From 074811bcc991032c7d91551688c5bd33b86b2b5c Mon Sep 17 00:00:00 2001
From: Reynold Tan <reynold@rain.baskt.bioinfo>
Date: Wed, 19 Jun 2019 14:58:30 -0600
Subject: [PATCH 1/8] Phenotype Ontology field file structure

---
 .../analyzedphenotypes.fields.inc             |  51 ++++++
 .../ncit__synonym/ncit__synonym.inc           | 151 ++++++++++++++++++
 .../ncit__synonym/ncit__synonym_formatter.inc |  57 +++++++
 .../ncit__synonym/ncit__synonym_widget.inc    | 126 +++++++++++++++
 4 files changed, 385 insertions(+)
 create mode 100644 includes/TripalFields/ncit__synonym/ncit__synonym.inc
 create mode 100644 includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
 create mode 100644 includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc

diff --git a/includes/TripalFields/analyzedphenotypes.fields.inc b/includes/TripalFields/analyzedphenotypes.fields.inc
index 57cdae4..892836a 100644
--- a/includes/TripalFields/analyzedphenotypes.fields.inc
+++ b/includes/TripalFields/analyzedphenotypes.fields.inc
@@ -135,6 +135,25 @@ function analyzedphenotypes_bundle_fields_info($entity_type, $bundle) {
 	      'type' => 'field_chado_storage',
       ),
     );
+
+    // Phenotype Ontology.
+    tripal_insert_cvterm(array(
+      'id' => 'NCIT:c52469',
+      'name' => 'Synonym',
+      'cv_name' => 'NCIT',
+      'definition' => 'A word having the same or nearly the same meaning as another word or other words in a language; a word or an expression that serves as a figurative or symbolic substitute for another',
+    ));
+    $field_name = 'ncit__synonym';
+    $field_type = 'ncit__synonym';
+    $fields[$field_name] = array(
+      'field_name' => $field_name,
+      'type' => $field_type,
+      'cardinality' => 1,
+      'locked' => FALSE,
+      'storage' => array(
+	      'type' => 'field_chado_storage',
+      ),
+    );
   }
 
   // IN GERMPLASM PAGE ONLY:
@@ -433,6 +452,38 @@ function analyzedphenotypes_bundle_instances_info($entity_type, $bundle) {
         ),
       ),
     );
+
+    // Phenotype Ontology - Synonym.
+    $field_name = 'ncit__synonym';
+    $field_type = 'ncit__synonym';
+    $instances[$field_name] =  array(
+      'field_name' => $field_name,
+      'entity_type' => $entity_type,
+      'bundle' => $bundle->name,
+      'label' => 'Phenotype Ontology',
+      'description' => 'Phenotype Ontology.',
+      'required' => FALSE,
+      'settings' => array(
+        'term_vocabulary' => 'NCIT',
+        'term_name' => 'Synonym',
+        'term_accession' => 'c52469',
+        'auto_attach' => FALSE,
+        'chado_table' => $bundle->data_table,
+        'chado_column' => 'cvterm_id',
+        'base_table' => $bundle->data_table,
+      ),
+      'widget' => array(
+        'type' => 'ncit__synonym_widget',
+        'settings' => array(),
+      ),
+      'display' => array(
+        'default' => array(
+          'label' => 'hidden',
+          'type' => 'ncit__synonym_formatter',
+          'settings' => array(),
+        ),
+      ),
+    );
   }
 
   // IN GERMPLASM PAGE ONLY:
diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym.inc b/includes/TripalFields/ncit__synonym/ncit__synonym.inc
new file mode 100644
index 0000000..5052f3e
--- /dev/null
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym.inc
@@ -0,0 +1,151 @@
+<?php
+/**
+ * @class
+ * Purpose: Provide quick browse functionality for entity pages
+ *
+ * Data: No data.
+ * Assumptions:
+ */
+class ncit__synonym extends TripalField {
+  // --------------------------------------------------------------------------
+  //                     EDITABLE STATIC CONSTANTS
+  //
+  // The following constants SHOULD be set for each descendant class.  They are
+  // used by the static functions to provide information to Drupal about
+  // the field and it's default widget and formatter.
+  // --------------------------------------------------------------------------
+  // The default label for this field.
+  public static $default_label = 'Phenotype Ontology';
+  // The default description for this field.
+  public static $default_description = 'Phenotype Ontology';
+  // The default widget for this field.
+  public static $default_widget = 'ncit__synonym_widget';
+  // The default formatter for this field.
+  public static $default_formatter = 'ncit__synonym_formatter';
+  // The module that manages this field.
+  public static $module = 'analyzedphenotypes';
+
+  // A list of global settings. These can be accessed within the
+  // globalSettingsForm.  When the globalSettingsForm is submitted then
+  // Drupal will automatically change these settings for all fields.
+  // Once instances exist for a field type then these settings cannot be
+  // changed.
+  public static $default_settings = array(
+    'storage' => 'tripal_no_storage',
+    // It is expected that all fields set a 'value' in the load() function.
+    // In many cases, the value may be an associative array of key/value pairs.
+    // In order for Tripal to provide context for all data, the keys should
+    // be a controlled vocabulary term (e.g. rdfs:type). Keys in the load()
+    // function that are supported by the query() function should be
+    // listed here.
+    'browseable_keys' => array(),
+  );
+
+  // Provide a list of instance specific settings. These can be access within
+  // the instanceSettingsForm.  When the instanceSettingsForm is submitted
+  // then Drupal with automatically change these settings for the instance.
+  // It is recommended to put settings at the instance level whenever possible.
+  // If you override this variable in a child class be sure to replicate the
+  // term_name, term_vocab, term_accession and term_fixed keys as these are
+  // required for all TripalFields.
+  public static $default_instance_settings = array(
+    // The short name for the vocabulary (e.g. schema, SO, GO, PATO, etc.).
+    'term_vocabulary' => 'NCIT',
+    // The name of the term.
+    'term_name' => 'Synonym',
+    // The unique ID (i.e. accession) of the term.
+    'term_accession' => 'c52469',
+    // Set to TRUE if the site admin is not allowed to change the term
+    // type, otherwise the admin can change the term mapped to a field.
+    'term_fixed' => FALSE,
+    // Indicates if this field should be automatically attached to display
+    // or web services or if this field should be loaded separately. This
+    // is convenient for speed.  Fields that are slow should for loading
+    // should have auto_attach set to FALSE so tha their values can be
+    // attached asynchronously.
+    'auto_attach' => FALSE,
+    // The table where the options for this specific field are stored.
+    // This can be one of trpfancy_browse_options or trpfancy_browse_options_per_entity
+    // based on admin configuration. Default: trpfancy_browse_options.
+    'option_storage' => '',
+    // A list of browser types this field intends to provide.
+    'browser_types' => '',
+  );
+
+  // A boolean specifying that users should not be allowed to create
+  // fields and instances of this field type through the UI. Such
+  // fields can only be created programmatically with field_create_field()
+  // and field_create_instance().
+  public static $no_ui = FALSE;
+  // A boolean specifying that the field will not contain any data. This
+  // should exclude the field from web services or downloads.  An example
+  // could be a quick browse field that appears on the page that redirects
+  // the user but otherwise provides no data.
+  public static $no_data = TRUE;
+
+ /**
+   * Loads the field values from the underlying data store.
+   *
+   * @param $entity
+   *
+   * @return
+   *   An array of the following format:
+   *     $entity->{$field_name}['und'][0]['value'] = $value;
+   *   where:
+   *     - $entity is the entity object to which this field is attached.
+   *     - $field_name is the name of this field
+   *     - 'und' is the language code (in this case 'und' == undefined)
+   *     - 0 is the cardinality.  Increment by 1 when more than one item is
+   *       available.
+   *     - 'value' is the key indicating the value of this field. It should
+   *       always be set.  The value of the 'value' key will be the contents
+   *       used for web services and for downloadable content.  The value
+   *       should be of the follow format types: 1) A single value (text,
+   *       numeric, etc.) 2) An array of key value pair. 3) If multiple entries
+   *       then cardinality should incremented and format types 1 and 2 should
+   *       be used for each item.
+   *   The array may contain as many other keys at the same level as 'value'
+   *   but those keys are for internal field use and are not considered the
+   *   value of the field.
+   *
+   *
+   */
+  public function load($entity) {
+    $field_name = $this->instance['field_name'];
+
+    $entity->{$field_name}['und'][0]['value']['local:number of experiments'] = 1;
+  }
+
+  /**
+   * Provides a form for the 'Field Settings' of an instance of this field.
+   *
+   * This function corresponds to the hook_field_instance_settings_form()
+   * function of the Drupal Field API.
+   *
+   * Validation of the instance settings form is not supported by Drupal, but
+   * the TripalField class does provide a mechanism for supporting validation.
+   * To allow for validation of your setting form you must call the parent
+   * in your child class:
+   *
+   * @code
+   *   $element = parent::instanceSettingsForm();
+   * @endcode
+   *
+   * Please note, the form generated with this function does not easily
+   * support AJAX calls in the same way that other Drupal forms do.  If you
+   * need to use AJAX you must manually alter the $form in your ajax call.
+   * The typical way to handle updating the form via an AJAX call is to make
+   * the changes in the form function itself but that doesn't work here.
+   */
+  public function instanceSettingsForm() {
+
+    // Retrieve the current settings.
+    // If this field was just created these will contain the default values.
+    $settings = $this->instance['settings'];
+
+    // Allow the parent Tripal Field to set up the form element for us.
+    $element = parent::instanceSettingsForm();
+
+    return $element;
+  }
+}
diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc b/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
new file mode 100644
index 0000000..261fdbb
--- /dev/null
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
@@ -0,0 +1,57 @@
+<?php
+/**
+ * @class
+ * Purpose: Provide a quick search on entity pages which submits/redirects to a full search.
+ *
+ * Display: A simple textfield search form.
+ * Configuration:
+ *   - path to the full search.
+ *   - the URL token (query parameter) the value applies to.
+ *   - help text.
+ *   - textfield placeholder.
+ *   - search button text.
+ *   - autocomplete path.
+ */
+class ncit__synonym_formatter extends TripalFieldFormatter {
+  // The default label for this field.
+  public static $default_label = 'Phenotype Ontology';
+
+  // The list of field types for which this formatter is appropriate.
+  public static $field_types = array('ncit__synonym');
+
+  /**
+   *  Provides the display for a field
+   *
+   * This function corresponds to the hook_field_formatter_view()
+   * function of the Drupal Field API.
+   *
+   *  This function provides the display for a field when it is viewed on
+   *  the web page.  The content returned by the formatter should only include
+   *  what is present in the $items[$delta]['values] array. This way, the
+   *  contents that are displayed on the page, via webservices and downloaded
+   *  into a CSV file will always be identical.  The view need not show all
+   *  of the data in the 'values' array.
+   *
+   *  @param $element
+   *  @param $entity_type
+   *  @param $entity
+   *  @param $langcode
+   *  @param $items
+   *  @param $display
+   *
+   *  @return
+   *    An element array compatible with that returned by the
+   *    hook_field_formatter_view() function.
+   */
+  public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
+
+    // All set, render items.
+    $element[0] = array(
+      '#type' => 'markup',
+      '#markup' => 'lorem',
+    );
+
+
+    return $element;
+  }
+}
diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc b/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
new file mode 100644
index 0000000..a7f1528
--- /dev/null
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
@@ -0,0 +1,126 @@
+<?php
+/**
+ * @class
+ * Purpose: Provide a graphical summary of data stored in a materialized view.
+ *   This is a generic, configurable fields to make it easier to add charts
+ *   to Tripal Content pages.
+ *
+ * Allowing edit? No
+ */
+class ncit__synonym_widget extends TripalFieldWidget {
+
+  // The default lable for this field.
+  public static $default_label = 'No Edits';
+
+  // The list of field types for which this formatter is appropriate.
+  public static $field_types = array('ncit__synonym');
+
+  /**
+   * Provides the form for editing of this field.
+   *
+   * This function corresponds to the hook_field_widget_form()
+   * function of the Drupal Field API.
+   *
+   * This form is diplayed when the user creates a new entity or edits an
+   * existing entity.  If the field is attached to the entity then the form
+   * provided by this function will be displayed.
+   *
+   * At a minimum, the form must have a 'value' element.  For Tripal, the
+   * 'value' element of a field always corresponds to the value that is
+   * presented to the end-user either directly on the page (with formatting)
+   * or via web services, or some other mechanism.  However, the 'value' is
+   * sometimes not enough for a field.  For example, the Tripal Chado module
+   * maps fields to table columns and sometimes those columns are foreign keys
+   * therefore, the Tripal Chado modules does not just use the 'value' but adds
+   * additional elements to help link records via FKs.  But even in this case
+   * the 'value' element must always be present in the return form and in such
+   * cases it's value should be set equal to that added in the 'load' function.
+   *
+   * @param $widget
+   * @param $form
+   *   The form structure where widgets are being attached to. This might be a
+   *   full form structure, or a sub-element of a larger form.
+   * @param $form_state
+   *   An associative array containing the current state of the form.
+   * @param $langcode
+   *   The language associated with $items.
+   * @param $items
+   *   Array of default values for this field.
+   * @param $delta
+   *   The order of this item in the array of subelements (0, 1, 2, etc).
+   * @param $element
+   * A form element array containing basic properties for the widget:
+   *  - #entity_type: The name of the entity the field is attached to.
+   *  - #bundle: The name of the field bundle the field is contained in.
+   *  - #field_name: The name of the field.
+   *  - #language: The language the field is being edited in.
+   *  - #field_parents: The 'parents' space for the field in the form. Most
+   *    widgets can simply overlook this property. This identifies the location
+   *    where the field values are placed within $form_state['values'], and is
+   *    used to access processing information for the field through the
+   *    field_form_get_state() and field_form_set_state() functions.
+   *  - #columns: A list of field storage columns of the field.
+   *  - #title: The sanitized element label for the field instance, ready for
+   *    output.
+   *  - #description: The sanitized element description for the field instance,
+   *    ready for output.
+   *  - #required: A Boolean indicating whether the element value is required;
+   *    for required multiple value fields, only the first widget's values are
+   *    required.
+   *  - #delta: The order of this item in the array of subelements; see
+   *    $delta above
+   */
+  public function form(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
+    parent::form($widget, $form, $form_state, $langcode, $items, $delta, $element);
+  }
+
+  /**
+   * Performs validation of the widgetForm.
+   *
+   * Use this validate to ensure that form values are entered correctly.
+   * The 'value' key of this field must be set in the $form_state['values']
+   * array anytime data is entered by the user.  It may be the case that there
+   * are other fields for helping select a value. In the end those helper
+   * fields must be used to set the 'value' field.
+   */
+  public function validate($element, $form, &$form_state, $langcode, $delta) {
+  }
+
+  /**
+   * Performs extra commands when the entity form is submitted.
+   *
+   * Drupal typically does not provide a submit hook for fields.  The
+   * TripalField provides one to allow for behind-the-scenes actions to
+   * occur.   This function should never be used for updates, deletes or
+   * inserts for the Chado table associated with the field.  Rather, the
+   * storage backend should be allowed to handle inserts, updates deletes.
+   * However, it is permissible to perform inserts, updates or deletions within
+   * Chado using this function.  Those operations can be performed if needed but
+   * on other tables not directly associated with the field.
+   *
+   * An example is the chado.feature_synonym table.  The chado_linker__synonym
+   * field allows the user to provide a brand new synonynm and it must add it
+   * to the chado.synonym table prior to the record in the
+   * chado.feature_synonym table.  This insert occurs in the widgetFormSubmit
+   * function.
+   *
+   *  @param $entity_type
+   *    The type of $entity.
+   *  @param $entity
+   *    The entity for the operation.
+   *  @param $field
+   *    The field structure for the operation.
+   *  @param $instance
+   *    The instance structure for $field on $entity's bundle.
+   *  @param $langcode
+   *    The language associated with $items.
+   *  @param $items
+   *    $entity->{$field['field_name']}[$langcode], or an empty array if unset.
+   *  @param $form
+   *    The submitted form array.
+   *  @param $form_state.
+   *    The form state array.
+   */
+  public function submit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
+  }
+}

From 7e45b5793849c85a951b484433191a3f74140186 Mon Sep 17 00:00:00 2001
From: Reynold Tan <reynold@rain.baskt.bioinfo>
Date: Fri, 21 Jun 2019 14:36:40 -0600
Subject: [PATCH 2/8] Working on ontology update form

---
 .../ncit__synonym/ncit__synonym.inc           | 63 ++++++++++-----
 .../ncit__synonym/ncit__synonym_formatter.inc |  9 ++-
 .../ncit__synonym/ncit__synonym_widget.inc    | 78 ++++++++++++++++++-
 3 files changed, 124 insertions(+), 26 deletions(-)

diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym.inc b/includes/TripalFields/ncit__synonym/ncit__synonym.inc
index 5052f3e..a6c023d 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym.inc
@@ -6,7 +6,7 @@
  * Data: No data.
  * Assumptions:
  */
-class ncit__synonym extends TripalField {
+class ncit__synonym extends ChadoField {
   // --------------------------------------------------------------------------
   //                     EDITABLE STATIC CONSTANTS
   //
@@ -31,14 +31,14 @@ class ncit__synonym extends TripalField {
   // Once instances exist for a field type then these settings cannot be
   // changed.
   public static $default_settings = array(
-    'storage' => 'tripal_no_storage',
+    'storage' => 'field_chado_storage',
     // It is expected that all fields set a 'value' in the load() function.
     // In many cases, the value may be an associative array of key/value pairs.
     // In order for Tripal to provide context for all data, the keys should
     // be a controlled vocabulary term (e.g. rdfs:type). Keys in the load()
     // function that are supported by the query() function should be
     // listed here.
-    'browseable_keys' => array(),
+    'searchable_keys' => array(),
   );
 
   // Provide a list of instance specific settings. These can be access within
@@ -64,12 +64,6 @@ class ncit__synonym extends TripalField {
     // should have auto_attach set to FALSE so tha their values can be
     // attached asynchronously.
     'auto_attach' => FALSE,
-    // The table where the options for this specific field are stored.
-    // This can be one of trpfancy_browse_options or trpfancy_browse_options_per_entity
-    // based on admin configuration. Default: trpfancy_browse_options.
-    'option_storage' => '',
-    // A list of browser types this field intends to provide.
-    'browser_types' => '',
   );
 
   // A boolean specifying that users should not be allowed to create
@@ -81,7 +75,7 @@ class ncit__synonym extends TripalField {
   // should exclude the field from web services or downloads.  An example
   // could be a quick browse field that appears on the page that redirects
   // the user but otherwise provides no data.
-  public static $no_data = TRUE;
+  public static $no_data = FALSE;
 
  /**
    * Loads the field values from the underlying data store.
@@ -111,9 +105,45 @@ class ncit__synonym extends TripalField {
    *
    */
   public function load($entity) {
-    $field_name = $this->instance['field_name'];
+    // Trait/cvterm record.
+    $record = $entity->chado_record;
 
-    $entity->{$field_name}['und'][0]['value']['local:number of experiments'] = 1;
+    if ($record) {
+      // Has record.
+      $settings = $this->instance['settings'];
+
+      // Define relationship between trait and ontology term by
+      // creating entry in cvterm_relationhip where subject id is the ontology term
+      // and object id being the trait. Relation is of type related (as configured).
+      $field_table = array(
+        'table' => 'cvterm_relationship',
+        'field' => 'subject_id'
+      );
+
+      $field_name = $this->field['field_name'];
+
+      // Set some defaults for the empty record.
+      $entity->{$field_name}['und'][0] = array(
+        'value' => array(),
+      );
+
+      // Requires ontology term for this trait in both Tripal Engine and End-user.
+      // @see api/ontology.api
+      $traitprop = ap_get_cvterm(
+        array('cvterm_id' => $entity->chado_record_id),
+        array('dataset' => 'fullset')
+      );
+
+      // To user (formmater):
+      if ($traitprop['crop_ontology']) {
+        $term_rel_subject = tripal_get_chado_semweb_term($field_table['table'], $field_table['field']);
+        $entity->{$field_name}['und'][0]['value'][ $term_rel_subject ] = $traitprop['crop_ontology'];
+      }
+
+      // To Tripal engine (widget):
+      $linker_field = 'chado-' . $field_table['table'] . '__' . $field_table['field'];
+      $entity->{$field_name}['und'][ $linker_field ] = 1;// $traitprop['crop_ontology'];
+    }
   }
 
   /**
@@ -138,14 +168,5 @@ class ncit__synonym extends TripalField {
    * the changes in the form function itself but that doesn't work here.
    */
   public function instanceSettingsForm() {
-
-    // Retrieve the current settings.
-    // If this field was just created these will contain the default values.
-    $settings = $this->instance['settings'];
-
-    // Allow the parent Tripal Field to set up the form element for us.
-    $element = parent::instanceSettingsForm();
-
-    return $element;
   }
 }
diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc b/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
index 261fdbb..4759e1f 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
@@ -12,13 +12,19 @@
  *   - search button text.
  *   - autocomplete path.
  */
-class ncit__synonym_formatter extends TripalFieldFormatter {
+class ncit__synonym_formatter extends ChadoFieldFormatter {
   // The default label for this field.
   public static $default_label = 'Phenotype Ontology';
 
   // The list of field types for which this formatter is appropriate.
   public static $field_types = array('ncit__synonym');
 
+
+
+  public function settingsForm($view_mode, $form, &$form_state) {
+
+  }
+
   /**
    *  Provides the display for a field
    *
@@ -44,7 +50,6 @@ class ncit__synonym_formatter extends TripalFieldFormatter {
    *    hook_field_formatter_view() function.
    */
   public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
-
     // All set, render items.
     $element[0] = array(
       '#type' => 'markup',
diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc b/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
index a7f1528..6bbe619 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
@@ -7,7 +7,7 @@
  *
  * Allowing edit? No
  */
-class ncit__synonym_widget extends TripalFieldWidget {
+class ncit__synonym_widget extends ChadoFieldWidget {
 
   // The default lable for this field.
   public static $default_label = 'No Edits';
@@ -71,7 +71,78 @@ class ncit__synonym_widget extends TripalFieldWidget {
    *    $delta above
    */
   public function form(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::form($widget, $form, $form_state, $langcode, $items, $delta, $element);
+    if (count($delta) == 1) {
+      // Create field element to allow user to modify trait ontology term.
+      $field_name = $this->field['field_name'];
+      $field_table = array(
+        'table' => 'cvterm_relationship',
+        'field' => 'subject_id'
+      );
+
+      $linker_field = 'chado-' . $field_table['table'] . '__' . $field_table['field'];
+
+      // Create or upldate.
+
+      // The value presented to the user via load.
+      // If $items['delta']['value'] is set then we are updating and already have this
+      // information. As such, simply save it again.
+      $widget['value'] = array(
+        '#type' => 'value',
+        '#value' => array_key_exists($delta, $items) ? $items[ $delta ]['value'] : '',
+      );
+
+      // Pull out the value previously saved to be used as the default.
+      $ontology_term = '';
+      if (count($items) > 0 && array_key_exists($linker_field, $items[0])) {
+        $ontology_term = $items[0][ $linker_field ];
+      }
+
+      // Autocomplete field - instance the same as the ontology field in upload.
+      // @see api/ontology api
+      //      upload.inc
+
+      // Search ontology terms in genus configuration:
+      $widget['ap_fieldset'] = array(
+        '#type' => 'fieldset',
+        '#title' => t('Crop Ontology'),
+      );
+
+      // Fetch all genus with ontology value set.
+      $cv_options = array();
+      $genus = ap_get_genus();
+      foreach($genus as $g) {
+        $genus_key = strtolower(str_replace(' ', '_', $g));
+        $conf = variable_get('analyzedphenotypes_systemvar_' . $genus_key . '_ontology');
+        if ($conf) {
+          $term_name = ap_get_cv(
+            array('cv_id' => $conf)
+          );
+
+          $cv_options[ $g ] = $g . ' : ' . $term_name['name'];
+        }
+      }
+
+      $widget['ap_fieldset']['ap_source_cv'] = array(
+        '#type' => 'select',
+        '#title' => t('CV'),
+        '#description' => t('Select ontology terms in Genus-CV configuration to limit/filter terms only to this option.'),
+        '#options' => array('Select') + $cv_options,
+      );
+
+      $widget['ap_fieldset'][ $linker_field ] = array(
+        '#type' => 'textfield',
+        '#title' => t('Trait Ontology'),
+        //'#default_value' => $ontology_term,
+        '#autocomplete_path' => 'admin/tripal/extension/analyzedphenotypes/json/ontology/Lens',
+      );
+    }
+    else {
+      // This field can only process one field per trait.
+      drupal_set_message('Please set the maximum number of values user can enter for this field to 1 in manage field.', 'status', FALSE);
+      $widget['no_field'] = array(
+        '#markup' => 'Field not available.',
+      );
+    }
   }
 
   /**
@@ -84,7 +155,8 @@ class ncit__synonym_widget extends TripalFieldWidget {
    * fields must be used to set the 'value' field.
    */
   public function validate($element, $form, &$form_state, $langcode, $delta) {
-  }
+
+ }
 
   /**
    * Performs extra commands when the entity form is submitted.

From 1e1dd2e372e704b6bb6cf1149340db3c5cbdf94a Mon Sep 17 00:00:00 2001
From: Reynold Tan <reynold@rain.baskt.bioinfo>
Date: Wed, 26 Jun 2019 14:17:29 -0600
Subject: [PATCH 3/8] Yes! this is a working field - it does save now

---
 .../analyzedphenotypes.fields.inc             |   2 +-
 .../ncit__synonym/ncit__synonym.inc           |  86 +++++------
 .../ncit__synonym/ncit__synonym_formatter.inc |  30 ++--
 .../ncit__synonym/ncit__synonym_widget.inc    | 136 ++++++++----------
 4 files changed, 126 insertions(+), 128 deletions(-)

diff --git a/includes/TripalFields/analyzedphenotypes.fields.inc b/includes/TripalFields/analyzedphenotypes.fields.inc
index 892836a..9b5ce9e 100644
--- a/includes/TripalFields/analyzedphenotypes.fields.inc
+++ b/includes/TripalFields/analyzedphenotypes.fields.inc
@@ -469,7 +469,7 @@ function analyzedphenotypes_bundle_instances_info($entity_type, $bundle) {
         'term_accession' => 'c52469',
         'auto_attach' => FALSE,
         'chado_table' => $bundle->data_table,
-        'chado_column' => 'cvterm_id',
+        'chado_column' => $bundle->data_table . '_id',
         'base_table' => $bundle->data_table,
       ),
       'widget' => array(
diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym.inc b/includes/TripalFields/ncit__synonym/ncit__synonym.inc
index a6c023d..7af3daf 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym.inc
@@ -15,9 +15,9 @@ class ncit__synonym extends ChadoField {
   // the field and it's default widget and formatter.
   // --------------------------------------------------------------------------
   // The default label for this field.
-  public static $default_label = 'Phenotype Ontology';
+  public static $default_label = 'Crop Ontology';
   // The default description for this field.
-  public static $default_description = 'Phenotype Ontology';
+  public static $default_description = 'Crop Ontology';
   // The default widget for this field.
   public static $default_widget = 'ncit__synonym_widget';
   // The default formatter for this field.
@@ -31,14 +31,14 @@ class ncit__synonym extends ChadoField {
   // Once instances exist for a field type then these settings cannot be
   // changed.
   public static $default_settings = array(
-    'storage' => 'field_chado_storage',
+    'storage' => 'tripal_no_storage',
     // It is expected that all fields set a 'value' in the load() function.
     // In many cases, the value may be an associative array of key/value pairs.
     // In order for Tripal to provide context for all data, the keys should
     // be a controlled vocabulary term (e.g. rdfs:type). Keys in the load()
     // function that are supported by the query() function should be
     // listed here.
-    'searchable_keys' => array(),
+    'browseable_keys' => array(),
   );
 
   // Provide a list of instance specific settings. These can be access within
@@ -64,6 +64,17 @@ class ncit__synonym extends ChadoField {
     // should have auto_attach set to FALSE so tha their values can be
     // attached asynchronously.
     'auto_attach' => FALSE,
+    // The table where the options for this specific field are stored.
+    // This can be one of trpfancy_browse_options or trpfancy_browse_options_per_entity
+    // based on admin configuration. Default: trpfancy_browse_options.
+    'option_storage' => '',
+    // A list of browser types this field intends to provide.
+    'browser_types' => '',
+
+    'chado_table' => 'cvterm_relationship',
+    'chado_column' => 'cvterm_relationship_id',
+    'base_table'    => 'cvterm_relationship'
+
   );
 
   // A boolean specifying that users should not be allowed to create
@@ -75,7 +86,7 @@ class ncit__synonym extends ChadoField {
   // should exclude the field from web services or downloads.  An example
   // could be a quick browse field that appears on the page that redirects
   // the user but otherwise provides no data.
-  public static $no_data = FALSE;
+  public static $no_data = TRUE;
 
  /**
    * Loads the field values from the underlying data store.
@@ -105,45 +116,29 @@ class ncit__synonym extends ChadoField {
    *
    */
   public function load($entity) {
-    // Trait/cvterm record.
-    $record = $entity->chado_record;
-
-    if ($record) {
-      // Has record.
-      $settings = $this->instance['settings'];
-
-      // Define relationship between trait and ontology term by
-      // creating entry in cvterm_relationhip where subject id is the ontology term
-      // and object id being the trait. Relation is of type related (as configured).
-      $field_table = array(
-        'table' => 'cvterm_relationship',
-        'field' => 'subject_id'
-      );
-
-      $field_name = $this->field['field_name'];
+    // We need the term configuration for term Related used when creating relationship.
+    $sysvar = ap_get_variablenames(
+      array('variablename' => 'related'),
+      array('set' => 'terms')
+    );
+    $sysvar_related = variable_get($sysvar);
 
-      // Set some defaults for the empty record.
-      $entity->{$field_name}['und'][0] = array(
-        'value' => array(),
-      );
+    $m = chado_query("SELECT cvterm_relationship_id AS id, subject_id AS synonym_id
+      FROM {cvterm_relationship} WHERE type_id = :type_id AND object_id = :trait_id limit 1",
+      array(':type_id' => $sysvar_related, ':trait_id' => $entity->chado_record_id))
+    ->fetchObject();
 
-      // Requires ontology term for this trait in both Tripal Engine and End-user.
-      // @see api/ontology.api
-      $traitprop = ap_get_cvterm(
-        array('cvterm_id' => $entity->chado_record_id),
-        array('dataset' => 'fullset')
-      );
+    $this->instance['settings']['chado_table'] = 'cvterm_relationship';
+    $field_table = $this->instance['settings']['chado_table'];
 
-      // To user (formmater):
-      if ($traitprop['crop_ontology']) {
-        $term_rel_subject = tripal_get_chado_semweb_term($field_table['table'], $field_table['field']);
-        $entity->{$field_name}['und'][0]['value'][ $term_rel_subject ] = $traitprop['crop_ontology'];
-      }
-
-      // To Tripal engine (widget):
-      $linker_field = 'chado-' . $field_table['table'] . '__' . $field_table['field'];
-      $entity->{$field_name}['und'][ $linker_field ] = 1;// $traitprop['crop_ontology'];
-    }
+    $field_name = $this->field['field_name'];
+    $entity->{$field_name}['und'][0] = array(
+      'value' => '',
+      'chado-' . $field_table . '__cvterm_relationship_id' => $m->id,
+      'chado-' . $field_table . '__type_id' => $sysvar_related,
+      'chado-' . $field_table . '__object_id' => $entity->chado_record_id,
+      'chado-' . $field_table . '__subject_id' => $m->synonym_id
+    );
   }
 
   /**
@@ -168,5 +163,14 @@ class ncit__synonym extends ChadoField {
    * the changes in the form function itself but that doesn't work here.
    */
   public function instanceSettingsForm() {
+
+    // Retrieve the current settings.
+    // If this field was just created these will contain the default values.
+    $settings = $this->instance['settings'];
+
+    // Allow the parent Tripal Field to set up the form element for us.
+    $element = parent::instanceSettingsForm();
+
+    return $element;
   }
 }
diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc b/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
index 4759e1f..87f1449 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
@@ -12,19 +12,13 @@
  *   - search button text.
  *   - autocomplete path.
  */
-class ncit__synonym_formatter extends ChadoFieldFormatter {
+class ncit__synonym_formatter extends TripalFieldFormatter {
   // The default label for this field.
-  public static $default_label = 'Phenotype Ontology';
+  public static $default_label = 'Crop Ontology';
 
   // The list of field types for which this formatter is appropriate.
   public static $field_types = array('ncit__synonym');
 
-
-
-  public function settingsForm($view_mode, $form, &$form_state) {
-
-  }
-
   /**
    *  Provides the display for a field
    *
@@ -50,13 +44,25 @@ class ncit__synonym_formatter extends ChadoFieldFormatter {
    *    hook_field_formatter_view() function.
    */
   public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
-    // All set, render items.
-    $element[0] = array(
-      '#type' => 'markup',
-      '#markup' => 'lorem',
+    $trait_id = $items[0]['chado-cvterm_relationship__object_id'];
+    dpm($trait_id);
+
+    // Requires ontology term for this trait in both Tripal Engine and End-user.
+    // @see api/ontology.api
+    $traitprop = ap_get_cvterm(
+      array('cvterm_id' => $trait_id),
+      array('dataset' => 'fullset')
     );
 
 
+    if ($traitprop[0]['crop_ontology']) {
+      $element[0] = array(
+        '#type' => 'markup',
+        '#markup' => $traitprop[0]['crop_ontology'],
+      );
+    }
+
+
     return $element;
   }
 }
diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc b/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
index 6bbe619..fd9a075 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
@@ -7,7 +7,7 @@
  *
  * Allowing edit? No
  */
-class ncit__synonym_widget extends ChadoFieldWidget {
+class ncit__synonym_widget extends TripalFieldWidget {
 
   // The default lable for this field.
   public static $default_label = 'No Edits';
@@ -71,78 +71,55 @@ class ncit__synonym_widget extends ChadoFieldWidget {
    *    $delta above
    */
   public function form(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    if (count($delta) == 1) {
-      // Create field element to allow user to modify trait ontology term.
-      $field_name = $this->field['field_name'];
-      $field_table = array(
-        'table' => 'cvterm_relationship',
-        'field' => 'subject_id'
-      );
-
-      $linker_field = 'chado-' . $field_table['table'] . '__' . $field_table['field'];
-
-      // Create or upldate.
-
-      // The value presented to the user via load.
-      // If $items['delta']['value'] is set then we are updating and already have this
-      // information. As such, simply save it again.
-      $widget['value'] = array(
-        '#type' => 'value',
-        '#value' => array_key_exists($delta, $items) ? $items[ $delta ]['value'] : '',
-      );
-
-      // Pull out the value previously saved to be used as the default.
-      $ontology_term = '';
-      if (count($items) > 0 && array_key_exists($linker_field, $items[0])) {
-        $ontology_term = $items[0][ $linker_field ];
-      }
-
-      // Autocomplete field - instance the same as the ontology field in upload.
-      // @see api/ontology api
-      //      upload.inc
-
-      // Search ontology terms in genus configuration:
-      $widget['ap_fieldset'] = array(
-        '#type' => 'fieldset',
-        '#title' => t('Crop Ontology'),
-      );
-
-      // Fetch all genus with ontology value set.
-      $cv_options = array();
-      $genus = ap_get_genus();
-      foreach($genus as $g) {
-        $genus_key = strtolower(str_replace(' ', '_', $g));
-        $conf = variable_get('analyzedphenotypes_systemvar_' . $genus_key . '_ontology');
-        if ($conf) {
-          $term_name = ap_get_cv(
-            array('cv_id' => $conf)
-          );
-
-          $cv_options[ $g ] = $g . ' : ' . $term_name['name'];
-        }
-      }
-
-      $widget['ap_fieldset']['ap_source_cv'] = array(
-        '#type' => 'select',
-        '#title' => t('CV'),
-        '#description' => t('Select ontology terms in Genus-CV configuration to limit/filter terms only to this option.'),
-        '#options' => array('Select') + $cv_options,
-      );
-
-      $widget['ap_fieldset'][ $linker_field ] = array(
-        '#type' => 'textfield',
-        '#title' => t('Trait Ontology'),
-        //'#default_value' => $ontology_term,
-        '#autocomplete_path' => 'admin/tripal/extension/analyzedphenotypes/json/ontology/Lens',
-      );
-    }
-    else {
-      // This field can only process one field per trait.
-      drupal_set_message('Please set the maximum number of values user can enter for this field to 1 in manage field.', 'status', FALSE);
-      $widget['no_field'] = array(
-        '#markup' => 'Field not available.',
-      );
-    }
+    parent::form($widget, $form, $form_state, $langcode, $items, $delta, $element);
+
+    $field_name = $this->field['field_name'];
+    $field_type = $this->field['type'];
+
+    $this->instance['settings']['chado_table'] = 'cvterm_relationship';
+    $field_table = $this->instance['settings']['chado_table'];
+
+    $this->instance['settings']['chado_column'] = 'cvterm_relationship_id';
+    $field_column = $this->instance['settings']['chado_column'];
+
+    $this->instance['settings']['base_table'] = 'cvterm_relationship';
+    $base_table = $this->instance['settings']['base_table'];
+
+    $widget['#table_name'] = $field_table;
+
+    $widget['value'] = array(
+      '#type' => 'value',
+      '#value' => $items[$delta]['chado-cvterm__cvterm_relationship_id'],
+    );
+
+    $widget['chado-cvterm_relationship__cvterm_relationship_id'] = array(
+      '#type' => 'value',
+      '#value' => $items[$delta]['chado-cvterm_relationship__cvterm_relationship_id'],
+    );
+
+    $widget['chado-cvterm_relationship__type_id'] = array(
+      '#type' => 'value',
+      '#value' => $items[$delta]['chado-cvterm_relationship__type_id'],
+    );
+
+    $widget['chado-cvterm_relationship__object_id'] = array(
+      '#type' => 'value',
+      '#value' => $items[$delta]['chado-cvterm_relationship__object_id'],
+    );
+
+    $widget['chado-cvterm_relationship__subject_id'] = array(
+      '#type' => 'value',
+      '#value' => $items[$delta]['chado-cvterm_relationship__subject_id'],
+    );
+
+
+    $widget['new_term'] = array(
+      '#type'   => 'select',
+      '#title'   => 'Trait Ontology',
+      '#options' => array(4010=>'Subset Traits: # Pods (count)',  6086 => 'Chickpea Traits', 5705 => 'Lentil Traits'),
+      //'#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/cvterm/2',
+      '#default_value' => $m->subject_id,
+    );
   }
 
   /**
@@ -155,8 +132,19 @@ class ncit__synonym_widget extends ChadoFieldWidget {
    * fields must be used to set the 'value' field.
    */
   public function validate($element, $form, &$form_state, $langcode, $delta) {
+    $field_name = $this->field['field_name'];
 
- }
+
+    ///////////////
+    $this->instance['settings']['chado_table'] = 'cvterm_relationship';
+    $field_table = $this->instance['settings']['chado_table'];
+
+    $form_state['values'][$field_name][$langcode][$delta]['value'] = $form_state['values'][$field_name][$langcode][$delta]['value'];
+    $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__cvterm_relationship_id'] = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__cvterm_relationship_id'];
+    $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__object_id'] = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__object_id'];
+    $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__subject_id'] = $form_state['values'][$field_name][$langcode][$delta]['new_term'];
+    $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__type_id'] = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__type_id'];
+  }
 
   /**
    * Performs extra commands when the entity form is submitted.

From ba0a269cbf4da276024c5fde580ed7b07b1e371d Mon Sep 17 00:00:00 2001
From: Reynold Tan <reynold@rain.baskt.bioinfo>
Date: Tue, 2 Jul 2019 14:47:59 -0600
Subject: [PATCH 4/8] Create and Update work

---
 .../ncit__synonym/ncit__synonym.inc           |  74 +++++--
 .../ncit__synonym/ncit__synonym_formatter.inc |  17 +-
 .../ncit__synonym/ncit__synonym_widget.inc    | 199 ++++++++++++++----
 3 files changed, 208 insertions(+), 82 deletions(-)

diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym.inc b/includes/TripalFields/ncit__synonym/ncit__synonym.inc
index 7af3daf..d7e9557 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym.inc
@@ -116,29 +116,57 @@ class ncit__synonym extends ChadoField {
    *
    */
   public function load($entity) {
-    // We need the term configuration for term Related used when creating relationship.
-    $sysvar = ap_get_variablenames(
-      array('variablename' => 'related'),
-      array('set' => 'terms')
-    );
-    $sysvar_related = variable_get($sysvar);
-
-    $m = chado_query("SELECT cvterm_relationship_id AS id, subject_id AS synonym_id
-      FROM {cvterm_relationship} WHERE type_id = :type_id AND object_id = :trait_id limit 1",
-      array(':type_id' => $sysvar_related, ':trait_id' => $entity->chado_record_id))
-    ->fetchObject();
-
-    $this->instance['settings']['chado_table'] = 'cvterm_relationship';
-    $field_table = $this->instance['settings']['chado_table'];
-
-    $field_name = $this->field['field_name'];
-    $entity->{$field_name}['und'][0] = array(
-      'value' => '',
-      'chado-' . $field_table . '__cvterm_relationship_id' => $m->id,
-      'chado-' . $field_table . '__type_id' => $sysvar_related,
-      'chado-' . $field_table . '__object_id' => $entity->chado_record_id,
-      'chado-' . $field_table . '__subject_id' => $m->synonym_id
-    );
+    $record = $entity->chado_record_id;
+
+    if ($record) {
+      // We need the term configuration for term Related used when creating relationship.
+      $sysvar = ap_get_variablenames(
+        array('variablename' => 'related'),
+        array('set' => 'terms')
+      );
+      $sysvar_related = variable_get($sysvar);
+
+      if ($sysvar_related) {
+        $identifiers = array(
+          'column' => array('cvterm_relationship_id', 'subject_id'),
+          'value'  => array('type_id' => $sysvar_related, 'object_id' => $record)
+        );
+        $rel = chado_select_record('cvterm_relationship', $identifiers['column'], $identifiers['value']);
+
+        $field_name = $this->field['field_name'];
+        $field_table = 'cvterm_relationship';
+
+        if ($rel) {
+          // Has crop ontology.
+
+          // For chado mechnanism.
+          $entity->{$field_name}['und'][0] = array(
+            'chado-' . $field_table . '__cvterm_relationship_id' => $rel[0]->cvterm_relationship_id,
+            'chado-' . $field_table . '__type_id' => $sysvar_related,
+            'chado-' . $field_table . '__object_id' => $entity->chado_record_id,
+            'chado-' . $field_table . '__subject_id' => $rel[0]->subject_id
+          );
+
+          // For end user.
+          $relationship_term = tripal_get_chado_semweb_term('cvterm_relationship', 'subject_id');
+
+          $traitprop = ap_get_cvterm(
+            array('cvterm_id' => $record),
+            array('dataset' => 'fullset')
+          );
+
+          $entity->{$field_name}['und'][0]['value'][ $relationship_term ] = $traitprop[0]['crop_ontology'];
+        }
+        else {
+          // Crop ontology not set.
+          $entity->{$field_name}['und'][0] = array(
+            'value' => array(),
+            'chado-' . $field_table . '__object_id' => $entity->chado_record_id,
+            'chado-' . $field_table . '__type_id' => $sysvar_related,
+          );
+        }
+      }
+    }
   }
 
   /**
diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc b/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
index 87f1449..ca7133b 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
@@ -44,25 +44,14 @@ class ncit__synonym_formatter extends TripalFieldFormatter {
    *    hook_field_formatter_view() function.
    */
   public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
-    $trait_id = $items[0]['chado-cvterm_relationship__object_id'];
-    dpm($trait_id);
-
-    // Requires ontology term for this trait in both Tripal Engine and End-user.
-    // @see api/ontology.api
-    $traitprop = ap_get_cvterm(
-      array('cvterm_id' => $trait_id),
-      array('dataset' => 'fullset')
-    );
-
-
-    if ($traitprop[0]['crop_ontology']) {
+    // Render crop ontology for this trait.
+    if ($items[0]['value']) {
       $element[0] = array(
         '#type' => 'markup',
-        '#markup' => $traitprop[0]['crop_ontology'],
+        '#markup' => current($items[0]['value']),
       );
     }
 
-
     return $element;
   }
 }
diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc b/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
index fd9a075..2b0f475 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
@@ -71,55 +71,115 @@ class ncit__synonym_widget extends TripalFieldWidget {
    *    $delta above
    */
   public function form(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    parent::form($widget, $form, $form_state, $langcode, $items, $delta, $element);
+    if (count($delta) == 1) {
+      // By the default, field allows for multiple/unlimited values to be entered. AP only
+      // supports 1 and only 1 crop ontology term per trait name.
 
-    $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
+      parent::form($widget, $form, $form_state, $langcode, $items, $delta, $element);
+
+      // Field name.
+      $field_name = $this->field['field_name'];
+
+      // Elements of chado.cvterm_relationship table:
+      $chado_table = 'chado-cvterm_relationship__';
+
+      // Column - cvterm_relationship_id primary key.
+      $widget['value'] = array(
+        '#type' => 'value',
+        '#value' => $items[$delta][ $chado_table . 'cvterm_relationship_id' ] ?? '',
+      );
+
+      // Column - cvterm_relationship_id primary key.
+      $widget[ $chado_table . 'cvterm_relationship_id' ] = array(
+        '#type' => 'value',
+        '#value' => $items[$delta][ $chado_table . 'cvterm_relationship_id' ] ?? '',
+      );
+
+      // Column - object_id, the trait id (cvterm_id) # the crop ontology term maps to.
+      // Has value even when trait has no crop ontology.
+      $widget[ $chado_table . 'object_id' ] = array(
+        '#type' => 'value',
+        '#value' => $items[$delta][ $chado_table . 'object_id' ],
+      );
 
-    $this->instance['settings']['chado_table'] = 'cvterm_relationship';
-    $field_table = $this->instance['settings']['chado_table'];
+      // Column - subject_id, the crop ontology id (cvterm_id) that maps to a trait.
+      $widget[ $chado_table . 'subject_id' ] = array(
+        '#type' => 'value',
+        '#value' => $items[$delta][ $chado_table . 'subject_id' ] ?? '',
+      );
 
-    $this->instance['settings']['chado_column'] = 'cvterm_relationship_id';
-    $field_column = $this->instance['settings']['chado_column'];
+      // Column - type_id, refers to ontology term Related in AP configuration.
+      // Has value even when trait has no crop ontology.
+      $widget[ $chado_table . 'type_id' ] = array(
+        '#type' => 'value',
+        '#value' => $items[$delta][ $chado_table . 'type_id' ],
+      );
 
-    $this->instance['settings']['base_table'] = 'cvterm_relationship';
-    $base_table = $this->instance['settings']['base_table'];
+      // FORM ELEMENTS:
+      // Current crop ontology.
+      $relationship_term = tripal_get_chado_semweb_term('cvterm_relationship', 'subject_id');
+      $ontology = $items[$delta]['value'][ $relationship_term ] ?? 'Crop ontology not set';
 
-    $widget['#table_name'] = $field_table;
+      // FIELDSET - Main fieldset - search ontology terms.
+      $widget['ap_fieldset'] = array(
+        '#type' => 'fieldset',
+        '#title' => t('Crop Ontology'),
+      );
 
-    $widget['value'] = array(
-      '#type' => 'value',
-      '#value' => $items[$delta]['chado-cvterm__cvterm_relationship_id'],
-    );
+      // MARKUP - Show current record if any.
+      $widget['ap_fieldset']['ap_ontology'] = array(
+        '#type' => 'markup',
+        '#markup' => '<h2 style="font-style: italic">' . $ontology . '</h2>',
+      );
 
-    $widget['chado-cvterm_relationship__cvterm_relationship_id'] = array(
-      '#type' => 'value',
-      '#value' => $items[$delta]['chado-cvterm_relationship__cvterm_relationship_id'],
-    );
+      $vocs = [];
+      $vocs = chado_get_cv_select_options();
+      $cv_id = isset($form_state['values'][$field_name][$langcode][$delta]['ap_fieldset']['ap_ajax_response']['ap_source_cv'])
+        ? $form_state['values'][$field_name][$langcode][$delta]['ap_fieldset']['ap_ajax_response']['ap_source_cv'] : 0;
 
-    $widget['chado-cvterm_relationship__type_id'] = array(
-      '#type' => 'value',
-      '#value' => $items[$delta]['chado-cvterm_relationship__type_id'],
-    );
+      // ITEM - Describe both CV field and CV Term field.
+      $widget['ap_fieldset']['ap_describe'] = array(
+        '#type' => 'item',
+        '#title' => t('CV and Term'),
+        '#description' => t('Select CV and Term to change the ontology term for this trait.'),
+      );
 
-    $widget['chado-cvterm_relationship__object_id'] = array(
-      '#type' => 'value',
-      '#value' => $items[$delta]['chado-cvterm_relationship__object_id'],
-    );
+      // MARKUP - AJAX response wrapper. Update CV id filter in autocomplete field below.
+      $widget['ap_fieldset']['ap_ajax_response'] = array(
+        '#prefix' => '<div id="ap-ajax-response">',
+        '#suffix' => '</div>',
+      );
 
-    $widget['chado-cvterm_relationship__subject_id'] = array(
-      '#type' => 'value',
-      '#value' => $items[$delta]['chado-cvterm_relationship__subject_id'],
-    );
 
+      // FIELD SELECT - Select CV.
+      $widget['ap_fieldset']['ap_ajax_response']['ap_source_cv'] = array(
+        '#type' => 'select',
+        '#options' => $vocs,
+        '#theme_wrappers' => array(),
+        '#ajax' => array(
+          'callback' => 'analyzedphentypes_synonym_callback',
+          'wrapper' => 'ap-ajax-response',
+          'method' => 'replace',
+        ),
+      );
 
-    $widget['new_term'] = array(
-      '#type'   => 'select',
-      '#title'   => 'Trait Ontology',
-      '#options' => array(4010=>'Subset Traits: # Pods (count)',  6086 => 'Chickpea Traits', 5705 => 'Lentil Traits'),
-      //'#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/cvterm/2',
-      '#default_value' => $m->subject_id,
-    );
+      // FIELD AUTOCOMPLETE - Search term in a CV.
+      $widget['ap_fieldset']['ap_ajax_response']['ap_ontology_term'] = array(
+        '#type' => 'textfield',
+        '#size' => 60,
+        '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/cvterm/' . $cv_id,
+        '#disabled' => TRUE,
+        '#theme_wrappers' => array(),
+        '#attributes' => array(
+          'style' => 'margin: 0 10px;'
+        ),
+      );
+
+      if (isset($cv_id)) {
+        // Enable field when a cv selected.
+        $widget['ap_fieldset']['ap_ajax_response']['ap_ontology_term']['#disabled'] = FALSE;
+      }
+    }
   }
 
   /**
@@ -134,16 +194,46 @@ class ncit__synonym_widget extends TripalFieldWidget {
   public function validate($element, $form, &$form_state, $langcode, $delta) {
     $field_name = $this->field['field_name'];
 
+    if (isset($form_state['values'][$field_name][$langcode][$delta])) {
+      $form_values = $form_state['values'][$field_name][$langcode][$delta];
+
+      if (isset($form_values['ap_fieldset']['ap_ajax_response']['ap_source_cv'])
+        && isset($form_values['ap_fieldset']['ap_ajax_response']['ap_ontology_term'])) {
+
+          $termprop = chado_generate_var('cvterm', array(
+            'cv_id' => $form_values['ap_fieldset']['ap_ajax_response']['ap_source_cv'],
+            'name' => $form_values['ap_fieldset']['ap_ajax_response']['ap_ontology_term'],
+          ));
+
+          if ($termprop && $termprop->cvterm_id > 0) {
+            // Term is valid.
+
+            // From this point on, set the chado_table settings to cvterm_relationship from cvterm.
+            $this->instance['settings']['chado_table'] = 'cvterm_relationship';
+            $field_table = $this->instance['settings']['chado_table'];
 
-    ///////////////
-    $this->instance['settings']['chado_table'] = 'cvterm_relationship';
-    $field_table = $this->instance['settings']['chado_table'];
 
-    $form_state['values'][$field_name][$langcode][$delta]['value'] = $form_state['values'][$field_name][$langcode][$delta]['value'];
-    $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__cvterm_relationship_id'] = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__cvterm_relationship_id'];
-    $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__object_id'] = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__object_id'];
-    $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__subject_id'] = $form_state['values'][$field_name][$langcode][$delta]['new_term'];
-    $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__type_id'] = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__type_id'];
+            // Create or Update?
+
+            if (empty($form_values['value'])) {
+              // Create.
+              $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__object_id'] = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__object_id'];
+              $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__type_id'] = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__type_id'];
+
+              // As entered in the autocomplete field.
+              $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__subject_id'] = $termprop->cvterm_id;
+            }
+            else {
+              // Update.
+              // As entered in the autocomplete field.
+              $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__subject_id'] = $termprop->cvterm_id;
+           }
+
+           // After create or update, restore chado_table setting to original value (cvterm).
+           $this->instance['settings']['chado_table'] = 'cvterm';
+         }
+      }
+    }
   }
 
   /**
@@ -184,3 +274,22 @@ class ncit__synonym_widget extends TripalFieldWidget {
   public function submit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
   }
 }
+
+
+/**
+ * Function callback - AJAX response.
+ * @credits to Tripal developer - sbo relationship.
+ */
+function analyzedphentypes_synonym_callback($form, $form_state) {
+  // Get the triggering element
+  $form_element_name = $form_state['triggering_element']['#name'];
+  preg_match('/(.+?)\[(.+?)\]\[(.+?)\]/', $form_element_name, $matches);
+  $field = $matches[1];
+  $lang = $matches[2];
+  $delta = $matches[3];
+
+  // Return the widget that triggered the AJAX call, but only the ontology section.
+  if (isset($form[$field][$lang][$delta])) {
+    return $form[$field][$lang][$delta]['ap_fieldset']['ap_ajax_response'];
+  }
+}

From 5bd2c986fef0d083be378c9b6d4738e79c1b39ea Mon Sep 17 00:00:00 2001
From: Reynold Tan <reynold@rain.baskt.bioinfo>
Date: Wed, 3 Jul 2019 10:43:42 -0600
Subject: [PATCH 5/8] Ready for review

---
 .../ncit__synonym/ncit__synonym.inc           |  42 +++++--
 .../ncit__synonym/ncit__synonym_formatter.inc |  14 ++-
 .../ncit__synonym/ncit__synonym_widget.inc    | 117 ++++++++++++------
 .../ncit__synonym/theme/.DS_Store             | Bin 0 -> 6148 bytes
 .../theme/style_cp_synonym_field.css          |  27 ++++
 5 files changed, 145 insertions(+), 55 deletions(-)
 create mode 100644 includes/TripalFields/ncit__synonym/theme/.DS_Store
 create mode 100644 includes/TripalFields/ncit__synonym/theme/style_cp_synonym_field.css

diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym.inc b/includes/TripalFields/ncit__synonym/ncit__synonym.inc
index d7e9557..999e606 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym.inc
@@ -127,6 +127,10 @@ class ncit__synonym extends ChadoField {
       $sysvar_related = variable_get($sysvar);
 
       if ($sysvar_related) {
+        // Inspect to see if this trait has crop ontology set in chado.cvterm_relationship
+        // using what is known - type_id of ontology Related (in configuration) and the object_id
+        // which is the current trait.
+
         $identifiers = array(
           'column' => array('cvterm_relationship_id', 'subject_id'),
           'value'  => array('type_id' => $sysvar_related, 'object_id' => $record)
@@ -134,31 +138,43 @@ class ncit__synonym extends ChadoField {
         $rel = chado_select_record('cvterm_relationship', $identifiers['column'], $identifiers['value']);
 
         $field_name = $this->field['field_name'];
-        $field_table = 'cvterm_relationship';
+        $field_table = 'chado-cvterm_relationship__';
 
         if ($rel) {
           // Has crop ontology.
 
           // For chado mechnanism.
           $entity->{$field_name}['und'][0] = array(
-            'chado-' . $field_table . '__cvterm_relationship_id' => $rel[0]->cvterm_relationship_id,
-            'chado-' . $field_table . '__type_id' => $sysvar_related,
-            'chado-' . $field_table . '__object_id' => $entity->chado_record_id,
-            'chado-' . $field_table . '__subject_id' => $rel[0]->subject_id
+            // Row id #.
+            $field_table . 'cvterm_relationship_id' => $rel[0]->cvterm_relationship_id,
+            // Relationship details.
+            $field_table . 'type_id' => $sysvar_related,
+            $field_table . 'object_id' => $entity->chado_record_id,
+            $field_table . 'subject_id' => $rel[0]->subject_id
           );
 
           // For end user.
-          $relationship_term = tripal_get_chado_semweb_term('cvterm_relationship', 'subject_id');
-
-          $traitprop = ap_get_cvterm(
-            array('cvterm_id' => $record),
-            array('dataset' => 'fullset')
-          );
-
-          $entity->{$field_name}['und'][0]['value'][ $relationship_term ] = $traitprop[0]['crop_ontology'];
+          // Sending the term, accession and cv name. Last two items are used to constuct
+          // direct link to vocabulary lookup to a more details about a term.
+          $termprop = chado_generate_var('cvterm', array(
+            'cvterm_id' => $rel[0]->subject_id
+          ));
+
+            // Term.
+            $relationship_term = tripal_get_chado_semweb_term('cvterm_relationship', 'subject_id');
+            $entity->{$field_name}['und'][0]['value'][ $relationship_term ] = $termprop->name;
+
+            // Accession.
+            $accession = tripal_get_chado_semweb_term('dbxref', 'accession');
+            $entity->{$field_name}['und'][0]['value'][ $accession ] = $termprop->dbxref_id->accession;
+
+            // CV.
+            $cv_term = tripal_get_chado_semweb_term('cv', 'name');
+            $entity->{$field_name}['und'][0]['value'][ $cv_term ] = $termprop->cv_id->name;
         }
         else {
           // Crop ontology not set.
+          // Nothing here, just forward what we know so far, Related term and the trait id.
           $entity->{$field_name}['und'][0] = array(
             'value' => array(),
             'chado-' . $field_table . '__object_id' => $entity->chado_record_id,
diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc b/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
index ca7133b..7be8301 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
@@ -44,11 +44,23 @@ class ncit__synonym_formatter extends TripalFieldFormatter {
    *    hook_field_formatter_view() function.
    */
   public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
+    // No show when no crop ontology for a trait.
+    $element = null;
+
     // Render crop ontology for this trait.
     if ($items[0]['value']) {
+      // Style information.
+      drupal_add_css(drupal_get_path('module', 'analyzedphenotypes') . '/includes/TripalFields/ncit__synonym/theme/style_cp_synonym_field.css');
+
+      // Refer to this ID for CSS styling.
+      $id = 'ap-field-crop_ontology_synonym';
+
+      list($term, $accession, $cv) = array_values($items[0]['value']);
+      $cvterm_lookup = l('Vocabulary Details', 'cv/lookup/' .  $cv . '/' . $accession, array('attributes' => array('target' => '_blank')));
+
       $element[0] = array(
         '#type' => 'markup',
-        '#markup' => current($items[0]['value']),
+        '#markup' => '<div id="' . $id . '">' . $term . '</div> ' . $cvterm_lookup,
       );
     }
 
diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc b/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
index 2b0f475..fcf070a 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
@@ -83,6 +83,8 @@ class ncit__synonym_widget extends TripalFieldWidget {
       // Elements of chado.cvterm_relationship table:
       $chado_table = 'chado-cvterm_relationship__';
 
+
+      // FOR CHADO MECHNANISM:
       // Column - cvterm_relationship_id primary key.
       $widget['value'] = array(
         '#type' => 'value',
@@ -115,10 +117,25 @@ class ncit__synonym_widget extends TripalFieldWidget {
         '#value' => $items[$delta][ $chado_table . 'type_id' ],
       );
 
-      // FORM ELEMENTS:
+
+      // CURRENT SETTINGS:
+      // Style information.
+      drupal_add_css(drupal_get_path('module', 'analyzedphenotypes') . '/includes/TripalFields/ncit__synonym/theme/style_cp_synonym_field.css');
+
       // Current crop ontology.
-      $relationship_term = tripal_get_chado_semweb_term('cvterm_relationship', 'subject_id');
-      $ontology = $items[$delta]['value'][ $relationship_term ] ?? 'Crop ontology not set';
+      list($term, $accession, $cv) = array_values($items[0]['value']);
+
+      if (empty($term)) {
+        $crop_ontology = 'Crop ontology not set ';
+        $cvterm_lookup = '';
+      }
+      else {
+        // Refer to this ID for CSS styling.
+        $id = 'ap-field-crop_ontology_synonym';
+
+        $crop_ontology = '<div id="' . $id . '">' . $term . '</div> ';
+        $cvterm_lookup = l('Vocabulary Details', 'cv/lookup/' .  $cv . '/' . $accession, array('attributes' => array('target' => '_blank'))) . ' | ';
+      }
 
       // FIELDSET - Main fieldset - search ontology terms.
       $widget['ap_fieldset'] = array(
@@ -129,9 +146,12 @@ class ncit__synonym_widget extends TripalFieldWidget {
       // MARKUP - Show current record if any.
       $widget['ap_fieldset']['ap_ontology'] = array(
         '#type' => 'markup',
-        '#markup' => '<h2 style="font-style: italic">' . $ontology . '</h2>',
+        '#markup' => $crop_ontology . $cvterm_lookup . l('Update term', '#', array('attributes' => array('class' => 'ap-link-form-revel'))),
       );
 
+
+      // FORM ELEMENTS:
+      // @credits to Tripal developer - sbo relationship.
       $vocs = [];
       $vocs = chado_get_cv_select_options();
       $cv_id = isset($form_state['values'][$field_name][$langcode][$delta]['ap_fieldset']['ap_ajax_response']['ap_source_cv'])
@@ -142,43 +162,55 @@ class ncit__synonym_widget extends TripalFieldWidget {
         '#type' => 'item',
         '#title' => t('CV and Term'),
         '#description' => t('Select CV and Term to change the ontology term for this trait.'),
+        //
+        // Wrap.
+        '#prefix' => '<div id="ap-crop-ontology-form-fields">',
       );
 
-      // MARKUP - AJAX response wrapper. Update CV id filter in autocomplete field below.
-      $widget['ap_fieldset']['ap_ajax_response'] = array(
-        '#prefix' => '<div id="ap-ajax-response">',
-        '#suffix' => '</div>',
-      );
-
-
-      // FIELD SELECT - Select CV.
-      $widget['ap_fieldset']['ap_ajax_response']['ap_source_cv'] = array(
-        '#type' => 'select',
-        '#options' => $vocs,
-        '#theme_wrappers' => array(),
-        '#ajax' => array(
-          'callback' => 'analyzedphentypes_synonym_callback',
-          'wrapper' => 'ap-ajax-response',
-          'method' => 'replace',
-        ),
-      );
-
-      // FIELD AUTOCOMPLETE - Search term in a CV.
-      $widget['ap_fieldset']['ap_ajax_response']['ap_ontology_term'] = array(
-        '#type' => 'textfield',
-        '#size' => 60,
-        '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/cvterm/' . $cv_id,
-        '#disabled' => TRUE,
-        '#theme_wrappers' => array(),
-        '#attributes' => array(
-          'style' => 'margin: 0 10px;'
-        ),
-      );
-
-      if (isset($cv_id)) {
-        // Enable field when a cv selected.
-        $widget['ap_fieldset']['ap_ajax_response']['ap_ontology_term']['#disabled'] = FALSE;
-      }
+        // MARKUP - AJAX response wrapper. Update CV id filter in autocomplete field below.
+        $widget['ap_fieldset']['ap_ajax_response'] = array(
+          '#prefix' => '<div id="ap-ajax-response">',
+          '#suffix' => '</div>',
+        );
+
+        // FIELD SELECT - Select CV.
+        $widget['ap_fieldset']['ap_ajax_response']['ap_source_cv'] = array(
+          '#type' => 'select',
+          '#options' => $vocs,
+          '#theme_wrappers' => array(),
+          '#ajax' => array(
+            'callback' => 'analyzedphentypes_synonym_callback',
+            'wrapper' => 'ap-ajax-response',
+            'method' => 'replace',
+          ),
+        );
+
+        // FIELD AUTOCOMPLETE - Search term in a CV.
+        $widget['ap_fieldset']['ap_ajax_response']['ap_ontology_term'] = array(
+          '#type' => 'textfield',
+          '#size' => 60,
+          '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/cvterm/' . $cv_id,
+          '#disabled' => TRUE,
+          '#theme_wrappers' => array(),
+          '#attributes' => array('style' => 'margin: 0 10px;'),
+          //
+          // Wrap.
+          '#suffix' => '</div>',
+        );
+
+        if (isset($cv_id)) {
+          // Enable field when a cv selected.
+          $widget['ap_fieldset']['ap_ajax_response']['ap_ontology_term']['#disabled'] = FALSE;
+        }
+
+        // Listen to link to update ontology term.
+        drupal_add_js("jQuery('.ap-link-form-revel').click(function(e) {
+          e.preventDefault();
+          jQuery('#ap-crop-ontology-form-fields').fadeIn();
+        })", array('type' => 'inline', 'scope' => 'footer'));
+    }
+    else {
+      drupal_set_message('Crop ontology configuration can only be set to a single value. Please set the allowed value to one in mange field.', 'warning');
     }
   }
 
@@ -217,8 +249,11 @@ class ncit__synonym_widget extends TripalFieldWidget {
 
             if (empty($form_values['value'])) {
               // Create.
-              $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__object_id'] = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__object_id'];
-              $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__type_id'] = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__type_id'];
+              $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__object_id']
+                = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__object_id'];
+
+              $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__type_id']
+                = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__type_id'];
 
               // As entered in the autocomplete field.
               $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__subject_id'] = $termprop->cvterm_id;
diff --git a/includes/TripalFields/ncit__synonym/theme/.DS_Store b/includes/TripalFields/ncit__synonym/theme/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..b21d3a41c40c7013b11eb5437fc7b4cd6a3f4342
GIT binary patch
literal 6148
zcmeHKJx{|x41I<Ul~_6=rW=`%m|0F$J23MDKy5)n3Jp@|kS!ZO8=gNvM4>AKvL*Z7
z`TXvZH^eyrvOMgrfdzm$T@mjZrl#xa6FZ5F5b50G5%<{Qm9d*t|DI6p1*_lCqZ#pg
z?9tMDyl}rKJae_d4p%&(LwDP>+fCDM$k&Izp<jNOag>${qynixDv%1K0>>24-b<UG
zIc7`+Qh`+9TLJw(6uM#!931V_!C+Sa;*4oCj_oc%ESezJz`>CjnmCo{REaBwIGy<t
zbv1BsbUMUN=00(<#0^F4bmohdL#kuOR3H@?D{$)5h4%k7{mA`)Ov+g*kP7@O1!T6m
zTP^uY(OV}kr@gk&ALw7kS}SL;R!p>3%!#(*^B;9Z$6T+0gQL-zH##wY1XP!_RNyZZ
F_yjABA)WvL

literal 0
HcmV?d00001

diff --git a/includes/TripalFields/ncit__synonym/theme/style_cp_synonym_field.css b/includes/TripalFields/ncit__synonym/theme/style_cp_synonym_field.css
new file mode 100644
index 0000000..83fa488
--- /dev/null
+++ b/includes/TripalFields/ncit__synonym/theme/style_cp_synonym_field.css
@@ -0,0 +1,27 @@
+/**
+ * @file
+ * Style NCIT synonym - crop ontology.
+ */
+
+/* Term wrapper */
+#ap-field-crop_ontology_synonym {
+  background-color: #3A7f21;
+  color: #FFFFFF;
+  display: inline-block;
+  font-family: sans-serif;
+  margin-right: 20px;
+  padding: 10px;
+
+  -webkit-border-radius: 5px;
+  -moz-border-radius: 5px;
+  border-radius: 5px;
+
+  letter-spacing: 1px;
+  word-spacing: 1px;
+}
+
+/* Update ontology formset wrapper */
+#ap-crop-ontology-form-fields {
+  display: none;
+  margin: 15px 0 0 0;
+}

From f2fa2ce28e6ad4637c95c23515df0f032559a329 Mon Sep 17 00:00:00 2001
From: Reynold Tan <reynold@rain.baskt.bioinfo>
Date: Wed, 3 Jul 2019 13:45:12 -0600
Subject: [PATCH 6/8] Limit # of allowed values

---
 .../ncit__synonym/ncit__synonym_widget.inc             | 10 +++++-----
 .../ncit__synonym/theme/style_cp_synonym_field.css     |  5 +++--
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc b/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
index fcf070a..dd0e944 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
@@ -71,12 +71,12 @@ class ncit__synonym_widget extends TripalFieldWidget {
    *    $delta above
    */
   public function form(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
-    if (count($delta) == 1) {
+    parent::form($widget, $form, $form_state, $langcode, $items, $delta, $element);
+
+    if ($delta == 0) {
       // By the default, field allows for multiple/unlimited values to be entered. AP only
       // supports 1 and only 1 crop ontology term per trait name.
 
-      parent::form($widget, $form, $form_state, $langcode, $items, $delta, $element);
-
       // Field name.
       $field_name = $this->field['field_name'];
 
@@ -126,7 +126,7 @@ class ncit__synonym_widget extends TripalFieldWidget {
       list($term, $accession, $cv) = array_values($items[0]['value']);
 
       if (empty($term)) {
-        $crop_ontology = 'Crop ontology not set ';
+        $crop_ontology = 'Crop ontology not set | ';
         $cvterm_lookup = '';
       }
       else {
@@ -210,7 +210,7 @@ class ncit__synonym_widget extends TripalFieldWidget {
         })", array('type' => 'inline', 'scope' => 'footer'));
     }
     else {
-      drupal_set_message('Crop ontology configuration can only be set to a single value. Please set the allowed value to one in mange field.', 'warning');
+      drupal_set_message('Crop ontology configuration can only be set to a single value. Please set the allowed value to one in mange field.', 'warning', FALSE);
     }
   }
 
diff --git a/includes/TripalFields/ncit__synonym/theme/style_cp_synonym_field.css b/includes/TripalFields/ncit__synonym/theme/style_cp_synonym_field.css
index 83fa488..2cc13bc 100644
--- a/includes/TripalFields/ncit__synonym/theme/style_cp_synonym_field.css
+++ b/includes/TripalFields/ncit__synonym/theme/style_cp_synonym_field.css
@@ -5,12 +5,13 @@
 
 /* Term wrapper */
 #ap-field-crop_ontology_synonym {
-  background-color: #3A7f21;
+  background-color: #3A7F21;
   color: #FFFFFF;
   display: inline-block;
   font-family: sans-serif;
+  font-weight: 300;
   margin-right: 20px;
-  padding: 10px;
+  padding: 5px 7px;
 
   -webkit-border-radius: 5px;
   -moz-border-radius: 5px;

From 3f201146994567fd7b873600e82f0bbd5b8e7635 Mon Sep 17 00:00:00 2001
From: Reynold Tan <reynold@rain.baskt.bioinfo>
Date: Wed, 3 Jul 2019 14:19:19 -0600
Subject: [PATCH 7/8] Bug fix - undefined index when no crop ontology set

---
 .../TripalFields/ncit__synonym/ncit__synonym.inc    |  4 ++--
 .../ncit__synonym/ncit__synonym_widget.inc          | 13 ++++++-------
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym.inc b/includes/TripalFields/ncit__synonym/ncit__synonym.inc
index 999e606..fd5580d 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym.inc
@@ -177,8 +177,8 @@ class ncit__synonym extends ChadoField {
           // Nothing here, just forward what we know so far, Related term and the trait id.
           $entity->{$field_name}['und'][0] = array(
             'value' => array(),
-            'chado-' . $field_table . '__object_id' => $entity->chado_record_id,
-            'chado-' . $field_table . '__type_id' => $sysvar_related,
+            $field_table . 'object_id' => $entity->chado_record_id,
+            $field_table . 'type_id' => $sysvar_related,
           );
         }
       }
diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc b/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
index dd0e944..946ff97 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym_widget.inc
@@ -123,19 +123,18 @@ class ncit__synonym_widget extends TripalFieldWidget {
       drupal_add_css(drupal_get_path('module', 'analyzedphenotypes') . '/includes/TripalFields/ncit__synonym/theme/style_cp_synonym_field.css');
 
       // Current crop ontology.
-      list($term, $accession, $cv) = array_values($items[0]['value']);
-
-      if (empty($term)) {
-        $crop_ontology = 'Crop ontology not set | ';
-        $cvterm_lookup = '';
-      }
-      else {
+      if (count($items[0]['value']) > 0) {
+        @list($term, $accession, $cv) = array_values($items[0]['value']);
         // Refer to this ID for CSS styling.
         $id = 'ap-field-crop_ontology_synonym';
 
         $crop_ontology = '<div id="' . $id . '">' . $term . '</div> ';
         $cvterm_lookup = l('Vocabulary Details', 'cv/lookup/' .  $cv . '/' . $accession, array('attributes' => array('target' => '_blank'))) . ' | ';
       }
+      else {
+        $crop_ontology = 'Crop ontology not set | ';
+        $cvterm_lookup = '';
+      }
 
       // FIELDSET - Main fieldset - search ontology terms.
       $widget['ap_fieldset'] = array(

From f3d8b50f486793febcf38e509dbb5a4a54657921 Mon Sep 17 00:00:00 2001
From: Reynold Tan <reynold@rain.baskt.bioinfo>
Date: Wed, 3 Jul 2019 15:31:39 -0600
Subject: [PATCH 8/8] Added a check to see if term can be search in term lookup
 module before supplying a link to vocab details

---
 .../ncit__synonym/ncit__synonym_formatter.inc          | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc b/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
index 7be8301..50b6bb7 100644
--- a/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
+++ b/includes/TripalFields/ncit__synonym/ncit__synonym_formatter.inc
@@ -56,7 +56,15 @@ class ncit__synonym_formatter extends TripalFieldFormatter {
       $id = 'ap-field-crop_ontology_synonym';
 
       list($term, $accession, $cv) = array_values($items[0]['value']);
-      $cvterm_lookup = l('Vocabulary Details', 'cv/lookup/' .  $cv . '/' . $accession, array('attributes' => array('target' => '_blank')));
+
+      // If we can't find the term then do not provide the link as it will just cause a term not found
+      // in the term lookup module.
+      // @see tripal_vocabulary_lookup_term_page()
+      // Tripal.term_lookup.inc.
+      $lookterm = tripal_get_term_details($cv, $accession);
+
+      $cvterm_lookup = (!$lookterm) ? ''
+        : l('Vocabulary Details', 'cv/lookup/' .  $cv . '/' . $accession, array('attributes' => array('target' => '_blank')));
 
       $element[0] = array(
         '#type' => 'markup',