Added administrative interface for migrating Tripal v2 content.

tripal/api/tripal.entities.api.inc

@@ -2,9 +2,9 @@
 
 function tripal_chado_migrate_form($form, &$form_state) {
 
-  $content_type = 'all';
+  $chado_content = 'all';
   if (array_key_exists('values', $form_state)) {
-    $content_type = $form_state['values']['content_type'];
+    $chado_content = $form_state['values']['chado_content'];
   }
     
   // Get all available Tripal v2 chado tables
@@ -27,12 +27,12 @@ function tripal_chado_migrate_form($form, &$form_state) {
     }
   }
   
-  $form['content_type'] = array(
+  $form['chado_content'] = array(
     '#type' => 'select',
-    '#title' => 'Content Type',
-    '#description' => t('Select the content type to migrate.'),
+    '#title' => 'Chado Content',
+    '#description' => t('Select the chado content to migrate.'),
     '#options' => $options,
-    '#default_value' => $content_type,
+    '#default_value' => $chado_content,
     '#ajax' => array(
       'callback' => "tripal_chado_migrate_form_ajax_callback",
       'wrapper' => "tripal-chado-migrate-form",
@@ -41,10 +41,65 @@ function tripal_chado_migrate_form($form, &$form_state) {
     ),
   );
   
+  // Add a review button that allows reviewing migratable content types
+  if ($chado_content != 'all') {
+    $form['review'] = array(
+      '#type' => 'fieldset',
+      '#title' => 'Review Content Type',
+      '#description' => 'By clicking on the Review button, Tripal will gather information from
+      existing database and list content types which can be mapped to a Tripal v3 content 
+      type. (may take a while depending on the size of your database.). This allows you 
+      to migrate only the types of your selection.'
+    );
+    $form['review']['review_btn'] = array(
+      '#type' => 'button',
+      '#name' => 'review_btn',
+      '#value' => "Review",
+      '#ajax' => array(
+        'callback' => "tripal_chado_migrate_form_ajax_callback",
+        'wrapper' => "tripal-chado-migrate-form",
+        'effect' => 'fade',
+        'method' => 'replace'
+      ),
+    );
+    if ($form_state['clicked_button']['#name'] == 'review_btn') {
+      // Get all Tripal v2 node types from the chad_* linking table
+        $table = str_replace('chado_', '', $chado_content);
+        $schema = chado_get_schema($table);
+        $pkey = $schema['primary key'][0];
+        $fkeys = $schema['foreign keys'];
+        $counter = 0;
+        if (key_exists('cvterm', $fkeys) && key_exists('type_id', $fkeys['cvterm']['columns'])) {
+          $sql = 
+            "SELECT DISTINCT V.name AS type, X.accession, db.name AS namespace 
+                FROM chado.$table T
+                INNER JOIN $chado_content CT ON T.$pkey = CT.$pkey
+                INNER JOIN chado.cvterm V ON V.cvterm_id = T.type_id
+                INNER JOIN chado.dbxref X ON X.dbxref_id = V.dbxref_id
+                INNER JOIN chado.db ON db.db_id = X.db_id";
+        $subtypes = db_query($sql);
+         while($subtype = $subtypes->fetchObject()) {
+          $form['review']['chado_content_type--' . $subtype->namespace . '--' . $subtype->type] = array(
+            '#type' => 'checkbox',
+            '#title' => $subtype->type,
+          );
+          $counter ++;
+        }
+      }
+      // No subtype exists, migrate all
+      if ($counter == 0) {
+        $form['review']['nosubtype'] = array(
+          '#markup' => t("<br>Type not found. Migrate all $options[$chado_content]."),
+        );
+      }
+    }
+  }
+  
+  // Submit button
   $form['migrate_btn'] = array(
     '#type' => 'submit',
     '#name' => 'migrate_btn',
-    '#value' => "Migrate $options[$content_type] Content Type",
+    '#value' => "Migrate $options[$chado_content]",
   );
 
   $form['#prefix'] = '<div id="tripal-chado-migrate-form">';
@@ -60,26 +115,28 @@ function tripal_chado_migrate_form_submit($form, &$form_state) {
   if ($form_state['clicked_button']['#name'] == 'migrate_btn') {
     global $user;
     $values = $form_state['values'];
-    $all = $form_state['values']['all'];
-    $migration = array();
+    $chado_contents = $form_state['values']['chado_content'];
+    $subtypes = array();
     foreach ($values AS $key => $value) {
-      if ($all) {
-        if (preg_match('/^chado_/', $key)) {
-          array_push($migration, $key);
-        }
-      } else {
-        if (preg_match('/^chado_/', $key) && $value) {
-          array_push($migration, $key);
+      if ($chado_contents != 'all') {
+        if (preg_match('/^chado_content_type--(.+)--(.+)/', $key, $matches) && $value == 1) {
+          $namespace = $matches[1];
+          $accession = $matches[2];          
+          $subtypes [$namespace] = $accession;
         }
       }
     }
     
     // Submit a job to migrate content
-    dpm($migration);
-    /* $term_id = $form_state['values']['term_id'];
-    $bundle_name = 'bio-data_' . $term_id;
-    $bundle = tripal_load_bundle_entity(array('name' => $bundle_name)); */
-
+    global $user;
+    $args = array(
+      array(
+        'chado_content' => $chado_contents,
+        'subtypes' => $subtypes
+      ),
+    );
+    $includes = array();
+    return tripal_add_job("Migrate $chado_contents.", 'tripal_chado', 'tripal_chado_migrate_records', $args, $user->uid, 10, $includes);
   }
 }
 /**