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@@ -144,7 +144,7 @@ function chado_pub_form($node, $form_state) {
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$num_properties += chado_pub_node_form_add_pubprop_table_props($form, $form_state, $pub_id, $d_properties, $d_removed);
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// add in any new properties that have been added by the user through an AHAH callback
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- $num_properties += chado_pub_node_form_add_new_props($form, $form_state, $num_new, $d_properties, $d_removed);
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+ $num_new = chado_pub_node_form_add_new_props($form, $form_state, $d_properties, $d_removed);
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// add an empty row of field to allow for addition of a new property
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chado_pub_node_form_add_new_empty_props($form, $properties_select);
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@@ -159,6 +159,10 @@ function chado_pub_form($node, $form_state) {
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'#type' => 'hidden',
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'#value' => $num_new,
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);
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+ $form['num_properties'] = array(
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+ '#type' => 'hidden',
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+ '#value' => $num_properties,
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+ );
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$form['is_obsolete'] = array(
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'#type' => 'checkbox',
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@@ -189,7 +193,9 @@ function chado_pub_validate($node, &$form) {
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$pubplace = trim($node->pubplace);
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$is_obsolete = $node->is_obsolete;
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$pub_id = $node->pub_id;
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-
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+ $num_properties = $node->num_properties;
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+ $num_new = $node->num_new;
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+
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// if this is a delete then don't validate
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if($node->op == 'Delete') {
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return;
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@@ -206,49 +212,128 @@ function chado_pub_validate($node, &$form) {
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$options = array('statement_name' => 'sel_pub_ty');
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$cvterm = tripal_core_chado_select('cvterm', array('name'), $values, $options);
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if (count($cvterm) == 0) {
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- $message = t('Invalided publication type.');
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+ $message = t('Invalid publication type.');
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form_set_error('type_id', $message);
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return;
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}
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-
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- // on an insert (no $pub_id) make sure the publication doesn't already exist
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- if (!$pub_id) {
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- $results = tripal_pub_get_pubs_by_title_type_pyear($title, $cvterm[0]->name, $pyear);
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- if (count($results) > 0) {
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- $message = t('A publication with this title, type and publication year, already exists. Cannot add this publication');
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- form_set_error('pyear', $message);
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- return;
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+
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+ // get the media name looking at the properties
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+ foreach ($node as $element => $value) {
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+ // if this is an existing property (either previously in the database or
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+ // added via AHAH/AJAX callback)
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+ if (preg_match('/^prop_value-(\d+)-(\d+)$/', $element, $matches)) {
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+ $prop_type_id = $matches[1];
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+ $prop_type = tripal_cv_get_cvterm_by_id($prop_type_id);
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+ if($prop_type->name == 'Conference Name' or $prop_type->name == 'Journal Name') {
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+ $series_name = $value;
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+ }
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+ if($prop_type->name == 'Citation') {
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+ $uniquename = $value;
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+ }
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+ }
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+ // if this is a new property (added by this submit of the form)
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+ elseif ($element = 'new_id') {
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+ $prop_type = tripal_cv_get_cvterm_by_id($value);
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+ if($prop_type->name == 'Conference Name' or $prop_type->name == 'Journal Name') {
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+ $series_name = $node->new_value;
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+ }
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+ if($prop_type->name == 'Citation') {
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+ $uniquename = $value;
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+ }
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}
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}
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- // on an update, make sure that if the title has changed that it doesn't
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- // conflict with any other publication
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+ $skip_duplicate_check = 0;
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+
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+ // if this publication is a Patent then skip the validation below. Patents can have the title
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+ // name and year but be different
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+ if (strcmp($cvterm[0]->name,'Patent') == 0) {
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+ $skip_duplicate_check = 1;
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+ }
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+
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+ // on an update ($pub_id is set), check to see if there have been changes to fields that
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+ // are used to check for duplicates. If not, then no need to check for duplicates
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if ($pub_id) {
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// first get the original title, type and year before it was changed
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$values = array('pub_id' => $pub_id);
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- $columns = array('title','pyear','type_id');
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+ $columns = array('title', 'pyear', 'type_id', 'series_name');
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$options = array('statement_name' => 'sel_pub_id');
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- $pub = tripal_core_chado_select('pub', $columns, $values, $options);
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-
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- // if the title or year doesn't match then it was changed and we want to make
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- // sure it doesn't already exist in another publication
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- if((strcmp($pub[0]->title, $title) != 0) or
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- ($pub[0]->type_id != $type_id) or
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- ($pub[0]->year != $pyear)) {
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- $results = tripal_pub_get_pubs_by_title_type_pyear($title, $cvterm[0]->name, $pyear);
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+ $pub = tripal_core_chado_select('pub', $columns, $values, $options);
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- // make sure we don't capture our pub_id in the list (remove it)
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- foreach ($results as $index => $found_pub_id) {
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- if($found_pub_id == $pub_id){
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- unset($results[$index]);
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- }
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- }
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- if (count($results) > 0) {
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- $message = t('A publication with this title and publication year, already exists. Cannot update this publication');
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- form_set_error('pyear', $message);
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- }
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+ // if the title, type, year or series_name have changed then check the pub
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+ // to see if it is a duplicate of another
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+ if((strcmp(strtolower($pub[0]->title), strtolower($title)) == 0) and
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+ (strcmp(strtolower($pub[0]->series_name), strtolower($series_name)) == 0) and
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+ ($pub[0]->type_id == $type_id) and
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+ ($pub[0]->year == $pyear)) {
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+ $skip_duplicate_check = 1;
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}
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+ }
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+
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+ // check to see if a duplicate publication already exists
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+ if (!$skip_duplicate_check) {
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+
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+ // make sure the publication is unique using the prefereed import duplication check
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+ $import_dups_check = variable_get('tripal_pub_import_duplicate_check', 'title_year_media');
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+ switch ($import_dups_check) {
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+ case 'title_year':
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+ $results = tripal_pub_get_pubs_by_title_type_pyear_series($title, NULL, $pyear, NULL);
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+ // make sure we don't capture our pub_id in the list (remove it)
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+ foreach ($results as $index => $found_pub_id) {
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+ if($found_pub_id == $pub_id){
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+ unset($results[$index]);
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+ }
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+ }
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+ if (count($results) > 0) {
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+ $message = t('A publication with this title and publication year, already exists.');
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+ form_set_error('pyear', $message);
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+ }
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+ break;
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+ case 'title_year_type':
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+ $results = tripal_pub_get_pubs_by_title_type_pyear_series($title, $cvterm[0]->name, $pyear, NULL);
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+
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+ // make sure we don't capture our pub_id in the list (remove it)
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+ foreach ($results as $index => $found_pub_id) {
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+ if($found_pub_id == $pub_id){
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+ unset($results[$index]);
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+ }
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+ }
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+ if (count($results) > 0) {
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+ $message = t('A publication with this title, type and publication year, already exists.');
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+ form_set_error('pyear', $message);
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+ }
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+ break;
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+ case 'title_year_media':
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+ $results = tripal_pub_get_pubs_by_title_type_pyear_series($title, NULL, $pyear, $series_name);
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+
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+ // make sure we don't capture our pub_id in the list (remove it)
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+ foreach ($results as $index => $found_pub_id) {
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+ if($found_pub_id == $pub_id){
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+ unset($results[$index]);
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+ }
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+ }
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+ if (count($results) > 0) {
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+ $message = t('A publication with this title, media name (e.g. Journal Name) and publication year, already exists.');
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+ form_set_error('pyear', $message);
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+ }
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+ break;
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+ }
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}
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+ // even though we are skipping the duplication checks above we must make sure the uniquename is unique
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+ // as that is the offical table constraint
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+ else {
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+ $results = tripal_pub_get_pub_by_uniquename($uniquename);
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+ // make sure we don't capture our pub_id in the list (remove it)
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+ foreach ($results as $index => $found_pub_id) {
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+ if($found_pub_id == $pub_id){
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+ unset($results[$index]);
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+ }
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+ }
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+ if (count($results) > 0) {
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+ $message = t('A publication with this unique citation already exists.');
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+ form_set_error('uniquename', $message);
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+ }
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+ }
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}
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/*
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*
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@@ -289,7 +374,7 @@ function chado_pub_node_form_add_new_empty_props(&$form, $properties_select) {
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/*
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*
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*/
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-function chado_pub_node_form_add_new_props(&$form, $form_state, $num_new, &$d_properties, &$d_removed) {
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+function chado_pub_node_form_add_new_props(&$form, $form_state, &$d_properties, &$d_removed) {
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// first, add in all of the new properties that were added through a previous AHAH callback
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$j = 0;
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Stephen Ficklin