StructureFeatures.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/ProtocolFeatures.cc
/// @brief  report protocol level features to features statistics scientific benchmark
/// @author Matthew O'Meara

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

// Project Headers
#include <basic/database/sql_utils.hh>
#include <core/io/silent/BinaryProteinSilentStruct.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <utility/exit.hh>
#include <utility/sql_database/DatabaseSessionManager.hh>
#include <utility/vector1.hh>
#include <utility/tools/make_vector.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/inout.OptionKeys.gen.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/Job.hh>
#include <numeric/random/random.hh>

#include <basic/database/schema_generator/PrimaryKey.hh>
#include <basic/database/schema_generator/ForeignKey.hh>
#include <basic/database/schema_generator/Column.hh>
#include <basic/database/schema_generator/Schema.hh>

#include <basic/database/insert_statement_generator/InsertGenerator.hh>
#include <basic/database/insert_statement_generator/RowData.hh>

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

// Boost Headers
#include <boost/uuid/uuid.hpp>
#include <boost/uuid/uuid_generators.hpp>
#include <boost/uuid/uuid_io.hpp>
#include <boost/lexical_cast.hpp>

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

//Basic Headers
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/inout.OptionKeys.gen.hh>

static basic::Tracer TR("protocols.features.StructureFeatures");

namespace protocols{
namespace features{

using std::string;
using std::stringstream;
using std::endl;
using basic::database::safely_prepare_statement;
using boost::hash_value;
using core::Size;
using core::io::silent::BinaryProteinSilentStruct;
using core::pose::Pose;
using core::pose::tag_from_pose;
using core::pose::tag_into_pose;
using utility::vector1;
using utility::sql_database::sessionOP;
using cppdb::statement;
using cppdb::result;
using basic::database::insert_statement_generator::InsertGenerator;
using basic::database::insert_statement_generator::RowData;
using basic::database::insert_statement_generator::RowDataBaseOP;

StructureFeatures::StructureFeatures(){}

StructureFeatures::StructureFeatures( StructureFeatures const & ) :
  FeaturesReporter()
{}

StructureFeatures::~StructureFeatures(){}

string
StructureFeatures::type_name() const { return "StructureFeatures"; }

void
StructureFeatures::write_schema_to_db(
  sessionOP db_session
) const {
  using namespace basic::database::schema_generator;

  //Don't autoincrement the struct_id because it is a UUID generated here
  Column struct_id("struct_id", new DbUUID(), false /*not null*/, false /*don't autoincrement*/);
  Column batch_id("batch_id", new DbInteger());
  Column tag("tag", new DbText(255));
  Column input_tag("input_tag", new DbText());

  /***structures***/
  Schema structures("structures", PrimaryKey(struct_id));

  structures.add_foreign_key(ForeignKey(batch_id, "batches", "batch_id", true /*defer*/));
  structures.add_column( tag );
  structures.add_column( input_tag );

  structures.write(db_session);

  /***sampled_structures***/
  Schema sampled_structures("sampled_structures");
  sampled_structures.add_foreign_key(ForeignKey(batch_id, "batches", "batch_id", true /*defer*/));

  sampled_structures.add_column( tag );
  sampled_structures.add_column( input_tag );

  utility::vector1<Column> unique_cols;
  unique_cols.push_back(tag);
  unique_cols.push_back(batch_id);
  sampled_structures.add_constraint(new UniqueConstraint(unique_cols));

  sampled_structures.write(db_session);
}

utility::vector1<std::string>
StructureFeatures::features_reporter_dependencies() const {
  utility::vector1<std::string> dependencies;
  dependencies.push_back("ProtocolFeatures");
  return dependencies;
}


//@details missing struct_id and input/output tags
boost::uuids::uuid
StructureFeatures::report_features(
  vector1< bool > const & relevant_residues,
  Size batch_id,
  sessionOP db_session
){
  string const output_tag(protocols::jd2::JobDistributor::get_instance()->current_output_name());
  string const input_tag(protocols::jd2::JobDistributor::get_instance()->current_job()->input_tag());
  boost::uuids::uuid struct_id(
    report_features(relevant_residues, batch_id,
      db_session, output_tag, input_tag));
  return struct_id;
}

//@details missing struct_id and input/output tags
boost::uuids::uuid
StructureFeatures::report_features(
  vector1< bool > const &,
  Size batch_id,
  sessionOP db_session,
  string const & tag,
  string const & input_tag
){

  boost::uuids::basic_random_generator<numeric::random::RandomGenerator>
    uuids_rng(numeric::random::RG);
  boost::uuids::uuid struct_id = uuids_rng();

  InsertGenerator structures_insert("structures");
  structures_insert.add_column("struct_id");
  structures_insert.add_column("batch_id");
  structures_insert.add_column("tag");
  structures_insert.add_column("input_tag");

  RowDataBaseOP struct_id_data = new RowData<boost::uuids::uuid>("struct_id",struct_id);
  RowDataBaseOP batch_id_data = new RowData<Size>("batch_id",batch_id);
  RowDataBaseOP tag_data = new RowData<string>("tag",tag);
  RowDataBaseOP input_tag_data = new RowData<string>("input_tag",input_tag);

  structures_insert.add_row(utility::tools::make_vector(struct_id_data,batch_id_data,tag_data,input_tag_data));
  structures_insert.write_to_database(db_session);

  return struct_id;
}

void StructureFeatures::mark_structure_as_sampled(
  core::Size batch_id,
  std::string const & tag,
  std::string const & input_tag,
  utility::sql_database::sessionOP db_session
){

  InsertGenerator sampled_insert("sampled_structures");
  sampled_insert.add_column("batch_id");
  sampled_insert.add_column("tag");
  sampled_insert.add_column("input_tag");

  RowDataBaseOP batch_id_data = new RowData<Size>("batch_id",batch_id);
  RowDataBaseOP tag_data = new RowData<string>("tag",tag);
  RowDataBaseOP input_tag_data = new RowData<string>("input_tag",input_tag);

  sampled_insert.add_row(utility::tools::make_vector(batch_id_data,tag_data,input_tag_data));
  sampled_insert.write_to_database(db_session);
}

void StructureFeatures::delete_record(
  boost::uuids::uuid struct_id,
  utility::sql_database::sessionOP db_session
){

  std::string statement_string = "DELETE FROM structures WHERE struct_id = ?;";
  statement stmt(basic::database::safely_prepare_statement(statement_string,db_session));
  stmt.bind(1,struct_id);
  basic::database::safely_write_to_database(stmt);

}

void
StructureFeatures::load_into_pose(
  sessionOP db_session,
  boost::uuids::uuid struct_id,
  Pose & pose
){
  load_tag(db_session, struct_id, pose);
}

void
StructureFeatures::load_tag(
  sessionOP db_session,
  boost::uuids::uuid struct_id,
  Pose & pose) {

  std::string statement_string =
    "SELECT\n"
    " tag\n"
    "FROM\n"
    " structures\n"
    "WHERE\n"
    " structures.struct_id=?";

  statement stmt(basic::database::safely_prepare_statement(statement_string, db_session)) ;
  stmt.bind(1,struct_id);


  result res(basic::database::safely_read_from_database(stmt));
  if(!res.next()){
    stringstream error_message;
    error_message << "Unable to locate structure with struct_id '"
      << struct_id << "'." << endl;
    utility_exit_with_message(error_message.str());
  }
  string tag;
  res >> tag;
  tag_into_pose(pose,tag);
}

boost::uuids::uuid
StructureFeatures::get_struct_id(
  sessionOP db_session,
  string const & tag,
  core::Size const & protocol_id
){

  std::string statement_string =
    "SELECT\n"
    " structures.struct_id\n"
    "FROM\n"
    " protocols\n"
    "JOIN batches ON\n"
    " protocols.protocol_id = batches.protocol_id\n"
    "JOIN structures ON\n"
    " batches.batch_id = structures.batch_id\n"
    "WHERE\n"
    " structures.tag=? AND protocols.protocol_id=?;";

  statement stmt(basic::database::safely_prepare_statement(statement_string,db_session));
  stmt.bind(1,tag);
  stmt.bind(2,protocol_id);

  result res(basic::database::safely_read_from_database(stmt));
  if(!res.next()){
    stringstream error_message;
    error_message << "Unable to locate structure with tag '"<<tag<<"'."<<endl;
    utility_exit_with_message(error_message.str());
  }
  boost::uuids::uuid struct_id;
  res >> struct_id;
  return struct_id;
}

} // namesapce
} // namespace