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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:

  • -h, --help: Shows a help text with a brief description of all options and arguments.
  • -s <base URL>, --server-base-url=<base URL>: The base URL of the openBIS server. If not specified the URL from the file .openBIS-default will be used.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

Parameter:

  • <control layout code>: Code of the control layout. The command list-control-layouts lists all available values.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

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:

  • -v <version number>, --attachmentVersion=<version number>: Version of the requested file. Has to be a number greater or equals 1. Without this option the latest version will be downloaded.

Parameter:

  • <project code>: Code of the project to which the experiment belongs.
  • <experiment code>: Code of the experiment. Available experiments can be listed by the command list-experiments.
  • <file name>: Name of the file to be downloaded.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

Parameter:

  • <project code>: Code of the project to which the experiments belong.
  • <experiment code>: Codes of the experiments. Exactly one experiment has to be specified. Available experiments can be listed by the command list-experiments.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

Parameter:

  • <experiment type code>: The experiment. The command list-experiments lists all available values.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

Parameter:

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

get-plate-info

Description: Gets detailed information about a plate.

Usage:

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

Options:

  • -b, --buffer: If specified, the output on the console is stopped when the screen is full. By pressing space key or enter key output will be continued. By pressing 'q' output is quited.
  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.
    Parameter:
  • <plate code>: Code of the plate to be shown.

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:

  • -a, --show-also-invalid: Also locations of invalid plates are shown if this flag is specified.
  • -i, --gene-id: Parameter <gene-symbol or id> is interpreted as gene id if this flag is specified.
  • -p <project code>, --project=<project code>: Code of a project. This restricts the query. Available projects can be listed by the command list-projects.
  • -e <experiment code>, --experiment=<experiment code>: Code of an experiment. Will be ignored if option -p is not also specified. This restricts the query to one specific experiment. Available experiments can be listed by the command list-experiments.
  • -o <study object code>, --study-object=<material code>: Material code of the object to be studied. This restricts the query.
  • -t <time interval>, --time-interval=<time interval>: A query restriction on the time interval. For the format see here. Only those experiments are taken into account which have an overlap of the specified time interval with the time interval defined by the experiment registration date and the registration date of the last registered data set.

Parameter:

  • <gene-symbol or id>: The gene symbol. Because the gene symbol is not unique the gene id can be used if the option -i is specified.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

Parameter:

  • <sample type code>: The plate type. The command list-plate-types lists all available values.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

Parameter:

  • <vocabulary-code>: Code of the controlled vocabulary set.

list-contacts

Description: Lists all persons who used the system.

Usage:

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

Options:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

Parameter:

  • <project code>: Code of the project to which the experiments belong.
  • <experiment code>: Codes of the experiments. Exactly one experiment has to be specified. Available experiments can be listed by the command list-experiments.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

Parameter:

  • <project code>: Code of the project to which the experiments belong.
  • <experiment code>: Codes of the experiments. Exactly one experiment has to be specified. Available experiments can be listed by the command list-experiments.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

Parameter:

  • <project code>: Code of the project to which the experiments belong.
  • <experiment code>: Codes of the experiments. Exactly one experiment has to be specified. Available experiments can be listed by the command list-experiments.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

Parameter: No parameters.

list-experiment-types

Description: Lists all experiment types.

Usage:

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

Options:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

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:

  • -a, --show-also-invalid: Also invalid experiments are shown if this flag is specified.
  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.
  • -p <project code>, --project=<project code>: Code of a project. This restricts the query. Available projects can be listed by the command list-projects.
  • -o <study object code>, --study-object=<material code>: Material code of the object to be studied. This restricts the query.
  • -t <time interval>, --time-interval=<time interval>: A query restriction on the time interval. For the format see here. Only those experiments are taken into account which have an overlap of the specified time interval with the time interval defined by the experiment registration date and the registration date of the last registered data set.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

Parameter: No parameters.

list-material-types

Description: Lists all material types.

Usage:

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

Options:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

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:

  • -b, --buffer: If specified, the output on the console is stopped when the screen is full. By pressing space key or enter key output will be continued. By pressing 'q' output is quited.
  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.
  • -l <number of lines>, --limit=<number of lines>: Maximum number of lines to be shown.
  • ["<pattern>" ...]: Restricts the query to those materials whose code matches the specified wild card pattern (* = any string, ? = any character). Pattern should be placed inside the quotation marks.

Parameter:

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

list-plate-types

Description: Lists all plate types.

Usage:

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

Options:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

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:

  • -a, --show-also-invalid: Also invalid plates are shown if this flag is specified.
  • -b, --buffer: If specified, the output on the console is stopped when the screen is full. By pressing space key or enter key output will be continued. By pressing 'q' output is quited.
  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.
  • -l <number of lines>, --limit=<number of lines>: Maximum number of lines to be shown.
  • -n, --no-experiment: Only plates registered to an experiment are shown.
  • ["<pattern>" ...]: Restricts the query to those plates whose code matches the specified wild card pattern (* = any string, ? = any character). Pattern should be placed inside the quotation marks.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

Parameter:

  • <project code>: Code of the project to which the experiments belong.
  • <experiment code>: Codes of the experiments. Exactly one experiment has to be specified. Available experiments can be listed by the command list-experiments.

list-projects

Description: Lists all projects.

Usage:

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

Options:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

Parameter: No parameters.

list-property-types

Description: Lists all property types.

Usage:

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

Options:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

Parameter: No parameters.

list-control-layouts

Description: Lists all control layouts.

Usage:

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

Options:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

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:

  • -P, --pretty-print: Shows the data in a pretty printed format which is more human readable than the tab-separated one. For more details see here.

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:

  • -u <login name>, --username=<login name>: The login name of the user to be authenticated. If not specified the user will be asked.
  • -p <password>, --password=<password>: The password of the user to be authenticated. If not specified the user will be asked. This option should only be used in scripts calling this command.

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:

  • <project code>: Code of the project to which the experiment belongs.
  • <experiment code>: Code of the experiment. Available experiments can be listed by the command list-experiments.
  • <file path>: Path to the file to be uploaded.

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:

  • -c <control layout code>, --control-layout=<control layout code>: Control layout code which will be used for all plates whose control layout has not been specified in the plate file.

Parameter:

  • <cell plate file>: A tab-separated file with at least two columns: code and parent. The first column contains unique and currently not registered cell plate codes (maximum length: 20 characters). The second column contains codes of already registered dilution plates (registered by the command register-dilution-plates). In an optional column control_layout individual control layout codes (registered by the command register-control-layout) can be specified for chosen cell plates. exampleCellPlates.txt or exampleCellPlatesWithControl.txt can serve as templates. Additional columns may or must appear if properties have been assigned to cell plates.

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:

  • The file name without the extension serves as the code of the control layout to be registered.
  • Property PLATE_GEOMETRY is mandatory for control layouts and must be specified. Available plate geometries can be listed using get-vocabulary-info PLATE_GEOMETRY command.

Usage:

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

Options:

  • -p <property code>=<property value>, --property=<property code>=<property value>: Setting the value of the property named <property code>. This can only be used for setting one property. If you want or have to set more than one property, use the -f option with a properties file.
  • -f <properties file>, --properties-file=<properties file>: A tab-separated file with two columns (named code and value) for all properties to be set.

Parameter:

  • <control layout file>: A tab-separated file with at two columns: code and materialCode. The first column contains well codes in the format <row letter><two colum digits>. The second column contains codes of already registered materials of type CONTROL (registered by the command register-materials). CL1.txt can serve as template. As the file name (without the extension) specifies the control layout code, only valid characters can be used (letters, numbers and underscore).

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:

  • -c <control layout code>, --control-layout=<control layout code>: Control layout code which will be used for all plates whose control layout has not been specified in the plate file.

Parameter:

  • <dilution plate file>: A tab-separated file with at least two columns: Dilution Plate and Master Plate. The first column contains unique and currently not registered dilution plate codes (maximum length: 20 characters). The second column contains codes of already registered master plates (registered by the command register-master-plate). In an optional column Control Layout individual control layout codes (registered by the command register-control-layout) can be specified for chosen dilution plates. exampleDilutionPlates.txt or exampleDilutionPlatesWithControl.txt can serve as templates. Additional columns may or must appear if properties have been assigned to dilution plates.

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:

  • -d <root directory>, --root-dir=<root directory>: Root directory of <experiment file> and all files referred inside an experiment file.

Parameter:

  • <experiment-type-code>: Code of an existing experiment type. The allowed experiment types can be obtained by the command list-experiment-types.
  • <experiment file>: File specifying the experiments to be registered. A tab-separated experiment file contains the following columns (order is irrelevant):

    Column name

    Mandatory?

    Description

    project

    yes

    Code of a registered project.

    code

    yes

    Experiment code which has to be unique in the specified project. It has to be no longer than 20 characters and cannot contain any dashes.

    study_object

    yes

    Code of a registered material of the type specified by study_object_type.

    study_object_type

    yes

    Code of a registered material type.

    cell_plates

    yes/no

    File of cell plates associated with this experiment. The file path has to be relative to the above-mentioned root directory. The path has to be prefixed by '>'. The file has no header and contains one cell plate code per line. This column is optional if the workflow-code is plates-on-demand (i.e. old IMSB workflow). cellPlates.txt is an example.

    control_layout

    no/yes

    Code of a registered control layout. This is a mandatory column if the workflow-code is plates-on-demand. Otherwise this column is not allowed.

    user.description

    no

    A brief description of the purpose of the experiment to be registered.

    processing_instructions

    no

    Processing instructions for the ETL Server. The instructions are specified in a file whose path is relative to the root directory. The path has to be prefixed by '>'. A processing instruction file is a tab-separated file with the mandatory columns procedure_type and path. The procedure type code has to be either DATA_ACQUISITION or IMAGE_ANALYSIS. Optional columns are description and parameters. The last one denotes the path (relative to the above-mentioned root directory and with prefix '>') of the processing parameters which will be uploaded. exampleProcessingInstructions.txt can serve as a template.

    exampleExperiments.txt can serve as a template if the workflow-code is plates-on-demand. Otherwise exampleExperimentsWithCellPlates.txt can serve as a template.

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:

  • -c <control layout code>, --control-layout=<control layout code>: Code of the control layout which will be used for all reinfection plates whose control layout has not been specified in the reinfection plate file.

Parameter:

  • <reinfection plate file>: A tab-separated file with at least two columns: code and parent. The first column contains unique and currently not registered reinfection plate codes (maximum length: 20 characters). The second column contains codes of already registered cell plates (registered by the command register-cell-plates). In an optional column control_layout individual control layout codes (registered by the command register-control-layout) can be specified for chosen cell plates. exampleReinfectionPlates.txt or exampleReinfectionPlatesWithControl.txt can serve as templates. Additional columns may or must appear if properties have been assigned to reinfection plates.

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:

  • -f <file path>, --load-values=<file path>: A tab-separated text file (specified by <file path> with two colums: code (here control layout code) and value. example file
  • -g <global default value>, --global=<global default value>: A global default value for entities that are not specified in <file path>.
  • -m[=<mandatory flag>], --mandatory[=<mandatory flag>]: If <mandatory flag> is true or missing the assign property type will be a mandatory one. If this option is not specified it will be optional.

Parameter:

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

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:

  • -f <file path>, --load-values=<file path>: A tab-separated text file (specified by <file path> with three colums: code (here experiment code) , project and value. example file
  • -g <global default value>, --global=<global default value>: A global default value for entities that are not specified in <file path>.
  • -m[=<mandatory flag>], --mandatory[=<mandatory flag>]: If <mandatory flag> is true or missing the assign property type will be a mandatory one. If this option is not specified it will be optional.

Parameter:

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

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:

  • -f <file path>, --load-values=<file path>: A tab-separated text file (specified by <file path> with two colums: code (here material code) and value. example file
  • -g <global default value>, --global=<global default value>: A global default value for entities that are not specified in <file path>.
  • -m[=<mandatory flag>], --mandatory[=<mandatory flag>]: If <mandatory flag> is true or missing the assign property type will be a mandatory one. If this option is not specified it will be optional.

Parameter:

  • <material type code>: Code of the material type. The command list-material-types lists all available values.
  • <property type code>: Code of the property type. The command list-property-types lists all available values.

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:

  • -f <file path>, --load-values=<file path>: A tab-separated text file (specified by <file path> with two colums: code (here plate code) and value. example file
  • -g <global default value>, --global=<global default value>: A global default value for entities that are not specified in <file path>.
  • -m[=<mandatory flag>], --mandatory[=<mandatory flag>]: If <mandatory flag> is true or missing the assign property type will be a mandatory one. If this option is not specified it will be optional.

Parameter:

  • <plate type code>: Code of the sample type. The command list-plates-types lists all available values.
  • <property type code>: Code of the property type. The command list-property-types lists all available values.

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:

  • -r <invalidation-reason>, --invalidation-reason=<invalidation-reason>: Brief description why the experiment is invalidated. If the description contains spaces, it should be surrounded by quote signs, e.g. "operator error".

Parameter:

  • <project code>: Code of the project to which the experiment belongs.
  • <experiment code>: Code of the experiment. Available experiments can be listed by the command list-experiments.

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:

  • Control layouts can not be invalidated.
  • All subordinated plates will also be invalidated. Plates hierarchy is as follows: master plate > dilution plate > cell plate > reinfection plate. For example, invalidation of a dilution plate means also invalidation of all cell plates derived from this dilution plate. In addition all reinfection plates of those cell plates are also invalidated.

Usage:

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

Options:

  • -r <invalidation-reason>, --invalidation-reason=<invalidation-reason>: Brief description why the plates will be invalidated.
  • -f <file with plate codes>, --plate-names-file=<file with plate codes>: File with codes (one per line) of all plates to be invalidated. Invalid_plates.txt can serve as template.

Parameter:

  • <plate code>: Zero or more plate codes.

register-master-plate

Description: Registers a master plate from a specified file.

Note:

  • The name of the file without extension serves as the code of the master plate.
  • Property PLATE_GEOMETRY is mandatory for master plates and must be specified. Available plate geometries can be listed using get-vocabulary-info PLATE_GEOMETRY command.

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:

  • -c <control layout code>, --control-layout=<control layout code>: Code of a control layout which is optionally associated with the master plate to be registered. The command list-control-layouts lists all available values.
  • -p <property code>=<property value>, --property=<property code>=<property value>: Setting the value of the property named <property code>. This can only be used for setting one property. If you want or have to set more than one property, use the -f option with a properties file.
  • -f <properties file>, --properties-file=<properties file>: A tab-separated file with two columns (named code and value) for all properties to be set.
  • --empty <empty-plate-name>: should be used to create an empty master plate. When this option is given, master plate file should not be specified.

Parameter:

  • <master plate file>: A tab-separated file with the following mandatory colums (see MP001-1.txt as an example):
    • code: The well code specified in the format <row letter><two colum digits>.
    • material: The code of the material of type specified in column material_type.
    • material_type: The code of a material type. The command list-material-types lists all available values.
  • <material batch code>: An arbitrary text specifying the instance of all materials associated in the master plate to be registered.

register-materials

Description: Registers materials from a specified file.

Usage:

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

Options: No additional options.

Parameter:

  • <material type code>: The code of the type of materials to be registered. The command list-material-types lists all available values.
  • <material file>: Tab-separated file which contains one material and its properties per line. It has the mandatory column code which contains the material code which has to be unique for the specified material type (maximum length: 20 characters). The column inhibitor_code contains the code of the material which is inhibited by the material to be registered. This is a mandatory column if the material type is OLIGO.
    Additional columns are determined by the property types assigned to the specified material type. The command get-material-type-info lists all available columns. The name of the column in the material file has to be the same (ignoring case) as the property type code. Columns of non-mandatory properties are optional in the material file.
    See exampleGenes.txt, exampleOligos.txt, controls.txt, viruses.txt for example input files.

register-project

Description: Registers a new project.

Usage:

prompt> bis register-project <project code>

Options: No additional options.

Parameter:

  • <project code>: Code of the new project. It has to be unique and not more than 20 characters long.

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:

  • <property types file>: A tab-separated file with the following mandatory columns (see examplePropertyTypes.txt for an example):
    • code: Code (i.e. name) of the property type to be registered. It has to be unique and not more than 20 characters long.
    • label: Label to be used for human readable output.
    • description: A brief description.
    • data_type: Code of the type of data associated with the property type to be registered. The following data types are available:

      Data type code

      Description

      VARCHAR

      Text with not more than 1024 characters.

      INTEGER

      32-bit integer number.

      REAL

      Double precision floating point number.

      BOOLEAN

      Boolean value: Either true or false ignoring case.

      TIMESTAMP

      Time stamp (i.e. date and time).

      CONTROLLEDVOCABULARY

      This type is useful when you want to have a text property, but its values should be restricted to a certain set of controlled vocabularies. In the
      vocabulary column the name of the set should be specified if this type is used.

      When the property has a TIMESTAMP type, it's value can be specified in following formats:
      • full format with time zone (yyyy-MM-dd HH:mm:ss Z), e.g. 2007-12-24 16:59:59 +0200.
      • without a time zone (yyyy-MM-dd HH:mm:ss), e.g. 2007-12-24 16:59:59. The local timezone will be assumed.
      • without specifying seconds (yyyy-MM-dd HH:mm), e.g. 2007-12-24 16:59.
      • specyfing just a date, without the time (yyyy-MM-dd), e.g. 2007-12-24. The midnight of that day in the local time zone will be assumed as the time.
        where yyyy is the year, MM is the month (as number), dd is the day in the month, HH is the hour (0-23), mm is the minute, ss is the second, and Z is the time zone.
    • vocabulary: Optional, should be specified only when data_type is CONTROLLEDVOCABULARY. The value should be the name of the controlled vocabulary set which restricts the set of allowed values (see examplePropertyTypesWithVocabularies.txt for an example). The available vocabularies can be displayed by list-vocabularies command.

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:

  • --add-terms: If specified, the terms from <vocabulary-terms-file> will be added to already existing <vocabulary-name>.

Parameter:

  • <vocabulary-name>: Name of the controlled vocabulary set
  • <vocabulary-terms-file>: The file with vocabulary terms. Each term should be in one line. There should be no header. The following file can serve as an example: exampleVocabularyTermsOrganism.txt

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:

  • --force: Attempts to unassign the property type without asking the user for confirmation.

Parameter:

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

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:

  • --force: Attempts to unassign the property type without asking the user for confirmation.

Parameter:

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

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:

  • --force: Attempts to unassign the property type without asking the user for confirmation.

Parameter:

  • <material type code>: Code of the material type. The command list-material-types lists all available values.
  • <property type code>: Code of the property type. The command list-property-types lists all available values.

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:

  • --force: Attempts to unassign the property type without asking the user for confirmation.

Parameter:

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