From 4acb18416281778e360bc3767f0d7672850be41e Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Tue, 24 Oct 2023 12:53:07 +0000
Subject: [PATCH 01/22] add video tutorials

---
 frontend-v2/package.json                  |  3 +
 frontend-v2/src/features/help/Help.tsx    | 72 ++++++++++++++++++-----
 frontend-v2/src/features/help/HelpTab.tsx | 62 +++++++++++++------
 frontend-v2/src/setupProxy.js             | 14 ++---
 frontend-v2/yarn.lock                     | 42 ++++++++++++-
 5 files changed, 151 insertions(+), 42 deletions(-)

diff --git a/frontend-v2/package.json b/frontend-v2/package.json
index e87dec8d..679f117d 100644
--- a/frontend-v2/package.json
+++ b/frontend-v2/package.json
@@ -16,10 +16,12 @@
     "@types/react": "^18.0.6",
     "@types/react-dom": "^18.0.2",
     "http-proxy-middleware": "^2.0.6",
+    "papaparse": "^5.4.1",
     "plotly.js": "^2.23.2",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
     "react-hook-form": "^7.43.9",
+    "react-player": "^2.13.0",
     "react-plotly.js": "^2.6.0",
     "react-redux": "^8.0.1",
     "react-scripts": "5.0.1",
@@ -54,6 +56,7 @@
   },
   "devDependencies": {
     "@babel/plugin-proposal-private-property-in-object": "^7.21.11",
+    "@types/papaparse": "^5.3.10",
     "@types/react-plotly.js": "^2.6.0",
     "cypress": "^12.16.0",
     "start-server-and-test": "^2.0.0"
diff --git a/frontend-v2/src/features/help/Help.tsx b/frontend-v2/src/features/help/Help.tsx
index db058416..d26e9ae0 100644
--- a/frontend-v2/src/features/help/Help.tsx
+++ b/frontend-v2/src/features/help/Help.tsx
@@ -1,12 +1,46 @@
+import React, { useEffect } from 'react';
 import { DynamicTabs, TabPanel } from '../../components/DynamicTabs';
 import HelpTab from './HelpTab';
+import { parse } from 'papaparse';
+import { set } from 'react-hook-form';
 
 export type Question = {
   question: string;
   answer: string;
 }
 
+export type TutorialVideo = {
+  title: string;
+  type: string;
+  link: string;
+  keywords: string[];
+}
+
+const tutorialVideosUrl: string = '/backend/tutorial_videos.csv';
+
 const Help: React.FC = () => {
+  const [ tutorialVideos, setTutorialVideos ] = React.useState<TutorialVideo[]>([]);
+  useEffect(() => {
+    parse(tutorialVideosUrl, {
+      download: true,
+      error: (err) => {
+        console.error('Error downloading tutorial videos:', err);
+      },
+      complete: (results) => {
+        setTutorialVideos(
+          results.data.map((row) => {
+            const rowList = row as string[];
+            return {
+              title: rowList[0],
+              type: rowList[1],
+              link: rowList[2],
+              keywords: rowList[3].split(',').map((keyword) => keyword.trim())
+            };
+          })
+        );
+      }
+    })
+  }, []);
   let generic_questions: Question[] = Array(5).fill({
     question: "Question 1?",
     answer: "Answer 1"
@@ -16,6 +50,22 @@ const Help: React.FC = () => {
       question: `Question ${index + 1}?`,
       answer: `Answer ${index + 1}: Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.`
     }});
+  
+  const questions = [
+    generic_questions.slice(0, 2),
+    generic_questions.slice(0, 4),
+    generic_questions.slice(0, 3),
+    generic_questions.slice(0, 5),
+    generic_questions.slice(0, 1),
+  ]
+  const tutorials = [
+    tutorialVideos.filter((video) => video.type.includes('Tutorial')),
+    tutorialVideos.filter((video) => video.type === 'Project'),
+    tutorialVideos.filter((video) => video.type === 'Drug'),
+    tutorialVideos.filter((video) => video.type === 'Model'),
+    tutorialVideos.filter((video) => video.type === 'Trial Design'),
+    tutorialVideos.filter((video) => video.type === 'Simulation'),
+  ]
     
   const project_questions = generic_questions.slice(0, 2);
   const drug_questions = generic_questions.slice(0, 4)
@@ -24,22 +74,12 @@ const Help: React.FC = () => {
   const simulation_questions = generic_questions.slice(0, 1)
 
   return (
-    <DynamicTabs tabNames={["Projects", "Drug", "Model", "Trial Design", "Simulation"]}>
-      <TabPanel>
-        <HelpTab questions={project_questions} />
-      </TabPanel>
-      <TabPanel>
-        <HelpTab questions={drug_questions} />
-      </TabPanel>
-      <TabPanel>
-        <HelpTab questions={model_questions} />
-      </TabPanel>
-      <TabPanel>
-        <HelpTab questions={trial_questions} />
-      </TabPanel>
-      <TabPanel>
-        <HelpTab questions={simulation_questions} />
-      </TabPanel>
+    <DynamicTabs tabNames={["Tutorials", "Projects", "Drug", "Model", "Trial Design", "Simulation"]}>
+      { questions.map((question, index) => (
+        <TabPanel key={index}>
+          <HelpTab questions={question} videos={tutorials[index]} />
+        </TabPanel>
+      ))}
     </DynamicTabs>
   );
 }
diff --git a/frontend-v2/src/features/help/HelpTab.tsx b/frontend-v2/src/features/help/HelpTab.tsx
index f4ab1a68..18d49661 100644
--- a/frontend-v2/src/features/help/HelpTab.tsx
+++ b/frontend-v2/src/features/help/HelpTab.tsx
@@ -1,29 +1,57 @@
-import { Accordion, AccordionDetails, AccordionSummary, Typography } from "@mui/material";
+import { Accordion, AccordionDetails, AccordionSummary, Chip, Stack, Typography } from "@mui/material";
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
-import { Question } from "./Help";
+import { Question, TutorialVideo } from "./Help";
+import ReactPlayer from 'react-player/youtube'
+
 
 interface Props {
   questions: Question[];
+  videos: TutorialVideo[];
 }
 
 // tab that lists questions as mui accordian components
-const HelpTab: React.FC<Props> = ({ questions }) => {
+const HelpTab: React.FC<Props> = ({ questions, videos }) => {
   return (
     <div>
-      {questions.map((question, index) => {
-        return (
-          <Accordion key={index}>
-            <AccordionSummary
-              expandIcon={<ExpandMoreIcon />}
-            >
-              <Typography>{question.question}</Typography>
-            </AccordionSummary>
-            <AccordionDetails>
-              <Typography>{question.answer}</Typography>
-            </AccordionDetails>
-          </Accordion>
-        )
-      })}
+      <Stack spacing={1} sx={{ marginBottom: 2 }}>
+        {questions.map((question, index) => {
+          return (
+            <Accordion key={index}>
+              <AccordionSummary
+                expandIcon={<ExpandMoreIcon />}
+              >
+                <Typography>{question.question}</Typography>
+              </AccordionSummary>
+              <AccordionDetails>
+                <Typography>{question.answer}</Typography>
+              </AccordionDetails>
+            </Accordion>
+          )
+        })}
+      </Stack>
+      <Stack spacing={2}>
+        {videos.map((video, index) => {
+          return (
+            <div key={index}>
+              <Typography variant='h6' >{video.title}</Typography>
+              <Stack direction="row" spacing={1} sx={{ marginBottom: 1 }}>
+              { video.keywords.map((keyword, index) => {
+                return (
+                  <Chip size="small" label={keyword} />
+                )
+              })}
+              </Stack>
+              <iframe
+                key={index}
+                allowFullScreen
+                src={video.link}
+                style={{ border: "none", width: "100%", aspectRatio: "16/9" }}
+                title={video.title}
+              />
+            </div>
+          )
+        })}
+      </Stack>
     </div>
   );
 }
diff --git a/frontend-v2/src/setupProxy.js b/frontend-v2/src/setupProxy.js
index 787a43d2..606ea6e2 100644
--- a/frontend-v2/src/setupProxy.js
+++ b/frontend-v2/src/setupProxy.js
@@ -1,11 +1,11 @@
 const { createProxyMiddleware } = require('http-proxy-middleware');
 
 module.exports = function(app) {
-  app.use(
-    '/api',
-    createProxyMiddleware({
-      target: 'http://localhost:8000',
-      changeOrigin: true,
-    })
-  );
+  const backend = createProxyMiddleware({
+    target: 'http://localhost:8000',
+    changeOrigin: true,
+    pathRewrite: { '^/backend': '/static' },
+  });
+  app.use('/api', backend);
+  app.use('/backend', backend);
 };
\ No newline at end of file
diff --git a/frontend-v2/yarn.lock b/frontend-v2/yarn.lock
index e06ef058..6a4756e4 100644
--- a/frontend-v2/yarn.lock
+++ b/frontend-v2/yarn.lock
@@ -2544,6 +2544,13 @@
   resolved "https://registry.yarnpkg.com/@types/node/-/node-17.0.45.tgz#2c0fafd78705e7a18b7906b5201a522719dc5190"
   integrity sha512-w+tIMs3rq2afQdsPJlODhoUEKzFP1ayaoyl1CcnwtIlsVe7K7bA1NGm4s3PraqTLlXnbIN84zuBlxBWo1u9BLw==
 
+"@types/papaparse@^5.3.10":
+  version "5.3.10"
+  resolved "https://registry.yarnpkg.com/@types/papaparse/-/papaparse-5.3.10.tgz#d315347dfafd0458aa25062ec9e3dcebb948b6de"
+  integrity sha512-mS1Fta/xJ9EDYmAvpeWzcV9Gr0cOl1ClpW7di9+wSUNDIDO55tBtyXg97O7K+Syrd9rDEmuejM2iqmJIJ1SO5g==
+  dependencies:
+    "@types/node" "*"
+
 "@types/parse-json@^4.0.0":
   version "4.0.0"
   resolved "https://registry.yarnpkg.com/@types/parse-json/-/parse-json-4.0.0.tgz#2f8bb441434d163b35fb8ffdccd7138927ffb8c0"
@@ -4700,7 +4707,7 @@ deep-is@^0.1.3, deep-is@~0.1.3:
   resolved "https://registry.yarnpkg.com/deep-is/-/deep-is-0.1.4.tgz#a6f2dce612fadd2ef1f519b73551f17e85199831"
   integrity sha512-oIPzksmTg4/MriiaYGO+okXDT7ztn/w3Eptv/+gSIdMdKsJo0u4CfYNFJPy+4SKMuCqGw2wxnA+URMg3t8a/bQ==
 
-deepmerge@^4.2.2:
+deepmerge@^4.0.0, deepmerge@^4.2.2:
   version "4.3.1"
   resolved "https://registry.yarnpkg.com/deepmerge/-/deepmerge-4.3.1.tgz#44b5f2147cd3b00d4b56137685966f26fd25dd4a"
   integrity sha512-3sUqbMEc77XqpdNO7FRyRog+eW3ph+GYCbj+rK+uYyRMuwsVy0rMiVtPn+QJlKFvWP/1PYpapqYn0Me2knFn+A==
@@ -7895,6 +7902,11 @@ listr2@^3.8.3:
     through "^2.3.8"
     wrap-ansi "^7.0.0"
 
+load-script@^1.0.0:
+  version "1.0.0"
+  resolved "https://registry.yarnpkg.com/load-script/-/load-script-1.0.0.tgz#0491939e0bee5643ee494a7e3da3d2bac70c6ca4"
+  integrity sha512-kPEjMFtZvwL9TaZo0uZ2ml+Ye9HUMmPwbYRJ324qF9tqMejwykJ5ggTyvzmrbBeapCAbk98BSbTeovHEEP1uCA==
+
 loader-runner@^4.2.0:
   version "4.3.0"
   resolved "https://registry.yarnpkg.com/loader-runner/-/loader-runner-4.3.0.tgz#c1b4a163b99f614830353b16755e7149ac2314e1"
@@ -8111,6 +8123,11 @@ memfs@^3.1.2, memfs@^3.4.3:
   dependencies:
     fs-monkey "^1.0.4"
 
+memoize-one@^5.1.1:
+  version "5.2.1"
+  resolved "https://registry.yarnpkg.com/memoize-one/-/memoize-one-5.2.1.tgz#8337aa3c4335581839ec01c3d594090cebe8f00e"
+  integrity sha512-zYiwtZUcYyXKo/np96AGZAckk+FWWsUdJ3cHGGmld7+AhvcWmQyGCYUh1hc4Q/pkOhb65dQR/pqCyK0cOaHz4Q==
+
 merge-descriptors@1.0.1:
   version "1.0.1"
   resolved "https://registry.yarnpkg.com/merge-descriptors/-/merge-descriptors-1.0.1.tgz#b00aaa556dd8b44568150ec9d1b953f3f90cbb61"
@@ -8616,6 +8633,11 @@ p-try@^2.0.0:
   resolved "https://registry.yarnpkg.com/p-try/-/p-try-2.2.0.tgz#cb2868540e313d61de58fafbe35ce9004d5540e6"
   integrity sha512-R4nPAVTAU0B9D35/Gk3uJf/7XYbQcyohSKdvAxIRSNghFl4e71hVoGnBNQz9cWaXxO2I10KTC+3jMdvvoKw6dQ==
 
+papaparse@^5.4.1:
+  version "5.4.1"
+  resolved "https://registry.yarnpkg.com/papaparse/-/papaparse-5.4.1.tgz#f45c0f871853578bd3a30f92d96fdcfb6ebea127"
+  integrity sha512-HipMsgJkZu8br23pW15uvo6sib6wne/4woLZPlFf3rpDyMe9ywEXUsuD7+6K9PRkJlVT51j/sCOYDKGGS3ZJrw==
+
 param-case@^3.0.4:
   version "3.0.4"
   resolved "https://registry.yarnpkg.com/param-case/-/param-case-3.0.4.tgz#7d17fe4aa12bde34d4a77d91acfb6219caad01c5"
@@ -9487,7 +9509,7 @@ prompts@^2.0.1, prompts@^2.4.2:
     kleur "^3.0.3"
     sisteransi "^1.0.5"
 
-prop-types@^15.6.2, prop-types@^15.8.1:
+prop-types@^15.6.2, prop-types@^15.7.2, prop-types@^15.8.1:
   version "15.8.1"
   resolved "https://registry.yarnpkg.com/prop-types/-/prop-types-15.8.1.tgz#67d87bf1a694f48435cf332c24af10214a3140b5"
   integrity sha512-oj87CgZICdulUohogVAR7AjlC0327U4el4L6eAvOqCeudMDVU0NThNaV+b9Df4dXgSP1gXMTnPdhfe/2qDH5cg==
@@ -9657,6 +9679,11 @@ react-error-overlay@^6.0.11:
   resolved "https://registry.yarnpkg.com/react-error-overlay/-/react-error-overlay-6.0.11.tgz#92835de5841c5cf08ba00ddd2d677b6d17ff9adb"
   integrity sha512-/6UZ2qgEyH2aqzYZgQPxEnz33NJ2gNsnHA2o5+o4wW9bLM/JYQitNP9xPhsXwC08hMMovfGe/8retsdDsczPRg==
 
+react-fast-compare@^3.0.1:
+  version "3.2.2"
+  resolved "https://registry.yarnpkg.com/react-fast-compare/-/react-fast-compare-3.2.2.tgz#929a97a532304ce9fee4bcae44234f1ce2c21d49"
+  integrity sha512-nsO+KSNgo1SbJqJEYRE9ERzo7YtYbou/OqjSQKxV7jcKox7+usiUVZOAC+XnDOABXggQTno0Y1CpVnuWEc1boQ==
+
 react-hook-form@^7.43.9:
   version "7.47.0"
   resolved "https://registry.yarnpkg.com/react-hook-form/-/react-hook-form-7.47.0.tgz#a42f07266bd297ddf1f914f08f4b5f9783262f31"
@@ -9677,6 +9704,17 @@ react-is@^18.0.0, react-is@^18.2.0:
   resolved "https://registry.yarnpkg.com/react-is/-/react-is-18.2.0.tgz#199431eeaaa2e09f86427efbb4f1473edb47609b"
   integrity sha512-xWGDIW6x921xtzPkhiULtthJHoJvBbF3q26fzloPCK0hsvxtPVelvftw3zjbHWSkR2km9Z+4uxbDDK/6Zw9B8w==
 
+react-player@^2.13.0:
+  version "2.13.0"
+  resolved "https://registry.yarnpkg.com/react-player/-/react-player-2.13.0.tgz#b6fb252bf70574608ac711f6c83d7057c8fb0c14"
+  integrity sha512-gkY7ZdbVFztlKFFhCPcnDrFQm+L399b8fhWsKatZ+b2wpKJwfUHBXQFMRxqYQGT0ic1/wQ7D7EZEWy7ZBqk2pw==
+  dependencies:
+    deepmerge "^4.0.0"
+    load-script "^1.0.0"
+    memoize-one "^5.1.1"
+    prop-types "^15.7.2"
+    react-fast-compare "^3.0.1"
+
 react-plotly.js@^2.6.0:
   version "2.6.0"
   resolved "https://registry.yarnpkg.com/react-plotly.js/-/react-plotly.js-2.6.0.tgz#ad6b68ee64f1b5cfa142ee92c59687f9c2c09209"

From bbe38953f820117575e3455da632d5bcc841dc09 Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Tue, 24 Oct 2023 13:35:45 +0000
Subject: [PATCH 02/22] replace view with preview

---
 frontend-v2/src/features/help/Help.tsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/frontend-v2/src/features/help/Help.tsx b/frontend-v2/src/features/help/Help.tsx
index d26e9ae0..fd512957 100644
--- a/frontend-v2/src/features/help/Help.tsx
+++ b/frontend-v2/src/features/help/Help.tsx
@@ -33,7 +33,7 @@ const Help: React.FC = () => {
             return {
               title: rowList[0],
               type: rowList[1],
-              link: rowList[2],
+              link: rowList[2].replace('view?usp=sharing', 'preview'),
               keywords: rowList[3].split(',').map((keyword) => keyword.trim())
             };
           })

From 3f03e00f23551089f6f5af8c4a87ea97985aff23 Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Tue, 24 Oct 2023 14:03:59 +0000
Subject: [PATCH 03/22] update nginx config

---
 nginx.default.template | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/nginx.default.template b/nginx.default.template
index 6a8f0d44..e8e91819 100644
--- a/nginx.default.template
+++ b/nginx.default.template
@@ -57,4 +57,18 @@ server {
       proxy_read_timeout 20d;
       proxy_buffering off;
     }
+    
+    # or /backend -> /static
+    location /backend {
+      proxy_pass http://app_server/static;
+      proxy_set_header X-Real-IP  $remote_addr;
+      proxy_set_header X-Forwarded-For $remote_addr;
+      proxy_set_header Host $host;
+      proxy_set_header X-Forwarded-Proto $scheme;
+      proxy_redirect http://app_server/static $scheme://$http_host;
+      proxy_http_version 1.1;
+      proxy_set_header Upgrade $http_upgrade;
+      proxy_read_timeout 20d;
+      proxy_buffering off;
+    }
 }

From debeebb5fac2688994f325563b3fd08a48d5668f Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Fri, 27 Oct 2023 17:28:38 +0000
Subject: [PATCH 04/22] make sure we update model after updating mappings (plus
 test)

---
 pkpdapp/pkpdapp/api/serializers/models.py     |  21 ++-
 .../tests/test_views/test_combined_model.py   | 178 ++++++++++++++++++
 .../tests/test_views/test_dosed_pk_model.py   |  41 ----
 3 files changed, 192 insertions(+), 48 deletions(-)
 create mode 100644 pkpdapp/pkpdapp/tests/test_views/test_combined_model.py
 delete mode 100644 pkpdapp/pkpdapp/tests/test_views/test_dosed_pk_model.py

diff --git a/pkpdapp/pkpdapp/api/serializers/models.py b/pkpdapp/pkpdapp/api/serializers/models.py
index 409ab25c..66558668 100644
--- a/pkpdapp/pkpdapp/api/serializers/models.py
+++ b/pkpdapp/pkpdapp/api/serializers/models.py
@@ -68,8 +68,8 @@ def get_components(self, m):
         return [_serialize_component(m, c, model) for c in model.components(sort=True)]
 
     def create(self, validated_data):
-        mappings_data = validated_data.pop("mappings")
-        derived_variables_data = validated_data.pop("derived_variables")
+        mappings_data = validated_data.pop("mappings", [])
+        derived_variables_data = validated_data.pop("derived_variables", [])
         new_pkpd_model = BaseDosedPharmacokineticSerializer().create(validated_data)
         for field_datas, Serializer in [
             (mappings_data, PkpdMappingSerializer),
@@ -83,13 +83,17 @@ def create(self, validated_data):
         return new_pkpd_model
 
     def update(self, instance, validated_data):
-        mappings_data = validated_data.pop("mappings")
-        derived_var_data = validated_data.pop("derived_variables")
+        mappings_data = validated_data.pop("mappings", [])
+        derived_var_data = validated_data.pop("derived_variables", [])
         old_mappings = list((instance.mappings).all())
         old_derived_vars = list((instance.derived_variables).all())
 
-        pk_model_changed = instance.pk_model != validated_data.get("pk_model")
-        pd_model_changed = instance.pd_model != validated_data.get("pd_model")
+        pk_model_changed = False
+        if "pk_model" in validated_data:
+            pk_model_changed = instance.pk_model != validated_data.get("pk_model")
+        pd_model_changed = False
+        if "pd_model" in validated_data:
+            pd_model_changed = instance.pd_model != validated_data.get("pd_model")
 
         new_pkpd_model = BaseDosedPharmacokineticSerializer().update(
             instance, validated_data
@@ -130,12 +134,15 @@ def update(self, instance, validated_data):
                     mapping["pkpd_model"] = new_pkpd_model
                     new_model = serializer.create(mapping)
 
-        # delete any remaining old mappings
+        # delete any remaining old mappings and derived variables
         for old_model in old_mappings:
             old_model.delete()
         for old_model in old_derived_vars:
             old_model.delete()
 
+        # update model since mappings might have changed
+        new_pkpd_model.update_model()
+
         return new_pkpd_model
 
 
diff --git a/pkpdapp/pkpdapp/tests/test_views/test_combined_model.py b/pkpdapp/pkpdapp/tests/test_views/test_combined_model.py
new file mode 100644
index 00000000..aece7677
--- /dev/null
+++ b/pkpdapp/pkpdapp/tests/test_views/test_combined_model.py
@@ -0,0 +1,178 @@
+#
+# This file is part of PKPDApp (https://github.com/pkpdapp-team/pkpdapp) which
+# is released under the BSD 3-clause license. See accompanying LICENSE.md for
+# copyright notice and full license details.
+#
+
+import pkpdapp.tests  # noqa: F401
+from rest_framework import status
+from rest_framework.test import APITestCase, APIClient
+from django.contrib.auth.models import User
+from pkpdapp.models import Project, PharmacokineticModel, CombinedModel, PharmacodynamicModel
+import numpy as np
+
+
+class CombinedModelTestCase(APITestCase):
+    def setUp(self):
+        user = User.objects.get(username='demo')
+        self.client = APIClient()
+        self.client.force_authenticate(user=user)
+
+    def test_pk_project_filter(self):
+        response = self.client.get("/api/combined_model/?project_id=1")
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        response_data = response.data
+        self.assertEqual(len(response_data), 1)
+
+    def test_cannot_create_in_read_only_project(self):
+        user = User.objects.get(username='demo2')
+        self.client = APIClient()
+        self.client.force_authenticate(user=user)
+
+        project = Project.objects.get(name='demo')
+        response = self.client.post(
+            "/api/combined_model/",
+            data={
+                'name': 'test',
+                'project': project.id
+            }
+        )
+        self.assertEqual(
+            response.status_code, status.HTTP_403_FORBIDDEN
+        )
+    
+    def create_combined_model(self, name, pd=None):
+        project = Project.objects.get(name='demo')
+        pk = PharmacokineticModel.objects.get(
+            name='one_compartment_clinical',
+        )
+        data={
+            'name': name,
+            'project': project.id,
+            'pk_model': pk.id,
+            'mappings': [],
+            'derived_variables': [],
+        }
+        if pd is not None:
+            data['pd_model'] = pd.id
+        response = self.client.post(
+            "/api/combined_model/",
+            data=data,
+            format='json'
+        )
+        self.assertEqual(response.status_code, status.HTTP_201_CREATED)
+        cm = CombinedModel.objects.get(pk=response.data['id'])
+
+        # set up a protocol
+        response = self.client.post(
+            "/api/protocol/",
+            data={
+                'name': 'test protocol',
+                'project': project.id,
+                'doses': [
+                    {
+                        'start_time': 0,
+                        'amount': 1,
+                        'duration': 0.001,
+                        'repeat_interval': 1,
+                        'repeats': 1,
+                    }
+                ]
+            },
+            format='json'
+        )
+        self.assertEqual(response.status_code, status.HTTP_201_CREATED)
+
+        # attach it to the A1 variables
+        a1 = cm.variables.get(name='A1')
+        response = self.client.patch(
+            f"/api/variable/{a1.id}/",
+            data={
+                'protocol': response.data['id'],
+            },
+            format='json'
+        )
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+
+        if pd is not None:
+            c1 = cm.variables.get(name='C1')
+            drug_c = cm.variables.get(name='C_Drug')
+
+            response = self.client.patch(
+                f"/api/combined_model/{cm.id}/",
+                data={
+                    'mappings': [
+                        {
+                            'pk_variable': c1.id,
+                            'pd_variable': drug_c.id,
+                        }
+                    ],
+                    'derived_variables': [],
+                },
+                format='json'
+            )
+            self.assertEqual(response.status_code, status.HTTP_200_OK)
+
+        return response.data
+    
+    def simulate_combined_model(self, id):
+        response = self.client.post(
+            f"/api/combined_model/{id}/simulate",
+            data={
+                'outputs': ['PDCompartment.C_Drug', 'PKCompartment.C1', 'PDCompartment.E'],
+                'variables': {},
+            },
+            format='json'
+        )
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        keys= [ key for key in response.data['outputs'].keys() ]
+        return response.data['outputs'][keys[0]], response.data['outputs'][keys[1]], response.data['outputs'][keys[2]]
+
+    
+    def test_swap_mapped_pd_model(self):
+        pd1 = PharmacodynamicModel.objects.get(
+            name='indirect_effects_stimulation_elimination',
+        )
+        pd2 = PharmacodynamicModel.objects.get(
+            name='indirect_effects_inhibition_elimination',
+        )
+        model1 = self.create_combined_model('test1', pd1)
+        model2 = self.create_combined_model('test2', pd2)
+        c_drug1, c1_1, e1 = self.simulate_combined_model(model1['id'])
+        c_drug2, c1_2, e2 = self.simulate_combined_model(model2['id'])
+
+        # c_drug should be mapped to c1 and equal 
+        np.testing.assert_allclose(c_drug1, c1_1, atol=1e-5, rtol=1e-5)
+
+        # swap the pd model for model 1, old mappings should be updated
+        cm = CombinedModel.objects.get(pk=model1['id'])
+        c1 = cm.variables.get(name='C1')
+        c_drug = cm.variables.get(name='C_Drug')
+        response = self.client.patch(
+            f"/api/combined_model/{model1['id']}/",
+            data={
+                'pd_model': pd2.id,
+                'mappings': [
+                    {
+                        'pk_variable': c1.id,
+                        'pd_variable': c_drug.id,
+                    }
+                ],
+            },
+            format='json'
+        )
+        model1 = response.data
+
+        # simulate the model again
+        c_drug3, c1_3, e3 = self.simulate_combined_model(model1['id'])
+
+        # c_drug3 should be mapped to c3 and equal 
+        np.testing.assert_allclose(c_drug3, c1_3, atol=1e-5, rtol=1e-5)
+
+        # check that the data is the same as the second simulation
+        np.testing.assert_allclose(c_drug3, c_drug2, atol=1e-5, rtol=1e-5)
+        np.testing.assert_allclose(c1_3, c1_2, atol=1e-5, rtol=1e-5)
+        np.testing.assert_allclose(e3, e2, atol=1e-5, rtol=1e-5)
+
+
+
diff --git a/pkpdapp/pkpdapp/tests/test_views/test_dosed_pk_model.py b/pkpdapp/pkpdapp/tests/test_views/test_dosed_pk_model.py
deleted file mode 100644
index dc604f5d..00000000
--- a/pkpdapp/pkpdapp/tests/test_views/test_dosed_pk_model.py
+++ /dev/null
@@ -1,41 +0,0 @@
-#
-# This file is part of PKPDApp (https://github.com/pkpdapp-team/pkpdapp) which
-# is released under the BSD 3-clause license. See accompanying LICENSE.md for
-# copyright notice and full license details.
-#
-
-import pkpdapp.tests  # noqa: F401
-from rest_framework import status
-from rest_framework.test import APITestCase, APIClient
-from django.contrib.auth.models import User
-from pkpdapp.models import Project
-
-
-class DosedPkModelTestCase(APITestCase):
-    def setUp(self):
-        user = User.objects.get(username='demo')
-        self.client = APIClient()
-        self.client.force_authenticate(user=user)
-
-    def test_pk_project_filter(self):
-        response = self.client.get("/api/combined_model/?project_id=1")
-        self.assertEqual(response.status_code, status.HTTP_200_OK)
-        response_data = response.data
-        self.assertEqual(len(response_data), 1)
-
-    def test_cannot_create_in_read_only_project(self):
-        user = User.objects.get(username='demo2')
-        self.client = APIClient()
-        self.client.force_authenticate(user=user)
-
-        project = Project.objects.get(name='demo')
-        response = self.client.post(
-            "/api/combined_model/",
-            data={
-                'name': 'test',
-                'project': project.id
-            }
-        )
-        self.assertEqual(
-            response.status_code, status.HTTP_403_FORBIDDEN
-        )

From 4609794a0a7d425fdfbbc4a785baa43f72c56924 Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Mon, 30 Oct 2023 09:44:34 +0000
Subject: [PATCH 05/22] update default parameters and make variables in tmdd
 models consistent

---
 .../src/features/model/param_default.ts       | 266 +++++++++---------
 .../models/ParametersValue_Species.xlsx       | Bin 26067 -> 25694 bytes
 ...SS_ConstTarget_1cmpt_PK_Model_Clinical.mmt |   4 +-
 ...ConstTarget_1cmpt_PK_Model_Preclinical.mmt |   4 +-
 ...SS_ConstTarget_2cmpt_PK_Model_clinical.mmt |   4 +-
 ...ConstTarget_2cmpt_PK_Model_preclinical.mmt |   4 +-
 6 files changed, 141 insertions(+), 141 deletions(-)

diff --git a/frontend-v2/src/features/model/param_default.ts b/frontend-v2/src/features/model/param_default.ts
index 1d5c2e40..7aa597e3 100644
--- a/frontend-v2/src/features/model/param_default.ts
+++ b/frontend-v2/src/features/model/param_default.ts
@@ -261,41 +261,41 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         Km: {
             M: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             R: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             K: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             H: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
@@ -304,7 +304,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         ke0: {
             M: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -314,7 +314,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             R: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -324,7 +324,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             K: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -334,7 +334,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             H: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -347,7 +347,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         Kpu: {
             M: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -357,7 +357,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             R: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -367,7 +367,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             K: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -377,7 +377,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             H: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -737,41 +737,41 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         Km: {
             M: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             R: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             K: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             H: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
@@ -780,7 +780,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         ke0: {
             M: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -790,7 +790,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             R: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -800,7 +800,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             K: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -810,7 +810,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             H: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -823,7 +823,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         Kpu: {
             M: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -833,7 +833,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             R: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -843,7 +843,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             K: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -853,12 +853,12 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             H: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
                     value: 0.2,
-                unit: 'dimensionless',
+                    unit: 'dimensionless',
                 },
             },
             
@@ -1095,27 +1095,27 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             R: {
                 SM: {
                     value: 1,
-                    unit: 'None',
+                    unit: 'L/kg',
                 },
                 LM: {
                     value: 20,
-                    unit: 'None',
+                    unit: 'mL/kg',
                 },
             },
             K: {
                 SM: {
                     value: 1,
-                    unit: 'None',
+                    unit: 'L/kg',
                 },
                 LM: {
                     value: 20,
-                    unit: 'None',
+                    unit: 'mL/kg',
                 },
             },
             H: {
                 SM: {
                     value: 75,
-                    unit: 'None',
+                    unit: 'L',
                 },
                 LM: {
                     value: 1500,
@@ -1224,31 +1224,31 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             R: {
                 SM: {
                     value: 33,
-                    unit: 'None',
+                    unit: 'mL/h/kg',
                 },
                 LM: {
                     value: 0.04,
-                    unit: 'None',
+                    unit: 'mL/h/kg',
                 },
             },
             K: {
                 SM: {
                     value: 26,
-                    unit: 'None',
+                    unit: 'mL/h/kg',
                 },
                 LM: {
                     value: 0.025,
-                    unit: 'None',
+                    unit: 'mL/h/kg',
                 },
             },
             H: {
                 SM: {
                     value: 1,
-                    unit: 'None',
+                    unit: 'L/h',
                 },
                 LM: {
                     value: 0.8,
-                    unit: 'None',
+                    unit: 'mL/h',
                 },
             },
             
@@ -1299,41 +1299,41 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         Km: {
             M: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             R: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             K: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             H: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
@@ -1342,7 +1342,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         ke0: {
             M: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -1352,7 +1352,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             R: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -1362,7 +1362,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             K: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -1372,7 +1372,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             H: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -1385,7 +1385,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         Kpu: {
             M: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -1395,7 +1395,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             R: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -1405,7 +1405,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             K: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -1415,7 +1415,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             H: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -1646,7 +1646,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         ke0: {
             M: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -1656,7 +1656,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             R: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -1666,7 +1666,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             K: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -1676,7 +1676,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             H: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -1689,7 +1689,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         Kp: {
             M: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -1699,7 +1699,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             R: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -1709,7 +1709,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             K: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -1719,7 +1719,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             H: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -1775,41 +1775,41 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         KD: {
             M: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             R: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             K: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             H: {
                 SM: {
-                    value: 5000,
+                    value: 10000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
@@ -1947,41 +1947,41 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         KSS: {
             M: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             R: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             K: {
                 SM: {
-                    value: 5000,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             H: {
                 SM: {
-                    value: 5000,
+                    value: 10000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
@@ -2255,7 +2255,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
                     unit: 'mL/h/kg',
                 },
                 LM: {
-                    value: 1.8,
+                    value: 1.75,
                     unit: 'mL/h/kg',
                 },
             },
@@ -2294,7 +2294,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         ke0: {
             M: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -2304,7 +2304,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             R: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -2314,7 +2314,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             K: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -2324,7 +2324,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             H: {
                 SM: {
-                    value: 0.1,
+                    value: 0.5,
                     unit: '1/h',
                 },
                 LM: {
@@ -2337,7 +2337,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         Kp: {
             M: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -2347,7 +2347,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             R: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -2357,7 +2357,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             K: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -2367,7 +2367,7 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
             },
             H: {
                 SM: {
-                    value: 0.01,
+                    value: 0.02,
                     unit: 'dimensionless',
                 },
                 LM: {
@@ -2423,41 +2423,41 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         KD: {
             M: {
                 SM: {
-                    value: 0.5,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 0.5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             R: {
                 SM: {
-                    value: 0.5,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 0.5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             K: {
                 SM: {
-                    value: 0.5,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 0.5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             H: {
                 SM: {
-                    value: 0.5,
+                    value: 10000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 0.5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
@@ -2466,41 +2466,41 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         koff: {
             M: {
                 SM: {
-                    value: 0.693,
+                    value: 0.6931471805599453,
                     unit: '1/h',
                 },
                 LM: {
-                    value: 0.693,
+                    value: 0.6931471805599453,
                     unit: '1/h',
                 },
             },
             R: {
                 SM: {
-                    value: 0.693,
+                    value: 0.6931471805599453,
                     unit: '1/h',
                 },
                 LM: {
-                    value: 0.693,
+                    value: 0.6931471805599453,
                     unit: '1/h',
                 },
             },
             K: {
                 SM: {
-                    value: 0.693147181,
+                    value: 0.6931471805599453,
                     unit: '1/h',
                 },
                 LM: {
-                    value: 0.693147181,
+                    value: 0.6931471805599453,
                     unit: '1/h',
                 },
             },
             H: {
                 SM: {
-                    value: 0.693147181,
+                    value: 0.6931471805599453,
                     unit: '1/h',
                 },
                 LM: {
-                    value: 0.693,
+                    value: 0.6931471805599453,
                     unit: '1/h',
                 },
             },
@@ -2509,41 +2509,41 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         kdeg: {
             M: {
                 SM: {
-                    value: 0.0712,
+                    value: 0.07124809851593399,
                     unit: '1/h',
                 },
                 LM: {
-                    value: 0.0712,
+                    value: 0.07124809851593399,
                     unit: '1/h',
                 },
             },
             R: {
                 SM: {
-                    value: 0.0401,
+                    value: 0.04006575013674287,
                     unit: '1/h',
                 },
                 LM: {
-                    value: 0.0401,
+                    value: 0.04006575013674287,
                     unit: '1/h',
                 },
             },
             K: {
                 SM: {
-                    value: 0.020712917,
+                    value: 0.020712917213851895,
                     unit: '1/h',
                 },
                 LM: {
-                    value: 0.020712917,
+                    value: 0.020712917213851895,
                     unit: '1/h',
                 },
             },
             H: {
                 SM: {
-                    value: 0.00963,
+                    value: 0.009627044174443685,
                     unit: '1/h',
                 },
                 LM: {
-                    value: 0.00963,
+                    value: 0.009627044174443685,
                     unit: '1/h',
                 },
             },
@@ -2552,41 +2552,41 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         kint: {
             M: {
                 SM: {
-                    value: 0.356,
+                    value: 0.3562404925796699,
                     unit: '1/h',
                 },
                 LM: {
-                    value: 0.356,
+                    value: 0.3562404925796699,
                     unit: '1/h',
                 },
             },
             R: {
                 SM: {
-                    value: 0.2,
+                    value: 0.20032875068371434,
                     unit: '1/h',
                 },
                 LM: {
-                    value: 0.2,
+                    value: 0.20032875068371434,
                     unit: '1/h',
                 },
             },
             K: {
                 SM: {
-                    value: 0.103564586,
+                    value: 0.10356458606925947,
                     unit: '1/h',
                 },
                 LM: {
-                    value: 0.103564586,
+                    value: 0.10356458606925947,
                     unit: '1/h',
                 },
             },
             H: {
                 SM: {
-                    value: 0.04814,
+                    value: 0.04813522087221842,
                     unit: '1/h',
                 },
                 LM: {
-                    value: 0.04814,
+                    value: 0.04813522087221842,
                     unit: '1/h',
                 },
             },
@@ -2595,41 +2595,41 @@ export const param_default: {[key: string]: {[key: string]: {[key: string]: {[ke
         KSS: {
             M: {
                 SM: {
-                    value: 0.5,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 0.5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             R: {
                 SM: {
-                    value: 0.5,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 0.5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             K: {
                 SM: {
-                    value: 0.5,
+                    value: 1000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 0.5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
             H: {
                 SM: {
-                    value: 0.5,
+                    value: 10000,
                     unit: 'nmol/L',
                 },
                 LM: {
-                    value: 0.5,
+                    value: 1,
                     unit: 'nmol/L',
                 },
             },
diff --git a/pkpdapp/pkpdapp/migrations/models/ParametersValue_Species.xlsx b/pkpdapp/pkpdapp/migrations/models/ParametersValue_Species.xlsx
index fe49f08168f8c55559ea0d4bb99bfee76073bdb6..3919d9933c6031bad405e9a6b0896127ead7af78 100644
GIT binary patch
delta 14560
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zr{xe<z~&ajTf<l(WcGKqcA<T#@=2kRnZ#~_ar$F~j(%&5gJ-iYFAK9C_DDc}zs8ai
z8qGnxTgv^qx#uPMe-|z;03PtJ$pa_=75(d#^{~2hP+&v(J~o2jGq^X2;YP#9o=)-A
zo<xs4NFLrmTWb4i#22-MBOWPmn@!sU8XPO+u3dSOpPH;{47$UgrzHUiUEq^6um!ut
zfcpMZhC57Dl%?7aaggjeJStgH2_1V4y*ANjJ<Z%N=<xgrT#4F9Mtb_H;;6>rBML(d
zg~XFdEZ{U3nGPV{E~`Bh_4NxGLk~v}6BYM##jRw!6mqAGR!yrlAOMFx7uE(1NdW3$
zMsK?4;d@>h3H{jG*N-VSc6V{i?t*I-i?o|4+7+5sc-%ahZ+=2bHD~FiMl2`Qd|O=j
znNDcqAG3^F12(3nxen#w;T}`h4Sb^0{C7BM5e({DX9EZYUH(pe$J|vEu&mY#|N5(*
zijfeqiG8O6sqjIAbyBj)u;cXzn`Es+Qj!pf66!jE^F6q;St^=2FLQNlFcx%R9j%H5
zhYPckd=`@}fI@pj=qCk!@g}bi)(?jHKc9s_FpSk;>yZHf$TTt$1Z<2+^505y0D$2A
zru_GZg9f=U#(S?#$0Po4A>;oV<wDMl8A<+MAqLC;j;9g-$BBXo9?5^-#r&_4E%kql
z65fsepRV%%^TfscAEPA`R_Jjq2$Crc$^T}R|2_3ML5Q3wImtiBk%9sM_THl=?te$$
zTbUvdUvYd$hUrIW95KkF6fp!-5*hO6y^AOQpDw2v7c_yydy@tdWA+i6SQ3I^P7T>G
zV}&l2dvEeXvdxH~xmEwOH_RN5<bPxCe`o8}hP0Sd!v0(8kWF)ZXe&L)ow+bHtRaNQ
Mf)f75_@Cwf2d(wY*#H0l

diff --git a/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_1cmpt_PK_Model_Clinical.mmt b/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_1cmpt_PK_Model_Clinical.mmt
index 23a93093..b064b492 100644
--- a/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_1cmpt_PK_Model_Clinical.mmt
+++ b/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_1cmpt_PK_Model_Clinical.mmt
@@ -63,7 +63,7 @@ c_term = C1_t * KSS in [pmol/L*pmol/L]
 C1_t = A1_t/V1 in [pmol/L]
     desc: Total concentration of drug in the central compartment	
 
-CT1_t = CT1_0 in [pmol/L]	
+CT1_t = CT1_b + CT1_f in [pmol/L]	
 	desc: Total concentration of target in the central compartment	
 	
 C1_f = 0.5 * (b_term + (b_term^2+4*c_term)^0.5) in [pmol/L]
@@ -75,7 +75,7 @@ C1_b = C1_t-C1_f in [pmol/L]
 CT1_b = C1_b in [pmol/L]
 	desc: Bound concentration of target in the central compartment
 
-CT1_f = CT1_t-CT1_b in [pmol/L]
+CT1_f = CT1_0-CT1_b in [pmol/L]
 	desc: Free concentration of target in the central compartment
 	
 RO_Model = CT1_b/CT1_t*100 in [dimensionless]
diff --git a/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_1cmpt_PK_Model_Preclinical.mmt b/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_1cmpt_PK_Model_Preclinical.mmt
index 67e39fea..50260312 100644
--- a/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_1cmpt_PK_Model_Preclinical.mmt
+++ b/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_1cmpt_PK_Model_Preclinical.mmt
@@ -63,7 +63,7 @@ c_term = C1_t * KSS in [pmol/L*pmol/L]
 C1_t = A1_t/V1 in [pmol/L]
     desc: Total concentration of drug in the central compartment	
 
-CT1_t = CT1_0 in [pmol/L]	
+CT1_t = CT1_b + CT1_f in [pmol/L]	
 	desc: Total concentration of target in the central compartment	
 	
 C1_f = 0.5 * (b_term + (b_term^2+4*c_term)^0.5) in [pmol/L]
@@ -75,7 +75,7 @@ C1_b = C1_t-C1_f in [pmol/L]
 CT1_b = C1_b in [pmol/L]
 	desc: Bound concentration of target in the central compartment
 
-CT1_f = CT1_t-CT1_b in [pmol/L]
+CT1_f = CT1_0-CT1_b in [pmol/L]
 	desc: Free concentration of target in the central compartment
 	
 	
diff --git a/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_2cmpt_PK_Model_clinical.mmt b/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_2cmpt_PK_Model_clinical.mmt
index 6d2c5707..27df8b01 100644
--- a/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_2cmpt_PK_Model_clinical.mmt
+++ b/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_2cmpt_PK_Model_clinical.mmt
@@ -70,7 +70,7 @@ c_term = C1_t * KSS in [pmol/L * pmol/L]
 C1_t = A1_t/V1 in [pmol/L]
     desc: Total concentration of drug in the central compartment
 
-CT1_t = CT1_0 in [pmol/L]	
+CT1_t = CT1_b + CT1_f in [pmol/L]	
 	desc: Total concentration of target in the central compartment
 	
 C1_f = 0.5 * (b_term + (b_term^2+4*c_term)^0.5) in [pmol/L]
@@ -85,7 +85,7 @@ C2 = A2/V2 in [pmol/L]
 CT1_b = C1_b in [pmol/L]
 	desc: Bound concentration of target in the central compartment
 
-CT1_f = CT1_t-CT1_b in [pmol/L]
+CT1_f = CT1_0-CT1_b in [pmol/L]
 	desc: Free concentration of target in the central compartment
 	
 	
diff --git a/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_2cmpt_PK_Model_preclinical.mmt b/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_2cmpt_PK_Model_preclinical.mmt
index d0221863..f0965b89 100644
--- a/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_2cmpt_PK_Model_preclinical.mmt
+++ b/pkpdapp/pkpdapp/migrations/models/TMDD_QSS_ConstTarget_2cmpt_PK_Model_preclinical.mmt
@@ -70,7 +70,7 @@ c_term = C1_t * KSS in [pmol/L * pmol/L]
 C1_t = A1_t/V1 in [pmol/L]
     desc: Total concentration of drug in the central compartment
 
-CT1_t = CT1_0 in [pmol/L]	
+CT1_t = CT1_b + CT1_f in [pmol/L]	
 	desc: Total concentration of target in the central compartment
 	
 C1_f = 0.5 * (b_term + (b_term^2+4*c_term)^0.5) in [pmol/L]
@@ -85,7 +85,7 @@ C2 = A2/V2 in [pmol/L]
 CT1_b = C1_b in [pmol/L]
 	desc: Bound concentration of target in the central compartment
 
-CT1_f = CT1_t-CT1_b in [pmol/L]
+CT1_f = CT1_0-CT1_b in [pmol/L]
 	desc: Free concentration of target in the central compartment
 	
 	

From 9fd40135c68d5d8e3bcbbf7e414336523fad994d Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Tue, 31 Oct 2023 15:41:20 +0000
Subject: [PATCH 06/22] move set defaults to backend, any change to pk model
 triggers

---
 frontend-v2/src/app/api.ts                    |  3 +
 frontend-v2/src/app/backendApi.ts             | 25 ++++--
 frontend-v2/src/features/help/HelpTab.tsx     |  2 +-
 .../src/features/model/MapVariablesTab.tsx    | 21 ++---
 frontend-v2/src/features/model/Model.tsx      | 82 ++++++++++++-----
 .../src/features/model/PKPDModelTab.tsx       | 23 +++--
 .../src/features/model/ParametersTab.tsx      | 88 ++++---------------
 .../src/features/model/VariableRow.tsx        |  7 +-
 .../features/model/resetToSpeciesDefaults.ts  | 71 +++++++++++++++
 frontend-v2/src/features/projects/Project.tsx | 21 ++---
 pkpdapp/pkpdapp/api/views/models.py           | 25 +++++-
 pkpdapp/pkpdapp/models/combined_model.py      | 31 ++++++-
 pkpdapp/pkpdapp/models/mechanistic_model.py   |  1 +
 .../test_models/test_mechanistic_model.py     | 11 +++
 pkpdapp/pkpdapp/utils/default_params.py       | 43 +++++++++
 pkpdapp/schema.yml                            | 39 ++++++--
 requirements.txt                              |  1 +
 17 files changed, 351 insertions(+), 143 deletions(-)
 create mode 100644 frontend-v2/src/features/model/resetToSpeciesDefaults.ts
 create mode 100644 pkpdapp/pkpdapp/utils/default_params.py

diff --git a/frontend-v2/src/app/api.ts b/frontend-v2/src/app/api.ts
index b5753111..853052d8 100644
--- a/frontend-v2/src/app/api.ts
+++ b/frontend-v2/src/app/api.ts
@@ -79,6 +79,9 @@ export const api = backendApi.enhanceEndpoints({
       ],
     },
     // CombinedModel
+    combinedModelSetParamsToDefaultsUpdate: {
+      invalidatesTags: (result, error, { id }) => [{ type: 'Variable', id: 'LIST' }],
+    },
     combinedModelList: {
       providesTags: (result) =>
         result
diff --git a/frontend-v2/src/app/backendApi.ts b/frontend-v2/src/app/backendApi.ts
index 75b4b2f3..d3f07c32 100644
--- a/frontend-v2/src/app/backendApi.ts
+++ b/frontend-v2/src/app/backendApi.ts
@@ -157,6 +157,16 @@ const injectedRtkApi = api.injectEndpoints({
         method: "DELETE",
       }),
     }),
+    combinedModelSetParamsToDefaultsUpdate: build.mutation<
+      CombinedModelSetParamsToDefaultsUpdateApiResponse,
+      CombinedModelSetParamsToDefaultsUpdateApiArg
+    >({
+      query: (queryArg) => ({
+        url: `/api/combined_model/${queryArg.id}/set_params_to_defaults/`,
+        method: "PUT",
+        body: queryArg.combinedModel,
+      }),
+    }),
     combinedModelSetVariablesFromInferenceUpdate: build.mutation<
       CombinedModelSetVariablesFromInferenceUpdateApiResponse,
       CombinedModelSetVariablesFromInferenceUpdateApiArg
@@ -849,10 +859,7 @@ const injectedRtkApi = api.injectEndpoints({
     unitList: build.query<UnitListApiResponse, UnitListApiArg>({
       query: (queryArg) => ({
         url: `/api/unit/`,
-        params: {
-          compound_id: queryArg.compoundId,
-          is_target: queryArg.isTarget,
-        },
+        params: { compound_id: queryArg.compoundId },
       }),
     }),
     unitCreate: build.mutation<UnitCreateApiResponse, UnitCreateApiArg>({
@@ -1092,6 +1099,13 @@ export type CombinedModelDestroyApiArg = {
   /** A unique integer value identifying this combined model. */
   id: number;
 };
+export type CombinedModelSetParamsToDefaultsUpdateApiResponse =
+  /** status 200  */ CombinedModelRead;
+export type CombinedModelSetParamsToDefaultsUpdateApiArg = {
+  /** A unique integer value identifying this combined model. */
+  id: number;
+  combinedModel: CombinedModel;
+};
 export type CombinedModelSetVariablesFromInferenceUpdateApiResponse =
   /** status 200  */ CombinedModelRead;
 export type CombinedModelSetVariablesFromInferenceUpdateApiArg = {
@@ -1522,8 +1536,6 @@ export type UnitListApiResponse = /** status 200  */ UnitRead[];
 export type UnitListApiArg = {
   /** Enable conversions based on compound information */
   compoundId?: number;
-  /** (optional, default=false) true if unit is a target concentration unit */
-  isTarget?: boolean;
 };
 export type UnitCreateApiResponse = /** status 201  */ UnitRead;
 export type UnitCreateApiArg = {
@@ -2717,6 +2729,7 @@ export const {
   useCombinedModelUpdateMutation,
   useCombinedModelPartialUpdateMutation,
   useCombinedModelDestroyMutation,
+  useCombinedModelSetParamsToDefaultsUpdateMutation,
   useCombinedModelSetVariablesFromInferenceUpdateMutation,
   useCombinedModelSimulateCreateMutation,
   useCompoundListQuery,
diff --git a/frontend-v2/src/features/help/HelpTab.tsx b/frontend-v2/src/features/help/HelpTab.tsx
index 18d49661..7c8afb55 100644
--- a/frontend-v2/src/features/help/HelpTab.tsx
+++ b/frontend-v2/src/features/help/HelpTab.tsx
@@ -37,7 +37,7 @@ const HelpTab: React.FC<Props> = ({ questions, videos }) => {
               <Stack direction="row" spacing={1} sx={{ marginBottom: 1 }}>
               { video.keywords.map((keyword, index) => {
                 return (
-                  <Chip size="small" label={keyword} />
+                  <Chip key={index} size="small" label={keyword} />
                 )
               })}
               </Stack>
diff --git a/frontend-v2/src/features/model/MapVariablesTab.tsx b/frontend-v2/src/features/model/MapVariablesTab.tsx
index e43f13f0..6392180d 100644
--- a/frontend-v2/src/features/model/MapVariablesTab.tsx
+++ b/frontend-v2/src/features/model/MapVariablesTab.tsx
@@ -1,29 +1,22 @@
 import * as React from 'react';
-import { CombinedModel, CombinedModelRead, Project, ProjectRead, Variable, VariableRead, useCompoundRetrieveQuery, useUnitListQuery, useUnitRetrieveQuery } from '../../app/backendApi';
-import { Control, useFieldArray } from 'react-hook-form';
+import { CombinedModelRead, CompoundRead, ProjectRead, UnitRead, VariableRead } from '../../app/backendApi';
+import { Control } from 'react-hook-form';
 import { Table, TableBody, TableCell, TableContainer, TableHead, TableRow, Tooltip } from '@mui/material';
 import VariableRow from './VariableRow';
 import HelpButton from '../../components/HelpButton';
+import { FormData } from './Model';
 
 interface Props {
     model: CombinedModelRead;
     project: ProjectRead;
-    control: Control<CombinedModel>;
+    control: Control<FormData>;
     variables: VariableRead[];
+    units: UnitRead[];
+    compound: CompoundRead;
 }
 
-const MapVariablesTab: React.FC<Props> = ({ model, project, control, variables }: Props ) => {
+const MapVariablesTab: React.FC<Props> = ({ model, project, control, variables, units, compound }: Props ) => {
     
-    const { data: units, isLoading: isLoadingUnits } = useUnitListQuery({ compoundId: project.compound}, { skip: !project.compound });
-    const { data: compound, isLoading: isLoadingCompound } = useCompoundRetrieveQuery({id: project.compound})
-
-    if (isLoadingUnits || isLoadingCompound) {
-      return null;
-    }
-    if (units === undefined || compound === undefined) {
-      return null;
-    }
-
     const concentrationUnit = units.find((unit) => unit.symbol === "pmol/L");
     const amountUnit = units.find((unit) => unit.symbol === "pmol");
     if (concentrationUnit === undefined || amountUnit === undefined) {
diff --git a/frontend-v2/src/features/model/Model.tsx b/frontend-v2/src/features/model/Model.tsx
index e4e40aec..e1de26a6 100644
--- a/frontend-v2/src/features/model/Model.tsx
+++ b/frontend-v2/src/features/model/Model.tsx
@@ -1,6 +1,6 @@
 import { useSelector } from 'react-redux';
 import { RootState } from '../../app/store';
-import { CombinedModel, CombinedModelRead, useCombinedModelListQuery, useCombinedModelUpdateMutation, useProjectRetrieveQuery, useProtocolDestroyMutation, useProtocolListQuery, useSimulationListQuery, useSimulationUpdateMutation, useVariableListQuery } from '../../app/backendApi';
+import { CombinedModel, CombinedModelRead, ProjectRead, useCombinedModelListQuery, useCombinedModelSetParamsToDefaultsUpdateMutation, useCombinedModelUpdateMutation, useCompoundRetrieveQuery, usePharmacokineticListQuery, usePharmacokineticRetrieveQuery, useProjectRetrieveQuery, useProjectUpdateMutation, useProtocolDestroyMutation, useProtocolListQuery, useSimulationListQuery, useSimulationUpdateMutation, useUnitListQuery, useVariableListQuery, useVariableUpdateMutation } from '../../app/backendApi';
 import { useForm } from 'react-hook-form';
 import { useEffect, useMemo } from 'react';
 import { DynamicTabs, TabPanel } from '../../components/DynamicTabs';
@@ -8,21 +8,30 @@ import MapVariablesTab from './MapVariablesTab';
 import PKPDModelTab from './PKPDModelTab';
 import ParametersTab from './ParametersTab';
 import useDirty from '../../hooks/useDirty';
+import { getConstVariables, resetToSpeciesDefaults } from './resetToSpeciesDefaults';
 
+export type FormData = {
+  project: ProjectRead;
+  model: CombinedModel;
+};
 
 const Model: React.FC = () => {
   const projectId = useSelector((state: RootState) => state.main.selectedProject);
   const { data: project, isLoading: isProjectLoading } = useProjectRetrieveQuery({id: projectId || 0}, { skip: !projectId })
+  const { data: compound, isLoading: isLoadingCompound } = useCompoundRetrieveQuery({ id: project?.compound || 0}, { skip: !project || !project.compound});
   const { data: models, isLoading: isModelsLoading } = useCombinedModelListQuery({projectId: projectId || 0}, { skip: !projectId})
   const { data: protocols, error: protocolsError, isLoading: isProtocolsLoading } = useProtocolListQuery({projectId: projectId || 0}, { skip: !projectId})
   const model = models?.[0] || null;
   const [ updateModel ]  = useCombinedModelUpdateMutation()
   const { data: variables, isLoading: isVariablesLoading } = useVariableListQuery({ dosedPkModelId: model?.id || 0 }, { skip: !model?.id })
-  const { data: simulations, isLoading: isSimulationsLoading } = useSimulationListQuery({projectId: projectId || 0}, { skip: !projectId })
+  const { data: simulations, isLoading: isSimulationsLoading } = useSimulationListQuery({projectId: projectId || 0 }, { skip: !projectId })
+  const { data: units, isLoading: isLoadingUnits } = useUnitListQuery({ compoundId: project?.compound}, { skip: !project || !project.compound});
   const [updateSimulation] = useSimulationUpdateMutation();
   const simulation = useMemo(() => {
     return simulations?.[0] || undefined
   }, [simulations]);
+  const [ updateProject, { isLoading: isUpdatingProject } ] = useProjectUpdateMutation()
+  const [ setParamsToDefault ] = useCombinedModelSetParamsToDefaultsUpdateMutation();
 
 
   const defaultModel: CombinedModelRead = {
@@ -37,35 +46,68 @@ const Model: React.FC = () => {
     time_unit: 0,
     is_library_model: false,
   };
-  const { reset, handleSubmit, control, formState: { isDirty } } = useForm<CombinedModel>({
-    defaultValues: model || defaultModel
+  const defaultProject: ProjectRead = {
+    id: 0,
+    user_access: [],
+    name: '',
+    created: '',
+    compound: 0,
+    users: [],
+    protocols: [],
+  }
+  
+  const defaultValues: FormData = {
+    project: defaultProject,
+    model: defaultModel,
+  };
+
+  const { reset, handleSubmit, control, formState: { isDirty } } = useForm<FormData>({
+    defaultValues,
   });
-  useDirty(isDirty);
 
+  useDirty(isDirty);
   
   useEffect(() => {
-    if (model) {
-      reset(model);
+    if (model && project) {
+      reset({ model, project });
     }
-  }, [model, reset]);
+  }, [model, project, reset]);
 
-  const submit = handleSubmit((data: CombinedModel) => {
-    if (!model) {
+  const submit = handleSubmit((data: FormData) => {
+    if (!model || !project) {
       return;
     }
     
     // if only pd_model has changed, need to clear pd_model2
-    if (data.pd_model !== model?.pd_model) {
-      data.pd_model2 = null;
+    if (data.model.pd_model !== model?.pd_model) {
+      data.model.pd_model2 = null;
     }
-
-    return updateModel({ id: model.id, combinedModel: data }).then((response) => {
+    
+    // if species changed then update project
+    if (data.project.species !== project.species) {
+      updateProject({ id: project.id, project: { ...project, species: data.project.species }, });
+
+      // if species has changed, then clear the models
+      data.model.pk_model = null;
+      data.model.pd_model = null;
+      data.model.pd_model2 = null;
+    }
+    return updateModel({ id: model.id, combinedModel: data.model }).then((response) => {
       if ('data' in response) {
-        // if the pk_model has changed, need to reset the simulation time_max_unit
-        if ((data.pk_model !== model?.pk_model) && simulation) {
+        // if the pk_model has changed, need to reset the simulation time_max_unit and set default parameters again
+        if ((data.model.pk_model !== model?.pk_model) && simulation) {
           const time_max_unit = response.data.time_unit;
           updateSimulation({ id: simulation.id, simulation: { ...simulation, time_max_unit } });
         }
+        // if the pk model has changed or any of the checkboxes have changed, need to reset the parameters
+        if (
+          (data.model.pk_model !== model?.pk_model) || 
+          (data.model.has_bioavailability !== model.has_bioavailability) || 
+          (data.model.has_effect !== model.has_effect) ||
+          (data.model.has_saturation !== model.has_saturation)
+        ) {
+          setParamsToDefault({ id: model.id, combinedModel: data.model });
+        }
       }
     });
   });
@@ -84,11 +126,11 @@ const Model: React.FC = () => {
   }, [submit, isDirty]);
 
 
-  if (isProjectLoading || isModelsLoading || isVariablesLoading) {
+  if (isProjectLoading || isModelsLoading || isVariablesLoading || isProtocolsLoading || isSimulationsLoading || isLoadingCompound || isLoadingUnits) {
     return <div>Loading...</div>;
   }
 
-  if (!model || !project || !variables) {
+  if (!model || !project || !variables || !protocols || !compound || !units) {
     return <div>Not found</div>;
   }
 
@@ -110,10 +152,10 @@ const Model: React.FC = () => {
         <PKPDModelTab model={model} project={project} control={control} updateModel={updateModel} />
       </TabPanel>
       <TabPanel>
-        <MapVariablesTab model={model} project={project} control={control} variables={variables} />
+        <MapVariablesTab model={model} project={project} control={control} variables={variables} units={units} compound={compound} />
       </TabPanel>
       <TabPanel>
-        <ParametersTab model={model} project={project} control={control} variables={variables} />
+        <ParametersTab model={model} project={project} control={control} variables={variables} units={units} compound={compound} />
       </TabPanel>
     </DynamicTabs>
   );
diff --git a/frontend-v2/src/features/model/PKPDModelTab.tsx b/frontend-v2/src/features/model/PKPDModelTab.tsx
index da955912..b4e64aea 100644
--- a/frontend-v2/src/features/model/PKPDModelTab.tsx
+++ b/frontend-v2/src/features/model/PKPDModelTab.tsx
@@ -5,11 +5,13 @@ import { FormControlLabel, Stack, Typography, Grid, Checkbox as MuiCheckbox, Too
 import SelectField from '../../components/SelectField';
 import Checkbox from '../../components/Checkbox';
 import HelpButton from '../../components/HelpButton';
+import { FormData } from './Model';
+import { speciesOptions } from '../projects/Project';
 
 interface Props {
     model: CombinedModelRead;
     project: ProjectRead;
-    control: Control<CombinedModel>;
+    control: Control<FormData>;
     updateModel: (data: CombinedModelUpdateApiArg) => void;
 }
 
@@ -64,10 +66,13 @@ const PKPDModelTab: React.FC<Props> = ({ model, project, control }: Props ) => {
 
     return (
       <Grid container spacing={2}>
+        <Grid item xs={5}>
+          <SelectField label="Species" name="project.species" control={control} options={speciesOptions} formControlProps={{ fullWidth: true }}/>
+        </Grid>
         <Grid container item spacing={2}>
           <Grid item xs={5}>
             <Stack direction="row" alignItems="center" spacing={1}>
-            <SelectField label="PK Model" name="pk_model" control={control} options={pk_model_options} formControlProps={{ fullWidth: true }}/>
+            <SelectField label="PK Model" name="model.pk_model" control={control} options={pk_model_options} formControlProps={{ fullWidth: true }}/>
             <>
             { model.pk_model && 
               <HelpButton title={pk_model_map[model.pk_model].name}>
@@ -83,22 +88,22 @@ const PKPDModelTab: React.FC<Props> = ({ model, project, control }: Props ) => {
           <Stack direction="row" alignItems="center" spacing={1}>
           <Tooltip title="Includes Michaellis-Menten parameters (CLmax and Km)">
           <div>
-          <Checkbox label="Saturation" name="has_saturation" control={control} checkboxFieldProps={{ disabled: isTMDDmodel || !model.pk_model }} />
+          <Checkbox label="Saturation" name="model.has_saturation" control={control} checkboxFieldProps={{ disabled: isTMDDmodel || !model.pk_model }} />
           </div>
           </Tooltip>
           <Tooltip title="Includes an effect compartment">
           <div>
-          <Checkbox label="Effect Compartment" name="has_effect" control={control} checkboxFieldProps={{ disabled: !model.pk_model }}  />
+          <Checkbox label="Effect Compartment" name="model.has_effect" control={control} checkboxFieldProps={{ disabled: !model.pk_model }}  />
           </div>
           </Tooltip>
           <Tooltip title="Includes a time delay following PO of SC administration">
           <div>
-          <Checkbox label="Lag Time" name="has_lag" control={control} checkboxFieldProps={{ disabled: !model.pk_model }}  />
+          <Checkbox label="Lag Time" name="model.has_lag" control={control} checkboxFieldProps={{ disabled: !model.pk_model }}  />
           </div>
           </Tooltip>
           <Tooltip title="Includes bioavailability (F), if not selected F=1">
           <div>
-          <Checkbox label="Bioavailability" name="has_bioavailability" control={control} checkboxFieldProps={{ disabled: !model.pk_model }}  />
+          <Checkbox label="Bioavailability" name="model.has_bioavailability" control={control} checkboxFieldProps={{ disabled: !model.pk_model }}  />
           </div>
           </Tooltip>
           </Stack>
@@ -107,7 +112,7 @@ const PKPDModelTab: React.FC<Props> = ({ model, project, control }: Props ) => {
         <Grid container item spacing={2}>
           <Grid item xs={5}>
             <Stack direction="row" alignItems="center" spacing={1}>
-            <SelectField label="PD Model" name="pd_model" control={control} options={pd_model_options}  formControlProps={{ fullWidth: true }}/>
+            <SelectField label="PD Model" name="model.pd_model" control={control} options={pd_model_options}  formControlProps={{ fullWidth: true }}/>
             <>
             { model.pd_model && 
               <HelpButton title={pd_model_map[model.pd_model].name}>
@@ -123,7 +128,7 @@ const PKPDModelTab: React.FC<Props> = ({ model, project, control }: Props ) => {
             { model.pd_model && (
               <Tooltip title="Includes the Hill coefficient to the PD response">
               <div>
-              <Checkbox label="Hill Coefficient" name="has_hill_coefficient" control={control} checkboxFieldProps={{ disabled: !model.pd_model }} />
+              <Checkbox label="Hill Coefficient" name="model.has_hill_coefficient" control={control} checkboxFieldProps={{ disabled: !model.pd_model }} />
               </div>
               </Tooltip>
             )}
@@ -132,7 +137,7 @@ const PKPDModelTab: React.FC<Props> = ({ model, project, control }: Props ) => {
           <>
             <Grid item xs={5}>
             <Stack direction="row" alignItems="center" spacing={1}>
-              <SelectField label="Secondary PD Model" name="pd_model2" control={control} options={pd_model2_options} formControlProps={{ fullWidth: true }}/>
+              <SelectField label="Secondary PD Model" name="model.pd_model2" control={control} options={pd_model2_options} formControlProps={{ fullWidth: true }}/>
               <>
               {model.pd_model2 && (
                 <HelpButton title={pd_model_map[model.pd_model2].name}>
diff --git a/frontend-v2/src/features/model/ParametersTab.tsx b/frontend-v2/src/features/model/ParametersTab.tsx
index 71761467..8caea8eb 100644
--- a/frontend-v2/src/features/model/ParametersTab.tsx
+++ b/frontend-v2/src/features/model/ParametersTab.tsx
@@ -1,99 +1,43 @@
 import * as React from 'react';
-import { CombinedModel, CombinedModelRead, ProjectRead, VariableRead, useCompoundRetrieveQuery, usePharmacokineticRetrieveQuery, useUnitListQuery, useVariableUpdateMutation } from '../../app/backendApi';
+import { CombinedModel, CombinedModelRead, CompoundRead, ProjectRead, UnitRead, VariableRead, useCombinedModelSetParamsToDefaultsUpdateMutation, useCompoundRetrieveQuery, usePharmacokineticRetrieveQuery, useUnitListQuery, useVariableUpdateMutation } from '../../app/backendApi';
 import { Control } from 'react-hook-form';
 import { TableContainer, Table, TableHead, TableRow, TableCell, TableBody, Stack, Button, Tooltip } from '@mui/material';
 import ParameterRow from './ParameterRow';
-import { param_default as paramDefaults } from './param_default';
 import HelpButton from '../../components/HelpButton';
 import paramPriority from './paramPriority';
+import { getConstVariables, getNoReset, resetToSpeciesDefaults } from './resetToSpeciesDefaults';
+import { FormData } from './Model';
 
 interface Props {
     model: CombinedModelRead;
     project: ProjectRead;
-    control: Control<CombinedModel>;
+    control: Control<FormData>;
     variables: VariableRead[];
+    compound: CompoundRead;
+    units: UnitRead[];
 }
 
 
-const ParametersTab: React.FC<Props> = ({ model, project, control, variables }) => {
+const ParametersTab: React.FC<Props> = ({ model, project, control, variables, compound, units }) => {
 
-    const { data: compound, isLoading: isLoadingCompound } = useCompoundRetrieveQuery({ id: project.compound}, { skip: !project.compound});
-    const [updateVariable] = useVariableUpdateMutation();
-    const { data: pkModel } = usePharmacokineticRetrieveQuery({ id: model.pk_model || 0}, { skip: !model.pk_model });
-    const { data: units, isLoading: isLoadingUnits } = useUnitListQuery({ compoundId: project.compound}, { skip: !project.compound});
+    const [ setParamsToDefault ] = useCombinedModelSetParamsToDefaultsUpdateMutation();
 
-    if (isLoadingUnits || isLoadingCompound) {
-        return <div>Loading...</div>;
-    }
-
-    if (!units || !compound) {
-        return <div>Units not found</div>;
-    }
-
-    let constVariables = variables.filter(variable => variable.constant);
-    if (model.is_library_model) {
-      constVariables = constVariables.filter(variable => variable.name !== "C_Drug");
-    }
-    constVariables.sort((a, b) => {
-      const overallOrder = paramPriority(a) - paramPriority(b);
-      if (overallOrder !== 0) {
-        // first sort by priority
-        return overallOrder;
-      } else {
-        // otherwise use alphabetical ordering
-        return a.name.localeCompare(b.name);
-      }
-    })
-
-    const noReset = !pkModel || !project.species || project.species === 'O';
-
-    const resetToSpeciesDefaults = () => {
-        if (noReset || !project.species) {
-            return;
-        }
-        const modelName: string = pkModel.name
-          .replace("_clinical", "")
-          .replace("_preclinical", "")
-          .replace("tmdd_full_constant_target", "tmdd")
-          .replace("tmdd_QSS_constant_target", "tmdd")
-          .replace("tmdd_full", "tmdd")
-          .replace("tmdd_QSS", "tmdd")
-          .replace("production", "")
-          .replace("elimination", "");
-        const species: string = project.species;
-        const compoundType: string = compound.compound_type || "SM";
-        for (const variable of constVariables) {
-            const varName = variable.name;
-            let defaultVal = paramDefaults[modelName]?.[varName]?.[species]?.[compoundType];
-            if (defaultVal?.unit === "dimensionless") {
-              defaultVal.unit = '';
-            }
-            let defaultUnitId: number | undefined = defaultVal ? units.find(unit => unit.symbol === defaultVal.unit)?.id : undefined;
-            let defaultValue: number | undefined = defaultVal?.value;
-            if (varName.endsWith("_RO_KD")) {
-              defaultValue = compound.dissociation_constant || undefined;
-              defaultUnitId = compound.dissociation_unit;
-            } else if (varName.endsWith("_RO_TC")) {
-              defaultValue = compound.target_concentration || undefined;
-              defaultUnitId = compound.target_concentration_unit;
-            }
-            if (!defaultValue || !defaultUnitId) {
-              continue;
-            }
-            if (defaultUnitId) {
-                updateVariable({ id: variable.id, variable: { ...variable, default_value: defaultValue, unit: defaultUnitId }});
-            }
-        }
+    const constVariables = getConstVariables(variables, model);
+    const noReset = getNoReset(project);
+    
+    
+    const myResetToSpeciesDefaults = () =>  {
+      setParamsToDefault({id: model.id, combinedModel: model });
     }
 
     return (
       <Stack spacing={2}>
       {noReset ? (
       <Tooltip title='No default parameters as "Other" has been selected as species (in "Projects")'>
-        <span><Button variant="contained" color="primary" onClick={resetToSpeciesDefaults} disabled={noReset} sx={{width: 270}}>Reset to Species Defaults</Button></span>
+        <span><Button variant="contained" color="primary" onClick={myResetToSpeciesDefaults} disabled={noReset} sx={{width: 270}}>Reset to Species Defaults</Button></span>
       </Tooltip>
       ) : (
-        <Button variant="contained" color="primary" onClick={resetToSpeciesDefaults} disabled={noReset} sx={{width: 270}}>Reset to Species Defaults</Button>
+        <Button variant="contained" color="primary" onClick={myResetToSpeciesDefaults} disabled={noReset} sx={{width: 270}}>Reset to Species Defaults</Button>
       )}
       <TableContainer>
       <Table>
diff --git a/frontend-v2/src/features/model/VariableRow.tsx b/frontend-v2/src/features/model/VariableRow.tsx
index 270eedd1..9ca1a5cb 100644
--- a/frontend-v2/src/features/model/VariableRow.tsx
+++ b/frontend-v2/src/features/model/VariableRow.tsx
@@ -12,13 +12,14 @@ import {
 } from "@mui/material";
 import { CombinedModel, Variable, useVariableUpdateMutation, useProtocolCreateMutation, useProtocolDestroyMutation, Dose, CombinedModelRead, CompoundRead, ProjectRead, UnitRead, VariableRead, DoseRead } from "../../app/backendApi";
 import useDirty from "../../hooks/useDirty";
+import { FormData } from "./Model";
 
 interface Props {
   project: ProjectRead;
   compound: CompoundRead;
   model: CombinedModelRead;
   variable: VariableRead;
-  control: Control<CombinedModel>;
+  control: Control<FormData>;
   effectVariable: VariableRead | undefined;
   units: UnitRead[];
   timeVariable: VariableRead | undefined;
@@ -31,11 +32,11 @@ const VariableRow: React.FC<Props> = ({ project, compound, model, variable, cont
 
   const { fields: mappings, append: appendMapping, remove: removeMapping } = useFieldArray({
       control,
-      name: "mappings",
+      name: "model.mappings",
   });
   const { fields: derivedVariables, append: derivedVariablesAppend, remove: derivedVariablesRemove } = useFieldArray({
       control,
-      name: "derived_variables",
+      name: "model.derived_variables",
   });
 
   const { control: controlVariable, handleSubmit, reset, setValue, formState: { isDirty: isDirtyForm }, watch} = useForm<Variable>(
diff --git a/frontend-v2/src/features/model/resetToSpeciesDefaults.ts b/frontend-v2/src/features/model/resetToSpeciesDefaults.ts
new file mode 100644
index 00000000..8f1a0dc8
--- /dev/null
+++ b/frontend-v2/src/features/model/resetToSpeciesDefaults.ts
@@ -0,0 +1,71 @@
+import { MutationTrigger } from "@reduxjs/toolkit/dist/query/react/buildHooks";
+import { CombinedModelRead, CompoundRead, PharmacokineticRead, Project, ProjectRead, UnitRead, VariableRead, VariableUpdateApiArg, useVariableUpdateMutation } from "../../app/backendApi";
+import paramPriority from "./paramPriority";
+import { param_default as paramDefaults } from './param_default';
+import { MutationDefinition, BaseQueryFn, FetchArgs, FetchBaseQueryError, FetchBaseQueryMeta } from "@reduxjs/toolkit/dist/query";
+
+// filter out parameters from all variables, and sort them by priority
+export const getConstVariables = (variables: VariableRead[], model: CombinedModelRead) => {
+  let constVariables = variables.filter(variable => variable.constant);
+  if (model.is_library_model) {
+    constVariables = constVariables.filter(variable => variable.name !== "C_Drug");
+  }
+  constVariables.sort((a, b) => {
+    const overallOrder = paramPriority(a) - paramPriority(b);
+    if (overallOrder !== 0) {
+      // first sort by priority
+      return overallOrder;
+    } else {
+      // otherwise use alphabetical ordering
+      return a.name.localeCompare(b.name);
+    }
+  })
+  return constVariables;
+}
+
+export const getNoReset = (project: ProjectRead) => !project.species || project.species === 'O';
+
+type VariableMutation = MutationTrigger<MutationDefinition<VariableUpdateApiArg, BaseQueryFn<string | FetchArgs, unknown, FetchBaseQueryError, {}, FetchBaseQueryMeta>, never, VariableRead, "api">>
+
+export function resetToSpeciesDefaults(pkModel: PharmacokineticRead, project: ProjectRead, compound: CompoundRead, constVariables: VariableRead[], units: UnitRead[], updateVariable: VariableMutation) {
+  if (getNoReset(project) || !project.species) {
+      return;
+  }
+  console.log('resetting to species defaults')
+  const modelName: string = pkModel.name
+    .replace("_clinical", "")
+    .replace("_preclinical", "")
+    .replace("tmdd_full_constant_target", "tmdd")
+    .replace("tmdd_QSS_constant_target", "tmdd")
+    .replace("tmdd_full", "tmdd")
+    .replace("tmdd_QSS", "tmdd")
+    .replace("production", "")
+    .replace("elimination", "");
+  const species: string = project.species;
+  const compoundType: string = compound.compound_type || "SM";
+  console.log(modelName, species, compoundType)
+  for (const variable of constVariables) {
+    const varName = variable.name;
+    let defaultVal = paramDefaults[modelName]?.[varName]?.[species]?.[compoundType];
+    console.log(variable.name, defaultVal)
+    if (defaultVal?.unit === "dimensionless") {
+      defaultVal.unit = '';
+    }
+    let defaultUnitId: number | undefined = defaultVal ? units.find(unit => unit.symbol === defaultVal.unit)?.id : undefined;
+    let defaultValue: number | undefined = defaultVal?.value;
+    if (varName.endsWith("_RO_KD")) {
+      defaultValue = compound.dissociation_constant || undefined;
+      defaultUnitId = compound.dissociation_unit;
+    } else if (varName.endsWith("_RO_TC")) {
+      defaultValue = compound.target_concentration || undefined;
+      defaultUnitId = compound.target_concentration_unit;
+    }
+    if (!defaultValue || !defaultUnitId) {
+      continue;
+    }
+    console.log(defaultValue, defaultUnitId)
+    if (defaultUnitId) {
+      updateVariable({ id: variable.id, variable: { ...variable, default_value: defaultValue, unit: defaultUnitId }});
+    }
+  }
+}
\ No newline at end of file
diff --git a/frontend-v2/src/features/projects/Project.tsx b/frontend-v2/src/features/projects/Project.tsx
index 859a7385..4ac65df0 100644
--- a/frontend-v2/src/features/projects/Project.tsx
+++ b/frontend-v2/src/features/projects/Project.tsx
@@ -7,11 +7,10 @@ import {
   TableRow,
   IconButton,
   Radio,
-  Box,
+  Typography,
 } from "@mui/material";
 import { Delete, PersonAdd } from "@mui/icons-material";
 import { Compound, Project, ProjectAccess, useProjectDestroyMutation, useCompoundRetrieveQuery, useCompoundUpdateMutation, useProjectUpdateMutation, CompoundRead, ProjectRead } from "../../app/backendApi";
-import SelectField from "../../components/SelectField";
 import UserAccess from "./UserAccess";
 import { setProject } from "../main/mainSlice";
 import TextField from "../../components/TextField";
@@ -29,6 +28,14 @@ export interface FormData {
   compound: Compound;
 }
 
+export const speciesOptions = [
+    { value: "M", label: "Mouse" },
+    { value: "R", label: "Rat" },
+    { value: "K", label: "Monkey" },
+    { value: "H", label: "Human" },
+    { value: "O", label: "Other" },
+  ]
+
 const ProjectRow: React.FC<Props> = ({ project, isSelected, otherProjectNames }) => {
   const dispatch = useDispatch();
   const [
@@ -130,13 +137,7 @@ const ProjectRow: React.FC<Props> = ({ project, isSelected, otherProjectNames })
     fullWidth: true,
   }
 
-  const speciesOptions = [
-    { value: "M", label: "Mouse" },
-    { value: "R", label: "Rat" },
-    { value: "K", label: "Monkey" },
-    { value: "H", label: "Human" },
-    { value: "O", label: "Other" },
-  ]
+  
 
   const validateName = (value: string) => {
     if (otherProjectNames.includes(value)) {
@@ -155,7 +156,7 @@ const ProjectRow: React.FC<Props> = ({ project, isSelected, otherProjectNames })
         <TextField name="project.name" control={control} textFieldProps={defaultProps} rules={{ required: true, validate: validateName }} /> 
       </TableCell>
       <TableCell>
-        <SelectField name="project.species" options={speciesOptions} control={control} selectProps={defaultProps} /> 
+        <Typography>{ speciesOptions.find(s => s.value === project.species)?.label }</Typography>
       </TableCell>
       <TableCell>
         <TextField name="compound.name" control={control} textFieldProps={defaultProps} rules={{ required: true }} /> 
diff --git a/pkpdapp/pkpdapp/api/views/models.py b/pkpdapp/pkpdapp/api/views/models.py
index a0ca364a..413059d7 100644
--- a/pkpdapp/pkpdapp/api/views/models.py
+++ b/pkpdapp/pkpdapp/api/views/models.py
@@ -74,7 +74,30 @@ def set_variables_from_inference(self, request, pk):
         obj.set_variables_from_inference(inference)
         serializer = self.serializer_class(obj)
         return response.Response(serializer.data)
-
+    
+    @decorators.action(
+        detail=True,
+        methods=['PUT'],
+        serializer_class=CombinedModelSerializer,
+    )
+    def set_params_to_defaults(self, request, pk):
+        obj = self.get_object()
+        project = obj.get_project()
+        if project is None:
+            return response.Response(
+                {'project': 'project not found'},
+                status.HTTP_400_BAD_REQUEST
+            )
+        compound = project.compound
+        if compound is None:
+            return response.Response(
+                {'compound': 'compound not found'},
+                status.HTTP_400_BAD_REQUEST
+            )
+        print('setting params to defaults', project.species, compound.compound_type)
+        obj.reset_params_to_defaults(project.species, compound.compound_type)
+        serializer = self.serializer_class(obj)
+        return response.Response(serializer.data)
 
 class PharmacodynamicView(viewsets.ModelViewSet):
     queryset = PharmacodynamicModel.objects.all()
diff --git a/pkpdapp/pkpdapp/models/combined_model.py b/pkpdapp/pkpdapp/models/combined_model.py
index da7cde89..c64b9d54 100644
--- a/pkpdapp/pkpdapp/models/combined_model.py
+++ b/pkpdapp/pkpdapp/models/combined_model.py
@@ -16,6 +16,7 @@
 from django.db import models
 from django.urls import reverse
 import logging
+from pkpdapp.utils.default_params import defaults
 
 logger = logging.getLogger(__name__)
 
@@ -534,6 +535,32 @@ def save(self, force_insert=False, force_update=False, *args, **kwargs):
         self.__original_has_lag = self.has_lag
         self.__original_has_hill_coefficient = self.has_hill_coefficient
         self.__original_has_bioavailability = self.has_bioavailability
+        
+    def reset_params_to_defaults(self, species, compoundType):
+        if self.is_library_model:
+            model_name = self.pk_model.name\
+                .replace("_clinical", "")\
+                .replace("_preclinical", "")\
+                .replace("tmdd_full_constant_target", "tmdd")\
+                .replace("tmdd_QSS_constant_target", "tmdd")\
+                .replace("tmdd_full", "tmdd")\
+                .replace("tmdd_QSS", "tmdd")\
+                .replace("production", "")\
+                .replace("elimination", "")
+            for v in self.variables.all():
+                varName = v.name;
+                defaultVal = defaults.get(model_name, {}).get(varName, {}).get(species, {}).get(compoundType, None)
+                if defaultVal is None:
+                    continue
+                if defaultVal.get('unit', '') == "dimensionless":
+                  defaultVal['unit'] = '';
+                unit = Unit.objects.filter(symbol=defaultVal.get('unit', '')).first()
+                value = defaultVal.get('value', None)
+                if value is None or unit is None:
+                  continue;
+                v.default_value = value
+                v.unit = unit
+                v.save()
 
 
 class PkpdMapping(StoredModel):
@@ -599,7 +626,9 @@ def create_stored_mapping(self, new_pkpd_model, new_variables):
         }
         stored_mapping = PkpdMapping.objects.create(**stored_kwargs)
         return stored_mapping
-
+    
+    
+  
 
 class DerivedVariable(StoredModel):
     pkpd_model = models.ForeignKey(
diff --git a/pkpdapp/pkpdapp/models/mechanistic_model.py b/pkpdapp/pkpdapp/models/mechanistic_model.py
index 5d013dae..b68268e2 100644
--- a/pkpdapp/pkpdapp/models/mechanistic_model.py
+++ b/pkpdapp/pkpdapp/models/mechanistic_model.py
@@ -70,3 +70,4 @@ def clean(self):
             self.create_myokit_model()
         except Exception as e:
             raise ValidationError({'mmt': str(e)})
+        
diff --git a/pkpdapp/pkpdapp/tests/test_models/test_mechanistic_model.py b/pkpdapp/pkpdapp/tests/test_models/test_mechanistic_model.py
index 53651347..54248126 100644
--- a/pkpdapp/pkpdapp/tests/test_models/test_mechanistic_model.py
+++ b/pkpdapp/pkpdapp/tests/test_models/test_mechanistic_model.py
@@ -89,6 +89,17 @@ def test_store_model(self):
         v = stored_model.variables.get(qname='PKCompartment.A1')
         self.assertEqual(v.protocol.name, 'my_cool_protocol')
         self.assertNotEqual(v.protocol.id, self.p.id)
+        
+    def test_reset_to_default(self):
+        v = self.model.variables.get(qname='PKCompartment.CL')
+        self.assertNotEqual(v.default_value, 8)
+        self.assertNotEqual(v.unit.symbol, 'mL/h')
+
+        self.model.reset_params_to_defaults('H', 'LM')
+
+        v = self.model.variables.get(qname='PKCompartment.CL')
+        self.assertEqual(v.default_value, 8)
+        self.assertEqual(v.unit.symbol, 'mL/h')
 
     def test_myokit_model(self):
         model = self.model.get_myokit_model()
diff --git a/pkpdapp/pkpdapp/utils/default_params.py b/pkpdapp/pkpdapp/utils/default_params.py
new file mode 100644
index 00000000..a0b393ee
--- /dev/null
+++ b/pkpdapp/pkpdapp/utils/default_params.py
@@ -0,0 +1,43 @@
+# This file is part of PKPDApp (https://github.com/pkpdapp-team/pkpdapp) which
+# is released under the BSD 3-clause license. See accompanying LICENSE.md for
+# copyright notice and full license details.
+#
+import openpyxl
+
+
+# Load the workbook
+workbook = openpyxl.load_workbook(
+    'pkpdapp/migrations/models/ParametersValue_Species.xlsx', data_only=True)
+
+sheet_names = ['1cmpt_PK_Model', '2cmpt_PK_Model',
+               '3cmpt_PK_Model', '1cmpt_TMDD_Model',
+               '2cmpt_TMDD_Model']
+model_names = ['one_compartment', 'two_compartment',
+               'three_compartment', 'one_compartment_tmdd',
+               'two_compartment_tmdd']
+species_list = ['M', 'R', 'K', 'H']
+compound_type = ['SM', 'LM']
+clinical = [False, False, False, True]
+
+defaults = {}
+
+for sheet_name, model_name in zip(sheet_names, model_names):
+    worksheet = workbook[sheet_name]
+
+    defaults[model_name] = {}
+    for row in worksheet.iter_rows():
+        parameter = row[0].value
+        if parameter is None:
+            continue
+        defaults[model_name][parameter] = {}
+        for i, species in enumerate(species_list):
+            defaults[model_name][parameter][species] = {}
+            for j, ctype in enumerate(compound_type):
+                rowi = i * 4 + j * 2 + 1
+                value = row[rowi].value
+                unit = row[rowi + 1].value
+                if_clinical = clinical[i]
+                defaults[model_name][parameter][species][ctype] = {
+                    'value': value,
+                    'unit': unit,
+                }
\ No newline at end of file
diff --git a/pkpdapp/schema.yml b/pkpdapp/schema.yml
index 5ae83c30..d7b85b2d 100644
--- a/pkpdapp/schema.yml
+++ b/pkpdapp/schema.yml
@@ -443,6 +443,39 @@ paths:
       responses:
         '204':
           description: No response body
+  /api/combined_model/{id}/set_params_to_defaults/:
+    put:
+      operationId: combined_model_set_params_to_defaults_update
+      parameters:
+      - in: path
+        name: id
+        schema:
+          type: integer
+        description: A unique integer value identifying this combined model.
+        required: true
+      tags:
+      - combined_model
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/CombinedModel'
+          application/x-www-form-urlencoded:
+            schema:
+              $ref: '#/components/schemas/CombinedModel'
+          multipart/form-data:
+            schema:
+              $ref: '#/components/schemas/CombinedModel'
+        required: true
+      security:
+      - cookieAuth: []
+      responses:
+        '200':
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/CombinedModel'
+          description: ''
   /api/combined_model/{id}/set_variables_from_inference/:
     put:
       operationId: combined_model_set_variables_from_inference_update
@@ -2551,12 +2584,6 @@ paths:
         schema:
           type: integer
         description: Enable conversions based on compound information
-      - in: query
-        name: is_target
-        schema:
-          type: boolean
-        description: (optional, default=false) true if unit is a target concentration
-          unit
       tags:
       - unit
       security:
diff --git a/requirements.txt b/requirements.txt
index dd593197..f605bedb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -24,3 +24,4 @@ pymc3>=3.11.5
 django-auth-ldap>=4.1.0
 pyyaml>=6.0.0
 drf-spectacular>=0.26.2
+openpyxl>=3.1.2
\ No newline at end of file

From 477acbcd50a59b9ec9523edb21e126a1c7f605df Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Wed, 1 Nov 2023 10:02:56 +0000
Subject: [PATCH 07/22] Add to the title the "Name" of the project as defined
 in Project's page

---
 frontend-v2/src/features/main/Sidebar.tsx | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/frontend-v2/src/features/main/Sidebar.tsx b/frontend-v2/src/features/main/Sidebar.tsx
index 85d30bee..da5d6e1f 100644
--- a/frontend-v2/src/features/main/Sidebar.tsx
+++ b/frontend-v2/src/features/main/Sidebar.tsx
@@ -26,7 +26,7 @@ import { logout } from '../login/loginSlice';
 import { useAppDispatch } from '../../app/hooks';
 import ErrorIcon from '@mui/icons-material/Error';
 import { Tooltip } from '@mui/material';
-import { useCombinedModelListQuery, useProtocolListQuery } from '../../app/backendApi';
+import { useCombinedModelListQuery, useProjectRetrieveQuery, useProtocolListQuery } from '../../app/backendApi';
 import { Protocol } from "../../app/backendApi";
 
 const drawerWidth = 240;
@@ -41,6 +41,7 @@ export default function Sidebar() {
   const { data: models, isLoading: isModelsLoading } = useCombinedModelListQuery({projectId: projectId || 0}, { skip: !projectId})
   const { data: protocols, error: protocolsError, isLoading: isProtocolsLoading } = useProtocolListQuery({projectId: projectId || 0}, { skip: !projectId})
   const model = models?.[0] || null;
+  const { data: project, isLoading: isProjectLoading } = useProjectRetrieveQuery({id: projectId || 0}, { skip: !projectId })
 
   let errors: { [key: string]: string } = {};
   if ((model && model.pk_model === null) || (model && model.pd_model && model.mappings.length === 0) || (protocols && protocols.length === 0)) {
@@ -143,7 +144,8 @@ export default function Sidebar() {
             <MenuIcon />
           </IconButton>
           <Typography variant="h6" noWrap component="div" sx={{ flexGrow: 1 }}>
-            PK/PD Simulator
+            
+            PK/PD Simulator {project && ` - ${project.name}`}
           </Typography>
           <IconButton
             onClick={() => dispatch(logout())}

From eb23ec67a33630056a4053aa0682f476bb3220fe Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Wed, 1 Nov 2023 10:50:30 +0000
Subject: [PATCH 08/22] export to csv button

---
 .../src/features/simulation/Simulations.tsx   | 70 +++++++++++++++----
 1 file changed, 58 insertions(+), 12 deletions(-)

diff --git a/frontend-v2/src/features/simulation/Simulations.tsx b/frontend-v2/src/features/simulation/Simulations.tsx
index 7312ad36..d3fca731 100644
--- a/frontend-v2/src/features/simulation/Simulations.tsx
+++ b/frontend-v2/src/features/simulation/Simulations.tsx
@@ -1,4 +1,4 @@
-import { Alert, Container, Grid, Snackbar, Stack, Typography } from '@mui/material';
+import { Alert, Button, Container, Grid, Snackbar, Stack, Typography } from '@mui/material';
 import { useSelector } from 'react-redux';
 import { RootState } from '../../app/store';
 import { Simulate, SimulateResponse, Simulation, SimulationPlotRead, SimulationRead, SimulationSlider, SimulationSliderRead, UnitRead, VariableRead, useCombinedModelListQuery, useCombinedModelSimulateCreateMutation, useCompoundRetrieveQuery, useProjectRetrieveQuery, useProtocolListQuery, useSimulationListQuery, useSimulationUpdateMutation, useUnitListQuery, useVariableListQuery, useVariableUpdateMutation } from '../../app/backendApi';
@@ -7,7 +7,7 @@ import { useEffect, useMemo, useState } from 'react';
 import SimulationPlotView from './SimulationPlotView';
 import SimulationSliderView from './SimulationSliderView';
 import DropdownButton from '../../components/DropdownButton';
-import { Add } from '@mui/icons-material';
+import { Add, NorthWestSharp } from '@mui/icons-material';
 import FloatField from '../../components/FloatField';
 import useDirty from '../../hooks/useDirty';
 import UnitField from '../../components/UnitField';
@@ -19,7 +19,7 @@ interface ErrorObject {
   error: string;
 };
 
-const getSimulateInput = (simulation: Simulation, sliderValues: SliderValues, variables?: VariableRead[], timeMax?: number ): Simulate => {
+const getSimulateInput = (simulation: Simulation, sliderValues: SliderValues, variables?: VariableRead[], timeMax?: number, allOutputs: boolean = false ): Simulate => {
     let outputs: string[] = [];
     let simulateVariables: {[key: string]: number} = {};
     for (const slider of simulation?.sliders || []) {
@@ -30,11 +30,19 @@ const getSimulateInput = (simulation: Simulation, sliderValues: SliderValues, va
         }
       }
     }
-    for (const plot of simulation?.plots || []) {
-      for (const y_axis of plot.y_axes) {
-        const variable = variables?.find((v) => v.id === y_axis.variable);
-        if (variable && !outputs.includes(variable.name)) {
-          outputs.push(variable.qname);
+    if (allOutputs) {
+      for (const v of variables || []) {
+        if (!v.constant) {
+          outputs.push(v.qname);
+        }
+      }
+    } else {
+      for (const plot of simulation?.plots || []) {
+        for (const y_axis of plot.y_axes) {
+          const variable = variables?.find((v) => v.id === y_axis.variable);
+          if (variable && !outputs.includes(variable.name)) {
+            outputs.push(variable.qname);
+          }
         }
       }
     }
@@ -124,14 +132,19 @@ const Simulations: React.FC = () => {
       reset(simulation);
     }
   }, [simulation, reset, variables]);
+  
+  const getTimeMax = (simulation: SimulationRead, variables: VariableRead[]): number => {
+    const timeMaxUnit = units?.find((u) => u.id === simulation.time_max_unit);
+    const compatibleTimeUnit = timeMaxUnit?.compatible_units?.find((u) => parseInt(u.id) === model?.time_unit); 
+    const timeMaxConversionFactor = compatibleTimeUnit ? parseFloat(compatibleTimeUnit.conversion_factor) : 1.0;
+    const timeMax = (simulation?.time_max || 0) * timeMaxConversionFactor;
+    return timeMax;
+  }
 
   // generate a simulation if slider values change
   useEffect(() => {
     if (simulation?.id && sliderValues && variables && model && protocols && compound) {
-      const timeMaxUnit = units?.find((u) => u.id === simulation.time_max_unit);
-      const compatibleTimeUnit = timeMaxUnit?.compatible_units?.find((u) => parseInt(u.id) === model.time_unit); 
-      const timeMaxConversionFactor = compatibleTimeUnit ? parseFloat(compatibleTimeUnit.conversion_factor) : 1.0;
-      const timeMax = (simulation?.time_max || 0) * timeMaxConversionFactor;
+      const timeMax = getTimeMax(simulation, variables);
       simulate({ id: model.id, simulate: getSimulateInput(simulation, sliderValues, variables, timeMax)})
       .then((response) => {
         setLoadingSimulate(false);
@@ -142,6 +155,38 @@ const Simulations: React.FC = () => {
       });
     }
   }, [simulation, simulate, sliderValues, model, protocols, variables, compound]);
+  
+  const exportSimulation = () => {
+    if (simulation && variables && model && protocols && compound && sliderValues && project) {
+      const timeMax = getTimeMax(simulation, variables);
+      simulate({ id: model.id, simulate: getSimulateInput(simulation, sliderValues, variables, timeMax, true)})
+      .then((response) => {
+        if ("data" in response) {
+          const data = response.data as SimulateResponse;
+          const nrows = data.outputs[Object.keys(data.outputs)[0]].length;
+          const cols = Object.keys(data.outputs)
+          const vars = cols.map((vid) => variables.find((v) => v.id === parseInt(vid)));
+          const varNames = vars.map((v) => v?.qname || '');
+          const ncols = cols.length;
+          let rows = new Array(nrows + 1);
+          rows[0] = varNames;
+          for (let i = 0; i < nrows; i++) {
+            rows[i + 1] = new Array(ncols);
+            for (let j = 0; j < ncols; j++) {
+              rows[i + 1][j] = data.outputs[cols[j]][i];
+            }
+          }
+          const csvContent = rows.map(e => e.join(",")).join("\n");
+          const blob = new Blob([csvContent], { type: 'text/csv;charset=utf-8;' });
+          const url = URL.createObjectURL(blob);
+          const link = document.createElement('a');
+          link.download = `${project.name}.csv`;
+          link.href = url;
+          link.click();
+        }
+      });
+    }
+  }
 
   
   // save simulation every second if dirty
@@ -295,6 +340,7 @@ const Simulations: React.FC = () => {
         <Stack direction={'row'} alignItems={'center'} spacing={2} justifyContent="flex-start">
           <FloatField label="Simulation Duration" name="time_max" control={control} />
           <UnitField label="Unit" name="time_max_unit" baseUnit={units.find(u => u.id === simulation?.time_max_unit)} control={control} selectProps={{ style: { flexShrink: 0 }}} />
+          <Button variant="contained" onClick={exportSimulation}>Export to CSV</Button>
         </Stack>
         <Stack direction={'row'} alignItems={'center'}>
           <Typography variant="h6">Parameters</Typography>

From 77b40157e4a8d1daa112f3d5d448bdc3259c8838 Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Wed, 1 Nov 2023 13:19:22 +0000
Subject: [PATCH 09/22] fix amount unit for preclinical models

---
 frontend-v2/src/features/model/MapVariablesTab.tsx | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/frontend-v2/src/features/model/MapVariablesTab.tsx b/frontend-v2/src/features/model/MapVariablesTab.tsx
index 6392180d..a956de63 100644
--- a/frontend-v2/src/features/model/MapVariablesTab.tsx
+++ b/frontend-v2/src/features/model/MapVariablesTab.tsx
@@ -17,8 +17,9 @@ interface Props {
 
 const MapVariablesTab: React.FC<Props> = ({ model, project, control, variables, units, compound }: Props ) => {
     
+    const isPreclinical = project.species !== 'H' && model.is_library_model;
     const concentrationUnit = units.find((unit) => unit.symbol === "pmol/L");
-    const amountUnit = units.find((unit) => unit.symbol === "pmol");
+    const amountUnit = isPreclinical ? units.find((unit) => unit.symbol === "pmol/kg") : units.find((unit) => unit.symbol === "pmol");
     if (concentrationUnit === undefined || amountUnit === undefined) {
       return (<>No concentration or amount unit found</>);
     }
@@ -38,8 +39,8 @@ const MapVariablesTab: React.FC<Props> = ({ model, project, control, variables,
       const bIsConcentration = concentrationUnit?.compatible_units.find((unit) => parseInt(unit.id) === b.unit) !== undefined;
       const bIsAmount = amountUnit?.compatible_units.find((unit) => parseInt(unit.id) === b.unit) !== undefined;
 
-      const aValue = aIsConcentration ? 1 : (aIsAmount ? 2 : 0);
-      const bValue = bIsConcentration ? 1 : (bIsAmount ? 2 : 0);
+      const aValue = aIsConcentration ? 2 : (aIsAmount ? 1 : 0);
+      const bValue = bIsConcentration ? 2 : (bIsAmount ? 1 : 0);
 
       if (aValue !== bValue) {
         return bValue - aValue;

From c0eb2bfe26e54549a80f6bfadc5d236bf970cf1b Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Wed, 1 Nov 2023 13:28:13 +0000
Subject: [PATCH 10/22] filter out F and ka for library models if Aa is not
 dosed

---
 frontend-v2/src/features/model/ParametersTab.tsx | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/frontend-v2/src/features/model/ParametersTab.tsx b/frontend-v2/src/features/model/ParametersTab.tsx
index 8caea8eb..8c1ca84a 100644
--- a/frontend-v2/src/features/model/ParametersTab.tsx
+++ b/frontend-v2/src/features/model/ParametersTab.tsx
@@ -22,10 +22,15 @@ const ParametersTab: React.FC<Props> = ({ model, project, control, variables, co
 
     const [ setParamsToDefault ] = useCombinedModelSetParamsToDefaultsUpdateMutation();
 
-    const constVariables = getConstVariables(variables, model);
+    // if Aa is not dosed, then we will filter out F and ka (for library models)
+    const aaIsNotDosed = variables.filter((variable) => variable.protocol && variable.name === 'Aa').length === 0;
+    const willFilterFandKa = model.is_library_model && aaIsNotDosed;
+    let constVariables = getConstVariables(variables, model);
+    if (willFilterFandKa) {
+      constVariables = constVariables.filter((variable) => !['F', 'ka'].includes(variable.name));
+    }
     const noReset = getNoReset(project);
     
-    
     const myResetToSpeciesDefaults = () =>  {
       setParamsToDefault({id: model.id, combinedModel: model });
     }

From a9295855c6fc9473d5db90ee63b1d0ce9cc2f449 Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Wed, 1 Nov 2023 13:30:32 +0000
Subject: [PATCH 11/22] add variable description for slider add pulldown

---
 frontend-v2/src/features/simulation/Simulations.tsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/frontend-v2/src/features/simulation/Simulations.tsx b/frontend-v2/src/features/simulation/Simulations.tsx
index d3fca731..0c75a4a4 100644
--- a/frontend-v2/src/features/simulation/Simulations.tsx
+++ b/frontend-v2/src/features/simulation/Simulations.tsx
@@ -263,7 +263,7 @@ const Simulations: React.FC = () => {
   inputs.sort((a, b) => { return paramPriority(a) - paramPriority(b) });
   const addPlotOptions = outputsSorted.map((variable) => ({ value: variable.id, label: variable.description ? `${variable.name} (${variable.description})` : variable.name }));
   const sliderVarIds = sliders.map(v => v.variable)
-  const addSliderOptions = inputs.filter(v => !sliderVarIds.includes(v.id)).map((variable) => ({ value: variable.id, label: variable.name }));
+  const addSliderOptions = inputs.filter(v => !sliderVarIds.includes(v.id)).map((variable) => ({ value: variable.id, label: `${variable.name} (${variable.description})` }));
 
   const handleAddPlot = (variableId: number) => {
     const variable = variables?.find((v) => v.id === variableId);

From 119942cec36034bf83621bd2f3fc80d6f103946b Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Wed, 1 Nov 2023 14:16:02 +0000
Subject: [PATCH 12/22] improve display of help videos

---
 frontend-v2/src/features/help/Help.tsx    |  1 +
 frontend-v2/src/features/help/HelpTab.tsx | 16 ++++++++--------
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/frontend-v2/src/features/help/Help.tsx b/frontend-v2/src/features/help/Help.tsx
index fd512957..89240f44 100644
--- a/frontend-v2/src/features/help/Help.tsx
+++ b/frontend-v2/src/features/help/Help.tsx
@@ -3,6 +3,7 @@ import { DynamicTabs, TabPanel } from '../../components/DynamicTabs';
 import HelpTab from './HelpTab';
 import { parse } from 'papaparse';
 import { set } from 'react-hook-form';
+import { Container } from '@mui/material';
 
 export type Question = {
   question: string;
diff --git a/frontend-v2/src/features/help/HelpTab.tsx b/frontend-v2/src/features/help/HelpTab.tsx
index 7c8afb55..0e0d2484 100644
--- a/frontend-v2/src/features/help/HelpTab.tsx
+++ b/frontend-v2/src/features/help/HelpTab.tsx
@@ -1,4 +1,4 @@
-import { Accordion, AccordionDetails, AccordionSummary, Chip, Stack, Typography } from "@mui/material";
+import { Accordion, AccordionDetails, AccordionSummary, Box, Card, Chip, Grid, Stack, Typography } from "@mui/material";
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
 import { Question, TutorialVideo } from "./Help";
 import ReactPlayer from 'react-player/youtube'
@@ -29,18 +29,18 @@ const HelpTab: React.FC<Props> = ({ questions, videos }) => {
           )
         })}
       </Stack>
-      <Stack spacing={2}>
+      <Box sx={{ display: 'flex', flexWrap: 'wrap' }}>
         {videos.map((video, index) => {
           return (
-            <div key={index}>
+            <Card sx={{ width: '500px', margin: 2, padding: 1 }}>
               <Typography variant='h6' >{video.title}</Typography>
-              <Stack direction="row" spacing={1} sx={{ marginBottom: 1 }}>
+              <Box sx={{ display: 'flex', flexWrap: 'wrap' }}>
               { video.keywords.map((keyword, index) => {
                 return (
-                  <Chip key={index} size="small" label={keyword} />
+                  <Chip key={index} size="small" label={keyword} sx={{ margin: 0.2 }} />
                 )
               })}
-              </Stack>
+              </Box>
               <iframe
                 key={index}
                 allowFullScreen
@@ -48,10 +48,10 @@ const HelpTab: React.FC<Props> = ({ questions, videos }) => {
                 style={{ border: "none", width: "100%", aspectRatio: "16/9" }}
                 title={video.title}
               />
-            </div>
+            </Card>
           )
         })}
-      </Stack>
+      </Box>
     </div>
   );
 }

From 922f5b880f84498428429414ddb2e1b143422cb7 Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Wed, 1 Nov 2023 14:18:44 +0000
Subject: [PATCH 13/22] parameter slidesr

---
 frontend-v2/src/features/simulation/Simulations.tsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/frontend-v2/src/features/simulation/Simulations.tsx b/frontend-v2/src/features/simulation/Simulations.tsx
index 0c75a4a4..a9786f65 100644
--- a/frontend-v2/src/features/simulation/Simulations.tsx
+++ b/frontend-v2/src/features/simulation/Simulations.tsx
@@ -343,7 +343,7 @@ const Simulations: React.FC = () => {
           <Button variant="contained" onClick={exportSimulation}>Export to CSV</Button>
         </Stack>
         <Stack direction={'row'} alignItems={'center'}>
-          <Typography variant="h6">Parameters</Typography>
+          <Typography variant="h6">Parameter Sliders</Typography>
           <DropdownButton options={addSliderOptions} onOptionSelected={handleAddSlider}  data_cy="add-parameter-slider">
             <Add />
           </DropdownButton>

From 19bc44d577f72127f874454d77bba0078f81bd73 Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Wed, 1 Nov 2023 14:20:57 +0000
Subject: [PATCH 14/22] remove cm units

---
 pkpdapp/pkpdapp/migrations/0007_initial_units.py | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/pkpdapp/pkpdapp/migrations/0007_initial_units.py b/pkpdapp/pkpdapp/migrations/0007_initial_units.py
index 47923675..1fab8799 100644
--- a/pkpdapp/pkpdapp/migrations/0007_initial_units.py
+++ b/pkpdapp/pkpdapp/migrations/0007_initial_units.py
@@ -183,14 +183,6 @@ def load_units(apps, schema_editor):
             'symbol': '1/L',
             'unit': 1 / L
         },
-        {
-            'symbol': 'cm^3',
-            'unit': (1e-2 * m)**3,
-        },
-        {
-            'symbol': 'cm^3/d',
-            'unit': (1e-2 * m)**3 / (24 * h),
-        },
         {
             'symbol': 'kg',
             'unit': 1e3 * g,

From 0e8dd852c64dfb1f73fa6f86cd00efc4b496e901 Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Mon, 6 Nov 2023 09:59:13 +0000
Subject: [PATCH 15/22] remove tlag dv when tlag checkbox unchecked

---
 frontend-v2/src/features/model/Model.tsx | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/frontend-v2/src/features/model/Model.tsx b/frontend-v2/src/features/model/Model.tsx
index e1de26a6..d1171bcd 100644
--- a/frontend-v2/src/features/model/Model.tsx
+++ b/frontend-v2/src/features/model/Model.tsx
@@ -77,6 +77,11 @@ const Model: React.FC = () => {
     if (!model || !project) {
       return;
     }
+
+    // if tlag checkbox is unchecked, then remove tlag derived variables
+    if (data.model.has_lag !== model.has_lag && !data.model.has_lag) {
+      data.model.derived_variables = data.model.derived_variables.filter((dv) => dv.type !== 'TLG');
+    }
     
     // if only pd_model has changed, need to clear pd_model2
     if (data.model.pd_model !== model?.pd_model) {

From c48e2160aeb7344f67e1612de36e0424a6dd6826 Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Mon, 6 Nov 2023 12:44:57 +0000
Subject: [PATCH 16/22] auto default new params

---
 frontend-v2/src/features/model/Model.tsx     | 9 ++-------
 pkpdapp/pkpdapp/api/views/models.py          | 1 +
 pkpdapp/pkpdapp/models/combined_model.py     | 6 ++++--
 pkpdapp/pkpdapp/models/myokit_model_mixin.py | 8 ++++++++
 4 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/frontend-v2/src/features/model/Model.tsx b/frontend-v2/src/features/model/Model.tsx
index d1171bcd..2ff6aa0b 100644
--- a/frontend-v2/src/features/model/Model.tsx
+++ b/frontend-v2/src/features/model/Model.tsx
@@ -104,13 +104,8 @@ const Model: React.FC = () => {
           const time_max_unit = response.data.time_unit;
           updateSimulation({ id: simulation.id, simulation: { ...simulation, time_max_unit } });
         }
-        // if the pk model has changed or any of the checkboxes have changed, need to reset the parameters
-        if (
-          (data.model.pk_model !== model?.pk_model) || 
-          (data.model.has_bioavailability !== model.has_bioavailability) || 
-          (data.model.has_effect !== model.has_effect) ||
-          (data.model.has_saturation !== model.has_saturation)
-        ) {
+        // if the pk model has changed, need to reset the parameters
+        if (data.model.pk_model !== model?.pk_model) {
           setParamsToDefault({ id: model.id, combinedModel: data.model });
         }
       }
diff --git a/pkpdapp/pkpdapp/api/views/models.py b/pkpdapp/pkpdapp/api/views/models.py
index 413059d7..cb80344a 100644
--- a/pkpdapp/pkpdapp/api/views/models.py
+++ b/pkpdapp/pkpdapp/api/views/models.py
@@ -99,6 +99,7 @@ def set_params_to_defaults(self, request, pk):
         serializer = self.serializer_class(obj)
         return response.Response(serializer.data)
 
+
 class PharmacodynamicView(viewsets.ModelViewSet):
     queryset = PharmacodynamicModel.objects.all()
     serializer_class = PharmacodynamicSerializer
diff --git a/pkpdapp/pkpdapp/models/combined_model.py b/pkpdapp/pkpdapp/models/combined_model.py
index c64b9d54..0caa2c04 100644
--- a/pkpdapp/pkpdapp/models/combined_model.py
+++ b/pkpdapp/pkpdapp/models/combined_model.py
@@ -536,7 +536,7 @@ def save(self, force_insert=False, force_update=False, *args, **kwargs):
         self.__original_has_hill_coefficient = self.has_hill_coefficient
         self.__original_has_bioavailability = self.has_bioavailability
         
-    def reset_params_to_defaults(self, species, compoundType):
+    def reset_params_to_defaults(self, species, compoundType, variables=None):
         if self.is_library_model:
             model_name = self.pk_model.name\
                 .replace("_clinical", "")\
@@ -547,7 +547,9 @@ def reset_params_to_defaults(self, species, compoundType):
                 .replace("tmdd_QSS", "tmdd")\
                 .replace("production", "")\
                 .replace("elimination", "")
-            for v in self.variables.all():
+            if variables is None:
+                variables = self.variables.all()
+            for v in variables:
                 varName = v.name;
                 defaultVal = defaults.get(model_name, {}).get(varName, {}).get(species, {}).get(compoundType, None)
                 if defaultVal is None:
diff --git a/pkpdapp/pkpdapp/models/myokit_model_mixin.py b/pkpdapp/pkpdapp/models/myokit_model_mixin.py
index 2c64d513..d9a509f7 100644
--- a/pkpdapp/pkpdapp/models/myokit_model_mixin.py
+++ b/pkpdapp/pkpdapp/models/myokit_model_mixin.py
@@ -269,6 +269,14 @@ def update_model(self):
                     f"{v.qname}, id = {v.id} "
                     f"constant = {v.constant}, state = {v.state}"
                 )
+        
+        # for library models: set new variables to defaults
+        if self.is_library_model and hasattr(self, "reset_params_to_defaults"):
+            project = self.get_project()
+            if project is not None:
+                species = project.species
+                compound_type = project.compound.compound_type
+                self.reset_params_to_defaults(species, compound_type, all_new_variables)
 
         # delete all variables that are not in new
         for variable in self.variables.all():

From d2e7651173124cbac57043c3e4234246e0a2c1fc Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Mon, 6 Nov 2023 12:49:28 +0000
Subject: [PATCH 17/22] plot default pan

---
 frontend-v2/src/features/simulation/SimulationPlotView.tsx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/frontend-v2/src/features/simulation/SimulationPlotView.tsx b/frontend-v2/src/features/simulation/SimulationPlotView.tsx
index c50f126b..557a4211 100644
--- a/frontend-v2/src/features/simulation/SimulationPlotView.tsx
+++ b/frontend-v2/src/features/simulation/SimulationPlotView.tsx
@@ -282,6 +282,7 @@ const SimulationPlotView: React.FC<SimulationPlotProps> = ({ index, plot, data,
 
 
   const plotLayout: Partial<Layout> = {
+    dragmode: 'pan',
     shapes: icLines.map((icLine, i) => {
       return {
         type: 'line',

From 162086be24e280158d94c5f71686c34a85f2ab3c Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Mon, 6 Nov 2023 12:57:37 +0000
Subject: [PATCH 18/22] fix default params for qss constant target models

---
 pkpdapp/pkpdapp/models/combined_model.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pkpdapp/pkpdapp/models/combined_model.py b/pkpdapp/pkpdapp/models/combined_model.py
index 0caa2c04..eed04fbc 100644
--- a/pkpdapp/pkpdapp/models/combined_model.py
+++ b/pkpdapp/pkpdapp/models/combined_model.py
@@ -542,11 +542,12 @@ def reset_params_to_defaults(self, species, compoundType, variables=None):
                 .replace("_clinical", "")\
                 .replace("_preclinical", "")\
                 .replace("tmdd_full_constant_target", "tmdd")\
-                .replace("tmdd_QSS_constant_target", "tmdd")\
+                .replace("tmdd_qss_constant_target", "tmdd")\
                 .replace("tmdd_full", "tmdd")\
                 .replace("tmdd_QSS", "tmdd")\
                 .replace("production", "")\
                 .replace("elimination", "")
+            print('resetting params to defaults', model_name, species, compoundType, self.pk_model.name)
             if variables is None:
                 variables = self.variables.all()
             for v in variables:

From 429947c80b2e0449cf050aa0fe082bd26a581de0 Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Fri, 10 Nov 2023 11:58:00 +0000
Subject: [PATCH 19/22] remove questions, help label

---
 frontend-v2/src/features/help/Help.tsx     | 16 +++++-----------
 frontend-v2/src/features/main/mainSlice.ts |  2 +-
 2 files changed, 6 insertions(+), 12 deletions(-)

diff --git a/frontend-v2/src/features/help/Help.tsx b/frontend-v2/src/features/help/Help.tsx
index 89240f44..33da4112 100644
--- a/frontend-v2/src/features/help/Help.tsx
+++ b/frontend-v2/src/features/help/Help.tsx
@@ -53,11 +53,11 @@ const Help: React.FC = () => {
     }});
   
   const questions = [
-    generic_questions.slice(0, 2),
-    generic_questions.slice(0, 4),
-    generic_questions.slice(0, 3),
-    generic_questions.slice(0, 5),
-    generic_questions.slice(0, 1),
+    generic_questions.slice(0, 0),
+    generic_questions.slice(0, 0),
+    generic_questions.slice(0, 0),
+    generic_questions.slice(0, 0),
+    generic_questions.slice(0, 0),
   ]
   const tutorials = [
     tutorialVideos.filter((video) => video.type.includes('Tutorial')),
@@ -68,12 +68,6 @@ const Help: React.FC = () => {
     tutorialVideos.filter((video) => video.type === 'Simulation'),
   ]
     
-  const project_questions = generic_questions.slice(0, 2);
-  const drug_questions = generic_questions.slice(0, 4)
-  const model_questions = generic_questions.slice(0, 3);
-  const trial_questions = generic_questions.slice(0, 5);
-  const simulation_questions = generic_questions.slice(0, 1)
-
   return (
     <DynamicTabs tabNames={["Tutorials", "Projects", "Drug", "Model", "Trial Design", "Simulation"]}>
       { questions.map((question, index) => (
diff --git a/frontend-v2/src/features/main/mainSlice.ts b/frontend-v2/src/features/main/mainSlice.ts
index 7db75cf3..dfbfa3c1 100644
--- a/frontend-v2/src/features/main/mainSlice.ts
+++ b/frontend-v2/src/features/main/mainSlice.ts
@@ -7,7 +7,7 @@ export enum PageName {
   DATA = 'Data',
   TRIAL_DESIGN = 'Trial Design',
   SIMULATIONS = 'Simulations',
-  HELP = 'Help',
+  HELP = 'Help & Feedback',
 }
 
 interface MainState {

From 663edde03cbedec9c101e30479c9d052b7ec230d Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Fri, 10 Nov 2023 12:25:35 +0000
Subject: [PATCH 20/22] add proper icons

---
 frontend-v2/src/features/main/Sidebar.tsx | 19 ++++++++++++++++++-
 frontend-v2/src/hooks/useDirty.ts         |  1 -
 2 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/frontend-v2/src/features/main/Sidebar.tsx b/frontend-v2/src/features/main/Sidebar.tsx
index da5d6e1f..ffa4ec37 100644
--- a/frontend-v2/src/features/main/Sidebar.tsx
+++ b/frontend-v2/src/features/main/Sidebar.tsx
@@ -28,6 +28,13 @@ import ErrorIcon from '@mui/icons-material/Error';
 import { Tooltip } from '@mui/material';
 import { useCombinedModelListQuery, useProjectRetrieveQuery, useProtocolListQuery } from '../../app/backendApi';
 import { Protocol } from "../../app/backendApi";
+import DnsIcon from '@mui/icons-material/Dns';
+import BiotechIcon from '@mui/icons-material/Biotech';
+import FunctionsIcon from '@mui/icons-material/Functions';
+import VaccinesIcon from '@mui/icons-material/Vaccines';
+import SsidChartIcon from '@mui/icons-material/SsidChart';
+import ContactSupportIcon from '@mui/icons-material/ContactSupport';
+import TableViewIcon from '@mui/icons-material/TableView';
 
 const drawerWidth = 240;
 
@@ -56,6 +63,16 @@ export default function Sidebar() {
       </Tooltip>
     )
   }
+  
+  let icons: { [key: string]: React.ReactNode } = {
+    [PageName.PROJECTS]: <DnsIcon />,
+    [PageName.DRUG]: <BiotechIcon />,
+    [PageName.MODEL]: <FunctionsIcon />,
+    [PageName.TRIAL_DESIGN]: <VaccinesIcon />,
+    [PageName.DATA]: <TableViewIcon />,
+    [PageName.SIMULATIONS]: <SsidChartIcon />,
+    [PageName.HELP]: <ContactSupportIcon />,
+  };
 
   const handleDrawerToggle = () => {
     setMobileOpen(!mobileOpen);
@@ -111,7 +128,7 @@ export default function Sidebar() {
           <ListItem key={key} disablePadding selected={isPageSelected(key)}>
             <ListItemButton onClick={handlePageClick(key)} disabled={isPageDisabled(key)} disableRipple={true}>
               <ListItemIcon>
-                {value in errorComponents ? errorComponents[value] : index % 2 === 0 ? <InboxIcon /> : <MailIcon />}
+                {value in errorComponents ? errorComponents[value] : icons[value]}
               </ListItemIcon>
               <ListItemText primary={value} />
             </ListItemButton>
diff --git a/frontend-v2/src/hooks/useDirty.ts b/frontend-v2/src/hooks/useDirty.ts
index 0b766213..2a504137 100644
--- a/frontend-v2/src/hooks/useDirty.ts
+++ b/frontend-v2/src/hooks/useDirty.ts
@@ -1,7 +1,6 @@
 import { useDispatch } from "react-redux";
 import { decrementDirtyCount, incrementDirtyCount } from "../features/main/mainSlice";
 import { useEffect, useState } from "react";
-import usePrevious from "./usePrevious";
 
 function useDirty(isDirty: boolean) {
   const dispatch = useDispatch();

From b41530de65b3d7acdc0b10d22dd1cbe554841b53 Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Mon, 20 Nov 2023 11:49:00 +0000
Subject: [PATCH 21/22] flake8

---
 pkpdapp/pkpdapp/api/views/models.py           |  77 ++--
 .../pkpdapp/migrations/0007_initial_units.py  | 347 ++++++++----------
 pkpdapp/pkpdapp/models/combined_model.py      |  50 ++-
 pkpdapp/pkpdapp/models/mechanistic_model.py   |  39 +-
 pkpdapp/pkpdapp/models/myokit_model_mixin.py  |   2 +-
 .../test_models/test_mechanistic_model.py     |  67 ++--
 .../tests/test_views/test_combined_model.py   | 149 ++++----
 pkpdapp/pkpdapp/utils/default_params.py       |  33 +-
 8 files changed, 365 insertions(+), 399 deletions(-)

diff --git a/pkpdapp/pkpdapp/api/views/models.py b/pkpdapp/pkpdapp/api/views/models.py
index cb80344a..41600985 100644
--- a/pkpdapp/pkpdapp/api/views/models.py
+++ b/pkpdapp/pkpdapp/api/views/models.py
@@ -3,9 +3,7 @@
 # is released under the BSD 3-clause license. See accompanying LICENSE.md for
 # copyright notice and full license details.
 #
-from rest_framework import (
-    viewsets, response, parsers, status, decorators
-)
+from rest_framework import viewsets, response, parsers, status, decorators
 from drf_spectacular.utils import extend_schema, OpenApiParameter
 from drf_spectacular.types import OpenApiTypes
 from rest_framework.permissions import IsAuthenticated
@@ -16,10 +14,7 @@
     CombinedModelSerializer,
     PharmacodynamicSbmlSerializer,
 )
-from pkpdapp.api.views import (
-    ProjectFilter,
-    CheckAccessToProject
-)
+from pkpdapp.api.views import ProjectFilter, CheckAccessToProject
 from pkpdapp.models import (
     PharmacokineticModel,
     PharmacodynamicModel,
@@ -31,27 +26,23 @@
 class PharmacokineticView(viewsets.ModelViewSet):
     queryset = PharmacokineticModel.objects.all()
     serializer_class = PharmacokineticSerializer
-    permission_classes = [
-        IsAuthenticated & CheckAccessToProject
-    ]
+    permission_classes = [IsAuthenticated & CheckAccessToProject]
 
 
 class CombinedModelView(viewsets.ModelViewSet):
     queryset = CombinedModel.objects.all()
     serializer_class = CombinedModelSerializer
     filter_backends = [ProjectFilter]
-    permission_classes = [
-        IsAuthenticated & CheckAccessToProject
-    ]
+    permission_classes = [IsAuthenticated & CheckAccessToProject]
 
     @extend_schema(
         parameters=[
             OpenApiParameter(
-                name='project_id',
-                description='Filter results by project ID',
+                name="project_id",
+                description="Filter results by project ID",
                 required=False,
                 type=OpenApiTypes.INT,
-                location=OpenApiParameter.QUERY
+                location=OpenApiParameter.QUERY,
             ),
         ],
     )
@@ -60,24 +51,25 @@ def list(self, request, *args, **kwargs):
 
     @decorators.action(
         detail=True,
-        methods=['PUT'],
+        methods=["PUT"],
         serializer_class=CombinedModelSerializer,
     )
     def set_variables_from_inference(self, request, pk):
         obj = self.get_object()
         try:
-            inference = Inference.objects.get(id=request.data['inference_id'])
+            inference = Inference.objects.get(id=request.data["inference_id"])
         except Inference.DoesNotExist:
-            return response.Response({'inference_id': 'inference not found'},
-                                     status.HTTP_400_BAD_REQUEST)
+            return response.Response(
+                {"inference_id": "inference not found"}, status.HTTP_400_BAD_REQUEST
+            )
 
         obj.set_variables_from_inference(inference)
         serializer = self.serializer_class(obj)
         return response.Response(serializer.data)
-    
+
     @decorators.action(
         detail=True,
-        methods=['PUT'],
+        methods=["PUT"],
         serializer_class=CombinedModelSerializer,
     )
     def set_params_to_defaults(self, request, pk):
@@ -85,16 +77,14 @@ def set_params_to_defaults(self, request, pk):
         project = obj.get_project()
         if project is None:
             return response.Response(
-                {'project': 'project not found'},
-                status.HTTP_400_BAD_REQUEST
+                {"project": "project not found"}, status.HTTP_400_BAD_REQUEST
             )
         compound = project.compound
         if compound is None:
             return response.Response(
-                {'compound': 'compound not found'},
-                status.HTTP_400_BAD_REQUEST
+                {"compound": "compound not found"}, status.HTTP_400_BAD_REQUEST
             )
-        print('setting params to defaults', project.species, compound.compound_type)
+        print("setting params to defaults", project.species, compound.compound_type)
         obj.reset_params_to_defaults(project.species, compound.compound_type)
         serializer = self.serializer_class(obj)
         return response.Response(serializer.data)
@@ -104,56 +94,51 @@ class PharmacodynamicView(viewsets.ModelViewSet):
     queryset = PharmacodynamicModel.objects.all()
     serializer_class = PharmacodynamicSerializer
     filter_backends = [ProjectFilter]
-    permission_classes = [
-        IsAuthenticated & CheckAccessToProject
-    ]
+    permission_classes = [IsAuthenticated & CheckAccessToProject]
 
     @decorators.action(
         detail=True,
-        methods=['PUT'],
+        methods=["PUT"],
         serializer_class=PharmacodynamicSbmlSerializer,
         parser_classes=[parsers.MultiPartParser],
     )
     def sbml(self, request, pk):
         obj = self.get_object()
-        serializer = self.serializer_class(obj, data=request.data,
-                                           partial=True)
+        serializer = self.serializer_class(obj, data=request.data, partial=True)
         if serializer.is_valid():
             serializer.save()
             return response.Response(serializer.data)
-        print('xXXXXXx', serializer.errors)
-        return response.Response(serializer.errors,
-                                 status.HTTP_400_BAD_REQUEST)
+        print("xXXXXXx", serializer.errors)
+        return response.Response(serializer.errors, status.HTTP_400_BAD_REQUEST)
 
     @decorators.action(
         detail=True,
-        methods=['PUT'],
+        methods=["PUT"],
         serializer_class=PharmacodynamicSerializer,
         parser_classes=[parsers.MultiPartParser],
     )
     def mmt(self, request, pk):
         obj = self.get_object()
-        serializer = self.serializer_class(obj, data=request.data,
-                                           partial=True)
+        serializer = self.serializer_class(obj, data=request.data, partial=True)
         if serializer.is_valid():
             serializer.save()
             return response.Response(serializer.data)
-        return response.Response(serializer.errors,
-                                 status.HTTP_400_BAD_REQUEST)
+        return response.Response(serializer.errors, status.HTTP_400_BAD_REQUEST)
 
     @decorators.action(
         detail=True,
-        methods=['PUT'],
+        methods=["PUT"],
         serializer_class=PharmacodynamicSerializer,
     )
     def set_variables_from_inference(self, request, pk):
         obj = self.get_object()
         try:
-            print('got request', request.data)
-            inference = Inference.objects.get(id=request.data['inference_id'])
+            print("got request", request.data)
+            inference = Inference.objects.get(id=request.data["inference_id"])
         except Inference.DoesNotExist:
-            return response.Response({'inference_id': 'inference not found'},
-                                     status.HTTP_400_BAD_REQUEST)
+            return response.Response(
+                {"inference_id": "inference not found"}, status.HTTP_400_BAD_REQUEST
+            )
 
         obj.set_variables_from_inference(inference)
         serializer = self.serializer_class(obj)
diff --git a/pkpdapp/pkpdapp/migrations/0007_initial_units.py b/pkpdapp/pkpdapp/migrations/0007_initial_units.py
index 1fab8799..57e55c4c 100644
--- a/pkpdapp/pkpdapp/migrations/0007_initial_units.py
+++ b/pkpdapp/pkpdapp/migrations/0007_initial_units.py
@@ -10,342 +10,313 @@
 
 def load_units(apps, schema_editor):
     Unit = apps.get_model("pkpdapp", "Unit")
-    m = myokit.Unit.parse_simple('m')
-    L = myokit.Unit.parse_simple('L')
-    cL = myokit.Unit.parse_simple('cL')
-    h = myokit.Unit.parse_simple('h')
-    g = myokit.Unit.parse_simple('g')
-    mol = myokit.Unit.parse_simple('mol')
+    L = myokit.Unit.parse_simple("L")
+    cL = myokit.Unit.parse_simple("cL")
+    h = myokit.Unit.parse_simple("h")
+    g = myokit.Unit.parse_simple("g")
+    mol = myokit.Unit.parse_simple("mol")
     dimensionless = myokit.Unit()
 
     units = [
         {
-            'symbol': 'nmol/L',
-            'unit': 1e-9 * mol / L,
+            "symbol": "nmol/L",
+            "unit": 1e-9 * mol / L,
         },
         {
-            'symbol': 'mol',
-            'unit': mol,
+            "symbol": "mol",
+            "unit": mol,
         },
         {
-            'symbol': 'nmol',
-            'unit': 1e-9 * mol,
+            "symbol": "nmol",
+            "unit": 1e-9 * mol,
         },
         {
-            'symbol': 'pmol',
-            'unit': 1e-12 * mol,
+            "symbol": "pmol",
+            "unit": 1e-12 * mol,
         },
         {
-            'symbol': 'µmol',
-            'unit': 1e-6 * mol,
+            "symbol": "µmol",
+            "unit": 1e-6 * mol,
         },
         {
-            'symbol': 'pmol/L',
-            'unit': 1e-12 * mol / L,
+            "symbol": "pmol/L",
+            "unit": 1e-12 * mol / L,
         },
         {
-            'symbol': 'µmol/L',
-            'unit': 1e-6 * mol / L,
+            "symbol": "µmol/L",
+            "unit": 1e-6 * mol / L,
         },
         {
-            'symbol': 'nmol/L',
-            'unit': 1e-9 * mol / L,
+            "symbol": "nmol/L",
+            "unit": 1e-9 * mol / L,
         },
         {
-            'symbol': 'µL/min/mg',
-            'unit': 1e-6 * L / (60 * h * 1e-3 * g),
+            "symbol": "µL/min/mg",
+            "unit": 1e-6 * L / (60 * h * 1e-3 * g),
         },
         {
-            'symbol': 'h',
-            'unit': h,
+            "symbol": "h",
+            "unit": h,
         },
         {
-            'symbol': '1/h',
-            'unit': 1 / h,
+            "symbol": "1/h",
+            "unit": 1 / h,
         },
         {
-            'symbol': 'mg',
-            'unit': 1e-3 * g,
+            "symbol": "mg",
+            "unit": 1e-3 * g,
         },
         {
-            'symbol': 'day',
-            'unit': 24 * h,
+            "symbol": "day",
+            "unit": 24 * h,
         },
         {
-            'symbol': '1/day',
-            'unit': 1 / (24 * h),
+            "symbol": "1/day",
+            "unit": 1 / (24 * h),
         },
         {
-            'symbol': 'week',
-            'unit': 7 * 24 * h,
+            "symbol": "week",
+            "unit": 7 * 24 * h,
         },
         {
-            'symbol': '1/week',
-            'unit': 1 / (7 * 24 * h),
+            "symbol": "1/week",
+            "unit": 1 / (7 * 24 * h),
         },
         {
-            'symbol': 'min',
-            'unit': h / 60,
+            "symbol": "min",
+            "unit": h / 60,
         },
         {
-            'symbol': 's',
-            'unit': h / 3600,
+            "symbol": "s",
+            "unit": h / 3600,
         },
         {
-            'symbol': 'L/mg/day',
-            'unit': L / (1e-3 * g * 24 * h),
+            "symbol": "L/mg/day",
+            "unit": L / (1e-3 * g * 24 * h),
         },
         {
-            'symbol': 'L/h/kg',
-            'unit': L / (h * 1e3 * g),
+            "symbol": "L/h/kg",
+            "unit": L / (h * 1e3 * g),
         },
         {
-            'symbol': 'mL/h/kg',
-            'unit': 1e-3 * L / (h * 1e3 * g),
+            "symbol": "mL/h/kg",
+            "unit": 1e-3 * L / (h * 1e3 * g),
         },
         {
-            'symbol': 'L/day/kg',
-            'unit': L / (24 * h * 1e3 * g),
+            "symbol": "L/day/kg",
+            "unit": L / (24 * h * 1e3 * g),
         },
         {
-            'symbol': 'mL/day/kg',
-            'unit': 1e-3 * L / (24 * h * 1e3 * g),
+            "symbol": "mL/day/kg",
+            "unit": 1e-3 * L / (24 * h * 1e3 * g),
         },
         {
-            'symbol': 'L/h/pmol',
-            'unit': L / (h * 1e-12 * mol),
+            "symbol": "L/h/pmol",
+            "unit": L / (h * 1e-12 * mol),
         },
         {
-            'symbol': 'L/day/pmol',
-            'unit': L / (24 * h * 1e-12 * mol),
+            "symbol": "L/day/pmol",
+            "unit": L / (24 * h * 1e-12 * mol),
         },
         {
-            'symbol': 'mL/day/pmol',
-            'unit': 1e-3 * L / (24 * h * 1e-12 * mol),
+            "symbol": "mL/day/pmol",
+            "unit": 1e-3 * L / (24 * h * 1e-12 * mol),
         },
         {
-            'symbol': 'L/h/nmol',
-            'unit': L / (h * 1e-9 * mol),
+            "symbol": "L/h/nmol",
+            "unit": L / (h * 1e-9 * mol),
         },
         {
-            'symbol': 'L/day/nmol',
-            'unit': L / (24 * h * 1e-9 * mol),
+            "symbol": "L/day/nmol",
+            "unit": L / (24 * h * 1e-9 * mol),
         },
         {
-            'symbol': 'mL/day/nmol',
-            'unit': 1e-3 * L / (24 * h * 1e-9 * mol),
+            "symbol": "mL/day/nmol",
+            "unit": 1e-3 * L / (24 * h * 1e-9 * mol),
         },
         {
-            'symbol': 'L/h/µmol',
-            'unit': L / (h * 1e-6 * mol),
+            "symbol": "L/h/µmol",
+            "unit": L / (h * 1e-6 * mol),
         },
         {
-            'symbol': 'L/day/µmol',
-            'unit': L / (24 * h * 1e-6 * mol),
+            "symbol": "L/day/µmol",
+            "unit": L / (24 * h * 1e-6 * mol),
         },
         {
-            'symbol': 'mL/day/µmol',
-            'unit': 1e-3 * L / (24 * h * 1e-6 * mol),
+            "symbol": "mL/day/µmol",
+            "unit": 1e-3 * L / (24 * h * 1e-6 * mol),
         },
+        {"symbol": "L", "unit": L},
+        {"symbol": "mL", "unit": 1e-3 * L},
+        {"symbol": "L/kg", "unit": L / (1e3 * g)},
+        {"symbol": "L/h", "unit": L / h},
+        {"symbol": "L/day", "unit": L / (24 * h)},
+        {"symbol": "mL/day", "unit": 1e-3 * L / (24 * h)},
+        {"symbol": "mL/h", "unit": 1e-3 * L / h},
+        {"symbol": "µL/h", "unit": 1e-6 * L / h},
+        {"symbol": "1/L", "unit": 1 / L},
         {
-            'symbol': 'L',
-            'unit': L
+            "symbol": "kg",
+            "unit": 1e3 * g,
         },
         {
-            'symbol': 'mL',
-            'unit': 1e-3 * L
+            "symbol": "g",
+            "unit": g,
         },
         {
-            'symbol': 'L/kg',
-            'unit': L / (1e3 * g)
+            "symbol": "ng",
+            "unit": 1e-9 * g,
         },
         {
-            'symbol': 'L/h',
-            'unit': L / h
+            "symbol": "ng/mL",
+            "unit": 1e-9 * g / (1e-3 * L),
         },
         {
-            'symbol': 'L/day',
-            'unit': L / (24 * h)
+            "symbol": "mg/L",
+            "unit": 1e-3 * g / L,
         },
         {
-            'symbol': 'mL/day',
-            'unit': 1e-3 * L / (24 * h)
+            "symbol": "ng/L",
+            "unit": 1e-9 * g / L,
         },
         {
-            'symbol': 'mL/h',
-            'unit': 1e-3 * L / h
+            "symbol": "g/L",
+            "unit": g / L,
         },
         {
-            'symbol': 'µL/h',
-            'unit': 1e-6 * L / h
+            "symbol": "pg/mL",
+            "unit": 1e-12 * g / (1e-3 * L),
         },
         {
-            'symbol': '1/L',
-            'unit': 1 / L
+            "symbol": "ng/mL",
+            "unit": 1e-9 * g / (1e-3 * L),
         },
         {
-            'symbol': 'kg',
-            'unit': 1e3 * g,
+            "symbol": "µg/mL",
+            "unit": 1e-6 * g / (1e-3 * L),
         },
         {
-            'symbol': 'g',
-            'unit': g,
+            "symbol": "10^6/mcL",
+            "unit": 1e6 / (1e-3 * cL),
         },
         {
-            'symbol': 'ng',
-            'unit': 1e-9 * g,
+            "symbol": "10^3/mcL",
+            "unit": 1e3 / (1e-3 * cL),
         },
         {
-            'symbol': 'ng/mL',
-            'unit': 1e-9 * g / (1e-3 * L),
+            "symbol": "g/dL",
+            "unit": g / (10 * cL),
         },
         {
-            'symbol': 'mg/L',
-            'unit': 1e-3 * g / L,
+            "symbol": "",
+            "unit": dimensionless,
         },
         {
-            'symbol': 'ng/L',
-            'unit': 1e-9 * g / L,
+            "symbol": "g/mol",
+            "unit": g / mol,
         },
         {
-            'symbol': 'g/L',
-            'unit': g / L,
+            "symbol": "g/nmol",
+            "unit": g / (1e-6 * mol),
         },
         {
-            'symbol': 'pg/mL',
-            'unit': 1e-12 * g / (1e-3 * L),
+            "symbol": "h*pmol/L",
+            "unit": h * 1e-12 * mol / L,
         },
         {
-            'symbol': 'ng/mL',
-            'unit': 1e-9 * g / (1e-3 * L),
+            "symbol": "h*nmol/L",
+            "unit": h * 1e-9 * mol / L,
         },
         {
-            'symbol': 'µg/mL',
-            'unit': 1e-6 * g / (1e-3 * L),
+            "symbol": "h*µmol/L",
+            "unit": h * 1e-6 * mol / L,
         },
         {
-            'symbol': '10^6/mcL',
-            'unit': 1e6 / (1e-3 * cL),
+            "symbol": "h*ng/mL",
+            "unit": h * 1e-9 * g / (1e-3 * L),
         },
         {
-            'symbol': '10^3/mcL',
-            'unit': 1e3 / (1e-3 * cL),
+            "symbol": "h*µg/mL",
+            "unit": h * 1e-6 * g / (1e-3 * L),
         },
         {
-            'symbol': 'g/dL',
-            'unit': g / (10 * cL),
+            "symbol": "day*pmol/L",
+            "unit": 24 * h * 1e-12 * mol / L,
         },
         {
-            'symbol': '',
-            'unit': dimensionless,
+            "symbol": "day*nmol/L",
+            "unit": 24 * h * 1e-9 * mol / L,
         },
         {
-            'symbol': 'g/mol',
-            'unit': g / mol,
+            "symbol": "day*µmol/L",
+            "unit": 24 * h * 1e-6 * mol / L,
         },
         {
-            'symbol': 'g/nmol',
-            'unit': g / (1e-6 * mol),
+            "symbol": "day*ng/mL",
+            "unit": 24 * h * 1e-9 * g / (1e-3 * L),
         },
         {
-            'symbol': 'h*pmol/L',
-            'unit': h * 1e-12 * mol / L,
+            "symbol": "day*µg/mL",
+            "unit": 24 * h * 1e-6 * g / (1e-3 * L),
         },
         {
-            'symbol': 'h*nmol/L',
-            'unit': h * 1e-9 * mol / L,
+            "symbol": "mg/kg",
+            "unit": 1e-3 * g / (1e3 * g),
         },
         {
-            'symbol': 'h*µmol/L',
-            'unit': h * 1e-6 * mol / L,
+            "symbol": "pg/kg",
+            "unit": 1e-12 * g / (1e3 * g),
         },
         {
-            'symbol': 'h*ng/mL',
-            'unit': h * 1e-9 * g / (1e-3 * L),
+            "symbol": "ng/kg",
+            "unit": 1e-9 * g / (1e3 * g),
         },
         {
-            'symbol': 'h*µg/mL',
-            'unit': h * 1e-6 * g / (1e-3 * L),
+            "symbol": "µg/kg",
+            "unit": 1e-6 * g / (1e3 * g),
         },
         {
-            'symbol': 'day*pmol/L',
-            'unit': 24 * h * 1e-12 * mol / L,
+            "symbol": "pmol/kg",
+            "unit": 1e-12 * mol / (1e3 * g),
         },
         {
-            'symbol': 'day*nmol/L',
-            'unit': 24 * h * 1e-9 * mol / L,
+            "symbol": "nmol/kg",
+            "unit": 1e-9 * mol / (1e3 * g),
         },
         {
-            'symbol': 'day*µmol/L',
-            'unit': 24 * h * 1e-6 * mol / L,
+            "symbol": "µmol/kg",
+            "unit": 1e-6 * mol / (1e3 * g),
         },
         {
-            'symbol': 'day*ng/mL',
-            'unit': 24 * h * 1e-9 * g / (1e-3 * L),
+            "symbol": "mL/kg",
+            "unit": 1e-3 * L / (1e3 * g),
         },
         {
-            'symbol': 'day*µg/mL',
-            'unit': 24 * h * 1e-6 * g / (1e-3 * L),
-        },
-        {
-            'symbol': 'mg/kg',
-            'unit': 1e-3 * g / (1e3 * g),
-        },
-        {
-            'symbol': 'pg/kg',
-            'unit': 1e-12 * g / (1e3 * g),
-        },
-        {
-            'symbol': 'ng/kg',
-            'unit': 1e-9 * g / (1e3 * g),
-        },
-        {
-            'symbol': 'µg/kg',
-            'unit': 1e-6 * g / (1e3 * g),
-        },
-        {
-            'symbol': 'pmol/kg',
-            'unit': 1e-12 * mol / (1e3 * g),
-        },
-        {
-            'symbol': 'nmol/kg',
-            'unit': 1e-9 * mol / (1e3 * g),
-        },
-        {
-            'symbol': 'µmol/kg',
-            'unit': 1e-6 * mol / (1e3 * g),
-        },
-        {
-            'symbol': 'mL/kg',
-            'unit': 1e-3 * L / (1e3 * g),
-        },
-        {
-            'symbol': 'L/kg',
-            'unit': L / (1e3 * g),
+            "symbol": "L/kg",
+            "unit": L / (1e3 * g),
         },
     ]
 
     for u in units:
         try:
-            Unit.objects.get(symbol=u['symbol'])
+            Unit.objects.get(symbol=u["symbol"])
         except Unit.DoesNotExist:
             Unit.objects.create(
-                symbol=u['symbol'],
-                g=u['unit'].exponents()[0],
-                m=u['unit'].exponents()[1],
-                s=u['unit'].exponents()[2],
-                A=u['unit'].exponents()[3],
-                K=u['unit'].exponents()[4],
-                cd=u['unit'].exponents()[5],
-                mol=u['unit'].exponents()[6],
-                multiplier=u['unit'].multiplier_log_10(),
+                symbol=u["symbol"],
+                g=u["unit"].exponents()[0],
+                m=u["unit"].exponents()[1],
+                s=u["unit"].exponents()[2],
+                A=u["unit"].exponents()[3],
+                K=u["unit"].exponents()[4],
+                cd=u["unit"].exponents()[5],
+                mol=u["unit"].exponents()[6],
+                multiplier=u["unit"].multiplier_log_10(),
             )
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
-        ('pkpdapp', '0001_initial'),
+        ("pkpdapp", "0001_initial"),
     ]
 
     operations = [
diff --git a/pkpdapp/pkpdapp/models/combined_model.py b/pkpdapp/pkpdapp/models/combined_model.py
index eed04fbc..1e972f3e 100644
--- a/pkpdapp/pkpdapp/models/combined_model.py
+++ b/pkpdapp/pkpdapp/models/combined_model.py
@@ -535,32 +535,44 @@ def save(self, force_insert=False, force_update=False, *args, **kwargs):
         self.__original_has_lag = self.has_lag
         self.__original_has_hill_coefficient = self.has_hill_coefficient
         self.__original_has_bioavailability = self.has_bioavailability
-        
+
     def reset_params_to_defaults(self, species, compoundType, variables=None):
         if self.is_library_model:
-            model_name = self.pk_model.name\
-                .replace("_clinical", "")\
-                .replace("_preclinical", "")\
-                .replace("tmdd_full_constant_target", "tmdd")\
-                .replace("tmdd_qss_constant_target", "tmdd")\
-                .replace("tmdd_full", "tmdd")\
-                .replace("tmdd_QSS", "tmdd")\
-                .replace("production", "")\
+            model_name = (
+                self.pk_model.name.replace("_clinical", "")
+                .replace("_preclinical", "")
+                .replace("tmdd_full_constant_target", "tmdd")
+                .replace("tmdd_qss_constant_target", "tmdd")
+                .replace("tmdd_full", "tmdd")
+                .replace("tmdd_QSS", "tmdd")
+                .replace("production", "")
                 .replace("elimination", "")
-            print('resetting params to defaults', model_name, species, compoundType, self.pk_model.name)
+            )
+            print(
+                "resetting params to defaults",
+                model_name,
+                species,
+                compoundType,
+                self.pk_model.name,
+            )
             if variables is None:
                 variables = self.variables.all()
             for v in variables:
-                varName = v.name;
-                defaultVal = defaults.get(model_name, {}).get(varName, {}).get(species, {}).get(compoundType, None)
+                varName = v.name
+                defaultVal = (
+                    defaults.get(model_name, {})
+                    .get(varName, {})
+                    .get(species, {})
+                    .get(compoundType, None)
+                )
                 if defaultVal is None:
                     continue
-                if defaultVal.get('unit', '') == "dimensionless":
-                  defaultVal['unit'] = '';
-                unit = Unit.objects.filter(symbol=defaultVal.get('unit', '')).first()
-                value = defaultVal.get('value', None)
+                if defaultVal.get("unit", "") == "dimensionless":
+                    defaultVal["unit"] = ""
+                unit = Unit.objects.filter(symbol=defaultVal.get("unit", "")).first()
+                value = defaultVal.get("value", None)
                 if value is None or unit is None:
-                  continue;
+                    continue
                 v.default_value = value
                 v.unit = unit
                 v.save()
@@ -629,9 +641,7 @@ def create_stored_mapping(self, new_pkpd_model, new_variables):
         }
         stored_mapping = PkpdMapping.objects.create(**stored_kwargs)
         return stored_mapping
-    
-    
-  
+
 
 class DerivedVariable(StoredModel):
     pkpd_model = models.ForeignKey(
diff --git a/pkpdapp/pkpdapp/models/mechanistic_model.py b/pkpdapp/pkpdapp/models/mechanistic_model.py
index b68268e2..74c97d40 100644
--- a/pkpdapp/pkpdapp/models/mechanistic_model.py
+++ b/pkpdapp/pkpdapp/models/mechanistic_model.py
@@ -13,50 +13,44 @@ class MechanisticModel(models.Model, MyokitModelMixin):
     """
     A PK or PD model, represented using mmt
     """
-    DEFAULT_MMT = (
-        '[[model]]\n'
-        '\n'
-        '[myokit]\n'
-        'time = 0 bind time'
-    )
+
+    DEFAULT_MMT = "[[model]]\n" "\n" "[myokit]\n" "time = 0 bind time"
 
     DEFAULT_SBML = (
         '<?xml version="1.0" encoding="UTF-8"?>'
-        '<sbml '
+        "<sbml "
         'xmlns="http://www.sbml.org/sbml/level3/version2/core" '
         'level="3" version="2"'
-        '>'
+        ">"
         '<model id="default">'
-        '</model>'
-        '</sbml>'
+        "</model>"
+        "</sbml>"
     )
 
-    name = models.CharField(max_length=100, help_text='name of the model')
+    name = models.CharField(max_length=100, help_text="name of the model")
     description = models.TextField(
-        help_text='short description of the model',
-        blank=True, default=''
+        help_text="short description of the model", blank=True, default=""
     )
     mmt = models.TextField(
         help_text=(
-            'the model represented using mmt '
-            '(see https://myokit.readthedocs)'
+            "the model represented using mmt " "(see https://myokit.readthedocs)"
         ),
         default=DEFAULT_MMT,
     )
     time_max = models.FloatField(
         default=30,
         help_text=(
-            'suggested maximum time to simulate for this model (in the time '
-            'units specified by the mmt model)'
-        )
+            "suggested maximum time to simulate for this model (in the time "
+            "units specified by the mmt model)"
+        ),
     )
 
     is_library_model = models.BooleanField(
         default=False,
         help_text=(
-            'whether this model is a library model (i.e. it is not an '
-            'uploaded user model)'
-        )
+            "whether this model is a library model (i.e. it is not an "
+            "uploaded user model)"
+        ),
     )
 
     class Meta:
@@ -69,5 +63,4 @@ def clean(self):
         try:
             self.create_myokit_model()
         except Exception as e:
-            raise ValidationError({'mmt': str(e)})
-        
+            raise ValidationError({"mmt": str(e)})
diff --git a/pkpdapp/pkpdapp/models/myokit_model_mixin.py b/pkpdapp/pkpdapp/models/myokit_model_mixin.py
index d9a509f7..9f824b3a 100644
--- a/pkpdapp/pkpdapp/models/myokit_model_mixin.py
+++ b/pkpdapp/pkpdapp/models/myokit_model_mixin.py
@@ -269,7 +269,7 @@ def update_model(self):
                     f"{v.qname}, id = {v.id} "
                     f"constant = {v.constant}, state = {v.state}"
                 )
-        
+
         # for library models: set new variables to defaults
         if self.is_library_model and hasattr(self, "reset_params_to_defaults"):
             project = self.get_project()
diff --git a/pkpdapp/pkpdapp/tests/test_models/test_mechanistic_model.py b/pkpdapp/pkpdapp/tests/test_models/test_mechanistic_model.py
index 54248126..38e93670 100644
--- a/pkpdapp/pkpdapp/tests/test_models/test_mechanistic_model.py
+++ b/pkpdapp/pkpdapp/tests/test_models/test_mechanistic_model.py
@@ -5,9 +5,12 @@
 #
 from django.test import TestCase
 from pkpdapp.models import (
-    PharmacodynamicModel, Protocol, PharmacokineticModel,
+    PharmacodynamicModel,
+    Protocol,
+    PharmacokineticModel,
     CombinedModel,
-    Dose, Unit,
+    Dose,
+    Unit,
 )
 import myokit
 from django.core.exceptions import ValidationError
@@ -22,37 +25,34 @@ def setUp(self):
     def test_model_bad_mmt(self):
         with self.assertRaises(myokit.ParseError):
             PharmacodynamicModel.objects.create(
-                name='my_cool_model',
-                description='description for my cool model',
-                mmt='this is not sbml'
+                name="my_cool_model",
+                description="description for my cool model",
+                mmt="this is not sbml",
             )
 
     def test_model_clean(self):
         m = PharmacodynamicModel(
-            name='my_cool_model',
-            description='description for my cool model',
-            mmt='this is not xml'
+            name="my_cool_model",
+            description="description for my cool model",
+            mmt="this is not xml",
         )
         with self.assertRaises(ValidationError):
             m.clean()
 
     def test_model_creation(self):
         m = PharmacodynamicModel.objects.create(
-            name='my_cool_model',
-            description='description for my cool model',
+            name="my_cool_model",
+            description="description for my cool model",
         )
         self.assertTrue(isinstance(m, PharmacodynamicModel))
 
     def test_myokit_model(self):
         m = PharmacodynamicModel.objects.get(
-            name='tumour_growth_gompertz',
+            name="tumour_growth_gompertz",
         )
         model = m.get_myokit_model()
         model_variables = [v.name() for v in model.variables()]
-        test_model_variables = [
-            'TS0', 'TSmax', 'beta',
-            'Growth', 'TS', 't'
-        ]
+        test_model_variables = ["TS0", "TSmax", "beta", "Growth", "TS", "t"]
         self.assertCountEqual(model_variables, test_model_variables)
 
 
@@ -60,7 +60,7 @@ class TestDosedPharmokineticModel(TestCase):
     def setUp(self):
         cache.clear()
         self.pk = PharmacokineticModel.objects.get(
-            name='one_compartment_clinical',
+            name="one_compartment_clinical",
         )
 
         self.model = CombinedModel.objects.create(
@@ -68,13 +68,13 @@ def setUp(self):
         )
 
         self.p = Protocol.objects.create(
-            amount_unit=Unit.objects.get(symbol='pmol'),
-            time_unit=Unit.objects.get(symbol='h'),
-            name='my_cool_protocol',
+            amount_unit=Unit.objects.get(symbol="pmol"),
+            time_unit=Unit.objects.get(symbol="h"),
+            name="my_cool_protocol",
             dose_type=Protocol.DoseType.INDIRECT,
         )
 
-        v = self.model.variables.get(qname='PKCompartment.A1')
+        v = self.model.variables.get(qname="PKCompartment.A1")
         v.protocol = self.p
         v.save()
 
@@ -83,23 +83,22 @@ def test_store_model(self):
         self.assertTrue(isinstance(stored_model, CombinedModel))
         self.assertTrue(stored_model.read_only)
         self.assertEqual(
-            len(stored_model.variables.all()),
-            len(self.model.variables.all())
+            len(stored_model.variables.all()), len(self.model.variables.all())
         )
-        v = stored_model.variables.get(qname='PKCompartment.A1')
-        self.assertEqual(v.protocol.name, 'my_cool_protocol')
+        v = stored_model.variables.get(qname="PKCompartment.A1")
+        self.assertEqual(v.protocol.name, "my_cool_protocol")
         self.assertNotEqual(v.protocol.id, self.p.id)
-        
+
     def test_reset_to_default(self):
-        v = self.model.variables.get(qname='PKCompartment.CL')
+        v = self.model.variables.get(qname="PKCompartment.CL")
         self.assertNotEqual(v.default_value, 8)
-        self.assertNotEqual(v.unit.symbol, 'mL/h')
+        self.assertNotEqual(v.unit.symbol, "mL/h")
 
-        self.model.reset_params_to_defaults('H', 'LM')
+        self.model.reset_params_to_defaults("H", "LM")
 
-        v = self.model.variables.get(qname='PKCompartment.CL')
+        v = self.model.variables.get(qname="PKCompartment.CL")
         self.assertEqual(v.default_value, 8)
-        self.assertEqual(v.unit.symbol, 'mL/h')
+        self.assertEqual(v.unit.symbol, "mL/h")
 
     def test_myokit_model(self):
         model = self.model.get_myokit_model()
@@ -127,11 +126,11 @@ def test_myokit_model(self):
         sim = self.model.get_myokit_simulator()
 
         output = sim.run(self.model.time_max)
-        index = np.where(np.array(output['environment.t']) > 0.5)[0][0]
-        self.assertGreater(output['PKCompartment.C1'][index], 0.01)
+        index = np.where(np.array(output["environment.t"]) > 0.5)[0][0]
+        self.assertGreater(output["PKCompartment.C1"][index], 0.01)
 
         # non-dosed model should have a concentration at t ~ 0.5 of near zero
         pk_sim = self.pk.get_myokit_simulator()
         output = pk_sim.run(self.pk.time_max)
-        index = np.where(np.array(output['environment.t']) > 0.5)[0][0]
-        self.assertLess(output['PKCompartment.C1'][index], 1e-6)
+        index = np.where(np.array(output["environment.t"]) > 0.5)[0][0]
+        self.assertLess(output["PKCompartment.C1"][index], 1e-6)
diff --git a/pkpdapp/pkpdapp/tests/test_views/test_combined_model.py b/pkpdapp/pkpdapp/tests/test_views/test_combined_model.py
index aece7677..1fb18cd2 100644
--- a/pkpdapp/pkpdapp/tests/test_views/test_combined_model.py
+++ b/pkpdapp/pkpdapp/tests/test_views/test_combined_model.py
@@ -8,13 +8,18 @@
 from rest_framework import status
 from rest_framework.test import APITestCase, APIClient
 from django.contrib.auth.models import User
-from pkpdapp.models import Project, PharmacokineticModel, CombinedModel, PharmacodynamicModel
+from pkpdapp.models import (
+    Project,
+    PharmacokineticModel,
+    CombinedModel,
+    PharmacodynamicModel,
+)
 import numpy as np
 
 
 class CombinedModelTestCase(APITestCase):
     def setUp(self):
-        user = User.objects.get(username='demo')
+        user = User.objects.get(username="demo")
         self.client = APIClient()
         self.client.force_authenticate(user=user)
 
@@ -25,154 +30,148 @@ def test_pk_project_filter(self):
         self.assertEqual(len(response_data), 1)
 
     def test_cannot_create_in_read_only_project(self):
-        user = User.objects.get(username='demo2')
+        user = User.objects.get(username="demo2")
         self.client = APIClient()
         self.client.force_authenticate(user=user)
 
-        project = Project.objects.get(name='demo')
+        project = Project.objects.get(name="demo")
         response = self.client.post(
-            "/api/combined_model/",
-            data={
-                'name': 'test',
-                'project': project.id
-            }
-        )
-        self.assertEqual(
-            response.status_code, status.HTTP_403_FORBIDDEN
+            "/api/combined_model/", data={"name": "test", "project": project.id}
         )
-    
+        self.assertEqual(response.status_code, status.HTTP_403_FORBIDDEN)
+
     def create_combined_model(self, name, pd=None):
-        project = Project.objects.get(name='demo')
+        project = Project.objects.get(name="demo")
         pk = PharmacokineticModel.objects.get(
-            name='one_compartment_clinical',
+            name="one_compartment_clinical",
         )
-        data={
-            'name': name,
-            'project': project.id,
-            'pk_model': pk.id,
-            'mappings': [],
-            'derived_variables': [],
+        data = {
+            "name": name,
+            "project": project.id,
+            "pk_model": pk.id,
+            "mappings": [],
+            "derived_variables": [],
         }
         if pd is not None:
-            data['pd_model'] = pd.id
-        response = self.client.post(
-            "/api/combined_model/",
-            data=data,
-            format='json'
-        )
+            data["pd_model"] = pd.id
+        response = self.client.post("/api/combined_model/", data=data, format="json")
         self.assertEqual(response.status_code, status.HTTP_201_CREATED)
-        cm = CombinedModel.objects.get(pk=response.data['id'])
+        cm = CombinedModel.objects.get(pk=response.data["id"])
 
         # set up a protocol
         response = self.client.post(
             "/api/protocol/",
             data={
-                'name': 'test protocol',
-                'project': project.id,
-                'doses': [
+                "name": "test protocol",
+                "project": project.id,
+                "doses": [
                     {
-                        'start_time': 0,
-                        'amount': 1,
-                        'duration': 0.001,
-                        'repeat_interval': 1,
-                        'repeats': 1,
+                        "start_time": 0,
+                        "amount": 1,
+                        "duration": 0.001,
+                        "repeat_interval": 1,
+                        "repeats": 1,
                     }
-                ]
+                ],
             },
-            format='json'
+            format="json",
         )
         self.assertEqual(response.status_code, status.HTTP_201_CREATED)
 
         # attach it to the A1 variables
-        a1 = cm.variables.get(name='A1')
+        a1 = cm.variables.get(name="A1")
         response = self.client.patch(
             f"/api/variable/{a1.id}/",
             data={
-                'protocol': response.data['id'],
+                "protocol": response.data["id"],
             },
-            format='json'
+            format="json",
         )
         self.assertEqual(response.status_code, status.HTTP_200_OK)
 
         if pd is not None:
-            c1 = cm.variables.get(name='C1')
-            drug_c = cm.variables.get(name='C_Drug')
+            c1 = cm.variables.get(name="C1")
+            drug_c = cm.variables.get(name="C_Drug")
 
             response = self.client.patch(
                 f"/api/combined_model/{cm.id}/",
                 data={
-                    'mappings': [
+                    "mappings": [
                         {
-                            'pk_variable': c1.id,
-                            'pd_variable': drug_c.id,
+                            "pk_variable": c1.id,
+                            "pd_variable": drug_c.id,
                         }
                     ],
-                    'derived_variables': [],
+                    "derived_variables": [],
                 },
-                format='json'
+                format="json",
             )
             self.assertEqual(response.status_code, status.HTTP_200_OK)
 
         return response.data
-    
+
     def simulate_combined_model(self, id):
         response = self.client.post(
             f"/api/combined_model/{id}/simulate",
             data={
-                'outputs': ['PDCompartment.C_Drug', 'PKCompartment.C1', 'PDCompartment.E'],
-                'variables': {},
+                "outputs": [
+                    "PDCompartment.C_Drug",
+                    "PKCompartment.C1",
+                    "PDCompartment.E",
+                ],
+                "variables": {},
             },
-            format='json'
+            format="json",
         )
         self.assertEqual(response.status_code, status.HTTP_200_OK)
-        keys= [ key for key in response.data['outputs'].keys() ]
-        return response.data['outputs'][keys[0]], response.data['outputs'][keys[1]], response.data['outputs'][keys[2]]
+        keys = [key for key in response.data["outputs"].keys()]
+        return (
+            response.data["outputs"][keys[0]],
+            response.data["outputs"][keys[1]],
+            response.data["outputs"][keys[2]],
+        )
 
-    
     def test_swap_mapped_pd_model(self):
         pd1 = PharmacodynamicModel.objects.get(
-            name='indirect_effects_stimulation_elimination',
+            name="indirect_effects_stimulation_elimination",
         )
         pd2 = PharmacodynamicModel.objects.get(
-            name='indirect_effects_inhibition_elimination',
+            name="indirect_effects_inhibition_elimination",
         )
-        model1 = self.create_combined_model('test1', pd1)
-        model2 = self.create_combined_model('test2', pd2)
-        c_drug1, c1_1, e1 = self.simulate_combined_model(model1['id'])
-        c_drug2, c1_2, e2 = self.simulate_combined_model(model2['id'])
+        model1 = self.create_combined_model("test1", pd1)
+        model2 = self.create_combined_model("test2", pd2)
+        c_drug1, c1_1, e1 = self.simulate_combined_model(model1["id"])
+        c_drug2, c1_2, e2 = self.simulate_combined_model(model2["id"])
 
-        # c_drug should be mapped to c1 and equal 
+        # c_drug should be mapped to c1 and equal
         np.testing.assert_allclose(c_drug1, c1_1, atol=1e-5, rtol=1e-5)
 
         # swap the pd model for model 1, old mappings should be updated
-        cm = CombinedModel.objects.get(pk=model1['id'])
-        c1 = cm.variables.get(name='C1')
-        c_drug = cm.variables.get(name='C_Drug')
+        cm = CombinedModel.objects.get(pk=model1["id"])
+        c1 = cm.variables.get(name="C1")
+        c_drug = cm.variables.get(name="C_Drug")
         response = self.client.patch(
             f"/api/combined_model/{model1['id']}/",
             data={
-                'pd_model': pd2.id,
-                'mappings': [
+                "pd_model": pd2.id,
+                "mappings": [
                     {
-                        'pk_variable': c1.id,
-                        'pd_variable': c_drug.id,
+                        "pk_variable": c1.id,
+                        "pd_variable": c_drug.id,
                     }
                 ],
             },
-            format='json'
+            format="json",
         )
         model1 = response.data
 
         # simulate the model again
-        c_drug3, c1_3, e3 = self.simulate_combined_model(model1['id'])
+        c_drug3, c1_3, e3 = self.simulate_combined_model(model1["id"])
 
-        # c_drug3 should be mapped to c3 and equal 
+        # c_drug3 should be mapped to c3 and equal
         np.testing.assert_allclose(c_drug3, c1_3, atol=1e-5, rtol=1e-5)
 
         # check that the data is the same as the second simulation
         np.testing.assert_allclose(c_drug3, c_drug2, atol=1e-5, rtol=1e-5)
         np.testing.assert_allclose(c1_3, c1_2, atol=1e-5, rtol=1e-5)
         np.testing.assert_allclose(e3, e2, atol=1e-5, rtol=1e-5)
-
-
-
diff --git a/pkpdapp/pkpdapp/utils/default_params.py b/pkpdapp/pkpdapp/utils/default_params.py
index a0b393ee..243a017b 100644
--- a/pkpdapp/pkpdapp/utils/default_params.py
+++ b/pkpdapp/pkpdapp/utils/default_params.py
@@ -7,16 +7,25 @@
 
 # Load the workbook
 workbook = openpyxl.load_workbook(
-    'pkpdapp/migrations/models/ParametersValue_Species.xlsx', data_only=True)
+    "pkpdapp/migrations/models/ParametersValue_Species.xlsx", data_only=True
+)
 
-sheet_names = ['1cmpt_PK_Model', '2cmpt_PK_Model',
-               '3cmpt_PK_Model', '1cmpt_TMDD_Model',
-               '2cmpt_TMDD_Model']
-model_names = ['one_compartment', 'two_compartment',
-               'three_compartment', 'one_compartment_tmdd',
-               'two_compartment_tmdd']
-species_list = ['M', 'R', 'K', 'H']
-compound_type = ['SM', 'LM']
+sheet_names = [
+    "1cmpt_PK_Model",
+    "2cmpt_PK_Model",
+    "3cmpt_PK_Model",
+    "1cmpt_TMDD_Model",
+    "2cmpt_TMDD_Model",
+]
+model_names = [
+    "one_compartment",
+    "two_compartment",
+    "three_compartment",
+    "one_compartment_tmdd",
+    "two_compartment_tmdd",
+]
+species_list = ["M", "R", "K", "H"]
+compound_type = ["SM", "LM"]
 clinical = [False, False, False, True]
 
 defaults = {}
@@ -38,6 +47,6 @@
                 unit = row[rowi + 1].value
                 if_clinical = clinical[i]
                 defaults[model_name][parameter][species][ctype] = {
-                    'value': value,
-                    'unit': unit,
-                }
\ No newline at end of file
+                    "value": value,
+                    "unit": unit,
+                }

From 9bc95b69457377649f472204d624841fc427f79b Mon Sep 17 00:00:00 2001
From: martinjrobins <martinjrobins@gmail.com>
Date: Mon, 20 Nov 2023 12:45:29 +0000
Subject: [PATCH 22/22] copyright

---
 pkpdapp/pkpdapp/utils/default_params.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pkpdapp/pkpdapp/utils/default_params.py b/pkpdapp/pkpdapp/utils/default_params.py
index 243a017b..614e5aa7 100644
--- a/pkpdapp/pkpdapp/utils/default_params.py
+++ b/pkpdapp/pkpdapp/utils/default_params.py
@@ -1,3 +1,4 @@
+#
 # This file is part of PKPDApp (https://github.com/pkpdapp-team/pkpdapp) which
 # is released under the BSD 3-clause license. See accompanying LICENSE.md for
 # copyright notice and full license details.