This topic is under construction for the 23.3 (March 2023) release of LabKey Server. For current documentation of this feature, click here.
Exporting a study is a use case of exporting a folder
. Study data and metadata are copied to a set of .xml and .tsv files in a specific folder archive format. You can export in an exploded individual file structure or as a single zipped ".folder.zip" archive.
As part of the folder export process, you can choose which study elements are included in the archive, including all the elements available in folder exports, plus datasets, cohort assignments, participant views, etc.
To export a study folder:
- Go to (Admin) > Manage Study (or click the Manage tab).
- Click the Export Study button at the bottom of the page.
Note: This page is also accessible at (Admin) > Folder > Management > Export tab
, as described in Export / Import a Folder
Study Folder Objects to Export
When you export a study, you can choose which items to include in the archive. In addition to queries, grid views, reports, and settings available when exporting any type of folder
, the study folder enables the export of study related objects and properties.
- Select the checkboxes for folder and study objects you wish to export. The list will look something like the following:
- Use the Clear All Objects button to clear all the checkboxes (then select a minimal set).
- Use the Reset button to reset the default set of checkboxes (and add/remove as needed from there).
In addition to the objects available when exporting any folder
, the study checkbox allows you to include the following Study
- Assay Schedule: Exports assay schedule .tsv files to a directory parallel to datasets in the archive including definitions of which assays are included in the study and expectations for which visits assay data will be uploaded.
- Cohort Settings: This option exports the cohort definitions to "cohorts.xml." If defined, SubjectCount and Description for cohorts are included.
- Custom Participant View: For a study where the admin has pasted in a custom Participant HTML page, the custom participant view is exported as participant.html.
- Datasets: For each category of datasets, the definitions and data can be exported independently. Exporting definitions without data is useful for creating new template studies for new data collection. Exporting data without definitions could be used as part of audit or setting up to refresh data without changing any definitions. Definitions, or the fields and types for the dataset, aka the metadata, will be written to "datasets_manifest.xml". Data exported will be written to .tsv files. See Study Object Files and Formats for more details.
- Datasets: Assay Dataset Definitions: Include definitions for datasets created by linking assay data into a study.
- Datasets: Assay Dataset Data: Include the data contained in assay datasets.
- Datasets: Sample Dataset Definitions: Include definitions for datasets created by linking sample data into a study.
- Datasets: Sample Dataset Data: Include the data contained in sample datasets.
- Datasets: Study Dataset Definitions: Include definitions of study datasets (previously known as "CRF Datasets"), including demographic, clinical, and additional key datasets. This category includes all datasets not created by linking assays or samples to the study.
- Datasets: Study Dataset Data: Include the data contained in study datasets.
- Participant Comment Settings: This option exports participant comment settings, if present.
- Participant Groups: This option exports the study's participant groups. In addition to label, type, and datasetID, the autoUpdate attribute will record whether the group should be updated automatically. The file generated is "participant_groups.xml."
- Permissions for Custom Study Security: Include the custom study security configuration in the archive. Study security policies can also be exported separately; for details see Manage Study Security.
- Protocol Documents: This option exports the study protocol documents to a "protocolDocs" folder.
- Treatment Data: Include information about study products and immunization treatments including immunogens, adjuvants, doses, and routes.
- Visit Map: This option exports a "visit_map.xml" file detailing the baseline and visit schedule for the exported study.
If the study folder has any subfolders, you can use the checkbox to Include Subfolders
in the export if you like.
You can also control the amount of Protected Health Information (PHI) that is included in the export.
- Include PHI Columns: Select which PHI columns are included in the archive. Options:
- Restricted, Full, and Limited PHI: Include all columns.
- Full and Limited PHI: Exclude only Restricted columns.
- Limited PHI: Exclude Restricted and Full PHI columns.
- To exclude all columns marked as PHI at any level, uncheck the checkbox.
- Learn more in this topic: Protecting PHI Data
- Shift Participant Dates: Selecting this option will shift date values associated with a participant by a random participant-specific offset from 1 to 365.
- The offset is applied to all dates for a specific participant, maintaining the time between dates but obscuring actual dates.
- If you want to exclude certain date fields from this shifting, you can exclude them in the advanced properties for the field. Learn more in this topic.
- Export Alternate Participant IDs: Selecting this option will replace each participant ID with an alternate randomly generated ID.
- Mask Clinic Names: Selecting this option will change the labels for the clinics in the exported list of locations to a generic label (i.e. Clinic).
Select the destination for your export from the following options:
- Pipeline root "export" directory, as individual files: In the folder pipeline root, an "export" directory is created if it does not exist. The individual files are exported to this directory.
- Pipeline root "export" directory, as zip file: In the folder pipeline root, an "export" directory is created if it does not exist. A zip file archive is exported to that location.
- Browser as zip file: Default. A zip file will be downloaded to the destination connected to your browser, such as a "Downloads" folder. You will typically see a box with a link to the export in the bottom of the browser window.