Fixed issues with re-setting Feature URLs and node languages. Also started to fix same for stocks but can't create a stock... need to debug that

tripal_core/api/tripal_core.chado_general.api.inc

@@ -231,8 +231,7 @@ $cv_name, $value, $update_if_present = 0) {
     }
   }
 
-  // make sure the cvterm exists.  Otherwise we'll get an error with
-  // prepared statements not matching
+  // make sure the cvterm exists.  
   $values = array(
     'cv_id' => array(
       'name' => $cv_name,

tripal_core/api/tripal_core.chado_nodes.api.inc

@@ -237,15 +237,14 @@ function chado_node_sync_form($form, &$form_state) {
         $form['sync']['ids'] = array(
           '#title'         => 'Avaliable ' . $args['record_type_title']['plural'],
           '#type'          => 'checkboxes',
-          '#description'   => t("The above  %title_plural have not been synced. Check those to be synced or leave all unchecked to sync them all.",
-            array(
-              '%title_singular' => strtolower($args['record_type_title']['singular']),
-              '%title_plural'   => strtolower($args['record_type_title']['plural'])
-            )),
           '#options'       => $values,
           '#default_value' => (isset($form_state['values']['ids'])) ? $form_state['values']['ids'] : array(),
-          '#prefix'        => '<div style="height: 200px; overflow: scroll">',
           '#suffix'        => '</div><br>',
+          '#prefix'       => t("The following  %title_plural have not been synced. Check those to be synced or leave all unchecked to sync them all.",
+              array(
+                '%title_singular' => strtolower($args['record_type_title']['singular']),
+                '%title_plural'   => strtolower($args['record_type_title']['plural'])
+              )) . '<div style="height: 200px; overflow: scroll">',
         );
       }
       else {
@@ -476,7 +475,7 @@ function chado_node_sync_records($base_table, $max_sync = FALSE, $organism_id =
   // execute the query
   $results = chado_query($query, $sql_args);
 
-  // Iterate through features that need to be synced
+  // Iterate through records that need to be synced
   $count = $results->rowCount();
   $interval = intval($count * 0.01);
   if ($interval < 1) {
@@ -490,7 +489,7 @@ function chado_node_sync_records($base_table, $max_sync = FALSE, $organism_id =
   try {
     foreach ($results as $record) {
 
-      print "\nLoading $base_table " . ($i + 1) . " of $count ($base_table_id=".$record->{$base_table_id}.")...";
+      print "\nLoading $base_table " . ($i + 1) . " of $count ($base_table_id=" . $record->{$base_table_id} . ")...";
 
       // update the job status every 1% features
       if ($job_id and $i % $interval == 0) {
@@ -500,7 +499,7 @@ function chado_node_sync_records($base_table, $max_sync = FALSE, $organism_id =
       }
 
       // Check if it is in the chado linking table (ie: check to see if it is already linked to a node)
-      $result = db_select('chado_'.$base_table, 'lnk')
+      $result = db_select('chado_' . $base_table, 'lnk')
         ->fields('lnk',array('nid'))
         ->condition($base_table_id, $record->{$base_table_id}, '=')
         ->execute()
@@ -517,6 +516,7 @@ function chado_node_sync_records($base_table, $max_sync = FALSE, $organism_id =
         $new_node->uid = $user->uid;
         $new_node->{$base_table_id} = $record->{$base_table_id};
         $new_node->$base_table = $record;
+        //$new_node->language = LANGUAGE_NONE;
 
         // TODO: should we get rid of this hook and use hook_node_presave() instead?
         // allow base module to set additional fields as needed

tripal_core/api/tripal_core.chado_query.api.inc

@@ -843,7 +843,6 @@ function chado_delete_record($table, $match, $options = NULL) {
   $args = array();
   foreach ($delete_matches as $field => $value) {
     // if we have an array values then this is an "IN" clasue.
-    // we cannot use prepared statements with these
 
     if (count($value) > 1) {
       $sql .= "$field IN (";
@@ -1180,15 +1179,11 @@ function chado_select_record($table, $columns, $values, $options = NULL) {
   }
 
 
-  // now build the SQL and prepared SQL statements. We may not use
-  // the prepared statement if it wasn't requested in the options or if the
-  // argument in a where statement has multiple values.
+  // now build the SQL 
   if (empty($where)) {
     // sometimes want to select everything
     $sql  = "SELECT " . implode(', ', $columns) . " ";
     $sql .= 'FROM {' . $table . '} ';
-    // we don't prepare a statement if there is no where clause
-    $prepared = FALSE;
   }
   else {
     $sql  = "SELECT " . implode(', ', $columns) . " ";

tripal_core/tripal_core.install

@@ -349,49 +349,69 @@ function tripal_core_custom_tables_schema() {
  *
  */
 function tripal_core_update_7200() {
-
-  // add an mview column to the tripal_custom_tables table so we
-  // can associate which of the custom tables are also mviews
-  if (!db_field_exists('tripal_custom_tables', 'mview_id')) {
-    $spec = array(
-      'type' => 'int',
-      'not NULL' => FALSE
-    );
-    $keys = array(
-      'foreign keys' => array(
-        'tripal_mviews' => array(
-          'table' => 'tripal_mviews',
-          'columns' => array(
-            'mview_id' => 'mview_id'
+  try {
+    // add an mview column to the tripal_custom_tables table so we
+    // can associate which of the custom tables are also mviews
+    if (!db_field_exists('tripal_custom_tables', 'mview_id')) {
+      $spec = array(
+        'type' => 'int',
+        'not NULL' => FALSE
+      );
+      $keys = array(
+        'foreign keys' => array(
+          'tripal_mviews' => array(
+            'table' => 'tripal_mviews',
+            'columns' => array(
+              'mview_id' => 'mview_id'
+            ),
           ),
         ),
-      ),
-    );
-    db_add_field('tripal_custom_tables', 'mview_id', $spec, $keys);
+      );
+      db_add_field('tripal_custom_tables', 'mview_id', $spec, $keys);
+      
+      // the foreign key specification doesn't really add one to the
+      // Drupal schema, it is just used internally, but we want one
+      db_query('
+        ALTER TABLE {tripal_custom_tables}
+        ADD CONSTRAINT tripal_custom_tables_fk1
+        FOREIGN KEY (mview_id) REFERENCES {tripal_mviews} (mview_id)
+        ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+      ');
+    }
     
-    // the foreign key specification doesn't really add one to the
-    // Drupal schema, it is just used internally, but we want one
-    db_query('
-      ALTER TABLE {tripal_custom_tables}
-      ADD CONSTRAINT tripal_custom_tables_fk1
-      FOREIGN KEY (mview_id) REFERENCES {tripal_mviews} (mview_id)
-      ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
-    ');
+    // now link the materialized view to it's custom table entry
+    $mviews = db_select('tripal_mviews', 'tmv')
+      ->fields('tmv', array('mview_id', 'mv_table'))
+      ->execute();
+    foreach ($mviews as $mview) {
+      db_update('tripal_custom_tables')
+       ->fields(array(
+         'mview_id' => $mview->mview_id
+       ))
+       ->condition('table_name', $mview->mv_table)
+       ->execute();
+    }
   }
-  
-  // now link the materialized view to it's custom table entry
-  $mviews = db_select('tripal_mviews', 'tmv')
-    ->fields('tmv', array('mview_id', 'mv_table'))
-    ->execute();
-  foreach ($mviews as $mview) {
-    db_update('tripal_custom_tables')
-     ->fields(array(
-       'mview_id' => $mview->mview_id
-     ))
-     ->condition('table_name', $mview->mv_table)
-     ->execute();
-     
-     
+  catch (\PDOException $e) {
+    $error = $e->getMessage();
+    throw new DrupalUpdateException('Could not update tripal_mviews table and link to custom tables: '. $error);
+  }
+}
+
+/**
+ * Fixes missing language for nodes and URL aliases. This may take awhile...
+ *
+ */
+function tripal_core_update_7201() {
+
+  try {
+    $sql = "UPDATE {node} SET language = :language WHERE language = ''";
+    db_query($sql, array(':language' => LANGUAGE_NONE));
+    $sql = "UPDATE {url_alias} SET language = :language WHERE language = ''";
+    db_query($sql, array(':language' => LANGUAGE_NONE));
+  }
+  catch (\PDOException $e) {
+    $error = $e->getMessage();
+    throw new DrupalUpdateException('Could not reset language for nodes and url aliases: '. $error);
   }
-  
 }

tripal_cv/includes/tripal_cv.cvterm_form.inc

@@ -204,6 +204,7 @@ function tripal_cv_add_cvterm_form_fields(&$form, $form_state, $cv_id = 0, $cvte
     '#type'          => 'textfield',
     '#title'         => t("Term Name"),
     '#default_value' => $name,
+    '#description'   => t('The term must be unique within the database selected below.'),
     '#required'      => TRUE,
   );
 
@@ -238,7 +239,7 @@ function tripal_cv_add_cvterm_form_fields(&$form, $form_state, $cv_id = 0, $cvte
   $form['fields']['db_id'] = array(
     '#type'         => 'select',
     '#title'         => t('Database'),
-    '#description'   => t('All terms must be assocated with a database. If the term you are adding is custom for this database, consider creating a database specific for your site and use that anytime you would like to add terms.'),
+    '#description'   => t('All terms must be assocated with a database. If there is no database for this term (e.g. it is a custom term specific to this site) then select the database \'null\' or consider creating a database specific for your site and use that anytime you would like to add terms.'),
     '#options'      => $dbs,
     '#default_value' => $db_id,
     '#required' => TRUE,
@@ -250,8 +251,7 @@ function tripal_cv_add_cvterm_form_fields(&$form, $form_state, $cv_id = 0, $cvte
     '#description'   => t('If this term has an existing accession (unique identifier) in the database
        please enter that here.  If the accession is numeric with a database prefix (e.g. GO:003023), please
        enter just the numeric value.  The database prefix will be appended whenever the term is displayed.
-       If the accession is not numeric then enter it as is.  If no value is provied, the term name
-       provided above will be used as the accession.'),
+       If you do not have a numeric value consider entering the term name as the accession.'),
     '#required'      => TRUE,
     '#default_value' => $accession,
   );

tripal_feature/includes/tripal_feature.admin.inc

@@ -50,7 +50,7 @@ function tripal_feature_admin() {
   $form['title'] = array(
     '#type' => 'fieldset',
     '#title' => t('Feature Page Titles'),
-    '#collapsible' => TRUE,
+    '#collapsible' => FALSE,
     '#collapsed' => FALSE,
   );
   $form['title']['desc'] = array(
@@ -82,7 +82,7 @@ function tripal_feature_admin() {
   $form['url'] = array(
     '#type' => 'fieldset',
     '#title' => t('Feature URL Path'),
-    '#collapsible' => TRUE,
+    '#collapsible' => FALSE,
     '#collapsed' => FALSE,
   );
   
@@ -143,7 +143,7 @@ function tripal_feature_admin() {
   $form['browser'] = array(
      '#type' => 'fieldset',
      '#title' => t('Feature Browser'),
-     '#collapsible' => TRUE,
+     '#collapsible' => FALSE,
      '#collapsed' => FALSE,
   );
   $form['browser']['browser_desc'] = array(
@@ -172,7 +172,7 @@ function tripal_feature_admin() {
   $form['summary'] = array(
      '#type' => 'fieldset',
      '#title' => t('Feature Summary Report'),
-     '#collapsible' => TRUE,
+     '#collapsible' => FALSE,
      '#collapsed' => FALSE,
   );
   $form['summary']['feature_mapping'] = array(
@@ -213,10 +213,12 @@ function tripal_feature_admin_validate($form, &$form_state) {
       break;
 
     case t('Set Feature URLs') :
-      variable_set('chado_feature_url', $form_state['values']['feature_url']);
+      variable_set('chado_feature_url_string', $form_state['values']['chado_feature_url_string']);
       tripal_add_job('Set Feature URLs', 'tripal_feature',
         'tripal_feature_set_urls', $job_args, $user->uid);
       break;
   }
 
 }
+
+

tripal_feature/includes/tripal_feature.chado_node.inc

@@ -901,6 +901,86 @@ function tripal_feature_get_feature_url($node, $url_alias = NULL) {
 
   return $url_alias;
 }
+/**
+ * Resets all of the URL alias for all features.  This function is meant to
+ * be run using Tripal's job managmenet interface
+ *  
+ * @param $na
+ *   Tripal expects all jobs to have at least one argument. For this function
+ *   we don't need any, so we have this dummy argument as a filler
+ * @param $job_id
+ * 
+ * @ingroup tripal_feature
+ */
+function tripal_feature_set_urls($na = NULL, $job = NULL) {
+
+  $transaction = db_transaction();
+
+  print "\nNOTE: Setting of URLs is performed using a database transaction. \n" .
+      "If the load fails or is terminated prematurely then the entire set of \n" .
+      "new URLs will be rolled back and no changes will be made\n\n";
+
+  try {
+    // get the number of records we need to set URLs for
+    $csql = "SELECT count(*) FROM {chado_feature}";
+    $num_nodes = db_query($csql)->fetchField();
+
+    // calculate the interval at which we will print an update on the screen
+    $num_set = 0;
+    $num_per_interval = 100;
+
+    // prepare the statements which will quickly add url alias. Because these
+    // are not Chado tables we must manually prepare them
+    $dsql = "DELETE FROM {url_alias} WHERE source = :source";
+    $isql = "INSERT INTO url_alias (source, alias, language) VALUES (:source, :alias, :language)";
+
+    // get the URL alias syntax string
+    $url_alias = variable_get('chado_feature_url_string', '/feature/[genus]/[species]/[type]/[uniquename]');
+    $url_alias = preg_replace('/^\//', '', $url_alias); // remove any preceeding forward slash
+
+    // get the list of features that have been synced
+    $sql = "SELECT * FROM {chado_feature}";
+    $nodes = db_query($sql);
+    foreach ($nodes as $node) {
+       
+      // get the URL alias
+      $src = "node/$node->nid";
+      $dst = tripal_feature_get_feature_url($node, $url_alias);
+
+      // if the src and dst is the same (the URL alias couldn't be set)
+      // then skip to the next one. There's nothing we can do about this one.
+      if($src == $dst) {
+        continue;
+      }
+
+      // remove any previous alias and then add the new one
+      db_query($dsql, array(':source' => $src));
+      db_query($isql, array(':source' => $src, ':alias' => $dst, ':language' => LANGUAGE_NONE));
+
+      // update the job status every 1% features
+      if ($job and $num_set % $num_per_interval == 0) {
+        $percent = ($num_set / $num_nodes) * 100;
+        tripal_job_set_progress($job, intval($percent));
+        $percent = sprintf("%.2f", $percent);
+        print "Setting URLs (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
+
+      }
+      $num_set++;
+    }
+    $percent = ($num_set / $num_nodes) * 100;
+    tripal_job_set_progress($job, intval($percent));
+    $percent = sprintf("%.2f", $percent);
+    print "Setting URLs (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
+    print "\nDone. Set " . number_format($num_set) . " URLs\n";
+
+  }
+  catch (Exception $e) {
+    $transaction->rollback();
+    print "\n"; // make sure we start errors on new line
+    watchdog_exception('tripal_feature', $e);
+    watchdog('trp-seturl', "Failed Removing URL Alias: %src", array('%src' => $src), WATCHDOG_ERROR);
+  }
+}
 
 /**
  * Implements hook_node_view().

tripal_feature/includes/tripal_feature.gff_loader.inc

@@ -899,8 +899,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
     }
   }
   catch (Exception $e) {
-    print "\n"; // make sure we start errors on new line
-    watchdog_exception('T_gff3_loader', $e);
+    print "\n"; // make sure we start errors on new line    
     if ($use_transaction) {
       $transaction->rollback();
       print "FAILED: Rolling back database changes...\n";
@@ -908,6 +907,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
     else {
       print "FAILED\n";
     }
+    watchdog_exception('T_gff3_loader', $e);
     return 0;
   }
 

tripal_feature/theme/tripal_feature.theme.inc

@@ -725,11 +725,11 @@ function tripal_feature_load_organism_feature_counts($organism) {
   // get the feature counts.  This is dependent on a materialized view
   // installed with the organism module
   $sql = "
-  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 = :organism_id
-  ORDER BY num_features desc
+    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 = :organism_id
+    ORDER BY num_features desc
   ";
   $args[':organism_id'] = $organism->organism_id;
   $org_features = chado_query($sql, $args);

tripal_stock/includes/tripal_stock.chado_node.inc

@@ -1000,4 +1000,84 @@ function tripal_stock_get_stock_url($node, $url_alias = NULL) {
   }
 
   return $url_alias;
+}
+/**
+ * Resets all of the URL alias for all stocks.  This function is meant to
+ * be run using Tripal's job managmenet interface
+ *
+ * @param $na
+ *   Tripal expects all jobs to have at least one argument. For this function
+ *   we don't need any, so we have this dummy argument as a filler
+ * @param $job_id
+ *
+ * @ingroup tripal_stock
+ */
+function tripal_stock_set_urls($na = NULL, $job = NULL) {
+
+  $transaction = db_transaction();
+
+  print "\nNOTE: Setting of URLs is performed using a database transaction. \n" .
+      "If the load fails or is terminated prematurely then the entire set of \n" .
+      "new URLs will be rolled back and no changes will be made\n\n";
+
+  try {
+    // get the number of records we need to set URLs for
+    $csql = "SELECT count(*) FROM {chado_stock}";
+    $num_nodes = db_query($csql)->fetchField();
+
+    // calculate the interval at which we will print an update on the screen
+    $num_set = 0;
+    $num_per_interval = 100;
+
+    // prepare the statements which will quickly add url alias. Because these
+    // are not Chado tables we must manually prepare them
+    $dsql = "DELETE FROM {url_alias} WHERE source = :source";
+    $isql = "INSERT INTO url_alias (source, alias, language) VALUES (:source, :alias, :language)";
+
+    // get the URL alias syntax string
+    $url_alias = variable_get('chado_stock_url_string', '/stock/[genus]/[species]/[type]/[uniquename]');
+    $url_alias = preg_replace('/^\//', '', $url_alias); // remove any preceeding forward slash
+
+    // get the list of stocks that have been synced
+    $sql = "SELECT * FROM {chado_stock}";
+    $nodes = db_query($sql);
+    foreach ($nodes as $node) {
+       
+      // get the URL alias
+      $src = "node/$node->nid";
+      $dst = tripal_stock_get_stock_url($node, $url_alias);
+
+      // if the src and dst is the same (the URL alias couldn't be set)
+      // then skip to the next one. There's nothing we can do about this one.
+      if($src == $dst) {
+        continue;
+      }
+
+      // remove any previous alias and then add the new one
+      db_query($dsql, array(':source' => $src));
+      db_query($isql, array(':source' => $src, ':alias' => $dst, ':language' => LANGUAGE_NONE));
+
+      // update the job status every 1% stocks
+      if ($job and $num_set % $num_per_interval == 0) {
+        $percent = ($num_set / $num_nodes) * 100;
+        tripal_job_set_progress($job, intval($percent));
+        $percent = sprintf("%.2f", $percent);
+        print "Setting URLs (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
+
+      }
+      $num_set++;
+    }
+    $percent = ($num_set / $num_nodes) * 100;
+    tripal_job_set_progress($job, intval($percent));
+    $percent = sprintf("%.2f", $percent);
+    print "Setting URLs (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
+    print "\nDone. Set " . number_format($num_set) . " URLs\n";
+
+  }
+  catch (Exception $e) {
+    $transaction->rollback();
+    print "\n"; // make sure we start errors on new line
+    watchdog_exception('tripal_stock', $e);
+    watchdog('trp-seturl', "Failed Removing URL Alias: %src", array('%src' => $src), WATCHDOG_ERROR);
+  }
 }

tripal_stock/tripal_stock.install

@@ -49,6 +49,11 @@ function tripal_stock_requirements($phase) {
 function tripal_stock_install() {
   // create the module's data directory
   tripal_create_files_dir('tripal_stock');
+  
+  // add some controlled vocabularies 
+  tripal_stock_add_cvs();
+  
+  tripal_stock_add_cvterms();
 
   // set the default vocabularies
   tripal_set_default_cv('stock', 'type_id', 'stock_type');
@@ -301,7 +306,7 @@ function tripal_stock_update_7200() {
 }
 
 /**
- * Upgrade to 7.x-2.0.1-alpha
+ * Add materialized views
  */
 function tripal_stock_update_7201() {