Merge pull request #116 from TripalCultivate/g4.91-removeOldDesignRem…

…nants G4.91 Remove all deprecations
TripalCultivate · Nov 4, 2024 · bb0dc68 · bb0dc68
2 parents 7551244 + 1461f72
commit bb0dc68
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diff --git a/.devcontainer.json b/.devcontainer.json
@@ -24,6 +24,7 @@
         "ms-azuretools.vscode-docker",
         "github.vscode-github-actions",
         "GitHub.vscode-pull-request-github"
+        //"valeryanm.vscode-phpsab"
       ],
       "settings": {
         // This turns off basic PHP suggestions provided by Visual Studio Code (in lieu of Intelephense's).
@@ -116,6 +117,22 @@
         "composer.bin": "/usr/local/bin/composer",
         "tws.trimOnSave": true,
         "tws.highlightTrailingWhiteSpace": true
+      	/* PHP Sniffer & Beautifier */
+        /**
+      	"phpsab.snifferEnable": true,
+      	"phpsab.executablePathCS": "/var/www/drupal/vendor/bin/phpcs",
+      	"phpsab.fixerEnable": true,
+      	"phpsab.executablePathCBF": "/var/www/drupal/vendor/bin/phpcbf",
+      	"phpsab.standard": "Drupal,DrupalPractice",
+      	"phpsab.snifferMode": "onType",
+      	"phpsab.debug": false,
+      	"phpsab.fixerArguments": [
+      		"--extensions=inc,theme,install,module,profile,php,phtml"
+      	],
+      	"phpsab.snifferArguments": [
+      		"--extensions=inc,theme,install,module,profile,php,phtml"
+      	]
+        */
       }
     }
   },

diff --git a/...ultivate_phenotypes/src/Plugin/TripalImporter/TripalCultivatePhenotypesTraitsImporter.php b/...ultivate_phenotypes/src/Plugin/TripalImporter/TripalCultivatePhenotypesTraitsImporter.php
diff --git a/...phenotypes/src/TripalCultivateValidator/Annotation/TripalCultivatePhenotypesValidator.php b/...phenotypes/src/TripalCultivateValidator/Annotation/TripalCultivatePhenotypesValidator.php
@@ -34,16 +34,6 @@ class TripalCultivatePhenotypesValidator extends Plugin {
    */
   public $validator_name;
 
-  /**
-   * The scope a validator will perform a check
-   * ie. FILE level check, Project/Genus level check or Data Values level check.
-   *
-   * @deprecated Remove in issue #91
-   *
-   * @var string.
-   */
-  public $validator_scope;
-
   /**
    * The type of the data this validator supports validating.
    *

diff --git a/...tivate_phenotypes/src/TripalCultivateValidator/TripalCultivatePhenotypesValidatorBase.php b/...tivate_phenotypes/src/TripalCultivateValidator/TripalCultivatePhenotypesValidatorBase.php
@@ -7,6 +7,36 @@
 
 abstract class TripalCultivatePhenotypesValidatorBase extends PluginBase implements TripalCultivatePhenotypesValidatorInterface {
 
+  /**
+   * An associative array containing the needed context, which is dependant
+   * on the validator. For example, instead of validating each cell by default,
+   * a validator may need a list of indices which correspond to the columns in
+   * the row for which the validator should act on.
+   *
+   * Key-value pairs are set by the setter methods in ValidatorTraits.
+   */
+  protected array $context = [];
+
+  /**
+   * A mapping of supported file mime-types and their supported delimiters.
+   *
+   * More specifically, the file is split based on the appropriate delimiter
+   * for the mime-type passed in. For example, the mime-type
+   * "text/tab-separated-values" maps to the tab (i.e. "\t") delimiter.
+   *
+   * By using this mapping approach we can actually support a number of different
+   * file types with different delimiters for the same importer while keeping
+   * the performance hit to a minimum. Especially as in many cases, this is a
+   * one-to-one mapping.
+   *
+   * @var array
+   */
+  public static array $mime_to_delimiter_mapping = [
+    'text/tab-separated-values' => ["\t"],
+    'text/csv' => [','],
+    'text/plain' => ["\t", ','],
+  ];
+
   /**
    * Get validator plugin validator_name definition annotation value.
    *
@@ -45,37 +75,6 @@ public function checkInputTypeSupported(string $input_type) {
     return FALSE;
   }
 
-  /**
-   * An associative array containing the needed context, which is dependant
-   * on the validator. For example, instead of validating each cell by default,
-   * a validator may need a list of indices which correspond to the columns in
-   * the row for which the validator should act on.
-   *
-   * Key-value pairs are set by the setter methods in ValidatorTraits.
-   */
-  protected array $context = [];
-
-  /**
-   * A mapping of supported file mime-types and their supported delimiters.
-   *
-   * More specifically, the file is split based on the appropriate delimiter
-   * for the mime-type passed in. For example, the mime-type
-   * "text/tab-separated-values" maps to the tab (i.e. "\t") delimiter.
-   *
-   * By using this mapping approach we can actually support a number of different
-   * file types with different delimiters for the same importer while keeping
-   * the performance hit to a minimum. Especially as in many cases, this is a
-   * one-to-one mapping.
-   *
-   * @var array
-   */
-  public static array $mime_to_delimiter_mapping = [
-    'text/tab-separated-values' => ["\t"],
-    'text/csv' => [','],
-    'text/plain' => ["\t", ','],
-  ];
-
-
   /**
    * {@inheritdoc}
    */
@@ -108,91 +107,6 @@ public function validateRawRow(string $raw_row) {
     throw new \Exception("Method validateRawRow() from base class called for $plugin_name. If this plugin wants to support this type of validation then they need to override it.");
   }
 
-  /**
-   * {@inheritdoc}
-   * @deprecated Remove in issue #91
-   */
-  public function validate() {
-    $plugin_name = $this->getValidatorName();
-    throw new \Exception("Method validate() from base class called for $plugin_name. This method is being deprecated and should be upgraded to validateMetadata(), validateFile() or validateRow().");
-  }
-
-  /**
-   * Project name/title.
-   * @deprecated Remove in issue #91
-   */
-  public $project;
-
-  /**
-   * Genus.
-   * @deprecated Remove in issue #91
-   */
-  public $genus;
-
-  /**
-   * Drupal File ID Number.
-   * @deprecated Remove in issue #91
-   */
-  public $file_id;
-
-  /**
-   * Required column headers as defined in the importer.
-   * @deprecated Remove in issue #91
-   */
-  public $column_headers;
-
-  /**
-   * Skip flag, indicate validator not to execute validation logic and
-   * set the validator as upcoming or todo.
-   * @deprecated Remove in issue #91
-   */
-  public $skip;
-
-  /**
-   * Load phenotypic data upload assets to validated.
-   *
-   * @deprecated Remove in issue #91
-   *
-   * @param $project
-   *   String, Project name/title - chado.project: name.
-   * @param $genus
-   *   String, Genus - chado.organism: genus.
-   * @param $file_id
-   *   Integer, Drupal file id number.
-   * @param $headers
-   *   Array, required column headers defined in the importer.
-   * @param $skip
-   *   Boolean, skip flag when set to true will skip the validation
-   *   logic and set the validator as upcoming/todo.
-   *   Default: false - execute validation process.
-   */
-  public function loadAssets($project, $genus, $file_id, $headers, $skip = 0) {
-    // Prepare assets:
-
-    // Project.
-    $this->project = $project;
-    // Genus.
-    $this->genus = $genus;
-    // File id.
-    $this->file_id = $file_id;
-    // Column Headers.
-    $this->column_headers = $headers;
-    // Skip.
-    $this->skip = $skip;
-  }
-
-  /**
-   * Get validator plugin validator_scope definition annotation value.
-   *
-   * @deprecated Remove in issue #91
-   *
-   * @return string
-   *   The validator plugin scope annotation definition value.
-   */
-  public function getValidatorScope() {
-    return (array_key_exists('validator_scope', $this->pluginDefinition)) ? $this->pluginDefinition['validator_scope'] : NULL;
-  }
-
   /**
    * {@inheritdoc}
    */

diff --git a/...e_phenotypes/src/TripalCultivateValidator/TripalCultivatePhenotypesValidatorInterface.php b/...e_phenotypes/src/TripalCultivateValidator/TripalCultivatePhenotypesValidatorInterface.php
@@ -56,11 +56,6 @@ public function checkInputTypeSupported(string $input_type);
    *      For example, if this validator checks a specific set of form elements,
    *      then this array should be keyed by the form element key and the value
    *      matches what was provided by the user input in form_values.
-   *  The old style keys we are deprecating are:
-   *    @deprecated Remove in issue #91
-   *  - title: the title of the validation (shown both when passes or fails).
-   *  - details: string describing the failure to users with failed items embedded.
-   *  - status: one of 'pass' or 'fail'
    */
   public function validateMetadata(array $form_values);
 
@@ -84,11 +79,6 @@ public function validateMetadata(array $form_values);
    *      For example, if this validator checks the permissions of the file, then
    *      this array might contain the permissions the file actually had that
    *      did not match what was expected.
-   *  The old style keys we are deprecating are:
-   *    @deprecated Remove in issue #91
-   *  - title: the title of the validation (shown both when passes or fails).
-   *  - details: string describing the failure to users with failed items embedded.
-   *  - status: one of 'pass' or 'fail'
    */
   public function validateFile(string $filename, int $fid);
 
@@ -112,11 +102,6 @@ public function validateFile(string $filename, int $fid);
    *      if this validator checks that a number of indices have values in a
    *      specific list, then this array would use the index as the key and
    *      the value the column actually had, for each failed column.
-   *  The old style keys we are deprecating are:
-   *    @deprecated Remove in issue #91
-   *  - title: the title of the validation (shown both when passes or fails).
-   *  - details: string describing the failure to users with failed items embedded.
-   *  - status: one of 'pass' or 'fail'
    */
   public function validateRow(array $row_values);
 
@@ -173,51 +158,6 @@ public function validateRawRow(string $raw_row);
    */
   public function checkIndices($row_values, $indices);
 
-  /**
-   * Return the scope of the validator.
-   *
-   * @deprecated Remove in issue #91
-   *
-   * @return string.
-   */
-  public function getValidatorScope();
-
-  /**
-   * Load data file import assets Project title, Genus and Data File Id
-   * as entered in the Importer form.
-   *
-   * @deprecated Remove in issue #91
-   *
-   * @param $project
-   *   String, Project name/title - chado.project: name.
-   * @param $genus
-   *   String, Genus - chado.organism: genus.
-   * @param $file_id
-   *   Integer, Drupal file id number.
-   * @param $headers
-   *   Array, required column headers defined in the importer.
-   * @param $skip
-   *   Boolean, skip flag when set to true will skip the validation
-   *   logic and set the validator as upcoming/todo.
-   *   Default: false - execute validation process.
-   *
-   * @return void.
-   */
-  public function loadAssets($project, $genus, $file_id, $headers, $skip);
-
-  /**
-   * Validate items in the phenotypic data upload assets.
-   *
-   * @deprecated Remove in issue #91
-   *
-   * @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 validate();
-
   /**
    * Traits, method and unit may be created/inserted through
    * the phenotypic data importer using the configuration allow new.
@@ -228,7 +168,7 @@ public function validate();
    *   validation error and will not permit creation of terms.
    */
   public function getConfigAllowNew();
-  
+
   /**
    * Split or explode a data file line/row values into an array using a delimiter.
    *

diff --git a/...ate_phenotypes/src/TripalCultivateValidator/TripalCultivatePhenotypesValidatorManager.php b/...ate_phenotypes/src/TripalCultivateValidator/TripalCultivatePhenotypesValidatorManager.php
@@ -39,40 +39,4 @@ public function __construct(\Traversable $namespaces, CacheBackendInterface $cac
     $this->alterInfo('trpcultivate_phenotypes_validators_info');
     $this->setCacheBackend($cache_backend, 'tripalcultivate_phenotypes_validators');
   }
-
-  /**
-   * Retrieve validator implementation with a specific scope.
-   *
-   * @deprecated Remove in issue #91
-   *
-   * @param string $scope
-   *   The validator_scope you are interested in.
-   *
-   * @return string
-   *   The id of the validator with that scope based on it's annotation.
-   */
-  public function getValidatorIdWithScope($scope) {
-    $plugins = $this->getDefinitions();
-    $plugin_definitions = array_values($plugins);
-    $plugin_with_scope = [];
-
-    // Remove all plugins without scope.
-    foreach($plugin_definitions as $i => $plugin) {
-      if (!isset($plugin['validator_scope'])) {
-        continue;
-      }
-
-      array_push($plugin_with_scope, $plugin);
-    }
-
-    unset($plugin_definitions);
-    $plugin_definitions = $plugin_with_scope;
-
-    $plugin_key = array_search(
-      $scope,
-      array_column($plugin_definitions, 'validator_scope')
-    );
-
-    return $plugin_definitions[ $plugin_key ]['id'];
-  }
 }
diff --git a/trpcultivate_phenotypes/templates/trpcultivate-phenotypes-template-importer-header.html.twig b/trpcultivate_phenotypes/templates/trpcultivate-phenotypes-template-importer-header.html.twig
@@ -5,20 +5,20 @@
  *
  * Available variables:
  * - header_notes: array of headers keyed by the header name. Value is description and expected value.
- * - template_file: a file name of a template file. 
+ * - template_file: a file name of a template file.
  */
 #}
 
 {{ attach_library('trpcultivate_phenotypes/trpcultivate-phenotypes-style-importer-header') }}
 
 <div id="tcp-header-notes">
   <p>This should be a tab-separated file with the following columns:</p>
-  
+
   <ol id="tcp-header-notes">
-    {% for header,description in data.headers %}
+    {% for header in data.headers %}
     <li>
-      <strong>{{header}}</strong>: {{description}}
-    </li>  
+      <strong>{{header['name']}}</strong>: {{header['description']}} ({{header['type']}})
+    </li>
     {% endfor %}
   </ol>
 </div>
@@ -27,4 +27,4 @@
   <a href="{{data.template_file}}" target="_blank">Download a template file</a>
 </div>
 
-<br />
+<br />
diff --git a/...types/tests/src/Fixtures/TraitImporterFiles/correct_header_emptycell_after_empty_line.tsv b/...types/tests/src/Fixtures/TraitImporterFiles/correct_header_emptycell_after_empty_line.tsv
@@ -0,0 +1,4 @@
+Trait Name	Trait Description	Method Short Name	Collection Method	Unit	Type
+trait1	trait1 description	method1	Collect measurements for the trait by the best method possible.	unit1	Quantitative
+
+trait2	trait2 description		Collect measurements for the trait by the best method possible.	unit2	Qualitative