Merge pull request #77 from TripalCultivate/g4.76-divideTraitImportValue

G4.76 STEP 1 --Divides trait import value plugin instance into 3 separate instances

trpcultivate_phenotypes/src/Plugin/TripalImporter/TripalCultivatePhenotypesTraitsImporter.php

@@ -224,6 +224,7 @@ public function formValidate($form, &$form_state) {
     $headers = array_keys($this->headers);
 
     $scopes = ['GENUS', 'FILE', 'HEADERS', 'TRAIT IMPORT VALUES'];
+    //$scopes = ['GENUS', 'FILE', 'HEADERS', 'FILE ROW'];
 
     // Array to hold all validation result for each level.
     // Each result is keyed by the scope.

trpcultivate_phenotypes/src/Plugin/Validators/DuplicateTraits.php

@@ -0,0 +1,186 @@
+<?php
+
+/**
+ * @file
+ * Contains validator plugin definition.
+ */
+
+namespace Drupal\trpcultivate_phenotypes\Plugin\Validators;
+
+use Drupal\Core\Plugin\ContainerFactoryPluginInterface;
+use Drupal\trpcultivate_phenotypes\Service\TripalCultivatePhenotypesTraitsService;
+use Drupal\trpcultivate_phenotypes\TripalCultivatePhenotypesValidatorBase;
+use Symfony\Component\DependencyInjection\ContainerInterface;
+
+/**
+ * Validate duplicate traits within a file
+ *
+ * @TripalCultivatePhenotypesValidator(
+ *   id = "trpcultivate_phenotypes_validator_duplicate_traits",
+ *   validator_name = @Translation("Duplicate Traits Validator"),
+ *   validator_scope = "FILE ROW",
+ * )
+ */
+class DuplicateTraits extends TripalCultivatePhenotypesValidatorBase implements ContainerFactoryPluginInterface {
+
+  /**
+   * A nested array of already validated values forming the unique trait name +
+   *   method name + unit combinations that have been encountered by this
+   *   validator so far within the input file. More specifically,
+   *   - TRAIT-NAME: array of methods associated with this trait.
+   *     - METHOD-NAME: array of units associated with this trait-method combo
+   *       - UNIT-NAME: 1 (indicates this full trait-method-unit combo exists)
+   *
+   *   NOTE: All capital words are intended to be replaced by the actual full
+   *   name of the term.
+   */
+  protected $unique_traits = [];
+
+  /**
+   * Traits Service
+   */
+  protected $service_traits;
+
+  /**
+   * Constructor.
+   */
+  public function __construct(array $configuration, $plugin_id, $plugin_definition, TripalCultivatePhenotypesTraitsService $service_traits) {
+    parent::__construct($configuration, $plugin_id, $plugin_definition);
+
+    $this->service_traits = $service_traits;
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function create(ContainerInterface $container, array $configuration, $plugin_id, $plugin_definition){
+    return new static(
+      $configuration,
+      $plugin_id,
+      $plugin_definition,
+      $container->get('trpcultivate_phenotypes.traits')
+    );
+  }
+
+  /**
+   * Validate the values within the cells of this row.
+   *
+   * @param array $row_values
+   *   The contents of the file's row where each value within a cell is
+   *   stored as an array element
+   * @param array $context
+   *   An associative array with the following keys:
+   *   - indices => an associative array with the following keys:
+   *     - 'trait': int, the index of the trait name column in $row_values
+   *     - 'method': int, the index of the method name column in $row_values
+   *     - 'unit': int, the index of the unit column in $row_values
+   *
+   * @return array
+   *   An associative array with the following keys:
+   *   - title: string, section or title of the validation as it appears in the result window.
+   *   - status: string, pass if it passed the validation check/test, fail string otherwise and todo string if validation was not applied.
+   *   - details: details about the offending field/value.
+   */
+  public function validateRow($row_values, $context) {
+
+    // Check the indices provided are valid in the context of the row.
+    // Will throw an exception if there's a problem.
+    // Typically checkIndices() doesn't take an associative array but
+    // because it checks the values not the keys, it will work in this
+    // case as well.
+    $this->checkIndices($row_values, $context['indices']);
+
+    // Grab our trait, method and unit values from the $row_values array
+    // using the indices stored in our $context array
+    // We need to ensure that each array key we expect in $context['indices']
+    // exists, otherwise throw an exception
+    if (!isset($context['indices']['trait'])) {
+      throw new \Exception(t('The trait name (key: trait) was not set in the $context[\'indices\'] array'));
+    }
+    if (!isset($context['indices']['method'])) {
+       throw new \Exception(t('The method name (key: method) was not set in the $context[\'indices\'] array'));
+    }
+    if (!isset($context['indices']['unit'])) {
+       throw new \Exception(t('The unit (key: unit) was not set in the $context[\'indices\'] array'));
+    }
+
+    $trait = $row_values[$context['indices']['trait']];
+    $method = $row_values[$context['indices']['method']];
+    $unit = $row_values[$context['indices']['unit']];
+
+    // Set our flags for tracking database and input file duplicates
+    $duplicate_in_file = FALSE;
+    $duplicate_in_db = FALSE;
+
+    // Now check for the presence of our array within our global array
+    // ie. has this trait combination been seen in this input file before?
+    if (!empty($this->unique_traits)) {
+      if (isset($this->unique_traits[$trait][$method][$unit])) {
+        // Then we've found a duplicate
+        $duplicate_in_file = TRUE;
+      }
+    }
+
+    // Check if our trait combo exists at the database level
+    // Grab our traits service
+    $trait_combo = $this->service_traits->getTraitMethodUnitCombo($trait, $method, $unit);
+    if (!empty($trait_combo)) {
+      // Duplicate found
+      $duplicate_in_db = TRUE;
+    }
+
+    // Finally, add to the global array as a row we've now seen
+    $this->unique_traits[$trait][$method][$unit] = 1;
+
+    // Then set the status of the validation
+    if($duplicate_in_file) {
+      if ($duplicate_in_db) {
+        // This row is a duplicate of another row AND in the database
+        $validator_status = [
+          'title' => 'Duplicate trait combo in file + database',
+          'status' => 'fail',
+          'details' => 'A duplicate trait was found within both the input file and the database.'
+        ];
+      }
+      else {
+        $validator_status = [
+          'title' => 'Duplicate Trait Name + Method Short Name + Unit combination',
+          'status' => 'fail',
+          'details' => 'A duplicate trait was found within the input file'
+        ];
+      }
+    }
+    else if ($duplicate_in_db) {
+      $validator_status = [
+        'title' => 'Duplicate Trait Name + Method Short Name + Unit combination',
+        'status' => 'fail',
+        'details' => 'The combination of ' . $trait . ', ' . $method . ', and ' . $unit . ' is already found in the database.'
+      ];
+    }
+    // If not seen before in the file or in the database, then set the validation to pass
+    else {
+      $validator_status = [
+        'title' => 'Unique Trait Name + Method Short Name + Unit combination',
+        'status' => 'pass',
+        'details' => 'Confirmed that the current trait being validated is unique.'
+      ];
+    }
+    return $validator_status;
+  }
+
+  /**
+   * Getter for the $unique_traits array.
+   *
+   * @return $unique_traits
+   *   The array of unique trait name + method name + unit combinations that
+   *   have been encountered by this validator so far within the input file
+   *   More specifically, the array is as follows with capitalized words replaced
+   *   by the term name.
+   *   - TRAIT-NAME: array of methods associated with this trait.
+   *     - METHOD-NAME: array of units associated with this trait-method combo
+   *       - UNIT-NAME: 1 (indicates this full trait-method-unit combo exists)
+   */
+  public function getUniqueTraits() {
+    return $this->unique_traits;
+  }
+}

trpcultivate_phenotypes/src/Plugin/Validators/EmptyCell.php

@@ -0,0 +1,97 @@
+<?php
+
+/**
+ * @file
+ * Contains validator plugin definition.
+ */
+
+namespace Drupal\trpcultivate_phenotypes\Plugin\Validators;
+
+use Drupal\trpcultivate_phenotypes\TripalCultivatePhenotypesValidatorBase;
+use Drupal\Core\Plugin\ContainerFactoryPluginInterface;
+use Symfony\Component\DependencyInjection\ContainerInterface;
+
+/**
+ * Validate empty cells of an importer.
+ *
+ * @TripalCultivatePhenotypesValidator(
+ *   id = "trpcultivate_phenotypes_validator_empty_cell",
+ *   validator_name = @Translation("Empty Cell Validator"),
+ *   validator_scope = "FILE ROW",
+ * )
+ */
+class EmptyCell extends TripalCultivatePhenotypesValidatorBase implements ContainerFactoryPluginInterface {
+  /**
+   * Constructor.
+   */
+  public function __construct(array $configuration, $plugin_id, $plugin_definition) {
+    parent::__construct($configuration, $plugin_id, $plugin_definition);
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function create(ContainerInterface $container, array $configuration, $plugin_id, $plugin_definition){
+    return new static(
+      $configuration,
+      $plugin_id,
+      $plugin_definition
+    );
+  }
+
+  /**
+   * Validate the values within the cells of this row.
+   *
+   * @param array $row_values
+   *   The contents of the file's row where each value within a cell is
+   *   stored as an array element
+   * @param array $context
+   *   An associative array with the following key:
+   *   - indices => an array of indices corresponding to the cells in $row_values to act on
+   *
+   * @return array
+   *   An associative array with the following keys.
+   *   - title: string, section or title of the validation as it appears in the result window.
+   *   - status: string, pass if it passed the validation check/test, fail string otherwise and todo string if validation was not applied.
+   *   - details: details about the offending field/value.
+   */
+  public function validateRow($row_values, $context) {
+
+    // Check the indices provided are valid in the context of the row.
+    // Will throw an exception if there's a problem
+    $this->checkIndices($row_values, $context['indices']);
+
+    $empty = FALSE;
+    $failed_indices = [];
+    // Iterate through our array of row values
+    foreach($row_values as $index => $cell) {
+      // Only validate the values in which their index is also within our
+      // context array of indices
+      if (in_array($index, $context['indices'])) {
+        // First trim the contents of our cell in case we have whitespace
+        $cell = trim($cell);
+        // Check if our content is empty and report an error if it is
+        if (!isset($cell) || empty($cell)) {
+          $empty = TRUE;
+          array_push($failed_indices, $index);
+        }
+      }
+    }
+    // Check if empty values were found that should not be empty
+    if ($empty) {
+      $failed_list = implode(', ', $failed_indices);
+      $validator_status = [
+        'title' => 'Empty value found in required column(s)',
+        'status' => 'fail',
+        'details' => 'Empty values at index: ' . $failed_list
+      ];
+    } else {
+      $validator_status = [
+        'title' => 'No empty values found in required column(s)',
+        'status' => 'pass',
+        'details' => ''
+      ];
+    }
+    return $validator_status;
+  }
+}