tripal/tripal_pub/includes/pub_form.inc

<?php

/**
 * This is the chado_pub node form callback. The arguments
 * are out of order from a typical form because it's a defined callback
 */

function chado_pub_form($node, $form_state) {
  tripal_core_ahah_init_form();
  $form = array();

  $pub = $node->pub;
  $pub_id = $pub->pub_id;

  $d_title        = $form_state['values']['pubtitle']     ? $form_state['values']['pubtitle']    : $pub->title;
  $d_uniquename   = $form_state['values']['uniquename']   ? $form_state['values']['uniquename']  : $pub->uniquename;
  $d_type_id      = $form_state['values']['type_id']      ? $form_state['values']['type_id']     : $pub->type_id->cvterm_id;
  $d_volume       = $form_state['values']['volume']       ? $form_state['values']['volume']      : $pub->volume;
  $d_volumetitle  = $form_state['values']['volumetitle']  ? $form_state['values']['volumetitle'] : $pub->volumetitle;
  $d_series_name  = $form_state['values']['series_name']  ? $form_state['values']['series_name'] : $pub->series_name;
  $d_issue        = $form_state['values']['issue']        ? $form_state['values']['issue']       : $pub->issue;
  $d_pyear        = $form_state['values']['pyear']        ? $form_state['values']['pyear']       : $pub->pyear;
  $d_pages        = $form_state['values']['pages']        ? $form_state['values']['pages']       : $pub->pages;
  $d_miniref      = $form_state['values']['miniref']      ? $form_state['values']['miniref']     : $pub->miniref;
  $d_publisher    = $form_state['values']['publisher']    ? $form_state['values']['publisher']   : $pub->publisher;
  $d_pubplace     = $form_state['values']['pubplace']     ? $form_state['values']['pubplace']    : $pub->pubplace;
  $d_is_obsolete  = $form_state['values']['is_obsolete']  ? $form_state['values']['is_obsolete'] : $pub->is_obsolete;

  // if the obsolete value is set by the database then it is in the form of
  // 't' or 'f', we need to convert to 1 or 0
  $d_is_obsolete = $d_is_obsolete == 't' ? 1 : $d_is_obsolete;
  $d_is_obsolete = $d_is_obsolete == 'f' ? 0 : $d_is_obsolete;

  // on AHAH callbacks we want to keep a list of all the properties that have been removed
  // we'll store this info in a hidden field and retrieve it here
  $d_removed = $form_state['values']['removed'];

  // get the number of new fields that have been aded via AHAH callbacks
  $num_new = $form_state['values']['num_new'] ? $form_state['values']['num_new'] : 0;

  // initialze default properties array. This is where we store the property defaults
  $d_properties = array();

  // get the list of publication types.  In the Tripal publication
  // ontologies these are all grouped under the term 'Publication Type'
  // we want the default to be 'Journal Article'
  $sql = "
    SELECT 
      CVTS.cvterm_id, CVTS.name
    FROM {cvtermpath} CVTP
      INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
      INNER JOIN {cvterm} CVTO ON CVTP.object_id  = CVTO.cvterm_id
      INNER JOIN {cv}          ON CVTO.cv_id      = CV.cv_id
    WHERE 
      CV.name = 'tripal_pub' AND CVTO.name = 'Publication Type' AND 
      NOT CVTS.is_obsolete = 1
    ORDER BY CVTS.name ASC 
  ";
  $results = chado_query($sql);
  $pub_types = array();
  while ($pub_type = $results->fetchObject()) {
    $pub_types[$pub_type->cvterm_id] = $pub_type->name;
    // if we don't have a default type then set the default to be 'Journal Article'
    if (strcmp($pub_type->name,"Journal Article") == 0 and !$d_type_id) {
      $d_type_id = $pub_type->cvterm_id;
    }
  }
  
  // reset the default to use the stored variable if one exists
  $d_type_id = variable_get('tripal_pub_default_type', $d_type_id);

  // get publication properties list
  $properties_select = array();
  $properties_select[] = 'Select a Property';
  $properties_list = array();
  $sql = "
    SELECT 
      DISTINCT CVTS.cvterm_id, CVTS.name, CVTS.definition
    FROM {cvtermpath} CVTP
      INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
      INNER JOIN {cvterm} CVTO ON CVTP.object_id  = CVTO.cvterm_id
      INNER JOIN {cv}          ON CVTO.cv_id      = CV.cv_id
    WHERE CV.name = 'tripal_pub' and 
      (CVTO.name = 'Publication Details' OR CVTS.name = 'Publication Type') AND 
      NOT CVTS.is_obsolete = 1
    ORDER BY CVTS.name ASC 
  ";
  $prop_types = chado_query($sql);
  while ($prop = $prop_types->fetchObject()) {
    // the 'Citation' term is special because it serves
    // both as a property and as the uniquename for the publiation table
    if ($prop->name != "Citation") {
      $properties_select[$prop->cvterm_id] = $prop->name;
    }
    $properties_list[$prop->cvterm_id] = $prop;
  }

  $form['pub_id'] = array(
    '#type' => 'hidden',
    '#value' => $pub_id,
  );

  // a drupal title can only be 255 characters, but the Chado title can be much longer.
  // we use the publication title as the drupal title, but we'll need to truncate it.
  $form['title'] = array(
    '#type' => 'hidden',
    '#value' => substr($d_title, 0, 255),
  );

  $form['pubtitle'] = array(
    '#type' => 'textarea',
    '#title' => t('Publication Title'),
    '#default_value' => $d_title,
    '#required' => TRUE,
  );

  $form['type_id'] = array(
    '#type' => 'select',
    '#title' => t('Publication Type'),
    '#options' => $pub_types,
    '#required' => TRUE,
    '#default_value' => $d_type_id,
  );

  $form['pyear'] = array(
    '#type' => 'textfield',
    '#title' => t('Publication Year'),
    '#default_value' => $d_pyear,
    '#required' => TRUE,
    '#size' => 5,
    '#description' => t('Enter the year of publication. Also, if available, please add a <b>Publication Date</b> property to specify the full date of publication.'),
  );
  $form['uniquename'] = array(
    '#type' => 'textarea',
    '#title' => t('Citation'),
    '#default_value' => $d_uniquename,
    '#description' => t('All publications must have a unique citation. 
      <b>Please enter the full citation for this publication or leave blank and one will be generated 
      automatically if possible</b>.  For PubMed style citations list 
      the last name of the author followed by initials. Each author should be separated by a comma. Next comes 
      the title, followed by the series title (e.g. journal name), publication date (4 digit year, 3 character Month, day), volume, issue and page numbers. You may also use HTML to provide a link in the citation.  
      Below is an example: <pre>Medeiros PM, Ladio AH, Santos AM, Albuquerque UP. <a href="http://www.ncbi.nlm.nih.gov/pubmed/23462414" target="_blank">Does the selection of medicinal plants by Brazilian local populations 
        suffer taxonomic influence?</a> J Ethnopharmacol. 2013 Apr 19; 146(3):842-52.</pre>'),
  );


  // add in the properties that are actually stored in the pub table fields.
  $num_properties = chado_pub_node_form_add_pub_table_props($form, $form_state, $properties_list,
  $d_properties, $d_removed, $d_volume, $d_volumetitle, $d_issue, $d_pages, $d_series_name);

  // add in the properties from the pubprop table
  $num_properties += chado_pub_node_form_add_pubprop_table_props($form, $form_state, $pub_id, $d_properties, $d_removed);

  // add in any new properties that have been added by the user through an AHAH callback
  $num_new = chado_pub_node_form_add_new_props($form, $form_state, $d_properties, $d_removed);

  // add an empty row of field to allow for addition of a new property
  chado_pub_node_form_add_new_empty_props($form, $properties_select);


  $form['removed'] = array(
    '#type' => 'hidden',
    '#value' => $d_removed,
  );

  $form['num_new'] = array(
    '#type' => 'hidden',
    '#value' => $num_new,
  );
  $form['num_properties'] = array(
    '#type' => 'hidden',
    '#value' => $num_properties,
  );

  $form['is_obsolete'] = array(
    '#type' => 'checkbox',
    '#title' => t('Is Obsolete? (Check for Yes)'),
    '#required' => TRUE,
    '#default_value' => $d_is_obsolete,
  );
  return $form;

}
/*
 *
 */
function chado_pub_validate($node, &$form) {

  // get the submitted values
  $title        = trim($node->pubtitle);
  $uniquename   = trim($node->uniquename);
  $type_id      = trim($node->type_id);
  $volume       = trim($node->volume);
  $volumetitle  = trim($node->volumetitle);
  $series_name  = trim($node->series_name);
  $issue        = trim($node->issue);
  $pyear        = trim($node->pyear);
  $pages        = trim($node->pages);
  $miniref      = trim($node->miniref);
  $publisher    = trim($node->publisher);
  $pubplace     = trim($node->pubplace);
  $is_obsolete  = $node->is_obsolete;
  $pub_id       = $node->pub_id;
  $num_properties = $node->num_properties;
  $num_new = $node->num_new;
  
  $pub = array();

  // if this is a delete then don't validate
  if($node->op == 'Delete') {
    return;
  }
  

  // make sure the year is four digits
  if(!preg_match('/^\d{4}$/', $pyear)){
    form_set_error('pyear', t('The publication year should be a 4 digit year.'));
    return;
  }

  // get the type of publication
  $values = array('cvterm_id' => $type_id);
  $options = array('statement_name' => 'sel_pub_ty');
  $cvterm = tripal_core_chado_select('cvterm', array('name'), $values, $options);
  if (count($cvterm) == 0) {
    $message = t('Invalid publication type.');
    form_set_error('type_id', $message);
    return;
  }  

  // get the media name looking at the properties  
  foreach ($node as $element => $value) {
    // if this is an existing property (either previously in the database or
    // added via AHAH/AJAX callback)
    if (preg_match('/^prop_value-(\d+)-(\d+)$/', $element, $matches)) {
      $prop_type_id = $matches[1];
      $prop_type = tripal_cv_get_cvterm_by_id($prop_type_id);
      if($prop_type->name == 'Conference Name' or $prop_type->name == 'Journal Name') {
        $series_name = $value;
      }
      if($prop_type->name == 'Citation') {
        $uniquename = $value;
      }
      $pub[$prop_type->name] = $value;
    }
    // if this is a new property (added by this submit of the form)
    elseif ($element == 'new_id') {    	 
      $prop_type = tripal_cv_get_cvterm_by_id($value);
      if($prop_type->name == 'Conference Name' or $prop_type->name == 'Journal Name') {
        $series_name = $node->new_value;
      }
      if($prop_type->name == 'Citation') {
        $uniquename = $node->new_value;
      }
      $pub[$prop_type->name] = $node->new_value;
    }
  }
  // if the citation is missing then try to generate one
  if (!$uniquename) {
    $pub['Title'] = $title;
    $pub['Publication Type'][0] = $cvterm[0]->name;
    $pub['Year'] = $pyear;
    $uniquename = tripal_pub_create_citation($pub);
    if (!$uniquename) {
      form_set_error('uniquename', "Cannot automatically generate a citation for this publication type. Please add one manually.");
    }
  }

  $skip_duplicate_check = 0;

  // if this publication is a Patent then skip the validation below.  Patents can have the title
  // name and year but be different
  if (strcmp($cvterm[0]->name,'Patent') == 0) {
    $skip_duplicate_check = 1;
  }

  // on an update ($pub_id is set), check to see if there have been  changes to fields that
  // are used to check for duplicates. If not, then no need to check for duplicates
  if ($pub_id) {
    // first get the original title, type and year before it was changed
    $values = array('pub_id' => $pub_id);
    $columns =  array('title', 'pyear', 'type_id', 'series_name');
    $options = array('statement_name' => 'sel_pub_id');
    $pub = tripal_core_chado_select('pub', $columns, $values, $options);

    // if the title, type,  year or series_name have changed then check the pub
    // to see if it is a duplicate of another
    if((strcmp(strtolower($pub[0]->title), strtolower($title)) == 0) and
       (strcmp(strtolower($pub[0]->series_name), strtolower($series_name)) == 0) and
       ($pub[0]->type_id == $type_id) and
       ($pub[0]->year == $pyear)) {
      $skip_duplicate_check = 1;
    }
  }

  // check to see if a duplicate publication already exists
  if (!$skip_duplicate_check) {

    // make sure the publication is unique using the prefereed import duplication check
    $import_dups_check = variable_get('tripal_pub_import_duplicate_check', 'title_year_media');
    switch ($import_dups_check) {
      case 'title_year':
        $results = tripal_pub_get_pubs_by_title_type_pyear_series($title, NULL, $pyear, NULL);
        // make sure we don't capture our pub_id in the list (remove it)
        foreach ($results as $index => $found_pub_id) {
          if($found_pub_id == $pub_id){
            unset($results[$index]);
          }
        }
        if (count($results) > 0) {
          $message = t('A publication with this title and publication year, already exists.');
          form_set_error('pyear', $message);
        }
        break;
      case 'title_year_type':
        $results = tripal_pub_get_pubs_by_title_type_pyear_series($title, $cvterm[0]->name, $pyear, NULL);

        // make sure we don't capture our pub_id in the list (remove it)
        foreach ($results as $index => $found_pub_id) {
          if($found_pub_id == $pub_id){
            unset($results[$index]);
          }
        }
        if (count($results) > 0) {
          $message = t('A publication with this title, type and publication year, already exists.');
          form_set_error('pyear', $message);
        }
        break;
      case 'title_year_media':
        $results = tripal_pub_get_pubs_by_title_type_pyear_series($title, NULL, $pyear, $series_name);

        // make sure we don't capture our pub_id in the list (remove it)
        foreach ($results as $index => $found_pub_id) {
          if($found_pub_id == $pub_id){
            unset($results[$index]);
          }
        }
        if (count($results) > 0) {
          $message = t('A publication with this title, media name (e.g. Journal Name) and publication year, already exists.');
          form_set_error('pyear', $message);
        }
        break;
    }
  }
  // even though we are skipping the duplication checks above we must make sure the uniquename is unique
  // as that is the offical table constraint
  else {
    $results = tripal_pub_get_pub_by_uniquename($uniquename);
    // make sure we don't capture our pub_id in the list (remove it)
    foreach ($results as $index => $found_pub_id) {
      if($found_pub_id == $pub_id){
        unset($results[$index]);
      }
    }
    if (count($results) > 0) {
      $message = t('A publication with this unique citation already exists.');
      form_set_error('uniquename', $message);
    }
  }
}
/*
 *
 */
function chado_pub_node_form_add_new_empty_props(&$form, $properties_select) {

  // add one more blank set of property fields
  $form['properties']['new']["new_id"] = array(
    '#type'          => 'select',
    '#options'       => $properties_select,
    '#ahah' => array(
      'path'    => "tripal_pub/properties/description",
      'wrapper' => 'tripal-pub-new_value-desc',
      'event'   => 'change',
      'method'  => 'replace',          
  ),
  );
  $form['properties']['new']["new_value"] = array(
    '#type'          => 'textarea',
    '#default_value' => '',
    '#cols'          => 5,
    '#rows'          => $rows,
    '#description'   => '<div id="tripal-pub-new_value-desc"></div>'
    );
    $form['properties']['new']["add"] = array(
    '#type'         => 'image_button',      
    '#value'        => t('Add'),
    '#src'          => drupal_get_path('theme', 'tripal') . '/images/add.png',
    '#ahah' => array(
      'path'    => "tripal_pub/properties/add",
      'wrapper' => 'tripal-pub-edit-properties-table',
      'event'   => 'click',
      'method'  => 'replace',          
    ),
    '#attributes' => array('onClick' => 'return false;'),
    );
}
/*
 *
 */
function chado_pub_node_form_add_new_props(&$form, $form_state, &$d_properties, &$d_removed) {
   
  // first, add in all of the new properties that were added through a previous AHAH callback
  $j = 0;
  $num_properties++;

  // we need to find the
  if ($form_state['values']) {
    foreach ($form_state['values'] as $element_name => $value) {
      if (preg_match('/new_value-(\d+)-(\d+)/', $element_name, $matches)) {
        $new_id = $matches[1];
        $rank = $matches[2];

        // skip any properties that the user requested to delete through a previous
        // AHAH callback or through the current AHAH callback
        if($d_removed["$new_id-$rank"]) {
          continue;
        }
        if($form_state['post']['remove-' . $new_id . '-' . $rank]) {
          $d_removed["$new_id-$rank"] = 1;
          continue;
        }

        // get this new_id information
        $cvterm = tripal_core_chado_select('cvterm', array('name', 'definition'), array('cvterm_id' => $new_id));

        // add it to the $d_properties array
        $d_properties[$new_id][$rank]['name']  = $cvterm->name;
        $d_properties[$new_id][$rank]['id']    = $new_id;
        $d_properties[$new_id][$rank]['value'] = $value;
        $d_properties[$new_id][$rank]['definition']  = $cvterm->definition;
        $num_properties++;

        // determine how many rows we need in the textarea
        $rows = 1;
        if (preg_match('/Abstract/', $cvterm[0]->name)) {
          $rows = 10;
        }
        if ($cvterm[0]->name == 'Authors') {
          $rows = 2;
        }

        // add the new fields
        $form['properties']['new'][$new_id][$rank]["new_id-$new_id-$rank"] = array(
          '#type'          => 'item',
          '#value'         => $cvterm[0]->name
        );
        $form['properties']['new'][$new_id][$rank]["new_value-$new_id-$rank"] = array(
          '#type'          => 'textarea',
          '#default_value' => $value,
          '#cols'          => 50,
          '#rows'          => $rows,
          '#description'   => $cvterm->definition,
        );

        $form['properties']['new'][$new_id][$rank]["remove-$new_id-$rank"] = array(
          '#type'         => 'image_button',
          '#value'        => t('Remove'),
          '#src'          => drupal_get_path('theme', 'tripal') . '/images/minus.png',
          '#ahah' => array(
            'path'    => "tripal_pub/properties/minus/$new_id/$rank",
            'wrapper' => 'tripal-pub-edit-properties-table',
            'event'   => 'click',
            'method'  => 'replace',
        ),
          '#attributes' => array('onClick' => 'return false;'),
        );
      }
    }
  }


  // second add in any new properties added during this callback
  if($form_state['post']['add']) {
    $new_id = $form_state['values']['new_id'];
    $new_value = $form_state['values']['new_value'];

    // get the rank by counting the number of entries
    $rank = count($d_properties[$new_id]);

    // get this new_id information
    $cvterm = tripal_core_chado_select('cvterm', array('name', 'definition'), array('cvterm_id' => $new_id));

    // add it to the $d_properties array
    $d_properties[$new_id][$rank]['name']  = $cvterm->name;
    $d_properties[$new_id][$rank]['id']    = $new_id;
    $d_properties[$new_id][$rank]['value'] = $value;
    $d_properties[$new_id][$rank]['definition']  = $cvterm->definition;
    $num_properties++;

    // determine how many rows we need in the textarea
    $rows = 1;
    if (preg_match('/Abstract/', $cvterm[0]->name)) {
      $rows = 10;
    }
    if ($cvterm[0]->name == 'Authors') {
      $rows = 2;
    }

    // add the new fields
    $form['properties']['new'][$new_id][$rank]["new_id-$new_id-$rank"] = array(
      '#type'          => 'item',
      '#value'         => $cvterm[0]->name
    );
    $form['properties']['new'][$new_id][$rank]["new_value-$new_id-$rank"] = array(
      '#type'          => 'textarea',
      '#default_value' => $new_value,
      '#cols'          => 50,
      '#rows'          => $rows,
      '#description'   => $cvterm->definition,
    );

    $form['properties']['new'][$new_id][$rank]["remove-$new_id-$rank"] = array(
      '#type'         => 'image_button',
      '#value'        => t('Remove'),
      '#src'          => drupal_get_path('theme', 'tripal') . '/images/minus.png',
      '#ahah' => array(
        'path'    => "tripal_pub/properties/minus/$new_id/$rank",
        'wrapper' => 'tripal-pub-edit-properties-table',
        'event'   => 'click',
        'method'  => 'replace',
    ),
      '#attributes' => array('onClick' => 'return false;'),
    );

  }

  return $num_properties;
}
/*
 *
 */
function chado_pub_node_form_add_pubprop_table_props(&$form, $form_state, $pub_id, &$d_properties, &$d_removed) {

  // get the properties for this publication
  $num_properties = 0;

  if(!$pub_id) {
    return $num_properties;
  }

  $sql = "
    SELECT CVT.cvterm_id, CVT.name, CVT.definition, PP.value, PP.rank
    FROM {pubprop} PP
      INNER JOIN {cvterm} CVT on CVT.cvterm_id = PP.type_id
    WHERE PP.pub_id = :pub_id
    ORDER BY CVT.name, PP.rank
  ";
  $pub_props = chado_query($sql, array(':pub_id' => $pub_id));
  while ($prop = $pub_props->fetchObject()) {

    $type_id = $prop->cvterm_id;
    $rank = count($d_properties[$type_id]);

    // skip properties that are found in the pub table
    if($prop->name == "Volume" or $prop->name == "Volume Title" or
    $prop->name == "Issue"  or $prop->name == "Pages" or
    $prop->name == "Citation" or $prop->name == "Journal Name") {
      continue;
    }

    // skip any properties that the user requested to delete through a previous
    // AHAH callback or through the current AHAH callback
    if($d_removed["$type_id-$rank"]) {
      continue;
    }
    if($form_state['post']['remove-' . $type_id . '-' . $rank]) {
      $d_removed["$type_id-$rank"] = 1;
      continue;
    }

    $d_properties[$type_id][$rank]['name']  = $prop->name;
    $d_properties[$type_id][$rank]['id']    = $type_id;
    $d_properties[$type_id][$rank]['value'] = $prop->value;
    $d_properties[$type_id][$rank]['definition']  = $prop->definition;
    $num_properties++;

    // determine how many rows we need in the textarea
    $rows = 1;
    if (preg_match('/Abstract/', $prop->name)) {
      $rows = 10;
    }
    if ($prop->name == 'Authors') {
      $rows = 2;
    }

    $form['properties'][$type_id][$rank]["prop_id-$type_id-$rank"] = array(
      '#type'          => 'item',
      '#value'         => $prop->name,
    );
    $form['properties'][$type_id][$rank]["prop_value-$type_id-$rank"] = array(
      '#type'          => 'textarea',
      '#default_value' => $prop->value,
      '#cols'          => 50,
      '#rows'          => $rows,
      '#description'   => $prop->definition,
    );

    $form['properties'][$type_id][$rank]["remove-$type_id-$rank"] = array(
      '#type'         => 'image_button',
      '#value'        => t('Remove'),
      '#src'          => drupal_get_path('theme', 'tripal') . '/images/minus.png',
      '#ahah' => array(
        'path'    => "tripal_pub/properties/minus/$type_id/$rank",
        'wrapper' => 'tripal-pub-edit-properties-table',
        'event'   => 'click',
        'method'  => 'replace',
    ),
      '#attributes' => array('onClick' => 'return false;'),
    );
  }
  return $num_properties;
}
/*
 *
 */
function chado_pub_node_form_add_pub_table_props(&$form, $form_state, $properties_list,
&$d_properties, &$d_removed, $d_volume, $d_volumetitle, $d_issue, $d_pages, $d_series_name) {

  $num_properties = 0;
  $rank = 0;

  // add properties that are actually part of the pub table
  foreach($properties_list as $type_id => $prop) {

    // skip any properties that the user requested to delete through a previous
    // AHAH callback or through the current AHAH callback
    if($d_removed["$type_id-$rank"]) {
      continue;
    }
    if($form_state['post']["remove-$type_id-$rank"]) {
      $d_removed["$type_id-$rank"] = 1;
      continue;
    }

    // if any of the properties match the fields in the pub table then we
    // want to include those automatically
    if (($prop->name == 'Volume' and $d_volume) or
    ($prop->name == 'Issue' and $d_issue) or
    ($prop->name == 'Pages' and $d_pages) or
    ($prop->name == 'Volume Title' and $d_volumetitle) or
    ($prop->name == 'Journal Name' and $d_series_name)) {

      $d_properties[$type_id][$rank]['name']  = $prop->name;
      $d_properties[$type_id][$rank]['id']    = $type_id;
      $d_properties[$type_id][$rank]['definition']  = $prop->definition;
      $num_properties++;

      if ($prop->name == 'Volume') {
        $d_properties[$type_id][$rank]['value'] = $d_volume;
      }
      if ($prop->name == 'Issue') {
        $d_properties[$type_id][$rank]['value'] = $d_issue;
      }
      if ($prop->name == 'Pages') {
        $d_properties[$type_id][$rank]['value'] = $d_pages;
      }
      if ($prop->name == 'Volume Title') {
        $d_properties[$type_id][$rank]['value'] = $d_volumetitle;
      }
      if ($prop->name == 'Journal Name') {
        $d_properties[$type_id][$rank]['value'] = $d_series_name;
      }

      // determine how many rows we need in the textarea
      $rows = 1;
      if (preg_match('/Abstract/', $prop->name)) {
        $rows = 10;
      }
      if ($prop->name == 'Authors') {
        $rows = 2;
      }

      // add in the fields
      $form['properties'][$type_id][$rank]["prop_id-$type_id-$rank"] = array(
        '#type'          => 'item',
        '#value'         => $prop->name
      );
      $form['properties'][$type_id][$rank]["prop_value-$type_id-$rank"] = array(
        '#type'          => 'textarea',
        '#default_value' => $d_properties[$type_id][$rank]['value'],
        '#cols'          => 50,
        '#rows'          => $rows,
        '#description'   => $description,
      );

      $form['properties'][$type_id][$rank]["remove-$type_id-$rank"] = array(
        '#type'         => 'image_button',
        '#value'        => t('Remove'),
        '#src'          => drupal_get_path('theme', 'tripal') . '/images/minus.png',
        '#ahah' => array(
          'path'    => "tripal_pub/properties/minus/$type_id/$rank",
          'wrapper' => 'tripal-pub-edit-properties-table',
          'event'   => 'click',
          'method'  => 'replace',
      ),
        '#attributes' => array('onClick' => 'return false;'),
      );
    }
  }
  return $num_properties;
}
/*
 *
 */
function theme_chado_pub_node_form($form) {

  $properties_table = tripal_pub_theme_node_form_properties($form);

  $markup  = drupal_render($form['pub_id']);
  $markup .= drupal_render($form['pubtitle']);
  $markup .= drupal_render($form['type_id']);
  $markup .= drupal_render($form['series_name']);
  $markup .= drupal_render($form['pyear']);
  $markup .= drupal_render($form['uniquename']);
  $markup .= "<b>Include Additional Details</b><br>You may add additional properties to this publication by scrolling to the bottom of this table, selecting a property type from the dropdown and adding text.  You may add as many properties as desired by clicking the plus button on the right.  To remove a property, click the minus button";
  $markup .= $properties_table;
  $markup .= drupal_render($form['is_obsolete']);

  $form['properties'] = array(
    '#type' => 'markup',
    '#value' =>  $markup,
  );
  return drupal_render($form);
}

/*
 *
 */
function tripal_pub_theme_node_form_properties($form) {
  $rows = array();

  if ($form['properties']) {

    // first add in the properties derived from the pub and pubprop tables
    // the array tree for these properties looks like this:
    // $form['properties'][$type_id][$rank]["prop_id-$type_id-$rank"]
    foreach ($form['properties'] as $type_id => $elements) {
      // there are other fields in the properties array so we only
      // want the numeric ones those are our type_id
      if (is_numeric($type_id)) {
        foreach ($elements as $rank => $element) {
          if (is_numeric($rank)) {
            $rows[] = array(
            drupal_render($element["prop_id-$type_id-$rank"]),
            drupal_render($element["prop_value-$type_id-$rank"]),
            drupal_render($element["remove-$type_id-$rank"]),
            );
          }
        }
      }
    }

    // second, add in any new properties added by the user through AHAH callbacks
    // the array tree for these properties looks like this:
    // $form['properties']['new'][$type_id][$rank]["new_id-$new_id-$rank"]
    foreach ($form['properties']['new'] as $type_id => $elements) {
      if (is_numeric($type_id)) {
        foreach ($elements as $rank => $element) {
          if (is_numeric($rank)) {
            $rows[] = array(
            drupal_render($element["new_id-$type_id-$rank"]),
            drupal_render($element["new_value-$type_id-$rank"]),
            drupal_render($element["remove-$type_id-$rank"]),
            );
          }
        }
      }
    }

    // finally add in a set of blank field for adding a new property
    $rows[] = array(
    drupal_render($form['properties']['new']['new_id']),
    drupal_render($form['properties']['new']['new_value']),
    drupal_render($form['properties']['new']['add']),
    );
  }

  $headers = array('Property Type','Value', '');
  return theme('table', $headers, $rows, array('id'=> "tripal-pub-edit-properties-table"));
}

/*
 *
 */
function tripal_pub_property_add() {
  $status = TRUE;

  // prepare and render the form
  $form = tripal_core_ahah_prepare_form();

  // we only want to return the properties as that's all we'll replace with this AHAh callback
  $data = tripal_pub_theme_node_form_properties($form);

  // bind javascript events to the new objects that will be returned
  // so that AHAH enabled elements will work.
  $settings = tripal_core_ahah_bind_events();

  // return the updated JSON
  drupal_json(
  array(
      'status'   => $status, 
      'data'     => $data,
      'settings' => $settings,
  )
  );
}
/*
 *
 */
function tripal_pub_property_delete() {
  $status = TRUE;

  // prepare and render the form
  $form = tripal_core_ahah_prepare_form();

  // we only want to return the properties as that's all we'll replace with this AHAh callback
  $data = tripal_pub_theme_node_form_properties($form);

  // bind javascript events to the new objects that will be returned
  // so that AHAH enabled elements will work.
  $settings = tripal_core_ahah_bind_events();

  // return the updated JSON
  drupal_json(
  array(
      'status'   => $status, 
      'data'     => $data,
      'settings' => $settings,
  )
  );
}
/*
 *
 */
function tripal_pub_property_get_description() {
  $new_id = $_POST['new_id'];

  $values = array('cvterm_id' => $new_id);
  $cvterm = tripal_core_chado_select('cvterm', array('definition'), $values);

  $description = '&nbsp;';
  if ($cvterm[0]->definition) {
    $description = $cvterm[0]->definition;
  }
  drupal_json(
  array(
      'status' => TRUE,
      'data'   => '<div id="tripal-pub-new_value-desc">' . $description . '</div>',
  )
  );
}