[Feature Branch] Analysis Discussion Section - Phase 1 (#161)

* [Frontend] Create a new discussion component to be displayed in an Analysis view (#139)

* Updating the paper to include the country for each affiliation which is required for publication.

* Updated the system tests workflow to use electron (#140)

* Added a DiscussionsSection.vue in AnalysisView components, updated the analysis model to return an injected discussion object, and updating the styling of the buttons to match figma more closely

* The discussion collapse works

* Looks ready for a pull request

* Tests should be working now

* Left out the node test

* Updating CSS in a few places

* Updating the DiscussionSection values

---------

Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>

* Created a discussions property in each of the analyses with several posts within them. Removed the temp fixture used in the frontend (#141)

* Fixed frontend unit test with AnalysisView

* fixed line too long

* Missed the updated json

* Changed formatting on the /etc/fixtures/analyses.json

* removed the etc/.certificate files

* Displaying discussion posts (#150)

* New Discussions post button, text field, and save/publish buttons

* Creating temporary discussion API mock api endpoints to test integrating them into the frontend

* Displaying posts from an analysis

* Hooked up the discussion post to the backend and return a mock discussions post. Added styling to the discussion posts

* Updated CSS to alternate discussion post colors

* Added more unit test coverage on the frontend and linted

* Added system tests and data-test attributes to go along with it

---------

Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>

* [Frontend] Clicking the "New Discussion" button opens a field below the header line divider to enter an opinion (#151)

* New Discussions post button, text field, and save/publish buttons

* Displaying posts from an analysis

* Added more unit test coverage on the frontend and linted

* Toggles New Discussion Field

* added system and unit tests for the discussion section

* forgot to add the system test

* Minor CSS fixes

* [Backend] Add a new route and repository to handle an incoming post and save it in Mongo (#153)

* Added a new collection to update a new post along with a test and linting

* Fixing python unit test

* Integration test and linting

* Updated the analysis_collection add_discussion_post function to use pymongo find_one_and_update function to simplify how posts are added to discussions in analyses

* linting

* New migration script to ensure both supporting_evidence_files and discussions keys are added to each analysis object in the analyses collection (#154)

* Updated phenotips importer to include supporting_evidence_files and discussions field. Updated the analyses fixture to include these fields as well (#155)

* Adding context menu to discussion posts (#156)

* added actions to the discussion post context menus

* Changed the backend user object to send back the clientId in the basic user object, this is used to check if the user made a post and present a context menu

* new ContextMenu.vue duplicates the DropDownMenu.vue functionality and turns it from hover to click. This is not quite right

* lots of changes: swapped dropdown and contextmenu icons, contextmenu will now open on click and close when unfocused or an action is taken on the menu. ContextMenu styling changes

* Fixed frontend test

* Lots of fixes, trying to figure out how to test this

* Frontend linting

* Removed a .only in front end test

* [Backend] Remove and edit post route and methods to update and delete a post from the discussion section (#157)

* Added a delete route and delete post analysis collection function

* Added a new route for editing a post and matching collection function, also added error checking for different situations in modifying discussion posts in an analysis

* Change responsibilities of routes and put helper function to find discussion post in analysis model

* proper error handling for discussion posts in progress

* Removed the discussion fixtures and properly gets the discussion posts from the analysis

* Finished integration and unit tests for updating and deleting a discussion post

* Formatting/linting

* Fixed integration test

* Added unit and integration tests for analysis model and routers

* Update backend/src/routers/analysis_discussion_router.py

Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>
Signed-off-by: James Scherer <james.m.scherer@gmail.com>

* Update backend/tests/integration/test_analysis_routers.py

Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>
Signed-off-by: James Scherer <james.m.scherer@gmail.com>

* linting

---------

Signed-off-by: James Scherer <james.m.scherer@gmail.com>
Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>

* [Frontend] The vertical '...' context menu functions to delete posts (#158)

* Frontend discussion post deletion working, complete with notification dialog

* Adding a system test for successfully deleting a new discussion post

* fixing frontend unit tests and adding an extra system test

* Linting

* Changed the delete action in the context menu to have an emit key and chain the emits down the section to be called in the view to delete a post

* Linting and changing var names

* Lots of frontend unit tests, but not yet finished

* Added more tests and linting

* Fixed issue with contextId being renamed

* Removed console log

* [Frontend] The vertical '...' context menu functions to edit posts (#160)

* Frontend discussion post deletion working, complete with notification dialog

* Adding a system test for successfully deleting a new discussion post

* fixing frontend unit tests and adding an extra system test

* Linting

* Changed the delete action in the context menu to have an emit key and chain the emits down the section to be called in the view to delete a post

* Linting and changing var names

* Lots of frontend unit tests, but not yet finished

* Added more tests and linting

* Fixed issue with contextId being renamed

* Removed console log

* Edit post emit chain working and backend is saving properly, it's just the discussion content is the same as what's posted

* Now editing a post works, it edits the post in place

* More styling for the post editing

* Frontend linting

* Frontend tests and linting

* Added system tests for post editing

* Update .github/workflows/system-tests.yml

Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>
Signed-off-by: James Scherer <james.m.scherer@gmail.com>

* Update backend/src/routers/analysis_router.py

Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>
Signed-off-by: James Scherer <james.m.scherer@gmail.com>

* skipping the a test in rosalution_analysis to match main, will come back later

---------

Signed-off-by: James Scherer <james.m.scherer@gmail.com>
Co-authored-by: Angelina Uno-Antonison <ange.unoantonison@gmail.com>

backend/src/core/phenotips_importer.py

@@ -42,6 +42,8 @@ def import_phenotips_json(self, phenotips_json_data):
 
  analysis_data = self.import_analysis_data(phenotips_json_data, phenotips_variants, phenotips_json_data["genes"])
 
+ analysis_data['discussions'] = []
+ analysis_data['supporting_evidence_files'] = []
  analysis_data['timeline'] = []
  return analysis_data
 

backend/src/models/analysis.py

@@ -80,6 +80,7 @@ class Analysis(BaseAnalysis):
 
  genomic_units: List[GenomicUnit] = []
  sections: List[Section] = []
+ discussions: List = []
  supporting_evidence_files: List = []
 
  def units_to_annotate(self):
@@ -105,3 +106,29 @@ def units_to_annotate(self):
  })
 
  return units
+
+ def find_discussion_post(self, discussion_post_id):
+ """
+ Finds a specific discussion post in an analysis by the discussion post id otherwise returns none
+ if no discussion with that post id in the analysis.
+ """
+ for discussion in self.discussions:
+ if discussion['post_id'] == discussion_post_id:
+ return discussion
+
+ return None
+
+ def find_authored_discussion_post(self, discussion_post_id, client_id):
+ """
+ Finds a discussion post from a user that authored the post in an analysis otherwise returns none if the post
+ was found, but the user did not author the post
+ """
+ discussion_post = self.find_discussion_post(discussion_post_id)
+
+ if discussion_post is None:
+ raise ValueError(f"Post '{discussion_post_id}' does not exist.")
+
+ if discussion_post['author_id'] == client_id:
+ return discussion_post
+
+ return None

backend/src/models/user.py

@@ -14,11 +14,11 @@ class User(BaseModel):
  full_name: Optional[str] = None
  disabled: Optional[bool] = None
  scope: Optional[str] = None
+ client_id: str
 
 
 class AccessUserAPI(User):
  """ This extends the user class to include the user's credentials for API access """
- client_id: str
  client_secret: Optional[str] = None
 
 

backend/src/repository/analysis_collection.py

@@ -486,3 +486,39 @@ def remove_section_supporting_evidence(self, analysis_name: str, section_name: s
  return_field = {"header": section_name, "field": field_name}
 
  return return_field
+
+ def add_discussion_post(self, analysis_name: str, discussion_post: object):
+ """ Appends a new discussion post to an analysis """
+
+ updated_document = self.collection.find_one_and_update({"name": analysis_name},
+ {"$push": {"discussions": discussion_post}},
+ return_document=ReturnDocument.AFTER)
+
+ updated_document.pop("_id", None)
+
+ return updated_document['discussions']
+
+ def updated_discussion_post(self, discussion_post_id: str, discussion_content: str, analysis_name: str):
+ """ Edits a discussion post from an analysis to update the discussion post's content """
+
+ updated_document = self.collection.find_one_and_update({"name": analysis_name}, {
+ "$set": {"discussions.$[item].content": discussion_content}
+ },
+ array_filters=[{"item.post_id": discussion_post_id}],
+ return_document=ReturnDocument.AFTER)
+
+ updated_document.pop("_id", None)
+
+ return updated_document['discussions']
+
+ def delete_discussion_post(self, discussion_post_id: str, analysis_name: str):
+ """ Removes a discussion post from an analysis """
+
+ updated_document = self.collection.find_one_and_update({"name": analysis_name}, {
+ "$pull": {"discussions": {"post_id": discussion_post_id}}
+ },
+ return_document=ReturnDocument.AFTER)
+
+ updated_document.pop("_id", None)
+
+ return updated_document['discussions']

backend/src/routers/analysis_discussion_router.py

@@ -0,0 +1,139 @@
+# pylint: disable=too-many-arguments
+# Due to adding scope checks, it's adding too many arguments (7/6) to functions, so diabling this for now.
+# Need to refactor later.
+""" Analysis endpoint routes that provide an interface to interact with an Analysis' discussions """
+from datetime import datetime, timezone
+import logging
+from uuid import uuid4
+
+from fastapi import (APIRouter, Depends, Form, Security, HTTPException, status)
+
+from ..dependencies import database
+from ..models.user import VerifyUser
+from ..models.analysis import Analysis
+from ..security.security import get_current_user
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(tags=["analysis"], dependencies=[Depends(database)])
+
+
+@router.get("/{analysis_name}/discussions")
+def get_analysis_discussions(analysis_name: str, repositories=Depends(database)):
+ """ Returns a list of discussion posts for a given analysis """
+ logger.info("Retrieving the analysis '%s' discussions ", analysis_name)
+
+ found_analysis = repositories['analysis'].find_by_name(analysis_name)
+
+ if not found_analysis:
+ raise HTTPException(
+ status_code=status.HTTP_404_NOT_FOUND, detail=f"Analysis '{analysis_name}' does not exist.'"
+ )
+
+ analysis = Analysis(**found_analysis)
+
+ return analysis.discussions
+
+
+@router.post("/{analysis_name}/discussions")
+def add_analysis_discussion(
+ analysis_name: str,
+ discussion_content: str = Form(...),
+ repositories=Depends(database),
+ client_id: VerifyUser = Security(get_current_user)
+):
+ """ Adds a new analysis topic """
+ logger.info("Adding the analysis '%s' from user '%s'", analysis_name, client_id)
+ logger.info("The message: %s", discussion_content)
+
+ found_analysis = repositories['analysis'].find_by_name(analysis_name)
+
+ if not found_analysis:
+ raise HTTPException(
+ status_code=status.HTTP_404_NOT_FOUND, detail=f"Analysis '{analysis_name}' does not exist.'"
+ )
+
+ analysis = Analysis(**found_analysis)
+ current_user = repositories["user"].find_by_client_id(client_id)
+
+ new_discussion_post = {
+ "post_id": str(uuid4()),
+ "author_id": client_id,
+ "author_fullname": current_user["full_name"],
+ "publish_timestamp": datetime.now(timezone.utc),
+ "content": discussion_content,
+ "attachments": [],
+ "thread": [],
+ }
+
+ return repositories['analysis'].add_discussion_post(analysis.name, new_discussion_post)
+
+
+@router.put("/{analysis_name}/discussions/{discussion_post_id}")
+def update_analysis_discussion_post(
+ analysis_name: str,
+ discussion_post_id: str,
+ discussion_content: str = Form(...),
+ repositories=Depends(database),
+ client_id: VerifyUser = Security(get_current_user)
+):
+ """ Updates a discussion post's content in an analysis by the discussion post id """
+ logger.info(
+ "Editing post '%s' by user '%s' from the analysis '%s' with new content: '%s'", discussion_post_id, client_id,
+ analysis_name, discussion_content
+ )
+
+ found_analysis = repositories['analysis'].find_by_name(analysis_name)
+
+ if not found_analysis:
+ raise HTTPException(
+ status_code=status.HTTP_404_NOT_FOUND,
+ detail=f"Analysis '{analysis_name}' does not exist. Unable to update discussion post.'"
+ )
+
+ analysis = Analysis(**found_analysis)
+
+ try:
+ valid_post = analysis.find_authored_discussion_post(discussion_post_id, client_id)
+ except ValueError as e:
+ raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail=str(e)) from e
+
+ if not valid_post:
+ raise HTTPException(
+ status_code=status.HTTP_401_UNAUTHORIZED, detail="User cannot update post they did not author."
+ )
+
+ return repositories['analysis'].updated_discussion_post(valid_post['post_id'], discussion_content, analysis.name)
+
+
+@router.delete("/{analysis_name}/discussions/{discussion_post_id}")
+def delete_analysis_discussion(
+ analysis_name: str,
+ discussion_post_id: str,
+ repositories=Depends(database),
+ client_id: VerifyUser = Security(get_current_user)
+):
+ """ Deletes a discussion post in an analysis by the discussion post id """
+ logger.info("Deleting post %s by user '%s' from the analysis '%s'", discussion_post_id, client_id, analysis_name)
+
+ found_analysis = repositories['analysis'].find_by_name(analysis_name)
+
+ if not found_analysis:
+ raise HTTPException(
+ status_code=status.HTTP_404_NOT_FOUND,
+ detail=f"Analysis '{analysis_name}' does not exist. Unable to delete discussion post.'"
+ )
+
+ analysis = Analysis(**found_analysis)
+
+ try:
+ valid_post = analysis.find_authored_discussion_post(discussion_post_id, client_id)
+ except ValueError as e:
+ raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail=str(e)) from e
+
+ if not valid_post:
+ raise HTTPException(
+ status_code=status.HTTP_401_UNAUTHORIZED, detail="User cannot delete post they did not author."
+ )
+
+ return repositories['analysis'].delete_discussion_post(valid_post['post_id'], analysis.name)

backend/src/routers/analysis_router.py

@@ -21,10 +21,12 @@
 from ..models.phenotips_json import BasePhenotips
 from ..models.user import VerifyUser
 from ..security.security import get_authorization, get_current_user
+from . import analysis_discussion_router
 
 logger = logging.getLogger(__name__)
 
 router = APIRouter(prefix="/analysis", tags=["analysis"], dependencies=[Depends(database)])
+router.include_router(analysis_discussion_router.router)
 
 
 @router.get("/", response_model=List[Analysis])

backend/tests/fixtures/analysis-CPAM0002.json

@@ -222,6 +222,7 @@
  ]
  }
  ],
+ "discussions":[],
  "supporting_evidence_files": [
  {
  "name": "test.txt", 

backend/tests/fixtures/empty-pedigree.json

@@ -216,6 +216,7 @@
  ]
  }
  ],
+ "discussions":[],
  "supporting_evidence_files": [
  {
  "name": "test.txt",

backend/tests/integration/conftest.py

@@ -74,7 +74,7 @@ def mock_current_user():
 @pytest.fixture(name="mock_user")
 def test_auth_user():
  """A mocked user that can be used to generate an OAuth2 access token"""
- return {"sub": "johndoe", "scopes": ["read", "write"]}
+ return {"sub": "johndoe-client-id", "scopes": ["read", "write"]}
 
 
 @pytest.fixture(name="mock_access_token")