icsearch/icbasic.install

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<?php
// $Id: icbasic.install,v 1.9 2010-01-02 17:06:45 alexie Exp $


function icbasic_install() {
  //  drupal_uninstall_schema('icbasic');
  global $db_url;
  if (strpos($db_url['default'], 'pgsql://') === FALSE && strpos($db_url, 'pgsql://') === FALSE) {
    drupal_set_message("The icbasic module was not installed: it requires a PostgreSQL database due to integration with GMOD and chado ($db_url).", 'error', FALSE);
    return FALSE;
  }

  drupal_install_schema('icbasic');
  // organism 1 will always be the 'construct' one, e.g used in constructs
  db_query('ALTER table {ic_feature} add timestamp timestamp with time zone default now()');
  db_query('ALTER table {ic_resource} add timestamp timestamp with time zone default now()');
  db_query("INSERT INTO {ic_organism} (tax_order,tax_family,genus,species) VALUES ('general','general','general','general')");
  db_query("INSERT INTO {ic_db} (name) VALUES ('local publication')");
  db_query("INSERT INTO {ic_db} (name) VALUES ('local study')");
  db_query("INSERT INTO {ic_db} (name) VALUES ('local feature')");
  db_query("INSERT INTO {ic_db} (name) VALUES ('local resource')");
  db_query("INSERT INTO {ic_dbxref} (db_id,accession) VALUES (1,'Unpublished')");
  db_query("INSERT INTO {ic_cv} (name) VALUES ('resource_property')");
  db_query("INSERT INTO {ic_cv} (name) VALUES ('relationship')");
  db_query("INSERT INTO {ic_cvterm} (cv_id,name) VALUES ((SELECT cv_id from {ic_cv} where name='relationship'),'uses')");
  db_query("INSERT INTO {ic_cvterm} (cv_id,name) VALUES ((SELECT cv_id from {ic_cv} where name='relationship'),'part_of')");
  db_query("INSERT INTO {ic_pub} (dbxref_id,uniquename) VALUES (1,'none')");
}

function icbasic_uninstall() {
  //because of foreign keys, we have to drop the tables, manually.
  $drop_sql = 'DROP TABLE %s CASCADE';
  $tables = array('{ic_pub}', '{ic_db}', '{ic_dbxref}', '{ic_author}', '{ic_pub_author}', '{ic_organism}', '{ic_feature}', '{ic_cv}',
    '{ic_cvterm}', '{ic_feature_cvterm}', '{ic_featureprop}', '{ic_resource}', '{ic_resource_cvterm}', '{ic_resourceprop}',
    '{ic_resource_resource}',
  );
  $table_str = implode(',', $tables);
  db_query($drop_sql, $table_str);
}

function icbasic_enable() {}

function icbasic_disable() {}

function icbasic_schema() {
  $schema['ic_pub'] = array(
    'fields' => array(
      'pub_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ),
      'dbxref_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'type_id' => array(
        'type' => 'int',
      ),
      'uniquename' => array(
        'type' => 'text',
        'not null' => TRUE,
      ),
      'passkey' => array(
        'type' => 'varchar',
        'length' => 15,
        'not null' => FALSE,
      ),
    ),
    'unique keys' => array(
      'pub_uidx1' => array('uniquename'),
    ),
    'primary key' => array('pub_id'),
  );
  $schema['ic_db'] = array(
    'fields' => array(
      'db_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ),
      'name' => array(
        'type' => 'text',
        'not null' => TRUE,
      ), 'description' => array(
        'type' => 'text',
      ),
    ),
    'unique keys' => array(
      'db_uidx1' => array('name'),
    ),
    'primary key' => array('db_id'),
  );
  $schema['ic_dbxref'] = array(
    'fields' => array(
      'dbxref_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ),
      'accession' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE,
      ), 'description' => array(
        'type' => 'text',
      ),
      'db_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
    ),
    'unique keys' => array(
      'pub_uidx1' => array('db_id', 'accession'),
    ),
    'primary key' => array('dbxref_id'),
  );
  $schema['ic_author'] = array(
    'fields' => array(
      'author_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ),
      'first_names' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE,
      ),
      'last_names' => array(
        'type' => 'varchar',
        'length' => 255,
        'not null' => TRUE,
      ),
      'email' => array(
        'type' => 'varchar',
        'length' => 127,
        'not null' => TRUE,
      ),
      'address' => array(
        'type' => 'text',
      ),
    ),
    'primary key' => array('author_id'),
    'unique keys' => array(
      array('last_names', 'first_names', 'email'),
    ),
  );
  $schema['ic_pub_author'] = array(
    'fields' => array(
      'author_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'pub_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'rank' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
    ),
    'primary key' => array('author_id', 'pub_id', 'rank'),
  );
  $schema['ic_organism'] = array(
    'fields' => array(
      'organism_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ), 'tax_order' => array(
        'type' => 'varchar',
        'not null' => TRUE,
        'length' => 128,
      ), 'tax_family' => array(
        'type' => 'varchar',
        'not null' => TRUE,
        'length' => 128,
      ), 'genus' => array(
        'type' => 'varchar',
        'not null' => TRUE,
        'length' => 128,
      ), 'species' => array(
        'type' => 'varchar',
        'not null' => TRUE,
        'length' => 128,
      ), 'ncbi_taxid' => array(
        'type' => 'int',
      ),
    ),
    'primary key' => array('organism_id'),
    'unique keys' => array(
      'organism_uidx1' => array('tax_order', 'tax_family', 'genus', 'species'),
    ),
  );
  $schema['ic_feature'] = array(
    'fields' => array(
      'feature_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ), 'uniquename' => array(
        'type' => 'text',
        'not null' => TRUE,
      ), 'dbxref_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'type_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'residues' => array(
        'type' => 'text',
      ), 'organism_id' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 1,
      ), 'passkey' => array(
        'type' => 'varchar',
        'length' => 15,
        'not null' => TRUE,
      ),
    ),
    'primary key' => array('feature_id'),
    'unique keys' => array(
      'feature_uidx1' => array('uniquename'),
    ),
  );
  $schema['ic_cv'] = array(
    'fields' => array(
      'cv_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ), 'name' => array(
        'type' => 'text',
        'not null' => TRUE,
      ),
    ),
    'primary key' => array('cv_id'),
    'unique keys' => array(
      'cv_uidx1' => array('name'),
    ),
  );
  $schema['ic_cvterm'] = array(
    'fields' => array(
      'cvterm_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ), 'name' => array(
        'type' => 'text',
        'not null' => TRUE,
      ), 'cv_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'definition' => array(
        'type' => 'text',
      ),
    ),
    'primary key' => array('cvterm_id'),
    'unique keys' => array(
      'cvterm_uidx1' => array('name', 'cv_id'),
    ),
  );
  $schema['ic_feature_cvterm'] = array(
    'fields' => array(
      'feature_cvterm_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ), 'feature_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'cvterm_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
    ),
    'primary key' => array('feature_cvterm_id'),
    'indexes' => array(
      'feature_cvterm_idx1' => array('feature_id', 'cvterm_id'),
    ),
  );
  $schema['ic_featureprop'] = array(
    'fields' => array(
      'featureprop_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ), 'feature_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'type_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'value' => array(
        'type' => 'text',
      ),
    ),
    'primary key' => array('featureprop_id'),
  );
  $schema['ic_resource'] = array(
    'fields' => array(
      'resource_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ), 'uniquename' => array(
        'type' => 'text',
        'not null' => TRUE,
        // 1 if none
      ), 'organism_id' => array(
        'type' => 'int',
        'not null' => TRUE,
        'default' => 1,
        // e.g. Stock center
      ), 'dbxref_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'passkey' => array(
        'type' => 'varchar',
        'length' => 15,
        'not null' => FALSE,
        // type of material (in RNAi will just be one thing: experimental animal
      ), 'type_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'description' => array(
        'type' => 'text',
      ),
    ), 'unique keys' => array(
      'resource_uidx1' => array('uniquename'),
    ),
    'primary key' => array('resource_id'),
  );
  $schema['ic_resource_cvterm'] = array(
    'fields' => array(
      'resource_cvterm_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ), 'resource_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'cvterm_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
    ),
    'primary key' => array('resource_cvterm_id'),
    'indexes' => array(
      'resource_cvterm_idx1' => array('resource_id', 'cvterm_id'),
    ),
  );
  $schema['ic_resourceprop'] = array(
    'fields' => array(
      'resourceprop_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ), 'resource_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'type_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'value' => array(
        'type' => 'text',
      ), 'rank' => array(
        'type' => 'int',
        'default' => 0,
      ),
    ),
    'primary key' => array('resourceprop_id'),
  );
  $schema['ic_resource_resource'] = array(
    'fields' => array(
      'resource_resource_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ), 'subject_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'object_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'type_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
    ),
    'primary key' => array('resource_resource_id'),
    'unique keys' => array(
      'resource_resource_uidx1' => array('subject_id', 'object_id'),
    ),
  );

  return $schema;
}

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