| 1 | #include <boost/regex.hpp>
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| 2 | #include <boost/filesystem.hpp>
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| 3 | #include <boost/algorithm/string/join.hpp>
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| 4 |
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| 5 | #include "Database.h"
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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 "zfits.h"
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| 12 |
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| 13 | using namespace std;
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| 14 | namespace fs = boost::filesystem;
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| 15 |
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| 16 | // ------------------------------------------------------------------------
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| 17 |
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| 18 | struct Map : pair<string, string>
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| 19 | {
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| 20 | Map() { }
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| 21 | };
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| 22 |
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| 23 | std::istream &operator>>(std::istream &in, Map &m)
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| 24 | {
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| 25 | const istreambuf_iterator<char> eos;
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| 26 | string txt(istreambuf_iterator<char>(in), eos);
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| 27 |
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| 28 | const boost::regex expr("((.*)[^\\\\])/(.*)");
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| 29 | boost::smatch match;
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| 30 | if (!boost::regex_match(txt, match, expr))
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| 31 | throw runtime_error("Could not evaluate map argument: "+txt);
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| 32 |
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| 33 | m.first = match[1].str();
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| 34 | m.second = match[3].str();
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| 35 |
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| 36 | return in;
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| 37 | }
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| 38 |
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| 39 |
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| 40 | void SetupConfiguration(Configuration &conf)
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| 41 | {
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| 42 | po::options_description control("Root to SQL");
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| 43 | control.add_options()
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| 44 | ("uri,u", var<string>()->required(), "Database link as in\n\tuser:password@server[:port]/database[?compress=0|1].")
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| 45 | ("file", var<string>()->required(), "The root file to read from")
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| 46 | ("create", po_switch(), "Create the database if not existing")
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| 47 | ("drop", po_switch(), "Drop the table (implies create)")
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| 48 | ("extension,e", var<string>(""), "Name of the fits extension (table) to convert")
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| 49 | ("table", var<string>(""), "Name of the table to use (default is the tree name)")
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| 50 | ("map", vars<Map>(), "A regular expression which is applied to the leaf name befoee it is used as SQL column name)")
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| 51 | ("sql-type", vars<Map>(), "Allows to overwrite the calculated SQL type for a given column e.g. 'sql-column-name/UNSIGNED IN'")
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| 52 | ("ignore", vars<string>(), "Ignore the given leaf, if the given regular expression matches")
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| 53 | ("unsigned", vars<string>(), "In fits files per default columns are signed. This interpretss the column as unsigned value. Use the FITS column name.")
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| 54 | ("primary", vars<string>(), "List of columns to be used as primary keys during table creation (in connection with --create)")
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| 55 | ("first", var<size_t>(size_t(0)), "First event to start with (default: 0), mainly for test purpose")
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| 56 | ("max", var<size_t>(size_t(0)), "Maximum number of events to process (0: all), mainly for test purpose")
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| 57 | ("engine", var<string>(""), "Database engine to be used when a new table is created")
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| 58 | ("row-format", var<string>(""), "Defines the ROW_FORMAT keyword for table creation")
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| 59 | ("duplicate", vars<string>(), "Specifies an assignment_list for an 'ON DUPLICATE KEY UPDATE' expression")
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| 60 | ("ignore-errors", po_switch(), "Adds the IGNORE keyword to the INSERT query (turns errors into warnings, ignores rows with errors)")
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| 61 | ("const.*", var<string>(), "Insert a constant number into the given column (--const.mycolumn=5). A special case is `/.../.../`")
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| 62 | ("conditional", po_switch(), "Conditional insert. Only insert if no entry exists yet with the constants defined by --const")
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| 63 | ("delete", po_switch(), "Delete all entries first which fit all constant columns defined by --const")
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| 64 | ("index", po_switch(), "If a table is created, all const columns are used as a single index")
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| 65 | ;
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| 66 |
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| 67 | po::options_description debug("Debug options");
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| 68 | debug.add_options()
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| 69 | ("no-insert", po_switch(), "Does not insert any data into the table")
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| 70 | ("dry-run", po_switch(), "Skip any query which changes the databse (might result in consecutive failures)")
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| 71 | ("print-extensions", po_switch(), "Print extensions (tables) from fits file")
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| 72 | ("print-connection", po_switch(), "Print database connection information")
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| 73 | ("print-columns", po_switch(), "Print columns in fits table")
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| 74 | ("print-insert", po_switch(), "Print the INSERT query (note that it contains all data)")
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| 75 | ("print-create", po_switch(), "Print the CREATE query")
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| 76 | ("print-select", po_switch(), "Print the SELECT query for the conditional execution")
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| 77 | ("print-delete", po_switch(), "Print the DELETE query")
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| 78 | ("verbose,v", var<uint16_t>(1), "Verbosity (0: quiet, 1: default, 2: more, 3, ...)")
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| 79 | ;
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| 80 |
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| 81 | po::positional_options_description p;
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| 82 | p.add("file", 1); // The 1st positional options (n=1)
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| 83 |
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| 84 | conf.AddOptions(control);
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| 85 | conf.AddOptions(debug);
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| 86 | conf.SetArgumentPositions(p);
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| 87 | }
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| 88 |
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| 89 | void PrintUsage()
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| 90 | {
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| 91 | cout <<
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| 92 | "fits2sql - Fills the data from a fits file into a database\n"
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| 93 | "\n"
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| 94 | "For convenience, this documentation uses the extended version of the options, "
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| 95 | "refer to the output below to get the abbreviations.\n"
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| 96 | "\n"
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| 97 | "This is a general purpose tool to fill the contents of a fite file into a database.\n"
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| 98 | "\n"
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| 99 | "Each fits file contians several table, so called extenbsions. Each tables has "
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| 100 | "a number of columns compilsed from basic data types. The default extension to "
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| 101 | "read from is the first one on the file but the name can be overwritten using "
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| 102 | "--extension. The default table name to fill the data into is identical to "
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| 103 | "the extension name. It can be overwritten using --table.\n"
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| 104 | "\n"
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| 105 | "The name of each column to which data is filled is obtained from "
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| 106 | "the fits column names. The column names can be checked using --print-columns. "
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| 107 | "Sometimes these names might not be convenient. To allow to simplify or replace "
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| 108 | "column names, regular expressions (using boost's regex) can be defined to change "
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| 109 | "the names. Note that these regular expressions are applied one by one on each "
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| 110 | "columns's name. A valid expression could "
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| 111 | "be:\n"
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| 112 | " --map=MHillas\\.f/\n"
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| 113 | "which would remove all occurances of 'MHillas.f'. This option can be used more than "
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| 114 | "once. They are applied in sequence. A single match does not stop the sequence.\n"
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| 115 | "\n"
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| 116 | "Sometimes it might also be convenient to skip a column. This can be done with "
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| 117 | "the --ignore resource. If the given regular expresion yields a match, the "
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| 118 | "column will be ignored. Note that the regular expression works on the raw-name "
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| 119 | "of the column not the readily mapped SQL column names. Example:\n"
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| 120 | " --ignore=ThetaSq\\..*\n"
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| 121 | "will skip all leaved which start with 'ThetaSq.'. This option can be used"
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| 122 | "more than once.\n"
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| 123 | "\n"
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| 124 | "The data type of each column is kept as close as possible to the columns' data "
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| 125 | "types. If for some reason this is not wanted, the data type of the SQL column "
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| 126 | "can be overwritten with --sql-type sql-column/sql-ytpe, for example:\n"
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| 127 | " --sql-type=FileId/UNSIGNED INT\n"
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| 128 | "while the first argument of the name of the SQL column to which the data type "
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| 129 | "should be applied. The second column is the basic SQL data type. The option can "
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| 130 | "be given more than once.\n"
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| 131 | "\n"
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| 132 | "Database interaction:\n"
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| 133 | "\n"
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| 134 | "To drop an existing table, --drop can be used.\n"
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| 135 | "\n"
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| 136 | "To create a table according to theSQL column names and data types, --create "
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| 137 | "can be used. The query used can be printed with --print-create even --create "
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| 138 | "has not been specified.\n"
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| 139 | "\n"
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| 140 | "To choose the columns which should become primary keys, use --primary, "
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| 141 | "for example:\n"
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| 142 | " --primary=col1\n"
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| 143 | "To define more than one column as primary key, the option can be given more than "
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| 144 | "once. Note that the combination of these columns must be unique.\n"
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| 145 | "\n"
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| 146 | "All columns are created as NOT NULL as default. To force a database engine "
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| 147 | "and/or a storage format, use --engine and --rot-format.\n"
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| 148 | "\n"
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| 149 | "Usually, the INSERT query would fail if the PRIMARY key exists already. "
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| 150 | "This can be avoided using the 'ON DUPLICATE KEY UPDATE' directive. With the "
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| 151 | "--duplicate, you can specify what should be updated in case of a duplicate key. "
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| 152 | "To keep the row untouched, you can just update the primary key "
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| 153 | "with the identical primary key, e.g. --duplicate='MyPrimary=VALUES(MyPrimary)'. "
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| 154 | "The --duplicate resource can be specified more than once to add more expressions "
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| 155 | "to the assignment_list. For more details, see the MySQL manual.\n"
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| 156 | "\n"
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| 157 | "Another possibility is to add the IGNORE keyword to the INSERT query by "
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| 158 | "--ignore-errors, which essentially ignores all errors and turns them into "
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| 159 | "warnings which are printed after the query succeeded.\n"
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| 160 | "\n"
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| 161 | "For debugging purpose, or to just create or drop a table, the final insert "
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| 162 | "query can be skipped using --no-insert. Note that for performance reason, "
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| 163 | "all data is collected in memory and a single INSERT query is issued at the "
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| 164 | "end.\n"
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| 165 | "\n"
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| 166 | "Using a higher verbosity level (-v), an overview of the written columns or all "
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| 167 | "processed leaves is printed depending on the verbosity level. The output looks "
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| 168 | "like the following\n"
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| 169 | " Leaf name [root data type] (SQL name)\n"
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| 170 | "for example\n"
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| 171 | " MTime.fTime.fMilliSec [Long64_t] (MilliSec)\n"
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| 172 | "which means that the leaf MTime.fTime.fMilliSec is detected to be a Long64_t "
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| 173 | "which is filled into a column called MilliSec. Leaves with non basic data types "
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| 174 | "are ignored automatically and are marked as (-n/a-). User ignored columnd "
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| 175 | "are marked as (-ignored-).\n"
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| 176 | "\n"
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| 177 | "A constant value for the given file can be inserted by using the --const directive. "
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| 178 | "For example --const.mycolumn=42 would insert 42 into a column called mycolumn. "
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| 179 | "The column is created as INT UNSIGNED as default which can be altered by "
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| 180 | "--sql-type. A special case is a value of the form `/regex/format/`. Here, the given "
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| 181 | "regular expression is applied to the filename and it is newly formated with "
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| 182 | "the new format string. For details on how backreferences work, see for example "
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| 183 | "the man-page of the sed utility.\n"
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| 184 | "\n"
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| 185 | "Usually the previously defined constant values are helpful to create an index "
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| 186 | "which relates unambiguously the inserted data to the file. It might be useful "
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| 187 | "to delete all data which belongs to this particular file before new data is "
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| 188 | "entered. This can be achieved with the `--delete` directive. It deletes all "
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| 189 | "data from the table before inserting new data which fulfills the condition "
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| 190 | "defined by the `--const` directives.\n"
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| 191 | "\n"
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| 192 | "The constant values can also be used for a conditional execution (--conditional). "
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| 193 | "If any row with the given constant values are found, the execution is stopped "
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| 194 | "(note that this happend after the table drop/create but before the delete/insert.\n"
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| 195 | "\n"
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| 196 | "To ensure efficient access for a conditonal execution, it makes sense to have "
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| 197 | "an index created for those columns. This can be done during table creation "
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| 198 | "with the --index option.\n"
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| 199 | "\n"
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| 200 | "To create the index as a UNIQUE INDEX, you can use the --unique option which "
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| 201 | "implies --index.\n"
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| 202 | "\n"
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| 203 | "If a query failed, the query is printed to stderr together with the error message. "
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| 204 | "For the main INSERT query, this is only true if the verbosity level is at least 2 "
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| 205 | "or the query has less than 80*25 bytes.\n"
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| 206 | "\n"
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| 207 | "In case of success, 0 is returned, a value>0 otherwise.\n"
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| 208 | "\n"
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| 209 | "Usage: fits2sql [options] --uri URI fitsfile.fits[.gz]\n"
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| 210 | "\n"
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| 211 | ;
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| 212 | cout << endl;
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| 213 | }
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| 214 |
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| 215 | enum BasicType_t
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| 216 | {
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| 217 | kNone = 0,
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| 218 | kConst,
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| 219 | kVarchar,
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| 220 | kBool,
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| 221 | kFloat,
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| 222 | kDouble,
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| 223 | kInt8,
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| 224 | kUInt8,
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| 225 | kInt16,
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| 226 | kUInt16,
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| 227 | kInt32,
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| 228 | kUInt32,
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| 229 | kInt64,
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| 230 | kUInt64,
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| 231 | // kMJD,
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| 232 | };
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| 233 |
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| 234 | static const map<char, pair<BasicType_t, string>> ConvFits =
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| 235 | {
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| 236 | { 'A', { kVarchar, "VARCHAR" } },
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| 237 | { 'a', { kVarchar, "VARCHAR" } },
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| 238 | { 'L', { kBool, "BOOLEAN" } },
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| 239 | { 'l', { kBool, "BOOLEAN" } },
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| 240 | { 'B', { kInt8, "TINYINT" } },
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| 241 | { 'b', { kUInt8, "TINYINT UNSIGNED" } },
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| 242 | { 'I', { kInt16, "SMALLINT" } },
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| 243 | { 'i', { kUInt16, "SMALLINT UNSIGNED" } },
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| 244 | { 'J', { kInt32, "INT" } },
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| 245 | { 'j', { kUInt32, "INT UNSIGNED" } },
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| 246 | { 'K', { kInt64, "BIGINT" } },
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| 247 | { 'k', { kUInt64, "BIGINT UNSIGNED" } },
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| 248 | { 'E', { kFloat, "FLOAT" } },
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| 249 | { 'e', { kFloat, "FLOAT" } },
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| 250 | { 'D', { kDouble, "DOUBLE" } },
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| 251 | { 'd', { kDouble, "DOUBLE" } },
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| 252 | };
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| 253 |
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| 254 | struct Container
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| 255 | {
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| 256 | string branch; // fits column name
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| 257 | string column; // sql column name
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| 258 | BasicType_t type;
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| 259 | size_t num;
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| 260 | // double offset;
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| 261 | void *ptr;
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| 262 |
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| 263 | Container(const string &b, const string &c, const BasicType_t &t, const size_t &n/*, const double &offset=0*/) : branch(b), column(c), type(t), num(n), ptr(0)
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| 264 | {
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| 265 | }
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| 266 | Container(const string &c, const string &value) : branch(value), column(c), type(kConst), num(1), ptr(0)
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| 267 | {
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| 268 | }
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| 269 | ~Container()
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| 270 | {
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| 271 | }
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| 272 |
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| 273 | string fmt(const size_t &index) const
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| 274 | {
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| 275 | ostringstream str;
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| 276 |
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| 277 | switch (type)
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| 278 | {
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| 279 | //case kVarchar: str << string(reinterpret_cast<char*>(ptr), num); break;
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| 280 | case kVarchar: str << string(reinterpret_cast<char*>(ptr), num).c_str(); break;
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| 281 | case kFloat: str << setprecision(8) << reinterpret_cast<float*>(ptr)[index]; break;
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| 282 | // case kMJD: str << setprecision(16) << reinterpret_cast<double*>(ptr)[0]+offset; break;
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| 283 | case kDouble: str << setprecision(16) << reinterpret_cast<double*>(ptr)[index]; break;
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| 284 | case kBool:
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| 285 | case kInt8: str << int32_t(reinterpret_cast<int8_t*>(ptr)[index]); break;
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| 286 | case kUInt8: str << uint32_t(reinterpret_cast<uint8_t*>(ptr)[index]); break;
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| 287 | case kInt16: str << reinterpret_cast<int16_t*>(ptr)[index]; break;
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| 288 | case kUInt16: str << reinterpret_cast<uint16_t*>(ptr)[index]; break;
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| 289 | case kInt32: str << reinterpret_cast<int32_t*>(ptr)[index]; break;
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| 290 | case kUInt32: str << reinterpret_cast<uint32_t*>(ptr)[index]; break;
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| 291 | case kInt64: str << reinterpret_cast<int64_t*>(ptr)[index]; break;
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| 292 | case kUInt64: str << reinterpret_cast<uint64_t*>(ptr)[index]; break;
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| 293 | case kConst: str << branch; break;
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| 294 | case kNone:
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| 295 | break;
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| 296 | }
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| 297 |
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| 298 | return str.str();
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| 299 | }
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| 300 | };
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| 301 |
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| 302 | int main(int argc, const char* argv[])
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| 303 | {
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| 304 | Time start;
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| 305 |
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| 306 | Configuration conf(argv[0]);
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| 307 | conf.SetPrintUsage(PrintUsage);
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| 308 | SetupConfiguration(conf);
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| 309 |
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| 310 | if (!conf.DoParse(argc, argv))
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| 311 | return 127;
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| 312 |
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| 313 | // ----------------------------- Evaluate options --------------------------
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| 314 | const string uri = conf.Get<string>("uri");
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| 315 | const string file = conf.Get<string>("file");
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| 316 | const string extension = conf.Get<string>("extension");
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| 317 | string table = conf.Get<string>("table");
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| 318 |
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| 319 | const uint16_t verbose = conf.Get<uint16_t>("verbose");
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| 320 | const size_t first = conf.Get<size_t>("first");
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| 321 | const size_t max = conf.Get<size_t>("max");
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| 322 |
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| 323 | const bool drop = conf.Get<bool>("drop");
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| 324 | const bool create = conf.Get<bool>("create") || drop;
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| 325 | const bool noinsert = conf.Get<bool>("no-insert");
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| 326 | const bool dry_run = conf.Get<bool>("dry-run");
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| 327 | const bool conditional = conf.Get<bool>("conditional");
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| 328 | const bool run_delete = conf.Get<bool>("delete");
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| 329 | const bool index = conf.Get<bool>("index");
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| 330 | const bool unique = conf.Get<bool>("unique");
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| 331 |
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| 332 | const string engine = conf.Get<string>("engine");
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| 333 | const string row_format = conf.Get<string>("row-format");
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| 334 |
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| 335 | const bool ignore_errors = conf.Get<bool>("ignore-errors");
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| 336 |
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| 337 | const bool print_connection = conf.Get<bool>("print-connection");
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| 338 | const bool print_extensions = conf.Get<bool>("print-extensions");
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| 339 | const bool print_columns = conf.Get<bool>("print-columns");
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| 340 | const bool print_create = conf.Get<bool>("print-create");
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| 341 | const bool print_insert = conf.Get<bool>("print-insert");
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| 342 | const bool print_select = conf.Get<bool>("print-select");
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| 343 | const bool print_delete = conf.Get<bool>("print-delete");
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| 344 |
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| 345 | const vector<Map> mymap = conf.Vec<Map>("map");
|
|---|
| 346 | const vector<Map> sqltypes = conf.Vec<Map>("sql-type");
|
|---|
| 347 | const vector<string> _ignore = conf.Vec<string>("ignore");
|
|---|
| 348 | const vector<string> primary = conf.Vec<string>("primary");
|
|---|
| 349 |
|
|---|
| 350 | const vector<string> duplicate = conf.Vec<string>("duplicate");
|
|---|
| 351 | const vector<string> notsigned = conf.Vec<string>("unsigned");
|
|---|
| 352 |
|
|---|
| 353 | if (first>=max)
|
|---|
| 354 | cerr << "WARNING: Resource `first` (" << first << ") exceeds `max` (" << max << ")" << endl;
|
|---|
| 355 |
|
|---|
| 356 |
|
|---|
| 357 | // -------------------------------------------------------------------------
|
|---|
| 358 |
|
|---|
| 359 | if (verbose>0)
|
|---|
| 360 | {
|
|---|
| 361 | cout << "\n-------------------------- Evaluating file -------------------------" << endl;
|
|---|
| 362 | cout << "Start Time: " << Time::sql << Time(Time::local) << endl;
|
|---|
| 363 | }
|
|---|
| 364 |
|
|---|
| 365 | zfits f(file.c_str(), extension.c_str());
|
|---|
| 366 | if (!f)
|
|---|
| 367 | {
|
|---|
| 368 | cerr << "Could not open file " << file << ": " << strerror(errno) << endl;
|
|---|
| 369 | return 1;
|
|---|
| 370 | }
|
|---|
| 371 |
|
|---|
| 372 | if (verbose>0)
|
|---|
| 373 | cout << "File: " << file << endl;
|
|---|
| 374 |
|
|---|
| 375 | if (!extension.empty() && extension!=f.Get<string>("EXTNAME"))
|
|---|
| 376 | {
|
|---|
| 377 | cerr << "Extension " << extension << " not found in file." << endl;
|
|---|
| 378 | return 2;
|
|---|
| 379 | }
|
|---|
| 380 |
|
|---|
| 381 | if (print_extensions)
|
|---|
| 382 | {
|
|---|
| 383 | cout << "\nTables:\n - " << boost::join(f.GetTables(), "\n - ") << '\n' << endl;
|
|---|
| 384 | return 3;
|
|---|
| 385 | }
|
|---|
| 386 |
|
|---|
| 387 | if (verbose>0)
|
|---|
| 388 | cout << "FITS extension [table]: " << f.Get<string>("EXTNAME") << endl;
|
|---|
| 389 |
|
|---|
| 390 | if (table.empty())
|
|---|
| 391 | table = f.Get<string>("EXTNAME");
|
|---|
| 392 |
|
|---|
| 393 | if (verbose>0)
|
|---|
| 394 | cout << "SQL table: " << table << endl;
|
|---|
| 395 |
|
|---|
| 396 | // const double mjdref = f.Get("MJDREF", double(0));
|
|---|
| 397 |
|
|---|
| 398 | if (print_columns)
|
|---|
| 399 | {
|
|---|
| 400 | cout << '\n';
|
|---|
| 401 | f.PrintColumns();
|
|---|
| 402 | cout << '\n';
|
|---|
| 403 | }
|
|---|
| 404 |
|
|---|
| 405 | const auto cols = f.GetColumns();
|
|---|
| 406 |
|
|---|
| 407 | if (verbose>0)
|
|---|
| 408 | {
|
|---|
| 409 | cout << f.GetNumRows() << " events found." << endl;
|
|---|
| 410 | cout << cols.size() << " columns found." << endl;
|
|---|
| 411 | }
|
|---|
| 412 |
|
|---|
| 413 | string query =
|
|---|
| 414 | "CREATE TABLE IF NOT EXISTS `"+table+"`\n"
|
|---|
| 415 | "(\n";
|
|---|
| 416 |
|
|---|
| 417 | vector<Container> vec;
|
|---|
| 418 |
|
|---|
| 419 | const auto fixed = conf.GetWildcardOptions("const.*");
|
|---|
| 420 |
|
|---|
| 421 | string where;
|
|---|
| 422 | vector<string> vindex;
|
|---|
| 423 | for (auto it=fixed.cbegin(); it!=fixed.cend(); it++)
|
|---|
| 424 | {
|
|---|
| 425 | const string name = it->substr(6);
|
|---|
| 426 | string val = conf.Get<string>(*it);
|
|---|
| 427 |
|
|---|
| 428 | boost::smatch match;
|
|---|
| 429 | if (boost::regex_match(val, match, boost::regex("\\/(.+)(?<!\\\\)\\/(.*)(?<!\\\\)\\/")))
|
|---|
| 430 | {
|
|---|
| 431 | const string reg = match[1];
|
|---|
| 432 | const string fmt = match[2];
|
|---|
| 433 |
|
|---|
| 434 | val = boost::regex_replace(file, boost::regex(reg), fmt.empty()?"$0":fmt,
|
|---|
| 435 | boost::regex_constants::format_default|boost::regex_constants::format_no_copy);
|
|---|
| 436 |
|
|---|
| 437 | if (verbose>0)
|
|---|
| 438 | {
|
|---|
| 439 | cout << "Regular expression detected for constant column `" << *it << "`\n";
|
|---|
| 440 | cout << "Filename converted with /" << reg << "/ to /" << fmt << "/\n";
|
|---|
| 441 | cout << "Filename: " << file << '\n';
|
|---|
| 442 | cout << "Result: " << val << endl;
|
|---|
| 443 | }
|
|---|
| 444 | }
|
|---|
| 445 |
|
|---|
| 446 | if (verbose==2)
|
|---|
| 447 | cout << "\n" << val << " [-const-]";
|
|---|
| 448 | if (verbose>1)
|
|---|
| 449 | cout << " (" << name << ")";
|
|---|
| 450 |
|
|---|
| 451 | string sqltype = "INT UNSIGNED";
|
|---|
| 452 |
|
|---|
| 453 | for (auto m=sqltypes.cbegin(); m!=sqltypes.cend(); m++)
|
|---|
| 454 | if (m->first==name)
|
|---|
| 455 | sqltype = m->second;
|
|---|
| 456 |
|
|---|
| 457 | if (!vec.empty())
|
|---|
| 458 | query += ",\n";
|
|---|
| 459 | query += " `"+name+"` "+sqltype+" NOT NULL COMMENT '--user--'";
|
|---|
| 460 |
|
|---|
| 461 | vec.emplace_back(name, val);
|
|---|
| 462 | where += " AND `"+name+"`="+val;
|
|---|
| 463 | vindex.emplace_back(name);
|
|---|
| 464 | }
|
|---|
| 465 |
|
|---|
| 466 | const size_t nvec = vec.size();
|
|---|
| 467 |
|
|---|
| 468 | for (auto ic=cols.cbegin(); ic!=cols.cend(); ic++)
|
|---|
| 469 | {
|
|---|
| 470 | const auto &col = ic->second;
|
|---|
| 471 |
|
|---|
| 472 | if (verbose>2)
|
|---|
| 473 | cout << '\n' << col.type << " " << ic->first << "[" << col.num << "]";
|
|---|
| 474 |
|
|---|
| 475 | string name = ic->first;
|
|---|
| 476 |
|
|---|
| 477 | bool found = false;
|
|---|
| 478 | for (auto b=_ignore.cbegin(); b!=_ignore.cend(); b++)
|
|---|
| 479 | {
|
|---|
| 480 | if (boost::regex_match(name, boost::regex(*b)))
|
|---|
| 481 | {
|
|---|
| 482 | found = true;
|
|---|
| 483 | if (verbose>2)
|
|---|
| 484 | cout << " (-ignored-)";
|
|---|
| 485 | break;
|
|---|
| 486 | }
|
|---|
| 487 | }
|
|---|
| 488 | if (found)
|
|---|
| 489 | continue;
|
|---|
| 490 |
|
|---|
| 491 | const char tn = find(notsigned.cbegin(), notsigned.cend(), ic->first)!=notsigned.cend() ?
|
|---|
| 492 | tolower(col.type) : toupper(col.type);
|
|---|
| 493 |
|
|---|
| 494 | auto it = ConvFits.find(tn);
|
|---|
| 495 | if (it==ConvFits.end())
|
|---|
| 496 | {
|
|---|
| 497 | if (verbose>2)
|
|---|
| 498 | cout << " (-n/a-)";
|
|---|
| 499 | continue;
|
|---|
| 500 | }
|
|---|
| 501 |
|
|---|
| 502 | if (verbose==2)
|
|---|
| 503 | cout << '\n' << name << " [" << tn << "]";
|
|---|
| 504 |
|
|---|
| 505 | for (auto m=mymap.cbegin(); m!=mymap.cend(); m++)
|
|---|
| 506 | name = boost::regex_replace(name, boost::regex(m->first), m->second);
|
|---|
| 507 |
|
|---|
| 508 | if (verbose>1)
|
|---|
| 509 | cout << " (" << name << ")";
|
|---|
| 510 |
|
|---|
| 511 | string sqltype = it->second.second;
|
|---|
| 512 |
|
|---|
| 513 | for (auto m=sqltypes.cbegin(); m!=sqltypes.cend(); m++)
|
|---|
| 514 | if (m->first==name)
|
|---|
| 515 | sqltype = m->second;
|
|---|
| 516 |
|
|---|
| 517 | if (!vec.empty())
|
|---|
| 518 | query += ",\n";
|
|---|
| 519 |
|
|---|
| 520 | const size_t N = col.type=='A' ? 1 : col.num;
|
|---|
| 521 | for (size_t i=0; i<N; i++)
|
|---|
| 522 | {
|
|---|
| 523 | query += " `"+name;
|
|---|
| 524 | if (N>1)
|
|---|
| 525 | query += "["+to_string(i)+"]";
|
|---|
| 526 | query += "` "+sqltype;
|
|---|
| 527 | if (col.type=='A')
|
|---|
| 528 | query += '('+to_string(col.num)+')';
|
|---|
| 529 | query += " NOT NULL COMMENT '"+ic->first;
|
|---|
| 530 | if (!col.unit.empty())
|
|---|
| 531 | query += "["+col.unit+"]";
|
|---|
| 532 | if (!col.comment.empty())
|
|---|
| 533 | query += ": "+col.comment;
|
|---|
| 534 | query += +"'";
|
|---|
| 535 | if (N>1 && i!=N-1)
|
|---|
| 536 | query += ",\n";
|
|---|
| 537 | }
|
|---|
| 538 |
|
|---|
| 539 | const BasicType_t bt =
|
|---|
| 540 | /*ic.first=="Time" && col.num==1 && col.unit=="MJD" && it->second.first==kDouble ?
|
|---|
| 541 | kMJD :*/ it->second.first;
|
|---|
| 542 |
|
|---|
| 543 | vec.emplace_back(ic->first, name, bt, col.num/*, mjdref*/);
|
|---|
| 544 | vec.back().ptr = f.SetPtrAddress(ic->first);
|
|---|
| 545 | }
|
|---|
| 546 |
|
|---|
| 547 | if (verbose>1)
|
|---|
| 548 | cout << "\n\n";
|
|---|
| 549 | if (verbose>0)
|
|---|
| 550 | {
|
|---|
| 551 | if (nvec>0)
|
|---|
| 552 | cout << nvec << " constant value column(s) configured." << endl;
|
|---|
| 553 | cout << vec.size()-nvec << " FITS columns setup for reading." << endl;
|
|---|
| 554 | }
|
|---|
| 555 |
|
|---|
| 556 | // -------------------------------------------------------------------------
|
|---|
| 557 | // Checking for database connection
|
|---|
| 558 | if (verbose>0)
|
|---|
| 559 | cout << "\n---------------------- Connecting database -------------------------" << endl;
|
|---|
| 560 |
|
|---|
| 561 | if (verbose>0)
|
|---|
| 562 | {
|
|---|
| 563 | cout << "Connecting to database...\n";
|
|---|
| 564 | cout << "Client Version: " << mysqlpp::Connection().client_version() << endl;
|
|---|
| 565 | }
|
|---|
| 566 |
|
|---|
| 567 | Database connection(uri); // Keep alive while fetching rows
|
|---|
| 568 |
|
|---|
| 569 | if (verbose>0)
|
|---|
| 570 | cout << "Server Version: " << connection.server_version() << endl;
|
|---|
| 571 |
|
|---|
| 572 | if (print_connection)
|
|---|
| 573 | {
|
|---|
| 574 | try
|
|---|
| 575 | {
|
|---|
| 576 | const auto &res1 = connection.query("SHOW STATUS LIKE 'Compression'").store();
|
|---|
| 577 | cout << "Compression of databse connection is " << string(res1[0][1]) << endl;
|
|---|
| 578 |
|
|---|
| 579 | const auto &res2 = connection.query("SHOW STATUS LIKE 'Ssl_cipher'").store();
|
|---|
| 580 | cout << "Connection to databases is " << (string(res2[0][1]).empty()?"UNENCRYPTED":"ENCRYPTED ("+string(res2[0][1])+")") << endl;
|
|---|
| 581 | }
|
|---|
| 582 | catch (const exception &e)
|
|---|
| 583 | {
|
|---|
| 584 | cerr << "\nSHOW STATUS LIKE COMPRESSION\n\n";
|
|---|
| 585 | cerr << "SQL query failed:\n" << e.what() << endl;
|
|---|
| 586 | return 4;
|
|---|
| 587 | }
|
|---|
| 588 | }
|
|---|
| 589 |
|
|---|
| 590 | // -------------------------------------------------------------------------
|
|---|
| 591 |
|
|---|
| 592 | if (verbose>0)
|
|---|
| 593 | cout << "\n--------------------------- Database Table -------------------------" << endl;
|
|---|
| 594 |
|
|---|
| 595 | if (!primary.empty())
|
|---|
| 596 | query += ",\n PRIMARY KEY USING BTREE (`"+boost::algorithm::join(primary, "`, `")+"`)";
|
|---|
| 597 |
|
|---|
| 598 | if (!vindex.empty() && (index || unique))
|
|---|
| 599 | query += ",\n "+string(unique?"UNIQUE ":"")+"INDEX USING BTREE (`"+boost::algorithm::join(vindex, "`, `")+"`)";
|
|---|
| 600 |
|
|---|
| 601 | query +=
|
|---|
| 602 | "\n)\n"
|
|---|
| 603 | "DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci\n";
|
|---|
| 604 | if (!engine.empty())
|
|---|
| 605 | query += "ENGINE="+engine+"\n";
|
|---|
| 606 | if (!row_format.empty())
|
|---|
| 607 | query += "ROW_FORMAT="+row_format+"\n";
|
|---|
| 608 | query += "COMMENT='created by "+fs::path(conf.GetName()).filename().string()+"'\n";
|
|---|
| 609 |
|
|---|
| 610 |
|
|---|
| 611 | // FIXME: Can we omit the catching to be able to print the
|
|---|
| 612 | // query 'autmatically'?
|
|---|
| 613 | try
|
|---|
| 614 | {
|
|---|
| 615 | if (drop)
|
|---|
| 616 | {
|
|---|
| 617 | // => Simple result
|
|---|
| 618 | if (!dry_run)
|
|---|
| 619 | connection.query("DROP TABLE `"+table+"`").execute();
|
|---|
| 620 | if (verbose>0)
|
|---|
| 621 | cout << "Table `" << table << "` dropped." << endl;
|
|---|
| 622 | }
|
|---|
| 623 | }
|
|---|
| 624 | catch (const exception &e)
|
|---|
| 625 | {
|
|---|
| 626 | cerr << "DROP TABLE `" << table << "`\n\n";
|
|---|
| 627 | cerr << "SQL query failed:\n" << e.what() << '\n' << endl;
|
|---|
| 628 | return 5;
|
|---|
| 629 | }
|
|---|
| 630 |
|
|---|
| 631 | try
|
|---|
| 632 | {
|
|---|
| 633 | if (create && !dry_run)
|
|---|
| 634 | connection.query(query).execute();
|
|---|
| 635 | }
|
|---|
| 636 | catch (const exception &e)
|
|---|
| 637 | {
|
|---|
| 638 | cerr << query << "\n\n";
|
|---|
| 639 | cerr << "SQL query failed:\n" << e.what() << '\n' << endl;
|
|---|
| 640 | return 6;
|
|---|
| 641 | }
|
|---|
| 642 |
|
|---|
| 643 | if (print_create)
|
|---|
| 644 | cout << query << endl;
|
|---|
| 645 |
|
|---|
| 646 | if (create && verbose>0)
|
|---|
| 647 | cout << "Table `" << table << "` created." << endl;
|
|---|
| 648 |
|
|---|
| 649 |
|
|---|
| 650 | try
|
|---|
| 651 | {
|
|---|
| 652 | if (conditional && !fixed.empty() && !drop)
|
|---|
| 653 | {
|
|---|
| 654 | const mysqlpp::StoreQueryResult res =
|
|---|
| 655 | connection.query("SELECT 1 FROM `"+table+"` WHERE 1"+where+" LIMIT 1").store();
|
|---|
| 656 |
|
|---|
| 657 | if (print_select)
|
|---|
| 658 | cout << "SELECT 1 FROM `"+table+"` WHERE 1" << where << " LIMIT 1" << endl;
|
|---|
| 659 |
|
|---|
| 660 | if (res.num_rows()>0)
|
|---|
| 661 | {
|
|---|
| 662 | if (verbose>0)
|
|---|
| 663 | {
|
|---|
| 664 | cout << "Conditional execution... detected existing rows!\n";
|
|---|
| 665 | cout << "Exit.\n" << endl;
|
|---|
| 666 | }
|
|---|
| 667 | return 0;
|
|---|
| 668 | }
|
|---|
| 669 | }
|
|---|
| 670 | }
|
|---|
| 671 | catch (const exception &e)
|
|---|
| 672 | {
|
|---|
| 673 | cerr << "SELECT 1 FROM `"+table+"` WHERE 1" << where << " LIMIT 1\n\n";
|
|---|
| 674 | cerr << "SQL query failed: " << e.what() << endl;
|
|---|
| 675 | return 7;
|
|---|
| 676 | }
|
|---|
| 677 |
|
|---|
| 678 | try
|
|---|
| 679 | {
|
|---|
| 680 | if (run_delete && !fixed.empty() && !drop && !dry_run)
|
|---|
| 681 | {
|
|---|
| 682 | const mysqlpp::SimpleResult res =
|
|---|
| 683 | connection.query("DELETE FROM `"+table+"` WHERE 1"+where).execute();
|
|---|
| 684 |
|
|---|
| 685 | if (verbose>0)
|
|---|
| 686 | cout << res.rows() << " row(s) deleted.\n" << endl;
|
|---|
| 687 | }
|
|---|
| 688 | }
|
|---|
| 689 | catch (const exception &e)
|
|---|
| 690 | {
|
|---|
| 691 | cerr << "DELETE FROM `" << table << "` WHERE 1" << where << "\n\n";
|
|---|
| 692 | cerr << "SQL query failed: " << e.what() << endl;
|
|---|
| 693 | return 8;
|
|---|
| 694 | }
|
|---|
| 695 |
|
|---|
| 696 | if (print_delete)
|
|---|
| 697 | cout << "DELETE FROM `" << table << "` WHERE 1" << where << endl;
|
|---|
| 698 |
|
|---|
| 699 | // -------------------------------------------------------------------------
|
|---|
| 700 |
|
|---|
| 701 | if (verbose>0)
|
|---|
| 702 | cout << "\n---------------------------- Reading file --------------------------" << endl;
|
|---|
| 703 |
|
|---|
| 704 | //query = update ? "UPDATE" : "INSERT";
|
|---|
| 705 | query = "INSERT ";
|
|---|
| 706 | if (ignore_errors)
|
|---|
| 707 | query += "IGNORE ";
|
|---|
| 708 | query += "`"+table+"`\n"
|
|---|
| 709 | "(\n";
|
|---|
| 710 |
|
|---|
| 711 | for (auto c=vec.cbegin(); c!=vec.cend(); c++)
|
|---|
| 712 | {
|
|---|
| 713 | if (c!=vec.cbegin())
|
|---|
| 714 | query += ",\n";
|
|---|
| 715 |
|
|---|
| 716 | const size_t N = c->type==kVarchar ? 1 : c->num;
|
|---|
| 717 | for (size_t i=0; i<N; i++)
|
|---|
| 718 | {
|
|---|
| 719 | if (N==1)
|
|---|
| 720 | query += " `"+c->column+"`";
|
|---|
| 721 | else
|
|---|
| 722 | query += " `"+c->column+"["+to_string(i)+"]`";
|
|---|
| 723 |
|
|---|
| 724 | if (N>1 && i!=N-1)
|
|---|
| 725 | query += ",\n";
|
|---|
| 726 | }
|
|---|
| 727 | }
|
|---|
| 728 |
|
|---|
| 729 | query +=
|
|---|
| 730 | "\n)\n"
|
|---|
| 731 | "VALUES\n";
|
|---|
| 732 |
|
|---|
| 733 | size_t count = 0;
|
|---|
| 734 |
|
|---|
| 735 | const size_t num = max>first && (max-first)<f.GetNumRows() ? (max-first) : f.GetNumRows();
|
|---|
| 736 | for (size_t j=first; j<num; j++)
|
|---|
| 737 | {
|
|---|
| 738 | f.GetRow(j);
|
|---|
| 739 |
|
|---|
| 740 | if (count>0)
|
|---|
| 741 | query += ",\n";
|
|---|
| 742 |
|
|---|
| 743 | query += "(\n";
|
|---|
| 744 |
|
|---|
| 745 | for (auto c=vec.cbegin(); c!=vec.cend(); c++)
|
|---|
| 746 | {
|
|---|
| 747 | if (c!=vec.cbegin())
|
|---|
| 748 | query += ",\n";
|
|---|
| 749 |
|
|---|
| 750 | const size_t N = c->type==kVarchar ? 1 : c->num;
|
|---|
| 751 | for (size_t i=0; i<N; i++)
|
|---|
| 752 | {
|
|---|
| 753 | if (c->type==kVarchar)
|
|---|
| 754 | query += " '"+c->fmt(i)+"'";
|
|---|
| 755 | else
|
|---|
| 756 | query += " "+c->fmt(i);
|
|---|
| 757 |
|
|---|
| 758 | if (print_insert && i==0)
|
|---|
| 759 | query += " /* "+c->column+" -> "+c->branch+" */";
|
|---|
| 760 |
|
|---|
| 761 | if (N>1 && i!=N-1)
|
|---|
| 762 | query += ",\n";
|
|---|
| 763 | }
|
|---|
| 764 | }
|
|---|
| 765 | query += "\n)";
|
|---|
| 766 |
|
|---|
| 767 | count ++;
|
|---|
| 768 | }
|
|---|
| 769 |
|
|---|
| 770 | if (!duplicate.empty())
|
|---|
| 771 | query += "\nON DUPLICATE KEY UPDATE\n " + boost::join(duplicate, ",\n ");
|
|---|
| 772 |
|
|---|
| 773 | if (verbose>0)
|
|---|
| 774 | cout << count << " out of " << num << " row(s) read from file [N=" << first << ".." << num-1 << "]." << endl;
|
|---|
| 775 |
|
|---|
| 776 | if (count==0)
|
|---|
| 777 | {
|
|---|
| 778 | if (verbose>0)
|
|---|
| 779 | {
|
|---|
| 780 | cout << "Total execution time: " << Time().UnixTime()-start.UnixTime() << "s\n";
|
|---|
| 781 | cout << "Success.\n" << endl;
|
|---|
| 782 | }
|
|---|
| 783 | return 0;
|
|---|
| 784 | }
|
|---|
| 785 |
|
|---|
| 786 | // -------------------------------------------------------------------------
|
|---|
| 787 |
|
|---|
| 788 | if (verbose>0)
|
|---|
| 789 | {
|
|---|
| 790 | cout << "\n--------------------------- Inserting data -------------------------" << endl;
|
|---|
| 791 | cout << "Sending INSERT query (" << query.length() << " bytes)" << endl;
|
|---|
| 792 | }
|
|---|
| 793 |
|
|---|
| 794 | try
|
|---|
| 795 | {
|
|---|
| 796 | if (!noinsert && !dry_run)
|
|---|
| 797 | {
|
|---|
| 798 | auto q = connection.query(query);
|
|---|
| 799 | q.execute();
|
|---|
| 800 | cout << q.info() << '\n' << endl;
|
|---|
| 801 | }
|
|---|
| 802 | else
|
|---|
| 803 | cout << "Insert query skipped!" << endl;
|
|---|
| 804 |
|
|---|
| 805 | if (print_insert)
|
|---|
| 806 | cout << query << endl;
|
|---|
| 807 | }
|
|---|
| 808 | catch (const exception &e)
|
|---|
| 809 | {
|
|---|
| 810 | if (verbose>1 || query.length()<80*25)
|
|---|
| 811 | cerr << query << "\n\n";
|
|---|
| 812 | cerr << "SQL query failed (" << query.length() << " bytes):\n" << e.what() << '\n' << endl;
|
|---|
| 813 | return 9;
|
|---|
| 814 | }
|
|---|
| 815 |
|
|---|
| 816 | if (verbose>0)
|
|---|
| 817 | {
|
|---|
| 818 | const auto sec = Time().UnixTime()-start.UnixTime();
|
|---|
| 819 | cout << "Total execution time: " << sec << "s ";
|
|---|
| 820 | cout << "(" << Tools::Fractional(sec/count) << "s/row)\n";
|
|---|
| 821 |
|
|---|
| 822 | try
|
|---|
| 823 | {
|
|---|
| 824 | const auto resw =
|
|---|
| 825 | connection.query("SHOW WARNINGS").store();
|
|---|
| 826 |
|
|---|
| 827 | for (size_t i=0; i<resw.num_rows(); i++)
|
|---|
| 828 | {
|
|---|
| 829 | const mysqlpp::Row &roww = resw[i];
|
|---|
| 830 |
|
|---|
| 831 | cout << roww["Level"] << '[' << roww["Code"] << "]: ";
|
|---|
| 832 | cout << roww["Message"] << '\n';
|
|---|
| 833 | }
|
|---|
| 834 | cout << endl;
|
|---|
| 835 |
|
|---|
| 836 | }
|
|---|
| 837 | catch (const exception &e)
|
|---|
| 838 | {
|
|---|
| 839 | cerr << "\nSHOW WARNINGS\n\n";
|
|---|
| 840 | cerr << "SQL query failed:\n" << e.what() << '\n' <<endl;
|
|---|
| 841 | return 10;
|
|---|
| 842 | }
|
|---|
| 843 | }
|
|---|
| 844 |
|
|---|
| 845 | if (print_connection)
|
|---|
| 846 | {
|
|---|
| 847 | try
|
|---|
| 848 | {
|
|---|
| 849 | // Exchange _send and _received as it is the view of the server
|
|---|
| 850 | const auto &res1 = connection.query("SHOW STATUS LIKE 'Bytes_%'").store();
|
|---|
| 851 | cout << left << setw(16) << res1[1]["Variable_name"] << ' ' << Tools::Scientific(res1[0]["Value"]) << endl;
|
|---|
| 852 | cout << left << setw(16) << res1[0]["Variable_name"] << ' ' << Tools::Scientific(res1[1]["Value"]) << endl;
|
|---|
| 853 | cout << endl;
|
|---|
| 854 | }
|
|---|
| 855 | catch (const exception &e)
|
|---|
| 856 | {
|
|---|
| 857 | cerr << "\nSHOW STATUS LIKE 'Bytes_%'\n\n";
|
|---|
| 858 | cerr << "SQL query failed:\n" << e.what() << endl;
|
|---|
| 859 | return 11;
|
|---|
| 860 | }
|
|---|
| 861 | }
|
|---|
| 862 |
|
|---|
| 863 | cout << "Success!\n" << endl;
|
|---|
| 864 | return 0;
|
|---|
| 865 | }
|
|---|