updated blast_ui.services.inc, remove word size 2 in option, set num_threads option in command

api/blast_ui.api.inc

@@ -144,6 +144,9 @@ 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.form_advanced_options.inc

@@ -1197,7 +1197,7 @@ 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.services.inc

@@ -1,96 +1,148 @@
 <?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(),
-         ),
-         '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(),
-         ),
-        ),
-       ),
-   );
+/**
+* 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
+                    )
+                )
+            ),
+            '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 information needed',
+                        '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 information needed',
+                        'source' => array(
+                            'path' => '0'
+                        ),
+                        'optional' => FALSE
+                    ),
+                    array(
+                        'name' => 'data',
+                        'type' => 'struct',
+                        'description' => 'The information needed',
+                        '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 information needed',
+                        '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(
+                '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
+                )
+            )
+        )
+    );
     
 }
 
@@ -98,77 +150,304 @@ function blast_ui_services_resources() {
 
 
 
-function _blast_ui_create($param) {
-  
- return services_error('Missing _blast_ui_create', 406);
+function _blast_ui_create($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 updating blast 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);
+ * Callback for deleting blast 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);
+/**
+ * Callback for Index blast services.
+ */
+
+function _blast_ui_index()
+{
+    return array(
+        
+        'query_type' => array(
+            '1' => 'nucleotide',
+            '2' => 'protein'
+        ),
+        'db_type' => array(
+            '1' => 'nucleotide',
+            '2' => 'protein'
+        ),
+        'blast_program' => array(
+            '1' => 'blastn',
+            '2' => 'blastx',
+            '3' => 'tblastn',
+            '4' => 'blastp'
+        )
+        
+    );
 }
 
-function _blast_ui_getDatabaseType() {
 
-    return array(
-      'Nucleotide' => array ( 
-        'Nucleotide' => 'blastn',
-      	'protein' => 'blastx',
-      ),
-      'Protein' => array ( 
-        'Nucleotide' => 'tblastn',
-      	'protein' => 'blastp',
-      ),
-    ); 
+
+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);
+    
+    
+    
+    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($blast_program),
+            'Default_Values' => _get_default_values('')
+        );
+    }
+    elseif ($blast_program == 'blastx')
+    {
+        return array(
+            'Select_Database' => $options_database,
+            'Max_target_sequences' => _get_max_target($blast_program),
+            'Word_size' => _get_word_size($blast_program),
+            'Matrix_options' => _get_matrix_options()
+            
+        );
+    }
+}
+
+
+function blast_validation($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[ Default_Values ]))
+            {
+                return services_error('Missing blast attribute $Default_Values [ query blast/getDatabaseOptions for options]', 406);
+            }
+            if (!isset($data[ seqQuery ]))
+            {
+                return services_error('Missing blast attribute  $seqQuery [ Add sequence query for blast]', 406);
+            }
+            
+        }
+        elseif ($db_type == 'protein')
+        {
+            
+            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 ]))
+            {
+                return services_error('Missing blast attribute  $seqQuery [ Add sequence query for blast]', 406);
+            }
+            
+        }
+    }
+    /*
+    elseif ($query_type == 'protein') {
+    if ($db_type == 'nucleotide') {
+    $blast_program = 'tblastn';
+    }
+    elseif ($db_type == 'protein') {
+    $blast_program = 'blastp';
+    }
+    }
+    
+    
+    */
+    
+}
+
+
+
+
+function _blast_ui_getJobId($data)
+{
+    
+    $query_type;
+    $db_type;
+    $eVal   = 0.001;
+    $qRange = 0;
+    
+    
+    
+    
+    /* check values in post query */
+    
+    if (!isset($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    = $data[ db_type ];
+    
+    blast_validation($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 ?
+            $wordvalue        = 11;
+            //     $wordvalue = intval($data[Word_size]);
+            $numAlign         = intval($data[ Max_target_sequences ]);
+            $options_database = get_blast_database_options($data[ db_type ]);
+            $Databasekey      = array_search($data[ Select_Database ], $options_database);
+            $advanced_options = advanced_options($blast_program, $data[ Gap_Costs ], $data[ Match_Mismatch_Scores ], $wordvalue, $numAlign, $eVal, $qRange);
+            
+        }
+        elseif ($db_type == 'protein')
+        {
+            $blast_program = 'blastx';
+            return 'working';
+        }
+    }
+    elseif ($query_type == 'protein')
+    {
+        if ($db_type == 'nucleotide')
+        {
+            $blast_program = 'tblastn';
+        }
+        elseif ($db_type == 'protein')
+        {
+            $blast_program = 'blastp';
+        }
+    }
+    
+    
+    return blast_ui_getblastJobId($data[ query_type ], $data[ db_type ], $data[ seqQuery ], $Databasekey, $advanced_options);
+    
+    
 }
 
+// Define the advanced Options for Blast 
 
-function _blast_ui_getDatabaseOption() {
 
- $db_type = 'nucleotide';
- $options = get_blast_database_options($db_type);
-return $options;
+function advanced_options($blast_program, $gapCost, $Match_Mismatch_Scores, $wordvalue, $numAlign, $eVal, $qRange)
+{
+    
+    $Data_GapCost = _get_gap($blast_program);
+    $gapkey       = array_search($gapCost, $Data_GapCost);
+    $gap          = _set_gap($gapkey);
+    
+    
+    $Data_Mismatch_Scores = _get_match_mismatch($blast_program);
+    $Mismatch_Scores_key  = array_search($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
+        
+    );
 }
 
 
@@ -177,6 +456,66 @@ return $options;
 
 
 
+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);
+}
 
 
 
@@ -188,5 +527,37 @@ 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 $job_res;  */
+}
+
+
+
+function getBlastData($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);
+    $file_path = str_replace('BLAST (blastn): /', '/', $file_path);
+    
+    if (file_exists($file_path))
+    {
+        $result = file_get_contents($file_path);
+    }
+    else
+    {
+        $result = "The file  $file_path does not exist";
+    }
+    return $result;
+}
+
+
+