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@@ -4,6 +4,10 @@
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* Management of importers
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*/
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+require_once('tripal_chado.pub_importer_AGL.inc');
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+require_once('tripal_chado.pub_importer_PMID.inc');
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+
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+
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/**
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* A function to generate a table containing the list of publication importers
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*
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@@ -13,7 +17,7 @@ function tripal_pub_importers_list() {
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// clear out the session variable when we view the list.
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unset($_SESSION['tripal_pub_import']);
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- $header = array('', 'Importer Name', 'Database', 'Search String', 'Disabled', 'Create Contact', '');
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+ $headers = array('', 'Importer Name', 'Database', 'Search String', 'Disabled', 'Create Contact', '');
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$rows = array();
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$importers = db_query("SELECT * FROM {tripal_pub_import} ORDER BY name");
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@@ -31,8 +35,8 @@ function tripal_pub_importers_list() {
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$rows[] = array(
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array(
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- 'data' => l(t('Edit/Test'), "admin/tripal/chado/tripal_pub/import/edit/$importer->pub_import_id") . '<br>' .
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- l(t('Import Pubs'), "admin/tripal/chado/tripal_pub/import/submit/$importer->pub_import_id"),
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+ 'data' => l(t('Edit/Test'), "admin/tripal/storage/chado/loaders/pub/edit/$importer->pub_import_id") . '<br>' .
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+ l(t('Import Pubs'), "admin/tripal/storage/chado/loaders/pub/submit/$importer->pub_import_id"),
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'nowrap' => 'nowrap'
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),
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$importer->name,
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@@ -40,13 +44,13 @@ function tripal_pub_importers_list() {
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$criteria_str,
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$importer->disabled ? 'Yes' : 'No',
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$importer->do_contact ? 'Yes' : 'No',
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- l(t('Delete'), "admin/tripal/chado/tripal_pub/import/delete/$importer->pub_import_id"),
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+ l(t('Delete'), "admin/tripal/storage/chado/loaders/pub/delete/$importer->pub_import_id"),
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);
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}
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$page = "<ul class='action-links'>";
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- $page .= ' <li>' . l('New Importer', 'admin/tripal/chado/tripal_pub/import/new') . '</li>';
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+ $page .= ' <li>' . l('New Importer', 'admin/tripal/storage/chado/loaders/pub/new') . '</li>';
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$page .= '</ul>';
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$page .= '<p>' . t(
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@@ -64,7 +68,19 @@ function tripal_pub_importers_list() {
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set the importers to run automatically.") . '</li>
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</ol><br>';
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- $page .= theme('table', array('header' => $header, 'rows' => $rows));
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+
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+ $table = array(
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+ 'header' => $headers,
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+ 'rows' => $rows,
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+ 'attributes' => array(
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+ ),
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+ 'caption' => '',
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+ 'sticky' => TRUE,
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+ 'colgroups' => array(),
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+ 'empty' => 'There are currently importers',
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+ );
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+
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+ $page .= theme_table($table);
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return $page;
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}
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@@ -105,7 +121,7 @@ function tripal_pub_importer_setup_page($action = 'new', $pub_import_id = NULL)
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// generate the search form
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$form = drupal_get_form('tripal_pub_importer_setup_form', $pub_import_id, $action);
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- $output = l("Return to publication importers list", "admin/tripal/chado/tripal_pub/import_list");
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+ $output = l("Return to publication importers list", "admin/tripal/storage/chado/loaders/pub");
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$output .= drupal_render($form);
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// retrieve any results
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@@ -145,7 +161,7 @@ function tripal_pub_importer_setup_page($action = 'new', $pub_import_id = NULL)
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$citation = htmlspecialchars($pub['Citation']);
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$raw_link = '';
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if($pub['Publication Dbxref']) {
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- $raw_link = l('raw', 'admin/tripal/chado/tripal_pub/import/raw/' . $pub['Publication Dbxref'], array('attributes' => array('target' => '_blank')));
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+ $raw_link = l('raw', 'admin/tripal/storage/chado/loaders/pub/raw/' . $pub['Publication Dbxref'], array('attributes' => array('target' => '_blank')));
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}
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$rows[] = array(
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number_format($i),
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@@ -308,8 +324,6 @@ function tripal_pub_importer_setup_form($form, &$form_state = NULL, $pub_import_
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$num_criteria--;
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}
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-
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-
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// set the values we need for later but that should not be shown on the form
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$form['num_criteria']= array(
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'#type' => 'value',
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@@ -333,7 +347,7 @@ function tripal_pub_importer_setup_form($form, &$form_state = NULL, $pub_import_
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'#required' => TRUE,
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);
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- $supported_dbs = variable_get('tripal_pub_supported_dbs', array());
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+ $supported_dbs = variable_get('tripal_pub_supported_dbs', array('PMID'));
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$remote_dbs = array();
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$values = array(
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'name' => $supported_dbs,
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@@ -693,7 +707,7 @@ function tripal_pub_importer_setup_form_submit($form, &$form_state) {
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if(drupal_write_record('tripal_pub_import', $record, 'pub_import_id')){
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unset($_SESSION['tripal_pub_import']);
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drupal_set_message('Publication import settings updated.');
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- drupal_goto('admin/tripal/chado/tripal_pub/import_list');
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+ drupal_goto('admin/tripal/storage/chado/loaders/pub');
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}
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else {
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drupal_set_message('Could not update publication import settings.', 'error');
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@@ -709,7 +723,7 @@ function tripal_pub_importer_setup_form_submit($form, &$form_state) {
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if ($form_state['values']['op'] == 'Save & Import Now') {
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tripal_execute_pub_importer($record['pub_import_id']);
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}
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- drupal_goto('admin/tripal/chado/tripal_pub/import_list');
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+ drupal_goto('admin/tripal/storage/chado/loaders/pub');
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}
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else {
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drupal_set_message('Could not save publication import settings.', 'error');
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@@ -721,7 +735,7 @@ function tripal_pub_importer_setup_form_submit($form, &$form_state) {
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$success = db_query($sql, array(':pub_import_id' => $pub_import_id));
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if ($success) {
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drupal_set_message('Publication importer deleted.');
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- drupal_goto('admin/tripal/chado/tripal_pub/import_list');
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+ drupal_goto('admin/tripal/storage/chado/loaders/pub');
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}
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else {
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drupal_set_message('Could not delete publication importer.', 'error');
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@@ -807,19 +821,37 @@ function theme_tripal_pub_importer_setup_form_elements($variables) {
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*/
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function tripal_pub_importer_submit_job($import_id) {
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global $user;
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-
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// get all of the loaders
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$args = array(':import_id' => $import_id);
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$sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = :import_id ";
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$import = db_query($sql, $args)->fetchObject();
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$args = array($import_id);
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- tripal_add_job("Import publications $import->name", 'tripal_pub',
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- 'tripal_execute_pub_importer', $args, $user->uid);
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+ $includes = array();
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+ $includes[] = module_load_include('inc', 'tripal_chado', 'includes/loaders/tripal_chado.pub_importers');
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+ tripal_add_job("Import publications $import->name", 'tripal_chado',
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+ 'tripal_execute_pub_importer', $args, $user->uid, 10, $includes);
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- drupal_goto('admin/tripal/chado/tripal_pub/import_list');
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+ drupal_goto('admin/tripal/storage/chado/loaders/pub');
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}
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+/**
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+ * Deletes a publication importer.
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+ *
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+ */
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+function tripal_pub_importer_delete($import_id) {
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+ $args = array(':import_id' => $import_id);
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+ $sql = "DELETE FROM {tripal_pub_import} WHERE pub_import_id = :import_id";
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+ $success = db_query($sql, $args);
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+
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+ if ($success) {
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+ drupal_set_message('Publication importer deleted.');
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+ drupal_goto('admin/tripal/storage/chado/loaders/pub');
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+ }
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+ else {
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+ drupal_set_message('Could not delete publication importer.', 'error');
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+ }
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+}
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/**
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* Adds publications that have been retrieved from a remote database and
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* consolidated into an array of details.
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@@ -1424,103 +1456,7 @@ function tripal_pub_get_publication_array($pub_id, $skip_existing = TRUE) {
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return $pub_array;
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}
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-/**
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- * Imports all publications for all active import setups.
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- *
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- * @param $report_email
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- * A list of email address, separated by commas, that should be notified
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- * once importing has completed
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- * @param $do_update
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- * If set to TRUE then publications that already exist in the Chado database
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- * will be updated, whereas if FALSE only new publications will be added
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- *
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- * @ingroup tripal_pub
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- */
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-function tripal_execute_active_pub_importers($report_email = FALSE, $do_update = FALSE) {
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- $num_to_retrieve = 100;
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- $page = 0;
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-
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- print "\nNOTE: Loading of publications is performed using a database transaction. \n" .
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- "If the load fails or is terminated prematurely then the entire set of \n" .
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- "insertions/updates is rolled back and will not be found in the database\n\n";
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- // start the transaction
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- $transaction = db_transaction();
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-
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- try {
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- // get all of the loaders
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- $args = array();
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- $sql = "SELECT * FROM {tripal_pub_import} WHERE disabled = 0 ";
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- $results = db_query($sql, $args);
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- $do_contact = FALSE;
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- $reports = array();
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- foreach ($results as $import) {
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- $page = 0;
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- print "Executing importer: '" . $import->name . "'\n";
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- // keep track if any of the importers want to create contacts from authors
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- if ($import->do_contact == 1) {
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- $do_contact = TRUE;
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- }
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- $criteria = unserialize($import->criteria);
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- $remote_db = $criteria['remote_db'];
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- do {
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- // retrieve the pubs for this page. We'll retreive 100 at a time
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- $results = tripal_get_remote_pubs($remote_db, $criteria, $num_to_retrieve, $page);
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- $pubs = $results['pubs'];
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- $reports[$import->name] = tripal_pub_add_publications($pubs, $import->do_contact, $do_update);
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- $page++;
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- }
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- // continue looping until we have a $pubs array that does not have
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- // our requested numer of records. This means we've hit the end
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- while (count($pubs) == $num_to_retrieve);
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- }
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-
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- // sync the newly added publications with Drupal. If the user
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- // requested a report then we don't want to print any syncing information
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- // so pass 'FALSE' to the sync call
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- print "Syncing publications with Drupal...\n";
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- chado_node_sync_records('pub');
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-
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- // iterate through each of the reports and generate a final report with HTML links
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- $HTML_report = '';
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- if ($report_email) {
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- $HTML_report .= "<html>";
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- global $base_url;
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- foreach ($reports as $importer => $report) {
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- $total = count($report['inserted']);
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- $HTML_report .= "<b>$total new publications from importer: $importer</b><br><ol>\n";
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- foreach ($report['inserted'] as $pub) {
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- $item = $pub['Title'];
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- if (array_key_exists('pub_id', $pub)) {
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- $item = l($pub['Title'], "$base_url/pub/" . $pub['pub_id']);
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- }
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- $HTML_report .= "<li>$item</li>\n";
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- }
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- $HTML_report .= "</ol>\n";
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- }
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- $HTML_report .= "</html>";
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- $site_email = variable_get('site_mail', '');
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- $params = array(
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- 'message' => $HTML_report
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- );
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- drupal_mail('tripal_pub', 'import_report', $report_email, language_default(), $params, $site_email, TRUE);
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- }
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-
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- // if any of the importers wanted to create contacts from the authors then sync them
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- if($do_contact) {
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- print "Syncing contacts with Drupal...\n";
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- chado_node_sync_records('contact');
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- }
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- }
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- catch (Exception $e) {
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- $transaction->rollback();
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- print "\n"; // make sure we start errors on new line
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- watchdog_exception('T_pub_import', $e);
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- print "FAILED: Rolling back database changes...\n";
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- return;
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- }
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- print "Done.\n";
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-}
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/**
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* Imports all publications for a given publication import setup.
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@@ -1568,16 +1504,20 @@ function tripal_execute_pub_importer($import_id, $job_id = NULL) {
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// our requested numer of records. This means we've hit the end
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while (count($pubs) == $num_to_retrieve);
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- // sync the newly added publications with Drupal. If the user
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- // requested a report then we don't want to print any syncing information
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- // so pass 'FALSE' to the sync call
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- print "Syncing publications with Drupal...\n";
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- chado_node_sync_records('pub');
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-
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- // if any of the importers wanted to create contacts from the authors then sync them
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- if($import->do_contact) {
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- print "Syncing contacts with Drupal...\n";
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- chado_node_sync_records('contact');
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+ // For backwards compatibility check to see if the legacy pub module
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+ // is enabled. If so, then sync the nodes.
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+ if (module_exists('tripal_pub')) {
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+ // sync the newly added publications with Drupal. If the user
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+ // requested a report then we don't want to print any syncing information
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+ // so pass 'FALSE' to the sync call
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+ print "Syncing publications with Drupal...\n";
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+ chado_node_sync_records('pub');
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+
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+ // if any of the importers wanted to create contacts from the authors then sync them
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+ if($import->do_contact) {
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+ print "Syncing contacts with Drupal...\n";
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+ chado_node_sync_records('contact');
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+ }
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}
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tripal_set_job_progress($job_id, '100');
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}
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@@ -1614,7 +1554,7 @@ function tripal_get_remote_pub($dbxref) {
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$accession = $matches[2];
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// check that the database is supported
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- $supported_dbs = variable_get('tripal_pub_supported_dbs', array());
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+ $supported_dbs = variable_get('tripal_pub_supported_dbs', array('PMID'));
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if(!in_array($remote_db, $supported_dbs)) {
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return FALSE;
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}
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@@ -1694,180 +1634,436 @@ function tripal_get_remote_pubs($remote_db, $search_array, $num_to_retrieve, $pa
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}
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/**
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- * Imports a singe publication specified by a remote database cross reference.
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+ * The admin form for submitting job to create citations
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*
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- * @param $pub_dbxref
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- * The unique database ID for the record to update. This value must
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- * be of the format DB_NAME:ACCESSION where DB_NAME is the name of the
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- * database (e.g. PMID or AGL) and the ACCESSION is the unique identifier
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- * for the record in the database.
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- * @param $do_contact
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- * Set to TRUE if authors should automatically have a contact record added
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- * to Chado.
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- * @param $do_update
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- * If set to TRUE then the publication will be updated if it already exists
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- * in the database.
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+ * @param $form_state
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*
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* @ingroup tripal_pub
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*/
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-function tripal_import_pub_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_update) {
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- $num_to_retrieve = 1;
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- $pager_id = 0;
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- $page = 0;
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- $num_pubs = 0;
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+function tripal_pub_citation_form($form, &$form_state) {
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+
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+ $form['instructions'] = array(
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+ '#markup' => '<p>Use this form to unify publication citations. Citations are created automtically when
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+ importing publications but citations are set by the user when publications are added manually.
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+ Or publications added to the Chado database by tools other than the Tripal Publication Importer may
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+ not have citations set. If you are certain that all necessary information for all publications is present (e.g.
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+ authors, volume, issue, page numbers, etc.) but citations are not consistent, then you can
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+ choose to update all citations for all publications using the form below. Alternatively, you
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+ can update citations only for publication that do not already have one.</p>'
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+ );
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- print "\nNOTE: Loading of publications is performed using a database transaction. \n" .
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- "If the load fails or is terminated prematurely then the entire set of \n" .
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- "insertions/updates is rolled back and will not be found in the database\n\n";
|
|
|
+ $form['options'] = array(
|
|
|
+ '#type' => 'radios',
|
|
|
+ '#options' => array(
|
|
|
+ 'all' => 'Create citation for all publications. Replace the existing citation if it exists.',
|
|
|
+ 'new' => 'Create citation for publication only if it does not already have one.'),
|
|
|
+ '#default_value' => 'all'
|
|
|
+ );
|
|
|
|
|
|
- $transaction = db_transaction();
|
|
|
- try {
|
|
|
- if(preg_match('/^(.*?):(.*?)$/', $pub_dbxref, $matches)) {
|
|
|
- $dbname = $matches[1];
|
|
|
- $accession = $matches[2];
|
|
|
-
|
|
|
- $criteria = array(
|
|
|
- 'num_criteria' => 1,
|
|
|
- 'remote_db' => $dbname,
|
|
|
- 'criteria' => array(
|
|
|
- '1' => array(
|
|
|
- 'search_terms' => "$dbname:$accession",
|
|
|
- 'scope' => 'id',
|
|
|
- 'operation' => '',
|
|
|
- 'is_phrase' => 0,
|
|
|
- ),
|
|
|
- ),
|
|
|
- );
|
|
|
- $remote_db = $criteria['remote_db'];
|
|
|
- $results = tripal_get_remote_pubs($remote_db, $criteria, $num_to_retrieve, $page);
|
|
|
- $pubs = $results['pubs'];
|
|
|
- $search_str = $results['search_str'];
|
|
|
- $total_records = $results['total_records'];
|
|
|
- $pub_id = tripal_pub_add_publications($pubs, $do_contact, $do_update);
|
|
|
- }
|
|
|
+ $form['submit'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => t('Submit')
|
|
|
+ );
|
|
|
|
|
|
- // sync the newly added publications with Drupal
|
|
|
- print "Syncing publications with Drupal...\n";
|
|
|
- chado_node_sync_records('pub');
|
|
|
+ return $form;
|
|
|
+}
|
|
|
|
|
|
- // if any of the importers wanted to create contacts from the authors then sync them
|
|
|
- if($do_contact) {
|
|
|
- print "Syncing contacts with Drupal...\n";
|
|
|
- chado_node_sync_records('contact');
|
|
|
- }
|
|
|
+/**
|
|
|
+ * Submit form. Create Tripal job for citations
|
|
|
+ *
|
|
|
+ * @param $form_state
|
|
|
+ *
|
|
|
+ * @ingroup tripal_pub
|
|
|
+ */
|
|
|
+function tripal_pub_citation_form_submit(&$form_state) {
|
|
|
+ $options [0] = $form_state['options']['#value'];
|
|
|
+ tripal_add_job("Create citations ($options[0])", 'tripal_pub', 'tripal_pub_create_citations', $options, $user->uid);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Launch the Tripal job to generate citations. Called by tripal jobs
|
|
|
+ *
|
|
|
+ * @param $options
|
|
|
+ * Options pertaining to what publications to generate citations for.
|
|
|
+ * One of the following must be present:
|
|
|
+ * - all: Create and replace citation for all pubs
|
|
|
+ * - new: Create citation for pubs that don't already have one
|
|
|
+ *
|
|
|
+ * @ingroup tripal_pub
|
|
|
+ */
|
|
|
+function tripal_pub_create_citations($options) {
|
|
|
+ $skip_existing = TRUE;
|
|
|
+ $sql = "
|
|
|
+ SELECT cvterm_id
|
|
|
+ FROM {cvterm}
|
|
|
+ WHERE
|
|
|
+ name = 'Citation' AND
|
|
|
+ cv_id = (SELECT cv_id FROM {cv} WHERE name = 'tripal_pub')
|
|
|
+ ";
|
|
|
+ $citation_type_id = chado_query($sql)->fetchField();
|
|
|
+
|
|
|
+ // Create and replace citation for all pubs
|
|
|
+ if ($options == 'all') {
|
|
|
+ $sql = "SELECT pub_id FROM {pub} P WHERE pub_id <> 1";
|
|
|
+ $skip_existing = FALSE;
|
|
|
}
|
|
|
- catch (Exception $e) {
|
|
|
- $transaction->rollback();
|
|
|
- print "\n"; // make sure we start errors on new line
|
|
|
- watchdog_exception('T_pub_import', $e);
|
|
|
- print "FAILED: Rolling back database changes...\n";
|
|
|
- return;
|
|
|
+ // Create citation for pubs that don't already have one
|
|
|
+ else if ($options == 'new') {
|
|
|
+ $sql = "
|
|
|
+ SELECT pub_id
|
|
|
+ FROM {pub} P
|
|
|
+ WHERE
|
|
|
+ (SELECT value
|
|
|
+ FROM {pubprop} PB
|
|
|
+ WHERE type_id = :type_id AND P.pub_id = PB.pub_id AND rank = 0) IS NULL
|
|
|
+ AND pub_id <> 1
|
|
|
+ ";
|
|
|
+ $skip_existing = TRUE;
|
|
|
}
|
|
|
|
|
|
- print "Done.\n";
|
|
|
+ $result = chado_query($sql, array(':type_id' => $citation_type_id));
|
|
|
+ $counter_updated = 0;
|
|
|
+ $counter_generated = 0;
|
|
|
+ while ($pub = $result->fetchObject()) {
|
|
|
+ $pub_arr = tripal_pub_get_publication_array($pub->pub_id, $skip_existing);
|
|
|
+ if ($pub_arr) {
|
|
|
+ $citation = tripal_pub_create_citation($pub_arr);
|
|
|
+ print $citation . "\n\n";
|
|
|
+ // Replace if citation exists. This condition is never TRUE if $skip_existing is TRUE
|
|
|
+ if ($pub_arr['Citation']) {
|
|
|
+ $sql = "
|
|
|
+ UPDATE {pubprop} SET value = :value
|
|
|
+ WHERE pub_id = :pub_id AND type_id = :type_id AND rank = :rank
|
|
|
+ ";
|
|
|
+ chado_query($sql, array(':value' => $citation, ':pub_id' => $pub->pub_id,
|
|
|
+ ':type_id' => $citation_type_id, ':rank' => 0));
|
|
|
+ $counter_updated ++;
|
|
|
+ // Generate a new citation
|
|
|
+ } else {
|
|
|
+ $sql = "
|
|
|
+ INSERT INTO {pubprop} (pub_id, type_id, value, rank)
|
|
|
+ VALUES (:pub_id, :type_id, :value, :rank)
|
|
|
+ ";
|
|
|
+ chado_query($sql, array(':pub_id' => $pub->pub_id, ':type_id' => $citation_type_id,
|
|
|
+ ':value' => $citation, ':rank' => 0));
|
|
|
+ $counter_generated ++;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ print "$counter_generated citations generated. $counter_updated citations updated.\n";
|
|
|
}
|
|
|
|
|
|
+
|
|
|
/**
|
|
|
- * Updates publication records that currently exist in the Chado pub table
|
|
|
- * with the most recent data in the remote database.
|
|
|
+ * This function generates citations for publications. It requires
|
|
|
+ * an array structure with keys being the terms in the Tripal
|
|
|
+ * publication ontology. This function is intended to be used
|
|
|
+ * for any function that needs to generate a citation.
|
|
|
*
|
|
|
- * @param $do_contact
|
|
|
- * Set to TRUE if authors should automatically have a contact record added
|
|
|
- * to Chado. Contacts are added using the name provided by the remote
|
|
|
- * database.
|
|
|
- * @param $dbxref
|
|
|
- * The unique database ID for the record to update. This value must
|
|
|
- * be of the format DB_NAME:ACCESSION where DB_NAME is the name of the
|
|
|
- * database (e.g. PMID or AGL) and the ACCESSION is the unique identifier
|
|
|
- * for the record in the database.
|
|
|
- * @param $db
|
|
|
- * The name of the remote database to update. If this value is provided and
|
|
|
- * no dbxref then all of the publications currently in the Chado database
|
|
|
- * for this remote database will be updated.
|
|
|
+ * @param $pub
|
|
|
+ * An array structure containing publication details where the keys
|
|
|
+ * are the publication ontology term names and values are the
|
|
|
+ * corresponding details. The pub array can contain the following
|
|
|
+ * keys with corresponding values:
|
|
|
+ * - Publication Type: an array of publication types. a publication can have more than one type
|
|
|
+ * - Authors: a string containing all of the authors of a publication
|
|
|
+ * - Journal Name: a string containing the journal name
|
|
|
+ * - Journal Abbreviation: a string containing the journal name abbreviation
|
|
|
+ * - Series Name: a string containing the series (e.g. conference proceedings) name
|
|
|
+ * - Series Abbreviation: a string containing the series name abbreviation
|
|
|
+ * - Volume: the serives volume number
|
|
|
+ * - Issue: the series issue number
|
|
|
+ * - Pages: the page numbers for the publication
|
|
|
+ * - Publication Date: A date in the format "Year Month Day"
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A text string containing the citation
|
|
|
*
|
|
|
* @ingroup tripal_pub
|
|
|
*/
|
|
|
-function tripal_reimport_publications($do_contact = FALSE, $dbxref = NULL, $db = NULL) {
|
|
|
+function tripal_pub_create_citation($pub) {
|
|
|
+ $citation = '';
|
|
|
+ $pub_type = '';
|
|
|
+
|
|
|
+ // An article may have more than one publication type. For example,
|
|
|
+ // a publication type can be 'Journal Article' but also a 'Clinical Trial'.
|
|
|
+ // Therefore, we need to select the type that makes most sense for
|
|
|
+ // construction of the citation. Here we'll iterate through them all
|
|
|
+ // and select the one that matches best.
|
|
|
+ if (is_array($pub['Publication Type'])) {
|
|
|
+ foreach ($pub['Publication Type'] as $ptype) {
|
|
|
+ if ($ptype == 'Journal Article' ) {
|
|
|
+ $pub_type = $ptype;
|
|
|
+ break;
|
|
|
+ }
|
|
|
+ else if ($ptype == 'Conference Proceedings'){
|
|
|
+ $pub_type = $ptype;
|
|
|
+ break;
|
|
|
+ }
|
|
|
+ else if ($ptype == 'Review') {
|
|
|
+ $pub_type = $ptype;
|
|
|
+ break;
|
|
|
+ }
|
|
|
+ else if ($ptype == 'Book') {
|
|
|
+ $pub_type = $ptype;
|
|
|
+ break;
|
|
|
+ }
|
|
|
+ else if ($ptype == 'Letter') {
|
|
|
+ $pub_type = $ptype;
|
|
|
+ break;
|
|
|
+ }
|
|
|
+ else if ($ptype == 'Book Chapter') {
|
|
|
+ $pub_type = $ptype;
|
|
|
+ break;
|
|
|
+ }
|
|
|
+ else if ($ptype == "Research Support, Non-U.S. Gov't") {
|
|
|
+ $pub_type = $ptype;
|
|
|
+ // we don't break because if the article is also a Journal Article
|
|
|
+ // we prefer that type
|
|
|
+ }
|
|
|
+ }
|
|
|
+ // If we don't have a recognized publication type, then just use the
|
|
|
+ // first one in the list.
|
|
|
+ if (!$pub_type) {
|
|
|
+ $pub_type = $pub['Publication Type'][0];
|
|
|
+ }
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $pub_type = $pub['Publication Type'];
|
|
|
+ }
|
|
|
+ //----------------------
|
|
|
+ // Journal Article
|
|
|
+ //----------------------
|
|
|
+ if ($pub_type == 'Journal Article') {
|
|
|
+ if (array_key_exists('Authors', $pub)) {
|
|
|
+ $citation = $pub['Authors'] . '. ';
|
|
|
+ }
|
|
|
|
|
|
- print "\nNOTE: Loading of publications is performed using a database transaction. \n" .
|
|
|
- "If the load fails or is terminated prematurely then the entire set of \n" .
|
|
|
- "insertions/updates is rolled back and will not be found in the database\n\n";
|
|
|
- $transaction = db_transaction();
|
|
|
- try {
|
|
|
+ $citation .= $pub['Title'] . '. ';
|
|
|
|
|
|
- // get a list of all publications by their Dbxrefs that have supported databases
|
|
|
- $sql = "
|
|
|
- SELECT DB.name as db_name, DBX.accession
|
|
|
- FROM pub P
|
|
|
- INNER JOIN pub_dbxref PDBX ON P.pub_id = PDBX.pub_id
|
|
|
- INNER JOIN dbxref DBX ON DBX.dbxref_id = PDBX.dbxref_id
|
|
|
- INNER JOIN db DB ON DB.db_id = DBX.db_id
|
|
|
- ";
|
|
|
- $args = array();
|
|
|
- if ($dbxref and preg_match('/^(.*?):(.*?)$/', $dbxref, $matches)) {
|
|
|
- $dbname = $matches[1];
|
|
|
- $accession = $matches[2];
|
|
|
- $sql .= "WHERE DBX.accession = :accession and DB.name = :dbname ";
|
|
|
- $args[':accession'] = $accession;
|
|
|
- $args[':dbname'] = $dbname;
|
|
|
+ if (array_key_exists('Journal Name', $pub)) {
|
|
|
+ $citation .= $pub['Journal Name'] . '. ';
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Journal Abbreviation', $pub)) {
|
|
|
+ $citation .= $pub['Journal Abbreviation'] . '. ';
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Series Name', $pub)) {
|
|
|
+ $citation .= $pub['Series Name'] . '. ';
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Series Abbreviation', $pub)) {
|
|
|
+ $citation .= $pub['Series Abbreviation'] . '. ';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Publication Date', $pub)) {
|
|
|
+ $citation .= $pub['Publication Date'];
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Year', $pub)) {
|
|
|
+ $citation .= $pub['Year'];
|
|
|
+ }
|
|
|
+ if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) {
|
|
|
+ $citation .= '; ';
|
|
|
}
|
|
|
- elseif ($db) {
|
|
|
- $sql .= " WHERE DB.name = :dbname ";
|
|
|
- $args[':dbname'] = $db;
|
|
|
+ if (array_key_exists('Volume', $pub)) {
|
|
|
+ $citation .= $pub['Volume'];
|
|
|
+ }
|
|
|
+ if (array_key_exists('Issue', $pub)) {
|
|
|
+ $citation .= '(' . $pub['Issue'] . ')';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Pages', $pub)) {
|
|
|
+ if (array_key_exists('Volume', $pub)) {
|
|
|
+ $citation .= ':';
|
|
|
+ }
|
|
|
+ $citation .= $pub['Pages'];
|
|
|
+ }
|
|
|
+ $citation .= '.';
|
|
|
+ }
|
|
|
+ //----------------------
|
|
|
+ // Review
|
|
|
+ //----------------------
|
|
|
+ if ($pub_type == 'Review') {
|
|
|
+ if (array_key_exists('Authors', $pub)) {
|
|
|
+ $citation = $pub['Authors'] . '. ';
|
|
|
}
|
|
|
- $sql .= "ORDER BY DB.name, P.pub_id";
|
|
|
- $results = chado_query($sql, $args);
|
|
|
|
|
|
- $num_to_retrieve = 100;
|
|
|
- $i = 0; // count the number of IDs. When we hit $num_to_retrieve we'll do the query
|
|
|
- $curr_db = ''; // keeps track of the current current database
|
|
|
- $ids = array(); // the list of IDs for the database
|
|
|
- $search = array(); // the search array passed to the search function
|
|
|
-
|
|
|
- // iterate through the pub IDs
|
|
|
- while ($pub = $results->fetchObject()) {
|
|
|
- $accession = $pub->accession;
|
|
|
- $remote_db = $pub->db_name;
|
|
|
-
|
|
|
- // here we need to only update publications for databases we support
|
|
|
- $supported_dbs = variable_get('tripal_pub_supported_dbs', array());
|
|
|
- if(!in_array($remote_db, $supported_dbs)) {
|
|
|
- continue;
|
|
|
+ $citation .= $pub['Title'] . '. ';
|
|
|
+
|
|
|
+ if (array_key_exists('Journal Name', $pub)) {
|
|
|
+ $citation .= $pub['Journal Name'] . '. ';
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Journal Abbreviation', $pub)) {
|
|
|
+ $citation .= $pub['Journal Abbreviation'] . '. ';
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Series Name', $pub)) {
|
|
|
+ $citation .= $pub['Series Name'] . '. ';
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Series Abbreviation', $pub)) {
|
|
|
+ $citation .= $pub['Series Abbreviation'] . '. ';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Publication Date', $pub)) {
|
|
|
+ $citation .= $pub['Publication Date'];
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Year', $pub)) {
|
|
|
+ $citation .= $pub['Year'];
|
|
|
+ }
|
|
|
+ if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) {
|
|
|
+ $citation .= '; ';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Volume', $pub)) {
|
|
|
+ $citation .= $pub['Volume'];
|
|
|
+ }
|
|
|
+ if (array_key_exists('Issue', $pub)) {
|
|
|
+ $citation .= '(' . $pub['Issue'] . ')';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Pages', $pub)) {
|
|
|
+ if (array_key_exists('Volume', $pub)) {
|
|
|
+ $citation .= ':';
|
|
|
}
|
|
|
- $search = array(
|
|
|
- 'num_criteria' => 1,
|
|
|
- 'remote_db' => $remote_db,
|
|
|
- 'criteria' => array(
|
|
|
- '1' => array(
|
|
|
- 'search_terms' => "$remote_db:$accession",
|
|
|
- 'scope' => 'id',
|
|
|
- 'operation' => '',
|
|
|
- 'is_phrase' => 0,
|
|
|
- ),
|
|
|
- ),
|
|
|
- );
|
|
|
- $pubs = tripal_get_remote_pubs($remote_db, $search, 1, 0);
|
|
|
- tripal_pub_add_publications($pubs, $do_contact, TRUE);
|
|
|
+ $citation .= $pub['Pages'];
|
|
|
+ }
|
|
|
+ $citation .= '.';
|
|
|
+ }
|
|
|
+ //----------------------
|
|
|
+ // Research Support, Non-U.S. Gov't
|
|
|
+ //----------------------
|
|
|
+ elseif ($pub_type == "Research Support, Non-U.S. Gov't") {
|
|
|
+ if (array_key_exists('Authors', $pub)) {
|
|
|
+ $citation = $pub['Authors'] . '. ';
|
|
|
+ }
|
|
|
+
|
|
|
+ $citation .= $pub['Title'] . '. ';
|
|
|
|
|
|
- $i++;
|
|
|
+ if (array_key_exists('Journal Name', $pub)) {
|
|
|
+ $citation .= $pub['Journal Name'] . '. ';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Publication Date', $pub)) {
|
|
|
+ $citation .= $pub['Publication Date'];
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Year', $pub)) {
|
|
|
+ $citation .= $pub['Year'];
|
|
|
+ }
|
|
|
+ $citation .= '.';
|
|
|
+ }
|
|
|
+ //----------------------
|
|
|
+ // Letter
|
|
|
+ //----------------------
|
|
|
+ elseif ($pub_type == 'Letter') {
|
|
|
+ if (array_key_exists('Authors', $pub)) {
|
|
|
+ $citation = $pub['Authors'] . '. ';
|
|
|
}
|
|
|
|
|
|
- // sync the newly added publications with Drupal
|
|
|
- print "Syncing publications with Drupal...\n";
|
|
|
- chado_node_sync_records('pub');
|
|
|
+ $citation .= $pub['Title'] . '. ';
|
|
|
+ if (array_key_exists('Journal Name', $pub)) {
|
|
|
+ $citation .= $pub['Journal Name'] . '. ';
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Journal Abbreviation', $pub)) {
|
|
|
+ $citation .= $pub['Journal Abbreviation'] . '. ';
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Series Name', $pub)) {
|
|
|
+ $citation .= $pub['Series Name'] . '. ';
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Series Abbreviation', $pub)) {
|
|
|
+ $citation .= $pub['Series Abbreviation'] . '. ';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Publication Date', $pub)) {
|
|
|
+ $citation .= $pub['Publication Date'];
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Year', $pub)) {
|
|
|
+ $citation .= $pub['Year'];
|
|
|
+ }
|
|
|
+ if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) {
|
|
|
+ $citation .= '; ';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Volume', $pub)) {
|
|
|
+ $citation .= $pub['Volume'];
|
|
|
+ }
|
|
|
+ if (array_key_exists('Issue', $pub)) {
|
|
|
+ $citation .= '(' . $pub['Issue'] . ')';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Pages', $pub)) {
|
|
|
+ if (array_key_exists('Volume', $pub)) {
|
|
|
+ $citation .= ':';
|
|
|
+ }
|
|
|
+ $citation .= $pub['Pages'];
|
|
|
+ }
|
|
|
+ $citation .= '.';
|
|
|
+ }
|
|
|
+ //-----------------------
|
|
|
+ // Conference Proceedings
|
|
|
+ //-----------------------
|
|
|
+ elseif ($pub_type == 'Conference Proceedings') {
|
|
|
+ if (array_key_exists('Authors', $pub)) {
|
|
|
+ $citation = $pub['Authors'] . '. ';
|
|
|
+ }
|
|
|
|
|
|
- // if the caller wants to create contacts then we should sync them
|
|
|
- if ($do_contact) {
|
|
|
- print "Syncing contacts with Drupal...\n";
|
|
|
- chado_node_sync_records('contact');
|
|
|
+ $citation .= $pub['Title'] . '. ';
|
|
|
+ if (array_key_exists('Conference Name', $pub)) {
|
|
|
+ $citation .= $pub['Conference Name'] . '. ';
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Series Name', $pub)) {
|
|
|
+ $citation .= $pub['Series Name'] . '. ';
|
|
|
}
|
|
|
+ elseif (array_key_exists('Series Abbreviation', $pub)) {
|
|
|
+ $citation .= $pub['Series Abbreviation'] . '. ';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Publication Date', $pub)) {
|
|
|
+ $citation .= $pub['Publication Date'];
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Year', $pub)) {
|
|
|
+ $citation .= $pub['Year'];
|
|
|
+ }
|
|
|
+ if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) {
|
|
|
+ $citation .= '; ';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Volume', $pub)) {
|
|
|
+ $citation .= $pub['Volume'];
|
|
|
+ }
|
|
|
+ if (array_key_exists('Issue', $pub)) {
|
|
|
+ $citation .= '(' . $pub['Issue'] . ')';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Pages', $pub)) {
|
|
|
+ if (array_key_exists('Volume', $pub)) {
|
|
|
+ $citation .= ':';
|
|
|
+ }
|
|
|
+ $citation .= $pub['Pages'];
|
|
|
+ }
|
|
|
+ $citation .= '.';
|
|
|
}
|
|
|
- catch (Exception $e) {
|
|
|
- $transaction->rollback();
|
|
|
- print "\n"; // make sure we start errors on new line
|
|
|
- watchdog_exception('T_pub_import', $e);
|
|
|
- print "FAILED: Rolling back database changes...\n";
|
|
|
- return;
|
|
|
+ //-----------------------
|
|
|
+ // Default
|
|
|
+ //-----------------------
|
|
|
+ else {
|
|
|
+ if (array_key_exists('Authors', $pub)) {
|
|
|
+ $citation = $pub['Authors'] . '. ';
|
|
|
+ }
|
|
|
+ $citation .= $pub['Title'] . '. ';
|
|
|
+ if (array_key_exists('Series Name', $pub)) {
|
|
|
+ $citation .= $pub['Series Name'] . '. ';
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Series Abbreviation', $pub)) {
|
|
|
+ $citation .= $pub['Series Abbreviation'] . '. ';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Publication Date', $pub)) {
|
|
|
+ $citation .= $pub['Publication Date'];
|
|
|
+ }
|
|
|
+ elseif (array_key_exists('Year', $pub)) {
|
|
|
+ $citation .= $pub['Year'];
|
|
|
+ }
|
|
|
+ if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) {
|
|
|
+ $citation .= '; ';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Volume', $pub)) {
|
|
|
+ $citation .= $pub['Volume'];
|
|
|
+ }
|
|
|
+ if (array_key_exists('Issue', $pub)) {
|
|
|
+ $citation .= '(' . $pub['Issue'] . ')';
|
|
|
+ }
|
|
|
+ if (array_key_exists('Pages', $pub)) {
|
|
|
+ if (array_key_exists('Volume', $pub)) {
|
|
|
+ $citation .= ':';
|
|
|
+ }
|
|
|
+ $citation .= $pub['Pages'];
|
|
|
+ }
|
|
|
+ $citation .= '.';
|
|
|
}
|
|
|
- print "Done.\n";
|
|
|
-}
|
|
|
+
|
|
|
+ return $citation;
|
|
|
+}
|
Stephen Ficklin