2.1.0

LICENSE

@@ -0,0 +1,121 @@
+Creative Commons Legal Code
+
+CC0 1.0 Universal
+
+    CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE
+    LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN
+    ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS
+    INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES
+    REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS
+    PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM
+    THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED
+    HEREUNDER.
+
+Statement of Purpose
+
+The laws of most jurisdictions throughout the world automatically confer
+exclusive Copyright and Related Rights (defined below) upon the creator
+and subsequent owner(s) (each and all, an "owner") of an original work of
+authorship and/or a database (each, a "Work").
+
+Certain owners wish to permanently relinquish those rights to a Work for
+the purpose of contributing to a commons of creative, cultural and
+scientific works ("Commons") that the public can reliably and without fear
+of later claims of infringement build upon, modify, incorporate in other
+works, reuse and redistribute as freely as possible in any form whatsoever
+and for any purposes, including without limitation commercial purposes.
+These owners may contribute to the Commons to promote the ideal of a free
+culture and the further production of creative, cultural and scientific
+works, or to gain reputation or greater distribution for their Work in
+part through the use and efforts of others.
+
+For these and/or other purposes and motivations, and without any
+expectation of additional consideration or compensation, the person
+associating CC0 with a Work (the "Affirmer"), to the extent that he or she
+is an owner of Copyright and Related Rights in the Work, voluntarily
+elects to apply CC0 to the Work and publicly distribute the Work under its
+terms, with knowledge of his or her Copyright and Related Rights in the
+Work and the meaning and intended legal effect of CC0 on those rights.
+
+1. Copyright and Related Rights. A Work made available under CC0 may be
+protected by copyright and related or neighboring rights ("Copyright and
+Related Rights"). Copyright and Related Rights include, but are not
+limited to, the following:
+
+  i. the right to reproduce, adapt, distribute, perform, display,
+     communicate, and translate a Work;
+ ii. moral rights retained by the original author(s) and/or performer(s);
+iii. publicity and privacy rights pertaining to a person's image or
+     likeness depicted in a Work;
+ iv. rights protecting against unfair competition in regards to a Work,
+     subject to the limitations in paragraph 4(a), below;
+  v. rights protecting the extraction, dissemination, use and reuse of data
+     in a Work;
+ vi. database rights (such as those arising under Directive 96/9/EC of the
+     European Parliament and of the Council of 11 March 1996 on the legal
+     protection of databases, and under any national implementation
+     thereof, including any amended or successor version of such
+     directive); and
+vii. other similar, equivalent or corresponding rights throughout the
+     world based on applicable law or treaty, and any national
+     implementations thereof.
+
+2. Waiver. To the greatest extent permitted by, but not in contravention
+of, applicable law, Affirmer hereby overtly, fully, permanently,
+irrevocably and unconditionally waives, abandons, and surrenders all of
+Affirmer's Copyright and Related Rights and associated claims and causes
+of action, whether now known or unknown (including existing as well as
+future claims and causes of action), in the Work (i) in all territories
+worldwide, (ii) for the maximum duration provided by applicable law or
+treaty (including future time extensions), (iii) in any current or future
+medium and for any number of copies, and (iv) for any purpose whatsoever,
+including without limitation commercial, advertising or promotional
+purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each
+member of the public at large and to the detriment of Affirmer's heirs and
+successors, fully intending that such Waiver shall not be subject to
+revocation, rescission, cancellation, termination, or any other legal or
+equitable action to disrupt the quiet enjoyment of the Work by the public
+as contemplated by Affirmer's express Statement of Purpose.
+
+3. Public License Fallback. Should any part of the Waiver for any reason
+be judged legally invalid or ineffective under applicable law, then the
+Waiver shall be preserved to the maximum extent permitted taking into
+account Affirmer's express Statement of Purpose. In addition, to the
+extent the Waiver is so judged Affirmer hereby grants to each affected
+person a royalty-free, non transferable, non sublicensable, non exclusive,
+irrevocable and unconditional license to exercise Affirmer's Copyright and
+Related Rights in the Work (i) in all territories worldwide, (ii) for the
+maximum duration provided by applicable law or treaty (including future
+time extensions), (iii) in any current or future medium and for any number
+of copies, and (iv) for any purpose whatsoever, including without
+limitation commercial, advertising or promotional purposes (the
+"License"). The License shall be deemed effective as of the date CC0 was
+applied by Affirmer to the Work. Should any part of the License for any
+reason be judged legally invalid or ineffective under applicable law, such
+partial invalidity or ineffectiveness shall not invalidate the remainder
+of the License, and in such case Affirmer hereby affirms that he or she
+will not (i) exercise any of his or her remaining Copyright and Related
+Rights in the Work or (ii) assert any associated claims and causes of
+action with respect to the Work, in either case contrary to Affirmer's
+express Statement of Purpose.
+
+4. Limitations and Disclaimers.
+
+ a. No trademark or patent rights held by Affirmer are waived, abandoned,
+    surrendered, licensed or otherwise affected by this document.
+ b. Affirmer offers the Work as-is and makes no representations or
+    warranties of any kind concerning the Work, express, implied,
+    statutory or otherwise, including without limitation warranties of
+    title, merchantability, fitness for a particular purpose, non
+    infringement, or the absence of latent or other defects, accuracy, or
+    the present or absence of errors, whether or not discoverable, all to
+    the greatest extent permissible under applicable law.
+ c. Affirmer disclaims responsibility for clearing rights of other persons
+    that may apply to the Work or any use thereof, including without
+    limitation any person's Copyright and Related Rights in the Work.
+    Further, Affirmer disclaims responsibility for obtaining any necessary
+    consents, permissions or other rights required for any use of the
+    Work.
+ d. Affirmer understands and acknowledges that Creative Commons is not a
+    party to this document and has no duty or obligation with respect to
+    this CC0 or use of the Work.

MANIFEST.in

@@ -0,0 +1,4 @@
+recursive-include bycon/config *.*
+recursive-include bycon/rsrc *.*
+recursive-include bycon/schemas *.*
+include config.yaml

README.md

@@ -0,0 +1,24 @@
+[![License: CC0-1.0](https://img.shields.io/badge/License-CC0%201.0-lightgrey.svg)](http://creativecommons.org/publicdomain/zero/1.0/)
+
+# Bycon - a Python-based environment for the Beacon v2 genomics API
+
+The `bycon` project - at least at its current stage - is a mix of _Progenetix_ (i.e. GA4GH object model derived, _MongoDB_ implemented) - data management, and the implementation of middleware & server for the Beacon API.
+
+In its current state the `bycon` package is undergoing a transition from resource
+specific to general use environment. There is still some entanglement between
+code and use case specific definitions (e.g. database definitions inside the
+distribution) though this is (early 2023) in a process of "disentanglement".
+
+## More Documentation
+
+Documentation has been moved to [`bycon.progenetix.org`](http://bycon.progenetix.org).
+W/ the rapid code development it is recommended to keep following the [Changes](http://bycon.progenetix.org/changes/)
+page.
+
+### Installation
+
+The installation is documented [`on the website`](http://bycon.progenetix.org/installation/)
+(and in the page's Markdown [source here](./docs/installation.md)).
+
+Since version `1.0.55` (2023-06-22) additional "services" may be installed from
+the [`byconaut`](https://github.com/progenetix/byconaut/) repository.

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/bin/env 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
+}