Merge branch '7.x-3.x' into collections

.gitignore

@@ -1 +1,4 @@
 .DS_Store
+composer.lock
+vendor/*
+tests/.env

.travis.yml

@@ -0,0 +1,37 @@
+language: php
+
+services:
+  - docker
+
+sudo: required
+
+before_script:
+  - docker pull statonlab/drupal7
+
+script:
+  # Set branch name
+  - export REPO=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_REPO_SLUG; else echo $TRAVIS_PULL_REQUEST_SLUG; fi)
+  - export BRANCH=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_BRANCH; else echo $TRAVIS_PULL_REQUEST_BRANCH; fi)
+  #  Travis does a shallow clone and we need a full clone to test Tripal v2 to v3 upgrade
+  - cd .. && rm -rf tripal && git clone https://github.com/$REPO.git tripal && cd tripal
+  - git checkout $BRANCH
+  # Test tripal 3 installation
+  - docker run -it -d --rm --name tripal3 -v "$(pwd)":/modules/tripal statonlab/drupal7
+  - sleep 15
+  - docker exec -it tripal3 drush en -y tripal tripal_chado tripal_chado_views tripal_ds tripal_ws
+  # Prepare Chado
+  - docker exec -it tripal3 drush eval "module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.install'); tripal_chado_load_drush_submit('Install Chado v1.3');"
+  - docker exec -it tripal3 drush trp-run-jobs --username=admin
+  # Prepare Drupal
+  - docker exec -it tripal3 drush eval "module_load_include('inc', 'tripal_chado', 'includes/setup/tripal_chado.setup'); tripal_chado_prepare_drush_submit();"
+  - docker exec -it tripal3 drush trp-run-jobs --username=admin
+  # Run PHPUnit tests
+  - docker exec -it tripal3 bash -c "cd /modules/tripal && composer install && DRUPAL_ROOT=/var/www/html ./vendor/bin/phpunit"
+  # Test Tripal v2 to v3 upgrade steps
+  - git checkout 7.x-2.x
+  - docker run -it -d --rm --name tripal2 -v "$(pwd)":/modules/tripal statonlab/drupal7
+  - sleep 15
+  - docker exec -it tripal2 drush en -y tripal_core
+  - docker exec -it tripal2 drush pm-disable tripal_core -y
+  - git checkout $BRANCH
+  - docker exec -it tripal2 drush en -y tripal

README.md

@@ -1,3 +1,5 @@
+[![7.x-3.x Build Status](https://travis-ci.org/tripal/tripal.svg?branch=7.x-3.x)](https://travis-ci.org/tripal/tripal)
+
 ![alt tag](https://raw.githubusercontent.com/tripal/tripal/7.x-3.x/tripal/theme/images/tripal_logo.png)
 
 Tripal is a toolkit for construction of online biological (genetics, genomics,
@@ -111,3 +113,15 @@ precise customizations as required by the community. A well-developed
 Tripal API provides a uniform set of variables and functions for 
 accessing any and all data within the Chado database. See the Tripal 3.x
 Developer's Handbook for additional details.
+
+
+# Development Testing
+
+To run PHP unit tests on your local system, simply create a `.env` file in your `/Tests/` directory that defines the `DRUPAL_ROOT` variable, for example 
+
+```
+DRUPAL_ROOT=/var/www/html
+```
+Then run PHPUnit from your root Tripal directory.
+
+PHPUnit tests will also be run in the Travis CI build.

composer.json

@@ -0,0 +1,5 @@
+{
+  "require-dev": {
+    "phpunit/phpunit": "^7"
+  }
+}

phpunit.xml

@@ -0,0 +1,11 @@
+<phpunit xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:noNamespaceSchemaLocation="phpunit.xsd"
+         bootstrap="tests/bootstrap.php"
+         verbose="true"
+         colors="true">
+    <testsuites>
+        <testsuite name="default">
+            <directory suffix=".test">./tests/</directory>
+        </testsuite>
+    </testsuites>
+</phpunit>

tests/TripalJobsTest.test

@@ -0,0 +1,21 @@
+<?php
+
+use PHPUnit\Framework\TestCase;
+
+class TripalJobsTest extends TestCase {
+
+  /**
+   * Tests the ability to create a tripal job.
+   *
+   * @test
+   */
+  public function should_create_a_tripal_job() {
+    $job_id = tripal_add_job('Test adding jobs', 'tripal', 'tripal_tripal_cron_notification', [], 1);
+    $this->assertTrue(is_numeric($job_id));
+
+    // Clean up
+    if($job_id) {
+      db_query('DELETE FROM {tripal_jobs} WHERE job_id = :id', [':id' => $job_id]);
+    }
+  }
+}

tests/bootstrap.php

@@ -0,0 +1,39 @@
+<?php
+// Set environment variables
+test_suite_read_and_set_environment_variables();
+
+// Get Drupal root path
+$drupal_root = getenv('DRUPAL_ROOT');
+define('DRUPAL_ROOT', $drupal_root ?: '/var/www/html');
+
+// Get Drupal bootstrap functions
+require_once DRUPAL_ROOT.'/includes/bootstrap.inc';
+$_SERVER['REMOTE_ADDR'] = '127.0.0.1';
+
+// Bootstrap Drupal.
+$current_dir = getcwd();
+chdir(DRUPAL_ROOT);
+drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
+chdir($current_dir);
+
+/**
+ * Get and set environment variables from .env file if it exists.
+ *
+ * @throws \Exception
+ */
+function test_suite_read_and_set_environment_variables() {
+  $filename = __DIR__.'/.env';
+  if(file_exists($filename)) {
+    $file = fopen($filename, 'r');
+    while ($line = str_replace("\n", '', fgets($file))) {
+      // break line into key value
+      $env = explode('=', $line);
+      if(count($env) === 2) {
+        putenv($line);
+      } else {
+        throw new Exception('Invalid environment line: ' . $line);
+      }
+    }
+    fclose($file);
+  }
+}

tripal/tripal.install

@@ -115,8 +115,10 @@ function tripal_enable() {
   }
 
   // schema change
-  $sql = "ALTER TABLE tripal_jobs ADD COLUMN includes text";
-  db_query($sql);
+  if (!db_field_exists('tripal_jobs', 'includes')) {
+    $sql = "ALTER TABLE tripal_jobs ADD COLUMN includes text";
+    db_query($sql);
+  }
 
   tripal_add_variables();
 }

tripal_chado/api/tripal_chado.property.api.inc

@@ -169,6 +169,7 @@ function chado_insert_property($record, $property, $options = array()) {
   $cv_id       = array_key_exists('cv_id', $property) ? $property['cv_id'] : '';
   $value       = array_key_exists('value', $property) ? $property['value'] : '';
   $rank        = array_key_exists('rank', $property) ? $property['rank'] : 0;
+  $cvalue_id   = array_key_exists('cvalue_id', $property) ? $property['cvalue_id'] : '';
 
   $update_if_present = array_key_exists('update_if_present', $options) ? $options['update_if_present'] : FALSE;
   $force_rank = array_key_exists('force_rank', $options) ? $options['force_rank'] : FALSE;
@@ -249,6 +250,20 @@ function chado_insert_property($record, $property, $options = array()) {
       array('%property' => print_r($property, TRUE)));    return FALSE;
   }
 
+
+    //Check that the cvalue property exists
+    if ($cvalue_id){
+        $term = chado_select_record('cvterm', array('cvterm_id'), array('cvterm_id' => $cvalue_id), $options);
+       if (!$term or count($term) == 0) {
+            tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_insert_property: " .
+                "Cannot find the term for the property value described by: %property.",
+                array('%property' => print_r($property, TRUE)));
+           return FALSE;
+    }
+    $values['cvalue'] = $cvalue_id;
+  }
+
+
   // Get the foreign key for this property table
   $table_desc = chado_get_schema($base_table . 'prop');
   $fkcol = key($table_desc['foreign keys'][$base_table]['columns']);
@@ -287,6 +302,9 @@ function chado_insert_property($record, $property, $options = array()) {
  *     -cv_name: The name of the CV that contains the term.
  *     -value: The specific value for the property.
  *     -rank: The specific rank for the property.
+ *     -cvalue_id: The cvterm_id of the value for the property.
+ *      **note** cvalue_id is an anticipated column in the the next Chado release (1.4).  It is included here for early adopters.
+ *
  * @param $options
  *   An associative array containing the following keys:
  *     -insert_if_missing: A boolean indicating whether a record should be
@@ -310,6 +328,7 @@ function chado_update_property($record, $property, $options = array()) {
   $cv_id       = array_key_exists('cv_id', $property) ? $property['cv_id'] : '';
   $value       = array_key_exists('value', $property) ? $property['value'] : '';
   $rank        = array_key_exists('rank', $property) ? $property['rank'] : 0;
+  $cvalue_id   = array_key_exists('cvalue_id', $property) ? $property['cvalue_id'] : '';
 
   $insert_if_missing = array_key_exists('insert_if_missing', $options) ? $options['insert_if_missing'] : FALSE;
 
@@ -385,6 +404,18 @@ function chado_update_property($record, $property, $options = array()) {
     $values['rank'] = $rank;
   }
 
+  // If a cvalue_id is supplied, check that it is a valid cvterm
+    if ($cvalue_id) {
+        $term = chado_select_record('cvterm', array('cvterm_id'), array('cvterm_id' => $cvalue_id), $options);
+        if (!$term or count($term) == 0) {
+            tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_insert_property: " .
+                "Cannot find the term for the property value described by: %property.",
+                array('%property' => print_r($property, TRUE)));
+            return FALSE;
+    }
+    $values['cvalue_id'] = $cvalue_id;
+  }
+
   // If we have the unique property_id then we can also update the type
   // thus add it to the values to be updated
   if ($prop_id) {
@@ -516,6 +547,9 @@ function chado_delete_property($record, $property) {
  *     -cv_name: The name of the CV that contains the term.
  *     -value: The specific value for the property.
  *     -rank: The specific rank for the property.
+ *     -cvalue_id: The cvterm_id of the value for the property.
+ *      **note** cvalue_id is an anticipated column in the the next Chado release (1.4).  It is included here for early adopters.
+ * 
  * @param $options
  *   An array of options supported by chado_generate_var(). These keys
  *   are used for generating the cvterm objects returned by this function.

tripal_chado/api/tripal_chado.schema.api.inc

@@ -41,9 +41,19 @@
  */
 function chado_table_exists($table) {
 
+  // Get the default database and chado schema.
   global $databases;
-
   $default_db = $databases['default']['default']['database'];
+  $chado_schema = tripal_get_schema_name('chado');
+
+  // If we've already lookup up this table then don't do it again, as
+  // we don't need to keep querying the database for the same tables.
+  if (array_key_exists("chado_tables", $GLOBALS) and
+      array_key_exists($default_db, $GLOBALS["chado_tables"]) and
+      array_key_exists($chado_schema, $GLOBALS["chado_tables"][$default_db]) and
+      array_key_exists($table, $GLOBALS["chado_tables"][$default_db][$chado_schema])) {
+    return TRUE;
+  }
 
   $sql = "
     SELECT 1
@@ -55,7 +65,7 @@ function chado_table_exists($table) {
   ";
   $args = array(
     ':table_name' => $table,
-    ':chado' => tripal_get_schema_name('chado'),
+    ':chado' => $chado_schema,
     ':default_db' => $default_db
   );
   $results = db_query($sql, $args);
@@ -63,6 +73,9 @@ function chado_table_exists($table) {
   if (!$exists) {
     return FALSE;
   }
+
+  // Set this table in the GLOBALS so we don't query for it again the next time.
+  $GLOBALS["chado_tables"][$default_db][$chado_schema][$table] = TRUE;
   return TRUE;
 }
 /**

tripal_chado/tripal_chado.module

@@ -85,6 +85,7 @@ function tripal_chado_set_globals() {
     $GLOBALS["chado_is_local"]      = chado_is_local();
     $GLOBALS["chado_version"]       = chado_get_version();
     $GLOBALS["exact_chado_version"] = chado_get_version(TRUE);
+    $GLOBALS["chado_tables"] = array();
   }
 }
 

tripal_ds/api/tripal_ds.pane.api.inc

@@ -31,11 +31,12 @@
  *  field_create_instance($instance);
  *  tripal_ds_field_create_field($field_label, $field, $bundle);
  */
-function tripal_ds_field_create_field($field_label, $field, $bundle_name) {
+function tripal_ds_create_field($field_label, $field_name, $bundle_name) {
+  $field_name = str_replace(' ', '_', strtolower($field_name));
   //Build the rest of the passes parameters.
-  $group_field_name = 'gp_'.$field['field_name'];
+  $group_field_name = 'gp_'.$field_name;
   //Create the field groups.
-  _additional_fields_field_group_info($bundle_name, $field_label, $group_field_name, $field);
+  tripal_ds_additional_fields_field_group_info($bundle_name, $field_label, $group_field_name, $field_name);
   //Place the field groups in the layout.
-  tripal_ds_update_ds_layout($bundle_name, $field, $group_field_name);
+  tripal_ds_update_ds_layout($bundle_name, $field_name, $group_field_name);
 }

tripal_ds/includes/tripal_ds.ds.inc

@@ -134,7 +134,7 @@ function _ds_layout_settings_info($bundle_name, $instances) {
         // Add random numbers to ensure the field name is unique within the 32
         // character limit of the field.
         $group_field_name = $group_field_name.rand(0, 99999);
-        _additional_fields_field_group_info($bundle_name, $other_field['label'], $group_field_name, $other_field['field_name']);
+        tripal_ds_additional_fields_field_group_info($bundle_name, $other_field['label'], $group_field_name, $other_field['field_name']);
       }
     }
 
@@ -328,7 +328,7 @@ function _ds_layout_pub_settings_info($bundle_name, $instances) {
       $group_field_name = $group_field_name.rand(0, 99999);
 
       // Build the field group.
-      _additional_fields_field_group_info($bundle_name, $other_field['label'], $group_field_name, $other_field['field_name']);
+      tripal_ds_additional_fields_field_group_info($bundle_name, $other_field['label'], $group_field_name, $other_field['field_name']);
 
       // Update arrays.
       array_push($temporary_field, $group_field_name, $other_field['field_name']);

tripal_ds/includes/tripal_ds.field_group.inc

@@ -230,7 +230,7 @@ function _data_sequence_field_group_info($bundle_name, $fields){
  * @param $field_name
  *  Machine name of the child element.
  */
-function _additional_fields_field_group_info($bundle_name, $field_label, $group_field_name, $field_name){
+function tripal_ds_additional_fields_field_group_info($bundle_name, $field_label, $group_field_name, $field_name){
   //Write to the tripal_ds table to record the new tripal pane.
   tripal_ds_bundle_menu_item($bundle_name, $field_label, $group_field_name, 'TripalEntity');
 

tripal_ds/tripal_ds.module

@@ -4,6 +4,10 @@ require_once "includes/tripal_ds.inc";
 require_once "includes/tripal_ds.ds.inc";
 require_once "includes/tripal_ds.field_group.inc";
 require_once "includes/tripal_ds.field_formatter.inc";
+require_once "includes/tripal_ds.field_formatter.inc";
+
+// Import the full Tripal_DS API into scope.
+tripal_ds_import_api();
 
 /**
  * Implements hook_init().
@@ -376,12 +380,9 @@ function tripal_ds_pane_addition_button_form_submit($form, &$form_state) {
   $bundle_name = $form_state['build_info']['args'][0];
   //Build the rest of the passed variables.
   $field_name = $form_state['input']['field_name'];
-  $group_field_name = 'gp_'.$form_state['input']['field_name'];
-  //Create the field groups, last passed parameter is NULL because there are no
-  //children.
-  _additional_fields_field_group_info($bundle_name, $field_name, $group_field_name, NULL);
-  //Place the field groups in the layout.
-  tripal_ds_update_ds_layout($bundle_name, NULL, $group_field_name);
+  $field_label = $form_state['input']['field_name'];
+
+  tripal_ds_create_field($field_label, $field_name, $bundle_name);
   drupal_goto("admin/structure/bio_data/manage/$bundle_name/display");
 }
 
@@ -583,3 +584,11 @@ function tripal_ds_toc_order($bundle, $fields = array()){
   }
 }
 
+/**
+ * Imports all of the Tripal_DS API into scope.
+ *
+ *
+ */
+function tripal_ds_import_api() {
+  module_load_include('inc', 'tripal_ds', 'api/tripal_ds.pane.api');
+}