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File Watchers let administrators set up the monitoring of directories on the file system and perform specific actions when desired files appear. This topic describes the various pipeline tasks available. The configuration options for file watcher triggers and specifics about type of files eligible vary based on the type of file watcher, and the tasks available vary by folder type.

File Watcher Tasks

Reload Folder Archive (Any folder)

This option is available in any folder type and reloads an unzipped folder archive. It will not accept compressed (.zip) folder archives.

The reloader expects a folder.xml in the base directory of the archive. To create an unzipped folder archive, export the folder to your browser as a .zip file and then unzip it.

Reload Lists Using Data File (Any folder)

This option is available in any folder type and imports data to existing lists from source files. It can also infer non-key column changes. Note that this task cannot create a new list definition: the list definition must already exist on the server. The list module must also be enabled in the folder.

Custom Parameter: mergeData

By default, this task replaces list data using the contents of the source files. You may merge data by including the custom parameter: "mergeData": "true".

Move Files Across the Server (Any folder)

This option is available in any folder type. It moves and/or copies files around the server without analyzing the contents of those files.

Import/Reload Study Datasets Using Data File (Study folders only)

This option is available in a study folder and creates and/or loads data into study datasets from source files. Source data can be in TSV, Excel, or text files. This task can also create dataset definitions if they do not already exist in the study.

Custom Parameter: "default.action"

Whether data is appended to existing data or replaces it entirely is controlled by adding a custom parameter to the file watcher trigger. To append data to the target table, when defining the trigger, set "default.action" to "append". If you do not include this parameter, or set it to "replace", the new data will replace all existing data.

Reload Study (Study folders only)

This option reloads or populates a study from an unzipped study archive. This task is triggered by a .txt file (i.e. studyload.txt) and reloads a study (both its datasets and study configurations such as cohort assignments). To create a study archive, see Export a Study.

Import a Directory of FCS Files (Flow folders only)

Import flow files to the flow module. This type of file watcher is only available in Flow folders. It supports a process where FCS flow data is deposited in a common location by a number of users, with each data export placed into a subdirectory of the watched folder, perhaps in a separate subdirectory per user.

When the File Watcher finds these files, they are placed into a new location under the folder pipeline root based on the current user and date. Example: @pipeline/${username}/${date('YYYY-MM')}

LabKey then imports the FCS data to that container. All FCS files within a single directory are imported as a single experiment run in the flow module.

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