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@@ -1075,10 +1075,8 @@ function chado_cleanup_orphaned_nodes_part($table, $job_id = NULL, $nentries,
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$clsql= "
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$clsql= "
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SELECT *
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SELECT *
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FROM {" . $linking_table . "} LT
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FROM {" . $linking_table . "} LT
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- INNER JOIN {node} N ON N.nid = LT.nid
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- WHERE N.type = :node_type
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ORDER BY LT.nid LIMIT $nentries OFFSET $offset";
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ORDER BY LT.nid LIMIT $nentries OFFSET $offset";
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- $res = db_query($clsql, array(':node_type' => $node_type));
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+ $res = db_query($clsql);
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foreach ($res as $node) {
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foreach ($res as $node) {
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$cnodes[$count] = $node;
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$cnodes[$count] = $node;
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$count++;
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$count++;
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@@ -1093,40 +1091,40 @@ function chado_cleanup_orphaned_nodes_part($table, $job_id = NULL, $nentries,
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if ($interval < 1) {
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if ($interval < 1) {
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$interval = 1;
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$interval = 1;
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}
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}
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- foreach ($cnodes as $nid) {
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+ foreach ($cnodes as $linker) {
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// Update the job status every 1% analyses
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// Update the job status every 1% analyses
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if ($job_id and $i % $interval == 0) {
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if ($job_id and $i % $interval == 0) {
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$percent = sprintf("%.2f", ($i / $count) * 100);
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$percent = sprintf("%.2f", ($i / $count) * 100);
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tripal_set_job_progress($job_id, intval($percent));
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tripal_set_job_progress($job_id, intval($percent));
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- print "Percent complete: $percent%. Memory: " . number_format(memory_get_usage()) . " bytes.\r";
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+ print "Percent complete: $percent%. Memory: " . number_format(memory_get_usage()) . " bytes.\n";
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}
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}
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// See if the node exits, if not remove the entry from linking table table.
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// See if the node exits, if not remove the entry from linking table table.
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- $nsql = "SELECT * FROM {node} WHERE nid = :nid";
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- $results = db_query($nsql, array(':nid' => $nid->nid));
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+ $nsql = "SELECT * FROM {node} WHERE nid = :nid AND type = :node_type";
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+ $results = db_query($nsql, array(':nid' => $linker->nid, ':node_type' => $node_type));
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$node = $results->fetchObject();
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$node = $results->fetchObject();
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if (!$node) {
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if (!$node) {
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$deleted++;
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$deleted++;
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- db_query("DELETE FROM {" . $linking_table . "} WHERE nid = :nid", array(':nid' => $nid->nid));
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- //print "$linking_table missing node.... DELETING: $nid->nid\n";
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+ db_query("DELETE FROM {" . $linking_table . "} WHERE nid = :nid", array(':nid' => $linker->nid));
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+ //print "$linking_table missing node.... DELETING where nid=".$linker->nid." $linking_table entry.\n";
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}
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}
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// Does record in chado exists, if not remove entry from $linking_table.
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// Does record in chado exists, if not remove entry from $linking_table.
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$table_id = $table . "_id";
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$table_id = $table . "_id";
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- $lsql = "SELECT * FROM {" . $table . "} where " . $table . "_id = :" . $table . "_id";
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- $results = chado_query($lsql, array(":" . $table . "_id" => $nid->$table_id));
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+ $lsql = "SELECT * FROM {" . $table . "} where " . $table_id . " = :chado_id";
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+ $results = chado_query($lsql, array(":chado_id" => $linker->$table_id));
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$record = $results->fetchObject();
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$record = $results->fetchObject();
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if (!$record) {
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if (!$record) {
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$deleted++;
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$deleted++;
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- $sql = "DELETE FROM {" . $linking_table . "} WHERE " . $table . "_id = :" . $table . "_id";
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- db_query($sql, array(":" . $table . "_id" => $nid->$table_id));
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- //print "$linking_table missing $table.... DELETING entry.\n";
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+ $sql = "DELETE FROM {" . $linking_table . "} WHERE " . $table_id . " = :chado_id";
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+ db_query($sql, array(":chado_id" => $linker->$table_id));
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+ //print "$linking_table missing $table.... DELETING where $table_id=".$linker->$table_id." $linking_table entry.\n";
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}
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}
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$i++;
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$i++;
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}
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}
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$percent = sprintf("%.2f", ($i / $count) * 100);
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$percent = sprintf("%.2f", ($i / $count) * 100);
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tripal_set_job_progress($job_id, intval($percent));
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tripal_set_job_progress($job_id, intval($percent));
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- print "Percent complete: $percent%. Memory: " . number_format(memory_get_usage()) . " bytes.\r";
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+ print "Percent complete: $percent%. Memory: " . number_format(memory_get_usage()) . " bytes.\n";
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}
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}
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print "\nDeleted $deleted record(s) from $linking_table missing either a node or chado entry.\n";
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print "\nDeleted $deleted record(s) from $linking_table missing either a node or chado entry.\n";
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