Loading of Ontologies is converted to 7.x

tripal_core/api/tripal_core_chado.api.inc

@@ -2697,7 +2697,7 @@ function tripal_get_chado_custom_schema($table) {
  * @return
  *   TRUE/FALSE depending upon whether it exists
  */
-function tripal_chado_table_exists($table) {
+function chado_table_exists($table) {
 	global $databases;
 	
 	$default_db = $databases['default']['default']['database'];

tripal_core/api/tripal_core_custom_tables.api.inc

@@ -113,7 +113,7 @@ function tripal_core_create_custom_table($table, $schema, $skip_creation = 1) {
   $centry = $results->fetchObject();
   
   // check to see if the table already exists in the chado schema
-  $exists = tripal_chado_table_exists($table); 
+  $exists = chado_table_exists($table); 
   
   // if the table does not exist then create it
   if (!$exists) { 

tripal_core/api/tripal_core_mviews.api.inc

@@ -78,12 +78,10 @@ function tripal_add_mview($name, $modulename, $mv_table, $mv_specs, $indexed,
   if (drupal_write_record('tripal_mviews', $record)) {
 
     // drop the table from chado if it exists
-    $previous_db = tripal_db_set_active('chado');  // use chado database
-    if (db_table_exists($mv_table)) {
-      $sql = "DROP TABLE $mv_table";
-      db_query($sql);
+    if (chado_table_exists($mv_table)) {
+      $sql = "DROP TABLE {$mv_table}";
+      chado_query($sql);
     }
-    tripal_db_set_active($previous_db);  // now use drupal database
 
     // now construct the indexes
     $index = '';
@@ -297,8 +295,7 @@ function tripal_mviews_get_mview_id($view_name) {
  */
 function tripal_mviews_action($op, $mview_id, $redirect = FALSE) {
   global $user;
-
-  $args = array("$mview_id");
+  
   if (!$mview_id) {
     return '';
   }
@@ -310,6 +307,7 @@ function tripal_mviews_action($op, $mview_id, $redirect = FALSE) {
 
   // add a job or perform the action based on the given operation
   if ($op == 'update') {
+  	$args = array("$mview_id");
     tripal_add_job("Populate materialized view '$mview->name'", 'tripal_core',
        'tripal_update_mview', $args, $user->uid);
   }
@@ -321,7 +319,7 @@ function tripal_mviews_action($op, $mview_id, $redirect = FALSE) {
     // drop the table from chado if it exists
     $previous_db = tripal_db_set_active('chado');  // use chado database
     if (db_table_exists($mview->mv_table)) {
-      $sql = "DROP TABLE $mview->mv_table";
+      $sql = "DROP TABLE " . $mview->mv_table;
       db_query($sql);
     }
     tripal_db_set_active($previous_db);  // now use drupal database

tripal_cv/api/tripal_cv.api.inc

@@ -151,10 +151,9 @@ function tripal_cv_get_cv_by_id($cv_id) {
  */
 function tripal_cv_get_cv_id($cv_name) {
 
-  $sql = "
-    SELECT cv_id FROM {cv} WHERE name = '%s'
-  ";
-  $cv = db_fetch_object(chado_query($sql, $cv_name));
+  $sql = "SELECT cv_id FROM {cv} WHERE name = :name";
+  $result = chado_query($sql, array(':name' => $cv_name));
+  $cv = $result->fetchObject();
 
   return $cv->cv_id;
 }
@@ -368,13 +367,24 @@ function tripal_cv_update_cvtermpath($cvid, $job_id = NULL) {
   // TODO: need better error checking in this function
 
   // first get the controlled vocabulary name:
-  $cv = db_fetch_object(chado_query("SELECT * FROM {cv} WHERE cv_id = %d", $cvid));
+  $sql = "SELECT * FROM {cv} WHERE cv_id = :cv_id";
+  $result = chado_query($sql, array(':cv_id' => $cvid));
+  $cv = $result->fetchObject();
+  
   print "\nUpdating cvtermpath for $cv->name...\n";
-
-  // now fill the cvtermpath table
-  // @coder-ignore: using a function rather then tablename therefore table prefixing doesn't apply
-  $sql = "SELECT * FROM fill_cvtermpath('%s')";
-  $success = chado_query($sql, $cv->name); 
+  
+  $previous = tripal_db_set_active('chado');
+  try {
+    $sql = "SELECT * FROM fill_cvtermpath(':name')";
+    db_query($sql, array(':name' => $cv->name));
+    tripal_db_set_active($previous); 
+  }
+  catch (Exception $e) {
+    tripal_db_set_active($previous);	
+    $error = $e->getMessage();
+    watchdog('tripal_cv', "Could not fill cvtermpath table: @error", array('@error' => $error), WATCHDOG_ERROR);
+    return FALSE;
+  }
 
   return TRUE;
 }
@@ -548,22 +558,15 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
   // here for easy reference below.  Because CV terms can change their names
   // but accessions don't change, the following SQL finds cvterms based on
   // their accession rather than the name
-  if (!tripal_core_is_sql_prepared('sel_cvterm_by_accession')) {
-    $pcvtermsql = "
-      PREPARE sel_cvterm_by_accession(text, text) AS
-      SELECT CVT.name, CVT.cvterm_id, CV.cv_id, CV.name as cvname, 
-        DB.name as dbname, DB.db_id, DBX.accession 
-      FROM {cvterm} CVT
-        INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
-        INNER JOIN {db} DB on DBX.db_id = DB.db_id
-        INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
-      WHERE DBX.accession = $1 and DB.name = $2";
-    if (!tripal_core_chado_prepare('sel_cvterm_by_accession', $pcvtermsql, array('text', 'text'))) {
-      watchdog('tripal_cv', "Cannot prepare statement 'sel_cvterm_by_accession'", NULL, WATCHDOG_WARNING);
-      return 0; 
-    }
-  } 
-  $cvtermsql = "EXECUTE sel_cvterm_by_accession('%s','%s')";  
+  $cvtermsql = "     
+    SELECT CVT.name, CVT.cvterm_id, CV.cv_id, CV.name as cvname, 
+      DB.name as dbname, DB.db_id, DBX.accession 
+    FROM {cvterm} CVT
+      INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
+      INNER JOIN {db} DB on DBX.db_id = DB.db_id
+      INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
+    WHERE DBX.accession = :accession and DB.name = :name
+  ";    
   
   // add the database. The function will just return the DB object if the
   // database already exists.
@@ -676,7 +679,8 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
         }
       }        
       // get the original cvterm with the same name and return that.
-      $cvterm = db_fetch_object(chado_query($cvtermsql, $dbxref->accession, $dbname));
+      $result = chado_query($cvtermsql, array(':accession' => $dbxref->accession, ':name' => $dbname));
+      $cvterm = $result->fetchObject();
       return $cvterm;
     }
     
@@ -685,10 +689,8 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
   }
   
   // get the CVterm record
-  $cvterm = db_fetch_object(chado_query($cvtermsql, $accession, $dbname)); 
-  //print "$pcvtermsql\n$cvtermsql\n$accession, $dbname\n";
-  //print "CVTERM:\n";
-  //print_r($cvterm);
+  $result = chado_query($cvtermsql, array(':accession' => $accession, ':name' => $dbname));
+  $cvterm = $result->fetchObject();
   if (!$cvterm) {
 
     // check to see if the dbxref exists if not, add it
@@ -731,8 +733,9 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
     else {
       watchdog('tripal_cv', "The dbxref already exists for another cvterm record: $name (cv: " . $cvname . " db: $dbname)", NULL, WATCHDOG_WARNING);
       return 0;
-    }    
-    $cvterm = db_fetch_object(chado_query($cvtermsql, $accession, $dbname));
+    } 
+    $result = chado_query($cvtermsql, array(':accession' => $accession, ':name' => $dbname));
+    $cvterm = $result->fetchObject();   
   }
   // upate the cvterm
   elseif ($update) { 
@@ -749,7 +752,8 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
       watchdog('tripal_cv', "Failed to update the term: $name", NULL, WATCHDOG_WARNING);
       return 0;
     }
-    $cvterm = db_fetch_object(chado_query($cvtermsql, $accession, $dbname));
+    $result = chado_query($cvtermsql, array(':accession' => $accession, ':name' => $dbname));
+    $cvterm = $result->fetchObject();
   } 
   else {
      // do nothing, we have the cvterm but we don't want to update
@@ -832,9 +836,9 @@ function tripal_cv_submit_obo_job($obo_id = NULL, $obo_name = NULL, $obo_url = N
   global $user;
 
   if ($obo_id) {
-    $sql = "SELECT * FROM {tripal_cv_obo} WHERE obo_id = %d";
-    $obo = db_fetch_object(db_query($sql, $obo_id));
-    
+    $sql = "SELECT * FROM {tripal_cv_obo} WHERE obo_id = :obo_id";
+    $obo = db_query($sql, array(':obo_id' => $obo_id))->fetchObject();
+        
     $args = array($obo_id);
     return tripal_add_job("Load OBO $obo->name", 'tripal_cv',
        "tripal_cv_load_obo_v1_2_id", $args, $user->uid);

tripal_cv/includes/obo_loader.inc

@@ -13,7 +13,7 @@
  *
   * @ingroup tripal_obo_loader
  */
-function tripal_cv_obo_form(&$form_state = NULL) {
+function tripal_cv_obo_form($form, &$form_state) {
 
   // get a list of db from chado for user to choose
   $sql = "SELECT * FROM {tripal_cv_obo} ORDER BY name";
@@ -21,7 +21,7 @@ function tripal_cv_obo_form(&$form_state = NULL) {
 
   $obos = array();
   $obos[] = '';
-  while ($obo = db_fetch_object($results)) {
+  foreach ($results as $obo) {
 //    $obos[$obo->obo_id] = "$obo->name  | $obo->path";
     $obos[$obo->obo_id] = $obo->name;
   }
@@ -41,21 +41,18 @@ function tripal_cv_obo_form(&$form_state = NULL) {
                    installation of the Tripal CV module or were added from a previous upload.  Select
                    an OBO, then click the submit button to load the vocabulary into the database.  If the
                    vocabularies already exist then the ontology will be updated.'),
-    '#weight'        => -1
   );
 
   $form['obo_existing']['obo_id'] = array(
     '#title' => t('Ontology OBO File Reference'),
     '#type' => 'select',
     '#options' => $obos,
-    '#weight'        => 0
   );
 
   $form['obo_new']['path_instructions']= array(
     '#value' => t('Provide the name and path for the OBO file.  If the vocabulary OBO file
                    is stored local to the server provide a file name. If the vocabulry is stored remotely,
                    provide a URL.  Only provide a URL or a local file, not both.'),
-    '#weight'        => 0
   );
 
   $form['obo_new']['obo_name']= array(
@@ -63,7 +60,6 @@ function tripal_cv_obo_form(&$form_state = NULL) {
     '#title'         => t('New Vocabulary Name'),
     '#description'   => t('Please provide a name for this vocabulary.  After upload, this name will appear in the drop down
                            list above for use again later.'),
-    '#weight'        => 1
   );
 
   $form['obo_new']['obo_url']= array(
@@ -71,8 +67,6 @@ function tripal_cv_obo_form(&$form_state = NULL) {
     '#title'         => t('Remote URL'),
     '#description'   => t('Please enter a URL for the online OBO file.  The file will be downloaded and parsed.
                            (e.g. http://www.obofoundry.org/ro/ro.obo'),
-    '#default_value' => $default_desc,
-    '#weight'        => 2
   );
 
   $form['obo_new']['obo_file']= array(
@@ -81,14 +75,11 @@ function tripal_cv_obo_form(&$form_state = NULL) {
     '#description'   => t('Please enter the full system path for an OBO definition file, or a path within the Drupal
                            installation (e.g. /sites/default/files/xyz.obo).  The path must be accessible to the
                            server on which this Drupal instance is running.'),
-    '#default_value' => $default_desc,
-    '#weight'        => 3
   );
 
   $form['submit'] = array(
     '#type'         => 'submit',
     '#value'        => t('Submit'),
-    '#weight'       => 5,
     '#executes_submit_callback' => TRUE,
   );
 
@@ -125,7 +116,7 @@ function tripal_cv_cvtermpath_form() {
 
   $cvs = array();
   $cvs[] = '';
-  while ($cv = db_fetch_object($results)) {
+  foreach ($results as $cv) {
     $cvs[$cv->cv_id] = $cv->name;
   }
 
@@ -161,8 +152,8 @@ function tripal_cv_cvtermpath_form() {
 function tripal_cv_load_obo_v1_2_id($obo_id, $jobid = NULL) {
 
   // get the OBO reference
-  $sql = "SELECT * FROM {tripal_cv_obo} WHERE obo_id = %d";
-  $obo = db_fetch_object(db_query($sql, $obo_id));
+  $sql = "SELECT * FROM {tripal_cv_obo} WHERE obo_id = :obo_id";
+  $obo = db_query($sql, array(':obo_id' => $obo_id))->fetchObject();
 
   // if the reference is for a remote URL then run the URL processing function
   if (preg_match("/^http:\/\//", $obo->path) or preg_match("/^ftp:\/\//", $obo->path)) {
@@ -274,9 +265,9 @@ function tripal_cv_load_obo_v1_2($file, $jobid = NULL, &$newcvs) {
     
   // make sure our temporary table exists
   $ret = array(); 
-  if (!db_table_exists('tripal_obo_temp')) { 
+  if (!chado_table_exists('tripal_obo_temp')) { 
     $schema = tripal_cv_get_custom_tables('tripal_obo_temp');  
-    $success = tripal_core_create_custom_table($ret, 'tripal_obo_temp', $schema['tripal_obo_temp']);
+    $success = tripal_core_create_custom_table('tripal_obo_temp', $schema['tripal_obo_temp']);
     if (!$success) {
       watchdog('T_obo_loader', "Cannot create temporary loading table", array(), WATCHDOG_ERROR); 
       return;
@@ -286,20 +277,6 @@ function tripal_cv_load_obo_v1_2($file, $jobid = NULL, &$newcvs) {
   $sql = "DELETE FROM {tripal_obo_temp}";
   chado_query($sql);
 
-  // get a persistent connection
-  $connection = tripal_db_persistent_chado();
-  if (!$connection) {
-     print "A persistant connection was not obtained. Loading will be slow\n";
-  }
-          
-  // if we cannot get a connection then let the user know the loading will be slow
-  tripal_db_start_transaction();
-  if ($connection) {
-     print "\nNOTE: Loading of this OBO file is performed using a database transaction. \n" .
-           "If the load fails or is terminated prematurely then the entire set of \n" .
-           "insertions/updates is rolled back and will not be found in the database\n\n";
-  }
-
   print "Step 1: Preloading File $file\n";  
 
   // make sure we have an 'internal' and a '_global' database
@@ -350,19 +327,15 @@ function tripal_cv_obo_quiterror($message) {
  * 
  */
 function tripal_cv_obo_load_typedefs($defaultcv, $newcvs, $default_db, $jobid){
-  $sql = "
-    SELECT * 
-    FROM tripal_obo_temp
-    WHERE type = 'Typedef' 
-  ";
+  $sql = "SELECT * FROM {tripal_obo_temp} WHERE type = 'Typedef' ";
   $typedefs = chado_query($sql);
   
-    $sql = "
+  $sql = "
     SELECT count(*) as num_terms
-    FROM tripal_obo_temp
+    FROM {tripal_obo_temp}
     WHERE type = 'Typedef'     
   "; 
-  $result = db_fetch_object(chado_query($sql));
+  $result = chado_query($sql)->fetchObject();
   $count = $result->num_terms;
   
   // calculate the interval for updates
@@ -371,7 +344,7 @@ function tripal_cv_obo_load_typedefs($defaultcv, $newcvs, $default_db, $jobid){
     $interval = 1;
   }
   $i = 0;
-  while ($typedef = db_fetch_object($typedefs)) {
+  foreach ($typedefs as $typedef) {
     $term = unserialize(base64_decode($typedef->stanza));
     
     // update the job status every interval
@@ -419,7 +392,7 @@ function tripal_cv_obo_process_terms($defaultcv, $jobid = NULL, &$newcvs, $defau
     FROM {tripal_obo_temp}
     WHERE type = 'Term'     
   "; 
-  $result = db_fetch_object(chado_query($sql));
+  $result = chado_query($sql)->fetchObject();
   $count = $result->num_terms;
   
   // calculate the interval for updates
@@ -427,7 +400,7 @@ function tripal_cv_obo_process_terms($defaultcv, $jobid = NULL, &$newcvs, $defau
   if ($interval < 1) {
     $interval = 1;
   }
-  while($t = db_fetch_object($terms)) {
+  foreach ($terms as $t) {
     $term = unserialize(base64_decode($t->stanza));
     
     // update the job status every interval

tripal_cv/tripal_cv.info

@@ -1,8 +1,8 @@
 name = Tripal CV
 description = The controlled vocabulary module for the Tripal package that integrates Drupal and GMOD chado. This module provides support for managing and viewing controlled vocabularies.
-core = 6.x
+core = 7.x
 project = tripal_cv
 package = Tripal
-version = 6.x-1.1
+version = 7.x-2.0
 dependencies[] = tripal_core
 dependencies[] = tripal_db

tripal_cv/tripal_cv.install

@@ -31,8 +31,8 @@ function tripal_cv_install() {
     // SQL statement that populates the view
     'SELECT DISTINCT CVT.name,CVT.cvterm_id, CV.cv_id, CV.name
      FROM {cvterm_relationship} CVTR
-       INNER JOIN cvterm CVT on CVTR.object_id = CVT.cvterm_id
-       INNER JOIN CV on CV.cv_id = CVT.cv_id
+       INNER JOIN {cvterm} CVT on CVTR.object_id = CVT.cvterm_id
+       INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
      WHERE CVTR.object_id not in
        (SELECT subject_id FROM {cvterm_relationship}) ',
     // special index
@@ -40,27 +40,9 @@ function tripal_cv_install() {
   );
 
   // create the tables that correlate OBO files/references with a chado CV
-  drupal_install_schema('tripal_cv');
   tripal_cv_add_obo_defaults();
 }
 
-/**
- *  This update adds the new tripal_obo table.  This is an upgrade from
- *  Tripal version 0.2
- *
- * @ingroup tripal_cv
- */
-
-function tripal_cv_update_6000() {
-  drupal_install_schema('tripal_cv');
-  tripal_cv_add_obo_defaults();
-  $ret = array(
-    '#finished' => 1,
-  );
-
-  return $ret;
-}
-
 /**
  * Implementation of hook_uninstall().
  *
@@ -73,8 +55,6 @@ function tripal_cv_uninstall() {
   if ($mview) {
     tripal_mviews_action('delete', $mview);
   }
-
-  drupal_uninstall_schema('tripal_cv');
 }
 
 /**
@@ -83,21 +63,6 @@ function tripal_cv_uninstall() {
  * @ingroup tripal_cv
  */
 function tripal_cv_schema() {
-  $schema = tripal_cv_get_schemas();
-  return $schema;
-}
-
-/**
- * This function simply defines all tables needed for the module to work
- * correctly.  By putting the table definitions in a separate function we
- * can easily provide the entire list for hook_install or individual
- * tables for an update.
- *
- * @ingroup tripal_cv
- */
-function tripal_cv_get_schemas() {
-  $schema = array();
-
   $schema['tripal_cv_obo'] = array(
     'fields' => array(
       'obo_id' => array('type' => 'serial', 'unsigned' => TRUE, 'not null' => TRUE),
@@ -131,13 +96,8 @@ function tripal_cv_add_obo_defaults() {
     array('Plant Growth and Development Stages Ontology', 'http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_temporal.obo?view=co')
   );
   foreach ($ontologies as $o) {
-    db_query(
-      "INSERT INTO {tripal_cv_obo} (name,path) VALUES ('%s','%s')",
-      $o[0],
-      $o[1]
-    );
+    db_query("INSERT INTO {tripal_cv_obo} (name,path) VALUES (:name, :path)", array(':name' => $o[0], ':path' => $o[1]));
   }
-
 }
 
 /**

tripal_cv/tripal_cv.module

@@ -191,9 +191,12 @@ function tripal_cv_menu() {
  *
  * @ingroup tripal_cv
  */
-function tripal_cv_perm() {
+function tripal_cv_permission() {
   return array(
-    'administer controlled vocabularies',
+    'administer controlled vocabularies' => array(
+      'title' => t('Administer controlled vocabularies (CVs).'),
+      'description' => t('Allow a user to add, edit and delete controlled vocabularies as well as add and edit terms.')
+    ),
   );
 }
 

tripal_db/api/tripal_db.api.inc

@@ -84,11 +84,8 @@ function tripal_db_get_db($select_values) {
  */
 function tripal_db_get_db_by_db_id($db_id) {
 
-  $r = db_fetch_object(chado_query(
-    "SELECT * FROM {db} WHERE db_id=%d", $db_id
-  ));
-
-  return $r;
+  $r = chado_query("SELECT * FROM {db} WHERE db_id = :db_id", array(':db_id' => $db_id ));
+  return $r->fetchObject();
 }
 
 /**
@@ -142,12 +139,10 @@ function tripal_db_get_db_by_name($name) {
  */
 function tripal_db_get_db_options() {
 
-  $result = chado_query(
-    "SELECT db_id, name FROM {db}"
-  );
+  $result = chado_query("SELECT db_id, name FROM {db}");
 
   $options = array();
-  while ( $r = db_fetch_object($result) ) {
+  foreach ($result as $r) {
     $options[$r->db_id] = $r->name;
   }
 
@@ -257,19 +252,15 @@ function tripal_db_get_dbxref($select_values) {
 function tripal_db_get_dbxref_by_accession($accession, $db_id=0) {
 
   if (!empty($db_id)) {
-    $r = db_fetch_object(chado_query(
-      "SELECT * FROM {dbxref} WHERE accession='%s' AND db_id=%d",
-      $accession, $db_id
-    ));
+  	$sql = "SELECT * FROM {dbxref} WHERE accession = :accession AND db_id = :db_id";
+    $r = chado_query($sql, array(':accession' => $accession, ':db_id' => $db_id));
   }
   else {
-    $r = db_fetch_object(chado_query(
-      "SELECT * FROM {dbxref} WHERE accession='%s'",
-      $accession
-    ));
+  	$sql = "SELECT * FROM {dbxref} WHERE accession = :accession";
+    $r = chado_query($sql, array(':accession' => $accession));
   }
 
-  return $r;
+  return $r->fetchObject();
 }
 
 /**

tripal_db/tripal_db.module

@@ -86,21 +86,6 @@ function tripal_db_views_api() {
   return array('api' => 2.0);
 }
 
-function tripal_db_form_alter(&$form, &$form_state, $form_id) {
-  if ($form_id == "tripal_db_form") {    
-    // updating the form through the ahah callback sets the action of
-    // the form to the ahah callback URL. We need to set it back
-    // to the normal form URL 
-    if (array_key_exists('values', $form_state)) {
-	    if ($form_state['values']['form_action'] == 'Update') {
-	      $form['#action'] = url("admin/tripal/tripal_db/edit_db");
-	    }
-	    if ($form_state['values']['form_action'] == 'Add') {
-	      $form['#action'] = url("admin/tripal/tripal_db/add_db");
-	    }
-    }
-  } 
-}
 
 /**
  *  We need to let drupal know about our theme functions and their arguments.