small fix to blast database node page to ensure if linkout not set we don't know errors and empty rows ;)

includes/blast_ui.custom.inc

@@ -1,129 +0,0 @@
-<?php
-/*
- * customized for PeanutBase
- *
- */
- 
-function tripal_custom_generate_linkout($url_prefix, $hit, $info, $options = array()) {
-// uncomment to see contents of hit object
-//echo "hit:<pre>";var_dump($hit);echo "</pre>";
-// uncomment to see contents of info object
-//echo "info:<pre>";var_dump($info);echo "</pre>";
-
-  $url = false;
-  $hit_name = $hit->{'Hit_def'};
-//echo "hit name: $hit_name ... ";
-
-  if ($info['Target'] == 'All genomes') {
-    // default regex
-    $regex = "/^\w+\.(\S+).*/";
-    
-    if (preg_match('/^aradu/', $hit_name) == 1) {
-      $blastdb_name = 'PeanutBase_aradu_gbrowse';
-    }
-    else if (preg_match('/^araip/', $hit_name) == 1) {
-      $blastdb_name = 'PeanutBase_araip_gbrowse';
-    }
-    else if (preg_match('/^cajca/', $hit_name) == 1) {
-      $blastdb_name = 'LegumeInfo_cajca_gbrowse';
-    }
-    else if (preg_match('/^cicar/', $hit_name) == 1) {
-      $blastdb_name = 'LegumeInfo_cicar_gbrowse';
-    }
-    else if (preg_match('/^glyma/', $hit_name) == 1) {
-      $blastdb_name = 'SoyBase_glyma_gbrowse';
-    }
-    else if (preg_match('/^lotja/', $hit_name) == 1) {
-      $blastdb_name = 'LegumeInfo_lotja_gbrowse';
-    }
-    else if (preg_match('/^medtr/', $hit_name) == 1) {
-      $blastdb_name = 'LegumeInfo_medtr_gbrowse';
-    }
-    else if (preg_match('/^phavu/', $hit_name) == 1) {
-      $blastdb_name = 'LegumeInfo_phavu_gbrowse';
-    }
-    else if (preg_match('/^vigra/', $hit_name) == 1) {
-      $blastdb_name = 'LegumeInfo_vigra_gbrowse';
-    }
-    else {
-      // Don't know what to do with this hit
-      drupal_set_message("Don't know how to create GBrowse linkout for $hit_name", 'error');
-    }  
-
-    $hit_name = preg_replace($regex, '$1', $hit_name);
-    $hit->{'linkout_id'} = $hit_name;
-    if ($blastdb_info = tripal_custom_getBLASTdbinfo($blastdb_name)) {
-//echo "generate gbrowse link with " . $blastdb_info['urlprefix'] . " $hit<br>";
-      $url = tripal_blast_generate_linkout_gbrowse($blastdb_info['urlprefix'], $hit, $info, $options);
-    }
-  }//handle All genomes BLAST target
-  
-  else {
-    // default regex:
-    $regex = "/^\w+\.(\S+)/";
-    
-    if (preg_match('/^aradu/', $hit_name) == 1) {
-      $blastdb_name = 'PeanutBase_aradu_gene';
-    }
-    else if (preg_match('/^araip/', $hit_name) == 1) {
-      $blastdb_name = 'PeanutBase_araip_gene';
-    }
-    else if (preg_match('/^cajca/', $hit_name) == 1) {
-      $blastdb_name = 'LegumeInfo_cajca_gene';
-    }
-    else if (preg_match('/^cicar/', $hit_name) == 1) {
-      $blastdb_name = 'LegumeInfo_cicar_gene';
-    }
-    else if (preg_match('/^glyma/', $hit_name) == 1) {
-      $blastdb_name = 'LegumeInfo_glyma_gene';
-      if (preg_match("/^\w+\.(\S+)\.p/", $hit_name)) {
-        //glyma protein
-        $regex = "/^\w+\.(\S+)\.p/";
-      }
-    }
-    else if (preg_match('/^lotja/', $hit_name) == 1) {
-      $blastdb_name = 'LegumeInfo_lotja_gene';
-    }
-    else if (preg_match('/^medtr/', $hit_name) == 1) {
-      $blastdb_name = 'LegumeInfo_medtr_gene';
-    }
-    else if (preg_match('/^phavu/', $hit_name) == 1) {
-      $blastdb_name = 'LegumeInfo_phavu_gene';
-    }
-    else if (preg_match('/^vigra/', $hit_name) == 1) {
-      $blastdb_name = 'LegumeInfo_vigra_gene';
-    }
-    else {
-      // Don't know what to do with this hit
-      drupal_set_message("Don't know how to create linkout for $hit_name", 'error');
-    }  
-
-    $hit_name = preg_match($regex, $hit_name, $matches);
-//echo "<br>Using $regex, found matches:<pre>" . var_dump($matches);echo "</pre>";
-//echo "<br>Use [" . $matches[1] . "]<br>";
-    $hit->{'linkout_id'} = $matches[1];
-//echo "look for gene link for $blastdb_name with " . $hit->{'linkout_id'} . "<br>";
-    if ($blastdb_info = tripal_custom_getBLASTdbinfo($blastdb_name)) {
-//echo "generate gbrowse link with " . $blastdb_info['urlprefix'] . " $hit<br>";
-      $url = tripal_blast_generate_linkout_link($blastdb_info['urlprefix'], $hit, $info, $options);
-    }
-  }
-  return $url;
-}
-
-
-function tripal_custom_getBLASTdbinfo($blastdb_name) {
-  $sql = "
-    SELECT urlprefix 
-    FROM {db} WHERE name='$blastdb_name'";
-//echo "$sql<br>";
-  if ($res = chado_query($sql)) {
-    if ($row=$res->fetchObject()) {
-      return array(
-        'urlprefix' => $row->urlprefix, 
-      );
-    }
-  }
-  
-  return false;
-}//tripal_custom_getBLASTdbinfo

theme/node--blastdb.tpl.php

@@ -99,10 +99,12 @@
       <tr><th>Human-Readable Name</th><td><?php print $node->db_name; ?></td></tr>
       <tr><th>Database Path</th><td><?php print $node->db_path; ?></td></tr>
       <tr><th>Database Type</th><td><?php print $node->db_dbtype; ?></td></tr>
+<?php if ($node->linkout->none === FALSE ) { ?>
       <tr><th>FASTA Header Format</th><td><?php print $node->linkout->regex_type; ?></td></tr>
       <tr><th>External Database</th><td><?php print $node->linkout->db_id->name; ?></td></tr>
       <tr><th>RegEx</th><td><?php print $node->linkout->regex; ?></td></tr>
       <tr><th>Link-out Type</th><td><?php print $node->linkout->type; ?></td></tr>
+<?php } ?>
     </table>
 
     <?php