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@@ -50,7 +50,7 @@ function tripal_feature_fasta_load_form( ) {
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'#type' => 'textfield',
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'#title' => t('Sequence Type'),
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'#required' => TRUE,
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- '#description' => t('Please enter the Sequence Ontology term that describes the sequences in the FASTA file.'),
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+ '#description' => t('Please enter the Sequence Ontology (SO) term name that describes the sequences in the FASTA file (e.g. gene, mRNA, protein, etc...)'),
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);
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@@ -99,18 +99,17 @@ function tripal_feature_fasta_load_form( ) {
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t('Name'),
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t('Unique name'),
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),
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- '#description' => t('Feature data is stored in Chado with both a human-readable
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- name and a unique name. If the features in your FASTA file are identified using
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+ '#description' => t('Used for "updates only" or "insert and update" methods. Not required if method type is "insert".
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+ Feature data is stored in Chado with both a human-readable
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+ name and a unique name. If the features in your FASTA file are uniquely identified using
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a human-readable name then select the "Name" button. If your features are
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- identified using the unique name then select the "Unique name" button. If you
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+ uniquely identified using the unique name then select the "Unique name" button. If you
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loaded your features first using the GFF loader then the unique name of each
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features were indicated by the "ID=" attribute and the name by the "Name=" attribute.
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By default, the FASTA loader will use the first word (character string
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before the first space) as the name for your feature. If
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this does not uniquely identify your feature consider specifying a regular expression in the advanced section below.
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- Additionally, you may import both a name and a unique name for each sequence using the advanced options.
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- When updating a sequence, the value selected here will be used to identify the sequence in the
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- database in combination with any regular expression provided below.'),
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+ Additionally, you may import both a name and a unique name for each sequence using the advanced options.'),
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'#default_value' => 1,
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);
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@@ -484,6 +483,11 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
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$interval = 1;
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}
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$inv_read = 0;
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+
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+ // we need to get the table schema to make sure we don't overrun the
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+ // size of fields with what our regular expressions retrieve
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+ $feature_tbl = tripal_core_get_chado_table_schema('feature');
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+ $dbxref_tbl = tripal_core_get_chado_table_schema('dbxref');
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//foreach ($lines as $line_num => $line) {
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while ($line = fgets($fh)) {
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@@ -496,7 +500,7 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
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if (preg_match('/^>/', $line)) {
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// if we have a feature name then we are starting a new sequence
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// so lets handle the previous one before moving on
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- if ($name or $uname) {
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+ if ($name or $uname) {
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tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id,
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$accession, $subject, $rel_type, $parent_type, $analysis_id, $organism_id, $cvterm,
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$source, $residues, $method, $re_name, $match_type, $parentcvterm, $relcvterm);
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@@ -505,26 +509,42 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
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$uname = '';
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}
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- $line = preg_replace("/^>/", '', $line);
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+ $line = preg_replace("/^>/", '', $line); // remove the > symbol from the defline
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+
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// get the feature name
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if ($re_name) {
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if (!preg_match("/$re_name/", $line, $matches)) {
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- print "WARNING: Regular expression for the feature name finds nothing\n";
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+ watchdog('trp-fasta', "ERROR: Regular expression for the feature name finds nothing. Line %line.", array('%line' => $i), 'error');
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+ }
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+ elseif (strlen($matches[1]) > $feature_tbl['fields']['name']['length']) {
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+ watchdog('trp-fasta', "WARNING: Regular expression retrieves a value too long for the feature name. Line %line.", array('%line' => $i), 'error');
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}
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- $name = trim($matches[1]);
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+ else {
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+ $name = trim($matches[1]);
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+ }
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}
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else {
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// if the match_type is name and no regular expression was provided
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// then use the first word as the name, otherwise we don't set the name
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if (strcmp($match_type, 'Name')==0) {
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- preg_match("/^\s*(.*?)[\s\|].*$/", $line, $matches);
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- $name = trim($matches[1]);
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+ if(preg_match("/^\s*(.*?)[\s\|].*$/", $line, $matches)){
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+ if (strlen($matches[1]) > $feature_tbl['fields']['name']['length']) {
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+ watchdog('trp-fasta', "WARNING: Regular expression retrieves a feature name too long for the feature name. Line %line.", array('%line' => $i), 'error');
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+ }
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+ else {
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+ $name = trim($matches[1]);
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+ }
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+ }
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+ else {
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+ watchdog('trp-fasta', "ERROR: Cannot find a feature name. Line %line.", array('%line' => $i), 'error');
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+ }
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}
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}
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+
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// get the feature unique name
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if ($re_uname) {
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if (!preg_match("/$re_uname/", $line, $matches)) {
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- print "WARNING: Regular expression for the feature unique name finds nothing\n";
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+ watchdog('trp-fasta', "ERROR: Regular expression for the feature unique name finds nothing. Line %line.", array('%line' => $i), 'error');
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}
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$uname = trim($matches[1]);
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}
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@@ -532,13 +552,22 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
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// if the match_type is name and no regular expression was provided
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// then use the first word as the name, otherwise, we don't set the unqiuename
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if (strcmp($match_type, 'Unique name')==0) {
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- preg_match("/^\s*(.*?)[\s\|].*$/", $line, $matches);
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- $uname = trim($matches[1]);
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+ if(preg_match("/^\s*(.*?)[\s\|].*$/", $line, $matches)){
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+ $uname = trim($matches[1]);
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+ }
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+ else {
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+ watchdog('trp-fasta', "ERROR: Cannot find a feature unique name. Line %line.", array('%line' => $i), 'error');
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+ }
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}
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}
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// get the accession
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preg_match("/$re_accession/", $line, $matches);
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- $accession = trim($matches[1]);
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+ if (strlen($matches[1]) > $dbxref_tbl['fields']['accession']['length']) {
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+ watchdog('trp-fasta', "WARNING: Regular expression retrieves an accession too long for the feature name. Cannot add cross reference. Line %line.", array('%line' => $i), 'warning');
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+ }
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+ else {
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+ $accession = trim($matches[1]);
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+ }
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// get the relationship subject
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preg_match("/$re_subject/", $line, $matches);
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@@ -552,16 +581,17 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
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$intv_read = 0;
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$percent = sprintf("%.2f", ($num_read / $filesize) * 100);
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if ($name) {
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- print "Parsing Line $i (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes. Parsing: $name\r";
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+ print "Parsing Line $i (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes. Current feature: $name\r";
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}
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else {
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- print "Parsing Line $i (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes. Parsing: $uname\r";
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+ print "Parsing Line $i (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes. Current feature: $uname\r";
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}
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tripal_job_set_progress($job, intval(($num_read / $filesize) * 100));
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}
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}
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}
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- // now load the last sequence in the file
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+
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+ // now load the last sequence in the file
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tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id,
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$accession, $subject, $rel_type, $parent_type, $analysis_id, $organism_id, $cvterm,
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$source, $residues, $method, $re_name, $match_type, $parentcvterm, $relcvterm);
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@@ -596,7 +626,7 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
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}
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if (count($results) == 1) {
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$feature = $results[0];
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- }
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+ }
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}
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// check to see if this feature already exists if the match_type is 'Unique Name'
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if (strcmp($match_type, 'Unique name')==0) {
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@@ -615,14 +645,20 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
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}
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if (count($results) == 1) {
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$feature = $results[0];
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+ }
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+
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+ // if the feature exists but this is an "insert only" method then skip this feature
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+ if ($feature and (strcmp($method, 'Insert only')==0)) {
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+ watchdog('T_fasta_loader', "Feature already exists '%name' ('%uname') while matching on %type. Skipping insert.",
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+ array('%name' => $name, '%uname' => $uname, '%type' => drupal_strtolower($match_type)), WATCHDOG_WARNING);
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+ return 0;
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}
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}
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// if we don't have a feature and we're doing an insert then do the insert
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$inserted = 0;
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if (!$feature and (strcmp($method, 'Insert only')==0 or strcmp($method, 'Insert and update')==0)) {
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- // if we have a unique name but not a name then set them to be the same
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- // and vice versa
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+ // if we have a unique name but not a name then set them to be the same and vice versa
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if (!$uname) {
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$uname = $name;
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}
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@@ -666,23 +702,40 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
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watchdog('T_fasta_loader', "Failed to retreive newly inserted feature '%name (%uname)'",
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array('%name' => $name, '%uname' => $numane), WATCHDOG_ERROR);
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return 0;
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- }
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+ }
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}
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- // if we don't have a feature and the uesr wants to do an update then fail
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+ // if we don't have a feature and the user wants to do an update then fail
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if (!$feature and (strcmp($method, 'Update only')==0 or drupal_strcmp($method, 'Insert and update')==0)) {
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- watchdog('T_fasta_loader', "Failed to find feature '%name' ('%uiname') while matching on " .
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- drupal_strtolower($match_type), array('%name' => $name, '%uiname' => $uname), WATCHDOG_ERROR);
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+ watchdog('T_fasta_loader', "Failed to find feature '%name' ('%uname') while matching on " .
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+ drupal_strtolower($match_type), array('%name' => $name, '%uname' => $uname), WATCHDOG_ERROR);
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return 0;
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}
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-
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+
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// if we do have a feature and this is an update then proceed with the update
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if ($feature and !$inserted and (strcmp($method, 'Update only')==0 or strcmp($method, 'Insert and update')==0)) {
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// if the user wants to match on the Name field
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if (strcmp($match_type, 'Name')==0) {
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- // if we're matching on the name but do not have a new unique name then we don't want to update the uniquename.
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+ // if we're matching on the name but do not have a unique name then we don't want to update the uniquename.
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$values = array();
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if ($uname) {
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+ // first check to make sure that by changing the unique name of this feature that we won't conflict with
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+ // another existing feature of the same name
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+ $values = array(
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+ 'organism_id' => $organism_id,
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+ 'uniquename' => $uname,
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+ 'type_id' => $cvterm->cvterm_id,
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+ );
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+ $options = array('statement_name' => 'sel_feature_oruqty');
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+ $results = tripal_core_chado_select('feature', array('feature_id'), $values, $options);
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+ if (count($results) > 0) {
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+ watchdog('T_fasta_loader', "Cannot update the feature '%name' with a uniquename of '%uname' and type of '%type' as it
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+ conflicts with an existing feature with the same uniquename and type.",
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+ array('%name' => $name, '%uname' => $uname, '%type' => $type));
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+ return 0;
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+ }
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+
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+ // the changes to the uniquename don't conflict so proceed with the update
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$values = array(
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'uniquename' => $uname,
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'residues' => $residues,
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@@ -698,7 +751,7 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
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);
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$options = array('statement_name' => 'upd_feature_resemdisis_naorty_un');
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}
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- // if we have a unique name then update it after matching by the name
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+ // if we do not have a new unique name then don't change the existing uniquename field
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else {
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$values = array(
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'residues' => $residues,
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@@ -714,6 +767,8 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
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);
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$options = array('statement_name' => 'upd_feature_unresemdisis_naorty');
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}
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+
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+ // perform the update
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$success = tripal_core_chado_update('feature', $match, $values, $options);
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if (!$success) {
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watchdog('T_fasta_loader', "Failed to update feature '%name' ('%name')",
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@@ -812,6 +867,9 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
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array('%name' => $name, '%uname' => $numane), WATCHDOG_ERROR);
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return 0;
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}
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+ }
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+ else {
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+ $dbxref = $results[0];
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}
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// check to see if the feature dbxref record exists if not, then add it
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@@ -851,13 +909,13 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
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// check to see if the relationship already exists if not then add it
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$values = array(
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'subject_id' => $feature->feature_id,
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- 'ojbect_id' => $parent_feature->feature_id,
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+ 'object_id' => $parent_feature->feature_id,
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'type_id' => $relcvterm->cvterm_id,
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);
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$sel_options = array('statement_name' => 'sel_featurerelationship_suojty');
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- $results = tripal_core_chado_select('feature_relationship', array('feature_relationships_id'), $values, $sel_options);
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+ $results = tripal_core_chado_select('feature_relationship', array('feature_relationship_id'), $values, $sel_options);
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if (count($results) == 0) {
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- $ins_options = array('statement_name' => 'sel_featurerelationship_suojty');
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+ $ins_options = array('statement_name' => 'ins_featurerelationship_suojty');
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$success = tripal_core_chado_insert('feature_relationship', $values, $ins_options);
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if (!$success) {
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watchdog('T_fasta_loader', "Failed to add associate database accession '%accession' with feature",
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Lacey Sanderson