Removed the old cvterm.php file as those API functions have been replaced. All call to those old functions have been removed

extensions/tripal_search_unigene/tripal_search_unigene.install

@@ -35,7 +35,7 @@ function tripal_search_unigene_install(){
    							  ";
    
    $index = "feature_id, go_term, unigene, blast_value, kegg_value, interpro_value";
-   $singlet_type_id = tripal_get_cvterm_id('singlet_in_analysis');
+   $singlet_type_id = tripal_cv_get_cvterm_by_name('singlet_in_analysis');
    if ($singlet_type_id) {
    	$singlet_condition = " AND F.feature_id NOT IN (SELECT feature_id from feature
    						   WHERE type_id = (select cvterm_id from cvterm where name = 'EST')

extensions/tripal_search_unigene/views_handler_filter_analysis_name.inc

@@ -1,10 +1,13 @@
 <?php
 class views_handler_filter_analysis_name extends views_handler_filter_string {
 	function value_form(&$form, &$form_state) {
-		$type_id = tripal_get_cvterm_id("analysis_type");
-		$sql = "SELECT name, A.analysis_id FROM {analysis} A INNER JOIN {analysisprop} AP ON A.analysis_id = AP.analysis_id WHERE type_id = $type_id AND value = 'tripal_analysis_unigene'";
+		$type_id = tripal_cv_get_cvterm_by_name("analysis_type");
+		$sql = "SELECT name, A.analysis_id 
+		        FROM {analysis} A 
+		           INNER JOIN {analysisprop} AP ON A.analysis_id = AP.analysis_id 
+		        WHERE type_id = %d AND value = 'tripal_analysis_unigene'";
 
-		$results = chado_query($sql);
+		$results = chado_query($sql,$typ_id->cvterm_id);
 		$analyses = array();
 		$block_ana = array();
 		$counter = 0;
@@ -47,4 +50,4 @@ class views_handler_filter_analysis_name extends views_handler_filter_string {
 			'=' => t('Is equal to')
 		);
 	}
-}
+}

tripal_analysis/tripal_analysis.install

@@ -29,10 +29,10 @@ function tripal_analysis_install() {
 	}
 	tripal_db_set_active($previous_db);
 
-   tripal_add_cvterms('analysis_type','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_add_cvterms('analysis_date','The date that an analysis was performed.');
-	tripal_add_cvterms('analysis_short_name','A computer legible (no spaces '.
-      'or special characters) abbreviation for the analysis.');
+   tripal_cv_add_cvterm(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',0,1,'tripal');
+	tripal_cv_add_cvterm(array('name' => 'analysis_date','def' => 'The date that an analysis was performed.'),'tripal',0,1,'tripal');
+	tripal_cv_add_cvterm(array('name' => 'analysis_short_name','def' => 'A computer legible (no spaces '.
+      'or special characters) abbreviation for the analysis.'),'tripal',0,1,'tripal');
 }
 
 /*******************************************************************************
@@ -131,10 +131,10 @@ function tripal_analysis_requirements($phase) {
  */
 function tripal_analysis_update_6001(){
    // we have some new cvterms to add
-   tripal_add_cvterms('based_on_analysis','The analysis that this analysis was based on. For example, blast/kegg/interpro analyses are based on a unigene analysis. The unigene analysis_id should be stored in analysisprop as the rank using this cvterm. The name of said unigene analysis can be inserted as the value in analysisprop.');
-   tripal_add_cvterms('additional_files', 'Additional files for this analysis. Each file should be separated by a semi-colon and have this format: <file description>, <file path>;');
+   tripal_cv_add_cvterm(array('name' => 'based_on_analysis','def' => 'The analysis that this analysis was based on. For example, blast/kegg/interpro analyses are based on a unigene analysis. The unigene analysis_id should be stored in analysisprop as the rank using this cvterm. The name of said unigene analysis can be inserted as the value in analysisprop.'),'tripal',0,1,'tripal');
+   tripal_cv_add_cvterm(array('name' => 'additional_files', 'def' => 'Additional files for this analysis. Each file should be separated by a semi-colon and have this format: <file description>, <file path>;'),'tripal',0,1,'tripal');
    $ret = array(
       '#finished' => 1,
    );   
    return $ret;
-}
+}

tripal_core/cvterms.php

@@ -1,124 +0,0 @@
-<?php
-
-/** 
- * @defgroup tripal_core_cv_api Core Module CV API
- * @{
- * For working with controlled vocabularies see the Controlled Vocabulary
- * API.  However, there are cases where a CV does not exist. For example in
- * some cases a module may want to support adding of properties (such as to
- * for an analysis) to a record but an organized CV does not exist.  The 
- * progammer may create their own ontology and populate it, or they may use
- * the basic CV interface provided by Tripal.  Tripal provides a CV named
- * 'Tripal' and modules may add terms to this CV to support the functionality
- * of their modules.  
- * @}
- * @ingroup tripal_api
- */
-
-/**
- * DEPRECATED: This function should no longer be used. But rather the
- * tripal_cv_add_cvterm function should be used. 
- * 
- * This function adds a term to the cvterm table of Chado.
- *
- * @param $name 
- *   The name of the term
- * @param $definition 
- *   The definition for the term
- * @param $cv_name 
- *   The name of the controlled vocabulary to which the term will be added.
- *   The default CV is 'tripal'.
- * @param $db_name 
- *   CV records also have a corresponding database reference.  This argument
- *   specifies the name of the database to which this term belongs. The default
- *   database name is 'tripal'.
- *
- * @ingroup tripal_core_cv_api
- */
-function tripal_add_cvterms ($name,$definition,$cv_name = 'tripal',$db_name='tripal'){
-   
-   
-   $previous_db = tripal_db_set_active('chado');  // use chado database
-   $cv = db_fetch_object(db_query("SELECT * FROM {cv} WHERE name = '$cv_name'"));
-   if (!$cv->cv_id) {
-      tripal_db_set_active($previous_db);
-      tripal_add_cv('tripal', 'Terms used by Tripal for modules to manage data such as that 
-                               stored in property tables like featureprop, analysisprop, etc');
-      tripal_db_set_active('chado');
-      $cv = db_fetch_object(db_query("SELECT * FROM {cv} WHERE name = '$cv_name'"));
-   }
-   $db = db_fetch_object(db_query("SELECT * FROM {db} WHERE name = '$db_name'"));
-	if (!$db->db_id) {
-	   tripal_db_set_active($previous_db);
-	   tripal_add_db('tripal', 'Used as a database placeholder for tripal defined objects such as tripal cvterms', '', '');
-	   tripal_db_set_active('chado');
-	   $db = db_fetch_object(db_query("SELECT * FROM {db} WHERE name = '$db_name'"));
-	}
-
-	// check to see if the dbxref already exists if not then add it
-	$sql = "SELECT * FROM {dbxref} WHERE db_id = $db->db_id and accession = '$name'";
-	$dbxref = db_fetch_object(db_query($sql));
-	if(!$dbxref){
-	   db_query("INSERT INTO {dbxref} (db_id,accession) VALUES ($db->db_id,'$name')");
-		$dbxref = db_fetch_object(db_query($sql));
-	}
-
-   
-   // now add the cvterm only if it doesn't already exist
-	$sql = "SELECT * FROM {cvterm} ".
-	       "WHERE cv_id = $cv->cv_id and dbxref_id = $dbxref->dbxref_id and name = '$name'";
-	$cvterm = db_fetch_object(db_query($sql));
-	if(!$cvterm){
-      $result = db_query("INSERT INTO {cvterm} (cv_id,name,definition,dbxref_id) ".
-                         "VALUES ($cv->cv_id,'$name','$definition',$dbxref->dbxref_id)");
-	}
-   tripal_db_set_active($previous_db);  // now use drupal database	
-	
-   if(!$result){
-     // TODO -- ERROR HANDLING
-   }
-}
-/**
- * Add a database to the Chado 'db' table.
- * NOTE: This function is deprecated and may not be used in future releases of Tripal
- *  
- * @ingroup tripal_core_cv_api
- */
-function tripal_add_db($db_name,$description,$urlprefix,$url){
-   $previous_db = tripal_db_set_active('chado');  // use chado database
-
-   // use this SQL statement to get the db_id for the database name
-   $id_sql = "SELECT db_id FROM {db} WHERE name = '%s'";
-
-   $db = db_fetch_object(db_query($id_sql,$db_name));
-
-   // if the database doesn't exist then let's add it.
-   if(!$db->db_id){
-      $sql = "
-         INSERT INTO {db} (name,description,urlprefix,url) VALUES 
-         ('%s','%s','%s','%s');
-      ";
-      db_query($sql,$db_name,$description,$urlprefix,$url);
-    
-      # now get the id for this new db entry
-      $db = db_fetch_object(db_query($id_sql,$db_name));
-   }
-   tripal_db_set_active($previous_db);  // now use drupal database	
-   return $db->db_id;
-}
-
-
-/**
- * Get cvterm_id for a tripal term by passing its name
- * NOTE: This function is deprecated and may not be used in future releases of Tripal
- *  
- * @ingroup tripal_core_cv_api
- */
-function tripal_get_cvterm_id ($cvterm){
-	$sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT
-         	    INNER JOIN cv ON cv.cv_id = CVT.cv_id 
-            	 WHERE CVT.name = '$cvterm' 
-                AND CV.name = 'tripal'";
-	return db_result(chado_query($sql));
-}
-

tripal_core/tripal_core.module

@@ -2,7 +2,6 @@
 
 require_once "jobs.php";
 require_once "mviews.php";
-require_once "cvterms.php";
 require_once "chado_install.php";
 require_once "tripal_core.api.inc";
 

tripal_cv/tripal_cv.api.inc

@@ -166,28 +166,46 @@ function tripal_cv_get_cv_options() {
  *   the cvterm.name
  * @param $cv_id
  *   the cv_id of the term you are looking for
+ * @param $cv_name
+ *   the name of the CV
  *
  * @return 
  *   cvterm object
  *
  * @ingroup tripal_cv_api
  */
-function tripal_cv_get_cvterm_by_name ($name, $cv_id=0) {
+function tripal_cv_get_cvterm_by_name ($name, $cv_id=0,$cv_name='tripal') {
 
-  if (!empty($cv_id)) {
-    $sql = "SELECT * FROM cvterm WHERE name='%s' AND cv_id=%d";
-    $previous_db = tripal_db_set_active('chado');
-    $r = db_fetch_object(db_query($sql, $name, $cv_id));
-    tripal_db_set_active($previous_db);
-  } else {
-    $sql = "SELECT * FROM cvterm WHERE name='%s'";
-    $previous_db = tripal_db_set_active('chado');
-    $r = db_fetch_object(db_query($sql, $name));
-    tripal_db_set_active($previous_db);
+  if ($cv_id) {
+    $values = array(
+       'name' => $name,
+       'cv_id' => $cv_id,
+    );
+    $r = tripal_core_chado_select('cvterm',array('*'),$values);
+  } 
+  elseif($cv_name){
+    $values = array(
+       'name' => $name,
+       'cv_id' => array(
+          'name' => $cv_name,
+       ),
+    );
+    $r = tripal_core_chado_select('cvterm',array('*'),$values);
+  }
+  else {
+    $values = array(
+       'name' => $name,
+    );
+    $r = tripal_core_chado_select('cvterm',array('*'),$values);
   }
   
-  return $r;
-  
+  if(!$r){
+     return FALSE;
+  }
+  if(count($r) > 0){
+     return FALSE;
+  }
+  return $r[0];
 }
 
 /**
@@ -319,10 +337,11 @@ function tripal_cv_add_cv($name,$comment){
 *   the database to which the cvterm belongs and the <ACCESSION> is the 
 *   term's accession number in the database.
 * @param $defaultcv
-*   Optional. A CV object populated with the fields of the CV to which the term 
+*   Optional. The CV name to which the term 
 *   belongs.  If this arugment is null or not provided then the function tries
 *   to find a record in the CV table with the same name provided in the 
-*   $term[namespace]. 
+*   $term[namespace].  If this field is provided then it overrides what the 
+*   value in $term[namespace] 
 * @param $is_relationship
 *   If this term is a relationship term then this value should be 1.
 * @param $update
@@ -337,7 +356,7 @@ function tripal_cv_add_cv($name,$comment){
 *
 * @ingroup tripal_cv_api
 */
-function tripal_cv_add_cvterm($term,$defaultcv=NULL,$is_relationship = 0,$update = 1,$dbname=NULL){
+function tripal_cv_add_cvterm($term,$defaultcv='',$is_relationship = 0,$update = 1,$dbname=NULL){
 
    // get the term properties
    $id = $term['id'];
@@ -348,8 +367,18 @@ function tripal_cv_add_cvterm($term,$defaultcv=NULL,$is_relationship = 0,$update
    if(isset($term['is_obsolete']) and  strcmp($term['is_obsolete'],'true')==0){
      $is_obsolete = 1;
    }
+   if(!$name and !$id){
+      watchdog('tripal_cv', "Cannot find cvterm without 'id' or 'name'",NULL,WATCHDOG_WARNING);
+      return 0;
+   }
+   if(!$id){
+      $id = $name;
+   }
+   if(!$name){
+      $name = $id;
+   }
    if(!$cvname){
-      $cvname = $defaultcv->name;
+      $cvname = $defaultcv;
    }
    // make sure the CV name exists
    $cv = tripal_cv_add_cv($cvname,'');

tripal_feature/gff_loader.php

@@ -865,7 +865,7 @@ function tripal_feature_load_gff3_alias($feature,$aliases){
          'definition' => array(''),
          'is_obsolete' => array(0),
       );
-      $syntype = tripal_cv_add_cvterm($term,$syncv,0,1);
+      $syntype = tripal_cv_add_cvterm($term,$syncv->name,0,1);
       if(!$syntype){
          print("Cannot add synonym type: internal:$type");
          return 0;

tripal_library/tripal_library.install

@@ -16,14 +16,14 @@ function tripal_library_install(){
    // Insert cvterm 'library_description' into cvterm table of chado
    // database. This CV term is used to keep track of the library
    // description in the libraryprop table.
-   tripal_add_cvterms('library_description','Description of a library');
+   tripal_cv_add_cvterm(array('name' => 'library_description','def' => 'Description of a library'),'tripal',0,1,'tripal');
    
    // Add CVTerms for the library types
-   tripal_add_cvterms('cdna_library','cDNA Library');
-   tripal_add_cvterms('bac_library','BAC Library');
-   tripal_add_cvterms('fosmid_library','FOSMID Library');
-   tripal_add_cvterms('cosmid_library','COSMID Library');
-   tripal_add_cvterms('yac_library','YAC Library');
+   tripal_cv_add_cvterm(array('name' => 'cdna_library','def' => 'cDNA Library'),'tripal',0,1,'tripal');
+   tripal_cv_add_cvterm(array('name' => 'bac_library','def' => 'BAC Library'),'tripal',0,1,'tripal');
+   tripal_cv_add_cvterm(array('name' => 'fosmid_library','def' => 'FOSMID Library'),'tripal',0,1,'tripal');
+   tripal_cv_add_cvterm(array('name' => 'cosmid_library','def' => 'COSMID Library'),'tripal',0,1,'tripal');
+   tripal_cv_add_cvterm(array('name' => 'yac_library','def' => 'YAC Library'),'tripal',0,1,'tripal');
 
    // Add the materialized view needed to count the features for the library
    // Drop the MView table if it exists