FeaturesReporter.cc

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   protocols/features/FeaturesReporter.cc
/// @brief  Base class to report geometry and scores to features Statistics Scientific Benchmark
/// @author Matthew O'Meara

// Unit Headers
#include <protocols/features/FeaturesReporter.hh>

//External
#include <boost/uuid/uuid.hpp>
#include <boost/uuid/uuid_io.hpp>

// Project Headers
#include <basic/Tracer.hh>
#include <basic/database/sql_utils.hh>
#include <utility/sql_database/DatabaseSessionManager.hh>
#include <utility/string_util.hh>
#include <utility/tag/Tag.hh>
#include <utility/vector1.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/datacache/CacheableString.hh>
#include <core/pose/Pose.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/pose/PDBInfo.hh>
#include <basic/database/sql_utils.hh>

// Boost Headers
#include <boost/foreach.hpp>
#include <boost/tokenizer.hpp>
#define foreach BOOST_FOREACH

// External Headers
#include <cppdb/frontend.h>

// C++ Headers
#include <string>
#include <sstream>
#include <iostream>

#include <utility/vector0.hh>


namespace protocols {
namespace features {

/// @details Auto-generated virtual destructor
FeaturesReporter::~FeaturesReporter() {}

using basic::Tracer;
using basic::datacache::CacheableString;
using boost::char_separator;
using boost::tokenizer;
using core::Size;
using core::pose::Pose;
using cppdb::statement;
using cppdb::cppdb_error;
using protocols::filters::Filters_map;
using protocols::jd2::JobDistributor;
using protocols::moves::DataMap;
using protocols::moves::Movers_map;
using std::endl;
using std::string;
using std::stringstream;
using utility::tag::TagPtr;
using basic::database::safely_prepare_statement;
using basic::database::safely_write_to_database;
using utility::trim;
using utility::vector1;
using utility::sql_database::sessionOP;

static Tracer TR("protocols.features.FeaturesReporter");

void
FeaturesReporter::write_schema_to_db(
  sessionOP db_session
) const {

  string schema_str(schema());
  try{
    basic::database::write_schema_to_database(schema_str,db_session);
  } catch (cppdb::cppdb_error error){
    stringstream err_msg;
    err_msg
      << "Failed to write database schema for '" << type_name() << "'" << endl
      << "Error Message:" << endl << error.what() << endl
      << "Schema:" << endl << schema_str << endl;
    utility_exit_with_message(err_msg.str());
  }
}

///@details Extract all features from the pose to the database.  The
///input parent_id can be used to connect the features with the rest
///of the database.  Usually the parent_id will be struct_id which
///uniquely identifies each structure in the database.  The feature
///reporter can return a parent_id.
Size
FeaturesReporter::report_features(
  Pose const & pose,
  boost::uuids::uuid parent_id,
  sessionOP db_session
){
  vector1<bool> relevant_residues(true, pose.total_residue());
  return report_features(pose, relevant_residues, parent_id, db_session);
}

///@details Extract all features from the pose to the database.  The
///input parent_id can be used to connect the features with the rest
///of the database.  Usually the parent_id will be struct_id which
///uniquely identifies each structure in the database.  The feature
///reporter can return a parent_id.
Size
FeaturesReporter::report_features(
  Pose const & /*pose*/,
  vector1< bool > const & /*relevant_residues*/,
  boost::uuids::uuid /*parent uuid*/,
  sessionOP /*db_session*/
){
  Size dummy_parent_id(0);
  return dummy_parent_id;
}


void
FeaturesReporter::parse_my_tag(
  TagPtr const tag,
  DataMap & /*data*/,
  Filters_map const & /*filters*/,
  Movers_map const & /*movers*/,
  Pose const & /*pose*/
) {
  runtime_assert(tag->getName() == "feature");
}


string
FeaturesReporter::find_tag(
  Pose const & pose
) const {
  //silent files and pdbs set the name of the pose differently
  string name = "";
  if (pose.pdb_info()){
    name = pose.pdb_info()->name();
  }
  if (name == ""){
    if (pose.data().has(core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG)) {
      name = static_cast< basic::datacache::CacheableString const & >
        (pose.data().get(core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG)).str();
    } else {
      name = JobDistributor::get_instance()->current_output_name();
    }
  }
  return name;
}

void
FeaturesReporter::delete_records_from_table(
  string const & table_name,
  boost::uuids::uuid struct_id,
  sessionOP db_session){
  stringstream sql;
  sql << "DELETE FROM " << table_name << " WHERE struct_id = ?;";
  statement stmt(safely_prepare_statement(sql.str(), db_session));
  stmt.bind(1,struct_id);
  safely_write_to_database(stmt);
}

} // namespace
} // namespace