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Export a Specimen Archive

Documentation: Version 21.7

Export a Specimen Archive

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Premium Resource - Specimen functionality is a legacy feature available with Premium Editions of LabKey Server. For new installations, we recommend using Sample Manager instead. Learn more or contact LabKey.

When you export a study, you have the option to include specimen repository settings and specimen data with the rest of the study archive. If you only need to export the data itself, you can export a standalone specimen archive independently as described in this topic.

An exported specimen archive can be imported into a new study, or reimported into the original study, such as after updating the included data.

Note that if you have added or customized specimen properties, you must export the complete study to include the customized fields. Specimen request settings, such as requestability rules or notification settings, are only exported and reimported as part of a full study archive.

To export a standalone specimen archive:

  • Navigate to the Manage tab of your study.
  • Click the Export Study button at the bottom of the page.
  • Select Study from the Folder Objects list.
  • Unselect all the study objects except Specimens and Specimen Settings.
  • Under Options, select the desired behavior.
  • Under Export To, select Pipeline root export directory, as individual files.
  • Click Export.
  • Under Files, navigate to export > study > specimens. Look for a file named <StudyName>.specimens, where <StudyName> is the name of your study. This is the specimen archive. It is a .zip file, renamed as a .specimen file.
  • Download the .specimen file to your machine.

The exported .specimens file can now be imported into another study or location. For import details, see Import a Specimen Archive.

Exporting and Importing Specimen Settings

Some but not all specimen settings are exported in a standalone archive. To determine which settings are included, you can unpack the zipped archive and view the contents of the included .xml files. To include custom properties and request settings, for example, you must export the entire study archive.

Upon reimport of a specimen repository, some rules about some settings are observed. For example, any status or actor that is currently in use in the specimen repository will not be replaced. When you import an in-use Actor, the membership emails for that actor will be replaced.

The full XML schema description can be found in: LabKey XML Schema Reference.

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