BatchKi Reference Manual

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Command Line Interface

The examples in this section are based on the Microsoft Windows command line interpreter. The examples assume that the BatchKi executable file batchki.exe is installed in the directory J:/batchki. With trivial modifications, the examples given here are applicable to other operating systems, and to other installations of the web server.

Typing batchki.exe on the command line displays the following usage banner:

J:\batchki>batchki.exe
BatchKi ver. 4.07.015 [07/23/2004]
Copyright (c) 1999-2004 BioKin Ltd.  All rights reserved.

Usage:

BatchKi F .................... process single file
BatchKi F web P S ............ server run
BatchKi F web P S O .......... output to arbitrary directory
BatchKi F web P S O I ........ input arbitrary control file

F = data file name
P = relative path (usually `.')
S = data file signature
O = arbitrary output directory name
I = arbitrary control (settings) file name

Accordingly, there are four ways to execute the BatchKi numerical engine from the command line (or from within other programs, such as the CGI interface).

Default initialization file

According to this method, the command line contains a single parameter representing the file name to be processed.

batchki.exe <filename>

The <filename> stands for a BatchKi data file as described in Chapter 5.

Example 1

J:\>batchki.exe ./input/JDOE-data.xml

In this example, several things are implicitly assumed with regard to the location of files and directories.

• The initialization file settings.ini is located in the default directory ./system/BatchKi, where `.' stands for the directory in which the executable file batchki.exe itself is installed.
• There exist output directories named ./output/p0001, ./output/p0002, etc., depending on the number of plate-reader files being processed simultaneously.
• The main output file is named ./output/index.html.

Thus, the presumed layout of files and directories corresponding to Example 1 is shown in Figure 3.1.

Figure 3.1: File and directory layout for command line Example 1

Specified initialization file

Using this method, the command line has the following syntax:

batchki.exe <filename> web <path> <signature>

As before, the <filename> parameter is the relative path to the XML datafile. The second parameter (web) signals to the BatchKi numerical engine not to use the default initialization file ./system/BatchKi/settings.ini. Instead, the software is instructed to look for a specific initialization file named <signature>settings.ini, located in the directory ./input. In this version of BatchKi, the <path> command-line parameter should always be simply the period (``.''), representing ``current directory''.

Example 2

J:\>batchki.exe ./input/JDOE-data.xml web . JDOE-

In this example, the following assumptions are made with regard to the location of files and directories:

• The initialization file is assumed to be named JDOE-1234-settings.ini, where the JDOE-1234- is the fourth command line parameter (<signature> above).
• The initialization file is assumed to be located in the same directory where the data file is also located, in this case the directory ./input.
• As before in Example 1, The output directories are ./output/p0001, ./output/p0002, etc., depending on the number of plate-reader files being processed simultaneously.
• The main output file is named JDOE-1234-index.html.

The layout of files and directories assumed in Example 2 is summarized in Figure 3.2.

Figure 3.2: File and directory layout for command line Example 2

Specified output directory

Using this method, the command line has the following syntax:

batchki.exe <filename> web <path> <signature> <output_directory>

The fifth command line parameter in this syntax allows redirection of the output files into an arbitrary output directory (for example, in the ``HTML'' tree of the server's file system, as opposed to the ``CGI-BIN'' tree). In fact, this is how BatchKi is deployed in the distributed installation package.

Example 3

J:\>batchki.exe ./input/JDOE-data.xml web . JDOE- ../results

In this example, the implicitly assumed location of files and directories is shown in Figure 3.3. Please note the location the arbitrary output directory results, relative to the main installation directory.

Figure 3.3: File and directory layout for command line Example 3

Specified output directory and initialization file

The final example of command line syntax for the BatchKi numerical engine involves six command line parameters. The last command line parameter represents a fully qualified path name for an arbitrary initialization file. In contrast to Example 2 above, the initialization file is no longer assumed to be present in the same directory as the data file, and it can have an arbitrary name, rather than being tied to the signature parameter.

Example 4

J:\>batchki.exe ./input/JDOE-1-data.xml web . JDOE-1- ../results ./input/TEST.ini
J:\>batchki.exe ./input/JDOE-2-data.xml web . JDOE-2- ../results ./input/TEST.ini
J:\>batchki.exe ./input/JDOE-3-data.xml web . JDOE-3- ../results ./input/TEST.ini

The layout of files and directories assumed in Example 4 is shown in Figure 3.4. This particular command line syntax allows to perform the analysis of many BatchKi formatted input files at once, while all analyses utilize a single initialization file (in this example TEST.ini). We have used this syntax for massive data review sessions, involving tens of thousands of inhibitors and thousands of plate-reader output files.

Figure 3.4: File and directory layout for command line Example 4

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Petr Kuzmic | Jul 12 2008