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@@ -0,0 +1,212 @@
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+<?php
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+
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+/**
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+ *
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+ */
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+function tripal_organism_sync () {
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+ $form = array();
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+
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+ get_tripal_organism_admin_form_sync_set($form);
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+ get_tripal_organism_admin_form_cleanup_set($form);
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+
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+ return $form;
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+}
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+
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+/**
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+ *
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+ *
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+ * @ingroup tripal_organism
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+ */
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+function get_tripal_organism_admin_form_cleanup_set(&$form) {
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+ $form['cleanup'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => t('Clean Up'),
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+ '#description' => t("With Drupal and chado residing in different databases or database schemas " .
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+ "it is possible that nodes in Drupal and organisms in Chado become " .
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+ "\"orphaned\". This can occur if an organism node in Drupal is " .
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+ "deleted but the corresponding chado organism is not and/or vice " .
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+ "versa. Click the button below to resolve these discrepancies."),
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+ );
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+ $form['cleanup']['button'] = array(
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+ '#type' => 'submit',
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+ '#value' => t('Clean up orphaned organisms'),
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+ );
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+}
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+/**
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+ *
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+ * @ingroup tripal_organism
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+ */
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+function get_tripal_organism_admin_form_sync_set(&$form) {
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+ // define the fieldsets
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+ $form['sync'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => t('Sync Organisms')
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+ );
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+
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+ // get the list of organisms
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+ $sql = "SELECT * FROM {Organism} ORDER BY genus,species";
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+ $org_rset = chado_query($sql);
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+
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+ // if we've added any organisms to the list that can be synced
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+ // then we want to build the form components to allow the user
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+ // to select one or all of them. Otherwise, just present
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+ // a message stating that all organisms are currently synced.
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+ $org_boxes = array();
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+ $added = 0;
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+ foreach ($org_rset as $organism) {
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+ // check to see if the organism is already present as a node in drupal.
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+ // if so, then skip it.
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+ $sql = "SELECT * FROM {chado_organism} WHERE organism_id = :organism_id";
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+ if (!db_query($sql, array(':organism_id' => $organism->organism_id))->fetchObject()) {
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+ $org_boxes[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
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+ $added++;
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+ }
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+ }
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+
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+ // if we have organisms we need to add to the checkbox then
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+ // build that form element
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+ if ($added > 0) {
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+ $org_boxes['all'] = "All Organisms";
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+
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+ $form['sync']['organisms'] = array(
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+ '#title' => t('Available Organisms'),
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+ '#type' => t('checkboxes'),
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+ '#description' => t("Check the organisms you want to sync. Drupal content will be created for each of the organisms listed above. Select 'All Organisms' to sync all of them."),
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+ '#required' => FALSE,
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+ '#prefix' => '<div id="org_boxes">',
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+ '#suffix' => '</div>',
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+ '#options' => $org_boxes,
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+ );
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+ $form['sync']['button'] = array(
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+ '#type' => 'submit',
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+ '#value' => t('Submit Sync Job')
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+ );
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+ }
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+ // we don't have any organisms to select from
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+ else {
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+ $form['sync']['value'] = array(
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+ '#markup' => t('All organisms in Chado are currently synced with Drupal.')
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+ );
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+ }
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+}
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+
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+/**
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+ *
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+ * @ingroup tripal_organism
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+ */
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+function tripal_organism_sync_submit($form, &$form_state) {
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+ global $user; // we need access to the user info
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+ $job_args = array();
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+
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+ if ($form_state['values']['op'] == t('Submit Sync Job')) {
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+
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+ // check to see if the user wants to sync chado and drupal. If
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+ // so then we need to register a job to do so with tripal
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+ $organisms = $form_state['values']['organisms'];
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+ $do_all = FALSE;
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+ $to_sync = array();
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+
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+ foreach ($organisms as $organism_id) {
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+ if (preg_match("/^all$/i" , $organism_id)) {
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+ $do_all = TRUE;
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+ }
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+ if ($organism_id and preg_match("/^\d+$/i" , $organism_id)) {
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+ // get the list of organisms
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+ $sql = "SELECT * FROM {organism} WHERE organism_id = :organism_id";
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+ $organism = chado_query($sql, array(':organism_id' => $organism_id))->fetchObject();
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+ $to_sync[$organism_id] = "$organism->genus $organism->species";
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+ }
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+ }
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+
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+ // submit the job the tripal job manager
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+ if ($do_all) {
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+ tripal_add_job('Sync all organisms' , 'tripal_organism',
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+ 'tripal_organism_sync_organisms' , $job_args , $user->uid);
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+ }
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+ else{
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+ foreach ($to_sync as $organism_id => $name) {
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+ $job_args[0] = $organism_id;
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+ tripal_add_job("Sync organism: $name" , 'tripal_organism',
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+ 'tripal_organism_sync_organisms' , $job_args , $user->uid);
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+ }
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+ }
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+ }
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+
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+ // -------------------------------------
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+ // Submit the Cleanup Job if selected
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+ if ($form_state['values']['op'] == t('Clean up orphaned organisms')) {
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+ tripal_add_job('Cleanup orphaned organisms', 'tripal_organism',
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+ 'tripal_organism_cleanup', $job_args, $user->uid);
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+ }
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+}
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+/**
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+ * Synchronize organisms from chado to drupal
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+ *
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+ * @ingroup tripal_organism
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+ */
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+function tripal_organism_sync_organisms($organism_id = NULL, $job_id = NULL) {
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+ global $user;
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+ $page_content = '';
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+
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+ if (!$organism_id) {
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+ $sql = "SELECT * FROM {Organism} O";
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+ $results = chado_query($sql);
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+ }
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+ else {
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+ $sql = "SELECT * FROM {organism} WHERE organism_id = :organism_id";
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+ $results = chado_query($sql, array(':organism_id' => $organism_id));
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+ }
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+
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+ // We'll use the following SQL statement for checking if the organism
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+ // already exists as a drupal node.
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+ $sql = "SELECT * FROM {chado_organism} " .
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+ "WHERE organism_id = :organism_id";
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+
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+ foreach ($results as $organism) {
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+
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+ // check if this organism already exists in the drupal database. if it
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+ // does then skip this organism and go to the next one.
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+ if (!db_query($sql, array(':organism_id' => $organism->organism_id))->fetchObject()) {
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+
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+ $new_node = new stdClass();
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+ $new_node->type = 'chado_organism';
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+ $new_node->uid = $user->uid;
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+ $new_node->title = "$organism->genus $organism->species";
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+ $new_node->organism_id = $organism->organism_id;
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+ $new_node->genus = $organism->genus;
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+ $new_node->species = $organism->species;
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+ $new_node->description = '';
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+ $form = array(); // dummy variable
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+ $form_state = array(); // dummy variable
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+ node_validate($new_node, $form, $form_state);
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+ if (!form_get_errors()) {
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+ $node = node_submit($new_node);
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+ node_save($node);
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+ if ($node->nid) {
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+ print "Added $organism->common_name\n";
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+ }
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+ }
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+ else {
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+ print "Failed to insert organism $organism->common_name\n";
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+ }
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+ }
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+ else {
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+ print "Skipped $organism->common_name\n";
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+ }
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+ }
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+ return $page_content;
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+}
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+/**
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+ * Remove orphaned drupal nodes
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+ *
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+ * @param $dummy
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+ * Not Used -kept for backwards compatibility
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+ * @param $job_id
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+ * The id of the tripal job executing this function
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+ *
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+ * @ingroup tripal_organism
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+ */
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+function tripal_organism_cleanup($dummy = NULL, $job_id = NULL) {
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+
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+ return tripal_core_clean_orphaned_nodes('organism', $job_id);
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+}
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Stephen Ficklin