Started adding code for analysis proprties, but then commented out because didn't have time to finish. Also, updated the tripal pub obo

tripal_analysis/tripal_analysis.install

@@ -34,6 +34,18 @@ function tripal_analysis_update_6100() {
   // add the new materialized view
   tripal_analysis_add_mview_analysis_organism();
   
+  // move the analysis_type property into a new CV so that user's can change this property if
+  // they want too  
+  tripal_cv_add_cv('tripal_analysis', 'Terms used for managing analyses in Tripal');
+  
+  $sql = "
+    UPDATE {cvterm} SET cv_id = 
+      (SELECT cv_id FROM {cv} WHERE name = 'tripal_analysis')
+    WHERE cv_id = (SELECT cv_id FROM {cv} WHERE name = 'tripal') AND
+      name = 'analysis_type'
+  ";
+  chado_query($sql);
+  
   $ret = array(
     '#finished' => 1,
   );
@@ -65,28 +77,34 @@ function tripal_analysis_create_analysisfeatureprop(){
  */
 function tripal_analysis_add_cvterms(){
   
-  // add analysis_type
+  tripal_cv_add_cv('tripal_analysis', 'Terms used for managing analyses in Tripal');
+  
+  // add analysis_type. This goes in the 'tripal_analysis' CV so that site admins
+  // change change this property
   $term = array(
     'name' => 'analysis_type', 
     'def' => 'The type of analysis was performed. This value is automatically set by '.
              'each Tripal Analysis module and should be equal to the module name '.
              '(e.g. tripal_analysis_blast, tripal_analysis_go).'
   );
-  tripal_cv_add_cvterm($term, 'tripal', 0, 1, 'tripal');
+  tripal_cv_add_cvterm($term, 'tripal_analysis', 0, 1, 'tripal');
   
-  // add analysis_date
+  // add analysis_date.  This is no longer used (as far as we can tell) but we don't
+  // get rid of it in case it is used, so just keep it in the Tripal CV
   $term = array(
     'name' => 'analysis_date', 
     'def' => 'The date that an analysis was performed.'
   );
   tripal_cv_add_cvterm($term, 'tripal', 0, 1, 'tripal');
   
-  // add analysis_short_name
+  // add analysis_short_name.  This is no longer used (as far as we can tell) but we don't
+  // get rid of it in case it is used, so just keep it in the Tripal CV
   $term = array(
     'name' => 'analysis_short_name', 
     'def' => 'A computer legible (no spaces or special characters) abbreviation for the analysis.'
   );     
-  tripal_cv_add_cvterm($term, 'tripal', 0, 1 , 'tripal'); 
+  tripal_cv_add_cvterm($term, 'tripal', 0, 1 , 'tripal');     
+  
 }
 /**
  * Implementation of hook_uninstall().

tripal_analysis/tripal_analysis.module

@@ -17,7 +17,7 @@
 require('api/tripal_analysis.api.inc');
 require('includes/tripal_analysis_privacy.inc');
 require('includes/tripal_analysis.admin.inc');
-
+require('includes/tripal_analysis-properties.inc');
 
 
 /**
@@ -63,8 +63,37 @@ function tripal_analysis_menu() {
       'type' => MENU_NORMAL_ITEM,
       'file' => 'includes/tripal_analysis.admin.inc',
   );
+  
+  //Edit/Deleting Properties-------------
+/*  $items['node/%ta_node/edit_analysis_properties'] = array(
+    'title' => 'Edit Properties',
+    'description' => 'Analysis Properties',
+    'page callback' => 'tripal_analysis_edit_ALL_properties_page',
+    'page arguments' => array(1),
+    'access arguments' => array('edit chado_analysis content'),
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 8,
+  );*/
   return $items;
 }
+/**
+ * Implements Menu wildcard_load hook
+ * Purpose: Allows the node ID of a chado analysis to be dynamically
+ *   pulled from the path. The node is loaded from this node ID
+ *   and supplied to the page as an arguement
+ *
+ * @ingroup tripal_analysis
+ */
+function ta_node_load($nid) {  
+  if (is_numeric($nid)) {
+    $node = node_load($nid);
+    $analysis_id = chado_get_id_for_node('analysis', $node);
+    if ($analysis_id) {
+      return $node;
+    }
+  }
+  return FALSE;
+}
 
 /**
  * Provide information to drupal about the node types that we're creating
@@ -738,3 +767,4 @@ function tripal_analysis_views_api() {
 }
 
 
+

tripal_pub/files/tpub.obo

@@ -1391,6 +1391,12 @@ name: Media Code
 relationship: part_of TPUB:0000037 ! Publication Details
 def: A unique special code for a journal, book, conference proceeding, etc
 
+[Term]
+id: TPUB:0000254
+name: Publication Code
+relationship: part_of TPUB:0000037 ! Publication Details
+def: A unique special code for journal article, book, book chapter or any publication type.
+
 [Typedef]
 id: is_a
 name: is a