Removed materialized view unigene_libraries_mview. This mview exited to associate a unigene with all

the libraries represented by sequences in that unigene.  Also removed code to display these libraries
in the tab on the organism ungiene page.

Altered the unigene_mview not to include "short_name".  This is niether a standard Tripal cvterm nor
used in the display of the unigene.

tripal_analysis_unigene/tripal_analysis_unigene.install

@@ -30,30 +30,30 @@ function tripal_analysis_unigene_install() {
      "specific unigene version (e.g. v1, v2, etc...). The value specified ".
      "should match that of the unigene_version");
 
-   tripal_add_mview('unigene_libraries_mview',
-     'tripal_analysis_unigene',
-     'unigene_libraries_mview',
-     'analysis_name character varying(255), analysis_id integer,  '.
-     'organism_common_name character varying(255), organism_id integer, '.
-     'library_name character varying(255), library_id integer, '.
-     'library_type character varying(255)',
-     'analysis_id,organism_id,library_id',
-     "select A.name as analysis_name, A.analysis_id, ".
-     "         O.common_name as organism_common_name, O.organism_id, ".
-     "         L.name as library_name, L.library_id,".
-     "         CV.name as library_type ".
-     "FROM {Analysis} A ".
-     "INNER JOIN Analysisfeature AF ON A.analysis_id = AF.analysis_ID ".
-     "INNER JOIN Featureloc FL ON AF.feature_id = FL.feature_ID ".
-     "INNER JOIN Feature F ON FL.srcfeature_id = F.feature_id ".
-     "INNER JOIN Organism O ON F.organism_id = O.organism_id ".
-     "INNER JOIN Library_feature LF ON F.feature_id = LF.feature_id ".
-     "INNER JOIN Library L ON LF.library_id = L.library_id ".
-     "INNER JOIN CVterm CV ON L.type_id = CV.cvterm_id ".
-     "GROUP BY A.analysis_id, A.name, O.common_name, O.organism_id, ".
-     "   L.library_id, L.name, CV.name",
-     ''
-   );
+   //tripal_add_mview('unigene_libraries_mview',
+     //'tripal_analysis_unigene',
+     //'unigene_libraries_mview',
+     //'analysis_name character varying(255), analysis_id integer,  '.
+     //'organism_common_name character varying(255), organism_id integer, '.
+     //'library_name character varying(255), library_id integer, '.
+     //'library_type character varying(255)',
+     //'analysis_id,organism_id,library_id',
+     //"select A.name as analysis_name, A.analysis_id, ".
+     //"         O.common_name as organism_common_name, O.organism_id, ".
+     //"         L.name as library_name, L.library_id,".
+     //"         CV.name as library_type ".
+     //"FROM {Analysis} A ".
+     //"INNER JOIN Analysisfeature AF ON A.analysis_id = AF.analysis_ID ".
+     //"INNER JOIN Featureloc FL ON AF.feature_id = FL.feature_ID ".
+     //"INNER JOIN Feature F ON FL.srcfeature_id = F.feature_id ".
+     //"INNER JOIN Organism O ON F.organism_id = O.organism_id ".
+     //"INNER JOIN Library_feature LF ON F.feature_id = LF.feature_id ".
+     //"INNER JOIN Library L ON LF.library_id = L.library_id ".
+     //"INNER JOIN CVterm CV ON L.type_id = CV.cvterm_id ".
+     //"GROUP BY A.analysis_id, A.name, O.common_name, O.organism_id, ".
+     //"   L.library_id, L.name, CV.name",
+     //''
+   //);
 
    tripal_add_mview('unigene_mview',
       'tripal_analysis_unigene',
@@ -63,12 +63,12 @@ function tripal_analysis_unigene_install() {
       'algorithm character varying(255), sourcename character varying(255), '.
       'sourceversion character varying(255), sourceuri text, '.
       'timeexecuted timestamp,  organism_id integer, '.
-      'uversion text, adate text, short_name text, num_ests integer, '.
+      'uversion text, adate text, num_ests integer, '.
 		'num_contigs integer, num_singlets integer',
 	   'analysis_id, organism_id',
 	   "SELECT Distinct A.analysis_id, A.name, A.description, A.program, A.programversion, A.algorithm, ".
       "  A.sourcename, A.sourceversion, A.sourceuri, A.timeexecuted, O.organism_id, ".
-      "  AP.value as uversion, AP2.value as adate, AP3.value as short_name,   ".
+      "  AP.value as uversion, AP2.value as adate,    ".
       " (SELECT count(*) FROM {feature} F  ".
       "   INNER JOIN CVTerm CVT on F.type_id = CVT.cvterm_id  ".
       "   INNER JOIN CV on CVT.cv_id = CV.cv_id ".
@@ -104,10 +104,6 @@ function tripal_analysis_unigene_install() {
       "    ON A.analysis_id = AP2.analysis_id ".
       "  INNER JOIN CVterm CV2 ".
       "    ON AP2.type_id = CV2.cvterm_ID   ".
-      "  INNER JOIN Analysisprop AP3 ".
-      "    ON A.analysis_id = AP3.analysis_id ".
-      "  INNER JOIN CVterm CV3 ".
-      "    ON AP3.type_id = CV3.cvterm_ID   ".
       "  INNER JOIN Analysisfeature AF ".
       "    ON A.analysis_id = AF.analysis_ID ".
       "  INNER JOIN Feature F  ".
@@ -119,10 +115,9 @@ function tripal_analysis_unigene_install() {
       "WHERE ".
       "  CV.name = 'unigene_version' ".
       "  AND CV2.name = 'analysis_date' ".
-      "  AND CV3.name = 'analysis_short_name' ".
       "GROUP BY A.analysis_id, A.name, A.description, A.program, ".
       "   A.programversion, A.algorithm, A.sourcename, A.sourceversion, ".
-      "   A.sourceuri, A.timeexecuted, AP.value, AP2.value, AP3.value, O.organism_id", 
+      "   A.sourceuri, A.timeexecuted, AP.value, AP2.value, O.organism_id", 
 	   ''
    );
 }

tripal_analysis_unigene/tripal_analysis_unigene.module

@@ -482,27 +482,28 @@ function tripal_analysis_unigene_organism_add($node){
    $previous_db = db_set_active('chado');  // use chado database
    $results = db_query($sql,$org_id->organism_id);
    db_set_active($previous_db);  // now use drupal database
-   $i = 0;
-   while ($assembly = db_fetch_object($results)){
+
+   //$i = 0;
+   //while ($assembly = db_fetch_object($results)){
       // get information about this organism and add it to the items in this node
-      $libraries = array();
-      $libraries_sql = "SELECT library_id, library_name ".
-                       "FROM {unigene_libraries_mview} ".
-                       "WHERE analysis_id = %d ";
-      $previous_db = db_set_active('chado');  // use chado database
-      $libraries_result = db_query($libraries_sql,$assembly->analysis_id);
-      db_set_active($previous_db);  // now use drupal database
-      $library_sql = "SELECT * FROM {chado_library} WHERE library_id = %d";
-      $k = 0;
-      while ($library = db_fetch_object($libraries_result)){
-          $library_node = db_fetch_object(db_query($library_sql,$library->library_id));
-          $library->node_id = $library_node->nid;
-          $libraries[$k++] = $library;
-      }      
-      $assembly->libraries = $libraries;
-      $assemblies[$i++] = $assembly;
-
-   } 
+      //$libraries = array();
+      //$libraries_sql = "SELECT library_id, library_name ".
+                       //"FROM {unigene_libraries_mview} ".
+                       //"WHERE analysis_id = %d ";
+      //$previous_db = db_set_active('chado');  // use chado database
+      //$libraries_result = db_query($libraries_sql,$assembly->analysis_id);
+      //db_set_active($previous_db);  // now use drupal database
+      //$library_sql = "SELECT * FROM {chado_library} WHERE library_id = %d";
+      //$k = 0;
+      //while ($library = db_fetch_object($libraries_result)){
+          //$library_node = db_fetch_object(db_query($library_sql,$library->library_id));
+          //$library->node_id = $library_node->nid;
+          //$libraries[$k++] = $library;
+      //}      
+      //$assembly->libraries = $libraries;
+      //$assemblies[$i++] = $assembly;
+   //} 
+
    // if this content is intended to be a menu item the 
    // we need to know so we can format the content slightly different
    $box_status =variable_get("tripal_analysis_unigene-box-assembly","menu_off");
@@ -533,10 +534,10 @@ function tripal_analysis_unigene_organism_add($node){
              "    <td class=\"dbfieldvalue\">$assembly->description         </td></tr>".
              "<tr><td class=\"dbfieldname\"> Libraries Included in Assembly </td>".
              "    <td class=\"dbfieldvalue\"> ";
-# TODO: THIS SHOULD NOT HAVE A LINK IF THERE IS NO LIBRARY NODE IN DRUPAL
-             foreach($assembly->libraries as $library){
-               $content .= "<a href=\"/node/$library->node_id\">$library->library_name</a> ";
-             }
+//# TODO: THIS SHOULD NOT HAVE A LINK IF THERE IS NO LIBRARY NODE IN DRUPAL
+             //foreach($assembly->libraries as $library){
+               //$content .= "<a href=\"/node/$library->node_id\">$library->library_name</a> ";
+             //}
              $content .= " </td></tr>".
              "</table>";