| 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 | ("explain", po_switch(), "Requests an EXPLAIN from the server (shows the serveroptimized query)")
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| 39 | ("var.*", var<string>(), "Predefined SQL user variables (@VAR)")
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| 40 | ("env.*", vars<string>(), "Predefined environment for substitutions in the query ($ENV)")
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| 41 | ("verbose,v", var<uint16_t>(1), "Verbosity (0: quiet, 1: default, 2: more, 3, ...)")
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| 42 | ;
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| 43 |
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| 44 | po::positional_options_description p;
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| 45 | p.add("file", 1); // The 1st positional options (n=1)
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| 46 | p.add("out", 1); // The 2nd positional options (n=1)
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| 47 |
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| 48 | conf.AddOptions(control);
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| 49 | conf.SetArgumentPositions(p);
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| 50 | }
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| 51 |
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| 52 | void PrintUsage()
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| 53 | {
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| 54 | cout <<
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| 55 | "rootifysql - Converts the result of a mysql query into a root file\n"
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| 56 | "\n"
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| 57 | "For convenience, this documentation uses the extended version of the options, "
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| 58 | "refer to the output below to get the abbreviations.\n"
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| 59 | "\n"
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| 60 | "Writes the result of a mysql query into a root file. For each column, a branch is "
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| 61 | "created of type double with the field name as name. This is usually the column name "
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| 62 | "if not specified otherwise by the AS mysql directive.\n"
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| 63 | "\n"
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| 64 | "Columns with CHAR or VARCHAR as field type are ignored. DATETIME, DATE and TIME "
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| 65 | "columns are converted to unix time (time_t). Rows containing any file which is "
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| 66 | "NULL are skipped if not suppressed by the --ignore-null option. Ideally, the query "
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| 67 | "is compiled in a way that no NULL field is returned. With the --display option the "
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| 68 | "result of the request is printed on the screen (NULL skipping still in action). "
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| 69 | "This can be useful to create an ascii file or to show results as 'SHOW DATABASES' "
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| 70 | "or 'EXPLAIN table'. To redirect the contents into an ascii file, the option -v0 "
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| 71 | "is useful. To suppredd writing to an output file --null can be used.\n"
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| 72 | "\n"
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| 73 | "The default is to read the query from a file called rootify.sql. Except if a different "
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| 74 | "filename is specified by the --file option or a query is given with --query.\n"
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| 75 | "\n"
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| 76 | "As a trick, the rootify.sql file can be made excutable (chmod u+x rootify.sql). "
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| 77 | "If the first line contains '#!rootifysql', the script can be executed directly.\n"
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| 78 | "\n"
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| 79 | "Columns whose name start with @ are skipped. If you want them in your output file "
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| 80 | "give them a name using AS, e.g. 'SELECT @A:=5 AS A'.\n"
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| 81 | "\n"
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| 82 | "You can use variables in your sql query like @MyVar and define them on the "
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| 83 | "command line. In this example with --var.MyVar=5\n"
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| 84 | "\n"
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| 85 | "You can use environment definitions for substitutions in your SQL query. "
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| 86 | "For example --env.TEST=5 would replace $TEST or ${TEST} in your query by 5."
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| 87 | "If you specifiy one environmentvariable more than once, a list is created. "
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| 88 | "For example --env.TEST=1 --env.TEST=2 --env.TEST=3 would substitute "
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| 89 | "$TEST or ${TEST} by '1, 2, 3'. This is useful for the SQL `IN` keyword.\n"
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| 90 | "\n"
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| 91 | "Comments in the query-file can be placed according to the SQL standard inline "
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| 92 | "/*comment*/ or introduced with # (shell script style) or -- (SQL style).\n"
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| 93 | "\n"
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| 94 | "In case of succes, 0 is returned, a value>0 otherwise.\n"
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| 95 | "\n"
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| 96 | "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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| 97 | "\n"
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| 98 | ;
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| 99 | cout << endl;
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| 100 | }
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| 101 |
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| 102 | int main(int argc, const char* argv[])
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| 103 | {
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| 104 | Time start;
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| 105 |
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| 106 | gROOT->SetBatch();
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| 107 |
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| 108 | Configuration conf(argv[0]);
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| 109 | conf.SetPrintUsage(PrintUsage);
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| 110 | SetupConfiguration(conf);
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| 111 |
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| 112 | if (!conf.DoParse(argc, argv))
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| 113 | return 127;
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| 114 |
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| 115 | // ----------------------------- Evaluate options --------------------------
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| 116 | const string uri = conf.Get<string>("uri");
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| 117 | const string out = conf.Get<string>("out");
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| 118 | const string file = conf.Get<string>("file");
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| 119 | const string tree = conf.Get<string>("tree");
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| 120 | const bool force = conf.Get<bool>("force");
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| 121 | const bool ignorenull = conf.Get<bool>("ignore-null");
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| 122 | const bool update = conf.Get<bool>("update");
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| 123 | const bool display = conf.Get<bool>("display");
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| 124 | const bool noout = conf.Get<bool>("null");
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| 125 | const bool nofill = conf.Get<bool>("no-fill");
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| 126 | const bool explain = conf.Get<bool>("explain");
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| 127 | const uint16_t verbose = conf.Get<uint16_t>("verbose");
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| 128 | const uint16_t compression = conf.Get<uint16_t>("compression");
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| 129 | const string delimiter = conf.Get<string>("delimiter");
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| 130 | const vector<string> _ignore = conf.Vec<string>("ignore");
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| 131 | //const vector<Map> mymap = conf.Vec<Map>("map");
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| 132 |
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| 133 | // -------------------------------------------------------------------------
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| 134 |
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| 135 | const auto vars = conf.GetWildcardOptions("var.*");
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| 136 |
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| 137 | vector<string> variables;
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| 138 | for (const auto &var : vars)
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| 139 | variables.emplace_back('@'+var.substr(4)+":="+Tools::Trim(conf.Get<string>(var)));
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| 140 |
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| 141 | // -------------------------------------------------------------------------
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| 142 |
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| 143 | if (verbose>0)
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| 144 | cout << "\n--------------------- Rootify SQL ----------------------" << endl;
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| 145 |
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| 146 | string query = conf.Get<string>("query");
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| 147 | if (query.empty())
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| 148 | {
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| 149 | if (verbose>0)
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| 150 | cout << "Reading query from file '" << file << "'." << endl;
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| 151 |
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| 152 | ifstream fin(file);
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| 153 | if (!fin)
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| 154 | {
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| 155 | cerr << "Could not open '" << file << "': " << strerror(errno) << endl;
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| 156 | return 1;
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| 157 | }
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| 158 | getline(fin, query, (char)fin.eof());
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| 159 | }
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| 160 |
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| 161 | if (query.empty())
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| 162 | {
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| 163 | cerr << "No query specified." << endl;
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| 164 | return 2;
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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 | const auto envs = conf.GetWildcardOptions("env.*");
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| 170 |
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| 171 | for (const auto &env : envs)
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| 172 | {
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| 173 | regex r1("\\$\\{"+env.substr(4)+"\\}");
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| 174 | regex r2("\\$"+env.substr(4)+"\\b");
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| 175 |
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| 176 | const string repl = boost::join(conf.Vec<string>(env), ", ");
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| 177 |
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| 178 | query = regex_replace(query, r1, repl);
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| 179 | query = regex_replace(query, r2, repl);
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| 180 | }
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| 181 |
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| 182 | // -------------------------- Check for file permssion ---------------------
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| 183 | // Strictly speaking, checking for write permission and existance is not necessary,
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| 184 | // but it is convenient that the user does not find out that it failed after
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| 185 | // waiting long for the query result
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| 186 | //
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| 187 | // I am using root here instead of boost to be
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| 188 | // consistent with the access pattern by TFile
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| 189 | TString path(noout?"/dev/null":out.c_str());
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| 190 | gSystem->ExpandPathName(path);
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| 191 |
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| 192 | if (!noout)
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| 193 | {
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| 194 | FileStat_t stat;
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| 195 | const Int_t exist = !gSystem->GetPathInfo(path, stat);
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| 196 | const Bool_t write = !gSystem->AccessPathName(path, kWritePermission) && R_ISREG(stat.fMode);
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| 197 |
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| 198 | if ((update && !exist) || (update && exist && !write) || (force && exist && !write))
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| 199 | {
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| 200 | cerr << "File '" << path << "' is not writable." << endl;
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| 201 | return 3;
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| 202 | }
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| 203 |
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| 204 | if (!update && !force && exist)
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| 205 | {
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| 206 | cerr << "File '" << path << "' already exists." << endl;
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| 207 | return 4;
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| 208 | }
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| 209 | }
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| 210 |
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| 211 | Time start2;
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| 212 |
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| 213 | // --------------------------- Connect to database -------------------------------------------------
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| 214 |
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| 215 | if (query.back()!='\n')
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| 216 | query += '\n';
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| 217 |
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| 218 | if (verbose>0)
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| 219 | cout << "Connecting to database..." << endl;
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| 220 |
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| 221 |
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| 222 | Database connection(uri); // Keep alive while fetching rows
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| 223 |
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| 224 | // -------------------------- Set user defined variables -------------------
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| 225 | if (variables.size()>0)
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| 226 | {
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| 227 | if (verbose>0)
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| 228 | cout << "Setting user defined variables..." << endl;
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| 229 |
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| 230 | const string varset =
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| 231 | "SET\n "+boost::algorithm::join(variables, ",\n ");
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| 232 |
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| 233 | try
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| 234 | {
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| 235 | connection.query(varset).execute();
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| 236 | }
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| 237 | catch (const exception &e)
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| 238 | {
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| 239 | cerr << varset << "\n\n";
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| 240 | cerr << "SQL query failed:\n" << e.what() << endl;
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| 241 | return 5;
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| 242 | }
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| 243 |
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| 244 | if (verbose>2)
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| 245 | cout << '\n' << varset << '\n' << endl;
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| 246 | }
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| 247 |
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| 248 | // ------------------------- Explain query if requested --------------------
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| 249 |
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| 250 | if (explain)
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| 251 | {
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| 252 | try
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| 253 | {
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| 254 | const auto res0 =
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| 255 | connection.query("EXPLAIN FORMAT=JSON "+query).store();
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| 256 |
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| 257 | cout << res0[0][0] << endl;
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| 258 | cout << endl;
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| 259 |
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| 260 | const mysqlpp::StoreQueryResult res1 =
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| 261 | connection.query("EXPLAIN "+query).store();
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| 262 |
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| 263 | for (size_t i=0; i<res1.num_rows(); i++)
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| 264 | {
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| 265 | const mysqlpp::Row &row = res1[i];
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| 266 |
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| 267 | cout << "\nid : " << row["id"];
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| 268 | cout << "\nselect type : " << row["select_type"];
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| 269 |
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| 270 | if (!row["table"].is_null())
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| 271 | cout << "\ntable : " << row["table"];
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| 272 |
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| 273 | if (!row["partitions"].is_null())
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| 274 | cout << "\npartitions : " << row["partitions"];
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| 275 |
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| 276 | if (!row["key"].is_null())
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| 277 | cout << "\nselected key : " << row["key"] << " [len=" << row["key_len"] << "] out of (" << row["possible_keys"] << ")";
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| 278 |
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| 279 | if (!row["type"].is_null())
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| 280 | cout << "\njoin type : " << row["type"];
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| 281 |
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| 282 | //if (!row["possible_keys"].is_null())
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| 283 | // cout << "\npossible_keys: " << row["possible_keys"];
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| 284 |
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| 285 | //if (!row["key_len"].is_null())
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| 286 | // cout << "\nkey_len : " << row["key_len"];
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| 287 |
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| 288 | if (!row["ref"].is_null())
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| 289 | cout << "\nref : (" << row["ref"] << ") compared to the index";
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| 290 |
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| 291 | if (!row["rows"].is_null())
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| 292 | cout << "\nrows : " << row["rows"];
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| 293 |
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| 294 | if (!row["filtered"].is_null())
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| 295 | cout << "\nfiltered : " << row["filtered"];
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| 296 |
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| 297 | if (!row["extra"].is_null())
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| 298 | cout << "\nExtra : " << row["extra"];
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| 299 |
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| 300 | cout << endl;
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| 301 | }
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| 302 |
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| 303 | cout << endl;
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| 304 |
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| 305 | return 0;
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| 306 |
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| 307 | const mysqlpp::StoreQueryResult res2 =
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| 308 | connection.query("SHOW WARNINGS").store();
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| 309 |
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| 310 | for (size_t i=0; i<res2.num_rows(); i++)
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| 311 | {
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| 312 | const mysqlpp::Row &row = res2[i];
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| 313 |
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| 314 | // 1003 //
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| 315 | cout << row["Level"] << '[' << row["Code"] << "]:\n";
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| 316 | cout << row["Message"] << '\n' << endl;
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| 317 |
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| 318 | }
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| 319 |
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| 320 | }
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| 321 | catch (const exception &e)
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| 322 | {
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| 323 | cerr << query << "\n\n";
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| 324 | cerr << "SQL query failed:\n" << e.what() << endl;
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| 325 | return 6;
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| 326 | }
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| 327 |
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| 328 | return 0;
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| 329 | }
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| 330 |
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| 331 | // -------------------------- Request data from database -------------------
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| 332 | if (verbose>0)
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| 333 | cout << "Requesting data..." << endl;
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| 334 |
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| 335 | if (verbose>2)
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| 336 | cout << '\n' << query << endl;
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| 337 |
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| 338 | const mysqlpp::UseQueryResult res =
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| 339 | connection.query(query).use();
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| 340 |
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| 341 | // -------------------------------------------------------------------------
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| 342 |
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| 343 | if (verbose>0)
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| 344 | cout << "Opening file '" << path << "' [compression=" << compression << "]..." << endl;
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| 345 |
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| 346 | // ----------------------------- Open output file --------------------------
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| 347 | TFile tfile(path, update?"UPDATE":(force?"RECREATE":"CREATE"), "Rootify SQL", compression);
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| 348 | if (tfile.IsZombie())
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| 349 | return 7;
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| 350 |
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| 351 | // -------------------------------------------------------------------------
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| 352 |
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| 353 | // get the first row to get the field description
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| 354 | mysqlpp::Row row = res.fetch_row();
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| 355 | if (!row)
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| 356 | {
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| 357 | cerr << "Empty set returned... nothing to write." << endl;
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| 358 | return 8;
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| 359 | }
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| 360 |
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| 361 | if (verbose>0)
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| 362 | cout << "Trying to setup " << row.size() << " branches..." << endl;
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| 363 |
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| 364 | if (verbose>1)
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| 365 | cout << endl;
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| 366 |
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| 367 | const mysqlpp::FieldNames &l = *row.field_list().list;
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| 368 |
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| 369 | vector<double> buf(l.size());
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| 370 | vector<uint8_t> typ(l.size(),'n'); // n=number [double], d is used for DateTime
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| 371 |
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| 372 | UInt_t cols = 0;
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| 373 |
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| 374 |
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| 375 | // -------------------- Configure branches of TTree ------------------------
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| 376 | TTree *ttree = new TTree(tree.c_str(), query.c_str());
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| 377 |
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| 378 | size_t skipat = 0;
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| 379 | size_t skipreg = 0;
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| 380 | for (size_t i=0; i<l.size(); i++)
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| 381 | {
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| 382 | const string t = row[i].type().sql_name();
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| 383 |
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| 384 | if (t.find("DATETIME")!=string::npos)
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| 385 | typ[i] = 'd';
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| 386 | else
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| 387 | if (t.find("DATE")!=string::npos)
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| 388 | typ[i] = 'D';
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| 389 | else
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| 390 | if (t.find("TIME")!=string::npos)
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| 391 | typ[i] = 'T';
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| 392 | else
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| 393 | if (t.find("VARCHAR")!=string::npos)
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| 394 | typ[i] = 'V';
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| 395 | else
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| 396 | if (t.find("CHAR")!=string::npos)
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| 397 | typ[i] = 'C';
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| 398 |
|
|---|
| 399 | bool found = false;
|
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| 400 | for (const auto &pattern: _ignore)
|
|---|
| 401 | {
|
|---|
| 402 | if (regex_match(l[i], regex(pattern)))
|
|---|
| 403 | {
|
|---|
| 404 | found = true;
|
|---|
| 405 | typ[i] = '-';
|
|---|
| 406 | skipreg++;
|
|---|
| 407 | break;
|
|---|
| 408 | }
|
|---|
| 409 | }
|
|---|
| 410 |
|
|---|
| 411 | if (l[i][0]=='@')
|
|---|
| 412 | {
|
|---|
| 413 | typ[i] = '@';
|
|---|
| 414 | skipat++;
|
|---|
| 415 | }
|
|---|
| 416 |
|
|---|
| 417 | const bool use = l[i][0]!='@' && typ[i]!='V' && typ[i]!='C' && !found;
|
|---|
| 418 |
|
|---|
| 419 | if (verbose>1)
|
|---|
| 420 | cout << (use?" + ":" - ") << l[i].c_str() << " [" << t << "] {" << typ[i] << "}\n";
|
|---|
| 421 |
|
|---|
| 422 | if (use)
|
|---|
| 423 | {
|
|---|
| 424 | // string name = l[i];
|
|---|
| 425 | // for (const auto &m: mymap)
|
|---|
| 426 | // name = boost::regex_replace(l[i], boost::regex(m.first), m.second);
|
|---|
| 427 |
|
|---|
| 428 | ttree->Branch(l[i].c_str(), buf.data()+i);
|
|---|
| 429 | cols++;
|
|---|
| 430 | }
|
|---|
| 431 | }
|
|---|
| 432 | // -------------------------------------------------------------------------
|
|---|
| 433 |
|
|---|
| 434 | if (verbose>1)
|
|---|
| 435 | cout << endl;
|
|---|
| 436 | if (verbose>0)
|
|---|
| 437 | {
|
|---|
| 438 | if (skipreg)
|
|---|
| 439 | cout << skipreg << " branches skipped due to ignore list." << endl;
|
|---|
| 440 | if (skipat)
|
|---|
| 441 | cout << skipat << " branches skipped due to name starting with @." << endl;
|
|---|
| 442 | cout << "Configured " << cols << " branches.\nFilling branches..." << endl;
|
|---|
| 443 | }
|
|---|
| 444 |
|
|---|
| 445 | if (display)
|
|---|
| 446 | {
|
|---|
| 447 | cout << endl;
|
|---|
| 448 | cout << "#";
|
|---|
| 449 | for (size_t i=0; i<l.size(); i++)
|
|---|
| 450 | cout << ' ' << l[i].c_str();
|
|---|
| 451 | cout << endl;
|
|---|
| 452 | }
|
|---|
| 453 |
|
|---|
| 454 | // ---------------------- Fill TTree with DB data --------------------------
|
|---|
| 455 | size_t count = 0;
|
|---|
| 456 | size_t skip = 0;
|
|---|
| 457 | do
|
|---|
| 458 | {
|
|---|
| 459 | count++;
|
|---|
| 460 |
|
|---|
| 461 | ostringstream sout;
|
|---|
| 462 |
|
|---|
| 463 | size_t idx=0;
|
|---|
| 464 | for (auto col=row.begin(); col!=row.end(); col++, idx++)
|
|---|
| 465 | {
|
|---|
| 466 | if (display)
|
|---|
| 467 | {
|
|---|
| 468 | if (idx>0)
|
|---|
| 469 | sout << (delimiter.empty()?"\t":delimiter);
|
|---|
| 470 | sout << col->c_str();
|
|---|
| 471 | }
|
|---|
| 472 |
|
|---|
| 473 | if (!ignorenull && col->is_null())
|
|---|
| 474 | {
|
|---|
| 475 | skip++;
|
|---|
| 476 | break;
|
|---|
| 477 | }
|
|---|
| 478 |
|
|---|
| 479 | switch (typ[idx])
|
|---|
| 480 | {
|
|---|
| 481 | case 'd':
|
|---|
| 482 | buf[idx] = time_t((mysqlpp::DateTime)(*col));
|
|---|
| 483 | break;
|
|---|
| 484 |
|
|---|
| 485 | case 'D':
|
|---|
| 486 | buf[idx] = time_t((mysqlpp::Date)(*col));
|
|---|
| 487 | break;
|
|---|
| 488 |
|
|---|
| 489 | case 'T':
|
|---|
| 490 | buf[idx] = time_t((mysqlpp::Time)(*col));
|
|---|
| 491 | break;
|
|---|
| 492 |
|
|---|
| 493 | case 'V':
|
|---|
| 494 | case 'C':
|
|---|
| 495 | case '-':
|
|---|
| 496 | case '@':
|
|---|
| 497 | break;
|
|---|
| 498 |
|
|---|
| 499 | default:
|
|---|
| 500 | buf[idx] = atof(col->c_str());
|
|---|
| 501 | }
|
|---|
| 502 | }
|
|---|
| 503 |
|
|---|
| 504 | if (idx==row.size())
|
|---|
| 505 | {
|
|---|
| 506 | if (!nofill)
|
|---|
| 507 | ttree->Fill();
|
|---|
| 508 |
|
|---|
| 509 | if (display)
|
|---|
| 510 | cout << sout.str() << endl;
|
|---|
| 511 | }
|
|---|
| 512 |
|
|---|
| 513 | row = res.fetch_row();
|
|---|
| 514 |
|
|---|
| 515 |
|
|---|
| 516 | } while (row);
|
|---|
| 517 |
|
|---|
| 518 | // -------------------------------------------------------------------------
|
|---|
| 519 |
|
|---|
| 520 | if (display)
|
|---|
| 521 | cout << '\n' << endl;
|
|---|
| 522 |
|
|---|
| 523 | if (verbose>0)
|
|---|
| 524 | {
|
|---|
| 525 | cout << count << " rows fetched." << endl;
|
|---|
| 526 | if (skip>0)
|
|---|
| 527 | cout << skip << " rows skipped due to NULL field." << endl;
|
|---|
| 528 |
|
|---|
| 529 | cout << ttree->GetEntries() << " rows filled into tree." << endl;
|
|---|
| 530 | }
|
|---|
| 531 |
|
|---|
| 532 | ttree->Write();
|
|---|
| 533 | tfile.Close();
|
|---|
| 534 |
|
|---|
| 535 | if (verbose>0)
|
|---|
| 536 | {
|
|---|
| 537 | cout << "File closed.\n";
|
|---|
| 538 | cout << "Execution time: " << Time().UnixTime()-start.UnixTime() << "s\n";
|
|---|
| 539 | cout << "--------------------------------------------------------" << endl;
|
|---|
| 540 | }
|
|---|
| 541 |
|
|---|
| 542 | return 0;
|
|---|
| 543 | }
|
|---|
