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@@ -318,588 +318,598 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
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chado_query($sql);
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// begin the transaction
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+ $transaction = null;
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if ($use_transaction) {
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- $transaction = tripal_db_start_transaction();
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+ $transaction = db_transaction();
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print "\nNOTE: Loading of this GFF file 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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}
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-
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- // check to see if the file is located local to Drupal
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- $dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $gff_file;
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- if (!file_exists($dfile)) {
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- // if not local to Drupal, the file must be someplace else, just use
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- // the full path provided
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- $dfile = $gff_file;
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- }
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- if (!file_exists($dfile)) {
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- watchdog('T_gff3_loader', "Cannot find the file: %dfile",
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- array('%dfile' => $dfile), WATCHDOG_ERROR);
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- return 0;
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- }
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-
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- print "Opening $gff_file\n";
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-
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- //$lines = file($dfile,FILE_SKIP_EMPTY_LINES);
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- $fh = fopen($dfile, 'r');
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- if (!$fh) {
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- watchdog('T_gff3_loader', "cannot open file: %dfile",
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- array('%dfile' => $dfile), WATCHDOG_ERROR);
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- return 0;
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- }
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- $filesize = filesize($dfile);
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-
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- // get the controlled vocaubulary that we'll be using. The
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- // default is the 'sequence' ontology
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- $sql = "SELECT * FROM {cv} WHERE name = :cvname";
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- $cv = chado_query($sql, array(':cvname' => 'sequence'))->fetchObject();
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- if (!$cv) {
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- watchdog('T_gff3_loader', "Cannot find the 'sequence' ontology",
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- array(), WATCHDOG_ERROR);
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- return '';
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- }
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-
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- // get the organism for which this GFF3 file belongs
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- $sql = "SELECT * FROM {organism} WHERE organism_id = :organism_id";
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- $organism = chado_query($sql, array(':organism_id' => $organism_id))->fetchObject();
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-
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- $interval = intval($filesize * 0.0001);
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- if ($interval == 0) {
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- $interval = 1;
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- }
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- $in_fasta = 0;
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- $line_num = 0;
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- $num_read = 0;
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- $intv_read = 0;
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-
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- // prepare the statement used to get the cvterm for each feature.
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- $psql = "
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- PREPARE sel_cvterm_idnasy (int, text, text) AS
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- SELECT CVT.cvterm_id, CVT.cv_id, CVT.name, CVT.definition,
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- CVT.dbxref_id, CVT.is_obsolete, CVT.is_relationshiptype
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- FROM {cvterm} CVT
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- INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
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- LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
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- WHERE CV.cv_id = $1 and
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- (lower(CVT.name) = lower($2) or lower(CVTS.synonym) = lower($3))
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- ";
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- $status = chado_query($psql);
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- if (!$status) {
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- watchdog('T_gff3_loader', 'cannot prepare statement \'sel_cvterm_idnasy\'.',
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- array(), WATCHDOG_ERROR);
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- return '';
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- }
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-
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- // iterate through each line of the GFF file
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- print "Parsing Line $line_num (0.00%). Memory: " . number_format(memory_get_usage()) . " bytes\r";
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- while ($line = fgets($fh)) {
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- $line_num++;
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- $size = drupal_strlen($line);
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- $num_read += $size;
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- $intv_read += $size;
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-
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- if ($line_num < $start_line) {
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- continue;
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- }
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-
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- // update the job status every 1% features
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- if ($job and $intv_read >= $interval) {
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- $intv_read = 0;
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- $percent = sprintf("%.2f", ($num_read / $filesize) * 100);
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- print "Parsing Line $line_num (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
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- tripal_job_set_progress($job, intval(($num_read / $filesize) * 100));
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- }
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-
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- // check to see if we have FASTA section, if so then set the variable
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- // to start parsing
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- if (preg_match('/^##FASTA/i', $line)) {
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- if ($remove) {
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- // we're done because this is a delete operation so break out of the loop.
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- break;
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- }
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- tripal_feature_load_gff3_fasta($fh, $interval, $num_read, $intv_read, $line_num);
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- continue;
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+ try {
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+
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+ // check to see if the file is located local to Drupal
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+ $dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $gff_file;
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+ if (!file_exists($dfile)) {
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+ // if not local to Drupal, the file must be someplace else, just use
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+ // the full path provided
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+ $dfile = $gff_file;
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}
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- // if the ##sequence-region line is present then we want to add a new feature
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- if (preg_match('/^##sequence-region (.*?) (\d+) (\d+)$/i', $line, $region_matches)) {
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- $rid = $region_matches[1];
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- $rstart = $region_matches[2];
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- $rend = $region_matches[3];
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- if ($landmark_type) {
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- $result = chado_query("EXECUTE sel_cvterm_idnasy (:cv_id, :name, :synonym)",
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- array(':cv_id' => $cv->cv_id, ':name' => $landmark_type, ':synonym' => $landmark_type));
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- $cvterm = $result->fetchObject();
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- if (!$cvterm) {
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- watchdog('T_gff3_loader', 'cannot find feature type \'%landmark_type\' on line %line_num of the GFF file',
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- array('%landmark_type' => $landmark_type, '%line_num' => $line_num), WATCHDOG_ERROR);
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- return '';
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- }
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- tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $rid,
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- $rid, '', 'f', 'f', 1, 0);
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- }
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- continue;
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+ if (!file_exists($dfile)) {
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+ watchdog('T_gff3_loader', "Cannot find the file: %dfile",
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+ array('%dfile' => $dfile), WATCHDOG_ERROR);
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+ return 0;
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}
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-
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- // skip comments
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- if (preg_match('/^#/', $line)) {
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- continue;
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+
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+ print "Opening $gff_file\n";
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+
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+ //$lines = file($dfile,FILE_SKIP_EMPTY_LINES);
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+ $fh = fopen($dfile, 'r');
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+ if (!$fh) {
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+ watchdog('T_gff3_loader', "cannot open file: %dfile",
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+ array('%dfile' => $dfile), WATCHDOG_ERROR);
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+ return 0;
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}
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-
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- // skip empty lines
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- if (preg_match('/^\s*$/', $line)) {
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- continue;
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- }
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-
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- // get the columns
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- $cols = explode("\t", $line);
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- if (sizeof($cols) != 9) {
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- watchdog('T_gff3_loader', 'improper number of columns on line %line_num',
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- array('%line_num' => $line_num), WATCHDOG_ERROR);
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+ $filesize = filesize($dfile);
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+
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+ // get the controlled vocaubulary that we'll be using. The
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+ // default is the 'sequence' ontology
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+ $sql = "SELECT * FROM {cv} WHERE name = :cvname";
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+ $cv = chado_query($sql, array(':cvname' => 'sequence'))->fetchObject();
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+ if (!$cv) {
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+ watchdog('T_gff3_loader', "Cannot find the 'sequence' ontology",
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+ array(), WATCHDOG_ERROR);
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return '';
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}
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-
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- // get the column values
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- $landmark = $cols[0];
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- $source = $cols[1];
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- $type = $cols[2];
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- $start = $cols[3];
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- $end = $cols[4];
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- $score = $cols[5];
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- $strand = $cols[6];
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- $phase = $cols[7];
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- $attrs = explode(";", $cols[8]); // split by a semicolon
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-
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- // ready the start and stop for chado. Chado expects these positions
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- // to be zero-based, so we substract 1 from the fmin
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- $fmin = $start - 1;
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- $fmax = $end;
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- if ($end < $start) {
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- $fmin = $end - 1;
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- $fmax = $start;
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- }
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-
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- // format the strand for chado
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- if (strcmp($strand, '.') == 0) {
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- $strand = 0;
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- }
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- elseif (strcmp($strand, '+') == 0) {
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- $strand = 1;
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- }
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- elseif (strcmp($strand, '-') == 0) {
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- $strand = -1;
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- }
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- if (strcmp($phase, '.') == 0) {
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- $phase = '';
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- }
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- $result = chado_query("EXECUTE sel_cvterm_idnasy (:cv_id, :name, :synonym)",
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- array(':cv_id' => $cv->cv_id, ':name' => $type, ':synonym' => $type));
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-
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- $cvterm = $result->fetchObject();
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- if (!$cvterm) {
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- watchdog('T_gff3_loader', 'cannot find feature term \'%type\' on line %line_num of the GFF file',
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- array('%type' => $type, '%line_num' => $line_num), WATCHDOG_ERROR);
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- return '';
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+ // get the organism for which this GFF3 file belongs
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+ $sql = "SELECT * FROM {organism} WHERE organism_id = :organism_id";
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+ $organism = chado_query($sql, array(':organism_id' => $organism_id))->fetchObject();
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+
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+ $interval = intval($filesize * 0.0001);
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+ if ($interval == 0) {
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+ $interval = 1;
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}
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-
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- // break apart each of the attributes
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- $tags = array();
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- $attr_name = '';
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- $attr_uniquename = '';
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- $attr_residue_info = '';
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- $attr_locgroup = 0;
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- $attr_fmin_partial = 'f';
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- $attr_fmax_partial = 'f';
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- $attr_is_obsolete = 'f';
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- $attr_is_analysis = 'f';
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- $attr_others = '';
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- $residues = '';
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+ $in_fasta = 0;
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+ $line_num = 0;
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+ $num_read = 0;
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+ $intv_read = 0;
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- // the organism to which a feature belongs can be set in the GFF
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- // file using the 'organism' attribute. By default we
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- // set the $feature_organism variable to the default organism for the landmark
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- $attr_organism = '';
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- $feature_organism = $organism;
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-
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- foreach ($attrs as $attr) {
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- $attr = rtrim($attr);
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- $attr = ltrim($attr);
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- if (strcmp($attr, '')==0) {
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+ // prepare the statement used to get the cvterm for each feature.
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+ $psql = "
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+ PREPARE sel_cvterm_idnasy (int, text, text) AS
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+ SELECT CVT.cvterm_id, CVT.cv_id, CVT.name, CVT.definition,
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+ CVT.dbxref_id, CVT.is_obsolete, CVT.is_relationshiptype
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+ FROM {cvterm} CVT
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+ INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
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+ LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
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+ WHERE CV.cv_id = $1 and
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+ (lower(CVT.name) = lower($2) or lower(CVTS.synonym) = lower($3))
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+ ";
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+ $status = chado_query($psql);
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+ if (!$status) {
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+ watchdog('T_gff3_loader', 'cannot prepare statement \'sel_cvterm_idnasy\'.',
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+ array(), WATCHDOG_ERROR);
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+ return '';
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+ }
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+
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+ // iterate through each line of the GFF file
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+ print "Parsing Line $line_num (0.00%). Memory: " . number_format(memory_get_usage()) . " bytes\r";
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+ while ($line = fgets($fh)) {
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+ $line_num++;
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+ $size = drupal_strlen($line);
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+ $num_read += $size;
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+ $intv_read += $size;
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+
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+ if ($line_num < $start_line) {
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continue;
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+ }
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+
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+ // update the job status every 1% features
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+ if ($job and $intv_read >= $interval) {
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+ $intv_read = 0;
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+ $percent = sprintf("%.2f", ($num_read / $filesize) * 100);
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+ print "Parsing Line $line_num (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
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+ tripal_job_set_progress($job, intval(($num_read / $filesize) * 100));
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}
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- if (!preg_match('/^[^\=]+\=.+$/', $attr)) {
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- watchdog('T_gff3_loader', 'Attribute is not correctly formatted on line %line_num: %attr',
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- array('%line_num' => $line_num, '%attr' => $attr), WATCHDOG_ERROR);
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- return '';
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+
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+ // check to see if we have FASTA section, if so then set the variable
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+ // to start parsing
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+ if (preg_match('/^##FASTA/i', $line)) {
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+ if ($remove) {
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+ // we're done because this is a delete operation so break out of the loop.
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+ break;
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+ }
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+ tripal_feature_load_gff3_fasta($fh, $interval, $num_read, $intv_read, $line_num);
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+ continue;
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+ }
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+ // if the ##sequence-region line is present then we want to add a new feature
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+ if (preg_match('/^##sequence-region (.*?) (\d+) (\d+)$/i', $line, $region_matches)) {
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+ $rid = $region_matches[1];
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+ $rstart = $region_matches[2];
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+ $rend = $region_matches[3];
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+ if ($landmark_type) {
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+ $result = chado_query("EXECUTE sel_cvterm_idnasy (:cv_id, :name, :synonym)",
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+ array(':cv_id' => $cv->cv_id, ':name' => $landmark_type, ':synonym' => $landmark_type));
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+ $cvterm = $result->fetchObject();
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+ if (!$cvterm) {
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+ watchdog('T_gff3_loader', 'cannot find feature type \'%landmark_type\' on line %line_num of the GFF file',
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+ array('%landmark_type' => $landmark_type, '%line_num' => $line_num), WATCHDOG_ERROR);
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+ return '';
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+ }
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+ tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $rid,
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+ $rid, '', 'f', 'f', 1, 0);
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+ }
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+ continue;
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}
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-
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- // break apart each tag
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- $tag = preg_split("/=/", $attr, 2); // split by equals sign
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- // multiple instances of an attribute are separated by commas
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- $tag_name = $tag[0];
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- if (!array_key_exists($tag_name, $tags)) {
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- $tags[$tag_name] = array();
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+ // skip comments
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+ if (preg_match('/^#/', $line)) {
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+ continue;
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+ }
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+
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+ // skip empty lines
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+ if (preg_match('/^\s*$/', $line)) {
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+ continue;
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+ }
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+
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+ // get the columns
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+ $cols = explode("\t", $line);
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+ if (sizeof($cols) != 9) {
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+ watchdog('T_gff3_loader', 'improper number of columns on line %line_num',
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+ array('%line_num' => $line_num), WATCHDOG_ERROR);
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+ return '';
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}
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- $tags[$tag_name] = array_merge($tags[$tag_name], explode(",", $tag[1])); // split by comma
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+ // get the column values
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+ $landmark = $cols[0];
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+ $source = $cols[1];
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+ $type = $cols[2];
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+ $start = $cols[3];
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+ $end = $cols[4];
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+ $score = $cols[5];
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+ $strand = $cols[6];
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+ $phase = $cols[7];
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+ $attrs = explode(";", $cols[8]); // split by a semicolon
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- // replace the URL escape codes for each tag
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|
|
- for ($i = 0; $i < count($tags[$tag_name]); $i++) {
|
|
|
- $tags[$tag_name][$i] = urldecode($tags[$tag_name][$i]);
|
|
|
+ // ready the start and stop for chado. Chado expects these positions
|
|
|
+ // to be zero-based, so we substract 1 from the fmin
|
|
|
+ $fmin = $start - 1;
|
|
|
+ $fmax = $end;
|
|
|
+ if ($end < $start) {
|
|
|
+ $fmin = $end - 1;
|
|
|
+ $fmax = $start;
|
|
|
}
|
|
|
|
|
|
- // get the name and ID tags
|
|
|
- $skip_feature = 0; // if there is a problem with any of the attributes this variable gets set
|
|
|
- if (strcmp($tag_name, 'ID') == 0) {
|
|
|
- $attr_uniquename = urldecode($tag[1]);
|
|
|
+ // format the strand for chado
|
|
|
+ if (strcmp($strand, '.') == 0) {
|
|
|
+ $strand = 0;
|
|
|
}
|
|
|
- elseif (strcmp($tag_name, 'Name') == 0) {
|
|
|
- $attr_name = urldecode($tag[1]);
|
|
|
+ elseif (strcmp($strand, '+') == 0) {
|
|
|
+ $strand = 1;
|
|
|
}
|
|
|
- elseif (strcmp($tag_name, 'organism') == 0) {
|
|
|
- $attr_organism = urldecode($tag[1]);
|
|
|
- $org_matches = array();
|
|
|
- if (preg_match('/^(.*?):(.*?)$/', $attr_organism, $org_matches)) {
|
|
|
- $values = array(
|
|
|
- 'genus' => $org_matches[1],
|
|
|
- 'species' => $org_matches[2],
|
|
|
- );
|
|
|
- $options = array('statement_name' => 'sel_organism_gesp');
|
|
|
- $org = tripal_core_chado_select('organism', array("*"), $values, $options);
|
|
|
- if (count($org) == 0) {
|
|
|
- if ($create_organism) {
|
|
|
- $options = array('statement_name' => 'ins_organism_gesp');
|
|
|
- $feature_organism = (object) tripal_core_chado_insert('organism', $values, $options);
|
|
|
- if (!$feature_organism) {
|
|
|
- watchdog('T_gff3_loader', "Could not add the organism, '%org', from line %line. Skipping this line. ",
|
|
|
+ elseif (strcmp($strand, '-') == 0) {
|
|
|
+ $strand = -1;
|
|
|
+ }
|
|
|
+ if (strcmp($phase, '.') == 0) {
|
|
|
+ $phase = '';
|
|
|
+ }
|
|
|
+
|
|
|
+ $result = chado_query("EXECUTE sel_cvterm_idnasy (:cv_id, :name, :synonym)",
|
|
|
+ array(':cv_id' => $cv->cv_id, ':name' => $type, ':synonym' => $type));
|
|
|
+
|
|
|
+ $cvterm = $result->fetchObject();
|
|
|
+ if (!$cvterm) {
|
|
|
+ watchdog('T_gff3_loader', 'cannot find feature term \'%type\' on line %line_num of the GFF file',
|
|
|
+ array('%type' => $type, '%line_num' => $line_num), WATCHDOG_ERROR);
|
|
|
+ return '';
|
|
|
+ }
|
|
|
+
|
|
|
+ // break apart each of the attributes
|
|
|
+ $tags = array();
|
|
|
+ $attr_name = '';
|
|
|
+ $attr_uniquename = '';
|
|
|
+ $attr_residue_info = '';
|
|
|
+ $attr_locgroup = 0;
|
|
|
+ $attr_fmin_partial = 'f';
|
|
|
+ $attr_fmax_partial = 'f';
|
|
|
+ $attr_is_obsolete = 'f';
|
|
|
+ $attr_is_analysis = 'f';
|
|
|
+ $attr_others = '';
|
|
|
+ $residues = '';
|
|
|
+
|
|
|
+ // the organism to which a feature belongs can be set in the GFF
|
|
|
+ // file using the 'organism' attribute. By default we
|
|
|
+ // set the $feature_organism variable to the default organism for the landmark
|
|
|
+ $attr_organism = '';
|
|
|
+ $feature_organism = $organism;
|
|
|
+
|
|
|
+ foreach ($attrs as $attr) {
|
|
|
+ $attr = rtrim($attr);
|
|
|
+ $attr = ltrim($attr);
|
|
|
+ if (strcmp($attr, '')==0) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ if (!preg_match('/^[^\=]+\=.+$/', $attr)) {
|
|
|
+ watchdog('T_gff3_loader', 'Attribute is not correctly formatted on line %line_num: %attr',
|
|
|
+ array('%line_num' => $line_num, '%attr' => $attr), WATCHDOG_ERROR);
|
|
|
+ return '';
|
|
|
+ }
|
|
|
+
|
|
|
+ // break apart each tag
|
|
|
+ $tag = preg_split("/=/", $attr, 2); // split by equals sign
|
|
|
+
|
|
|
+ // multiple instances of an attribute are separated by commas
|
|
|
+ $tag_name = $tag[0];
|
|
|
+ if (!array_key_exists($tag_name, $tags)) {
|
|
|
+ $tags[$tag_name] = array();
|
|
|
+ }
|
|
|
+ $tags[$tag_name] = array_merge($tags[$tag_name], explode(",", $tag[1])); // split by comma
|
|
|
+
|
|
|
+
|
|
|
+ // replace the URL escape codes for each tag
|
|
|
+ for ($i = 0; $i < count($tags[$tag_name]); $i++) {
|
|
|
+ $tags[$tag_name][$i] = urldecode($tags[$tag_name][$i]);
|
|
|
+ }
|
|
|
+
|
|
|
+ // get the name and ID tags
|
|
|
+ $skip_feature = 0; // if there is a problem with any of the attributes this variable gets set
|
|
|
+ if (strcmp($tag_name, 'ID') == 0) {
|
|
|
+ $attr_uniquename = urldecode($tag[1]);
|
|
|
+ }
|
|
|
+ elseif (strcmp($tag_name, 'Name') == 0) {
|
|
|
+ $attr_name = urldecode($tag[1]);
|
|
|
+ }
|
|
|
+ elseif (strcmp($tag_name, 'organism') == 0) {
|
|
|
+ $attr_organism = urldecode($tag[1]);
|
|
|
+ $org_matches = array();
|
|
|
+ if (preg_match('/^(.*?):(.*?)$/', $attr_organism, $org_matches)) {
|
|
|
+ $values = array(
|
|
|
+ 'genus' => $org_matches[1],
|
|
|
+ 'species' => $org_matches[2],
|
|
|
+ );
|
|
|
+ $options = array('statement_name' => 'sel_organism_gesp');
|
|
|
+ $org = tripal_core_chado_select('organism', array("*"), $values, $options);
|
|
|
+ if (count($org) == 0) {
|
|
|
+ if ($create_organism) {
|
|
|
+ $options = array('statement_name' => 'ins_organism_gesp');
|
|
|
+ $feature_organism = (object) tripal_core_chado_insert('organism', $values, $options);
|
|
|
+ if (!$feature_organism) {
|
|
|
+ watchdog('T_gff3_loader', "Could not add the organism, '%org', from line %line. Skipping this line. ",
|
|
|
+ array('%org' => $attr_organism, '%line' => $line_num), WATCHDOG_ERROR);
|
|
|
+ $skip_feature = 1;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ watchdog('T_gff3_loader', "The organism attribute '%org' on line %line does not exist. Skipping this line. ",
|
|
|
array('%org' => $attr_organism, '%line' => $line_num), WATCHDOG_ERROR);
|
|
|
- $skip_feature = 1;
|
|
|
+ $skip_feature = 1;
|
|
|
}
|
|
|
- }
|
|
|
+ }
|
|
|
else {
|
|
|
- watchdog('T_gff3_loader', "The organism attribute '%org' on line %line does not exist. Skipping this line. ",
|
|
|
- array('%org' => $attr_organism, '%line' => $line_num), WATCHDOG_ERROR);
|
|
|
- $skip_feature = 1;
|
|
|
+ // we found the organism in the database so use it
|
|
|
+ $feature_organism = $org[0];
|
|
|
}
|
|
|
- }
|
|
|
+ }
|
|
|
else {
|
|
|
- // we found the organism in the database so use it
|
|
|
- $feature_organism = $org[0];
|
|
|
+ watchdog('T_gff3_loader', "The organism attribute '%org' on line %line is not properly formated. It " .
|
|
|
+ "should be of the form: organism=Genus:species. Skipping this line.",
|
|
|
+ array('%org' => $attr_organism, '%line' => $line_num), WATCHDOG_ERROR);
|
|
|
+ $skip_feature = 1;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ // get the list of non-reserved attributes
|
|
|
+ elseif (strcmp($tag_name, 'Alias') != 0 and strcmp($tag_name, 'Parent') != 0 and
|
|
|
+ strcmp($tag_name, 'Target') != 0 and strcmp($tag_name, 'Gap') != 0 and
|
|
|
+ strcmp($tag_name, 'Derives_from') != 0 and strcmp($tag_name, 'Note') != 0 and
|
|
|
+ strcmp($tag_name, 'Dbxref') != 0 and strcmp($tag_name, 'Ontology_term') != 0 and
|
|
|
+ strcmp($tag_name, 'Is_circular') != 0 and strcmp($tag_name, 'target_organism') != 0 and
|
|
|
+ strcmp($tag_name, 'target_type') != 0 and strcmp($tag_name, 'organism' != 0)) {
|
|
|
+ foreach ($tags[$tag_name] as $value) {
|
|
|
+ $attr_others[$tag_name][] = $value;
|
|
|
}
|
|
|
- }
|
|
|
- else {
|
|
|
- watchdog('T_gff3_loader', "The organism attribute '%org' on line %line is not properly formated. It " .
|
|
|
- "should be of the form: organism=Genus:species. Skipping this line.",
|
|
|
- array('%org' => $attr_organism, '%line' => $line_num), WATCHDOG_ERROR);
|
|
|
- $skip_feature = 1;
|
|
|
- }
|
|
|
- }
|
|
|
- // get the list of non-reserved attributes
|
|
|
- elseif (strcmp($tag_name, 'Alias') != 0 and strcmp($tag_name, 'Parent') != 0 and
|
|
|
- strcmp($tag_name, 'Target') != 0 and strcmp($tag_name, 'Gap') != 0 and
|
|
|
- strcmp($tag_name, 'Derives_from') != 0 and strcmp($tag_name, 'Note') != 0 and
|
|
|
- strcmp($tag_name, 'Dbxref') != 0 and strcmp($tag_name, 'Ontology_term') != 0 and
|
|
|
- strcmp($tag_name, 'Is_circular') != 0 and strcmp($tag_name, 'target_organism') != 0 and
|
|
|
- strcmp($tag_name, 'target_type') != 0 and strcmp($tag_name, 'organism' != 0)) {
|
|
|
- foreach ($tags[$tag_name] as $value) {
|
|
|
- $attr_others[$tag_name][] = $value;
|
|
|
}
|
|
|
}
|
|
|
- }
|
|
|
-
|
|
|
- if ($skip_line) {
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- // if neither name nor uniquename are provided then generate one
|
|
|
- if (!$attr_uniquename and !$attr_name) {
|
|
|
- // check if an alternate ID field is suggested, if so, then use
|
|
|
- // that for the name
|
|
|
- if (array_key_exists($alt_id_attr, $tags)) {
|
|
|
- $attr_uniquename = $tags[$alt_id_attr][0];
|
|
|
- $attr_name = $attr_uniquename;
|
|
|
+
|
|
|
+ if ($skip_line) {
|
|
|
+ continue;
|
|
|
}
|
|
|
- // if the row has a parent then generate a uniquename using the parent name
|
|
|
- // add the date to the name in the event there are more than one child with
|
|
|
- // the same parent.
|
|
|
- elseif (array_key_exists('Parent', $tags)) {
|
|
|
- $date = getdate();
|
|
|
- $attr_uniquename = $tags['Parent'][0] . "-$type-$landmark-" . $date[0] . ":" . ($fmin + 1) . ".." . $fmax;
|
|
|
+
|
|
|
+ // if neither name nor uniquename are provided then generate one
|
|
|
+ if (!$attr_uniquename and !$attr_name) {
|
|
|
+ // check if an alternate ID field is suggested, if so, then use
|
|
|
+ // that for the name
|
|
|
+ if (array_key_exists($alt_id_attr, $tags)) {
|
|
|
+ $attr_uniquename = $tags[$alt_id_attr][0];
|
|
|
+ $attr_name = $attr_uniquename;
|
|
|
+ }
|
|
|
+ // if the row has a parent then generate a uniquename using the parent name
|
|
|
+ // add the date to the name in the event there are more than one child with
|
|
|
+ // the same parent.
|
|
|
+ elseif (array_key_exists('Parent', $tags)) {
|
|
|
+ $date = getdate();
|
|
|
+ $attr_uniquename = $tags['Parent'][0] . "-$type-$landmark-" . $date[0] . ":" . ($fmin + 1) . ".." . $fmax;
|
|
|
+ $attr_name = $attr_uniquename;
|
|
|
+ }
|
|
|
+ // generate a unique name based on the date, type and location
|
|
|
+ // and set the name to simply be the type
|
|
|
+ else {
|
|
|
+ $date = getdate();
|
|
|
+ $attr_uniquename = $date[0] . "-$type-$landmark:" . ($fmin + 1) . ".." . $fmax;
|
|
|
+ $attr_name = $type;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // if a name is not specified then use the unique name as the name
|
|
|
+ if (strcmp($attr_name, '')==0) {
|
|
|
$attr_name = $attr_uniquename;
|
|
|
}
|
|
|
- // generate a unique name based on the date, type and location
|
|
|
- // and set the name to simply be the type
|
|
|
- else {
|
|
|
+
|
|
|
+ // if an ID attribute is not specified then use the attribute name plus the date
|
|
|
+ if (!$attr_uniquename) {
|
|
|
$date = getdate();
|
|
|
- $attr_uniquename = $date[0] . "-$type-$landmark:" . ($fmin + 1) . ".." . $fmax;
|
|
|
- $attr_name = $type;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // if a name is not specified then use the unique name as the name
|
|
|
- if (strcmp($attr_name, '')==0) {
|
|
|
- $attr_name = $attr_uniquename;
|
|
|
- }
|
|
|
-
|
|
|
- // if an ID attribute is not specified then use the attribute name plus the date
|
|
|
- if (!$attr_uniquename) {
|
|
|
- $date = getdate();
|
|
|
- $attr_uniquename = $attr_name . '-' . $date[0];
|
|
|
- }
|
|
|
-
|
|
|
- // make sure the landmark sequence exists in the database. If the user
|
|
|
- // has not specified a landmark type (and it's not requiredin the GFF foramt)
|
|
|
- // then We don't know the type of the landmark so we'll hope that it's unique across
|
|
|
- // all types for the orgnaism. Only do this test if the landmark and the feature are
|
|
|
- // different.
|
|
|
- if (!$remove and !(strcmp($landmark, $attr_uniquename) == 0 or strcmp($landmark, $attr_name) == 0)) {
|
|
|
- $select = array(
|
|
|
- 'organism_id' => $organism->organism_id,
|
|
|
- 'uniquename' => $landmark,
|
|
|
- );
|
|
|
- $columns = array('count(*) as num_landmarks');
|
|
|
- $options = array('statement_name' => 'sel_feature_numland');
|
|
|
- if ($landmark_type) {
|
|
|
- $select['type_id'] = array(
|
|
|
- 'name' => $landmark_type,
|
|
|
- );
|
|
|
- $options = array('statement_name' => 'sel_feature_numlandty');
|
|
|
- }
|
|
|
- $count = tripal_core_chado_select('feature', $columns, $select, $options);
|
|
|
- if (!$count or count($count) == 0 or $count[0]->num_landmarks == 0) {
|
|
|
- // now look for the landmark using the name rather than uniquename.
|
|
|
+ $attr_uniquename = $attr_name . '-' . $date[0];
|
|
|
+ }
|
|
|
+
|
|
|
+ // make sure the landmark sequence exists in the database. If the user
|
|
|
+ // has not specified a landmark type (and it's not requiredin the GFF foramt)
|
|
|
+ // then We don't know the type of the landmark so we'll hope that it's unique across
|
|
|
+ // all types for the orgnaism. Only do this test if the landmark and the feature are
|
|
|
+ // different.
|
|
|
+ if (!$remove and !(strcmp($landmark, $attr_uniquename) == 0 or strcmp($landmark, $attr_name) == 0)) {
|
|
|
$select = array(
|
|
|
'organism_id' => $organism->organism_id,
|
|
|
- 'name' => $landmark,
|
|
|
- );
|
|
|
+ 'uniquename' => $landmark,
|
|
|
+ );
|
|
|
$columns = array('count(*) as num_landmarks');
|
|
|
- $options = array('statement_name' => 'sel_feature_numlandna');
|
|
|
+ $options = array('statement_name' => 'sel_feature_numland');
|
|
|
if ($landmark_type) {
|
|
|
$select['type_id'] = array(
|
|
|
'name' => $landmark_type,
|
|
|
);
|
|
|
- $options = array('statement_name' => 'sel_feature_numlandnaty');
|
|
|
+ $options = array('statement_name' => 'sel_feature_numlandty');
|
|
|
+ }
|
|
|
+ $count = tripal_core_chado_select('feature', $columns, $select, $options);
|
|
|
+ if (!$count or count($count) == 0 or $count[0]->num_landmarks == 0) {
|
|
|
+ // now look for the landmark using the name rather than uniquename.
|
|
|
+ $select = array(
|
|
|
+ 'organism_id' => $organism->organism_id,
|
|
|
+ 'name' => $landmark,
|
|
|
+ );
|
|
|
+ $columns = array('count(*) as num_landmarks');
|
|
|
+ $options = array('statement_name' => 'sel_feature_numlandna');
|
|
|
+ if ($landmark_type) {
|
|
|
+ $select['type_id'] = array(
|
|
|
+ 'name' => $landmark_type,
|
|
|
+ );
|
|
|
+ $options = array('statement_name' => 'sel_feature_numlandnaty');
|
|
|
+ }
|
|
|
+ $count = tripal_core_chado_select('feature', $columns, $select, $options);
|
|
|
+ if (!$count or count($count) == 0 or $count[0]->num_landmarks == 0) {
|
|
|
+ watchdog('T_gff3_loader', "The landmark '%landmark' cannot be found for this organism (%species) " .
|
|
|
+ "Please add the landmark and then retry the import of this GFF3 " .
|
|
|
+ "file", array('%landmark' => $landmark, '%species' => $organism->genus . " " . $organism->species), WATCHDOG_ERROR);
|
|
|
+ return '';
|
|
|
+ }
|
|
|
+ elseif ($count[0]->num_landmarks > 1) {
|
|
|
+ watchdog('T_gff3_loader', "The landmark '%landmark' has more than one entry for this organism (%species) " .
|
|
|
+ "Cannot continue", array('%landmark' => $landmark, '%species' => $organism->genus . " " . $organism->species), WATCHDOG_ERROR);
|
|
|
+ return '';
|
|
|
+ }
|
|
|
+
|
|
|
}
|
|
|
- $count = tripal_core_chado_select('feature', $columns, $select, $options);
|
|
|
- if (!$count or count($count) == 0 or $count[0]->num_landmarks == 0) {
|
|
|
- watchdog('T_gff3_loader', "The landmark '%landmark' cannot be found for this organism (%species) " .
|
|
|
- "Please add the landmark and then retry the import of this GFF3 " .
|
|
|
- "file", array('%landmark' => $landmark, '%species' => $organism->genus . " " . $organism->species), WATCHDOG_ERROR);
|
|
|
+ if ($count[0]->num_landmarks > 1) {
|
|
|
+ watchdog('T_gff3_loader', "The landmark '%landmark' is not unique for this organism. " .
|
|
|
+ "The features cannot be associated", array('%landmark' => $landmark), WATCHDOG_ERROR);
|
|
|
return '';
|
|
|
- }
|
|
|
- elseif ($count[0]->num_landmarks > 1) {
|
|
|
- watchdog('T_gff3_loader', "The landmark '%landmark' has more than one entry for this organism (%species) " .
|
|
|
- "Cannot continue", array('%landmark' => $landmark, '%species' => $organism->genus . " " . $organism->species), WATCHDOG_ERROR);
|
|
|
- return '';
|
|
|
- }
|
|
|
-
|
|
|
+ }
|
|
|
}
|
|
|
- if ($count[0]->num_landmarks > 1) {
|
|
|
- watchdog('T_gff3_loader', "The landmark '%landmark' is not unique for this organism. " .
|
|
|
- "The features cannot be associated", array('%landmark' => $landmark), WATCHDOG_ERROR);
|
|
|
- return '';
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // if the option is to remove or refresh then we want to remove
|
|
|
- // the feature from the database.
|
|
|
- if ($remove or $refresh) {
|
|
|
- $sql = "DELETE FROM {feature}
|
|
|
- WHERE organism_id = %d and uniquename = '%s' and type_id = %d";
|
|
|
- $match = array(
|
|
|
- 'organism_id' => $feature_organism->organism_id,
|
|
|
- 'uniquename' => $attr_uniquename,
|
|
|
- 'type_id' => $cvterm->cvterm_id
|
|
|
- );
|
|
|
- $result = tripal_core_chado_delete('feature', $match);
|
|
|
- if (!$result) {
|
|
|
- watchdog('T_gff3_loader', "cannot delete feature %attr_uniquename",
|
|
|
- array('%attr_uniquename' => $attr_uniquename), WATCHDOG_ERROR);
|
|
|
+
|
|
|
+ // if the option is to remove or refresh then we want to remove
|
|
|
+ // the feature from the database.
|
|
|
+ if ($remove or $refresh) {
|
|
|
+ $sql = "DELETE FROM {feature}
|
|
|
+ WHERE organism_id = %d and uniquename = '%s' and type_id = %d";
|
|
|
+ $match = array(
|
|
|
+ 'organism_id' => $feature_organism->organism_id,
|
|
|
+ 'uniquename' => $attr_uniquename,
|
|
|
+ 'type_id' => $cvterm->cvterm_id
|
|
|
+ );
|
|
|
+ $result = tripal_core_chado_delete('feature', $match);
|
|
|
+ if (!$result) {
|
|
|
+ watchdog('T_gff3_loader', "cannot delete feature %attr_uniquename",
|
|
|
+ array('%attr_uniquename' => $attr_uniquename), WATCHDOG_ERROR);
|
|
|
+ }
|
|
|
+ $feature = 0;
|
|
|
+ unset($result);
|
|
|
}
|
|
|
- $feature = 0;
|
|
|
- unset($result);
|
|
|
- }
|
|
|
-
|
|
|
- // add or update the feature and all properties
|
|
|
- if ($update or $refresh or $add_only) {
|
|
|
+
|
|
|
+ // add or update the feature and all properties
|
|
|
+ if ($update or $refresh or $add_only) {
|
|
|
+
|
|
|
+ // add/update the feature
|
|
|
+ $feature = tripal_feature_load_gff3_feature($feature_organism, $analysis_id, $cvterm,
|
|
|
+ $attr_uniquename, $attr_name, $residues, $attr_is_analysis,
|
|
|
+ $attr_is_obsolete, $add_only, $score);
|
|
|
+
|
|
|
+ if ($feature) {
|
|
|
+
|
|
|
+ // add a record for this feature to the tripal_gff_temp table for
|
|
|
+ // later lookup
|
|
|
+ $values = array(
|
|
|
+ 'feature_id' => $feature->feature_id,
|
|
|
+ 'organism_id' => $feature->organism_id,
|
|
|
+ 'type_name' => $type,
|
|
|
+ 'uniquename' => $feature->uniquename
|
|
|
+ );
|
|
|
+ // make sure this record doesn't already exist in oru temp table
|
|
|
+ $options = array('statement_name' => 'sel_tripalgfftemp_all');
|
|
|
+ $results = tripal_core_chado_select('tripal_gff_temp', array('*'), $values, $options);
|
|
|
+
|
|
|
+ if (count($results) == 0) {
|
|
|
+ $options = array('statement_name' => 'ins_tripalgfftemp');
|
|
|
+ $result = tripal_core_chado_insert('tripal_gff_temp', $values, $options);
|
|
|
+ if (!$result) {
|
|
|
+ watchdog('T_gff3_loader', "Cound not save record in temporary table, Cannot continue.", array(), WATCHDOG_ERROR);
|
|
|
+ exit;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ // add/update the featureloc if the landmark and the ID are not the same
|
|
|
+ // if they are the same then this entry in the GFF is probably a landmark identifier
|
|
|
+ if (strcmp($landmark, $attr_uniquename) !=0 ) {
|
|
|
+ tripal_feature_load_gff3_featureloc($feature, $organism,
|
|
|
+ $landmark, $fmin, $fmax, $strand, $phase, $attr_fmin_partial,
|
|
|
+ $attr_fmax_partial, $attr_residue_info, $attr_locgroup);
|
|
|
+ }
|
|
|
|
|
|
- // add/update the feature
|
|
|
- $feature = tripal_feature_load_gff3_feature($feature_organism, $analysis_id, $cvterm,
|
|
|
- $attr_uniquename, $attr_name, $residues, $attr_is_analysis,
|
|
|
- $attr_is_obsolete, $add_only, $score);
|
|
|
-
|
|
|
- if ($feature) {
|
|
|
-
|
|
|
- // add a record for this feature to the tripal_gff_temp table for
|
|
|
- // later lookup
|
|
|
- $values = array(
|
|
|
- 'feature_id' => $feature->feature_id,
|
|
|
- 'organism_id' => $feature->organism_id,
|
|
|
- 'type_name' => $type,
|
|
|
- 'uniquename' => $feature->uniquename
|
|
|
- );
|
|
|
- // make sure this record doesn't already exist in oru temp table
|
|
|
- $options = array('statement_name' => 'sel_tripalgfftemp_all');
|
|
|
- $results = tripal_core_chado_select('tripal_gff_temp', array('*'), $values, $options);
|
|
|
-
|
|
|
- if (count($results) == 0) {
|
|
|
- $options = array('statement_name' => 'ins_tripalgfftemp');
|
|
|
- $result = tripal_core_chado_insert('tripal_gff_temp', $values, $options);
|
|
|
- if (!$result) {
|
|
|
- watchdog('T_gff3_loader', "Cound not save record in temporary table, Cannot continue.", array(), WATCHDOG_ERROR);
|
|
|
- exit;
|
|
|
+ // add any aliases for this feature
|
|
|
+ if (array_key_exists('Alias', $tags)) {
|
|
|
+ tripal_feature_load_gff3_alias($feature, $tags['Alias']);
|
|
|
+ }
|
|
|
+ // add any dbxrefs for this feature
|
|
|
+ if (array_key_exists('Dbxref', $tags)) {
|
|
|
+ tripal_feature_load_gff3_dbxref($feature, $tags['Dbxref']);
|
|
|
}
|
|
|
- }
|
|
|
- // add/update the featureloc if the landmark and the ID are not the same
|
|
|
- // if they are the same then this entry in the GFF is probably a landmark identifier
|
|
|
- if (strcmp($landmark, $attr_uniquename) !=0 ) {
|
|
|
- tripal_feature_load_gff3_featureloc($feature, $organism,
|
|
|
- $landmark, $fmin, $fmax, $strand, $phase, $attr_fmin_partial,
|
|
|
- $attr_fmax_partial, $attr_residue_info, $attr_locgroup);
|
|
|
- }
|
|
|
-continue;
|
|
|
- // add any aliases for this feature
|
|
|
- if (array_key_exists('Alias', $tags)) {
|
|
|
- tripal_feature_load_gff3_alias($feature, $tags['Alias']);
|
|
|
- }
|
|
|
- // add any dbxrefs for this feature
|
|
|
- if (array_key_exists('Dbxref', $tags)) {
|
|
|
- tripal_feature_load_gff3_dbxref($feature, $tags['Dbxref']);
|
|
|
- }
|
|
|
- // add any ontology terms for this feature
|
|
|
- if (array_key_exists('Ontology_term', $tags)) {
|
|
|
- tripal_feature_load_gff3_ontology($feature, $tags['Ontology_term']);
|
|
|
- }
|
|
|
- // add parent relationships
|
|
|
- if (array_key_exists('Parent', $tags)) {
|
|
|
- tripal_feature_load_gff3_parents($feature, $cvterm, $tags['Parent'], $feature_organism->organism_id, $fmin);
|
|
|
- }
|
|
|
- // add target relationships
|
|
|
- if (array_key_exists('Target', $tags)) {
|
|
|
- tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $target_type, $create_target, $attr_locgroup);
|
|
|
- }
|
|
|
- // add gap information. This goes in simply as a property
|
|
|
- if (array_key_exists('Gap', $tags)) {
|
|
|
- foreach ($tags['Gap'] as $value) {
|
|
|
- tripal_feature_load_gff3_property($feature, 'Gap', $value);
|
|
|
+ // add any ontology terms for this feature
|
|
|
+ if (array_key_exists('Ontology_term', $tags)) {
|
|
|
+ tripal_feature_load_gff3_ontology($feature, $tags['Ontology_term']);
|
|
|
+ }
|
|
|
+ // add parent relationships
|
|
|
+ if (array_key_exists('Parent', $tags)) {
|
|
|
+ tripal_feature_load_gff3_parents($feature, $cvterm, $tags['Parent'], $feature_organism->organism_id, $fmin);
|
|
|
+ }
|
|
|
+ // add target relationships
|
|
|
+ if (array_key_exists('Target', $tags)) {
|
|
|
+ tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $target_type, $create_target, $attr_locgroup);
|
|
|
}
|
|
|
- }
|
|
|
- // add notes. This goes in simply as a property
|
|
|
- if (array_key_exists('Note', $tags)) {
|
|
|
- foreach ($tags['Note'] as $value) {
|
|
|
- tripal_feature_load_gff3_property($feature, 'Note', $value);
|
|
|
+ // add gap information. This goes in simply as a property
|
|
|
+ if (array_key_exists('Gap', $tags)) {
|
|
|
+ foreach ($tags['Gap'] as $value) {
|
|
|
+ tripal_feature_load_gff3_property($feature, 'Gap', $value);
|
|
|
+ }
|
|
|
}
|
|
|
- }
|
|
|
- // add the Derives_from relationship (e.g. polycistronic genes).
|
|
|
- if (array_key_exists('Derives_from', $tags)) {
|
|
|
- tripal_feature_load_gff3_derives_from($feature, $tags['Derives_from'][0], $feature_organism);
|
|
|
- }
|
|
|
- // add in the GFF3_source dbxref so that GBrowse can find the feature using the source column
|
|
|
- $source_ref = array('GFF_source:' . $source);
|
|
|
- tripal_feature_load_gff3_dbxref($feature, $source_ref);
|
|
|
- // add any additional attributes
|
|
|
- if ($attr_others) {
|
|
|
- foreach ($attr_others as $tag_name => $values) {
|
|
|
- foreach ($values as $value) {
|
|
|
- tripal_feature_load_gff3_property($feature, $tag_name, $value);
|
|
|
+ // add notes. This goes in simply as a property
|
|
|
+ if (array_key_exists('Note', $tags)) {
|
|
|
+ foreach ($tags['Note'] as $value) {
|
|
|
+ tripal_feature_load_gff3_property($feature, 'Note', $value);
|
|
|
}
|
|
|
}
|
|
|
+ // add the Derives_from relationship (e.g. polycistronic genes).
|
|
|
+ if (array_key_exists('Derives_from', $tags)) {
|
|
|
+ tripal_feature_load_gff3_derives_from($feature, $tags['Derives_from'][0], $feature_organism);
|
|
|
+ }
|
|
|
+ // add in the GFF3_source dbxref so that GBrowse can find the feature using the source column
|
|
|
+ $source_ref = array('GFF_source:' . $source);
|
|
|
+ tripal_feature_load_gff3_dbxref($feature, $source_ref);
|
|
|
+ // add any additional attributes
|
|
|
+ if ($attr_others) {
|
|
|
+ foreach ($attr_others as $tag_name => $values) {
|
|
|
+ foreach ($values as $value) {
|
|
|
+ tripal_feature_load_gff3_property($feature, $tag_name, $value);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
}
|
|
|
-
|
|
|
}
|
|
|
}
|
|
|
- }
|
|
|
-
|
|
|
- if (!$remove) {
|
|
|
- print "\nSetting ranks of children...\n";
|
|
|
-
|
|
|
- // get features in a relationship that are also children of an alignment
|
|
|
- $sql = "
|
|
|
- SELECT DISTINCT F.feature_id, F.organism_id, F.type_id,
|
|
|
- F.uniquename, FL.strand
|
|
|
- FROM {tripal_gff_temp} TGT
|
|
|
- INNER JOIN {feature} F ON TGT.feature_id = F.feature_id
|
|
|
- INNER JOIN {feature_relationship} FR ON FR.object_id = TGT.feature_id
|
|
|
- INNER JOIN {cvterm} CVT ON CVT.cvterm_id = FR.type_id
|
|
|
- INNER JOIN {featureloc} FL ON FL.feature_id = F.feature_id
|
|
|
- WHERE CVT.name = 'part_of'
|
|
|
- ";
|
|
|
- $parents = chado_query($sql);
|
|
|
-
|
|
|
- // build and prepare the SQL for selecting the children relationship
|
|
|
- $sql = "";
|
|
|
-
|
|
|
- $sql = "
|
|
|
- PREPARE sel_gffchildren (int) AS
|
|
|
- SELECT DISTINCT FR.feature_relationship_id, FL.fmin, FR.rank
|
|
|
- FROM {feature_relationship} FR
|
|
|
- INNER JOIN {featureloc} FL on FL.feature_id = FR.subject_id
|
|
|
- WHERE FR.object_id = \$1 ORDER BY FL.fmin ASC
|
|
|
- ";
|
|
|
- $success = chado_query('sel_gffchildren', $sql);
|
|
|
- if (!$success) {
|
|
|
- watchdog("T_gff3_loader", "Cannot prepare statement 'sel_gffchildren' and cannot set children ranks.",
|
|
|
- array(), WATCHDOG_WARNING);
|
|
|
- return 0;
|
|
|
- }
|
|
|
-
|
|
|
- // now set the rank of any parent/child relationships. The order is based
|
|
|
- // on the fmin. The start rank is 1. This allows features with other
|
|
|
- // relationships to be '0' (the default), and doesn't interfer with the
|
|
|
- // ordering defined here.
|
|
|
- while ($parent = $parents->fetchObject()) {
|
|
|
-
|
|
|
- // get the children
|
|
|
- if ($connection) {
|
|
|
- $result = chado_query('EXECUTE sel_gffchildren (:feature_id)', array(':feature_id' => $parent->feature_id));
|
|
|
- }
|
|
|
- else {
|
|
|
- $result = chado_query($sql, array(':feature_id' => $parent->feature_id));
|
|
|
- }
|
|
|
+
|
|
|
+ if (!$remove) {
|
|
|
+ print "\nSetting ranks of children...\n";
|
|
|
|
|
|
- // build an array of the children
|
|
|
- $children = array();
|
|
|
- while ($child = $result->fetchObject()) {
|
|
|
- $children[] = $child;
|
|
|
- }
|
|
|
+ // get features in a relationship that are also children of an alignment
|
|
|
+ $sql = "
|
|
|
+ SELECT DISTINCT F.feature_id, F.organism_id, F.type_id,
|
|
|
+ F.uniquename, FL.strand
|
|
|
+ FROM {tripal_gff_temp} TGT
|
|
|
+ INNER JOIN {feature} F ON TGT.feature_id = F.feature_id
|
|
|
+ INNER JOIN {feature_relationship} FR ON FR.object_id = TGT.feature_id
|
|
|
+ INNER JOIN {cvterm} CVT ON CVT.cvterm_id = FR.type_id
|
|
|
+ INNER JOIN {featureloc} FL ON FL.feature_id = F.feature_id
|
|
|
+ WHERE CVT.name = 'part_of'
|
|
|
+ ";
|
|
|
+ $parents = chado_query($sql);
|
|
|
|
|
|
- // the children list comes sorted in ascending fmin
|
|
|
- // but if the parent is on the reverse strand we need to
|
|
|
- // reverse the order of the children.
|
|
|
- if ($parent->strand == -1) {
|
|
|
- arsort($children);
|
|
|
- }
|
|
|
+ // build and prepare the SQL for selecting the children relationship
|
|
|
+ $sql = "";
|
|
|
|
|
|
- // first set the ranks to a negative number so that we don't
|
|
|
- // get a duplicate error message when we try to change any of them
|
|
|
- $rank = -1;
|
|
|
- foreach ($children as $child) {
|
|
|
- $match = array('feature_relationship_id' => $child->feature_relationship_id);
|
|
|
- $options = array('statement_name' => 'upd_featurerelationship_rank');
|
|
|
- $values = array('rank' => $rank);
|
|
|
- tripal_core_chado_update('feature_relationship', $match, $values, $options);
|
|
|
- $rank--;
|
|
|
+ $sql = "
|
|
|
+ PREPARE sel_gffchildren (int) AS
|
|
|
+ SELECT DISTINCT FR.feature_relationship_id, FL.fmin, FR.rank
|
|
|
+ FROM {feature_relationship} FR
|
|
|
+ INNER JOIN {featureloc} FL on FL.feature_id = FR.subject_id
|
|
|
+ WHERE FR.object_id = \$1 ORDER BY FL.fmin ASC
|
|
|
+ ";
|
|
|
+ $success = chado_query('sel_gffchildren', $sql);
|
|
|
+ if (!$success) {
|
|
|
+ watchdog("T_gff3_loader", "Cannot prepare statement 'sel_gffchildren' and cannot set children ranks.",
|
|
|
+ array(), WATCHDOG_WARNING);
|
|
|
+ return 0;
|
|
|
}
|
|
|
- // now set the rank correctly. The rank should start at 0.
|
|
|
- $rank = 0;
|
|
|
- foreach ($children as $child) {
|
|
|
- $match = array('feature_relationship_id' => $child->feature_relationship_id);
|
|
|
- $options = array('statement_name' => 'upd_featurerelationship_rank');
|
|
|
- $values = array('rank' => $rank);
|
|
|
- //print "Was: " . $child->rank . " now $rank ($parent->strand)\n" ;
|
|
|
- tripal_core_chado_update('feature_relationship', $match, $values, $options);
|
|
|
- $rank++;
|
|
|
+
|
|
|
+ // now set the rank of any parent/child relationships. The order is based
|
|
|
+ // on the fmin. The start rank is 1. This allows features with other
|
|
|
+ // relationships to be '0' (the default), and doesn't interfer with the
|
|
|
+ // ordering defined here.
|
|
|
+ while ($parent = $parents->fetchObject()) {
|
|
|
+
|
|
|
+ // get the children
|
|
|
+ if ($connection) {
|
|
|
+ $result = chado_query('EXECUTE sel_gffchildren (:feature_id)', array(':feature_id' => $parent->feature_id));
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $result = chado_query($sql, array(':feature_id' => $parent->feature_id));
|
|
|
+ }
|
|
|
+
|
|
|
+ // build an array of the children
|
|
|
+ $children = array();
|
|
|
+ while ($child = $result->fetchObject()) {
|
|
|
+ $children[] = $child;
|
|
|
+ }
|
|
|
+
|
|
|
+ // the children list comes sorted in ascending fmin
|
|
|
+ // but if the parent is on the reverse strand we need to
|
|
|
+ // reverse the order of the children.
|
|
|
+ if ($parent->strand == -1) {
|
|
|
+ arsort($children);
|
|
|
+ }
|
|
|
+
|
|
|
+ // first set the ranks to a negative number so that we don't
|
|
|
+ // get a duplicate error message when we try to change any of them
|
|
|
+ $rank = -1;
|
|
|
+ foreach ($children as $child) {
|
|
|
+ $match = array('feature_relationship_id' => $child->feature_relationship_id);
|
|
|
+ $options = array('statement_name' => 'upd_featurerelationship_rank');
|
|
|
+ $values = array('rank' => $rank);
|
|
|
+ tripal_core_chado_update('feature_relationship', $match, $values, $options);
|
|
|
+ $rank--;
|
|
|
+ }
|
|
|
+ // now set the rank correctly. The rank should start at 0.
|
|
|
+ $rank = 0;
|
|
|
+ foreach ($children as $child) {
|
|
|
+ $match = array('feature_relationship_id' => $child->feature_relationship_id);
|
|
|
+ $options = array('statement_name' => 'upd_featurerelationship_rank');
|
|
|
+ $values = array('rank' => $rank);
|
|
|
+ //print "Was: " . $child->rank . " now $rank ($parent->strand)\n" ;
|
|
|
+ tripal_core_chado_update('feature_relationship', $match, $values, $options);
|
|
|
+ $rank++;
|
|
|
+ }
|
|
|
}
|
|
|
}
|
|
|
}
|
|
|
-
|
|
|
- // commit the transaction
|
|
|
- if ($use_transaction) {
|
|
|
- tripal_db_commit_transaction();
|
|
|
+ catch (Exception $e) {
|
|
|
+ print "\n"; // make sure we start errors on new line
|
|
|
+ watchdog_exception('T_gff3_loader', $e);
|
|
|
+ if ($use_transaction) {
|
|
|
+ $transaction->rollback();
|
|
|
+ print "FAILED: Rolling back database changes...\n";
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ print "FAILED\n";
|
|
|
+ }
|
|
|
+ return 0;
|
|
|
}
|
|
|
+
|
|
|
print "Done\n";
|
|
|
-
|
|
|
return 1;
|
|
|
}
|
|
|
/**
|
Stephen Ficklin