tripal/tripal_chado/includes/tripal_chado.fields.inc

<?php

/**
 * Implements hook_field_create_info().
 *
 * This is a Tripal defined hook that supports integration with the
 * TripalEntity field.
 */
function tripal_chado_bundle_create_fields($entity_type, $bundle) {

  $chado_bundle = db_select('chado_bundle', 'cb')
    ->fields('cb')
    ->condition('bundle_id', $bundle->id)
    ->execute()
    ->fetchObject();

  // Get the details about the mapping of this bundle to the Chado table:
  $details = array(
    'chado_cvterm_id' => $chado_bundle->type_id,
    'chado_table' => $chado_bundle->data_table,
    'chado_type_table' => $chado_bundle->type_linker_table,
    'chado_type_column' => $chado_bundle->type_column,
  );

  $info = array();

  // Create the fields for each column in the table.
  tripal_chado_bundle_create_fields_base($info, $details, $entity_type, $bundle);

  // Create custom fields.
  tripal_chado_bundle_create_fields_custom($info, $details, $entity_type, $bundle);

  // Create fields for linking tables.
  tripal_chado_bundle_create_fields_linker($info, $details, $entity_type, $bundle);

  return $info;

}
/**
 *
 * @param unknown $details
 */
function tripal_chado_bundle_create_fields_base(&$info, $details, $entity_type, $bundle) {

  $table_name = $details['chado_table'];
  $type_table = $details['chado_type_table'];
  $type_field = $details['chado_type_column'];
  $cvterm_id  = $details['chado_cvterm_id'];

  // Iterate through the columns of the table and see if fields have been
  // created for each one. If not, then create them.
  $schema = chado_get_schema($table_name);
  if (!$schema) {
    return;
  }

  $pkey = $schema['primary key'][0];


  // Get the list of columns for this table and create a new field for each one.
  $columns = $schema['fields'];
  foreach ($columns as $column_name => $details) {
    // Don't create base fields for the primary key and the type_id field.
    if ($column_name == $pkey or $column_name == $type_field) {
      continue;
    }
    $cvterm = tripal_get_chado_semweb_term($table_name, $column_name, array('return_object' => TRUE));
    if (!$cvterm) {
      tripal_report_error('tripal', TRIPAL_ERROR,
        'Cannot create field for "%table_name.%column_name". Missing an appropriate vocabulary term',
         array('%table_name' => $table_name, '%column_name' => $column_name));
      drupal_set_message(t('Cannot create field for "%table_name.%column_name". Missing an appropriate vocabulary term',
        array('%table_name' => $table_name, '%column_name' => $column_name)), 'error');
      continue;
    }
    $field_name = strtolower($cvterm->dbxref_id->db_id->name . '__' . preg_replace('/ /', '_', $cvterm->name));
    $field_name = substr($field_name, 0, 32);

    // Skip the primary key field.
    if ($column_name == $schema['primary key'][0]) {
      continue;
    }

    // Skip the type field that will always be custom
    if (($table_name == $type_table and $column_name == $type_field) or
         $column_name == 'type_id') {
      continue;
    }

    // Set some defaults for the field.
    $base_info = array(
      'field_name' => $field_name,
      'type' => '',
      'cardinality' => 1,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );

    // Alter the field info array depending on the column details.
    switch($details['type']) {
      case 'char':
        $base_info['type'] = 'text';
        $base_info['settings']['max_length'] = $details['length'];
        break;
      case 'varchar':
        $base_info['type'] = 'text';
        $base_info['settings']['max_length'] = $details['length'];
        break;
      case 'text':
        $base_info['type'] = 'text';
        $base_info['settings']['max_length'] = 17179869184;
        $base_info['settings']['text_processing'] = 1;
        break;
      case 'blob':
        // not sure how to support a blob field.
        continue;
        break;
      case 'int':
        $base_info['type'] = 'number_integer';
        break;
      case 'float':
        $base_info['type'] = 'number_float';
        $base_info['settings']['precision'] = 10;
        $base_info['settings']['scale'] = 2;
        $base_info['settings']['decimal_separator'] = '.';
        break;
      case 'numeric':
        $base_info['type'] = 'number_decimal';
        break;
      case 'serial':
        // Serial fields are most likely not needed as a field.
        break;
      case 'boolean':
        $base_info['type'] = 'list_boolean';
        $base_info['settings']['allowed_values'] = array(0 => "No", 1 => "Yes");
        break;
      case 'datetime':
        // Use the Drupal Date and Date API to create the field/widget
        $base_info['type'] = 'datetime';
        break;
    }

    // Set some default semantic web information
    if ($column_name == 'uniquename') {
      $base_info['settings']['text_processing'] = 0;
    }
    //
    // PUB TABLE
    //
    elseif ($table_name == 'pub' and $column_name == 'uniquename') {
      $base_info['type'] = 'text';
      $base_info['settings']['text_processing'] = 0;
    }

    //
    // ANALYSIS TABLE
    //
    elseif ($table_name == 'analysis' and $column_name == 'sourceuri') {
      $base_info['type'] = 'text';
      $base_info['settings']['text_processing'] = 0;
    }

    $info[$field_name] = $base_info;
  }
}

/**
 *
 * @param unknown $details
 */
function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type, $bundle) {
  $table_name = $details['chado_table'];
  $type_table = $details['chado_type_table'];
  $type_field = $details['chado_type_column'];
  $cvterm_id  = $details['chado_cvterm_id'];

  $schema = chado_get_schema($table_name);

  // BASE TYPE_ID
  // Exclude the type_id field on base tables where content types are mapped
  // by the type_id field or on the organism table where the type_id is mean
  // as an infraspecific name type.
  if (array_key_exists('type_id', $schema['fields']) and
      $table_name != 'organism' and $type_field != 'type_id') {
    $field_name = 'schema__additional_type';
    $field_type = 'schema__additional_type';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => 1,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // BASE ORGANISM_ID
  if ($table_name != 'organism' and
      array_key_exists('organism_id', $schema['fields'])) {
    $field_name = 'obi__organism';
    $field_type = 'obi__organism';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => 1,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // BASE DBXREF
  if (array_key_exists('dbxref_id', $schema['fields'])) {
    $field_name = 'data__accession';
    $field_type = 'data__accession';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => 1,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // FEATURE MD5CHECKSUM
  if ($table_name == 'feature') {
    $field_name = 'data__sequence_checksum';
    $field_type = 'data__sequence_checksum';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => 1,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // FEATURE RESIDUES
  if ($table_name == 'feature') {
    $field_name = 'data__sequence';
    $field_type = 'data__sequence';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => 1,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // FEATURE SEQLEN
  if ($table_name == 'feature') {
    $field_name = 'data__sequence_length';
    $field_type = 'data__sequence_length';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => 1,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // GENE TRANSCRIPTS
  $rel_table = $table_name . '_relationship';
  if (chado_table_exists($rel_table) and $bundle->label == 'gene') {
    $field_name = 'so__transcript';
    $field_type = 'so__transcript';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // ORGANISM TYPE_ID
//   if ($table_name == 'organism' and array_key_exists('type_id', $schema['fields'])) {
//     $field_name = 'taxarank__infraspecific_taxon';
//     $field_type = 'taxarank__infraspecific_taxon';
//     $info[$field_name] = array(
//       'field_name' => $field_name,
//       'type' => $field_type,
//       'cardinality' => 1,
//       'locked' => FALSE,
//       'storage' => array(
//         'type' => 'field_chado_storage',
//       ),
//       'settings' => array(
//       ),
//     );
//   }

  // FEATUREMAP UNITTYPE_ID
  if ($table_name == 'featuremap') {
    $field_name = 'uo__unit';
    $field_type = 'uo__unit';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => 1,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // Add an image field to the Organism type.  This is a Drupal field and
  // not stored in Chado, but is used for backwards compatibility.
  if ($table_name == 'organism') {
    $field_name = 'data__image';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => 'image',
      'cardinality' => 1,
      'locked' => FALSE,
    );
  }
}

/**
 *
 * @param unknown $details
 */
function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type, $bundle) {

  $table_name = $details['chado_table'];
  $type_table = $details['chado_type_table'];
  $type_field = $details['chado_type_column'];
  $cvterm_id  = $details['chado_cvterm_id'];

  // CONTACTS
  $contact_table = $table_name . '_contact';
  if (chado_table_exists($contact_table)) {
    $schema = chado_get_schema($contact_table);
    $pkey = $schema['primary key'][0];
    $field_name = $table_name . '_contact';
    $field_type = 'chado_linker__contact';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // DBXREF
  $dbxref_table = $table_name . '_dbxref';
  if (chado_table_exists($dbxref_table)) {
    $field_name = 'sbo__database_cross_reference';
    $field_type = 'sbo__database_cross_reference';
    $info[$field_name] = array(
      'field_name' =>  $field_name,
      'type' => $field_type,
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // EXPRESSION
  $expression_table = $table_name . '_expression';
  if (chado_table_exists($expression_table)) {
    $field_name = 'go__gene_expression';
    $field_type = 'go__gene_expression';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // FEATURELOC
  if ($table_name == 'feature') {
    $field_name = 'data__sequence_coordinates';
    $field_type = 'data__sequence_coordinates';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // FEATUREPOS
  if ($table_name == 'feature') {
    $field_name = 'ogi__location_on_map';
    $field_type = 'ogi__location_on_map';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // GENOTYPE
  $genotype_table = $table_name . '_genotype';
  if (chado_table_exists($genotype_table)) {
    $field_name = 'so__genotype';
    $field_type = 'so__genotype';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // PHENOTYPE
  $phenotype_table = $table_name . '_phenotype';
  if (chado_table_exists($phenotype_table)) {
    $field_name = 'sbo__phenotype';
    $field_type = 'sbo__phenotype';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // PROPERTIES
  $prop_table = $table_name . 'prop';
  if (chado_table_exists($prop_table)) {
    // Get the list of existing property types for this table.
    $sql = 'SELECT DISTINCT type_id FROM {' . $prop_table . '}';
    $props = chado_query($sql);
    while ($prop = $props->fetchObject()) {
      $term = chado_generate_var('cvterm', array('cvterm_id' => $prop->type_id));

      // The tripal_analysis_KEGG, tripal_analysis_blast, and
      // tripal_analysis_interpro modules store results in the analysisprop
      // table which is probably not the best place, but we don't want to
      // create a ton of fields for this.
      if ($prop_table == 'analysisprop' and
          ($term->dbxref_id->db_id->name == 'KEGG_BRITE' or
           $term->dbxref_id->db_id->name == 'tripal')) {
        continue;
      }

      $field_name = strtolower(preg_replace('/[^\w]/','_', $term->dbxref_id->db_id->name . '__' . $term->name));
      $field_name = substr($field_name, 0, 32);
      $field_type = 'chado_linker__prop';
      $info[$field_name] = array(
        'field_name' => $field_name,
        'type' => $field_type,
        'cardinality' => 1,
        'locked' => FALSE,
        'storage' => array(
          'type' => 'field_chado_storage',
        ),
      );
    }
  }

  // PUBLICATIONS
  $pub_table = $table_name . '_pub';
  if (chado_table_exists($pub_table)) {
    $field_name = 'schema__publication';
    $field_type = 'schema__publication';
    $info[$field_name] =  array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // PUBLICATIONS (in reverse)
  // We want to be able to show all of the content that a publication links
  // to. The sio__references field does that.
  if ($table_name == 'pub') {
    $field_name = 'sio__references';
    $field_type = 'sio__references';
    $info[$field_name] =  array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // RELATIONSHIPS
  // If the linker table does not exists then we don't want to add attach.
  $rel_table = $table_name . '_relationship';
  if (chado_table_exists($rel_table)) {
    $field_name = 'sbo__relationship';
    $field_type = 'sbo__relationship';
    $info[$field_name] =  array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
    );
  }

  // SYNONYMS
  $syn_table = $table_name . '_synonym';
  if (chado_table_exists($syn_table)) {
    $field_name = 'schema__alternate_name';
    $field_type = 'schema__alternate_name';
    $info[$field_name] =  array(
      'field_name' => $field_name,
      'type' => $field_type,
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
      'settings' => array(
      ),
    );
  }
}

/**
 * Impelments hook_create_tripalfield_instance().
 *
 * This is a Tripal defined hook that supports integration with the
 * TripalEntity field.
 */
function tripal_chado_bundle_create_instances($entity_type, $bundle) {

  $chado_bundle = db_select('chado_bundle', 'cb')
    ->fields('cb')
    ->condition('bundle_id', $bundle->id)
    ->execute()
    ->fetchObject();

  $details = array(
    'chado_cvterm_id' => $chado_bundle->type_id,
    'chado_table' => $chado_bundle->data_table,
    'chado_type_table' => $chado_bundle->type_linker_table,
    'chado_type_column' => $chado_bundle->type_column,
  );

  $info = array();
  tripal_chado_bundle_create_instances_base($info, $entity_type, $bundle, $details);
  tripal_chado_bundle_create_instances_custom($info, $entity_type, $bundle, $details);
  tripal_chado_bundle_create_instances_linker($info, $entity_type, $bundle, $details);

  return $info;

}


/**
 * Helper function for the hook_create_tripalfield_instance().
 *
 * Add the field instances that corresond to the columns of the base table.
 *
 * @param $entity_type
 * @param $bundle
 * @param $details
 */
function tripal_chado_bundle_create_instances_base(&$info, $entity_type, $bundle, $details) {
  $fields = array();

  // Get Chado information
  $table_name = $details['chado_table'];
  $type_table = $details['chado_type_table'];
  $type_field = $details['chado_type_column'];
  $cvterm_id  = $details['chado_cvterm_id'];

  // Iterate through the columns of the table and see if fields have been
  // created for each one. If not, then create them.
  $schema = chado_get_schema($table_name);
  if (!$schema) {
    return;
  }

  $pkey = $schema['primary key'][0];

  $columns = $schema['fields'];
  foreach ($columns as $column_name => $details) {
    // Don't create base fields for the primary key and the type_id field.
    if ($column_name == $pkey or $column_name == $type_field) {
      continue;
    }

    // Skip the type field that will always be custom
    if (($table_name == $type_table and $column_name == $type_field) or
        $column_name == 'type_id') {
      continue;
    }

    $cvterm = tripal_get_chado_semweb_term($table_name, $column_name, array('return_object' => TRUE));
    if (!$cvterm) {
      // We already provided an error when creating the base field.  So
      // don't create another one here.
      continue;
    }

    $field_name = strtolower($cvterm->dbxref_id->db_id->name . '__' . preg_replace('/ /', '_', $cvterm->name));
    $field_name = substr($field_name, 0, 32);

    // Skip the primary key field.
    if ($column_name == $schema['primary key'][0]) {
      continue;
    }

    // Skip the type field.
    if ($table_name == $type_table and $column_name == $type_field) {
      continue;
    }

    $base_info =  array(
      'field_name' => $field_name,
      'entity_type' => 'TripalEntity',
      'bundle' => $bundle->name,
      'label' => ucwords(preg_replace('/_/', ' ', $column_name)),
      'description' => '',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => TRUE,
        'term_vocabulary' => $cvterm->dbxref_id->db_id->name,
        'term_name' => $cvterm->name,
        'term_accession' => $cvterm->dbxref_id->accession,
        'chado_table' => $table_name,
        'chado_column' => $column_name,
        'base_table' => $table_name,
      ),
      'widget' => array(
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'inline',
          'region' =>'Left',
          'settings' => array(),
        ),
      ),
    );

    // Determine if the field is required.
    if (array_key_exists('not null', $details) and $details['not null'] === TRUE) {
      $base_info['required'] = TRUE;
    }

    // Alter the field info array depending on the column details.
    switch($details['type']) {
      case 'char':
        $base_info['widget']['type'] = 'text_textfield';
        break;
      case 'varchar':
        $base_info['widget']['type'] = 'text_textfield';
        break;
      case 'text':
        $base_info['display']['default']['label'] = 'above';
        $base_info['widget']['type'] = 'text_textarea';
        $base_info['settings']['text_processing'] = '1';
        $base_info['settings']['format'] = 'full_html';
        break;
      case 'blob':
        // not sure how to support a blob field.
        continue;
        break;
      case 'int':
        $base_info['widget']['type'] = 'number';
        break;
      case 'float':
        $base_info['widget']['type'] = 'number';
        break;
      case 'numeric':
        $base_info['widget']['type'] = 'number';
        break;
      case 'serial':
        // Serial fields are most likely not needed as a field.
        break;
      case 'boolean':
        $base_info['widget']['type'] = 'options_onoff';
        $base_info['required'] = FALSE;
        break;
      case 'datetime':
        $base_info['widget']['type'] = 'date_select';
        $base_info['widget']['settings']['increment'] = 1;
        $base_info['widget']['settings']['tz_handling'] = 'none';
        $base_info['widget']['settings']['collapsible'] = TRUE;

        // TODO: Add settings so that the minutes increment by 1.
        // And turn off the timezone, as the Chado field doesn't support it.
        break;
    }

    // Set some default semantic web information
    if ($column_name == 'uniquename') {
      $base_info['label'] = 'Identifier';
      $base_info['widget_type'] = 'text_textfield';
    }
    elseif ($base_info['label'] == 'Timeaccessioned') {
      $base_info['label'] = 'Time Accessioned';
      $base_info['description'] = 'Please enter the time that this record was first added to the database.';
    }
    elseif ($base_info['label'] == 'Timelastmodified') {
      $base_info['label'] = 'Time Last Modified';
      $base_info['description'] = 'Please enter the time that this record was last modified. The default is the current time.';
    }
    //
    // ORGANISM TABLE
    //
    elseif ($table_name == 'organism' and $column_name == 'comment') {
      $base_info['label'] = 'Description';
    }
    //
    // PUB TABLE
    //
    elseif ($table_name == 'pub' and $column_name == 'uniquename') {
      $base_info['widget_type'] = 'text_textfield';
    }

    //
    // ANALYSIS TABLE
    //
    elseif ($table_name == 'analysis' and $column_name == 'program') {
      $base_info['description'] = 'The program name (e.g. blastx, blastp, sim4, genscan. If the analysis was not derived from a software package then provide a very brief description of the pipeline, workflow or method.';
      $base_info['label'] = 'Program, Pipeline, Workflow or Method Name';
    }
    elseif ($table_name == 'analysis' and $column_name == 'sourceuri') {
      $base_info['widget_type'] = 'text_textfield';
      $base_info['label'] = 'Source URL';
      $base_info['description'] = 'The URL where the original source data was derived.  Ideally, this should link to the page where more information about the source data can be found.';
    }
    elseif ($table_name == 'analysis' and $column_name == 'sourcename') {
      $base_info['label'] = 'Source Name';
      $base_info['description'] = 'The name of the source data. This could be a file name, data set or a small description for how the data was collected. For long descriptions use the larger description field.';
    }
    elseif ($table_name == 'analysis' and $column_name == 'sourceversion') {
      $base_info['label'] = 'Source Version';
      $base_info['description'] = 'If the source data set has a version include it here.';
    }
    elseif ($table_name == 'analysis' and $column_name == 'algorithm') {
      $base_info['label'] = 'Source Version';
      $base_info['description'] = 'The name of the algorithm used to produce the dataset if different from the program.';
    }
    elseif ($table_name == 'analysis' and $column_name == 'programversion') {
      $base_info['label'] = 'Program Version';
      $base_info['description'] = 'The version of the program used to perform this analysis. (e.g. TBLASTX 2.0MP-WashU [09-Nov-2000]. Enter "n/a" if no version is available or applicable.';
    }
    //
    // PROJECT TABLE
    //
    elseif ($table_name == 'project' and $column_name == 'description') {
      $base_info['label'] = 'Short Description';
    }
    $info[$field_name] = $base_info;
  }
}

/**
 * Helper function for the hook_create_tripalfield_instance().
 *
 * Adds custom fields for base fields.  These override the settings provided
 * in the tripal_chado_create_tripalfield_instance_base() function.
 *
 * @param $entity_type
 * @param $bundle
 * @param $details
 */
function tripal_chado_bundle_create_instances_custom(&$info, $entity_type, $bundle, $details) {
  $table_name = $details['chado_table'];
  $type_table = $details['chado_type_table'];
  $type_field = $details['chado_type_column'];
  $cvterm_id  = $details['chado_cvterm_id'];
  $schema = chado_get_schema($table_name);

  // BASE TYPE_ID
  // Exclude the type_id field on base tables where content types are mapped
  // by the type_id field or on the organism table where the type_id is mean
  // as an infraspecific name type.
  if (array_key_exists('type_id', $schema['fields']) and
      $table_name != 'organism' and $type_field != 'type_id') {
    $field_name = 'schema__additional_type';
    $is_required = FALSE;
    if (array_key_exists('not null', $schema['fields']['type_id']) and
        $schema['fields']['type_id']['not null']) {
      $is_required = TRUE;
    }
    $info[$field_name] =  array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Type',
      'description' => 'Select a type for this record.',
      'required' => $is_required,
      'settings' => array(
        'auto_attach' => TRUE,
        'chado_table' => $table_name,
        'chado_column' => 'type_id',
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'schema__additional_type_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'inline',
          'type' => 'schema__additional_type_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // BASE ORGANISM_ID
  if ($table_name != 'organism' and array_key_exists('organism_id', $schema['fields'])) {
    $field_name = 'obi__organism';
    $is_required = FALSE;
    if (array_key_exists('not null', $schema['fields']['organism_id']) and
        $schema['fields']['organism_id']['not null']) {
      $is_required = TRUE;
    }
    $info[$field_name] =  array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Organism',
      'description' => 'Select an organism.',
      'required' => $is_required,
      'settings' => array(
        'auto_attach' => TRUE,
        'chado_table' => $table_name,
        'chado_column' => 'organism_id',
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'obi__organism_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'inline',
          'type' => 'obi__organism_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // BASE DBXREF
  if (array_key_exists('dbxref_id', $schema['fields'])) {
    $field_name = 'data__accession';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Accession',
      'description' => 'This field specifies the unique stable accession (ID) for
        this record. It requires that this site have a database entry.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => TRUE,
        'chado_table' => $table_name,
        'chado_column' => 'dbxref_id',
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'data__accession_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'inline',
          'type' => 'data__accession_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // FEATURE MD5CHECKSUM
  if ($table_name == 'feature') {
    $field_name = 'data__sequence_checksum';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Sequence Checksum',
      'description' => 'The MD5 checksum for the sequence. The checksum here
        will always be unique for the raw unformatted sequence. To verify that the
        sequence has not been corrupted, download the raw sequence and use an MD5 tool
        to calculate the value. If the value calculated is identical the one shown
        here, then the downloaded sequence is uncorrupted.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => TRUE,
        'chado_table' => $table_name,
        'chado_column' => 'md5checksum',
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'data__sequence_checksum_widget',
        'settings' => array(
          'display_label' => 1,
          'md5_fieldname' => 'feature__md5checksum',
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'inline',
          'type' => 'data__sequence_checksum_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // FEATURE RESIDUES
  if ($table_name == 'feature') {
    $field_name = 'data__sequence';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Sequence',
      'description' => 'All available sequences for this record.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => FALSE,
        'chado_table' => $table_name,
        'chado_column' => 'residues',
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'data__sequence_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'above',
          'type' => 'data__sequence_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // FEATURE SEQLEN
  if ($table_name == 'feature') {
    $field_name = 'data__sequence_length';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Sequence Length',
      'description' => 'The number of residues in the raw sequence.  This length
        is only for the assigned raw sequence and does not represent the length of any
        sequences derived from alignments. If this value is zero but aligned sequences
        are present then this record has no official assigned sequence.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => TRUE,
        'chado_table' => $table_name,
        'chado_column' => 'seqlen',
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'data__sequence_length_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'inline',
          'type' => 'data__sequence_length_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // GENE TRANSCRIPTS
  $rel_table = $table_name . '_relationship';
  if (chado_table_exists($rel_table) and $bundle->label == 'gene') {
    $field_name = 'so__transcript';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Transcripts',
      'description' => 'Transcripts that are part of this gene.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => FALSE,
        'chado_table' => $rel_table,
        'chado_column' => '',
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'so__transcript_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'above',
          'type' => 'so__transcript_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // ORGANISM TYPE_ID
//   if ($table_name == 'organism' and array_key_exists('type_id', $schema['fields'])) {
//     $field_name = 'taxarank__infraspecific_taxon';
//     $info[$field_name] = array(
//       'field_name' => $field_name,
//       'entity_type' => $entity_type,
//       'bundle' => $bundle->name,
//       'label' => 'Infraspecific Taxon',
//       'description' => 'The Infraspecific Taxon.',
//       'required' => FALSE,
//       'settings' => array(
//         'auto_attach' => TRUE,
//         'chado_table' => 'organism',
//         'chado_column' => 'type_id',
//         'base_table' => 'organism',
//       ),
//       'widget' => array(
//         'type' => 'taxarank__infraspecific_taxon_widget',
//         'settings' => array(
//           'display_label' => 1,
//         ),
//       ),
//       'display' => array(
//         'default' => array(
//           'label' => 'inline',
//           'type' => 'taxarank__infraspecific_taxon_formatter',
//           'settings' => array(),
//         ),
//       ),
//     );
//   }


  // FEATURE SEQLEN
  if ($table_name == 'featuremap') {
    $field_name = 'uo__unit';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Units',
      'description' => 'The map\'s unit type.',
      'required' => TRUE,
      'settings' => array(
        'auto_attach' => TRUE,
        'chado_table' => $table_name,
        'chado_column' => 'unittype_id',
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'uo__unit_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'inline',
          'type' => 'uo__unit_formatter',
          'settings' => array(),
        ),
      ),
    );
  }
  // Add an image field to the Organism type.  This is a Drupal field and
  // not stored in Chado, but is used for backwards compatibility.
  if ($table_name == 'organism') {
    $field_name = 'data__image';
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Organism Image',
      'description' => 'An image for the organism',
      'required' => FALSE,
      'display' => array(
        'default' => array(
          'label' => 'hidden',
        ),
      ),
    );
  }
}

/**
 *
 * @param unknown $entity_type
 * @param unknown $bundle
 * @param unknown $details
 */
function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bundle, $details) {

  $table_name = $details['chado_table'];
  $type_table = $details['chado_type_table'];
  $type_field = $details['chado_type_column'];
  $cvterm_id  = $details['chado_cvterm_id'];

  // CONTACTS
  $contact_table = $table_name . '_contact';
  if (chado_table_exists($contact_table)) {
    $field_name = $table_name . '_contact';
    $info[$field_name] =     $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Contact',
      'description' => 'Associates an indviddual or organization with this record',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => FALSE,
        'chado_table' => $contact_table,
        'base_table' => $table_name,
        'chado_column' => 'contact_id',
      ),
      'widget' => array(
        'type' => 'local__contact_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'above',
          'type' => 'local__contact_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // DBXREF
  $dbxref_table = $table_name . '_dbxref';
  if (chado_table_exists($dbxref_table)) {
    $field_name = 'sbo__database_cross_reference';
    $schema = chado_get_schema($dbxref_table);
    $pkey = $schema['primary key'][0];
    $info[$field_name] =  array(
      'field_name' =>  $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Database Cross Reference',
      'description' => 'The IDs where this record may be available in other external online databases.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => FALSE,
        'chado_table' => $dbxref_table,
        'chado_column' => $pkey,
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'sbo__database_cross_reference_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'inline',
          'type' => 'sbo__database_cross_reference_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // EXPRESSION
  $expression_table = $table_name . '_expression';
  if (chado_table_exists($expression_table)) {
    $field_name = 'go__gene_expression';
    $schema = chado_get_schema($expression_table);
    $pkey = $schema['primary key'][0];
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Gene expression',
      'description' => 'Information about the expression of this record.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => FALSE,
        'chado_table' => $expression_table,
        'chado_column' => $pkey,
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'go__gene_expression_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'above',
          'type' => 'go__gene_expression_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // FEATURELOC
  if ($table_name == 'feature') {
    $field_name = 'data__sequence_coordinates';
    $schema = chado_get_schema('featureloc');
    $pkey = $schema['primary key'][0];
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Sequence Coordinates',
      'description' => 'The locations on other genomic sequences where this
        record has been aligned.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => FALSE,
        'chado_table' => 'featureloc',
        'chado_column' => $pkey,
        'base_table' => 'feature',
      ),
      'widget' => array(
        'type' => 'data__sequence_coordinates_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'above',
          'type' => 'data__sequence_coordinates_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // FEATUREPOS
  if ($table_name == 'feature') {
    $field_name = 'ogi__location_on_map';
    $schema = chado_get_schema('featurepos');
    $pkey = $schema['primary key'][0];
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Location on Map',
      'description' => 'The positions on a genetic map.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => FALSE,
        'chado_table' => 'featurepos',
        'chado_column' => $pkey,
        'base_table' => 'feature',
      ),
      'widget' => array(
        'type' => 'ogi__location_on_map_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'above',
          'type' => 'ogi__location_on_map_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // GENOTYPE
  $genotype_table = $table_name . '_genotype';
  if (chado_table_exists($genotype_table)) {
    $field_name = 'so__genotype';
    $schema = chado_get_schema($genotype_table);
    $pkey = $schema['primary key'][0];
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Genotype',
      'description' => 'The genotypes associated with this record.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => FALSE,
        'chado_table' => $genotype_table,
        'chado_column' => $pkey,
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'so__genotype_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'above',
          'type' => 'so__genotype_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // PHENOTYPE
  $phenotype_table = $table_name . '_phenotype';
  if (chado_table_exists($phenotype_table)) {
    $field_name = 'sbo__phenotype';
    $schema = chado_get_schema($phenotype_table);
    $pkey = $schema['primary key'][0];
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Phenotype',
      'description' => 'The phenotypes associated with this record.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => FALSE,
        'chado_table' => $phenotype_table,
        'chado_column' => $pkey,
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'sbo__phenotype_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'above',
          'type' => 'sbo__phenotype_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // PROPERTIES
  $prop_table = $table_name . 'prop';
  if (chado_table_exists($prop_table)) {
     $tschema = chado_get_schema($table_name);
     $schema = chado_get_schema($prop_table);
     $tpkey = $tschema['primary key'][0];
     $pkey = $schema['primary key'][0];
     // Get the list of existing property types for this table.
     $args = array();
     $sql = "
       SELECT DISTINCT P.type_id
       FROM {" . $prop_table . "} P
     ";
     if ($type_field) {
       $sql .= "
           INNER JOIN {" . $table_name . "} T on T.$tpkey = P.$tpkey
         WHERE T.type_id = :cvterm_id
       ";
       $args[':cvterm_id'] = $cvterm_id;
     }
     $props = chado_query($sql, $args);
     while ($prop = $props->fetchObject()) {

       $term = chado_generate_var('cvterm', array('cvterm_id' => $prop->type_id));

       // The tripal_analysis_KEGG, tripal_analysis_blast, and
       // tripal_analysis_interpro modules store results in the analysisprop
       // table which is probably not the best place, but we don't want to
       // create a ton of fields for this.
       if ($prop_table == 'analysisprop' and
           ($term->dbxref_id->db_id->name == 'KEGG_BRITE' or
            $term->dbxref_id->db_id->name == 'tripal')) {
         continue;
       }

       $field_name = strtolower(preg_replace('/[^\w]/','_', $term->dbxref_id->db_id->name . '__' . $term->name));
       $field_name = substr($field_name, 0, 32);
       $info[$field_name] = array(
         'field_name' => $field_name,
         'entity_type' => $entity_type,
         'bundle' => $bundle->name,
         'label' => ucwords(preg_replace('/_/', ' ', $term->name)),
         'description' => $term->definition,
         'required' => FALSE,
         'settings' => array(
           'auto_attach' => TRUE,
           'term_vocabulary' => $term->dbxref_id->db_id->name,
           'term_accession' => $term->dbxref_id->accession,
           'term_name' => $term->name,
           'base_table' => $table_name,
           'chado_table' => $prop_table,
           'chado_column' => $pkey,
         ),
         'widget' => array(
           'type' => 'chado_linker__prop_widget',
           'settings' => array(
             'display_label' => 1,
           ),
         ),
         'display' => array(
           'default' => array(
             'label' => 'inline',
             'type' => 'chado_linker__prop_formatter',
             'settings' => array(),
           ),
         ),
       );
     }
   }


  // PUBLICATIONS
  $pub_table = $table_name . '_pub';
  if (chado_table_exists($pub_table)) {
    $field_name = 'schema__publication';
    $schema = chado_get_schema($pub_table);
    $pkey = $schema['primary key'][0];
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Publication',
      'description' => 'This record has been referenced or is sourced from these publications.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => FALSE,
        'chado_table' => $pub_table,
        'chado_column' => $pkey,
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'schema__publication_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'above',
          'type' => 'schema__publication_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // PUBLICATIONS (in reverse)
  // We want to be able to show all of the content that a publication links
  // to. The sio__references field does that.
  if ($table_name == 'pub') {
    $field_name = 'sio__references';
    $schema = chado_get_schema($table_name);
    $pkey = $schema['primary key'][0];
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'References',
      'description' => 'Records that are referred to by the publication.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => FALSE,
        'chado_table' => $table_name,
        'chado_column' => $pkey,
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'sio__references_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'above',
          'type' => 'sio__references_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // RELATIONSHIPS
  // If the linker table does not exists then we don't want to add attach.
  $rel_table = $table_name . '_relationship';
  if (chado_table_exists($rel_table)) {
    $field_name = 'sbo__relationship';
    $schema = chado_get_schema($rel_table);
    $pkey = $schema['primary key'][0];
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Relationship',
      'description' => 'Other records with relationships to this record.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => FALSE,
        'chado_table' => $rel_table,
        'chado_column' => $pkey,
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'sbo__relationship_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'above',
          'type' => 'sbo__relationship_formatter',
          'settings' => array(),
        ),
      ),
    );
  }

  // SYNONYMS
  $syn_table = $table_name . '_synonym';
  if (chado_table_exists($syn_table)) {
    $field_name = 'schema__alternate_name';
    $schema = chado_get_schema($syn_table);
    $pkey = $schema['primary key'][0];
    $info[$field_name] = array(
      'field_name' => $field_name,
      'entity_type' => $entity_type,
      'bundle' => $bundle->name,
      'label' => 'Synonyms',
      'description' => 'Alternate names, aliases or synonyms for this record.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => FALSE,
        'chado_table' => $syn_table,
        'chado_column' => $pkey,
        'base_table' => $table_name,
      ),
      'widget' => array(
        'type' => 'schema__alternate_name_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'default' => array(
          'label' => 'inline',
          'type' => 'schema__alternate_name_formatter',
          'settings' => array(),
        ),
      ),
    );
  }
}

/**
 * Implements hook_bundle_create_user_field().
 *
 * A priviledged user has the ability to add new fields to the bundle. The
 * chado_linker__prop and chado_linker__cvterm fields are allowed to be
 * added dynamically by the user.  But, Drupal doesn't know whot to deal with
 * it, so this function is called for any field attached to a TripalEntity
 * bundle type. Any fields whose TripalField::$module argument is set to
 * 'tripal_chado' and that can be added dynamically will result in a call
 * to this function.
 */
function tripal_chado_bundle_create_user_field($new_field, $bundle) {

  // Get the table this bundle is mapped to.
  $term = tripal_load_term_entity(array('term_id' => $bundle->term_id));
  $vocab = $term->vocab;
  $params = array(
    'vocabulary' => $vocab->vocabulary,
    'accession' => $term->accession,
  );
  $mapped_table = chado_get_cvterm_mapping($params);
  $chado_table = $mapped_table->chado_table;
  $chado_type_table = $mapped_table->chado_table;
  $chado_type_column = $mapped_table->chado_field;

  // We allow site admins to add new chado_linker__prop fields to an entity.
  // This function will allow us to properly add them.  But at this point we
  // don't know the controlled vocabulary term.  We'll have to use the
  // defaults and let the user set it using the interface.
  if ($new_field['type'] == 'chado_linker__prop') {
    $table_name = $chado_table . 'prop';

    if (chado_table_exists($table_name)) {
      $schema = chado_get_schema($table_name);
      $pkey = $schema['primary key'][0];
      $field_name = $new_field['field_name'];
      $field_type = 'chado_linker__prop';

      // First add the field.
      field_create_field(array(
        'field_name' => $field_name,
        'type' => $field_type,
        'cardinality' => FIELD_CARDINALITY_UNLIMITED,
        'locked' => FALSE,
        'storage' => array(
          'type' => 'field_chado_storage',
        ),
      ));

      // Now add the instance
      field_create_instance(array(
        'field_name' => $field_name,
        'entity_type' => 'TripalEntity',
        'bundle' => $bundle->name,
        'label' => $new_field['label'],
        'description' => '',
        'required' => FALSE,
        'settings' => array(
          'auto_attach' => TRUE,
          'base_table' => $chado_table,
          'chado_table' => $table_name,
          'chado_column' => $pkey,
          'term_vocabulary' => $vocab->vocabulary,
          'term_accession' => $term->accession,
          'term_name' => $term->name
        ),
        'widget' => array(
          'type' => 'chado_linker__prop_widget',
          'settings' => array(
            'display_label' => 1,
          ),
        ),
        'display' => array(
          'default' => array(
            'label' => 'inline',
            'type' => 'chado_linker__prop_formatter',
            'settings' => array(),
          ),
        ),
      ));
    }
    else {
      drupal_set_message('Cannot add a property field to this entity. Chado does not support properties for this data type.', 'error');
    }
  }

  // We allow site admins to add new chado_linker__cvterm fields to an entity.
  // This function will allow us to properly add them.  But at this point we
  // don't know the controlled vocabulary term.  We'll have to use the
  // defaults and let the user set it using the interface.

  if ($new_field['type'] == 'chado_linker__cvterm') {
    $table_name = $chado_table . '_cvterm';

    if (chado_table_exists($table_name)) {
      $schema = chado_get_schema($table_name);
      $pkey = $schema['primary key'][0];
      $field_name = $new_field['field_name'];
      $field_type = 'chado_linker__cvterm';

      // First add the field.
      field_create_field(array(
        'field_name' => $field_name,
        'type' => $field_type,
        'cardinality' => FIELD_CARDINALITY_UNLIMITED,
        'locked' => FALSE,
        'storage' => array(
          'type' => 'field_chado_storage',
        ),
        'settings' => array(
          'base_table' => $chado_table,
          'chado_table' => $table_name,
          'chado_column' => $pkey,
        ),
      ));

      // Now add the instance
      field_create_instance(array(
        'field_name' => $field_name,
        'entity_type' => 'TripalEntity',
        'bundle' => $bundle->name,
        'label' => $new_field['label'],
        'description' => '',
        'required' => FALSE,
        'settings' => array(
          'auto_attach' => TRUE,
        ),
        'widget' => array(
          'type' => 'chado_linker__cvterm_widget',
          'settings' => array(
            'display_label' => 1,
          ),
        ),
        'display' => array(
          'default' => array(
            'label' => 'above',
            'type' => 'chado_linker__cvterm_formatter',
            'settings' => array(),
          ),
        ),
      ));
    }
    else {
      drupal_set_message('Cannot add a property field to this entity. Chado does not support annotations for this data type.', 'error');
    }
  }
}


/**
 * Allows for altering of a field's instance setting form.
 *
 * This appears to be a Drupal hook but is actually a custom function created
 * by this module. It is called by the tripal_form_alter() function of this
 * module.
 *
 * Here we put additional form elements for any field, regardless if it is
 * a tripalField or not.
 *
 * @param $form
 *   The form array.  Alterations to the form can be made within this array.
 * @param $form_state
 *   The form state array.
 */
function tripal_chado_field_instance_settings_form_alter(&$form, $form_state) {
  global $language;
  $field = $form['#field'];
  $instance = $form['#instance'];

  $base_table = array_key_exists('base_table', $instance['settings']) ? $instance['settings']['base_table'] : '';
  $chado_table = array_key_exists('chado_table', $instance['settings']) ? $instance['settings']['chado_table'] : '';
  $chado_column = array_key_exists('chado_column', $instance['settings']) ? $instance['settings']['chado_column'] : '';


  if ($chado_table) {
    // Construct a table for the vocabulary information.
    $headers = array();
    $rows = array();
    $rows[] = array(
      array(
        'data' => 'Base Table',
        'header' => TRUE,
        'width' => '20%',
      ),
      $base_table
    );
    $rows[] = array(
      array(
        'data' => 'Record Table',
        'header' => TRUE,
        'width' => '20%',
      ),
      $chado_table
    );
    $rows[] = array(
      array(
        'data' => 'ID Column',
        'header' => TRUE,
        'width' => '20%',
      ),
      $chado_column
    );
    $table = array(
      'header' => $headers,
      'rows' => $rows,
      'attributes' => array(
      ),
      'sticky' => FALSE,
      'caption' => '',
      'colgroups' => array(),
      'empty' => '',
    );

    $form['chado_mapping'] = array(
      '#type' => 'fieldset',
      '#title' => 'Chado Mapping',
      '#description' => t('This field maps to data in Chado to the following table:'),
    );
    $form['chado_mapping']['details'] = array(
      '#type' => 'item',
      '#markup' => theme_table($table),
    );
  }
}

/**
 * Implements hook_form_FROM_ID_alter()
 */
function tripal_chado_form_tripalbundle_form_alter(&$form, $form_state) {
  global $language;
  $bundle = $form['#bundle'];

  $term = entity_load('TripalTerm', array('id' => $bundle->term_id));
  $term = reset($term);
  $vocab = $term->vocab;
  $params = array(
    'vocabulary' => $vocab->vocabulary,
    'accession' => $term->accession,
  );
  $mapped_table = chado_get_cvterm_mapping($params);
  $chado_table = $mapped_table->chado_table;
  $chado_column = $mapped_table->chado_field;

  // Construct a table for the vocabulary information.
  $headers = array();
  $rows = array();
  $rows[] = array(
    array(
      'data' => 'Chado Table',
      'header' => TRUE,
      'width' => '20%',
    ),
    $chado_table
  );
  $rows[] = array(
    array(
      'data' => 'Type Column',
      'header' => TRUE,
      'width' => '20%',
    ),
    $chado_column
  );
  $table = array(
    'header' => $headers,
    'rows' => $rows,
    'attributes' => array(
    ),
    'sticky' => FALSE,
    'caption' => '',
    'colgroups' => array(),
    'empty' => '',
  );

  $form['chado_mapping'] = array(
    '#type' => 'item',
    '#title' => 'Chado Mapping',
    '#markup' => theme_table($table),
    '#description' => t('This content type maps to the table in Chado
        listed above.  Chado allows multiple data types to be housed
        in a single table. Therefore, the column that is used to
        differentiate between data types is also listed above.'),
    '#weight' => 0,
  );
}