Pull request for linkout repairs

api/blast_ui.api.inc

@@ -1,5 +1,101 @@
 <?php
 
+/**
+ * This program is used for services module specifically.
+ * Run BLAST (should be called from the command-line)
+ *
+ * @param $program
+ *   Which BLAST program to run (ie: 'blastn', 'tblastn', tblastx', 'blastp','blastx')
+ * @param $query
+ *   The full path and filename of the query FASTA file
+ * @param $database
+ *   The full path and filename prefix (excluding .nhr, .nin, .nsq, etc.)
+ * @param $output_filestub
+ *   The filename (not including path) to give the results. Should not include file type suffix
+ * @param $options
+ *   An array of additional option where the key is the name of the option used by
+ *   BLAST (ie: 'num_alignments') and the value is relates to this particular
+ *   BLAST job (ie: 250)
+ * @param $format 
+ *   Which specifies Json or asn format of file or program
+ * @param  $format_type 
+ * which specify the number of format used by BLAST e.g json has 11 and json as 12. 
+ */
+
+
+function run_BLAST_tripal_job_services($program, $query, $database, $output_filestub, $options, $format, $format_type,  $job_id = NULL) {
+
+
+
+  $output_file = file_directory_temp() .  DIRECTORY_SEPARATOR . $output_filestub . '.blast.' . $format_type;
+
+
+ // $output_file = file_directory_temp() .  DIRECTORY_SEPARATOR . $output_filestub . '.blast.json';
+
+  $output_dir = variable_get('file_public_path', conf_path() . '/files') 
+              . DIRECTORY_SEPARATOR . 'tripal' . DIRECTORY_SEPARATOR . 'tripal_blast';
+
+  print "\nExecuting $program\n\n";
+  print "Query: $query\n";
+  print "Database: $database\n";
+  print "Results File: $output_file\n";
+
+  print "Options:\n";
+
+  // Allow administrators to use an absolute path for these commands.
+  // Defaults to using $PATH.
+	$blast_path    = variable_get('blast_path', '');
+	$blast_threads = variable_get('blast_threads', '');
+
+	// Strip the extension off the BLAST target
+	$database = preg_replace("/(.*)\.[pn]\w\w/", '$1', $database);
+
+	// The executables:
+	$program       = $blast_path . $program;
+	$blast_formatter_command = $blast_path . 'blast_formatter';
+
+  //$blast_cmd = "$program -query '$query' -db '$database' -out '$output_file' -outfmt=11";
+  $blast_cmd = "$program -query '$query' -db '$database' -out '$output_file' -outfmt=".$format;
+
+   if (!empty($options)) {
+    foreach ($options as $opt => $val) {
+      if ($val) {
+        print "\t$opt: $val\n";
+        $blast_cmd .= " -$opt $val";
+      }
+    }
+  }
+
+  // Setting the value of threads by admin page
+ $blast_cmd .= " -num_threads ".$blast_threads;
+
+  print "\nExecuting the following BLAST command:\n" . $blast_cmd . "\n";
+
+  system($blast_cmd);
+
+  if (!file_exists($output_file)) {
+    tripal_report_error(
+      'blast_ui',
+      TRIPAL_ERROR,
+      "BLAST did not complete successfully as is implied by the lack of output file (%file). The command run was @command",
+      array('%file' => $output_file, '@command' => $blast_cmd),
+      array('print' => TRUE)
+    );
+    return FALSE;
+ }
+  print "\nDone!\n";
+
+}
+
+
+
+
+
+
+
+
+
+
 /**
  * @file
  * Contains more generally applicable functions as well as some meant to help developers
@@ -84,8 +180,11 @@ function get_blast_database_options($type) {
     }
   }
 
+  // Sort alphabetically
   asort($options);
-  $options[0] = 'Select a Dataset';
+
+  // Prepend prompt; note that array_unshift() will re-index the array
+  $options = array('Select a Dataset') + $options;
 
   return $options;
 }
@@ -668,4 +767,4 @@ function generate_blast_hit_image($acc = '', $scores, $hits, $tsize, $qsize, $na
   ob_end_clean();
 
   return $b64_img;
-}
+}

blast_ui.module

@@ -266,10 +266,13 @@ function show_blast_output($job_string) {
  *  
  */
 function blast_ui_ctools_plugin_api($owner, $api) {
+   $webservices = variable_get('Enable_webservices');
+  if($webservices == 1){
   if ($owner == 'services' && $api == 'services') {
     return array(
       'version' => 3,
       'file' => 'includes/blast_ui.services.inc'
     );
   }
+ }
 }

includes/blast_ui.admin.inc

@@ -31,19 +31,26 @@ function blast_ui_admin_form($form, $form_state) {
 
    $form['general']['eVal']= array(
     '#type' => 'textfield',
-    '#title' => t('e-Value (Expected Threshold)'),
-    '#description' => t('Expected number of chance matches in a random model. This number should be give in a decimal format.'),
+    '#title' => t('Default e-value (Expected Threshold)'),
+    '#description' => t('Expected number of chance matches in a random model. This number should be given in a decimal format.'),
      '#default_value' => variable_get('eVal', 0.001),
     //'#default_value' => variable_get('blast_threads', 1),
   );
 
   $form['general']['qRange']= array(
     '#type' => 'textfield',
-    '#title' => t('Max matches in a query range'),
+    '#title' => t('Default max matches in a query range'),
     '#description' => t('Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query.'),
     '#default_value' => variable_get('qRange', 0),
   );
 
+   $form['general']['Enable_webservices'] = array(
+    '#type' => 'checkbox',
+    '#title' => 'Enable webservices of blast',
+    '#description' => 'When checked, a blast webservices gets enabled.',
+    '#default_value' => variable_get('Enable_webservices', true),
+  );
+
   $form['file_upload'] = array(
     '#type' => 'fieldset',
     '#title' => 'Allow File Upload',
@@ -156,6 +163,99 @@ function blast_ui_admin_form_validate($form, &$form_state) {
 
 }
 
+/*
+**
+** custom method disabled the web services 
+**
+*/
+
+function disable_web_services()
+{
+    $ar=array('services', 'rest_server');
+  	$result = module_disable($ar,true);
+  	try{
+  	$eid = 1;
+    $num_deleted = db_delete('services_endpoint')->condition('eid', $eid)->execute();  
+    } catch(Exception $e){
+    //drupal_set_message(t("Web-Services of blast are already disabled"), 'error');
+   }
+
+}
+
+/*
+** custom method enable the web services 
+**
+*/
+
+function enable_web_services()
+{
+    $ar=array('services', 'rest_server');
+    $result = module_enable($ar, true);
+    if (empty($result)) {
+     throw new DrupalUpdateException(implode(', ', $ar) . ' or dependencies could not be enabled, please install services ');
+   }
+
+   $server_settings = array(
+  'formatters' => array(
+    'bencode' => TRUE,
+    'json' => TRUE,
+    'jsonp' => TRUE,
+    'php' => TRUE,
+    'xml' => TRUE,
+  ),
+  'parsers' => array(
+    'application/json' => TRUE,
+    'application/vnd.php.serialized' => TRUE,
+    'application/x-www-form-urlencoded' => TRUE,
+    'application/xml' => TRUE,
+    'multipart/form-data' => TRUE,
+    'text/xml' => TRUE,
+  ),
+);
+
+$resources = array(
+  'blast' => array(
+    'operations' => array(
+      'retrieve' => array(
+        'enabled' => '1',
+      ),
+      'index' => array(
+        'enabled' => '1',
+      ),
+    ),
+    'actions' => array(
+      'getJobId' => array(
+        'enabled' => '1',
+      ),
+      'getBlastStatus' => array(
+        'enabled' => '1',
+      ),
+      'getDatabaseOptions' => array(
+        'enabled' => '1',
+      ),
+    ),
+  ),
+);
+
+  try{
+   $nid = db_insert('services_endpoint')->fields(
+    array(
+    'eid' => 1,
+    'debug'  => 1,
+    'name' => 'restapi',
+    'server' => 'rest_server',
+    'path' => 'restapi',
+    'resources' =>  serialize($resources),   //'a:1:{s:5:"blast";a:2:{s:10:"operations";a:2:{s:8:"retrieve";a:1:{s:7:"enabled";s:1:"1";}s:5:"index";a:1:{s:7:"enabled";s:1:"1";}}s:7:"actions";a:2:{s:8:"getJobId";a:1:{s:7:"enabled";s:1:"1";}s:18:"getDatabaseOptions";a:1:{s:7:"enabled";s:1:"1";}}}}',
+     'server_settings' => serialize($server_settings),
+    'authentication' => 'a:0:{}',
+  ))->execute();
+}
+ catch(Exception $e){
+    //drupal_set_message(t("Web-Services of blast are already Enabled"), 'error');
+   }
+
+}
+
 /**
  * Submit the Admin/settings form.
  */
@@ -167,9 +267,17 @@ function blast_ui_admin_form_submit($form, $form_state) {
   variable_set('eVal', $form_state['values']['eVal']);
   variable_set('qRange', $form_state['values']['qRange']);
 
+  // Logic to enable web services on single click
+  variable_set('Enable_webservices', $form_state['values']['Enable_webservices']);
   variable_set('blast_ui_allow_query_upload', $form_state['values']['query_upload']);	
   variable_set('blast_ui_allow_target_upload', $form_state['values']['target_upload']);
 
   variable_set('blast_ui_nucleotide_example_sequence', $form_state['values']['nucleotide_example']);
   variable_set('blast_ui_protein_example_sequence', $form_state['values']['protein_example']);
-}
+
+  if($form_state['values']['Enable_webservices'] == 1){
+  	enable_web_services();
+  }else{
+    disable_web_services();
+  }
+}