In this section all commands are listed (in alphabetical order) and described. By just typing bis (or bis.sh for Linux and MacOS) all commands are listed.

The following options are applicable for all commands and therefore not mentioned in the descriptions of the commands below:

To have an overview of all command line options, have a look on this page.

Browsing commands

get-control-layout-info

Description: Shows the code of the material of type CONTROL for each well (specified in the format <row letter><two colum digits>) of the control layout.

Usage:

prompt> bis get-control-layout-info [--pretty-print] <control layout code>

Options:

Parameter:

get-control-layout-type-info

Description: Lists the property types assigned to control layouts.

Usage:

prompt> bis get-control-layout-type-info [--pretty-print]

Options:

get-experiment-attachment

Description: Downloads a specified file which has been attached to a specified experiment by the command add-experiment-attachment.

Usage:

prompt> bis get-experiment-attachment [-v <version number>] <project code> <experiment code> <file name>

Options:

Parameter:

get-experiment-info

Description: Gets basic information about a specified experiments.

Usage:

prompt> bis get-experiment-info [--pretty-print] <project code> <experiment code>

Other detailed information about the experiment can be obtained by commands:

Options:

Parameter:

get-experiment-type-info

Description: Lists the property types assigned to a specified experiment type.

Usage:

prompt> bis get-experiment-type-info [--pretty-print] <experiment type code>

Options:

Parameter:

get-material-type-info

Description: Lists the property types assigned to a specified material type.

Usage:

prompt> bis get-material-type-info [--pretty-print] <material type code>

Options:

Parameter:

get-plate-info

Description: Gets detailed information about a plate.

Usage:

prompt> bis get-plate-info [-b] [--pretty-print] <plate code>

Options:

get-plate-locations

Description: Lists for a specified gene its locations in all plates for all valid experiments. The set of experiments can be restricted by various options.

Usage:

prompt> bis get-plate-locations [-a] [-p <project code>] [-e <experiment code>] [-i] [-o <study object code>] [-t [<from>]:[<until>]] <gene-symbol or id>

Options:

Parameter:

get-plate-type-info

Description: Lists the property types assigned to a specified plate type.

Usage:

prompt> bis get-plate-type-info [--pretty-print] <sample type code>

Options:

Parameter:

get-vocabulary-info

Description: Lists all terms in a given controlled vocabulary set. To see available vocabulary sets, use list-vocabularies command.

Usage:

prompt> bis get-vocabulary-info [--pretty-print] <vocabulary-code>

Options:

Parameter:

list-contacts

Description: Lists all persons who used the system.

Usage:

prompt> bis list-contacts [--pretty-print]

Options:

Parameter: No parameters.

list-experiment-attachments

Description: Prints information about all the documents attached to a specified experiment.
Additionally basic information about the experiment (as in get-experiment-info) are listed.

Usage:

prompt> bis list-experiment-attachments [--pretty-print] <project code> <experiment code>

Other detailed information about the experiment can be obtained by commands:

Options:

Parameter:

list-experiment-datasets

Description: Prints information about all datasets produced in a specified experiment.
Additionally basic information about the experiment (as in get-experiment-info) are listed.

Usage:

prompt> bis list-experiment-datasets [--pretty-print] <project code> <experiment code>

Other detailed information about the experiment can be obtained by commands:

Options:

Parameter:

list-experiment-plates

Description: Prints information about all plates that are connected with a specified experiment.
Additionally basic information about the experiment (as in get-experiment-info) are listed.

Usage:

prompt> bis list-experiment-plates [--pretty-print] <project code> <experiment code>

Other detailed information about the experiment can be obtained by commands:

Options:

Parameter:

list-experiment-property-types

Description: Lists all property types for experiment and also show the assignment, which property type is used for which assignment and if the property type is mandatory.

Usage:

prompt> bis list-experiment-property-types [--pretty-print]

If you want to see the other assignent:

Options:

Parameter: No parameters.

list-experiment-types

Description: Lists all experiment types.

Usage:

prompt> bis list-experiment-types [--pretty-print]

Options:

Parameter: No parameters.

list-experiments

Description: Lists all valid experiments. The set of experiments can be restricted by various options.

Usage:

prompt> bis list-experiments [-a] [--pretty-print] [-p <project code>] [-o <study object code>] [-t [<from>]:[<until>]] <experiment type code>

Options:

Parameter: <experiment type code>: Code of the experiment type. The command list-experiment-types lists all available values.

list-material-property-types

Description: Lists all property types for material and also show the assignment, which property type is used for which assignment and if the property type is mandatory.

Usage:

prompt> bis list-material-property-types [--pretty-print]

If you want to see the other assigment:

Options:

Parameter: No parameters.

list-material-types

Description: Lists all material types.

Usage:

prompt> bis list-material-types [--pretty-print]

Options:

Parameter: No parameters.

list-materials

Description: Lists all materials of a specified type.

Usage:

prompt> bis list-materials [-b] [--pretty-print] [-l <number of lines>] <material type code> ["<pattern>" ...]

Options:

Parameter:

list-plate-types

Description: Lists all plate types.

Usage:

prompt> bis list-plate-types [--pretty-print]

Options:

Parameter: No parameters.

list-plates

Description: Lists all plates of a specified type. Various command line options may restrict or expand the list.

Usage:

prompt> bis list-plates [-a] [-b] [--pretty-print] [-l <number of lines>] [-n] <plate type code> ["<pattern>" ...]

Options:

Parameter: <plate type code>: Code of the plate type. The command list-plate-types lists all available values.

list-processing-instructions

Description: Prints information about all processing instructions in a specified experiment.
Additionally basic information about the experiment (as in get-experiment-info) are listed.

Usage:

prompt> bis list-processing-instructions <project code> <experiment code>

Other detailed information about the experiment can be obtained by commands:

Options:

Parameter:

list-projects

Description: Lists all projects.

Usage:

prompt> bis list-project [--pretty-print]

Options:

Parameter: No parameters.

list-property-types

Description: Lists all property types.

Usage:

prompt> bis list-property-types [--pretty-print]

Options:

Parameter: No parameters.

list-plate-property-types

Description: Lists all property types for plate and also show the assignment, which property type is used for which assignment and if the property type is mandatory.

Usage:

prompt> bis list-plate-property-types [--pretty-print]

If you want to see the other assignment:

Options:

Parameter: No parameters.

list-control-layout-property-types

Description: Lists all property types for control layout and also show the assignment, which property type is used for which assignment and if the property type is mandatory.

Usage:

prompt> bis list-control-layout-property-types [--pretty-print]

If you want to see the other assignment:

Options:

Parameter: No parameters.

list-control-layouts

Description: Lists all control layouts.

Usage:

prompt> bis list-control-layouts [--pretty-print]

Options:

Parameter: No parameters.

list-vocabularies

Description: Lists all available vocabularies. A vocabulary is a collection of terms. This set can be used as a data type for a property type.
To see terms available in a given vocabulary set, use get-vocabulary-info command.

Usage:

prompt> bis list-vocabularies [--pretty-print]

Options:

Parameter: No parameters.

login

Description: Authenticates the specified user and establishes a connection to the openBIS server. A connection will be automatically closed after some idle time.

An authenticated user has a role which may restrict the set of commands he or she is allowed to execute.

Usage:

prompt> bis login [-u <login name>] [-p <password>]

Options:

Blank option value (uniquely composed of whitespace, empty ("")) are considered by the system as not provided and will throw an error.

Parameter: No parameters.

logout

Description: Closes the connection to the openBIS server.

Usage:

prompt> bis logout

Options: No additional options.

Parameter: No parameters.

Commands for Users and Administrators

add-experiment-attachment

Description: Uploads and attaches an arbitrary file to a specified experiment. The file name is used to identify the attachment and to download it with command get-experiment-attachment.

A new version can be uploaded by this command. All versions are available for downloading.

Usage:

prompt> bis add-experiment-attachment <project code> <experiment code> <file path>

Options: no additional options.

Parameter:

register-cell-plates

Description: Registers all cell plates specified in a file. For each cell plate a corresponding dilution plate has to be specified.

Usage:

prompt> bis register-cell-plates [-c <control layout code>] <cell plate file>

Options:

Parameter:

register-control-layout

Description: Registers a control layout specified in a file. This command specifies for certain wells a certain material of type CONTROL.

Note:

Usage:

prompt> bis register-control-layout [-p <property code>=<property value>] [-f <properties file>] <control layout file>

Options:

Parameter:

register-dilution-plates

Description: Registers all dilution plates specified in a file. For each dilution plate a corresponding master plate has to be specified. Optional a control layout can be associated.

Usage:

prompt> bis register-dilution-plates [-c <control layout code>] [-c <control layout code>] <dilution plate file>

Options:

Parameter:

register-experiments

Description: Registers one or more experiments as specified in the file.

Usage:

prompt> bis register-experiments [-d <root directory>] <experiment-type-code> <experiment file> 

Options:

Parameter:

register-reinfection-plates

Description: Registers reinfection plates specified in a file. For each reinfection plate a corresponding cell plate has to be specified. Optionally a control layout can be associated.

Usage:

prompt> bis register-reinfection-plates [-c <control layout code>] <reinfection plate file>

Options:

Parameter:

Commands for Administrators only

assign-control-layout-property-type

Description: Assigns a property type to a control layout. The assigned property type can be optional or mandatory. This can be changed by executing this command again.

If an optional property type is changed to a mandatory one it might be necessary to specify a file with values for this property. This tab-separated file has to provide a value for all control layouts which do not have a value for the property which had become mandatory.

Usage:

prompt> bis assign-control-layout-property-type [-f <file path>] [-g <global default value>] [-m[=<mandatory flag>]] <property type code>

Options:

Parameter:

assign-experiment-property-type

Description: Assigns a property type to an experiment type. The assigned property type can be optional or mandatory. This can be changed by executing this command again.

If an optional property type is changed to a mandatory one it might be necessary to specify a file with values for this property. This tab-separated file has to provide a value for all experiments of all projects which do not have a value for the property which had become mandatory.

Usage:

prompt> bis assign-experiment-property-type [-f <file path>] [-g <global default value>] [-m[=<mandatory flag>]] <experiment type code> <property type code>

Options:

Parameter:

assign-material-property-type

Description: Assigns a property type to a material type. The assigned property type can be optional or mandatory. This can be changed by executing this command again.

If an optional property type is changed to a mandatory one it might be necessary to specify a file with values for this property. This tab-separated file has to provide a value for all materials which do not have a value for the property which had become mandatory.

Usage:

prompt> bis assign-material-property-type [-f <file path>] [-g <global default value>] [-m[=<mandatory flag>]] <material type code> <property type code>

Options:

Parameter:

assign-plate-property-type

Description: Assigns a property type to a plate type. The assigned property type can be optional or mandatory. This can be changed by executing this command again.

If an optional property type is changed to a mandatory one it might be necessary to specify a file with values for this property. This tab-separated file has to provide a value for all plates which do not have a value for the property which had become mandatory.

Usage:

prompt> bis assign-plate-property-type [-f <file path>] [-g <global default value>] [-m[=<mandatory flag>]] <plate type code> <property type code>

Options:

Parameter:

invalidate-experiment

Description: Invalidates a specified experiment. After invalidation the plates which were used in the invalidated experiment can be reused in another experiment.

Usage:

prompt> bis invalidate-experiment [-r <invalidation-reason>] <project code> <experiment code>

Options:

Parameter:

invalidate-plates

Description: Invalidates one or more plates. The plates are specified by their codes in the command line and/or in a specified file.

Note:

Usage:

prompt> bis invalidate-plates [-r <invalidation-reason>] [-f <file with plate codes>] [<plate code> ...]

Options:

Parameter:

register-master-plate

Description: Registers a master plate from a specified file.

Note:

Usage:

prompt> bis register-master-plate [-p <property code>=<property value>] [-f <properties file>] [-c <control layout code>] <master plate file> <material batch code>

Options:

Parameter:

register-materials

Description: Registers materials from a specified file.

Usage:

prompt> bis register-materials <material type code> <material file>

Options: No additional options.

Parameter:

register-project

Description: Registers a new project.

Usage:

prompt> bis register-project <project code>

Options: No additional options.

Parameter:

register-property-types

Description: Registers property types from a specified file.

Usage:

prompt> bis register-property-types <property types file>

Options: No additional options.

Parameter:

register-vocabulary

Description: Registers controlled vocabulary set with given terms. To browse existsting controlled vocabulary set see list-vocabularies and get-vocabulary-info commands.

Usage:

prompt> bis register-vocabulary <vocabulary-name> <vocabulary-terms-file>

Options:

Parameter:

unassign-control-layout-property-type

Description: Unassigns a property type from control layout.

Note: This automatically deletes all values of the specified property type for all control layouts.

Usage:

prompt> bis unassign-control-layout-property-type [--force] <property type code>

Options:

Parameter:

unassign-experiment-property-type

Description: Unassigns a property type from an experiment type.

Note: This automatically deletes all values of the specified property type for all experiments of the specified type.

Usage:

prompt> bis unassign-experiment-property-type [--force] <experiment type code> <property type code>

Options:

Parameter:

unassign-material-property-type

Description: Unassigns a property type from a material type.

Note: This automatically deletes all values of the specified property type for all materials of the specified type.

Usage:

prompt> bis unassign-material-property-type [--force] <material type code> <property type code>

Options:

Parameter:

unassign-plate-property-type

Description: Unassigns a property type from a plate type.

Note: This automatically deletes all values of the specified property type for all plates of the specified type.

Usage:

prompt> bis unassign-plate-property-type [--force] <plate type code> <property type code>

Options:

Parameter: