Oops forgot to add tripal_cv_admin.inc to the includes list

tripal_cv/includes/tripal_cv_admin.inc

@@ -0,0 +1,916 @@
+<?php
+/**
+ * Purpose: Provide Guidance to new Tripal Admin
+ *
+ * @return HTML Formatted text
+ *
+ * @ingroup tripal_cv
+ */
+function tripal_cv_module_description_page() {
+  $text = '';
+
+  $text = '<br><h3>Tripal Controlled Vocabulary Administrative Tools Quick Links</h3>';
+    $text .= '<ul>';
+      $text .= '<li>' . l('Add a Vocabulary', 'admin/tripal/tripal_cv/cv/add') . '</li>';
+      $text .= '<li>' . l('Edit a Vocabulary', 'admin/tripal/tripal_cv/cv/edit') . '</li>';
+      $text .= '<li>' . l('Load ontology with OBO file', 'admin/tripal/tripal_cv/obo_loader') . '</li>';
+      $text .= '<li>' . l('Add a Term', 'admin/tripal/tripal_cv/cvterm/add') . '</li>';
+      $text .= '<li>' . l('Edit a Term', 'admin/tripal/tripal_cv/cvterm/edit') . '</li>';      
+      $text .= '<li>' . l('Update cvtermpath', 'admin/tripal/tripal_cv/cvtermpath') . '</li>';
+    $text .= '</ul>';
+
+
+  $text .= '<h3>Module Description:</h3>';
+  $text .= '<p>The Tripal CV (Controlled Vocabularies) Module provides
+    functionality for managing controlled vocabularies and the terms they are
+    comprised of. The flexibility and extendibility of the chado schema depends
+    on controlled vocabularies. For example, by using a controlled vocabulary for
+    feature types the chado schema can describe features of any type, even those
+    we have not concieved of yet.</p>';
+
+  $text .= '<h3>Setup Instructions:</h3>';
+  $text .= '<p>After installation of the controlled vocabulary module, the following tasks should be performed:</p>';
+    $text .= '<ol>';
+      $text .= '<li><p><b>Set Permissions</b>: The cv module supports the Drupal user permissions interface for
+               controlling access to cv content and functions. These permissions include viewing,
+               creating, editing or administering of
+               cv content. The default is that only the original site administrator has these
+               permissions.  You can <a href="' . url('admin/user/roles') . '">add roles</a> for classifying users,
+               <a href="' . url('admin/user/user') . '">assign users to roles</a> and
+               <a href="' . url('admin/user/permissions') . '">assign permissions</a> for the cv content to
+               those roles.  For a simple setup, allow anonymous users access to view organism content and
+               allow the site administrator all other permissions.</p></li>';
+      $text .= '<li><b>Loading of Ontologies/Controlled Vocabularies</b>: You can access this loader at '.
+        l('Admin->Tripal Management->Tripal CV->Load Ontology With OBO File', 'admin/tripal/tripal_cv/obo_loader')
+        .'. This loader allows you to choose from a list of common ontologies or
+        enter the URL or location to an OBO file. Even the list of common
+        ontologies is using a URL ensuring you get the most up to date ontology.</p>';
+      $text .= '<p>This loader adds a Tripal Job which then waits in a queue to
+        be launched. To launch Tripal Jobs either navidate to the root of your
+        drupal installation and execute "php sites/all/modules/tripal/tripal_core/
+        tripal_launch_jobs.php <drupal user>" or set up a cron job (See user manual
+        for more details).</p>';
+      $text .= '<p>NOTE: in some cases, community developed ontologies for your
+        data may not yet be developed. In this case, it is suggested that you begin
+        developement of an ontology using one of the online tools. You might find
+        that many researchers are trying to deal with the same data and are willing
+        to help you in this endevor. You can ' . l('create a controlled vocabulary', 'admin/tripal/tripal_cv/add_cv') . ' and '
+        . l('add terms to it', 'admin/tripal/tripal_cv/add_cvterm')  . ' to provide functionality to your site while you are waiting
+        for the ontology to be developed.</p></li>';
+    $text .= '</ol>';
+
+  $text .= '<h3>Features of this Module:</h3>';
+  $text .= '<p>Aside from the data loading described above, the Tripal Controlled Vocabulary (CV) module also provides the following functionality:</p>';
+    $text .= '<ul>';
+      $text .= '<li><b>Create/Update/Delete A Controlled Vocaulbulary</b>: to create your own controlled vocabulary go to '.
+        l('Admin->Tripal Management->Tripal CV->Add a Controlled Vocabulary', 'admin/tripal/tripal_cv/add_cv')
+        .' and fill out the form provided.To Update/Delete a controlled vocabulary
+        go to ' . l('Admin->Tripal Management->Tripal CV->Update/Delete Controlled Vocabulary', 'admin/tripal/tripal_cv/edit_cv')
+        .', select the existing controlled vocabulary you want to modify and then
+        edit it as desired. This only modifies the name, description of a
+        controlled vocabulary. See the next section for adding, removing, editing
+        the term a controlled vocabulary contains.</li>';
+
+      $text .= '<li><b>Create a Controlled Vocaulbulary Term</b>: To Add a term to an already existing controlled vocabulary
+        go to ' . l('Admin->Tripal Management->Tripal CV->Add a Controlled Vocabulary Term', 'admin/tripal/tripal_cv/add_cvterm')
+        .', select the controlled vocabulary you want to add terms to and then fill
+        out the form.</li>';
+      $text .= '<li><b>Controlled Vocabulary Term Browser</b>: This module provides a ' . l('basic listing', 'admin/tripal/tripal_cv/list_cvterms') . ' of controlled vocabulry terms for
+              for all vocabularies currently in chado. It does not require indexing for Drupal searching but relies on Drupal Views.
+              <a href="http://drupal.org/project/views">Drupal Views</a> must be installed.</li>';
+      $text .= '<li><p><b>Integration with Drupal Views</b>: <a href="http://drupal.org/project/views">Drupal Views</a> is
+              a powerful tool that allows the site administrator to create lists or basic searching forms of Chado content.
+              It provides a graphical interface within Drupal to allow the site admin to directly query the Chado database
+              and create custom lists without PHP programming or customization of Tripal source code.  Views can also
+              be created to filter content that has not yet been synced with Druapl in order to protect access to non
+              published data (only works if Chado was installed using Tripal).  You can see a list of available pre-existing
+              Views <a href="' . url('admin/build/views/') . '">here</a>, as well as create your own. </p></li>';
+    $text .= '</ul>';
+
+  return $text;
+}
+
+/**
+ * Purpose: Provides the form for Updating and Deleteing existing
+ *   chado controlled vocabularies (See chado cv table)
+ *
+ * @ingroup tripal_cv
+ */
+function tripal_cv_edit_page() {
+  $output .= drupal_get_form('tripal_cv_select_form');
+  $output .= '<div id="db-edit-div">Please select a vocabulary above to view or edit</div>';
+
+  return $output;
+}
+
+/**
+ * Purpose: Provides the actual "Select CV" form on the Update/Delete Controlled
+ *   Vocabulary page. This form also triggers the edit javascript
+ * @todo Modify this form to use Drupal AJAX
+ *
+ * @ingroup tripal_cv
+ */
+function tripal_cv_select_form() {
+
+  // get a list of db from chado for user to choose
+  $sql = "SELECT * FROM {cv} WHERE NOT name = 'tripal' ORDER BY name ";
+  $results = chado_query($sql);
+
+  $cvs = array();
+  $cvs[] = '';
+  while ($cv = db_fetch_object($results)) {
+    $cvs[$cv->cv_id] = $cv->name;
+  }
+
+  $form['cvid'] = array(
+    '#title' => t('Controlled Vocabulary/Ontology Name'),
+    '#type' => 'select',
+    '#options' => $cvs,
+    '#ahah' => array(
+      'path' => 'admin/tripal/tripal_cv/cv/edit/js',
+      'wrapper' => 'db-edit-div',
+      'effect' => 'fade',
+      'event' => 'change',
+      'method' => 'replace',
+    ),
+  );
+
+  return $form;
+}
+
+/**
+ * Purpose: The edit controlled vocabulary javascript
+ *
+ * @ingroup tripal_cv
+ */
+function tripal_ajax_cv_edit() {
+
+  // get the database id, build the form and then return the JSON object
+  $cvid = filter_xss($_POST['cvid']);
+  $form = drupal_get_form('tripal_cv_edit_form', $cvid);
+  drupal_json(array('status' => TRUE, 'data' => $form));
+
+}
+
+/**
+ * Purpose: Provides a form to allow updating/deleteing of controlled vocabularies
+ *
+ * @ingroup tripal_cv
+ */
+function tripal_cv_edit_form(&$form_state = NULL, $cvid = NULL) {
+
+  $sql = "SELECT * FROM {cv} WHERE cv_id = %d ";
+  $cv = db_fetch_object(chado_query($sql, $cvid));
+
+  // set the default values.  If there is a value set in the
+  // form_state then let's use that, otherwise, we'll pull
+  // the values from the database
+  $default_db = $form_state['values']['name'];
+  $default_desc = $form_state['values']['description'];
+  $default_url = $form_state['values']['url'];
+  $default_urlprefix = $form_state['values']['urlprefix'];
+  if (!$default_db) {
+    $default_cv = $cv->name;
+  }
+  if (!$default_desc) {
+    $default_desc = $cv->definition;
+  }
+
+  $form['cvid'] = array(
+    '#type' => 'hidden',
+    '#value' => $cvid
+  );
+
+  $form['name']= array(
+    '#type'          => 'textfield',
+    '#title'         => t("Controlled Vocabulary name"),
+    '#description'   => t('Please enter the name for this vocabulary.'),
+    '#required'      => FALSE,
+    '#default_value' => $default_cv,
+    '#weight'        => 1
+  );
+
+  $form['definition']= array(
+    '#type'          => 'textarea',
+    '#title'         => t('Description'),
+    '#description'   => t('Please enter a description for this vocabulary'),
+    '#default_value' => $default_desc,
+    '#weight'        => 2
+  );
+
+  $form['update'] = array(
+    '#type'         => 'submit',
+    '#value'        => t('Update'),
+    '#weight'       => 5,
+    '#executes_submit_callback' => TRUE,
+  );
+  $form['delete'] = array(
+    '#type'         => 'submit',
+    '#value'        => t('Delete'),
+    '#weight'       => 6,
+    '#executes_submit_callback' => TRUE,
+  );
+
+  $form['#redirect'] = 'admin/tripal/tripal_cv';
+
+
+  return $form;
+}
+
+/**
+ * Purpose: The submit function of the update/delete controlled vocabulary form
+ *
+ * @ingroup tripal_cv
+ */
+function tripal_cv_edit_form_submit($form, &$form_state) {
+
+  $name =  $form_state['values']['name'];
+  $desc =  $form_state['values']['definition'];
+  $cvid =  $form_state['values']['cvid'];
+  $op   =  $form_state['values']['op'];
+
+  if (strcmp($op, 'Update') == 0) {
+    $sql = "
+       UPDATE {cv} SET
+         name = '%s',
+         definition = '%s'
+       WHERE cv_id = %d
+    ";
+    $db = chado_query($sql, $name, $desc, $cvid);
+    if ($db) {
+      drupal_set_message(t("Controlled vocabulary updated"));
+    }
+    else {
+      drupal_set_message(t("Failed to update controlled vocabulary."), 'error');
+    }
+  }
+  if (strcmp($op, 'Delete')==0) {
+    $sql = "
+       DELETE FROM {cv}
+       WHERE cv_id = %d
+    ";
+    $db = chado_query($sql, $cvid);
+    if ($db) {
+      drupal_set_message(t("Controlled vocabulary deleted"));
+    }
+    else {
+      drupal_set_message(t("Failed to delete controlled vocabulary."), 'error');
+    }
+  }
+
+}
+
+
+/**
+ * Purpose: Provides the Add controlled vocabulary form
+ *
+  * @ingroup tripal_cv
+ */
+function tripal_cv_add_form(&$form_state = NULL) {
+
+  $form['cvid'] = array(
+    '#type' => 'hidden',
+    '#value' => $cvid
+  );
+
+  $form['name']= array(
+    '#type'          => 'textfield',
+    '#title'         => t("Controlled Vocabulary name"),
+    '#description'   => t('Please enter the name for this vocabulary.  This field will be ignored if an OBO file or URL is provided above'),
+    '#required'      => FALSE,
+    '#default_value' => $default_cv,
+    '#weight'        => 1
+  );
+
+  $form['definition']= array(
+    '#type'          => 'textarea',
+    '#title'         => t('Description'),
+    '#description'   => t('Please enter a description for this vocabulary'),
+    '#default_value' => $default_desc,
+    '#weight'        => 2
+  );
+
+  $form['add'] = array(
+    '#type'         => 'submit',
+    '#value'        => t('Add'),
+    '#weight'       => 5,
+    '#executes_submit_callback' => TRUE,
+  );
+
+  $form['#redirect'] = 'admin/tripal/tripal_cv';
+
+  return $form;
+}
+
+/**
+ * Purpose: The submit function for the add controlled vocabulary form
+ *
+ * @ingroup tripal_cv
+ */
+function tripal_cv_add_form_submit($form, &$form_state) {
+
+  $name =  $form_state['values']['name'];
+  $desc =  $form_state['values']['definition'];
+
+  $sql = "
+    INSERT INTO {cv}
+     (name,definition)
+    VALUES
+     ('%s','%s')
+  ";
+  $db = chado_query($sql, $name, $desc);
+  if ($db) {
+    drupal_set_message(t("Controlled vocabulary added"));
+  }
+  else {
+    drupal_set_message(t("Failed to add controlled vocabulary."), 'error');
+  }
+
+}
+
+/**
+ * Purpose: Provides the form that allows adding of terms to an existing
+ *   controlled vocabulary
+ *
+  * @ingroup tripal_cv
+ */
+function tripal_cv_cvterm_form(&$form_state, $action = 'add') {
+  tripal_core_ahah_init_form();
+  
+  $form = array();
+
+  // get defaults  
+  $cv_id = $form_state['values']['cv_id'] ? $form_state['values']['cv_id'] : FALSE;
+  $name  = $form_state['values']['name'] ? $form_state['values']['name'] : '';
+  
+  // if we have a cv_id and a term name then get the rest of the term details
+  if ($cv_id and $name) {
+     $values = array(
+       'cv_id' => $cv_id,
+       'name' => $name,
+     );     
+     $results = tripal_core_chado_select('cvterm', array('*'), $values);
+     if (!$results or count($results) == 0) {
+       // we can't find the cvterm so reset the name to blank
+       $name = '';
+     }
+     else {
+       $cvterm = $results[0];
+       $definition = $cvterm->definition;
+       $is_relationshiptype = $cvterm->is_relationshiptype;
+       $is_obsolete = $cvterm->is_obsolete;
+       
+       // now get the database
+       $values = array('dbxref_id' => $cvterm->dbxref_id);
+       $results = tripal_core_chado_select('dbxref', array('*'), $values);
+       $dbxref = $results[0];
+       $accession = $dbxref->accession;
+       $db_id = $dbxref->db_id;
+     }
+  }
+  
+  $values = array();
+  $columns = array('cv_id', 'name');
+  $options = array('order_by' => array('name' => 'ASC'));
+  $results = tripal_core_chado_select('cv', $columns, $values, $options);
+  $cvs = array();
+  $cvs[] = '';
+  foreach ($results as $cv) {
+    $cvs[$cv->cv_id] = $cv->name;
+  }
+
+  $form['wrapper-top'] = array(
+    '#type' => 'markup',
+    '#value' => '<div id="cvterm-form">', 
+  );
+  
+  $form['form_action'] = array(
+    '#type' => 'hidden',
+    '#value' => $action, 
+  );   
+  
+  $form['cv_id'] = array(
+    '#title' => t('Controlled Vocabulary (Ontology) Name'),
+    '#type' => 'select',
+    '#options' => $cvs,
+    '#required' => TRUE,
+    '#default_value' => $cv_id,
+    '#ahah' => array(
+       'path'    => 'admin/tripal/tripal_cv/cvterm/ahah',
+       'wrapper' => 'cvterm-form',
+       'event'   => 'change',
+       'method'  => 'replace',
+    ),    
+  );
+  
+  if ($cv_id) {
+    $form['add_cvterm'] = array(
+      '#type'           => 'fieldset',
+      '#title'          => t('Term Details'),
+      '#prefix'         => '<div id="cvterm-add-div">',
+      '#suffix'         => '</div>'
+    );
+    $description = t('Please enter the name for this vocabulary term.');
+    if ($action == 'edit') {
+      $description = t('Enter the name of the term to edit.  This field will update automatically as you type. Click outside of the box after entering the term.');
+    }
+    $form['add_cvterm']['name']= array(
+      '#type'          => 'textfield',
+      '#title'         => t("Term Name"),
+      '#description'   => $description,
+      '#default_value' => $name,
+      '#required'      => TRUE,
+    );
+    if ($action == 'edit') {
+      if ($name) {
+        $form['add_cvterm']['name']['#attributes'] = array('readonly' => 'readonly');
+        $form['add_cvterm']['name']['#description'] = 'The term name cannot be changed. If the name is incorrect, please create a new term and make this one as obsolete.';
+      } else {
+        $form['add_cvterm']['name']['#autocomplete_path'] = "admin/tripal/tripal_cv/cvterm/auto_name/$cv_id";
+        $form['add_cvterm']['name']['#ahah'] = array(
+           'path'    => 'admin/tripal/tripal_cv/cvterm/ahah',
+           'wrapper' => 'cvterm-form',
+           'method'  => 'replace',
+        );
+      }
+    }   
+
+    if ($action == 'add' or $name) { 
+      
+      
+      $form['add_cvterm']['definition']= array(
+        '#type'          => 'textarea',
+        '#title'         => t('Description'),
+        '#description'   => t('Please enter a description for this term'),
+        '#default_value' => $definition,
+      );
+  
+      $form['add_cvterm']['is_relationshiptype'] = array(
+        '#type'          => 'checkbox',
+        '#title'         => t('This term describes a relationship?'),
+        '#default_value' => $is_relationshiptype,
+      );
+  
+      $form['add_cvterm']['is_obsolete'] = array(
+        '#type'          => 'checkbox',
+        '#title'         => t('This term is obsolete?'),
+        '#default_value' => $is_obsolete,
+      );
+  
+      $values = array();
+      $columns = array('db_id', 'name');
+      $options = array('order_by' => array('name' => 'ASC'));
+      $results = tripal_core_chado_select('db', $columns, $values, $options);
+      $dbs = array();
+      $dbs[] = '';
+      foreach ($results as $db) {
+        $dbs[$db->db_id] = $db->name;
+      }
+      $form['add_cvterm']['db_id'] = array(
+        '#type'         => 'select',
+        '#title'         => t('Database'),
+        '#description'   => t('All terms must be assocated with an external database.
+                            Please select the external database to associate with
+                            this term'),
+        '#options'      => $dbs,
+        '#default_value' => $db_id,
+        '#required' => TRUE,
+      );
+      if ($action == 'edit') {
+        // we don't want to allow the user to change the database on an edit.
+        $form['add_cvterm']['db_id']['#disabled'] = TRUE;
+        $form['add_cvterm']['db_id']['#description'] = 'The database to which this term belongs cannot be changed.';
+      }
+      
+      $form['add_cvterm']['accession']= array(
+        '#type'          => 'textfield',
+        '#title'         => t("Accession"),
+        '#description'   => t('If this term has an existing accession (unique identifier) in the database 
+           please enter that here.  If the accession is numeric with a database prefix (e.g. GO:003023), please
+           enter just the numeric value.  The database prefix will be appended whenever the term is displayed. 
+           If the accession is not numeric then enter it as is.  If no value is provied, the term name 
+           provided above will be used as the accession.'),
+        '#required'      => FALSE,
+        '#default_value' => $accession,
+      );
+      if ($action == 'edit') {
+        $form['add_cvterm']['accession']['#attributes'] = array('readonly' => 'readonly');
+        $form['add_cvterm']['accession']['#description'] = 'Cannot change the term accession.';
+      }
+      $button_text = 'Add Term';
+      if ($action == 'edit') {
+        $button_text = 'Update Term';
+      }
+      $form['add_cvterm']['submit'] = array(
+        '#type'  => 'submit',
+        '#value' => $button_text,
+      );
+    } // end if name selected (or action == 'add')
+  } //end of if cv selected
+    
+  
+  $form['wrapper-bottom'] = array(
+    '#type' => 'markup',
+    '#value' => '</div>',
+  );
+
+  return $form;
+}
+
+/*
+ * @ingroup tripal_cv
+ */
+function tripal_cv_cvterm_name_autocomplete($cv_id, $string = '') {
+  $sql = "SELECT cvterm_id, name FROM cvterm WHERE cv_id = %d and name like '%s%%' ORDER by name";
+  $results = chado_query($sql, $cv_id, $string);
+  $items = array();
+  while($term = db_fetch_object($results)) {
+     $items[$term->name] = $term->name;
+  }  
+  drupal_json($items);   
+}
+/**
+ * Purpose: Validates the input for adding a cvterm
+ *
+  * @ingroup tripal_cv
+ */
+function tripal_cv_cvterm_form_validate($form, &$form_state) {
+
+  // Ensure that submit does not get called unless the AHAH in the form was called
+  if (!empty($form_state['ahah_submission'])) {
+    return;
+  }
+
+}
+
+/**
+ * Purpose: Adds terms to an existing controlled vocabulary
+ *
+ * @ingroup tripal_cv
+ */
+function tripal_cv_cvterm_form_submit($form, &$form_state) {
+
+  // Ensure the AHAH in the form was called
+  if (!empty($form_state['ahah_submission'])) {
+    return;
+  }
+    
+  // get the database
+  $values = array('db_id' => $form_state['values']['db_id']);
+  $results = tripal_core_chado_select('db', array('name'), $values);
+  if (!$results or count($results) == 0){
+    drupal_set_message(t('Unable to add term.  Cannot find the database.'), 'error');
+    return;
+  }
+  $db = $results[0];
+  
+  // get the cv
+  $values = array('cv_id' => $form_state['values']['cv_id']);
+  $results = tripal_core_chado_select('cv', array('name'), $values);
+  if (!$results or count($results) == 0){
+    drupal_set_message(t('Unable to add term.  Cannot find the vocabulary.'), 'error');
+    return;
+  }
+  $cv = $results[0];
+  
+  // get the accession for this term
+  $accession = $form_state['values']['accession'];
+  if (!$accession) {
+    $accession = $form_state['values']['name'];
+  }  
+  if (is_numeric($accession)) {
+    $accession = $db->name . ":" . $accession;
+  }
+  
+  
+  $update = 0;
+  if ($form_state['values']['form_action'] == 'edit') {
+    $update = 1;
+  }
+  
+  // now add the term
+  $term = array(    
+    'name' => $form_state['values']['name'],
+    'namespace' => $cv->name,
+    'id' => $accession,
+    'def' => $form_state['values']['definition'],
+    'is_obsolete' => $form_state['values']['is_obsolete'],
+  );  
+  
+  $is_relationship = $form_state['values']['is_relationshiptype'];
+  $cvterm = tripal_cv_add_cvterm($term, $cv->name, $is_relationship, $update, $db->name);
+  if ($cvterm) {
+    if (!$update) {
+      drupal_set_message('Term added successfully.');
+    }
+    else {
+      drupal_set_message('Term updated successfully.');
+    }
+  } 
+  else {
+    drupal_set_message('Could not add term. Check Drupal recent logs for error messages.', 'error');  
+  }
+
+}
+
+/**
+ * Purpose: This function gets called when the selecting of a cv from
+ *   the select list triggers it. This function simply rebuilds the form
+ *   with new information. No elements are created here
+ *
+ * @ingroup tripal_cv
+ */
+function tripal_cv_cvterm_callback() {
+  $status = TRUE;
+
+  // prepare and render the form
+  $form = tripal_core_ahah_prepare_form();   
+  $data = drupal_render($form);  
+
+  // bind javascript events to the new objects that will be returned 
+  // so that AHAH enabled elements will work.
+  $settings = tripal_core_ahah_bind_events();
+   
+  // return the updated JSON
+  drupal_json(
+    array(
+      'status'   => $status, 
+      'data'     => $data,
+      'settings' => $settings,
+    )  
+  );
+}
+
+///////////////////////////////
+// Ontology Loader
+//////////////////////////////
+
+/**
+ * Purpose: Provides the form to load an already existing controlled
+ *  Vocabulary into chado
+ *
+  * @ingroup tripal_obo_loader
+ */
+function tripal_cv_obo_form(&$form_state = NULL) {
+
+  // get a list of db from chado for user to choose
+  $sql = "SELECT * FROM {tripal_cv_obo} ORDER BY obo_id";
+  $results = db_query($sql);
+
+  $obos = array();
+  $obos[] = '';
+  while ($obo = db_fetch_object($results)) {
+    $obos[$obo->obo_id] = "$obo->name  | $obo->path";
+  }
+
+  $form['obo_existing'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('Use a Saved Ontology OBO Reference')
+  );
+
+  $form['obo_new'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('Use a New Ontology OBO Reference')
+  );
+
+  $form['obo_existing']['existing_instructions']= array(
+    '#value' => t('The Ontology OBO files listed in the drop down below have been automatically added upon
+                   installation of the Tripal CV module or were added from a previous upload.  Select
+                   an OBO, then click the submit button to load the vocabulary into the database.  If the
+                   vocabularies already exist then the ontology will be updated.'),
+    '#weight'        => -1
+  );
+
+  $form['obo_existing']['obo_id'] = array(
+    '#title' => t('Ontology OBO File Reference'),
+    '#type' => 'select',
+    '#options' => $obos,
+    '#weight'        => 0
+  );
+
+  $form['obo_new']['path_instructions']= array(
+    '#value' => t('Provide the name and path for the OBO file.  If the vocabulary OBO file
+                   is stored local to the server provide a file name. If the vocabulry is stored remotely,
+                   provide a URL.  Only provide a URL or a local file, not both.'),
+    '#weight'        => 0
+  );
+
+  $form['obo_new']['obo_name']= array(
+    '#type'          => 'textfield',
+    '#title'         => t('New Vocabulary Name'),
+    '#description'   => t('Please provide a name for this vocabulary.  After upload, this name will appear in the drop down
+                           list above for use again later.'),
+    '#weight'        => 1
+  );
+
+  $form['obo_new']['obo_url']= array(
+    '#type'          => 'textfield',
+    '#title'         => t('Remote URL'),
+    '#description'   => t('Please enter a URL for the online OBO file.  The file will be downloaded and parsed.
+                           (e.g. http://www.obofoundry.org/ro/ro.obo'),
+    '#default_value' => $default_desc,
+    '#weight'        => 2
+  );
+
+  $form['obo_new']['obo_file']= array(
+    '#type'          => 'textfield',
+    '#title'         => t('Local File'),
+    '#description'   => t('Please enter the full system path for an OBO definition file, or a path within the Drupal
+                           installation (e.g. /sites/default/files/xyz.obo).  The path must be accessible to the
+                           server on which this Drupal instance is running.'),
+    '#default_value' => $default_desc,
+    '#weight'        => 3
+  );
+
+  $form['submit'] = array(
+    '#type'         => 'submit',
+    '#value'        => t('Submit'),
+    '#weight'       => 5,
+    '#executes_submit_callback' => TRUE,
+  );
+
+  $form['#redirect'] = 'admin/tripal/tripal_cv/obo_loader';
+
+  return $form;
+}
+
+/**
+ * Purpose: The submit function for the load ontology form. It registers a
+ *   tripal job to run the obo_loader.php script
+ *
+   * @ingroup tripal_obo_loader
+ */
+function tripal_cv_obo_form_submit($form, &$form_state) {
+  global $user;
+
+  $obo_id =  $form_state['values']['obo_id'];
+  $obo_name =  $form_state['values']['obo_name'];
+  $obo_url =  $form_state['values']['obo_url'];
+  $obo_file  = $form_state['values']['obo_file'];
+
+  $sql = "SELECT * FROM {tripal_cv_obo} WHERE obo_id = %d";
+  $obo = db_fetch_object(db_query($sql, $obo_id));
+
+  if ($obo_id) {
+    $args = array($obo_id);
+    tripal_add_job("Load OBO $obo->name", 'tripal_cv',
+       "tripal_cv_load_obo_v1_2_id", $args, $user->uid);
+  }
+  else {
+    if ($obo_url) {
+      $args = array($obo_name, $obo_url);
+      tripal_add_job("Load OBO $obo_name", 'tripal_cv',
+        "tripal_cv_load_obo_v1_2_url", $args, $user->uid);
+    }
+    elseif ($obo_file) {
+      $args = array($obo_name, $obo_file);
+      tripal_add_job("Load OBO $obo_name", 'tripal_cv',
+        "tripal_cv_load_obo_v1_2_file", $args, $user->uid);
+    }
+  }
+
+}
+
+////////////////////////////////////
+// cvterm path management
+///////////////////////////////////
+
+/**
+ * Form for re-doing the cvterm path
+ *
+ * @ingroup tripal_cv
+ */
+function tripal_cv_cvtermpath_form() {
+
+  // get a list of db from chado for user to choose
+  $sql = "SELECT * FROM {cv} WHERE NOT name = 'tripal' ORDER BY name ";
+  $results = chado_query($sql);
+
+  $cvs = array();
+  $cvs[] = '';
+  while ($cv = db_fetch_object($results)) {
+    $cvs[$cv->cv_id] = $cv->name;
+  }
+
+  $form['cvid'] = array(
+    '#title' => t('Controlled Vocabulary/Ontology Name'),
+    '#type' => 'select',
+    '#options' => $cvs,
+    '#description' => t('The Chado cvtermpath is a database table that provides lineage for ontology terms 
+      and is useful for quickly finding any ancestor parent of a term.  This table must be populated for each
+      ontology.  Select a controlled vocabulary for which you would like to upate the cvtermpath.'),
+  );
+
+  $form['description'] = array(
+    '#type' => 'item',
+    '#value' => t("Submit a job to update chado cvtermpath table."),
+    '#weight' => 1,
+  );
+
+  $form['button'] = array(
+    '#type' => 'submit',
+    '#value' => t('Update cvtermpath'),
+    '#weight' => 2,
+  );
+
+  return $form;
+}
+
+/**
+ * Cvterm path form submit
+ *
+ * @ingroup tripal_cv
+ */
+function tripal_cv_cvtermpath_form_submit($form, &$form_state) {
+  global $user;
+
+  $cvid =  $form_state['values']['cvid'];
+
+  // first get the controlled vocabulary name:
+  $cv = db_fetch_object(chado_query("SELECT * FROM {cv} WHERE cv_id = %d", $cvid));
+
+  // Submit a job to update cvtermpath
+  $job_args = array($cvid);
+  if ($form_state['values']['op'] == t('Update cvtermpath')) {
+    tripal_add_job("Update cvtermpath: $cv->name", 'tripal_cv',
+       'tripal_cv_update_cvtermpath', $job_args, $user->uid);
+  }
+}
+
+/**
+ * Update the cvtermpath table
+ *
+ * @ingroup tripal_cv
+ */
+function tripal_cv_update_cvtermpath($cvid = NULL, $job_id = NULL) {
+
+  // first get the controlled vocabulary name:
+  $cv = db_fetch_object(chado_query("SELECT * FROM {cv} WHERE cv_id = %d", $cvid));
+  print "\nUpdating cvtermpath for $cv->name...\n";
+
+  // now fill the cvtermpath table
+  // @coder-ignore: using a function rather then tablename therefore table prefixing doesn't apply
+  $sql = "SELECT * FROM fill_cvtermpath('%s')";
+  chado_query($sql, $cv->name);
+
+  return;
+}
+
+//////////////////////////////////////
+// @section Miscellaneous
+// @todo check to see if these functions are still needed and/or if they
+//   should be moved to the api file
+//////////////////////////////////////
+
+/**
+ * Get the CV ID based on name
+ *
+ * @ingroup tripal_cv
+ */
+function tripal_cv_get_cv_id($cv_name) {
+
+  $sql = "
+    SELECT cv_id FROM {cv} WHERE name = '%s'
+  ";
+  $cv = db_fetch_object(chado_query($sql, $cv_name));
+
+  return $cv->cv_id;
+}
+
+/**
+ * Returns a themed cvterm definition table
+ *
+ * @ingroup tripal_cv
+ */
+function tripal_cv_cvterm_edit($cvterm_id) {
+
+  $sql = "
+    SELECT CVT.name as cvtermname, CVT.definition, CV.name as cvname
+    FROM {CVTerm} CVT
+      INNER JOIN CV on CVT.cv_id = CV.cv_id
+    WHERE CVT.cvterm_id = %d
+  ";
+  $cvterm = db_fetch_object(chado_query($sql, $cvterm_id));
+
+  return theme('tripal_cv_cvterm_edit', $cvterm);
+}
+
+/**
+ * Does the actual themeing of the cvterm definition table
+ *
+ * @ingroup tripal_cv
+ */
+function theme_tripal_cv_cvterm_edit(&$cvterm) {
+
+  $output = "
+    <div id=\"cvterm\">
+    <table>
+      <tr><th>Term</th><td>$cvterm->cvtermname</td></tr>
+      <tr><th>Vocabulary</th><td>$cvterm->cvname</td></tr>
+      <tr><th>Definition</th><td>$cvterm->definition</td></tr>
+    </table>
+    </div>
+  ";
+
+  return $output;
+}