Merge pull request #197 from AberystwythSystemsBiology/feature/admin-…

…cart

New feature on admin-cart , and improved sample index, and audit report

services/web/app/admin/routes/audit.py

@@ -22,6 +22,10 @@
 from datetime import datetime
 from ..enums import *
 
+from flask import make_response, json
+import gzip
+from ...sample.routes import compress_response
+
 
 @admin.route("/audit/index", methods=["GET", "POST"])
 @login_required
@@ -37,18 +41,18 @@ def audit_index():
         sites = sites_response.json()["content"]["choices"]
 
     sites.append((99999, "Bots"))
-    users_by_site = {s[0]: [] for s in sites}
+    # users_by_site = {s[0]: [] for s in sites}
     sites_dict = {s[0]: s[1] for s in sites}
 
     auth_response = requests.get(
-        url_for("api.auth_home", _external=True),
+        url_for("api.auth_home_tokenuser", _external=True),
         headers=get_internal_api_header(),
     )
 
     users = []
     if auth_response.status_code == 200:
         auth_info = auth_response.json()["content"]
-
+        # print("auth_info", auth_info)
         for user in auth_info:
             if user["site_id"]:
                 site_id = user["site_id"]
@@ -81,14 +85,20 @@ def audit_query():
 
     args["start_date"] = start_date
     args["end_date"] = end_date
+    time1 = datetime.now()
+
     audit_response = requests.get(
         url_for("api.audit_query", _external=True),
         headers=get_internal_api_header(),
         json=args,
     )
 
-    if audit_response.status_code != 200:
-        abort(audit_response.status_code)
+    time2 = datetime.now()
+    td1 = time2 - time1
+    print("api call audit_query took %0.3f ms" % (td1.microseconds / 1000))
+
+    if audit_response.status_code == 200:
+        return compress_response(audit_response.json())
 
     return audit_response.json()
 

services/web/app/admin/views.py

@@ -287,7 +287,7 @@ class Meta:
     reference_id = masql.auto_field()
     event = ma.Nested(AuditInfoEventSchema)
     protocol_id = masql.auto_field()
-    # protocol = ma.Nested(BasicProtocolTemplateSchema)
+    protocol = ma.Nested(BasicProtocolTemplateSchema)
     created_on = masql.auto_field()
     author = ma.Nested(UserAccountSearchSchema, many=False)
     updated_on = masql.auto_field()
@@ -451,14 +451,14 @@ class Meta:
     reduced_quantity = masql.auto_field()
     event = ma.Nested(AuditInfoEventSchema)
     protocol_id = masql.auto_field()
-    # protocol = ma.Nested(BasicProtocolTemplateSchema)
+    protocol = ma.Nested(BasicProtocolTemplateSchema)
 
     created_on = masql.auto_field()
-    author_id = masql.auto_field
-    # author = ma.Nested(UserAccountSearchSchema, many=False)
+    # author_id = masql.auto_field
+    author = ma.Nested(UserAccountSearchSchema, many=False)
     updated_on = masql.auto_field()
-    editor_id = masql.auto_field
-    # editor = ma.Nested(UserAccountSearchSchema, many=False)
+    # editor_id = masql.auto_field
+    editor = ma.Nested(UserAccountSearchSchema, many=False)
     operation_type = masql.auto_field()
     transaction_id = masql.auto_field()
     end_transaction_id = masql.auto_field()
@@ -529,54 +529,58 @@ class Meta:
 
 class AuditEntityToStorageSchema(masql.SQLAlchemySchema):
     class Meta:
-        # model = version_class(EntityToStorage)
-        model = EntityToStorage
+        model = version_class(EntityToStorage)
+        # model = EntityToStorage
 
     id = masql.auto_field()
     storage_type = EnumField(EntityToStorageType)
 
     rack = ma.Nested(BasicSampleRackSchema, many=False)
     shelf = ma.Nested(BasicColdStorageShelfSchema, many=False)
+    sample_id = masql.auto_field()
     # rack_id = masql.auto_field()
     # shelf_id = masql.auto_field()
     row = masql.auto_field()
     col = masql.auto_field()
     entry_datetime = masql.auto_field()
     entry = masql.auto_field()
+    removed = masql.auto_field()
 
     created_on = masql.auto_field()
     author = ma.Nested(UserAccountSearchSchema, many=False)
     updated_on = masql.auto_field()
     editor = ma.Nested(UserAccountSearchSchema, many=False)
-    # operation_type = masql.auto_field() #masql.Enum(Operation, by_value=True)
-    # transaction_id = masql.auto_field()
-    # end_transaction_id = masql.auto_field()
+    operation_type = masql.auto_field()  # masql.Enum(Operation, by_value=True)
+    transaction_id = masql.auto_field()
+    end_transaction_id = masql.auto_field()
     object = fields.Constant("EntityToStorage")
 
 
 class AuditBasicEntityToStorageSchema(masql.SQLAlchemySchema):
     class Meta:
-        # model = version_class(EntityToStorage)
-        model = EntityToStorage
+        model = version_class(EntityToStorage)
+        # model = EntityToStorage
 
     id = masql.auto_field()
     storage_type = EnumField(EntityToStorageType)
     rack_id = masql.auto_field()
     # rack = ma.Nested(BasicSampleRackSchema, many=False)
     shelf_id = masql.auto_field()
     # shelf = ma.Nested(BasicColdStorageShelfSchema, many=False)
+    sample_id = masql.auto_field()
     row = masql.auto_field()
     col = masql.auto_field()
     entry_datetime = masql.auto_field()
     entry = masql.auto_field()
+    removed = masql.auto_field()
 
     created_on = masql.auto_field()
     author = ma.Nested(UserAccountSearchSchema, many=False)
     updated_on = masql.auto_field()
     editor = ma.Nested(UserAccountSearchSchema, many=False)
-    # operation_type = masql.auto_field()
-    # transaction_id = masql.auto_field()
-    # end_transaction_id = masql.auto_field()
+    operation_type = masql.auto_field()
+    transaction_id = masql.auto_field()
+    end_transaction_id = masql.auto_field()
     object = fields.Constant("EntityToStorage")
 
 
@@ -770,8 +774,8 @@ class Meta:
     remaining_quantity = masql.auto_field()
     comments = masql.auto_field()
     barcode = masql.auto_field()
-    sample_to_type_id = masql.auto_field()
-    # sample_type_information = ma.Nested(SampleTypeSchema)
+    # sample_to_type_id = masql.auto_field()
+    sample_type_information = ma.Nested(SampleTypeSchema)
 
     colour = EnumField(Colour, by_value=True)
     source = EnumField(SampleSource, by_value=True)

services/web/app/api/filters.py

@@ -30,7 +30,7 @@ def get_filters_and_joins(args: object, model: object) -> object:
 
 def generate_base_query_filters(tokenuser: UserAccount, type: str):
 
-    if tokenuser.account_type.value is "Administrator":
+    if tokenuser.account_type.value == "Administrator":
         return {}, True
 
     else:

services/web/app/auth/routes.py

@@ -38,6 +38,7 @@ def login():
         user = (
             db.session.query(UserAccount)
             .filter(func.lower(UserAccount.email) == func.lower(form.email.data))
+            .filter_by(is_locked=False)
             .first()
         )
 

services/web/app/auth/views.py

@@ -173,7 +173,7 @@ class Meta:
 
     id = masql.auto_field()
 
-    title = EnumField(Title, by_value=True)
+    title = EnumField(Title)  # , by_value=True)
 
     email = masql.auto_field()
     first_name = masql.auto_field()

services/web/app/donor/api/base.py

@@ -54,7 +54,8 @@
     new_donor_diagnosis_event_schema,
     donor_diagnosis_event_schema,
     new_donor_protocol_event_schema,
-    # donor_protocol_event_info_schema,
+    # donor_protocol_events_info_schema,
+    NewDonorProtocolEventSchema,
 )
 
 from ...event.views import new_event_schema
@@ -67,6 +68,22 @@
 )
 
 
+@api.route("/donor/get_study_reference", methods=["GET"])
+@use_args(NewDonorProtocolEventSchema(), location="json")
+@token_required
+def donor_study_reference(args, tokenuser: UserAccount):
+    study_id = args.pop("protocol_id", None)
+    reference_id = args.pop("reference_id", None)
+    refs = (
+        db.session.query(DonorProtocolEvent)
+        .filter_by(protocol_id=study_id, reference_id=reference_id)
+        .all()
+    )
+    donor_study_references_schema = NewDonorProtocolEventSchema(many=True)
+
+    return success_with_content_response(donor_study_references_schema.dump(refs))
+
+
 @api.route("/donor")
 @token_required
 def donor_home(tokenuser: UserAccount):

services/web/app/donor/forms.py

@@ -276,12 +276,28 @@ def validate(self):
                     )
                     return False
 
+            if len(data["questions"]) == 0:
+                validate_answers = True
+            else:
+                validate_answers = False
+                for question in data["questions"]:
+                    if self[str(question["id"])].data:
+                        validate_answers = True
+                        break
+
+            if not validate_answers:
+                self.submit.errors.append(
+                    "None of the questions has been checked for consent!!"
+                )
+                return False
+
             return True
 
     for question in data["questions"]:
         checked = ""
         if "checked" in question:
             checked = question["checked"]
+
         setattr(
             StaticForm,
             str(question["id"]),

services/web/app/donor/routes.py

@@ -99,6 +99,20 @@ def view_endpoint(id):
         return response.json()
 
 
+@donor.route("/get_study_reference", methods=["POST"])
+@login_required
+def get_study_reference():
+    response = requests.get(
+        url_for("api.donor_study_reference", _external=True),
+        headers=get_internal_api_header(),
+        json=request.json,
+    )
+    if response.status_code == 200:
+        return response.json()
+    else:
+        abort(response.status_code)
+
+
 # TODO sample to donor association:
 #  should done by sample basic edit and change the consent form
 @donor.route("/LIMBDON-<id>/associate/sample", methods=["GET", "POST"])