<?php
//$Id:
/*******************************************************************************
* Implementation of hook_install().
*/
function tripal_analysis_blast_install() {
// create the module's data directory
tripal_create_moddir('tripal_analysis_blast');
// We need to register to tripal_analysis module so it can provide a control
// for our blast result. Basically the registration is done by inserting
// modulename into the drupal {tripal_analysis} table AND inserting required
// information to the chado Analysis table. Also in tripal_analysis_blast.module,
// we need to define HOOK_get_settings() for the module to work properly.
// Register the analysis type
tripal_analysis_register_child('tripal_analysis_blast');
// Add cvterms
tripal_analysis_blast_add_cvterms();
// Create a tripal_analysis_blast table to store parsers
drupal_install_schema('tripal_analysis_blast');
// Create default parser for swissprot, DB:genbank, and go-seqdb
$sql_db = "SELECT db_id, name FROM {db} WHERE name like '%s'";
$sql_parser = "INSERT INTO {tripal_analysis_blast} ".
" (db_id, displayname, regex_hit_id, regex_hit_def, regex_hit_accession, genbank_style) ".
"VALUES (%d, '%s', '%s', '%s', '%s', %d)";
// Add swissprot parser
$previous_db = tripal_db_set_active ('chado');
$results = db_query($sql_db, "%swissprot%");
tripal_db_set_active($previous_db);
while ($db = db_fetch_object($results)) {
db_query($sql_parser, $db->db_id, 'ExPASy Swissprot', '^sp\|.*?\|(.*?)\s.*?$', '^sp\|.*?\|.*?\s(.*)$', 'sp\|(.*?)\|.*?\s.*?$', 0);
}
// Add trembl parser
$previous_db = tripal_db_set_active ('chado');
$results = db_query($sql_db, "%trembl%");
tripal_db_set_active($previous_db);
while ($db = db_fetch_object($results)) {
db_query($sql_parser, $db->db_id, 'ExPASy TrEMBL', '^.*?\|(.*?)\s.*?$', '^.*?\|.*?\s(.*)$', '^(.*?)\|.*?\s.*?$', 0);
}
// Add NCBI genbank parser
$previous_db = tripal_db_set_active ('chado');
$results = db_query($sql_db, "%genbank%");
tripal_db_set_active($previous_db);
while ($db = db_fetch_object($results)) {
db_query($sql_parser, $db->db_id, 'Genbank', '', '', '', 1);
}
}
/*******************************************************************************
* Implementation of hook_uninstall().
*/
function tripal_analysis_blast_uninstall() {
// Delete all information associate with the module
// Drupal complains when the user tries to uninstall tripal_analysis
// and tripal_analysis_blast at the same time. This is because Drupal drops
// the {tripal_analysis} table before we can delete anything from it. Thus,
// we perform a db_table_exists() check before the deletion
//Delete the settings from {tripal_analysis} table
tripal_analysis_unregister_child('tripal_analysis_blast');
// Delete module's variables from variables table.
db_query("DELETE FROM {variable} WHERE name='%s'",
'tripal_analysis_blast_setting');
// Delete a tripal_analysis_blast table
drupal_uninstall_schema('tripal_analysis_blast');
}
/*******************************************************************************
* Implementation of hook_schema(). This table stores the parsers for blast xml
* xml results.
*/
function tripal_analysis_blast_schema() {
$schema = array();
$schema['tripal_analysis_blast'] = array(
'fields' => array(
'db_id' => array(
'type' => 'int',
'unsigned' => TRUE,
'not null' => TRUE,
'default' => 0
),
'displayname' => array(
'type' => 'varchar',
'length' => 100,
'not null' => TRUE,
),
'regex_hit_id' => array(
'type' => 'varchar',
'length' => 30,
),
'regex_hit_def' => array(
'type' => 'varchar',
'length' => 30,
),
'regex_hit_accession' => array(
'type' => 'varchar',
'length' => 30,
),
'genbank_style' => array(
'type' => 'int',
'unsigned' => TRUE,
'default' => 0
),
),
'indexes' => array(
'db_id' => array('db_id')
),
'primary key' => array('db_id'),
);
return $schema;
}
/*******************************************************************************
* Implementation of hook_requirements(). Make sure 'Tripal Core' and 'Tripal
* Analysis' are enabled before installation
*/
function tripal_analysis_blast_requirements($phase) {
$requirements = array();
if ($phase == 'install') {
if (!function_exists('tripal_create_moddir') || !function_exists('tripal_analysis_register_child')) {
$requirements ['tripal_analysis_blast'] = array(
'title' => "tripal_analysis_blast",
'value' => "error. Some required modules are just being installed. Please try again.",
'severity' => REQUIREMENT_ERROR,
);
}
}
return $requirements;
}
/*******************************************************************************
* Provide update script for adding new cvterms
*/
function tripal_analysis_blast_update_6000(){
// we have some new cvterms to add
tripal_analysis_blast_add_cvterms();
$ret = array(
'#finished' => 1,
);
return $ret;
}
/*******************************************************************************
* Function for adding cvterms
*/
function tripal_analysis_blast_add_cvterms () {
// Add the cvterms for the anlysisprop table
tripal_add_cvterms('analysis_blast_settings', 'Settings of a blast analysis, '.
'including db_id, output file, and run parameters separated by a bar |');
tripal_add_cvterms('analysis_blast_blastdb','The database used for blasting');
tripal_add_cvterms('analysis_blast_blastfile','The input file or directory that contains the XML blast output');
tripal_add_cvterms('analysis_blast_blastparameters','The parameters used when performing blast.');
tripal_add_cvterms('analysis_blast_no_parsed','Indicates if the input file should be parsed to map results to features');
tripal_add_cvterms('analysis_blast_query_re','The regular expression for finding the feature name in the query definition line of the blast results');
tripal_add_cvterms('analysis_blast_query_type','The feature type (e.g. mRNA, polypeptide) of the query input file. This type is used to identify the query feature when multiple features have the same name');
tripal_add_cvterms('analysis_blast_query_uniquename','Indicates if the matched name in the query definition line of the blast results is feature uniquename');
tripal_add_cvterms('analysis_blast_blastfile_ext','Indicates the extension of the blast files. This is required if the blastfile setting is a directory.');
tripal_add_cvterms('analysis_blast_is_concat','Indicates if the blast results XML file is a series of concatenated XML results. Such is the case, for example, if Blast2GO was used to perform the analysis.');
// Add cvterm 'analysis_blast_output_iteration_hits' for inserting into featureprop table
tripal_add_cvterms('analysis_blast_output_iteration_hits', 'Hits of a blast '.
'output iteration. Each iteration corresponds to a chado feature, and is '.
'the content between <iteration> and </iteration> tags in the blast xml '.
'output file. This cvterm represents all hits in the iteration');
tripal_add_cvterms('analysis_blast_besthit_query', 'query name of the best hit
associated with a feature and a blast analysis ');
tripal_add_cvterms('analysis_blast_besthit_match', 'match name of the best hit
associated with a feature and a blast analysis ');
tripal_add_cvterms('analysis_blast_besthit_description', 'description of the best hit
associated with a feature and a blast analysis ');
tripal_add_cvterms('analysis_blast_besthit_evalue', 'evalue of the best hit
associated with a feature and a blast analysis ');
tripal_add_cvterms('analysis_blast_besthit_identity', 'identity (%) of the best hit
associated with a feature and a blast analysis ');
tripal_add_cvterms('analysis_blast_besthit_length', 'length of the best hit
associated with a feature and a blast analysis ');
}