feat: findings

epiviz-ws_api/app/db.py

@@ -19,13 +19,31 @@
     sqlalchemy.Column('workspace_uuid', sqlalchemy.String, unique=True, index=True)
 )
 
+findings = sqlalchemy.Table(
+    'findings',
+    metadata,
+    sqlalchemy.Column('id', sqlalchemy.Integer, primary_key=True, index=True),
+    sqlalchemy.Column('user_id', sqlalchemy.String, index=True),
+    sqlalchemy.Column('title', sqlalchemy.String, index=True),
+    sqlalchemy.Column('description', sqlalchemy.String, index=True),
+    sqlalchemy.Column('gene', sqlalchemy.ARRAY(sqlalchemy.String), nullable=True, index=True),
+    sqlalchemy.Column('genes_in_view', sqlalchemy.ARRAY(sqlalchemy.String), nullable=True),
+    sqlalchemy.Column('chart_markers', sqlalchemy.ARRAY(sqlalchemy.String), nullable=True),
+    sqlalchemy.Column('datasets', sqlalchemy.ARRAY(sqlalchemy.String), nullable=True),
+    sqlalchemy.Column('chr', sqlalchemy.String, index=True),
+    sqlalchemy.Column('start', sqlalchemy.Integer, index=True),
+    sqlalchemy.Column('end', sqlalchemy.Integer, index=True),
+    sqlalchemy.Column('workspace_id', sqlalchemy.Integer, index=True),
+    sqlalchemy.Column('workspace_uuid', sqlalchemy.String, index=True)
+)
+
 # sqlalchemy.Column('workspace_uuid', sqlalchemy.String)
 
 engine = sqlalchemy.create_engine(DATABASE_URI)
 metadata.create_all(engine)
 
 # https://alembic.sqlalchemy.org/en/latest/cookbook.html#building-an-up-to-date-database-from-scratch
-from alembic.config import Config
-from alembic import command
-alembic_cfg = Config("alembic.ini")
-command.stamp(alembic_cfg, "head")
+# from alembic.config import Config
+# from alembic import command
+# alembic_cfg = Config("alembic.ini")
+# command.stamp(alembic_cfg, "head")

epiviz-ws_api/app/db_manager.py

@@ -1,7 +1,8 @@
-from app.db import database, workspaces
+from app.db import database, workspaces, findings
 from app import models
 from uuid import uuid4
 
+# Workspaces
 async def get_all_workspaces():
     query = workspaces.select()
     return await database.fetch_all(query)
@@ -43,4 +44,42 @@ async def update_workspace(id: int, ws: models.WorkspaceUpdate):
             .where(workspaces.c.id == id)
             .values(**ws.dict())
     )
-    return await database.execute(query=query)
+    return await database.execute(query=query)
+
+async def get_workspace_findings(id:int):
+    query = findings.select(findings.c.workspace_id == id)
+    res =  await database.fetch_all(query)
+    print(res)
+    return res
+
+# Findings
+async def get_all_findings():
+    query = findings.select()
+    return await database.fetch_all(query)
+
+async def get_user_findings(user_id: str):
+    query = findings.select(findings.c.user_id == user_id)
+    return await database.fetch_all(query)
+
+async def get_finding(id: int):
+    query = findings.select(findings.c.id == id)
+    return await database.fetch_one(query)
+
+async def add_finding(fd: models.FindingCreate):
+    tfd = fd.dict()
+    query = findings.insert().values(tfd)
+    return await database.execute(query)
+
+async def delete_finding(id: int):
+    query = findings.delete().where(findings.c.id == id)
+    return await database.execute(query)
+
+async def update_finding(id: int, fd: models.FindingUpdate):
+    query = (
+        findings
+            .update()
+            .where(findings.c.id == id)
+            .values(**fd.dict())
+    )
+    return await database.execute(query=query)
+

epiviz-ws_api/app/findings.py

@@ -0,0 +1,59 @@
+from typing import List, Optional
+from datetime import datetime
+from fastapi import Header, APIRouter, Depends, HTTPException
+
+from app import models
+from app import db_manager
+from app.auth import get_user_from_header
+
+findings = APIRouter()
+
+@findings.get('/', response_model=List[models.Finding])
+async def index():
+    return await db_manager.get_all_findings()
+
+@findings.get('/user/{user_id}', response_model=List[models.Finding])
+async def get_user_findings(user_id: str, user: models.User = Depends(get_user_from_header)):
+    if user_id == user.username:
+        return await db_manager.get_user_findings(user_id)
+    else: 
+        raise HTTPException(status_code=404, detail="UnixID does not match token")
+
+@findings.get('/{id}', response_model=models.Finding)
+async def get_finding(id: int):
+    return await db_manager.get_finding(id)
+
+@findings.post('/', response_model=models.Finding)
+async def add_finding(payload: models.FindingCreate):
+    id = await db_manager.add_finding(payload)
+    response = {
+        'id': id,
+        **payload.dict()
+    }
+
+    return response
+
+@findings.put('/{id}')
+async def update_finding(id: int, payload: models.FindingUpdate, user: models.User = Depends(get_user_from_header)):
+    fd = await db_manager.get_finding(id)
+    if not fd:
+        raise HTTPException(status_code=404, detail="Finding not found")
+
+    if fd.get("user_id") == user.username or "admin" in user.roles:
+        update_data = payload.dict(exclude_unset=True)
+        fd_in_db = models.findingUpdate(**fd)
+        updated_fd = fd_in_db.copy(update=update_data)
+        return await db_manager.update_finding(id, updated_fd)    
+    else:
+        raise HTTPException(status_code=404, detail="UnixID does not match token")
+
+@findings.delete('/{id}')
+async def delete_finding(id: int, user: models.User = Depends(get_user_from_header)):
+    fd = await db_manager.get_finding(id)
+    if not fd:
+        raise HTTPException(status_code=404, detail="finding not found")
+
+    if fd.get("user_id") == user.username:
+        return await db_manager.delete_finding(id)
+    else:
+        raise HTTPException(status_code=404, detail="UnixID does not match token")

epiviz-ws_api/app/main.py

@@ -3,6 +3,7 @@
 from fastapi import FastAPI, Depends
 from app.db import database
 from app.workspaces import workspaces
+from app.findings import findings
 from fastapi.middleware.cors import CORSMiddleware
 import os
 
@@ -30,5 +31,6 @@ async def shutdown():
     await database.disconnect()
 
 app.include_router(workspaces, prefix='/api/v1', tags=['workspaces'])
+app.include_router(findings, prefix='/api/v1/findings', tags=['findings'])
 
 

epiviz-ws_api/app/models.py

@@ -28,4 +28,28 @@ class User(BaseModel):
     username: str
     email: Optional[str] = None
     full_name: Optional[str] = None
-    roles: Optional[List[str]] = None
+    roles: Optional[List[str]] = None
+
+class FindingBase(BaseModel):
+    user_id: str
+    title: str
+    description: str
+    gene: Optional[List[str]]
+    genes_in_view: Optional[List[str]]
+    chart_markers: Optional[List[str]]
+    datasets: Optional[List[str]]
+    chr: str
+    start: int
+    end: int
+    workspace_id: int
+    workspace_uuid: str
+
+class FindingCreate(FindingBase):
+    pass
+
+class Finding(FindingBase):
+    id: int
+
+class FindingUpdate(FindingBase):
+    title: Optional[str] = None
+    description: Optional[str] = None

epiviz-ws_api/app/workspaces.py

@@ -23,6 +23,10 @@ async def get_user_workspaces(user_id: str, user: models.User = Depends(get_user
 async def get_workspace(id: int):
     return await db_manager.get_workspace(id)
 
+@workspaces.get('/{id}/findings', response_model=List[models.Finding])
+async def get_workspace_findings(id: int):
+    return await db_manager.get_workspace_findings(id)
+
 @workspaces.get('/uuid/{uuid}', response_model=models.Workspace)
 async def get_workspace_uuid(uuid: str):
     return await db_manager.get_workspace_uuid(uuid)