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