dh_ecology.install

<?php

function dh_ecology_schema() {
  // 
  // temp//
  if (db_field_exists('dh_ecology_isolate', 'sequence')) {
    $seqcol = 'sequence';
  } else {
    $seqcol = 'its_sequence';
  }
  $schema['dh_ecology_isolate'] = array (
    'description' => 'Repository of plant sample DNA isolate',
    'fields' => array(
      'iid' => array(
        'description' => 'Isolate ID - Primary key for Variables',
        'type' => 'serial',
        'unsigned' => TRUE,
        'not null' => TRUE,
      ),
      'source' => array(
        'description' => 'Data Source (lab or collector)',
         'type' => 'varchar',
         'length' => 128,
         'not null' => FALSE,
         'default' => '',
       ),
      'isolate' => array(
         'description' => 'Isolate Unique Text Identifier',
         'type' => 'varchar',
         'length' => 64,
         'not null' => TRUE,
         'default' => '',
       ),
      'species' => array(
         'description' => 'Species',
         'type' => 'varchar',
         'length' => 255,
         'not null' => FALSE,
         'default' => '',
       ),
      'genus' => array(
         'description' => 'Genus',
         'type' => 'varchar',
         'length' => 255,
         'not null' => FALSE,
         'default' => '',
       ),
      'host_organism' => array(
         'description' => 'Host',
         'type' => 'varchar',
         'length' => 255,
         'not null' => FALSE,
         'default' => '',
       ),
      'acquisition_num' => array(
         'description' => 'Acquisition Number (Gen Bank)',
         'type' => 'varchar',
         'length' => 32,
         'not null' => FALSE,
         'default' => '',
       ),
      'primer_f' => array(
         'description' => 'Primer (forward)',
         'type' => 'varchar',
         'length' => 32,
         'not null' => FALSE,
         'default' => '',
       ),
      'primer_r' => array(
         'description' => 'Primer (reverse)',
         'type' => 'varchar',
         'length' => 32,
         'not null' => FALSE,
         'default' => '',
       ),
      $seqcol => array(
         'description' => 'DNA Sequence',
         'type' => 'text',
         'size' => 'big',
         'not null' => FALSE,
         'default' => '',
         'translatable' => false,
       ),
      'ecology' => array(
        'description' => 'Ecology Type (pathogen/non-pathogen/unknown))) ',
        'type' => 'varchar',
		    'length' => 64,
        'not null' => TRUE,
		    'default' => 'unknown',
      ),
      'sequence_location' => array(
        'description' => 'Sequence Location ',
        'type' => 'varchar',
        'length' => 64,
        'not null' => FALSE,
        'default' => 'undefined',
      ),
      'modified' => array(
        'description' => 'Type Specimen',
			  'type' => 'int',
			  'not null' => FALSE,
			  'size' => 'small',
      ),
      'modified' => array(
        'description' => 'Modified Date',
			  'type' => 'int',
			  'not null' => FALSE,
			  'size' => 'big',
      ),
      'bundle' => array(
        'description' => 'Isolate Type / Location / Bundle (machine name)) ',
        'type' => 'varchar',
		    'length' => 64,
        'not null' => TRUE,
		    'default' => 'dh_ecology_isolate',
      ),
      'type_specimen' => array(
        'description' => 'Type Specimen',
			  'type' => 'int',
			  'not null' => FALSE,
			  'size' => 'small',
      ),
      'uid' => array(
        'description' => 'Record Owner',
			  'type' => 'int',
			  'not null' => FALSE,
			  'size' => 'big',
      ),

     ) + entity_exportable_schema_fields(),
     'primary key' => array('iid'),
     'indexes' => array(
       'de_iso_iix' => array('iid'),
       'de_iso_isix' => array('isolate'),
       'de_iso_six' => array('source'),
       'de_iso_spix' => array('species'),
       'de_iso_aix' => array('acquisition_num'),
       'de_iso_itsix' => array($seqcol),
    )
  );
	if (db_field_exists('dh_ecology_isolate', 'sequence_location')) {
    $schema['dh_ecology_isolate']['sequence_location'] = array(
      'description' => 'Sequence Location ',
      'type' => 'varchar',
      'length' => 64,
      'not null' => FALSE,
      'default' => 'undefined',
    );
  }
  
  $schema['dh_ecology_isolate_type'] = array (
    'description' => 'Repository of plant sample DNA isolate',
    'fields' => array(
      'itid' => array(
         'description' => 'Isolate Type ID - Primary key',
         'type' => 'serial',
         'unsigned' => TRUE,
         'not null' => TRUE,
      ),
      'name' => array(
        'description' => 'Isolate Type Name ',
        'type' => 'varchar',
		    'length' => 64,
        'not null' => TRUE,
		    'default' => '',
      ),
      'bundle' => array(
        'description' => 'Isolate Type / Bundle (machine name)) ',
        'type' => 'varchar',
		    'length' => 64,
        'not null' => TRUE,
		    'default' => 'dh_ecology_isolate',
      ),
      'description' => array(
        'description' => 'Description of this Isolate Class',
        'type' => 'varchar',
		    'length' => 255,
        'not null' => TRUE,
		    'default' => '',
      ),
    ) + entity_exportable_schema_fields(),
    'primary key' => array('itid'),
    'indexes' => array(
      'de_isot_iix' => array('itid'),
      'de_isot_bix' => array('bundle'),
    )
  );

  return $schema;
}

function dh_ecology_uninstall() {
}


function dh_ecology_references() {
  $refdefs = array();
  $feature_bundles = dh_feature_get_types();
  // add references
  $refdefs[] = array(
    'fieldname' => 'dh_link_isolate_mps',
    'src_type' => 'dh_ecology_isolate',
    'src_bundle' => 'dh_ecology_isolate',
    'dest_type' => 'dh_feature',
    // could link to all features but not yet implemented
    //'dest_bundle' => $feature_bundles,
    'dest_bundle' => array('plant_tissue_sample'),
    'label' => 'Source Plant Tissue Sample',
    'select_type' => 'entityreference_autocomplete'
  );
  
  // link sample point to submittal
  $refdefs[] = array(
    'fieldname' => 'dh_link_feature_submittal',
    'src_type' => 'dh_adminreg_feature',
    'src_bundle' => 'submittal',
    'dest_type' => 'dh_feature',
    'dest_bundle' => 'plant_tissue_sample',
    'label' => 'Link Submittal Record to dH Feature',
    'select_type' => 'entityreference_autocomplete'
  );
  
  return $refdefs;
}

function dh_ecology_install() {  
  // shared ID key
  //$thistable = 'dh_ecology_isolate';
  //db_query("alter table {$thistable} alter column iid set default nextval('{dh_feature}_hydroid_seq')");
  // hack to make this work
  //db_query("insert into {dh_adminreg_feature} (admincode,name,bundle,status) values('dummy','dummy','facility','expired'); ");
  // add bundles
  dh_ecology_add_bundles();
  dh_ecology_isolate_add_bundles();
  //dh_ecology_add_views();
  
  // add references
  $refdefs = dh_ecology_references();
  dh_add_references($refdefs);
  
  // set up fields here
  $fields_fields = array(
    'plant_tissue_sample' => array(
      'dh_geofield' => array('label' => 'Geometry', 'type' => 'geofield', 'display' => 'geofield_wkt', 'widget' => 'geofield_wkt'),
    ),
  );
  foreach ($fields_fields as $key => $thistype) {
    dh_initialize_fields($key, '', 'dh_feature', $fields_fields);
  }
}

function dh_ecology_add_bundles() {
  $typedefs = array(
    'plant_tissue_sample' => array('bundle' => 'plant_tissue_sample', 'name' => 'Plant Tissue Sample', 'description' => 'dH Ecology Plant Tissue Sample and Site'),
  );

  foreach ($typedefs as $key => $thistype) {
    dh_base_feature_type_save($thistype);
    //dh_initialize_fields($key);
  }
}

function dh_ecology_isolate_add_bundles() {
  $iso_types = dh_define_isolate_bundles();
  foreach ($iso_types as $tn => $thistype) {
    if ($e = entity_create('dh_ecology_isolate_type', $thistype)) {
      $e->save();
    } else {
      drupal_set_message("Failed adding bundle $tn - $e: </pre>" . print_r($thistype,1) . "</pre>");
    }
  }
}
function dh_define_isolate_bundles() {
  $typedefs = array(
    'dh_ecology_isolate' => array('bundle' => 'dh_ecology_isolate', 'name' => 'Default Isolate Type', 'description' => 'dH Basic Isolate'),
    'its' => array('bundle' => 'its', 'name' => 'ITS Sequence', 'description' => 'ITS Sequence'),
  );
  return $typedefs;
}

function dh_ecology_isolate_type_save($info) {
  // set the base dh_ecology_isolate_type entries
  // modeled after node_type_save
  $existing_type = !empty($info['old_bundle']) ? $info['old_bundle'] : $info['bundle'];
  $is_existing = (bool) db_query_range('SELECT 1 FROM {dh_ecology_isolate_type} WHERE bundle = :bundle', 0, 1, array(':bundle' => $existing_type))->fetchField();

  $fields = array(
    'bundle' => $info['bundle'],
    'name' => $info['name'],
    'description' => $info['description'],
  );

  if ($is_existing) {
  error_log("Updating an existing bundle"); 
    db_update('dh_ecology_isolate_type')
      ->fields($fields)
      ->condition('bundle', $existing_type)
      ->execute();

    if (!empty($info['old_bundle']) && $info['old_bundle'] != $info['bundle']) {
      field_attach_rename_bundle('dh_ecology_isolate', $info['old_bundle'], $info['bundle']);
    }
	 // need equivalent?
    //module_invoke_all('node_type_update', $type);
    $status = SAVED_UPDATED;
  }
  else {
    db_insert('dh_ecology_isolate_type')
      ->fields($fields)
      ->execute();

    field_attach_create_bundle('dh_ecology_isolate', $info['bundle']);

    $status = SAVED_NEW;
  }

  // Clear the node type cache.
  // hmmm ... do we need to supply an equivalent to this?
  // node_type_cache_reset();
  dh_ecology_isolate_type_cache_reset();

  return $status;
}

function dh_ecology_isolate_type_cache_reset() {
  cache_clear_all('dh_ecology_isolate_type:', 'cache', TRUE);
  //drupal_static_reset('_node_types_build');
}


function dh_ecology_define_views() {
  $views = array();
  /*
  $views['dh_views_last_weather24'] = "  create or replace view {dh_views_last_weather24} as ";
  $views['dh_views_last_weather24'] .= " select a.featureid, ";
  $views['dh_views_last_weather24'] .= "   a.tstime as tsendtime, min(b.tstime) as tstime, ";
  $views['dh_views_last_weather24'] .= "   sum(b.rain) as rain, sum(b.wet_min) as wet_min, ";
  $views['dh_views_last_weather24'] .= "   avg(b.temp) as temp, avg(b.rh) as rh ";
  $views['dh_views_last_weather24'] .= " from ( ";
  $views['dh_views_last_weather24'] .= "   select a.featureid, max(a.tstime) as tstime ";
  $views['dh_views_last_weather24'] .= "   from {dh_timeseries_weather} as a ";
  $views['dh_views_last_weather24'] .= "   left outer join {dh_variabledefinition} as b ";
  $views['dh_views_last_weather24'] .= "   on ( a.varid = b.varid and b.varkey = 'weather_obs' ) ";
  $views['dh_views_last_weather24'] .= "   where b.varid is not null ";
  $views['dh_views_last_weather24'] .= " ) as a ";
  */
  return $views;
}

function dh_ecology_add_views($views = array()) {
  $allviews = dh_ecology_define_views();
  if (count($views) == 0) {
    $views = array_keys($allviews);
  }
  foreach ($views as $viewname => $viewsql) {
    db_query( $viewsql );
  }
}
  
function dh_ecology_update_7101() {
// this seems not to be needed as submittal can connect to any feature
/*
  $refdefs = array();
  // link sample point to submittal
  $refdefs[] = array(
    'fieldname' => 'dh_link_feature_submittal',
    'src_type' => 'dh_adminreg_feature',
    'src_bundle' => 'submittal',
    'dest_type' => 'dh_feature',
    'dest_bundle' => 'plant_tissue_sample',
    'label' => 'Link Submittal Record to dH Feature',
    'select_type' => 'entityreference_autocomplete'
  );
  dh_add_references($refdefs, false);
*/
}

function dh_ecology_update_7102() {
  db_query("alter table {dh_ecology_isolate} add column bundle varchar(64) default 'dh_ecology_isolate'");
}

function dh_ecology_update_7103() {
  $schema = dh_ecology_schema();
	if (!db_table_exists('dh_ecology_isolate_type')) {
    db_create_table('dh_ecology_isolate_type', $schema['dh_ecology_isolate_type']);
  }
	if (!db_field_exists('dh_ecology_isolate', 'bundle')) {
    db_query("alter table {dh_ecology_isolate} add column bundle varchar(64) default 'dh_ecology_isolate'");
  }
  db_query("alter table {dh_ecology_isolate} alter column bundle set default 'dh_ecology_isolate'");
}

function dh_ecology_update_7105() {
  $schema = dh_ecology_schema();
	if (!db_table_exists('dh_ecology_isolate_type')) {
    db_create_table('dh_ecology_isolate_type', $schema['dh_ecology_isolate_type']);
  }
}

function dh_ecology_update_7108() {
  dh_ecology_isolate_add_bundles();
}

function dh_ecology_update_7109() {
  // rename its_sequence to sequence
	if (db_field_exists('dh_ecology_isolate', 'its_sequence')) {
    db_query("alter table {dh_ecology_isolate} rename column its_sequence TO sequence ");
  }
  // sequence_location 
  db_query("alter table {dh_ecology_isolate} add column sequence_location varchar(64) default 'unknown' ");
  // create bundle its_sequence - sequence_location = its
  $tn = 'its';
  $thistype = array('bundle' => 'its', 'name' => 'ITS Sequence', 'description' => 'ITS Sequence');
  if ($e = entity_create('dh_ecology_isolate_type', $thistype)) {
    $e->save();
  } else {
    drupal_set_message("Failed adding bundle $tn - $e: </pre>" . print_r($thistype,1) . "</pre>");
  }
}

function dh_ecology_update_7110() {
  $schema = dh_ecology_schema();
  $uid = $schema['dh_ecology_isolate']['fields']['uid'];
  dpm($uid, 'Adding uid field');
  db_add_field( 'dh_ecology_isolate', 'uid', $uid);
}

function dh_ecology_update_7111() {
  // type_specimen 
  db_query("alter table {dh_ecology_isolate} add column type_specimen INTEGER default 0 ");
}