Working on showing remote content within the layout on this site

tripal_chado/includes/fields/chado_base__organism_id.inc

@@ -178,7 +178,7 @@ class chado_base__organism_id extends TripalField {
       $field, $instance, $langcode, $items, $display) {
 
     if (count($items) > 0) {
-      $content =  $items[0]['value'];
+      $content = $items[0]['value']['label'];
       if (array_key_exists('entity', $items[0]['value'])) {
         list($entity_type, $entity_id) = explode(':', $items[0]['value']['entity']);
         $content = l(strip_tags($items[0]['value']['label']), 'bio_data/' . $entity_id);

tripal_chado/includes/fields/chado_feature__residues.inc

@@ -155,7 +155,6 @@ class chado_feature__residues extends TripalField {
     );
 
     $num_bases = 50;
-    $feature = $entity->chado_record;
     foreach ($items as $delta => $item) {
       // If there are no residues then skip this one.
       if (!is_array($item['value']) or !array_key_exists('residues', $item['value'])) {

tripal_chado/includes/fields/chado_gene__transcripts.inc

@@ -174,7 +174,6 @@ class chado_gene__transcripts extends TripalField {
 
     // Get the settings
     $settings = $display['settings'];
-    $record = $entity->chado_record;
 
     $headers = array('Transcript Name', 'Identifier', 'Type', 'Location');
     $rows = array();

tripal_chado/includes/fields/chado_linker__contact.inc

@@ -80,7 +80,7 @@ class chado_linker__contact extends TripalField {
       ),
       'settings' => array(
         'chado_table' => $contact_table,
-        'chado_column' => $pkey,
+        'chado_column' => 'contact_id',
         'base_table' => $table_name,
         'semantic_web' => 'local:contact'
       ),
@@ -162,7 +162,6 @@ class chado_linker__contact extends TripalField {
       $field, $instance, $langcode, $items, $display) {
     // Get the settings
     $settings = $display['settings'];
-    $record = $entity->chado_record;
 
     $headers = array('Name', 'Description', 'Type');
     $rows = array();

tripal_chado/includes/fields/chado_linker__expression.inc

@@ -157,7 +157,6 @@ class chado_linker__expression extends TripalField {
 
     // Get the settings
     $settings = $display['settings'];
-    $record = $entity->chado_record;
 
     $content = '';
     $rows = array();

tripal_chado/includes/fields/chado_linker__genotype.inc

@@ -156,7 +156,6 @@ class chado_linker__genotype extends TripalField {
 
     // Get the settings
     $settings = $display['settings'];
-    $record = $entity->chado_record;
 
     $headers = array('Name', 'Description', 'Type');
     $rows = array();

tripal_chado/includes/fields/chado_linker__phenotype.inc

@@ -156,7 +156,6 @@ class chado_linker__phenotype extends TripalField {
       $field, $instance, $langcode, $items, $display) {
     // Get the settings
     $settings = $display['settings'];
-    $record = $entity->chado_record;
 
     $headers = array('Name', 'Value', 'Type');
     $rows = array();

tripal_chado/includes/tripal_chado.field_storage.inc

@@ -405,20 +405,6 @@ function tripal_chado_field_storage_expand_field($item_name, $value) {
      return array($item_name => $value);
    }
 }
-
-/**
- * Implements hook_field_storage_query().
- *
- * Used by EntityFieldQuery to find the entities having certain field values.
- *
- * We do not support use of the EntityFieldQuery API for Tripal based fields
- * because EFQ doesn't support when multiple storage backends are used. Instead
- * use the TripalFieldQuery class and implement the hook_storage_tquery()
- * function.
- */
-function tripal_chado_field_storage_query($query) {
-
-}
 /**
  * Implements hook_field_storage_tquery().
  *
@@ -446,6 +432,7 @@ function tripal_chado_field_storage_tquery($conditions) {
     // Set the value for this field search.
     $value = NULL;
     $subfields = explode('.', $filter);
+    print_r($subfields);
     if (count($subfields) > 1) {
       // Get the term for this field's column and replace the field_name with
       // the term.  We need to do this for the recursive function to work.
@@ -461,6 +448,7 @@ function tripal_chado_field_storage_tquery($conditions) {
       $value = $condition['value'];
     }
 
+
     // Use the appropriate operator.
     $operator = $condition['operator'];
     switch ($operator) {
@@ -503,6 +491,8 @@ function tripal_chado_field_storage_tquery($conditions) {
   // Iterate through the filters and perform the query
   $entity_ids = array();
   foreach ($filters as $chado_table => $values) {
+    print_r($chado_table);
+    print_r($values);
     // First get the matching record IDs from the Chado table.
     $schema = chado_get_schema($chado_table);
     $pkey = $schema['primary key'][0];

tripal_ws/includes/tripal_ws.admin.inc

@@ -1,7 +1,7 @@
 <?php
 /**
  * Provide form to store information of other Tripal sites
- * 
+ *
  * @param unknown $form
  * @param unknown $form_state
  */
@@ -10,8 +10,8 @@ function tripal_ws_tripal_sites_form($form, &$form_state) {
   $form = array();
   $values = key_exists('values', $form_state) ? $form_state['values'] : NULL;
   $tripal_site = $values ? $values['tripal_site'] : 0;
-  
-  $results = 
+
+  $results =
     db_select('tripal_sites', 'ts')
       ->fields('ts')
       ->execute();
@@ -33,14 +33,27 @@ function tripal_ws_tripal_sites_form($form, &$form_state) {
   if (count($rows) == 0) {
     $rows[] = array('No configured Tripal site.', array('colspan' => 5));
   }
-  $output = theme('table', array(
-      'header' => $headers,
-      'rows' => $rows,
-    ));
-    $form['table'] = array(
-      '#markup' => $output
-    );
-  
+
+  $table = array(
+    'header' => $headers,
+    'rows' => $rows,
+    'attributes' => array(),
+    'sticky' => FALSE,
+    'caption' => '',
+    'colgroups' => array(),
+    'empty' => '',
+  );
+  $output = theme_table($table);
+
+  $form['instructions'] = array(
+    '#type' => 'item',
+    '#markup' => t('The following is a list of remote Tripal sites with which
+        this site can communicate. You may add and remove site as needed.')
+  );
+  $form['table'] = array(
+    '#markup' => $output
+  );
+
   return $form;
 }
 
@@ -112,7 +125,7 @@ function tripal_ws_tripal_sites_edit_form($form, &$form_state, $tripal_site_id =
     '#name' => 'cancel_button',
     '#limit_validation_errors' => array()
   );
-  
+
   return $form;
 }
 
@@ -283,6 +296,6 @@ function tripal_ws_tripal_sites_remove_form_submit($form, &$form_state) {
       ->condition('id', $id)
       ->execute();
     drupal_set_message('The Tripal site \'' .$name . '\' has been removed.');
-  }    
+  }
   drupal_goto('/admin/tripal/storage/ws/tripal_sites');
 }

tripal_ws/tripal_ws.install

@@ -53,7 +53,10 @@ function tripal_ws_tripal_sites_schema() {
       'url' => array('url'),
       'description' => array('description'),
     ),
-    'unique keys' => array('url' => array('url')),
+    'unique keys' => array(
+      'tripal_sites_c1' => array('url', 'version'),
+      'tripal_sites_c2' => array('name')
+    ),
     'primary key' => array('id'),
   );
   return $schema;

tripal_ws/tripal_ws.module

@@ -36,10 +36,17 @@ function tripal_ws_menu() {
     'type' => MENU_CALLBACK,
   );
 
+  $items['remote/%/%/%/%'] = array(
+    'page callback' => 'tripal_ws_load_remote_entity',
+    'page arguments' => array(1, 2, 3, 4),
+    'access arguments' => array('access content'),
+    'type' => MENU_CALLBACK,
+  );
+
   // Tripal Web Services setting groups
   $items['admin/tripal/storage/ws'] = array(
-    'title' => 'Web Services',
-    'description' => t("Import data from other Tripal sites using the web services."),
+    'title' => 'Remote Tripal Sites',
+    'description' => t("Create mashups of content using data from this site and remote Tripal sites."),
     'weight' => 20,
     'page callback' => 'system_admin_menu_block_page',
     'access arguments' => array('administer tripal'),
@@ -47,7 +54,7 @@ function tripal_ws_menu() {
     'file path' => drupal_get_path('module', 'system'),
   );
   $items['admin/tripal/storage/ws/tripal_sites'] = array(
-    'title' => 'Other Tripal Sites',
+    'title' => 'Configuration',
     'description' => t('Provides information about other Tripal sites.
         This allows data exchange and communication betwen Tripal
         enabled sites through the web services.'),
@@ -118,4 +125,71 @@ function tripal_ws_services() {
 
   drupal_add_http_header('Content-Type', 'application/ld+json');
   print drupal_json_encode($response);
+}
+
+function tripal_ws_entity_load($entities, $type) {
+  foreach ($entities as $entity) {
+    //if ($entiy->type = 'TripalEntity') {
+      dpm($entity);
+    //}
+  }
+}
+
+function tripal_ws_load_remote_entity($site_id, $api_version, $ctype, $id) {
+
+  // Get the content from the web services of the remote site.
+  $url = "https://dev.bioinfo.wsu.edu/~ccheng/tripal3/ws/v0.1/content/gene/12";
+  $json = file_get_contents($url);
+  $response = json_decode($json, TRUE);
+  dpm($response);
+
+  // Set the title for this page to match the title provided.
+  drupal_set_title($response['label']);
+
+  // Attribute this data to the proper source.
+  $source_url = l($response['label'], $response['itemPage'], array('attributes' => array('target' => '_blank')));
+  $content = '<div><strong>Source:</strong> Chun-huai\'s amazing test site: ' . $source_url . '</div>';
+
+  // Fake an entity so we can display this content using the same
+  // entity type on this site.
+  $entity = new TripalEntity(array(), 'TripalEntity');
+  $entity->id = 807;
+  $entity->type = 'TripalEntity';
+  $entity->bundle = 'bio_data_266';
+  $entity->term_id = 266;
+  $entity->title = $response['label'];
+  $entity->uid = 1;
+  $entity->status = 1;
+
+  // Add fields.
+  $entity->feature__name = array(
+    'und' => array(
+      0 => array(
+        'value' => $response['name'],
+      ),
+    ),
+  );
+  $entity->feature__organism_id = array(
+    'und' => array(
+      0 => array(
+        'value' => $response['organism'],
+      ),
+    ),
+  );
+  $sequences_json = file_get_contents($response['sequence']);
+  $sequences = json_decode($sequences_json, TRUE);
+  $entity->feature__residues = array();
+  foreach ($sequences['member'] as $delta => $value) {
+    $entity->feature__residues['und'][$delta]['value'] = $sequences['member'][$delta];
+  }
+  dpm($entity);
+
+  // Generate the View for this entity
+  $entities = array();
+  $entities[] = $entity;
+  $view = entity_view('TripalEntity', $entities);
+  $content .= drupal_render($view['TripalEntity'][807]);
+
+  return $content;
+
 }