When you export a study, the server copies the study data into an archive file format consisting of TSV files (to hold the core data) and XML files (to hold the study properties and metadata). You have the option to receive these files in an exploded format, or as a single zip file (a ".folder.zip" file). As part of the study export process, you can choose which study elements copied into the archive, including specimens, cohort assignments, datasets, 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
Folder Objects to Export
When you export a study, you can choose which items to include in the archive. In addition to queries, views, reports, and settings available when exporting any type of folder
, the study folder enables the export of study related properties.
To export a study:
- Go to the Manage tab.
- Click Export Study at the bottom of the page.
- Select the checkboxes for folder and study objects you wish to export. The list will look something like the following:
- Assay Datasets - This option exports assay dataset information, writing metadata to "datasets_manifest.xml" and data to .tsv files. See Study Archive Files and Formats for more details.
- 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.
- Categories - This option exports the Categories for report grouping to "view_categories.xml."
- Cohort Settings - This option exports the cohort definitions to "cohorts.xml." If defined, SubjectCount and Description for cohorts are included.
- CRF Datasets - This option exports Case Report Form dataset information, aka, the Demographic and Clinical datasets in the study. Selecting this option only exports the dataset metadata, that is, the field names and data types, but not the data contained in the datasets. To export the data, select "Dataset Data" below. Dataset metadata is written to "datasets_manifest.xml" and "datasets_metadata.xml" files. If data is exported, it is written to .tsv files. See Study Archive Files and Formats for more details.
- 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.
- Dataset Data - Export data in datasets; omitting this object creates a study template useful for creating empty clone studies.
- 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."
- Protocol Documents - This option exports the study protocol documents to a "protocolDocs" folder.
- QC State Settings - This option exports a "quality_control_states.xml" file that includes QC state definitions including custom states, descriptions, default states for the different import pathways and the default blank QC state.
- Specimen Settings - This option exports a "specimen_settings.xml" file containing the groupings, location types, statuses, actors, and requirements you have defined. If you later import 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 from the imported archive. When you import an in-use actor, the membership emails for that actor will be replaced. Note that there are some settings associated with specimen repositories which are not covered by this option. For example, custom properties defined for specimen tables are only exported in a full study archive. For additional information about specimen repository settings and options, see Specimens: Administrator Guide.
- Specimens - This option exports a "specimens" directory containing the specimen archive itself as a .specimens file. For more about specimen archives, see Specimen Archive File Reference. Note that this archive includes the data only - select export of specimen repository settings separately as described above.
- 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.
- Shift Participant Dates: Selecting this option will shift selected date values associated with a participant by a random participant-specific offset from 1 to 365.
- 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.