Merge pull request #114 from ssi-dk/feat/use-csv-in-workspace-data

feat: use csv in workspace data

web/requirements.txt

@@ -24,4 +24,5 @@ openapi-spec-validator==0.2.9
 pydantic==2.8.2
 hkdf
 python-keycloak
-flask-cors
+flask-cors
+flask

web/src/SAP/src/controllers/WorkspacesController.py

@@ -50,4 +50,4 @@ def get_workspace_data(user, token_info, workspace_id):
     if res is None:
         return abort(404)
 
-    return jsonify(res["values"])
+    return res

web/src/SAP/src/repositories/workspaces.py

@@ -1,36 +1,46 @@
 from typing import Any, Dict, List, TypedDict, Union
-
 from bson.objectid import ObjectId
-
 from ...src.security.permission_check import authorized_columns
-
 from ...generated.models.update_workspace import UpdateWorkspace
-from ...src.repositories.analysis import get_analysis_with_metadata, get_single_analysis_by_object_id
+from ...src.repositories.analysis import (
+    get_analysis_with_metadata,
+    get_single_analysis_by_object_id,
+)
 from ...common.database import get_collection, WORKSPACES_COL_NAME
 from ...generated.models import CreateWorkspace
 from ...generated.models import CloneWorkspace
+import io
+from flask import send_file
+
 
 def trim(item):
     item["id"] = str(item["_id"])
     item.pop("_id", None)
     item.pop("username", None)
     return item
 
+
 def get_sequence(sample_id: str):
     single = get_single_analysis_by_object_id(sample_id)
     sequence = get_analysis_with_metadata(single["sequence_id"])
     return sequence
 
+
 def get_workspaces(user: str):
     workspaces = get_collection(WORKSPACES_COL_NAME)
     return list(map(trim, workspaces.find({"created_by": user})))
 
+
 def get_workspace(user: str, workspace_id: str):
     workspaces = get_collection(WORKSPACES_COL_NAME)
     if ObjectId.is_valid(workspace_id):
-        workspace = trim(workspaces.find_one({"created_by": user, "_id": ObjectId(workspace_id)}))
+        workspace = trim(
+            workspaces.find_one({"created_by": user, "_id": ObjectId(workspace_id)})
+        )
     else:
-        workspace = trim(workspaces.find_one({"created_by": user, "name": workspace_id}))
+        workspace = trim(
+            workspaces.find_one({"created_by": user, "name": workspace_id})
+        )
 
     if workspace is None:
         return workspace
@@ -42,42 +52,40 @@ def get_workspace(user: str, workspace_id: str):
 
     return workspace
 
-WorkspaceData = TypedDict('WorkspaceData', {'keys': List[str], 'values': List[List[Any]]})
 
-def get_workspace_data(user: str, token_info: Dict[str, str], workspace_id: str) -> Union[WorkspaceData,None]:
+def get_workspace_data(user: str, token_info: Dict[str, str], workspace_id: str):
     workspace = get_workspace(user, workspace_id)
 
     if workspace is None:
-        return workspace
+        return None
 
     authorized = authorized_columns(token_info)
 
-    values = []
+    if len(authorized) == 0:
+        return None
+
+    csv = ",".join(f'"{column}"' for column in authorized)
     for sample in workspace["samples"]:
-        row = []
-        for column in authorized:
-            if column in sample:
-                row.append(sample[column])
-            else:
-                row.append("")
-        values.append(row)
-
-    return {
-        "keys": authorized, 
-        "values": values
-    }
+        csv += "\n" + ",".join(
+            f'"{sample[column]}"' if sample[column] else ""
+            for column in authorized
+            if column in sample
+        )
+
+    file = io.BytesIO(bytes(csv, "utf-8"))
+    return send_file(file, download_name="proj.csv", mimetype="text/csv")
+
 
 def delete_workspace(user: str, workspace_id: str):
     workspaces = get_collection(WORKSPACES_COL_NAME)
 
-    return workspaces.delete_one(
-        {"_id": ObjectId(workspace_id), "created_by": user}
-    )
+    return workspaces.delete_one({"_id": ObjectId(workspace_id), "created_by": user})
+
 
 def delete_workspace_sample(user: str, workspace_id: str, sample_id: str):
     workspaces = get_collection(WORKSPACES_COL_NAME)
 
-    update_filter = {'created_by': user, '_id': ObjectId(workspace_id)}
+    update_filter = {"created_by": user, "_id": ObjectId(workspace_id)}
     update = {"$pull": {"samples": sample_id}}
     return workspaces.update_one(update_filter, update, upsert=True)
 
@@ -87,36 +95,53 @@ def create_workspace(user: str, workspace: CreateWorkspace):
 
     if workspace.samples is None:
         workspace.samples = []
-    
+
     record = {**workspace.to_dict(), "created_by": user}
-    return workspaces.update_one({'created_by': user, 'name': workspace.name}, {"$set": record}, upsert=True)
+    return workspaces.update_one(
+        {"created_by": user, "name": workspace.name}, {"$set": record}, upsert=True
+    )
+
 
 def clone_workspace(user: str, cloneWorkspaceInfo: CloneWorkspace):
     workspaces = get_collection(WORKSPACES_COL_NAME)
 
     if ObjectId.is_valid(cloneWorkspaceInfo.id):
-        workspace = trim(workspaces.find_one({"created_by": user, "_id": ObjectId(cloneWorkspaceInfo.id)}))
+        workspace = trim(
+            workspaces.find_one(
+                {"created_by": user, "_id": ObjectId(cloneWorkspaceInfo.id)}
+            )
+        )
     else:
-        workspace = trim(workspaces.find_one({"created_by": user, "name": cloneWorkspaceInfo.id}))
+        workspace = trim(
+            workspaces.find_one({"created_by": user, "name": cloneWorkspaceInfo.id})
+        )
 
     if workspace is None:
         return None
 
-    if workspace["samples"] is None:    
+    if workspace["samples"] is None:
         workspace["samples"] = []
 
-    return workspaces.insert_one({'created_by': user, 'name': cloneWorkspaceInfo.name, 'samples': workspace["samples"]})
+    return workspaces.insert_one(
+        {
+            "created_by": user,
+            "name": cloneWorkspaceInfo.name,
+            "samples": workspace["samples"],
+        }
+    )
+
 
 def update_workspace(user: str, workspace_id: str, workspace: UpdateWorkspace):
     workspaces = get_collection(WORKSPACES_COL_NAME)
 
-    update_filter = {'created_by': user, '_id': ObjectId(workspace_id)}
-    update = {"$addToSet": {"samples": { "$each": workspace.samples}}}
+    update_filter = {"created_by": user, "_id": ObjectId(workspace_id)}
+    update = {"$addToSet": {"samples": {"$each": workspace.samples}}}
     return workspaces.update_one(update_filter, update, upsert=True)
 
+
 def update_microreact(microreact_reference):
     workspaces = get_collection(WORKSPACES_COL_NAME)
 
-    update_filter = {'_id': ObjectId(microreact_reference['id'])}
-    update = {"$set": {"microreact": microreact_reference['microreact']}}
+    update_filter = {"_id": ObjectId(microreact_reference["id"])}
+    update = {"$set": {"microreact": microreact_reference["microreact"]}}
     return workspaces.update_one(update_filter, update, upsert=True)