tripal_qtl.install

<?php

/**
 * @file
 * Prepares the site for tripal_genentic module.
 */

/**
 * Implements hook_enable().
 */
function tripal_qtl_enable() {

  // Add cvterms needed for the feature map loader.
  // map_type.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:map_type',
    'name' => 'map_type',
    'cv_name' => 'MAIN',
    'definition' => 'The type of feature map (e.g. genetic, cytogenetic, physical, sequence).',
  ));

  // published_map_name.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:published_map_name',
    'name' => 'published_map_name',
    'cv_name' => 'MAIN',
    'definition' => 'The name of the map in the linked publication.',
  ));

  // population_type.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:population_type',
    'name' => 'population_type',
    'cv_name' => 'MAIN',
    'definition' => 'The type of population used to generate a map (e.g. F2, BC1, RIL, ABC)',
  ));

  // population_size.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:population_size',
    'name' => 'population_size',
    'cv_name' => 'MAIN',
    'definition' => 'The number of individuals in the population used to generate the map.',
  ));

  // locus.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:marker_locus',
    'name' => 'marker_locus',
    'cv_name' => 'MAIN',
    'definition' => 'The position of a gene or a chromosomal marker on a chromosome; also, a stretch of DNA at a particular place on a particular chromosome. The use of locus is sometimes restricted to mean regions of DNA that are expressed..',
  ));

  // start: used for marker positions.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:start',
    'name' => 'start',
    'cv_name' => 'MAIN',
    'definition' => 'The start position.',
  ));

  // end: used for marker positions.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:end',
    'name' => 'end',
    'cv_name' => 'MAIN',
    'definition' => 'The end position.',
  ));

  // instance_of.
  tripal_insert_cvterm(array(
    'id' => 'OBO_REL:instance_of',
    'name' => 'instance_of',
    'cv_name' => 'relationship',
    'definition' => '',
  ));

  // marker_type.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:marker_type',
    'name' => 'marker_type',
    'cv_name' => 'MAIN',
    'definition' => '',
  ));

  // CVterms needed for QTL.
  // published_symbol.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:published_symbol',
    'name' => 'published_symbol',
    'cv_name' => 'MAIN',
    'definition' => '',
  ));

  // site_name.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:site_name',
    'name' => 'site_name',
    'cv_name' => 'MAIN',
    'definition' => '',
  ));

  // lod.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:lod',
    'name' => 'lod',
    'cv_name' => 'MAIN',
    'definition' => '',
  ));

  // r2.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:r2',
    'name' => 'r2',
    'cv_name' => 'MAIN',
    'definition' => '',
  ));

  // additive_effect.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:additive_effect',
    'name' => 'additive_effect',
    'cv_name' => 'MAIN',
    'definition' => '',
  ));

  // direction.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:direction',
    'name' => 'direction',
    'cv_name' => 'MAIN',
    'definition' => '',
  ));

  // qtl_peak.
  tripal_insert_cvterm(array(
    'id' => 'MAIN:qtl_peak',
    'name' => 'qtl_peak',
    'cv_name' => 'MAIN',
    'definition' => '',
  ));
  
  // @todo File an issue with github/GMOD/chado to add this table to 1.4.
  $table = 'featuremap_analysis';
  $schema = [
    'table' => 'featuremap_analysis',
    'description' => 'Maps analysis to the featuremaps they generated.',
    'fields' => [
      'featuremap_analysis_id' => [
        'type' => 'serial',
        'not null' => TRUE,
      ],
      'featuremap_id' => [
        'size' => 'big',
        'type' => 'int',
        'not null' => TRUE,
      ],
      'analysis_id' => [
        'size' => 'big',
        'type' => 'int',
        'not null' => TRUE,
      ],
    ],
    'primary key' => [
      'featuremap_analysis_id',
    ],
    'indexes' => [
      'featuremap_analysis_idx1' => [
        0 => 'featuremap_id',
      ],
      'featuremap_analysis_idx2' => [
        0 => 'analysis_id',
      ],
    ],
    'foreign keys' => [
      'featuremap' => [
        'table' => 'featuremap',
        'columns' => [
          'featuremap_id' => 'featuremap_id',
        ],
      ],
      'analysis' => [
        'table' => 'analysis',
        'columns' => [
          'analysis_id' => 'analysis_id',
        ],
      ],
    ],
  ];
  chado_create_custom_table($table, $schema, TRUE, NULL, FALSE);

}