2.1.2

.github/workflows/mk-bycon-docs.yaml

@@ -16,4 +16,6 @@ jobs:
       - run: pip install pymdown-extensions
       - run: pip install mkdocs-mermaid2-plugin
       - run: pip install mdx_gh_links
+      - run: pip install mkdocstrings-python
+      - run: pip install mkdocs-include-markdown-plugin
       - run: mkdocs gh-deploy --force

.gitignore

@@ -1,18 +1,17 @@
 .DS_Store
-rsrc/remnants
+*remnants
 remnants
 *~lock*
 *.ods#
 *__pycache__*
 site
+logs
 build
 bycon.egg-info
 dist
 bycon/beaconServer/local/*
-.idea/bycon.iml
-.idea/misc.xml
-.idea/vcs.xml
-.idea/bycon.iml
-.idea/bycon.iml
-.idea/misc.xml
-.idea/vcs.xml
+.idea
+beaconplusWeb/.next
+beaconplusWeb/node_modules
+beaconplusWeb/out
+

beaconServer/README.md

@@ -0,0 +1,4 @@
+## `bycon/beaconServer` directory
+
+This directory contains the Beacon app, calling the individual v2
+endpoints.

beaconServer/beacon.py

@@ -0,0 +1,48 @@
+#!/usr/local/bin/python3
+
+from bycon import (
+    BYC,
+    BeaconDataResponse,
+    BeaconErrorResponse,
+    BeaconInfoResponse,
+    prdbug,
+    print_json_response
+)
+
+################################################################################
+
+def main():
+    """
+    The type of execution depends on the requested entity defined in the
+    `request_entity_path_id` (or aliases) in `entity_defaults`.
+    The entity is determined from different potential inputs and overwritten
+    by the next one in the order, if existing:
+
+    1. from the path (element after "beacon", e.g. `biosamples` from
+       `/beacon/biosamples/...`)
+    2. from a form value, e.g. `?requestEntityPathId=biosamples`
+    3. from a command line argument, e.g. `--requestEntityPathId biosamples`
+
+    Fallback is `/info` - so the 422 shouldn't be a thing...
+    """
+
+    b_r_c = BYC.get("bycon_response_class", "___none___")
+
+    r = None
+    if b_r_c == "BeaconInfoResponse":
+        r = BeaconInfoResponse().populatedInfoResponse()
+    elif b_r_c == "BeaconDataResponse":
+        r = BeaconDataResponse().dataResponseFromEntry()
+    BeaconErrorResponse().respond_if_errors()
+    if r:
+        print_json_response(r)
+
+    BYC["ERRORS"].append("No correct service path provided. Please refer to the documentation at http://docs.progenetix.org")
+    BeaconErrorResponse().respond_if_errors()
+
+
+################################################################################
+################################################################################
+
+if __name__ == '__main__':
+    main()

beaconplusWeb/.babelrc

@@ -0,0 +1,3 @@
+{
+  "presets": ["next/babel"]
+}

beaconplusWeb/.eslintrc.json

@@ -0,0 +1,34 @@
+{
+  "env": {
+    "browser": true,
+    "es2020": true,
+    "jest": true,
+    "node": true
+  },
+  "extends": [
+    "eslint:recommended",
+    "plugin:react/recommended",
+    "plugin:react-hooks/recommended"
+  ],
+  "parserOptions": {
+    "ecmaFeatures": {
+      "jsx": true
+    },
+    "ecmaVersion": 11,
+    "sourceType": "module"
+  },
+  "plugins": ["react"],
+  "rules": {
+    "react/react-in-jsx-scope": "off",
+    "react/prop-types": "off",
+    "no-unused-vars": [
+      "error",
+      {
+        "ignoreRestSiblings": true
+      }
+    ]
+  },
+  "globals": {
+    "React": "writable"
+  }
+}

beaconplusWeb/.prettierrc

@@ -0,0 +1,6 @@
+{
+  "trailingComma": "none",
+  "tabWidth": 2,
+  "semi": false,
+  "singleQuote": false
+}

beaconplusWeb/env/development

@@ -0,0 +1,3 @@
+NEXT_PUBLIC_API_PATH=/api/
+NEXT_PUBLIC_USE_PROXY=true
+NEXT_PUBLIC_SITE_URL=http://beaconplus.test/

beaconplusWeb/env/local

@@ -0,0 +1,5 @@
+SERVER=http://beaconplus.test/
+NEXT_PUBLIC_API_PATH=http://beaconplus.test/
+NEXT_PUBLIC_PREFETCH_API_PATH=http://beaconplus.test/
+NEXT_PUBLIC_USE_PROXY=false
+NEXT_PUBLIC_SITE_URL=http://beaconplus.test/

beaconplusWeb/env/production

@@ -0,0 +1,3 @@
+NEXT_PUBLIC_API_PATH=/
+NEXT_PUBLIC_USE_PROXY=false
+NEXT_PUBLIC_SITE_URL=https://beaconplus.progenetix.org/

beaconplusWeb/env/staging

@@ -0,0 +1,5 @@
+SERVER=https://staging.beaconplus.org/
+NEXT_PUBLIC_API_PATH=/
+NEXT_PUBLIC_PREFETCH_API_PATH=$SERVER
+NEXT_PUBLIC_USE_PROXY=false
+NEXT_PUBLIC_SITE_URL=$SERVER

beaconplusWeb/jest.config.js

@@ -0,0 +1,8 @@
+module.exports = {
+  collectCoverageFrom: ["**/*.{js,jsx}", "!**/node_modules/**"],
+  testPathIgnorePatterns: ["/node_modules/", "/.next/"],
+  transform: {
+    "^.+\\.(js|jsx)$": "<rootDir>/node_modules/babel-jest"
+  },
+  transformIgnorePatterns: ["/node_modules/"]
+}

beaconplusWeb/next.config.js

@@ -0,0 +1,12 @@
+module.exports = {
+  // eslint-disable-next-line no-unused-vars
+  webpack(config, options) {
+    config.module.rules.push({
+      test: /\.ya?ml$/,
+      use: "js-yaml-loader"
+    })
+    return config
+  },
+  trailingSlash: true,
+  productionBrowserSourceMaps: true
+}