<?php

function tripal_chado_install() {
  // Unfortunately, some Chado base tables do not have a type_id, so we must
  // take special action for those tables.  These include: organism and
  // analysis. Until we can find an appropriate controlled vocabulary
  // that is well supported by the community with types for these tables we
  // will have to use in-house terms.

  // Add a term to be used for an inherent 'type_id' for the organism table.
  tripal_insert_cvterm(array(
    'id' => 'local:organism',
    'name' => 'organism',
    'definition' => 'An individual form of life, such as a bacterium, protist, ' .
    'fungus, plant, or animal, composed of a single cell or a complex of cells  ' .
    'in which organelles or organs work together to carry out the various  ' .
    'processes of life. (American Heritage® Dictionary of the English ' .
    'Language, Fifth Edition. Copyright © 2011 by Houghton Mifflin ' .
    'Harcourt Publishing Company).',
    'cv_name' => 'local',
  ));

  // Add a term to be used for an inherent 'type_id' for the organism table.
  tripal_insert_cvterm(array(
    'id' => 'local:analysis',
    'name' => 'analysis',
    'definition' => 'A process as a method of studying the nature of something ' .
    'or of determining its essential features and their relations. ' .
    '(Random House Kernerman Webster\'s College Dictionary, © 2010 K ' .
    'Dictionaries Ltd).',
    'cv_name' => 'local',
  ));

  tripal_insert_cvterm(array(
    'id' => 'local:project',
    'name' => 'project',
    'definition' => 'A plan or proposal for accomplishing something. ' .
    '(American Heritage® Dictionary of the English Language, Fifth Edition. ' .
    'Copyright © 2011 by Houghton Mifflin Harcourt Publishing Company).',
    'cv_name' => 'local',
  ));

  // For the TripalBundle entities we will want to associate the cvterm_id,
  // and the chado table and field that it maps to.  We will use a few
  // variables to do this:
  tripal_insert_variable('chado_cvterm_id', 'The cvterm_id that a TripalBundle maps to.');
  tripal_insert_variable('chado_table', 'The name of the table to which a TripalBundle maps.');
  tripal_insert_variable('chado_column', 'The name of the column within the table that a TripalBundle maps to.');

  // We want to provide a set of commonly used entity types by default. This
  // way when a user first installs Tripal there are some commonly used
  // formats.
  module_load_include('inc', 'tripal_entities', 'api/tripal_entities.api');
  module_load_include('inc', 'tripal_entities', 'includes/tripal_entities.admin');

  // Create the 'Organism' entity type. This uses the local:organism term.
  $error = '';
  $term = array('name' => 'organism', 'cv_id' => array('name' => 'local'));
  $cvterm = chado_generate_var('cvterm', $term);
  if (!tripal_create_bundle('local', 'organism', 'organism', $error)) {
    throw new Exception($error);
  }

  // Create the 'Analysis' entity type. This uses the local:analysis term.
  $error = '';
  $term = array('name' => 'analysis', 'cv_id' => array('name' => 'local'));
  $cvterm = chado_generate_var('cvterm', $term);
  if (!tripal_create_bundle('local', 'analysis', 'analysis', $error)) {
    throw new Exception($error);
  }

  // Create the 'Project' entity type. This uses the local:project term.
  $error = '';
  $term = array('name' => 'project', 'cv_id' => array('name' => 'local'));
  $cvterm = chado_generate_var('cvterm', $term);
  if (!tripal_create_bundle('local', 'project', 'project', $error)) {
    throw new Exception($error);
  }
}


/**
 * Implements hook_schema().
 */
function tripal_chado_schema() {

  // Links TripalEntity entities to the chado record.
  $schema['chado_entity'] = tripal_chado_chado_entity_schema();

  return $schema;
}

/**
 * @section
 * Schema Definitions.
 */


/**
 * Links Biological Data Entities to the chado "base" table the data is stored in.
 * This is where we would specify that a particular gene maps to the record in the
 * chado.feature table with a feature_id=2432;
 */
function tripal_chado_chado_entity_schema() {

  $schema = array(
    'description' => 'The linker table that associates an enitity from the public.tripal_entity table with a "base" record in Chado',
    'fields' => array(
      'chado_entity_id' => array(
        'description' => 'The primary identifier for this table.',
        'type' => 'serial',
        'unsigned' => TRUE,
        'not null' => TRUE,
      ),
      'entity_id' => array(
        'description' => 'The unique entity id.',
        'type' => 'int',
        'not null' => TRUE,
      ),
      'record_id' => array(
        'description' => 'The unique numerical identifier for the record that this entity is associated with (e.g. feature_id, stock_id, library_id, etc.).',
        'type' => 'int',
        'not null' => TRUE,
      ),
      'data_table' => array(
        'description' => 'Indicates the table in Chado that this term services (e.g. feature, stock, library, etc.)',
        'type' => 'varchar',
        'length' => 128,
        'not null' => TRUE,
        'default' => '',
      ),
      'type_table' => array(
        'description' => 'Sometimes the record in the data table doesn’t have a field that specifies  the record type.  For example, an analysis type is stored in the analysisprop table.  If the data_table does have a type field then this value will be the same as the data_table.',
        'type' => 'varchar',
        'length' => 128,
        'not null' => TRUE,
        'default' => '',
      ),
      'field' => array(
        'description' => 'The name of the field in the typetable that contains the cvterm record.',
        'type' => 'varchar',
        'length' => 128,
        'not null' => FALSE,
        'default' => ''
      ),
    ),
    'indexes' => array(
      'record_id' => array('record_id'),
      'entity_id' => array('entity_id'),
      'data_table' => array('data_table'),
    ),
    'unique keys' => array(
      'record' => array('data_table', 'record_id'),
      'entity_id' => array('entity_id'),
    ),
    'primary key' => array('chado_entity_id'),
  );
  return $schema;
}