Merge upstream

• merge upstream
• remove galaxy link
• add link to phaeo wbesite and genomic resources
• remove "other organisms are available at"
• fix structural annotation feature count when there is no genes (count mRNA instead)
• update readme

template.php

@@ -92,7 +92,7 @@ function abims_process_page(&$variables) {
   if ($variables['is_front']) {
     $variables['page']['analyses'] = abims_get_analyses_from_chado();
   }
-  $variables['page']['organisms'] = abims_get_organisms_from_chado();
+  $variables['page']['organisms'] = abims_get_organisms_with_versions_from_chado();
 }
 
 function abims_get_analyses_from_chado() {
@@ -133,6 +133,9 @@ function abims_get_analyses_from_chado() {
     if (preg_match('/.*\s\(?(OGS\s?[0-9.]+)\)?\b.*/i', $an->name, $m) && count($m) == 2) {
       $an->guessed_version = str_replace(' ', '', $m[1]);
     }
+    else if (preg_match('/.*\s\(?v([0-9.]+)\)?\b.*/i', $an->name, $m) && count($m) == 2) {
+      $an->guessed_version = str_replace(' ', '', $m[1]);
+    }
     else if (preg_match('/.*\s\(?v?([0-9.]+)\)?\b.*/i', $an->name, $m) && count($m) == 2) {
       $an->guessed_version = str_replace(' ', '', $m[1]);
     }
@@ -156,7 +159,10 @@ function abims_get_analyses_from_chado() {
 
   // Fix feature_counts for structural annots
   $csql = "SELECT a.analysis_id, count(af.feature_id) as feature_count FROM {analysis} a LEFT JOIN {analysisfeature} af ON a.analysis_id = af.analysis_id LEFT JOIN {feature} f ON af.feature_id = f.feature_id WHERE f.type_id=:term GROUP BY a.analysis_id ORDER BY a.name";
-   $counts = chado_query($csql, array(':term' => $gene_term));
+  $counts = chado_query($csql, array(':term' => $gene_term));
+  if (!$counts->rowCount()) {
+    $counts = chado_query($csql, array(':term' => $mRNA_term));
+  }
   foreach ($counts as $count) {
     if (in_array($count->analysis_id, $structural_ids)) {
       $analysis_list[$count->analysis_id]->feature_count = $count->feature_count;
@@ -250,6 +256,51 @@ function abims_get_organisms_from_chado() {
   return $organism_list;
 }
 
+function abims_get_organisms_with_versions_from_chado() {
+  $organism_list = array();
+
+  $csql =  "SELECT * FROM {organism} ORDER BY genus, species";
+  $organisms = chado_query($csql);
+
+  $csql =  "SELECT name FROM {analysis} order by analysis_id desc";
+  $analyses = chado_query($csql);
+
+  $versions = array();
+  foreach ($analyses as $an) {
+    if ((preg_match('/assembly/i', $an->name) || preg_match('/genome/i', $an->name)) && !preg_match('/transcriptome/i', $an->name)) {
+      if (preg_match('/([A-Za-z0-9]+ [A-Za-z0-9]+).+v\.?([0-9.]+)/', $an->name, $matches)) {
+        if (!array_key_exists($matches[1], $versions) || version_compare($matches[2], $versions[$matches[1]], '>')) {
+          $versions[$matches[1]] = $matches[2];
+        }
+      }
+      if (preg_match('/([A-Za-z0-9]+ [A-Za-z0-9]+ [A-Za-z0-9]+).+v\.?([0-9.]+)/', $an->name, $matches)) {
+        if (!array_key_exists($matches[1], $versions) || version_compare($matches[2], $versions[$matches[1]], '>')) {
+          $versions[$matches[1]] = $matches[2];
+        }
+      }
+      if (preg_match('/v\.?([0-9.]+).+ ([A-Za-z0-9]+ [A-Za-z0-9]+ [A-Za-z0-9]+)$/', $an->name, $matches)) {
+        if (!array_key_exists($matches[2], $versions) || version_compare($matches[1], $versions[$matches[2]], '>')) {
+          $versions[$matches[2]] = $matches[1];
+        }
+      }
+      if (preg_match('/v\.?([0-9.]+).+ ([A-Za-z0-9]+ [A-Za-z0-9]+)$/', $an->name, $matches)) {
+        if (!array_key_exists($matches[2], $versions) || version_compare($matches[1], $versions[$matches[2]], '>')) {
+          $versions[$matches[2]] = $matches[1];
+        }
+      }
+    }
+  }
+
+  foreach ($organisms as $organism) {
+    if (array_key_exists($organism->genus . ' ' . $organism->species, $versions)) {
+        $organism->version = $versions[$organism->genus . ' ' . $organism->species];
+      }
+    $organism_list[$organism->organism_id] = $organism;
+  }
+
+  return $organism_list;
+}
+
 /**
  * Implements hook_preprocess_maintenance_page().
  */