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Overview of the MS2 Notification APIs

LabKey Server includes two server APIs and associated java-language wrappers that support automatic processing of MS spectra files as they are produced by the mass spectrometer, without operator intervention. This document describes their configuration and use:


A few excerpts from this document:

The LabKey Server Enterprise Pipeline is designed to be used in a shared file system configuration with the MS instrument. In this configuration data files are copied from the instrument to a directory shared with the LabKey Server and with its remote task runners. From the LabKey Server's perspective, this directory lives under the Pipeline root directory for a given folder. Once the raw data files are copied, the Pipeline web part can be used to manually select a search protocol and initiate search processing. Alternately, these notification APIs can be called by a batch processing step after the copy to the shared pipeline directory is complete.

  • The StartSearchCommand initiates MS2 searching on one or more specified data files using a named, pre-configured search protocol. If a data file is not found in the specified location at the time this command is called, the search job will still be initiated and will enter a "File Waiting" status.
  • The FileNotificationCommand tells LabKey Server to check for any jobs in a given folder that are in the File Waiting status. A File Waiting status is cleared if the specified file being waited for is found in the expected pipeline location. If the waited-for file is not present the File Waiting status remains until it is checked again the next time a FileNotificationCommand is called on that folder.
In addition, LabKey Server includes two wrapper classes to make these APIs easier to call from a batch file:
  • The MS2SearchClient class takes data file and protocol information from a CSV file and uses it to call StartSearchCommand one or more times. The CSV file contents are also saved at the server using the SubmitAssayBatches API. MS2SearchClient is designed to be called in a batch file.
  • The PipelineFileAvailableClient is a simple wrapper over FileNotificationCommand to enable calling from a batch file.
LabKey Server does not try to detect partially-copied files, so these APIs should be called at a time when there are no file copies in progress.

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