Sampletype fix - actually some fixes for storage

.env.example

@@ -11,4 +11,5 @@ ONTOLOGY_DIRECTORY=/limbus/ontologies/
 DEBUG=True
 LC_ALL=C.UTF-8
 LANG=C.UTF-8
-DOID_PATH=https://users.aber.ac.uk/keo7/doid.xrdf
+## DOID_PATH=https://users.aber.ac.uk/keo7/doid.xrdf
+DOID_PATH=/limbus/ontologies/doid.xrdf ## https://www.dropbox.com/s/1v3b69iw7o1nibs/doid.xrdf

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

@@ -65,6 +65,7 @@ def sites_new_site():
             "street_address_one": form.address_line_one.data,
             "street_address_two": form.address_line_two.data,
             "city": form.city.data,
+            "county": form.county.data,
             "country": form.country.data,
             "post_code": form.post_code.data,
         }

services/web/app/api/generics.py

@@ -58,19 +58,18 @@ def generic_lock(
     view_schema: masql.SQLAlchemySchema,
     tokenuser: UserAccount,
 ):
-    existing = Model.query.filter_by(id=id).first()
+    existing = model.query.filter_by(id=id).first()
 
     if not existing:
         return not_found()
 
     existing.is_locked = not existing.is_locked
     existing.editor_id = tokenuser.id
 
-    db.session.add(existing)
     db.session.commit()
     db.session.flush()
 
-    return success_with_content_response(view_schema.dump(existing))
+    return success_with_content_response(existing.is_locked)
 
 
 def generic_edit(
@@ -128,4 +127,3 @@ def generic_delete(
 
     #return success_with_content_response()
     return success_without_content_response()
-

services/web/app/api/responses.py

@@ -21,19 +21,32 @@ def not_found():
         {"ContentType": "application/json"},
     )
 
-def locked():
-    return (
-        {"success": False, "message": "Data locked"},
-        404,
-        {"ContentType": "application/json"},
+def sample_assigned_delete_response():
+    return(
+        {"success": False, "message":"Can't delete assigned samples"},
+        400,
+        {"ContentType":"application/json"}
     )
+
+def in_use_response(entity):
+    return(
+        {"success": False, "message":"Has associated " + entity},
+        400,
+        {"ContentType":"application/json"}
+    )
+
 def no_values_response():
     return (
         {"success": False, "message": "No input data provided"},
         400,
         {"ContentType": "application/json"},
     )
 
+def locked_response():
+    return({"success": False, "message": "Entity is locked"},
+            400,
+            {"ContentType": "application/json"})
+
 
 def invalid_query_response():
     return (

services/web/app/decorators.py

@@ -30,6 +30,15 @@ def decorated_function(*args, **kwargs):
 
     return decorated_function
 
+def check_if_locked(model):
+    def inner(f):
+        def wrapper(*args,**kwargs):
+            if(model.query.filter_by(id=kwargs["id"]).is_locked):
+                return abort(401)
+            return f(*args,**kwargs)
+        return wrapper
+    return inner
+
 
 def requires_access_level(f):
     @wraps(f)

services/web/app/misc/models.py

@@ -38,6 +38,7 @@ class SiteInformation(Base, RefAuthorMixin):
     miabis_id = db.Column(db.String(128))
     acronym = db.Column(db.String(64))
     name = db.Column(db.String(128))
+    is_locked = db.Column(db.Boolean,default=False)
     description = db.Column(db.String(128))
     url = db.Column(db.String(128))
     address_id = db.Column(db.Integer, db.ForeignKey("address.id"), nullable=False)

services/web/app/static/css/global.css

@@ -58,6 +58,34 @@ nav img {
     color: #000;
 }
 
+.btn-cancel {
+    background-color: #eb4034;
+    color: #ffffff;
+    margin-right:0.5em;
+}
+
+.btn-cancel:hover {
+    background-color:#a62b23;
+    color: #ffffff;
+}
+
+.btn-delete{
+    background-color: #ffffff;
+    color: #eb4034;
+    border: 1px #eb4034 solid;
+}
+
+
+
+.btn-form{
+    background-color: #007bff;
+    color:white
+}
+.btn-form:hover{
+    background-color: #0062cc;
+    color: white;
+}
+
 #wmd-preview {
     background-color: #f5f5f5;
     padding:1em;

services/web/app/static/css/storage/navbar.css

@@ -12,7 +12,7 @@
     overflow: auto;
     top: 30px;
     left: 0;
-    z-index: 998;
+    z-index: 997;
     transition: all 0.3s;
 }
 
@@ -23,7 +23,7 @@
 #sidebar-collapse {
     float: right;
     margin: 0;
-    z-index: 999;
+    z-index: 998;
     position: relative;
     margin-top: 50%;
     right: -1em;
@@ -36,4 +36,29 @@
 
 #sidebar.active #sidebar-collapse {
     right: -3em;
+}
+
+/* The Modal (background) */
+.modal-delete {
+    display: none; /* Hidden by default */
+    position: fixed; /* Stay in place */
+    z-index: 999; /* Sit on top */
+    left: 0;
+    top: 15%;
+    width: 100%; /* Full width */
+    height: 100%; /* Full height */
+    overflow: auto; /* Enable scroll if needed */
+    /*background-color: #474e5d;*/
+    padding-top: 50px;
+}
+
+/* Modal Content/Box */
+.modal-delete-content {
+    color:black;
+    background-color: #fefefe;
+    margin: 5% auto 15% auto; /* 5% from the top, 15% from the bottom and centered */
+    border: 2px solid #000;
+    border-radius: 0;
+    width: 70%; /* Could be more or less, depending on screen size */
+    height: fit-content;
 }

services/web/app/static/js/storage/delete.js

@@ -0,0 +1,26 @@
+/*
+Copyright (C) 2020 Keiron O'Shea <keo7@aber.ac.uk>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+*/
+
+// Get the modal
+var modal = document.getElementById('delete-confirmation');
+
+// When the user clicks anywhere outside of the modal, close it
+window.onclick = function(event) {
+    if (event.target === modal) {
+        modal.style.display = "none";
+    }
+}

services/web/app/static/js/storage/navtree.js

@@ -15,6 +15,7 @@ You should have received a copy of the GNU General Public License
 along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
 
+
 function sap2tree(sap) {
     var sites = sap["content"];
 

services/web/app/static/js/storage/panel.js

@@ -38,7 +38,7 @@ function get_panel_information() {
 
 function render_counts(basic_statistics) {
     $("#site_count").html(basic_statistics["site_count"]);
-    $("#room_count").html(basic_statistics["site_count"]);
+    $("#room_count").html(basic_statistics["room_count"]);
     $("#building_count").html(basic_statistics["building_count"]);
     $("#cold_storage_count").html(basic_statistics["cold_storage_count"]);
 

services/web/app/static/js/storage/rack/view.js

@@ -265,9 +265,12 @@ function render_sample_table(samples) {
                             return sample_type_information["fluid_type"];
                         }
                         else if (data["sample"]["base_type"] == "Cellular") {
-                            return sample_type_information["cellular_type"] + " > " + sample_type_information["tiss_type"];
+                            return sample_type_information["cellular_type"]; // + " > " + sample_type_information["tissue_type"];
                         }
-
+                        else if (data["sample"]["base_type"] == "Molecular") {
+                            return sample_type_information["molecular_type"]; // + " > " + sample_type_information["tissue_type"];
+                        }
+
 
                     }
                 },

services/web/app/storage/api/building.py

@@ -13,14 +13,20 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-from flask import request, current_app, jsonify, send_file
+from flask import request, current_app, jsonify, send_file,url_for
 
 from ...api import api
 from ...api.responses import *
 from ...api.filters import generate_base_query_filters, get_filters_and_joins
-from ...decorators import token_required
+from ...decorators import token_required,check_if_locked
 from ...webarg_parser import use_args, use_kwargs, parser
-from ...database import db, Building, UserAccount
+from ...database import db, Building, UserAccount,Room
+from ..api.room import func_room_delete
+
+
+import requests
+from ...misc import get_internal_api_header
+
 
 
 from marshmallow import ValidationError
@@ -93,11 +99,53 @@ def storage_lock_building(id: int, tokenuser: UserAccount):
     building.is_locked = not building.is_locked
     building.editor_id = tokenuser.id
 
-    db.session.add(building)
     db.session.commit()
     db.session.flush()
 
-    return success_with_content_response(basic_building_schema.dump(building))
+    return success_with_content_response(building.is_locked)
+
+
+@api.route("/storage/building/LIMBBUILD-<id>/delete", methods=["PUT"])
+@token_required
+def storage_building_delete(id, tokenuser: UserAccount):
+    existing = Building.query.filter_by(id=id).first()
+
+    if not existing:
+        return not_found()
+
+    if existing.is_locked:
+        return locked_response()
+
+    existing.editor_id = tokenuser.id
+
+    code = delete_buildings_func(existing)
+
+    siteID = existing.site_id
+
+    if code == "success":
+        return success_with_content_response(siteID)
+    elif code == "cold storage":
+        return in_use_response(code)
+    elif code == "locked":
+        return locked_response()
+    else:
+        return no_values_response()
+
+def delete_buildings_func(record):
+    attachedRooms = Room.query.filter(Room.building_id == record.id).all()
+    for rooms in attachedRooms:
+        code = func_room_delete(rooms)
+        if code == "cold storage":
+            return "cold storage"
+        elif code == "locked" or record.is_locked:
+            return "locked"
+
+    try:
+        db.session.delete(record)
+        db.session.commit()
+        return "success"
+    except Exception as err:
+        return transaction_error_response(err)
 
 
 @api.route("/storage/building/LIMBBUILD-<id>/edit", methods=["PUT"])
@@ -108,6 +156,8 @@ def storage_edit_building(id: int, tokenuser: UserAccount):
 
     if not building:
         return not_found()
+    if building.is_locked:
+        return not_allowed()
 
     values = request.get_json()