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@@ -335,8 +335,8 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
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$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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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "Cannot find the file: %dfile",
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+ array('%dfile' => $dfile));
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return 0;
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}
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@@ -345,8 +345,8 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
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//$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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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "cannot open file: %dfile",
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+ array('%dfile' => $dfile));
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return 0;
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}
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$filesize = filesize($dfile);
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@@ -355,9 +355,9 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
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// default is the 'sequence' ontology
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$sql = "SELECT * FROM {cv} WHERE name = :cvname";
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$cv = chado_query($sql, array(':cvname' => 'sequence'))->fetchObject();
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- if (!$cv) {
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- watchdog('T_gff3_loader', "Cannot find the 'sequence' ontology",
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- array(), WATCHDOG_ERROR);
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+ if (!$tripal_core_report_error) {
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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR "Cannot find the 'sequence' ontology",
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+ array());
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return '';
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}
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@@ -424,8 +424,8 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
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$result = chado_query($sel_cvterm_sql, 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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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, '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' => $line_num));
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return '';
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}
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tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $rid,
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@@ -447,8 +447,8 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
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// get the columns
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$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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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, 'improper number of columns on line %line_num',
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+ array('%line_num' => $line_num));
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return '';
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}
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@@ -489,8 +489,8 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
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$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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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, 'cannot find feature term \'%type\' on line %line_num of the GFF file',
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+ array('%type' => $type, '%line_num' => $line_num));
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return '';
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}
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@@ -520,8 +520,8 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
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continue;
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}
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if (!preg_match('/^[^\=]+\=.+$/', $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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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, 'Attribute is not correctly formatted on line %line_num: %attr',
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+ array('%line_num' => $line_num, '%attr' => $attr));
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return '';
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}
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@@ -562,14 +562,14 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
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if ($create_organism) {
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$feature_organism = (object) tripal_core_chado_insert('organism', $values);
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if (!$feature_organism) {
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- watchdog('T_gff3_loader', "Could not add the organism, '%org', from line %line. Skipping this line. ",
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- array('%org' => $attr_organism, '%line' => $line_num), WATCHDOG_ERROR);
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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "Could not add the organism, '%org', from line %line. Skipping this line. ",
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+ array('%org' => $attr_organism, '%line' => $line_num));
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$skip_feature = 1;
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}
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}
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else {
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- watchdog('T_gff3_loader', "The organism attribute '%org' on line %line does not exist. Skipping this line. ",
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- array('%org' => $attr_organism, '%line' => $line_num), WATCHDOG_ERROR);
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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "The organism attribute '%org' on line %line does not exist. Skipping this line. ",
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+ array('%org' => $attr_organism, '%line' => $line_num));
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$skip_feature = 1;
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}
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}
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@@ -579,9 +579,9 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
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}
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}
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else {
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- watchdog('T_gff3_loader', "The organism attribute '%org' on line %line is not properly formated. It " .
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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "The organism attribute '%org' on line %line is not properly formated. It " .
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"should be of the form: organism=Genus:species. Skipping this line.",
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- array('%org' => $attr_organism, '%line' => $line_num), WATCHDOG_ERROR);
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+ array('%org' => $attr_organism, '%line' => $line_num));
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$skip_feature = 1;
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}
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}
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@@ -669,21 +669,21 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
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}
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$count = tripal_core_chado_select('feature', $columns, $select);
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if (!$count or count($count) == 0 or $count[0]->num_landmarks == 0) {
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- watchdog('T_gff3_loader', "The landmark '%landmark' cannot be found for this organism (%species) " .
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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "The landmark '%landmark' cannot be found for this organism (%species) " .
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"Please add the landmark and then retry the import of this GFF3 " .
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- "file", array('%landmark' => $landmark, '%species' => $organism->genus . " " . $organism->species), WATCHDOG_ERROR);
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+ "file", array('%landmark' => $landmark, '%species' => $organism->genus . " " . $organism->species));
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return '';
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}
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elseif ($count[0]->num_landmarks > 1) {
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- watchdog('T_gff3_loader', "The landmark '%landmark' has more than one entry for this organism (%species) " .
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- "Cannot continue", array('%landmark' => $landmark, '%species' => $organism->genus . " " . $organism->species), WATCHDOG_ERROR);
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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "The landmark '%landmark' has more than one entry for this organism (%species) " .
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+ "Cannot continue", array('%landmark' => $landmark, '%species' => $organism->genus . " " . $organism->species));
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return '';
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}
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}
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if ($count[0]->num_landmarks > 1) {
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- watchdog('T_gff3_loader', "The landmark '%landmark' is not unique for this organism. " .
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- "The features cannot be associated", array('%landmark' => $landmark), WATCHDOG_ERROR);
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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "The landmark '%landmark' is not unique for this organism. " .
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+ "The features cannot be associated", array('%landmark' => $landmark));
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return '';
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}
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}
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@@ -700,8 +700,8 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
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);
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$result = tripal_core_chado_delete('feature', $match);
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if (!$result) {
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- watchdog('T_gff3_loader', "cannot delete feature %attr_uniquename",
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- array('%attr_uniquename' => $attr_uniquename), WATCHDOG_ERROR);
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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "cannot delete feature %attr_uniquename",
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+ array('%attr_uniquename' => $attr_uniquename));
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}
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$feature = 0;
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unset($result);
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@@ -731,7 +731,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
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if (count($results) == 0) {
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$result = tripal_core_chado_insert('tripal_gff_temp', $values);
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if (!$result) {
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- watchdog('T_gff3_loader', "Cound not save record in temporary table, Cannot continue.", array(), WATCHDOG_ERROR);
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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "Cound not save record in temporary table, Cannot continue.", array());
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exit;
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}
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}
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@@ -908,7 +908,7 @@ function tripal_feature_load_gff3_derives_from($feature, $subject, $organism) {
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);
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$result = tripal_core_chado_select('tripal_gff_temp', array('type_name'), $values);
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if (count($result) == 0) {
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- watchdog("T_gff3_loader", "Cannot find subject type for feature in 'derives_from' relationship: %subject", array('%subject' => $subject), WATCHDOG_WARNING);
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+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find subject type for feature in 'derives_from' relationship: %subject", array('%subject' => $subject));
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return '';
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}
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$subject_type = $result[0]->type_name;
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@@ -926,9 +926,9 @@ function tripal_feature_load_gff3_derives_from($feature, $subject, $organism) {
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);
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$sfeature = tripal_core_chado_select('feature', array('feature_id'), $match);
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if (count($sfeature)==0) {
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- watchdog('T_gff3_loader', "Could not add 'Derives_from' relationship " .
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+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "Could not add 'Derives_from' relationship " .
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"for %uniquename and %subject. Subject feature, '%subject', " .
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- "cannot be found", array('%uniquename' => $feature->uniquename, '%subject' => $subject), WATCHDOG_ERROR);
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+ "cannot be found", array('%uniquename' => $feature->uniquename, '%subject' => $subject));
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return;
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}
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@@ -952,8 +952,8 @@ function tripal_feature_load_gff3_derives_from($feature, $subject, $organism) {
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// finally insert the relationship if it doesn't exist
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$ret = tripal_core_chado_insert('feature_relationship', $values);
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if (!$ret) {
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- watchdog("T_gff3_loader", "Could not add 'Derives_from' relationship for $feature->uniquename and $subject",
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- array(), WATCHDOG_WARNING);
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+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Could not add 'Derives_from' relationship for $feature->uniquename and $subject",
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+ array());
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}
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}
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/**
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@@ -985,7 +985,7 @@ function tripal_feature_load_gff3_parents($feature, $cvterm, $parents, $organism
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);
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$result = tripal_core_chado_select('tripal_gff_temp', array('type_name'), $values);
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if (count($result) == 0) {
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- watchdog("T_gff3_loader", "Cannot find parent: %parent", array('%parent' => $parent), WATCHDOG_WARNING);
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+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find parent: %parent", array('%parent' => $parent));
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return '';
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}
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$parent_type = $result[0]->type_name;
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@@ -1023,14 +1023,14 @@ function tripal_feature_load_gff3_parents($feature, $cvterm, $parents, $organism
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);
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$result = tripal_core_chado_insert('feature_relationship', $values);
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if (!$result) {
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- watchdog("T_gff3_loader", "Failed to insert feature relationship '$uname' ($type) $rel_type '$parent' ($parent_type)",
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- array(), WATCHDOG_WARNING);
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+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert feature relationship '$uname' ($type) $rel_type '$parent' ($parent_type)",
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+ array());
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}
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}
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}
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else {
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- watchdog("T_gff3_loader", "Cannot establish relationship '$uname' ($type) $rel_type '$parent' ($parent_type): Cannot find the parent",
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- array(), WATCHDOG_WARNING);
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+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot establish relationship '$uname' ($type) $rel_type '$parent' ($parent_type): Cannot find the parent",
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+ array());
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}
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}
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}
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@@ -1072,7 +1072,7 @@ function tripal_feature_load_gff3_dbxref($feature, $dbxrefs) {
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$db = tripal_core_chado_select('db', array('db_id'), $values);
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}
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else {
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- watchdog("T_gff3_loader", "Cannot find or add the database $dbname", array(), WATCHDOG_WARNING);
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+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find or add the database $dbname", array());
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return 0;
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}
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}
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@@ -1117,7 +1117,7 @@ function tripal_feature_load_gff3_dbxref($feature, $dbxrefs) {
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);
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$success = tripal_core_chado_insert('feature_dbxref', $values);
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if (!$success) {
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- watchdog("T_gff3_loader", "Failed to insert Dbxref: $dbname:$accession", array(), WATCHDOG_WARNING);
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+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert Dbxref: $dbname:$accession", array());
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return 0;
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}
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}
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@@ -1145,7 +1145,7 @@ function tripal_feature_load_gff3_ontology($feature, $dbxrefs) {
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// now look for the name without the 'DB:' prefix.
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$db = tripal_core_chado_select('db', array('db_id'), array('name' => "$dbname"));
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|
if (sizeof($db) == 0) {
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|
|
- watchdog("T_gff3_loader", "Database, $dbname, is not present. Cannot associate term: $dbname:$accession", array(), WATCHDOG_WARNING);
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|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Database, $dbname, is not present. Cannot associate term: $dbname:$accession", array());
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return 0;
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|
}
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|
}
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@@ -1155,7 +1155,7 @@ function tripal_feature_load_gff3_ontology($feature, $dbxrefs) {
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|
|
$dbxref = tripal_core_chado_select('dbxref', array('dbxref_id'),
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|
|
array('accession' => $accession, 'db_id' => $db->db_id));
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|
|
if (sizeof($dbxref) == 0) {
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|
|
- watchdog("T_gff3_loader", "Accession, $accession is missing for reference: $dbname:$accession", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Accession, $accession is missing for reference: $dbname:$accession", array());
|
|
|
return 0;
|
|
|
}
|
|
|
$dbxref = $dbxref[0];
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|
@@ -1168,7 +1168,7 @@ function tripal_feature_load_gff3_ontology($feature, $dbxrefs) {
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|
|
$cvterm = tripal_core_chado_select('cvterm_dbxref', array('cvterm_id'), array(
|
|
|
'dbxref_id' => $dbxref->dbxref_id));
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|
|
if (sizeof($cvterm) == 0) {
|
|
|
- watchdog("T_gff3_loader", "CV Term is missing for reference: $dbname:$accession", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "CV Term is missing for reference: $dbname:$accession", array());
|
|
|
return 0;
|
|
|
}
|
|
|
}
|
|
|
@@ -1191,7 +1191,7 @@ function tripal_feature_load_gff3_ontology($feature, $dbxrefs) {
|
|
|
$success = tripal_core_chado_insert('feature_cvterm', $values);
|
|
|
|
|
|
if (!$success) {
|
|
|
- watchdog("T_gff3_loader", "Failed to insert ontology term: $dbname:$accession", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert ontology term: $dbname:$accession", array());
|
|
|
return 0;
|
|
|
}
|
|
|
}
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|
|
@@ -1217,7 +1217,7 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
|
|
|
);
|
|
|
$success = tripal_core_chado_insert('cv', $values);
|
|
|
if (!$success) {
|
|
|
- watchdog("T_gff3_loader", "Failed to add the synonyms type vocabulary", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to add the synonyms type vocabulary", array());
|
|
|
return 0;
|
|
|
}
|
|
|
// now that we've added the cv we need to get the record
|
|
|
@@ -1247,7 +1247,7 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
|
|
|
);
|
|
|
$syntype = tripal_cv_add_cvterm($term, $syncv->name, 0, 1);
|
|
|
if (!$syntype) {
|
|
|
- watchdog("T_gff3_loader", "Cannot add synonym type: internal:$type", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add synonym type: internal:$type", array());
|
|
|
return 0;
|
|
|
}
|
|
|
}
|
|
|
@@ -1273,7 +1273,7 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
|
|
|
);
|
|
|
$success = tripal_core_chado_insert('synonym', $values);
|
|
|
if (!$success) {
|
|
|
- watchdog("T_gff3_loader", "Cannot add alias $alias to synonym table", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add alias $alias to synonym table", array());
|
|
|
return 0;
|
|
|
}
|
|
|
$result = tripal_core_chado_select('synonym', array('*'), $select);
|
|
|
@@ -1299,14 +1299,14 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
|
|
|
";
|
|
|
$status = chado_query($psql);
|
|
|
if (!$status) {
|
|
|
- watchdog("T_gff3_loader", "Cannot prepare statement 'ins_pub_uniquename_typeid", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot prepare statement 'ins_pub_uniquename_typeid", array());
|
|
|
return 0;
|
|
|
}
|
|
|
|
|
|
// insert the null pub
|
|
|
$result = chado_query($pub_sql, array(':uname' => 'null', ':type_id' => 'null'))->fetchObject();
|
|
|
if (!$result) {
|
|
|
- watchdog("T_gff3_loader", "Cannot add null publication needed for setup of alias", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add null publication needed for setup of alias", array());
|
|
|
return 0;
|
|
|
}
|
|
|
$result = tripal_core_chado_select('pub', array('*'), $select);
|
|
|
@@ -1334,7 +1334,7 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
|
|
|
$success = tripal_core_chado_insert('feature_synonym', $values);
|
|
|
|
|
|
if (!$success) {
|
|
|
- watchdog("T_gff3_loader", "Cannot add alias $alias to feature synonym table", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add alias $alias to feature synonym table", array());
|
|
|
return 0;
|
|
|
}
|
|
|
}
|
|
|
@@ -1391,7 +1391,7 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
|
|
|
);
|
|
|
$result = tripal_core_chado_insert('feature', $values);
|
|
|
if (!$result) {
|
|
|
- watchdog("T_gff3_loader", "Failed to insert feature '$uniquename' ($cvterm->name)", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert feature '$uniquename' ($cvterm->name)", array());
|
|
|
return 0;
|
|
|
}
|
|
|
}
|
|
|
@@ -1411,7 +1411,7 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
|
|
|
);
|
|
|
$result = tripal_core_chado_update('feature', $match, $values);
|
|
|
if (!$result) {
|
|
|
- watchdog("T_gff3_loader", "Failed to update feature '$uniquename' ($cvterm->name)", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to update feature '$uniquename' ($cvterm->name)", array());
|
|
|
return 0;
|
|
|
}
|
|
|
}
|
|
|
@@ -1438,7 +1438,7 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
|
|
|
$af_values['significance'] = $score;
|
|
|
}
|
|
|
if (!tripal_core_chado_insert('analysisfeature', $af_values)) {
|
|
|
- watchdog("T_gff3_loader", "Could not add analysisfeature record: $analysis_id, $feature->feature_id", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Could not add analysisfeature record: $analysis_id, $feature->feature_id", array());
|
|
|
}
|
|
|
}
|
|
|
else {
|
|
|
@@ -1453,7 +1453,7 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
|
|
|
if (!$add_only) {
|
|
|
$ret = tripal_core_chado_update('analysisfeature', $af_values, $new_vals);
|
|
|
if (!$ret) {
|
|
|
- watchdog("T_gff3_loader", "Could not update analysisfeature record: $analysis_id, $feature->feature_id", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Could not update analysisfeature record: $analysis_id, $feature->feature_id", array());
|
|
|
}
|
|
|
}
|
|
|
}
|
|
|
@@ -1514,24 +1514,24 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
|
|
|
);
|
|
|
$results = tripal_core_chado_insert('feature', $values);
|
|
|
if (!$results) {
|
|
|
- watchdog("T_gff3_loader", "Cannot find landmark feature: '%landmark', nor could it be inserted",
|
|
|
- array('%landmark' => $landmark), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find landmark feature: '%landmark', nor could it be inserted",
|
|
|
+ array('%landmark' => $landmark));
|
|
|
return 0;
|
|
|
}
|
|
|
$srcfeature = new stdClass();
|
|
|
$srcfeature->feature_id = $results['feature_id'];
|
|
|
}
|
|
|
else {
|
|
|
- watchdog("T_gff3_loader", "Cannot find unique landmark feature: '%landmark'.",
|
|
|
- array('%landmark' => $landmark), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find unique landmark feature: '%landmark'.",
|
|
|
+ array('%landmark' => $landmark));
|
|
|
return 0;
|
|
|
}
|
|
|
}
|
|
|
}
|
|
|
elseif (count($results) > 1) {
|
|
|
- watchdog("T_gff3_loader", "multiple landmarks exist with the name: '%landmark'. Cannot
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "multiple landmarks exist with the name: '%landmark'. Cannot
|
|
|
resolve which one to use. Cannot add the feature location record",
|
|
|
- array('%landmark' => $landmark), WATCHDOG_WARNING);
|
|
|
+ array('%landmark' => $landmark));
|
|
|
return 0;
|
|
|
}
|
|
|
else {
|
|
|
@@ -1539,9 +1539,9 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
|
|
|
}
|
|
|
}
|
|
|
elseif (count($results) > 1) {
|
|
|
- watchdog("T_gff3_loader", "multiple landmarks exist with the name: '%landmark'. Cannot
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "multiple landmarks exist with the name: '%landmark'. Cannot
|
|
|
resolve which one to use. Cannot add the feature location record",
|
|
|
- array('%landmark' => $landmark), WATCHDOG_WARNING);
|
|
|
+ array('%landmark' => $landmark));
|
|
|
return 0;
|
|
|
}
|
|
|
else {
|
|
|
@@ -1629,7 +1629,7 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
|
|
|
}
|
|
|
$success = tripal_core_chado_insert('featureloc', $values);
|
|
|
if (!$success) {
|
|
|
- watchdog("T_gff3_loader", "Failed to insert featureloc", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert featureloc", array());
|
|
|
exit;
|
|
|
return 0;
|
|
|
}
|
|
|
@@ -1662,7 +1662,7 @@ function tripal_feature_load_gff3_property($feature, $property, $value) {
|
|
|
);
|
|
|
$cvterm = (object) tripal_cv_add_cvterm($term, 'feature_property', 0, 0);
|
|
|
if (!$cvterm) {
|
|
|
- watchdog("T_gff3_loader", "Cannot add cvterm, $property", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add cvterm, $property", array());
|
|
|
return 0;
|
|
|
}
|
|
|
}
|
|
|
@@ -1703,7 +1703,7 @@ function tripal_feature_load_gff3_property($feature, $property, $value) {
|
|
|
);
|
|
|
$result = tripal_core_chado_insert('featureprop', $values);
|
|
|
if (!$result) {
|
|
|
- watchdog("T_gff3_loader", "cannot add featureprop, $property", array(), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "cannot add featureprop, $property", array());
|
|
|
}
|
|
|
}
|
|
|
}
|
|
|
@@ -1745,8 +1745,8 @@ function tripal_feature_load_gff3_fasta($fh, $interval, &$num_read, &$intv_read,
|
|
|
$values = array('uniquename' => $id);
|
|
|
$result = tripal_core_chado_select('tripal_gff_temp', array('*'), $values);
|
|
|
if (count($result) == 0) {
|
|
|
- watchdog('T_gff3_loader', 'Cannot find feature to assign FASTA sequence: %uname',
|
|
|
- array('%uname' => $id), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error('T_gff3_loader', TRIPAL_WARNING, 'Cannot find feature to assign FASTA sequence: %uname',
|
|
|
+ array('%uname' => $id));
|
|
|
}
|
|
|
else {
|
|
|
// if we have a feature then add the residues
|
|
|
@@ -1770,8 +1770,8 @@ function tripal_feature_load_gff3_fasta($fh, $interval, &$num_read, &$intv_read,
|
|
|
$values = array('uniquename' => $id);
|
|
|
$result = tripal_core_chado_select('tripal_gff_temp', array('*'), $values);
|
|
|
if (count($result) == 0) {
|
|
|
- watchdog('T_gff3_loader', 'Cannot find feature to assign FASTA sequence: %uname',
|
|
|
- array('%uname' => $id), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error('T_gff3_loader', TRIPAL_WARNING, 'Cannot find feature to assign FASTA sequence: %uname',
|
|
|
+ array('%uname' => $id));
|
|
|
}
|
|
|
else {
|
|
|
// if we have a feature then add the residues
|
|
|
@@ -1839,15 +1839,15 @@ function tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $
|
|
|
$t_organism_id = $torganism[0]->organism_id;
|
|
|
}
|
|
|
else {
|
|
|
- watchdog('T_gff3_loader', "Cannot find organism for target %target.",
|
|
|
- array('%target' => $gff_target_organism), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error('T_gff3_loader', TRIPAL_WARNING, "Cannot find organism for target %target.",
|
|
|
+ array('%target' => $gff_target_organism));
|
|
|
$t_organism_id = '';
|
|
|
}
|
|
|
}
|
|
|
else {
|
|
|
- watchdog('T_gff3_loader', "The target_organism attribute is improperly formatted: %target.
|
|
|
+ tripal_core_report_error('T_gff3_loader', TRIPAL_WARNING, "The target_organism attribute is improperly formatted: %target.
|
|
|
It should be target_organism=genus:species.",
|
|
|
- array('%target' => $gff_target_organism), WATCHDOG_WARNING);
|
|
|
+ array('%target' => $gff_target_organism));
|
|
|
$t_organism_id = '';
|
|
|
}
|
|
|
}
|
|
|
@@ -1867,8 +1867,8 @@ function tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $
|
|
|
$t_type_id = $type[0]->cvterm_id;
|
|
|
}
|
|
|
else {
|
|
|
- watchdog('T_gff3_loader', "The target type does not exist in the sequence ontology: %type. ",
|
|
|
- array('%type' => $target_type), WATCHDOG_ERROR);
|
|
|
+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "The target type does not exist in the sequence ontology: %type. ",
|
|
|
+ array('%type' => $target_type));
|
|
|
exit;
|
|
|
}
|
|
|
}
|
|
|
@@ -1899,8 +1899,8 @@ function tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $
|
|
|
$t_type_id = $synonym->cvterm_id;
|
|
|
}
|
|
|
else {
|
|
|
- watchdog('T_gff3_loader', "The target_type attribute does not exist in the sequence ontology: %type. ",
|
|
|
- array('%type' => $gff_target_type), WATCHDOG_WARNING);
|
|
|
+ tripal_core_report_error('T_gff3_loader', TRIPAL_WARNING, "The target_type attribute does not exist in the sequence ontology: %type. ",
|
|
|
+ array('%type' => $gff_target_type));
|
|
|
$t_type_id = '';
|
|
|
}
|
|
|
}
|
|
|
@@ -1914,7 +1914,7 @@ function tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $
|
|
|
}
|
|
|
// the target attribute is not correctly formatted
|
|
|
else {
|
|
|
- watchdog('T_gff3_loader', "Could not add 'Target' alignment as it is improperly formatted: '%target'",
|
|
|
- array('%target' => $tags['Target'][0]), WATCHDOG_ERROR);
|
|
|
+ tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "Could not add 'Target' alignment as it is improperly formatted: '%target'",
|
|
|
+ array('%target' => $tags['Target'][0]));
|
|
|
}
|
|
|
}
|
Stephen Ficklin