extract

Extract a copy of objects from the package

Overview

The tool extracts a copy of specified objects from a package and writes to a directory

Example Usage

Extract subject S1234 to /path/to/outdir

squirrel extract <package> --object subject --objectid S1234 --outdir /path/to/outdir

Options

--object

--object <object> can be one of the following

• package

• subject

• study

• series

• analysis

• intervention

• observation

• experiment

• pipeline

• groupanalysis

• datadictionary

--outdir

--outdir <outdir> specifies a path to which the object(s) will be written. Filenames(s) will reflect the object IDs or names.

--objectid

--objectid <id> specifies the ID or name of the object to extract. For example: subject with ID S1234 or experiment named MyExperiment.

--recurse

If specified, --recurse will extract all child objects of the specified object. If option is not set, only the specified object will be extracted.

--subjectid

--subjectid <id> specifies the subject ID when extracting study, series, intervention, observation, or analysis objects.

--studynum

--studynum <num> specifies the study number when extracting series and analysis objects. Must be used with --subjectid option.