| 1 | #include "Database.h"
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| 2 |
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| 3 | #include <regex>
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| 4 |
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| 5 | #include <boost/algorithm/string/join.hpp>
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| 6 |
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| 7 | #include "tools.h"
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| 8 | #include "Time.h"
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| 9 | #include "Configuration.h"
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| 10 |
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| 11 | #include <TROOT.h>
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| 12 | #include <TSystem.h>
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| 13 | #include <TFile.h>
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| 14 | #include <TTree.h>
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| 15 |
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| 16 | using namespace std;
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| 17 |
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| 18 | // ------------------------------------------------------------------------
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| 19 |
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| 20 | void SetupConfiguration(Configuration &conf)
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| 21 | {
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| 22 | po::options_description control("Rootify SQL");
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| 23 | control.add_options()
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| 24 | ("uri,u", var<string>()->required(), "Database link as in\n\tuser:password@server[:port]/database.")
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| 25 | ("query,q", var<string>(""), "MySQL query (overwrites --file)")
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| 26 | ("file", var<string>("rootify.sql"), "An ASCII file with the MySQL query (overwrites --query)")
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| 27 | ("ignore-null,i", po_switch(), "Do not skip rows containing any NULL field")
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| 28 | ("out,o", var<string>("rootify.root"), "Output root file name")
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| 29 | ("force,f", po_switch(), "Force overwriting an existing root file ('RECREATE')")
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| 30 | ("update", po_switch(), "Update an existing root file with the new tree ('UPDATE')")
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| 31 | ("compression,c", var<uint16_t>(1), "zlib compression level for the root file")
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| 32 | ("tree,t", var<string>("Result"), "Name of the root tree")
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| 33 | ("ignore", vars<string>(), "Ignore the given columns")
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| 34 | ("display,d", po_switch(), "Displays contents on the screen (most usefull in combination with mysql statements as SHOW or EXPLAIN)")
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| 35 | ("null,n", po_switch(), "Redirect the output file to /dev/null (mainly for debugging purposes, e.g. performance studies)")
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| 36 | ("no-fill", po_switch(), "Do not fill events into the root file (mainly for debugging purposes, e.g. performance studies)")
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| 37 | ("delimiter", var<string>(""), "The delimiter used if contents are displayed with --display (default=\\t)")
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| 38 | ("var.*", var<string>(), "Predefined SQL user variables (@VAR)")
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| 39 | ("env.*", vars<string>(), "Predefined environment for substitutions in the query ($ENV)")
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| 40 | ("verbose,v", var<uint16_t>(1), "Verbosity (0: quiet, 1: default, 2: more, 3, ...)")
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| 41 | ;
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| 42 |
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| 43 | po::positional_options_description p;
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| 44 | p.add("file", 1); // The 1st positional options (n=1)
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| 45 | p.add("out", 1); // The 2nd positional options (n=1)
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| 46 |
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| 47 | conf.AddOptions(control);
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| 48 | conf.SetArgumentPositions(p);
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| 49 | }
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| 50 |
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| 51 | void PrintUsage()
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| 52 | {
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| 53 | cout <<
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| 54 | "rootifysql - Converts the result of a mysql query into a root file\n"
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| 55 | "\n"
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| 56 | "For convenience, this documentation uses the extended version of the options, "
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| 57 | "refer to the output below to get the abbreviations.\n"
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| 58 | "\n"
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| 59 | "Writes the result of a mysql query into a root file. For each column, a branch is "
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| 60 | "created of type double with the field name as name. This is usually the column name "
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| 61 | "if not specified otherwise by the AS mysql directive.\n"
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| 62 | "\n"
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| 63 | "Columns with CHAR or VARCHAR as field type are ignored. DATETIME, DATE and TIME "
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| 64 | "columns are converted to unix time (time_t). Rows containing any file which is "
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| 65 | "NULL are skipped if not suppressed by the --ignore-null option. Ideally, the query "
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| 66 | "is compiled in a way that no NULL field is returned. With the --display option the "
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| 67 | "result of the request is printed on the screen (NULL skipping still in action). "
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| 68 | "This can be useful to create an ascii file or to show results as 'SHOW DATABASES' "
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| 69 | "or 'EXPLAIN table'. To redirect the contents into an ascii file, the option -v0 "
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| 70 | "is useful. To suppredd writing to an output file --null can be used.\n"
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| 71 | "\n"
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| 72 | "The default is to read the query from a file called rootify.sql. Except if a different "
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| 73 | "filename is specified by the --file option or a query is given with --query.\n"
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| 74 | "\n"
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| 75 | "As a trick, the rootify.sql file can be made excutable (chmod u+x rootify.sql). "
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| 76 | "If the first line contains '#!rootifysql', the script can be executed directly.\n"
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| 77 | "\n"
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| 78 | "Columns whose name start with @ are skipped. If you want them in your output file "
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| 79 | "give them a name using AS, e.g. 'SELECT @A:=5 AS A'.\n"
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| 80 | "\n"
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| 81 | "You can use variables in your sql query like @MyVar and define them on the "
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| 82 | "command line. In this example with --var.MyVar=5\n"
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| 83 | "\n"
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| 84 | "You can use environment definitions for substitutions in your SQL query. "
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| 85 | "For example --env.TEST=5 would replace $TEST or ${TEST} in your query by 5."
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| 86 | "If you specifiy one environmentvariable more than once, a list is created. "
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| 87 | "For example --env.TEST=1 --env.TEST=2 --env.TEST=3 would substitute "
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| 88 | "$TEST or ${TEST} by '1, 2, 3'. This is useful for the SQL `IN` keyword.\n"
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| 89 | "\n"
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| 90 | "Comments in the query-file can be placed according to the SQL standard inline "
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| 91 | "/*comment*/ or introduced with # (shell script style) or -- (SQL style).\n"
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| 92 | "\n"
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| 93 | "In case of succes, 0 is returned, a value>0 otherwise.\n"
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| 94 | "\n"
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| 95 | "Usage: rootifysql [rootify.sql [rootify.root]] [-u URI] [-q query|-f file] [-i] [-o out] [-f] [-cN] [-t tree] [-vN]\n"
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| 96 | "\n"
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| 97 | ;
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| 98 | cout << endl;
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| 99 | }
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| 100 |
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| 101 | int main(int argc, const char* argv[])
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| 102 | {
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| 103 | Time start;
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| 104 |
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| 105 | gROOT->SetBatch();
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| 106 |
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| 107 | Configuration conf(argv[0]);
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| 108 | conf.SetPrintUsage(PrintUsage);
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| 109 | SetupConfiguration(conf);
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| 110 |
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| 111 | if (!conf.DoParse(argc, argv))
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| 112 | return 127;
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| 113 |
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| 114 | // ----------------------------- Evaluate options --------------------------
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| 115 | const string uri = conf.Get<string>("uri");
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| 116 | const string out = conf.Get<string>("out");
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| 117 | const string file = conf.Get<string>("file");
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| 118 | const string tree = conf.Get<string>("tree");
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| 119 | const bool force = conf.Get<bool>("force");
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| 120 | const bool ignorenull = conf.Get<bool>("ignore-null");
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| 121 | const bool update = conf.Get<bool>("update");
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| 122 | const bool display = conf.Get<bool>("display");
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| 123 | const bool noout = conf.Get<bool>("null");
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| 124 | const bool nofill = conf.Get<bool>("no-fill");
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| 125 | const uint16_t verbose = conf.Get<uint16_t>("verbose");
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| 126 | const uint16_t compression = conf.Get<uint16_t>("compression");
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| 127 | const string delimiter = conf.Get<string>("delimiter");
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| 128 | const vector<string> _ignore = conf.Vec<string>("ignore");
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| 129 | //const vector<Map> mymap = conf.Vec<Map>("map");
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| 130 |
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| 131 | // -------------------------------------------------------------------------
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| 132 |
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| 133 | const auto vars = conf.GetWildcardOptions("var.*");
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| 134 |
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| 135 | vector<string> variables;
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| 136 | for (const auto &var : vars)
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| 137 | variables.emplace_back('@'+var.substr(4)+":="+Tools::Trim(conf.Get<string>(var)));
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| 138 |
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| 139 | // -------------------------------------------------------------------------
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| 140 |
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| 141 | if (verbose>0)
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| 142 | cout << "\n--------------------- Rootify SQL ----------------------" << endl;
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| 143 |
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| 144 | string query = conf.Get<string>("query");
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| 145 | if (query.empty())
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| 146 | {
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| 147 | if (verbose>0)
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| 148 | cout << "Reading query from file '" << file << "'." << endl;
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| 149 |
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| 150 | ifstream fin(file);
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| 151 | if (!fin)
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| 152 | {
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| 153 | cerr << "Could not open '" << file << "': " << strerror(errno) << endl;
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| 154 | return 1;
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| 155 | }
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| 156 | getline(fin, query, (char)fin.eof());
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| 157 | }
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| 158 |
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| 159 | if (query.empty())
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| 160 | {
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| 161 | cerr << "No query specified." << endl;
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| 162 | return 2;
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| 163 | }
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| 164 |
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| 165 | // -------------------------------------------------------------------------
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| 166 |
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| 167 | const auto envs = conf.GetWildcardOptions("env.*");
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| 168 |
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| 169 | for (const auto &env : envs)
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| 170 | {
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| 171 | regex r1("\\$\\{"+env.substr(4)+"\\}");
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| 172 | regex r2("\\$"+env.substr(4)+"\\b");
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| 173 |
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| 174 | const string repl = boost::join(conf.Vec<string>(env), ", ");
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| 175 |
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| 176 | query = regex_replace(query, r1, repl);
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| 177 | query = regex_replace(query, r2, repl);
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| 178 | }
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| 179 |
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| 180 | // -------------------------- Check for file permssion ---------------------
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| 181 | // Strictly speaking, checking for write permission and existance is not necessary,
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| 182 | // but it is convenient that the user does not find out that it failed after
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| 183 | // waiting long for the query result
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| 184 | //
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| 185 | // I am using root here instead of boost to be
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| 186 | // consistent with the access pattern by TFile
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| 187 | TString path(noout?"/dev/null":out.c_str());
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| 188 | gSystem->ExpandPathName(path);
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| 189 |
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| 190 | if (!noout)
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| 191 | {
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| 192 | FileStat_t stat;
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| 193 | const Int_t exist = !gSystem->GetPathInfo(path, stat);
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| 194 | const Bool_t write = !gSystem->AccessPathName(path, kWritePermission) && R_ISREG(stat.fMode);
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| 195 |
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| 196 | if ((update && !exist) || (update && exist && !write) || (force && exist && !write))
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| 197 | {
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| 198 | cerr << "File '" << path << "' is not writable." << endl;
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| 199 | return 3;
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| 200 | }
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| 201 |
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| 202 | if (!update && !force && exist)
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| 203 | {
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| 204 | cerr << "File '" << path << "' already exists." << endl;
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| 205 | return 4;
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| 206 | }
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| 207 | }
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| 208 |
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| 209 | Time start2;
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| 210 |
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| 211 | // --------------------------- Connect to database -------------------------------------------------
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| 212 |
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| 213 | if (query.back()!='\n')
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| 214 | query += '\n';
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| 215 |
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| 216 | if (verbose>0)
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| 217 | cout << "Connecting to database..." << endl;
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| 218 |
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| 219 |
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| 220 | Database connection(uri); // Keep alive while fetching rows
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| 221 |
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| 222 | // -------------------------- Set user defined variables -------------------
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| 223 | if (variables.size()>0)
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| 224 | {
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| 225 | if (verbose>0)
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| 226 | cout << "Setting user defined variables..." << endl;
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| 227 |
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| 228 | const string varset =
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| 229 | "SET\n "+boost::algorithm::join(variables, ",\n ");
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| 230 |
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| 231 | try
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| 232 | {
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| 233 | connection.query(varset).execute();
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| 234 | }
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| 235 | catch (const exception &e)
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| 236 | {
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| 237 | cerr << varset << "\n\n";
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| 238 | cerr << "SQL query failed:\n" << e.what() << endl;
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| 239 | return 5;
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| 240 | }
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| 241 |
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| 242 | if (verbose>2)
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| 243 | cout << '\n' << varset << '\n' << endl;
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| 244 | }
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| 245 |
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| 246 | // -------------------------- Request data from database -------------------
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| 247 | if (verbose>0)
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| 248 | cout << "Requesting data..." << endl;
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| 249 |
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| 250 | if (verbose>2)
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| 251 | cout << '\n' << query << endl;
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| 252 |
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| 253 | const mysqlpp::UseQueryResult res =
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| 254 | connection.query(query).use();
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| 255 |
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| 256 | // -------------------------------------------------------------------------
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| 257 |
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| 258 | if (verbose>0)
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| 259 | cout << "Opening file '" << path << "' [compression=" << compression << "]..." << endl;
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| 260 |
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| 261 | // ----------------------------- Open output file --------------------------
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| 262 | TFile tfile(path, update?"UPDATE":(force?"RECREATE":"CREATE"), "Rootify SQL", compression);
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| 263 | if (tfile.IsZombie())
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| 264 | return 6;
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| 265 |
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| 266 | // -------------------------------------------------------------------------
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| 267 |
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| 268 | // get the first row to get the field description
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| 269 | mysqlpp::Row row = res.fetch_row();
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| 270 | if (!row)
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| 271 | {
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| 272 | cerr << "Empty set returned... nothing to write." << endl;
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| 273 | return 7;
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| 274 | }
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| 275 |
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| 276 | if (verbose>0)
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| 277 | cout << "Trying to setup " << row.size() << " branches..." << endl;
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| 278 |
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| 279 | if (verbose>1)
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| 280 | cout << endl;
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| 281 |
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| 282 | const mysqlpp::FieldNames &l = *row.field_list().list;
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| 283 |
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| 284 | vector<double> buf(l.size());
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| 285 | vector<uint8_t> typ(l.size(),'n'); // n=number [double], d is used for DateTime
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| 286 |
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| 287 | UInt_t cols = 0;
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| 288 |
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| 289 |
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| 290 | // -------------------- Configure branches of TTree ------------------------
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| 291 | TTree *ttree = new TTree(tree.c_str(), query.c_str());
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| 292 |
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| 293 | size_t skipat = 0;
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| 294 | size_t skipreg = 0;
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| 295 | for (size_t i=0; i<l.size(); i++)
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| 296 | {
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| 297 | const string t = row[i].type().sql_name();
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| 298 |
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| 299 | if (t.find("DATETIME")!=string::npos)
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| 300 | typ[i] = 'd';
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| 301 | else
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| 302 | if (t.find("DATE")!=string::npos)
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| 303 | typ[i] = 'D';
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| 304 | else
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| 305 | if (t.find("TIME")!=string::npos)
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| 306 | typ[i] = 'T';
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| 307 | else
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| 308 | if (t.find("VARCHAR")!=string::npos)
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| 309 | typ[i] = 'V';
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| 310 | else
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| 311 | if (t.find("CHAR")!=string::npos)
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| 312 | typ[i] = 'C';
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| 313 |
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| 314 | bool found = false;
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| 315 | for (const auto &pattern: _ignore)
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| 316 | {
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| 317 | if (regex_match(l[i], regex(pattern)))
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| 318 | {
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| 319 | found = true;
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| 320 | typ[i] = '-';
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| 321 | skipreg++;
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| 322 | break;
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| 323 | }
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| 324 | }
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| 325 |
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| 326 | if (l[i][0]=='@')
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| 327 | {
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| 328 | typ[i] = '@';
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| 329 | skipat++;
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| 330 | }
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| 331 |
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| 332 | const bool use = l[i][0]!='@' && typ[i]!='V' && typ[i]!='C' && !found;
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| 333 |
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| 334 | if (verbose>1)
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| 335 | cout << (use?" + ":" - ") << l[i].c_str() << " [" << t << "] {" << typ[i] << "}\n";
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| 336 |
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| 337 | if (use)
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| 338 | {
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| 339 | // string name = l[i];
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| 340 | // for (const auto &m: mymap)
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| 341 | // name = boost::regex_replace(l[i], boost::regex(m.first), m.second);
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| 342 |
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| 343 | ttree->Branch(l[i].c_str(), buf.data()+i);
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| 344 | cols++;
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| 345 | }
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| 346 | }
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| 347 | // -------------------------------------------------------------------------
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| 348 |
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| 349 | if (verbose>1)
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| 350 | cout << endl;
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| 351 | if (verbose>0)
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| 352 | {
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| 353 | if (skipreg)
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| 354 | cout << skipreg << " branches skipped due to ignore list." << endl;
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| 355 | if (skipat)
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| 356 | cout << skipat << " branches skipped due to name starting with @." << endl;
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| 357 | cout << "Configured " << cols << " branches.\nFilling branches..." << endl;
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| 358 | }
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| 359 |
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| 360 | if (display)
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| 361 | {
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| 362 | cout << endl;
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| 363 | cout << "#";
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| 364 | for (size_t i=0; i<l.size(); i++)
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| 365 | cout << ' ' << l[i].c_str();
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| 366 | cout << endl;
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| 367 | }
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| 368 |
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| 369 | // ---------------------- Fill TTree with DB data --------------------------
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| 370 | size_t count = 0;
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| 371 | size_t skip = 0;
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| 372 | do
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| 373 | {
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| 374 | count++;
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| 375 |
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| 376 | ostringstream sout;
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| 377 |
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| 378 | size_t idx=0;
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| 379 | for (auto col=row.begin(); col!=row.end(); col++, idx++)
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| 380 | {
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| 381 | if (display)
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| 382 | {
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| 383 | if (idx>0)
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| 384 | sout << (delimiter.empty()?"\t":delimiter);
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| 385 | sout << col->c_str();
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| 386 | }
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| 387 |
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| 388 | if (!ignorenull && col->is_null())
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| 389 | {
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| 390 | skip++;
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| 391 | break;
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| 392 | }
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| 393 |
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| 394 | switch (typ[idx])
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| 395 | {
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| 396 | case 'd':
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| 397 | buf[idx] = time_t((mysqlpp::DateTime)(*col));
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| 398 | break;
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| 399 |
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| 400 | case 'D':
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| 401 | buf[idx] = time_t((mysqlpp::Date)(*col));
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| 402 | break;
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| 403 |
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| 404 | case 'T':
|
|---|
| 405 | buf[idx] = time_t((mysqlpp::Time)(*col));
|
|---|
| 406 | break;
|
|---|
| 407 |
|
|---|
| 408 | case 'V':
|
|---|
| 409 | case 'C':
|
|---|
| 410 | case '-':
|
|---|
| 411 | case '@':
|
|---|
| 412 | break;
|
|---|
| 413 |
|
|---|
| 414 | default:
|
|---|
| 415 | buf[idx] = atof(col->c_str());
|
|---|
| 416 | }
|
|---|
| 417 | }
|
|---|
| 418 |
|
|---|
| 419 | if (idx==row.size())
|
|---|
| 420 | {
|
|---|
| 421 | if (!nofill)
|
|---|
| 422 | ttree->Fill();
|
|---|
| 423 |
|
|---|
| 424 | if (display)
|
|---|
| 425 | cout << sout.str() << endl;
|
|---|
| 426 | }
|
|---|
| 427 |
|
|---|
| 428 | row = res.fetch_row();
|
|---|
| 429 |
|
|---|
| 430 |
|
|---|
| 431 | } while (row);
|
|---|
| 432 |
|
|---|
| 433 | // -------------------------------------------------------------------------
|
|---|
| 434 |
|
|---|
| 435 | if (display)
|
|---|
| 436 | cout << '\n' << endl;
|
|---|
| 437 |
|
|---|
| 438 | if (verbose>0)
|
|---|
| 439 | {
|
|---|
| 440 | cout << count << " rows fetched." << endl;
|
|---|
| 441 | if (skip>0)
|
|---|
| 442 | cout << skip << " rows skipped due to NULL field." << endl;
|
|---|
| 443 |
|
|---|
| 444 | cout << ttree->GetEntries() << " rows filled into tree." << endl;
|
|---|
| 445 | }
|
|---|
| 446 |
|
|---|
| 447 | ttree->Write();
|
|---|
| 448 | tfile.Close();
|
|---|
| 449 |
|
|---|
| 450 | if (verbose>0)
|
|---|
| 451 | {
|
|---|
| 452 | cout << "File closed.\n";
|
|---|
| 453 | cout << "Execution time: " << Time().UnixTime()-start.UnixTime() << "s\n";
|
|---|
| 454 | cout << "--------------------------------------------------------" << endl;
|
|---|
| 455 | }
|
|---|
| 456 |
|
|---|
| 457 | return 0;
|
|---|
| 458 | }
|
|---|
