Merge pull request #8 from UofS-Pulse-Binfo/github-actions-integration

Implements GitHub Actions

.github/workflows/phpunit.yml

@@ -0,0 +1,86 @@
+
+name: Run PHPUnit Tests
+
+# Controls when the workflow will run.
+# Run this workflow every time a new commit is pushed to your repository
+on: [push, pull_request]
+
+jobs:
+  # This key is the name of the job.
+  run-tests:
+    # The type of system that the job will run on.
+    runs-on: ubuntu-latest
+    # Matrix Build for this job.
+    strategy:
+      matrix:
+        php-versions: ['7.1', '7.2']
+    # Name the matrix build so we can tell them apart.
+    name: PHP Unit Testing of Tripal QTL Module (PHP ${{ matrix.php-versions }})
+
+    # Service containers to run with `run-tests`
+    services:
+      # Label used to access the service container
+      postgres:
+        # Docker Hub image
+        image: postgres
+        env:
+          POSTGRES_USER: tripaladmin
+          POSTGRES_PASSWORD: somesupersecurepassword
+          POSTGRES_DB: testdb
+        # Set health checks to wait until postgres has started
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          # Maps tcp port 5432 on service container to the host
+          - 5432:5432
+
+    steps:
+    # 1) Checkout the repository and setup workspace.
+    - uses: actions/checkout@v2
+
+    # 2) Setup PHP according to the version passed in.
+    - name: Setup PHP
+      uses: shivammathur/setup-php@v2
+      with:
+        php-version: ${{ matrix.php-versions }}
+        extensions: mbstring, intl, php-pgsql, php-gd, php-xml
+        ini-values: memory_limit=2G
+        coverage: xdebug
+        tools: composer, phpunit
+
+    # 3) Install Drush/Drupal/Tripal
+    - name: Setup Drush, Drupal 7.x, Tripal 3.x
+      id: tripalsetup
+      uses: tripal/[email protected]
+      with:
+        postgres_user: tripaladmin
+        postgres_pass: somesupersecurepassword
+        postgres_db: testdb
+
+    # 4) Install Tripal QTL
+    - name: Install Tripal QTL
+      id: installtripalqtl
+      env:
+        DRUSH: ${{ steps.tripalsetup.outputs.drush_path }}
+        DRUPAL_ROOT: ${{ steps.tripalsetup.outputs.drupal_root }}
+      run: |
+        mkdir -p $DRUPAL_ROOT/sites/all/modules/tripal_qtl
+        cp -R * $DRUPAL_ROOT/sites/all/modules/tripal_qtl
+        cd $DRUPAL_ROOT
+        $DRUSH en -y tripal_qtl
+
+    # 5) Runs the PHPUnit tests.
+    # https://github.com/mheap/phpunit-github-actions-printer is used
+    # to report PHPUnit fails in a meaningful way to github in PRs.
+    - name: PHPUnit Tests
+      env:
+        DRUSH: ${{ steps.tripalsetup.outputs.drush_path }}
+        DRUPAL_ROOT: ${{ steps.tripalsetup.outputs.drupal_root }}
+      run: |
+        cd $DRUPAL_ROOT/sites/all/modules/tripal_qtl
+        composer require --dev mheap/phpunit-github-actions-printer --quiet
+        composer update --quiet
+        ./vendor/bin/phpunit --printer mheap\\GithubActionsReporter\\Printer

includes/TripalImporter/QTLImporter.inc

@@ -5,7 +5,7 @@
  * Provides support for loading of MST map files.
  */
 class QTLImporter extends TripalImporter {
-
+  
   /**
    * The name of this loader.
    *
@@ -130,7 +130,7 @@ class QTLImporter extends TripalImporter {
   /**
    * Import the map.
    */
-  public function run() {
+  public function run($f_id = null) {
 
     // All values provided by the user in the Importer's form widgets are
     // made available to us here by the Class' arguments member variable.
@@ -147,7 +147,8 @@ class QTLImporter extends TripalImporter {
     $file_path = $this->arguments['files'][0]['file_path'];
 
     // Retrieve map to add QTL Data to.
-    $featuremap_id = $arguments['featuremap_name'];
+    $featuremap_id = ($f_id && $f_id > 1) ? $f_id : $arguments['featuremap_name'];
+
     if (!$featuremap_id) {
       $this->logMessage('An Error was encountered retrieving the genetic map.');
       return FALSE;

tests/QTLImporterTest.php

@@ -110,7 +110,7 @@ public function testRun() {
     $importer->prepareFiles();
 
     // Now we run the importer!
-    $success = $importer->run();
+    $success = $importer->run($mapdetails['featuremap_id']);
     $this->assertNotFalse($success,
       "The importer returned an error.");