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@@ -429,41 +429,29 @@ function chado_import_pub_by_dbxref($pub_dbxref, $do_contact = FALSE,
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function chado_execute_active_pub_importers($report_email = FALSE,
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$publish = TRUE, $do_update = FALSE) {
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+ $report = [];
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+ $report['error'] = [];
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+ $report['inserted'] = [];
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+ $report['skipped'] = [];
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+ $report['updated'] = [];
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+
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// Get all of the loaders.
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$args = array();
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$sql = "SELECT * FROM {tripal_pub_import} WHERE disabled = 0 ";
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$importers = db_query($sql, $args);
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$do_contact = FALSE;
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- $reports = array();
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while ($import = $importers->fetchObject()) {
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- chado_execute_pub_importer($import->pub_import_id, $publish, $do_update);
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- }
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-
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- // Iterate through each of the reports and generate a final report with HTML
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- // 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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+ $importer_report = chado_execute_pub_importer($import->pub_import_id, $publish, $do_update);
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+ foreach ($importer_report as $action => $pubs) {
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+ $report[$action] = array_merge($report[$action], $pubs);
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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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+ $site_email = variable_get('site_mail', '');
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+ $params = array(
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+ 'report' => $report
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+ );
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+ drupal_mail('tripal_chado', 'import_report', $report_email, language_default(), $params, $site_email, TRUE);
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print "Done.\n";
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}
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@@ -488,12 +476,20 @@ function chado_execute_active_pub_importers($report_email = FALSE,
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* this function is run directly.
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*
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* @return
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- * TRUE if importing occured with on errors. FALSE otherwise. If failed,
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- * all database changes are rolled back.
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+ * Returns an array containing the number of publications that were
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+ * inserted, updated, skipped and which had an error during import.
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*
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* @ingroup tripal_pub
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*/
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-function chado_execute_pub_importer($import_id, $publish = TRUE, $do_update = FALSE, $job = NULL) {
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+function chado_execute_pub_importer($import_id, $publish = TRUE,
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+ $do_update = FALSE, $job = NULL) {
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+
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+ // Holds the list of imported pubs which includes their ID and Citation.
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+ $report = [];
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+ $report['error'] = [];
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+ $report['inserted'] = [];
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+ $report['skipped'] = [];
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+ $report['updated'] = [];
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// These are options for the tripal_report_error function. We do not
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// want to log messages to the watchdog but we do for the job and to
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@@ -538,15 +534,18 @@ function chado_execute_pub_importer($import_id, $publish = TRUE, $do_update = FA
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tripal_report_error($message_type, TRIPAL_INFO,
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"Querying !remote_db for up to !num pubs that match the criteria.",
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['!num' => $num_to_retrieve, '!remote_db' => $remote_db], $message_opts);
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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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+ $results = tripal_get_remote_pubs($remote_db, $criteria, $num_to_retrieve, $page);
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+ $pubs = $results['pubs'];
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$num_pubs = $results['total_records'];
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$total_pubs += $num_pubs;
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tripal_report_error($message_type, TRIPAL_INFO,
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- "Adding %num new publications.",
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+ "Found %num publications.",
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['%num' => $num_pubs], $message_opts);
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- tripal_pub_add_publications($pubs, $import->do_contact, $do_update, $job);
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+ $subset_report = tripal_pub_add_publications($pubs, $import->do_contact, $do_update, $job);
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+ foreach ($subset_report as $action => $pubs) {
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+ $report[$action] = array_merge($report[$action], $pubs);
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+ }
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$page++;
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}
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while (count($pubs) == $num_to_retrieve);
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@@ -570,7 +569,7 @@ function chado_execute_pub_importer($import_id, $publish = TRUE, $do_update = FA
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tripal_report_error($message_type, TRIPAL_INFO,
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"Done.", [], $message_opts);
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- return TRUE;
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+ return $report;
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}
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Stephen Ficklin