<?php
/**
* @file
* 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.
*/
/**
* Implements hook_install().
*/
function blast_ui_install() {
tripal_create_files_dir('tripal_blast');
}
/**
* Implements hook_uninstall().
*/
function blast_ui_uninstall() {
// Remove all nodes of type blastdb
$query = new EntityFieldQuery();
$query->entityCondition('entity_type', 'node')
// Restrict to BLASTDB nodes.
->entityCondition('bundle', 'blastdb')
// Restrict to Published nodes.
->propertyCondition('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
$nodes = node_load_multiple(array_keys($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;
}
/**
* 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
)
);
}