dump accumuilated organisms prior to test

tests/tripal_chado/loaders/TaxonomyImporterTest.php

@@ -26,6 +26,10 @@ class TaxonomyImporterTest extends TripalTestCase {
       'type_id' => NULL,
     ];
 
+    $prev_db = chado_set_active('chado');
+    chado_query('TRUNCATE TABLE {organism} CASCADE');
+    chado_set_active($prev_db);
+
     $organism = factory('chado.organism')->create($org);
     //  $this->publish('organism');
     $file = [];

tripal_chado/includes/TripalImporter/TaxonomyImporter.inc

@@ -1,921 +0,0 @@
-<?php
-
-class TaxonomyImporter extends TripalImporter {
-  /**
-   * The name of this loader.  This name will be presented to the site
-   * user.
-   */
-  public static $name = 'Chado NCBI Taxonomy Loader';
-
-  /**
-   * The machine name for this loader. This name will be used to construct
-   * the URL for the loader.
-   */
-  public static $machine_name = 'chado_taxonomy';
-
-  /**
-   * A brief description for this loader.  This description will be
-   * presented to the site user.
-   */
-  public static $description = 'Imports new organisms from NCBI using taxonomy IDs, or loads taxonomic details about existing organisms.';
-
-  /**
-   * An array containing the extensions of allowed file types.
-   */
-  public static $file_types = array();
-
-
-  /**
-   * Provides information to the user about the file upload.  Typically this
-   * may include a description of the file types allowed.
-   */
-  public static $upload_description = '';
-
-  /**
-   * The title that should appear above the upload button.
-   */
-  public static $upload_title = 'File Upload';
-
-  /**
-   * If the loader should require an analysis record.  To maintain provenance
-   * we should always indiate where the data we are uploading comes from.
-   * The method that Tripal attempts to use for this by associating upload files
-   * with an analysis record.  The analysis record provides the details for
-   * how the file was created or obtained. Set this to FALSE if the loader
-   * should not require an analysis when loading. if $use_analysis is set to
-   * true then the form values will have an 'analysis_id' key in the $form_state
-   * array on submitted forms.
-   */
-  public static $use_analysis = FALSE;
-
-  /**
-   * If the $use_analysis value is set above then this value indicates if the
-   * analysis should be required.
-   */
-  public static $require_analysis = FALSE;
-
-  /**
-   * Text that should appear on the button at the bottom of the importer
-   * form.
-   */
-  public static $button_text = 'Import from NCBI Taxonomy';
-
-  /**
-   * Indicates the methods that the file uploader will support.
-   */
-  public static $methods = array(
-    // Allow the user to upload a file to the server.
-    'file_upload' => FALSE,
-    // Allow the user to provide the path on the Tripal server for the file.
-    'file_local' => FALSE,
-    // Allow the user to provide a remote URL for the file.
-    'file_remote' => FALSE,
-  );
-
-  /**
-   * Indicates if the file must be provided.  An example when it may not be
-   * necessary to require that the user provide a file for uploading if the
-   * loader keeps track of previous files and makes those available for
-   * selection.
-   */
-  public static $file_required = FALSE;
-
-
-  /**
-   * The array of arguments used for this loader.  Each argument should
-   * be a separate array containing a machine_name, name, and description
-   * keys.  This information is used to build the help text for the loader.
-   */
-  public static $argument_list = array();
-
-
-  /**
-   * Indicates how many files are allowed to be uploaded.  By default this is
-   * set to allow only one file.  Change to any positive number. A value of
-   * zero indicates an unlimited number of uploaded files are allowed.
-   */
-  public static $cardinality = 0;
-
-  /**
-   * Holds the list of all orgainsms currently in Chado. This list
-   * is needed when checking to see if an organism has already been
-   * loaded.
-   */
-  private  $all_orgs = array();
-
-  /**
-   * The record from the Chado phylotree table that refers to this
-   * Taxonomic tree.
-   */
-  private $phylotree = NULL;
-
-  /**
-   * The temporary tree array used by the Tripal Phylotree API for
-   * importing a new tree.
-   */
-  private $tree = NULL;
-
-  /**
-   * @see TripalImporter::form()
-   */
-  public function form($form, &$form_state) {
-
-    $form['instructions'] = array(
-      '#type' => 'fieldset',
-      '#title' => 'instructions',
-      '#description' => t('This form is used to import species from the NCBI
-        Taxonomy database into this site. Alternatively, it can import details
-        about organisms from the NCBI Taxonomy database for organisms that
-        already exist on this site.  This loader will also construct
-        the taxonomic tree for the species loaded.'),
-    );
-    $form['taxonomy_ids'] = array(
-      '#type' => 'textarea',
-      '#title' => 'Taxonomy ID',
-      '#description' => t('Please provide a list of NCBI taxonomy IDs separated
-        by spaces, tabs or new lines.
-        The information about these organisms will be downloaded and new organism
-        records will be added to this site.')
-    );
-
-    $form['import_existing'] = array(
-      '#type' => 'checkbox',
-      '#title' => 'Import details for existing species.',
-      '#description' =>  t('The NCBI Taxonomic Importer examines the organisms
-        currently present in the database and queries NCBI for the
-        taxonomic details.  If the importer is able to match the
-        genus and species with NCBI the species details will be imported,
-        and a page containing the taxonomic tree will be created.'),
-      '#default value' => 1,
-    );
-    return $form;
-  }
-
-  /**
-   * @see TripalImporter::formValidate()
-   */
-  public function formValidate($form, &$form_state) {
-    global $user;
-
-    $import_existing = $form_state['values']['import_existing'];
-    $taxonomy_ids = $form_state['values']['taxonomy_ids'];
-
-    // make sure that we have numeric values, one per line.
-    if ($taxonomy_ids) {
-      $tax_ids = preg_split("/[\s\n\t\r]+/", $taxonomy_ids);
-      $bad_ids = array();
-      foreach ($tax_ids as $tax_id) {
-        $tax_id = trim($tax_id);
-        if (!preg_match('/^\d+$/', $tax_id)) {
-          $bad_ids[] = $tax_id;
-        }
-      }
-      if (count($bad_ids) > 0) {
-        form_set_error('taxonomy_ids',
-            t('Taxonomy IDs must be numeric. The following are not valid: "@ids".',
-                array('@ids' => implode('", "', $bad_ids))));
-      }
-    }
-  }
-
-  /**
-   * Performs the import.
-   */
-  public function run() {
-    global $site_name;
-
-
-    $arguments = $this->arguments['run_args'];
-    $taxonomy_ids = $arguments['taxonomy_ids'];
-    $import_existing = $arguments['import_existing'];
-
-    // Get the list of all organisms as we'll need this to lookup existing
-    // organisms.
-    if (chado_get_version() > 1.2) {
-      $sql = "
-        SELECT O.*, CVT.name as type
-        FROM {organism} O
-         LEFT JOIN {cvterm} CVT ON CVT.cvterm_id = O.type_id
-        ORDER BY O.genus, O.species
-      ";
-    }
-    else {
-      $sql = "
-        SELECT O.*, '' as type
-        FROM {organism} O
-        ORDER BY O.genus, O.species
-      ";
-    }
-    $results = chado_query($sql);
-    while ($item = $results->fetchObject()) {
-      $this->all_orgs[] = $item;
-    }
-
-    // Get the phylotree object.
-    $this->logMessage('Initializing Tree...');
-    $this->phylotree = $this->initTree();
-    $this->logMessage('Rebuilding Tree...');
-    $this->tree = $this->rebuildTree();
-
-    // Clean out the phnylondes for this tree in the event this is a reload
-    chado_delete_record('phylonode', array('phylotree_id' => $this->phylotree->phylotree_id));
-
-    // Get the taxonomy IDs provided by the user (if any).
-    $tax_ids = array();
-    if ($taxonomy_ids) {
-      $tax_ids = preg_split("/[\s\n\t\r]+/", $taxonomy_ids);
-    }
-
-    // Set the number of items to handle.
-    if ($taxonomy_ids and $import_existing) {
-      $this->setTotalItems(count($this->all_orgs) + count($tax_ids));
-    }
-    if ($taxonomy_ids and !$import_existing) {
-      $this->setTotalItems(count($tax_ids));
-    }
-    if (!$taxonomy_ids and $import_existing) {
-      $this->setTotalItems(count($this->all_orgs));
-    }
-    $this->setItemsHandled(0);
-
-    // If the user wants to import new taxonomy IDs then do that.
-    if ($taxonomy_ids){
-      $this->logMessage('Importing Taxonomy IDs...');
-      foreach ($tax_ids as $tax_id) {
-        $tax_id = trim($tax_id);
-        $this->importRecord($tax_id);
-        $this->addItemsHandled(1);
-      }
-    }
-
-    // If the user wants to update existing records then do that.
-    if ($import_existing) {
-      $this->logMessage('Updating Existing...');
-      $this->updateExisting();
-    }
-
-    // Now import the tree.
-    $options = array('taxonomy' => 1);
-    chado_phylogeny_import_tree($this->tree, $this->phylotree, $options);
-  }
-
-
-  /**
-   * Create the taxonomic tree in Chado.
-   *
-   * If the tree already exists it will not be recreated.
-   *
-   * @throws Exception
-   * @return
-   *   Returns the phylotree object.
-   */
-  private function initTree() {
-    // Add the taxonomy tree record into the phylotree table. If the tree
-    // already exists then don't insert it again.
-    $site_name = variable_get('site_name');
-    $tree_name = $site_name . 'Taxonomy Tree';
-    $phylotree = chado_select_record('phylotree', array('*'), array('name' => $tree_name));
-    if (count($phylotree) == 0) {
-      // Add the taxonomic tree.
-      $phylotree = array(
-        'name' =>  $site_name . 'Taxonomy Tree',
-        'description' => 'A phylogenetic tree based on taxonomic rank.',
-        'leaf_type' => 'taxonomy',
-        'tree_file' => '/dev/null',
-        'format' => 'taxonomy',
-        'no_load' => TRUE,
-      );
-      $errors = array();
-      $warnings = array();
-      $success = tripal_insert_phylotree($phylotree, $errors, $warnings);
-      if (!$success) {
-        throw new Exception("Cannot add the Taxonomy Tree record.");
-      }
-      $phylotree = (object) $phylotree;
-    }
-    else {
-      $phylotree = $phylotree[0];
-    }
-    return $phylotree;
-  }
-
-
-
-  /**
-   * Iterates through all existing organisms and rebuilds the taxonomy tree.
-   *
-   * The phloytree API doesn't support adding nodes to existing trees only
-   * importing whole trees. So, we must rebuild the tree using the current
-   * organisms and then we can add to it.
-   *
-   */
-  private function rebuildTree() {
-    $lineage_nodes[] = array();
-
-    // Get the "rank" cvterm. It requires that the TAXRANK vocabulary is loaded.
-    $rank_cvterm = chado_get_cvterm(array(
-      'name' => 'rank',
-      'cv_id' => array('name' => 'local')
-    ));
-
-    // The taxonomic tree must have a root, so create that first.
-    $tree = array(
-      'name' => 'root',
-      'depth' => 0,
-      'is_root' => 1,
-      'is_leaf' => 0,
-      'is_internal' => 0,
-      'left_index' => 0,
-      'right_index' => 0,
-      'branch_set' => array(),
-    );
-
-    $total = count($this->all_orgs);
-    $j = 1;
-    foreach ($this->all_orgs as $organism) {
-      $sci_name = chado_get_organism_scientific_name($organism);
-      //$this->logMessage("- " . ($j++) . " of $total. Adding @organism", array('@organism' => $sci_name));
-
-      // First get the phylonode record for this organism.
-      $sql = "
-        SELECT P.*
-        FROM {phylonode} P
-         INNER JOIN {phylonode_organism} PO on PO.phylonode_id = P.phylonode_id
-        WHERE P.phylotree_id = :phylotree_id AND PO.organism_id = :organism_id
-      ";
-      $args = array(
-        ':phylotree_id' => $this->phylotree->phylotree_id,
-        ':organism_id' => $organism->organism_id,
-      );
-      $result = chado_query($sql, $args);
-      if (!$result) {
-        continue;
-      }
-      $phylonode = $result->fetchObject();
-
-      // Next get the lineage for this organism.
-      $lineage = $this->getProperty($organism->organism_id, 'lineage');
-      if (!$lineage) {
-        continue;
-      }
-      $lineage_depth = preg_split('/;\s*/', $lineage->value);
-
-      // Now rebuild the tree by first creating the nodes for the full
-      // lineage and then adding the organism as a leaf node.
-      $parent = $tree;
-      $i = 1;
-      $lineage_good = TRUE;
-      foreach ($lineage_depth as $child) {
-        // We need to find the node in the phylotree for this level of the
-        // lineage, but there's a lot of repeats and we don't want to keep
-        // doing the same queries over and over, so we store the nodes
-        // we've already seen in the $lineage_nodes array for fast lookup.
-        if (array_key_exists($child, $lineage_nodes)) {
-          $phylonode = $lineage_nodes[$child];
-          if (!$phylonode) {
-            $lineage_good = FALSE;
-            continue;
-          }
-        }
-        else {
-          $values = array(
-            'phylotree_id' => $this->phylotree->phylotree_id,
-            'label' => $child,
-          );
-          $columns = array('*');
-          $phylonode = chado_select_record('phylonode', $columns, $values);
-          if (count($phylonode) == 0) {
-            $lineage_nodes[$child] = NULL;
-            $lineage_good = FALSE;
-            continue;
-          }
-          $phylonode = $phylonode[0];
-          $lineage_nodes[$child] = $phylonode;
-
-
-          $values = array(
-            'phylonode_id' => $phylonode->phylonode_id,
-            'type_id' => $rank_cvterm->cvterm_id,
-          );
-          $columns = array('*');
-          $phylonodeprop = chado_select_record('phylonodeprop', $columns, $values);
-        }
-        $name = $child;
-        $node_rank = (string) $child->Rank;
-        $node = array(
-          'name' => $name,
-          'depth' => $i,
-          'is_root' => 0,
-          'is_leaf' => 0,
-          'is_internal' => 1,
-          'left_index' => 0,
-          'right_index' => 0,
-          'parent' => $parent,
-          'branch_set' => array(),
-          'parent' => $parent['name'],
-          'properties' => array(
-            $rank_cvterm->cvterm_id => $phylonodeprop[0]->value,
-          ),
-        );
-        $parent = $node;
-        $this->addTaxonomyNode($tree, $node, $lineage_depth);
-        $i++;
-      } // end foreach ($lineage_depth as $child) { ...
-
-      // If $stop is set then we had problems setting the lineage so
-      // skip adding the leaf node below.
-      if (!$lineage_good) {
-        continue;
-      }
-
-      $rank_type = 'species';
-      if (property_exists($organism, 'type_id') and $organism->type_id) {
-        $rank_type = $organism->type;
-      }
-
-      // Now add in the leaf node
-      $sci_name = chado_get_organism_scientific_name($organism);
-      $node = array(
-        'name' => $sci_name,
-        'depth' => $i,
-        'is_root' => 0,
-        'is_leaf' => 1,
-        'is_internal' => 0,
-        'left_index' => 0,
-        'right_index' => 0,
-        'parent' => $parent['name'],
-        'organism_id' => $organism->organism_id,
-        'properties' => array(
-          $rank_cvterm->cvterm_id => $rank_type,
-        ),
-      );
-      $this->addTaxonomyNode($tree, $node, $lineage_depth);
-
-      // Set the indecies for the tree.
-      chado_assign_phylogeny_tree_indices($tree);
-    }
-
-    return $tree;
-  }
-
-  /**
-   * Imports details from NCBI Taxonomy for organisms that alrady exist.
-   */
-  private function updateExisting() {
-
-    foreach ($this->all_orgs as $organism) {
-      // If the organism record is marked as new then let's skip it because
-      // it was newly added and should have the updated information already.
-      if ($organism->is_new) {
-        continue;
-      }
-
-      // TODO: we should check if the organism already has a taxonomy ID.
-      // if so we should use that instead of the scientific name.
-
-      // Build the query string to get the information about this species.
-      $sci_name = chado_get_organism_scientific_name($organism);
-      $sci_name = urlencode($sci_name);
-      $search_url = "http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?".
-          "db=taxonomy" .
-          "&term=$sci_name";
-
-      // Get the search response from NCBI.
-      $rfh = fopen($search_url, "r");
-      $xml_text = '';
-      while (!feof($rfh)) {
-        $xml_text .= fread($rfh, 255);
-      }
-      fclose($rfh);
-
-      // Parse the XML to get the taxonomy ID
-      $xml = new SimpleXMLElement($xml_text);
-      if ($xml) {
-        $taxid = (string) $xml->IdList->Id;
-        if ($taxid) {
-          $this->importRecord($taxid, $organism);
-        }
-      }
-      $this->addItemsHandled(1);
-    }
-  }
-
-  /**
-   * Checks the Chado database to see if the organism already exists.
-   *
-   * @param $taxid
-   *   The taxonomic ID for the organism.
-   * @param $sci_name
-   *   The scientific name for the organism as returned by NCBI
-   */
-  private function findOrganism($taxid, $sci_name) {
-    $organism = NULL;
-
-    // First check the taxid to see if it's present and assocaited with an
-    // organism already.
-    $values = array(
-      'db_id' => array(
-        'name' => 'NCBITaxon'
-      ),
-      'accession' => $taxid,
-    );
-    $columns = array('dbxref_id');
-    $dbxref = chado_select_record('dbxref', $columns, $values);
-    if (count($dbxref) > 0) {
-      $columns = array('organism_id');
-      $values = array('dbxref_id' => $dbxref[0]->dbxref_id);
-      $organism_dbxref = chado_select_record('organism_dbxref', $columns, $values);
-      if (count($organism_dbxref) >0) {
-        $organism_id = $organism_dbxref[0]->organism_id;
-        $columns = array('*');
-        $values = array('organism_id' => $organism_id);
-        $organism = chado_select_record('organism', $columns, $values);
-        if (count($organism) > 0) {
-          $organism = $organism[0];
-        }
-      }
-    }
-
-    // If the caller did not provide an organism then we want to try and
-    // add one. But, it only makes sense to add one if this record
-    // is of rank species.
-    // First check if the full name (including the infrasepcific name)
-    // are all present in the genus and species name.  This would have
-    // been the Chado v1.2 (or less) of storing species.
-    if (!$organism) {
-      $sql = "
-          SELECT organism_id
-          FROM {organism}
-          WHERE concat(genus, ' ', species) = :sci_name
-        ";
-      $results = chado_query($sql, array(':sci_name' => $sci_name));
-      $item = $results->fetchObject();
-      if ($item) {
-        $columns = array('*');
-        $values = array('organism_id' => $item->organism_id);
-        $organism = chado_select_record('organism', $columns, $values);
-        if (count($organism) > 0) {
-          $organism = $organism[0];
-        }
-      }
-    }
-    // Second, check if the full name includes the infraspecific name.
-    if (!$organism) {
-      foreach ($this->all_orgs as $item) {
-        $internal_sci_name = chado_get_organism_scientific_name($item);
-        if ($sci_name == $internal_sci_name) {
-          $organism = $item;
-        }
-      }
-    }
-    return $organism;
-  }
-  /**
-   * Adds a new organism record to Chado.
-   *
-   * @param sci_name
-   *   The scientific name as provied by NCBI Taxonomy.
-   * @param $rank
-   *   The rank of the organism as provied by NCBI Taxonomy.
-   */
-  private function addOrganism($sci_name, $rank) {
-
-    $organism = NULL;
-    $matches = array();
-    $genus = '';
-    $species = '';
-    $infra = '';
-    $values = array();
-
-    // Check if the scientific name has an infraspecific part or is just
-    // a species name.
-    if (preg_match('/^(.+?)\s+(.+?)\s+(.+)$/', $sci_name, $matches)) {
-      $genus = $matches[1];
-      $species = $matches[2];
-      $infra = $matches[3];
-
-      // Get the CV term for the rank.
-      $type = chado_get_cvterm(array(
-        'name' => preg_replace('/ /','_', $rank),
-        'cv_id' => array('name' => 'taxonomic_rank')
-      ));
-
-      // Remove the rank from the infraspecific name.
-      $abbrev = chado_abbreviate_infraspecific_rank($rank);
-      $infra = preg_replace("/$abbrev/", "", $infra);
-      $infra = trim($infra);
-
-      $values = array(
-        'genus' => $genus,
-        'species' => $species,
-        'abbreviation' => $genus[0] . '. ' . $species,
-        'type_id' => $type->cvterm_id,
-        'infraspecific_name' => $infra,
-      );
-      $organism = chado_insert_record('organism', $values);
-      $organism = (object) $organism;
-      $organism->type = $rank;
-    }
-    else if (preg_match('/^(.+?)\s+(.+?)$/', $sci_name, $matches)) {
-      $genus = $matches[1];
-      $species = $matches[2];
-      $infra = '';
-      $values = array(
-        'genus' => $genus,
-        'species' => $species,
-        'abbreviation' => $genus[0] . '. ' . $species,
-      );
-      $organism = chado_insert_record('organism', $values);
-      $organism = (object) $organism;
-    }
-    if ($organism) {
-      $organism->is_new = TRUE;
-      $this->all_orgs[] = $organism;
-    }
-
-    return $organism;
-  }
-
-  /**
-   * Imports an organism from the NCBI taxonomy DB by its taxonomy ID
-   *
-   * @param $taxid
-   *   The NCBI Taxonomy ID.
-   * @param $organism
-   *   The organism object to which this taxonomy belongs.  If the organism
-   *   is NULL then it will be created.
-   */
-  private function importRecord($taxid, $organism = NULL) {
-    $adds_organism = $organism ? FALSE : TRUE;
-
-    // Get the "rank" cvterm. It requires that the TAXRANK vocabulary is loaded.
-    $rank_cvterm = chado_get_cvterm(array(
-      'name' => 'rank',
-      'cv_id' => array('name' => 'local')
-    ));
-
-    // Get the details for this taxonomy.
-    $fetch_url = "http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?".
-        "db=taxonomy" .
-        "&id=$taxid";
-
-    // Get the search response from NCBI.
-    $rfh = fopen($fetch_url, "r");
-    $xml_text = '';
-    while (!feof($rfh)) {
-      $xml_text .= fread($rfh, 255);
-    }
-    fclose($rfh);
-
-    $xml = new SimpleXMLElement($xml_text);
-    if ($xml) {
-      $taxon = $xml->Taxon;
-
-      // Get the genus and species from the xml.
-      $parent = (string) $taxon->ParentTaxId;
-      $rank = (string) $taxon->Rank;
-      $sci_name = (string) $taxon->ScientificName;
-      //$this->logMessage(' - Importing @sci_name', array('@sci_name' => $sci_name));
-
-      // If we don't have an organism record provided then see if there
-      // is one provided by Chado, if not, the try to add one.
-      if (!$organism) {
-        $organism = $this->findOrganism($taxid, $sci_name);
-        if (!$organism) {
-          $organism = $this->addOrganism($sci_name, $rank);
-          if (!$organism) {
-            throw new Exception(t('Cannot add organism: @sci_name', array('@sci_name' => $sci_name)));
-          }
-        }
-      }
-
-      // Associate the Dbxref with the organism.
-      $this->addDbxref($organism->organism_id, $taxid);
-
-      // Get properties for this organism.
-      $lineage = (string) $taxon->Lineage;
-      $genetic_code = (string) $taxon->GeneticCode->GCId;
-      $genetic_code_name = (string) $taxon->GeneticCode->GCName;
-      $mito_genetic_code = (string) $taxon->MitoGeneticCode->MGCId;
-      $mito_genetic_code_name = (string) $taxon->MitoGeneticCode->MGCName;
-      $division = (string) $taxon->Division;
-
-      // Add in the organism properties.
-      $this->addProperty($organism->organism_id, 'division', $division);
-      $this->addProperty($organism->organism_id, 'mitochondrial_genetic_code_name', $mito_genetic_code_name);
-      $this->addProperty($organism->organism_id, 'mitochondrial_genetic_code', $mito_genetic_code);
-      $this->addProperty($organism->organism_id, 'genetic_code_name', $genetic_code_name);
-      $this->addProperty($organism->organism_id, 'lineage', $lineage);
-      $this->addProperty($organism->organism_id, 'genetic_code', $genetic_code);
-
-      $name_ranks = array();
-      if ($taxon->OtherNames->children) {
-        foreach ($taxon->OtherNames->children() as $child) {
-          $type = $child->getName();
-          $name = (string) $child;
-          if (!array_key_exists($type, $name_ranks)) {
-            $name_ranks[$type] = 0;
-          }
-          switch ($type) {
-            case 'GenbankCommonName':
-              $this->addProperty($organism->organism_id, 'genbank_common_name', $name, $name_ranks[$type]);
-              break;
-            case 'Synonym':
-            case 'GenbankSynonym':
-              $this->addProperty($organism->organism_id, 'synonym', $name, $name_ranks[$type]);
-              break;
-            case 'CommonName':
-              // If we had to add the organism then include the commone name too.
-              if ($adds_organism) {
-                $organism->common_name = $name;
-                $values = array('organism_id' => $organism->id);
-                chado_update_record('organism', $values, $organism);
-              }
-            case 'Includes':
-              $this->addProperty($organism->organism_id, 'other_name', $name, $name_ranks[$type]);
-              break;
-            case 'EquivalentName':
-              $this->addProperty($organism->organism_id, 'equivalent_name', $name, $name_ranks[$type]);
-              break;
-            case 'Anamorph':
-              $this->addProperty($organism->organism_id, 'anamorph', $name, $name_ranks[$type]);
-              break;
-            case 'Name':
-              // skip the Name stanza
-              break;
-            default:
-              print "NOTICE: Skipping unrecognzed name type: $type\n";
-              // do nothing for unrecognized types
-          }
-          $name_ranks[$type]++;
-        }
-      }
-
-      // Generate a nested array structure that can be used for importing the tree.
-      $lineage_depth = preg_split('/;\s*/', $lineage);
-      $parent = $this->tree;
-      $i = 1;
-      foreach ($taxon->LineageEx->children() as $child) {
-        $tid = (string) $child->TaxID;
-        $name = (string) $child->ScientificName;
-        $node_rank = (string) $child->Rank;
-        $node = array(
-          'name' => $name,
-          'depth' => $i,
-          'is_root' => 0,
-          'is_leaf' => 0,
-          'is_internal' => 1,
-          'left_index' => 0,
-          'right_index' => 0,
-          'parent' => $parent,
-          'branch_set' => array(),
-          'parent' => $parent['name'],
-          'properties' => array(
-            $rank_cvterm->cvterm_id => $node_rank,
-          ),
-        );
-        $parent = $node;
-        $this->addTaxonomyNode($this->tree, $node, $lineage_depth);
-        $i++;
-      }
-      // Now add in the leaf node
-      $node = array(
-        'name' => $sci_name,
-        'depth' => $i,
-        'is_root' => 0,
-        'is_leaf' => 1,
-        'is_internal' => 0,
-        'left_index' => 0,
-        'right_index' => 0,
-        'parent' => $parent['name'],
-        'organism_id' => $organism->organism_id,
-        'properties' => array(
-          $rank_cvterm->cvterm_id => $rank,
-        ),
-      );
-      $this->addTaxonomyNode($this->tree, $node, $lineage_depth);
-
-      // Set the indecies for the tree.
-      chado_assign_phylogeny_tree_indices($this->tree);
-    }
-  }
-  /**
-   *
-   */
-  private function addTaxonomyNode(&$tree, $node, $lineage_depth) {
-
-    // Get the branch set for the tree root.
-    $branch_set = &$tree['branch_set'];
-
-    // Iterate through the tree up until the depth where this node will
-    // be placed.
-    $node_depth = $node['depth'];
-    for ($i = 1; $i <= $node_depth; $i++) {
-      // Iterate through any existing nodes in the branch set to see if
-      // the node name matches the correct name for the lineage at this
-      // depth. If it matches then it is inside of this branch set that
-      // we will place the node.
-      for ($j = 0; $j < count($branch_set); $j++) {
-        // If this node already exists in the tree then return.
-        if ($branch_set[$j]['name'] == $node['name'] and
-            $branch_set[$j]['depth'] = $node['depth']) {
-          return;
-        }
-        // Otherwise, set the branch to be the current branch and continue.
-        if ($branch_set[$j]['name'] == $lineage_depth[$i-1]) {
-          $branch_set = &$branch_set[$j]['branch_set'];
-          break;
-        }
-      }
-    }
-    // Add the node to the last branch set.  This should be where this node goes.
-    $branch_set[] = $node;
-  }
-
-  /**
-   * Retrieves a property for a given organism.
-   *
-   * @param $organism_id
-   *   The organism ID to which the property is added.
-   * @param $term_name
-   *   The name of the organism property term.  This term must be
-   *   present in the 'organism_property' cv.
-   * @param $rank
-   *   The order for this property. The first instance of this term for
-   *   this organism should be zero. Defaults to zero.
-   * @return
-   *   The property object.
-   */
-  private function getProperty($organism_id, $term_name, $rank = 0) {
-    $record = array(
-      'table' => 'organism',
-      'id' => $organism_id
-    );
-    $property = array(
-      'type_name' => $term_name,
-      'cv_name' => 'organism_property',
-      'value' => $value,
-      'rank' => $rank
-    );
-
-    return chado_get_property($record, $property);
-  }
-
-  /**
-   * Adds a property to an organism node.
-   *
-   * @param $organism_id
-   *   The organism ID to which the property is added.
-   * @param $term_name
-   *   The name of the organism property term.  This term must be
-   *   present in the 'organism_property' cv.
-   * @param $value
-   *   The value of the property.
-   * @param $rank
-   *   The order for this property. The first instance of this term for
-   *   this organism should be zero. Defaults to zero.
-   */
-  private function addProperty($organism_id, $term_name, $value, $rank = 0) {
-    if (!$value) {
-      return;
-    }
-
-    $record = array(
-      'table' => 'organism',
-      'id' => $organism_id
-    );
-    $property = array(
-      'type_name' => $term_name,
-      'cv_name' => 'organism_property',
-      'value' => $value
-    );
-    // Delete all properties of this type if the rank is zero.
-    if ($rank == 0) {
-      chado_delete_property($record, $property);
-    }
-    chado_insert_property($record, $property);
-  }
-
-  /**
-   *
-   * @param unknown $organism_id
-   * @param unknown $taxId
-   */
-  private function addDbxref($organism_id, $taxId) {
-    $db = chado_get_db(array('name' => 'NCBITaxon'));
-    $values = array(
-      'db_id' => $db->db_id,
-      'accession' => $taxId
-    );
-    $dbxref = chado_insert_dbxref($values);
-
-    $values = array(
-      'dbxref_id' => $dbxref->dbxref_id,
-      'organism_id' => $organism_id,
-    );
-
-   if (!chado_select_record('organism_dbxref', ['organism_dbxref_id'], $values)) {
-     chado_insert_record('organism_dbxref', $values);
-   }
-  }
-}