App::combinesheets

- NAME
- VERSION
- SYNOPSIS
- DESCRIPTION
  - Duplicated values in the matching columns
- ADVANCED USAGE
  - Calculated columns by external programs
  - Calculated columns by a Perl subroutine
- ARGUMENTS and OPTIONS
- ENVIRONMENT VARIABLES
  - COMBINE_SHEETS_EXT_PATH
- DEPENDENCIES
- KNOWN BUGS, MISSING FEATURES
- SUPPORT
- AUTHOR
- COPYRIGHT AND LICENSE

# NAME

App::combinesheets - command-line tool merging CSV and TSV spreadsheets

# VERSION

version 0.2.12

# SYNOPSIS

       combinesheets -h
       combinesheets -help
       combinesheets -man
       combinesheets -version

       combinesheets -config <config-file> -inputs <input-files> [<options>] [-outfile <output-file>]

          where <input-files> has the form: <input-ID>=<filename> [<input-ID>=<filename>...]
          where <options> are: -check

# DESCRIPTION

combinesheets is a command-line tool merging together two or more spreadsheets. The spreadsheets can be COMMA-separated or TAB-separated files, each of them having the first line with column headers. Data in one of the column (it can be a different column in each input spreadsheet) serve to match lines. For example, having two spreadsheets, PERSON and CAR, with the following contents:

       persons.tsv:

       Surname      First name  Sex  Age  Nickname
       Novak        Jan         M    52   Honza
       Gudernova    Jitka       F    56
       Senger       Martin      M    61   Tulak

       cars.tsv:

       Model  Year  Owned by
       Praga  1936  Someone else
       Mini   1968  Gudernova
       Skoda  2002  Senger

we want to merge these spreadsheet by `Surname` in persons.tsv and by `Owned by` in cars.tsv. There are two possible results, depending which spreadsheet is used as the first one (a primary one). If the persons.tsv is the first, the result will be (which columns are included in the result will be described later in this document):

       combinesheets -cfg config.cfg -in PERSON=persons.tsv CAR=cars.csv

       First name  Surname    Model  Sex  Nickname  Age  Year  Owned by
       Jitka       Gudernova  Mini   F              56   1968  Gudernova
       Jan         Novak             M    Honza     52
       Martin      Senger     Skoda  M    Tulak     61   2002  Senger

Or, if the cars.tsv is the first, the result will be:

       combinesheets -cfg config.cfg -in CAR=cars.csv PERSON=persons.tsv

       First name  Surname    Model  Sex  Nickname  Age  Year  Owned by
       Jitka       Gudernova  Mini   F              56   1968  Gudernova
       Martin      Senger     Skoda  M    Tulak     61   2002  Senger
                              Praga                      1936  Someone else

Of course, if both input spreadsheets have only the matching lines, both results will be the same (it will not matter which one of them is considered the primary one).

The rows in the resulting spreadsheet are sorted by values in the column that was used as a matching column in the primary input.

The information which columns should be used to match the input spreadsheets and which columns should appear in the resulting spreadsheet is read from a configuration file (see the `-config` - or `-cfg` - argument).

The command-line arguments and options can be specified with single or double dash. Most of them can be abbreviated to the nearest non-biased length. They are case-sensitive.

## Duplicated values in the matching columns

If there are repeated (the same) values in the column that serves as matching criterion then the resulting spreadsheet will have as many output lines (for a particular matching value) as is the number of all combinations of the lines with that matching values in all input spreadsheets. For example, let's have `books.tsv` and `authors.tsv`, assuming that a book can have more authors and any author can contribute to any number of books:

       books.tsv:
       Title   Note    Author
       Book 1  from B1-a       Kim
       Book 2  from B2-b       Kim
       Book 3  from B3-c       Katrin
       Book 1  from B1-d       Blanka
       Book 2  from B2-e       Katrin

       authors.tsv:
       Age     Name
       28      Kim
       20      Katrin
       30      Blanka
       50      Lazy author

The output (again, depending on which input is considered a primary input) will be (a list of included column is defined in the configuration file - see later):

       combinesheets -cfg books_to_authors.cfg -in BOOK=books.tsv AUTHOR=authors.tsv

       Name    Title   Age Note
       Blanka  Book 1  30  from B1-d
       Katrin  Book 3  20  from B3-c
       Katrin  Book 2  20  from B2-e
       Kim     Book 1  28  from B1-a
       Kim     Book 2  28  from B2-b

       combinesheets -cfg books_to_authors.cfg -in AUTHOR=authors.tsv BOOK=books.tsv

       Name        Title   Age  Note
       Blanka      Book 1  30   from B1-d
       Katrin      Book 3  20   from B3-c
       Katrin      Book 2  20   from B2-e
       Kim         Book 1  28   from B1-a
       Kim         Book 2  28   from B2-b
       Lazy author         50

# ADVANCED USAGE

Additionally to the merging columns from one or more spreadsheets, this script can also add completely new columns to the resulting spreadsheet, the columns that do not exist in any of the input spreadsheet. Such columns are called `calculated columns`.

Each `calculated column` is created either by an external, command-line driven, program, or by a Perl subroutine. In both cases, the user must create (write) such external program or such Perl subroutine. Therefore, this usage is meant more for developers than for the end users.

Note that this advanced feature is meant only for new columns, not for new rows. Therefore, it cannot be used, for example, to create rows with totals of columns.

## Calculated columns by external programs

If specified, an external program is invoked for each row. It can be specified either by a keyword PROG or by a keyword PROGS - see syntax in the configuration section. In both cases, the value of the standard output of these programs become the value of the calculated column (a trailing newline of this standard output is removed and other newlines are replaced by spaces).

A program defined by the PROGS is called without any arguments (`S` in PROGS stands for a Simple). That's why it does not have any knowledge for which row it has been invoked. Its usage is, therefore, for column values that are not dependent on other values from the spreadsheet. For example, for the `cars.tsv` shown above, you can add a column `Last updated` by calling a UNIX program `date` - again, see an example the configuration section.

A program defined by the PROG is called with one argument which is a filename. This file contains the current row; each of its lines has two, TAB-separated, fields. The first field is the column name and the second field is the column value. For example, when processing the last row of the `cars.tsv` given above, the file will have the following content:

       Model       Skoda
       Year        2002
       Owned by    Senger

The files are only temporary and will be removed when `combinesheets` finishes.

## Calculated columns by a Perl subroutine

If specified by the keyword PERL, a Perl subroutine is called for each row with the three arguments:

1. A hashref with information about the current column. Not often used but may be handy if the same subroutine deals with more columns and, therefore, needs to know for which column it was invoked. See the flights example in the configuration section.
2. An arrayref with all column names.
3. An arrayref with all column values - in the same order as the column names.

Actually, depending how the subroutine is defined in the configuration, it may get as the first argument the module/class name where it belongs to. If you define it like this:

       PERL   Module::Example::test

the `test` subroutine is called, indeed, with the three arguments as described above. However, if your definition is rather:

       PERL   Module::Example->test

then the `test` subroutine is considered a Perl method and its first argument is the module/class name. It is up to you to decide how you want/need to write your functions. Again, an example is available in the configuration section.

The return value of the subroutine will become a new value in the calculated column. Do not return undef but rather an empty string if the value cannot be created.

What is an advantage of writing my own module/package if I can simply write an external program (perhaps also in Perl) doing exactly the same? The Perl module stays in the memory for the whole time of processing all input rows and, therefore, you can re-use some calculations done for the previous rows. An example about it (`flights`) is given in the configuration section.

# ARGUMENTS and OPTIONS

-config <config-file>

  A filename with a configuration file. This is a mandatory parameter. The configuration file describes:

  - which columns in individual input spreadsheets should be included in the resulting spreadsheet,
  - what names should be given to the resulting columns
  - in which order should be the columns in the resulting spreadsheet
  - which columns should be used to match individual lines,

  The configuration file is a TAB-separated file (with no header line). Empty lines and lines starting with a "#" character are ignored. Each line has two columns, in some cases there is an optional third column. Here is a configuration file used in the example above:

         # Columns to match records from individual inputs
         MATCH   PERSON=Surname
         MATCH   CAR=Owned by
         MATCH   CHILD=Parent

         # Columns - how they be in rows
         PERSON  First name
         PERSON  Surname
         CAR     Model
         PERSON  Sex
         CHILD   Name
         CHILD   Born
         PERSON  Nickname
         PERSON  Age
         CAR     Year
         CAR     Owned by

  The first column is either a reserved word `MATCH`, or an identifier of an input spreadsheet. There are also few other reserved words - see more about them a bit later.

  The identifier can be almost anything (and it does not appear in the input spreadsheet itself). It is also used in the command-line argument `-inputs` where it corresponds to a real file name of the input. The lines with identifiers define what columns will be in the result: the second column is the header of the wanted columns and an optional third column (not used in the example above) is the header used in the result. The resulting columns will be in the same order as are these lines in the configuration file.

  The reserved word `MATCH` is used to define how to match lines in the input spreadsheets. The format of its second column is:

         <input-ID>=<column-header>

  There should be one MATCH line for each input spreadsheet. The data in the column defined by the "column-header" will be used to find the corresponding lines. In our example, the data in the column Surname in the `persons.tsv` will be matched with the data in the column Owned by in the `cars.tsv` (the rows having the same values in these two columns will be merged into one resulting row).

  Advanced configuration

  If you want to add so-called calculated columns as described in the "ADVANCED USAGE" you need to use few additional reserved words in the configuration file. These words are PROG, PROGS and/or PERL. They are used in the place where the new calculated column should be placed. Their lines have the program name or the Perl subroutine name in the second column, and they have mandatory third column with the resulting name of the calculated column.

  For example, we wish to add two columns to the input spreadsheet `cars.tsv`. The input file (the same as in the introduction) is:

         Model  Year  Owned by
         Praga  1936  Someone else
         Mini   1968  Gudernova
         Skoda  2002  Senger

  We wish to add a column Car age that shows the difference between the actual year and the value from the Year column. We have a shell script `age.sh` doing it:

         #!/bin/bash
         YEAR=`grep Year $1 | cut -f2`
         NOW=`date +%Y`
         echo $(($NOW-$YEAR))

  The configuration file `cars.cfg` (assuming that we want the other columns to remain the same) is:

         MATCH   CAR=Owned by

         CAR     Owned by
         CAR     Model
         CAR     Year
         PROG    age.sh  Car age

  When we run:

         combinesheets -config cars.cfg -inputs CAR=cars.tsv

  we get this result:

         Owned by        Model   Year    Car age
         Gudernova       Mini    1968    44
         Senger          Skoda   2002    10
         Someone else    Praga   1936    76

  You can see that there is no need to use `combinesheets` for really combining more sheets, an input can be just one sheet.

  Another example adds a fixed column to the same input, a column named Last updated that gets its value from a UNIX command `date`. This program does not get any information which row it has been invoked for. The configuration file is now (note the new line with the PROGS):

         MATCH   CAR=Owned by

         CAR     Owned by
         CAR     Model
         CAR     Year
         PROG    age.sh  Car age
         PROGS   date    Last updated

  and the result is now:

         Owned by        Model   Year    Car age   Last updated
         Gudernova       Mini    1968    44        Mon Feb 27 12:32:04 AST 2012
         Senger          Skoda   2002    10        Mon Feb 27 12:32:04 AST 2012
         Someone else    Praga   1936    76        Mon Feb 27 12:32:04 AST 2012

  The last possibility is to call a Perl subroutine - using the reserved word PERL in the configuration file. Let's have an input spreadsheet (`flights.tsv`) with data about flights:

         Date         Flight    Airport From      Airport To
         2009-01-18   AY838     London LHR        Helsinki Vantaa
         2009-01-22   AY839     Helsinki Vantaa   London LHR
         2009-03-15   NW2       Manila            Tokyo Narita
         2009-03-21   NW1       Tokyo Narita      Manila
         2011-05-06   SV326     Sharm El Sheik    Jeddah
         2011-07-31   RJ700     Amman             Jeddah
         2011-09-21   ME369     Jeddah            Beirut
         2011-09-24   ME368     Beirut            Jeddah
         2011-12-02   EZY3064   Prague            London Stansted
         2011-12-09   EZY3067   London Stansted   Prague
         2012-01-26   MS663     Cairo             Jeddah

  We want to add columns with the international airport codes for both Airport From and Airport To. The new columns will be named Code From and Code To. The Perl subroutine will use a web service to find the code. The subroutine will use a closure that will remember already fetched codes so the web service does not need to be called several times for the same airport name.

  The configuration file `flights.cfg` is:

         MATCH   FLY=Date

         FLY     Date
         FLY     Flight
         FLY     Airport From
         PERL    Airport->find_code      Code From
         FLY     Airport To
         PERL    Airport->find_code      Code To

  The name of the subroutine is attached to the module where it comes from by either :: or -> notation.

  The invocation is:

         combinesheets -config flights.cfg -inputs FLY=flights.tsv

  The full code for the module `Airport`, the file `Airport.pm` is here:

         package Airport;
         use warnings;
         use strict;

         use LWP::Simple;
         use JSON;

         # preparing a closure in order not to fetch the same airport code again and again
         my $already_found = make_already_found();
         sub make_already_found {
            my $already_found = {};
            return sub {
               my ($airport_name, $airport_code) = @_;
               if (exists $already_found->{$airport_name}) {
                  if ($airport_code) {
                      $already_found->{$airport_name} = $airport_code;
                  }
                  return $already_found->{$airport_name};
               } else {
                  $already_found->{$airport_name} = ($airport_code ? $airport_code : 1);
                  return 0;
               }
            }
         }

         sub find_code {
            my ($class, $column, $header_line, $data_line) = @_;

            my $column_with_airport_name = $column->{ocol};
            $column_with_airport_name =~ s{Code}{Airport};

            my $airport_name;
            for (my $i = 0; $i < @$header_line; $i++) {
               if ($header_line->[$i] eq $column_with_airport_name) {
                  $airport_name = $data_line->[$i];
                  last;
               }
            }
            return '' unless $airport_name;

            # now we have an airport name...
            my $airport_code = $already_found->($airport_name);
            return $airport_code if $airport_code;

            #... go and find its airport code
            $airport_code = '';
            my $escaped_airport_name = $airport_name;
            $escaped_airport_name =~ tr{ }{+};
            my $url = "http://airportcode.riobard.com/search?q=$escaped_airport_name&fmt=json";
            my $content = get ($url);
            warn "Cannot get a response for '$url'\n"
               unless defined $content;
            my $json = JSON->new->allow_nonref;
            my $data = $json->decode ($content);
            foreach my $code (@$data) {
               $airport_code .= $code->{code} . ",";
            }
            chop ($airport_code) if $airport_code;  # removing the trailing comma

            $already_found->($airport_name, $airport_code);
            return $airport_code;
         }
         1;

  When run it creates the following output. Note that some airports have more than one code because the name was ambiguous. Well, this is just an example, isn't it?

         Date         Flight    Airport From      Code From   Airport To       Code To
         2009-01-18   AY838     London LHR        LHR         Helsinki Vantaa  HEL
         2009-01-22   AY839     Helsinki Vantaa   HEL         London LHR       LHR
         2009-03-15   NW2       Manila            MXA,MNL     Tokyo Narita     NRT
         2009-03-21   NW1       Tokyo Narita      NRT         Manila           MXA,MNL
         2011-05-06   SV326     Sharm El Sheik    SSH         Jeddah           JED
         2011-07-31   RJ700     Amman             ADJ,AMM     Jeddah           JED
         2011-09-21   ME369     Jeddah            JED         Beirut           BEY
         2011-09-24   ME368     Beirut            BEY         Jeddah           JED
         2011-12-02   EZY3064   Prague            PRG         London Stansted  STN
         2011-12-09   EZY3067   London Stansted   STN         Prague           PRG
         2012-01-26   MS663     Cairo             CAI,CIR     Jeddah           JED

-inputs <input_ID=<filename> [<input_ID>=<filename>...]>

  Each `-inputs` can have one or more file names, and there can be one or more `-inputs` arguments. It defines what are the input spreadsheets and how they are identified in the configuration file (see the `-config` argument). For example, the inputs for our example above can be specified in any of these ways:

         -inputs PERSON=persons.tsv -inputs CAR=cars.tsv
         -inputs PERSON=persons.tsv CAR=cars.tsv
         -inputs PERSON=persons.tsv,CAR=cars.tsv

  The first file name is considered to be the `primary` input (see the description above): the resulting spreadsheet will have the same number of lines as the primary input.

  The file names ending with the `.csv` are considered to be in the COMMA-separated formats, all others are considered to be TAB-separated.

  This is a mandatory parameter.

-outfile <output-file>

  An optional parameter specifying a filename of the combined result. By default, it is created on STDOUT. It is always in the TAB-separated format.

-check

  This option causes that the configuration file and the input files (only their header lines will be read) will be checked for errors but no resulting spreadsheet will be created.

-ignorecases

  Not yet implemented.

General options
  -h

    Print a brief usage message and exits.

  -help

    Print a brief usage message with options and exit.

  -man

    Print a full usage message and exit.

  -version

    Print the version and exit.

# ENVIRONMENT VARIABLES

### COMBINE_SHEETS_EXT_PATH

It contains a path that is used when looking for external programs (when the reserved words PROG or PROGS are used). For example, the `examples` directory in the source distribution of this package has an external program `age.sh`. The full invocation can be done by:

       COMBINE_SHEETS_EXT_PATH=examples bin/combinesheets -cfg examples/cars.cfg --inputs CAR=examples/cars.csv

# DEPENDENCIES

In order to run this tool you need Perl and the following Perl modules to be installed:

       App::Cmd::Simple
       Text::CSV::Simple
       Text::CSV_XS
       File::BOM
       Getopt::Long::Descriptive
       Pod::Usage
       Algorithm::Loops

Optionally (if your configuration file uses the reserved word PROG or PROGS for calculated columns):

       IO::CaptureOutput

# KNOWN BUGS, MISSING FEATURES

- Columns are identified by their header names. There is no way to identify them simply by their order (column number).
- The input spreadsheet are read first into memory. Which may be a problem with really huge spreadsheets.
- The inputs can be COMMA-separated or TAB-separated. It would be perhaps nice to allow also the Excel spreadsheets.
- Comparing header names and rows is case-sensitive only. There is a plan to implement the option `-ignorecases`,

Some of these missing features may be implemented later.

# SUPPORT

You can find documentation for this module with the perldoc command.

        perldoc App::combinesheets

You can also look for information at:

- RT: CPAN's request tracker

  http://rt.cpan.org/NoAuth/Bugs.html?Dist=App-combinesheets

- AnnoCPAN: Annotated CPAN documentation

  http://annocpan.org/dist/App-combinesheets

- CPAN Ratings

  http://cpanratings.perl.org/d/App-combinesheets

- Search CPAN

  http://search.cpan.org/dist/App-combinesheets/

# AUTHOR

Martin Senger <martin.senger@gmail.com>

# COPYRIGHT AND LICENSE

This software is copyright (c) 2012 by Martin Senger, CBRC - KAUST (Computational Biology Research Center - King Abdullah University of Science and Technology) All Rights Reserved..

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.