Added back in pub module from branch 6.x-1661416-fix_pub_module

tripal_pub/e_utilities.pl

@@ -0,0 +1,61 @@
+#!/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

@@ -0,0 +1,2687 @@
+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# ""
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+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# ""
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+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# ""
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+

tripal_pub/tripal_pub.info

@@ -0,0 +1,9 @@
+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

@@ -0,0 +1,91 @@
+<?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

@@ -0,0 +1,1729 @@
+<?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

@@ -0,0 +1,71 @@
+<?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(
+
+    ),
+  );
+}