Merge pull request #3 from LegumeFederation/7.x-1.x

Merging in the changed from the LegumeFederation.

api/blast_ui.api.inc

@@ -197,6 +197,9 @@ function run_BLAST_tripal_job($program, $query, $database, $output_filestub, $op
     }
   }
 
+ // 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);

includes/blast_ui.admin.inc

@@ -29,6 +29,21 @@ function blast_ui_admin_form($form, $form_state) {
     '#default_value' => variable_get('blast_threads', 1),
   );
   
+   $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.'),
+     '#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'),
+    '#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),
+  );
+  
   $form['file_upload'] = array(
     '#type' => 'fieldset',
     '#title' => 'Allow File Upload',
@@ -48,7 +63,7 @@ function blast_ui_admin_form($form, $form_state) {
 
   $form['file_upload']['target_upload'] = array(
     '#type' => 'checkbox',
-    '#title' => 'Enable Taget Sequence Upload',
+    '#title' => 'Enable Target Sequence Upload',
     '#description' => 'When checked, a target file upload field will be available on BLAST request forms.',
     '#default_value' => FALSE,
     '#default_value' => variable_get('blast_ui_allow_target_upload', FALSE)
@@ -149,6 +164,9 @@ function blast_ui_admin_form_submit($form, $form_state) {
   variable_set('blast_path', $form_state['values']['blast_path']);
   variable_set('blast_threads', $form_state['values']['blast_threads']);
   
+  variable_set('eVal', $form_state['values']['eVal']);
+  variable_set('qRange', $form_state['values']['qRange']);
+  
   variable_set('blast_ui_allow_query_upload', $form_state['values']['query_upload']);	
   variable_set('blast_ui_allow_target_upload', $form_state['values']['target_upload']);
   

includes/blast_ui.form_advanced_options.inc

@@ -1206,7 +1206,7 @@ function _get_word_size($which) {
     case 'blastp':
     case 'tblastn':
     	return array(
-        2 => t('2'),
+      //  2 => t('2'),
         3 => t('3'),
         6 => t('6'),
       );

includes/blast_ui.form_per_program.inc

@@ -202,14 +202,17 @@ function blast_ui_per_blast_program_form($form, $form_state) {
 
   // BLAST DATABASE
   //.........................
-
+  $target_upload_text = '';
+  if (variable_get('blast_ui_allow_target_upload', FALSE)) {
+    $target_upload_text = 'You can also use the browse button to upload a '
+                        . 'file from your local disk. The file may contain '
+                        . 'a single sequence or a list of sequences. ';
+  }
   $form['B']['DB'] = array(
     '#type' => 'fieldset',
     '#title' => t('Choose Search Target'),
     '#description' => t('Choose from one of the %type BLAST databases listed '
-      . 'below. You can also use the browse button to upload a file from your '
-      . 'local disk. The file may contain a single sequence or a list of '
-      . 'sequences. ',
+                        . 'below. ' . $target_upload_text,
       array('%type' => $db_type)),
     '#collapsible' => TRUE,
     '#collapsed' => FALSE,

includes/blast_ui.node.inc

@@ -364,12 +364,23 @@ function blastdb_load($nodes) {
   $result = db_query($sql, array(':nids' => array_keys($nodes)));
 
   foreach ($result as $record) {
+    // Does this BLAST node have a custom linkout? 
+    //   (Is there a better way to determine this?)
+    $custom_linkout = ($record->dbxref_linkout_type != '' 
+                         && $record->dbxref_linkout_type != 'link' 
+                         && $record->dbxref_linkout_type != 'gbrowse'
+                         && $record->dbxref_linkout_type != 'jbrowse');
+
     $nodes[$record->nid]->db_name = $record->name;
     $nodes[$record->nid]->db_path = $record->path;
     $nodes[$record->nid]->title = $record->name;
     $nodes[$record->nid]->db_dbtype = $record->dbtype;
 
-    if ($record->dbxref_id_regex AND $record->dbxref_db_id) {
+    // There will be a hit linkout if there is a regex pattern for the id
+    //   and a database (db record) to generate a URL
+    //   OR if a custom linkout has been set, which may or may not require a 
+    //   regex and/or database.
+    if ($record->dbxref_id_regex AND $record->dbxref_db_id || $custom_linkout) {
       $nodes[$record->nid]->linkout = new stdClass();
 
       if (preg_match('/\/.*\//', $record->dbxref_id_regex)) {
@@ -400,6 +411,7 @@ function blastdb_load($nodes) {
       }
     }
     else {
+      // No linkout
       $nodes[$record->nid]->linkout = new stdClass();
       $nodes[$record->nid]->linkout->regex = '';
       $nodes[$record->nid]->linkout->db_id = 0;

includes/blast_ui.services.inc

@@ -1,182 +1,584 @@
 <?php
-function blast_ui_services_resources() {
-  return array(
-    'blast' => array(
-      'retrieve' => array(
-        'help' => 'Retrieves a blast_ui',       
-        'callback' => '_blast_ui_retrieve',
-         'access callback' => 'user_access',
-        'access arguments' => array('access user profiles'),
-        'args' => array(),
-      ),
-      'create' => array(
-        'help' => 'Creates a blast_ui',
-        'callback' => '_blast_ui_create',
-        'access arguments' => array('access content'),
-        'access arguments append' => false,
-        'args' => array(
-           array(
-              'name' => 'param',
-              'type' => 'array',
-              'description' => 'The node information',
-              'source' => 'data',
-              'optional' => FALSE,
-          ),
-        ),
-      ),
-        'update' => array(
-        'help' => 'Updates a blast_ui',
-        'callback' => '_blast_ui_update',
-       'access callback' => 'user_access',
-        'access arguments' => array('access user profiles'),
-        'args' => array(
-          array(
-            'name' => 'id',
-            'type' => 'int',
-            'description' => 'The id of the node to update',
-            'source' => array('path' => '0'),
-            'optional' => FALSE,
-          ),
-          array(
-            'name' => 'data',
-            'type' => 'struct',
-            'description' => 'The node data object',
-            'source' => 'data',
-            'optional' => FALSE,
-          ),
-        ),
-      ),
-      'delete' => array(
-        'help' => 'Deletes a blast_ui',
-        'callback' => '_blast_ui_delete',
-         'access callback' => 'user_access',
-       'access arguments' => array('access content'),
-        'access arguments append' => TRUE,
-        'args' => array(
-          array(
-            'name' => 'nid',
-            'type' => 'int',
-            'description' => 'The id of the note to delete',
-            'source' => array('path' => '0'),
-            'optional' => FALSE,
-          ),
-        ),
-      ),
-      'index' => array(
-        'help' => 'Retrieves a listing of blast_ui',
-        'callback' => '_blast_ui_index',
-        'access callback' => 'user_access',
-        'access arguments' => array('access content'),
-        'access arguments append' => FALSE,
-        'args' => array(),
-        ),
-     
-       'actions' => array(
-    	'getDatabaseType' => array(
-    	'help' => 'Retrieves a listing of database',
-        'callback' => '_blast_ui_getDatabaseType',
-        'access callback' => 'user_access',
-        'access arguments' => array('access content'),
-        'access arguments append' => FALSE,
-        'args' => array(),
+/**
+ * Implements hook_services_resources().
+ * Hooks provided by Services for the definition of new services,
+ */
+
+function blast_ui_services_resources()
+ {
+   return array(
+       'blast' => array(
+          'retrieve' => array(
+             'help' => 'Retrieves a blastResult',
+            'callback' => 'getBlastData',
+            'access callback' => 'user_access',
+            'access arguments' => array(
+                'access content' 
+            ),
+            'access arguments append' => FALSE,
+            'args' => array(
+                array(
+                   'name' => 'job_id',
+                  'type' => 'int',
+                  'description' => 'The information needed',
+                  'source' => array(
+                      'path' => '0' 
+                  ),
+                  'optional' => FALSE 
+               ) 
+            ) 
          ),
-         'getDatabaseOptions' => array(
-    	'help' => 'Retrieves a listing of database',
-        'callback' => '_blast_ui_getDatabaseOption',
-        'access callback' => 'user_access',
-        'access arguments' => array('access content'),
-        'access arguments append' => FALSE,
-        'args' => array(),
+         'index' => array(
+             'help' => 'Retrieves a listing of blast_ui',
+            'callback' => '_blast_ui_index',
+            'access callback' => 'user_access',
+            'access arguments' => array(
+                'access content' 
+            ),
+            'access arguments append' => FALSE,
+            'args' => array ()
          ),
-        ),
-       ),
+         
+         'actions' => array(
+             'getJobId' => array(
+                'help' => 'Retrieves a listing of database',
+               'callback' => '_blast_ui_getJobId',
+               'access callback' => 'user_access',
+               'access arguments' => array(
+                   'access content' 
+               ),
+               'args' => array(
+                   array(
+                      'name' => 'data',
+                     'type' => 'array',
+                     'description' => 'Retrieve blast job id',
+                     'source' => 'data',
+                     'optional' => FALSE 
+                  ) 
+               ),
+               'access arguments append' => FALSE 
+            ),
+            
+            'getDatabaseOptions' => array(
+                'help' => 'Retrieves a listing of database',
+               'callback' => '_blast_ui_getDatabaseOption',
+               'access callback' => 'user_access',
+               'access arguments' => array(
+                   'access content' 
+               ),
+               'args' => array(
+                   array(
+                      'name' => 'data',
+                     'type' => 'array',
+                     'description' => 'The set database_type information',
+                     'source' => 'data',
+                     'optional' => FALSE 
+                  ) 
+               ),
+               'access arguments append' => false 
+            ) 
+         ) 
+      ) 
    );
-    
-}
-
-
-
+ }
 
 
-function _blast_ui_create($param) {
-  
- return services_error('Missing _blast_ui_create', 406);
-}
 
-
-/**
-* Callback for updating note services.
-*
-* @param int $id
-* @param object $data
-* @return object
-*/
-function _blast_ui_update($id, $data) {
-  return services_error('Missing _blast_ui_update', 406);
-} 
 /**
-* Callback for retrieving note services.
-*
-* @param int $id
-* @return object
-*/
-function _blast_ui_retrieve($id) {
- return services_error('Missing _blast_ui_retrieve', 406);
-}
+ * Callback for retrieving blast services.
+ *
+ * @param int $id
+ * @return object
+ */
+function _blast_ui_retrieve( $id )
+ {
+   return getBlastData( $id );
+ }
 
 /**
-* Callback for deleting note services.
-*
-* @param int $id
-* @return object
-*/
-function _blast_ui_delete($id) {
-  return services_error('Missing _blast_ui_delete', 406);
-}
-
-function _blast_ui_index($page, $parameters) {
- return array(
-      'Nucleotide' => array ( 
-        'Nucleotide' => 'blastn',
-      	'protein' => 'blastx',
-      ),
-      'Protein' => array ( 
-        'Nucleotide' => 'tblastn',
-      	'protein' => 'blastp',
-      ),
-    ); 
-  
-//  return services_error('Missing _blast_ui_index solved', 406);
-}
-
-function _blast_ui_getDatabaseType() {
+ * Callback for Index blast services.
+ * @return object
+ */
 
-    return array(
-      'Nucleotide' => array ( 
-        'Nucleotide' => 'blastn',
-      	'protein' => 'blastx',
+function _blast_ui_index()
+ {
+   return array(
+      
+       'query_type' => array(
+          '1' => 'nucleotide',
+         '2' => 'protein' 
       ),
-      'Protein' => array ( 
-        'Nucleotide' => 'tblastn',
-      	'protein' => 'blastp',
+      'db_type' => array(
+          '1' => 'nucleotide',
+         '2' => 'protein' 
       ),
-    ); 
-}
+      'blast_program' => array(
+          '1' => 'blastn',
+         '2' => 'blastx',
+         '3' => 'tblastn',
+         '4' => 'blastp' 
+      ) 
+   );
+ }
 
+/*
+ **  Method returns Advanced options and Database Type
+ **  @param Object $data
+ **  web service url :  http://localhost:8080/restapi/blast/getDatabaseOptions.json
+ */
 
-function _blast_ui_getDatabaseOption() {
+function _blast_ui_getDatabaseOption( $data )
+ {
+   
+   if ( !isset( $data[ query_type ] ) )
+    {
+      return services_error( 'Missing blast attribute $query_type [ set necleotide or protein in post request of query_type ]', 406 );
+    }
+   if ( !isset( $data[ db_type ] ) )
+    {
+      return services_error( 'Missing blast attribute $db_type [ set necleotide or protein in post request of db_type ]', 406 );
+    }
+   if ( !isset( $data[ blast_program ] ) )
+    {
+      return services_error( 'Missing blast attribute $blast_program [ set blastn, blastx, tblastn, blastp in post request of blast_program ]', 406 );
+    }
+   
+   $query_type       = $data[ db_type ];
+   $db_type          = $data[ db_type ];
+   $blast_program    = $data[ blast_program ];
+   $options_database = get_blast_database_options( $db_type );
+   
+   // Data Set send to user for selection of Blastn
+   if ( $blast_program == 'blastn' )
+    {
+      return array(
+          'Select_Database' => $options_database,
+         'Max_target_sequences' => _get_max_target( $blast_program ),
+         'Word_size' => _get_word_size( $blast_program ),
+         'Match_Mismatch_Scores' => _get_match_mismatch( $blast_program ),
+         'Gap_Costs' => _get_gap( $blast_program ) 
+      );
+    }
+   // Data Set send to user for selection of Blastx
+   elseif ( $blast_program == 'blastx' )
+    {
+      return array(
+          'Select_Database' => $options_database,
+         'Max_target_sequences' => _get_max_target( $blast_program ),
+         'Word_size' => _get_word_size( $blast_program ),
+         'Matrix_options' => _get_matrix_options() 
+         
+      );
+    }
+   //Data Set send to user for selection of tblastn
+   elseif ( $blast_program == 'tblastn' )
+    {
+      return array(
+          'Select_Database' => $options_database,
+         'Max_target_sequences' => _get_max_target( $blast_program ),
+         'Word_size' => _get_word_size( $blast_program ),
+         'Matrix_options' => _get_matrix_options(),
+         'Gap_Costs' => getGap_cost() 
+      );
+    }
+   //Data Set send to user for selection of blastp
+   elseif ( $blast_program == 'blastp' )
+    {
+      return array(
+          'Select_Database' => $options_database,
+         'Max_target_sequences' => _get_max_target( $blast_program ),
+         'Word_size' => _get_word_size( $blast_program ),
+         'Matrix_options' => _get_matrix_options(),
+         'Gap_Costs' => getGap_cost() 
+      );
+    }
+ }
 
- $db_type = 'nucleotide';
- $options = get_blast_database_options($db_type);
-return $options;
-}
+/*
+ ** validate the data  			           
+ */
 
+function blast_validation( $query_type, $db_type, $data )
+ {
+   if ( $query_type == 'nucleotide' )
+    {
+      if ( $db_type == 'nucleotide' )
+       {
+         
+         if ( !isset( $data[ Select_Database ] ) )
+          {
+            return services_error( 'Missing blast attribute $Select_Database [ query blast/getDatabaseOptions for options :- Add database you need to use]', 406 );
+          }
+         if ( !isset( $data[ Max_target_sequences ] ) )
+          {
+            return services_error( 'Missing blast attribute $Max_target_sequences [ query blast/getDatabaseOptions for options ]', 406 );
+          }
+         if ( !isset( $data[ Word_size ] ) )
+          {
+            return services_error( 'Missing blast attribute $Word_size [ query blast/getDatabaseOptions for options ]', 406 );
+          }
+         if ( !isset( $data[ Match_Mismatch_Scores ] ) )
+          {
+            return services_error( 'Missing blast attribute $Match_Mismatch_Scores [ query blast/getDatabaseOptions for options]', 406 );
+          }
+         if ( !isset( $data[ Gap_costs ] ) )
+          {
+            return services_error( 'Missing blast attribute $Gap_Costs [ query blast/getDatabaseOptions for options ]', 406 );
+          }
+         if ( isset( $data[ seqQuery ] ) )
+          {
+            if ( validate_fasta_sequence( $query_type, $data[ seqQuery ] ) == 1 )
+             {
+               return services_error( 'Please enter validate_fasta_sequence', 406 );
+             }
+          }
+         else
+          {
+            return services_error( 'Missing blast attribute data[seqQuery]', 406 );
+          }
+       }
+      else
+       {
+         
+         if ( !isset( $data[ Select_Database ] ) )
+          {
+            return services_error( 'Missing blast attribute $Select_Database [ query blast/getDatabaseOptions for options :- Add database used by you]', 406 );
+          }
+         if ( !isset( $data[ Max_target_sequences ] ) )
+          {
+            return services_error( 'Missing blast attribute $Max_target_sequences [ query blast/getDatabaseOptions for options ]', 406 );
+          }
+         if ( !isset( $data[ Word_size ] ) )
+          {
+            return services_error( 'Missing blast attribute $Word_size [ query blast/getDatabaseOptions for options ]', 406 );
+          }
+         if ( !isset( $data[ Matrix_options ] ) )
+          {
+            return services_error( 'Missing blast attribute $Matrix_options [ query blast/getDatabaseOptions for options ]', 406 );
+          }
+         if ( isset( $data[ seqQuery ] ) )
+          {
+            if ( validate_fasta_sequence( $query_type, $data[ seqQuery ] ) == 1 )
+             {
+               return services_error( 'Please enter validate_fasta_sequence', 406 );
+             }
+          }
+         else
+          {
+            return services_error( 'Missing blast attribute data[seqQuery]', 406 );
+          }
+         
+       }
+    }
+   else
+    {
+      if ( $db_type == 'nucleotide' )
+       {
+         if ( !isset( $data[ Select_Database ] ) )
+          {
+            return services_error( 'Missing blast attribute $Select_Database [ query blast/getDatabaseOptions for options :- Add database you need to use]', 406 );
+          }
+         if ( !isset( $data[ Max_target_sequences ] ) )
+          {
+            return services_error( 'Missing blast attribute $Max_target_sequences [ query blast/getDatabaseOptions for options ]', 406 );
+          }
+         if ( !isset( $data[ Word_size ] ) )
+          {
+            return services_error( 'Missing blast attribute $Word_size [ query blast/getDatabaseOptions for options ]', 406 );
+          }
+         if ( !isset( $data[ Matrix_options ] ) )
+          {
+            return services_error( 'Missing blast attribute $Matrix_options [ query blast/getDatabaseOptions for options ]', 406 );
+          }
+         if ( !isset( $data[ Gap_costs ] ) )
+          {
+            return services_error( 'Missing blast attribute [ query blast/getDatabaseOptions for options ]', 406 );
+          }
+         
+         if ( isset( $data[ seqQuery ] ) )
+          {
+            if ( validate_fasta_sequence( $query_type, $data[ seqQuery ] ) == 1 )
+             {
+               return services_error( 'Please enter validate_fasta_sequence', 406 );
+             }
+          }
+         else
+          {
+            return services_error( 'Missing blast attribute data[seqQuery]', 406 );
+          }
+       }
+      else
+       {
+         
+         //return $data;
+         
+         if ( !isset( $data[ Select_Database ] ) )
+          {
+            return services_error( 'Missing blast attribute $Select_Database [ query blast/getDatabaseOptions for options :- Add database used by you]', 406 );
+          }
+         if ( !isset( $data[ Max_target_sequences ] ) )
+          {
+            return services_error( 'Missing blast attribute $Max_target_sequences [ query blast/getDatabaseOptions for options ]', 406 );
+          }
+         if ( !isset( $data[ Word_size ] ) )
+          {
+            return services_error( 'Missing blast attribute $Word_size [ query blast/getDatabaseOptions for options ]', 406 );
+          }
+         if ( !isset( $data[ Matrix_options ] ) )
+          {
+            return services_error( 'Missing blast attribute $Matrix_options [ query blast/getDatabaseOptions for options ]', 406 );
+          }
+         if ( isset( $data[ seqQuery ] ) )
+          {
+            if ( validate_fasta_sequence( $query_type, $data[ seqQuery ] ) == 1 )
+             {
+               return services_error( 'Please enter validate_fasta_sequence', 406 );
+             }
+          }
+         else
+          {
+            return services_error( 'Missing blast attribute data[seqQuery]', 406 );
+          }
+       }
+    }
+ }
 
+/*
+ ** Method call the blast_ui_getblastJobId by setting all the needed
+ ** parameters
+ ** web service url :  http://localhost:8080/restapi/blast/getJobId.json
+ */
 
 
+function _blast_ui_getJobId( $data )
+ {
+   
+   $query_type;
+   $db_type;
+   // Setting the default value of qRange and eValue from blast_ui.admin
+   $eVal   = variable_get( 'eVal', '' );
+   $qRange = variable_get( 'qRange', '' );
+   
+   /* check values in post query */
+   
+   if ( !isset( $data[ query_type ] ) )
+    {
+      return services_error( 'Missing blast attribute $query_type [ set necleotide or protein in post request of query_type ]', 406 );
+    }
+   if ( !isset( $data[ db_type ] ) )
+    {
+      return services_error( 'Missing blast attribute $db_type [ set necleotide or protein in post request of db_type ]', 406 );
+    }
+   
+   $query_type = $data[ query_type ];
+   $db_type    = $data[ db_type ];
+   
+   // check the user input in $data
+   blast_validation( $query_type, $db_type, $data );
+   
+   
+   if ( isset( $data[ $eVal ] ) )
+    {
+      $eVal = $data[ $eVal ];
+    }
+   if ( isset( $data[ $culling_limit ] ) )
+    {
+      $qRange = $data[ $culling_limit ];
+    }
+   
+   if ( $query_type == 'nucleotide' )
+    {
+      if ( $db_type == 'nucleotide' )
+       {
+         $blast_program    = 'blastn';
+         // code not working for wordvalue = 7 ?
+         $options_database = get_blast_database_options( $data[ db_type ] );
+         $Databasekey      = array_search( $data[ Select_Database ], $options_database );
+         $advanced_options = advanced_options( $blast_program, $eVal, $qRange, $data );
+         
+       }
+      elseif ( $db_type == 'protein' )
+       {
+         $blast_program    = 'blastx';
+         // how to get gap cost - question
+         $options_database = get_blast_database_options( $data[ db_type ] );
+         $Databasekey      = array_search( $data[ Select_Database ], $options_database );
+         $advanced_options = advanced_options( $blast_program, $eVal, $qRange, $data );
+       }
+    }
+   elseif ( $query_type == 'protein' )
+    {
+      if ( $db_type == 'nucleotide' )
+       {
+         $blast_program    = 'tblastn';
+         $options_database = get_blast_database_options( $data[ db_type ] );
+         $Databasekey      = array_search( $data[ Select_Database ], $options_database );
+         $advanced_options = advanced_options( $blast_program, $eVal, $qRange, $data );
+         
+       }
+      elseif ( $db_type == 'protein' )
+       {
+         $blast_program    = 'blastp';
+         $options_database = get_blast_database_options( $data[ db_type ] );
+         $Databasekey      = array_search( $data[ Select_Database ], $options_database );
+         $advanced_options = advanced_options( $blast_program, $eVal, $qRange, $data );
+       }
+    }
+   
+   
+   return blast_ui_getblastJobId( $data[ query_type ], $data[ db_type ], $data[ seqQuery ], $Databasekey, $advanced_options );
+   
+   
+ }
+/*
+ ** Define the advanced Options for Blast 
+ ** @return : advanced_options according to blast_program
+ */
+function advanced_options( $blast_program, $eVal, $qRange, $data )
+ {
+   
+   if ( $blast_program == 'blastn' )
+    {
+      $wordvalue = intval( $data[ Word_size ] );
+      $numAlign  = intval( $data[ Max_target_sequences ] );
+      
+      $Data_GapCost = _get_gap( $blast_program );
+      $gapkey       = array_search( $data[ Gap_Costs ], $Data_GapCost );
+      
+      $gap                  = _set_gap( $gapkey );
+      $Data_Mismatch_Scores = _get_match_mismatch( $blast_program );
+      
+      $Mismatch_Scores_key = array_search( $data[ Match_Mismatch_Scores ], $Data_Mismatch_Scores );
+      $m_m                 = _set_match_mismatch( $Mismatch_Scores_key );
+      
+      return array(
+          'max_target_seqs' => $numAlign,
+         'evalue' => $eVal,
+         'word_size' => $wordvalue,
+         'gapopen' => $gap[ 'gapOpen' ],
+         'gapextend' => $gap[ 'gapExtend' ],
+         'penalty' => $m_m[ 'penalty' ],
+         'reward' => $m_m[ 'reward' ],
+         'culling_limit' => $qRange 
+      );
+      
+    }
+   elseif ( $blast_program == 'blastx' )
+    {
+      $wordSize = intval( $data[ Word_size ] );
+      $numAlign = intval( $data[ Max_target_sequences ] );
+      $matrix   = $data[ Matrix_options ];
+      $gap      = getGap( $matrix, 1 );
+      
+      return array(
+          'max_target_seqs' => $numAlign,
+         'evalue' => $eVal,
+         'word_size' => $wordSize,
+         'gapopen' => $gap[ 'gapOpen' ],
+         'gapextend' => $gap[ 'gapExtend' ],
+         'culling_limit' => $qRange,
+         'matrix' => $matrix 
+      );
+    }
+   elseif ( $blast_program == 'tblastn' )
+    {
+      $wordSize = intval( $data[ Word_size ] );
+      $numAlign = intval( $data[ Max_target_sequences ] );
+      $matrix   = $data[ Matrix_options ];
+      $gap      = getGap( $matrix, 1 );
+      
+      return array(
+          'max_target_seqs' => $numAlign,
+         'evalue' => $eVal,
+         'word_size' => $wordSize,
+         'gapopen' => $gap[ 'gapOpen' ],
+         'gapextend' => $gap[ 'gapExtend' ],
+         'culling_limit' => $qRange,
+         'matrix' => $matrix 
+      );
+    }
+   elseif ( $blast_program == 'blastp' )
+    {
+      $wordSize = intval( $data[ Word_size ] );
+      $numAlign = intval( $data[ Max_target_sequences ] );
+      $matrix   = $data[ Matrix_options ];
+      $gap      = getGap( $matrix, 1 );
+      
+      return array(
+          'max_target_seqs' => $numAlign,
+         'evalue' => $eVal,
+         'word_size' => $wordSize,
+         'gapopen' => $gap[ 'gapOpen' ],
+         'gapextend' => $gap[ 'gapExtend' ],
+         'culling_limit' => $qRange,
+         'matrix' => $matrix 
+      );
+    }
+ }
 
 
+/*
+ ** Call the core API of Triple
+ ** @return :  Job_ID 
+ */
 
+function blast_ui_getblastJobId( $query_type, $db_type, $seqQuery, $Databasekey, $adv_options )
+ {
+   if ( $query_type == 'nucleotide' )
+    {
+      if ( $db_type == 'nucleotide' )
+       {
+         $blast_program = 'blastn';
+       }
+      elseif ( $db_type == 'protein' )
+       {
+         $blast_program = 'blastx';
+       }
+    }
+   elseif ( $query_type == 'protein' )
+    {
+      if ( $db_type == 'nucleotide' )
+       {
+         $blast_program = 'tblastn';
+       }
+      elseif ( $db_type == 'protein' )
+       {
+         $blast_program = 'blastp';
+       }
+    }
+   
+   $query = '/tmp/' . date( 'YMd_His' ) . '_query.fasta';
+   file_put_contents( $query, $seqQuery );
+   $blastdb_node      = node_load( $Databasekey );
+   $blastdb_name      = $blastdb_node->db_name;
+   $blastdb_with_path = $blastdb_node->db_path;
+   
+   // Now let each program process its own advanced options.
+   
+   
+   $advanced_options = $adv_options;
+   global $user;
+   
+   $output_filestub = date( 'YMd_His' );
+   $job_args        = array(
+       'program' => $blast_program,
+      'query' => $query,
+      'database' => $blastdb_with_path,
+      'output_filename' => $output_filestub,
+      'options' => $advanced_options 
+   );
+   
+   $job_id = tripal_add_job( t( 'BLAST (@program): @query', array(
+       '@program' => $blast_program,
+      '@query' => $query 
+   ) ), 'blast_job', 'run_BLAST_tripal_job', $job_args, $user->uid );
+   
+   ob_start();
+   tripal_launch_job( 1, $job_id );
+   ob_end_clean();
+   return $job_id;
+   // return getBlastData($job_id);
+ }
 
 
 
@@ -184,9 +586,442 @@ return $options;
 
 
 
+function getBlaststatus( $job_id )
+ {
+   /* $sql =  "SELECT status FROM tripal_jobs WHERE job_id = :job_id ";
+   $job_res = db_query($sql, array(':job_id' => $job_id))->fetchField();
+   return $job_res;  */
+ }
 
 
+/*
+ **Method returns file output data 
+ **  @param int $job_id
+ **  web service url :  http://localhost:8080/restapi/blast/job_id
+ */
 
+function getBlastData( $job_id )
+ {
+   $result;
+   $sql     = "SELECT job_name FROM tripal_jobs WHERE job_id = :job_id ";
+   $job_res = db_query( $sql, array(
+       ':job_id' => $job_id 
+   ) )->fetchField();
+   
+   $file_path = str_replace( '_query.fasta', '.blast.asn', $job_res );
+   
+   
+   if ( stristr( $file_path, "tblastn" ) )
+    {
+      $file_path = str_replace( 'BLAST (tblastn): /', '/', $file_path );
+    }
+   elseif ( stristr( $file_path, "blastx" ) )
+    {
+      $file_path = str_replace( 'BLAST (blastx): /', '/', $file_path );
+    }
+   elseif ( stristr( $file_path, "blastn" ) )
+    {
+      $file_path = str_replace( 'BLAST (blastn): /', '/', $file_path );
+    }
+   elseif ( stristr( $file_path, "blastp" ) )
+    {
+      $file_path = str_replace( 'BLAST (blastp): /', '/', $file_path );
+    }
+   
+   
+   if ( file_exists( $file_path ) )
+    {
+      $result = file_get_contents( $file_path );
+    }
+   else
+    {
+      $result = "The file  $file_path does not exist";
+    }
+   return $result;
+ }
 
+/*
+ **Method Used for tblastn and blastx
+ **  @return  int $gapOpen and $gapExtend
+ */
 
+function getGap( $matrix, $gapkey )
+ {
+   switch ( $matrix )
+   {
+      case 'PAM30':
+         switch ( $gapKey )
+         {
+            case 0:
+               $gapOpen   = 7;
+               $gapExtend = 2;
+               break;
+            case 1:
+               $gapOpen   = 6;
+               $gapExtend = 2;
+               break;
+            case 2:
+               $gapOpen   = 5;
+               $gapExtend = 2;
+               break;
+            case 3:
+               $gapOpen   = 10;
+               $gapExtend = 1;
+               break;
+            case 4:
+               $gapOpen   = 9;
+               $gapExtend = 1;
+               break;
+            case 5:
+               $gapOpen   = 8;
+               $gapExtend = 1;
+               break;
+         }
+         break;
+      case 'PAM70':
+         switch ( $gapKey )
+         {
+            case 0:
+               $gapOpen   = 8;
+               $gapExtend = 2;
+               break;
+            case 1:
+               $gapOpen   = 7;
+               $gapExtend = 2;
+               break;
+            case 2:
+               $gapOpen   = 6;
+               $gapExtend = 2;
+               break;
+            case 3:
+               $gapOpen   = 11;
+               $gapExtend = 1;
+               break;
+            case 4:
+               $gapOpen   = 10;
+               $gapExtend = 1;
+               break;
+            case 5:
+               $gapOpen   = 9;
+               $gapExtend = 1;
+               break;
+         }
+         break;
+      case 'PAM250':
+         switch ( $gapKey )
+         {
+            case 0:
+               $gapOpen   = 15;
+               $gapExtend = 3;
+               break;
+            case 1:
+               $gapOpen   = 14;
+               $gapExtend = 3;
+               break;
+            case 2:
+               $gapOpen   = 13;
+               $gapExtend = 3;
+               break;
+            case 3:
+               $gapOpen   = 12;
+               $gapExtend = 3;
+               break;
+            case 4:
+               $gapOpen   = 11;
+               $gapExtend = 3;
+               break;
+            case 5:
+               $gapOpen   = 17;
+               $gapExtend = 2;
+               break;
+            case 6:
+               $gapOpen   = 16;
+               $gapExtend = 2;
+               break;
+            case 7:
+               $gapOpen   = 15;
+               $gapExtend = 2;
+               break;
+            case 8:
+               $gapOpen   = 14;
+               $gapExtend = 2;
+               break;
+            case 9:
+               $gapOpen   = 13;
+               $gapExtend = 2;
+               break;
+            case 10:
+               $gapOpen   = 21;
+               $gapExtend = 1;
+               break;
+            case 11:
+               $gapOpen   = 20;
+               $gapExtend = 1;
+               break;
+            case 12:
+               $gapOpen   = 19;
+               $gapExtend = 1;
+               break;
+            case 13:
+               $gapOpen   = 18;
+               $gapExtend = 1;
+               break;
+            case 14:
+               $gapOpen   = 17;
+               $gapExtend = 1;
+               break;
+         }
+         break;
+      case 'BLOSUM80':
+         switch ( $gapKey )
+         {
+            case 0:
+               $gapOpen   = 8;
+               $gapExtend = 2;
+               break;
+            case 1:
+               $gapOpen   = 7;
+               $gapExtend = 2;
+               break;
+            case 2:
+               $gapOpen   = 6;
+               $gapExtend = 2;
+               break;
+            case 3:
+               $gapOpen   = 11;
+               $gapExtend = 1;
+               break;
+            case 4:
+               $gapOpen   = 10;
+               $gapExtend = 1;
+               break;
+            case 5:
+               $gapOpen   = 9;
+               $gapExtend = 1;
+               break;
+         }
+         break;
+      case 'BLOSUM62':
+         switch ( $gapKey )
+         {
+            case 0:
+               $gapOpen   = 11;
+               $gapExtend = 2;
+               break;
+            case 1:
+               $gapOpen   = 10;
+               $gapExtend = 2;
+               break;
+            case 2:
+               $gapOpen   = 9;
+               $gapExtend = 2;
+               break;
+            case 3:
+               $gapOpen   = 8;
+               $gapExtend = 2;
+               break;
+            case 4:
+               $gapOpen   = 7;
+               $gapExtend = 2;
+               break;
+            case 5:
+               $gapOpen   = 6;
+               $gapExtend = 2;
+               break;
+            case 6:
+               $gapOpen   = 13;
+               $gapExtend = 1;
+               break;
+            case 7:
+               $gapOpen   = 12;
+               $gapExtend = 1;
+               break;
+            case 8:
+               $gapOpen   = 11;
+               $gapExtend = 1;
+               break;
+            case 9:
+               $gapOpen   = 10;
+               $gapExtend = 1;
+               break;
+            case 10:
+               $gapOpen   = 9;
+               $gapExtend = 1;
+               break;
+         }
+         break;
+      case 'BLOSUM45':
+         switch ( $gapKey )
+         {
+            case 0:
+               $gapOpen   = 13;
+               $gapExtend = 3;
+               break;
+            case 1:
+               $gapOpen   = 12;
+               $gapExtend = 3;
+               break;
+            case 2:
+               $gapOpen   = 11;
+               $gapExtend = 3;
+               break;
+            case 3:
+               $gapOpen   = 10;
+               $gapExtend = 3;
+               break;
+            case 4:
+               $gapOpen   = 15;
+               $gapExtend = 2;
+               break;
+            case 5:
+               $gapOpen   = 14;
+               $gapExtend = 2;
+               break;
+            case 6:
+               $gapOpen   = 13;
+               $gapExtend = 2;
+               break;
+            case 7:
+               $gapOpen   = 12;
+               $gapExtend = 2;
+               break;
+            case 8:
+               $gapOpen   = 19;
+               $gapExtend = 1;
+               break;
+            case 9:
+               $gapOpen   = 18;
+               $gapExtend = 1;
+               break;
+            case 10:
+               $gapOpen   = 17;
+               $gapExtend = 1;
+               break;
+            case 11:
+               $gapOpen   = 16;
+               $gapExtend = 1;
+               break;
+         }
+         break;
+      case 'BLOSUM50':
+         switch ( $gapKey )
+         {
+            case 0:
+               $gapOpen   = 13;
+               $gapExtend = 3;
+               break;
+            case 1:
+               $gapOpen   = 12;
+               $gapExtend = 3;
+               break;
+            case 2:
+               $gapOpen   = 11;
+               $gapExtend = 3;
+               break;
+            case 3:
+               $gapOpen   = 10;
+               $gapExtend = 3;
+               break;
+            case 4:
+               $gapOpen   = 9;
+               $gapExtend = 3;
+               break;
+            case 5:
+               $gapOpen   = 16;
+               $gapExtend = 2;
+               break;
+            case 6:
+               $gapOpen   = 15;
+               $gapExtend = 2;
+               break;
+            case 7:
+               $gapOpen   = 14;
+               $gapExtend = 2;
+               break;
+            case 8:
+               $gapOpen   = 13;
+               $gapExtend = 2;
+               break;
+            case 9:
+               $gapOpen   = 12;
+               $gapExtend = 2;
+               break;
+            case 10:
+               $gapOpen   = 19;
+               $gapExtend = 1;
+               break;
+            case 11:
+               $gapOpen   = 18;
+               $gapExtend = 1;
+               break;
+            case 12:
+               $gapOpen   = 17;
+               $gapExtend = 1;
+               break;
+            case 13:
+               $gapOpen   = 16;
+               $gapExtend = 1;
+               break;
+            case 14:
+               $gapOpen   = 15;
+               $gapExtend = 1;
+               break;
+         }
+         break;
+      case 'BLOSUM90':
+         switch ( $gapKey )
+         {
+            case 0:
+               $gapOpen   = 9;
+               $gapExtend = 2;
+               break;
+            case 1:
+               $gapOpen   = 8;
+               $gapExtend = 2;
+               break;
+            case 2:
+               $gapOpen   = 7;
+               $gapExtend = 2;
+               break;
+            case 3:
+               $gapOpen   = 6;
+               $gapExtend = 2;
+               break;
+            case 4:
+               $gapOpen   = 11;
+               $gapExtend = 1;
+               break;
+            case 5:
+               $gapOpen   = 10;
+               $gapExtend = 1;
+               break;
+            case 6:
+               $gapOpen   = 9;
+               $gapExtend = 1;
+               break;
+         }
+         break;
+         
+   }
+   return array(
+       'gapOpen' => $gapOpen,
+      'gapExtend' => $gapExtend 
+   );
+ }
 
+/*
+ ** Used for tblastn
+ */
+function getGap_cost()
+ {
+   return array(
+       'PAM30' => _get_gap_for_matrix( 'PAM30' ),
+      'PAM70' => _get_gap_for_matrix( 'PAM70' ),
+      'PAM250' => _get_gap_for_matrix( 'PAM250' ),
+      'BLOSUM80' => _get_gap_for_matrix( 'BLOSUM80' ),
+      'BLOSUM62' => _get_gap_for_matrix( 'BLOSUM62' ),
+      'BLOSUM45' => _get_gap_for_matrix( 'BLOSUM45' ),
+      'BLOSUM50' => _get_gap_for_matrix( 'BLOSUM50' ),
+      'BLOSUM90' => _get_gap_for_matrix( 'BLOSUM90' ) 
+   );
+ }

theme/blast_report.tpl.php

@@ -22,6 +22,7 @@ if ($blast_job->blastdb->linkout->none === FALSE) {
   }
 }
 
+
 // Handle no hits. This following array will hold the names of all query
 // sequences which didn't have any hits.
 $query_with_no_hits = array();
@@ -262,6 +263,9 @@ and click the <em>target name </em> to get more information about the target hit
                   $hit_url,
                   array('attributes' => array('target' => '_blank'))
                 );
+                
+                //HACK: change '%3F' to '?' to work around a Drupal bug"
+                $hit_name = str_replace('%3F', '?', $hit_name);
               }
             }
                         

theme/blast_user_menupage.tpl.php

@@ -1,10 +1,8 @@
 <?php
-
 /**
  * @file
  *
  */
-
 ?>
 
 <p>In bioinformatics, BLAST (Basic Local Alignment Search Tool) is an algorithm
@@ -37,7 +35,7 @@ local alignment search tool. J. Mol. Biol., 215, 403–410.</blockquote>
     <th>BLAST Program</th>
   </tr>
   <tr>
-    <td  rowspan="2"><?php print l('Nucleotide', './blast/nucleotide');?></td>
+    <td rowspan="2"><?php print l('Nucleotide', './blast/nucleotide');?></td>
     <td>Nucleotide</td>
     <td><?php print l('blastn', './blast/nucleotide/nucleotide');?>:
       Search a nucleotide database using a nucleotide query.</td>
@@ -48,7 +46,7 @@ local alignment search tool. J. Mol. Biol., 215, 403–410.</blockquote>
       Search protein database using a translated nucleotide query.</td>
   </tr>
   <tr>
-    <td  rowspan="2"><?php print l('Protein', './blast/protein');?></td>
+    <td rowspan="2"><?php print l('Protein', './blast/protein');?></td>
     <td>Nucleotide</td>
     <td><?php print l('tblastn', './blast/protein/nucleotide');?>:
       Search translated nucleotide database using a protein query.</td>