Merge branch 'master' into dependabot/pip/django-3.2.19

.env

@@ -1,26 +1 @@
-PORT=8020
-DEBUG=1
-HOST_NAME=monkshood
-SECRET_KEY=aLargeRandomSecretKey
-DJANGO_SUPERUSER_USERNAME=admin
-DJANGO_SUPERUSER_PASSWORD=sekret1
-DJANGO_SUPERUSER_EMAIL=[email protected]
-EMAIL_HOST=in-v3.mailjet.com
-EMAIL_PORT=25
-EMAIL_HOST_USER=email_username
-EMAIL_HOST_PASSWORD=email_password
-DEFAULT_FROM_EMAIL=[email protected]
-POSTGRES_PASSWORD=sekret2
-DATABASE_URL=postgres://postgres:sekret2@postgres:5432/postgres
-
-RABBITMQ_DEFAULT_USER=guest
-RABBITMQ_DEFAULT_PASS=guest
-
-AUTH_LDAP_USE=0
-AUTH_LDAP_SERVER_URI=ldap://ldap.forumsys.com:389 
-AUTH_LDAP_DIRECT_BIND=1
-AUTH_LDAP_BIND_DN_TEMPLATE=uid=%(user)s,dc=example,dc=com
-AUTH_LDAP_BIND_DN=cn=read-only-admin,dc=example,dc=com
-AUTH_LDAP_BIND_PASSWORD=password
-AUTH_LDAP_SEARCH_BASE=ou=mathematicians,dc=example,dc=com
-AUTH_LDAP_SEARCH_FILTER=(uid=%(user)s)
+DEBUG=1

.env.prod

@@ -0,0 +1,26 @@
+PORT=8020
+DEBUG=1
+HOST_NAME=monkshood
+SECRET_KEY=aLargeRandomSecretKey
+DJANGO_SUPERUSER_USERNAME=admin
+DJANGO_SUPERUSER_PASSWORD=sekret1
+DJANGO_SUPERUSER_EMAIL=[email protected]
+EMAIL_HOST=in-v3.mailjet.com
+EMAIL_PORT=25
+EMAIL_HOST_USER=email_username
+EMAIL_HOST_PASSWORD=email_password
+DEFAULT_FROM_EMAIL=[email protected]
+POSTGRES_PASSWORD=sekret2
+DATABASE_URL=postgres://postgres:sekret2@postgres:5432/postgres
+
+RABBITMQ_DEFAULT_USER=guest
+RABBITMQ_DEFAULT_PASS=guest
+
+AUTH_LDAP_USE=0
+AUTH_LDAP_SERVER_URI=ldap://ldap.forumsys.com:389 
+AUTH_LDAP_DIRECT_BIND=1
+AUTH_LDAP_BIND_DN_TEMPLATE=uid=%(user)s,dc=example,dc=com
+AUTH_LDAP_BIND_DN=cn=read-only-admin,dc=example,dc=com
+AUTH_LDAP_BIND_PASSWORD=password
+AUTH_LDAP_SEARCH_BASE=ou=mathematicians,dc=example,dc=com
+AUTH_LDAP_SEARCH_FILTER=(uid=%(user)s)

.flake8

@@ -1,4 +1,6 @@
 [flake8]
+max-line-length = 88
+extend-ignore = E203, W503
 
 exclude=
     .git,

.github/workflows/copyright-test.yml

@@ -17,10 +17,10 @@ jobs:
     steps:
       - uses: actions/checkout@v1
 
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/setup-python@v1
         with:
-          python-version: 3.9
+          python-version: '3.10'
           architecture: x64
 
       - name: install ldap 

.github/workflows/coverage-test.yml

@@ -17,10 +17,10 @@ jobs:
     steps:
       - uses: actions/checkout@v1
 
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/setup-python@v1
         with:
-          python-version: 3.9
+          python-version: '3.10'
           architecture: x64
 
       - name: install sundials

.github/workflows/style-test.yml

@@ -18,10 +18,10 @@ jobs:
     steps:
       - uses: actions/checkout@v1
 
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/setup-python@v1
         with:
-          python-version: 3.9
+          python-version: '3.10'
           architecture: x64
 
       - name: install ldap 

.github/workflows/unit-test-os-versions.yml

@@ -14,15 +14,15 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest]
 
     steps:
       - uses: actions/checkout@v1
 
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/setup-python@v1
         with:
-          python-version: 3.9
+          python-version: '3.10'
           architecture: x64
 
       - name: install sundials (ubuntu)

.github/workflows/unit-test-python-versions.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9, "3.10"]
+        python-version: ['3.10']
 
     steps:
       - uses: actions/checkout@v1

.gitignore

@@ -22,3 +22,5 @@ pkpdapp/static
 
 # nodemodules
 frontend/node_modules
+
+logfile.log*

Dockerfile

@@ -1,16 +1,16 @@
 # Using a 2-stage build. This is the builder for javascript frontend
 
-FROM node:lts as build
+FROM node:19 as build
 RUN mkdir -p /app/frontend
 WORKDIR /app/frontend
-COPY frontend/package.json /app/frontend
+COPY frontend-v2/package.json /app/frontend
 
-RUN npm install --legacy-peer-deps
+RUN npm install
 
-COPY frontend /app/frontend/
+COPY frontend-v2 /app/frontend/
 RUN npm run build
 
-FROM python:3.9
+FROM python:3.10
 
 # install libsundials-dev
 RUN apt-get update && apt-get upgrade -y
@@ -34,7 +34,7 @@ RUN rm -rf /var/lib/apt/lists/*
 # install dependencies
 COPY ./requirements.txt /
 RUN apt-get update && apt-get upgrade -y
-RUN apt-get install -y build-essential libsasl2-dev python-dev libldap2-dev libssl-dev
+RUN apt-get install -y build-essential libsasl2-dev python3-dev libldap2-dev libssl-dev
 
 RUN pip install  -r requirements.txt
 

README.md

@@ -136,7 +136,7 @@ described using the OpenAPI specification. To generate the OpenAPI
 specification, run the following command:
 
 ```bash
-python manage.py generateschema --file schema.yml
+python manage.py spectacular --color --file schema.yml
 ```
 
 ## Generating RTX Query API class

docker-compose.yml

@@ -9,14 +9,14 @@ services:
     ports:
       - "5432:5432"
     env_file:
-      - ./.env
+      - ./.env.prod
     restart: unless-stopped
     volumes: 
       - db:/var/lib/postgresql/data
   rabbitmq:
     image: rabbitmq:3-management-alpine
     env_file:
-      - ./.env
+      - ./.env.prod
     ports:
         - 5672:5672
         - 15672:15672
@@ -33,6 +33,6 @@ services:
       - "80:${PORT}"
     restart: unless-stopped
     env_file:
-     - ./.env
+     - ./.env.prod
 
 

frontend-v2/cypress.config.ts

@@ -0,0 +1,18 @@
+import { defineConfig } from "cypress";
+
+export default defineConfig({
+  e2e: {
+    setupNodeEvents(on, config) {
+      // implement node event listeners here
+    },
+    baseUrl: 'http://localhost:3000',
+
+  },
+
+  component: {
+    devServer: {
+      framework: "next",
+      bundler: "webpack",
+    },
+  },
+});

frontend-v2/cypress/.gitignore

@@ -0,0 +1,2 @@
+*.png
+*.mp4

frontend-v2/cypress/e2e/pkmodel.cy.js

@@ -0,0 +1,101 @@
+describe('landing page', () => {
+  beforeEach(() => {
+    const { username, password } = { username: 'demo', password: '12345'}
+    cy.login(username, password)
+  })
+
+  it('can create combined pk and pd model and simulate from it', () => {
+    // create a new project
+    cy.intercept('POST', '/api/project/').as('createProject')
+    cy.get('[data-cy="create-project"]').click()
+    cy.get('[data-cy="create-project-option-Small Molecule"]').click()
+    cy.wait('@createProject').then((interception) => {
+        const { id } = interception.response.body
+
+        // select the species
+        cy.get(`[data-cy="project-${id}"]`).find('[data-cy="select-project.species"]').click()
+        cy.get('[data-cy="select-option-project.species-Monkey"]').click()
+
+        // select the project
+        cy.get(`[data-cy="project-${id}"]`).find('[type=radio]').click()
+    });
+
+    cy.get('[data-cy="select-project.species"]').last().click()
+    cy.get('[data-cy="select-option-project.species-Monkey"]').last().click()
+
+
+    // go to model tab
+    cy.get('li').contains('Model').click()
+
+    // select one compartment model
+    cy.get('[data-cy="select-pk_model"]').click()
+    cy.get('[data-cy="select-option-pk_model-one_compartment_preclinical"]').click()
+
+    // select pd model
+    cy.get('[data-cy="select-pd_model"]').click()
+    cy.get('[data-cy="select-option-pd_model-indirect_effects_stimulation_elimination"]').click()
+
+    // go to map variables tab
+    cy.contains('button', 'Map Variables').click()
+
+    // dose into Aa compartment
+    cy.get('[data-cy="checkbox-dosing-Aa"]').click()
+
+    // map C1 to pd effect
+    cy.get('[data-cy="checkbox-map-to-pd-C1"]').click()
+
+    // go to parameters tab
+    cy.contains('button', 'Parameters').click()
+
+    cy.get('[data-cy="parameter-CL-value"]').find('input').then(($input) => {
+      const old_value = $input.val()
+
+      // reset to species defaults
+      cy.contains('button', 'Reset to Species Defaults').click()
+      cy.wait(1000)
+
+      // check that the value has changed
+      cy.get('[data-cy="parameter-CL-value"]').find('input').then(($input) => {
+        expect($input.val()).not.to.eq(old_value)
+      })
+    });
+
+    // go to trial design tab
+    cy.get('li').contains('Trial Design').click()
+
+    // set the dose
+    cy.get('input[name="doses.0.amount"]').clear().type('1')
+
+    // set the number of doses
+    cy.get('input[name="doses.0.repeats"]').clear().type('4')
+
+    // set the duration
+    cy.get('input[name="doses.0.duration"]').clear().type('0.1')
+
+    // set the interval
+    cy.get('input[name="doses.0.repeat_interval"]').clear().type('0.1')
+
+    // go to simulation tab
+    cy.get('li').contains('Simulations').click()
+
+    // should be no svg with class "main-svg"
+    cy.get('svg.main-svg').should('not.exist')
+
+    // add a plot of Aa
+    cy.get('[data-cy="add-plot"]').click()
+    cy.get('[data-cy^="add-plot-option-Aa"]').click()
+
+    // now there should be an svg with class "main-svg"
+    cy.get('svg.main-svg').should('exist')
+
+    // should be no CL slider
+    cy.get('[data-cy="parameter-slider-CL"]').should('not.exist')
+
+    // add a CL parameter slider
+    cy.get('[data-cy="add-parameter-slider"]').click()
+    cy.get('[data-cy="add-parameter-slider-option-CL"]').click()
+
+    // CL slider should exist
+    cy.get('[data-cy="parameter-slider-CL"]').should('exist')
+  });
+});

frontend-v2/cypress/support/commands.ts

@@ -0,0 +1,55 @@
+/// <reference types="cypress" />
+// ***********************************************
+// This example commands.ts shows you how to
+// create various custom commands and overwrite
+// existing commands.
+//
+// For more comprehensive examples of custom
+// commands please read more here:
+// https://on.cypress.io/custom-commands
+// ***********************************************
+//
+//
+// -- This is a parent command --
+// Cypress.Commands.add('login', (email, password) => { ... })
+//
+//
+// -- This is a child command --
+// Cypress.Commands.add('drag', { prevSubject: 'element'}, (subject, options) => { ... })
+//
+//
+// -- This is a dual command --
+// Cypress.Commands.add('dismiss', { prevSubject: 'optional'}, (subject, options) => { ... })
+//
+//
+// -- This will overwrite an existing command --
+// Cypress.Commands.overwrite('visit', (originalFn, url, options) => { ... })
+//
+// declare global {
+//   namespace Cypress {
+//     interface Chainable {
+//       login(email: string, password: string): Chainable<void>
+//       drag(subject: string, options?: Partial<TypeOptions>): Chainable<Element>
+//       dismiss(subject: string, options?: Partial<TypeOptions>): Chainable<Element>
+//       visit(originalFn: CommandOriginalFn, url: string, options: Partial<VisitOptions>): Chainable<Element>
+//     }
+//   }
+// }
+
+Cypress.Commands.add('login', (username, password) => {
+  cy.visit('/')
+
+  cy.get('input[name=username]').type(username)
+
+  // {enter} causes the form to submit
+  cy.get('input[name=password]').type(`${password}{enter}`, { log: false })
+
+  // we should be redirected to /
+  cy.url().should('not.contain', 'login')
+
+  // our auth cookies should be present
+  cy.getCookie('csrftoken').should('exist')
+  cy.getCookie('sessionid').should('exist')
+})
+
+export {}