Merge pull request #582 from tripal/290_newick_issues

resolve Phylotree TripalImporter errors

tripal_chado/api/modules/tripal_chado.phylotree.api.inc

@@ -3,7 +3,7 @@
 /**
  * @file
  * Provides API functions specificially for managing phylogenetic and taxonomic
- * tree records in Chado.  
+ * tree records in Chado.
  */
 
 /**
@@ -11,8 +11,8 @@
  * @ingroup tripal_chado_api
  * @{
  * Provides API functions specificially for managing phylogenetic and taxonomic
- * tree records in Chado.  The API consists of functions for creation, 
- * retrieval, update and deltion (CRUD) for phylogenetic tree records as 
+ * tree records in Chado.  The API consists of functions for creation,
+ * retrieval, update and deltion (CRUD) for phylogenetic tree records as
  * well as importing of trees in the newick file format.
  * @}
  */
@@ -85,10 +85,6 @@ function chado_validate_phylotree($val_type, &$options, &$errors, &$warnings) {
       $errors['description'] = t('Please provide a description for this tree.');
       return FALSE;
     }
-    if (!array_key_exists('tree_file', $options)) {
-      $errors['tree_file'] = t('Please provide either the full path to the tree_file or a Drupal managed file ID number.');
-      return FALSE;
-    }
     if (!array_key_exists('format', $options) or !$options['format']) {
       $errors['format'] = t('Please provide a file format for the tree file.');
       return FALSE;
@@ -202,12 +198,30 @@ function chado_validate_phylotree($val_type, &$options, &$errors, &$warnings) {
       ),
     );
     $dbxref = chado_generate_var('dbxref', $values);
+
     if (!$dbxref) {
-      $errors['dbxref'] = t('The dbxref provided does not exist in the database: %dbxref.', array('%dbxref' => $dbxref));
-      return FALSE;
+
+      $db = chado_generate_var('db', array( 'name' => $db_name));
+
+      if (!$db){
+              $errors['dbxref'] = t('
+              dbxref could not be created for db: %dbxref.', array('%dbxref' => $dbxref));
+              return FALSE;
+      }
+    $dbxref =  chado_insert_record('dbxref', $values);
+
+    if (!$dbxref){
+            $errors['dbxref'] = t('
+            dbxref could not be created for db: %dbxref.', array('%dbxref' => $dbxref));
+            return FALSE;
     }
+  }
+  if (is_array($dbxref)){
+    $options['dbxref_id'] = $dbxref['dbxref_id'];
+    }else {
     $options['dbxref_id'] = $dbxref->dbxref_id;
   }
+  }
 
   // Make sure the tree name is unique.
   if (array_key_exists('name', $options) and $options['name']) {
@@ -254,7 +268,7 @@ function chado_validate_phylotree($val_type, &$options, &$errors, &$warnings) {
  *     'tree_file':  The path of the file containing the phylogenetic tree to
  *                   import or a Drupal managed_file numeric ID.
  *     'format':     The file format. Currently only 'newick is supported'.
- * 
+ *
  *  Optional keys:
  *     'dbxref':     A database cross-reference of the form DB:ACCESSION.
  *                   Where DB is the database name, which is already present
@@ -312,6 +326,7 @@ function chado_insert_phylotree(&$options, &$errors, &$warnings) {
     'comment' => $options['description'],
     'type_id' => $options['type_id'],
   );
+
   $phylotree = chado_insert_record('phylotree', $values);
   if (!$phylotree) {
     drupal_set_message(t('Unable to add phylotree.'), 'warning');
@@ -675,7 +690,7 @@ function chado_phylogeny_import_tree(&$tree, $phylotree, $options, $vocab = arra
       if (!empty($tree['name']) and $tree['name'] != '') {
         if (!$options['taxonomy']) {
 
-          // This is a sequence-based tree. Try to match leaf nodes with 
+          // This is a sequence-based tree. Try to match leaf nodes with
           // features.
           // First, Get the Name and uniquename for the feature.
           $matches = array();
@@ -751,9 +766,9 @@ function chado_phylogeny_import_tree(&$tree, $phylotree, $options, $vocab = arra
 /**
  * Get the vocabulary terms used to describe nodes in the tree.
  *
- * @return 
+ * @return
  *  Array of vocab info or FALSE on failure.
- * 
+ *
  * @ingroup tripal_phylotree_api
  */
 function chado_phylogeny_get_node_types_vocab() {

tripal_chado/includes/TripalImporter/NewickImporter.inc

@@ -29,7 +29,7 @@ class NewickImporter extends TripalImporter {
    * Provides information to the user about the file upload.  Typically this
    * may include a description of the file types allowed.
    */
-  public static $upload_description = 'Please provide the Newick formatted tree file.  The file must have a .txt or .tree extension.';
+  public static $upload_description = 'Please provide the Newick formatted tree file (one tree per file only).  The file must have a .txt or .tree extension.';
 
   /**
    * The title that should appear above the file upload section.
@@ -125,7 +125,7 @@ class NewickImporter extends TripalImporter {
         tree. In this case, the word 'taxonomy' should be used."),
       '#required' => TRUE,
       '#default_value' => $leaf_type,
-      '#autocomplete_path' => "admin/tripal/legacy/tripal_cv/cvterm/auto_name/$cv_id",
+      '#autocomplete_path' => "admin/tripal/storage/chado/auto_name/cvterm/$cv_id",
     ];
 
     $form['dbxref'] = [
@@ -173,13 +173,11 @@ class NewickImporter extends TripalImporter {
   public function formValidate($form, &$form_state) {
 
     $values = $form_state['values'];
-
     $options = [
       'name' => trim($values["tree_name"]),
       'description' => trim($values["description"]),
       'analysis_id' => $values["analysis_id"],
       'leaf_type' => $values["leaf_type"],
-      'tree_file'    => $this->arguments['files'][0]['file_path'],
       'format' => 'newick',
       'dbxref' => trim($values["dbxref"]),
       'match' => $values["match"],
@@ -216,15 +214,15 @@ class NewickImporter extends TripalImporter {
     $arguments = $this->arguments['run_args'];
 
     $options = array(
-      'name'         => $this->arguments["tree_name"],
-      'description'  => $this->arguments["description"],
-      'analysis_id'  => $this->arguments["analysis_id"],
-      'leaf_type'    => $this->arguments["leaf_type"],
+      'name'         => $arguments["tree_name"],
+      'description'  => $arguments["description"],
+      'analysis_id'  => $arguments["analysis_id"],
+      'leaf_type'    => $arguments["leaf_type"],
       'tree_file'    => $this->arguments['files'][0]['file_path'],
       'format'       => 'newick',
-      'dbxref'       => $this->arguments["dbxref"],
-      'match'        => $this->arguments["match"],
-      'name_re'      => $this->arguments["name_re"],
+      'dbxref'       => $arguments["dbxref"],
+      'match'        => $arguments["match"],
+      'name_re'      => $arguments["name_re"],
     );
     $errors = array();
     $warnings = array();