Merge pull request #62 from matthiaskoenig/develop

pkpd-v0.1.0

.gitignore

@@ -6,9 +6,13 @@ __pycache__/
 # C extensions
 *.so
 
+# open/libre office
+*.ods#
+
+
 # Distribution / packaging
 .Python
-build/
+# build/
 develop-eggs/
 dist/
 downloads/
@@ -57,7 +61,7 @@ coverage.xml
 # Django stuff:
 *.log
 .static_storage/
-.media/
+media/
 local_settings.py
 
 # Flask stuff:
@@ -106,6 +110,12 @@ venv.bak/
 
 # django staticfiles
 /static
-/migrations
+
+*/migrations/
 # mypy
 .mypy_cache/
+pkdb_app/studies/migrations/00*.py
+pkdb_app/users/migrations/00*.py
+pkdb_app/subjects/migrations/00*.py
+pkdb_app/interventions/migrations/00*.py
+pkdb_app/comments/migrations/00*.py

Dockerfile

@@ -4,6 +4,8 @@ ENV PYTHONUNBUFFERED 1
 # Allows docker to cache installed dependencies between builds
 COPY ./requirements.txt requirements.txt
 RUN pip install -r requirements.txt
+#ENV DJANGO_SETTINGS_MODULE pkdb_app.config.local
+
 
 # Adds our application code to the image
 COPY . code

README.md

@@ -16,6 +16,13 @@ Database and web interface for storing pharmacokinetics information including
 <img src="./docs/images/data_extraction.png" width="600"/>
 Figure 1: Overview over data extraction.
 
+## Access
+http://localhost:8000/api/v1/
+http://localhost:8000/api/v1/studies/17955229/
+
+
+
+
 ## Data model
 Pharmacokinetics data is a special type of experimental data.
 Pharmacokinetics data like clearance, halflife, ... (with units and error measurements) are either directly reported in publications
@@ -51,6 +58,32 @@ Create a superuser to login to the admin:
 docker-compose run --rm web ./manage.py createsuperuser
 ```
 
+# Update after code change
+```
+# reset migrations
+sudo find . -path "*/migrations/*.py" -not -name "__init__.py" -delete && sudo find . -path "*/migrations/*.pyc"  -delete && sudo rm -r media/study/
+
+# rebuild container
+docker-compose down
+docker-compose up --build
+```
+
+
+# Fill database
+From console use the following
+```
+workon pkdb
+(pkdb) pip install -r requirements.txt --upgrade
+(pkdb) python ./pkdb_app/data_management/fill_database.py
+```
+
+
+# Connect database pycharm
+```
+DataSource -> postgres
+```
+Use port defined in `docker-compose.yml` (5433), database name and password in `docker-compose.yml`
+
 # Local Development
 Start the dev server for local development:
 
@@ -69,5 +102,14 @@ Example:
 ```
 
 ----
+# Client
+check out ./client/README.md.
+## Requirements
+- node.js
+- npm
+- vue.js
+
+
+
 
 &copy; 2018 Jan Grzegorzewski & Matthias König.

TODO.md

@@ -1,6 +1,47 @@
+# Small Tasks
+- change how to write characteristicy ("choice": "Y(3)||N(1)")
+
+- move reused information on groupset and interventionset, e.g., 
+  characteristica which are for all groups ✅
+- remove description from group & intervention ✅
+
+- add comments on group and intervention, groupset and intervention (serializer and data model)
+- use usernames for name (shorter and faster) ✅
+- remove NA from errors ✅
+- add substances on study (from categorials list of substances) ✅
+- update names changed in categorials ✅
+- add value field on valuable ✅, make sure means are stored as mean (i.e. values from a group with more than 1 subject)
+
+- remove choice from valuable ✅
+
+- add design to studies ✅
+
+- API endpoints
+    - reference
+    - study (complete JSON)
+    - groupset ()
+    - group
+    - characteristica
+    - individualset
+    - interventionset
+    - intervention
+    - outputset
+    - output
+- Documentation API (Swagger DRF/Open API)
+   (- show required fields & choices of choice fields if possible, test description for fields)
+
+- Group Timecourse with column selection based on Akinyinka2000_Fig1 & Akinyinka2000_Fig2
+
+- individualset similar to groupset (with characteristica on individualset for all individuals)
+    - first step list individual individually (no column mapping for now)
+
+- LATER: create list of allowed keywords and choices (for now looked up in categorials)
+
+#Questions Janek: 
+- do we need description on study? For now it is in.
+
 # Main Tasks
 
-* import existing data sets (caffeine & acetaminophen)
 * web interface for display
 * export to excel files and CSVs
 * web interface for curation
@@ -10,3 +51,54 @@ Have a look at genetic variants
 
 https://www.pharmvar.org/
 https://www.pharmvar.org/gene/CYP1A1
+
+## timescource example
+```json
+{ 
+"timecourse": [
+    {
+    "group": "col==subjects",
+    "intervention": "D1",
+    "source": "Akinyinka2000_Fig1.csv",
+    "format": "TSV",
+    "figure": "Akinyinka2000_Fig1.png",
+    "substance": "caffeine",
+    "tissue": "plasma",
+    "pktype": "concentration",
+    "times": "col==time",
+    "values": "col==caf",
+    "sd": "col==caf_sd",
+    "unit": "µg/ml"
+    }, 
+    {
+    "group": "col==subjects",
+    "intervention": "D1",
+    "source": "Akinyinka2000_Fig1.csv",
+    "format": "TSV",
+    "figure": "Akinyinka2000_Fig2.png",
+    "substance": "paraxanthine",
+    "tissue": "plasma",
+    "pktype": "concentration",
+    "times": "col==time",
+    "values": "col==px",
+    "sd": "col==px_sd",
+    "unit": "µg/ml"
+    }, 
+    {
+    "group": "col==subjects",
+    "intervention": "D1",
+    "source": "Akinyinka2000_Fig1.csv",
+    "format": "TSV",
+    "figure": "Akinyinka2000_Fig1.png && Akinyinka2000_Fig2.png",
+    "substance": "paraxanthine && caffeine",
+    "tissue": "plasma",
+    "pktype": "ratio",
+    "times": "col==time",
+    "values": "col==px_caf",
+    "sd": "col==px_caf_sd",
+    "unit": "-"
+    }
+    ]
+}
+```
+

client/.babelrc

@@ -0,0 +1,18 @@
+{
+  "presets": [
+    ["env", {
+      "modules": false,
+      "targets": {
+        "browsers": ["> 1%", "last 2 versions", "not ie <= 8"]
+      }
+    }],
+    "stage-2"
+  ],
+  "plugins": ["transform-vue-jsx", "transform-runtime"],
+  "env": {
+    "test": {
+      "presets": ["env", "stage-2"],
+      "plugins": ["transform-vue-jsx", "transform-es2015-modules-commonjs", "dynamic-import-node"]
+    }
+  }
+}

client/.editorconfig

@@ -0,0 +1,9 @@
+root = true
+
+[*]
+charset = utf-8
+indent_style = space
+indent_size = 2
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true

client/.eslintignore

@@ -0,0 +1,5 @@
+/build/
+/config/
+/dist/
+/*.js
+/test/unit/coverage/

client/.eslintrc.js

@@ -0,0 +1,29 @@
+// https://eslint.org/docs/user-guide/configuring
+
+module.exports = {
+  root: true,
+  parserOptions: {
+    parser: 'babel-eslint'
+  },
+  env: {
+    browser: true,
+  },
+  extends: [
+    // https://github.com/vuejs/eslint-plugin-vue#priority-a-essential-error-prevention
+    // consider switching to `plugin:vue/strongly-recommended` or `plugin:vue/recommended` for stricter rules.
+    'plugin:vue/essential', 
+    // https://github.com/standard/standard/blob/master/docs/RULES-en.md
+    'standard'
+  ],
+  // required to lint *.vue files
+  plugins: [
+    'vue'
+  ],
+  // add your custom rules here
+  rules: {
+    // allow async-await
+    'generator-star-spacing': 'off',
+    // allow debugger during development
+    'no-debugger': process.env.NODE_ENV === 'production' ? 'error' : 'off'
+  }
+}

client/.gitignore

@@ -0,0 +1,17 @@
+.DS_Store
+node_modules/
+/dist/
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+/test/unit/coverage/
+/test/e2e/reports/
+selenium-debug.log
+
+# Editor directories and files
+.idea
+.vscode
+*.suo
+*.ntvs*
+*.njsproj
+*.sln

client/.postcssrc.js

@@ -0,0 +1,10 @@
+// https://github.com/michael-ciniawsky/postcss-load-config
+
+module.exports = {
+  "plugins": {
+    "postcss-import": {},
+    "postcss-url": {},
+    // to edit target browsers: use "browserslist" field in package.json
+    "autoprefixer": {}
+  }
+}

client/README.md

@@ -0,0 +1,35 @@
+# frontend
+
+> pkdb
+
+## Build Setup
+
+``` bash
+# install dependencies
+npm install
+
+# serve with hot reload at localhost:8080
+npm run dev
+
+# build for production with minification
+npm run build
+
+# build for production and view the bundle analyzer report
+npm run build --report
+
+# run unit tests
+npm run unit
+
+# run e2e tests
+npm run e2e
+
+# run all tests
+npm test
+```
+
+For a detailed explanation on how things work, check out the [guide](http://vuejs-templates.github.io/webpack/) and [docs for vue-loader](http://vuejs.github.io/vue-loader).
+
+
+```
+sudo apt-get install npm
+```

client/build/build.js

@@ -0,0 +1,41 @@
+'use strict'
+require('./check-versions')()
+
+process.env.NODE_ENV = 'production'
+
+const ora = require('ora')
+const rm = require('rimraf')
+const path = require('path')
+const chalk = require('chalk')
+const webpack = require('webpack')
+const config = require('../config')
+const webpackConfig = require('./webpack.prod.conf')
+
+const spinner = ora('building for production...')
+spinner.start()
+
+rm(path.join(config.build.assetsRoot, config.build.assetsSubDirectory), err => {
+  if (err) throw err
+  webpack(webpackConfig, (err, stats) => {
+    spinner.stop()
+    if (err) throw err
+    process.stdout.write(stats.toString({
+      colors: true,
+      modules: false,
+      children: false, // If you are using ts-loader, setting this to true will make TypeScript errors show up during build.
+      chunks: false,
+      chunkModules: false
+    }) + '\n\n')
+
+    if (stats.hasErrors()) {
+      console.log(chalk.red('  Build failed with errors.\n'))
+      process.exit(1)
+    }
+
+    console.log(chalk.cyan('  Build complete.\n'))
+    console.log(chalk.yellow(
+      '  Tip: built files are meant to be served over an HTTP server.\n' +
+      '  Opening index.html over file:// won\'t work.\n'
+    ))
+  })
+})