Merge branch '7.x-2.x' of git.drupal.org:sandbox/spficklin/1337878 into 7.x-2.x

tripal_analysis/tripal_analysis.install

@@ -4,6 +4,24 @@
  * Implements hooks from the Schema API
  */
 
+/**
+ * Implementation of hook_requirements(). 
+ */
+function tripal_analysis_requirements($phase) {
+  $requirements = array();
+  if ($phase == 'install') {
+    // make sure chado is installed
+    if (!tripal_core_is_chado_installed()) {
+      $requirements ['tripal_analysis'] = array(
+            'title' => "tripal_analysis",
+            'value' => "ERROR: Chado most be installed before this module can be enabled",
+            'severity' => REQUIREMENT_ERROR,
+      );
+    }
+  }
+  return $requirements;
+}
+
 /**
  * Implementation of hook_install().
  */
@@ -22,6 +40,22 @@ function tripal_analysis_install() {
   tripal_analysis_add_mview_analysis_organism();
 }
 
+/**
+ * Implementation of hook_uninstall().
+ */
+function tripal_analysis_uninstall() {
+
+  // Remove analysis nodes from drupal.
+  $sql_ana_id = "
+    SELECT nid, vid
+    FROM {node}
+    WHERE type like 'chado_analysi%'
+  ";
+  $result = db_query($sql_ana_id);
+  while ($ana = $result->fetchObject()) {
+    node_delete($ana->nid);
+  }
+}
 /*
  * 
  */
@@ -29,17 +63,17 @@ function tripal_analysis_create_analysisfeatureprop() {
   
   // Create analysisfeatureprop table in chado.  This is needed for Chado 
   // version 1.11, the table exists in Chado 1.2. 
-  if (!db_table_exists('analysisfeatureprop')) {
-    $sql = "CREATE TABLE analysisfeatureprop (" .
-            "  analysisfeatureprop_id SERIAL PRIMARY KEY, " .
-            "  analysisfeature_id     INTEGER NOT NULL REFERENCES analysisfeature(analysisfeature_id) " .
-            "    ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, " .
-            "  type_id                INTEGER NOT NULL REFERENCES cvterm(cvterm_id) " .
-            "    ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, " .
-            "  value                  TEXT, " .
-            "  rank                   INTEGER NOT NULL, " .
-            "  CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank)" .
-            ")";
+  if (!db_table_exists('chado.analysisfeatureprop')) {
+    $sql = "
+      CREATE TABLE chado.analysisfeatureprop (
+        analysisfeatureprop_id SERIAL PRIMARY KEY, 
+        analysisfeature_id     INTEGER NOT NULL REFERENCES chado.analysisfeature(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, 
+        type_id                INTEGER NOT NULL REFERENCES chdo.cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED, 
+        value                  TEXT, 
+        rank                   INTEGER NOT NULL, 
+        CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank)
+      )
+    ";
     chado_query($sql);
   } 
 }
@@ -84,22 +118,6 @@ function tripal_analysis_add_cvterms() {
   tripal_cv_add_cvterm(array('name' => 'Analysis Type', 'def' => 'The type of analysis was performed.'), 
      'analysis_property', 0, 1, 'tripal');
 }
-/**
- * Implementation of hook_uninstall().
- */
-function tripal_analysis_uninstall() {
-
-  // Remove analysis nodes from drupal.
-  $sql_ana_id = "
-    SELECT nid, vid 
-    FROM {node} 
-    WHERE type like 'chado_analysi%'
-  ";
-  $result = db_query($sql_ana_id);
-  while ($ana = $result->fetchObject()) {
-    node_delete($ana->nid);
-  }
-}
 
 /**
  * Implementation of hook_schema() creates two tables.
@@ -111,6 +129,7 @@ function tripal_analysis_uninstall() {
  *     with this module.
  */
 function tripal_analysis_schema() {
+  
   // chado_analysis table
   $schema['chado_analysis'] = array(
     'fields' => array(
@@ -161,29 +180,13 @@ function tripal_analysis_schema() {
   return $schema;
 }
 
-/**
- * Implementation of hook_requirements(). 
- */
-function tripal_analysis_requirements($phase) {
-  $requirements = array();
-  if ($phase == 'install') {
-    // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
-      $requirements ['tripal_analysis'] = array(
-            'title' => "tripal_analysis",
-            'value' => "ERROR: Chado most be installed before this module can be enabled",
-            'severity' => REQUIREMENT_ERROR,
-      );
-    }
-  }
-  return $requirements;
-}
-
 /*
  * 
  * @ingroup tripal_network
  */
 function tripal_analysis_add_mview_analysis_organism() {
+  $view_name = 'analysis_organism';
+  $comment = t('This view is for associating an organism (via it\'s associated features) to an analysis.');
   
   // this is the SQL used to identify the organism to which an analsysis
   // has been used.  This is obtained though the analysisfeature -> feature -> organism
@@ -198,7 +201,8 @@ function tripal_analysis_add_mview_analysis_organism() {
   
   // the schema array for describing this view
   $schema = array(
-    'table' => 'analysis_organism',
+    'table' => $view_name,
+    'description' => $comment,
     'fields' => array(  
       'analysis_id' => array(
         'type' => 'int',
@@ -229,10 +233,6 @@ function tripal_analysis_add_mview_analysis_organism() {
     ),
   );
   
-  // add a comment to make sure this view makes sense to the site administator
-  $comment = t('This view is for associating an organism (via it\'s associated features) to an analysis.');
-  
   // add the view
-  tripal_add_mview('analysis_organism', 'tripal_analysis', NULL, NULL, NULL,
-    $sql, NULL, $comment, $schema);
-}
+  tripal_add_mview($view_name, 'tripal_analysis', $schema, $sql, $comment);
+}

tripal_contact/includes/contact_sync.inc

@@ -46,7 +46,7 @@ function tripal_contact_sync_contacts($job_id = NULL) {
   ";
   $results = db_query($sql);
 
-  while ($contact = db_fetch_object($results)) {
+  while ($contact = $results->fetchObject()) {
     $node = tripal_contact_sync_contact($contact);
   }
 }

tripal_contact/includes/tripal_contact.admin.inc

@@ -117,8 +117,8 @@ function tripal_contact_admin_validate($form, &$form_state) {
     foreach ($contacts as $contact_id) {
       if ($contact_id and preg_match("/^\d+$/i", $contact_id)) {
         // get the map info
-        $sql = "SELECT * FROM {contact} WHERE contact_id = %d";
-        $contact = db_fetch_object(chado_query($sql, $contact_id));
+        $sql = "SELECT * FROM {contact} WHERE contact_id = :contact_id";
+        $contact = db_fetch_object(chado_query($sql, array(':contact_id' => $contact_id)));
         $job_args[0] = $contact_id;
         tripal_add_job("Reindex features for map: $contact->name", 'tripal_contact',
          'tripal_contact_reindex_features', $job_args, $user->uid);

tripal_contact/includes/tripal_contact.form.inc

@@ -170,13 +170,13 @@ function chado_contact_validate($node, &$form) {
   if ($node->contact_id) {
     $sql = "
       SELECT * FROM {contact} 
-      WHERE name = '%s' AND NOT contact_id = %d
+      WHERE name = :name AND NOT contact_id = :contact_id
     ";
-    $contact = db_fetch_object(chado_query($sql, $title, $contact_id));
+    $contact = db_fetch_object(chado_query($sql, array(':name' => $title, ':contact_id' => $contact_id)));
   }
   else {
-    $sql = "SELECT * FROM {contact} WHERE name = '%s'";
-    $contact = db_fetch_object(chado_query($sql, $title));
+    $sql = "SELECT * FROM {contact} WHERE name = :name";
+    $contact = db_fetch_object(chado_query($sql, array(':name' => $title)));
   }
   if ($contact) {
     form_set_error('title', t('The contact name already exists. Please choose another'));
@@ -362,10 +362,10 @@ function chado_contact_node_form_add_contactprop_table_props(&$form, $form_state
     SELECT CVT.cvterm_id, CVT.name, CVT.definition, PP.value, PP.rank
     FROM {contactprop} PP
       INNER JOIN {cvterm} CVT on CVT.cvterm_id = PP.type_id
-    WHERE PP.contact_id = %d
+    WHERE PP.contact_id = :contact_id
     ORDER BY CVT.name, PP.rank
   ";
-  $contact_props = chado_query($sql, $contact_id);
+  $contact_props = chado_query($sql, array(':contact_id' => $contact_id));
   while ($prop = db_fetch_object($contact_props)) {
 
     $type_id = $prop->cvterm_id;

tripal_contact/tripal_contact.info

@@ -1,8 +1,8 @@
 name = Tripal Contact
-description = A module for interfacing the GMOD chado database with Drupal, providing viewing of Contacts
-core = 6.x
+description = A module for interfacing the GMOD chado database with Drupal, providing viewing of contacts such as people, organizations or entities.
+core = 7.x
 project = tripal_contact
 package = Tripal
-version = 6.x-1.1
+version = 7.x-2.0-beta1
 dependencies[] = tripal_core
 dependencies[] = tripal_cv

tripal_contact/tripal_contact.install

@@ -10,6 +10,24 @@
  * multiple contact/mysql instances as well as manage and create such contact instances
  */
 
+/**
+ * Implementation of hook_requirements().
+ *
+ */
+function tripal_contact_requirements($phase) {
+  $requirements = array();
+  if ($phase == 'install') {
+    // make sure chado is installed
+    if (!tripal_core_is_chado_installed()) {
+      $requirements ['tripal_contact'] = array(
+        'title' => "tripal_contact",
+        'value' => "ERROR: Chado most be installed before this module can be enabled",
+        'severity' => REQUIREMENT_ERROR,
+      );
+    }
+  }
+  return $requirements;
+}
 
 /**
  * Implementation of hook_install().
@@ -19,9 +37,6 @@ function tripal_contact_install() {
 	// create the module's data directory
   tripal_create_moddir('tripal_contact');
   
-  // add the tripal_contact table to Drupal
-  drupal_install_schema('tripal_contact');
-  
   // add the contactprop table to Chado
   tripal_contact_add_custom_tables();
   
@@ -35,7 +50,7 @@ function tripal_contact_install() {
  * Implementation of hook_uninstall().
  */
 function tripal_contact_uninstall() {
-  drupal_uninstall_schema('tripal_contact');
+
 }
 
 /**
@@ -74,24 +89,7 @@ function tripal_contact_schema() {
   return $schema;
 }
 
-/**
- * Implementation of hook_requirements(). 
- *
- */
-function tripal_contact_requirements($phase) {
-  $requirements = array();
-  if ($phase == 'install') {
-    // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
-      $requirements ['tripal_contact'] = array(
-            'title' => "tripal_contact",
-            'value' => "ERROR: Chado most be installed before this module can be enabled",
-            'severity' => REQUIREMENT_ERROR,
-      );
-    }
-  }
-  return $requirements;
-}
+
 /*
  * 
  */
@@ -154,25 +152,5 @@ function tripal_contact_add_custom_tables(){
       ),
     ),
   );
-  tripal_core_create_custom_table($ret, 'contactprop', $schema, TRUE);
-}
-/**
- *  Update for Drupal 6.x, Tripal 1.0
- *  This update
- *   - adds a new contact node
- *
- * @ingroup tripal_contact
- */
-function tripal_contact_update_6001() {
-  // add the tripal_contact table
-  drupal_install_schema('tripal_contact');
-  
-  // add the custom tables
-  tripal_contact_add_custom_tables();
-
-  // add loading of the the tripal contact ontology to the job queue
-  $obo_path =  realpath('./') . '/' . drupal_get_path('module', 'tripal_contact') . '/tcontact.obo';
-  $obo_id = tripal_cv_add_obo_ref('Tripal Contacts', $obo_path);
-  tripal_cv_submit_obo_job($obo_id);
-  return $ret;
+  tripal_core_create_custom_table('contactprop', $schema, TRUE);
 }

tripal_contact/tripal_contact.module

@@ -61,7 +61,7 @@ function tripal_contact_node_info() {
   return array(
     'chado_contact' => array(
       'name' => t('Contact'),
-      'module' => 'chado_contact',
+      'base' => 'chado_contact',
       'description' => t('A contact from the Chado database'),
       'title_label' => t('Article Title'),
       'body_label' => t('Abstract'),
@@ -147,15 +147,19 @@ function tripal_contact_theme() {
   return array(
     'tripal_contact_base' => array(
       'arguments' => array('node' => NULL),
+      'template' => 'tripal_contact_base',
     ),
     'tripal_contact_properties' => array(
-      'arguments' => array('node' => NULL)
+      'arguments' => array('node' => NULL),
+      'template' => 'tripal_contact_properties',
     ),
     'tripal_contact_relationships' => array(
-      'arguments' => array('node' => NULL)
+      'arguments' => array('node' => NULL),
+      'template' => 'tripal_contact_relationships',
     ),
     'tripal_contact_publications' => array(
-      'arguments' => array('node' => NULL)
+      'arguments' => array('node' => NULL),
+      'template' => 'tripal_contact_publications',
     ),
     'tripal_contact_admin' => array(
       'template' => 'tripal_contact_admin',  
@@ -169,17 +173,83 @@ function tripal_contact_theme() {
     ),
   );
 }
+/**
+ * @ingroup tripal_library
+ */
+function tripal_contact_block_info() {
+
+  $blocks['contbase']['info'] = t('Tripal Contact Details');
+  $blocks['contbase']['cache'] = BLOCK_NO_CACHE;
+
+  $blocks['contprops']['info'] = t('Tripal Contact Properties');
+  $blocks['contprops']['cache'] = BLOCK_NO_CACHE;
+
+  $blocks['contrels']['info'] = t('Tripal Contact Relationships');
+  $blocks['contrels']['cache'] = BLOCK_NO_CACHE;
+
+  $blocks['contpubs']['info'] = t('Tripal Cotact Publications');
+  $blocks['contpubs']['cache'] = BLOCK_NO_CACHE;
+
+  return $blocks;
+}
+/**
+ * @ingroup tripal_library
+ */
+function tripal_contact_block_view($delta = '') {
+
+  if (user_access('access chado_library content') and arg(0) == 'node' and is_numeric(arg(1))) {
+    $nid = arg(1);
+    $node = node_load($nid);
+
+    $block = array();
+    switch ($delta) {
+      case 'contbase':
+        $block['subject'] = t('Details');
+        $block['content'] = theme('tripal_contact_base', $node);
+        break;
+      case 'contprops':
+        $block['subject'] = t('Properties');
+        $block['content'] = theme('tripal_contact_properties', $node);
+        break;
+      case 'contrels':
+        $block['subject'] = t('Relationships');
+        $block['content'] = theme('tripal_contact_relationships', $node);
+        break;
+      case 'contpubs':
+        $block['subject'] = t('Publications');
+        $block['content'] = theme('tripal_contact_publications', $node);
+        break;
+      default :
+    }
+    return $block;
+  }
+}
 
 /**
  * Implement hook_perm().
  */
-function tripal_contact_perm() {
+function tripal_contact_permissions() {
   return array(
-    'access chado_contact content',
-    'create chado_contact content',
-    'delete chado_contact content',
-    'edit chado_contact content',
-    'administer tripal contacts',
+    'access chado_contact content' => array(
+      'title' => t('View Contacts'),
+      'description' => t('Allow users to view contact pages.'),
+    ),
+    'create chado_contact content' => array(
+      'title' => t('Create Contacts'),
+      'description' => t('Allow users to create new contact pages.'),
+    ),
+    'delete chado_contact content' => array(
+      'title' => t('Delete Contacts'),
+      'description' => t('Allow users to delete contact pages.'),
+    ),
+    'edit chado_contact content' => array(
+      'title' => t('Edit Contacts'),
+      'description' => t('Allow users to edit contact pages.'),
+    ),
+    'adminster tripal contact' => array(
+      'title' => t('Administer Contacts'),
+      'description' => t('Allow users to administer all contacts.'),
+    ),
   );
 }
 
@@ -188,12 +258,12 @@ function tripal_contact_perm() {
  *
  * This hook allows node modules to limit access to the node types they define.
  *
- *  @param $op
- *  The operation to be performed
- *
  *  @param $node
  *  The node on which the operation is to be performed, or, if it does not yet exist, the
  *  type of node to be created
+ *  
+ *  @param $op
+ *  The operation to be performed
  *
  *  @param $account
  *  A user object representing the user for whom the operation is to be performed
@@ -205,7 +275,7 @@ function tripal_contact_perm() {
  *  return TRUE if the permission is set.
  *
  */
-function chado_contact_access($op, $node, $account ) {
+function chado_contact_node_access($node, $op, $account ) {
   if ($op == 'create') {
     if (!user_access('create chado_contact content', $account)) {
       return FALSE;
@@ -284,7 +354,7 @@ function chado_contact_insert($node) {
       ORDER BY CVTS.name ASC 
     ";
     $prop_types = chado_query($sql);
-    while ($prop = db_fetch_object($prop_types)) {
+    while ($prop = $prop_types->fetchObject()) {
       $properties_list[$prop->cvterm_id] = $prop->name;
     }   
   
@@ -333,8 +403,8 @@ function chado_contact_insert($node) {
     if (!$contact_id) {
        // next add the item to the drupal table
       $sql = "INSERT INTO {chado_contact} (nid, vid, contact_id) ".
-             "VALUES (%d, %d, %d)";
-      db_query($sql, $node->nid, $node->vid, $contact['contact_id']);
+             "VALUES (:nid, :vid, :contact_id)";
+      db_query($sql, array(':nid'=> $node->nid, ':vid' => $node->vid, ':contact_id' => $contact['contact_id']));
     }
   }
   else {
@@ -367,8 +437,8 @@ function chado_contact_update($node) {
   $contact_id = chado_get_id_for_node('contact', $node->nid) ;
   
   // check to see if this contact name doens't already exists.    
-  $sql = "SELECT contact_id FROM {contact} WHERE NOT contact_id = %d AND name = '%s'";
-  $contact = db_fetch_object(chado_query($sql, $contact_id, $node->contact_name));
+  $sql = "SELECT contact_id FROM {contact} WHERE NOT contact_id = :contact_id AND name = :name";
+  $contact = chado_query($sql, array(':contact_id' => $contact_id, ':name' => $node->contact_name))->fetchObject();
   if ($contact) {
     drupal_set_message(t('A contact with this name already exists. Cannot perform update.'), 'warning');
     return;  
@@ -407,7 +477,7 @@ function chado_contact_update($node) {
     ORDER BY CVTS.name ASC 
   ";
   $prop_types = chado_query($sql);
-  while ($prop = db_fetch_object($prop_types)) {
+  while ($prop = $prop_types->fetchObject()) {
     $properties_list[$prop->cvterm_id] = $prop->name;
   }
   
@@ -520,22 +590,16 @@ function chado_contact_delete(&$node) {
 
   // Remove data from {chado_contact}, {node} and {node_revisions} tables of
   // drupal database
-  $sql_del = "DELETE FROM {chado_contact} ".
-             "WHERE nid = %d ".
-             "AND vid = %d";
-  db_query($sql_del, $node->nid, $node->vid);
-  $sql_del = "DELETE FROM {node_revisions} ".
-             "WHERE nid = %d ".
-             "AND vid = %d";
-  db_query($sql_del, $node->nid, $node->vid);
-  $sql_del = "DELETE FROM {node} ".
-             "WHERE nid = %d ".
-             "AND vid = %d";
-  db_query($sql_del, $node->nid, $node->vid);
+  $sql_del = "DELETE FROM {chado_contact} WHERE nid = :nid AND vid = :vid";
+  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
+  $sql_del = "DELETE FROM {node_revision} WHERE nid = :nid AND vid = :vid";
+  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
+  $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
+  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
 
   // Remove data from contact and contactprop tables of chado database as well
-  chado_query("DELETE FROM {contactprop} WHERE contact_id = %d", $contact_id);
-  chado_query("DELETE FROM {contact} WHERE contact_id = %d", $contact_id);
+  chado_query("DELETE FROM {contactprop} WHERE contact_id = :contact_id", array(':contact_id' => $contact_id));
+  chado_query("DELETE FROM {contact} WHERE contact_id = :contact_id", array(':contact_id' => $contact_id));
 }
 /**
  *
@@ -556,18 +620,18 @@ function tripal_contact_preprocess_tripal_contact_relationships(&$variables) {
       INNER JOIN {contact} C              ON PR.object_id  = C.contact_id
       INNER JOIN {cvterm} CVT             ON PR.type_id    = CVT.cvterm_id
       LEFT  JOIN public.chado_contact CP  ON C.contact_id  = CP.contact_id
-    WHERE PR.subject_id = %d
+    WHERE PR.subject_id = :contact_id
   ";
-  $as_subject = chado_query($sql, $contact->contact_id);
+  $as_subject = chado_query($sql, array(':contact_id' => $contact->contact_id));
   $sql = "
     SELECT C.name, C.contact_id, CP.nid, CVT.name as rel_type
     FROM contact_relationship PR
       INNER JOIN {contact} C              ON PR.subject_id = C.contact_id
       INNER JOIN {cvterm} CVT             ON PR.type_id    = CVT.cvterm_id
       LEFT  JOIN public.chado_contact CP  ON C.contact_id  = CP.contact_id
-    WHERE PR.object_id = %d
+    WHERE PR.object_id = :contact_id
   ";
-  $as_object = chado_query($sql, $contact->contact_id);
+  $as_object = chado_query($sql, array(':contact_id' => $contact->contact_id));
 
   // combine both object and subject relationshisp into a single array
   $relationships = array();
@@ -575,7 +639,7 @@ function tripal_contact_preprocess_tripal_contact_relationships(&$variables) {
   $relationships['subject'] = array();
 
   // iterate through the object relationships
-  while ($relationship = db_fetch_object($as_object)) {
+  while ($relationship = $as_object->fetchObject()) {
 
      // get the relationship and child types
      $rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
@@ -591,7 +655,7 @@ function tripal_contact_preprocess_tripal_contact_relationships(&$variables) {
   }
 
   // now add in the subject relationships
-  while ($relationship = db_fetch_object($as_subject)) {
+  while ($relationship = $as_subject->fetchObject()) {
 
      // get the relationship and child types
      $rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));

tripal_core/api/tripal_core_chado.api.inc

@@ -97,13 +97,11 @@ require_once "tripal_core.schema_v1.11.api.inc";
 function tripal_core_chado_insert($table, $values, $options = array()) {
 
   if (!is_array($values)) {
-    watchdog('tripal_core', 'Cannot pass non array as values for inserting.', array(),
-      WATCHDOG_ERROR);
+    watchdog('tripal_core', 'Cannot pass non array as values for inserting.', array(), WATCHDOG_ERROR);
     return FALSE;
   }
   if (count($values)==0) {
-    watchdog('tripal_core', 'Cannot pass an empty array as values for inserting.', array(),
-      WATCHDOG_ERROR);
+    watchdog('tripal_core', 'Cannot pass an empty array as values for inserting.', array(), WATCHDOG_ERROR);
     return FALSE;
   }
 
@@ -2426,15 +2424,19 @@ function tripal_core_chado_schema_exists() {
   // @coder-ignore: acting on pg_catalog schema rather then drupal schema therefore, table prefixing does not apply
   $sql = "
     SELECT nspname
-    FROM pg_catalog.pg_namespace
-    WHERE nspname = 'chado'
+    FROM pg_namespace
+    WHERE
+      has_schema_privilege(nspname, 'USAGE') AND
+      nspname = 'chado'
   ";
   $results = db_query($sql);
   $name = $results->fetchObject();
   if ($name) {
+    variable_set('chado_schema_exists', FALSE);
     return TRUE;
   }
   else {
+    variable_set('chado_schema_exists', TRUE);
     return FALSE;
   }
 }
@@ -2464,8 +2466,7 @@ function tripal_core_schema_exists($schema) {
   $name = $results->fetchObject();
   if (strcmp($name->nspname, $schema) != 0) {
     return FALSE;
-  }
-
+  }  
   return TRUE;
 }
 
@@ -2795,7 +2796,7 @@ function tripal_core_is_chado_installed() {
     return TRUE;
   }
 
-  // check to make sure the chado schema exists
+  // check to make sure the chado schema exists          
   return tripal_core_chado_schema_exists();
 }
 
@@ -2856,7 +2857,7 @@ function tripal_db_set_active($dbname  = 'default') {
   global $databases, $active_db;
 
   $chado_exists = variable_get('chado_schema_exists', FALSE);
-  if ($chado_exists) {
+  if ($dbname ) {
     if ($dbname == 'chado') {
       db_query('set search_path to chado');
       return 'default';
@@ -2872,4 +2873,4 @@ function tripal_db_set_active($dbname  = 'default') {
   elseif (array_key_exists($dbname, $databases)) {
     return db_set_active($dbname);
   }
-}
+}

tripal_core/api/tripal_core_custom_tables.api.inc

@@ -117,17 +117,13 @@ function tripal_core_create_custom_table($table, $schema, $skip_creation = 1) {
   
   // if the table does not exist then create it
   if (!$exists) { 
-    $previous_db = tripal_db_set_active('chado');  // use chado database   
-    try {      
-      $ret = db_create_table($table, $schema);
-      tripal_db_set_active($previous_db);  // now use drupal database
+    try {
+      $ret = db_create_table('chado.' . $table, $schema);
       $created = 1;
     }
     catch (Exception $e) {
-      tripal_db_set_active($previous_db);  // now use drupal database
       $error = $e->getMessage();
-      watchdog('tripal_core', "Error adding custom table: @message",
-        array('@message' => $error), WATCHDOG_ERROR);
+      watchdog('tripal_core', "Error adding custom table: @message", array('@message' => $error), WATCHDOG_ERROR);
       drupal_set_message("Could not add custom table. $error.", "error");
       return FALSE;
     }    
@@ -140,13 +136,10 @@ function tripal_core_create_custom_table($table, $schema, $skip_creation = 1) {
     // drop the table we'll recreate it with the new schema    
     try {      
       chado_query('DROP TABLE {' . $table . '}');
-      $previous_db = tripal_db_set_active('chado');  // use chado database
-      db_create_table($table, $schema);
-      tripal_db_set_active($previous_db);  // now use drupal database    
+      db_create_table('chado.' . $table, $schema);
       $recreated = 1;
     }
     catch (Exception $e) {
-      tripal_db_set_active('default');  // now use drupal database
       $error = $e->getMessage();
       watchdog('tripal_core', "Error adding custom table: @message",
         array('@message' => $error), WATCHDOG_ERROR);

tripal_core/api/tripal_core_jobs.api.inc

@@ -180,17 +180,21 @@ function tripal_jobs_get_end_time($job) {
  *
  * @param $job_id
  *   The job_id of the job to be re-ran
+ * @param $goto_jobs_page
+ *   If set to TRUE then after the re run job is added Drupal will redirect to the jobs page
  *
  * @ingroup tripal_jobs_api
  */
 function tripal_jobs_rerun($job_id, $goto_jobs_page = TRUE) {
   global $user;
+  
+  $user_id = $user->uid;
 
   $sql = "SELECT * FROM {tripal_jobs} WHERE job_id = :job_id";
   $results = db_query($sql, array(':job_id' => $job_id));
   $job = $results->fetchObject();
   $args = explode("::", $job->arguments);
-  $job_id = tripal_add_job($job->job_name, $job->modulename, $job->callback, $args, $user->uid, $job->priority);
+  $job_id = tripal_add_job($job->job_name, $job->modulename, $job->callback, $args, $user_id, $job->priority);
 
   if ($goto_jobs_page) {
     drupal_goto("admin/tripal/tripal_jobs");

tripal_core/api/tripal_core_mviews.api.inc

@@ -35,31 +35,11 @@
  *   currently not used
  * @param $comment
  *   A string containing a description of the materialized view
- * @param $mv_schema
- *   If using the newer Schema API array to define the materialized view then
- *   this variable should contain the array or a string representation of the 
- *   array.
- * 
+ *
  * @ingroup tripal_mviews_api
  */
-function tripal_add_mview($name, $modulename, $mv_table, $mv_specs, $indexed,
-  $query, $special_index, $comment = NULL, $mv_schema = NULL) {
-
-  // get the table name from the schema array
-  $schema_arr = array();
-  if ($mv_schema) {
-    // if the schema is provided as a string then convert it to an array
-    if (!is_array($mv_schema)) {
-      eval("\$schema_arr = $mv_schema;");
-    }
-    // if the schema is provided as an array then create a string
-    // copy of it for storage in the mview 
-    else {
-      $schema_arr = $mv_schema;
-      $mv_schema = var_export($schema_arr, 1);
-    }
-    $mv_table = $schema_arr['table'];
-  }
+function tripal_add_legacy_mview($name, $modulename, $mv_table, $mv_specs, $indexed,
+  $query, $special_index, $comment = NULL) {
 
   // Create a new record
   $record = new stdClass();
@@ -71,7 +51,6 @@ function tripal_add_mview($name, $modulename, $mv_table, $mv_specs, $indexed,
   $record->query = $query;
   $record->special_index = $special_index;
   $record->comment = $comment;
-  $record->mv_schema = $mv_schema;
 
   // add the record to the tripal_mviews table and if successful
   // create the new materialized view in the chado schema
@@ -93,30 +72,76 @@ function tripal_add_mview($name, $modulename, $mv_table, $mv_specs, $indexed,
         $field = trim($field);
         $index .= "CREATE INDEX idx_${mv_table}_${field} ON $mv_table ($field);";
       }
-    }
+    } 
+  }
 
-    // create the table differently depending on if it the traditional method
-    // or the Drupal Schema API method
-    if ($mv_schema) {
-      if (!tripal_core_create_custom_table ($mv_table, $schema_arr, 0)) {
-        drupal_set_message(t("Could not create the materialized view. Check Drupal error report logs."), 'error');
-      }
-      else {
-        drupal_set_message(t("View '%name' created", array('%name' => $name)));
-      }
+  // add the table to the database
+  $sql = "CREATE TABLE {$mv_table} ($mv_specs); $index";
+  $previous_db = tripal_db_set_active('chado');  // use chado database
+  $results = db_query($sql);
+  tripal_db_set_active($previous_db);  // now use drupal database
+  if ($results) {
+    drupal_set_message(t("View '%name' created", array('%name' => $name)));
+  }
+  else {
+    drupal_set_message(t("Failed to create the materialized view table: '%mv_table'", array('%mv_table' => $mv_table)), 'error');
+  }
+}
+/**
+ * Add a materialized view to the chado database to help speed data access. This
+ * function supports the older style where postgres column specifications
+ * are provided using the $mv_table, $mv_specs and $indexed variables. It also
+ * supports the newer preferred method where the materialized view is described
+ * using the Drupal Schema API array.
+ *
+ * @param $name
+ *   The name of the materialized view.
+ * @param $modulename
+ *   The name of the module submitting the materialized view (e.g. 'tripal_library')
+ * @param $mv_schema
+ *   If using the newer Schema API array to define the materialized view then
+ *   this variable should contain the array or a string representation of the 
+ *   array.
+ * @param $query
+ *   The SQL query that loads the materialized view with data
+ * @param $comment
+ *   A string containing a description of the materialized view 
+ *   
+ * @ingroup tripal_mviews_api
+ */
+function tripal_add_mview($name, $modulename, $schema_arr, $query, $comment = NULL) {
+  
+  $mv_table = $schema_arr['table'];
+  
+  if (!$mv_table) {
+     watchdog('tripal_core', 'Must have a table name when creating an mview.', array(), WATCHDOG_ERROR);
+     return NULL;
+  }
+
+  // Create a new record
+  $record = new stdClass();
+  $record->name = $name;
+  $record->modulename = $modulename;
+  $record->mv_table = $mv_table;
+  $record->query = $query;
+  $record->comment = $comment;
+  $record->mv_schema = $mv_schema;
+
+  // add the record to the tripal_mviews table and if successful
+  // create the new materialized view in the chado schema
+  if (drupal_write_record('tripal_mviews', $record)) {
+
+    // drop the table from chado if it exists
+    if (chado_table_exists($mv_table)) {
+      $sql = 'DROP TABLE {' . $mv_table . '}';
+      chado_query($sql);
+    }   
+    // create the table
+    if (!tripal_core_create_custom_table ($mv_table, $schema_arr, 0)) {
+      drupal_set_message(t("Could not create the materialized view. Check Drupal error report logs."), 'error');
     }
     else {
-      // add the table to the database
-      $sql = "CREATE TABLE {$mv_table} ($mv_specs); $index";
-      $previous_db = tripal_db_set_active('chado');  // use chado database
-      $results = db_query($sql);
-      tripal_db_set_active($previous_db);  // now use drupal database
-      if ($results) {
-        drupal_set_message(t("View '%name' created", array('%name' => $name)));
-      }
-      else {
-        drupal_set_message(t("Failed to create the materialized view table: '%mv_table'", array('%mv_table' => $mv_table)), 'error');
-      }
+      drupal_set_message(t("View '%name' created", array('%name' => $name)));
     }
   }
 }
@@ -311,18 +336,22 @@ function tripal_mviews_action($op, $mview_id, $redirect = FALSE) {
     tripal_add_job("Populate materialized view '$mview->name'", 'tripal_core',
        'tripal_update_mview', $args, $user->uid);
   }
+  
+  // if op is to delete then do so
   if ($op == 'delete') {
+    
     // remove the mview from the tripal_mviews table
-    $sql = "DELETE FROM {tripal_mviews} " .
-           "WHERE mview_id = $mview_id";
+    $sql = "DELETE FROM {tripal_mviews} WHERE mview_id = $mview_id";
     db_query($sql);
+    
+    // does the table already exist?
+    $mview_exists = db_table_exists('chado.' . $mview->mv_table);
+    
     // 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 " . $mview->mv_table;
-      db_query($sql);
+    if ($mview_exists) {
+      $sql = "DROP TABLE {" . $mview->mv_table . "}";
+      chado_query($sql);
     }
-    tripal_db_set_active($previous_db);  // now use drupal database
   }
 
   // Redirect the user

tripal_core/includes/custom_tables.inc

@@ -296,9 +296,7 @@ function tripal_custom_tables_form_validate($form, &$form_state) {
         $results = db_query($sql, array(':table_id' => $table_id));
         $ct = $results->fetchObject();
         if ($ct->table_name != $schema_array['table']) {
-          $previous_db = tripal_db_set_active('chado');
-          $exists = db_table_exists($schema_array['table']);
-          tripal_db_set_active($previous_db);        
+          $exists = db_table_exists('chado.' . $schema_array['table']);
           if ($exists) {
             form_set_error($form_state['values']['schema'],
               t("The table name already exists, please choose a different name."));  

tripal_core/includes/mviews.inc

@@ -25,14 +25,14 @@ function tripal_mview_report($mview_id) {
 
   // create a table with each row containig stats for
   // an individual job in the results set.
-  $output  = "<p>" . l("Return to table of materialized views", "admin/tripal/mviews/") . "</p>";
+  $output  = "<p>" . l("Return to table of materialized views", "admin/tripal/schema/mviews/") . "</p>";
   $output .= "<p>Details for <b>$mview->name</b>:</p>";
   
   // build the URLs using the url function so we can handle installations where
   // clean URLs are or are not used
-  $update_url = url("admin/tripal/mviews/action/update/$mview->mview_id");
-  $delete_url = url("admin/tripal/mviews/action/delete/$mview->mview_id");
-  $edit_url = url("admin/tripal/mviews/edit/$mview->mview_id");
+  $update_url = url("admin/tripal/schema/mviews/action/update/$mview->mview_id");
+  $delete_url = url("admin/tripal/schema/mviews/action/delete/$mview->mview_id");
+  $edit_url = url("admin/tripal/schema/mviews/edit/$mview->mview_id");
   $rows[] = array('Actions', "<a href='$update_url'>Populate</a>, <a href='$edit_url'>Edit</a>,  <a href='$delete_url'>Delete</a>");
   
   if ($mview->last_update > 0) {    
@@ -102,20 +102,20 @@ function tripal_mviews_report() {
     }
 
     $rows[] = array(
-      l(t('View'), "admin/tripal/mviews/report/$mview->mview_id") . " | " .
-      l(t('Edit'), "admin/tripal/mviews/edit/$mview->mview_id") . " | " .
-      l(t('Populate'), "admin/tripal/mviews/action/update/$mview->mview_id"),
+      l(t('View'), "admin/tripal/schema/mviews/report/$mview->mview_id") . " | " .
+      l(t('Edit'), "admin/tripal/schema/mviews/edit/$mview->mview_id") . " | " .
+      l(t('Populate'), "admin/tripal/schema/mviews/action/update/$mview->mview_id"),
       $mview->name,
       $update,
       $mview->status,
       $mview->comment,
-      l(t('Delete'), "admin/tripal/mviews/action/delete/$mview->mview_id"),
+      l(t('Delete'), "admin/tripal/schema/mviews/action/delete/$mview->mview_id"),
     );
   }
 
   $rows[] = array(
     'data' => array(
-      array('data' => l(t('Create a new materialized view.'), "admin/tripal/mviews/new"),
+      array('data' => l(t('Create a new materialized view.'), "admin/tripal/schema/mviews/new"),
         'colspan' => 6),
     )
   );
@@ -275,7 +275,7 @@ function tripal_mviews_form($form, &$form_state = NULL, $mview_id = NULL) {
   
   $form['return_link'] = array(
     '#type' => 'item',
-    '#description' => l("Return to table of materialized views", "admin/tripal/mviews/"),
+    '#description' => l("Return to table of materialized views", "admin/tripal/schema/mviews/"),
   );
   
 
@@ -391,7 +391,7 @@ function tripal_mviews_form($form, &$form_state = NULL, $mview_id = NULL) {
     '#weight'       => 9,
     '#executes_submit_callback' => TRUE,
   );
-  $form['#redirect'] = 'admin/tripal/mviews';
+  $form['#redirect'] = 'admin/tripal/schema/mviews';
 
   return $form;
 }

tripal_core/tripal_core.drush.inc

@@ -169,29 +169,38 @@ function tripal_core_drush_command() {
 }
 
 /**
- * Executes jobs in the Tripal Jobs Queue
- *
- * NOTE: The following code is executed when drush 'trpjob-run' or 'drush tripal-launch-jobs' is called
+ * 
+ * @param $username
  */
-function drush_tripal_core_tripal_jobs_launch($username) {
-  $parallel = drush_get_option('parallel');
-  $job_id = drush_get_option('job_id');
-
+function drush_tripal_core_set_user($username) {
   if ($username) {
     $sql = "SELECT uid FROM {users} WHERE name = :name";
     $results = db_query($sql, array(':name' => $username));
     $u = $results->fetchObject();
     if (!$u) {
-      drush_print('ERROR: Please provide a valid username for running this job.'); 
-      exit; 
+      drush_print('ERROR: Please provide a valid username for running this job.');
+      exit;
     }
     global $user;
     $user = user_load($u->uid);
+    return $u->uid;
   }
   else {
     drush_print('ERROR: Please provide a username for running this job.');
     return;
   }
+}
+
+/**
+ * Executes jobs in the Tripal Jobs Queue
+ *
+ * NOTE: The following code is executed when drush 'trpjob-run' or 'drush tripal-launch-jobs' is called
+ */
+function drush_tripal_core_tripal_jobs_launch($username) {
+  $parallel = drush_get_option('parallel');
+  $job_id = drush_get_option('job_id');  
+  
+  drush_tripal_core_set_user($username);
 
   if ($parallel) {
     drush_print("Tripal Job Launcher (in parallel)");
@@ -214,6 +223,7 @@ function drush_tripal_core_tripal_jobs_launch($username) {
  */
 function drush_tripal_core_tripal_jobs_rerun($username, $job_id) {
 
+  drush_tripal_core_set_user($username);  
   $new_job_id = tripal_jobs_rerun($job_id, FALSE);
   drush_tripal_core_tripal_jobs_launch($username, $new_job_id);
 
@@ -225,18 +235,22 @@ function drush_tripal_core_tripal_jobs_rerun($username, $job_id) {
  * NOTE: The following code is executed when 'drush trpjob-curr' or 'drush tripal-current-job' is called
  */
 function drush_tripal_core_tripal_jobs_current() {
-  $sql =  "SELECT * FROM {tripal_jobs} TJ " .
-            "WHERE TJ.end_time IS NULL and NOT TJ.start_time IS NULL ";
+  $sql =  "
+    SELECT * 
+    FROM {tripal_jobs} TJ 
+    WHERE TJ.end_time IS NULL and NOT TJ.start_time IS NULL 
+  ";
   $jobs = db_query($sql);
+  
   foreach ($jobs as $job) {
     $job_pid = $job->pid;
-    $output = "Name: " . $job->job_name . "\n"
-             . "Submitted: " . date(DATE_RFC822, $job->submit_date) . "\n"
-             . "Started: " . date(DATE_RFC822, $job->start_time) . "\n"
-             . "Module: " . $job->modulename . "\n"
-             . "Callback: " . $job->callback . "\n"
-             . "Process ID: " . $job->pid . "\n"
-             . "Progress: " . $job->progress . "%\n";
+    $output = "Name: " . $job->job_name . "\n" .
+              "Submitted: " . date(DATE_RFC822, $job->submit_date) . "\n" .
+              "Started: " . date(DATE_RFC822, $job->start_time) . "\n" .
+              "Module: " . $job->modulename . "\n" .
+              "Callback: " . $job->callback . "\n" .
+              "Process ID: " . $job->pid . "\n" .
+              "Progress: " . $job->progress . "%\n";
     drush_print($output);
   }
   if (!$job_pid) {

tripal_core/tripal_core.install

@@ -97,18 +97,67 @@ function tripal_core_mviews_schema() {
 
   $schema['tripal_mviews'] = array(
     'fields' => array(
-      'mview_id'      => array('type' => 'serial', 'unsigned' => TRUE, 'not NULL' => TRUE),
-      'name'          => array('type' => 'varchar', 'length' => 255, 'not NULL' => TRUE),
-      'modulename'    => array('type' => 'varchar', 'length' => 50, 'not NULL' => TRUE, 'description' => 'The module name that provides the callback for this job'),
-      'mv_table'      => array('type' => 'varchar', 'length' => 128, 'not NULL' => FALSE),
-      'mv_specs'      => array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE),
-      'mv_schema'     => array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE),
-      'indexed'       => array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE),
-      'query'         => array('type' => 'text', 'size' => 'normal', 'not NULL' => TRUE),
-      'special_index' => array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE),
-      'last_update'   => array('type' => 'int', 'not NULL' => FALSE, 'description' => 'UNIX integer time'),
-      'status'        => array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE),
-      'comment'       => array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE),
+      'mview_id' => array(
+        'type' => 'serial', 
+        'unsigned' => TRUE, 
+        'not NULL' => TRUE
+      ),
+      'name' => array(
+        'type' => 'varchar', 
+        'length' => 255, 
+        'not NULL' => TRUE
+      ),
+      'modulename' => array(
+        'type' => 'varchar', 
+        'length' => 50, 
+        'not NULL' => TRUE, 
+        'description' => 'The module name that provides the callback for this job'
+      ),    
+      'mv_table' => array(
+        'type' => 'varchar', 
+        'length' => 128, 
+        'not NULL' => FALSE
+      ),
+      'mv_specs' => array(
+        'type' => 'text', 
+        'size' => 'normal', 
+        'not NULL' => FALSE
+      ),
+      'mv_schema' => array(
+        'type' => 'text', 
+        'size' => 'normal', 
+        'not NULL' => FALSE
+      ),
+      'indexed' => array(
+        'type' => 'text', 
+        'size' => 'normal', 
+        'not NULL' => FALSE
+      ),
+      'query' => array(
+        'type' => 'text', 
+        'size' => 'normal', 
+        'not NULL' => TRUE
+      ),
+      'special_index' => array(
+        'type' => 'text', 
+        'size' => 'normal', 
+        'not NULL' => FALSE
+      ),
+      'last_update' => array(
+        'type' => 'int', 
+        'not NULL' => FALSE, 
+        'description' => 'UNIX integer time'
+      ),
+      'status'        => array(
+        'type' => 'text', 
+        'size' => 'normal', 
+        'not NULL' => FALSE
+      ),
+      'comment' => array(
+        'type' => 'text', 
+        'size' => 'normal', 
+        'not NULL' => FALSE
+      ),
     ),
     'indexes' => array(
       'mview_id' => array('mview_id')
@@ -134,22 +183,95 @@ function tripal_core_jobs_schema() {
   $schema = array();
   $schema['tripal_jobs'] = array(
     'fields' => array(
-      'job_id' => array('type' => 'serial', 'unsigned' => TRUE, 'not NULL' => TRUE),
-      'uid' => array('type' => 'int', 'unsigned' => TRUE, 'not NULL' => TRUE, 'description' => 'The Drupal userid of the submitee'),
-      'job_name' => array('type' => 'varchar', 'length' => 255, 'not NULL' => TRUE),
-      'modulename' => array('type' => 'varchar', 'length' => 50, 'not NULL' => TRUE, 'description' => 'The module name that provides the callback for this job'),
-      'callback' => array('type' => 'varchar', 'length' => 255, 'not NULL' => TRUE),
-      'arguments' => array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE),
-      'progress' => array('type' => 'int', 'unsigned' => TRUE, 'default' => 0, 'not NULL' => FALSE, 'description' => 'a value from 0 to 100 indicating percent complete'),
-      'status' => array('type' => 'varchar', 'length' => 50, 'not NULL' => TRUE),
-      'submit_date' => array('type' => 'int', 'not NULL' => TRUE, 'description' => 'UNIX integer submit time'),
-      'start_time' => array('type' => 'int', 'not NULL' => FALSE, 'description' => 'UNIX integer start time'),
-      'end_time' => array('type' => 'int', 'not NULL' => FALSE, 'description' => 'UNIX integer end time'),
-      'error_msg' => array('type' => 'text', 'size' => 'normal', 'not NULL' => FALSE),
-      'pid' => array('type' => 'int', 'unsigned' => TRUE, 'not NULL' => FALSE, 'description' => 'The process id for the job'),
-      'priority' => array('type' => 'int', 'unsigned' => TRUE, 'not NULL' => TRUE, 'default' => '0', 'description' => 'The job priority'),
-      'mlock' => array('type' => 'int', 'unsigned' => TRUE, 'not NULL' => FALSE, 'description' => 'If set to 1 then all jobs for the module are held until this one finishes'),
-      'lock' => array('type' => 'int', 'unsigned' => TRUE, 'not NULL' => FALSE, 'description' => 'If set to 1 then all jobs are held until this one finishes'),
+      'job_id' => array(
+        'type' => 'serial', 
+        'unsigned' => TRUE, 
+        'not NULL' => TRUE
+      ),
+      'uid' => array(
+        'type' => 'int', 
+        'unsigned' => TRUE, 
+        'not NULL' => TRUE, 
+        'description' => 'The Drupal userid of the submitee'
+      ),
+      'job_name' => array(
+        'type' => 'varchar', 
+        'length' => 255, 
+        'not NULL' => TRUE
+      ),
+      'modulename' => array(
+        'type' => 'varchar', 
+        'length' => 50, 
+        'not NULL' => TRUE, 
+        'description' => 'The module name that provides the callback for this job'
+      ),
+      'callback' => array(
+        'type' => 'varchar', 
+        'length' => 255, 
+        'not NULL' => TRUE
+      ),
+      'arguments' => array(
+        'type' => 'text', 
+        'size' => 'normal', 
+        'not NULL' => FALSE
+      ),
+      'progress' => array(
+        'type' => 'int', 
+        'unsigned' => TRUE, 
+        'default' => 0, 
+        'not NULL' => FALSE, 
+        'description' => 'a value from 0 to 100 indicating percent complete'
+      ),
+      'status' => array(
+        'type' => 'varchar', 
+        'length' => 50, 
+        'not NULL' => TRUE
+      ),
+      'submit_date' => array(
+        'type' => 'int', 
+        'not NULL' => TRUE, 
+        'description' => 'UNIX integer submit time'
+      ),
+      'start_time' => array(
+        'type' => 'int', 
+        'not NULL' => FALSE, 
+        'description' => 'UNIX integer start time'
+      ),
+      'end_time' => array(
+        'type' => 'int', 
+        'not NULL' => FALSE, 
+        'description' => 'UNIX integer end time'
+      ),
+      'error_msg' => array(
+        'type' => 'text', 
+        'size' => 'normal', 
+        'not NULL' => FALSE
+      ),
+      'pid' => array(
+        'type' => 'int', 
+        'unsigned' => TRUE, 
+        'not NULL' => FALSE, 
+        'description' => 'The process id for the job'
+      ),
+      'priority' => array(
+        'type' => 'int', 
+        'unsigned' => TRUE, 
+        'not NULL' => TRUE, 
+        'default' => '0', 
+        'description' => 'The job priority'
+      ),
+      'mlock' => array(
+        'type' => 'int', 
+        'unsigned' => TRUE, 
+        'not NULL' => FALSE, 
+        'description' => 'If set to 1 then all jobs for the module are held until this one finishes'
+      ),
+      'lock' => array(
+        'type' => 'int', 
+        'unsigned' => TRUE, 
+        'not NULL' => FALSE, 
+        'description' => 'If set to 1 then all jobs are held until this one finishes'
+      ),
     ),
     'indexes' => array(
       'job_id' => array('job_id'),
@@ -172,9 +294,20 @@ function tripal_core_custom_tables_schema() {
   $schema = array();
   $schema['tripal_custom_tables'] = array(
     'fields' => array(
-      'table_id' => array('type' => 'serial', 'unsigned' => TRUE, 'not NULL' => TRUE),
-      'table_name' => array('type' => 'varchar', 'length' => 255, 'not NULL' => TRUE),
-      'schema' => array('type' => 'text', 'not NULL' => TRUE),
+      'table_id' => array(
+        'type' => 'serial', 
+        'unsigned' => TRUE, 
+        'not NULL' => TRUE
+      ),
+      'table_name' => array(
+        'type' => 'varchar', 
+        'length' => 255, 
+        'not NULL' => TRUE
+      ),
+      'schema' => array(
+        'type' => 'text', 
+        'not NULL' => TRUE
+      ),
     ),
     'indexes' => array(
       'table_id' => array('table_id'),

tripal_core/tripal_core.module

@@ -65,7 +65,7 @@ function tripal_core_init() {
 
   // create the 'tripal' controlled volcabulary in chado but only if it doesn't already exist, and
   // only if the chado database is present.
-  if (tripal_core_is_chado_installed()) {
+  if (tripal_core_is_chado_installed()) {    
 
     // make sure the current version of chado is set
     tripal_core_set_chado_version();
@@ -242,7 +242,7 @@ function tripal_core_menu() {
     'title' => 'Materialized View',
     'description' => 'Materialized views are used to improve speed of large or complex queries. These are database views as compared to Drupal views.',
     'page callback' => 'tripal_mview_report',
-    'page arguments' => array(4),
+    'page arguments' => array(5),
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );
@@ -257,7 +257,7 @@ function tripal_core_menu() {
   $items['admin/tripal/schema/mviews/edit/%'] = array(
     'title' => 'Edit Materialized View',
     'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_mviews_form', 4),
+    'page arguments' => array('tripal_mviews_form', 5),
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );
@@ -265,7 +265,7 @@ function tripal_core_menu() {
     'title' => 'Create Materialized View',
     'description' => 'Materialized views are used to improve speed of large or complex queries.',
     'page callback' => 'tripal_mviews_action',
-    'page arguments' => array(4, 5, "1"),
+    'page arguments' => array(5, 6, "1"),
     'access arguments' => array('access administration pages'),
     'type' => MENU_CALLBACK,
   );

tripal_cv/tripal_cv.install

@@ -5,6 +5,23 @@
  * Contains functions executed only on install/uninstall of this module
  */
 
+/**
+ * Implementation of hook_requirements().
+ */
+function tripal_cv_requirements($phase) {
+  $requirements = array();
+  if ($phase == 'install') {
+    // make sure chado is installed
+    if (!tripal_core_is_chado_installed()) {
+      $requirements ['tripal_cv'] = array(
+        'title' => "tripal_cv",
+        'value' => "ERROR: Chado most be installed before this module can be enabled",
+        'severity' => REQUIREMENT_ERROR,
+      );
+    }
+  }
+  return $requirements;
+}
 /**
  * Implementation of hook_install().
  *
@@ -14,45 +31,21 @@ function tripal_cv_install() {
 
   // create the module's data directory
   tripal_create_moddir('tripal_cv');
-
-  // Create the MView
-  tripal_add_mview(
-    // view name
-    'cv_root_mview',
-    // module name
-    'tripal_cv',
-    // table name
-    'cv_root_mview',
-    // table schema
-    'name character varying(1024), cvterm_id integer, cv_id integer,
-     cv_name character varying(255)',
-    // indexed columns
-    'cvterm_id, cv_id',
-    // 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} CV on CV.cv_id = CVT.cv_id
-     WHERE CVTR.object_id not in
-       (SELECT subject_id FROM {cvterm_relationship}) ',
-    // special index
-    ''
-  );
-
+    
+  // add the cv_root_mview 
+  tripal_cv_add_cv_root_mview();
+  
   // create the tables that correlate OBO files/references with a chado CV
   tripal_cv_add_obo_defaults();
 }
-
 /**
  * Implementation of hook_uninstall().
  *
  * @ingroup tripal_cv
  */
 function tripal_cv_uninstall() {
-
   // remove the materialized view
-  $mview = tripal_mviews_get_mview_id('cv_root_mview');
-  if ($mview) {
+  if ($mview = tripal_mviews_get_mview_id('cv_root_mview')) {
     tripal_mviews_action('delete', $mview);
   }
 }
@@ -63,14 +56,25 @@ function tripal_cv_uninstall() {
  * @ingroup tripal_cv
  */
 function tripal_cv_schema() {
+  
   $schema['tripal_cv_obo'] = array(
     'fields' => array(
-      'obo_id' => array('type' => 'serial', 'unsigned' => TRUE, 'not null' => TRUE),
-      'name'  => array('type' => 'varchar', 'length' => 255),
-      'path'   => array('type' => 'varchar', 'length' => 1024),
+      'obo_id' => array(
+        'type' => 'serial', 
+        'unsigned' => TRUE, 
+        'not null' => TRUE
+      ),
+      'name' => array(
+        'type' => 'varchar', 
+         'length' => 255
+       ),
+      'path'  => array(
+        'type' => 'varchar', 
+        'length' => 1024
+      ),
     ),
     'indexes' => array(
-      'obo_id' => array('obo_id'),
+      'tripal_cv_obo_idx1' => array('obo_id'),
     ),
     'primary key' => array('obo_id'),
   );
@@ -78,6 +82,56 @@ function tripal_cv_schema() {
   return $schema;
 }
 
+/**
+ * 
+ * @ingroup tripal_cv
+ */
+function tripal_cv_add_cv_root_mview() {
+  $mv_name = 'cv_root_mview';
+  $comment = 'A list of the root terms for all controlled vocabularies. This is needed for viewing CV trees';
+  $schema = array(
+    'table' => $mv_name,
+    'description' => $comment,
+    'fields' => array(
+      'name' => array(
+        'type' => 'varchar',
+        'length' => 255,
+        'not null' => TRUE,
+      ),
+      'cvterm_id' => array(
+        'type' => 'int',
+        'not null' => TRUE,
+      ),
+      'cv_id' => array(
+        'type' => 'int',
+        'not null' => TRUE, 
+      ),
+      'cv_name' => array(
+        'type' => 'varchar',
+        'length' => 255,
+        'not null' => TRUE,
+      ),
+    ),
+    'indexes' => array(
+      'cv_root_mview_indx1' => array('cvterm_id'),
+      'cv_root_mview_indx2' => array('cv_id'),
+    ),
+  );
+  
+  $sql = "
+    SELECT DISTINCT CVT.name,CVT.cvterm_id, CV.cv_id, CV.name
+    FROM cvterm_relationship CVTR
+      INNER JOIN cvterm CVT on CVTR.object_id = CVT.cvterm_id
+      INNER JOIN cv CV on CV.cv_id = CVT.cv_id
+    WHERE CVTR.object_id not in
+      (SELECT subject_id FROM cvterm_relationship)
+  ";
+  
+  // Create the MView
+  tripal_add_mview($mv_name, 'tripal_cv', $schema, $sql, $comment);
+}
+
+
 /**
  * Add's defaults to the tripal_cv_obo table
  *
@@ -99,21 +153,3 @@ function tripal_cv_add_obo_defaults() {
     db_query("INSERT INTO {tripal_cv_obo} (name,path) VALUES (:name, :path)", array(':name' => $o[0], ':path' => $o[1]));
   }
 }
-
-/**
- * Implementation of hook_requirements(). 
- */
-function tripal_cv_requirements($phase) {
-  $requirements = array();
-  if ($phase == 'install') {
-    // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
-      $requirements ['tripal_cv'] = array(
-            'title' => "tripal_cv",
-            'value' => "ERROR: Chado most be installed before this module can be enabled",
-            'severity' => REQUIREMENT_ERROR,
-      );
-    }
-  }
-  return $requirements;
-}

tripal_db/tripal_db.install

@@ -5,6 +5,24 @@
  * Contains functions related to the installation of this module
  */
 
+/**
+ * Implementation of hook_requirements().
+ */
+function tripal_db_requirements($phase) {
+  $requirements = array();
+  if ($phase == 'install') {
+    // make sure chado is installed
+    if (!tripal_core_is_chado_installed()) {
+      $requirements ['tripal_db'] = array(
+          'title' => "tripal_db",
+          'value' => "ERROR: Chado most be installed before this module can be enabled",
+          'severity' => REQUIREMENT_ERROR,
+      );
+    }
+  }
+  return $requirements;
+}
+
 /**
  * Implementation of hook_install().
  *
@@ -26,20 +44,3 @@ function tripal_db_uninstall() {
 
 }
 
-/**
- * Implementation of hook_requirements(). 
- */
-function tripal_db_requirements($phase) {
-  $requirements = array();
-  if ($phase == 'install') {
-    // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
-      $requirements ['tripal_db'] = array(
-            'title' => "tripal_db",
-            'value' => "ERROR: Chado most be installed before this module can be enabled",
-            'severity' => REQUIREMENT_ERROR,
-      );
-    }
-  }
-  return $requirements;
-}

tripal_feature/api/tripal_feature.api.inc

@@ -515,8 +515,8 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
         watchdog('tripal_feature', "init: not able to prepare SQL statement '%name'", 
           array('%name' => 'feature_by_subject'), 'WATCHDOG ERROR');
       }    
-      $sql = "EXECUTE feature_rel_get_object(%d,'%s')";
-      $features = chado_query($sql, $feature_id, $relationship); 
+      $sql = "EXECUTE feature_rel_get_object(:feature_id, :relationship)";
+      $features = chado_query($sql, array(':feature_id' => $feature_id, ':relationship' => $relationship)); 
     }
     if ($rel_part == "object") {
       $psql = '
@@ -537,11 +537,11 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
         watchdog('tripal_feature', "init: not able to prepare SQL statement '%name'", 
           array('%name' => 'feature_by_object'), 'WATCHDOG ERROR');
       }
-      $sql = "EXECUTE feature_rel_get_subject(%d,'%s')";
-      $features = chado_query($sql, $feature_id, $relationship);     
+      $sql = "EXECUTE feature_rel_get_subject(:feature_id, :relationship)";
+      $features = chado_query($sql, array(':feature_id' => $feature_id, ':relationship' => $relationship));     
     }
     $sequences = '';
-    while ($feature = db_fetch_object($features)) {  
+    while ($feature = $features->fetchObject()) {  
 
       // recurse and get the sequences for these in the relationship
       if ($rel_part == "subject") {
@@ -625,11 +625,11 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
           END as downstream,  
           OF.residues                                                     
         FROM {featureloc} FL 
-          INNER JOIN {feature} SF on FL.feature_id = SF.feature_id
-          INNER JOIN {cvterm} SCVT on SF.type_id = SCVT.cvterm_id
-          INNER JOIN {feature} OF on FL.srcfeature_id = OF.feature_id                
-          INNER JOIN {cvterm} OCVT on OF.type_id = OCVT.cvterm_id
-          INNER JOIN {organism} OO on OF.organism_id = OO.organism_id
+          INNER JOIN {feature} SF   on FL.feature_id    = SF.feature_id
+          INNER JOIN {cvterm}  SCVT on SF.type_id       = SCVT.cvterm_id
+          INNER JOIN {feature} OF   on FL.srcfeature_id = OF.feature_id                
+          INNER JOIN {cvterm}  OCVT on OF.type_id       = OCVT.cvterm_id
+          INNER JOIN {organism} OO  on OF.organism_id   = OO.organism_id
         WHERE SF.feature_id = $3 and NOT (OF.residues = \'\' or OF.residues IS NULL)) as tbl1
     ';              
     $status = tripal_core_chado_prepare('sequence_by_parent', $psql, array('int', 'int', 'int'));
@@ -677,10 +677,10 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
   if ($derive_from_parent) {                  
     
     // execute the query to get the sequence from the parent
-    $sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
-    $parents = chado_query($sql, $upstream, $downstream, $feature_id);
+    $sql = "EXECUTE sequence_by_parent (:upstream, :downstream, :feature_id)";
+    $parents = chado_query($sql, array(':uptream' => $upstream, ':downstream' => $downstream, ':feature_id' => $feature_id));
 
-    while ($parent = db_fetch_object($parents)) {  
+    while ($parent = $parents->fetchObject()) {  
       $seq = '';  // initialize the sequence for each parent
 
       // if we are to aggregate then we will ignore the feature returned
@@ -688,16 +688,17 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
       if ($aggregate) {
         
         // now get the sub features that are located on the parent.
-        $sql = "EXECUTE sub_features (%d, %d)";
-        $children = chado_query($sql, $feature_id, $parent->srcfeature_id);
-        $sql = "EXECUTE count_sub_features (%d, %d)";
-        $num_children = db_fetch_object(chado_query($sql, $feature_id, $parent->srcfeature_id));
+        $sql = "EXECUTE sub_features (:feature_id, :srcfeature_id)";
+        $children = chado_query($sql, array(':feature_id' => $feature_id, ':srcfeature_id' => $parent->srcfeature_id));
+        $sql = "EXECUTE count_sub_features (:feature_id, :srcfeature_id)";
+        $sub_features = chado_query($sql, array(':feature_id' => $feature_id, ':srcfeature_id' => $parent->srcfeature_id));
+        $num_children = $sub_features->fetchObject();
                
         // iterate through the sub features and concat their sequences. They
         // should already be in order.
         $types = array();
         $i = 0;
-        while ($child = db_fetch_object($children)) {
+        while ($child = $children->fetchObject()) {
           // if the callee has specified that only certain sub features should be
           // included then continue if this child is not one of those allowed
           // subfeatures
@@ -710,7 +711,7 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
             $types[] = $child->type_name;
           }
           
-          $sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
+          $sql = "EXECUTE sequence_by_parent (:upstream, %d, :feature_id)";
 
           // if the first sub feature we need to include the upstream bases. first check if 
           // the feature is in the foward direction or the reverse.
@@ -718,13 +719,13 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
             // -------------------------- ref
             //    ....---->  ---->        
             //     up    1       2         
-            $q = chado_query($sql, $upstream, 0, $child->feature_id);
+            $q = chado_query($sql, array(':upstream' => $upstream, ':downstream' => 0, ':feature_id' => $child->feature_id));
           }
           elseif ($i == 0 and $parent->strand < 0) { // reverse direction
             // -------------------------- ref
             //    ....<----  <----
             //    down  1       2
-            $q = chado_query($sql, 0, $downstream, $child->feature_id);
+            $q = chado_query($sql, array(':upstream' => 0, ':downstream' => $downstream, ':feature_id' => $child->feature_id));
           }
                     
           // Next, if the last sub feature we need to include the downstream bases. first check if
@@ -733,22 +734,22 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
             // -------------------------- ref
             //        ---->  ---->....
             //          1       2 down
-            $q = chado_query($sql, 0, $downstream, $child->feature_id);
+            $q = chado_query($sql, array(':upstream' => 0, ':downstream' => $downstream, ':feature_id' => $child->feature_id));
           }
           elseif ($i == $num_children->num_children - 1 and $parent->strand < 0) { // reverse direction
             // -------------------------- ref
             //        <----  <----....
             //          1       2  up
-            $q = chado_query($sql, $upstream, 0, $child->feature_id);
+            $q = chado_query($sql, array(':upstream' => $upstream, ':downstream' => 0, ':feature_id' => $child->feature_id));
           }
           
           // for internal sub features we don't want upstream or downstream bases
           else {         
             $sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
-            $q = chado_query($sql, 0, 0, $child->feature_id);
+            $q = chado_query($sql, array(':upstream' => 0, ':downstream' => 0, ':feature_id' => $child->feature_id));
           }
           
-          while ($subseq = db_fetch_object($q)) {
+          while ($subseq = $q->fetchObject()) {
             // concatenate the sequences of all the sub features            
             if ($subseq->srcfeature_id == $parent->srcfeature_id) {
               $seq .= $subseq->residues;   
@@ -809,8 +810,8 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
   // if we are not getting the sequence from the parent sequence then
   // use what comes through from the feature record
   else {
-    $sql = "SELECT * FROM {feature} F WHERE feature_id = %d";
-    $values = db_fetch_object(chado_query($sql, $feature_id));
+    $sql = "SELECT * FROM {feature} F WHERE feature_id = :feature_id"; 
+    $values = chado_query($sql, array(':feature_id' => $feature_id))->fetchObject();
     $residues = $values->residues;
     if ($output_format == 'fasta_html') {
        $residues = wordwrap($residues, $num_bases_per_line, "<br>", TRUE);  
@@ -942,10 +943,9 @@ function tripal_feature_get_feature_relationships($feature) {
        // same landmark feature.
        $rel->child_featurelocs = array();     
        foreach ($cfeaturelocs as $featureloc) {
-          $res = chado_query("EXECUTE sel_featureloc_preprocess_relationships (%d, %d)", 
-            $relationship->subject_id->feature_id, 
-            $featureloc->srcfeature_id->feature_id);        
-          while ($loc = db_fetch_object($res)) {
+          $res = chado_query("EXECUTE sel_featureloc_preprocess_relationships (:relationship, :featureloc)", 
+            array(':relationship' => $relationship->subject_id->feature_id, ':featureloc' => $featureloc->srcfeature_id->feature_id));        
+          while ($loc = $res->fetchObject()) {
              // add in the node id of the src feature if it exists and save this location
              $loc->nid = $featureloc->srcfeature_id->nid;
              $rel->child_featurelocs[] = $loc;
@@ -958,8 +958,8 @@ function tripal_feature_get_feature_relationships($feature) {
        $child_type = $relationship->subject_id->type_id->name;
        
        // get the node id of the subject
-       $sql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d";
-       $n = db_fetch_object(db_query($sql, $relationship->subject_id->feature_id));
+       $sql = "SELECT nid FROM {chado_feature} WHERE feature_id = :feature_id";
+       $n = db_query($sql, array('feature_id' => $relationship->subject_id->feature_id))->fetchObject();
        if ($n) {
           $rel->record->nid = $n->nid;
        }
@@ -981,10 +981,9 @@ function tripal_feature_get_feature_relationships($feature) {
        // get locations where this feature overlaps with the parent
        $rel->parent_featurelocs = array();     
        foreach ($cfeaturelocs as $featureloc) {
-          $res = chado_query("EXECUTE sel_featureloc_preprocess_relationships (%d, %d)", 
-            $relationship->object_id->feature_id, 
-            $featureloc->srcfeature_id->feature_id);
-          while ($loc = db_fetch_object($res)) {
+          $res = chado_query("EXECUTE sel_featureloc_preprocess_relationships (:feature_id, :srcfeature_id)", 
+            array('feature_id' => $relationship->object_id->feature_id, ':srcfeature_id' => $featureloc->srcfeature_id->feature_id));
+          while ($loc = $res->fetchObject()) {
              // add in the node id of the src feature if it exists and save this location
              $loc->nid = $featureloc->srcfeature_id->nid;
              $rel->parent_featurelocs[] = $loc;
@@ -995,8 +994,8 @@ function tripal_feature_get_feature_relationships($feature) {
        $parent_type = $relationship->object_id->type_id->name;
        
        // get the node id of the subject
-       $sql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d";
-       $n = db_fetch_object(db_query($sql, $relationship->object_id->feature_id));
+       $sql = "SELECT nid FROM {chado_feature} WHERE feature_id = :feature_id";
+       $n = db_query($sql, array(':feature_id' => $relationship->object_id->feature_id))->fetchObject();
        if ($n) {
           $rel->record->nid = $n->nid;
        }

tripal_feature/includes/fasta_loader.inc

@@ -36,7 +36,7 @@ function tripal_feature_fasta_load_form( ) {
   $org_rset = chado_query($sql);
   $organisms = array();
   $organisms[''] = '';
-  while ($organism = db_fetch_object($org_rset)) {
+  while ($organism = $org_rset->fetchObject()) {
     $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
   }
   $form['organism_id'] = array(
@@ -63,7 +63,7 @@ function tripal_feature_fasta_load_form( ) {
   $lib_rset = chado_query($sql);
   $libraries = array();
   $libraries[''] = '';
-  while ($library = db_fetch_object($lib_rset)) {
+  while ($library = $lib_rset->fetchObject()) {
     $libraries[$library->library_id] = "$library->name ($library->type)";
   }
   //   $form['library_id'] = array (
@@ -132,7 +132,7 @@ function tripal_feature_fasta_load_form( ) {
   $org_rset = chado_query($sql);
   $analyses = array();
   $analyses[''] = '';
-  while ($analysis = db_fetch_object($org_rset)) {
+  while ($analysis = $org_rset->fetchObject()) {
     $analyses[$analysis->analysis_id] = "$analysis->name ($analysis->program $analysis->programversion, $analysis->sourcename)";
   }
   $form['analysis']['analysis_id'] = array(
@@ -202,7 +202,7 @@ function tripal_feature_fasta_load_form( ) {
   $db_rset = chado_query($sql);
   $dbs = array();
   $dbs[''] = '';
-  while ($db = db_fetch_object($db_rset)) {
+  while ($db = $db_rset->fetchObject()) {
     $dbs[$db->db_id] = "$db->name";
   }
   $form['advanced']['db']['db_id'] = array(
@@ -350,13 +350,13 @@ function tripal_feature_fasta_load_form_validate($form, &$form_state) {
                FROM {cvterm} CVT
                   INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
                   LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
-               WHERE cv.name = '%s' and (CVT.name = '%s' or CVTS.synonym = '%s')";
-  $cvterm = db_fetch_object(chado_query($cvtermsql, 'sequence', $type, $type));
+               WHERE cv.name = :cvname and (CVT.name = :name or CVTS.synonym = :synonym)";
+  $cvterm = chado_query($cvtermsql, array(':cvname' => 'sequence', ':name' => $type, ':synonym' => $type))->fetchObject();
   if (!$cvterm) {
     form_set_error('type', t("The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."));
   }
   if ($rel_type) {
-    $cvterm = db_fetch_object(chado_query($cvtermsql, 'sequence', $parent_type, $parent_type));
+    $cvterm = chado_query($cvtermsql, array(':cvname' => 'sequence', ':name' => $parent_type, ':synonym' => $parent_type))->fetchObject();
     if (!$cvterm) {
       form_set_error('parent_type', t("The Sequence Ontology (SO) term selected for the parent relationship is not available in the database. Please check spelling or select another."));
     }
@@ -444,21 +444,21 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
                FROM {cvterm} CVT
                   INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
                   LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
-               WHERE cv.name = '%s' and (CVT.name = '%s' or CVTS.synonym = '%s')";
-  $cvterm = db_fetch_object(chado_query($cvtermsql, 'sequence', $type, $type));     
+               WHERE cv.name = :cvname and (CVT.name = :name or CVTS.synonym = :synonym)";
+  $cvterm = chado_query($cvtermsql, array(':cvname' => 'sequence', ':name' => $type, ':synonym' => $type))->fetchObject();     
   if (!$cvterm) {
     watchdog("T_fasta_loader", "Cannot find the term type: '%type'", array('%type' => $type), WATCHDOG_ERROR);
     return 0;
   }
   if ($parent_type) {
-    $parentcvterm = db_fetch_object(chado_query($cvtermsql, 'sequence', $parent_type, $parent_type));
+    $parentcvterm = chado_query($cvtermsql, array(':cvname' => 'sequence', ':name' => $parent_type, ':synonym' => $parent_type))->fetchObject();
     if (!$parentcvterm) {
       watchdog("T_fasta_loader", "Cannot find the paretne term type: '%type'", array('%type' => $parentcvterm), WATCHDOG_ERROR);
       return 0;
     }
   }
   if ($rel_type) {
-    $relcvterm = db_fetch_object(chado_query($cvtermsql, 'relationship', $rel_type, $rel_type));
+    $relcvterm = chado_query($cvtermsql, array(':cvname' => 'relationship', ':name' => $rel_type, ':synonym' => $rel_type))->fetchObject();
     if (!$relcvterm) {
       watchdog("T_fasta_loader", "Cannot find the relationship term type: '%type'", array('%type' => $relcvterm), WATCHDOG_ERROR);
       return 0;

tripal_feature/includes/gff_loader.inc

@@ -33,7 +33,7 @@ function tripal_feature_gff3_load_form() {
   $org_rset = chado_query($sql);
   $organisms = array();
   $organisms[''] = '';
-  while ($organism = db_fetch_object($org_rset)) {
+  while ($organism = $org_rset->fetchObject()) {
     $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
   }
   $form['organism_id'] = array(
@@ -49,7 +49,7 @@ function tripal_feature_gff3_load_form() {
   $org_rset = chado_query($sql);
   $analyses = array();
   $analyses[''] = '';
-  while ($analysis = db_fetch_object($org_rset)) {
+  while ($analysis = $org_rset->fetchObject()) {
     $analyses[$analysis->analysis_id] = "$analysis->name ($analysis->program $analysis->programversion, $analysis->sourcename)";
   }
   $form['analysis_id'] = array(
@@ -372,8 +372,8 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
 
   // get the controlled vocaubulary that we'll be using.  The
   // default is the 'sequence' ontology
-  $sql = "SELECT * FROM {cv} WHERE name = '%s'";
-  $cv = db_fetch_object(chado_query($sql, 'sequence'));
+  $sql = "SELECT * FROM {cv} WHERE name = :cvname";
+  $cv = chado_query($sql, array(':cvname' => 'sequence'))->fetchObject();
   if (!$cv) {   
     watchdog('T_gff3_loader', "Cannot find the 'sequence' ontology", 
       array(), WATCHDOG_ERROR);
@@ -381,8 +381,8 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
   }
 
   // get the organism for which this GFF3 file belongs
-  $sql = "SELECT * FROM {organism} WHERE organism_id = %d";
-  $organism = db_fetch_object(chado_query($sql, $organism_id));
+  $sql = "SELECT * FROM {organism} WHERE organism_id = :organism_id";
+  $organism = chado_query($sql, array(':organism_id' => $organism_id))->fetchObject();
 
   $interval = intval($filesize * 0.0001);
   if ($interval == 0) {
@@ -448,8 +448,9 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
       $rstart = $region_matches[2];
       $rend = $region_matches[3];
       if ($landmark_type) {
-        $result = chado_query("EXECUTE sel_cvterm_idnasy (%d, '%s', '%s')", $cv->cv_id, $landmark_type, $landmark_type);
-        $cvterm = db_fetch_object($result);
+        $result = chado_query("EXECUTE sel_cvterm_idnasy (:cv_id, :name, :synonym)", 
+          array(':cv_id' => $cv->cv_id, ':name' => $landmark_type, ':synonym' => $landmark_type));
+        $cvterm = $result->fetchObject();
         if (!$cvterm) {
           watchdog('T_gff3_loader', 'cannot find feature type \'%landmark_type\' on line %line_num of the GFF file', 
             array('%landmark_type' => $landmark_type, '%line_num' => $line_num), WATCHDOG_ERROR);
@@ -513,9 +514,10 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
       $phase = '';
     }
   
-    $result = chado_query("EXECUTE sel_cvterm_idnasy (%d, '%s', '%s')", $cv->cv_id, $type, $type);
+    $result = chado_query("EXECUTE sel_cvterm_idnasy (:cv_id, :name, :synonym)", 
+      array(':cv_id' => $cv->cv_id, ':name' => $type, ':synonym' => $type));
 
-    $cvterm = db_fetch_object($result);
+    $cvterm = $result->fetchObject();
     if (!$cvterm) {
       watchdog('T_gff3_loader', 'cannot find feature term \'%type\' on line %line_num of the GFF file', 
         array('%type' => $type, '%line_num' => $line_num), WATCHDOG_ERROR);
@@ -847,10 +849,10 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
     
     // build and prepare the SQL for selecting the children relationship
     $sql = "SELECT DISTINCT FR.feature_relationship_id, FL.fmin, FR.rank
-            FROM {feature_relationship} FR              
+            FROM {feature_relationship} FR
               INNER JOIN {featureloc} FL on FL.feature_id = FR.subject_id";
     if (!$connection) {
-      $sql .= "WHERE FR.object_id = %d " .
+      $sql .= "WHERE FR.object_id = :feature_id " .
               "ORDER BY FL.fmin ASC ";
     }
     else {
@@ -869,19 +871,19 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
     // on the fmin.  The start rank is 1.  This allows features with other
     // relationships to be '0' (the default), and doesn't interfer with the
     // ordering defined here.        
-    while ($parent = db_fetch_object($parents)) {
+    while ($parent = $parents->fetchObject()) {
       
       // get the children
       if ($connection) {      
-        $result = chado_query('EXECUTE sel_gffchildren (%d)', $parent->feature_id);
+        $result = chado_query('EXECUTE sel_gffchildren (:feature_id)', array(':feature_id' => $parent->feature_id));
       }
       else {
-        $result = chado_query($sql, $parent->feature_id);
+        $result = chado_query($sql, array(':feature_id' => $parent->feature_id));
       }
       
       // build an array of the children
       $children = array();
-      while ($child = db_fetch_object($result)) {
+      while ($child = $result->fetchObject()) {
          $children[] = $child;  
       }
       
@@ -1032,8 +1034,10 @@ function tripal_feature_load_gff3_parents($feature, $cvterm, $parents, $organism
     $parent_type = $result[0]->type_name;
 
     // try to find the parent
-    $parentcvterm = db_fetch_object(chado_query("EXECUTE sel_cvterm_cvname_cvtname_synonym ('%s', '%s', '%s')", 'sequence', $parent_type, $parent_type));
-    $relcvterm = db_fetch_object(chado_query("EXECUTE sel_cvterm_cvname_cvtname_synonym ('%s', '%s', '%s')", 'relationship', $rel_type, $rel_type));
+    $parentcvterm = chado_query("EXECUTE sel_cvterm_cvname_cvtname_synonym (:cvname, :name, :synonym)", 
+      array(':cvname' => 'sequence', ':name' => $parent_type, ':synonym' => $parent_type))->fetchObject();
+    $relcvterm = chado_query("EXECUTE sel_cvterm_cvname_cvtname_synonym (:cvname, :name, :synonym)", 
+      array(':cvname' => 'relationship', ':name' => $rel_type, ':synonymn' => $rel_type))->fetchObject();
     $values = array(
         'organism_id' => $organism_id,
         'uniquename' => $parent,
@@ -1373,7 +1377,8 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
         } 
       }    
       // insert the null pub 
-      $result = db_fetch_object(chado_query("EXECUTE ins_pub_uniquename_typeid ('%s', '%s')", 'null', 'null'));
+      $result = chado_query("EXECUTE ins_pub_uniquename_typeid (:uname, :type_id)", 
+        array(':uname' => 'null', ':type_id' => 'null'))->fetchObject();
       if (!$result) {
         watchdog("T_gff3_loader", "Cannot add null publication needed for setup of alias", array(), WATCHDOG_WARNING);
         return 0;
@@ -1856,7 +1861,7 @@ function tripal_feature_load_gff3_fasta($fh, $interval, &$num_read, &$intv_read,
         }
         // if we have a feature then add the residues
         else {    
-          $feature = db_fetch_object($result);    
+          $feature = $result->fetchObject();    
           $values = array('residues' => $residues);
           $match = array('feature_id' => $feature->feature_id);
           $options = array('statement_name' => 'upd_feature_re');
@@ -1880,7 +1885,7 @@ function tripal_feature_load_gff3_fasta($fh, $interval, &$num_read, &$intv_read,
   }
   // if we have a feature then add the residues
   else {        
-    $feature = db_fetch_object($result);    
+    $feature = $result->fetchObject();    
     $values = array('residues' => $residues);
     $match = array('feature_id' => $feature->feature_id);
     $options = array('statement_name' => 'upd_feature_re');

tripal_feature/includes/seq_extract.inc

@@ -171,7 +171,7 @@ function tripal_feature_seq_extract_form(&$form_state = NULL) {
   $results = chado_query($sql);
   $genus = array();
   $genus[] = '';
-  while ($organism = db_fetch_object($results)) {
+  while ($organism = $results->fetchObject()) {
     $genus[$organism->genus] = $organism->genus;  
   }
   
@@ -196,11 +196,11 @@ function tripal_feature_seq_extract_form(&$form_state = NULL) {
     $sql = "
       SELECT DISTINCT species 
       FROM {organism} 
-      WHERE genus = '%s'
+      WHERE genus = :genus
       ORDER BY species
     ";
-    $results = chado_query($sql, $dgenus);
-    while ($organism = db_fetch_object($results)) {
+    $results = chado_query($sql, array(':genus' => $dgenus));
+    while ($organism = $results->fetchObject()) {
       $species[$organism->species] = $organism->species;  
     }
   }  
@@ -227,17 +227,17 @@ function tripal_feature_seq_extract_form(&$form_state = NULL) {
       FROM {analysis_organism} AO 
         INNER JOIN {analysis} A ON A.analysis_id = AO.analysis_id
         INNER JOIN {organism} O ON O.organism_id = AO.organism_id
-      WHERE O.genus = '%s'
+      WHERE O.genus = :genus
     ";
     $args = array();
-    $args[] = $dgenus;
+    $args[':genus'] = $dgenus;
     if ($dspecies) {
-      $sql .= " AND O.species = '%s' ";
-      $args[] = $dspecies;
+      $sql .= " AND O.species = :species ";
+      $args[':species'] = $dspecies;
     }
     $sql .=" ORDER BY A.name ";
     $results = chado_query($sql, $args);  
-    while ($analysis = db_fetch_object($results)) {
+    while ($analysis = $results->fetchObject()) {
       $analyses[$analysis->name] = $analysis->name;  
     }
   }
@@ -256,18 +256,18 @@ function tripal_feature_seq_extract_form(&$form_state = NULL) {
     $sql = "
       SELECT DISTINCT OFC.cvterm_id, OFC.feature_type
       FROM {organism_feature_count} OFC 
-      WHERE OFC.genus = '%s'
+      WHERE OFC.genus = :genus
     ";
     $args = array();
-    $args[] = $dgenus;
+    $args['genus'] = $dgenus;
     if ($dspecies) {
-      $sql .= " AND OFC.species = '%s'";
-      $args[] = $dspecies;
+      $sql .= " AND OFC.species = :species";
+      $args['species'] = $dspecies;
     }
     $sql .= " ORDER BY OFC.feature_type ";
     $results = chado_query($sql, $args);
     
-    while ($type = db_fetch_object($results)) {
+    while ($type = $results->fetchObject()) {
       $ftype[$type->feature_type] = $type->feature_type;  
     }
   }
@@ -481,45 +481,45 @@ function tripal_feature_seq_extract_get_features($org_commonname, $genus, $speci
   }         
   $sql .= "WHERE (1=1) ";
   if ($org_commonname) {
-    $sql .= "AND O.common_name = '%s' ";
-    $vars[] = $org_commonname;
+    $sql .= "AND O.common_name = :common_name ";
+    $vars[':common_name'] = $org_commonname;
   }
   if ($genus) {
-    $sql .= "AND O.genus = '%s' ";
-    $vars[] = $genus;
+    $sql .= "AND O.genus = :genus ";
+    $vars[':genus'] = $genus;
   }
   if ($species) {
-    $sql .= "AND O.species = '%s' ";
-    $vars[] = $species;
+    $sql .= "AND O.species = :species ";
+    $vars[':species'] = $species;
   }
   if ($type) {
-    $sql .= "AND CVT.name = '%s' ";
-    $vars[] = $type; 
+    $sql .= "AND CVT.name = ':cvtname ";
+    $vars[':cvtname'] = $type; 
   }
   if ($feature_name) {
     if (is_array($feature_name)) {
       $sql .= "AND F.name IN (";
       foreach ($feature_name as $i => $fname) {
-        $sql .= "'%s', ";
-        $vars[] = $fname;
+        $sql .= ":fname$i, ";
+        $vars[":fname$i"] = $fname;
       } 
       // remove the trailing comma and close the paren
       $sql = substr($sql, 0, -2) . ")";
     }
     else {
-      $sql .= "AND F.name = '%s'";
-      $vars[] = $feature_name;
+      $sql .= "AND F.name = :fname";
+      $vars[':fname'] = $feature_name;
     }
   }
   if ($analysis_name) {
-    $sql .= "AND A.name = '%s'";
-    $vars[] = $analysis_name;
+    $sql .= "AND A.name = :aname";
+    $vars[':aname'] = $analysis_name;
   }
   $num_bases_per_line = 50;
   $num_seqs = 0;
   $q = chado_query($sql, $vars);
   
-  while ($feature = db_fetch_object($q)) {
+  while ($feature = $q->fetchObject()) {
     
     $feature_id = $feature->feature_id;
     

tripal_feature/includes/tripal_feature-db_references.inc

@@ -1,357 +0,0 @@
-<?php
-
-/**
- * @file
- * @todo Add file header description
- */
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_add_ALL_dbreferences_page($node) {
-  $output = '';
-
-  $output .= tripal_feature_implement_add_chado_properties_progress('db_references') . '<br />';
-  $output .= '<b>All Database References should strictly pertain to THE CURRENT Individual</b><br />';
-  $output .= '<br /><b>Current Database References</b><br />';
-  $output .= list_dbreferences_for_node($node->db_references);
-  $output .= '<br /><br />';
-  $output .= drupal_get_form('tripal_feature_add_ONE_dbreference_form', $node);
-  $output .= '<br />';
-  $output .= drupal_get_form('tripal_feature_implement_add_chado_properties_navigate', 'db_references', $node->nid);
-  return $output;
-}
-
-/**
- * Implements Hook_form()
- * Handles adding of Database References to features
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_add_ONE_dbreference_form($form_state, $node) {
-
-  $form['nid'] = array(
-    '#type' => 'hidden',
-    '#value' => $node->nid
-  );
-
-  $form['feature_id'] = array(
-    '#type' => 'hidden',
-    '#value' => $node->feature->feature_id,
-  );
-
-  $form['add_dbreference'] = array(
-    '#type' => 'fieldset',
-    '#title' => t('Add Database References') . '<span class="form-optional" title="This field is optional">(optional)</span>',
-  );
-
-  $form['add_dbreference']['accession'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Accession'),
-    '#required' => TRUE,
-  );
-
-  $form['add_dbreference']['description'] = array(
-    '#type' => 'textarea',
-    '#title' => t('Description of Reference') . '<span class="form-optional" title="This field is optional">+</span>',
-    '#description' => t('Optionally enter a description about the database accession.'),
-  );
-
-  $db_options = tripal_db_get_db_options();
-  $db_options[0] = 'Select a Database';
-  ksort($db_options);
-  $form['add_dbreference']['db_id'] = array(
-    '#type' => 'select',
-    '#title' => t('Database'),
-    '#options' => $db_options,
-    '#required' => TRUE,
-  );
-
-  $form['add_dbreference']['submit'] = array(
-    '#type' => 'submit',
-    '#value' => t('Add Database Reference')
-  );
-
-  return $form;
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_add_ONE_dbreference_form_validate($form, &$form_state) {
-
-  $db_id = $form_state['values']['db_id'];
-  $accession = $form_state['values']['accession'];
-  $description = $form_state['values']['description'];
-  $feature_id = $form_state['values']['feature_id'];
-  $nid = $form_state['values']['nid'];
-
-  // Check database is valid db_id in chado
-  $tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {db} WHERE db_id=%d", $db_id));
-  if ($tmp_obj->count != 1) {
-    form_set_error('database', 'The database you selected is not valid. Please choose another one.');
-  }
-
-  // Check Accession is unique for database
-  $sql = "SELECT count(*) as count FROM {dbxref} WHERE accession='%s' and db_id = %d";
-  $tmp_obj = db_fetch_object(chado_query($sql, $accession, $db_id));
-
-  if ($tmp_obj->count > 0) {
-    form_set_error('accession', 'This accession has already been assigned to another feature in the selected database.');
-  }
-
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_add_ONE_dbreference_form_submit($form, &$form_state) {
-
-  $db_id = $form_state['values']['db_id'];
-  $accession = $form_state['values']['accession'];
-  $description = $form_state['values']['description'];
-  $feature_id = $form_state['values']['feature_id'];
-  $nid = $form_state['values']['nid'];
-
-  // create dbxref
-  $isql =  "INSERT INTO {dbxref} (db_id, accession, description) VALUES (%d, '%s', '%s')";
-  chado_query($isql, $db_id, $accession, $description);
-
-  //create feature_dbxref
-  $dbxref = tripal_db_get_dbxref( array('db_id' => array('type' => 'INT', 'value' => $form_state['values']['db_id']),
-                     'accession' => array('type' => 'STRING', 'exact' => TRUE, 'value' => $form_state['values']['accession']) ) );
-
-  if (!empty($dbxref->dbxref_id)) {
-      $isql = "INSERT INTO {feature_dbxref} (feature_id, dbxref_id) VALUES (%d, %d)";
-      chado_query($isql, $feature_id, $dbxref->dbxref_id);
-      drupal_set_message(t('Successfully Added Database Reference'));
-      drupal_goto('node/' . $nid);
-  }
-  else {
-    drupal_set_message(t('Database reference NOT successfully created...'), 'error');
-  } //end of if dbxref was created successfully
-
-}
-
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_edit_ALL_dbreferences_page($node) {
-  $output = '';
-
-  $output .= drupal_get_form('tripal_feature_edit_ALL_db_references_form', $node);
-  $output .= '<br />';
-  $output .= drupal_get_form('tripal_feature_add_ONE_dbreference_form', $node);
-  $output .= '<br />';
-  $output .= drupal_get_form('tripal_feature_implement_back_to_feature_button', $node->nid);
-
-  return $output;
-}
-
-/**
- * Implements Hook_form()
- * Handles adding of DB References to Features
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_edit_ALL_db_references_form($form_state, $node) {
-  $form = array();
-
-  $form['nid'] = array(
-    '#type' => 'hidden',
-    '#value' => $node->nid
-  );
-
-  $i=0;
-
-  $feature = $node->feature;
-  $references = tripal_feature_load_references($feature->feature_id);
-
-  // pre populate the database options
-  $db_options = tripal_db_get_db_options();
-  $db_options[0] = 'Select a Database';
-  ksort($db_options);
-
-  if (sizeof($references) != 0) {
-    foreach ($references as $ref) {
-      $i++;
-      $form["num-$i"] = array(
-        '#type' => 'fieldset',
-        '#title' => t("Database Reference") . " $i"
-      );
-
-      $form["num-$i"]["accession-$i"] = array(
-        '#type' => 'textfield',
-        '#title' => t('Accession'),
-        '#size' => 30,
-        '#required' => TRUE,
-        '#default_value' => $ref->accession
-      );
-
-      $form["num-$i"]["db_id-$i"] = array(
-        '#type' => 'select',
-        '#title' => t('Database'),
-        '#options' => $db_options,
-        '#required' => TRUE,
-        '#default_value' => $ref->db_id
-      );
-
-
-      $form["num-$i"]["dbxref_id-$i"] = array(
-        '#type' => 'hidden',
-        '#value' => $ref->dbxref_id
-      );
-
-      $form["num-$i"]["delete-$i"] = array(
-        '#type' => 'submit',
-        '#value' => t("Delete"),
-        '#name' => "delete-$i",
-      );
-
-      }
-
-      $form['num_db_references'] = array(
-        '#type' => 'hidden',
-        '#value' => $i
-      );
-
-      $form["submit-edits"] = array(
-        '#type' => 'submit',
-        '#value' => t('Update All References')
-      );
-  } //end of foreach db ref
-  return $form;
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_edit_ALL_db_references_form_submit($form, &$form_state) {
-
-  $num_refs = $form_state['values']['num_db_references'];
-  $action = $form_state['clicked_button']['#value'];
-  $button = $form_state['clicked_button']['#name'];
-  $nid = $form_state['values']['nid'];
-
-  if (strcmp($action, 'Update All References')==0) {
-    for ($i=1; $i<=$num_refs; $i++) {
-    $dbxref_id = $form_state['values']["dbxref_id-$i"];
-    $db_id = $form_state['values']["db_id-$i"];
-    $accession = $form_state['values']["accession-$i"];
-      tripal_feature_update_db_reference($dbxref_id, $db_id, $accession);
-    }
-    drupal_set_message(t("Updated all Database References"));
-    drupal_goto('node/' . $nid);
-  }
-  elseif (strcmp($action, 'Delete')==0) {
-    if (preg_match('/delete-(\d+)/', $button, $matches) ) {
-      $i = $matches[1];
-      $dbxref_id = $form_state['values']["dbxref_id-$i"];
-      tripal_feature_delete_db_reference($dbxref_id);
-      drupal_set_message(t("Deleted Database Reference"));
-      drupal_goto('node/' . $nid);
-    }
-    else {
-      drupal_set_message(t("Could not remove database reference:"), 'error');
-    }
-    }
-  else {
-    drupal_set_message(t("Unrecognized Button Pressed"), 'error');
-  }
-
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_update_db_reference($dbxref_id, $db_id, $accession) {
-
-  $sql =  "UPDATE {dbxref} SET db_id=%d, accession='%s' WHERE dbxref_id=%d";
-  chado_query($sql, $db_id, $accession, $dbxref_id);
-
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_delete_db_reference($dbxref_id) {
-
-  chado_query(
-    "DELETE FROM {dbxref} WHERE dbxref_id=%d",
-    $dbxref_id
-  );
-
-  chado_query(
-    "DELETE FROM {feature_dbxref} WHERE dbxref_id=%d",
-    $dbxref_id
-  );
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function theme_tripal_feature_edit_ALL_db_references_form($form) {
-  $output = '';
-
-  $output .= '<br /><fieldset>';
-  $output .= '<legend>Edit Existing Database References<span class="form-optional" title="This field is optional">(optional)</span></legend>';
-  $output .= '<p>Below is a list of already existing database references, one per line. When entering a database reference, the accession ' .
-             'is a unique identifier for this feature in the specified database.</p>';
-  $output .= '<table>';
-  $output .= '<tr><th>#</th><th>Database</th><th>Accession</th><th></th></tr>';
-
-  for ($i=1; $i<=$form['num_db_references']['#value']; $i++) {
-    $output .= '<tr><td>' . drupal_render($form["num-$i"]) . '</td><td>'
-             . drupal_render($form["database-$i"]) . '</td><td>'
-         . drupal_render($form["accession-$i"]) . '</td><td>'
-         . drupal_render($form["submit-$i"]) . '</td></tr>';
-  }
-
-  $output .= '</table><br />';
-  $output .= drupal_render($form);
-  $output .= '</fieldset>';
-
-  return $output;
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function list_dbreferences_for_node($db_references) {
-
-  if (!empty($db_references) ) {
-    $output = '<table>';
-    $output .= '<tr><th>Database</th><th>Accession</th></tr>';
-
-    foreach ($db_references as $db) {
-        $output .= '<tr><td>' . $db->db_name . '</td><td>' . $db->accession . '</td></tr>';
-    } // end of foreach db reference
-
-    $output .= '</table>';
-
-  }
-  else {
-    $output = 'No Database References Added to the Current Feature';
-  }
-
-  return $output;
-}

tripal_feature/includes/tripal_feature-delete.inc

@@ -10,7 +10,7 @@ function tripal_feature_delete_form() {
   $org_rset = chado_query($sql);
   $organisms = array();
   $organisms[''] = '';
-  while ($organism = db_fetch_object($org_rset)) {
+  while ($organism = $org_rset->fetchObject()) {
     $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
   }
   $form['desc'] = array(
@@ -50,7 +50,7 @@ function tripal_feature_delete_form() {
   $org_rset = chado_query($sql);
   $analyses = array();
   $analyses[''] = '';
-  while ($analysis = db_fetch_object($org_rset)) {
+  while ($analysis = $org_rset->fetchObject()) {
     $analyses[$analysis->analysis_id] = "$analysis->name ($analysis->program $analysis->programversion, $analysis->sourcename)";
   }
   //  TODO: ADD THIS BACK IN LATER
@@ -82,14 +82,18 @@ function tripal_feature_delete_form_validate($form, &$form_state) {
 
   // check to make sure the types exists
   if ($seq_type) {
-    $cvtermsql = "SELECT CVT.cvterm_id
-                  FROM {cvterm} CVT
-                     INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
-                     LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
-                  WHERE cv.name = '%s' and (CVT.name = '%s' or CVTS.synonym = '%s')";
-    $cvterm = db_fetch_object(chado_query($cvtermsql, 'sequence', $seq_type, $seq_type));
+    $cvtermsql = "
+      SELECT CVT.cvterm_id
+      FROM {cvterm} CVT
+        INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
+        LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
+      WHERE cv.name = :cvname and (CVT.name = :name or CVTS.synonym = :synonym)
+    ";
+    $cvterm = chado_query($cvtermsql, 
+      array(':cvname' => 'sequence', ':name' => $seq_type, ':synonym' => $seq_type))->fetchObject();
     if (!$cvterm) {
-      form_set_error('seq_type', t("The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."));
+      form_set_error('seq_type', t("The Sequence Ontology (SO) term selected for the " .
+      "sequence type is not available in the database. Please check spelling or select another."));
     }
   }
 }

tripal_feature/includes/tripal_feature-properties.inc

@@ -1,327 +0,0 @@
-<?php
-/**
- * @file
- * @todo Add file header description
- */
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_edit_ALL_properties_page($node) {
-  $output = '';
-
-  // get the list of properties for this feature
-  $values  = array('feature_id' => $node->feature->feature_id);
-  $options = array('order_by' => array('type_id' => 'ASC', 'rank' => 'ASC'));
-  $properties = tripal_core_generate_chado_var('featureprop', $values, $options);
-  $properties = tripal_core_expand_chado_vars($properties, 'field', 'featureprop.value');
-
-  $expand_add = (sizeof($properties)) ? FALSE : TRUE;
-
-  // add the appopriate form sections
-  $output .= drupal_get_form('tripal_feature_add_ONE_property_form', $node, $expand_add);
-  $output .= drupal_get_form('tripal_feature_edit_ALL_properties_form', $node, $properties);
-  $output .= drupal_get_form('tripal_feature_implement_back_to_feature_button', $node->nid);
-
-  return $output;
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_add_ONE_property_form($form_state, $node, $expand) {
-  $form = array();
-  $feature_id = $node->feature->feature_id;
-
-  $form['add_properties'] = array(
-    '#type' => 'fieldset',
-    '#title' => t('Add Property'),
-    '#collapsible' => TRUE,
-    '#collapsed' => ($expand) ? FALSE : TRUE,
-  );
-
-  $form['prop_nid'] = array(
-    '#type' => 'hidden',
-    '#value' => $node->nid
-  );
-
-  $form['add_properties']['feature_id'] = array(
-    '#type' => 'value',
-    '#value' => $feature_id,
-    '#required' => TRUE
-  );
-
-  // right now this defaults to the 'feature_property' CV
-  // but in the future it should be more flexible
-  $form['cv_name'] = array(
-    '#type' => 'hidden',
-    '#value' => 'feature_property'
-  );
-
-  // get the list of property types
-  $prop_type_options = array();
-  $columns = array('cvterm_id', 'name');
-  $values = array(
-    'cv_id' => array(
-      'name' => $form['cv_name']['#value'],
-    )
-  );
-  $results = tripal_core_chado_select('cvterm', $columns, $values);
-  foreach ($results as $r) {
-    $prop_type_options[$r->name] = $r->name;
-  }
-
-  $form['add_properties']['property'] = array(
-    '#type' => 'select',
-    '#title' => t('Type of Property'),
-    '#options' => $prop_type_options,
-  );
-
-  $form['add_properties']['prop_value'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Value'),
-  );
-
-  $form['add_properties']['submit-add'] = array(
-    '#type' => 'submit',
-    '#value' => t('Add Property')
-  );
-
-  return $form;
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_add_ONE_property_form_validate($form, &$form_state) {
-
-  // Only Require if Adding Property
-  if ($form_state['clicked_button']['#value'] == t('Add Property') ) {
-
-    // Check that there is a feature
-    if ( $form_state['values']['feature_id'] <= 0 ) {
-      form_set_error('feature_id', 'There is no associated feature.');
-    }
-
-    // Check that Selected a type
-    if ( !$form_state['values']['property']) {
-      form_set_error('property', 'Please select a type of property.');
-    }
-  }
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_add_ONE_property_form_submit($form, &$form_state) {
-  $feature_id = $form_state['values']['feature_id'];
-  $property = $form_state['values']['property'];
-  $value = $form_state['values']['prop_value'];
-  $cv_name = $form_state['values']['cv_name'];
-
-  $succes = tripal_feature_insert_property($feature_id, $property, $value, 0, $cv_name);
-  if ($succes) {
-    drupal_set_message(t("Successfully Added Property: %property => %value", array('%property' => $property), array('%value' => $value)));
-  }
-  else {
-    drupal_set_message(t("Failed to Add Property: %property => %value", array('%property' => $property), array('%value' => $value)));
-  }
-}
-
-/**
- * Implements Hook_form()
- * Handles adding of Properties for features
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_edit_ALL_properties_form($form_state, $node, $properties) {
-  $form = array();
-  $feature_id = $node->feature->feature_id;
-
-  $form['nid'] = array(
-    '#type' => 'hidden',
-    '#value' => $node->nid
-  );
-
-  $form['add_properties']['feature_id'] = array(
-    '#type' => 'value',
-    '#value' => $feature_id,
-    '#required' => TRUE
-  );
-
-  // right now this defaults to the 'feature_property' CV
-  // but in the future it should be more flexible
-  $form['cv_name'] = array(
-    '#type' => 'hidden',
-    '#value' => 'feature_property'
-  );
-
-  if (sizeof($properties)) {
-
-    // build the select box options for the property name
-    $prop_type_options = array();
-    $columns = array('cvterm_id', 'name');
-    $values = array(
-      'cv_id' => array(
-        'name' => $form['cv_name']['#value']
-      )
-    );
-    $results = tripal_core_chado_select('cvterm', $columns, $values);
-    foreach ($results as $r) {
-      $prop_type_options[$r->name] = $r->name;
-    }
-
-    // iterate through all of the properties and create a set of form elements
-  foreach ($properties as $i => $property) {
-    $form["num-$i"] = array(
-      '#type' => 'fieldset',
-      '#value' => "Property $i"
-    );
-    $form["num-$i"]["id-$i"] = array(
-      '#type' => 'hidden',
-      '#value' => $property->featureprop_id
-    );
-    $default = array_search($property->type, $prop_type_options);
-    $form["num-$i"]["type-$i"] = array(
-      '#type' => 'select',
-      '#options' => $prop_type_options,
-      '#default_value' => $property->type_id->name
-    );
-    $form["num-$i"]["value-$i"] = array(
-      '#type' => 'textfield',
-      '#default_value' => $property->value
-    );
-    $form["num-$i"]["delete-$i"] = array(
-      '#type' => 'submit',
-      '#value' => t("Delete"),
-      '#name' => "delete-$i",
-    );
-    } //end of foreach property
-
-    $form['num_properties'] = array(
-      '#type' => 'hidden',
-      '#value' => $i
-    );
-
-    $form["submit-edits"] = array(
-      '#type' => 'submit',
-      '#value' => t('Update All Properties')
-    );
-  }
-
-  return $form;
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_edit_ALL_properties_form_submit($form, &$form_state) {
-
-  $cv_name = $form_state['values']['cv_name'];
-  $feature_id = $form_state['values']["feature_id"];
-  $all_good = 1;
-
-  // if the update button was clicked then do the update
-  if ($form_state['clicked_button']['#value'] == t('Update All Properties') ) {
-    // iterate through each of the properties and set each one
-    for ($i=1; $i<=$form_state['values']['num_properties']; $i++) {
-      $featureprop_id = $form_state['values']["id-$i"];
-      $property = $form_state['values']["type-$i"];
-      $value = $form_state['values']["value-$i"];
-      $success = tripal_feature_update_property_by_id($featureprop_id, $property, $value, $cv_name);
-      if (!$success) {
-        drupal_set_message(t("Failed to Update Property: %property => %value", array('%property' => $property), array('%value' => $value)));
-        $all_good = 0;
-      }
-    }
-    if ($all_good) {
-      drupal_set_message(t("Updated all Properties"));
-    }
-    drupal_goto('node/' . $form_state['values']['nid']);
-  }
-  // if the delete button was clicked then remove the property
-  elseif (preg_match('/delete-(\d+)/', $form_state['clicked_button']['#name'], $matches) ) {
-    $i = $matches[1];
-    $featureprop_id = $form_state['values']["id-$i"];
-    $property = $form_state['values']["type-$i"];
-    $value = $form_state['values']["value-$i"];
-    $success = tripal_feature_delete_property_by_id($featureprop_id);
-    if ($success) {
-      drupal_set_message(t("Deleted Property"));
-    }
-    else {
-      drupal_set_message(t("Unable to Delete Property"));
-    }
-  }
-  else {
-    drupal_set_message(t("Unrecognized Button Pressed"), 'error');
-  }
-}
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function theme_tripal_feature_edit_ALL_properties_form($form) {
-  $output = '';
-
-  $output .= '<br /><fieldset>';
-  $output .= '<legend>Edit Already Existing Properties<span class="form-optional" title="This field is optional">(optional)</span></legend>';
-  $output .= '<p>Below is a list of already existing properties for this feature, one property per line. The type refers to the type of ' .
-             'property and the value is the value for that property. </p>';
-  $output .= '<table>';
-  $output .= '<tr><th>#</th><th>Type</th><th>Value</th><th></th></tr>';
-
-  for ($i=0; $i<=$form['num_properties']['#value']; $i++) {
-    if (isset($form["num-$i"])) {
-      $output .= '<tr><td>' . ($i+1) . '</td><td>' . drupal_render($form["num-$i"]["type-$i"]) . '</td><td>' . drupal_render($form["num-$i"]["value-$i"]) . '</td><td>' . drupal_render($form["num-$i"]["delete-$i"]) . '</td></tr>';
-      unset($form["num-$i"]);
-    }
-  }
-
-  $output .= '</table><br />';
-  $output .= drupal_render($form);
-  $output .= '</fieldset>';
-
-  return $output;
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_list_properties_for_node($properties) {
-
-  if (!empty($properties)) {
-    $output = '<table>';
-    $output .= '<tr><th>Type</th><th>Value</th></tr>';
-
-
-    if (!empty($properties) ) {
-      foreach ($properties as $p) {
-        $output .= '<tr><td>' . $p->type . '</td><td>' . $p->value . '</td></tr>';
-      } // end of foreach property
-    }
-
-    $output .= '</table>';
-
-  }
-  else {
-    $output = 'No properties exist for the current feature';
-  }
-
-  return $output;
-}
-
-

tripal_feature/includes/tripal_feature-relationships.inc

@@ -1,553 +0,0 @@
-<?php
-/**
- * @file
- * @todo Add file header description
- */
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_add_ALL_relationships_page($node) {
-  $output = '';
-
-  $output .= tripal_feature_implement_add_chado_properties_progress('relationships') . '<br />';
-  $output .= '<b>All Relationships should include the CURRENT Individual (' . $node->uniquename . ')</b><br />';
-  $output .= '<br /><b>Current Relationships</b><br />';
-  $output .= list_relationships_for_node($node->uniquename, $node->subject_relationships, $node->object_relationships);
-  $output .= '<br /><br />';
-  $output .= drupal_get_form('tripal_feature_add_ONE_relationship_form', $node);
-  $output .= '<br />';
-  $output .= drupal_get_form('tripal_feature_implement_add_chado_properties_navigate', 'relationships', $node->nid);
-  return $output;
-}
-
-/**
- * Implements Hook_form()
- * Handles adding of Relationships to Features
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_add_ONE_relationship_form($form_state, $node) {
-
-  $feature_id = $node->feature_id;
-  $organism_id = $node->organism->organism_id;
-  $_SESSION['organism'] = $organism_id; //needed for autocomplete enter feature to work
-
-  $form['rel_nid'] = array(
-    '#type' => 'hidden',
-    '#value' => $node->nid
-  );
-
-  $form['add_relationships'] = array(
-    '#type' => 'fieldset',
-    '#title' => t('Add Relationships') . '<span class="form-optional" title="This field is optional">(optional)</span>',
-  );
-
-  $form['add_relationships']['description'] = array(
-    '#type' => 'item',
-    '#value' => t('Relationships are specified as follows: (Subject) (Type of Relationship) (Object). For example, X part_of Y, where X & Y are genomic features.')
-  );
-
-  $form['add_relationships']['subject_id'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Subject'),
-    '#description' => 'The Uniquename, Name, Database Reference or Synonym of a Feature can be used here',
-  );
-
-  $cv = tripal_cv_get_cv_by_name('relationship');
-  $type_options = tripal_cv_get_cvterm_options($cv->cv_id);
-  $type_options[0] = 'Select a Type';
-  ksort($type_options);
-  $form['add_relationships']['type_id'] = array(
-    '#type' => 'select',
-    '#title' => t('Type of Relationship'),
-    '#options' => $type_options
-
-  );
-
-  $form['add_relationships']['object_id'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Object'),
-    '#description' => 'The Uniquename, Name, Database Reference or Synonym of a Feature can be used here',
-  );
-
-  $form['add_relationships']['r_description'] = array(
-    '#type' => 'textarea',
-    '#title' => t('Notes on the relationship') . '<span class="form-optional" title="This field is optional">+</span>',
-    '#description' => t('Should not include Genotypes and Phenotypes'),
-  );
-
-  $form['add_relationships']['submit'] = array(
-    '#type' => 'submit',
-    '#value' => t('Add a Relationship')
-  );
-
-  $form['add_relationships']['r_feature_id'] = array(
-    '#type' => 'value',
-    '#value' => $feature_id,
-    '#required' => TRUE
-
-  );
-
-  $form['add_relationships']['r_feature_uniquename'] = array(
-    '#type' => 'value',
-    '#value' => $node->uniquename,
-    '#required' => TRUE
-  );
-
-  return $form;
-
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_add_ONE_relationship_form_validate($form, &$form_state) {
-
-  //Require Validation if adding
-  if ($form_state['clicked_button']['#value'] == t('Add a Relationship') ) {
-
-    // check valid feature selected for subject
-    $criteria = array('unknown' => array('value' => $form_state['values']['subject_id'],
-                                          'columns' => array('name', 'uniquename', 'accession', 'synonym') ));
-    $subject_results = get_chado_stocks($criteria, 'ANY', $_SESSION['organism']);
-    if (sizeof($subject_results) > 1) {
-      $links= array();
-      for ($i=0; $i<sizeof($subject_results); $i++) {
-      $links[] = l($i+1, "node/" . $subject_results[$i]->nid); }
-      $message = t("Too many features match '%object'! Please refine your input to match
-        ONLY ONE feature. <br />To aid in this process, here are the features that
-        match your initial input: %features",
-        array('%object' => $form_state['values']['subject_id'],
-          '%features' => join(', ', $links)
-        )
-      );
-      form_set_error('subject_id', $message);
-    }
-    elseif (sizeof($subject_results) < 1) {
-      form_set_error('subject_id', t("There are no features matching your input. Please check your input for typos and/or lookup the feature <a href='!url'>here</a>", array('!url' => url('features'))));
-    }
-    elseif (sizeof($subject_results) == 1) {
-      $form_state['values']['subject_id'] = $subject_results[0]->stock_id;
-    }
-
-    // check valid stock selected for object
-    $criteria = array('unknown' => array('value' => $form_state['values']['object_id'],
-                                          'columns' => array('name', 'uniquename', 'accession', 'synonym') ));
-    $object_results = get_chado_stocks($criteria, 'ANY', $_SESSION['organism']);
-    if (sizeof($object_results) > 1) {
-      $links= array();
-      for ($i=0; $i<sizeof($object_results); $i++) {
-      $links[] = l($i+1, "node/" . $object_results[$i]->nid); }
-      $message = t("Too many features match '%object'! Please refine your input to match
-        ONLY ONE stock. <br />To aid in this process, here are the stocks that match
-        your initial input: %features",
-        array('%object' => $form_state['values']['object_id'],
-        '%features' => join(', ', $links)
-        )
-      );
-      form_set_error('object_id', $message);
-    }
-    elseif (sizeof($object_results) < 1) {
-      form_set_error('object_id', t("There are no features matching your input. Please check your input for typos and/or lookup the feature <a href='!url'>here</a>", array('!url' => url('features'))));
-    }
-    elseif (sizeof($object_results) == 1) {
-      $form_state['values']['object_id'] = $object_results[0]->stock_id;
-    }
-
-    // check valid type selected
-    if ($form_state['values']['type_id'] == 0) {
-      form_set_error('type_id', 'Please select a type of relationship.');
-    }
-    else {
-      $tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {cvterm} WHERE cvterm_id=%d", $form_state['values']['type_id']));
-
-      if ($tmp_obj->count != 1) {
-        form_set_error('type_id', 'The type you selected is not valid. Please choose another one.');
-      }
-    }
-
-    // check either subject or object is the current stock
-    if ( $subject_results[0]->nid != $form_state['values']['rel_nid'] ) {
-      if ( $object_results[0]->nid != $form_state['values']['rel_nid'] ) {
-        form_set_error('subject_id', 'Either Subject or Object must be the current stock (' . $form_state['values']['r_stock_uniquename'] . ').');
-      }
-    }
-  } //end of require validation if adding relationship
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_add_ONE_relationship_form_submit($form, &$form_state) {
-
-  if ($form_state['values']['subject_id'] > 0) {
-    chado_query(
-      "INSERT INTO {stock_relationship} (subject_id, type_id, object_id, value) VALUES (%d, %d, %d, '%s')",
-      $form_state['values']['subject_id'],
-      $form_state['values']['type_id'],
-      $form_state['values']['object_id'],
-      $form_state['values']['r_description']
-    );
-
-    drupal_set_message(t('Successfully Added Relationship.'));
-  } //end of insert relationship
-
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_edit_ALL_relationships_page($node) {
-  $output = '';
-
-  $output .= drupal_get_form('tripal_feature_edit_ALL_relationships_form', $node);
-  $output .= '<br />';
-  $output .= drupal_get_form('tripal_feature_add_ONE_relationship_form', $node);
-  $output .= '<br />';
-  $output .= drupal_get_form('tripal_feature_implement_back_to_feature_button', $node->nid);
-
-  return $output;
-}
-
-/**
- * Implements Hook_form()
- * Handles adding of Properties & Synonyms to Stocks
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_edit_ALL_relationships_form($form_state, $node) {
-  $form = array();
-
-  $form['nid'] = array(
-    '#type' => 'hidden',
-    '#value' => $node->nid
-  );
-
-  $form['r_feature_uniquename'] = array(
-    '#type' => 'hidden',
-    '#value' => $node->uniquename
-  );
-
-  $i=0;
-
-  $feature = $node->feature;
-  $orelationships = tripal_feature_load_relationships($feature->feature_id, 'as_object');
-  $srelationships = tripal_feature_load_relationships($feature->feature_id, 'as_subject');
-  $relationships = array_merge($orelationships, $srelationships);
-
-  if (sizeof($relationships) != 0) {
-    foreach ($relationships as $r) {
-
-      $i++;
-      $form["num-$i"] = array(
-        '#type' => 'fieldset',
-        '#title' => t("Relationship %i", array('%i' => $i)),
-      );
-
-      $form["num-$i"]["id-$i"] = array(
-        '#type' => 'hidden',
-        '#value' => $r->stock_relationship_id
-      );
-
-      //Enter relationship specific fields
-      if ( !empty($r->subject_id) ) {
-        $default = $r->subject_uniquename;
-        $description = l($r->subject_name, 'node/' . $r->subject_nid);
-      }
-      else {
-        $default = $node->uniquename;
-        $description = "Current Feature";
-      }
-      $description .= " (" . $r->subject_type . ")";
-      $form["num-$i"]["subject_id-$i"] = array(
-        '#type' => 'textfield',
-        //'#title' => t('Subject'),
-        '#required'   => TRUE,
-        '#size' => 30,
-        '#default_value' => $default,
-        '#description' => t('%description', array('%description' => $description)),
-      );
-
-      $cv = tripal_cv_get_cv_by_name('relationship');
-      $type_options = tripal_cv_get_cvterm_options($cv->cv_id);
-      ksort($type_options);
-      $form["num-$i"]["type_id-$i"] = array(
-        '#type' => 'select',
-        //'#title' => t('Type of Relationship'),
-        '#options' => $type_options,
-        '#required' => TRUE,
-        '#default_value' => $r->relationship_type_id
-      );
-
-      if (!empty($r->object_id) ) {
-        $default = $r->object_uniquename;
-        $description = l($r->object_name, 'node/' . $r->object_nid);
-      }
-      else {
-        $default = $node->uniquename;
-        $description = 'Current Feature';
-      }
-      $description .= " (" . $r->object_type . ")";
-      $form["num-$i"]["object_id-$i"] = array(
-        '#type' => 'textfield',
-        //'#title' => t('Object'),
-        '#required'   => TRUE,
-        '#size' => 30,
-        '#default_value' => $default,
-        '#description' => $description
-      );
-
-      $form["num-$i"]["delete-$i"] = array(
-        '#type' => 'submit',
-        '#value' => t("Delete"),
-        '#name' => "delete-$i",
-      );
-
-    } //end of foreach relationship
-    $form['num_relationships'] = array(
-      '#type' => 'hidden',
-      '#value' => $i
-    );
-
-    $form["submit-edits"] = array(
-      '#type' => 'submit',
-      '#value' => t('Update All Relationships')
-    );
-  }
-  else {
-    $form["info"] = array(
-      '#type' => 'markup',
-      '#value' => t('No relationships currently exist for this feature.')
-    );
-  }
-
-  return $form;
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_edit_ALL_relationships_form_validate($form, &$form_state) {
-
-  // Only Require if Updating Relationships
-  if ($form_state['clicked_button']['#value'] == t('Update All Relationships') ) {
-
-    for ($i=1; $i<=$form_state['values']['num_relationships']; $i++) {
-
-      // check valid stock selected for subject
-      $criteria = array('unknown' => array('value' => $form_state['values']["subject_id-$i"],
-                                          'columns' => array('name', 'uniquename', 'accession', 'synonym') ));
-      $subject_results = get_chado_stocks($criteria, 'ANY', $_SESSION['organism']);
-      if (sizeof($subject_results) > 1) {
-        $links= array();
-        for ($j=0; $j<sizeof($subject_results); $j++) {
-        $links[] = l($j+1, "node/" . $subject_results[$j]->nid); }
-        $message = t("Too many features match '%subject'!  Please refine your input to
-          match ONLY ONE feature. <br /> To aid in this process, here are the features that
-          match your initial input: %features",
-          array('%subject' => $form_state['values']["subject_id-$i"],
-            '%features' => join(', ', $links)
-          )
-        );
-        form_set_error("subject_id-$i", $message);
-      }
-      elseif (sizeof($subject_results) < 1) {
-        form_set_error("subject_id-$i", t("There are no features matching your input. Please check your input for typos and/or lookup the <a href='!url'>here</a>", array('!url' => url('features'))));
-      }
-      elseif (sizeof($subject_results) == 1) {
-        $form_state['values']["subject_id-$i"] = $subject_results[0]->stock_id;
-      }
-
-      // check valid stock selected for object
-      $criteria = array('unknown' => array('value' => $form_state['values']["object_id-$i"],
-                                          'columns' => array('name', 'uniquename', 'accession', 'synonym') ));
-      $object_results = get_chado_stocks($criteria, 'ANY' , $_SESSION['organism']);
-      if (sizeof($object_results) > 1) {
-        $links= array();
-        for ($j=0; $j<sizeof($object_results); $j++) {
-        $links[] = l($j+1, "node/" . $object_results[$j]->nid); }
-        $message = "Too many stocks match '" . $form_state['values']["object_id-$i"] . "'! "
-                 . "Please refine your input to match ONLY ONE stock. <br />"
-                 . "To aid in this process, here are the stocks that match your initial input: "
-                 . join(', ', $links);
-        form_set_error("object_id-$i", $message);
-      }
-      elseif (sizeof($object_results) < 1) {
-        form_set_error("object_id-$i", t("There are no features matching your input. Please check your input for typos and/or lookup the <a href='!url'>here</a>", array('!url' => url('features'))));
-      }
-      elseif (sizeof($object_results) == 1) {
-        $form_state['values']["object_id-$i"] = $object_results[0]->stock_id;
-      }
-
-      // check valid type selected
-      if ($form_state['values']["type_id-$i"] == 0) {
-        form_set_error('type_id', 'Please select a type of relationship.');
-      }
-      else {
-        $tmp_obj = db_fetch_object(chado_query("SELECT count(*) as count FROM {cvterm} WHERE cvterm_id=%d" , $form_state['values']["type_id-$i"]));
-
-        if ($tmp_obj->count != 1) {
-          form_set_error("type_id-$i", 'The type you selected is not valid. Please choose another one.');
-        }
-      }
-
-      // check either subject or object is the current stock
-      if ( $subject_results[0]->nid != $form_state['values']['nid'] ) {
-        if ( $object_results[0]->nid != $form_state['values']['nid'] ) {
-          form_set_error("subject_id-$i", 'Either Subject or Object must be the current stock (' . $form_state['values']['r_stock_uniquename'] . ').');
-        }
-      }
-
-    } // end of for each relationship
-  } //end of if updating relationships
-
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_edit_ALL_relationships_form_submit($form, &$form_state) {
-
-  if ($form_state['clicked_button']['#value'] == t('Update Relationships') ) {
-    //Update all
-    for ($i=1; $i<=$form_state['values']['num_relationships']; $i++) {
-
-      //process stock textfields
-      tripal_feature_update_relationship(
-        $form_state['values']["id-$i"],
-        $form_state['values']["subject_id-$i"],
-        $form_state['values']["type_id-$i"],
-        $form_state['values']["object_id-$i"]
-      );
-    }
-    drupal_set_message(t("Updated all Relationships"));
-    drupal_goto('node/' . $form_state['values']['nid']);
-
-  }
-  elseif ( preg_match('/Delete #(\d+)/', $form_state['clicked_button']['#value'], $matches) ) {
-
-    $i = $matches[1];
-    tripal_feature_delete_relationship($form_state['values']["id-$i"]);
-    drupal_set_message(t("Deleted Relationship"));
-
-  }
-  elseif ($form_state['clicked_button']['#value'] == t('Back to Stock') ) {
-    drupal_goto('node/' . $form_state['values']['nid']);
-  }
-  else {
-    drupal_set_message(t("Unrecognized Button Pressed"), 'error');
-  }
-
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_update_relationship($stock_relationship_id, $subject_id, $cvterm_id, $object_id) {
-
-  $previous_db = db_set_active('chado');
-  db_query(
-    "UPDATE {stock_relationship} SET subject_id=%d, type_id=%d, object_id=%d WHERE stock_relationship_id=%d",
-    $subject_id,
-    $cvterm_id,
-    $object_id,
-    $stock_relationship_id
-  );
-  db_set_active($previous_db);
-
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_delete_relationship($stock_relationship_id) {
-
-  $previous_db = db_set_active('chado');
-  db_query(
-    "DELETE FROM {stock_relationship} WHERE stock_relationship_id=%d",
-    $stock_relationship_id
-  );
-  db_set_active($previous_db);
-
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function theme_tripal_feature_edit_ALL_relationships_form($form) {
-  $output = '';
-
-  $output .= '<br /><fieldset>';
-  $output .= '<legend>Edit Already Existing Relationships<span class="form-optional" title="This field is optional">(optional)</span></legend>';
-  $output .= '<p>Each relationship for this stock is listed below, one per line. The textboxes indicating ' .
-             'the subject and object of the relationship can contain the uniquename, name, database ' .
-             'reference or synonym of a stock of the same organism.</p>';
-  $output .= '<table>';
-  $output .= '<tr><th>#</th><th>Subject</th><th>Type</th><th>Object</th><th></th></tr>';
-
-  for ($i=1; $i <= $form['num_relationships']['#value']; $i++) {
-    $output .= '<tr><td>' . drupal_render($form["num-$i"]) . '</td>' .
-              '<td>' . drupal_render($form["subject_id-$i"]) . '</td>' .
-              '<td>' . drupal_render($form["type_id-$i"]) . '</td>' .
-                '<td>' . drupal_render($form["object_id-$i"]) . '</td>' .
-              '<td>' . drupal_render($form["submit-$i"]) . '</td></tr>';
-  }
-
-  $output .= '</table><br />';
-  $output .= drupal_render($form);
-  $output .= '</fieldset>';
-
-  return $output;
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_list_relationships_for_node($feature_name, $subject_relationships, $object_relationships) {
-
-  if (!empty($subject_relationships) OR !empty($object_relationships) ) {
-    $output = '<table>';
-    $output .= '<tr><th>Subject</th><th>Relationship Type</th><th>Object</th></tr>';
-
-    if (!empty($subject_relationships) ) {
-      foreach ($subject_relationships as $s) {
-        $output .= '<tr><td>' . $s->subject_name . '</td><td>' . $s->relationship_type . '</td><td>' . $feature_name . '</td></tr>';
-      }
-    }
-
-    if (!empty($object_relationships) ) {
-      foreach ($object_relationships as $o) {
-        $output .= '<tr><td>' . $feature_name . '</td><td>' . $o->relationship_type . '</td><td>' . $o->object_name . '</td></tr>';
-      } // end of foreach property
-    }
-
-    $output .= '</table>';
-  }
-  else {
-    $output = 'No Relationships For the Current Feature';
-  }
-
-  return $output;
-
-}

tripal_feature/includes/tripal_feature-secondary_tables.inc

@@ -1,233 +0,0 @@
-<?php
-/**
- * @file
- * @todo Add file header description
- */
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_implement_back_to_feature_button($form_state, $nid) {
-  $form = array();
-
-  $form['nid'] = array(
-    '#type' => 'hidden',
-    '#value' => $nid
-  );
-
-  $form["submit-back"] = array(
-    '#type' => 'submit',
-    '#value' => t('Back to Stock')
-  );
-
-  return $form;
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_implement_back_to_feature_button_submit($form, $form_state) {
-  drupal_goto('node/' . $form_state['values']['nid']);
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_implement_add_chado_properties_progress($current) {
-
-    $value = '<div class="form_progress"><div class="form_progress-text">';
-
-    if ($current == 'main') {
-    $value .= '<span id="form-step-current">Create Basic Feature</span>'; }
-    else { $value .= '<span id="form-step">Create Basic Stock</span>'; }
-
-    $value .= '<span id="form-segway">  >>  </span>';
-
-    if ($current == 'properties') {
-    $value .= '<span id="form-step-current">Add Synonyms & Properties</span>'; }
-    else { $value .= '<span id="form-step">Add Synonyms & Properties</span>'; }
-
-    $value .= '<span id="form-segway">  >>  </span>';
-
-    if ($current == 'db_references') {
-    $value .= '<span id="form-step-current">Add Database References</span>'; }
-    else { $value .= '<span id="form-step">Add Database References</span>'; }
-
-    $value .= '<span id="form-segway">  >>  </span>';
-
-    if ($current == 'relationships') {
-    $value .= '<span id="form-step-current">Add Relationships</span>'; }
-    else { $value .= '<span id="form-step">Add Relationships</span>'; }
-
-    $value .= '</div></div>';
-
-    return $value;
-
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_implement_add_chado_properties_navigate($form_state, $step, $nid) {
-  $form = array();
-
-  $form['current_step'] = array(
-    '#type' => 'hidden',
-    '#value' => $step
-  );
-
-  // Use this field to set all the steps and the path to each form
-  // where each step is of the form name;path and each step is separated by ::
-  $steps =array(
-    'properties' => 'node/%node/properties',
-    'db_references' => 'node/%node/db_references',
-    'relationships' => 'node/%node/relationships'
-  );
-  $steps_value = array();
-  foreach ($steps as $k => $v) {
-  $steps_value[] = $k . ';' . $v; }
-  $form['steps'] = array(
-    '#type' => 'hidden',
-    '#value' => implode('::', $steps_value)
-  );
-
-  $form['first_step'] = array(
-    '#type' => 'hidden',
-    '#value' => 'properties'
-  );
-
-  $form['last_step'] = array(
-    '#type' => 'hidden',
-    '#value' => 'relationships'
-  );
-
-  $form['nid'] = array(
-    '#type' => 'hidden',
-    '#value' => $nid
-  );
-
-  if ($step != $form['first_step']['#value']) {
-    $form['submit-prev'] = array(
-      '#type' => 'submit',
-      '#value' => t('Previous Step')
-    );
-  }
-
-  if ($step != $form['last_step']['#value']) {
-    $form['submit-next'] = array(
-      '#type' => 'submit',
-      '#value' => t('Next Step')
-    );
-  }
-
-  if ($step == $form['last_step']['#value']) {
-    $form['submit-finish'] = array(
-      '#type' => 'submit',
-      '#value' => t('Finish')
-    );
-  }
-
-  return $form;
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_implement_add_chado_properties_navigate_submit($form, $form_state) {
-
-  $raw_steps = preg_split('/::/', $form_state['values']['steps']);
-
-  $steps = array();
-  $current_index = 'EMPTY';
-  $i=0;
-
-  foreach ($raw_steps as $raw_step) {
-    $step = preg_split('/;/', $raw_step);
-    $steps[$i] = $step;
-
-    if ($step[0] == $form_state['values']['current_step']) {
-      $current_index = $i;
-    }
-
-    $i++;
-  }
-  $num_steps = $i;
-
-  if (strcmp($current_index, 'EMPTY') == 0) {
-    // No Matching Step
-    drupal_set_message(t('Could not determine next step - %currentstep, please contact the administrator', array('%currentstep' => $form_state['values']['current_step'])), 'error');
-  }
-  elseif ($current_index == 0) {
-    $next_goto = $steps[$current_index+1][1];
-  }
-  elseif ($current_index == ($num_steps-1)) {
-    $prev_goto = $steps[$current_index-1][1];
-    $next_goto = 'node/%node';
-  }
-  else {
-    $prev_goto = $steps[$current_index-1][1];
-    $next_goto = $steps[$current_index+1][1];
-  }
-
-  if ($form_state['clicked_button']['#value'] == t('Previous Step') ) {
-    //replace %node
-    $prev_goto = preg_replace('/%node/', $form_state['values']['nid'], $prev_goto);
-    $_REQUEST['destination'] = $prev_goto;
-  }
-  elseif ($form_state['clicked_button']['#value'] == t('Next Step') ) {
-    $next_goto = preg_replace('/%node/', $form_state['values']['nid'], $next_goto);
-    $_REQUEST['destination'] = $next_goto;
-  }
-  elseif ($form_state['clicked_button']['#value'] == t('Finish') ) {
-    $next_goto = preg_replace('/%node/', $form_state['values']['nid'], $next_goto);
-    $_REQUEST['destination'] = $next_goto;
-  }
-
-}
-
-/**
- * Implements Hook_form()
- * Handles setting the is_obsolete property of stocks
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_is_obsolete_form($node, $stock_id) {
-
-  $form['make_obsolete'] = array(
-    '#type' => 'submit',
-    '#value' => t('Mark Stock as Obsolete')
-  );
-
-  $form['make_obsolete_stock_id'] = array(
-    '#type' => 'value',
-    '#value' => $stock_id,
-    '#required' => TRUE
-  );
-
-  return $form;
-}
-
-/**
- *
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_is_obsolete_form_submit($form, &$form_state) {
-
-  chado_query(
-    "UPDATE {stock} SET is_obsolete='t' WHERE stock_id=%d",
-    $form_state['values']['make_obsolete_stock_id']
-  );
-
-}
-

tripal_feature/includes/tripal_feature.admin.inc

@@ -420,14 +420,16 @@ function tripal_features_set_taxonomy($max_sync = 0, $job_id = NULL) {
 
   // iterate through all drupal feature nodes and set the taxonomy
   $results = db_query("SELECT * FROM {chado_feature}");
-  $nsql =  "SELECT * FROM {node} " .
-          "WHERE nid = %d";
+  $nsql =  "
+    SELECT * FROM {node} 
+    WHERE nid = :nid
+  ";
   $i = 0;
 
   // load into ids array
   $count = 0;
   $chado_features = array();
-  while ($chado_feature = db_fetch_object($results)) {
+  while ($chado_feature = $results->fetchObject()) {
     $chado_features[$count] = $chado_feature;
     $count++;
   }
@@ -441,7 +443,7 @@ function tripal_features_set_taxonomy($max_sync = 0, $job_id = NULL) {
     tripal_job_set_progress($job_id, intval(($i/$count)*100));
   }
   print "$i of $count: ";
-  $node = db_fetch_object(db_query($nsql, $chado_feature->nid));
+  $node = db_query($nsql, array(':nid' => $chado_feature->nid))->fetchObject();
   tripal_feature_set_taxonomy($node, $chado_feature->feature_id);
 
   $i++;
@@ -500,12 +502,14 @@ function tripal_feature_set_taxonomy($node, $feature_id) {
   }
 
   // get the cvterm and the organism for this feature
-  $sql = "SELECT CVT.name AS cvname, O.genus, O.species " .
-        "FROM {CVTerm} CVT " .
-        "  INNER JOIN {Feature} F on F.type_id = CVT.cvterm_id " .
-        "  INNER JOIN {Organism} O ON F.organism_id = O.organism_id " .
-        "WHERE F.feature_id = $feature_id";
-  $feature = db_fetch_object(chado_query($sql));
+  $sql = "
+    SELECT CVT.name AS cvname, O.genus, O.species 
+    FROM {CVTerm} CVT 
+      INNER JOIN {Feature} F on F.type_id = CVT.cvterm_id 
+      INNER JOIN {Organism} O ON F.organism_id = O.organism_id 
+    WHERE F.feature_id = :feature_id 
+  ";
+  $feature = chado_query($sql, array(':feature_id' => $feature_id))->fetchObject();
 
   // Set the feature type for this feature
   if ($do_ft && $ft_vid) {
@@ -518,11 +522,13 @@ function tripal_feature_set_taxonomy($node, $feature_id) {
 
   // get the library that this feature may belong to and add it as taxonomy
   if ($do_lb && $lb_vid) {
-    $sql = "SELECT L.name " .
-           "FROM {Library} L " .
-           "  INNER JOIN {Library_feature} LF ON LF.library_id = L.library_id " .
-           "WHERE LF.feature_id = %d ";
-    $library = db_fetch_object(chado_query($sql, $feature_id));
+    $sql = "
+      SELECT L.name 
+      FROM {Library} L 
+        INNER JOIN {Library_feature} LF ON LF.library_id = L.library_id 
+      WHERE LF.feature_id = :feature_id 
+    ";
+    $library = chado_query($sql, array(':feature_id' => $feature_id))->fetchObject();
     $tags["$lb_vid"] = "$library->name";
   }
 
@@ -534,13 +540,15 @@ function tripal_feature_set_taxonomy($node, $feature_id) {
   // get the analysis that this feature may belong to and add it as taxonomy
   // We'll add each one individually since there may be more than one analysis
   if ($do_an && $an_vid) {
-    $sql = "SELECT A.name " .
-           "FROM {Analysis} A " .
-           "  INNER JOIN {Analysisfeature} AF ON AF.analysis_id = A.analysis_id " .
-           "WHERE AF.feature_id = $feature_id ";
-    $results = chado_query($sql);
+    $sql = "
+      SELECT A.name 
+      FROM {Analysis} A 
+        INNER JOIN {analysisfeature} AF ON AF.analysis_id = A.analysis_id 
+      WHERE AF.feature_id = :feature_id 
+    ";
+    $results = chado_query($sql, array(':feature_id' => $feature_id));
     $analysis_terms = array();
-    while ($analysis=db_fetch_object($results)) {
+    while ($analysis = $results->fetchObject()) {
       $tags2["$an_vid"] = "$analysis->name";
       $terms['tags'] = $tags2;
       taxonomy_node_save($node, $terms);

tripal_feature/includes/tripal_feature.sync_features.inc

@@ -134,7 +134,7 @@ function tripal_feature_set_urls($na = NULL, $job = NULL) {
   
   // get the number of records we need to set URLs for
   $csql = "SELECT count(*) FROM {chado_feature}";
-  $num_nodes = db_result(db_query($csql));
+  $num_nodes = db_query($csql)->fetchField();
     
   // calculate the interval at which we will print an update on the screen
   $num_set = 0;
@@ -164,7 +164,7 @@ function tripal_feature_set_urls($na = NULL, $job = NULL) {
   // get the list of features that have been synced
   $sql = "SELECT * FROM {chado_feature}";
   $nodes = db_query($sql);  
-  while ($node = db_fetch_object($nodes)) {
+  while ($node = $nodes->fetchObject()) {
    
     // get the URL alias
     $src = "node/$node->nid";
@@ -183,7 +183,7 @@ function tripal_feature_set_urls($na = NULL, $job = NULL) {
     }
     
     // remove any previous alias and then add the new one
-    $success = db_query("EXECUTE del_url_alias_by_src('%s')", $src);    
+    $success = db_query("EXECUTE del_url_alias_by_src(:src)", array(':src' => $src));    
     if (!$success) {
       db_query('DEALLOCATE "del_url_alias_by_src"');
       db_query('DEALLOCATE "ins_url_alias_nisrds"');
@@ -191,7 +191,7 @@ function tripal_feature_set_urls($na = NULL, $job = NULL) {
       watchdog('trp-seturl', "Failed Removing URL Alias: %src", array('%src' => $src), WATCHDOG_ERROR);
       return;
     }
-    $success = db_query("EXECUTE ins_url_alias_nisrds('%s', '%s')", $src, $dst);
+    $success = db_query("EXECUTE ins_url_alias_nisrds(:src, :dst)", array(':src' => $src, ':dst' => $dst));
     if (!$success) {
       db_query('DEALLOCATE "del_url_alias_by_src"');
       db_query('DEALLOCATE "ins_url_alias_nisrds"');
@@ -315,6 +315,7 @@ function tripal_feature_sync_features($max_sync = 0, $organism_id = NULL,
 
   print "Looking for features of type: $allowed_types\n";
 
+  # TODO: fix the hard-coding of variables in this SQL statement
   $so_terms = split(' ', $allowed_types);
   $where_cvt = "";
   foreach ($so_terms as $term) {
@@ -341,12 +342,13 @@ function tripal_feature_sync_features($max_sync = 0, $organism_id = NULL,
   $where_org = drupal_substr($where_org, 0, drupal_strlen($where_org)-3);  # strip trailing 'OR'
 
   // use this SQL statement to get the features that we're going to upload
-  $sql = "SELECT feature_id " .
-        "FROM {FEATURE} F " .
-        "  INNER JOIN {Cvterm} CVT ON F.type_id = CVT.cvterm_id " .
-        "  INNER JOIN {CV} on CV.cv_id = CVT.cv_id " .
-        "WHERE ($where_cvt) AND ($where_org) AND CV.name = 'sequence' " .
-        "ORDER BY feature_id";
+  $sql = "
+    SELECT feature_id 
+    FROM {FEATURE} F 
+      INNER JOIN {Cvterm} CVT ON F.type_id = CVT.cvterm_id 
+      INNER JOIN {CV} on CV.cv_id = CVT.cv_id 
+    WHERE ($where_cvt) AND ($where_org) AND CV.name = 'sequence' 
+    ORDER BY feature_id";
 
   // get the list of features
   $results = chado_query($sql);
@@ -354,7 +356,7 @@ function tripal_feature_sync_features($max_sync = 0, $organism_id = NULL,
   // load into ids array
   $count = 0;
   $ids = array();
-  while ($id = db_fetch_object($results)) {
+  while ($id = $results->fetchObject()) {
     $ids[$count] = $id->feature_id;
     $count++;
   }
@@ -365,7 +367,7 @@ function tripal_feature_sync_features($max_sync = 0, $organism_id = NULL,
   // pre-create the SQL statement that will be used to check
   // if a feature has already been synced.  We skip features
   // that have been synced
-  $sql = "SELECT * FROM {chado_feature} WHERE feature_id = %d";
+  $sql = "SELECT * FROM {chado_feature} WHERE feature_id = :feature_id";
 
   // Iterate through features that need to be synced
   $interval = intval($count * 0.01);
@@ -384,7 +386,7 @@ function tripal_feature_sync_features($max_sync = 0, $organism_id = NULL,
     if ($max_sync and $i == $max_sync) {
       return '';
     }
-    if (!db_fetch_object(db_query($sql, $feature_id))) {
+    if (!db_query($sql, array(':feature_id' => $feature_id))->fetchObject()) {
 
       # parsing all the features can cause memory overruns
       # we are not sure why PHP does not clean up the memory as it goes
@@ -422,24 +424,28 @@ function tripal_feature_sync_feature($feature_id) {
   }
 
   // get information about this feature
-  $fsql = "SELECT F.feature_id, F.name, F.uniquename,O.genus, " .
-         "    O.species,CVT.name as cvname,F.residues,F.organism_id " .
-         "FROM {FEATURE} F " .
-         "  INNER JOIN {Cvterm} CVT ON F.type_id = CVT.cvterm_id " .
-         "  INNER JOIN {Organism} O ON F.organism_id = O.organism_ID " .
-         "WHERE F.feature_id = %d";
-  $feature = db_fetch_object(chado_query($fsql, $feature_id));
+  $fsql = "
+    SELECT F.feature_id, F.name, F.uniquename,O.genus, 
+      O.species,CVT.name as cvname,F.residues,F.organism_id 
+    FROM {FEATURE} F 
+      INNER JOIN {Cvterm} CVT ON F.type_id = CVT.cvterm_id 
+      INNER JOIN {Organism} O ON F.organism_id = O.organism_ID 
+    WHERE F.feature_id = :feature_id
+  ";
+  $feature = chado_query($fsql, array(':feature_id' => $feature_id))->fetchObject();
 
   // get the synonyms for this feature
-  $synsql = "SELECT S.name " .
-            "FROM {feature_synonym} FS " .
-            "  INNER JOIN {synonym} S on FS.synonym_id = S.synonym_id " .
-            "WHERE FS.feature_id = %d";
-  $synonyms = chado_query($synsql, $feature_id);
+  $synsql = "
+    SELECT S.name 
+    FROM {feature_synonym} FS 
+      INNER JOIN {synonym} S on FS.synonym_id = S.synonym_id 
+    WHERE FS.feature_id = :feature_id
+  ";
+  $synonyms = chado_query($synsql, array(':feature_id' => $feature_id));
 
   // now add these synonyms to the feature object as a single string
   $synstring = '';
-  while ($synonym = db_fetch_object($synonyms)) {
+  while ($synonym = $synonyms->fetchObject()) {
     $synstring .= "$synonym->name\n";
   }
   $feature->synonyms = $synstring;
@@ -448,14 +454,12 @@ function tripal_feature_sync_feature($feature_id) {
   // but without a corresponding entry in the chado_feature table if so then we want to
   // clean up that node.  (If a node is found we don't know if it belongs to our feature or
   // not since features can have the same name/title.)
-  $tsql =  "SELECT * FROM {node} N " .
-           "WHERE title = '%s'";
-  $cnsql = "SELECT * FROM {chado_feature} " .
-           "WHERE nid = %d";
-  $nodes = db_query($tsql, $feature->name);
+  $tsql =  "SELECT * FROM {node} N WHERE title = :title";
+  $cnsql = "SELECT * FROM {chado_feature} WHERE nid = :nid";
+  $nodes = db_query($tsql, array(':title' => $feature->name));
   // cycle through all nodes that may have this title
-  while ($node = db_fetch_object($nodes)) {
-    $feature_nid = db_fetch_object(db_query($cnsql, $node->nid));
+  while ($node = $nodes->fetchObject()) {
+    $feature_nid = db_query($cnsql, array(':nid' => $node->nid))->fetchObject();
     if (!$feature_nid) {
       drupal_set_message(t("%feature_id: A node is present but the chado_feature entry is missing... correcting", array('%feature_id' => $feature_id)));
       node_delete($node->nid);
@@ -464,21 +468,19 @@ function tripal_feature_sync_feature($feature_id) {
 
   // check if this feature already exists in the chado_feature table.
   // if we have a chado feature, we want to check to see if we have a node
-  $cfsql = "SELECT * FROM {chado_feature} " .
-           "WHERE feature_id = %d";
+  $cfsql = "SELECT * FROM {chado_feature} WHERE feature_id = :feature_id";
   // @coder-ignore: don't need to use db_rewrite_sql() since need all nodes regardless of access control
-  $nsql =  "SELECT * FROM {node} N " .
-           "WHERE nid = %d";
-  $chado_feature = db_fetch_object(db_query($cfsql, $feature->feature_id));
+  $nsql =  "SELECT * FROM {node} N WHERE nid = :nid";
+  $chado_feature = db_query($cfsql, array(':feature_id' => $feature->feature_id))->fetchObject();
   if ($chado_feature) {
     drupal_set_message(t("%feature_id: A chado_feature entry exists", array('%feature_id' => $feature_id)));
-    $node = db_fetch_object(db_query($nsql, $chado_feature->nid));
+    $node = db_query($nsql, array(':nid' => $chado_feature->nid))->fetchObject();
     if (!$node) {
       // if we have a chado_feature but not a node then we have a problem and
       // need to cleanup
       drupal_set_message(t("%feature_id: The node is missing, but has a chado_feature entry... correcting", array('%feature_id' => $feature_id)));
-      $df_sql = "DELETE FROM {chado_feature} WHERE feature_id = %d";
-      db_query($df_sql, $feature_id);
+      $df_sql = "DELETE FROM {chado_feature} WHERE feature_id = :feature_id";
+      db_query($df_sql, array(':feature_id' => $feature_id));
     }
     else {
       drupal_set_message(t("%feature_id: A corresponding node exists", array('%feature_id' => $feature_id)));
@@ -497,8 +499,8 @@ function tripal_feature_sync_feature($feature_id) {
   // will call the hook_submit function which
   if ($create_node) {
     // get the organism for this feature
-    $sql = "SELECT * FROM {organism} WHERE organism_id = %d";
-    $organism = db_fetch_object(chado_query($sql, $feature->organism_id));
+    $sql = "SELECT * FROM {organism} WHERE organism_id = :organism_id";
+    $organism = chado_query($sql, array(':organism_id' => $feature->organism_id))->fetchObject();
 
     drupal_set_message(t("%feature_id: Creating node $feature->name", array('%feature_id' => $feature_id)));
     $new_node = new stdClass();

tripal_feature/tripal_feature.install

@@ -4,6 +4,24 @@
  * @todo Add file header description
  */
 
+/**
+ * Implementation of hook_requirements().
+ */
+function tripal_feature_requirements($phase) {
+  $requirements = array();
+  if ($phase == 'install') {
+    // make sure chado is installed
+    if (!tripal_core_is_chado_installed()) {
+      $requirements ['tripal_feature'] = array(
+          'title' => "tripal_feature",
+          'value' => "ERROR: Chado most be installed before this module can be enabled",
+          'severity' => REQUIREMENT_ERROR,
+      );
+    }
+  }
+  return $requirements;
+}
+
 /**
  * Implementation of hook_install().
  *
@@ -15,136 +33,134 @@ function tripal_feature_install() {
 
   // add the materialized view
   tripal_feature_add_organism_count_mview();
-
-}
-/**
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_add_organism_count_mview() {
-  $view_name = 'organism_feature_count';
-
-  // Drop the MView table if it exists
-  $mview_id = tripal_mviews_get_mview_id($view_name);
-  if ($mview_id) {
-    tripal_mviews_action("delete", $mview_id);
-  }
-
-  // Create the MView
-  tripal_add_mview(
-    // view name
-    $view_name,
-    // tripal module name
-    'tripal_feature',
-    // table name
-    $view_name,
-    // table schema definition
-    'organism_id integer, genus character varying(255), ' .
-    '  species character varying(255), ' .
-    '  common_name character varying(255), ' .
-    '  num_features integer, cvterm_id integer, ' .
-    '  feature_type character varying(255)',
-    // columns for indexing
-    'organism_id,cvterm_id,feature_type',
-    // SQL statement to populate the view
-    'SELECT O.organism_id, O.genus, O.species, O.common_name,
-        count(F.feature_id) as num_features,
-        CVT.cvterm_id, CVT.name as feature_type
-     FROM Organism O
-        INNER JOIN Feature F           ON O.Organism_id = F.organism_id
-        INNER JOIN Cvterm CVT          ON F.type_id = CVT.cvterm_id
-     GROUP BY O.Organism_id, O.genus, O.species, O.common_name,
-        CVT.cvterm_id, CVT.name',
-    // special index
-    ''
-  );
-
+  
   // add a job to the job queue so this view gets updated automatically next
   // time the job facility is run
-  $mview_id = tripal_mviews_get_mview_id($view_name);
-  if ($mview_id) {
+  if ($mview_id = tripal_mviews_get_mview_id('organism_feature_count')) {
     tripal_mviews_action('update', $mview_id);
   }
 }
-/**
- * Implementation of hook_schema().
- *
- * @ingroup tripal_feature
- */
-function tripal_feature_schema() {
-  $schema = tripal_feature_get_schemas();
-  return $schema;
-}
+
 /**
  * Implementation of hook_uninstall().
  *
  * @ingroup tripal_feature
  */
 function tripal_feature_uninstall() {
-
   // Drop the MView table if it exists
-  $mview_id = tripal_mviews_get_mview_id('organism_feature_count');
-  if ($mview_id) {
+  if ($mview_id = tripal_mviews_get_mview_id('organism_feature_count')) {
     tripal_mviews_action("delete", $mview_id);
   }
-
-  // Get the list of nodes to remove
-  $sql_feature_id = "SELECT nid, vid " .
-               "FROM {node} " .
-               "WHERE type='chado_feature'";
-  $result = db_query($sql_feature_id);
-  while ($node = db_fetch_object($result)) {
-    node_delete($node->nid);
-  }
 }
-
+ 
 /**
- * This function simply defines all tables needed for the module to work
- * correctly.  By putting the table definitions in a separate function we
- * can easily provide the entire list for hook_install or individual
- * tables for an update.
+ * Implementation of hook_schema().
  *
  * @ingroup tripal_feature
  */
-function tripal_feature_get_schemas($table = NULL) {
-  $schema = array();
-
-
-  if (!$table or strcmp($table, 'chado_feature')==0) {
-    $schema['chado_feature'] = array(
-      'fields' => array(
-        'vid' => array('type' => 'int', 'unsigned' => TRUE, 'not null' => TRUE, 'default' => 0),
-        'nid' => array('type' => 'int', 'unsigned' => TRUE, 'not null' => TRUE, 'default' => 0),
-        'feature_id' => array('type' => 'int', 'not null' => TRUE, 'default' => 0),
-        'sync_date' => array('type' => 'int', 'not null' => FALSE, 'description' => 'UNIX integer sync date/time'),
-      ),
-      'indexes' => array(
-        'feature_id' => array('feature_id')
+function tripal_feature_schema() {
+  
+  $schema['chado_feature'] = array(
+    'fields' => array(
+      'vid' => array(
+        'type' => 'int', 
+        'unsigned' => TRUE, 
+        'not null' => TRUE, 
+        'default' => 0
+       ),
+      'nid' => array(
+        'type' => 'int', 
+        'unsigned' => TRUE, 
+        'not null' => TRUE, 
+        'default' => 0
+       ),
+      'feature_id' => array(
+        'type' => 'int', 
+        'not null' => TRUE, 
+        'default' => 0
       ),
-      'unique keys' => array(
-        'nid_vid' => array('nid', 'vid'),
-        'vid' => array('vid')
+      'sync_date' => array(
+        'type' => 'int', 
+        'not null' => FALSE, 
+        'description' => 'UNIX integer sync date/time'
       ),
-      'primary key' => array('nid'),
-    );
-  }
+    ),
+    'indexes' => array(
+      'chado_feature_idx1' => array('feature_id')
+    ),
+    'unique keys' => array(
+      'chado_feature_uq1' => array('nid', 'vid'),
+      'chado_feature_uq2' => array('vid')
+    ),
+    'primary key' => array('nid'),
+  );
+  
   return $schema;
 };
 
 /**
- * Implementation of hook_requirements(). 
+ *
+ * @ingroup tripal_feature
  */
-function tripal_feature_requirements($phase) {
-  $requirements = array();
-  if ($phase == 'install') {
-    // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
-      $requirements ['tripal_feature'] = array(
-            'title' => "tripal_feature",
-            'value' => "ERROR: Chado most be installed before this module can be enabled",
-            'severity' => REQUIREMENT_ERROR,
-      );
-    }
-  }
-  return $requirements;
+function tripal_feature_add_organism_count_mview() {
+  $view_name = 'organism_feature_count';
+  $comment = 'Stores the type and number of features per organism';
+
+  $schema = array(
+    'description' => $comment,
+    'table' => $view_name,
+    'fields' => array(
+      'organism_id' => array(
+        'type' => 'int',
+        'not null' => TRUE,
+      ),
+      'genus' => array(
+        'type' => 'varchar',
+        'length' => '255',
+        'not null' => TRUE,
+      ),
+      'species' => array(
+        'type' => 'varchar',
+        'length' => '255',
+        'not null' => TRUE,
+      ),
+      'common_name' => array(
+        'type' => 'varchar',
+        'length' => '255',
+        'not null' => FALSE,
+      ),
+      'num_features' => array(
+        'type' => 'int',
+        'not null' => TRUE,
+      ),
+      'cvterm_id' => array(
+        'type' => 'int',
+        'not null' => TRUE,
+      ),
+      'feature_type' => array(
+        'type' => 'varchar',
+        'length' => '255',
+        'not null' => TRUE,
+      ),
+    ),      
+    'indexes' => array(
+      'organism_feature_count_idx1' => array('organism_id'),
+      'organism_feature_count_idx2' => array('cvterm_id'),
+      'organism_feature_count_idx3' => array('feature_type'),
+    ),
+  );
+
+  $sql = "
+    SELECT
+        O.organism_id, O.genus, O.species, O.common_name,
+        count(F.feature_id) as num_features,
+        CVT.cvterm_id, CVT.name as feature_type
+     FROM organism O
+        INNER JOIN feature F  ON O.Organism_id = F.organism_id
+        INNER JOIN cvterm CVT ON F.type_id     = CVT.cvterm_id
+     GROUP BY
+        O.Organism_id, O.genus, O.species, O.common_name, CVT.cvterm_id, CVT.name
+  ";
+
+  tripal_add_mview($view_name, 'tripal_feature', $schema, $sql, $comment);
 }

tripal_feature/tripal_feature.module

@@ -13,20 +13,13 @@
  * @}
  */
 
+require_once "api/tripal_feature.api.inc";
 require_once "includes/tripal_feature.admin.inc";
 require_once "includes/tripal_feature.sync_features.inc";
 require_once "includes/fasta_loader.inc";
 require_once "includes/gff_loader.inc";
 require_once "includes/seq_extract.inc";
-
-require_once "api/tripal_feature.api.inc";
-
 require_once "includes/tripal_feature-delete.inc";
-//require_once "includes/tripal_feature-secondary_tables.inc";
-//require_once "includes/tripal_feature-properties.inc";
-//require_once "includes/tripal_feature-relationships.inc";
-//require_once "includes/tripal_feature-db_references.inc";
-
 
 /**
  *
@@ -524,14 +517,19 @@ function chado_feature_insert($node) {
 
   // make sure the entry for this feature doesn't already exist in the chado_feature table
   // if it doesn't exist then we want to add it.
-  $node_check_sql = "SELECT * FROM {chado_feature} " .
-                    "WHERE feature_id = '%s'";
-  $node_check = db_fetch_object(db_query($node_check_sql, $feature[0]->feature_id));
+  $node_check_sql = "
+    SELECT * FROM {chado_feature} 
+    WHERE feature_id = :feature_id
+  ";
+  $node_check = db_query($node_check_sql, array(':feature_id' => $feature[0]->feature_id))->fetchObject();
   if (!$node_check) {
     // next add the item to the drupal table
-    $sql = "INSERT INTO {chado_feature} (nid, vid, feature_id, sync_date) " .
-           "VALUES (%d, %d, %d, " . REQUEST_TIME . ")";
-      db_query($sql, $node->nid, $node->vid, $feature[0]->feature_id);
+    $sql = "
+      INSERT INTO {chado_feature} (nid, vid, feature_id, sync_date) 
+      VALUES (:nid, :vid, :feature_id, :time)
+    ";
+    db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid, 
+      ':feature_id' => $feature[0]->feature_id, ':time' => REQUEST_TIME));
   }
 }
 
@@ -610,24 +608,18 @@ function chado_feature_delete($node) {
   }
 
   // remove the drupal content
-  $sql_del = "DELETE FROM {chado_feature} " .
-             "WHERE nid = %d " .
-             "AND vid = %d";
-  db_query($sql_del, $node->nid, $node->vid);
-  $sql_del = "DELETE FROM {node} " .
-             "WHERE nid = %d " .
-             "AND vid = %d";
-  db_query($sql_del, $node->nid, $node->vid);
-  $sql_del = "DELETE FROM {node_revision} " .
-             "WHERE nid = %d " .
-             "AND vid = %d";
-  db_query($sql_del, $node->nid, $node->vid);
+  $sql_del = "DELETE FROM {chado_feature} WHERE nid = :nid AND vid = :vid";
+  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
+  $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
+  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
+  $sql_del = "DELETE FROM {node_revision} WHERE nid = :nid AND vid = :vid";
+  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
 
 
   // Remove data from feature tables of chado database.  This will
   // cause a cascade delete and remove all data in referencing tables
   // for this feature
-  chado_query("DELETE FROM {feature} WHERE feature_id = %d", $feature_id);
+  chado_query("DELETE FROM {feature} WHERE feature_id = :feature_id", array(':feature_id' => $feature_id));
 
   drupal_set_message(t("The feature and all associated data were removed from") .
   "chado");
@@ -648,8 +640,8 @@ function chado_feature_add_synonyms($synonyms, $feature_id) {
 
 
   // remove any old synonyms
-  $feature_syn_dsql = "DELETE FROM {feature_synonym} WHERE feature_id = %d";
-  if (!chado_query($feature_syn_dsql, $feature_id)) {
+  $feature_syn_dsql = "DELETE FROM {feature_synonym} WHERE feature_id = :feature_id";
+  if (!chado_query($feature_syn_dsql, array(':feature_id' => $feature_id))) {
     $error .= "Could not remove synonyms from feature. ";
   }
 
@@ -666,29 +658,32 @@ function chado_feature_add_synonyms($synonyms, $feature_id) {
     // check to see if we have this accession number already in the database
     // if so then don't add it again. it messes up drupal if the insert fails.
     // It is possible for the accession number to be present and not the feature
-    $synonym_sql = "SELECT synonym_id FROM {synonym} " .
-                   "WHERE name = '%s'";
-    $synonym = db_fetch_object(chado_query($synonym_sql, $syn));
+    $synonym_sql = "SELECT synonym_id FROM {synonym} WHERE name = :name";
+    $synonym = chado_query($synonym_sql, array(':name' => $syn))->fetchObject();
     if (!$synonym) {
-      $synonym_isql = "INSERT INTO {synonym} (name,synonym_sgml,type_id) " .
-                      "VALUES ('%s','%s', " .
-                      "   (SELECT cvterm_id " .
-                      "    FROM {CVTerm} CVT " .
-                      "    INNER JOIN CV ON CVT.cv_id = CV.cv_id " .
-                      "    WHERE CV.name = 'feature_property' and CVT.name = 'synonym'))";
-      if (!chado_query($synonym_isql, $syn, $syn)) {
+      $synonym_isql = "
+        INSERT INTO {synonym} (name, synonym_sgml, type_id) 
+        VALUES (:name, :synonym_sgml, 
+          (SELECT cvterm_id 
+           FROM {CVTerm} CVT 
+             INNER JOIN CV ON CVT.cv_id = CV.cv_id 
+           WHERE CV.name = 'feature_property' and CVT.name = 'synonym')
+          )
+      ";
+      if (!chado_query($synonym_isql, array(':name' => $syn, ':synonym_sgml' => $syn))) {
         $error .= "Could not add synonym. ";
       }
       // now get the synonym we just added
-      $synonym_sql = "SELECT synonym_id FROM {synonym} " .
-                     "WHERE name = '%s'";
-      $synonym = db_fetch_object(chado_query($synonym_sql, $syn));
+      $synonym_sql = "SELECT synonym_id FROM {synonym} WHERE name = :name";
+      $synonym = chado_query($synonym_sql, array(':name' => $syn))->fetchObject();
     }
 
     // now add in our new sysnonym
-    $feature_syn_isql = "INSERT INTO {feature_synonym} (synonym_id,feature_id,pub_id) " .
-                        "VALUES (%d,%d,1)";
-    if (!chado_query($feature_syn_isql, $synonym->synonym_id, $feature_id)) {
+    $feature_syn_isql = "
+      INSERT INTO {feature_synonym} (synonym_id,feature_id,pub_id) 
+      VALUES (:synonym_id, :feature_id, :pub_id)";
+    $args = array(':synonym_id' => $synonym->synonym_id, ':feature_id' => $feature_id, ':pub_id'=> 1);
+    if (!chado_query($feature_syn_isql, $args)) {
       $error .= "Could not add synonyms to feature. ";
     }
   }
@@ -707,13 +702,17 @@ function chado_feature_add_gbaccession($accession, $feature_id) {
   // use chado database
 
   // remove any old accession from genbank dbEST
-  $fdbxref_dsql = "DELETE FROM {feature_dbxref} " .
-                 "WHERE feature_id = %d and dbxref_id IN " .
-                 "   (SELECT DBX.dbxref_id FROM {dbxref} DBX " .
-                 "    INNER JOIN DB  ON DB.db_id = DBX.db_id " .
-                 "    INNER JOIN feature_dbxref FDBX ON DBX.dbxref_id = FDBX.dbxref_id " .
-                 "    WHERE DB.name = 'DB:Genbank' and FDBX.feature_id = %d)";
-  if (!chado_query($fdbxref_dsql, $feature_id, $feature_id)) {
+  $fdbxref_dsql = "
+    DELETE FROM {feature_dbxref} 
+    WHERE feature_id = :feature_id and dbxref_id IN 
+      (SELECT DBX.dbxref_id 
+       FROM {dbxref} DBX 
+         INNER JOIN DB  ON DB.db_id = DBX.db_id 
+         INNER JOIN feature_dbxref FDBX ON DBX.dbxref_id = FDBX.dbxref_id 
+       WHERE DB.name = 'DB:Genbank' and FDBX.feature_id = :feature_id
+      )
+  ";
+  if (!chado_query($fdbxref_dsql, array(':feature_id' => $feature_id))) {
     $error .= "Could not remove accession from feature. ";
   }
 
@@ -722,34 +721,29 @@ function chado_feature_add_gbaccession($accession, $feature_id) {
     return;
   }
   // get the db_id
-  $db_sql = "SELECT db_id FROM {DB} " .
-            "WHERE name = 'DB:Genbank_est'";
-  $db = db_fetch_object(chado_query($db_sql));
+  $db_sql = "SELECT db_id FROM {DB} WHERE name = 'DB:Genbank_est'";
+  $db = chado_query($db_sql)->fetchObject();
 
   // check to see if we have this accession number already in the database
   // if so then don't add it again. it messes up drupal if the insert fails.
   // It is possible for the accession number to be present and not the feature
-  $dbxref_sql = "SELECT dbxref_id FROM {dbxref} " .
-                "WHERE db_id = %d and accession = '%s'";
-  $dbxref = db_fetch_object(chado_query($dbxref_sql, $db->db_id, $accession));
+  $dbxref_sql = "SELECT dbxref_id FROM {dbxref} WHERE db_id = :db_id and accession = :accession";
+  $dbxref = chado_query($dbxref_sql, array(':db_id' => $db->db_id, ':accession' => $accession))->fetchObject();
   if (!$dbxref) {
     // add the accession number
-    $dbxref_isql = "INSERT INTO {dbxref} (db_id,accession) " .
-                   "  VALUES (%d, '%s') ";
-    if (!chado_query($dbxref_isql, $db->db_id, $accession)) {
+    $dbxref_isql = "INSERT INTO {dbxref} (db_id, accession) VALUES (:db_id, :accession) ";
+    if (!chado_query($dbxref_isql, array(':db_id' => $db->db_id, ':accession' => $accession))) {
       $error .= 'Could not add accession as a database reference ';
     }
     // get the dbxref_id for the just added accession number
-    $dbxref_sql = "SELECT dbxref_id FROM {dbxref} " .
-                  "WHERE db_id = %d and accession = '%s'";
-    $dbxref = db_fetch_object(chado_query($dbxref_sql, $db->db_id, $accession));
+    $dbxref_sql = "SELECT dbxref_id FROM {dbxref} WHERE db_id = :db_id and accession = :accession";
+    $dbxref = chado_query($dbxref_sql, array(':db_id' => $db->db_id, ':accession' => $accession))->fetchObject();
   }
 
 
   // associate the accession number with the feature
-  $feature_dbxref_isql = "INSERT INTO {feature_dbxref} (feature_id,dbxref_id) " .
-                         "  VALUES (%d, %d) ";
-  if (!chado_query($feature_dbxref_isql, $feature_id, $dbxref->dbxref_id)) {
+  $feature_dbxref_isql = "INSERT INTO {feature_dbxref} (feature_id, dbxref_id) VALUES (:feature_id, :dbxref_id) ";
+  if (!chado_query($feature_dbxref_isql, array(':feature_id' => $feature_id, ':dbxref_id' => $dbxref->dbxref_id))) {
     $error .= 'Could not add feature database reference. ';
   }
 
@@ -864,7 +858,7 @@ function chado_feature_form($node, $param) {
   $org_rset = chado_query($sql);
   $organisms = array();
   $organisms[''] = '';
-  while ($organism = db_fetch_object($org_rset)) {
+  while ($organism = $org_rset->fetchObject()) {
     $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
   }
   $form['organism_id'] = array(
@@ -934,12 +928,19 @@ function chado_feature_validate($node) {
   // the organism doesn't already have this uniquename. We don't want to give
   // two sequences the same uniquename
   if ($node->feature_id) {
-    $sql = "SELECT *
-            FROM {Feature} F
-              INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
-            WHERE uniquename = '%s'
-             AND organism_id = %d AND CVT.name = '%s' AND NOT feature_id = %d";
-    $result = db_fetch_object(chado_query($sql, $node->uniquename, $node->organism_id, $node->feature_type, $node->feature_id));
+    $sql = "
+      SELECT *
+      FROM {feature} F
+        INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
+      WHERE 
+        F.uniquename     = :uname AND 
+        F.organism_id    = :orgnism_id AND 
+        CVT.name         = :cvtname AND 
+        NOT f.feature_id = :feature_id
+    ";
+    $args = array(':uname' => $node->uniquename, ':organism_id' => $node->organism_id, 
+      ':cvtname' => $node->feature_type, ':feature_id' => $node->feature_id);
+    $result = chado_query($sql, $args)->fetchObject();
     if ($result) {
       form_set_error('uniquename', t("Feature update cannot proceed. The feature name '$node->uniquename' is not unique for this organism. Please provide a unique name for this feature."));
     }
@@ -948,12 +949,17 @@ function chado_feature_validate($node) {
   // if this is an insert then we just need to make sure this name doesn't
   // already exist for this organism if it does then we need to throw an error
   else {
-    $sql = "SELECT *
-            FROM {Feature} F
-              INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
-            WHERE uniquename = '%s'
-             AND organism_id = %d AND CVT.name = '%s'";
-    $result = db_fetch_object(chado_query($sql, $node->uniquename, $node->organism_id, $node->feature_type));
+    $sql = "
+      SELECT *
+      FROM {feature} F
+        INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
+      WHERE 
+        F.uniquename  = :name AND 
+        F.organism_id = :organism_id AND 
+        CVT.name      = :cvtname
+    ";
+    $args = array(':name' => $node->uniquename, ':organism_id' => $node->organism_id, ':cvtname' => $node->feature_type);
+    $result = chado_query($sql, $args)->fetchObject();
     if ($result) {
       form_set_error('uniquename', t("Feature insert cannot proceed. The feature name '$node->uniquename' already exists for this organism. Please provide a unique name for this feature."));
     }
@@ -1011,8 +1017,8 @@ function chado_feature_load($node) {
  */
 function tripal_feature_load_organism($organism_id) {
   // add organism details
-  $sql = "SELECT * FROM {organism} WHERE organism_id = %d";
-  $organism = db_fetch_object(chado_query($sql, $organism_id));
+  $sql = "SELECT * FROM {organism} WHERE organism_id = :organism_id";
+  $organism = chado_query($sql, array(':organism_id' => $organism_id))->fetchObject();
   return $organism;
 }
 /**
@@ -1022,16 +1028,17 @@ function tripal_feature_load_organism($organism_id) {
  */
 function tripal_feature_load_synonyms($feature_id) {
 
-  $sql = "SELECT S.name " .
-        "FROM {Feature_Synonym} FS " .
-        "  INNER JOIN {Synonym} S " .
-        "    ON FS.synonym_id = S.Synonym_id " .
-        "WHERE FS.feature_id = %d " .
-        "ORDER BY S.name ";
-  $results = chado_query($sql, $feature_id);
+  $sql = "
+    SELECT S.name 
+    FROM {feature_synonym} FS 
+      INNER JOIN {synonym} S  ON FS.synonym_id = S.Synonym_id 
+    WHERE FS.feature_id = :feature_id
+    ORDER BY S.name 
+   ";
+  $results = chado_query($sql, array(':feature_id' => $feature_id));
   $synonyms = array();
   $i=0;
-  while ($synonym = db_fetch_object($results)) {
+  while ($synonym = $results->fetchObject()) {
     $synonyms[$i++] = $synonym;
   }
   return $synonyms;
@@ -1043,20 +1050,24 @@ function tripal_feature_load_synonyms($feature_id) {
  */
 function tripal_feature_load_properties($feature_id) {
 
-  $sql = "SELECT CVT.name as cvname, FS.type_id, FS.value, FS.rank,
-           CVT.definition, CVT.is_obsolete,
-           DBX.dbxref_id,DBX.accession,DB.name as dbname,
-           DB.urlprefix, DB.description as db_description, DB.url
-         FROM {featureprop} FS
-           INNER JOIN {cvterm} CVT ON FS.type_id = CVT.cvterm_id
-           INNER JOIN {dbxref} DBX ON CVT.dbxref_id = DBX.dbxref_id
-           INNER JOIN {db} DB      ON DB.db_id = DBX.db_id
-         WHERE FS.feature_id = %d
-         ORDER BY FS.rank ASC";
-  $results = chado_query($sql, $feature_id);
+  $sql = "
+    SELECT 
+      CVT.name as cvname, CVT.definition, CVT.is_obsolete, 
+      FS.type_id, FS.value, FS.rank,      
+      DBX.dbxref_id,DBX.accession,DB.name as dbname,
+      DB.urlprefix, DB.description as db_description, DB.url
+    FROM {featureprop} FS
+      INNER JOIN {cvterm} CVT ON FS.type_id    = CVT.cvterm_id
+      INNER JOIN {dbxref} DBX ON CVT.dbxref_id = DBX.dbxref_id
+      INNER JOIN {db} DB      ON DB.db_id      = DBX.db_id
+    WHERE 
+      FS.feature_id = :feature_id
+    ORDER BY FS.rank ASC
+  ";
+  $results = chado_query($sql, array(':feature_id' => $feature_id));
   $i=0;
   $properties = array();
-  while ($property = db_fetch_object($results)) {
+  while ($property = $results->fetchObject()) {
     $properties[$i++] = $property;
   }
   return $properties;
@@ -1068,18 +1079,23 @@ function tripal_feature_load_properties($feature_id) {
  */
 function tripal_feature_load_references($feature_id) {
 
-  $sql = "SELECT F.uniquename,F.Feature_id,DBX.accession,DB.description as dbdesc, " .
-        "   DB.db_id, DB.name as db_name, DB.urlprefix,DBX.dbxref_id " .
-        "FROM {feature} F " .
-        "  INNER JOIN {feature_dbxref} FDBX on F.feature_id = FDBX.feature_id " .
-        "  INNER JOIN {dbxref} DBX on DBX.dbxref_id = FDBX.dbxref_id " .
-        "  INNER JOIN {db} on DB.db_id = DBX.db_id " .
-        "WHERE F.feature_id = %d " .
-        "ORDER BY DB.name ";
-  $results = chado_query($sql, $feature_id);
+  $sql = "
+    SELECT 
+       F.uniquename, F.Feature_id,
+       DB.description as dbdesc, DB.db_id, DB.name as db_name, DB.urlprefix,
+       DBX.accession, DBX.dbxref_id 
+    FROM {feature} F 
+      INNER JOIN {feature_dbxref} FDBX ON F.feature_id  = FDBX.feature_id 
+      INNER JOIN {dbxref} DBX          ON DBX.dbxref_id = FDBX.dbxref_id 
+      INNER JOIN {db}                  ON DB.db_id      = DBX.db_id 
+    WHERE 
+      F.feature_id = :feature_id
+    ORDER BY DB.name 
+  ";
+  $results = chado_query($sql, array(':feature_id' => $feature_id));
   $references = array();
   $i=0;
-  while ($accession = db_fetch_object($results)) {
+  while ($accession = $results->fetchObject()) {
     $references[$i++] = $accession;
   }
   return $references;
@@ -1091,40 +1107,38 @@ function tripal_feature_load_references($feature_id) {
  */
 function tripal_feature_load_featurelocs($feature_id, $side = 'as_parent', $aggregate = 1) {
 
-  $sql = "SELECT
-           F.name, F.feature_id, F.uniquename,
-           FS.name as src_name,
-           FS.feature_id as src_feature_id,
-           FS.uniquename as src_uniquename,
-           CVT.name as cvname, CVT.cvterm_id,
-           CVTS.name as src_cvname, CVTS.cvterm_id as src_cvterm_id,
-           FL.fmin, FL.fmax, FL.is_fmin_partial, FL.is_fmax_partial,FL.strand,
-           FL.phase
-         FROM {featureloc} FL
-            INNER JOIN {feature} F on FL.feature_id = F.feature_id
-            INNER JOIN {feature} FS on FS.feature_id = FL.srcfeature_id
-            INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id
-            INNER JOIN {cvterm} CVTS on FS.type_id = CVTS.cvterm_id
-         ";
+  $sql = "
+    SELECT
+       F.name, F.feature_id, F.uniquename,
+       FS.name as src_name, FS.feature_id as src_feature_id, FS.uniquename as src_uniquename,
+       CVT.name as cvname, CVT.cvterm_id,
+       CVTS.name as src_cvname, CVTS.cvterm_id as src_cvterm_id,
+       FL.fmin, FL.fmax, FL.is_fmin_partial, FL.is_fmax_partial,FL.strand, FL.phase
+     FROM {featureloc} FL
+       INNER JOIN {feature} F   ON FL.feature_id = F.feature_id
+       INNER JOIN {feature} FS  ON FS.feature_id = FL.srcfeature_id
+       INNER JOIN {cvterm} CVT  ON F.type_id     = CVT.cvterm_id
+       INNER JOIN {cvterm} CVTS ON FS.type_id    = CVTS.cvterm_id
+   ";
   if (strcmp($side, 'as_parent')==0) {
-    $sql .= "WHERE FL.srcfeature_id = %d ";
+    $sql .= "WHERE FL.srcfeature_id = :feature_id ";
   }
   if (strcmp($side, 'as_child')==0) {
-    $sql .= "WHERE FL.feature_id = %d ";
+    $sql .= "WHERE FL.feature_id = :feature_id ";
   }
-
-  $flresults = chado_query($sql, $feature_id);
+  
+  $flresults = chado_query($sql, array(':feature_id' => $feature_id));
 
   // copy the results into an array
   $i=0;
   $featurelocs = array();
-  while ($loc = db_fetch_object($flresults)) {
+  while ($loc = $flresults->fetchObject()) {
     // if a drupal node exists for this feature then add the nid to the
     // results object
-    $sql = 'SELECT nid FROM {chado_feature} WHERE feature_id = %d';
+    $sql = 'SELECT nid FROM {chado_feature} WHERE feature_id = :feature_id';
 
-    $ffeature = db_fetch_object(db_query($sql, $loc->feature_id));
-    $sfeature = db_fetch_object(db_query($sql, $loc->src_feature_id));
+    $ffeature = db_query($sql, array(':feature_id' => $loc->feature_id))->fetchObject();
+    $sfeature = db_query($sql, array(':feature_id' => $loc->src_feature_id))->fetchObject();
     $loc->fnid = $ffeature->nid;
     $loc->snid = $sfeature->nid;
     // add the result to the array
@@ -1164,50 +1178,44 @@ function tripal_feature_sort_locations($a, $b) {
 function tripal_feature_load_relationships($feature_id, $side = 'as_subject') {
   // get the relationships for this feature.  The query below is used for both
   // querying the object and subject relationships
-  $sql = "SELECT
-           FS.name as subject_name,
-           FS.uniquename as subject_uniquename,
-           CVTS.name as subject_type,
-           CVTS.cvterm_id as subject_type_id,
-           FR.subject_id,
-           FR.type_id as relationship_type_id,
-           CVT.name as rel_type,
-           FO.name as object_name,
-           FO.uniquename as object_uniquename,
-           CVTO.name as object_type,
-           CVTO.cvterm_id as object_type_id,
-           FR.object_id,
-           FR.rank
-         FROM {feature_relationship} FR
-           INNER JOIN {cvterm} CVT ON FR.type_id = CVT.cvterm_id
-           INNER JOIN {feature} FS ON FS.feature_id = FR.subject_id
-           INNER JOIN {feature} FO ON FO.feature_id = FR.object_id
-           INNER JOIN {cvterm} CVTO ON FO.type_id = CVTO.cvterm_id
-           INNER JOIN {cvterm} CVTS ON FS.type_id = CVTS.cvterm_id
+  $sql = "
+    SELECT
+      FS.name as subject_name, FS.uniquename as subject_uniquename,
+      CVTS.name as subject_type, CVTS.cvterm_id as subject_type_id,
+      FR.subject_id, FR.type_id as relationship_type_id, FR.object_id, FR.rank,
+      CVT.name as rel_type,
+      FO.name as object_name, FO.uniquename as object_uniquename,
+      CVTO.name as object_type, CVTO.cvterm_id as object_type_id      
+    FROM {feature_relationship} FR
+     INNER JOIN {cvterm} CVT  ON FR.type_id    = CVT.cvterm_id
+     INNER JOIN {feature} FS  ON FS.feature_id = FR.subject_id
+     INNER JOIN {feature} FO  ON FO.feature_id = FR.object_id
+     INNER JOIN {cvterm} CVTO ON FO.type_id    = CVTO.cvterm_id
+     INNER JOIN {cvterm} CVTS ON FS.type_id    = CVTS.cvterm_id
   ";
   if (strcmp($side, 'as_object')==0) {
-    $sql .= " WHERE FR.object_id = %d";
+    $sql .= " WHERE FR.object_id = :feature_id";
   }
   if (strcmp($side, 'as_subject')==0) {
-    $sql .= " WHERE FR.subject_id = %d";
+    $sql .= " WHERE FR.subject_id = :feature_id";
   }
   $sql .= " ORDER BY FR.rank";
 
   // get the relationships
-  $results = chado_query($sql, $feature_id);
+  $results = chado_query($sql, array(':feature_id' => $feature_id));
 
 
   // iterate through the relationships, put these in an array and add
   // in the Drupal node id if one exists
   $i=0;
-  $nodesql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d";
+  $nodesql = "SELECT nid FROM {chado_feature} WHERE feature_id = :feature_id";
   $relationships = array();
-  while ($rel = db_fetch_object($results)) {
-    $node = db_fetch_object(db_query($nodesql, $rel->subject_id));
+  while ($rel = $results->fetchObject()) {
+    $node = db_query($nodesql, array(':feature_id' => $rel->subject_id))->fetchObject();
     if ($node) {
       $rel->subject_nid = $node->nid;
     }
-    $node = db_fetch_object(db_query($nodesql, $rel->object_id));
+    $node = db_query($nodesql, array(':feature_id' => $rel->object_id))->fetchObject();
     if ($node) {
       $rel->object_nid = $node->nid;
     }
@@ -1289,9 +1297,11 @@ function tripal_feature_load_featureloc_sequences($feature_id, $featurelocs) {
   // where this feature is found.   We want to get the sequence for each
   // location and then annotate it with the parts found from the relationships
   // locations determiend above.
-  $sql = "SELECT substring(residues from %d for %d) as residues " .
-         "FROM {feature} " .
-         "WHERE feature_id = %d";
+  $sql = "
+    SELECT substring(residues from :start for :size) as residues 
+    FROM {feature} 
+    WHERE feature_id = :feature_id
+  ";
   $floc_sequences = array();
   foreach ($featurelocs as $featureloc) {
 
@@ -1340,7 +1350,8 @@ function tripal_feature_load_featureloc_sequences($feature_id, $featurelocs) {
 
       $floc_sequences[$src]['src'] = $src;
       $floc_sequences[$src]['type'] = $featureloc->feature_id->type_id->name;
-      $sequence = db_fetch_object(chado_query($sql, $featureloc->fmin + 1, ($featureloc->fmax - $featureloc->fmin), $featureloc->srcfeature_id->feature_id));
+      $args = array(':start' => $featureloc->fmin + 1, ':size' => ($featureloc->fmax - $featureloc->fmin), ':feature_id' => $featureloc->srcfeature_id->feature_id);
+      $sequence = chado_query($sql, $args)->fetchObject();
       $residues = $sequence->residues;
       if ($featureloc->strand < 0) {
          $residues = tripal_feature_reverse_complement($residues);
@@ -1383,43 +1394,46 @@ function tripal_feature_get_matched_alignments($feature) {
   // not want to include these, so we have to filter on the SO terms:
   // match, or %_match
   //
-   $sql = "SELECT  " .
-          "   FL1.featureloc_id    as left_featureloc_id, " .
-          "   FL1.srcfeature_id    as left_srcfeature_id, " .
-          "   FL1.feature_id       as left_feature_id, " .
-          "   FL1.fmin             as left_fmin, " .
-          "   FL1.is_fmin_partial  as left_is_fmin_partial, " .
-          "   FL1.fmax             as left_fmax, " .
-          "   FL1.is_fmax_partial  as left_is_fmax_partial, " .
-          "   FL1.strand           as left_strand,  " .
-          "   FL1.phase            as left_phase, " .
-          "   FL1.locgroup         as left_locgroup, " .
-          "   FL1.rank             as left_rank, " .
-          "   FL2.featureloc_id    as right_featureloc_id, " .
-          "   FL2.srcfeature_id    as right_srcfeature_id, " .
-          "   FL2.feature_id       as right_feature_id, " .
-          "   FL2.fmin             as right_fmin, " .
-          "   FL2.is_fmin_partial  as right_is_fmin_partial, " .
-          "   FL2.fmax             as right_fmax, " .
-          "   FL2.is_fmax_partial  as right_is_fmax_partial, " .
-          "   FL2.strand           as right_strand,  " .
-          "   FL2.phase            as right_phase, " .
-          "   FL2.locgroup         as right_locgroup, " .
-          "   FL2.rank             as right_rank " .
-          "FROM {feature} F1 " .
-          "  INNER JOIN {featureloc} FL1 on FL1.srcfeature_id = F1.feature_id " .
-          "  INNER JOIN {feature} F2 on FL1.feature_id = F2.feature_id " .
-          "  INNER JOIN {featureloc} FL2 on FL2.feature_id = F2.feature_id " .
-          "  INNER JOIN {cvterm} CVT2 on F2.type_id = CVT2.cvterm_id " .
-          "WHERE F1.feature_id = %d " .
-          "  AND (CVT2.name = 'match' or CVT2.name like '%_match') " .
-          "ORDER BY FL1.fmin";
-
-   $results = chado_query($sql, $feature->feature_id);
+   $sql = "
+     SELECT  
+       FL1.featureloc_id    as left_featureloc_id, 
+       FL1.srcfeature_id    as left_srcfeature_id, 
+       FL1.feature_id       as left_feature_id, 
+       FL1.fmin             as left_fmin, 
+       FL1.is_fmin_partial  as left_is_fmin_partial, 
+       FL1.fmax             as left_fmax, 
+       FL1.is_fmax_partial  as left_is_fmax_partial, 
+       FL1.strand           as left_strand,  
+       FL1.phase            as left_phase, 
+       FL1.locgroup         as left_locgroup, 
+       FL1.rank             as left_rank, 
+       FL2.featureloc_id    as right_featureloc_id, 
+       FL2.srcfeature_id    as right_srcfeature_id, 
+       FL2.feature_id       as right_feature_id, 
+       FL2.fmin             as right_fmin, 
+       FL2.is_fmin_partial  as right_is_fmin_partial, 
+       FL2.fmax             as right_fmax, 
+       FL2.is_fmax_partial  as right_is_fmax_partial, 
+       FL2.strand           as right_strand,  
+       FL2.phase            as right_phase, 
+       FL2.locgroup         as right_locgroup, 
+       FL2.rank             as right_rank 
+     FROM {feature} F1 
+       INNER JOIN {featureloc} FL1 on FL1.srcfeature_id = F1.feature_id 
+       INNER JOIN {feature} F2 on FL1.feature_id = F2.feature_id 
+       INNER JOIN {featureloc} FL2 on FL2.feature_id = F2.feature_id 
+       INNER JOIN {cvterm} CVT2 on F2.type_id = CVT2.cvterm_id 
+     WHERE 
+       F1.feature_id = :feature_id  AND 
+       (CVT2.name = 'match' or CVT2.name like '%_match') 
+     ORDER BY FL1.fmin
+   ";
+
+   $results = chado_query($sql, array(':feature_id' => $feature->feature_id));
 
    // iterate through the results and add them to our featurelocs array
    $featurelocs = array();
-   while ($fl = db_fetch_object($results)) {
+   while ($fl = $results->fetchObject()) {
      // ignore featurelocs where the left and right srcfeature is the same
      if (strcmp($fl->left_srcfeature_id, $fl->right_srcfeature_id) == 0) {
        continue;
@@ -1441,8 +1455,6 @@ function tripal_feature_load_organism_feature_counts($organism) {
   if (strcmp($show_counts, 'show_feature_summary')!=0) {
     return array('enabled' => FALSE );
   }
-
-
   $args = array();
   $names = array();
   $order = array();
@@ -1456,6 +1468,7 @@ function tripal_feature_load_organism_feature_counts($organism) {
   if ($temp) {
     $is_custom = 1;
     $temp = explode("\n", $temp);
+    $i = 0;
     foreach ($temp as $key => $value) {
       // separate the key value pairs
       $temp2 = explode("=", $value);
@@ -1465,12 +1478,13 @@ function tripal_feature_load_organism_feature_counts($organism) {
       // if a new name is provided then use that otherwise just
       // use the feature type
       if (count($temp2) == 2) {
-        $names[] = rtrim($temp2[1]);
+        $names[":name$i"] = rtrim($temp2[1]);
       }
       else {
-        $names[] = $feature_type;
+        $names[":name$i"] = $feature_type;
       }
-      $where .= "OFC.feature_type = '%s' OR \n";
+      $where .= " OFC.feature_type = :name$i OR ";
+      $i++;
     }
     if ($where) {
       $where = drupal_substr($where, 0, -5);  # remove OR from the end
@@ -1484,15 +1498,15 @@ function tripal_feature_load_organism_feature_counts($organism) {
     SELECT OFC.num_features,OFC.feature_type,CVT.definition
     FROM {organism_feature_count} OFC
       INNER JOIN {cvterm} CVT on OFC.cvterm_id = CVT.cvterm_id
-    WHERE $where organism_id = %d
+    WHERE $where organism_id = :organism_id
     ORDER BY num_features desc
   ";
-  $args[] = $organism->organism_id;
+  $args[':organism_id'] = $organism->organism_id;
   $org_features = chado_query($sql, $args);
 
   // iterate through the types
   $types = array();
-  while ($type = db_fetch_object($org_features)) {
+  while ($type = $org_features->fetchObject()) {
     $types[$type->feature_type] = $type;
     // if we don't have an order this means we didn't go through the loop
     // above to set the names, so do that now
@@ -1550,11 +1564,11 @@ function tripal_feature_load_organism_feature_browser($organism) {
   $pager = theme('pager');
 
   // add the node ids and types
-  $nsql = "SELECT nid FROM {chado_feature} WHERE feature_id = %d";
-  $tsql = "SELECT name FROM {cvterm} WHERE cvterm_id = %d";
+  $nsql = "SELECT nid FROM {chado_feature} WHERE feature_id = :feature_id";
+  $tsql = "SELECT name FROM {cvterm} WHERE cvterm_id = :cvterm_id";
   foreach ($features as $feature) {
-    $node = db_fetch_object(db_query($nsql, $feature->feature_id));
-    $type = db_fetch_object(chado_query($tsql, $feature->type_id));
+    $node = db_query($nsql, array(':feature_id' => $feature->feature_id))->fetchObject();
+    $type = chado_query($tsql, array(':cvterm_id' => $feature->type_id))->fetchObject();
     $feature->nid = $node->nid;
     $feature->type_name = $type->name;
   }
@@ -1583,39 +1597,46 @@ function tripal_feature_load_library_feature_browser($library) {
   $allowed_types = preg_replace("/[\s\n\r]+/", " ", $allowed_types);
   $so_terms = split(' ', $allowed_types);
   $where_cvt = "";
+  $args = array();
+  $i = 0;
   foreach ($so_terms as $term) {
-    $where_cvt .= "CVT.name = '$term' OR ";
+    $where_cvt .= "CVT.name = :cvtname$i OR ";
+    $args[':cvtname$i'] = $term;
+    $i++;
   }
   $where_cvt = drupal_substr($where_cvt, 0, drupal_strlen($where_cvt)-3);  # strip trailing 'OR'
 
   // get the features for this library
-  $sql  = "SELECT F.name,F.feature_id,F.uniquename,CVT.name as cvname " .
-         "FROM {feature} F " .
-            "  INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id " .
-            "  INNER JOIN {library_feature} LF on F.feature_id = LF.feature_id " .
-            "  INNER JOIN {library} L on LF.library_id = L.library_id " .
-          "WHERE LF.library_id = %d and ($where_cvt) " .
-          "ORDER BY feature_id ASC";
-
+  $sql  = "
+    SELECT F.name, F.feature_id, F.uniquename, CVT.name as cvname 
+    FROM {feature} F 
+      INNER JOIN {cvterm} CVT         ON F.type_id = CVT.cvterm_id 
+      INNER JOIN {library_feature} LF ON F.feature_id = LF.feature_id 
+      INNER JOIN {library} L          ON LF.library_id = L.library_id 
+    WHERE LF.library_id = :library_id and ($where_cvt) 
+    ORDER BY feature_id ASC
+  ";
+  $args[':library_id'] = $library->libary_id;
+  
   // the counting SQL
-  $csql  = "SELECT count(*) " .
-          "FROM {feature} F" .
-            "  INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id " .
-            "  INNER JOIN {library_feature} LF on F.feature_id = LF.feature_id " .
-            "  INNER JOIN {library} L on LF.library_id = L.library_id " .
-          "WHERE LF.library_id = %d and ($where_cvt) " .
-          "GROUP BY L.library_id ";
-
-  $org_features = chado_pager_query($sql, 10, 0, $csql, $library->library_id);
+  $csql  = "
+    SELECT count(*) 
+    FROM {feature} F
+      INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id 
+      INNER JOIN {library_feature} LF on F.feature_id = LF.feature_id 
+      INNER JOIN {library} L on LF.library_id = L.library_id 
+    WHERE LF.library_id = :library_id and ($where_cvt) 
+      GROUP BY L.library_id ";
+
+  $org_features = chado_pager_query($sql, 10, 0, $csql, $args);
   $pager = theme('pager');
 
   // prepare the query that will lookup node ids
-  $sql = "SELECT nid FROM {chado_feature} " .
-         "WHERE feature_id = %d";
+  $sql = "SELECT nid FROM {chado_feature} WHERE feature_id = :feature_id";
   $i=0;
   $features = array();
-  while ($feature = db_fetch_object($org_features)) {
-    $node = db_fetch_object(db_query($sql, $feature->feature_id));
+  while ($feature = $org_features->fetchObject()) {
+    $node = db_query($sql, array(':feature_id' => $feature->feature_id))->fetchObject();
     $feature->nid = $node->nid;
     $features[$i++] = $feature;
   }
@@ -1643,39 +1664,47 @@ function tripal_feature_load_analysis_feature_browser($analysis) {
   $allowed_types = preg_replace("/[\s\n\r]+/", " ", $allowed_types);
   $so_terms = split(' ', $allowed_types);
   $where_cvt = "";
+  $i = 0;
+  $args = array();
   foreach ($so_terms as $term) {
-    $where_cvt .= "CVT.name = '$term' OR ";
+    $where_cvt .= "CVT.name = :aname$i OR ";
+    $args[":aname$i"] = $term;
+    $i++;
   }
   $where_cvt = drupal_substr($where_cvt, 0, drupal_strlen($where_cvt)-3);  # strip trailing 'OR'
 
   // get the features for this library
-  $sql  = "SELECT F.name,F.feature_id,F.uniquename,CVT.name as cvname " .
-         "FROM {feature} F " .
-            "  INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id " .
-            "  INNER JOIN {analysisfeature} AF on F.feature_id = AF.feature_id " .
-            "  INNER JOIN {analysis} A on AF.analysis_id = A.analysis_id " .
-          "WHERE A.analysis_id = %d and ($where_cvt) " .
-          "ORDER BY feature_id ASC";
+  $sql  = "
+    SELECT F.name,F.feature_id,F.uniquename,CVT.name as cvname 
+    FROM {feature} F 
+      INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id 
+      INNER JOIN {analysisfeature} AF on F.feature_id = AF.feature_id 
+      INNER JOIN {analysis} A on AF.analysis_id = A.analysis_id 
+    WHERE A.analysis_id = :analysis_id and ($where_cvt) 
+    ORDER BY feature_id ASC
+  ";
+  $args[':analysis_id'] = $analysis->analysis_id;
 
   // the counting SQL
-  $csql  = "SELECT count(*) " .
-          "FROM {feature} F" .
-            "  INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id " .
-            "  INNER JOIN {analysisfeature} AF on F.feature_id = AF.feature_id " .
-            "  INNER JOIN {analysis} A on AF.analysis_id = A.analysis_id " .
-          "WHERE A.analysis_id = %d and ($where_cvt) " .
-          "GROUP BY A.analysis_id ";
-
-  $org_features = chado_pager_query($sql, 10, 0, $csql, $analysis->analysis_id);
+  $csql  = "
+    SELECT count(*) 
+    FROM {feature} F
+      INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id 
+      INNER JOIN {analysisfeature} AF on F.feature_id = AF.feature_id 
+      INNER JOIN {analysis} A on AF.analysis_id = A.analysis_id 
+    WHERE A.analysis_id = %d and ($where_cvt) 
+    GROUP BY A.analysis_id 
+  ";
+
+  $org_features = chado_pager_query($sql, 10, 0, $csql, $args);
   $pager = theme('pager');
 
   // prepare the query that will lookup node ids
-  $sql = "SELECT nid FROM {chado_feature} " .
-         "WHERE feature_id = %d";
+  $sql = "SELECT nid FROM {chado_feature} WHERE feature_id = :feature_id";
   $i=0;
   $features = array();
-  while ($feature = db_fetch_object($org_features)) {
-    $node = db_fetch_object(db_query($sql, $feature->feature_id));
+  while ($feature = $org_features->fetchObject()) {
+    $node = db_query($sql, array(':feature_id' => $feature->feature_id))->fetchObject();
     $feature->nid = $node->nid;
     $features[$i++] = $feature;
   }
@@ -1837,13 +1866,13 @@ function tripal_feature_node_insert($node) {
   switch ($node->type) {
     case 'chado_feature':
       if (!$node->feature_id) {
-        $sql = "SELECT * FROM {chado_feature} WHERE nid = %d";
-        $chado_feature = db_fetch_object(db_query($sql, $node->nid));
+        $sql = "SELECT * FROM {chado_feature} WHERE nid = :nid";
+        $chado_feature = db_query($sql, array(':nid' => $node->nid))->fetchObject();
         $node->feature_id = $chado_feature->feature_id;
       }
       
       // remove any previous alias
-      db_query("DELETE FROM {url_alias} WHERE src = '%s'", "node/$node->nid");
+      db_query("DELETE FROM {url_alias} WHERE src = :src", array(':src' => "node/$node->nid"));
       
       // set the URL for this feature page
       $url_alias = tripal_feature_get_feature_url($node);
@@ -1855,19 +1884,25 @@ function tripal_feature_node_insert($node) {
  *
  * @ingroup tripal_feature
  */
-function tripal_feature_node_update($node) {
-  
-  // set the URL path after inserting.  We do it here because we do not 
-  // know the feature_id in the presave  
+function tripal_feature_node_view($node, $view_mode, $langcode) {
   switch ($node->type) {
-    case 'chado_feature':
-      
-      // remove any previous alias
-      db_query("DELETE FROM {url_alias} WHERE src = '%s'", "node/$node->nid");
-      
-      // set the URL for this feature page
-      $url_alias = tripal_feature_get_feature_url($node);
-      path_set_alias("node/$node->nid", $url_alias);
+    case 'chado_organism':
+      // Show feature browser and counts
+      if ($view_mode == 'full') {
+        $node->content['tripal_organism_feature_counts'] = array(
+          '#value' => theme('tripal_organism_feature_counts', $node),
+        );
+        $node->content['tripal_organism_feature_browser'] = array(
+          '#value' => theme('tripal_organism_feature_browser', $node),
+        );
+      }
+      break;
+    // TODO: handle these node types. Should we also have a feature browser?
+    case 'chado_library':
+      break;
+    case 'chado_stock':
+      break;
+    case 'chado_analysis':
       break;
   }
 }
@@ -1879,18 +1914,14 @@ function tripal_feature_node_update($node) {
   
   // add items to other nodes, build index and search results
   switch ($node->type) {
-    case 'chado_organism':
-      // Show feature browser
-      $types_to_show = array('chado_organism', 'chado_library');
-      if (in_array($node->type, $types_to_show, TRUE)) {
-        $node->content['tripal_organism_feature_counts'] = array(
-          '#value' => theme('tripal_organism_feature_counts', $node),
-        );
-        $node->content['tripal_organism_feature_browser'] = array(
-          '#value' => theme('tripal_organism_feature_browser', $node),
-        );
-      }
-    break;
+    case 'chado_feature':
+      // remove any previous alias
+      db_query("DELETE FROM {url_alias} WHERE src = :src", array(':src' => "node/$node->nid"));
+      
+      // set the URL for this feature page
+      $url_alias = tripal_feature_get_feature_url($node);
+      path_set_alias("node/$node->nid", $url_alias);
+      break;
   }
 }
 
@@ -2311,13 +2342,13 @@ function tripal_feature_match_features_page($id) {
       LEFT JOIN {synonym} S on S.synonym_id = FS.synonym_id
       INNER JOIN public.chado_feature CF on CF.feature_id = F.feature_id
     WHERE
-      F.uniquename = '%s' or
-      F.name = '%s' or
-      S.name = '%s'
+      F.uniquename = :uname or
+      F.name = :fname' or
+      S.name = :sname
     GROUP BY F.name, F.uniquename, F.feature_id, O.genus, O.species,
       O.organism_id, CVT.cvterm_id, CVT.name, CF.nid
   ";
-  $results = chado_query($sql, $id, $id, $id);
+  $results = chado_query($sql, array(':uname' => $id, ':fname' => $id, ':sname' => $id));
 
   $num_matches = 0;
 
@@ -2325,7 +2356,7 @@ function tripal_feature_match_features_page($id) {
   $header = array('Uniquename', 'Name', 'Type', 'Species', 'Synonyms');
   $rows = array();
   $curr_match;
-  while ($match = db_fetch_object($results)) {
+  while ($match = $results->fetchObject()) {
     $curr_match = $match;
     $synonyms = $match->synonyms;
     $synonyms = preg_replace('/[\"\{\}]/', '', $synonyms);

tripal_featuremap/includes/tripal_featuremap.admin.inc

@@ -78,7 +78,7 @@ function get_tripal_featuremap_admin_form_taxonomy_set(&$form) {
 
   // iterate through all of the maps
   $lib_boxes = array();
-  while ($featuremap = db_fetch_object($lib_rset)) {
+  while ($featuremap = $lib_rset->fetchObject()) {
     $lib_boxes[$featuremap->featuremap_id] = "$featuremap->name";
   }
 
@@ -123,7 +123,7 @@ function get_tripal_featuremap_admin_form_reindex_set(&$form) {
 
   // iterate through all of the maps
   $lib_boxes = array();
-  while ($featuremap = db_fetch_object($lib_rset)) {
+  while ($featuremap = $lib_rset->fetchObject()) {
     $lib_boxes[$featuremap->featuremap_id] = "$featuremap->name";
   }
   $form['reindex']['description'] = array(
@@ -170,11 +170,11 @@ function get_tripal_featuremap_admin_form_sync_set(&$form) {
   // a message stating that all maps are currently synced.
   $lib_boxes = array();
   $added = 0;
-  while ($featuremap = db_fetch_object($lib_rset)) {
+  while ($featuremap = $lib_rset->fetchObject()) {
     // check to see if the map is already present as a node in drupal.
     // if so, then skip it.
-    $sql = "SELECT * FROM {chado_featuremap} WHERE featuremap_id = %d";
-    if (!db_fetch_object(db_query($sql, $featuremap->featuremap_id))) {
+    $sql = "SELECT * FROM {chado_featuremap} WHERE featuremap_id = :featuremap_id";
+    if (!db_query($sql, array(':featuremap_id' => $featuremap->featuremap_id))->fetchObject()) {
       $lib_boxes[$featuremap->featuremap_id] = "$featuremap->name";
       $added++;
     }
@@ -238,8 +238,8 @@ function tripal_featuremap_admin_validate($form, &$form_state) {
     }
     if ($featuremap_id and preg_match("/^\d+$/i", $featuremap_id)) {
       // get the map info
-      $sql = "SELECT * FROM {featuremap} WHERE featuremap_id = %d";
-      $featuremap = db_fetch_object(chado_query($sql, $featuremap_id));
+      $sql = "SELECT * FROM {featuremap} WHERE featuremap_id = :featuremap_id";
+      $featuremap = chado_query($sql, array(':featuremap_id' => $featuremap_id))->fetchObject();
       $to_sync[$featuremap_id] = $featuremap->name;
     }
   }
@@ -263,8 +263,8 @@ function tripal_featuremap_admin_validate($form, &$form_state) {
     foreach ($featuremaps as $featuremap_id) {
       if ($featuremap_id and preg_match("/^\d+$/i", $featuremap_id)) {
         // get the map info
-        $sql = "SELECT * FROM {featuremap} WHERE featuremap_id = %d";
-        $featuremap = db_fetch_object(chado_query($sql, $featuremap_id));
+        $sql = "SELECT * FROM {featuremap} WHERE featuremap_id = :featuremap_id";
+        $featuremap = chado_query($sql, array(':featuremap_id' => $featuremap_id))->fetchObject();
         $job_args[0] = $featuremap_id;
         tripal_add_job("Reindex features for map: $featuremap->name", 'tripal_featuremap',
          'tripal_featuremap_reindex_features', $job_args, $user->uid);
@@ -279,8 +279,8 @@ function tripal_featuremap_admin_validate($form, &$form_state) {
     foreach ($featuremaps as $featuremap_id) {
       if ($featuremap_id and preg_match("/^\d+$/i", $featuremap_id)) {
         // get the map info
-        $sql = "SELECT * FROM {featuremap} WHERE featuremap_id = %d";
-        $featuremap = db_fetch_object(chado_query($sql, $featuremap_id));
+        $sql = "SELECT * FROM {featuremap} WHERE featuremap_id = :featuremap_id";
+        $featuremap = chado_query($sql, array(':featuremap_id' => $featuremap_id))->fetchObject();
         $job_args[0] = $featuremap_id;
         tripal_add_job("Set taxonomy for features in map: $featuremap->name", 'tripal_featuremap',
          'tripal_featuremap_taxonify_features', $job_args, $user->uid);
@@ -307,24 +307,24 @@ function tripal_featuremap_sync_featuremaps($featuremap_id = NULL, $job_id = NUL
 
   // get the list of featuremaps and create new nodes
   if (!$featuremap_id) {
-    $sql = "SELECT * FROM {featuremap} L";
+    $sql = "SELECT * FROM {featuremap} F";
     $results = chado_query($sql);
   }
   else {
-    $sql = "SELECT * FROM {featuremap} L WHERE featuremap_id = %d";
-    $results = chado_query($sql, $featuremap_id);
+    $sql = "SELECT * FROM {featuremap} F WHERE featuremap_id = :featuremap_id";
+    $results = chado_query($sql, array(':featuremap_id' => $featuremap_id));
   }
 
   // We'll use the following SQL statement for checking if the map
   // already exists as a drupal node.
   $sql = "SELECT * FROM {chado_featuremap} ".
-        "WHERE featuremap_id = %d";
+        "WHERE featuremap_id = :featuremap_id";
 
-  while ($featuremap = db_fetch_object($results)) {
+  while ($featuremap = $results->fetchObject()) {
 
     // check if this map already exists in the drupal database. if it
     // does then skip this map and go to the next one.
-    if (!db_fetch_object(db_query($sql, $featuremap->featuremap_id))) {
+    if (!db_query($sql, array(':featuremap_id' => $featuremap->featuremap_id))->fetchObject()) {
 
     $new_node = new stdClass();
     $new_node->type = 'chado_featuremap';

tripal_featuremap/includes/tripal_featuremap.form.inc

@@ -55,7 +55,7 @@ function chado_featuremap_form($node) {
     ORDER BY CVT.name ASC 
   ";
   $prop_types = chado_query($sql);
-  while ($prop = db_fetch_object($prop_types)) {
+  while ($prop = $prop_types->fetchObject()) {
     $properties_select[$prop->cvterm_id] = $prop->name;
     $properties_list[$prop->cvterm_id] = $prop;
   }
@@ -129,13 +129,13 @@ function chado_featuremap_validate($node, &$form) {
   if ($node->featuremap_id) {
     $sql = "
       SELECT * FROM {featuremap} 
-      WHERE name = '%s' AND NOT featuremap_id = %d
+      WHERE name = :name AND NOT featuremap_id = :featuremap_id
     ";
-    $featuremap = db_fetch_object(chado_query($sql, $node->title, $node->featuremap_id));
+    $featuremap = chado_query($sql, array(':name' => $node->title, ':featurempa_id' => $node->featuremap_id))->fetchObject();
   }
   else {
-    $sql = "SELECT * FROM {featuremap} WHERE name = '%s'";
-    $featuremap = db_fetch_object(chado_query($sql, $node->title));
+    $sql = "SELECT * FROM {featuremap} WHERE name = :name";
+    $featuremap = chado_query($sql, array(':name' => $node->title))->fetchObject();
   }
   if ($featuremap) {
     form_set_error('name', t('The unique map name already exists. Please choose another'));
@@ -326,11 +326,11 @@ function chado_featuremap_node_form_add_featuremapprop_table_props(&$form, $form
     SELECT CVT.cvterm_id, CVT.name, CVT.definition, PP.value, PP.rank
     FROM {featuremapprop} PP
       INNER JOIN {cvterm} CVT on CVT.cvterm_id = PP.type_id
-    WHERE PP.featuremap_id = %d
+    WHERE PP.featuremap_id = :featuremap_id
     ORDER BY CVT.name, PP.rank
   ";
-  $featuremap_props = chado_query($sql, $featuremap_id);
-  while ($prop = db_fetch_object($featuremap_props)) {
+  $featuremap_props = chado_query($sql, array(':featuremap_id' => $featuremap_id));
+  while ($prop = $featuremap_props->fetchObject()) {
 
     $type_id = $prop->cvterm_id;
     $rank = count($d_properties[$type_id]);

tripal_featuremap/tripal_featuremap.info

@@ -1,9 +1,9 @@
 name = Tripal Feature Map
-description = A module for interfacing the GMOD chado database with Drupal, providing viewing, inserting and editing of maps.
-core = 6.x
+description = A module for interfacing the GMOD chado database with Drupal, providing viewing, inserting and editing of maps (e.g. genetic maps).
+core = 7.x
 project = tripal_featuremap
 package = Tripal
-version = 6.x-1.1
+version = 7.x-2.0-beta1
 dependencies[] = tripal_core
 dependencies[] = tripal_organism
 dependencies[] = tripal_feature

tripal_featuremap/tripal_featuremap.install

@@ -4,6 +4,24 @@
  * @todo Add file header description
  */
 
+/**
+ * Implementation of hook_requirements().
+ */
+function tripal_featuremap_requirements($phase) {
+  $requirements = array();
+  if ($phase == 'install') {
+    // make sure chado is installed
+    if (!tripal_core_is_chado_installed()) {
+      $requirements ['tripal_featuremap'] = array(
+        'title' => "tripal_featuremap",
+        'value' => "ERROR: Chado most be installed before this module can be enabled",
+        'severity' => REQUIREMENT_ERROR,
+      );
+    }
+  }
+  return $requirements;
+}
+
 /**
  * Implementation of hook_install().
  *
@@ -13,10 +31,6 @@ function tripal_featuremap_install() {
   // create the module's data directory
   tripal_create_moddir('tripal_featuremap');
 
-  // create the tables that correlate drupal nodes with chado
-  // features, maps, etc....
-  drupal_install_schema('tripal_featuremap');
-  
   // add the featuremapprop table to Chado
   tripal_featuremap_add_custom_tables();
   
@@ -25,44 +39,21 @@ function tripal_featuremap_install() {
 
 }
 
-/**
- * Implementation of hook_schema().
- *
- * @ingroup tripal_featuremap
- */
-function tripal_featuremap_schema() {
-  $schema = tripal_featuremap_get_schemas();
-  return $schema;
-}
-
 /**
  * Implementation of hook_uninstall().
  *
  * @ingroup tripal_featuremap
  */
 function tripal_featuremap_uninstall() {
-  drupal_uninstall_schema('tripal_featuremap');
 
-  // Get the list of nodes to remove
-  $sql_lib_id = "SELECT nid, vid ".
-                "FROM {node} ".
-                "WHERE type='chado_featuremap'";
-  $result = db_query($sql_lib_id);
-  while ($node = db_fetch_object($result)) {
-    node_delete($node->nid);
-  }
 }
 
 /**
- * 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.
+ * Implementation of hook_schema().
  *
  * @ingroup tripal_featuremap
  */
-function tripal_featuremap_get_schemas() {
-  $schema = array();
+function tripal_featuremap_schema() {
   $schema['chado_featuremap'] = array(
     'fields' => array(
       'vid' => array(
@@ -95,23 +86,7 @@ function tripal_featuremap_get_schemas() {
   return $schema;
 }
 
-/**
- * Implementation of hook_requirements(). 
- */
-function tripal_featuremap_requirements($phase) {
-  $requirements = array();
-  if ($phase == 'install') {
-    // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
-      $requirements ['tripal_featuremap'] = array(
-            'title' => "tripal_featuremap",
-            'value' => "ERROR: Chado most be installed before this module can be enabled",
-            'severity' => REQUIREMENT_ERROR,
-      );
-    }
-  }
-  return $requirements;
-}
+
 
 /*
  * 
@@ -218,7 +193,7 @@ function tripal_featuremap_add_custom_tables(){
       ),
     ),
   );  
-  tripal_core_create_custom_table($ret, 'featuremapprop', $schema, TRUE);
+  tripal_core_create_custom_table('featuremapprop', $schema, TRUE);
   
   // add the featuremap_dbxref table to Chado
   $schema = array (
@@ -270,7 +245,7 @@ function tripal_featuremap_add_custom_tables(){
     ),
     'referring_tables' => NULL,
   );
-  tripal_core_create_custom_table($ret, 'featuremap_dbxref', $schema, TRUE);
+  tripal_core_create_custom_table('featuremap_dbxref', $schema, TRUE);
   
   $schema = array (
     'table' => 'featureposprop',
@@ -330,23 +305,5 @@ function tripal_featuremap_add_custom_tables(){
       ),
     ),
   );
-  tripal_core_create_custom_table($ret, 'featureposprop', $schema, TRUE);
+  tripal_core_create_custom_table('featureposprop', $schema, TRUE);
 }
-
-/**
- *  Update for Drupal 6.x, Tripal 1.1, FeatureMap Module 1.1
- *  This update adds a new featuremapprop, featureposprop, and featuremap_dbxref tables and 
- *  CV terms for the featuremap_property CV
- *
- */
-function tripal_featuremap_update_6100() {
-
-  tripal_featuremap_add_custom_tables();  
-  tripal_featuremap_add_cvterms();
-   
-  $ret = array(
-    '#finished' => 1,
-  );
-
-  return $ret;
-}

tripal_featuremap/tripal_featuremap.module

@@ -53,7 +53,7 @@ function tripal_featuremap_node_info() {
   $nodes = array();
   $nodes['chado_featuremap'] = array(
       'name' => t('Map'),
-      'module' => 'chado_featuremap',
+      'base' => 'chado_featuremap',
       'description' => t('A feature map from the chado database (e.g. genetic map)'),
       'has_title' => FALSE,
       'title_label' => t('Feature Map'),
@@ -71,13 +71,28 @@ function tripal_featuremap_node_info() {
  *
  * @ingroup tripal_featuremap
  */
-function tripal_featuremap_perm() {
+function tripal_featuremap_permissions() {
   return array(
-    'access chado_featuremap content',
-    'create chado_featuremap content',
-    'delete chado_featuremap content',
-    'edit chado_featuremap content',
-    'administer tripal featuremap',
+    'access chado_featuremap content' => array(
+      'title' => t('View Maps'),
+      'description' => t('Allow users to view map pages.'),
+    ),
+    'create chado_featuremap content' => array(
+      'title' => t('Create Maps'),
+      'description' => t('Allow users to create new map pages.'),
+    ),
+    'delete chado_featuremap content' => array(
+      'title' => t('Delete Maps'),
+      'description' => t('Allow users to delete map pages.'),
+    ),
+    'edit chado_featuremap content' => array(
+      'title' => t('Edit Maps'),
+      'description' => t('Allow users to edit map pages.'),
+    ),
+    'adminster tripal featuremap' => array(
+      'title' => t('Administer Maps'),
+      'description' => t('Allow users to administer all maps.'),
+    ),
   );
 }
 /**
@@ -180,35 +195,6 @@ function tripal_featuremap_views_api() {
   );
 }
 
-
-
-/**
- * Implementation of hook_nodeapi().
- * Display map information for associated features or organisms
- * This function also provides contents for indexing
- *
- * @ingroup tripal_featuremap
- */
-function tripal_featuremap_nodeapi(&$node, $op, $teaser, $page) {
-
-  switch ($op) {
-    // Note that this function only adds map view to an organism/feature
-    // node.
-    case 'view':
-      // add the map to the organism/feature search indexing
-      if ($node->build_mode == NODE_BUILD_SEARCH_INDEX) {
-        $node->content['tripal_featuremap_index_version'] = array(
-          '#value' => theme('tripal_featuremap_search_index', $node),
-        );
-      }
-      elseif ($node->build_mode == NODE_BUILD_SEARCH_RESULT) {
-        $node->content['tripal_featuremap_index_version'] = array(
-          '#value' => theme('tripal_featuremap_search_result', $node),
-        );
-      }
-  }
-}
-
 /**
  *  We need to let drupal know about our theme functions and their arguments.
  *  We create theme functions to allow users of the module to customize the
@@ -257,6 +243,64 @@ function tripal_featuremap_theme() {
   );
 }
 
+/**
+ * @ingroup tripal_library
+ */
+function tripal_featuremap_block_info() {
+
+  $blocks['mapbase']['info'] = t('Tripal Map Details');
+  $blocks['mapbase']['cache'] = BLOCK_NO_CACHE;
+
+  $blocks['mapprops']['info'] = t('Tripal Map Properties');
+  $blocks['mapprops']['cache'] = BLOCK_NO_CACHE;
+  
+  $blocks['mappos']['info'] = t('Tripal Map Features');
+  $blocks['mappos']['cache'] = BLOCK_NO_CACHE;
+  
+  $blocks['mappubs']['info'] = t('Tripal Map Publications');
+  $blocks['mappubs']['cache'] = BLOCK_NO_CACHE;
+
+  $blocks['maprefs']['info'] = t('Tripal Map References');
+  $blocks['maprefs']['cache'] = BLOCK_NO_CACHE;
+    
+  return $blocks;
+}
+/**
+ * @ingroup tripal_library
+ */
+function tripal_featuremap_block_view($delta = '') {
+
+  if (user_access('access chado_library content') and arg(0) == 'node' and is_numeric(arg(1))) {
+    $nid = arg(1);
+    $node = node_load($nid);
+
+    $block = array();
+    switch ($delta) {
+      case 'mapbase':
+        $block['subject'] = t('Library Details');
+        $block['content'] = theme('tripal_featuremap_base', $node);
+        break;
+      case 'mapprops':
+        $block['subject'] = t('Properties');
+        $block['content'] = theme('tripal_featuremap_properties', $node);
+        break;
+      case 'mappos':
+        $block['subject'] = t('Features');
+        $block['content'] = theme('tripal_featuremap_featurepos', $node);
+        break;
+      case 'mappubs':
+        $block['subject'] = t('Publications');
+        $block['content'] = theme('tripal_featuremap_publication', $node);
+        break;
+      case 'maprefs':
+        $block['subject'] = t('References');
+        $block['content'] = theme('tripal_featuremap_references', $node);
+        break;
+      default :
+    }
+    return $block;
+  }
+}
 /**
  * This function is an extension of the chado_feature_view and
  * chado_organism_view by providing the markup for the map object
@@ -279,13 +323,13 @@ function tripal_featuremap_cron() {
  *
  * This hook allows node modules to limit access to the node types they define.
  *
- *  @param $op
- *  The operation to be performed
- *
  *  @param $node
  *  The node on which the operation is to be performed, or, if it does not yet exist, the
  *  type of node to be created
  *
+ *  @param $op
+ *  The operation to be performed
+ *
  *  @param $account
  *  A user object representing the user for whom the operation is to be performed
  *
@@ -297,7 +341,7 @@ function tripal_featuremap_cron() {
  *
  * @ingroup tripal_featuremap
  */
-function tripal_featuremap_map_access($op, $node, $account) {
+function chado_featuremap_node_access($node, $op, $account) {
   if ($op == 'create') {
     if (!user_access('create chado_featuremap content', $account)) {
       return FALSE;
@@ -375,7 +419,7 @@ function chado_featuremap_insert($node) {
       ORDER BY CVT.name ASC 
     ";
     $prop_types = chado_query($sql);
-    while ($prop = db_fetch_object($prop_types)) {
+    while ($prop = $prop_types->fetchObject()) {
       $properties_list[$prop->cvterm_id] = $prop->name;
     }   
   
@@ -441,14 +485,13 @@ function chado_featuremap_insert($node) {
     $featuremap_id = chado_get_id_for_node('featuremap', $node->nid) ;
     if (!$featuremap_id) {
        // next add the item to the drupal table
-      $sql = "INSERT INTO {chado_featuremap} (nid, vid, featuremap_id) VALUES (%d, %d, %d)";
-      db_query($sql, $node->nid, $node->vid, $featuremap['featuremap_id']);
-    }       
+      $sql = "
+        INSERT INTO {chado_featuremap} (nid, vid, featuremap_id) 
+        VALUES (:nid, :vid, :featuremap_id)
+      ";
+      db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid, ':featuremap_id' => $featuremap['featuremap_id']));
+    }
   }
-
-  
-  
-  
 }
 /**
  * Update nodes
@@ -494,7 +537,7 @@ function chado_featuremap_update($node) {
     ORDER BY CVT.name ASC 
   ";
   $prop_types = chado_query($sql);
-  while ($prop = db_fetch_object($prop_types)) {
+  while ($prop = $prop_types->fetchObject()) {
     $properties_list[$prop->cvterm_id] = $prop->name;
   }
   
@@ -613,32 +656,14 @@ function chado_featuremap_delete(&$node) {
 
   // Remove data from {chado_featuremap}, {node} and {node_revisions} tables of
   // drupal database
-  $sql_del = "DELETE FROM {chado_featuremap} ".
-            "WHERE nid = %d ".
-            "AND vid = %d";
-  db_query($sql_del, $node->nid, $node->vid);
-  $sql_del = "DELETE FROM {node} ".
-            "WHERE nid = %d ".
-            "AND vid = %d";
-  db_query($sql_del, $node->nid, $node->vid);
-  $sql_del = "DELETE FROM {node_revisions} ".
-            "WHERE nid = %d ".
-            "AND vid = %d";
-  db_query($sql_del, $node->nid, $node->vid);
+  $sql_del = "DELETE FROM {chado_featuremap} WHERE nid = :nid AND vid = :vid";
+  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
+  $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
+  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
+  $sql_del = "DELETE FROM {node_revisions} WHERE nid = :nid AND vid = :vid";
+  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
 
   // Remove data from map and mapprop tables of chado database as well
-  chado_query("DELETE FROM {featuremap} WHERE featuremap_id = %d", $featuremap_id);
-  chado_query("DELETE FROM {featuremapprop} WHERE featuremap_id = %d", $featuremap_id);
-}
-
-/*
- *
- */
-function theme_tripal_featuremap_search_result($node) {
-
+  chado_query("DELETE FROM {featuremap} WHERE featuremap_id = :featuremap_id", array(':featuremap_id' => $featuremap_id));
+  chado_query("DELETE FROM {featuremapprop} WHERE featuremap_id = :featuremap_id", array(':featuremap_id' => $featuremap_id));
 }
-
-function tripal_featuremap_form_alter(&$form, &$form_state, $form_id) {
-  if ($form_id == "chado_featuremap_node_form") {
-  }
-}

tripal_genetic/tripal_genetic.info

@@ -1,9 +1,9 @@
 name = Tripal Genetic
-description = A module for interfacing the GMOD chado database with Drupal, providing viewing of Genetic data
-core = 6.x
+description = A module for interfacing the GMOD chado database with Drupal, providing viewing of genetic data
+core = 7.x
 project = tripal_genetic
 package = Tripal
-version = 6.x-1.1
+version = 7.x-2.0-beta1
 dependencies[] = tripal_core
 dependencies[] = tripal_cv
 dependencies[] = tripal_feature

tripal_genetic/tripal_genetic.module

@@ -53,33 +53,33 @@ function tripal_genetic_theme() {
  *
  * @ingroup tripal_genetic
  */
-function tripal_genetic_nodeapi(&$node, $op, $teaser, $page) {
-  switch ($op) {
-    case 'view':
-      if ($node->type == 'chado_feature') {
-        // the tripal_natural_diversity module provides a tripal_feature_nd_genotype
-        // template.  The only difference between them is the addition of
-        // project information by this ND module's template.  Therefore,
-        // if the tripal_natural_diversity content is present then don't add the
-        // template from this module as the ND module would superceed this.
-        if (!array_key_exists('tripal_feature_nd_genotypes', $node->content)) {
-          $node->content['tripal_feature_genotypes'] = array(
-            '#value' => theme('tripal_feature_genotypes', $node),
-          );
-        }
+function tripal_genetic_node_view(&$node, $view_mode, $langcode) {
+  if ($node->type == 'chado_feature') {
+    // the tripal_natural_diversity module provides a tripal_feature_nd_genotype
+    // template.  The only difference between them is the addition of
+    // project information by this ND module's template.  Therefore,
+    // if the tripal_natural_diversity content is present then don't add the
+    // template from this module as the ND module would superceed this.
+    if ($view_mode == 'full') {
+      if (!array_key_exists('tripal_feature_nd_genotypes', $node->content)) {
+        $node->content['tripal_feature_genotypes'] = array(
+          '#value' => theme('tripal_feature_genotypes', $node),
+        );
       }
-      if ($node->type == 'chado_stock') {
-        // the tripal_natural_diversity module provides a tripal_stock_nd_genotype
-        // template.  The only difference between them is the addition of
-        // project information by this ND module's template.  Therefore,
-        // if the tripal_natural_diversity content is present then don't add the
-        // template from this module as the ND module would superceed this.
-        if (!array_key_exists('tripal_stock_nd_genotypes', $node->content)) {
-          $node->content['tripal_stock_genotypes'] = array(
-            '#value' => theme('tripal_stock_genotypes', $node),
-          );
-        }
+    }
+  }
+  if ($node->type == 'chado_stock') {
+    // the tripal_natural_diversity module provides a tripal_stock_nd_genotype
+    // template.  The only difference between them is the addition of
+    // project information by this ND module's template.  Therefore,
+    // if the tripal_natural_diversity content is present then don't add the
+    // template from this module as the ND module would superceed this.
+    if ($view_mode == 'full') {
+      if (!array_key_exists('tripal_stock_nd_genotypes', $node->content)) {
+        $node->content['tripal_stock_genotypes'] = array(
+          '#value' => theme('tripal_stock_genotypes', $node),
+        );
       }
-      break;
+    }
   }
 }

tripal_library/includes/tripal_library.admin.inc

@@ -126,7 +126,7 @@ function get_tripal_library_admin_form_reindex_set(&$form) {
 
   // iterate through all of the libraries
   $lib_boxes = array();
-  while ($library = db_fetch_object($lib_rset)) {
+  while ($library = $lib_rset->fetchObject()) {
     $lib_boxes[$library->library_id] = "$library->name";
   }
   $form['reindex']['description'] = array(
@@ -242,8 +242,8 @@ function tripal_library_admin_validate($form, &$form_state) {
     }
     if ($library_id and preg_match("/^\d+$/i", $library_id)) {
       // get the library info
-      $sql = "SELECT * FROM {Library} WHERE library_id = %d";
-      $library = db_fetch_object(chado_query($sql, $library_id));
+      $sql = "SELECT * FROM {library} WHERE library_id = :library_id";
+      $library = chado_query($sql, array(':library_id' => $library_id))->fetchObject();
       $to_sync[$library_id] = $library->name;
     }
   }
@@ -267,8 +267,8 @@ function tripal_library_admin_validate($form, &$form_state) {
     foreach ($libraries as $library_id) {
       if ($library_id and preg_match("/^\d+$/i", $library_id)) {
         // get the library info
-        $sql = "SELECT * FROM {Library} WHERE library_id = %d";
-        $library = db_fetch_object(chado_query($sql, $library_id));
+        $sql = "SELECT * FROM {Library} WHERE library_id = :library_id";
+        $library = chado_query($sql, array(':library_id' => $library_id))->fetchObject();
         $job_args[0] = $library_id;
         tripal_add_job("Reindex features for library: $library->name", 'tripal_library',
          'tripal_library_reindex_features', $job_args, $user->uid);
@@ -283,8 +283,8 @@ function tripal_library_admin_validate($form, &$form_state) {
     foreach ($libraries as $library_id) {
       if ($library_id and preg_match("/^\d+$/i", $library_id)) {
         // get the library info
-        $sql = "SELECT * FROM {Library} WHERE library_id = %d";
-        $library = db_fetch_object(chado_query($sql, $library_id));
+        $sql = "SELECT * FROM {Library} WHERE library_id = :libary_id";
+        $library = chado_query($sql, array(':library_id' => $library_id))->fetchObject();
         $job_args[0] = $library_id;
         tripal_add_job("Set taxonomy for features in library: $library->name", 'tripal_library',
          'tripal_library_taxonify_features', $job_args, $user->uid);
@@ -307,29 +307,18 @@ function tripal_library_admin_validate($form, &$form_state) {
  */
 function tripal_library_add_taxonomy($node, $library_id) {
 
-    //include the file containing the required functions.  We only have to
-    // do this because Drupal 6 fails to do this globally for us and
-    // the drupal_execute function below won't work
-    module_load_include('inc', 'taxonomy', 'taxonomy.admin');
-
-   /*   // get the vocabulary id
-    $vocabularies = taxonomy_get_vocabularies();
-    $vid = NULL;
-    foreach($vocabularies as $vocab){
-    if($vocab->name == 'DNA Libraries'){
-    $vid = $vocab->vid;
-    }
-    }
-
-    if(!$vid){  */
+  //include the file containing the required functions.  We only have to
+  // do this because Drupal 6 fails to do this globally for us and
+  // the drupal_execute function below won't work
+  module_load_include('inc', 'taxonomy', 'taxonomy.admin');
+    
    // add the vocabulary
   $vocab_form['values']['name'] = 'DNA Libraries';
   $vocab_form['values']['description'] = 'Allows for associating/searching of library features by library name';
   $vocab_form['values']['help'] = '';
   $vocab_form['values']['module'] = 'taxonomy';
-  drupal_execute('taxonomy_form_vocabulary', $vocab_form);
-  return;
-   //   }
+  drupal_form_submit('taxonomy_form_vocabulary', $vocab_form);
+  return;   
 
    // make sure this term doesn't already exist.  If it doesn't then add it
   if ($vid) {
@@ -346,7 +335,7 @@ function tripal_library_add_taxonomy($node, $library_id) {
       $form_state = array();
       $form_state['values']['name'] = $node->title;
       $form_state['values']['description'] = $library_id;
-      drupal_execute('taxonomy_form_term', $form_state, $vid);
+      drupal_form_submit('taxonomy_form_term', $form_state, $vid);
     }
   }
 }
@@ -364,24 +353,24 @@ function tripal_library_sync_libraries($library_id = NULL, $job_id = NULL) {
 
   // get the list of libraries and create new nodes
   if (!$library_id) {
-    $sql = "SELECT * FROM {Library} L";
+    $sql = "SELECT * FROM {library} L";
     $results = chado_query($sql);
   }
   else {
-    $sql = "SELECT * FROM {Library} L WHERE library_id = %d";
-    $results = chado_query($sql, $library_id);
+    $sql = "SELECT * FROM {library} L WHERE library_id = :library_id";
+    $results = chado_query($sql, array(':library_id' => $library_id));
   }
 
   // We'll use the following SQL statement for checking if the library
   // already exists as a drupal node.
   $sql = "SELECT * FROM {chado_library} ".
-        "WHERE library_id = %d";
+        "WHERE library_id = :libary_id";
 
-  while ($library = db_fetch_object($results)) {
+  while ($library = $results->fetchObject()) {
 
     // check if this library already exists in the drupal database. if it
     // does then skip this library and go to the next one.
-    if (!db_fetch_object(db_query($sql, $library->library_id))) {
+    if (!db_query($sql, array(':libary_id' => $library->library_id))->fetchObject()) {
 
     $new_node = new stdClass();
     $new_node->type = 'chado_library';
@@ -438,29 +427,35 @@ function tripal_library_feature_set_taxonomy($library_id = NULL) {
   // We'll use the following SQL statement for getting the node info
   if ($library_id) {
     print "Finding features for library with ID: $library_id\n";
-    $sql = "SELECT LF.feature_id, L.library_id, L.name as libname ".
-           "FROM {library_feature} LF ".
-           "INNER JOIN Library L ON LF.library_id = L.library_id ".
-           "WHERE L.library_id = $library_id ".
-           "ORDER BY LF.feature_id";
-    $features = chado_query($sql);
+    $sql = "
+      SELECT LF.feature_id, L.library_id, L.name as libname 
+      FROM {library_feature} LF 
+        INNER JOIN {library} L ON LF.library_id = L.library_id 
+      WHERE L.library_id = :library_id 
+      ORDER BY LF.feature_id
+    ";
+    $features = chado_query($sql, array(':library_id' => $library_id));
   }
   else {
     print "Finding features for all libraries\n";
-    $sql = "SELECT LF.feature_id, L.library_id, L.name as libname ".
-           "FROM {library_feature} LF ".
-           "INNER JOIN Library L ON LF.library_id = L.library_id ".
-           "ORDER BY LF.feature_id";
+    $sql = "
+      SELECT LF.feature_id, L.library_id, L.name as libname 
+      FROM {library_feature} LF 
+        INNER JOIN {library} L ON LF.library_id = L.library_id 
+      ORDER BY LF.feature_id
+    ";
     $features = chado_query($sql);
   }
 
-  $node_sql = "SELECT * FROM {chado_feature} CF ".
-             "  INNER JOIN {node} N ON CF.nid = N.nid ".
-             "WHERE feature_id = %d";
-
+  $node_sql = "
+    SELECT * 
+    FROM {chado_feature} CF 
+      INNER JOIN {node} N ON CF.nid = N.nid 
+    WHERE feature_id = :feature_id
+  ";
   // iterate through the features and add the taxonomy
-  while ($feature = db_fetch_object($features)) {
-    $node = db_fetch_object(db_query($node_sql, $feature->feature_id));
+  while ($feature = $features->fetchObject()) {
+    $node = db_query($node_sql, array(':feature_id' => $feature->feature_id))->fetchObject();
     $tags["$vid"] = $feature->libname;
     $terms['tags'] = $tags;
     taxonomy_node_save($node, $terms);
@@ -478,25 +473,29 @@ function tripal_library_reindex_features($library_id = NULL, $job_id = NULL) {
   // associated with the library. Otherwise get all sequences assoicated
   // with all libraries.
   if ($library_id) {
-    $sql = "SELECT LF.feature_id, L.library_id, L.name as libname ".
-           " FROM {library_feature} LF ".
-           "  INNER JOIN Library L ON LF.library_id = L.library_id ".
-           "WHERE L.library_id = $library_id ".
-           "ORDER BY LF.feature_id";
-    $results = chado_query($sql);
+    $sql = "
+      SELECT LF.feature_id, L.library_id, L.name as libname 
+      FROM {library_feature} LF 
+        INNER JOIN {library} L ON LF.library_id = L.library_id
+      WHERE L.library_id = :library_id 
+      ORDER BY LF.feature_id
+    ";
+    $results = chado_query($sql, array(':library_id' => $library_id));
   }
   else {
-    $sql = "SELECT LF.feature_id, L.library_id, L.name as libname ".
-           " FROM {library_feature} LF ".
-           "  INNER JOIN Library L ON LF.library_id = L.library_id ".
-           "ORDER BY LF.feature_id";
+    $sql = "
+      SELECT LF.feature_id, L.library_id, L.name as libname 
+      FROM {library_feature} LF 
+        INNER JOIN {library} L ON LF.library_id = L.library_id 
+      ORDER BY LF.feature_id
+    ";
     $results = chado_query($sql);
   }
 
    // load into ids array
   $count = 0;
   $ids = array();
-  while ($id = db_fetch_object($results)) {
+  while ($id = $results->fetchObject()) {
     $ids[$count] = $id->feature_id;
     $count++;
   }
@@ -521,25 +520,29 @@ function tripal_library_taxonify_features($library_id = NULL, $job_id = NULL) {
   // associated with the library. Otherwise get all sequences assoicated
   // with all libraries.
   if ($library_id) {
-    $sql = "SELECT LF.feature_id, L.library_id, L.name as libname ".
-           " FROM {library_feature} LF ".
-           "  INNER JOIN Library L ON LF.library_id = L.library_id ".
-           "WHERE L.library_id = $library_id ".
-           "ORDER BY LF.feature_id";
-    $results = chado_query($sql);
+    $sql = "
+      SELECT LF.feature_id, L.library_id, L.name as libname 
+      FROM {library_feature} LF 
+        INNER JOIN {library} L ON LF.library_id = L.library_id 
+      WHERE L.library_id = :library_id 
+      ORDER BY LF.feature_id
+    ";
+    $results = chado_query($sql, array(':library_id' => $library_id));
   }
   else {
-    $sql = "SELECT LF.feature_id, L.library_id, L.name as libname ".
-           " FROM {library_feature} LF ".
-           "  INNER JOIN Library L ON LF.library_id = L.library_id ".
-           "ORDER BY LF.feature_id";
+    $sql = "
+      SELECT LF.feature_id, L.library_id, L.name as libname 
+      FROM {library_feature} LF 
+        INNER JOIN {library} L ON LF.library_id = L.library_id 
+      ORDER BY LF.feature_id
+    ";
     $results = chado_query($sql);
   }
 
   // load into ids array
   $count = 0;
   $ids = array();
-  while ($id = db_fetch_object($results)) {
+  while ($id = $results->fetchObject()) {
     $ids[$count] = $id->feature_id;
     $count++;
   }
@@ -548,10 +551,12 @@ function tripal_library_taxonify_features($library_id = NULL, $job_id = NULL) {
   tripal_feature_set_vocabulary();
 
   // use this SQL for getting the nodes
-  $nsql =  "SELECT * FROM {chado_feature} CF ".
-          "  INNER JOIN {node} N ON N.nid = CF.nid ".
-          "WHERE feature_id = %d";
-
+  $nsql =  "
+    SELECT * 
+    FROM {chado_feature} CF 
+      INNER JOIN {node} N ON N.nid = CF.nid 
+    WHERE feature_id = :feature_id
+  ";
    // iterate through the features and set the taxonomy
   $interval = intval($count * 0.01);
   foreach ($ids as $feature_id) {
@@ -559,7 +564,7 @@ function tripal_library_taxonify_features($library_id = NULL, $job_id = NULL) {
     if ($job_id and $i % interval == 0) {
       tripal_job_set_progress($job_id, intval(($i/$count)*100));
     }
-      $node = db_fetch_object(db_query($nsql, $feature_id));
+      $node = db_query($nsql, array(':feature_id' => $feature_id))->fetchObject();
       tripal_feature_set_taxonomy($node, $feature_id);
       $i++;
   }

tripal_library/tripal_library.info

@@ -1,12 +1,12 @@
 name = Tripal Library
 description = A module for interfacing the GMOD chado database with Drupal, providing viewing, inserting and editing of lbraries.
-core = 6.x
+core = 7.x
 project = tripal_library
 package = Tripal
-version = 6.x-1.1
-dependencies[] = tripal_core
-dependencies[] = tripal_organism
+version = 7.x-2.0-beta1
 dependencies[] = search
 dependencies[] = path
+dependencies[] = tripal_core
+dependencies[] = tripal_organism
 dependencies[] = tripal_cv
 

tripal_library/tripal_library.install

@@ -4,92 +4,58 @@
  * @todo Add file header description
  */
 
+/**
+ * Implementation of hook_requirements().
+ */
+function tripal_library_requirements($phase) {
+  $requirements = array();
+  if ($phase == 'install') {
+    // make sure chado is installed
+    if (!tripal_core_is_chado_installed()) {
+      $requirements ['tripal_library'] = array(
+        'title' => "tripal_library",
+        'value' => "ERROR: Chado most be installed before this module can be enabled",
+        'severity' => REQUIREMENT_ERROR,
+      );
+    }
+  }
+  return $requirements;
+}
 /**
  * Implementation of hook_install().
  *
  * @ingroup tripal_library
  */
 function tripal_library_install() {
+  
   // create the module's data directory
   tripal_create_moddir('tripal_library');
 
-  // create the tables that correlate drupal nodes with chado
-  // features, librarys, etc....
-  drupal_install_schema('tripal_library');
-
-  // Add the materialized view needed to count the features for the library
-  // Create the MView
-  tripal_add_mview('library_feature_count', 'tripal_library',
-    'library_feature_count',
-    'library_id integer, name character varying(255), '.
-    '  num_features integer, feature_type character varying(255)',
-    'library_id',
-    'SELECT '.
-    '   L.library_id, '.
-    '   L.name, '.
-    '    count(F.feature_id) as num_features, '.
-    '    CVT.name as feature_type '.
-    'FROM Library L '.
-    '    INNER JOIN Library_Feature LF  ON LF.library_id = L.library_id '.
-    '    INNER JOIN Feature F           ON LF.feature_id = F.feature_id '.
-    '    INNER JOIN Cvterm CVT          ON F.type_id = CVT.cvterm_id '.
-    'GROUP BY L.library_id, L.name, CVT.name',
-    ''
-  );
+  // add the materialized view
+  tripal_library_add_mview_library_feature_count();
   
-  // Add cvterms
+  // add cvterms
   tripal_library_add_cvterms();
 }
 
-/**
- * Implementation of hook_schema().
- *
- * @ingroup tripal_library
- */
-function tripal_library_schema() {
-  $schema = tripal_library_get_schemas();
-  return $schema;
-}
-
 /**
  * Implementation of hook_uninstall().
  *
  * @ingroup tripal_library
  */
 function tripal_library_uninstall() {
-  drupal_uninstall_schema('tripal_library');
-
-  // remove the materialized view
-  $sql = "SELECT * FROM {tripal_mviews} ".
-        "WHERE name = 'library_feature_count'";
-
-  if (db_table_exists('tripal_mviews')) {
-    $mview = db_fetch_object(db_query($sql));
-    if ($mview) {
-      tripal_mviews_action('delete', $mview->mview_id);
-    }
-  }
-
-  // Get the list of nodes to remove
-  $sql_lib_id = "SELECT nid, vid ".
-               "FROM {node} ".
-               "WHERE type='chado_library'";
-  $result = db_query($sql_lib_id);
-  while ($node = db_fetch_object($result)) {
-    node_delete($node->nid);
+  // Drop the MView table if it exists
+  if ($mview_id = tripal_mviews_get_mview_id('library_feature_count')) {
+    tripal_mviews_action("delete", $mview_id);
   }
 }
 
 /**
- * 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.
+ * Implementation of hook_schema().
  *
  * @ingroup tripal_library
  */
-function tripal_library_get_schemas() {
-  $schema = array();
+function tripal_library_schema() {
   $schema['chado_library'] = array(
     'fields' => array(
       'vid' => array(
@@ -98,49 +64,82 @@ function tripal_library_get_schemas() {
         'not null' => TRUE,
         'default' => 0
       ),
-    'nid' => array(
-      'type' => 'int',
-      'unsigned' => TRUE,
-      'not null' => TRUE,
-      'default' => 0
+      'nid' => array(
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
+        'default' => 0
       ),
-    'library_id' => array(
-      'type' => 'int',
-      'not null' => TRUE,
-      'default' => 0
+      'library_id' => array(
+        'type' => 'int',
+        'not null' => TRUE,
+        'default' => 0
       )
-      ),
+    ),
     'indexes' => array(
-      'library_id' => array('library_id')
-      ),
+      'chado_library_idx1' => array('library_id')
+    ),
     'unique keys' => array(
-      'nid_vid' => array('nid', 'vid'),
-      'vid' => array('vid')
-      ),
+      'chado_library_uq1' => array('nid', 'vid'),
+      'chado_library_uq2' => array('vid')
+    ),
     'primary key' => array('nid'),
   );
   return $schema;
 }
+
 /**
- * Implementation of hook_requirements(). 
+ * @ingroup tripal_library
  */
-function tripal_library_requirements($phase) {
-  $requirements = array();
-  if ($phase == 'install') {
-    // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
-      $requirements ['tripal_library'] = array(
-        'title' => "tripal_library",
-        'value' => "ERROR: Chado most be installed before this module can be enabled",
-        'severity' => REQUIREMENT_ERROR,
-      );
-    }
-  }
-  return $requirements;
+function tripal_library_add_mview_library_feature_count(){
+  $view_name = 'library_feature_count';
+  $comment = 'Provides count of feature by type that are associated with all libraries';
+  
+  $schema = array(
+    'table' => $view_name,
+    'description' => $comment,
+    'fields' => array(
+      'library_id' => array(
+        'type' => 'int',
+        'not null' => TRUE,
+      ),
+      'name' => array(
+        'type' => 'varchar',
+        'length' => 255,
+        'not null' => TRUE,
+      ),
+      'num_features' => array(
+        'type' => 'int',
+        'not null' => TRUE,
+      ),
+      'feature_type' => array(
+        'type' => 'varchar',
+        'length' => 255,
+        'not null' => TRUE,
+      ),
+    ),
+    'indexes' => array(
+      'library_feature_count_idx1' => array('library_id'),
+    ),
+  );
+  
+  $sql = "
+    SELECT 
+      L.library_id, L.name, 
+      count(F.feature_id) as num_features, 
+      CVT.name as feature_type 
+    FROM library L 
+      INNER JOIN library_feature LF  ON LF.library_id = L.library_id 
+      INNER JOIN feature F           ON LF.feature_id = F.feature_id 
+      INNER JOIN cvterm CVT          ON F.type_id     = CVT.cvterm_id 
+    GROUP BY L.library_id, L.name, CVT.name
+  ";
+  
+  tripal_add_mview($view_name, 'tripal_library', $schema, $sql, $comment);
 }
 
-/*
- * 
+/**
+ * @ingroup tripal_library
  */
 function tripal_library_add_cvterms() {
   
@@ -163,17 +162,4 @@ function tripal_library_add_cvterms() {
     'tripal_library_types', 0, 1, 'tripal');
   tripal_cv_add_cvterm(array('name' => 'genomic_library','def' => 'Genomic Library'), 
     'tripal_library_types', 0, 1, 'tripal');
-}
-
-/**
- *  Update for Drupal 6.x, Tripal 1.0
- *  This update
- *   - adds the library types
- *
- * @ingroup tripal_library
- */
-function tripal_library_update_6000() {
-  // add in the missing library typ cv terms
-  tripal_library_add_cvterms();
-  return $ret;
 }

tripal_library/tripal_library.module

@@ -42,12 +42,11 @@ function tripal_library_node_info() {
   $nodes = array();
   $nodes['chado_library'] = array(
     'name' => t('Library'),
-    'module' => 'chado_library',
+    'base' => 'chado_library',
     'description' => t('A library from the chado database'),
     'has_title' => FALSE,
     'title_label' => t('Library'),
     'has_body' => FALSE,
-    'body_label' => t('Library Description'),
     'locked' => TRUE
   );
   return $nodes;
@@ -60,27 +59,42 @@ function tripal_library_node_info() {
  *
  * @ingroup tripal_library
  */
-function tripal_library_perm() {
+function tripal_library_permisssions() {
   return array(
-    'access chado_library content',
-    'create chado_library content',
-    'delete chado_library content',
-    'edit chado_library content',
-    'administer tripal libraries',
+    'access chado_library content' => array(
+      'title' => t('View Libraries'),
+      'description' => t('Allow users to view library pages.'),
+    ),
+    'create chado_library content' => array(
+      'title' => t('Create Libraries'),
+      'description' => t('Allow users to create new library pages.'),
+    ),
+    'delete chado_library content' => array(
+      'title' => t('Delete Libraries'),
+      'description' => t('Allow users to delete library pages.'),
+    ),
+    'edit chado_library content' => array(
+      'title' => t('Edit Libraries'),
+      'description' => t('Allow users to edit library pages.'),
+    ),
+    'adminster tripal library' => array(
+      'title' => t('Administer Libraries'),
+      'description' => t('Allow users to administer all libraries.'),
+    ),
   );
 }
 /**
  * Implement hook_access().
  *
  * This hook allows node modules to limit access to the node types they define.
- *
- *  @param $op
- *  The operation to be performed
- *
+ * 
  *  @param $node
  *  The node on which the operation is to be performed, or, if it does not yet exist, the
  *  type of node to be created
  *
+ *  @param $op
+ *  The operation to be performed
+ *
  *  @param $account
  *  A user object representing the user for whom the operation is to be performed
  *
@@ -92,7 +106,7 @@ function tripal_library_perm() {
  *
  * @ingroup tripal_library
  */
-function chado_library_access($op, $node, $account) {
+function chado_library_node_access($node, $op, $account) {
   if ($op == 'create') {
     if (!user_access('create chado_library content', $account)) {
       return FALSE;
@@ -169,49 +183,27 @@ function tripal_library_views_api() {
 }
 
 /**
- * Implementation of hook_nodeapi().
- * Display library information for associated features or organisms
- * This function also provides contents for indexing
- *
  * @ingroup tripal_library
  */
-function tripal_library_nodeapi(&$node, $op, $teaser, $page) {
-
-  switch ($op) {
-    // Note that this function only adds library view to an organism/feature
-    // node.
-    case 'view':
-      // add the library to the organism/feature search indexing
-    if ($node->build_mode == NODE_BUILD_SEARCH_INDEX) {
-      $node->content['tripal_library_index_version'] = array(
-    '#value' => theme('tripal_library_search_index', $node),
-      );
-    }
-    elseif ($node->build_mode == NODE_BUILD_SEARCH_RESULT) {
-      $node->content['tripal_library_index_version'] = array(
-    '#value' => theme('tripal_library_search_result', $node),
-      );
-    }
-    else {
-      switch ($node->type) {
-        case 'chado_organism':
-          // Show library if the organism/feature is not at teaser view
-          $node->content['tripal_organism_libraries'] = array(
-        '#value' => theme('tripal_organism_libraries', $node),
-          );
-        break;
-        case 'chado_feature':
-          // Show library if the organism/feature is not at teaser view
-          $node->content['tripal_feature_libraries'] = array(
-        '#value' => theme('tripal_feature_libraries', $node),
-          );
-        break;
-        }
+function tripal_library_node_view(&$node, $view_mode, $langcode) {
+
+  switch ($node->type) {
+    case 'chado_organism':
+      if ($view_mode == 'full') {
+        $node->content['tripal_organism_libraries'] = array(
+          '#value' => theme('tripal_organism_libraries', $node),
+        );
+      }
+      break;
+    case 'chado_feature':
+      if ($view_mode == 'full') {
+        $node->content['tripal_feature_libraries'] = array(
+          '#value' => theme('tripal_feature_libraries', $node),
+        );
       }
-    break;
+      break;
   }
 }
-
 /**
  *  We need to let drupal know about our theme functions and their arguments.
  *  We create theme functions to allow users of the module to customize the
@@ -265,7 +257,78 @@ function tripal_library_theme() {
     ),
   );
 }
+/**
+ * @ingroup tripal_library
+ */
+function tripal_library_block_info() {
+
+  $blocks['libreferences']['info'] = t('Tripal Library Cross References');
+  $blocks['libreferences']['cache'] = BLOCK_NO_CACHE;
+
+  $blocks['libbase']['info'] = t('Tripal Library Details');
+  $blocks['libbase']['cache'] = BLOCK_NO_CACHE;
+
+  $blocks['libterms']['info'] = t('Tripal Library Terms');
+  $blocks['libterms']['cache'] = BLOCK_NO_CACHE;
+
+  $blocks['libsynonyms']['info'] = t('Tripal Library Synonyms');
+  $blocks['libsynonyms']['cache'] = BLOCK_NO_CACHE;
+
+  $blocks['libproperties']['info'] = t('Tripal Library Properties');
+  $blocks['libproperties']['cache'] = BLOCK_NO_CACHE;
 
+  $blocks['featurelibs']['info'] = t('Tripal Feature Libraries');
+  $blocks['featurelibs']['cache'] = BLOCK_NO_CACHE;
+
+  $blocks['orglibs']['info'] = t('Tripal Organism Libraries');
+  $blocks['orglibs']['cache'] = BLOCK_NO_CACHE;
+
+  return $blocks;
+}
+/**
+ * @ingroup tripal_library
+ */
+function tripal_library_block_view($delta = '') {
+
+  if (user_access('access chado_library content') and arg(0) == 'node' and is_numeric(arg(1))) {
+    $nid = arg(1);
+    $node = node_load($nid);
+
+    $block = array();
+    switch ($delta) {
+    	case 'libreferences':
+    	  $block['subject'] = t('Cross References');
+    	  $block['content'] = theme('tripal_library_references', $node);
+    	  break;
+    	case 'libbase':
+    	  $block['subject'] = t('Library Details');
+    	  $block['content'] = theme('tripal_library_base', $node);
+    	  break;
+    	case 'libsynonyms':
+    	  $block['subject'] = t('Synonyms');
+    	  $block['content'] = theme('tripal_library_synonyms', $node);
+    	  break;
+    	case 'libproperties':
+    	  $block['subject'] = t('Properties');
+    	  $block['content'] = theme('tripal_library_properties', $node);
+    	  break;
+    	case 'libterms':
+    	  $block['subject'] = t('Library Terms');
+    	  $block['content'] = theme('tripal_library_terms', $node);
+    	  break;
+    	case 'featurelibs':
+    	  $block['subject'] = t('Libraries');
+    	  $block['content'] = theme('tripal_feature_libraries', $node);
+    	  break;
+    	case 'orglibs':
+    	  $block['subject'] = t('Libraries');
+    	  $block['content'] = theme('tripal_organism_libraries', $node);
+    	  break;
+    	default :
+    }
+    return $block;
+  }
+}
 /**
  * This function is an extension of the chado_feature_view and
  * chado_organism_view by providing the markup for the library object
@@ -278,17 +341,19 @@ function theme_tripal_library_search_index($node) {
   if ($node->type == 'chado_organism') {
     $content = "";
     // get the libraries for the organism
-    $sql = "SELECT * FROM {library} L ".
-            "WHERE L.organism_id = %d";
+    $sql = "SELECT * FROM {library} L WHERE L.organism_id = :organism_id";
     $libraries = array();
-    $results = chado_query($sql, $node->organism->organism_id);
-    while ($library = db_fetch_object($results)) {
+    $results = chado_query($sql, array(':organism_id' => $node->organism->organism_id));
+    while ($library = $results->fetchObject()) {
       // get the description
-      $sql = "SELECT * FROM {libraryprop} LP ".
-             "  INNER JOIN {CVTerm} CVT ON CVT.cvterm_id = LP.type_id ".
-            "WHERE LP.library_id = $library->library_id ".
-            "  AND CVT.name = 'library_description'";
-      $desc = db_fetch_object(chado_query($sql));
+      $sql = "
+        SELECT * 
+        FROM {libraryprop} LP 
+          INNER JOIN {cvterm} CVT ON CVT.cvterm_id = LP.type_id 
+        WHERE LP.library_id = :library_id
+          AND CVT.name = 'library_description'
+      ";
+      $desc = chado_query($sql, array(':library_id' => $library->library_id))->fetchObject();
       $library->description = $desc->value;
       $libraries[] = $library;
     }
@@ -303,12 +368,15 @@ function theme_tripal_library_search_index($node) {
   elseif ($node->type == 'chado_feature') {
     $content = "";
     $organism_id = $node->feature->organism_id;
-    $sql = "SELECT * FROM {library} L ".
-           "  INNER JOIN {Library_feature} LF ON L.library_id = LF.library_id ".
-            "WHERE LF.feature_id = " . $node->feature->feature_id;
+    $sql = "
+      SELECT * 
+      FROM {library} L 
+        INNER JOIN {library_feature} LF ON L.library_id = LF.library_id 
+      WHERE LF.feature_id = :feature_id
+    "; 
     $libraries = array();
-    $results = chado_query($sql);
-    while ($library = db_fetch_object($results)) {
+    $results = chado_query($sql, array(':feature_id' => $node->feature->feature_id));
+    while ($library = $results->fetchObject()) {
       $libraries[] = $library;
     }
     if (count($libraries) > 0) {
@@ -345,19 +413,22 @@ function theme_tripal_library_node_libraries($node) {
   // when a feature is previewed at its creation
   elseif ($node->type == 'chado_feature' && $node->feature->feature_id) {
     $organism_id = $node->feature->organism_id;
-    $sql = "SELECT * FROM {library} L ".
-           " INNER JOIN Library_feature LF ON L.library_id = LF.library_id ".
-            "WHERE LF.feature_id = " . $node->feature->feature_id;
+    $sql = "
+      SELECT * 
+      FROM {library} L 
+        INNER JOIN Library_feature LF ON L.library_id = LF.library_id 
+      WHERE LF.feature_id = :feature_id
+    ";
     $libraries = array();
-    $results = chado_query($sql);
-    while ($library = db_fetch_object($results)) {
+    $results = chado_query($sql, array(':feature_id' => $node->feature->feature_id));
+    while ($library = $results->fetchObject()) {
       $libraries[] = $library;
   }
   if (count($libraries) > 0) {
     $lib_additions = array();
     foreach ($libraries as $library) {
-      $sql = "SELECT nid FROM {chado_library} WHERE library_id = %d";
-      $lib_nid = db_result(db_query($sql, $library->library_id));
+      $sql = "SELECT nid FROM {chado_library} WHERE library_id = :library_id";
+      $lib_nid = db_query($sql, array(':library_id' => $library->library_id))->fetchField();
       if ($lib_nid) {
         $lib_url = url("node/$lib_nid");
       }
@@ -377,42 +448,6 @@ function theme_tripal_library_node_libraries($node) {
 function tripal_library_cron() {
 
 }
-/**
- *  The following function proves access control for users trying to
- *  perform actions on data managed by this module
- *
- * @ingroup tripal_library
- */
-function tripal_library_library_access($op, $node, $account) {
-  if ($op == 'create') {
-    if (!user_access('create chado_library content', $account)) {
-      return FALSE;
-    }
-  }
-
-  if ($op == 'update') {
-    if (!user_access('edit any chado_library content', $account) &&
-        !user_access('edit own chado_library content', $account)) {
-        return FALSE;
-    }
-    if (user_access('edit own chado_library content', $account) &&
-      $account->uid != $node->uid) {
-      return FALSE;
-    }
-  }
-
-  if ($op == 'delete') {
-    if (!user_access('delete any chado_library content', $account) &&
-      !user_access('delete own chado_library content', $account)) {
-      return FALSE;
-    }
-    if (user_access('delete own chado_library content', $account) &&
-      $account->uid != $node->uid) {
-      return FALSE;
-    }
-  }
-  return NULL;
-}
 
 
 /**
@@ -497,12 +532,12 @@ function chado_library_form($node) {
   );
 
   // get the list of organisms
-  $sql = "SELECT * FROM {Organism}";
+  $sql = "SELECT * FROM {organism}";
   $org_rset = chado_query($sql);
 
   $organisms = array();
   $organisms[''] = '';
-  while ($organism = db_fetch_object($org_rset)) {
+  while ($organism = $org_rset->fetchObject()) {
     $organisms[$organism->organism_id] =
     "$organism->genus $organism->species ($organism->common_name)";
   }
@@ -539,21 +574,19 @@ function chado_library_validate($node) {
   // check to make sure the unique name on the library is unique
   // before we try to insert into chado.
   if ($node->library_id) {
-    $sql = "SELECT * FROM ".
-           "{Library} WHERE ".
-           "uniquename = '%s' ".
-           "AND NOT library_id = %d";
-    $lib = db_fetch_object(chado_query($sql, $node->uniquename, $node->library_id));
+    $sql = "
+      SELECT * 
+      FROM {library} 
+      WHERE uniquename = :uname AND NOT library_id = :library_id
+    ";
+    $lib = chado_query($sql, array(':uname' => $node->uniquename, ':library_id' => $node->library_id))->fetchObject();
   }
   else {
-    $sql = "SELECT * FROM ".
-           "{Library} ".
-           "WHERE uniquename = '%s'";
-    $lib = db_fetch_object(chado_query($sql, $node->uniquename));
+    $sql = "SELECT * FROM {library} WHERE uniquename = :uname";
+    $lib = chado_query($sql, array(':uname' => $node->uniquename))->fetchObject();
   }
   if ($lib) {
-    form_set_error('uniquename', t('The unique library name already exists. '.
-                                  'Please choose another'));
+    form_set_error('uniquename', t('The unique library name already exists. Please choose another'));
   }
 }
 /**
@@ -588,18 +621,17 @@ function chado_library_insert($node) {
     $library_id = chado_get_id_for_node('library', $node->nid) ;
     if (!$library_id) {
        // next add the item to the drupal table
-      $sql = "INSERT INTO {chado_library} (nid, vid, library_id) ".
-             "VALUES (%d, %d, %d)";
-      db_query($sql, $node->nid, $node->vid, $library['library_id']);
+      $sql = "
+        INSERT INTO {chado_library} (nid, vid, library_id) 
+        VALUES (:nid, :vid, :library_id)
+      ";
+      db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid, ':library_id' => $library['library_id']));
     }
   }
   else {
     drupal_set_message(t('Unable to add library.', 'warning'));
-    watchdog('tripal_library',
-    'Insert feature: Unable to create library where values: %values',
-    array('%values' => print_r($values, TRUE)),
-    WATCHDOG_WARNING
-    );
+    watchdog('tripal_library', 'Insert feature: Unable to create library where values: %values',
+      array('%values' => print_r($values, TRUE)), WATCHDOG_WARNING);
   }
 }
 /**
@@ -663,8 +695,8 @@ function chado_library_view($node, $teaser = FALSE, $page = FALSE) {
     // but not genus/species/common_name. We need to get those from chado
     // database so they will show up in preview
     if (!$node->genus) {
-      $sql = "SELECT * FROM {organism} WHERE organism_id = %d";
-      $data = db_fetch_object(chado_query($sql, $node->organism_id));
+      $sql = "SELECT * FROM {organism} WHERE organism_id = :organism_id";
+      $data = chado_query($sql, array(':organism_id' => $node->organism_id))->fetchObject();
       $node->genus = $data->genus;
       $node->species = $data->species;
       $node->common_name = $data->common_name;
@@ -689,97 +721,16 @@ function chado_library_delete(&$node) {
 
   // Remove data from {chado_library}, {node} and {node_revisions} tables of
   // drupal database
-  $sql_del = "DELETE FROM {chado_library} ".
-            "WHERE nid = %d ".
-            "AND vid = %d";
-  db_query($sql_del, $node->nid, $node->vid);
-  $sql_del = "DELETE FROM {node_revisions} ".
-            "WHERE nid = %d ".
-            "AND vid = %d";
-  db_query($sql_del, $node->nid, $node->vid);
-  $sql_del = "DELETE FROM {node} ".
-            "WHERE nid = %d ".
-            "AND vid = %d";
-  db_query($sql_del, $node->nid, $node->vid);
+  $sql_del = "DELETE FROM {chado_library} WHERE nid = :nid AND vid = :vid";
+  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
+  $sql_del = "DELETE FROM {node_revision} WHERE nid = :nid AND vid = :vid";
+  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
+  $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
+  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
 
   // Remove data from library and libraryprop tables of chado database as well
-  chado_query("DELETE FROM {libraryprop} WHERE library_id = %d", $library_id);
-  chado_query("DELETE FROM {library} WHERE library_id = %d", $library_id);
+  chado_query("DELETE FROM {libraryprop} WHERE library_id = :library_id", array(':library_id' => $library_id));
+  chado_query("DELETE FROM {library} WHERE library_id = :library_id", array(':library_id' => $library_id));
 }
 
-/**
- * Display block with libraries
- * @param op    - parameter to define the phase being called for the block
- * @param delta - id of the block to return (ignored when op is list)
- * @param edit  - when op is save, contains the submitted form data
- *
- * @ingroup tripal_library
- */
-function tripal_library_block($op = 'list', $delta = '0', $edit = array()) {
-  switch ($op) {
-    case 'list':
-
-    $blocks['libreferences']['info'] = t('Tripal Library Cross References');
-    $blocks['libreferences']['cache'] = BLOCK_NO_CACHE;
-
-    $blocks['libbase']['info'] = t('Tripal Library Details');
-    $blocks['libbase']['cache'] = BLOCK_NO_CACHE;
-
-    $blocks['libterms']['info'] = t('Tripal Library Terms');
-    $blocks['libterms']['cache'] = BLOCK_NO_CACHE;
-
-    $blocks['libsynonyms']['info'] = t('Tripal Library Synonyms');
-    $blocks['libsynonyms']['cache'] = BLOCK_NO_CACHE;
-
-    $blocks['libproperties']['info'] = t('Tripal Library Properties');
-    $blocks['libproperties']['cache'] = BLOCK_NO_CACHE;
-
-    $blocks['featurelibs']['info'] = t('Tripal Feature Libraries');
-    $blocks['featurelibs']['cache'] = BLOCK_NO_CACHE;
-
-    $blocks['orglibs']['info'] = t('Tripal Organism Libraries');
-    $blocks['orglibs']['cache'] = BLOCK_NO_CACHE;
-
-    return $blocks;
-
-    case 'view':
-      if (user_access('access chado_library content') and arg(0) == 'node' and is_numeric(arg(1))) {
-        $nid = arg(1);
-        $node = node_load($nid);
-
-        $block = array();
-        switch ($delta) {
-          case 'libreferences':
-            $block['subject'] = t('Cross References');
-            $block['content'] = theme('tripal_library_references', $node);
-            break;
-          case 'libbase':
-            $block['subject'] = t('Library Details');
-            $block['content'] = theme('tripal_library_base', $node);
-            break;
-          case 'libsynonyms':
-            $block['subject'] = t('Synonyms');
-            $block['content'] = theme('tripal_library_synonyms', $node);
-            break;
-          case 'libproperties':
-            $block['subject'] = t('Properties');
-            $block['content'] = theme('tripal_library_properties', $node);
-            break;
-          case 'libterms':
-            $block['subject'] = t('Library Terms');
-            $block['content'] = theme('tripal_library_terms', $node);
-            break;
-          case 'featurelibs':
-            $block['subject'] = t('Libraries');
-            $block['content'] = theme('tripal_feature_libraries', $node);
-            break;
-          case 'orglibs':
-            $block['subject'] = t('Libraries');
-            $block['content'] = theme('tripal_organism_libraries', $node);
-            break;
-            default :
-        }
-        return $block;
-      }
-  }
-}
+

tripal_natural_diversity/tripal_natural_diversity.info

@@ -1,9 +1,9 @@
 name = Tripal Natural Diversity
 description = A module for interfacing the GMOD chado database with Drupal, providing viewing of Natural Diversity data
-core = 6.x
+core = 7.x
 project = tripal_natural_diversity
 package = Tripal
-version = 6.x-1.1
+version = 7.x-2.0-beta1
 dependencies[] = tripal_core
 dependencies[] = tripal_cv
 dependencies[] = tripal_db

tripal_natural_diversity/tripal_natural_diversity.install

@@ -4,6 +4,26 @@
  * Implements hooks from the Schema API
  */
 
+
+
+/**
+ * Implementation of hook_requirements().
+ */
+function tripal_natural_diversity_requirements($phase) {
+  $requirements = array();
+  if ($phase == 'install') {
+    // make sure chado is installed
+    if (!tripal_core_is_chado_installed()) {
+      $requirements ['tripal_natural_diversity'] = array(
+        'title' => "tripal_natural_diversity",
+        'value' => "ERROR: Chado most be installed before this module can be enabled",
+        'severity' => REQUIREMENT_ERROR,
+      );
+    }
+  }
+  return $requirements;
+}
+
 /**
  * Implementation of hook_install().
  */
@@ -18,20 +38,10 @@ function tripal_natural_diversity_install() {
 }
 
 /**
- *  Update for Drupal 6.x, Tripal 1.1, Natural Diversity Module 1.1
- *  This update adds new cvterms for experiment types
- *
+ * Implementation of hook_uninstall().
  */
-function tripal_natural_diversity_update_6100() {
-   
-  // add cvterms
-  tripal_natural_diversity_add_cvterms(); 
-  
-  $ret = array(
-    '#finished' => 1,
-  );
+function tripal_natural_diversity_uninstall() {
 
-  return $ret;
 }
 
 /*
@@ -48,28 +58,3 @@ function tripal_natural_diversity_add_cvterms(){
   tripal_cv_add_cvterm(array('name' => 'Location','def' => 'The name of the location.'), 
     'nd_geolocation_property', 0, 1, 'tripal');
 }
-/**
- * Implementation of hook_uninstall().
- */
-function tripal_natural_diversity_uninstall() {
-
-}
-
-
-/**
- * Implementation of hook_requirements(). 
- */
-function tripal_natural_diversity_requirements($phase) {
-  $requirements = array();
-  if ($phase == 'install') {
-    // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
-      $requirements ['tripal_natural_diversity'] = array(
-            'title' => "tripal_natural_diversity",
-            'value' => "ERROR: Chado most be installed before this module can be enabled",
-            'severity' => REQUIREMENT_ERROR,
-      );
-    }
-  }
-  return $requirements;
-}

tripal_natural_diversity/tripal_natural_diversity.module

@@ -52,19 +52,61 @@ function tripal_natural_diversity_theme() {
 }
 
 /**
- * Implements hook_nodeapi().
+ * @ingroup tripal_library
+ */
+function tripal_natural_diversity_block_info() {
+
+  $blocks['ndfgenotype']['info'] = t('Tripal Natural Diversity Feature Genotypes');
+  $blocks['ndfgenotype']['cache'] = BLOCK_NO_CACHE;
+
+  $blocks['ndsgenotype']['info'] = t('Tripal Natural Diversity Library Genotypes');
+  $blocks['ndsgenotype']['cache'] = BLOCK_NO_CACHE;
+
+  $blocks['ndsphenotype']['info'] = t('Tripal Natural Diversity Stock Phenotypes');
+  $blocks['ndsphenotype']['cache'] = BLOCK_NO_CACHE;
+
+  return $blocks;
+}
+/**
+ * @ingroup tripal_library
+ */
+function tripal_natural_diversity_block_view($delta = '') {
+
+  if (user_access('access chado_library content') and arg(0) == 'node' and is_numeric(arg(1))) {
+    $nid = arg(1);
+    $node = node_load($nid);
+
+    $block = array();
+    switch ($delta) {
+    	case 'ndfgenotype':
+    	  $block['subject'] = t('Genotypes');
+    	  $block['content'] = theme('tripal_feature_nd_genotypes', $node);
+    	  break;
+    	case 'ndsgenotype':
+    	  $block['subject'] = t('Stock Genotypes');
+    	  $block['content'] = theme('tripal_stock_nd_genotypes', $node);
+    	  break;
+    	case 'ndsphenotype':
+    	  $block['subject'] = t('Phenotypes');
+    	  $block['content'] = theme('tripal_stock_nd_phenotypes', $node);
+    	  break;
+    	default :
+    }
+    return $block;
+  }
+}
+/**
  *
  * @ingroup tripal_natural_diversity
  */
-function tripal_natural_diversity_nodeapi(&$node, $op, $teaser, $page){
-  switch ($op) {
-    case 'view':
-      if ($node->type == 'chado_feature') {
-        // the tripal_genetic module provides a tripal_feature_genotype
-        // template.  The only difference between them is the addition of
-        // project information by this module's template.  Therefore,
-        // if the tripal_genetic content is present get rid of as this
-        // module superceeds it.
+function tripal_natural_diversity_node_view(&$node, $view_mode, $langcode) {
+    if ($node->type == 'chado_feature') {
+      // the tripal_genetic module provides a tripal_feature_genotype
+      // template.  The only difference between them is the addition of
+      // project information by this module's template.  Therefore,
+      // if the tripal_genetic content is present get rid of as this
+      // module superceeds it.
+      if ($view_mode == 'full') {
         if (array_key_exists('tripal_feature_genotypes', $node->content)) {
           unset($node->content['tripal_feature_genotypes']);
         }
@@ -72,7 +114,9 @@ function tripal_natural_diversity_nodeapi(&$node, $op, $teaser, $page){
            '#value' => theme('tripal_feature_nd_genotypes', $node),
         );
       }
-      if ($node->type == 'chado_stock') {
+    }
+    if ($node->type == 'chado_stock') {
+      if ($view_mode == 'full') {
         $node->content['tripal_stock_nd_genotypes'] = array(
            '#value' => theme('tripal_stock_nd_genotypes', $node),
         );
@@ -80,15 +124,6 @@ function tripal_natural_diversity_nodeapi(&$node, $op, $teaser, $page){
            '#value' => theme('tripal_stock_nd_phenotypes', $node),
         );
       }
-      break;
-  }
-}
-
-/**
- *
- *
- * @ingroup tripal_natural_diversity
- */
-function tripal_natural_diversity_preprocess_tripal_stock_nd_genotypes(&$variables){
-
+    }
+    break;
 }

tripal_organism/tripal_organism.module

@@ -400,17 +400,11 @@ function chado_organism_delete($node) {
   }
 
   // Remove data from the {chado_organism}, {node}, and {node_revisions} tables
-  $sql_del = "DELETE FROM {chado_organism} " .
-             "WHERE nid = :nid " .
-             "AND vid = :vid";
+  $sql_del = "DELETE FROM {chado_organism} WHERE nid = :nid AND vid = :vid";
   db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
-  $sql_del = "DELETE FROM {node} " .
-             "WHERE nid = :nid " .
-             "AND vid = :vid";
+  $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
   db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
-  $sql_del = "DELETE FROM {node_revision} " .
-             "WHERE nid = ':nid' " .
-             "AND vid = ':vid'";
+  $sql_del = "DELETE FROM {node_revision} WHERE nid = ':nid' AND vid = ':vid'";
   db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
 
   // Test dependency before deleting from chado database. If a library or
@@ -426,8 +420,7 @@ function chado_organism_delete($node) {
   }
   else {
     drupal_set_message(t("Organism deleted from drupal. Warning: at least one " .
-                       "library or feature depends on this organism. It was " .
-               "not removed from chado."));
+      "library or feature depends on this organism. It was not removed from chado."));
   }
 }
 /**

tripal_phenotype/tripal_phenotype.info

@@ -1,9 +1,9 @@
 name = Tripal Phenotype
-description = A module for interfacing the GMOD chado database with Drupal, providing viewing of Phenotype Data
-core = 6.x
+description = A module for interfacing the GMOD chado database with Drupal providing viewing of phenotype data
+core = 7.x
 project = tripal_phenotype
 package = Tripal
-version = 6.x-1.1
+version = 7.x-2.0-beta1
 dependencies[] = tripal_core
 dependencies[] = tripal_cv
 dependencies[] = tripal_feature

tripal_project/includes/tripal_project.admin.inc

@@ -155,8 +155,8 @@ function tripal_project_admin_validate($form, &$form_state) {
       }
       if ($project_id and preg_match("/^\d+$/i" , $project_id)) {
         // get the list of projects
-        $sql = "SELECT * FROM {Project} WHERE project_id = %d";
-        $project = chado_query($sql, $project_id)->fetchObject();
+        $sql = "SELECT * FROM {project} WHERE project_id = :project_id";
+        $project = chado_query($sql, array(':project_id' => $project_id))->fetchObject();
         $to_sync[$project_id] = "$project->genus $project->species";
       }
     }
@@ -182,8 +182,8 @@ function tripal_project_admin_validate($form, &$form_state) {
     foreach ($projects as $project_id) {
       if ($project_id and preg_match("/^\d+$/i" , $project_id)) {
         // get the project info
-        $sql = "SELECT * FROM {project} WHERE project_id = %d";
-        $project = chado_query($sql , $project_id)->fetchObject();
+        $sql = "SELECT * FROM {project} WHERE project_id = :project_id";
+        $project = chado_query($sql , array(':project_id' => $project_id))->fetchObject();
         $job_args[0] = $project_id;
         tripal_add_job("Reindex features for project: $project->genus ".
          "$project->species", 'tripal_project' ,
@@ -199,8 +199,8 @@ function tripal_project_admin_validate($form, &$form_state) {
     foreach ($projects as $project_id) {
       if ($project_id and preg_match("/^\d+$/i", $project_id)) {
         // get the project info
-        $sql = "SELECT * FROM {project} WHERE project_id = %d";
-        $project = chado_query($sql , $project_id)->fetchObject();
+        $sql = "SELECT * FROM {project} WHERE project_id = :project_id";
+        $project = chado_query($sql , array(':project_id' => $project_id))->fetchObject();
         $job_args[0] = $project_id;
         tripal_add_job("Set taxonomy for features in project: ".
           "$project->genus $project->species" , 'tripal_project',
@@ -230,20 +230,19 @@ function tripal_project_sync_projects($project_id = NULL, $job_id = NULL) {
     $results = chado_query($sql);
   }
   else {
-    $sql = "SELECT * FROM {project} P WHERE project_id = %d";
-    $results = chado_query($sql, $project_id);
+    $sql = "SELECT * FROM {project} P WHERE project_id = :project_id";
+    $results = chado_query($sql, array(':project_id' => $project_id));
   }
 
   // We'll use the following SQL statement for checking if the project
   // already exists as a drupal node.
-  $sql = "SELECT * FROM {chado_project} ".
-         "WHERE project_id = %d";
+  $sql = "SELECT * FROM {chado_project} WHERE project_id = :project_id";
 
   while ($project = $results->fetchObject()) {
 
     // check if this project already exists in the drupal database. if it
     // does then skip this project and go to the next one.
-    if (!db_query($sql, $project->project_id)->fetchObject()) {
+    if (!db_query($sql, array(':project_id' => $project->project_id))->fetchObject()) {
 
       $new_node = new stdClass();
       $new_node->type = 'chado_project';

tripal_project/tripal_project.install

@@ -10,6 +10,24 @@
  * multiple project/mysql instances as well as manage and create such project instances
  */
 
+/**
+ * Implementation of hook_requirements().
+ *
+ */
+function tripal_project_requirements($phase) {
+  $requirements = array();
+  if ($phase == 'install') {
+    // make sure chado is installed
+    if (!tripal_core_is_chado_installed()) {
+      $requirements ['tripal_project'] = array(
+        'title' => "tripal_project",
+        'value' => "ERROR: Chado most be installed before this module can be enabled",
+        'severity' => REQUIREMENT_ERROR,
+      );
+    }
+  }
+  return $requirements;
+}
 /**
  * Implementation of hook_install().
  */
@@ -54,24 +72,6 @@ function tripal_project_schema() {
   return $schema;
 }
 
-/**
- * Implementation of hook_requirements(). 
- *
- */
-function tripal_project_requirements($phase) {
-  $requirements = array();
-  if ($phase == 'install') {
-    // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
-      $requirements ['tripal_project'] = array(
-            'title' => "tripal_project",
-            'value' => "ERROR: Chado most be installed before this module can be enabled",
-            'severity' => REQUIREMENT_ERROR,
-      );
-    }
-  }
-  return $requirements;
-}
 /*
  * 
  */

tripal_project/tripal_project.module

@@ -15,6 +15,30 @@ require('api/tripal_project.api.inc');
  * @ingroup tripal_modules
  */
 
+/**
+ * Implementation of hook_node_info().
+ *
+ * This node_info, is a simple node that describes the functionallity of the module. It specifies
+ * that the title(Project Name) and body(Description) set to true so that they information can be
+ * entered
+ *
+ *
+ * @ingroup tripal_project
+ */
+function tripal_project_node_info() {
+  return array(
+    'chado_project' => array(
+      'name' => t('Project'),
+      'base' => 'chado_project',
+      'description' => t('A module for interfacing the GMOD chado database with Drupal, providing viewing of projects'),
+      'has_title' => TRUE,
+      'title_label' => t('Project Name'),
+      'had_body' => TRUE,
+      'body_label' => t('Full Description'),
+    )
+  );
+}
+
 /**
  * Implements hook_views_api()
  *
@@ -158,29 +182,6 @@ function chado_project_node_access($node, $op, $account) {
   return NULL;
 }
 
-/**
- * Implementation of hook_node_info().
- *
- * This node_info, is a simple node that describes the functionallity of the module. It specifies
- * that the title(Project Name) and body(Description) set to true so that they information can be
- * entered
- *
- *
- * @ingroup tripal_project
- */
-function tripal_project_node_info() {
-  return array(
-    'chado_project' => array(
-      'name' => t('Project'),
-      'base' => 'chado_project',
-      'description' => t('A module for interfacing the GMOD chado database with Drupal, providing viewing of projects'),
-      'has_title' => TRUE,
-      'title_label' => t('Project Name'),
-      'had_body' => TRUE,
-      'body_label' => t('Full Description'),
-    )
-  );
-}
 /**
  *  We need to let drupal know about our theme functions and their arguments.
  *  We create theme functions to allow users of the module to customize the
@@ -342,8 +343,10 @@ function chado_project_insert($node) {
     $project_id = chado_get_id_for_node('project', $node->nid) ;
     if (!$project_id) {
        // next add the item to the drupal table
-      $sql = "INSERT INTO {chado_project} (nid, vid, project_id) ".
-             "VALUES (:nid, :vid, :project_id)";
+      $sql = "
+        INSERT INTO {chado_project} (nid, vid, project_id) 
+        VALUES (:nid, :vid, :project_id)
+      ";
       db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid, ':project_id' => $project['project_id']));
     }
   }
@@ -377,20 +380,13 @@ function chado_project_delete($node) {
 
   // Remove data from {chado_project}, {node} and {node_revisions} tables of
   // drupal database
-  $sql_del = "DELETE FROM {chado_project} ".
-             "WHERE nid = :nid ".
-             "AND vid = :vid";
+  $sql_del = "DELETE FROM {chado_project} WHERE nid = :nid AND vid = :vid";
   db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
-  $sql_del = "DELETE FROM {node_revision} ".
-             "WHERE nid = :nid ".
-             "AND vid = :vod";
+  $sql_del = "DELETE FROM {node_revision} WHERE nid = :nid AND vid = :vod";
   db_query($sql_del,  array(':nid' => $node->nid, ':vid' => $node->vid));
-  $sql_del = "DELETE FROM {node} ".
-             "WHERE nid = :nid ".
-             "AND vid = :vid";
+  $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
   db_query($sql_del,  array(':nid' => $node->nid, ':vid' => $node->vid));
 
-
   // Remove data from project and projectprop tables of chado database as well
   chado_query("DELETE FROM {projectprop} WHERE project_id = :project_id", array(':project_id' => $project_id));
   chado_query("DELETE FROM {project} WHERE project_id = :project_id", array(':project_id' => $project_id));
@@ -409,22 +405,18 @@ function chado_project_delete($node) {
 function chado_project_update($node) {
  if ($node->revision) {
     // there is no way to handle revisions in Chado but leave
-    // this here just to make not we've addressed it.
+    // this here just to make note we've addressed it.
   }
 
   // update the project and the description
   $project_id = chado_get_id_for_node('project', $node->nid) ;
-  $match = array(
-     'project_id' => $project_id,
-  );
+  $match = array('project_id' => $project_id);
   $values = array(
-     'name' => $node->title,
-     'description' => '',
+    'name' => $node->title,
+    'description' => '',
   );
   $status = tripal_core_chado_update('project', $match, $values);
   tripal_project_update_property($project_id, 'project_description', $node->project_description, 1);
-
-
 }
 
 /**

tripal_pub/api/tripal_pub.api.inc

@@ -840,7 +840,7 @@ function tripal_pub_add_authors($pub_id, $authors, $do_contact) {
     $values = array(
       'pub_id' => $pub_id,
       'rank' => $rank,
-      'surname' => $author['Surname'] ? $author['Surname'] : $author['Collective'],
+      'surname' => $author['Surname'] ? substr($author['Surname'], 0, 100) : substr($author['Collective'], 0, 100),
       'givennames' => $author['Given Name'],
       'suffix' => $author['Suffix'],
     );
@@ -1169,13 +1169,20 @@ function tripal_pub_create_citation($pub) {
       if ($ptype == 'Journal Article' ) {
         $pub_type = $ptype;
         break;
-      } else if ($ptype == 'Conference Proceedings'){ 
+      } 
+      else if ($ptype == 'Conference Proceedings'){ 
         $pub_type = $ptype;
         break;
-      } else if ($ptype == 'Book') {
+      } 
+      else if ($ptype == 'Book') {
         $pub_type = $ptype;
         break;
-      } else if ($ptype == 'Book Chapter') {
+      } 
+      else if ($ptype == 'Letter') {
+        $pub_type = $ptype;
+        break;
+      } 
+      else if ($ptype == 'Book Chapter') {
         $pub_type = $ptype;
         break;
       }
@@ -1231,6 +1238,47 @@ function tripal_pub_create_citation($pub) {
     $citation .= '.';
   }
   //----------------------
+  // Letter
+  //----------------------
+  elseif ($pub_type == 'Letter') {
+    $citation = $pub['Authors'] . '. ' . $pub['Title'] .  '. ';
+  
+    if ($pub['Journal Name']) {
+      $citation .= $pub['Journal Name'] . '. ';
+    }
+    elseif ($pub['Journal Abbreviation']) {
+      $citation .= $pub['Journal Abbreviation'] . '. ';
+    }
+    elseif ($pub['Series Name']) {
+      $citation .= $pub['Series Name'] . '. ';  
+    }
+    elseif ($pub['Series Abbreviation']) {
+      $citation .= $pub['Series Abbreviation'] . '. ';
+    }
+    if ($pub['Publication Date']) {
+      $citation .= $pub['Publication Date'];
+    }
+    elseif ($pub['Year']) {
+      $citation .= $pub['Year'];
+    }
+    if ($pub['Volume'] or $pub['Issue'] or $pub['Pages']) {
+      $citation .= '; ';
+    }
+    if ($pub['Volume']) {
+      $citation .= $pub['Volume'];
+    }
+    if ($pub['Issue']) {
+      $citation .= '(' . $pub['Issue'] . ')';
+    }
+    if ($pub['Pages']) {
+      if($pub['Volume']) {
+        $citation .= ':';
+      }
+      $citation .= $pub['Pages'];
+    }
+    $citation .= '.';
+  }
+  //----------------------
   // Book
   //----------------------
   elseif ($pub_type == 'Book') {
@@ -1282,4 +1330,4 @@ function tripal_pub_create_citation($pub) {
   }
 
   return $citation;
-}
+}

tripal_pub/includes/pub_form.inc

@@ -200,7 +200,6 @@ function chado_pub_validate($node, &$form) {
   $pub_id       = $node->pub_id;
   $num_properties = $node->num_properties;
   $num_new = $node->num_new;
-  dpm($node);
   
   $pub = array();
 
@@ -260,7 +259,7 @@ function chado_pub_validate($node, &$form) {
     $pub['Year'] = $pyear;
     $uniquename = tripal_pub_create_citation($pub);
     if (!$uniquename) {
-    	form_set_error('uniquename', 'Cannot automatically generate a citation for this publication type. Please add one manually.');
+      form_set_error('uniquename', "Cannot automatically generate a citation for this publication type. Please add one manually.");
     }
   }
 

tripal_pub/includes/pub_sync.inc

@@ -66,7 +66,8 @@ function tripal_pub_sync_pub($pub) {
   global $user;
 
   if(!$pub->pyear) {
-    watchdog('tpub_sync', "Skipping pub without published year: %title.", array('%title' => $pub->title), WATCHDOG_WARNING);
+    watchdog('tpub_sync', "Skipping pub without published year: %title.", 
+      array('%title' => $pub->title), WATCHDOG_WARNING);
     return FALSE;
   }
 
@@ -90,7 +91,8 @@ function tripal_pub_sync_pub($pub) {
       print "Added " . $pub->pub_id . "\n";
     }
     else {
-      watchdog('tpub_sync', "Unable to create publication node: %title.", array('%title' => $pub->title), WATCHDOG_ERROR);
+      watchdog('tpub_sync', "Unable to create publication node: %title.", 
+        array('%title' => $pub->title), WATCHDOG_ERROR);
       return FALSE;
     }
   }
@@ -98,7 +100,7 @@ function tripal_pub_sync_pub($pub) {
   else {
     form_set_error(NULL,'',TRUE);
     watchdog('tpub_sync', "Unable to create publication node: %title\n%errs",
-    array('%title' => $pub->title, '%errs' => print_r($errors, TRUE)), WATCHDOG_ERROR);
+      array('%title' => $pub->title, '%errs' => print_r($errors, TRUE)), WATCHDOG_ERROR);
     return FALSE;
   }
   return $node;

tripal_pub/tripal_pub.module

@@ -271,14 +271,14 @@ function tripal_pub_perm() {
  * Implement hook_access().
  *
  * This hook allows node modules to limit access to the node types they define.
- *
- *  @param $op
- *  The operation to be performed
- *
+ * 
  *  @param $node
  *  The node on which the operation is to be performed, or, if it does not yet exist, the
  *  type of node to be created
  *
+ *  @param $op
+ *  The operation to be performed
+ *
  *  @param $account
  *  A user object representing the user for whom the operation is to be performed
  *
@@ -289,7 +289,7 @@ function tripal_pub_perm() {
  *  return TRUE if the permission is set.
  *
  */
-function chado_pub_access($op, $node, $account ) {
+function chado_pub_node_access($node, $op, $account ) {
   if ($op == 'create') {
     if (!user_access('create chado_pub content', $account)) {
       return FALSE;
@@ -502,7 +502,7 @@ function chado_pub_insert($node) {
   else {
     drupal_set_message(t('Unable to add publication.', 'warning'));
     watchdog('tripal_pub', 'Insert publication: Unable to create pub where values: %values',
-    array('%values' => print_r($values, TRUE)), WATCHDOG_WARNING);
+      array('%values' => print_r($values, TRUE)), WATCHDOG_WARNING);
   }
 }
 

tripal_stock/tripal_stock.module

@@ -188,14 +188,14 @@ function tripal_stock_perm() {
  * Implement hook_access().
  *
  * This hook allows node modules to limit access to the node types they define.
- *
- *  @param $op
- *  The operation to be performed
- *
+ * 
  *  @param $node
  *  The node on which the operation is to be performed, or, if it does not yet exist, the
  *  type of node to be created
  *
+ *  @param $op
+ *  The operation to be performed
+ *
  *  @param $account
  *  A user object representing the user for whom the operation is to be performed
  *
@@ -207,7 +207,7 @@ function tripal_stock_perm() {
  *
  * @ingroup tripal_stock
  */
-function chado_stock_access($op, $node, $account) {
+function chado_stock_node_access($node, $op, $account) {
   if ($op == 'create') {
     if (!user_access('create chado_stock content', $account)) {
       return FALSE;