BioLockJ API#
BioLockJ comes with an API.
For the most up-to-date information about how to use the API, see the help menu:
biolockj-api help
BioLockJ API v1.4.2 - UNCC Fodor Lab
Usage:
(bash)
biolockj-api <query> [options...]
(java)
java -cp /path/to/BioLockJ.jar biolockj.api.BioLockJ_API <query> [options...]
For some uses, redirecting stderr is recommended:
biolockj-api <query> [options...] 2> /dev/null
Options shown in [ ] are optional for a given query.
Use biolockj-api without args to get help menu.
Options:
--external-modules <dir>
path to a directory containing additional modules
--module <module_path>
class path for a specific module
--property <property>
a specific property
--value <value>
a vlue to use for a specific property
--config <file>
file path for a configuration file giving one or more property values
--verbose true
flag indicating that all messages should go to standard err, including some that are typically disabled.
query:
last-pipeline
Returns the path to the most recent pipeline.
listModules [ --external-modules <dir> ]
Returns a list of classpaths to the classes that extend BioModule.
listApiModules [--external-modules <dir> ]
Like listModules but limit list to modules that implement the ApiModule interface.
listProps [ --module <module_path> ]
Returns a list of properties.
If no args, it returns the list of properties used by the BioLockJ backbone.
If a modules is given, then it returns a list of all properties used by
that module.
listAllProps [ --external-modules <dir> ]
Returns a list of all properties, include all backbone properties and all module properties.
Optionally supply the path to a directory containing additional modules to include their properties.
propType --property <property> [ --module <module_path> [ --external-modules <dir> ] ]
Returns the type expected for the property: String, list, integer, positive number, etc.
If a module is supplied, then the modules propType method is used.
describeProp --property <property> [ --module <module_path> [ --external-modules <dir> ] ]
Returns a description of the property.
If a module is supplied, then the modules getDescription method is used.
propValue --property <property> [ --config <file> ] [ --module <module_path> ]
Returns the value for that property given that config file (optional) or
no config file (ie the default value)
isValidProp --property <property> --value <value> [ --module <module_path> [--external-modules <dir>] ]
T/F/NA. Returns true if the value (val) for the property (prop) is valid;
false if prop is a property but val is not a valid value,
and NA if prop is not a recognized property.
IF a module is supplied, then additionally call the validateProp(key, value)
for that module, or for EACH module if a comma-separated list is given.
propInfo
Returns a json formatted list of the general properties (listProps)
with the type, descrption and default for each property
moduleInfo [--external-modules <dir>]
Returns a json formatted list of all modules and for each module that
implements the ApiModule interface, it lists the props used by the module,
and for each prop the type, descrption and default.
listMounts --config <file>
Returns a list of directories that would need to be mounted in order for
the files listed in the config file to be available to a pipeline running in docker.
listUploads --config <file>
Returns a list of file and directories that would need to be uploaded in order for
the files listed in the config file to be available to a pipeline running in the cloud.
help (or no args)
Print help menu.
listModules and listApiModules are nearly identical. The methods that allow the API to interface with modules are in the ApiModule interface, not all BioModules implement that interface. Once all of the build-in modules have those methods, then these two functions will be identical; the BioModule interface will absorb the ApiModule interface, and listApiModules will be depricated.
listAllProps is the union of all possible output from listProps.
propInfo returns information equivelent to calling biolockj_api listProps and creating a for-loop to call biolockj_api propType $PROP, biolockj_api describeProp $PROP and biolockj_api propValue $PROP for each PROP in the list.
moduleInfo returns information equivelent to calling biolockj_api listModules and creating a for-loop to call biolockj_api listProps $MODULE and for each of its properties.