WIP comparison service: operations

client/src/views/CompareView.vue

@@ -59,7 +59,7 @@ const onExport = () => {
 function load(operation) {
   records.value = undefined
   loading.value = true
-  HTTP.get('/compare', {
+  HTTP.get('/dataset/compare', {
     params: {
       reference: selectedDatasetA.value,
       comparison: selectedDatasetB.value,

server/src/scimodom/api/dataset.py

@@ -1,6 +1,8 @@
-from flask import Blueprint
+from flask import Blueprint, request, jsonify
+from flask_cors import cross_origin
 from flask_jwt_extended import jwt_required, get_jwt_identity
 
+from scimodom.services.comparison import get_comparison_service
 from scimodom.services.dataset import get_dataset_service
 from scimodom.services.user import get_user_service
 
@@ -21,3 +23,33 @@ def list_mine():
     email = get_jwt_identity()
     user = user_service.get_user_by_email(email)
     return dataset_service.get_datasets(user)
+
+
+@dataset_api.route("/compare", methods=["GET"])
+@cross_origin(supports_credentials=True)
+def compare():
+    """Compare dataset (Compare View)."""
+    reference_ids = request.args.getlist("reference", type=str)
+    comparison_ids = request.args.getlist("comparison", type=str)
+    upload_path = request.args.get("upload", type=str)
+    query_operation = request.args.get("operation", type=str)
+    print(f"{reference_ids}, {comparison_ids}, {upload_path}, {query_operation}")
+
+    # TODO
+    operation, strand = query_operation.split("S")
+    comparison_service = get_comparison_service(operation, eval(strand))
+    if upload_path:
+        try:
+            comparison_service.upload_records(upload_path)
+        except:  # FileNotFoundError, FailedUploadError, NoRecordsFoundError
+            pass
+    else:
+        try:
+            comparison_service.query_comparison_records(comparison_ids)
+        except:  # NoRecordsFoundErrror - querying from FE this will not occur...
+            pass
+    comparison_service.query_reference_records(reference_ids)
+    # try:
+    return comparison_service.compare_dataset()
+    # except: # what errors pybedtools can rise here?
+    #    return jsonify({"message": "Failed"}), 400

server/src/scimodom/api/public.py

@@ -6,7 +6,6 @@
 
 from scimodom.services.dataset import get_dataset_service
 from scimodom.services.public import get_public_service
-from scimodom.services.comparison import get_comparison_service
 
 api = Blueprint("api", __name__)
 
@@ -111,20 +110,6 @@ def get_search():
     return response
 
 
-@api.route("/compare", methods=["GET"])
-@cross_origin(supports_credentials=True)
-def get_compare():
-    """Compare view API."""
-    reference_ids = request.args.getlist("reference", type=str)
-    comparison_ids = request.args.getlist("comparison", type=str)
-    upload_path = request.args.get("upload", type=str)
-    query_operation = request.args.get("operation", type=str)
-
-    # TODO
-    compare_service = get_comparison_service()
-    return "Not implemented", 404
-
-
 @api.route("/upload", methods=["POST"])
 @cross_origin(supports_credentials=True)
 def upload_file():

server/src/scimodom/app.py

@@ -8,9 +8,7 @@
 from scimodom.api.public import api
 from scimodom.api.user import user_api
 from scimodom.api.dataset import dataset_api
-from scimodom.api.access import access_api
 from scimodom.api.management import management_api
-from scimodom.api.upload import upload_api
 from scimodom.api.transfer import transfer_api
 from scimodom.app_singleton import create_app_singleton
 from scimodom.database.database import make_session, init
@@ -28,9 +26,7 @@
 from scimodom.utils.url_routes import (
     API_PREFIX,
     USER_API_ROUTE,
-    ACCESS_API_ROUTE,
     DATASET_API_ROUTE,
-    UPLOAD_API_ROUTE,
     TRANSFER_API_ROUTE,
     DATA_MANAGEMENT_API_ROUTE,
 )
@@ -54,9 +50,7 @@ def create_app():
 
     app.register_blueprint(api, url_prefix=f"/{API_PREFIX}")
     app.register_blueprint(user_api, url_prefix=USER_API_ROUTE)
-    app.register_blueprint(access_api, url_prefix=ACCESS_API_ROUTE)
     app.register_blueprint(dataset_api, url_prefix=DATASET_API_ROUTE)
-    app.register_blueprint(upload_api, url_prefix=UPLOAD_API_ROUTE)
     app.register_blueprint(transfer_api, url_prefix=TRANSFER_API_ROUTE)
     app.register_blueprint(management_api, url_prefix=DATA_MANAGEMENT_API_ROUTE)