tripal_blast/blast_ui.install

<?php
/**
 * @file
 * .install file of BLAST UI.
 *
 * Contains hooks to handle installation of this module.
 *
 * Specifically, a database table (blastdb) is created to store additional information
 * related to blast database nodes such as the name/path to the NCBI BLAST database files
 * and the type (protein or nucleotide) of the database.
 */


use Drupal\node\Entity\Node;

/**
 * Implements hook_install().
 * 
 * @see tripal.info
 */
function blast_ui_install() {
  // Retreives the Drupal relative directory for a Tripal module.
  tripal_create_files_dir('tripal_blast');
}

/**
 * Implements hook_uninstall().
 */
function blast_ui_uninstall() {
  // Remove all nodes of type blastdb 
  $query = \Drupal::entityQuery('node')
    // Restrict to BLASTDB nodes.
    ->condition('bundle', 'blastdb')
    // Restrict to Published nodes.
    ->condition('status', 1)
    // Restrict to nodes the current user has permission to view.
    ->addTag('node_access');
  
  $entities = $query->execute();

  // Get all BlastDB nodes and delete them
  $nodes = Node::loadMultiple(array_keys($entities['node']));
  foreach ($nodes as $node) {
    print "Delete node " . $node->title . "\n";
    $nrs = node_revision_list($node);
    
    foreach ($nrs as $nr) {
      node_revision_delete($nr->vid);
    }
    node_delete($node->nid);
  }
}

/**
 * Implements hook_schema().
 * Create the blastdb database table for storing addditional info related to blastdb nodes.
 *
 * NOTE: This hook is called via Drupal magic during the installation process and no longer
 * needs to be called explicitly in hook_install().
 */
function blast_ui_schema() {
  // A table to keep extra information related to blastdb nodes.
  $schema['blastdb'] = array(
    'description' => t('The base table for blastdb node'),
    'fields' => array(
      'nid' => array(
        'description' => t('The primary identifier for a node.'),
        'type' => 'serial',
        'unsigned' => true,
        'not null' => true,
      ),
      'name' => array(
        'description' => t('The human-readable name of the blast database.'),
        'type' => 'varchar',
        'length' => 255,
        'not null' => true,
      ),
      'path' => array(
        'description' => t('The full path and filename prefix of the blast database.'),
        'type' => 'varchar',
        'length' => 1023,
        'not null' => true,
      ),
      'dbtype' => array(
        'description' => t('Type of the blast database. Should be either n for nucleotide or p for protein.'),
        'type' => 'varchar',
        'length' => 15,
        'not null' => true,
      ),
      'dbxref_id_regex' => array(
        'description' => t('The Regular Expression to use to extract the id from the FASTA header of the BLAST database hit.'),
        'type' => 'text',
      ),
      'dbxref_db_id' => array(
        'description' => t('The Database records from this BLAST Database reference.'),
        'type' => 'int',
      ),
      'dbxref_linkout_type' => array(
        'description' => t('Type of linkout to be used for this database reference.'),
        'type' => 'varchar',
        'length' => 50,
        'not null' => true,
        'default' => 'link'
      ),
      'cvitjs_enabled' => array(
        'description' => t('Indicate if CViTjs should be used to display hits on a whole genome'),
        'type' => 'int',
        'not null' => false,
        'default' => 0
      ),
    ),
    
    'indexes' => array(
      'name' => array('name'),
    ),
    
    'primary key' => array('nid'),
    'unique keys' => array(
       'nid' => array('nid'),
    ),
  );
  
  // BLAST JOBS
  // ------------------------
  // Keeps track of additional information related to tripal blast jobs.
  $schema['blastjob'] = array(
    'description' => t('Keeps track of additional information related to tripal blast jobs.'),
    'fields' => array(
      'job_id' => array(
        'description' => t('The Tripal job_id for the blast job.'),
        'type' => 'int',
        'unsigned' => true,
        'not null' => true,
      ),
      'blast_program' => array(
        'description' => t('The program to use to run the blast (ie: blastn, blastp, etc.).'),
        'type' => 'varchar',
        'length' => 20,
        'not null' => true,
      ),
      'target_blastdb' => array(
        'description' => t('The nid of the blastdb used to search against; NULL if target was uploaded.'),
        'type' => 'int',
        'unsigned' => true,
      ),
      'target_file' => array(
        'description' => t('The absolute path to the uploaded blast database after it was run through makeblastdb; NULL if target was NOT uploaded.'),
        'type' => 'text',
      ),
      'query_file' => array(
        'description' => t('The absolute path to the query file.'),
        'type' => 'text',
      ),
      'result_filestub' => array(
        'description' => t('The absolute path and filename (without extension) of the blast results.'),
        'type' => 'text',
      ),
      'options' => array(
        'description' => t('A serialized array of options selected for the blast job where the key is the machine name of the option used when calling blast (ie: gapextend) and the value is the value of the option.'),
        'type' => 'text',
      ),
    ),
    'primary key' => array('job_id'),
    'foreign keys' => array(
      'job_id' => array(
        'table' => 'tripal_jobs',
        'columns' => array(
          'job_id' => 'job_id',
        ),
      ),
    ),
  );
  
  return $schema;
}


// UPDATES:


/**
 * Make BlastDB type more readable & support Link-outs for BLAST Hits.
 */
function blast_ui_update_7101() {
  // Changing the length of the type field to allow it to be more readable.
  db_change_field('blastdb', 'dbtype', 'dbtype',
    array(
        'description' => t('Type of the blast database. Should be either n for nucleotide or p for protein.'),
        'type' => 'varchar',
        'length' => 15,
        'not null' => true,
    )
  );

  // Add fields related to Link-outs
  db_add_field(
    'blastdb',
    'dbxref_id_regex',
    array(
      'description' => t('The Regular Expression to use to extract the id from the FASTA header of the BLAST database hit.'),
      'type' => 'text',
    )
  );
  db_add_field(
    'blastdb',
    'dbxref_db_id',
    array(
      'description' => t('The Database records from this BLAST Database reference.'),
      'type' => 'int',
    )
  );
}

/**
 * Support complex types of link-outs such as GBrowse & JBrowse coordinate links.
 */
function blast_ui_update_7102() {
  db_add_field(
    'blastdb',
    'dbxref_linkout_type',
    array(
      'description' => t('Type of linkout to be used for this database reference.'),
      'type' => 'varchar',
      'length' => 50,
      'not null' => true,
      'default' => 'link'
    )
  );
}

/**
 * Add saving of blast job information for recent job list & resubmit functionality.
 */
function blast_ui_update_7103() {
  $schema = array();

  // Keeps track of additional information related to tripal blast jobs.
  $schema['blastjob'] = array(
    'description' => t('Keeps track of additional information related to tripal blast jobs.'),
    'fields' => array(
      'job_id' => array(
        'description' => t('The Tripal job_id for the blast job.'),
        'type' => 'int',
        'unsigned' => true,
        'not null' => true,
      ),
      'blast_program' => array(
        'description' => t('The program to use to run the blast (ie: blastn, blastp, etc.).'),
        'type' => 'varchar',
        'length' => 20,
        'not null' => true,
      ),
      'target_blastdb' => array(
        'description' => t('The nid of the blastdb used to search against; NULL if target was uploaded.'),
        'type' => 'int',
        'unsigned' => true,
      ),
      'target_file' => array(
        'description' => t('The absolute path to the uploaded blast database after it was run through makeblastdb; NULL if target was NOT uploaded.'),
        'type' => 'text',
      ),
      'query_file' => array(
        'description' => t('The absolute path to the query file.'),
        'type' => 'text',
      ),
      'result_filestub' => array(
        'description' => t('The absolute path and filename (without extension) of the blast results.'),
        'type' => 'text',
      ),
      'options' => array(
        'description' => t('A serialized array of options selected for the blast job where the key is the machine name of the option used when calling blast (ie: gapextend) and the value is the value of the option.'),
        'type' => 'text',
      ),
    ),
    'primary key' => array('job_id'),
    'foreign keys' => array(
      'job_id' => array(
        'table' => 'tripal_jobs',
        'columns' => array(
          'job_id' => 'job_id',
        ),
      ),
    ),
  );
  
  // First create the tables.
  db_create_table('blastjob', $schema['blastjob']);
}

/**
 * Add fields to blastp table for CViTjs support.
 */
function blast_ui_update_7104() {
  db_add_field(
    'blastdb',
    'cvitjs_enabled',
    array(
      'description' => t('Indicate if CViTjs should be used to display hits on a whole genome'),
      'type' => 'int',
      'not null' => false,
      'default' => 0
    )
  );
}