A specimen archive is a zip file with a .specimens
extension which contains a collection of .tsv
(tab-separated value) files.
When you import a Study
you can upload a specimen repository along with some specimen settings as part of that process. You can also import a specimen archive by itself into an existing study either to replace or add to an existing repository. Note: the study must be configured to use an Advanced Specimen Repository
to import an archive.
The import process has two basic steps: first upload the files to LabKey Server and then import the data into the study.
Upload a Specimen Archive
- Click the Specimen Data tab.
- In the Specimens web part, expand the Administration link if present.
- Click Import Specimens. A file browser will open showing the files already uploaded to the study. If your specimen archive is already uploaded to the file browser, skip the rest of this step.
- In a separate file explorer window, locate your specimen archive.
- Drag and drop it into the LabKey Server file browser panel.
When the files have been uploaded, you will see them in the file browser panel.
Import the Specimen Archive
- Select the files you wish to import, and click the Import Data link on the menu bar.
- On the Import Data pop up, select the specific import job you wish to run, by default Import Specimen Data and click Import.
- On the Import Study Batch page, you will see a list of files to be imported. If you are importing an archive to a folder already containing a previous archive, select either:
- Replace: Replace all of the existing specimens.
- Merge: Insert new specimens and update existing specimens.
If you are importing a specimen file to an existing editable repository, these options have important implications:
- Replace: Replaces the previous repository. Any changes you made to existing data will be lost.
- Merge: Any attempt to update specimens currently in the repository will result in an error. This only allows new specimens to be added and preserves all changes you may have made.
- Click Start Import.
To see uploaded specimens when the import is complete, return to the Specimen Data
tab. The new specimen data will be available for view via the links in the Specimens
If you encounter errors, please see Troubleshoot Specimen Import
to interpret .log files.
Note that creating a .specimen archive, changing the metadata file (specimens_metadata.xml) outside LabKey, and then importing the archive to create changes in the specimen repository, is not supported.
Import Specimen Settings
If specimen settings were exported with the repository, the archive will include a specimen_settings.xml
file containing Groupings, Location Types, Statuses, Actors, and Default Requirements
. If you are importing that archive into an existing specimen repository, any new specimen settings will be added. Any status or actor that is currently in use in the specimen repository will not be replaced, however. When you import an in-use Actor
, the membership emails for that actor will be replaced.