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@@ -586,7 +586,7 @@ class OBOImporter extends TripalImporter {
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continue;
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}
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if ($stanza === TRUE && (substr($line, 0, 3) === "id:")) {
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- $parts = explode(':', $line);
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+ $parts = explode(':', $line, 2);
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$short_name = strtolower($parts[1]);
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$short_name = preg_replace('/\s+/', '', $short_name);
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break;
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@@ -608,6 +608,8 @@ class OBOImporter extends TripalImporter {
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else {
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$results = $short_name;
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}
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+ print_r('$results');
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+ print_r($results);
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$defaultcv = tripal_insert_cv(strtoupper($results), '');
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$this->newcvs[$defaultcv->name] = $defaultcv->cv_id;
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}
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@@ -1199,8 +1201,8 @@ class OBOImporter extends TripalImporter {
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// Get the object term.
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if ($reference_term === TRUE && !empty($oterm)) {
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$objterm = array();
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- $objterm['id'] = $oterm['label'];
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- $objterm['name'] = $oterm['obo_id'];
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+ $objterm['id'] = $oterm['obo_id'];
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+ $objterm['name'] = $oterm['label'];
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if (array_key_exists('def', $oterm)) {
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$objterm['definition'] = $oterm['def'];
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}
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@@ -1239,6 +1241,8 @@ class OBOImporter extends TripalImporter {
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$objterm['cv_name' ] = $defaultcv;
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$objterm['is_relationship'] = $object_is_relationship;
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$objterm['db_name'] = $default_db;
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+ print_r('$objterm');
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+ print_r($objterm);
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$objcvterm = tripal_insert_cvterm($objterm, array('update_existing' => TRUE));
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if (!$objcvterm) {
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throw new Exception("Cannot add cvterm " . $objterm['name']);
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@@ -1505,6 +1509,8 @@ class OBOImporter extends TripalImporter {
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* @ingroup tripal_obo_loader
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*/
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private function addCvtermDbxref($cvterm, $xref) {
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+ print_r('addCvtermDbxref');
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+ print_r($cvterm);
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$dbname = preg_replace('/^(.+?):.*$/', '$1', $xref);
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$accession = preg_replace('/^.+?:\s*(.*?)(\{.+$|\[.+$|\s.+$|\".+$|$)/', '$1', $xref);
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