staging eosc gocbd

Snapshot of the current changes + configuration for the Staging instance of EOSC GOCDB

.codeclimate.yml

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+version: "2"
+plugins:
+  phpcodesniffer:
+    enabled: true
+    # Need the beta channel to enforce PSR12,
+    # see https://docs.codeclimate.com/docs/phpcodesniffer#standard.
+    channel: "beta"
+    config:
+      standard: "phpcs.xml"
+  phpmd:
+    enabled: true
+    config:
+      file_extensions: "php"
+      rulesets: "phpmd.xml"

.gitattributes

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+# This file sets the default file normalisation behavior, 
+# and is useful in case people don't have 'core.autocrlf' config variable set.
+# (When a text file is normalized, its line endings are converted to LF in the repo).
+# https://help.github.com/articles/dealing-with-line-endings/#platform-all
+
+# The 'core.autocrlf = true' is a config variable: set to true on Windows, input on *nix. 
+# Note, this does not force normalization of all text files, but does ensure that NEW 
+# text files that you introduce to the repo have their line endings normalized to LF 
+# when they are added, and that files that are already normalized in the repo stay normalized as LF. 
+# It will NOT normalise files existing in the repo that have CLRF endings !
+
+# To automatically normalize line endings to LF for all text-based files
+# and convert to NATIVE endings on checkout, use '* text=auto' 
+# https://git-scm.com/docs/gitattributes#_end_of_line_conversion
+
+* text=auto
+
+# Refreshing a repo to re-normalise: 
+# When text=auto normalization is enabled in an already EXISTING repository, any text 
+# files containing CRLFs in the repo need to be newly normalized! If they are not they will 
+# be normalized the next time someone tries to change them, causing unfortunate misattribution. 
+# To force a normalisation of all text files, see recipes at: 
+# https://git-scm.com/docs/gitattributes#_end_of_line_conversion
+# https://help.github.com/articles/dealing-with-line-endings/#platform-all
+# Or use a tool like eclipse to change all CRLFs to LFs and commit the file. 
+
+# To explicitly declare text files you want to always be normalized and converted
+# to NATIVE line endings on checkout: 
+*.c text
+*.h text
+*.php text
+*.xml text
+*.txt text
+*.xsd text
+*.md text
+
+# The eol attribute sets a specific line-ending style to be used in the WORKING DIRECTORY:
+
+# To normalize line endings to LF on checkin but prevent conversion to CRLF on checkout: 
+#*.css text eol=lf
+
+# To normalize line endings for this file on checkin and convert them to CRLF on checkout: 
+#*.sln text eol=crlf
+
+# Denote all files that are truly binary and should not be modified.
+*.png binary
+*.jpg binary
+*.gif binary

.github/actions/mysql_bootstrap_doctrine.php

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+<?php
+// bootstrap_doctrine.php
+
+// See :doc:`Configuration <../reference/configuration>` for up to date autoloading details.
+use Doctrine\ORM\Tools\Setup;
+use Doctrine\Common\EventManager;
+use Doctrine\DBAL\Event\Listeners\OracleSessionInit;
+
+require_once  __DIR__."/../../vendor/autoload.php";
+
+// Create a simple "default" Doctrine ORM configuration for XML Mapping
+$isDevMode = true;
+$config = Setup::createAnnotationMetadataConfiguration(array(__DIR__."/../../lib/Doctrine/entities"), $isDevMode);
+
+$conn = array(
+    'driver' => 'pdo_mysql',
+    'user' => 'user',
+    'password' => 'password',
+    'host' => '172.18.0.1',
+    'dbname' => 'doctrine',
+    'charset' => 'UTF8'
+);
+
+$evm = new EventManager();
+
+// obtaining the entity manager
+$entityManager = \Doctrine\ORM\EntityManager::create($conn, $config, $evm);

.github/actions/mysql_bootstrap_pdo.php

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+<?php
+
+/**
+ * Provides a connection to the test database. Copy this file and rename it
+ * to 'bootstrap_pdo.php' in the same directory.
+ * The DBUnit tests then require these methods to get a connection to the
+ * test db.
+ *
+ * @author David Meredith
+ */
+
+/**
+ * Returns the database connection to your test databse.
+ * Modify as required to return a connection to your test db.
+ * @return PHPUnit_Extensions_Database_DB_IDatabaseConnection
+ */
+function getConnectionToTestDB() {
+    $pdo = new PDO('mysql:host=172.18.0.1;dbname=doctrine;charset=UTF8', 'user', 'password');
+    return new PHPUnit_Extensions_Database_DB_DefaultDatabaseConnection($pdo);
+}

.github/actions/run_tests.sh

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+#!/bin/bash
+
+if [[ $GITHUB_ACTIONS ]]; then
+    # Check modified PHP files with PHP's internal syntax checker
+    git diff --name-only --diff-filter=ACMRTUXB HEAD^ | grep '\.php$' | xargs -r -n 1 php -l || exit 1
+
+    # Run test suite
+    vendor/bin/phpunit -c tests/phpunit.xml --coverage-clover=coverage.xml tests/DoctrineTestSuite1.php
+else
+    echo 'ABORTED: NOT RUNNING ON GITHUB ACTIONS'
+    exit 2
+fi

.github/actions/setup.sh

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+#!/bin/bash
+
+doctrine="$PWD/vendor/bin/doctrine"
+
+if [[ -n "$DB" ]]; then
+    echo "Configuring unit tests for a $DB database"
+    cp .github/actions/${DB}_bootstrap_doctrine.php tests/doctrine/bootstrap_doctrine.php
+    cp .github/actions/${DB}_bootstrap_pdo.php tests/doctrine/bootstrap_pdo.php
+    cd tests/doctrine
+    $doctrine orm:schema-tool:create
+    if [[ "$DB" = "mysql" ]]; then
+        mysql --host '172.18.0.1' -u root -e 'set global max_connections = 200;'
+    fi
+else
+    echo 'Cannot setup unit tests, $DB is not defined.'
+    exit 1
+fi

.github/actions/sqlite_bootstrap_doctrine.php

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+<?php
+// bootstrap_doctrine.php
+
+// See :doc:`Configuration <../reference/configuration>` for up to date autoloading details.
+use Doctrine\ORM\Tools\Setup;
+use Doctrine\Common\EventManager;
+use Doctrine\DBAL\Event\Listeners\OracleSessionInit;
+
+require_once  __DIR__."/../../vendor/autoload.php";
+
+// Create a simple "default" Doctrine ORM configuration for XML Mapping
+$isDevMode = true;
+$config = Setup::createAnnotationMetadataConfiguration(array(__DIR__."/../../lib/Doctrine/entities"), $isDevMode);
+
+$conn = array(
+    'driver' => 'pdo_sqlite',
+    'path' => '/tmp/gocdb.sqlite',
+);
+
+$evm = new EventManager();
+
+$entityManager = \Doctrine\ORM\EntityManager::create($conn, $config, $evm);

.github/actions/sqlite_bootstrap_pdo.php

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+<?php
+
+/**
+ * Provides a connection to the test database. Copy this file and rename it
+ * to 'bootstrap_pdo.php' in the same directory.
+ * The DBUnit tests then require these methods to get a connection to the
+ * test db.
+ *
+ * @author David Meredith
+ */
+
+/**
+ * Returns the database connection to your test databse.
+ * Modify as required to return a connection to your test db.
+ * @return PHPUnit_Extensions_Database_DB_IDatabaseConnection
+ */
+function getConnectionToTestDB() {
+    $sqliteFile = '/tmp/gocdb.sqlite';
+    $pdo = new PDO("sqlite:" . $sqliteFile);
+    return new PHPUnit_Extensions_Database_DB_DefaultDatabaseConnection($pdo, 'sqlite');
+}
+
+?>

.github/dependabot.yml

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+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+      # For GitHub Actions, "/" checks for workflow files in .github/workflows.
+    directory: "/"
+    schedule:
+      # By default, this is on Monday.
+      interval: "weekly"

.github/workflows/continuous-integration.yml

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+name: "Continuous Integration"
+
+on: [push, pull_request]
+
+jobs:
+
+  phpunit-mariadb:
+    name: "PHPUnit with MariaDB: ${{ matrix.mariadb-version }}, PHP: ${{ matrix.php-version }}, extension: ${{ matrix.extension }}"
+    runs-on: ubuntu-latest
+    strategy:
+      # If true, stop jobs if a required job fails:
+      fail-fast: false
+      matrix:
+        # Define jobs for all combinations of php, mariadb and extension, up to "include"
+        # Tests will be performed for each combination
+        php-version: ["5.4", "5.5", "5.6", "7.0", "7.1", "7.4"]
+        mariadb-version: ["10.3"]
+        extension: ["pdo_mysql"]
+        include:
+          - php-version: "5.4"
+            composer-json: "composer-5.4.json"
+          - php-version: "5.5"
+            composer-json: "composer-5.4.json"
+          - php-version: "5.6"
+            composer-json: "composer-5.4.json"
+          - php-version: "7.0"
+            composer-json: "composer-5.4.json"
+          - php-version: "7.1"
+            composer-json: "composer-5.4.json"
+          - php-version: "7.4"
+            composer-json: "composer.json"
+
+    services:
+      mariadb:
+        image: "mariadb:${{ matrix.mariadb-version }}"
+        env:
+          MYSQL_ALLOW_EMPTY_PASSWORD: yes
+          MYSQL_DATABASE: "doctrine"
+          MYSQL_USER: "user"
+          MYSQL_PASSWORD: "password"
+
+        options: --health-cmd="mysqladmin ping" --health-interval=5s --health-timeout=2s --health-retries=3
+        ports:
+          - "3306:3306"
+
+    steps:
+      - name: "Checkout"
+        uses: "actions/checkout@v4"
+        with:
+          fetch-depth: 2
+
+      - name: "Install PHP"
+        uses: "shivammathur/setup-php@v2"
+        with:
+          php-version: "${{ matrix.php-version }}"
+          coverage: "xdebug"
+          extensions: "${{ matrix.extension }}"
+
+      - name: Validate composer.json and composer.lock
+        run: composer validate
+
+      - name: Cache Composer packages
+        id: composer-cache
+        uses: actions/cache@v4
+        with:
+          path: vendor
+          key: ${{ runner.os }}-php-${{ hashFiles('**/composer.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-php-
+
+      - name: Install dependencies
+        env:
+          COMPOSER: ${{ matrix.composer-json }}
+        run: composer install --no-progress
+
+      - name: Set up unit testing
+        run: .github/actions/setup.sh
+        env:
+          DB: mysql
+
+      - name: Run unit tests
+        run: .github/actions/run_tests.sh
+
+      - name: "Upload to Codecov"
+        uses: "codecov/codecov-action@v4"

.gitignore

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+
+# Generic
+=====================
+*~
+
+# Project specific
+# ====================
+aup.pdf
+bootstrap_doctrine.php
+bootstrap_pdo.php
+bootstrap_doctrine_mysql.php
+bootstrap_doctrine_oracle.php
+vendor/
+compiledEntities/
+composer.phar
+composer.bat
+composer
+gocdb.log
+tests/coverageReports/
+privacy.pdf
+/.htaccess
+
+# Eclipse: https://github.com/github/gitignore/blob/master/Global/Eclipse.gitignore
+# =====================
+.metadata
+bin/
+tmp/
+*.tmp
+*.bak
+*.swp
+*~.nib
+local.properties
+.settings/
+.loadpath
+
+# Eclipse Core
+.project
+
+# External tool builders
+.externalToolBuilders/
+
+# Locally stored "Eclipse launch configurations"
+*.launch
+
+# PyDev specific (Python IDE for Eclipse)
+*.pydevproject
+
+# CDT-specific (C/C++ Development Tooling)
+.cproject
+
+# JDT-specific (Eclipse Java Development Tools)
+.classpath
+
+# Java annotation processor (APT)
+.factorypath
+
+# PDT-specific (PHP Development Tools)
+.buildpath
+
+# sbteclipse plugin
+.target
+
+# Tern plugin
+.tern-project
+
+# TeXlipse plugin
+.texlipse
+
+# STS (Spring Tool Suite)
+.springBeans
+
+# Code Recommenders
+.recommenders/
+
+
+
+# Netbeans: https://github.com/github/gitignore/blob/master/Global/NetBeans.gitignore
+# =====================
+nbproject/
+nbproject/private/
+build/
+nbbuild/
+dist/
+nbdist/
+nbactions.xml
+nb-configuration.xml
+
+#PhpStorm
+#================
+*.iml
+.idea/
+
+#wamp
+#==============
+error.log
+transfer.log
+Composer-Setup.exe

.gitold/HEAD

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+ref: refs/heads/dev

.gitold/config

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+[core]
+	repositoryformatversion = 0
+	filemode = true
+	bare = false
+	logallrefupdates = true
+[remote "origin"]
+	url = https://github.com/GOCDB/gocdb.git
+	fetch = +refs/heads/*:refs/remotes/origin/*
+[branch "dev"]
+	remote = origin
+	merge = refs/heads/dev