icsearch/dbsf.install

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<?php
// $Id: dbsf.install,v 1.1 2010-01-02 17:06:44 alexie Exp $


function dbsf_install() {
  global $db_url;
  if (strpos($db_url['default'], 'pgsql://') === FALSE && strpos($db_url, 'pgsql://') === FALSE) {
    drupal_set_message("The dbsf module was not installed: it requires a PostgreSQL database due to data integrity issues with MySQL and also PostgreSQL is need for integration with GMOD and chado.", 'error', FALSE);
    return FALSE;
  }

  drupal_install_schema('dbsf');
  db_query('ALTER TABLE {ic_software} ADD active boolean NOT NULL');
  db_query('ALTER TABLE {ic_software} ALTER active set default false');

  icbasic_add_cv('software_type', array('similarity search', 'de-novo prediction'));
  icbasic_add_cv('dataset_type', array('protein', 'nucleotide', 'both'));
  icbasic_add_cv('resource_type', array('software option', 'dataset', 'dataset_group', 'directory', 'filename'));
  icbasic_add_cv('software path', array('executable', 'data'));
  icbasic_add_cv('input type', array('select', 'textfield', 'textarea', 'checkbox', 'checkboxes', 'radio', 'radios'));

  // core plugin always installed
  $add_software_sql = "INSERT INTO {ic_software} (uniquename,description) VALUES ('%s','%s')";
  $software_core_avail = array(
    'blastall' => "BLAST from NCBI implementation from the C toolkit (BLASTALL)",
    'condor' => "If installed, searches will be launched via Condor",
  );
  foreach ($software_core_avail as $software_name => $description) {
    db_query($add_software_sql, $software_name, $description);
  }
  dbsf_add_software_blast();

  // determine which plugins exist
  $plugin_path = drupal_get_path('module', 'dbsf') .'/';
  $plugins = array();
  //    'annot8r'=>"GO/EC/KEGG annotation of proteins from Ralf Schmid as implemented in INSEARCH",
  if (file_exists($plugin_path .'dbsf_ssaha2.inc')) {
    $plugins['ssaha2']['file'] = $plugin_path .'dbsf_ssaha2.inc';
    $plugins['ssaha2']['desc'] = "SSAHA2 rapidly aligns reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) to reference databases";
  }
  foreach ($plugins as $plugin_name => $plugin_data) {
    require_once ($plugin_data['file']);
    switch ($plugin_name) {
      case 'ssaha2':
        db_query($add_software_sql, $plugin_name, $plugin_data['desc']);
        dbsf_add_software_ssaha2();
        break;
    }
    drupal_set_message($plugin_name .' plugin found and installed.', 'warning');
  }

  // A module specific directory with sites/.../files/ which will hold temporary data
  // symlinks don't work with file_create_path (if outside /files)
  $dirpath = file_create_path() .'/dbsf';
  file_check_directory($dirpath, FILE_CREATE_DIRECTORY);
  // prevent indexing via www
  touch($dirpath .'/index.html');
  touch($dirpath .'/index.php');
  //file_check_directory($dirpath, FILE_MODIFY_PERMISSIONS);
}

function dbsf_uninstall() {
  drupal_uninstall_schema('dbsf');
}

function dbsf_schema() {
  // each blastdb can have more than one role.
  $schema['ic_resource_role'] = array(
    'fields' => array(
      'resource_role_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ),
      'role_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
      'resource_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
    ),
    'unique keys' => array('ic_role_uidx' => array('resource_id', 'role_id')),
    'primary key' => array('resource_role_id'),
  );
  $schema['ic_software'] = array(
    'fields' => array(
      'software_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ),
      'uniquename' => array(
        'type' => 'varchar',
        'length' => 15,
        'not null' => TRUE,
      ),
      'description' => array(
        'type' => 'text',
      ),
    ),
    'unique keys' => array('ic_software_uidx' => array('uniquename')),
    'primary key' => array('software_id'),
  );
  $schema['ic_softwareprop'] = array(
    'fields' => array(
      'softwareprop_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ), 'software_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,
      ),
    ),
    'unique keys' => array('ic_softwareprop_uidx' => array('software_id', 'type_id', 'rank')),
    'primary key' => array('softwareprop_id'),
  );
  $schema['ic_software_resource'] = array(
    'fields' => array(
      'software_resource_id' => array(
        'type' => 'serial',
        'not null' => TRUE,
      ), 'software_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ), 'resource_id' => array(
        'type' => 'int',
        'not null' => TRUE,
      ),
    ),
    'unique keys' => array('ic_software_resource_uidx' => array('software_id', 'resource_id')),
    'primary key' => array('software_resource_id'),
  );
  return $schema;
}

function dbsf_add_software_option($name, $dbxref_id, $cvterm_id, $description = NULL) {
  if (empty($name) || empty($dbxref_id) || empty($cvterm_id)) {
    return FALSE;
  }
  db_query("DELETE FROM {ic_resource} where uniquename='%s'", $name);
  if (empty($description)) {
    db_query("INSERT INTO {ic_resource} (uniquename,organism_id,dbxref_id,type_id) " . "VALUES ('%s',1,%d,%d)", $name, $dbxref_id, $cvterm_id);
  }
  else {
    db_query("INSERT INTO {ic_resource} (uniquename,organism_id,dbxref_id,type_id,description) " . "VALUES ('%s',1,%d,%d,'%s')", $name, $dbxref_id, $cvterm_id, $description);
  }
  // Check:
  $res = db_fetch_array(db_query("SELECT resource_id from {ic_resource} where uniquename='%s' AND dbxref_id=%d and type_id=%d", $name, $dbxref_id, $cvterm_id));
  if (empty($res['uniquename'])) {
    drupal_set_message(t('Failed to add software option ') . $name .'.');
    return FALSE;
  }
  return TRUE;
}

function dbsf_add_software_blast() {
  db_query("INSERT INTO {ic_software} (uniquename,description) VALUES ('formatdb','Format reference sequence as a BLAST database - NCBI C toolkit. Required for blastall to work properly.')");
  db_query("INSERT INTO {ic_software} (uniquename,description) VALUES ('fastacmd','Retrieve data from formatted BLAST databases - NCBI C toolkit. Required for blastall to work properly.')");

  $dbxref_id = icbasic_get_add_dbxref_withnames('NCBI', 'BLASTALL');
  $cvterm_id = icbasic_get_add_cv_withnames('resource_type', 'software option');
  $link_sql  = 'INSERT INTO {ic_software_resource} (software_id,resource_id) VALUES (' . "(SELECT software_id from {ic_software} where uniquename='blastall')" . ",(SELECT resource_id from {ic_resource} where uniquename='%s')" . ')';

  $options_array = array(
    'Scoring matrix' => '',
    'Filtering' => '',
    'E-value cutoff' => '',
    'Advanced BLAST options' => '',
    'query genetic code' => '',
    'DB genetic code' => '',
    'Frame shift penalty' => '',
    'Number of results' => '',
  );
  foreach ($options_array as $option => $description) {
    dbsf_add_software_option($option, $dbxref_id, $cvterm_id, $description);
    switch ($option) {
      case 'Scoring matrix':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            'BLOSUM62', 'PAM30', 'PAM70', 'BLOSUM80', 'BLOSUM45',
          ));
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('select'));
        break;

      case 'Filtering':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            'Low complexity regions', 'Lower-case letters',
          ));
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('checkboxes'));
        break;

      case 'E-value cutoff':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            '1e-3', '1e-30', '1e-10', '1e-5', '0.1', '0', '10',
          ));
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('select'));
        break;

      case 'Advanced BLAST options':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            'ungapped', 'megablast',
          ));
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('checkboxes'));
        break;

      case 'query genetic code':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            'Standard', 'Vertebrate Mitochondrial', 'Yeast Mitochondrial', 'Mold, Protozoan, and Coelocoel Mitochondrial'
            , 'Invertebrate Mitochondrial', 'Ciliate Nuclear', 'Echinoderm Mitochondrial', 'Euplotid Nuclear'
            , 'Bacterial', 'Alternative Yeast Nuclear', 'Ascidian Mitochondrial', 'Flatworm Mitochondrial'
            , 'Blepharisma Macronuclear',
          ));
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('select'));
        break;

      case 'DB genetic code':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            'Standard', 'Vertebrate Mitochondrial', 'Yeast Mitochondrial', 'Mold, Protozoan, and Coelocoel Mitochondrial'
            , 'Invertebrate Mitochondrial', 'Ciliate Nuclear', 'Echinoderm Mitochondrial', 'Euplotid Nuclear'
            , 'Bacterial', 'Alternative Yeast Nuclear', 'Ascidian Mitochondrial', 'Flatworm Mitochondrial'
            , 'Blepharisma Macronuclear',
          ));
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('select'));
        break;

      case 'Frame shift penalty':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            '0',
          ));
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('textfield'));
        break;

      case 'Number of results':
        icbasic_populate_prop('ic_resource', $option, $cvterm_id, array(
            '10', '100', '1', '50',
          )
        );
        icbasic_populate_cvterms('ic_resource', $option, 'input type', array('select'));
        break;
    }
    //Now link them to the software
    db_query($link_sql, $option);
  }
  return TRUE;
}

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