#include #include #include #include "Database.h" #include "tools.h" #include "Time.h" #include "Configuration.h" #include "zfits.h" using namespace std; namespace fs = boost::filesystem; // ------------------------------------------------------------------------ struct Map : pair { Map() { } }; std::istream &operator>>(std::istream &in, Map &m) { const istreambuf_iterator eos; string txt(istreambuf_iterator(in), eos); const boost::regex expr("((.*)[^\\\\])/(.*)"); boost::smatch match; if (!boost::regex_match(txt, match, expr)) throw runtime_error("Could not evaluate map argument: "+txt); m.first = match[1].str(); m.second = match[3].str(); return in; } void SetupConfiguration(Configuration &conf) { po::options_description control("Root to SQL"); control.add_options() ("uri,u", var()->required(), "Database link as in\n\tuser:password@server[:port]/database[?compress=0|1].") ("file", var()->required(), "The root file to read from") ("create", po_switch(), "Create the database if not existing") ("drop", po_switch(), "Drop the table (implies create)") ("extension,e", var(""), "Name of the fits extension (table) to convert") ("table", var(""), "Name of the table to use (default is the tree name)") ("map", vars(), "A regular expression which is applied to the leaf name befoee it is used as SQL column name)") ("sql-type", vars(), "Allows to overwrite the calculated SQL type for a given column e.g. 'sql-column-name/UNSIGNED IN'") ("ignore", vars(), "Ignore the given leaf, if the given regular expression matches") ("unsigned", vars(), "In fits files per default columns are signed. This interpretss the column as unsigned value. Use the FITS column name.") ("primary", vars(), "List of columns to be used as primary keys during table creation (in connection with --create)") ("first", var(size_t(0)), "First event to start with (default: 0), mainly for test purpose") ("max", var(size_t(0)), "Maximum number of events to process (0: all), mainly for test purpose") ("engine", var(""), "Database engine to be used when a new table is created") ("row-format", var(""), "Defines the ROW_FORMAT keyword for table creation") ("duplicate", vars(), "Specifies an assignment_list for an 'ON DUPLICATE KEY UPDATE' expression") ("ignore-errors", po_switch(), "Adds the IGNORE keyword to the INSERT query (turns errors into warnings, ignores rows with errors)") ("const.*", var(), "Insert a constant number into the given column (--const.mycolumn=5). A special case is `/.../.../`") ("conditional", po_switch(), "Conditional insert. Only insert if no entry exists yet with the constants defined by --const") ("delete", po_switch(), "Delete all entries first which fit all constant columns defined by --const") ("index", po_switch(), "If a table is created, all const columns are used as a single index") ; po::options_description debug("Debug options"); debug.add_options() ("no-insert", po_switch(), "Does not insert any data into the table") ("dry-run", po_switch(), "Skip any query which changes the databse (might result in consecutive failures)") ("print-extensions", po_switch(), "Print extensions (tables) from fits file") ("print-connection", po_switch(), "Print database connection information") ("print-columns", po_switch(), "Print columns in fits table") ("print-insert", po_switch(), "Print the INSERT query (note that it contains all data)") ("print-create", po_switch(), "Print the CREATE query") ("print-select", po_switch(), "Print the SELECT query for the conditional execution") ("print-delete", po_switch(), "Print the DELETE query") ("verbose,v", var(1), "Verbosity (0: quiet, 1: default, 2: more, 3, ...)") ; po::positional_options_description p; p.add("file", 1); // The 1st positional options (n=1) conf.AddOptions(control); conf.AddOptions(debug); conf.SetArgumentPositions(p); } void PrintUsage() { cout << "fits2sql - Fills the data from a fits file into a database\n" "\n" "For convenience, this documentation uses the extended version of the options, " "refer to the output below to get the abbreviations.\n" "\n" "This is a general purpose tool to fill the contents of a fite file into a database.\n" "\n" "Each fits file contians several table, so called extenbsions. Each tables has " "a number of columns compilsed from basic data types. The default extension to " "read from is the first one on the file but the name can be overwritten using " "--extension. The default table name to fill the data into is identical to " "the extension name. It can be overwritten using --table.\n" "\n" "The name of each column to which data is filled is obtained from " "the fits column names. The column names can be checked using --print-columns. " "Sometimes these names might not be convenient. To allow to simplify or replace " "column names, regular expressions (using boost's regex) can be defined to change " "the names. Note that these regular expressions are applied one by one on each " "columns's name. A valid expression could " "be:\n" " --map=MHillas\\.f/\n" "which would remove all occurances of 'MHillas.f'. This option can be used more than " "once. They are applied in sequence. A single match does not stop the sequence.\n" "\n" "Sometimes it might also be convenient to skip a column. This can be done with " "the --ignore resource. If the given regular expresion yields a match, the " "column will be ignored. Note that the regular expression works on the raw-name " "of the column not the readily mapped SQL column names. Example:\n" " --ignore=ThetaSq\\..*\n" "will skip all leaved which start with 'ThetaSq.'. This option can be used" "more than once.\n" "\n" "The data type of each column is kept as close as possible to the columns' data " "types. If for some reason this is not wanted, the data type of the SQL column " "can be overwritten with --sql-type sql-column/sql-ytpe, for example:\n" " --sql-type=FileId/UNSIGNED INT\n" "while the first argument of the name of the SQL column to which the data type " "should be applied. The second column is the basic SQL data type. The option can " "be given more than once.\n" "\n" "Database interaction:\n" "\n" "To drop an existing table, --drop can be used.\n" "\n" "To create a table according to theSQL column names and data types, --create " "can be used. The query used can be printed with --print-create even --create " "has not been specified.\n" "\n" "To choose the columns which should become primary keys, use --primary, " "for example:\n" " --primary=col1\n" "To define more than one column as primary key, the option can be given more than " "once. Note that the combination of these columns must be unique.\n" "\n" "All columns are created as NOT NULL as default. To force a database engine " "and/or a storage format, use --engine and --rot-format.\n" "\n" "Usually, the INSERT query would fail if the PRIMARY key exists already. " "This can be avoided using the 'ON DUPLICATE KEY UPDATE' directive. With the " "--duplicate, you can specify what should be updated in case of a duplicate key. " "To keep the row untouched, you can just update the primary key " "with the identical primary key, e.g. --duplicate='MyPrimary=VALUES(MyPrimary)'. " "The --duplicate resource can be specified more than once to add more expressions " "to the assignment_list. For more details, see the MySQL manual.\n" "\n" "Another possibility is to add the IGNORE keyword to the INSERT query by " "--ignore-errors, which essentially ignores all errors and turns them into " "warnings which are printed after the query succeeded.\n" "\n" "For debugging purpose, or to just create or drop a table, the final insert " "query can be skipped using --no-insert. Note that for performance reason, " "all data is collected in memory and a single INSERT query is issued at the " "end.\n" "\n" "Using a higher verbosity level (-v), an overview of the written columns or all " "processed leaves is printed depending on the verbosity level. The output looks " "like the following\n" " Leaf name [root data type] (SQL name)\n" "for example\n" " MTime.fTime.fMilliSec [Long64_t] (MilliSec)\n" "which means that the leaf MTime.fTime.fMilliSec is detected to be a Long64_t " "which is filled into a column called MilliSec. Leaves with non basic data types " "are ignored automatically and are marked as (-n/a-). User ignored columnd " "are marked as (-ignored-).\n" "\n" "A constant value for the given file can be inserted by using the --const directive. " "For example --const.mycolumn=42 would insert 42 into a column called mycolumn. " "The column is created as INT UNSIGNED as default which can be altered by " "--sql-type. A special case is a value of the form `/regex/format/`. Here, the given " "regular expression is applied to the filename and it is newly formated with " "the new format string. For details on how backreferences work, see for example " "the man-page of the sed utility.\n" "\n" "Usually the previously defined constant values are helpful to create an index " "which relates unambiguously the inserted data to the file. It might be useful " "to delete all data which belongs to this particular file before new data is " "entered. This can be achieved with the `--delete` directive. It deletes all " "data from the table before inserting new data which fulfills the condition " "defined by the `--const` directives.\n" "\n" "The constant values can also be used for a conditional execution (--conditional). " "If any row with the given constant values are found, the execution is stopped " "(note that this happend after the table drop/create but before the delete/insert.\n" "\n" "To ensure efficient access for a conditonal execution, it makes sense to have " "an index created for those columns. This can be done during table creation " "with the --index option.\n" "\n" "To create the index as a UNIQUE INDEX, you can use the --unique option which " "implies --index.\n" "\n" "If a query failed, the query is printed to stderr together with the error message. " "For the main INSERT query, this is only true if the verbosity level is at least 2 " "or the query has less than 80*25 bytes.\n" "\n" "In case of success, 0 is returned, a value>0 otherwise.\n" "\n" "Usage: fits2sql [options] --uri URI fitsfile.fits[.gz]\n" "\n" ; cout << endl; } enum BasicType_t { kNone = 0, kConst, kVarchar, kBool, kFloat, kDouble, kInt8, kUInt8, kInt16, kUInt16, kInt32, kUInt32, kInt64, kUInt64, // kMJD, }; static const map> ConvFits = { { 'A', { kVarchar, "VARCHAR" } }, { 'a', { kVarchar, "VARCHAR" } }, { 'L', { kBool, "BOOLEAN" } }, { 'l', { kBool, "BOOLEAN" } }, { 'B', { kInt8, "TINYINT" } }, { 'b', { kUInt8, "TINYINT UNSIGNED" } }, { 'I', { kInt16, "SMALLINT" } }, { 'i', { kUInt16, "SMALLINT UNSIGNED" } }, { 'J', { kInt32, "INT" } }, { 'j', { kUInt32, "INT UNSIGNED" } }, { 'K', { kInt64, "BIGINT" } }, { 'k', { kUInt64, "BIGINT UNSIGNED" } }, { 'E', { kFloat, "FLOAT" } }, { 'e', { kFloat, "FLOAT" } }, { 'D', { kDouble, "DOUBLE" } }, { 'd', { kDouble, "DOUBLE" } }, }; struct Container { string branch; // fits column name string column; // sql column name BasicType_t type; size_t num; // double offset; void *ptr; Container(const string &b, const string &c, const BasicType_t &t, const size_t &n/*, const double &offset=0*/) : branch(b), column(c), type(t), num(n), ptr(0) { } Container(const string &c, const string &value) : branch(value), column(c), type(kConst), num(1), ptr(0) { } ~Container() { } string fmt(const size_t &index) const { ostringstream str; switch (type) { //case kVarchar: str << string(reinterpret_cast(ptr), num); break; case kVarchar: str << string(reinterpret_cast(ptr), num).c_str(); break; case kFloat: str << setprecision(8) << reinterpret_cast(ptr)[index]; break; // case kMJD: str << setprecision(16) << reinterpret_cast(ptr)[0]+offset; break; case kDouble: str << setprecision(16) << reinterpret_cast(ptr)[index]; break; case kBool: case kInt8: str << int32_t(reinterpret_cast(ptr)[index]); break; case kUInt8: str << uint32_t(reinterpret_cast(ptr)[index]); break; case kInt16: str << reinterpret_cast(ptr)[index]; break; case kUInt16: str << reinterpret_cast(ptr)[index]; break; case kInt32: str << reinterpret_cast(ptr)[index]; break; case kUInt32: str << reinterpret_cast(ptr)[index]; break; case kInt64: str << reinterpret_cast(ptr)[index]; break; case kUInt64: str << reinterpret_cast(ptr)[index]; break; case kConst: str << branch; break; case kNone: break; } return str.str(); } }; int main(int argc, const char* argv[]) { Time start; Configuration conf(argv[0]); conf.SetPrintUsage(PrintUsage); SetupConfiguration(conf); if (!conf.DoParse(argc, argv)) return 127; // ----------------------------- Evaluate options -------------------------- const string uri = conf.Get("uri"); const string file = conf.Get("file"); const string extension = conf.Get("extension"); string table = conf.Get("table"); const uint16_t verbose = conf.Get("verbose"); const size_t first = conf.Get("first"); const size_t max = conf.Get("max"); const bool drop = conf.Get("drop"); const bool create = conf.Get("create") || drop; const bool noinsert = conf.Get("no-insert"); const bool dry_run = conf.Get("dry-run"); const bool conditional = conf.Get("conditional"); const bool run_delete = conf.Get("delete"); const bool index = conf.Get("index"); const bool unique = conf.Get("unique"); const string engine = conf.Get("engine"); const string row_format = conf.Get("row-format"); const bool ignore_errors = conf.Get("ignore-errors"); const bool print_connection = conf.Get("print-connection"); const bool print_extensions = conf.Get("print-extensions"); const bool print_columns = conf.Get("print-columns"); const bool print_create = conf.Get("print-create"); const bool print_insert = conf.Get("print-insert"); const bool print_select = conf.Get("print-select"); const bool print_delete = conf.Get("print-delete"); const vector mymap = conf.Vec("map"); const vector sqltypes = conf.Vec("sql-type"); const vector _ignore = conf.Vec("ignore"); const vector primary = conf.Vec("primary"); const vector duplicate = conf.Vec("duplicate"); const vector notsigned = conf.Vec("unsigned"); if (first>=max) cerr << "WARNING: Resource `first` (" << first << ") exceeds `max` (" << max << ")" << endl; // ------------------------------------------------------------------------- if (verbose>0) { cout << "\n-------------------------- Evaluating file -------------------------" << endl; cout << "Start Time: " << Time::sql << Time(Time::local) << endl; } zfits f(file.c_str(), extension.c_str()); if (!f) { cerr << "Could not open file " << file << ": " << strerror(errno) << endl; return 1; } if (verbose>0) cout << "File: " << file << endl; if (!extension.empty() && extension!=f.Get("EXTNAME")) { cerr << "Extension " << extension << " not found in file." << endl; return 2; } if (print_extensions) { cout << "\nTables:\n - " << boost::join(f.GetTables(), "\n - ") << '\n' << endl; return 3; } if (verbose>0) cout << "FITS extension [table]: " << f.Get("EXTNAME") << endl; if (table.empty()) table = f.Get("EXTNAME"); if (verbose>0) cout << "SQL table: " << table << endl; // const double mjdref = f.Get("MJDREF", double(0)); if (print_columns) { cout << '\n'; f.PrintColumns(); cout << '\n'; } const auto cols = f.GetColumns(); if (verbose>0) { cout << f.GetNumRows() << " events found." << endl; cout << cols.size() << " columns found." << endl; } string query = "CREATE TABLE IF NOT EXISTS `"+table+"`\n" "(\n"; vector vec; const auto fixed = conf.GetWildcardOptions("const.*"); string where; vector vindex; for (auto it=fixed.cbegin(); it!=fixed.cend(); it++) { const string name = it->substr(6); string val = conf.Get(*it); boost::smatch match; if (boost::regex_match(val, match, boost::regex("\\/(.+)(?0) { cout << "Regular expression detected for constant column `" << *it << "`\n"; cout << "Filename converted with /" << reg << "/ to /" << fmt << "/\n"; cout << "Filename: " << file << '\n'; cout << "Result: " << val << endl; } } if (verbose==2) cout << "\n" << val << " [-const-]"; if (verbose>1) cout << " (" << name << ")"; string sqltype = "INT UNSIGNED"; for (auto m=sqltypes.cbegin(); m!=sqltypes.cend(); m++) if (m->first==name) sqltype = m->second; if (!vec.empty()) query += ",\n"; query += " `"+name+"` "+sqltype+" NOT NULL COMMENT '--user--'"; vec.emplace_back(name, val); where += " AND `"+name+"`="+val; vindex.emplace_back(name); } const size_t nvec = vec.size(); for (auto ic=cols.cbegin(); ic!=cols.cend(); ic++) { const auto &col = ic->second; if (verbose>2) cout << '\n' << col.type << " " << ic->first << "[" << col.num << "]"; string name = ic->first; bool found = false; for (auto b=_ignore.cbegin(); b!=_ignore.cend(); b++) { if (boost::regex_match(name, boost::regex(*b))) { found = true; if (verbose>2) cout << " (-ignored-)"; break; } } if (found) continue; const char tn = find(notsigned.cbegin(), notsigned.cend(), ic->first)!=notsigned.cend() ? tolower(col.type) : toupper(col.type); auto it = ConvFits.find(tn); if (it==ConvFits.end()) { if (verbose>2) cout << " (-n/a-)"; continue; } if (verbose==2) cout << '\n' << name << " [" << tn << "]"; for (auto m=mymap.cbegin(); m!=mymap.cend(); m++) name = boost::regex_replace(name, boost::regex(m->first), m->second); if (verbose>1) cout << " (" << name << ")"; string sqltype = it->second.second; for (auto m=sqltypes.cbegin(); m!=sqltypes.cend(); m++) if (m->first==name) sqltype = m->second; if (!vec.empty()) query += ",\n"; const size_t N = col.type=='A' ? 1 : col.num; for (size_t i=0; i1) query += "["+to_string(i)+"]"; query += "` "+sqltype; if (col.type=='A') query += '('+to_string(col.num)+')'; query += " NOT NULL COMMENT '"+ic->first; if (!col.unit.empty()) query += "["+col.unit+"]"; if (!col.comment.empty()) query += ": "+col.comment; query += +"'"; if (N>1 && i!=N-1) query += ",\n"; } const BasicType_t bt = /*ic.first=="Time" && col.num==1 && col.unit=="MJD" && it->second.first==kDouble ? kMJD :*/ it->second.first; vec.emplace_back(ic->first, name, bt, col.num/*, mjdref*/); vec.back().ptr = f.SetPtrAddress(ic->first); } if (verbose>1) cout << "\n\n"; if (verbose>0) { if (nvec>0) cout << nvec << " constant value column(s) configured." << endl; cout << vec.size()-nvec << " FITS columns setup for reading." << endl; } // ------------------------------------------------------------------------- // Checking for database connection if (verbose>0) cout << "\n---------------------- Connecting database -------------------------" << endl; if (verbose>0) { cout << "Connecting to database...\n"; cout << "Client Version: " << mysqlpp::Connection().client_version() << endl; } Database connection(uri); // Keep alive while fetching rows if (verbose>0) cout << "Server Version: " << connection.server_version() << endl; if (print_connection) { try { const auto &res1 = connection.query("SHOW STATUS LIKE 'Compression'").store(); cout << "Compression of databse connection is " << string(res1[0][1]) << endl; const auto &res2 = connection.query("SHOW STATUS LIKE 'Ssl_cipher'").store(); cout << "Connection to databases is " << (string(res2[0][1]).empty()?"UNENCRYPTED":"ENCRYPTED ("+string(res2[0][1])+")") << endl; } catch (const exception &e) { cerr << "\nSHOW STATUS LIKE COMPRESSION\n\n"; cerr << "SQL query failed:\n" << e.what() << endl; return 4; } } // ------------------------------------------------------------------------- if (verbose>0) cout << "\n--------------------------- Database Table -------------------------" << endl; if (!primary.empty()) query += ",\n PRIMARY KEY USING BTREE (`"+boost::algorithm::join(primary, "`, `")+"`)"; if (!vindex.empty() && (index || unique)) query += ",\n "+string(unique?"UNIQUE ":"")+"INDEX USING BTREE (`"+boost::algorithm::join(vindex, "`, `")+"`)"; query += "\n)\n" "DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci\n"; if (!engine.empty()) query += "ENGINE="+engine+"\n"; if (!row_format.empty()) query += "ROW_FORMAT="+row_format+"\n"; query += "COMMENT='created by "+fs::path(conf.GetName()).filename().string()+"'\n"; // FIXME: Can we omit the catching to be able to print the // query 'autmatically'? try { if (drop) { // => Simple result if (!dry_run) connection.query("DROP TABLE `"+table+"`").execute(); if (verbose>0) cout << "Table `" << table << "` dropped." << endl; } } catch (const exception &e) { cerr << "DROP TABLE `" << table << "`\n\n"; cerr << "SQL query failed:\n" << e.what() << '\n' << endl; return 5; } try { if (create && !dry_run) connection.query(query).execute(); } catch (const exception &e) { cerr << query << "\n\n"; cerr << "SQL query failed:\n" << e.what() << '\n' << endl; return 6; } if (print_create) cout << query << endl; if (create && verbose>0) cout << "Table `" << table << "` created." << endl; try { if (conditional && !fixed.empty() && !drop) { const mysqlpp::StoreQueryResult res = connection.query("SELECT 1 FROM `"+table+"` WHERE 1"+where+" LIMIT 1").store(); if (print_select) cout << "SELECT 1 FROM `"+table+"` WHERE 1" << where << " LIMIT 1" << endl; if (res.num_rows()>0) { if (verbose>0) { cout << "Conditional execution... detected existing rows!\n"; cout << "Exit.\n" << endl; } return 0; } } } catch (const exception &e) { cerr << "SELECT 1 FROM `"+table+"` WHERE 1" << where << " LIMIT 1\n\n"; cerr << "SQL query failed: " << e.what() << endl; return 7; } try { if (run_delete && !fixed.empty() && !drop && !dry_run) { const mysqlpp::SimpleResult res = connection.query("DELETE FROM `"+table+"` WHERE 1"+where).execute(); if (verbose>0) cout << res.rows() << " row(s) deleted.\n" << endl; } } catch (const exception &e) { cerr << "DELETE FROM `" << table << "` WHERE 1" << where << "\n\n"; cerr << "SQL query failed: " << e.what() << endl; return 8; } if (print_delete) cout << "DELETE FROM `" << table << "` WHERE 1" << where << endl; // ------------------------------------------------------------------------- if (verbose>0) cout << "\n---------------------------- Reading file --------------------------" << endl; //query = update ? "UPDATE" : "INSERT"; query = "INSERT "; if (ignore_errors) query += "IGNORE "; query += "`"+table+"`\n" "(\n"; for (auto c=vec.cbegin(); c!=vec.cend(); c++) { if (c!=vec.cbegin()) query += ",\n"; const size_t N = c->type==kVarchar ? 1 : c->num; for (size_t i=0; icolumn+"`"; else query += " `"+c->column+"["+to_string(i)+"]`"; if (N>1 && i!=N-1) query += ",\n"; } } query += "\n)\n" "VALUES\n"; size_t count = 0; const size_t num = max>first && (max-first)0) query += ",\n"; query += "(\n"; for (auto c=vec.cbegin(); c!=vec.cend(); c++) { if (c!=vec.cbegin()) query += ",\n"; const size_t N = c->type==kVarchar ? 1 : c->num; for (size_t i=0; itype==kVarchar) query += " '"+c->fmt(i)+"'"; else query += " "+c->fmt(i); if (print_insert && i==0) query += " /* "+c->column+" -> "+c->branch+" */"; if (N>1 && i!=N-1) query += ",\n"; } } query += "\n)"; count ++; } if (!duplicate.empty()) query += "\nON DUPLICATE KEY UPDATE\n " + boost::join(duplicate, ",\n "); if (verbose>0) cout << count << " out of " << num << " row(s) read from file [N=" << first << ".." << num-1 << "]." << endl; if (count==0) { if (verbose>0) { cout << "Total execution time: " << Time().UnixTime()-start.UnixTime() << "s\n"; cout << "Success.\n" << endl; } return 0; } // ------------------------------------------------------------------------- if (verbose>0) { cout << "\n--------------------------- Inserting data -------------------------" << endl; cout << "Sending INSERT query (" << query.length() << " bytes)" << endl; } try { if (!noinsert && !dry_run) { auto q = connection.query(query); q.execute(); cout << q.info() << '\n' << endl; } else cout << "Insert query skipped!" << endl; if (print_insert) cout << query << endl; } catch (const exception &e) { if (verbose>1 || query.length()<80*25) cerr << query << "\n\n"; cerr << "SQL query failed (" << query.length() << " bytes):\n" << e.what() << '\n' << endl; return 9; } if (verbose>0) { const auto sec = Time().UnixTime()-start.UnixTime(); cout << "Total execution time: " << sec << "s "; cout << "(" << Tools::Fractional(sec/count) << "s/row)\n"; try { const auto resw = connection.query("SHOW WARNINGS").store(); for (size_t i=0; i