Made corrections to core, anlaysis and feature modules accidentally in branch where working on new pub module, so had to merge. The pub module isn't quite ready for use but won't break anything

tripal_analysis/tripal_analysis.install

@@ -15,9 +15,18 @@ function tripal_analysis_install() {
   // Use schema API to create database table.
   drupal_install_schema('tripal_analysis');
 
-  // Create analysisfeatureprop table in chado. This cannot be accomplished
-  // by calling drupal_install_schema because it's not in the drupal db. This
-  // table is used to store Blast xml and Interpro html/goterms
+  // we may need the analysisfeatureprop table if it doesn't already exist
+  tripal_analysis_create_analysisfeatureprop();
+  
+  // add cvterms
+  tripal_analysis_add_cvterms();
+}
+/*
+ * 
+ */
+function tripal_analysis_create_analysisfeatureprop(){
+  // Create analysisfeatureprop table in chado.  This is needed for Chado 
+  // version 1.11, the table exists in Chado 1.2. 
   if (!db_table_exists('analysisfeatureprop')) {
     $sql = "CREATE TABLE analysisfeatureprop (".
             "  analysisfeatureprop_id SERIAL PRIMARY KEY, ".
@@ -30,9 +39,14 @@ function tripal_analysis_install() {
             "  CONSTRAINT analysisfeature_id_type_id_rank UNIQUE(analysisfeature_id, type_id, rank)".
             ")";
     chado_query($sql);
-  }
-
-  // add some cvterms
+  } 
+}
+/*
+ * 
+ */
+function tripal_analysis_add_cvterms(){
+  
+  // add analysis_type
   $term = array(
     'name' => 'analysis_type', 
     'def' => 'The type of analysis was performed. This value is automatically set by '.
@@ -40,18 +54,21 @@ function tripal_analysis_install() {
              '(e.g. tripal_analysis_blast, tripal_analysis_go).'
   );
   tripal_cv_add_cvterm($term, 'tripal', 0, 1, 'tripal');
+  
+  // add analysis_date
   $term = array(
     'name' => 'analysis_date', 
     'def' => 'The date that an analysis was performed.'
   );
   tripal_cv_add_cvterm($term, 'tripal', 0, 1, 'tripal');
+  
+  // add analysis_short_name
   $term = array(
     'name' => 'analysis_short_name', 
     'def' => 'A computer legible (no spaces or special characters) abbreviation for the analysis.'
   );     
-  tripal_cv_add_cvterm($term, 'tripal', 0, 1 , 'tripal');
+  tripal_cv_add_cvterm($term, 'tripal', 0, 1 , 'tripal'); 
 }
-
 /**
  * Implementation of hook_uninstall().
  */

tripal_analysis/tripal_analysis.module

@@ -16,6 +16,8 @@
 
 require('api/tripal_analysis.api.inc');
 require('includes/tripal_analysis_privacy.inc');
+require('includes/tripal_analysis.admin.inc');
+
 
 
 /**

tripal_core/api/tripal_core_chado.api.inc

@@ -2602,7 +2602,7 @@ function tripal_core_get_property($basetable, $record_id, $property, $cv_name) {
 
   // construct the array of values to be selected
   $values = array(
-  $fkcol => $record_id,
+    $fkcol => $record_id,
     'type_id' => array(
       'cv_id' => array(
         'name' => $cv_name,
@@ -2612,7 +2612,9 @@ function tripal_core_get_property($basetable, $record_id, $property, $cv_name) {
     ),
   );
   $results = tripal_core_generate_chado_var($basetable . 'prop', $values);
-  $results = tripal_core_expand_chado_vars($results, 'field', $basetable . 'prop.value');
+  if ($results) {
+    $results = tripal_core_expand_chado_vars($results, 'field', $basetable . 'prop.value');
+  }
 
   return $results;
 }
@@ -2680,26 +2682,40 @@ $cv_name, $value, $update_if_present = 0) {
     array('!prop_name' => $property), WATCHDOG_ERROR);
   }
 
-
+  // make sure the cvterm exists.  Otherwise we'll get an error with
+  // prepared statements not matching
+  $values = array(
+    'cv_id' => array(
+      'name' => $cv_name,
+    ),
+    'name' => $property,    
+  );
+  $options = array('statement_name' => 'sel_cvterm_cv');
+  $term = tripal_core_chado_select('cvterm', array('cvterm_id'), $values, $options);  
+  if(!$term or count($term) == 0) {
+    return FALSE;
+  }
+  
   // get the foreign key for this property table
   $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');
   $fkcol = key($table_desc['foreign keys'][$basetable]['columns']);
 
   // construct the array of values to be inserted
   $values = array(
-  $fkcol => $record_id,
+    $fkcol => $record_id,
     'type_id' => array(
       'cv_id' => array(
         'name' => $cv_name,
-  ),
+      ),
       'name' => $property,
-      'is_obsolete' => 0
-  ),
+    ),
     'value' => $value,
     'rank' => $rank,
   );
 
-  return tripal_core_chado_insert($basetable . 'prop', $values);
+  $options = array('statement_name' => 'ins_' . $basetable . 'prop_' . substr($fkcol, 0, 2) . 'tyvara');
+  $result = tripal_core_chado_insert($basetable . 'prop', $values, $options);
+  return $result;
 }
 
 /**

tripal_core/api/tripal_core_misc.api.inc

@@ -0,0 +1,53 @@
+<?php 
+/**
+ * This function implements a pager, similar to a pager for a database query
+ * using a non query.  Rather than pass a query as in pager_query function, a 
+ * callback function should recieve as it's first argument an array of the 
+ * argumetns passed to this function. The second argument should be the 
+ * number of results to retreive, and the third argument should be the the
+ * element index (same as with pager_query) function.  The callback function
+ * should always return an array. If no values are available then an empty 
+ * array should be returned.
+ * 
+ * @param $func
+ *  The name of the callback function used to retrieve the results. The
+ *  callback function should have three arguments: first, an array of values
+ *  passed into the tripal_pager_callback; second, the start index of
+ *  the paged values; third, the number of records to include.
+ * @param cfunc
+ *  The name of the callback function used to specify the total results. The
+ *  callback f unction should receive one argument: an array of values that
+ *  are passed into the tripal_pager_callbck function. 
+ * @param limit
+ *  The number of records to include in the paged results
+ * @param element
+ *  A unique integer ID if more than one pager exists on a page.  if multiple
+ *  types of pagers (e.g. pager_query, chado_pager_query) are on the same
+ *  page then this parameter should be unique amongst them all.
+ */
+function tripal_pager_callback($func, $cfunc, $limit = 9, $element = 0) {
+  
+  global $pager_page_array, $pager_total, $pager_total_items;
+  $page = isset($_GET['page']) ? $_GET['page'] : '';
+  
+  // Substitute in query arguments.
+  $args = func_get_args();
+  $args = array_slice($args, 3);
+  // Alternative syntax for '...'
+  if (isset($args[0]) && is_array($args[0])) {
+    $args = $args[0];
+  }
+
+  $count = $cfunc($args);  
+  
+  // Convert comma-separated $page to an array, used by other functions.
+  $pager_page_array = explode(',', $page);
+
+  // We calculate the total of pages as ceil(items / limit).
+  $pager_total_items[$element] = $count;
+  $pager_total[$element] = ceil($pager_total_items[$element] / $limit);
+  $pager_page_array[$element] = max(0, min((int)$pager_page_array[$element], ((int)$pager_total[$element]) - 1));
+  
+  // retrieve the results using the specified callback.
+  return $func($args, $pager_page_array[$element] * $limit, $limit);
+}

tripal_core/tripal_core.module

@@ -44,6 +44,7 @@ require_once "api/tripal_core_ahah.api.inc";
 require_once "api/tripal_core_custom_tables.api.inc";
 require_once "api/tripal_core_jobs.api.inc";
 require_once "api/tripal_core_mviews.api.inc";
+require_once "api/tripal_core_misc.api.inc";
 require_once "includes/jobs.php";
 require_once "includes/mviews.php";
 require_once "includes/custom_tables.php";

tripal_feature/api/tripal_feature.api.inc

@@ -87,8 +87,7 @@ function tripal_feature_analysis_get_property($analysis_id = NULL, $feature_id =
  * @ingroup tripal_feature_api
  */
 function tripal_feature_analysis_insert_property($analysis_id = NULL, $feature_id = NUll,
-  $analysisfeature_id = NULL, $property, $value, $update_if_present = 0,
-  $cv_name = 'tripal') {
+  $analysisfeature_id = NULL, $property, $value, $update_if_present = 0, $cv_name = 'tripal') {
 
   // check that the incoming arguments are correct
   if (($analysis_id and !$feature_id) or
@@ -107,8 +106,15 @@ function tripal_feature_analysis_insert_property($analysis_id = NULL, $feature_i
   }
 
   // insert the property.
-  return tripal_core_insert_property('analysisfeature', $analysisfeature_id,
+  $success = tripal_core_insert_property('analysisfeature', $analysisfeature_id,
     $property, $cv_name, $value, $update_if_present);
+  if (!$success) {
+     watchdog('tripal_feature',
+      'tripal_feature_analysis_insert_property: Failed to insert analysis feature property',
+       array(), WATCHDOG_WARNING);  
+     return FALSE;
+  }
+  return $success;
 }
 
 /**
@@ -928,4 +934,120 @@ function tripal_feature_get_feature_relationships($feature) {
     }
   }
   return $relationships;
-} 
+} 
+
+/*
+ * This function adds an entry to the feature_dbxref table.
+  *
+ * @param $feature_id
+ *   The numeric feature_if of the feature 
+ * @param $dbname
+ *   The name of the database to which the term belongs
+ * @param accession
+ *   The accession of the term   
+ *    
+ * @return
+ *   TRUE on success. FALSE on failure.
+ *
+ * @ingroup tripal_feature_api
+ */
+function tripal_feature_add_dbxref($feature_id, $dbname, $accession) {
+   
+  // make sure the db exists. If it doesn't, then add it
+  $values = array('name' => $dbname);
+  $options = array('statement_name' => 'sel_db_na');
+  $db = tripal_core_chado_select('db', array('db_id'), $values, $options);
+  if (!$db or count($db) == 0) {    
+    $options = array('statement_name' => 'ins_db_na');
+    $success = tripal_core_chado_insert('db', $values, $options);
+      if (!$success) {
+      watchdog('tripal_feature', 'tripal_feature_add_dbxref: The feature dbxref entry for feature, %feature_id, ". 
+        "could not be added because the database, %dbname, does not exist and cannot be added.', 
+        array('%feature_id' => $feature_id, '%dbname' => $dbname), WATCHDOG_WARNING);
+      return FALSE;
+    }
+  }
+  
+  // first make sure that the record doesn't already exist
+  $values = array(
+    'dbxref_id' => array(
+      'accession' => $accession,
+      'db_id' => array(
+        'name' => $dbname
+      ),
+    ),
+    'feature_id' => $feature_id,
+  );
+  $options = array('statement_name' => 'sel_featuredbxref_dbfe');
+  $xref = tripal_core_chado_select('feature_dbxref', array('feature_dbxref_id'), $values, $options);
+  if (count($xref) == 0) {    
+    // if the record doesn't exist then add it.
+    $options = array('statement_name' => 'ins_featuredbxref_dbfe');
+    $success = tripal_core_chado_insert('feature_dbxref', $values, $options);
+    if (!$success) {
+      watchdog('tripal_feature', 'tripal_feature_add_dbxref: The feature dbxref entry for feature, %feature_id, '. 
+        'could not be added: %db:%accession.', array('%feature_id' => $feature_id, '%db' => $dbname, 
+        '%accession' => $accession), WATCHDOG_WARNING);
+      return FALSE;
+    }
+  }
+  return TRUE;
+}
+
+/*
+ * This function adds an entry to the feature_cvterm table.
+  *
+ * @param $feature_id
+ *   The numeric feature_if of the feature 
+ * @param $cvname
+ *   The name of the controlled vocabulary to which the term belongs
+ * @param cvterm
+ *   The name of the cvterm  
+ *    
+ * @return
+ *   TRUE on success. FALSE on failure.
+ *
+ * @ingroup tripal_feature_api
+ */
+function tripal_feature_add_cvterm($feature_id, $cvname, $cvterm) {
+   
+  // make sure the cv exists. If it doesn't, then add it
+  $values = array('name' => $cvname);
+  $options = array('statement_name' => 'sel_cv_na');
+  $cv = tripal_core_chado_select('cv', array('cv_id'), $values, $options);
+  if (!$cv or count($cv) == 0) {    
+    $options = array('statement_name' => 'ins_cv_na');
+    $success = tripal_core_chado_insert('cv', $values, $options);
+      if (!$success) {
+      watchdog('tripal_feature', 'tripal_feature_add_cvterm: The feature cvterm entry for feature, %feature_id, ". 
+        "could not be added because the CV, %cvname, does not exist and cannot be added.', 
+        array('%feature_id' => $feature_id, '%cvname' => $cvname), WATCHDOG_WARNING);
+      return FALSE;
+    }
+  }
+  
+  // first make sure that the record doesn't already exist
+  $values = array(
+    'cvterm_id' => array(
+      'name' => $cvterm,
+      'cv_id' => array(
+        'name' => $cvname
+      ),
+    ),
+    'feature_id' => $feature_id,
+    'pub_id' => 1,
+  );
+  $options = array('statement_name' => 'sel_featuredcvterm_cvfepu');
+  $xref = tripal_core_chado_select('feature_cvterm', array('feature_cvterm_id'), $values, $options);
+  if (count($xref) == 0) {    
+    // if the record doesn't exist then add it.
+    $options = array('statement_name' => 'ins_featurecvterm_cvfepu');
+    $success = tripal_core_chado_insert('feature_cvterm', $values, $options);
+    if (!$success) {
+      watchdog('tripal_feature', 'tripal_feature_add_cvterm: The feature cvterm entry for feature, %feature_id, '. 
+        'could not be added: %cvterm.', array('%feature_id' => $feature_id, '%cvterm' => $cvterm), WATCHDOG_WARNING);
+      return FALSE;
+    }
+  }
+  return TRUE;
+}

tripal_project/tripal_project.module

@@ -39,6 +39,7 @@ function tripal_project_views_api() {
 function tripal_project_menu() {
   $items[ 'admin/tripal/tripal_project' ]= array(
     'title' => 'Projects',
+    'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of projects'),
     'page callback' => 'theme',
     'page arguments' => array('tripal_project_admin'),
     'access arguments' => array('adminster tripal projects'),

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/includes/pubmed.inc

@@ -0,0 +1,292 @@
+<?php 
+/**
+ * @file
+ * Tripal Pub PubMed Interface
+ *
+ * @defgroup tripal_pub_pubmed PubMed Interface
+ * @ingroup tripal_pub
+ */
+
+/**
+ *
+ */
+function tripal_pub_remote_search_pubmed($terms_str, $num_to_retrieve, $pager_id) {
+
+  // convert the terms list provicded by the caller into a string with words
+  // separated by a '+' symbol.
+  $search_terms = implode("+", preg_split('/\s+/', trim($terms_str)));
+
+  // we want to get the list of pubs using the search terms but using a Drupal style pager
+  $pubs = tripal_pager_callback('tripal_pub_remote_search_pubmed_range',
+    'tripal_pub_remote_search_pubmed_count', $num_to_retrieve, $pager_id, $search_terms);
+  
+  if ($pubs) {
+    foreach ($pubs as $pub) {
+      /*
+      $pmid = $output[$i];
+  
+      //aquiring the pubmed id from the pub table based on the uniquename
+      $values = array( 'uniquename' => $pmid);
+      $pubmed_id = tripal_core_chado_select('pub', array('pub_id'), $values); */
+    }
+  }
+  return $pubs;
+}
+
+/*
+ * This function is used as the callback function when used with the
+ * tripal_pager_callback function.  This function returns a count of
+ * the dataset to be paged.
+ */
+function tripal_pub_remote_search_pubmed_count($terms) {
+
+  // do a quick query using the provided terms, set the session variables
+  // so we can reuse this query and then return the total number of records.
+  $results = tripal_pub_remote_search_pubmed_query($terms);
+  $_SESSION['tripal_pub_pubmed_query']['WebEnv'] = $results['WebEnv'];
+  $_SESSION['tripal_pub_pubmed_query']['QueryKey'] = $results['QueryKey'];
+    
+  return $total_records;
+}
+
+/*
+ * This function is used as the callback function when used with the
+ * tripal_pager_callback function.  This function returns the results
+ * within the specified range
+ */
+function tripal_pub_remote_search_pubmed_range($terms, $start = 0, $limit = 10) {
+
+  // get the query_key and the web_env from the previous count query.
+  $query_key = $_SESSION['tripal_pub_pubmed_query']['QueryKey'];
+  $web_env = $_SESSION['tripal_pub_pubmed_query']['WebEnv'];
+     
+  // repeat the search performed previously (using WebEnv & QueryKey) to retrieve
+  // the PMID's within the range specied.  The PMIDs will be returned as a text list
+  $pmids_txt = tripal_pub_remote_search_pubmed_fetch($terms, $query_key, $web_env, 'uilist', $start, $limit);  
+  
+  // iterate through each PMID and get the publication record. This requires a new search and new fetch
+  $pmids = explode("\n", trim($pmids_txt));
+  $pubs = array();
+  foreach ($pmids as $pmid) {
+    
+    // first intialize the search for a single PMID. This will give us a new query key and Web env 
+    $term = $pmid . "[uid]";    
+    $query = tripal_pub_remote_search_pubmed_query($terms); 
+    
+    // second retrieve the individual record
+    $pub_xml = tripal_pub_remote_search_pubmed_fetch($terms, $query['QueryKey'], $query['WebEnv'], 'xml', 0, 1); 
+    $pubs[] = $pub_xml;
+    
+  } 
+  return $pubs;
+}
+
+/*
+ * 
+ */
+function tripal_pub_remote_search_pubmed_query($terms){
+   
+  // do a search for a single result so that we can establish a history, and get
+  // the number of records. Once we have the number of records we can retrieve
+  // those requested in the range.
+  $query_url = "http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=Pubmed&retmax=1&usehistory=y&term=$terms";
+  $rfh = fopen($query_url, "r");
+  if (!$rfh) {
+    drupal_set_message('Could not perform Pubmed query. Cannot connect to Entrez.', 'error');
+    return 0;    
+  }
+  
+  // retrieve the XML results
+  $query_xml = '';
+  while (!feof($rfh)) {
+    $query_xml .= fread($rfh, 255);
+  }
+  fclose($rfh);
+  $xml = new XMLReader();
+  $xml->xml($query_xml);
+  
+  // iterate though the child nodes of the <eSearchResult> tag and get the count, history and query_id
+  $result = array();
+  while ($xml->read()) {
+    if ($xml->nodeType == XMLReader::ELEMENT) {
+      $element = $xml->name;
+      $xml->read();
+      $value = $xml->value;
+      switch ($element) {
+        case 'Count':
+          $result['Count'] = $value;
+          break;        
+        case 'WebEnv':
+          $result['WebEnv'] = $value;
+          break;
+        case 'QueryKey':
+          $result['QueryKey'] = $value;
+          break;
+      }
+    }
+  }  
+  return $result;
+}
+
+/*
+ * 
+ */
+function tripal_pub_remote_search_pubmed_fetch($terms, $query_key, $web_env, $rettype = 'xml', $start = 0, $limit = 10){
+  
+  // repeat the search performed previously (using WebEnv & QueryKey) to retrieve
+  // the PMID's within the range specied.  The PMIDs will be returned as a text list
+  $fetch_url = "http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=$rettype&retmode=text&retstart=$start&retmax=$limit&db=Pubmed&query_key=$query_key&WebEnv=$web_env";
+  $rfh = fopen($fetch_url, "r");
+  $results = '';
+  while (!feof($rfh)) {
+    $results .= fread($rfh, 255);
+  }  
+  fclose($rfh);
+  
+  return $results;
+}
+
+/*
+ * This function parses the XML containing details of a publication and
+ * converts it into an associative array of where keys are Tripal Pub 
+ * ontology terms and the values are extracted from the XML. The
+ * XML should contain only a single publication record.
+ */
+function tripal_pub_remote_search_pubmed_parse_pubxml($pub_xml) {
+  $pub = array();
+  
+  // read the XML and iterate through it.
+  $xml = new XMLReader();
+  $xml->xml($pub_xml);
+  while ($xml->read()) {    
+    $element = $xml->name;    
+    if ($xml->nodeType == XMLReader::ELEMENT) {
+      $xml->read();
+      $value = $xml->value;
+      switch ($element) {
+        case 'PMID':
+          $pub['pub_accession'] = $value;
+          $pub['pub_database'] = 'PMID';
+          break;        
+        case 'Article':
+          tripal_pub_remote_search_pubmed_parse_article($xml, $pub);
+          break;
+      }
+    }
+  }
+  
+  return $pub;
+}
+
+/*
+ * 
+ */
+function tripal_pub_remote_search_pubmed_parse_article($xml, &$pub) {
+    
+  while ($xml->read()) {
+    $element = $xml->name;  
+    // if we're at the </Article> element then we're done with the article...
+    if ($xml->nodeType == XMLReader::END_ELEMENT and $element = 'Article') {
+      return;  
+    }
+    if ($xml->nodeType == XMLReader::ELEMENT) {
+      $element = $xml->name;
+      $xml->read();
+      $value = $xml->value;
+      switch ($element) {
+        case 'Journal':
+          tripal_pub_remote_search_pubmed_parse_journal($xml, $pub);
+          break;
+        case 'ArticleTitle':
+          break;
+        case 'AbstractText':
+          break;
+        case 'Affiliation':
+          break;
+        case 'AuthorList':
+          tripal_pub_remote_search_pubmed_parse_authorlist($xml, $pub);
+          break;
+        case 'Language':
+          break;
+        case 'ArticleDate':
+          break; 
+        default:
+          break;     
+      }
+    }
+  }
+}
+/*
+ * 
+ */
+function tripal_pub_remote_search_pubmed_parse_journal($xml, &$pub) {
+  
+  while ($xml->read()) {
+    $element = $xml->name;
+      
+    if ($xml->nodeType == XMLReader::END_ELEMENT){
+      // if we're at the </AuthorList> element then we're done with the article...
+      if($element = 'Journal') {
+        return;
+      }
+    }
+    if ($xml->nodeType == XMLReader::ELEMENT) {
+      $xml->read();
+      $value = $xml->value;
+      switch ($element) {
+        case 'ISSN':          
+          break;
+        case 'Volume':          
+          break;
+        case 'Year':          
+          break;
+        case 'Title':          
+          break;
+        case 'ISOAbbreviation':          
+          break;
+        default:
+          break;
+      }
+    }
+  }
+}
+/*
+ * 
+ */
+function tripal_pub_remote_search_pubmed_parse_authorlist($xml, &$pub) {
+  $authors = array();
+  $author = array();
+  $author_list = '';
+  
+  while ($xml->read()) {
+    $element = $xml->name;
+      
+    if ($xml->nodeType == XMLReader::END_ELEMENT){
+      // if we're at the </AuthorList> element then we're done with the article...
+      if($element = 'Article') {
+        return;
+      }
+      // if we're at the end </Author> element then we're done with the author and we can
+      // start a new one.
+      if($element = 'Author') {
+        return;
+      }  
+    }
+    if ($xml->nodeType == XMLReader::ELEMENT) {
+      $xml->read();
+      $value = $xml->value;
+      switch ($element) {
+        case 'Author':          
+          break;
+        case 'LastName':          
+          break;
+        case 'ForeName':          
+          break;
+        case 'Initials':          
+          break;
+        default:
+          break;
+      }
+    }
+  }
+}

tripal_pub/includes/remote_search.inc

@@ -0,0 +1,105 @@
+<?php
+/*
+ * 
+ */
+function tripal_pub_remote_search_page() {
+  global $pager_total;
+  
+  // generate the search form 
+  $form = drupal_get_form('tripal_pub_remote_search_form');
+
+  // retrieve any results
+  $remote_db = $_SESSION['tripal_pub_search_criteria']['remote_db'];
+  $search_terms = $_SESSION['tripal_pub_search_criteria']['search_terms'];  
+  $results = tripal_pub_get_remote_search_results($remote_db, $search_terms, 10, 0);
+  
+  // iterate through the results and construct the table displaying the publications
+  if (count($results) > 0) {
+  
+  }
+  
+  // generate the pager
+  $total_items = $pager_total[0];
+  $pager = theme('pager');
+  
+  // join all to form the final page
+  $output = $form . "<p><b>Found " . number_format($total_items) . " Results</b></br>" . $table . '</p>' . $pager;
+    dpm($results);
+  
+  return $output;
+}
+/*
+ * 
+ */
+function tripal_pub_get_remote_search_results($remote_db, $search_terms, $num_to_retrieve, $pager_id) {
+ 
+  $results = array();
+  $callback = 'tripal_pub_remote_search_' . strtolower($remote_db);
+  if (function_exists($callback) and $search_terms) {
+    $results = call_user_func($callback, $search_terms, $num_to_retrieve, $pager_id);
+  }    
+  
+  return $results;  
+}
+/**
+ * Purpose: Provides the form to search pubmed
+ *
+  * @ingroup tripal_pub
+ */
+function tripal_pub_remote_search_form(&$form_state = NULL) {
+  $remote_db = $_SESSION['tripal_pub_search_criteria']['remote_db'];
+  $search_terms = $_SESSION['tripal_pub_search_criteria']['search_terms'];
+  
+  $remote_dbs = array('Pubmed' => 'Pubmed');
+  $form['remote_db'] = array(
+    '#title' => t('Remote Publication Database'),
+    '#type' => 'select',
+    '#options' => $remote_dbs,
+    '#default_value' => $remote_db,
+  );
+
+  $form['search_terms']= array(
+    '#type'          => 'textfield',
+    '#title'         => t('Search Terms'),
+    '#description'   => t('Please provide a list of words, separated by spaces for searching'),
+    '#default_value' => $search_terms,
+  );
+
+  $form['submit'] = array(
+    '#type'         => 'submit',
+    '#value'        => t('Submit'),
+    '#executes_submit_callback' => TRUE,
+  );
+
+  return $form;
+}
+
+/**
+ *
+ */
+function tripal_pub_remote_search_form_validate($form, &$form_state) {
+  $remote_db =  $form_state['values']['remote_db'];
+  $search_terms =  $form_state['values']['search_terms'];
+}
+
+/**
+ *
+ */
+function tripal_pub_remote_search_form_submit($form, &$form_state) {
+  $remote_db =  $form_state['values']['remote_db'];
+  $search_terms =  $form_state['values']['search_terms'];
+  
+  // store the search settings in a session variable. Then when the page
+  // is refreshed these values will be available for the page to 
+  // generate results. 
+  if ($op == 'Reset') {   
+    unset($_SESSION['tripal_pub_search_criteria']); 
+    unset($form_state['values']);
+  }
+  else {
+    $_SESSION['tripal_pub_search_criteria'] = array(
+      'remote_db' => $remote_db,
+      'search_terms' => $search_terms,
+    );
+  }  
+}

tripal_pub/includes/tripal_pub.admin.inc

@@ -0,0 +1,119 @@
+<?php
+/**
+ * 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/publication.obo

@@ -0,0 +1,2687 @@
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+domain: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#Publication  ! Publication
+range: xsd:string 
+
+[Typedef]
+id: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#volume
+domain: __/home/obo/galaxy_dist/database/files/000/dataset_219.dat#__Description16 
+range: xsd:int 
+
+[Typedef]
+id: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#web
+domain: __/home/obo/galaxy_dist/database/files/000/dataset_219.dat#__Description14 
+range: xsd:string 
+
+[Typedef]
+id: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#year
+domain: http://mapekus.fiit.stuba.sk/mapekus/ontologies/v0.2/publication#Publication  ! Publication
+range: xsd:int 
+

tripal_pub/theme/tripal_pub_admin.tpl.php

@@ -0,0 +1,64 @@
+<br /><h3>Tripal Publication Administrative Tools Quick Links</h3>
+<ul>
+<li><?php print l('Configuration', 'admin/tripal/tripal_pub/configuration') ?></li>
+</ul>
+
+<h3>Module Description:</h3>
+<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>
+<h3>Setup Instructions:</h3>
+<ol>
+<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="<?php print url('admin/user/roles') ?>">add roles</a> for classifying users,
+               <a href="<?php print url('admin/user/user') ?>">assign users to roles</a> and
+               <a href="<?php print 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>
+<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="<?php print 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="<?php print url('admin/tripal/tripal_pub/configuration') ?>">Publication->Configuration</a>, select it in the controlled vocabulary '
+                select list and click save configuration.</p></li></ul>
+
+</ol>
+<h3>Features of this Module:</h3>
+<ul>
+<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>
+
+<li><b>Creating a Publication:</b>
+
+<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>
+

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 +1,106 @@
+<?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() {
+  
+  // create the module's data directory
+  tripal_create_moddir('tripal_pub');
+
+  // install the tripal_oub
+  drupal_install_schema('tripal_pub');
+  
+  // add any cvterms we need for this module
+  tripal_pub_add_cvterms();  
+}
+
+
+/*
+ * 
+ * 
+ */
+function tripal_pub_add_cvterms(){
+  
+  tripal_cv_add_cvterm(array('name' => 'abstract', 'def' => 'Publication abstract'), 
+    'tripal_pub', 0, 1, 'tripal');    
+}
+
+/**
+ * Implementation of hook_uninstall().
+ */
+function tripal_pub_uninstall() {
+  //Remove tables
+  drupal_uninstall_schema('tripal_pub');
+
+}
+
+
+/**
+ * Implementation of hook_schema().
+ */
+function tripal_pub_schema() {
+  
+  $schema['chado_pub'] = array(
+    'fields' => array(
+      'vid' => array('type' => 'int', 'unsigned' => TRUE, 'not null' => TRUE, 'default' => 0),
+      'nid' => array('type' => 'int', 'unsigned' => TRUE, 'not null' => TRUE, 'default' => 0),
+      'pub_id' => array('type' => 'int', 'not null' => TRUE, 'default' => 0),
+      'sync_date' => array('type' => 'int', 'not null' => FALSE, 'description' => 'UNIX integer sync date/time'),
+    ),
+    'indexes' => array(
+      'pub_id' => array('pub_id')
+    ),
+    'unique keys' => array(
+      'nid_vid' => array('nid', 'vid'),
+      'vid' => array('vid')
+    ),
+    'primary key' => array('nid'),
+  );
+      /*
+       //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.',
+      ),*/
+  return $schema;
+}
+
+
+
+/**
+ * Implementation of hook_requirements(). 
+ */
+function tripal_pub_requirements($phase) {
+  $requirements = array();
+  if ($phase == 'install') {
+    // make sure chado is installed
+    if (!tripal_core_is_chado_installed()) {
+      $requirements ['tripal_pub'] = array(
+        'title' => "tripal_pub",
+        'value' => "ERROR: Chado most be installed before this module can be enabled",
+        'severity' => REQUIREMENT_ERROR,
+      );
+    }
+  }
+  return $requirements;
+}

tripal_pub/tripal_pub.module

@@ -0,0 +1,1248 @@
+<?php
+
+//require_once('cron.php');
+require_once "includes/tripal_pub.admin.inc";
+require_once "includes/pubmed.inc";
+require_once "includes/remote_search.inc";
+
+/**
+ * @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.
+ */
+
+
+/**
+ * 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,
+    ),
+  );
+}
+
+/**
+ * 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' => 'theme',
+    'page arguments' => array('tripal_pub_admin'),
+    'access arguments' => array('administer tripal pubs'),
+    '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 tripal pubs'),
+    '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,
+  );
+  
+  $items['pub_finder'] = array(
+    'title' => t('Publication Finder'),
+    'description' => t('Finds publications using remote publication databases (e.g. PubMed).'),
+    'page callback' => 'tripal_pub_remote_search_page',
+    '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)
+    ),
+   'tripal_pub_admin' => array(
+      'template' => 'tripal_pub_admin',  
+      'arguments' =>  array(NULL),  
+      'path' => drupal_get_path('module', 'tripal_pub') . '/theme' 
+    ),
+  );
+}
+
+/**
+ * Implement hook_perm().
+ */
+function tripal_pub_perm() {
+  return array(
+    'access chado_pub content',
+    'create chado_pub content',
+    'delete chado_pub content',
+    'edit chado_pub content',
+    'administer tripal pubs',
+  );
+}
+
+
+/**
+ * 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, $account ) {
+  if ($op == 'create') {
+    if (!user_access('create chado_pub content', $account)) {
+      return FALSE;
+      }
+  }
+
+  if ($op == 'update') {
+    if (!user_access('edit chado_pub content', $account)) {
+      return FALSE;
+    }
+  }
+  if ($op == 'delete') {
+    if (!user_access('delete chado_pub content', $account)) {
+      return FALSE;
+    }
+  }
+  if ($op == 'view') {
+    if (!user_access('access chado_pub content', $account)) {
+      return FALSE;
+    }
+  }
+  return NULL;
+}
+
+
+/**
+ * Implementation of tripal_pub_form().
+ *
+ *
+ *
+ *  @parm &$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, $author);
+
+  }
+
+
+  if (isset($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 $node;
+
+}
+
+/**
+ * Submit handler for 'Add Author' button on node form.
+ */
+function tripal_pub_add_author_submit($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, $user->uid);
+
+      }
+
+}
+  */
+
+
+
+
+//-----------------------------------------------------------------------------
+//  SECTION: Custom form Elements
+//-----------------------------------------------------------------------------
+
+
+/*
+ * This fucnction tells the FAPI(Form-API) that this is a element that will carry a value, contains
+ * arrays of callback function names. Will declare an element will create a reuseable element type.
+ *
+ *  @return
+ *      An associative array with the name of each element type as a key and an
+ *      array of attributes describingthe type as a value
+ */
+function tripal_pub_elements() {
+
+      return array(
+          'publication_author' => array(
+               '#input' => TRUE,
+               '#process' => array('expand_publication_author'),
+               '#element_validate' => array('publication_author_validate'),
+              ),
+      );
+
+}
+
+
+/*
+ *
+ *
+ *
+ */
+function expand_publication_author($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.'));
+    }
+  }
+}
+
+
+

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(
+
+    ),
+  );
+}