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BioNetDB implements the bionetdb.sh command line with the following syntaxis:
bionetdb.sh [-h|--help] [--version] <command> [options]
In this section you will learn how to use the command lines, some examples are provided using bionetdb.sh command line.
BasicCommand Line Conventions
command line conventions
BioNetDB follows the most standard conventions when implementing command lines, the most relevant ones are:
- single-character parameters start with only one hyphen symbol and can be either lower-case or upper-case, e.g. -h to print the help or -S to provide session id; while multi-character parameters start with two hyphens and are always lower-case, e.g. --help to print the help or --name to provide a name.
- in the Usage the optional parameters are written always between [ square brackets ], in the following example help, version and option are not mandatory:
./opencga.sh [-h|--help] [--version] <command> [options]
- in the Usage the mandatory parameters are written between symbols < and >, like <command> in the previous example.
Executing the top level command line
You can execute the command line without any argument to get the usage help (you can also provide -h parameter):
Program: BioNetDB (OpenCB) Version: 1.0.0 Description: BioNetDB implements a storage engine to work with biological networks using Neo4j, a NoQSL Graph database Usage: bionetdb.sh [-h|--help] [--version] <command> [options] Commands: import Import the built data models in format CSV files into the database query Query and fetch data from BioNetDB database using this command line
Executing a specific command
When one command is executed without any other argument a specific help is shown, this specific help shows a brief description and the different options available with a brief description, as you can see in the following example:
Usage: bionetdb.sh import [options] Options: --create-csv-files Create the CSV files from the input biological files [false] create-csv-files parameter, it contains the biological files to convert to CSV files) [null] * -i, --input STRING Input directory where the CSV files are located (when used with -- -o, --output STRING Output directory where to save the CSV files to import (used with the - -create-csv-files parameter) [null] -L, --log-level STRING Set the logging level, accepted values are: debug, info, warn, error and fatal [info] -C, --conf STRING BioNetDB configuration.json file. [null] -h, --help Display this help and exit
Some of these options are available for most of the commands, these are:
-C, --conf: If not defined, the command line will assume that the configuration folder can be found in the parent folder where the executable is found (../conf). If that is not the case or if the user wants to use other configuration files available in a different path, the path should be provided.
-h, --help: Shows the help with the list of options. Generally this is not necessary because there is almost always a mandatory parameter to be provided, although it is needed in a few cases if user wants to see the options.
--log-file: By default, all the logs generated by the command lines are printed in the screen. However, the user might want to redirect the logs to another file. For those cases, the user will need to provide the file where the logs will be stored.
-L, --log-level: There are 5 different log levels: 'error', 'warn', 'info', 'debug', 'trace'
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