Ensure all fields describe elements using elementInfo().

UofS-Pulse-Binfo · Oct 7, 2020 · cc074fa · cc074fa
1 parent e922c01
commit cc074fa
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Showing 13 changed files with 307 additions and 22 deletions.
diff --git a/includes/TripalFields/hp__phenotypic_variability/hp__phenotypic_variability.inc b/includes/TripalFields/hp__phenotypic_variability/hp__phenotypic_variability.inc
@@ -292,10 +292,58 @@ class hp__phenotypic_variability extends ChadoField {
         'operations' => array('eq', 'ne', 'contains', 'starts'),
         'sortable' => TRUE,
         'searchable' => TRUE,
+        'elements' => array(
+          // Trait
+          'NCIT:C85496' => array(
+            'searchable' => FALSE,
+            'name' => 'Trait Name',
+            'operations' => array('eq', 'ne', 'contains', 'starts'),
+            'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
+          ),
+          // Experiment.
+          'SIO:001066' => array(
+            'searchable' => FALSE,
+            'name' => 'Experiment Name',
+            'operations' => array('eq', 'ne', 'contains', 'starts'),
+            'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
+          ),
+          // Method.
+          'NCIT:C71460' => array(
+            'searchable' => FALSE,
+            'name' => 'Methodology',
+            'operations' => array('eq', 'ne', 'contains', 'starts'),
+            'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
+          ),
+          // Unit.
+          'uo:unit' => array(
+            'searchable' => FALSE,
+            'name' => 'Unit',
+            'operations' => array('eq', 'ne', 'contains', 'starts'),
+            'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
+          ),
+          'schema:url' => array(
+            'searchable' => FALSE,
+            'name' => 'URL',
+            'operations' => array('eq', 'ne', 'contains', 'starts'),
+            'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
+          ),
+        ),
       ),
     );
   }
-
 }
-
-
diff --git a/includes/TripalFields/local__child_studies/local__child_studies.inc b/includes/TripalFields/local__child_studies/local__child_studies.inc
@@ -224,6 +224,32 @@ class local__child_studies extends TripalField {
 
     return $element;
   }
+
+  /**
+   * @see ChadoField::elementInfo()
+   *
+   */
+  public function elementInfo() {
+    $field_term = $this->getFieldTermID();
+    return array(
+      $field_term => array(
+        'operations' => array('eq', 'ne', 'contains', 'starts'),
+        'sortable' => TRUE,
+        'searchable' => TRUE,
+        'elements' => array(
+          'local:child_studies' => array(
+            'searchable' => FALSE,
+            'name' => 'Child Studies',
+            'operations' => array(),
+            'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
+          ),
+        ),
+      ),
+    );
+  }
 }
 
 /**

diff --git a/includes/TripalFields/local__magnitude_of_phenotypes/local__magnitude_of_phenotypes.inc b/includes/TripalFields/local__magnitude_of_phenotypes/local__magnitude_of_phenotypes.inc
@@ -213,6 +213,21 @@ class local__magnitude_of_phenotypes extends TripalField {
 
     return $element;
   }
+
+  /**
+   * @see ChadoField::elementInfo()
+   *
+   */
+  public function elementInfo() {
+    $field_term = $this->getFieldTermID();
+    return array(
+      $field_term => array(
+        'operations' => array('eq', 'ne', 'contains', 'starts'),
+        'sortable' => TRUE,
+        'searchable' => TRUE,
+      ),
+    );
+  }
 }
 
   /**

diff --git a/includes/TripalFields/local__number_of_experiments/local__number_of_experiments.inc b/includes/TripalFields/local__number_of_experiments/local__number_of_experiments.inc
@@ -178,4 +178,19 @@ class local__number_of_experiments extends TripalField {
 
     return $element;
   }
+
+  /**
+   * @see ChadoField::elementInfo()
+   *
+   */
+  public function elementInfo() {
+    $field_term = $this->getFieldTermID();
+    return array(
+      $field_term => array(
+        'operations' => array('eq', 'ne', 'contains', 'starts'),
+        'sortable' => TRUE,
+        'searchable' => TRUE,
+      ),
+    );
+  }
 }
diff --git a/includes/TripalFields/local__number_of_germplasm/local__number_of_germplasm.inc b/includes/TripalFields/local__number_of_germplasm/local__number_of_germplasm.inc
@@ -167,4 +167,19 @@ class local__number_of_germplasm extends TripalField {
 
     return $element;
   }
+
+  /**
+   * @see ChadoField::elementInfo()
+   *
+   */
+  public function elementInfo() {
+    $field_term = $this->getFieldTermID();
+    return array(
+      $field_term => array(
+        'operations' => array('eq', 'ne', 'contains', 'starts'),
+        'sortable' => TRUE,
+        'searchable' => TRUE,
+      ),
+    );
+  }
 }
diff --git a/includes/TripalFields/local__number_of_locations/local__number_of_locations.inc b/includes/TripalFields/local__number_of_locations/local__number_of_locations.inc
@@ -195,4 +195,19 @@ class local__number_of_locations extends TripalField {
 
     return $element;
   }
+
+  /**
+   * @see ChadoField::elementInfo()
+   *
+   */
+  public function elementInfo() {
+    $field_term = $this->getFieldTermID();
+    return array(
+      $field_term => array(
+        'operations' => array('eq', 'ne', 'contains', 'starts'),
+        'sortable' => TRUE,
+        'searchable' => TRUE,
+      ),
+    );
+  }
 }
diff --git a/includes/TripalFields/local__number_of_traits/local__number_of_traits.inc b/includes/TripalFields/local__number_of_traits/local__number_of_traits.inc
@@ -168,4 +168,19 @@ class local__number_of_traits extends TripalField {
 
     return $element;
   }
+
+  /**
+   * @see ChadoField::elementInfo()
+   *
+   */
+  public function elementInfo() {
+    $field_term = $this->getFieldTermID();
+    return array(
+      $field_term => array(
+        'operations' => array('eq', 'ne', 'contains', 'starts'),
+        'sortable' => TRUE,
+        'searchable' => TRUE,
+      ),
+    );
+  }
 }
diff --git a/includes/TripalFields/local__number_of_values_recorded/local__number_of_values_recorded.inc b/includes/TripalFields/local__number_of_values_recorded/local__number_of_values_recorded.inc
@@ -167,4 +167,19 @@ class local__number_of_values_recorded extends TripalField {
 
     return $element;
   }
+
+  /**
+   * @see ChadoField::elementInfo()
+   *
+   */
+  public function elementInfo() {
+    $field_term = $this->getFieldTermID();
+    return array(
+      $field_term => array(
+        'operations' => array('eq', 'ne', 'contains', 'starts'),
+        'sortable' => TRUE,
+        'searchable' => TRUE,
+      ),
+    );
+  }
 }
diff --git a/includes/TripalFields/local__number_of_years/local__number_of_years.inc b/includes/TripalFields/local__number_of_years/local__number_of_years.inc
@@ -195,4 +195,19 @@ class local__number_of_years extends TripalField {
 
     return $element;
   }
+
+  /**
+   * @see ChadoField::elementInfo()
+   *
+   */
+  public function elementInfo() {
+    $field_term = $this->getFieldTermID();
+    return array(
+      $field_term => array(
+        'operations' => array('eq', 'ne', 'contains', 'starts'),
+        'sortable' => TRUE,
+        'searchable' => TRUE,
+      ),
+    );
+  }
 }
diff --git a/includes/TripalFields/ncit__data/ncit__data.inc b/includes/TripalFields/ncit__data/ncit__data.inc
@@ -158,4 +158,39 @@ class ncit__data extends TripalField {
 
     return $element;
   }
+
+  /**
+   * @see ChadoField::elementInfo()
+   *
+   */
+  public function elementInfo() {
+    $field_term = $this->getFieldTermID();
+    return array(
+      $field_term => array(
+        'operations' => array('eq', 'ne', 'contains', 'starts'),
+        'sortable' => TRUE,
+        'searchable' => TRUE,
+        'elements' => array(
+          'NCIT:data' => array(
+            'searchable' => FALSE,
+            'name' => 'Data',
+            'operations' => array(),
+            'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
+          ),
+          'schema:additionalType' => array(
+            'searchable' => FALSE,
+            'name' => 'Type',
+            'operations' => array(),
+            'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
+          ),
+        ),
+      ),
+    );
+  }
 }
diff --git a/includes/TripalFields/ncit__image/ncit__image.inc b/includes/TripalFields/ncit__image/ncit__image.inc
@@ -122,4 +122,30 @@ class ncit__image extends ChadoField {
       $entity->{$field_name}['und'][0]['value'] = '';
     }
   }
+
+  /**
+   * @see ChadoField::elementInfo()
+   *
+   */
+  public function elementInfo() {
+    $field_term = $this->getFieldTermID();
+    return array(
+      $field_term => array(
+        'operations' => array('eq', 'ne', 'contains', 'starts'),
+        'sortable' => TRUE,
+        'searchable' => TRUE,
+        'elements' => array(
+          'NCIT:C48179' => array(
+            'searchable' => FALSE,
+            'name' => 'Data',
+            'operations' => array(),
+            'sortable' => FALSE,
+            'type' => 'xs:string',
+            'readonly' => TRUE,
+            'required' => FALSE,
+          ),
+        ),
+      ),
+    );
+  }
 }
diff --git a/includes/TripalFields/ncit__method/ncit__method.inc b/includes/TripalFields/ncit__method/ncit__method.inc
@@ -159,21 +159,6 @@ class ncit__method extends ChadoField {
     }
   }
 
-  /**
-   * @see ChadoField::query()
-   *
-   */
-  public function query($query, $condition) {
-  }
-
-  /**
-   * @see ChadoField::queryOrder()
-   *
-   */
-  public function queryOrder($query, $order) {
-  }
-
-
   /**
    * @see ChadoField::elementInfo()
    *
@@ -190,11 +175,20 @@ class ncit__method extends ChadoField {
         'type' => 'xs:complexType',
         'readonly' => TRUE,
         'elements' => array(
-          'NCIT:C71460' => array(
-            'searchable' => TRUE,
-            'name' => 'Phenotyping Method',
+          'schema:name' => array(
+            'searchable' => FALSE,
+            'name' => 'Method Name',
+            'operations' => ['eq', 'ne', 'contains', 'starts'],
+            'sortable' => FALSE,
+            'readonly' => TRUE,
+            'type' => 'xs:string',
+            'required' => FALSE,
+          ),
+          'IAO:0000115' => array(
+            'searchable' => FALSE,
+            'name' => 'Method description',
             'operations' => ['eq', 'ne', 'contains', 'starts'],
-            'sortable' => TRUE,
+            'sortable' => FALSE,
             'readonly' => TRUE,
             'type' => 'xs:string',
             'required' => FALSE,