<?php
//$Id:

/*******************************************************************************
 * Implementation of hook_install().
 */
function tripal_analysis_interpro_install() {
   // create the module's data directory
   tripal_create_moddir('tripal_analysis_interpro');

   // We need to register to tripal_analysis module so it can provide a control
   // for our interpro 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_interpro.module,
   // we need to define HOOK_get_settings() for the module to work properly.
   
   // Inert into drupal's {tripal_analysis}
   tripal_analysis_register_child('tripal_analysis_interpro');
   
   // add the CVterms needed for this module
   tripal_analysis_interpro_add_cvterms();
}

/*******************************************************************************
 * Implementation of hook_uninstall().
 */
function tripal_analysis_interpro_uninstall() {
   
   // Delete all information associate with the module
   // Drupal complains when the user tries to uninstall tripal_analysis 
   // and tripal_analysis_interpro 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_interpro');
   
   // Delete module's variables from variables table.
   db_query("DELETE FROM {variable} WHERE name='%s'",
            'tripal_analysis_interpro_setting');

}
/**
*
*/
function tripal_analysis_interpro_add_cvterms(){
   // Add cvterm 'analysis_interpro_output_iteration_hits' for inserting into featureprop table
   tripal_add_cvterms('analysis_interpro_output_hit', 'Hit in the interpro html output. Each hit belongs to a chado feature. This cvterm represents a hit in the output');
   tripal_add_cvterms('analysis_interpro_settings', 'Settings of an interpro analysis, including output file and run parameters separated by a bar |');
   tripal_add_cvterms('analysis_interpro_interproparameters','The parameters used when executing an InterProScan job');
   tripal_add_cvterms('analysis_interpro_interprofile','Used to hold the name of the XML file containing the InterProScan results');
   tripal_add_cvterms('analysis_interpro_parsego','Indicates whether or not the GO terms should be extracted when parsing the InterProScan XML file');
   tripal_add_cvterms('analysis_interpro_parseHTML','Indicates that the input file is in HTML format. This functionality is deprecated and may not work, but is provided for backwards compatability.');
   tripal_add_cvterms('analysis_interpro_query_re','The regular expression for finding the feature name in the query definition line of the InterPro results');
   tripal_add_cvterms('analysis_interpro_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_interpro_query_uniquename','Indicates if the matched name in the query definition line of the blast results is feature uniquename');
   tripal_add_cvterms('analysis_interpro_output_keywords', 'Selected keywords for interpro html output which are indexed for search.');
}
/**
 * 
 */
function tripal_analysis_interpro_update_6000(){

   // we have some new cvterms to add
   tripal_analysis_interpro_add_cvterms();

   $ret = array(
      '#finished' => 1,
   );
   
   return $ret;
}
/*******************************************************************************
 * Implementation of hook_requirements(). Make sure 'Tripal Core' and 'Tripal
 * Analysis' are enabled before installation
 */
function tripal_analysis_interpro_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
      if (!function_exists('tripal_create_moddir') || !function_exists('tripal_analysis_register_child')) {
         $requirements ['tripal_analysis_interpro'] = array(
            'title' => "tripal_analysis_interpro",
            'value' => "error. Some required modules are just being installed. Please try again.",
            'severity' => REQUIREMENT_ERROR,
         );
      }
   }
   return $requirements;
}