Forgot to commit the publish filee

tripal_chado/includes/tripal_chado.publish.inc

@@ -0,0 +1,174 @@
+<?php
+
+function tripal_chado_publish_form($form, &$form_state) {
+
+  $term_id = '';
+  if (array_key_exists('values', $form_state)) {
+    $term_id = $form_state['values']['term_id'];
+  }
+
+
+  $bundles = db_select('tripal_bundle', 'tb')
+    ->fields('tb')
+    ->orderBy('label', 'ASC')
+    ->execute();
+  $term_ids = array();
+  $term_ids[] = 'Select a Content Type';
+  while ($bundle = $bundles->fetchObject()) {
+    $term_ids[$bundle->term_id] = $bundle->label;
+  }
+
+  $form['term_id'] = array(
+    '#type' => 'select',
+    '#title' => 'Content Type',
+    '#description' => t('Select a content type to publish.  Only data that
+      is mapped to the selected vocabulary term will be published.'),
+    '#options' => $term_ids,
+    '#default_value' => $term_id,
+    '#ajax' => array(
+      'callback' => "tripal_chado_publish_form_ajax_callback",
+      'wrapper' => "tripal-chado-publish-form",
+      'effect' => 'fade',
+      'method' => 'replace'
+    ),
+  );
+
+  // If the user has selected a content type, then we need to
+  // show some filters.
+  if ($term_id) {
+    $form['filters'] = array(
+      '#type' => 'fieldset',
+      '#title' => 'Filters',
+      '#description' => t('Please provide any filters for limiting
+          the records. Only those that match the filters specified
+          below will be published.  To publish all records of this
+          type, leave all filters blank.'),
+      '#collapsed' => TRUE,
+      '#collapsible' => TRUE,
+    );
+
+    // Get the form for this bundle (content type).  Then iterate through
+    // the fields and include only those that are Chado fields.
+/*     $bundle_name = 'bio-data_' . $term_id;
+    $entity = entity_get_controller('TripalEntity')->create(array('bundle' => $bundle_name, 'term_id' => $term_id));
+    field_attach_form('TripalEntity', $entity, $form['filters'], $form_state);
+    foreach (element_children($form['filters']) as $field_name) {
+      $field = field_info_field($field_name);
+      if ($field and $field['storage']['type'] != 'field_chado_storage') {
+        unset($form['filters'][$field_name]);
+      }
+      // Ignore the KVPoperty field as this is just a field to
+      // allow the user to add new properties which isn't appropriate
+      // here.
+      if ($field['type'] == 'kvproperty_adder') {
+        unset($form['filters'][$field_name]);
+      }
+      // None of the fields should be required.
+
+      dpm($form['filters'][$field_name]);
+    } */
+
+    $form['publish_btn'] = array(
+      '#type' => 'submit',
+      '#name' => 'publish_btn',
+      '#value' => 'Publish',
+    );
+  }
+
+
+  $form['#prefix'] = '<div id="tripal-chado-publish-form">';
+  $form['#suffix'] = '</div>';
+  return $form;
+}
+
+function tripal_chado_publish_form_validate($form, &$form_state) {
+
+}
+
+function tripal_chado_publish_form_submit($form, &$form_state) {
+  if ($form_state['clicked_button']['#name'] == 'publish_btn') {
+    global $user;
+
+    $term_id = $form_state['values']['term_id'];
+    $bundle_name = 'bio-data_' . $term_id;
+    $bundle = tripal_load_bundle_entity(array('name' => $bundle_name));
+    $args = array($bundle_name);
+    $includes = array(
+      module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.publish'),
+    );
+    return tripal_add_job("Publish " . $bundle->label . " records.",
+      'tripal_chado', 'tripal_chado_publish_records', $args,
+      $user->uid, 10, $includes);
+  }
+}
+/**
+ *
+ */
+function tripal_chado_publish_form_ajax_callback($form, $form_state) {
+  return $form;
+}
+
+/**
+ *
+ */
+function tripal_chado_publish_records($bundle_name, $job_id = NULL) {
+  $bundle = tripal_load_bundle_entity(array('name' => $bundle_name));
+  $bundle_id = $bundle->id;
+  $table = tripal_get_bundle_variable('chado_table', $bundle_id);
+  $column = tripal_get_bundle_variable('chado_column', $bundle_id);
+  $cvterm_id = tripal_get_bundle_variable('chado_cvterm_id', $bundle_id);
+
+  // Get the table information
+  $table_schema = chado_get_schema($table);
+  $pkey_field = $table_schema['primary key'][0];
+
+  $where = '';
+  if ($table != 'analysis' and $table != 'organism') {
+    $where .= "AND $column = $cvterm_id";
+  }
+
+  $sql = "
+    SELECT $pkey_field as record_id
+    FROM {" . $table . "} T
+    LEFT JOIN public.chado_entity CE on CE.record_id = T.$pkey_field
+    AND CE.data_table = '$table'
+    WHERE CE.record_id IS NUll $where
+  ";
+  $records = chado_query($sql);
+  $num_published = 0;
+  try {
+    while($record = $records->fetchObject()) {
+
+      $record_id = $record->record_id;
+      $ec = entity_get_controller('TripalEntity');
+      $entity = $ec->create(array(
+        'bundle' => $bundle_name,
+        'term_id' => $bundle->term_id,
+      ));
+      $entity->save();
+
+      $record = array(
+        'entity_id' => $entity->id,
+        'record_id' => $record_id,
+        'data_table' => $table,
+        'type_table' => $table,
+        'field' => $column,
+      );
+      $success = drupal_write_record('chado_entity', $record);
+
+      $entity = entity_load('TripalEntity', array($entity->id));
+      $entity = reset($entity);
+      $title_format = tripal_get_title_format($bundle);
+      $title = tripal_replace_tokens($title_format, $entity, $bundle);
+      $ec->setTitle($entity, $title);
+      $num_published++;
+    }
+  }
+  catch (Exception $e) {
+    $error = $e->getMessage();
+    tripal_report_error('tripal_chado', TRIPAL_ERROR, "Could not publish record: @error", array('@error' => $error));
+    drupal_set_message('Failed publishing record. See recent logs for more details.', 'error');
+    return FALSE;
+  }
+  drupal_set_message("Succesfully published $num_published " . $bundle->label . " record(s).");
+}