Fixed a merging conflict

tripal_pub/e_utilities.pl

@@ -1,61 +0,0 @@
-#!/usr/bin/perl -w
-# ---------------------------------------------------------------------------
-# Define library for the 'get' function used in the next section.
-# $utils contains route for the utilities.
-# $db, $query, and $report may be supplied by the user when prompted; 
-# if not answered, default values, will be assigned as shown below.
-
-use LWP::Simple;
-use utf8;
-
-my $utils = "http://www.ncbi.nlm.nih.gov/entrez/eutils";
-
-my $db     = "Pubmed";
-my $query  = $ARGV[0];
-my $report = $ARGV[1];
-
-# ---------------------------------------------------------------------------
-# $esearch contÁins the PATH & parameters for the ESearch call
-# $esearch_result containts the result of the ESearch call
-# the results are displayed Ánd parsed into variables 
-# $Count, $QueryKey, and $WebEnv for later use and then displayed.
-
-my $esearch = "$utils/esearch.fcgi?" .
-              "db=$db&retmax=1&usehistory=y&term=";
-
-my $esearch_result = get($esearch . $query);
-
-
-
-$esearch_result =~ 
-  m|<Count>(\d+)</Count>.*<QueryKey>(\d+)</QueryKey>.*<WebEnv>(\S+)</WebEnv>|s;
-
-my $Count    = $1;
-my $QueryKey = $2;
-my $WebEnv   = $3;
-
-# ---------------------------------------------------------------------------
-# this area defines a loop which will display $retmax citation results from 
-# Efetch each time the the Enter Key is pressed, after a prompt.
-
-my $retstart;
-my $retmax=3;
-
-for($retstart = 0; $retstart < $Count; $retstart += $retmax) {
-  my $efetch = "$utils/efetch.fcgi?" .
-               "rettype=$report&retmode=text&retstart=$retstart&retmax=$retmax&" .
-               "db=$db&query_key=$QueryKey&WebEnv=$WebEnv";
-	
-  #print "\nEF_QUERY=$efetch\n";     
-
-
-  my $efetch_result = get($efetch);
-
-	#open( $fh, '>', \$efetch_result);
-
-  
-  print $efetch_result;
-    
-  #print binmode($fh, ":utf8");
-  
-}

tripal_pub/publication.obo

@@ -1,2687 +0,0 @@
-format-version: 1.2
-idspace: BIRN_ImagePhenotype http://ccdb.ucsd.edu/SAO/DPO/1.0/ImagePhenotype.owl ""
-idspace: BIRN_PDPO http://ccdb.ucsd.edu/PDPhenotypeOntology/1.0# ""
-idspace: BIRN_PDStage http://ccdb.ucsd.edu/PDStageOntology/1.0/ ""
-idspace: BIRN_SA http://ccdb.ucsd.edu/smart_atlas_ontology/sa.owl# ""
-idspace: NDPO http://ccdb.ucsd.edu/SAO/Disease/1.0/NDPO.owl# ""
-idspace: PKB http://ccdb.ucsd.edu/PKB/1.0/PKB.owl# ""
-idspace: SAO_HumanDPO http://ccdb.ucsd.edu/SAO/HumanDPO.owl# ""
-idspace: bfo http://www.ifomis.org/bfo/1.1# ""
-idspace: bfo1_0 http://www.ifomis.org/bfo/1.0# ""
-idspace: biopax1 http://www.biopax.org/release/biopax-level1.owl# ""
-idspace: birnlex_anatomy http://purl.org/nbirn/birnlex/ontology/BIRNLex-Anatomy.owl# ""
-idspace: birnlex_disease http://purl.org/nbirn/birnlex/ontology/BIRNLex-Disease.owl# ""
-idspace: birnlex_tax http://purl.org/nbirn/birnlex/ontology/BIRNLex-OrganismalTaxonomy.owl# ""
-idspace: c http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/cluster# ""
-idspace: daml http://www.daml.org/2001/03/daml+oil# ""
-idspace: dc http://purl.org/dc/elements/1.1/ ""
-idspace: dcterms http://purl.org/dc/terms/ ""
-idspace: eor http://dublincore.org/2000/03/13/eor# ""
-idspace: galen http://www.co-ode.org/ontologies/galen# ""
-idspace: mged http://mged.sourceforge.net/ontologies/MGEDOntology.owl# ""
-idspace: oban http://www.berkeleybop.org/ontologies/oban/alpha# ""
-idspace: obd http://www.bioontology.org/obd/obd-ontology# ""
-idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# ""
-idspace: owl http://www.w3.org/2002/07/owl# ""
-idspace: p http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/party# ""
-idspace: propreo http://lsdis.cs.uga.edu/projects/glycomics/propreo# ""
-idspace: r http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/region# ""
-idspace: rdf http://www.w3.org/1999/02/22-rdf-syntax-ns# ""
-idspace: rdfs http://www.w3.org/2000/01/rdf-schema# ""
-idspace: reactome http://www.reactome.org/biopax# ""
-idspace: sao http://ccdb.ucsd.edu/SAO/1.2# ""
-idspace: serql http://www.openrdf.org/schema/serql# ""
-idspace: skos http://www.w3.org/2004/02/skos/core# ""
-idspace: snap http://www.ifomis.org/bfo/1.1/snap# ""
-idspace: snap1_0 http://www.ifomis.org/bfo/1.0/snap# ""
-idspace: span http://www.ifomis.org/bfo/1.1/span# ""
-idspace: span1_0 http://www.ifomis.org/bfo/1.0/span# ""
-idspace: xsd http://www.w3.org/2001/XMLSchema# ""
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-[Term]
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-[Term]
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-[Term]
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-
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-
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-[Term]
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tripal_pub/tripal_pub.info

@@ -1,9 +0,0 @@
-name = Tripal Publication
-description = A module for interfacing the GMOD chado database with Drupal, providing viewing of publications
-core = 6.x
-project = tripal_pub
-package = Tripal
-version = 6.x-1.0
-dependencies[] = tripal_core
-dependencies[] = tripal_cv
-dependencies[] = tripal_db

tripal_pub/tripal_pub.install

@@ -1,91 +0,0 @@
-<?php
-
-/**
- * @file
- * This file contains all the functions which describe and implement drupal database tables
- * needed by this module. This module was developed by Chad N.A. Krilow and Lacey-Anne Sanderson,
- * University of Saskatchewan.
- *
- * The project manamgenet module allows you to sync data in a chado/Tripal instance with
- * multiple project/mysql instances as well as manage and create such project instances
- */
-
-
-/**
- * Implementation of hook_install().
- */
-function tripal_pub_install() {
-
-  drupal_install_schema('tripal_pub');
-  $dbxref = array('accession' => 'abstract', 'db_id' => array('name' => 'tripal'));
-  $success = tripal_core_chado_insert('dbxref', $dbxref);
-  if ($success) {
-    tripal_core_chado_insert('cvterm', array('name' => 'abstract', 'cv_id' => array('name' => 'tripal'), 'dbxref_id' => $dbxref));
-  }
-}
-
-
-/**
- * Implementation of hook_uninstall().
- */
-function tripal_pub_uninstall() {
-  //Remove tables
-  drupal_uninstall_schema('tripal_pub');
-
-}
-
-
-/**
- * Implementation of hook_schema().
- */
-function tripal_pub_schema() {
-//specification for 'tripal_pub_instances'
-  $schema['chado_pub'] = array(
-
-    'fields' => array(
-
-      //a int field that cannot be null and acts as a unique identifier for all nid's
-      'nid' => array(
-        'type' => 'int',
-        'unsigned' => TRUE,
-        'not null' => TRUE,
-        ),
-
-      //a int field that cannot be null and is vid
-      'vid' => array(
-          'type' => 'int',
-          'not null' => TRUE,
-      ),
-
-      //a intfield, not null and project_id is the unique_id of the project in chado
-       'pub_id' => array(
-          'type' => 'int',
-          'unsigned' => TRUE,
-          'not null' => TRUE,
-      ),
-
-       //a intfield, not null and project_id is the unique_id of the project in chado
-       'pubmed_id' => array(
-          'type' => 'int',
-          'unsigned' => TRUE,
-          'not null' => FALSE,
-      ),
-      'author' => array(
-        'type' => 'text',
-        'size' => 'normal',
-        'not null' => TRUE,
-        'default' => '',
-        'description' => 'The Author Name.',
-      ),
-      ),
-     //end of shema
-
-    'primary key' => array('nid'),
-
-  );
-
-  return $schema;
-}
-
-
-

tripal_pub/tripal_pub.module

@@ -1,1729 +0,0 @@
-<?php
-
-//require_once('cron.php');
-
-
-/**
- * @file
- * This file contains all the functions which provide functionality to this module.
- * This module was developed by Chad N.A. Krilow and Lacey-Anne Sanderson,
- * The University of Saskatchewan.
- *
- *
- * The Tripal Publication module allows you to search the PubMed databse for academic articles,
- * that relate to user specified tpoic\s. As well, it allows management of publications so that
- * a user can enter specified details regarding a desired publication. This allows all of the important
- * information that is unique to a Academic Publication to be stored for access.
- */
-
-
-//-----------------------------------------------------------------------------
-//  SECTION: Main Outline Menu for Tripal Publication
-//-----------------------------------------------------------------------------
-
-
-/**
- * Tripal-Publication-Menu
- *
- * Implemets hook_menu(): Adds menu items for the tripal_pub module menu. This section
- * gives the outline for the main menu of the Tripal-Publication module
- *
- * @return
- *   An array of menu items that is visible within the Drupal Menu, returned as soon
- *   as the program is ran
- */
-function tripal_pub_menu() {
-
-  $items = array();
-
-  $items[ 'admin/tripal/tripal_pub' ]= array(
-    'title' => 'Publications',
-    'description' => ('A module for interfacing the GMOD chado database with Drupal,
-    providing viewing of publications'),
-    'page callback' => 'administration_description_page',
-    'access arguments' => array('administer site configuration'),
-    'type' => MENU_NORMAL_ITEM
-  );
-
-  $items['admin/tripal/tripal_pub/configuration'] = array(
-    'title' => 'Configuration',
-    'description' => 'Configuration for this module',
-    'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_pub_configuration_form'),
-    'access arguments' => array('administer site configuration'),
-    'type' => MENU_NORMAL_ITEM
-    );
-
-  // Automatically generate checkboxes.
-  $items['node/add/tripal_pub/ahah_authors'] = array(
-    'title' => 'Add Additional Authors',
-    'page callback' => 'drupal_get_form',
-    'page arguments' => array('author_addition_fields_ahah_callback'),
-    'access callback' => TRUE,
-    'type' => MENU_CALLBACK,
-    'weight' => 2,
-  );
-
-  $items['tripal_pub/js/%'] = array(
-    'page callback' => 'tripal_pub_js',
-    'page arguments' => array(2),
-    'access arguments' => array('access content'),
-    'type ' => MENU_CALLBACK,
-  );
-
-  return $items;
-}
-
-
-/**
- * Implements hook_theme(): Register themeing functions for this module
- *
- *
- * @return
- *   An array of themeing functions to register
- *
- */
-function tripal_pub_theme() {
-
-  return array(
-    'tripal_pub_author_table' => array(
-      'arguments' => array('form' => NULL),
-    ),
-    'publication_author' => array(
-      'arguments' => array('element' => NULL)
-    ),
-  );
-}
-
-/**
- * Implement hook_perm().
- */
-function tripal_pub_perm() {
-
-  return array('edit own tripal_pub', 'edit tripal_pub', 'create tripal_pub');
-
-}
-
-
-/**
- * This section uses HTML to output the descriptions of the module, through the Tripal Management
- * Administation window.Any installation instructions are given as well as included features
- * as well as a overview of the purpose Module.
- *
- * @return
- *   Returns '$text'The HTML description of the Module, its instructions, features, and any other
- *   important aspects. This is returned when the Administration page is selected.
- */
-function administration_description_page() {
-
-  $text = '';
-
-  $text = '<br /><h3>Tripal Publication Administrative Tools Quick Links</h3>';
-  $text .= '<ul>';
-  $text .= '<li>' . l('Configuration', 'admin/tripal/tripal_pub/configuration') . '</li>';
-  $text .= '<li>' . l('Create A Publication', 'node/add/publication') . '</li>';
-
-  $text .= '</ul>';
-
-  $text .= '<h3>Module Description:</h3>';
-  //================================================================================
-$text .= '<p>The Tripal Publication Module provides the functionality for adding, editing, deleting and
-accessing academic publications, entered by the user.This module also allows a time limited search,
-specified by the user, which searches the PubMed extracts and saves acedemic puplications.
-
-
- </p>';
-
-  $text .= '<h3>Setup Instructions:</h3>';
-  //================================================================================
-  $text .= '<ol>';
-      $text .= '<ol type="i">';
-      $text .= '</ol>';
-
-  $text .= '<li><p><b>Set Permissions</b>: The publication module supports the Drupal user permissions interface for
-               controlling access to publlication content and functions. These permissions include viewing,
-               creating, editing or administering of
-               publication 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 publication content to
-               those roles.  For a simple setup, allow anonymous users access to view publication content and
-               allow the site administrator all other permissions.</p></li>';
-  $text .= '<li><p><b>Set Publication Type Controlled Vocabulary</b>: The select list for setting the publication '
-                . 'type is controlled be a controlled vocabulary (cv). '
-                . '<ul><li>Before you can add any publications you need '
-                . 'to create/load this cv. There is a limited cv included in this module. To use it, you need to '
-                . 'load it using the <a href="' . url('admin/tripal/tripal_cv/obo_loader') . '">OBO Loader included with Tripal</a>.</li>'
-                . '<li>After the controlled vocabulary is loaded you need to set it to be used for the publication '
-                . 'module. To do this, go to <a href="' . url('admin/tripal/tripal_pub/configuration') . '">Publication->Configuration</a>, select it in the controlled vocabulary '
-                . 'select list and click save configuration.</p></li></ul>';
-
-  $text .= '</ol>';
-  $text .= '<h3>Features of this Module:</h3>';
-  //================================================================================
-  $text .= '<ul>';
-
-
-
-
-  $text .= '<li><p><b>Configuration (Search For Academic Publications):</b>  The search capability implemented in
-  this module allows a user to search, by remote connection , the PubMEd database for articles
-  that relate to key search words, chosen by the user.The "search keys" are used to search through
-  Publication titles and when one of the key words is matched in a title, the recognized article will
-  be saved to the database.
-
-
-      <ul>
-
-      <li><b>Choose a Controlled Vocabulary:</b>The controlled vocabulary list is a set of terms
-
-      <li><b>Set Search Key Words:</b>The search keywords, are the user entered key terms, in which
-      the publications in the PubMed database can be recognized by. The user may enter any number
-      of search terms, as by adding more search terms, the search will limit the results to those
-      in which all of the search terms appear in the publication title.
-
-      <li><b>Set a time search interval:</b>The search term interval represents a pre-set ammount
-      of time for the search. The time search interval must be entered in minutes. This allows
-      the module to automatically search the PubMed database in a predetermined time interval.
-    </ul>
-
-
-
-
-
-
-  </p></li>';
-
-  $text .= '<li><b>Creating a Publication:</b>';
-
-  $text .= '<p>To <b>Create,update/delete a given property of a publication</b>:When Creating a Publication
-  it is neccessary to enter the requried fields in the form. These are marked with an astrix and
-  if they are not entered upon completion a warning will be issued and the user is forced to fill
-  in these entries. The author field, requires a given/surname/suffix to be entered. To add the
-  author to the publication, the add author button is to be pushed. The user is able to add as
-  many authors to the publication as needed.
-  </p>';
-
-
-
-
-
-  return $text;
-
-}
-
-
-//-----------------------------------------------------------------------------
-//  SECTION: Node Capability
-//-----------------------------------------------------------------------------
-
-
-/**
- * Implement hook_access().
- *
- * This hook allows node modules to limit access to the node types they define.
- *
- *  @param $op
- *  The operation to be performed
- *
- *  @param $node
- *  The node on which the operation is to be performed, or, if it does not yet exist, the
- *  type of node to be created
- *
- *  @param $account
- *  A user object representing the user for whom the operation is to be performed
- *
- *  @return
- *  TRUE
- *
- */
-function chado_pub_access($op, $node, $account ) {
-
-  global $user;
-
-  if (empty($account)) {
-    $account = $user;
-  }
-
-  if ($op != 'create') {
-    $node = (object)$node;
-  }
-
-  if ($op == 'create') {
-
-    if (user_access('create tripal_pub')) {
-
-        return TRUE;
-
-    }
-
-  }
-  elseif ($op == 'update' || $op == 'delete') {
-
-    if (user_access('edit tripal_pub')) {
-
-        return TRUE;
-    }
-    elseif (user_access('edit own tripal_pub') && $account->uid == $node->uid) {
-
-      return TRUE;
-    }
-
-  }
-
-/////////////////The following is taken from the tripal_pub module insert later////////////////////
-  /*
-  if ($op == 'create') {
-    // Only users with permission to do so may create this node type.
-<<<<<<< .mine
-    return user_access('create tripal_pub', $account);
-=======
-    if(!user_access('create tripal_pub', $account)){
-      return FALSE;
-    }
->>>>>>> .r25216
-  }
-
-  // Users who create a node may edit or delete it later, assuming they have the
-  // necessary permissions.
-  if ($op == 'update' || $op == 'delete') {
-    if (user_access('edit own tripal_pub',$account) && ($account->uid == $node->uid)) {
-      return TRUE;
-    }
-  }*/
-///////////////////////////////////////////////////////////////////////////////////////////////////
-
-}
-
-/**
- * Implementation of hook_tripal_pub_node_info().
- *
- * This node_info, is a simple node that describes the functionallity of the module.
- *
- */
-function tripal_pub_node_info() {
-
-  return array(
-    'chado_pub' => array(
-      'name' => t('Publication'),
-      'module' => 'chado_pub',
-      'description' => t('A module for interfacing the GMOD chado database with Drupal, providing viewing of publications'),
-      'title_label' => t('Article Title'),
-      'body_label' => t('Abstract'),
-      'has_title' => TRUE,
-      'has_body' => FALSE,
-    ),
-  );
-}
-
-
-/**
- * Implementation of tripal_pub_form().
- *
- *
- *
- *  @parm &$node
- *    The node that is created when the database is initialized
- *
- *  @parm $form_state
- *    The state of the form, that has the user entered information that is neccessary for, setting
- *    up the database tables for the publication
- *
- *  @return $form
- *    The information that was enterd allong with
- *
- */
-function chado_pub_form(&$node, $form_state) {
-
-  $type = node_get_types('type', $node);
-
-  // Article Title.
-  $form['title'] = array(
-    '#type' => 'textfield',
-    '#title' => check_plain($type->title_label),
-    '#default_value' => $node->title,
-    '#required' => TRUE,
-    '#weight' => 0,
-  );
-
-  // Abstract
-  $form['abstract'] = array(
-    '#title' => 'Abstract',
-    '#type' => 'textarea',
-    '#default_value' => isset($node->abstract) ? $node->abstract : ''
-  );
-
-  $form['pub_id'] = array(
-    '#type' => 'hidden',
-    '#value' => (isset($node->pub_id)) ? $node->pub_id->pub_id : NULL ,
-  );
-
-  $form['uniquename'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Unique Name'),
-    '#required' => TRUE,
-    '#description' => 'A unique name/identifier for this publication. If this article exists in pubmed, entering the pubmed ID here will ensure duplicate publication pages are not created.',
-    '#default_value' => isset($node->pub_id->uniquename) ? $node->pub_id->uniquename : ''
-  );
-
-  $values= array(
-    'cv_id' => variable_get('tripal_pub_types_cv', NULL),
-  );
-
-  //population select list with 'cvterm' names
-  $result = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), $values);
-
-  foreach ($result as $value) {
-    $newArray[$value->cvterm_id]=$value->name;     //options for the select list
-  }
-
-  $form['type_id'] = array(
-    '#type' => 'select',
-    '#title' => t('Publication Type'),
-    '#options' => $newArray,
-    '#required' => TRUE,
-    '#default_value' => isset($node->pub_id->type_id) ? $node->pub_id->type_id : ''
-  );
-
-  $form['author_wrapper'] = array(
-    '#tree' => FALSE,
-    '#prefix' => '<div class="clear-block" id="author-wrapper">',
-    '#suffix' => '</div>',
-  );
-
-  // Get number of authors
-  $author_count = empty($node->authors) ? 0 : count($node->authors);
-
-  // If a new author added, add to list and update the author count.
-  if (isset($form_state['new_author'])) {
-
-    if (!isset($node->authors)) {
-      $node->authors = array();
-    }
-
-    $node->authors = array_merge($node->authors, array($form_state['new_author']));
-    $author_count++;
-
-  }
-
-  // If a author removed, remove from list and update the author count.
-  $remove_delta = -1;
-
-  if (!empty($form_state['remove_delta'])) {
-
-      $remove_delta = $form_state['remove_delta'] - 1;
-
-      unset($node->authors[$remove_delta]);
-
-      // Re-number the values.
-      $node->authors = array_values($node->authors);
-
-      $author_count--;
-
-  }
-
-  // Container to display existing authors.
-  $form['author_wrapper']['authors'] = array(
-    '#prefix' => '<div id="publication-authors">',
-    '#suffix' => '</div>',
-    '#theme' => 'tripal_pub_author_table',
-  );
-
-  if (!isset($node->authors)) {
-
-    if (isset($node->new_author['new_author_name'])) {
-
-      $node->authors = array();
-
-      $node->authors[]['author_name'] = $node->new_author['new_author_name'];
-
-    }
-
-  }
-
-  //Add the existing authors to the form.
-  for ($delta = 0; $delta < $author_count; $delta++) {
-
-      $author = isset($node->authors[$delta]['author_name']) ? $node->authors[$delta] : array();
-
-      $form['author_wrapper']['authors'][$delta] = tripal_pub_author_display_form($delta, $author);
-
-  }
-
-  /////////////////////Edit authors//////////////////////////////////////////////////////////////////
-
-  if (isset($form_state['values']['edit_author'])) {
-
-      // Add new authors
-      $form['author_wrapper']['edit_author'] = array(
-        '#type' => 'fieldset',
-        '#title' => t('Current Publication Authors'),
-        '#tree' => FALSE,
-      );
-
-      // Define the form fields for the new author
-      $form['author_wrapper']['edit_author']['edit_author'] = array(
-        '#tree' => TRUE,
-        //'#default_value'=> '',
-        //'#theme' => 'author_add_author_form',
-      );
-
-      $form['author_wrapper']['edit_author']['edit_author']['delta'] = array(
-        '#type' => 'hidden',
-        '#value' => $form_state['values']['edit_author']['delta']
-      );
-
-      $form['author_wrapper']['edit_author']['edit_author']['edit_author_name'] = array(
-        '#type' => 'publication_author',
-        '#title' => t('Contributing Authors'),
-        '#default_value' => array(
-            'givennames' => $form_state['values']['edit_author']['author_name']['givennames'],
-            'surname' => $form_state['values']['edit_author']['author_name']['surname'],
-            'suffix' => $form_state['values']['edit_author']['author_name']['suffix'],
-          ),
-        '#weight' => 1,
-      );
-
-      // We name our button 'author_more' to avoid conflicts with other modules using
-      // AHAH-enabled buttons with the id 'more'.
-      $form['author_wrapper']['edit_author']['author_save'] = array(
-        '#type' => 'submit',
-        '#value' => t('Save Author'),
-        '#weight' => 0,
-        '#submit' => array('tripal_pub_edit_author_submit'),
-        '#ahah' => array(
-          'path' => 'tripal_pub/js/0',
-          'wrapper' => 'author-wrapper',
-          'method' => 'replace',
-          'effect' => 'fade',
-        ),
-      );
-
-  ////////////////////////////////////////////////////////////////////////////////////
-
-  }
-  else{
-
-      // Add new authors
-      $form['author_wrapper']['add_author'] = array(
-        '#type' => 'fieldset',
-        '#title' => t('Publication Authors'),
-        '#tree' => FALSE,
-      );
-
-      // Define the form fields for the new author
-      $form['author_wrapper']['add_author']['new_author'] = array(
-        '#tree' => TRUE,
-        //'#default_value'=> '',
-        '#theme' => 'author_add_author_form',
-      );
-
-      $form['author_wrapper']['add_author']['new_author']['new_author_name'] = array(
-        '#type' => 'publication_author',
-        '#title' => t('Contributing Authors'),
-        '#default_value' => '',
-        '#weight' => 1,
-      );
-
-      // We name our button 'author_more' to avoid conflicts with other modules using
-      // AHAH-enabled buttons with the id 'more'.
-      $form['author_wrapper']['add_author']['author_more'] = array(
-        '#type' => 'submit',
-        '#value' => t('Add Author'),
-        '#weight' => 0,
-        '#submit' => array('tripal_pub_add_author_submit'),
-        '#ahah' => array(
-          'path' => 'tripal_pub/js/0',
-          'wrapper' => 'author-wrapper',
-          'method' => 'replace',
-          'effect' => 'fade',
-        ),
-      );
-
-  }
-
-  ////////////////////////////////////////////////////////////////////////////////////////////////////
-
-
-  $form['volumetitle'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Volume Title'),
-    '#description' => t('Title of part if one of a series.'),
-    '#default_value' => isset($node->pub_id->volumetitle) ? $node->pub_id->volumetitle : ''
-  );
-
-  $form['volume'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Volume'),
-    '#default_value' => isset($node->pub_id->volume) ? $node->pub_id->volume : ''
-  );
-
-  $form['series_name'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Series Name'),
-    '#default_value' => isset($node->pub_id->series_name) ? $node->pub_id->series_name : ''
-  );
-
-  $form['issue'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Issue'),
-    '#default_value' => isset($node->pub_id->issue) ? $node->pub_id->issue : ''
-  );
-
-  $form['pyear'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Publication Year'),
-    '#default_value' => isset($node->pub_id->pyear) ? $node->pub_id->pyear : ''
-  );
-
-  $form['pages'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Pages'),
-    '#description' => t('Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.'),
-    '#default_value' => isset($node->pub_id->pages) ? $node->pub_id->pages : ''
-  );
-
-  $form['miniref'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Mini-Ref'),
-    '#required' => FALSE,
-    '#default_value' => isset($node->pub_id->miniref) ? $node->pub_id->miniref : ''
-  );
-
-  $form['is_obsolete'] = array(
-    '#type' => 'checkbox',
-    '#title' => t('Is Obsolete?(Check for Yes)'),
-    '#required' => TRUE,
-    '#default_value' => isset($node->pub_id->is_obsolete) ? $node->pub_id->is_obsolete : FALSE
-  );
-
-  $form['publisher'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Publisher Name'),
-    '#required' => FALSE,
-    '#default_value' => isset($node->pub_id->publisher) ? $node->pub_id->publisher : ''
-  );
-
-  $form['pubplace'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Place of Publication'),
-    '#required' => FALSE,
-    '#default_value' => isset($node->pub_id->pubplace) ? $node->pub_id->pubplace  : ''
-  );
-
-  return $form;
-
-}
-
-
-/**
- * Implementation of tripal_pub_insert().
- *
- * This function inserts user entered information pertaining to the Publication instance into the
- * 'pubauthor', 'pubprop', 'chado_pub', 'pub' talble of the database.
- *
- *  @parm $node
- *    Then node which contains the information stored within the node-ID
- *
- *
- */
-function chado_pub_insert($node) {
-
-  $values =  array(
-    'title' => $node->title,
-    'volumetitle' => $node->volumetitle,
-    'volume' => $node->volume,
-    'series_name' => $node->series_name,
-    'issue' => $node->issue,
-    'pyear' => $node->pyear,
-    'pages' => $node->pages,
-    'miniref' => $node->miniref,
-    'type_id' => $node->type_id,
-    'is_obsolete' => $node->is_obsolete,
-    'publisher' => $node->publisher,
-    'pubplace' => $node->pubplace,
-    'uniquename' => $node->uniquename,
-    'type_id' => $node->type_id
-  );
-
-  //inserts info into chado table
-  $result = tripal_core_chado_insert('pub', $values);
-
-
-  if (isset($result)) {
-
-          //inserts the row of vid,nid,project_id into the chado_pub table
-          db_query("INSERT INTO {chado_pub} (nid, vid, pub_id) VALUES (%d, %d, %d)",
-            $node->nid,
-            $node->vid,
-            $result['pub_id']
-          );
-
-          //Aquiring information for the abstract
-          $abstract_info = tripal_core_chado_select('cvterm', array('cvterm_id'),
-            array('name' => 'abstract', 'cv_id' => array('name' => 'tripal')
-            )
-          );
-
-          //Extracting the type_id
-          $type_id = $abstract_info[0]->cvterm_id;
-
-          //setting the abstract values
-          $abstract = array(
-            'pub_id' => $result['pub_id'],
-            'type_id' => $type_id,
-            'value' => $node->abstract,
-            'rank' => 1
-          );
-
-          //inserts info into chado pubpro table for abstract
-          tripal_core_chado_insert('pubprop', $abstract);
-
-          //counter for loop
-          for ($i=0; $i<=sizeof($node->authors); $i++) {
-
-              if (isset($node->authors[$i]['author_name'] )) {
-
-                $authors = array(
-                  'pub_id' => $result['pub_id'],
-                  'rank' => $i,
-                  'surname' => $node->authors[$i]['author_name']['surname'],
-                  'givennames' => $node->authors[$i]['author_name']['givennames'],
-                  'suffix' => $node->authors[$i]['author_name']['suffix'],
-                );
-
-                  //inserts info into chado pubpro table for abstract
-                  tripal_core_chado_insert('pubauthor', $authors);
-              }
-
-          }
-
-
-          if (!empty($node->new_author['new_author_name']['surname'])) {
-
-              $authors = array(
-                  'pub_id' => $result['pub_id'],
-                  'rank' => $i+1,
-                  'surname' => $node->new_author['new_author_name']['surname'],
-                  'givennames' => $node->new_author['new_author_name']['givennames'],
-                  'suffix' => $node->new_author['new_author_name']['suffix'],
-                );
-
-                  //inserts info into chado pubpro table for abstract
-                  tripal_core_chado_insert('pubauthor', $authors);
-
-          }
-
-
-      }
-      else{
-
-        druapl_set_message('Pub_id was not set, No information has been set.');
-
-    }
-
-}
-
-
-/**
- * Implementation of tripal_pub_delete().
- *
- * This function takes a node and if the delete button has been chosen by the user, the publication
- * and it's details will be removed.Following,given the node-ID, the instance will be deleted from
- * the 'chado_pub' table.
- *
- *  @parm $node
- *    Then node which contains the information stored within the node-ID
- *
- */
-function chado_pub_delete(&$node) {
-
-  // Matching all revision, by using the node's pub_id.
-  $values =  array(
-    'pub_id' => $node->pub_id->pub_id,
-  );
-
-  //deleting row in chado table
-  tripal_core_chado_delete('pub', $values);
-
-  //deleteing in drupal chado_project table
-  db_query('DELETE FROM {chado_pub} WHERE nid = %d', $node->nid);
-
-}
-
-
-/*
- *
- * Implements hook_update
- *
- * The purpose of the function is to allow the module to take action when an edited node is being
- * updated. It updates any name changes to the database tables that werec reated upon registering a Publication.
- * As well, the database will be changed, so the user changed information will be saved to the database.
- *
- * @param $node
- *   The node being updated
- *
- */
-function chado_pub_update($node) {
-
-
-  $values =  array(
-      'title' => $node->title,
-      'volumetitle' => $node->volumetitle,
-      'volume' => $node->volume,
-      'series_name' => $node->series_name,
-      'issue' => $node->issue,
-      'pyear' => $node->pyear,
-      'pages' => $node->pages,
-      'miniref' => $node->miniref,
-      'uniquename' => $node->uniquename,
-      'type_id' => $node->type_id,
-      'is_obsolete' => $node->is_obsolete,
-      'publisher' => $node->publisher,
-      'pubplace' => $node->pubplace,
-      'type_id' => $node->type_id
-    );
-
-  $result = db_fetch_object(db_query('SELECT pub_id FROM {chado_pub} WHERE nid=%d AND vid=%d ', $node->nid, $node->vid));
-
-  //extract pub_id from the chado table for update function
-  $match = array( 'pub_id' => $result->pub_id );
-
-  //$table to be updated, $match is the 'pub_id', $value are the values that are to be updated
-  $update_result = tripal_core_chado_update('pub', $match, $values);
-
-   //Aquiring information for the abstract
-  $abstract_info = tripal_core_chado_select('cvterm', array('cvterm_id'),
-    array('name' => 'abstract', 'cv_id' => array('name' => 'tripal')
-    )
-  );
-
-  //Grabbing the type id of the old abstract
-  $type_id = $abstract_info[0]->cvterm_id;
-
-  //Aquiring information for the abstract
-  $abstract = array(
-    'pub_id' => $result->pub_id,
-    'type_id' => $type_id,
-    'value' => $node->abstract,
-    'rank' => 1
-  );
-
-  //$table to be updated, $match is the 'pub_id', $value are the values that are to be updated
-  tripal_core_chado_update('pubprop', array('pub_id' => $result->pub_id, 'type_id' => $type_id, 'rank' => 1), $abstract);
-
-  //counter for loop
-  for ($i=0; $i<=sizeof($node->authors); $i++) {
-
-      if (isset($node->authors[$i]['author_name'] )) {
-
-          //if new insert
-          if (isset($node->authors[$i]['is_new'])) {
-
-              $authors = array(
-                  'pub_id' => $match['pub_id'],
-                  'rank' => $i+1,
-                  'surname' => $node->authors[$i]['author_name']['surname'],
-                  'givennames' => $node->authors[$i]['author_name']['givennames'],
-                  'suffix' => $node->authors[$i]['author_name']['suffix'],
-              );
-
-              //inserts info into chado pubpro table for abstract
-              tripal_core_chado_insert('pubauthor', $authors);
-
-          }
-          else{
-
-            //update
-            //$table=pubauthor to be updated, $match=author_match is the 'pub_id', $value=author are the values that are to be updated
-            tripal_core_chado_update('pubauthor', array('pub_id' => $match['pub_id'], 'rank' => $node->authors[$i]['author_name']['rank']), $node->authors[$i]['author_name']);
-
-          }
-
-      }
-
-  }
-
-
-}
-
-
-/**
- * Implementation of tripal_pub_load().
- *
- *
- * @param $node
- *   The node that is to be accessed from the database
- *
- * @return $node
- *   The node with the information to be loaded into the database
- *
- */
-function chado_pub_load($node) {
-
-  $result = db_fetch_object(db_query('SELECT * FROM {chado_pub} WHERE nid=%d AND vid=%d ', $node->nid, $node->vid));
-
-  $values = array(
-    'pub_id' => $result->pub_id,
-  );
-
-
-  if (empty($result->pub_id)) {
-
-    drupal_set_message(t("Unable to find publication"), 'error');
-
-  }
-  else{
-
-    $node->pub = tripal_core_generate_chado_var('pub', $values);
-
-    // add in authors
-    $authors = tripal_core_chado_select(
-      'pubauthor',
-      array('rank', 'surname', 'givennames', 'suffix'),
-      array('pub_id' => $node->pub->pub_id)
-    );
-    foreach ($authors as $author) {
-        $node->pub->authors[$author->rank] = $author;
-    }
-    ksort($node->pub->authors);
-
-  }
-
-  return $node;
-
-}
-
-
-//-----------------------------------------------------------------------------
-//  SECTION: Drupal AHAH Implementation & Edit Publication Section
-//-----------------------------------------------------------------------------
-
-
-/**
- * Submit handler for 'Add Author' button on node form.
- */
-function tripal_pub_add_author_submit($form, &$form_state) {
-
-    $form_state['remove_delta'] = 0;
-
-    // Set the form to rebuild and run submit handlers.
-    node_form_submit_build_node($form, $form_state);
-
-    // Make the changes we want to the form state.
-    if ($form_state['values']['author_more']) {
-
-      $new_author = array();
-
-      $new_author['author_name'] = $form_state['values']['new_author']['new_author_name'];
-      $new_author['is_new'] = TRUE;
-
-      $form_state['new_author'] = $new_author;
-
-    }
-
-
-
-}
-
-
-/**
- * Submit handler for 'Edit' button on node form.
- */
-function tripal_pub_edit_author_submit($form, &$form_state) {
-
-    // remember which author we're editing
-    $delta = $form_state['values']['edit_author']['delta'];
-
-    //add changes author details back
-    $rank = $form_state['values']['authors'][$delta]['author_name']['rank'];
-    $form_state['values']['authors'][$delta]['author_name'] = $form_state['values']['edit_author']['edit_author_name'];
-    $form_state['values']['authors'][$delta]['author_name']['rank'] = $rank;
-
-    //ensures that after they save their changes the edit fieldstate goes away
-    unset($form_state['values']['edit_author']);
-
-    // Set the form to rebuild and run submit handlers.
-    node_form_submit_build_node($form, $form_state);
-
-}
-
-
-/**
- * Submit handler for 'Edit' button on node form.
- */
-function tripal_pub_set_edit_author_submit($form, &$form_state) {
-
-  $form_state['remove_delta'] = 0;
-
-  // Make the changes we want to the form state
-  $edit_author = array();
-
-  if (preg_match('/edit_author_(\d+)/', $form_state['clicked_button']['#name'], $matches)) {
-
-
-    $delta = $matches[1];
-
-    $form_state['values']['edit_author'] = $form_state['values']['authors'][$delta];
-
-    $form_state['values']['edit_author']['delta'] = $delta;
-
-  }
-
-  // Set the form to rebuild and run submit handlers.
-  node_form_submit_build_node($form, $form_state);
-
-}
-
-
-/**
- * Submit handler for 'Remove' button on node form.
- */
-function tripal_pub_remove_row_submit($form, &$form_state) {
-
-
-  if (preg_match('/remove_author_(\d+)/', $form_state['clicked_button']['#name'], $matches)) {
-
-    $delta = $matches[1];
-
-    $form_state['values']['remove_author'] = $form_state['values']['authors'][$delta];
-
-    $form_state['values']['remove_author']['delta'] = $delta;
-
-  }
-
-  $values =  array(
-    'pub_id' => $form_state['values']['pub_id'],
-    'rank' => $form_state['values']['authors'][$delta]['author_name']['rank']
-
-    );
-
-  //deleting row in chado table
-  tripal_core_chado_delete('pubauthor', $values);
-
-
-  // Set the form to rebuild and run submit handlers.
-  node_form_submit_build_node($form, $form_state);
-
-}
-
-
-/*
- *
- *
- *
- */
-function tripal_pub_js($delta = 0) {
-
-    $form = tripal_pub_ajax_form_handler($delta);
-
-    // Render the new output.
-    $author_form = $form['author_wrapper']; //was ['author']
-
-    // Prevent duplicate wrappers.
-    unset($author_form['#prefix'], $author_form['#suffix']);
-
-    $output = theme('status_messages') . drupal_render($author_form);
-
-    // AHAH does not know about the "Remove" button.
-    // This causes it not to attach AHAH behaviours to it after modifying the form.
-    // So we need to tell it first.
-    $javascript = drupal_add_js(NULL, NULL);
-
-    if (isset($javascript['setting'])) {
-
-      $output .= '<script type="text/javascript">jQuery.extend(Drupal.settings, '. drupal_to_js(call_user_func_array('array_merge_recursive', $javascript['setting'])) .');</script>';
-
-    }
-
-    // Final rendering callback.
-    drupal_json(array('status' => TRUE, 'data' => $output));
-
-}
-
-
-/**
- * AJAX form handler.
- */
-function tripal_pub_ajax_form_handler($delta=0 ) {
-
-    // The form is generated in an include file which we need to include manually.
-    include_once 'modules/node/node.pages.inc';
-
-    $form_state = array('storage' => NULL, 'submitted' => FALSE);
-
-    $form_build_id = filter_xss($_POST['form_build_id']);
-
-    // Get the form from the cache.
-    $form = form_get_cache($form_build_id, $form_state);
-
-    $args = $form['#parameters'];
-
-    $form_id = array_shift($args);
-
-    // We need to process the form, prepare for that by setting a few internals.
-    $form_state['post'] = $form['#post'] = $_POST;
-
-    $form['#programmed'] = $form['#redirect'] = FALSE;
-
-    // Set up our form state variable, needed for removing authors.
-    $form_state['remove_delta'] = $delta;
-
-    // Build, validate and if possible, submit the form.
-    drupal_process_form($form_id, $form, $form_state);
-
-    // If validation fails, force form submission.
-    if (form_get_errors()) {
-
-      form_execute_handlers('submit', $form, $form_state);
-
-    }
-
-    // This call recreates the form relying solely on the form_state that the
-    // drupal_process_form set up.
-    $form = drupal_rebuild_form($form_id, $form_state, $args, $form_build_id);
-
-    return $form;
-}
-
-
-/*
- *
- *
- */
-function theme_tripal_pub_author_table($form) {
-
-  $rows = array();
-
-  $headers = array(
-    t('Givennames'),
-    t('Surname'),
-    t('Suffix'),
-    '',  // Blank header title for the remove link.
-  );
-
-  foreach (element_children($form) as $key) {
-
-    // No need to print the field title every time.
-    unset(
-      $form[$key]['author_name_text']['#title'],
-      $form[$key]['author_name_text-2']['#title'],
-      $form[$key]['author_name_text-3']['#title'],
-      $form[$key]['remove_author']['#title']
-    );
-
-    // Build the table row.
-    $row = array(
-      'data' => array(
-        array('data' => drupal_render($form[$key]['author_name']) . drupal_render($form[$key]['author_name_text']), 'class' => 'author-name'),
-        array('data' => drupal_render($form[$key]['author_name']) . drupal_render($form[$key]['author_name_text-2']), 'class' => 'author-name'),
-        array('data' => drupal_render($form[$key]['author_name']) . drupal_render($form[$key]['author_name_text-3']), 'class' => 'author-name'),
-        array('data' => drupal_render($form[$key]['edit_author']) . drupal_render($form[$key]['remove_author']), 'class' => 'remove-author'),
-      ),
-    );
-
-    // Add additional attributes to the row, such as a class for this row.
-    if (isset($form[$key]['#attributes'])) {
-
-      $row = array_merge($row, $form[$key]['#attributes']);
-
-    }
-
-    $rows[] = $row;
-
-  }
-
-  //$output = theme('table', $headers, $rows);
-
-  $output .= drupal_render($form);
-
-  return $output;
-
-}
-
-/**
- *
- * Helper function to define populated form field elements for publication node form.
- *
- */
-function tripal_pub_author_display_form($delta, $author) {
-
-  $form = array(
-    '#tree' => TRUE,
-  );
-
-  // Author Name
-  $form['author_name'] = array(
-    '#type' => 'hidden',
-    '#value' => $author,
-    '#parents' => array('authors', $delta),
-  );
-  $form['author_name_text'] = array(
-    '#type' => 'item',
-    '#title' => t('Givennames'),
-    '#parents' => array('authors', $delta),
-    '#value' => $author['author_name']['givennames'],
-  );
-
-  $form['author_name_text-2'] = array(
-    '#type' => 'item',
-    '#title' => t('Surname'),
-    '#parents' => array('authors', $delta),
-    '#value' => $author['author_name']['surname'],
-  );
-
-  $form['author_name_text-3'] = array(
-    '#type' => 'item',
-    '#title' => t('Suffix'),
-    '#parents' => array('authors', $delta),
-    '#value' => $author['author_name']['suffix'],
-  );
-
-    // Remove button.
-    $form['remove_author'] = array(
-        '#type' => 'submit',
-        '#name' => 'remove_author_' . $delta,
-        '#value' => t('Remove'),
-        '#submit' => array('tripal_pub_remove_row_submit'),
-        '#parents' => array('authors', $delta, 'remove_author'),
-        '#ahah' => array(
-          'path' => 'tripal_pub/js/0',
-          'wrapper' => 'author-wrapper',
-          'method' => 'replace',
-          'effect' => 'fade',
-        ),
-    );
-
-      // Edit Author button
-    $form['edit_author'] = array(
-        '#type' => 'submit',
-        '#name' => 'edit_author_' . $delta,
-        '#value' => t('Edit'),
-        '#submit' => array('tripal_pub_set_edit_author_submit'),
-        '#parents' => array('authors', $delta, 'edit_author'),
-        '#ahah' => array(
-          'path' => 'tripal_pub/js/0',
-          'wrapper' => 'author-wrapper',
-          'method' => 'replace',
-          'effect' => 'fade',
-        ),
-    );
-
-  return $form;
-}
-
-
-/*
- * This function executes commands periodically. This is called whenever a cron run occurs. This
- * function uses the time interval that the user has entered. This Publication module, requires
- * that the program is ran in pre-determined intervals, as desired by the user. By using a time stamp
- * and comparing the current time and the time that the last time a cron was ran, this program will
- *  be ran.
- *
- *
- * @TODO: The cron function is not working correctly, not sure why the cron is not working properly.
- *
- *
- *
- */
-/**
-function tripal_pub_cron(){
-
-      global $user;    //needed to make the current users details available so access of user id is available
-
-      //Aquiring the current time
-      $current_time = time();
-
-      //Aquiring the user entered time interval
-      $user_interval = variable_get('time_interval',NULL);
-
-      //converting the user entered interval into seconds for use with unix time stamp
-      $converted_interval = ($user_interval*60);
-
-      //Accessing database for time stamp from watchdog
-      $cron = db_result(db_query('select timestamp from {watchdog} where type="cron" order by timestamp desc limit 1'));
-
-      //debugging print statement
-      //print($cron);
-
-      //taking variable value & assigning for use
-      $cron_last = variable_get('cron', time());
-
-      $updated_interval = $cron_last - $converted_interval;
-
-      if($current_time >= $updated_interval ){
-
-        tripal_add_job('Search & Load PubMed Publications', 'tripal_pub', 'tripal_pub_search_load_pubmed_publications', $job_args, $user->uid);
-
-      }
-
-}
-  */
-
-//-----------------------------------------------------------------------------
-//  SECTION: Configuration form
-//-----------------------------------------------------------------------------
-
-
-/**
- * Implementation of tripal_pub_form().
- *
- *  This form takes the following information:A Publication Title,Volume title,Volume,Series Name,
- *  Issue,Publication Year,Pages where the Article is located, Miniref,Type-Id, if the article is Obsolete,
- *  Publishing company,Pubplication Place and a Uniquename for the the instance. It then puts the
- *  infromation into the Chado_project database table based on its 'pub_id'.
- *
- *
- *  @return $form
- *    An array of menu items '$form'
- *
- */
-function tripal_pub_configuration_form() {
-
-  $cv_options = tripal_cv_get_cv_options();
-
-  //Creating Fieldset for multiple fields in form
-  $form['node_form'] = array(
-    '#type' => 'fieldset',
-    '#title' => t('Create/Edit Publication Settings'),
-  );
-
-  $form['node_form']['tripal_pub_types_cv'] = array(
-    '#type' => 'select',
-    '#title' => t('Controlled Vocabularies'),
-    '#options' => $cv_options,
-    '#default_value' => variable_get('tripal_pub_types_cv', 0),
-    '#description' => 'Set the controlled vocabulary to pull publication type options from. Terms in this vocabulary will be available is the Publication Type select box on both the create and edit pages.',
-  );
-
-  $form['pubmed'] = array(
-    '#type' => 'fieldset',
-    '#title' => t('Create Nodes via PubMed Search'),
-  );
-
-  $form['pubmed']['description'] = array(
-    '#type' => 'item',
-    '#value' => 'Publication nodes are created based on the results of a PubMed publication search using '
-      .'the keywords entered below. No content is created until the sync is clicked below and the registered tripal job is '
-      .'run. This script attempts to only load new publications (ones which don\'t already have nodes from a previous search) '
-      .'by comparing the pub_id thus if a publication is added manually which also appears in the pubmed search it will likely '
-      .'get added twice.'
-  );
-
-  //define form elements for the node's title and body.
-  $form['pubmed']['unique_name'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Search Keywords'),
-    '#description' => t('Specific search terms. Must be seperated by a single space.'),
-    '#required' => FALSE,
-    '#default_value' => variable_get('unique_name', NULL)
-  );
-
-  //define form elements for the node's title and body.
-  /**
-  $form['set']['time_interval'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Time Search Interval (Minutes)'),
-    '#description'=>t(' The “Search Interval” set here determines when a drupal cron job should
-    schedule a tripal job. As such, in reality the time until publications are sync’d is “Search Interval”
-    + time remaining until drupal cron is run + time between drupal cron run and next tripal jobs run'),
-    '#required' => FALSE,
-    '#default_value' => variable_get('time_interval', NULL)
-  );
-  */
-
-  $form['pubmed']['sync_info'] = array(
-      '#type' => 'submit',
-      '#title' => t('Sync Publications Jobs'),
-      '#value' => t('Sync'),
-  );
-
-  $form['submit'] = array(
-    '#type' => 'submit',
-    '#weight' => 10,
-    '#value' => t('Save Configuration')
-  );
-
-  return $form;
-
-}
-
-
-/*
- * Pub Configuration-Form
- * This form submit uses variable_set to set the vocabularies that are used, as well as the
- * unique_name and time interval that was entered by the user. If the user selects the option
- * to Sync Publicatin Jobs, the 'tripal_add_job' function is called, and a tripal job
- * will be added.
- *
- * @param $form
- *    -The submitted form containing the user entered infromation
- * @param $form_state
- *    -Is the state of the form: i.e what button was pressed, what infromation was entered,etc.
- *    The key is the 'values'
- */
-function tripal_pub_configuration_form_submit($form, $form_state) {
-
-    global $user;    //needed to make the current users details available so access of user id is available
-
-    if ($form_state['values']['op'] == t('Save Configuration')) {
-
-        variable_set('tripal_pub_types_cv', $form_state['values']['tripal_pub_types_cv']);
-        variable_set('unique_name', $form_state['values']['unique_name'] );
-
-    }
-
-    //adding a tripal job if the user selects to Sync the Publications
-    if ($form_state['values']['op'] == t('Sync')) {
-
-        variable_set('unique_name', $form_state['values']['unique_name'] );
-        $job_args = array($form_state['values']['unique_name']);
-        $job_id = tripal_add_job('Search & Load PubMed Publications', 'tripal_pub', 'tripal_pub_search_load_pubmed_publications', $job_args, $user->uid);
-
-    }
-
-}
-
-
-/**
- * Tripal Pub Search Load Pubmed Publications
- *
- * This function takes a search term array and uses it as the parameters for the perl script
- * e_utiliies.pl, which needs to be included and installed in any system that wants full
- * functionality of this module, with respects to searching PubMed for relative articles.
- * When the function ends, and all of the form_state values are set, the drupal_execute()
- * function is called and retrieves a form using a form_id, populates it with $form_values,
- * processes it, and returns any validation errors that came up.
- *
- *
- *
- * @TODO: The loading of this function still needs to be fixed. When running the configuration, there
- * are still errors coming up, UFT8 warnings still come up, in random places. My guess, it is when
- * a article is found that is not in english
- *
- *
- *
- * @param $search_term_array
- *     -This arrary contains the search terms that were entered
- *
- *
- */
-function tripal_pub_search_load_pubmed_publications($search_term_array) {
-
-  $key_terms = preg_split('/\s+/', $search_term_array);
-
-  $search_terms= implode("+", $key_terms);
-
-  //Retrieving absolute path of current directory
-  $path = drupal_get_path('module', 'tripal_pub');
-
-  $i_path = realpath(".");
-
-  $absolute_path = $i_path . '/' . $path;
-
-  //perl file required for operating the NCBI PubMed database search, uses users working directory
-  $command = 'perl ' . $absolute_path  . '/e_utilities.pl' . ' ' . $search_terms . ' ' . 'uilist';
-
-  print "\nAccessing PubMed ID's\n";
-
-  exec($command, $output);
-
-
-  //for loop going through all the pub_med_id, creating a node for each one
-  for ($i=0; $i < sizeof($output); $i++) {
-
-    $pmid = $output[$i];
-
-    //aquiring the pubmed id from the pub table based on the uniquename
-    $pubmed_id = tripal_core_chado_select( 'pub', array('pub_id'), array( 'uniquename' => $pmid) );
-
-    //Checking that the pub-med id is not set & thus not in the database
-    if (!isset($pubmed_id[0]->pub_id)) {
-
-      print "\nRetrieving PubMed ID:" . $pmid . "\n";
-
-      $command = '';
-
-      $xml_report = '';
-
-      $newline_separated = '';
-
-      $xml = '';
-
-      //Uncomment below line to see any syntax errors within the perl script
-      //$command = 'perl ' ."-cs" .' ' . $absolute_path  .'/e_utilities.pl' .' ' .$pmid.'[uid] ' .'xml';
-
-      $command = 'perl ' . $absolute_path  . '/e_utilities.pl' . ' ' . $pmid . '[uid] ' . 'xml';
-
-      exec($command, $xml_report);
-
-      //adding the xml report once the new line characters have been removed
-      $newline_separated = implode("\n", $xml_report);
-
-      //relaying the xml output so it can be put in a string variable
-      $xml = simplexml_load_string($newline_separated);
-
-      //checking the Article Title exists, if so, procede with setting values
-      if (isset($xml->PubmedArticle->MedlineCitation->Article->ArticleTitle)) {
-
-        $form_id ='chado_pub_node_form';
-
-        $form_state = array();
-
-        module_load_include('inc', 'node', 'node.pages');
-
-        $node = array('type' => 'chado_pub');
-
-        $form_state = array();
-
-        $form_state['values']['title'] =
-        iconv(iconv_get_encoding((string)$xml->PubmedArticle->MedlineCitation->Article->ArticleTitle),
-        "UTF-8",
-        (string)$xml->PubmedArticle->MedlineCitation->Article->ArticleTitle);
-
-        $form_state['values']['abstract'] =
-        iconv(iconv_get_encoding((string)$xml->PubmedArticle),
-        "UTF-8",
-        (string)$xml->PubmedArticle);
-
-        $form_state['values']['authors'] =
-        iconv(iconv_get_encoding((string)$xml->PubmedArticle),
-        "UTF-8",
-        (string)$xml->PubmedArticle);
-
-        $form_state['values']['volumetitle'] =
-        iconv(iconv_get_encoding((string)$xml->PubmedArticle->MedlineCitation->Article->Journal->Title),
-        "UTF-8",
-        (string)$xml->PubmedArticle->MedlineCitation->Article->Journal->Title);
-
-        $form_state['values']['series_name'] =
-        iconv(iconv_get_encoding((string)$xml->PubmedArticle->MedlineCitation->Article->Journal->Title),
-        "UTF-8",
-        (string)$xml->PubmedArticle->MedlineCitation->Article->Journal->Title);
-
-        $form_state['values']['volume'] =
-        iconv(iconv_get_encoding((string)$xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->Volume),
-        "UTF-8",
-        (string)$xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->Volume);
-
-        $form_state['values']['issue'] =
-        iconv(iconv_get_encoding((string)$xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->Issue),
-        "UTF-8",
-        (string)$xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->Issue);
-
-        $form_state['values']['pyear'] =
-        iconv(iconv_get_encoding((string)$xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->PubDate->Year),
-        "UTF-8",
-        (string)$xml->PubmedArticle->MedlineCitation->Article->Journal->JournalIssue->PubDate->Year);
-
-        $form_state['values']['pages'] =
-        iconv(iconv_get_encoding((string)$xml->PubmedArticle->MedlineCitation->Article->Pagination->MedlinePgn),
-        "UTF-8",
-        (string)$xml->PubmedArticle->MedlineCitation->Article->Pagination->MedlinePgn);
-
-        $form_state['values']['uniquename'] =
-        iconv(iconv_get_encoding((string)$xml->PubmedArticle->MedlineCitation->PMID),
-        "UTF-8",
-        (string)$xml->PubmedArticle->MedlineCitation->PMID);
-
-        $type_id = tripal_core_chado_select( 'cvterm', array('cvterm_id'), array( 'name' => 'Article') );
-
-        $form_state['values']['type_id'] = $type_id[0]->cvterm_id;
-
-        $form_state['values']['is_obsolete']='f';
-
-        $form_state['values']['op'] = t('Save');
-
-        form_set_error(NULL, '', TRUE);
-
-        //If the required values & fields are not set, the drupal_execute function is not called and node is not added
-        if (isset($form_state['values']['volumetitle']) || isset($form_state['values']['series_name'])||
-            isset($form_state['values']['pages'])||isset($form_state['values']['uniquename'])) {
-
-          drupal_execute('tripal_pub_node_form', $form_state, (object)$node);
-
-        }
-
-        $errors = form_get_errors();
-
-        //if(isset($errors)){
-
-
-        if ( $errors !=
-          'Warning: pg_query(): Query failed: ERROR:  invalid byte sequence for encoding "UTF8": 0xfc
-          HINT:  This error can also happen if the byte sequence does not match the encoding expected
-          by the server, which is controlled by "client_encoding".') {
-
-          print "\nErrors:" . print_r($errors, TRUE) . "\n";
-
-          }
-          else{
-
-            print "\nErrors:" . print_r($errors, TRUE) . "\n";
-
-          }
-
-        }
-
-      }
-      elseif ($i==sizeof($output)) {
-
-        print "\n Search Completed Successfully \n";
-        print "\n Total Nodes Created:" . $i . "\n";
-
-      }
-      else{
-
-        print "\nERROR: The following PubMed ID:" . ' ' . $pubmed_id[0]->pub_id .  " Exists in database,skipped.\n";
-
-    }
-  }
-
-  }
-
-
-//-----------------------------------------------------------------------------
-//  SECTION: Custom form Elements
-//-----------------------------------------------------------------------------
-
-
-/*
- * This fucnction tells the FAPI(Form-API) that this is a element that will carry a value, contains
- * arrays of callback function names. Will declare an element will create a reuseable element type.
- *
- *  @return
- *      An associative array with the name of each element type as a key and an
- *      array of attributes describingthe type as a value
- */
-function tripal_pub_elements() {
-
-      return array(
-          'publication_author' => array(
-               '#input' => TRUE,
-               '#process' => array('expand_publication_author'),
-               '#element_validate' => array('publication_author_validate'),
-              ),
-      );
-
-}
-
-
-/*
- *
- *
- *
- */
-function expand_publication_author($element) {
-
-    if (empty($element['#value'])) {
-      $element['#value'] = array(
-              'givennames' => '',
-              'suffix' => '',
-              'surname' => '',
-            );
-
-    }
-
-    $element['#tree'] = TRUE;
-
-    $parents = $element['#parents'];
-
-    $parents[] = 'givennames';
-
-    $element['givennames'] = array(
-    '#type' => 'textfield',
-              '#size' => 10,
-              //'#maxlength' => TRUE,
-              //'#default_value'=> $element['#value']['#given'],
-              '#prefix' => 'Given Name',
-    );
-
-    if ($element['#default_value']) {
-
-      $element['givennames']['#default_value'] = $element['#default_value']['givennames'];
-
-    }
-
-    $parents = $element['#parents'];
-
-    $parents[]= 'surname';
-
-    $element['surname'] = array(
-    '#type' => 'textfield',
-              '#size' => 10,
-              //'#maxlength' => TRUE,
-              //'#default_value'=> $element['#value']['#surname'],
-              '#prefix' => 'Surname',
-    );
-
-    if ($element['#default_value']) {
-
-      $element['surname']['#default_value'] = $element['#default_value']['surname'];
-
-    }
-
-    $parents = $element['#parents'];
-
-    $parents[]= 'suffix';
-
-    $element['suffix'] = array(
-    '#type' => 'textfield',
-              '#size' => 5,
-              //'#maxlength' => TRUE,
-              //'#default_value'=> $element['#value']['#suffix'],
-              '#prefix' => 'suffix',
-    );
-
-    if ($element['#default_value']) {
-
-      $element['suffix']['#default_value'] = $element['#default_value']['suffix'];
-
-    }
-
-  return $element;
-
-}
-
-
-/*
- *
- *
- *
- */
-function theme_publication_author($element) {
-
-  return theme('form_element', $element, '<div class="container-inline">' . $element['#children'] . '</div>');
-
-}
-
-/*
- *
- *
- *
- */
-function publication_author_validate($element) {
-
-if ($element['#required']) {
-
-  if (trim($element['#value']['givennames']) == '' || trim($element['#value']['suffix']) == '' || trim($element['#value']['surname']) == '' ||
-
-      !is_string($element['#value']['givennames']) || !is_string($element['#value']['givennames']) || !is_string($element['#value']['surname'])) {
-
-      form_error($element, t('The Author name is required.'));
-
-    }
-
-  }
-
-
-}
-
-
-//-----------------------------------------------------------------------------
-//  End of Software
-//-----------------------------------------------------------------------------
-
-
-
-
-

tripal_pub/tripal_pub.views.inc

@@ -1,71 +0,0 @@
-<?php
-
-/**
- *  @file
- *  This file contains the basic functions for views integration of
- *  chado/tripal_pub tables. Supplementary functions can be found in
- *  ./views/
- *
- *  Documentation on views integration can be found at
- *  http://views2.logrus.com/doc/html/index.html.
- */
-
-/*************************************************************************
- * Implements hook_views_data()
- * Purpose: Describe chado/tripal tables & fields to views
- *
- * @return: a data array which follows the structure outlined in the
- *   views2 documentation for this hook. Essentially, it's an array of table
- *   definitions keyed by chado/tripal table name. Each table definition
- *   includes basic details about the table, fields in that table and
- *   relationships between that table and others (joins)
- */
-function tripal_pub_views_data()  {
-  $data = array();
-
-  if (module_exists('tripal_views')) {
-    $tables = array(
-      'pub'
-    );
-    foreach ($tables as $tablename) {
-      if (!tripal_views_is_integrated($tablename, 10)) {
-        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, TRUE);
-        tripal_views_integration_add_entry($table_integration_array);
-      }
-    }
-
-    $tables = array(
-      'pub_dbxref',
-      'pub_relationship',
-      'pubauthor',
-      'pubprop'
-    );
-    foreach ($tables as $tablename) {
-      if (!tripal_views_is_integrated($tablename, 10)) {
-        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, FALSE);
-        tripal_views_integration_add_entry($table_integration_array);
-      }
-    }
-  }
-
-  return $data;
-}
-
-/*************************************************************************
- * Implements hook_views_handlers()
- * Purpose: Register all custom handlers with views
- *   where a handler describes either "the type of field",
- *   "how a field should be filtered", "how a field should be sorted"
- *
- * @return: An array of handler definitions
- */
-function tripal_pub_views_handlers() {
-  return array(
-   'info' => array(
-     'path' => drupal_get_path('module', 'tripal_pub') . '/views/handlers',
-    ),
-   'handlers' => array(
-
-    ),
-  );
-}

tripal_views/tripal_views.api.inc

@@ -434,6 +434,20 @@ function tripal_views_get_integration_array_for_chado_table($table_name, $base_t
           'sort' => array('name' => 'chado_views_handler_sort'),
         );
       }
+      elseif (preg_match('/^boolean/', $field_schema['type'])) {
+        $defn_array['fields'][$field_name]['handlers'] = array(
+          'field' => array('name' => 'chado_views_handler_field_boolean'),
+          'filter' => array('name' => 'chado_views_handler_filter_boolean_operator'),
+          'sort' => array('name' => 'chado_views_handler_sort'),
+        );
+      }
+      elseif (preg_match('/^datetime/', $field_schema['type'])) {
+        $defn_array['fields'][$field_name]['handlers'] = array(
+          'field' => array('name' => 'chado_views_handler_field_date'),
+          'filter' => array('name' => 'chado_views_handler_filter_date'),
+          'sort' => array('name' => 'views_handler_sort_date'),
+        );
+      }
       else {
         $defn_array['fields'][$field_name]['handlers'] = array(
           'field' => array('name' => 'chado_views_handler_field'),
@@ -443,8 +457,8 @@ function tripal_views_get_integration_array_for_chado_table($table_name, $base_t
       }
 
       // Specify specialty handlers
-      if ($field_name == 'type_id') {
-        $defn_array['fields'][$field_name]['handlers']['filter']['name'] = 'views_handler_filter_chado_select_cvterm_name';
+      if ($field_name == 'type_id' OR $field_name == 'cvterm_id') {
+        $defn_array['fields'][$field_name]['handlers']['filter']['name'] = 'chado_views_handler_filter_select_cvterm';
       }
     }
   }
@@ -459,7 +473,7 @@ function tripal_views_get_integration_array_for_chado_table($table_name, $base_t
       $defn_array['fields'][$left_field]['joins'][ $foreign_key_schema['table'] ] = array(
         'table' => $foreign_key_schema['table'],
         'field' => $right_field,
-        'handler' => 'views_handler_join_chado_aggregtor'
+        'handler' => 'views_handler_join_chado_aggregator'
       );
     }
   }

tripal_views/tripal_views.views.inc

@@ -62,20 +62,27 @@ function tripal_views_views_handlers() {
     ),
     'handlers' => array(
 
+      // Custom Tripal Handlers
+      'views_handler_filter_file_upload' => array(
+        'parent' => 'views_handler_filter',
+      ),
+      'tripal_views_handler_filter_string_selectbox' => array(
+        'parent' => 'views_handler_filter_string',
+      ),
+      'views_handler_filter_no_results' => array(
+        'parent' => 'views_handler_filter'
+      ),
+
       // Custom Chado Handlers
       'chado_views_handler_field_aggregate' => array(
         'parent' => 'chado_views_handler_field',
       ),
-      // the following is deprecated but left for backwards compatibility
-      'views_handler_filter_chado_select_string' => array(
-        'parent' => 'views_handler_filter_string',
-      ),
-      'tripal_views_handler_filter_string_selectbox' => array(
-        'parent' => 'views_handler_filter_string',
+      'chado_views_handler_filter_select_cvterm' => array(
+        'parent' => 'views_handler_filter_chado_select_cvterm_name',
       ),
+      'chado_views_handler_filter_select_string' => array(
+        'parent' => 'chado_views_handler_filter_string',
 
-      'views_handler_filter_chado_select_cvterm_name' => array(
-        'parent' => 'views_handler_filter_string',
       ),
 
       // Join Handlers
@@ -86,12 +93,7 @@ function tripal_views_views_handlers() {
         'parent' => 'views_join',
       ),
 
-      // Other Custom Handlers
-      'views_handler_filter_no_results' => array(
-        'parent' => 'views_handler_filter'
-      ),
-
-      // Old Handlers
+      // Old Handlers no longer used (deprecated)
       'views_handler_field_node_optional' => array(
         'parent' => 'views_handler_field_node',
       ),
@@ -111,6 +113,13 @@ function tripal_views_views_handlers() {
         'parent' => 'views_handler_field',
       ),
 
+      // Old handlers with new counterparts (deprecated)
+      'views_handler_filter_chado_select_string' => array(
+        'parent' => 'views_handler_filter_string',
+      ),
+      'views_handler_filter_chado_select_cvterm_name' => array(
+        'parent' => 'views_handler_filter_string',
+      ),
 
       // Wrappers for Default Views Handlers-----
       // Field Handlers
@@ -160,10 +169,6 @@ function tripal_views_views_handlers() {
       'chado_views_handler_filter_numeric' => array(
         'parent' => 'views_handler_filter_numeric',
       ),
-      'views_handler_filter_file_upload' => array(
-        'parent' => 'views_handler_filter',
-      ),
-
       // Sort Handlers
       'chado_views_handler_sort' => array(
         'parent' => 'views_handler_sort'
@@ -726,12 +731,12 @@ function tripal_views_data_export_download_form(&$form_state, $view, $display_id
   $current_display = $view->current_display;
   foreach ($displays as $name => $display) {
     if (preg_match("/^views_data_export/", $name)) {
-    
-      // only add this display to the form if it is attached 
+
+      // only add this display to the form if it is attached
       $display_options = $display->display_options;
       if(strcmp($display_options['displays'][$current_display],$current_display)!=0){
          continue;
-      } 
+      }
 
       // set the first item as default
       if (!$default) {

tripal_views/tripal_views_integration.inc

@@ -606,7 +606,7 @@ function tripal_views_integration_form(&$form_state, $setup_id = NULL) {
       $default_join_handler = 0;
       if (isset($setup_id) && !isset($form_state['storage']["fields_join_handler_$table_id-$i"])) {
         $default_join_handler = $default_handlers[$column_name]['join']['handler_name'];
-        $form_state['storage']["fields_join_handler_$table_id-$i"]=$default_join_handler;
+        $form_state['storage']["fields_join_handler_$table_id-$i"] = $default_join_handler;
       }
       else {
         $default_join_handler = $form_state['storage']["fields_join_handler_$table_id-$i"];

tripal_views/views/handlers/chado_views_handler_field_boolean.inc

@@ -85,6 +85,32 @@ class chado_views_handler_field_boolean extends views_handler_field_boolean {
    *   The values retrieved from the database.
    */
   function render($values) {
+
+    // check to see if this is a t/f boolean field or a 1/0 boolean field
+    // parent render expects 1/0 so need to translate to that form before rendering
+    if (!is_array($values->{$this->field_alias})) {
+      if (!preg_match('/[01]/',$values->{$this->field_alias})) {
+        if (preg_match('/^[tT]/',$values->{$this->field_alias})) {
+          $values->{$this->field_alias} = 1;
+        }
+        elseif (preg_match('/^[fF]/',$values->{$this->field_alias})) {
+          $values->{$this->field_alias} = 0;
+        }
+      }
+    }
+    else {
+      if (!preg_match('/[01]/',$values->{$this->field_alias}[0])) {
+        foreach ($values->{$this->field_alias} as $k => $v) {
+          if (preg_match('/^[tT]/',$v)) {
+            $values->{$this->field_alias}[$k] = 1;
+          }
+          elseif (preg_match('/^[fF]/',$v)) {
+            $values->{$this->field_alias}[$k] = 0;
+          }
+        }
+      }
+    }
+
     return chado_wrapper_render_items($this, $values);
   }
 

tripal_views/views/handlers/chado_views_handler_field_date.inc

@@ -85,6 +85,22 @@ class chado_views_handler_field_date extends views_handler_field_date {
    *   The values retrieved from the database.
    */
   function render($values) {
+
+    // Check the format of the date is a UNIX timestamp and otherwise convert
+    if (!is_array($values->{$this->field_alias})) {
+      if (!preg_match('/^\d+$/',$values->{$this->field_alias})) {
+         $values->{$this->field_alias} = strtotime($values->{$this->field_alias});
+      }
+    }
+    else {
+      if (!preg_match('/^\d+$/',$values->{$this->field_alias}[0])) {
+        foreach ($values->{$this->field_alias} as $k => $v) {
+         $values->{$this->field_alias}[$k] = strtotime($v);
+        }
+      }
+    }
+
+    // render the items
     return chado_wrapper_render_items($this, $values);
   }
 

tripal_views/views/handlers/chado_views_handler_filter_boolean_operator.inc

@@ -30,14 +30,14 @@ class chado_views_handler_filter_boolean_operator extends views_handler_filter_b
       '#type' => 'checkbox',
       '#title' => t('Filter base table records'),
       '#description' => t('Filters %base_table to only those with the value in the aggregate array.', array('%base_table' => $this->view->base_table)),
-      '#default_value' => (isset($this->options['records_with'])) ? $this->options['records_with'] : TRUE,
+      '#default_value' => (isset($this->options['agg']['records_with'])) ? $this->options['agg']['records_with'] : TRUE,
     );
 
     $form['agg']['aggregates_with'] = array(
       '#type' => 'checkbox',
       '#title' => t('Filter aggregates displayed'),
       '#description' => t('Filters the aggregates shown based on the value. Doesn\'t affect the number of %base_table records.', array('%base_table' => $this->view->base_table)),
-      '#default_value' => (isset($this->options['aggregates_with'])) ? $this->options['aggregates_with'] : TRUE,
+      '#default_value' => (isset($this->options['agg']['aggregates_with'])) ? $this->options['agg']['aggregates_with'] : TRUE,
     );
 
   }
@@ -50,12 +50,13 @@ class chado_views_handler_filter_boolean_operator extends views_handler_filter_b
 
     // make optional
     // if it is not set or empty then don't restrict the query
-    if (!$this->value) {
+    if ($this->value == 'All') {
       return;
     }
 
     $this->ensure_my_table();
 
+    // determine whether it is aggregated or not
     $table = $this->query->get_table_info($this->table);
     if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
       $this->aggregated = TRUE;
@@ -64,8 +65,46 @@ class chado_views_handler_filter_boolean_operator extends views_handler_filter_b
       $this->aggregated = FALSE;
     }
 
+    // check if its a t/f or 1/0 boolean
+    $check = db_fetch_object(db_query("SELECT %s as val FROM %s LIMIT 1", $this->real_field, $this->table));
+    if (preg_match('/^[tTfF]/',$check->val)) {
+      $true = 't';
+      $false = 'f';
+    }
+    else {
+      $true = 1;
+      $false = 0;
+    }
+
     if (!$this->aggregated) {
-      parent::query();
+
+      // Only base records with value in the aggregated field
+      // This doesn't restrict the items in the aggregate field
+      if ($this->options['agg']['records_with']) {
+        $where = "$this->table_alias.$this->real_field ";
+        if (empty($this->value)) {
+          $where .= "= '".$false."'";
+          if ($this->accept_null) {
+            $where = '(' . $where . " OR $this->table_alias.$this->real_field IS NULL)";
+          }
+        }
+        else {
+          if (!empty($this->definition['use equal'])) {
+            $where .= "= '".$true."'";
+          }
+          else {
+            $where .= "<> '".$false."'";
+          }
+        }
+        $this->query->add_where($this->options['group'], $where);
+      }
+
+      // To restrict the items in the aggregate...
+      // Tell the join handler about the filter
+      // so it can be done in the join query
+      if ($this->options['agg']['aggregates_with']) {
+        //Do nothing b/c it's not aggregated!
+      }
     }
     else {
 
@@ -75,14 +114,24 @@ class chado_views_handler_filter_boolean_operator extends views_handler_filter_b
       $field = "$this->table_alias.$this->real_field";
       if ($this->options['agg']['records_with']) {
         $where = "'%s' = ANY($field)";
-        $this->query->add_where($this->options['group'], $where, $this->value);
+        if ($this->value) {
+          $this->query->add_where($this->options['group'], $where, $true);
+        }
+        else {
+          $this->query->add_where($this->options['group'], $where, $false);
+        }
       }
 
       // To restrict the items in the aggregate...
       // Tell the join handler about the filter
       // so it can be done in the join query
       if ($this->options['agg']['aggregates_with']) {
-        $table['join']->filter[] = $field . " = '" . $this->value . "'";
+        if ($this->value) {
+          $table['join']->filter[] = $field . " = '" . $true . "'";
+        }
+        else {
+          $table['join']->filter[] = $field . " = '" . $false . "'";
+        }
       }
     }
 

tripal_views/views/handlers/chado_views_handler_filter_date.inc

@@ -7,6 +7,8 @@
  * Handles fields which may be aggregated during the chado join process. There are options
  * to filter the base table based on an aggregated table or just filter the aggregated
  * table (showing blank for that field if there are no records in the aggregated table).
+ *
+ * @todo make handle aggregation
  */
 class chado_views_handler_filter_date extends views_handler_filter_date {
 
@@ -30,62 +32,128 @@ class chado_views_handler_filter_date extends views_handler_filter_date {
       '#type' => 'checkbox',
       '#title' => t('Filter base table records'),
       '#description' => t('Filters %base_table to only those with the value in the aggregate array.', array('%base_table' => $this->view->base_table)),
-      '#default_value' => (isset($this->options['records_with'])) ? $this->options['records_with'] : TRUE,
+      '#default_value' => (isset($this->options['agg']['records_with'])) ? $this->options['agg']['records_with'] : TRUE,
     );
 
     $form['agg']['aggregates_with'] = array(
       '#type' => 'checkbox',
       '#title' => t('Filter aggregates displayed'),
       '#description' => t('Filters the aggregates shown based on the value. Doesn\'t affect the number of %base_table records.', array('%base_table' => $this->view->base_table)),
-      '#default_value' => (isset($this->options['aggregates_with'])) ? $this->options['aggregates_with'] : TRUE,
+      '#default_value' => (isset($this->options['agg']['aggregates_with'])) ? $this->options['agg']['aggregates_with'] : TRUE,
     );
 
   }
 
   /**
-   * If the table to be filtered is not aggregated uses the parent::query()
-   * However, if it is uses postgresql any() function to compare
+   * Called by query if the operator is between
    */
-  function query() {
+  function op_between($field) {
 
-    // make optional
-    // if it is not set or empty then don't restrict the query
-    if (!$this->value) {
-      return;
+    // Check whether we have a UNIX timestamp or an ISO Timestamp
+    $check = db_fetch_object(db_query("SELECT $this->real_field as val FROM $this->table WHERE $this->real_field IS NOT NULL LIMIT 1"));
+    if (preg_match('/^\d+$/',$check->val)) {
+      // this is a unix timestamp
+      $is_unix = TRUE;
+    }
+    else {
+      // this is an ISO Timestamp
+      $is_unix = FALSE;
     }
 
-    $this->ensure_my_table();
+    if ($this->operator == 'between') {
+      $a = intval(strtotime($this->value['min'], 0));
+      $b = intval(strtotime($this->value['max'], 0));
+    }
+    else {
+      $a = intval(strtotime($this->value['max'], 0));
+      $b = intval(strtotime($this->value['min'], 0));
+    }
 
-    $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
-      $this->aggregated = TRUE;
+    if ($this->value['type'] == 'offset') {
+      $a = '***CURRENT_TIME***' . sprintf('%+d', $a); // keep sign
+      $b = '***CURRENT_TIME***' . sprintf('%+d', $b); // keep sign
+    }
+    // %s is safe here because strtotime scrubbed the input and we might
+    // have a string if using offset.
+    if ($is_unix) {
+      if ($this->operator == 'between') {
+        $this->query->add_where($this->options['group'], "$field >= %s", $a);
+        $this->query->add_where($this->options['group'], "$field <= %s", $b);
+      }
+      else {
+        $this->query->add_where($this->options['group'], "$field >= %s OR $field <= %s", array($a, $b));
+      }
     }
     else {
-      $this->aggregated = FALSE;
+      if ($this->operator == 'between') {
+        $this->query->add_where($this->options['group'], "CAST(EXTRACT(EPOCH FROM $field) as integer) >= %s", $a);
+        $this->query->add_where($this->options['group'], "CAST(EXTRACT(EPOCH FROM $field) as integer) <= %s", $b);
+      }
+      else {
+        $this->query->add_where($this->options['group'], "CAST(EXTRACT(EPOCH FROM $field) as integer) >= %s OR CAST(EXTRACT(EPOCH FROM $field) as integer) <= %s", array($a, $b));
+      }
     }
+  }
 
-    if (!$this->aggregated) {
-      parent::query();
+  /**
+   * Called by query if the operator is not between or empty
+   */
+  function op_simple($field) {
+    $value = intval(strtotime($this->value['value'], 0));
+
+    // Check whether we have a UNIX timestamp or an ISO Timestamp
+    $check = db_fetch_object(db_query("SELECT $this->real_field as val FROM $this->table WHERE $this->real_field IS NOT NULL LIMIT 1"));
+    if (preg_match('/^\d+$/',$check->val)) {
+      // this is a unix timestamp
+      $is_unix = TRUE;
     }
     else {
+      // this is an ISO Timestamp
+      $is_unix = FALSE;
+    }
 
-      // Only base records with value in the aggregated field
-      // This doesn't restrict the items in the aggregate field
-      $this->ensure_my_table();
-      $field = "$this->table_alias.$this->real_field";
-      if ($this->options['agg']['records_with']) {
-        $where = "'%s' = ANY($field)";
-        $this->query->add_where($this->options['group'], $where, $this->value);
+    if ($is_unix) {
+      if (!empty($this->value['type']) && $this->value['type'] == 'offset') {
+        $value = '***CURRENT_TIME***' . sprintf('%+d', $value); // keep sign
       }
-
-      // To restrict the items in the aggregate...
-      // Tell the join handler about the filter
-      // so it can be done in the join query
-      if ($this->options['agg']['aggregates_with']) {
-        $table['join']->filter[] = $field . " = '" . $this->value . "'";
+      $this->query->add_where($this->options['group'], "$field $this->operator %s", $value);
+    }
+    else {
+      if (!empty($this->value['type']) && $this->value['type'] == 'offset') {
+        $value = '***CURRENT_TIME***' . sprintf('%+d', $value); // keep sign
       }
+      $this->query->add_where($this->options['group'], "CAST(EXTRACT(EPOCH FROM $field) as integer) $this->operator %s", $value);
     }
+  }
 
+  /**
+   * Validate that the time values convert to something usable.
+   *
+   * We modify it to
+   * - fix a bug in the views handler for single values
+   *    $value['value'] didn't exist
+   * - fix a pass by reference error
+   *    changed form_error to form_set_error
+   */
+  function validate_valid_time(&$form, $operator, $value) {
+    $operators = $this->operators();
+
+    if ($operators[$operator]['values'] == 1) {
+      $convert = strtotime($value);
+      if (!empty($form) && ($convert == -1 || $convert === FALSE)) {
+        form_set_error($form['value'], t('Invalid date format.'));
+      }
+    }
+    elseif ($operators[$operator]['values'] == 2) {
+      $min = strtotime($value['min']);
+      if ($min == -1 || $min === FALSE) {
+        form_set_error($form['min'], t('Invalid date format.'));
+      }
+      $max = strtotime($value['max']);
+      if ($max == -1 || $max === FALSE) {
+        form_set_error($form['max'], t('Invalid date format.'));
+      }
+    }
   }
 
 }

tripal_views/views/handlers/chado_views_handler_filter_equality.inc

@@ -30,14 +30,14 @@ class chado_views_handler_filter_equality extends views_handler_filter_equality
       '#type' => 'checkbox',
       '#title' => t('Filter base table records'),
       '#description' => t('Filters %base_table to only those with the value in the aggregate array.', array('%base_table' => $this->view->base_table)),
-      '#default_value' => (isset($this->options['records_with'])) ? $this->options['records_with'] : TRUE,
+      '#default_value' => (isset($this->options['agg']['records_with'])) ? $this->options['agg']['records_with'] : TRUE,
     );
 
     $form['agg']['aggregates_with'] = array(
       '#type' => 'checkbox',
       '#title' => t('Filter aggregates displayed'),
       '#description' => t('Filters the aggregates shown based on the value. Doesn\'t affect the number of %base_table records.', array('%base_table' => $this->view->base_table)),
-      '#default_value' => (isset($this->options['aggregates_with'])) ? $this->options['aggregates_with'] : TRUE,
+      '#default_value' => (isset($this->options['agg']['aggregates_with'])) ? $this->options['agg']['aggregates_with'] : TRUE,
     );
 
   }

tripal_views/views/handlers/chado_views_handler_filter_float.inc

@@ -30,14 +30,14 @@ class chado_views_handler_filter_float extends views_handler_filter_float {
       '#type' => 'checkbox',
       '#title' => t('Filter base table records'),
       '#description' => t('Filters %base_table to only those with the value in the aggregate array.', array('%base_table' => $this->view->base_table)),
-      '#default_value' => (isset($this->options['records_with'])) ? $this->options['records_with'] : TRUE,
+      '#default_value' => (isset($this->options['agg']['records_with'])) ? $this->options['agg']['records_with'] : TRUE,
     );
 
     $form['agg']['aggregates_with'] = array(
       '#type' => 'checkbox',
       '#title' => t('Filter aggregates displayed'),
       '#description' => t('Filters the aggregates shown based on the value. Doesn\'t affect the number of %base_table records.', array('%base_table' => $this->view->base_table)),
-      '#default_value' => (isset($this->options['aggregates_with'])) ? $this->options['aggregates_with'] : TRUE,
+      '#default_value' => (isset($this->options['agg']['aggregates_with'])) ? $this->options['agg']['aggregates_with'] : TRUE,
     );
 
   }

tripal_views/views/handlers/chado_views_handler_filter_numeric.inc

@@ -30,14 +30,14 @@ class chado_views_handler_filter_numeric extends views_handler_filter_numeric {
       '#type' => 'checkbox',
       '#title' => t('Filter base table records'),
       '#description' => t('Filters %base_table to only those with the value in the aggregate array.', array('%base_table' => $this->view->base_table)),
-      '#default_value' => (isset($this->options['records_with'])) ? $this->options['records_with'] : TRUE,
+      '#default_value' => (isset($this->options['agg']['records_with'])) ? $this->options['agg']['records_with'] : TRUE,
     );
 
     $form['agg']['aggregates_with'] = array(
       '#type' => 'checkbox',
       '#title' => t('Filter aggregates displayed'),
       '#description' => t('Filters the aggregates shown based on the value. Doesn\'t affect the number of %base_table records.', array('%base_table' => $this->view->base_table)),
-      '#default_value' => (isset($this->options['aggregates_with'])) ? $this->options['aggregates_with'] : TRUE,
+      '#default_value' => (isset($this->options['agg']['aggregates_with'])) ? $this->options['agg']['aggregates_with'] : TRUE,
     );
 
   }

tripal_views/views/handlers/chado_views_handler_filter_boolean_operator_string.inc → tripal_views/views/handlers/chado_views_handler_filter_select_cvterm.inc

@@ -2,13 +2,26 @@
 
 /**
  * @file
- * A chado wrapper for the views_handler_filter_boolean_operator_string.
+ * Purpose: This Handler provides a select list for the type field
  *
- * Handles fields which may be aggregated during the chado join process. There are options
- * to filter the base table based on an aggregated table or just filter the aggregated
- * table (showing blank for that field if there are no records in the aggregated table).
+ *  NOTE: This handler only works when applied to the type_id field in the base_table of
+ *  this view.
+ *
+ * @ingroup views_filter_handlers
+ * @ingroup tripal_core
  */
-class chado_views_handler_filter_boolean_operator_string extends views_handler_filter_boolean_operator_string {
+class chado_views_handler_filter_select_cvterm extends views_handler_filter_chado_select_cvterm_name {
+
+ /**
+  * Executed when the field is added
+  * Determine which cv to limit the cvterms to
+  */
+  function init(&$view, $options) {
+
+    include_once('chado_wrapper_functions.inc');
+    parent::init($view, $options);
+
+  }
 
   /**
    * Defines the options form (form available to admin when they add a field to a view)
@@ -29,15 +42,15 @@ class chado_views_handler_filter_boolean_operator_string extends views_handler_f
     $form['agg']['records_with'] = array(
       '#type' => 'checkbox',
       '#title' => t('Filter base table records'),
-      '#description' => t('Filters %table to only those with the value in the aggregate array.', array('%table' => $this->view->base_table)),
-      '#default_value' => (isset($this->options['records_with'])) ? $this->options['records_with'] : TRUE,
+      '#description' => t('Filters %base_table to only those with the value in the aggregate array.', array('%base_table' => $this->view->base_table)),
+      '#default_value' => (isset($this->options['agg']['records_with'])) ? $this->options['agg']['records_with'] : TRUE,
     );
 
     $form['agg']['aggregates_with'] = array(
       '#type' => 'checkbox',
       '#title' => t('Filter aggregates displayed'),
-      '#description' => t('Filters the aggregates shown based on the value. Doesn\'t affect the number of %table records.', array('%table' => $this->view->base_table)),
-      '#default_value' => (isset($this->options['aggregates_with'])) ? $this->options['aggregates_with'] : TRUE,
+      '#description' => t('Filters the aggregates shown based on the value. Doesn\'t affect the number of %base_table records.', array('%base_table' => $this->view->base_table)),
+      '#default_value' => (isset($this->options['agg']['aggregates_with'])) ? $this->options['agg']['aggregates_with'] : TRUE,
     );
 
   }
@@ -82,10 +95,11 @@ class chado_views_handler_filter_boolean_operator_string extends views_handler_f
       // Tell the join handler about the filter
       // so it can be done in the join query
       if ($this->options['agg']['aggregates_with']) {
-        $table['join']->filter[] = $field . " = '" . $this->value . "'";
+        if (sizeof($this->value) == 1) {
+          $table['join']->filter[] = $field . " = '" . array_pop($this->value) . "'";
+        }
       }
     }
 
   }
-
 }

tripal_views/views/handlers/chado_views_handler_filter_select_string.inc

@@ -0,0 +1,364 @@
+<?php
+
+/**
+ * @file
+ * Purpose: This Handler provides a generic select list for any chado field that is a string
+ *  The select list includes all distinct values for that field.
+ *
+ * @ingroup views_filter_handlers
+ * @ingroup tripal_core
+ */
+class chado_views_handler_filter_select_string extends chado_views_handler_filter_string {
+
+  function options_form(&$form, &$form_state) {
+    parent::options_form($form, $form_state);
+
+    $form['values_form_type'] = array(
+      '#type' => 'radios',
+      '#title' => t('Filter Type'),
+      '#options' => array(
+        'textfield' => 'Text Field',
+        'select' => 'Drop-Down Box',
+      ),
+      '#default_value' => ($this->options['values_form_type']) ? $this->options['values_form_type'] : 'select',
+    );
+
+    $form['multiple'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Select Multiple'),
+      '#description' => t('Allows more then one option to be selected.'),
+      '#default_value' => (isset($this->options['multiple'])) ? $this->options['multiple'] : FALSE,
+    );
+
+    $form['optional'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Optional'),
+      '#description' => t('Adds --Any-- to the available options.'),
+      '#default_value' => (isset($this->options['optional'])) ? $this->options['optional'] : TRUE,
+    );
+
+    $form['max_length'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Max Width'),
+      '#description' => t('Specify the maximum width of the select box'),
+      '#default_value' => (isset($this->options['max_length'])) ? $this->options['max_length'] : 40,
+
+    );
+    $form['max_length'] = array(
+      '#type' => 'markup',
+      '#value' => t('<strong><font color="red">Note:</font></strong> If another filter exists for the same table then '.
+                    'the values shown in the drop box will only include those from rows that are not filtered.'),
+
+    );
+
+  }
+
+ /**
+  * Defines the value field in both the views filter options form
+  *   and the exposed form
+  */
+  function value_form(&$form, &$form_state) {
+    parent::value_form($form, $form_state);
+
+    if (preg_match('/textfield/', $this->options['values_form_type'])) {
+      $form['value'] = array(
+        '#type' => 'textfield',
+        '#title' => t('%label', array('%label' => $this->options['label'])),
+        '#default_value' => $this->value,
+      );
+
+    }
+    else {
+
+      // build a where clause that will filter the list in the drop box
+      // using fields that are not exposed and that are for the table
+      // from whcih the values in the drop box will be slected and
+      // we only want to use non-exposed fields because these are not
+      // available to the user to edit--their fixed.
+      $where = '';
+      $filters = ($this->view->filter) ? $this->view->filter : array();
+      foreach($filters as $filter_name => $details){
+         // we only want to inclue non-exposed filters
+         if($details->options['exposed'] == FALSE){
+            // we only want to filter on the table we're getting the list from
+            if(strcmp($details->table,$this->table)==0){
+              $where .= "$details->field $details->operator ". $details->value['value'];
+              $where .= ' AND ';
+            }
+         }
+      }
+      if($where){
+         $where = "WHERE $where";
+         $where = substr($where,0,-5); # remove the final ' AND '
+      }
+
+      // get the values from the table
+      $sql = "SELECT $this->real_field FROM $this->table $where ORDER BY $this->field ASC";
+      $previous_db = tripal_db_set_active('chado');  // use chado database
+      $results = db_query($sql);
+      tripal_db_set_active($previous_db);  // now use drupal database
+
+      // Build the select box options
+      $max_length = $this->options['max_length'];
+      if (!$max_length) {
+        $max_length = 40;
+      }
+      if ($this->options['optional']) {
+        //$options['<select '.$this->table.'>'] = '--None--';
+        $options['All'] = '--Any--';
+      }
+      while ($r = db_fetch_object($results)) {
+        if (drupal_strlen($r->{$this->field}) > $max_length) {
+          $options[$r->{$this->field}] = drupal_substr($r->{$this->field}, 0, $max_length) . '...';
+        }
+        else {
+          $options[$r->{$this->field}] = $r->{$this->field};
+        }
+      }
+
+      //Select List
+      $form['value'] = array(
+          '#type' => 'select',
+          '#title' => t('%label', array('%label' => $this->options['label'])),
+          '#options' => $options,
+          '#default_value' => $this->value,
+      );
+
+      if ($this->options['multiple']) {
+        $form['value']['#multiple'] = TRUE;
+      }
+    }
+  }
+
+ /**
+  * Ensures the select list gets rendered when the filter is exposed
+  */
+  function exposed_form(&$form, &$form_state) {
+    if (empty($this->options['exposed'])) {
+      return;
+    }
+
+    $value = $this->options['expose']['identifier'];
+    $this->value_form($form, $form_state);
+    $form[$value] = $form['value'];
+
+    if (isset($form[$value]['#title']) && !empty($form[$value]['#type']) && $form[$value]['#type'] != 'checkbox') {
+      unset($form[$value]['#title']);
+    }
+
+    $this->exposed_translate($form[$value], 'value');
+
+    if (!empty($form['#type']) && ($form['#type'] == 'checkboxes' || ($form['#type'] == 'select' && !empty($form['#multiple'])))) {
+      unset($form[$value]['#default_value']);
+    }
+
+    if (!empty($form['#type']) && $form['#type'] == 'select' && empty($form['#multiple'])) {
+      $form[$value]['#default_value'] = 'All';
+    }
+
+    if ($value != 'value') {
+      unset($form['value']);
+    }
+
+  }
+
+ /**
+  * Adds this filter to the where clause of the views query
+  */
+  function query() {
+
+    // make optional
+    // if it is not set or empty then don't restrict the query
+    if (!$this->value) {
+      return;
+    }
+
+    $this->ensure_my_table();
+
+    $table = $this->query->get_table_info($this->table);
+    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
+      $this->aggregated = TRUE;
+    }
+    else {
+      $this->aggregated = FALSE;
+    }
+
+    // filter the aggregates
+    if ($this->options['agg']['aggregates_with']) {
+      $this::query_restrict_curr_table_records();
+    }
+
+    // filter the base table
+    if ($this->options['agg']['records_with']) {
+      $this::query_restrict_base_records();
+    }
+
+
+
+
+  }
+
+  /**
+   * This function alters the query by adding the appropriate WHERE
+   * to filter the base table to only those with the value in the aggregate array.
+   *
+   * Note: this function is called only from query()
+   */
+  function query_restrict_base_records() {
+    if (!$this->aggregated) {
+      // Not Aggregated ---------------
+
+      $this->ensure_my_table();
+      $field = "$this->table_alias.$this->real_field";
+      $upper = $this->case_transform();
+
+      if ($this->options['multiple'] AND is_array($this->value)) {
+        // Remove any if it's there
+        unset($this->value['All']);
+
+        if (sizeof($this->value)) {
+          $holders = array();
+          foreach ($this->value as $v) {
+            if (preg_match('/^[\d\.]+$/', $v)) {
+              $holders[] = '%f';
+            }
+            else {
+              $holders[] = "'%s'";
+            }
+          }
+          $where = "$field IN (" . implode(", ", $holders) . ")";
+          $this->query->add_where($this->options['group'], $where, $this->value);
+        }
+      }
+      else {
+
+        // Deal with All/Any as value
+        if (preg_match('/All/', $this->value)) {
+          // Don't do anything
+        }
+        else {
+          $info = $this->operators();
+          if (!empty($info[$this->operator]['method'])) {
+            $this->{$info[$this->operator]['method']}($field, $upper);
+          }
+        }
+      }
+
+    }
+    else {
+      // Is Aggregated ----------------
+
+      $this->ensure_my_table();
+      $field = "$this->table_alias.$this->real_field";
+      $upper = $this->case_transform();
+
+      if ($this->options['multiple'] AND is_array($this->value)) {
+        // Remove any if it's there
+        unset($this->value['All']);
+
+        if (sizeof($this->value) > 1) {
+          $holders = array();
+          foreach ($this->value as $v) {
+            $holders[] = "'%s'";
+          }
+          $where = $field .' && ARRAY[' . implode(", ", $holders) . ']';
+          $this->query->add_where($this->options['group'], $where, $this->value);
+
+        }
+        elseif (sizeof($this->value) == 1) {
+          $where = "'%s' = ANY($field)";
+          $this->query->add_where($this->options['group'], $where, array_pop($this->value));
+        }
+      }
+      else {
+
+        // Deal with All/Any as value
+        if (preg_match('/All/', $this->value)) {
+          // Don't do anything
+        }
+        else {
+          $where = "'%s' = ANY($field)";
+          $this->query->add_where($this->options['group'], $where, $this->value);
+        }
+      }
+
+    }
+  }
+
+  /**
+   * This function alters the query by adding the appropriate WHERE
+   * to filter the aggregates shown based on the value. Doesn't affect
+   * the number of base table records.
+   *
+   * Note: this function is called only from query()
+   */
+  function query_restrict_curr_table_records() {
+
+    if (!$this->aggregated) {
+      // Not Aggregated ---------------
+      // Warn the admin/user that they have selected that the aggregates should be filtered
+      // on a field that isn't aggregated...
+      watchdog(
+        'tripal_views',
+        'You have chosen to filter the aggregates shown for %table %field
+          in %view; however, that field is not aggregated (ie: it is part of the base table
+          or is a 1:1 relationship to the base table)',
+        array(
+          '%field' => $this->field,
+          '%table' => $this->table,
+          '%view' => $this->view->name
+        ),
+        WATCHDOG_WARNING
+      );
+      // Do nothing!
+    }
+    else {
+      // Is Aggregated ----------------
+
+      $this->ensure_my_table();
+      $field = "$this->table_alias.$this->real_field";
+      $upper = $this->case_transform();
+
+      if ($this->options['multiple'] AND is_array($this->value)) {
+        // Remove any if it's there
+        unset($this->value['All']);
+
+        if (sizeof($this->value) > 1) {
+          $holders = array();
+          foreach ($this->value as $v) {
+            $holders[] = "'%s'";
+          }
+          $where = $field .' IN (' . implode(", ", $holders) . ')';
+          $where = vsprintf($where, $this->value);
+
+          // Add the where to the chado aggregated join object for this table
+          // then the views_handler_join_chado_aggregator will add this to the WHERE
+          // clause of the sub-query generating the aggregated listing
+          $this->query->table_queue[ $this->table ]['join']->filter[] = $where;
+
+        }
+        elseif (sizeof($this->value) == 1) {
+          $where = "$field = '%s'";
+          $where = vsprintf($where, $this->value);
+
+          // Add the where to the chado aggregated join object for this table
+          // then the views_handler_join_chado_aggregator will add this to the WHERE
+          // clause of the sub-query generating the aggregated listing
+          $this->query->table_queue[ $this->table ]['join']->filter[] = $where;
+        }
+      }
+      else {
+
+        // Deal with All/Any as value
+        if (preg_match('/All/', $this->value)) {
+          // Don't do anything
+        }
+        else {
+          $where = "'%s' = ANY($field)";
+          $this->query->add_where($this->options['group'], $where, $this->value);
+        }
+      }
+
+    }
+  }
+}

tripal_views/views/handlers/chado_views_handler_filter_string.inc

@@ -30,14 +30,14 @@ class chado_views_handler_filter_string extends views_handler_filter_string {
       '#type' => 'checkbox',
       '#title' => t('Filter base table records'),
       '#description' => t('Filters %base_table to only those with the value in the aggregate array.', array('%base_table' => $this->view->base_table)),
-      '#default_value' => (isset($this->options['records_with'])) ? $this->options['records_with'] : TRUE,
+      '#default_value' => (isset($this->options['agg']['records_with'])) ? $this->options['agg']['records_with'] : TRUE,
     );
 
     $form['agg']['aggregates_with'] = array(
       '#type' => 'checkbox',
       '#title' => t('Filter aggregates displayed'),
       '#description' => t('Filters the aggregates shown based on the value. Doesn\'t affect the number of %base_table records.', array('%base_table' => $this->view->base_table)),
-      '#default_value' => (isset($this->options['aggregates_with'])) ? $this->options['aggregates_with'] : TRUE,
+      '#default_value' => (isset($this->options['agg']['aggregates_with'])) ? $this->options['agg']['aggregates_with'] : TRUE,
     );
 
   }

tripal_views/views/handlers/chado_views_handler_sort_date.inc

@@ -1,58 +0,0 @@
-<?php
-
-/**
- * @file
- * A chado wrapper for the views_handler_sort_date.
- *
- * Handles fields which may be aggregated during the chado join process. Sorting of
- * aggregated fields required PostgreSQL 9.0 due to postgresql limitations. Sorting of
- * non-aggregated fields works for all PostgreSQL versions.
- */
-class chado_views_handler_sort extends views_handler_sort_date {
-
-  /**
-   * Defines the options form (form available to admin when they add a field to a view)
-   */
-  function options_form(&$form, &$form_state) {
-
-    $form['msg'] = array(
-      '#type' => 'item',
-      '#value' => '<b>Sorting of aggregated fields only works for PostgreSQL 9.0+. This is due to lack of support at the database level. With lower postgreSQL versions, no sorting is applied.</b>'
-    );
-
-    parent::options_form($form, $form_state);
-  }
-
-  /**
-   * Adds the sort to the query only if the field isn't aggregated
-   * If the field is aggregated then the sort has to be applied at the join handler level
-   */
-  function query() {
-
-    // Determine if the current field is part of an aggregated table
-    $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
-      $this->aggregated = TRUE;
-    }
-    else {
-      $this->aggregated = FALSE;
-    }
-
-    // One day when the aggregated sort will work (ie: Postgresql 9.0+)
-    // it will need to be applied in join handler
-    // thus tell join handler about the sort
-    $table['join']->sort[] = array(
-      'table' => $table['alias'],
-      'field' => $this->options['field'],
-      'order' => $this->options['order']
-    );
-
-
-    // if not then add the sort
-    if (!$this->aggregated) {
-      parent::query();
-    }
-
-  }
-
-}

tripal_views/views/handlers/chado_views_handler_sort_formula.inc

@@ -1,58 +0,0 @@
-<?php
-
-/**
- * @file
- * A chado wrapper for the views_handler_sort_formula.
- *
- * Handles fields which may be aggregated during the chado join process. Sorting of
- * aggregated fields required PostgreSQL 9.0 due to postgresql limitations. Sorting of
- * non-aggregated fields works for all PostgreSQL versions.
- */
-class chado_views_handler_sort extends views_handler_sort_formula {
-
-  /**
-   * Defines the options form (form available to admin when they add a field to a view)
-   */
-  function options_form(&$form, &$form_state) {
-
-    $form['msg'] = array(
-      '#type' => 'item',
-      '#value' => '<b>Sorting of aggregated fields only works for PostgreSQL 9.0+. This is due to lack of support at the database level. With lower postgreSQL versions, no sorting is applied.</b>'
-    );
-
-    parent::options_form($form, $form_state);
-  }
-
-  /**
-   * Adds the sort to the query only if the field isn't aggregated
-   * If the field is aggregated then the sort has to be applied at the join handler level
-   */
-  function query() {
-
-    // Determine if the current field is part of an aggregated table
-    $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
-      $this->aggregated = TRUE;
-    }
-    else {
-      $this->aggregated = FALSE;
-    }
-
-    // One day when the aggregated sort will work (ie: Postgresql 9.0+)
-    // it will need to be applied in join handler
-    // thus tell join handler about the sort
-    $table['join']->sort[] = array(
-      'table' => $table['alias'],
-      'field' => $this->options['field'],
-      'order' => $this->options['order']
-    );
-
-
-    // if not then add the sort
-    if (!$this->aggregated) {
-      parent::query();
-    }
-
-  }
-
-}

tripal_views/views/handlers/chado_views_handler_sort_menu_hierarchy.inc

@@ -1,58 +0,0 @@
-<?php
-
-/**
- * @file
- * A chado wrapper for the views_handler_sort_menu_hierarchy.
- *
- * Handles fields which may be aggregated during the chado join process. Sorting of
- * aggregated fields required PostgreSQL 9.0 due to postgresql limitations. Sorting of
- * non-aggregated fields works for all PostgreSQL versions.
- */
-class chado_views_handler_sort extends views_handler_sort_menu_hierarchy {
-
-  /**
-   * Defines the options form (form available to admin when they add a field to a view)
-   */
-  function options_form(&$form, &$form_state) {
-
-    $form['msg'] = array(
-      '#type' => 'item',
-      '#value' => '<b>Sorting of aggregated fields only works for PostgreSQL 9.0+. This is due to lack of support at the database level. With lower postgreSQL versions, no sorting is applied.</b>'
-    );
-
-    parent::options_form($form, $form_state);
-  }
-
-  /**
-   * Adds the sort to the query only if the field isn't aggregated
-   * If the field is aggregated then the sort has to be applied at the join handler level
-   */
-  function query() {
-
-    // Determine if the current field is part of an aggregated table
-    $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
-      $this->aggregated = TRUE;
-    }
-    else {
-      $this->aggregated = FALSE;
-    }
-
-    // One day when the aggregated sort will work (ie: Postgresql 9.0+)
-    // it will need to be applied in join handler
-    // thus tell join handler about the sort
-    $table['join']->sort[] = array(
-      'table' => $table['alias'],
-      'field' => $this->options['field'],
-      'order' => $this->options['order']
-    );
-
-
-    // if not then add the sort
-    if (!$this->aggregated) {
-      parent::query();
-    }
-
-  }
-
-}

tripal_views/views/handlers/chado_views_handler_sort_random.inc

@@ -1,58 +0,0 @@
-<?php
-
-/**
- * @file
- * A chado wrapper for the views_handler_sort_random.
- *
- * Handles fields which may be aggregated during the chado join process. Sorting of
- * aggregated fields required PostgreSQL 9.0 due to postgresql limitations. Sorting of
- * non-aggregated fields works for all PostgreSQL versions.
- */
-class chado_views_handler_sort extends views_handler_sort_random {
-
-  /**
-   * Defines the options form (form available to admin when they add a field to a view)
-   */
-  function options_form(&$form, &$form_state) {
-
-    $form['msg'] = array(
-      '#type' => 'item',
-      '#value' => '<b>Sorting of aggregated fields only works for PostgreSQL 9.0+. This is due to lack of support at the database level. With lower postgreSQL versions, no sorting is applied.</b>'
-    );
-
-    parent::options_form($form, $form_state);
-  }
-
-  /**
-   * Adds the sort to the query only if the field isn't aggregated
-   * If the field is aggregated then the sort has to be applied at the join handler level
-   */
-  function query() {
-
-    // Determine if the current field is part of an aggregated table
-    $table = $this->query->get_table_info($this->table);
-    if (preg_match('/aggregator/', $table['join']->definition['handler'])) {
-      $this->aggregated = TRUE;
-    }
-    else {
-      $this->aggregated = FALSE;
-    }
-
-    // One day when the aggregated sort will work (ie: Postgresql 9.0+)
-    // it will need to be applied in join handler
-    // thus tell join handler about the sort
-    $table['join']->sort[] = array(
-      'table' => $table['alias'],
-      'field' => $this->options['field'],
-      'order' => $this->options['order']
-    );
-
-
-    // if not then add the sort
-    if (!$this->aggregated) {
-      parent::query();
-    }
-
-  }
-
-}

tripal_views/views/handlers/chado_wrapper_functions.inc

@@ -65,7 +65,13 @@ function chado_wrapper_is_aggregated_by_join($handler) {
 function chado_wrapper_is_aggregated_by_result($handler, $values) {
   $aggregated = FALSE;
 
-  if (preg_match('/^{.*}$/', $values[0]->{$handler->field_alias})) {
+
+  $i = 0;
+  while (empty($values[$i]->{$handler->field_alias}) AND $i <= sizeof($values)) {
+    $i++;
+  }
+
+  if (preg_match('/^{.*}$/', $values[$i]->{$handler->field_alias})) {
     $aggregated = TRUE;
   }
 

tripal_views/views/handlers/views_handler_field_chado_tf_boolean.inc

@@ -1,39 +0,0 @@
-<?php
-
-/**
- * @file
- * A handler to provide proper displays for booleans.
- *
- * Allows for display of true/false, yes/no, on/off.
- *
- * Definition terms:
- *   - output formats: An array where the first entry is displayed on boolean false
- *      and the second is displayed on boolean true. An example for sticky is:
- *      @code
- *      'output formats' => array(
- *        'sticky' => array('', t('Sticky')),
- *      ),
- *      @endcode
- *
- * @ingroup views_field_handlers
- * @ingroup tripal_core
- */
-class views_handler_field_chado_tf_boolean extends views_handler_field_boolean {
-
-  // Changes the rendered value: t='Yes' & f='No'
-  // Rendered value depends on type of value chosen in options
-  function render($values) {
-    $value = $values->{$this->field_alias};
-    if (!empty($this->options['not'])) {
-      $value = !$value;
-    }
-
-    if (isset($this->formats[$this->options['type']])) {
-      return preg_match('/t/', $value) ? $this->formats[$this->options['type']][0] : $this->formats[$this->options['type']][1];
-    }
-    else {
-      return preg_match('/t/', $value) ? $this->formats['yes-no'][0] : $this->formats['yes-no'][1];
-    }
-  }
-
-}

tripal_views/views/handlers/views_handler_filter_chado_select_cvterm_name.inc

@@ -61,7 +61,7 @@ class views_handler_filter_chado_select_cvterm_name extends views_handler_filter
       // @coder-ignore: non-drupal schema therefore table prefixing does not apply
       $sql = "SELECT cvterm_id, name FROM cvterm WHERE cvterm_id IN (SELECT distinct(type_id) FROM %s)";
       $previous_db = tripal_db_set_active('chado');
-      $resource = db_query($sql, $this->view->base_table);
+      $resource = db_query($sql, $this->table);
       tripal_db_set_active($previous_db);
       $cvterms = array();
       while ( $r = db_fetch_object($resource) ) {