def get_analysis_discussions(
+    analysis_name: str,
+    repositories=Depends(database),
+    username: VerifyUser = Security(get_current_user)  #pylint: disable=unused-argument
+):
     """ Returns a list of discussion posts for a given analysis """
 
     found_analysis = repositories['analysis'].find_by_name(analysis_name)

backend/src/routers/analysis_router.py

@@ -29,7 +29,7 @@
 
 
 @router.get("", tags=["analysis"], response_model=List[Analysis])
-def get_all_analyses(repositories=Depends(database)):
+def get_all_analyses(repositories=Depends(database), username: VerifyUser = Security(get_current_user)):  #pylint: disable=unused-argument
     """Returns every analysis available"""
     return repositories["analysis"].all()
 
@@ -76,7 +76,11 @@ async def create_file(
 
 
 @router.get("/{analysis_name}", tags=["analysis"], response_model=Analysis, response_model_exclude_none=True)
-def get_analysis_by_name(analysis_name: str, repositories=Depends(database)):
+def get_analysis_by_name(
+    analysis_name: str,
+    repositories=Depends(database),
+    username: VerifyUser = Security(get_current_user)  #pylint: disable=unused-argument
+):
     """Returns analysis case data by calling method to find case by it's analysis_name"""
     analysis = repositories["analysis"].find_by_name(analysis_name)
 
@@ -116,15 +120,24 @@ def update_event(
         raise HTTPException(status_code=409, detail=str(exception)) from exception
 
 
-@router.get("/download/{file_id}")
-def download_file_by_id(file_id: str, repositories=Depends(database)):
+@router.get("/download/{file_id}", tags=["analysis"])
+def download_file_by_id(
+    file_id: str,
+    repositories=Depends(database),
+    username: VerifyUser = Security(get_current_user)  #pylint: disable=unused-argument
+):
     """ Returns a file from GridFS using the file's id """
     grid_fs_file = repositories['bucket'].stream_analysis_file_by_id(file_id)
     return StreamingResponse(grid_fs_file, media_type=grid_fs_file.content_type)
 
 
-@router.get("/{analysis_name}/download/{file_name}")
-def download(analysis_name: str, file_name: str, repositories=Depends(database)):
+@router.get("/{analysis_name}/download/{file_name}", tags=["analysis"])
+def download(
+    analysis_name: str,
+    file_name: str,
+    repositories=Depends(database),
+    username: VerifyUser = Security(get_current_user)  #pylint: disable=unused-argument
+):
     """ Returns a file saved to an analysis from GridFS by file name """
     # Does file exist by name in the given analysis?
     file = repositories['analysis'].find_file_by_name(analysis_name, file_name)
@@ -135,7 +148,7 @@ def download(analysis_name: str, file_name: str, repositories=Depends(database))
     return StreamingResponse(repositories['bucket'].stream_analysis_file_by_id(file['attachment_id']))
 
 
-@router.put("/{analysis_name}/attach/{third_party_enum}")
+@router.put("/{analysis_name}/attach/{third_party_enum}", tags=["analysis"])
 def attach_third_party_link(
     analysis_name: str,
     third_party_enum: ThirdPartyLinkType,

backend/src/routers/annotation_router.py

@@ -31,6 +31,7 @@ def annotate_analysis(
     background_tasks: BackgroundTasks,
     repositories=Depends(database),
     annotation_task_queue=Depends(annotation_queue),
+    authorized=Security(get_authorization, scopes=["write"])  #pylint: disable=unused-argument
 ):
     """
     Placeholder to initiate annotations for an analysis. This queueing/running

docker-compose.yml

@@ -1,5 +1,3 @@
-version: '3.5'
-
 services:
   reverse-proxy:
     image: traefik

frontend/Dockerfile

@@ -1,5 +1,5 @@
 # Local development stage
-FROM node:20.8-alpine3.18 as development-stage
+FROM node:20.8-alpine3.18 AS development-stage
 WORKDIR /app
 COPY package.json /app/
 COPY yarn.lock /app/
@@ -10,7 +10,7 @@ EXPOSE 3000
 ENTRYPOINT ["yarn", "dev:host"]
 
 # Production Build stage
-FROM node:20.8-alpine3.18 as production-build
+FROM node:20.8-alpine3.18 AS production-build
 WORKDIR /app
 COPY ./src /app/src/
 COPY package.json /app/
@@ -23,7 +23,7 @@ ENV VITE_ROSALUTION_VERSION=$VERSION_BUILD_TAG
 
 RUN yarn install --frozen-lockfile && yarn build --base=/rosalution/
 
-FROM nginx:1.25.2-alpine3.18 as production-stage
+FROM nginx:1.25.2-alpine3.18 AS production-stage
 
 COPY etc/default.conf /etc/nginx/conf.d/
 COPY --from=production-build /app/dist/ /usr/share/nginx/html/

frontend/package.json

@@ -21,7 +21,7 @@
     "@fortawesome/free-solid-svg-icons": "6.4.2",
     "@fortawesome/vue-fontawesome": "3.0.3",
     "@rollup/plugin-strip": "3.0.4",
-    "vue": "3.3.4",
+    "vue": "3.5.12",
     "vue-router": "4.2.5"
   },
   "devDependencies": {

frontend/src/components/AnalysisView/useActionMenu.js

@@ -0,0 +1,38 @@
+import {ref} from 'vue';
+import {StatusType, getWorkflowStatusIcon} from '@/config.js';
+
+
+/**
+ * Builds an actionMenu that can be used for the main header
+ * @return {Object} {actionChoices, builder} to return the actions to render and the builder to update the choices
+ */
+export function useActionMenu() {
+  const actionChoices = ref([]);
+
+  const builder = {
+    addWorkflowActions: (latest, operation) => {
+      if ( latest in StatusType ) {
+        for ( const [text, nextEvent, nextStatus] of StatusType[latest].transitions) {
+          builder.addMenuAction(text, getWorkflowStatusIcon(nextStatus), () => {
+            operation(nextEvent);
+          });
+        }
+      }
+    },
+    addMenuAction: (text, icon, operation) => {
+      actionChoices.value.push({
+        icon: icon,
+        text: text,
+        operation: operation,
+      });
+    },
+    addDivider: () => {
+      actionChoices.value.push({divider: true});
+    },
+    clear: () => {
+      actionChoices.value = [];
+    },
+  };
+
+  return {actionChoices, builder};
+}