Continued development of seq_extract form

tripal_analysis/tripal_analysis.install

@@ -246,7 +246,7 @@ function tripal_analysis_add_mview_analysis_organism() {
   );
   
   // add a comment to make sure this view makes sense to the site administator
-  $comment = t('This view is for associating an organism (via it\'s associated features) to an analaysis.');
+  $comment = t('This view is for associating an organism (via it\'s associated features) to an analysis.');
   
   // add the view
   tripal_add_mview('analysis_organism', 'tripal_analysis', NULL, NULL, NULL,

tripal_feature/includes/seq_extract.inc

@@ -3,6 +3,33 @@
  * 
  */
 function tripal_feature_seq_extract_page() {
+  if ($_SESSION['tripal_feature_seq_extract']){   
+    $genus      = $_SESSION['tripal_feature_seq_extract']['genus'];
+    $species    = $_SESSION['tripal_feature_seq_extract']['species'];
+    $analysis   = $_SESSION['tripal_feature_seq_extract']['analysis'];
+    $ftypes     = $_SESSION['tripal_feature_seq_extract']['ftypes'];
+    $fname      = $_SESSION['tripal_feature_seq_extract']['fname'];
+    $upstream   = $_SESSION['tripal_feature_seq_extract']['upstream'];
+    $downstream = $_SESSION['tripal_feature_seq_extract']['downstream'];
+    $format     = $_SESSION['tripal_feature_seq_extract']['format'];
+    $use_parent = $_SESSION['tripal_feature_seq_extract']['use_parent'];
+    $aggregate  = $_SESSION['tripal_feature_seq_extract']['aggregate'];
+    $agg_types  = $_SESSION['tripal_feature_seq_extract']['agg_types'];
+     
+    if ($format == 'fasta_html') {
+      drupal_set_header('Content-Type: text/html');
+    }
+    else {
+      drupal_set_header('Content-Type: text/plain');
+    }
+    tripal_feature_seq_extract_get_features(NULL, $genus, $species, $analysis, 
+      $ftypes, $fname, $upstream, $downstream, $format, $use_parent, $aggregate, $agg_types);
+      
+    unset($_SESSION['tripal_feature_seq_extract']);
+    return;
+  }
+ 
+  
   // generate the search form 
   $output .= '';
   if (user_access('access administration pages')) { 
@@ -77,7 +104,7 @@ function tripal_feature_seq_extract_form(&$form_state = NULL) {
   $ddownstream = $form_state['values']['downstream'];
   $dformat     = $form_state['values']['format'] ? $form_state['values']['format'] : 'fasta_txt';
   $duse_parent = $form_state['values']['use_parent'];
-  $aggregate   = $form_state['values']['aggregate'];
+  $daggregate  = $form_state['values']['aggregate'];
   $dagg_types  = $form_state['values']['agg_types'];
 
   $sql = "
@@ -331,3 +358,121 @@ function tripal_feature_seq_extract_set_source() {
     )  
   );
 }
+
+/**
+ * 
+ */
+function tripal_feature_seq_extract_form_validate($form, &$form_state) {
+  $genus      = $form_state['values']['genus'];
+  $species    = $form_state['values']['species'];
+  $analysis   = $form_state['values']['analysis'];
+  $ftypes     = $form_state['values']['ftypes'];
+  $fname      = $form_state['values']['fname'];
+  $upstream   = $form_state['values']['upstream'];
+  $downstream = $form_state['values']['downstream'];
+  $format     = $form_state['values']['format'];
+  $use_parent = $form_state['values']['use_parent'];
+  $aggregate  = $form_state['values']['aggregate'];
+  $agg_types  = $form_state['values']['agg_types'];  
+  
+  if ($upstream and !preg_match('/^\d+$/', $upstream)) {
+    form_set_error('upstream', 'Please enter a positive numeric value for the upstream bases');
+  }
+   if ($downstream and !preg_match('/^\d+$/', $downstream)) {
+    form_set_error('downstream', 'Please enter a positive numeric value for the downstream bases');
+  }
+}
+
+/**
+ * 
+ */
+function tripal_feature_seq_extract_form_submit($form, &$form_state) {
+  $genus      = $form_state['values']['genus'];
+  $species    = $form_state['values']['species'];
+  $analysis   = $form_state['values']['analysis'];
+  $ftypes     = $form_state['values']['ftypes'];
+  $fname      = $form_state['values']['fname'];
+  $upstream   = $form_state['values']['upstream'];
+  $downstream = $form_state['values']['downstream'];
+  $format     = $form_state['values']['format'];
+  $use_parent = $form_state['values']['use_parent'];
+  $aggregate  = $form_state['values']['aggregate'];
+  $agg_types  = $form_state['values']['agg_types'];
+  
+  $_SESSION['tripal_feature_seq_extract']['genus']      = $genus;
+  $_SESSION['tripal_feature_seq_extract']['species']    = $species;
+  $_SESSION['tripal_feature_seq_extract']['analysis']   = $analysis;
+  $_SESSION['tripal_feature_seq_extract']['ftypes']     = $ftypes;
+  $_SESSION['tripal_feature_seq_extract']['fname']      = $fname;
+  $_SESSION['tripal_feature_seq_extract']['upstream']   = $upstream;
+  $_SESSION['tripal_feature_seq_extract']['downstream'] = $downstream;
+  $_SESSION['tripal_feature_seq_extract']['format']     = $format;
+  $_SESSION['tripal_feature_seq_extract']['use_parent'] = $use_parent;
+  $_SESSION['tripal_feature_seq_extract']['aggregate']  = $aggregate;
+  $_SESSION['tripal_feature_seq_extract']['agg_types']  = $agg_types;
+}
+
+/*
+ * 
+ */
+function tripal_feature_seq_extract_get_features($org_commonname, $genus, $species, $analysis_name, 
+  $type, $feature_name, $upstream, $downstream, $output_format, $derive_from_parent, $aggregate, $child) {
+    
+  $sub_features = explode(',', $child);
+    
+  if (!$output_format) {
+     $output_format = 'fasta_txt';
+  }
+  
+  if (!$type and !$feature_name and !$org_commonname) {
+     print "Please provide a type, feature name or organism common name\n";
+     return;
+  }
+
+  // get the list of features
+  $vars = array();
+  $sql  = "SELECT DISTINCT F.feature_id, F.name, F.uniquename, O.genus, O.species, CVT.name as feature_type ".
+          "FROM {feature} F ".
+          "  INNER JOIN {organism} O on O.organism_id = F.organism_id ".
+          "  INNER JOIN {cvterm} CVT on CVT.cvterm_id = F.type_id ";
+  if ($analysis_name) {
+     $sql .= "  INNER JOIN {analysisfeature} AF on AF.feature_id = F.feature_id ".
+             "  INNER JOIN {analysis} A on AF.analysis_id = A.analysis_id ";
+  }         
+  $sql .= "WHERE (1=1) ";
+  if ($org_commonname) {
+     $sql .= "AND O.common_name = '%s' ";
+     $vars[] = $org_commonname;
+  }
+  if ($genus) {
+     $sql .= "AND O.genus = '%s' ";
+     $vars[] = $genus;
+  }
+  if ($species) {
+     $sql .= "AND O.species = '%s' ";
+     $vars[] = $species;
+  }
+  if ($type) {
+    $sql .= "AND CVT.name = '%s' ";
+    $vars[] = $type; 
+  }
+  if ($feature_name) {
+     $sql .= "AND F.name = '%s'";
+     $vars[] = $feature_name;
+  }
+  if ($analysis_name) {
+     $sql .= "AND A.name = '%s'";
+     $vars[] = $analysis_name;
+  }
+  $num_bases_per_line = 50;
+  $q = chado_query($sql, $vars);
+  while ($feature = db_fetch_object($q)) {
+    $feature_id = $feature->feature_id;
+    $feature_name = "$feature->uniquename $feature->name $feature->feature_type ($feature->genus $feature->species)";
+      
+    $sequence = tripal_feature_get_formatted_sequence($feature_id, $feature_name, 
+      $num_bases_per_line, $derive_from_parent, $aggregate, $output_format,
+      $upstream, $downstream, $sub_features);
+    print $sequence;
+  }
+}

tripal_feature/tripal_feature.drush.inc

@@ -80,63 +80,9 @@ function drush_tripal_feature_tripal_get_sequence() {
   $aggregate = drush_get_option('agg');
   $child = drush_get_option('child');
   
-  $sub_features = explode(',', $child);
-    
-  if (!$output_format) {
-     $output_format = 'fasta_txt';
-  }
-  
-  if (!$type and !$feature_name and !$org_commonname) {
-     print "Please provide a type, feature name or organism common name\n";
-     return;
-  }
-
-  // get the list of features
-  $vars = array();
-  $sql  = "SELECT DISTINCT F.feature_id, F.name, F.uniquename, O.genus, O.species, CVT.name as feature_type ".
-          "FROM {feature} F ".
-          "  INNER JOIN {organism} O on O.organism_id = F.organism_id ".
-          "  INNER JOIN {cvterm} CVT on CVT.cvterm_id = F.type_id ";
-  if ($analysis_name) {
-     $sql .= "  INNER JOIN {analysisfeature} AF on AF.feature_id = F.feature_id ".
-             "  INNER JOIN {analysis} A on AF.analysis_id = A.analysis_id ";
-  }         
-  $sql .= "WHERE (1=1) ";
-  if ($org_commonname) {
-     $sql .= "AND O.common_name = '%s' ";
-     $vars[] = $org_commonname;
-  }
-  if ($genus) {
-     $sql .= "AND O.genus = '%s' ";
-     $vars[] = $genus;
-  }
-  if ($species) {
-     $sql .= "AND O.species = '%s' ";
-     $vars[] = $species;
-  }
-  if ($type) {
-    $sql .= "AND CVT.name = '%s' ";
-    $vars[] = $type; 
-  }
-  if ($feature_name) {
-     $sql .= "AND F.name = '%s'";
-     $vars[] = $feature_name;
-  }
-  if ($analysis_name) {
-     $sql .= "AND A.name = '%s'";
-     $vars[] = $analysis_name;
-  }
-  $num_bases_per_line = 50;
-  $q = chado_query($sql, $vars);
-  while ($feature = db_fetch_object($q)) {
-    $feature_id = $feature->feature_id;
-    $feature_name = "$feature->uniquename $feature->name $feature->feature_type ($feature->genus $feature->species)";
-      
-    $sequence = tripal_feature_get_formatted_sequence($feature_id, $feature_name, 
-      $num_bases_per_line, $derive_from_parent, $aggregate, $output_format,
-      $upstream, $downstream, $sub_features);
-    print $sequence;
-  }
+  tripal_feature_seq_extract_get_features($org_commonname, $genus, $species, $analysis_name, 
+    $type, $feature_name, $upstream, $downstream, $output_format, $derive_from_parent, 
+    $aggregate, $child);   
 }
 /*
  * 

tripal_feature/tripal_feature.module

@@ -2342,3 +2342,18 @@ function tripal_feature_match_features_page($id) {
   $output .= theme_table($header, $rows, $table_attrs, $caption);
   return $output;
 }
+
+/**
+ * 
+ * @param unknown_type $form
+ * @param unknown_type $form_state
+ * @param unknown_type $form_id
+ */
+function tripal_feature_form_alter(&$form, &$form_state, $form_id) {
+  if ($form_id == "tripal_feature_seq_extract_form") {    
+    // updating the form through the ahah callback sets the action of
+    // the form to the ahah callback URL. We need to set it back
+    // to the normal form URL
+    $form['#action'] = url("seq_extract");
+  }
+}