The Experiment module supports other modules in providing functionality that is particular to different kinds of experiments. For example, the MS2 module provides code that knows how to load different types of output files from mass spectrometers, and code that knows how to provide a rich UI around that data. The Experiment module provides the general framework for dealing with samples, runs, data files, and more, and will delegate to other modules when loading information from a XAR, when rendering it in the experiment tables, when exporting it to a XAR, and so forth.
The ExperimentDataHandler interface allows a module to handle specific kinds of files that might be present in a XAR. When loading from a XAR, the Experiment module will keep track of all the data files that it encounters. After the general, Experiment-level information is fully imported, it will call into the ExperimentDataHandlers that other modules have registered. This gives other modules a chance to load data into the database or otherwise prepare it for later display. The XAR load will fail if an ExperimentDataHandler throws an ExperimentException, indicating that the data file was not as expected.
Similarly, when exporting a set of runs as a XAR, the Experiment module will call any registered ExperimentDataHandlers to allow them to transform the contents of the file before it is written to the compressed archive. The default exportFile() implementation, provided by AbstractExperimentDataHandler, simply exports the file as it exists on disk.
The ExperimentDataHandlers are also interrogated to determine if any modules provide UI for viewing the contents of the data files. By default, users can download the content of the file, but if the ExperimentDataHandler provides a URL, it will also be available. For example, the MS2 module provides an ExperimentDataHandler that hands out the URL to view the peptides and proteins for a .pep.xml file.
Prior to deleting a data object, the Experiment module will call the associated ExperimentDataHandler so that it can do whatever cleanup is necessary, like deleting any rows that have been inserted into the database for that data object.
ExperimentDataHandlers are registered by implementing the getDataHandlers() method on Module.org.labkey.api.exp.RunExpansionHandler
RunExpansionHandlers allow other modules to modify the XML document that describes the XAR before it is imported. This means that modules have a chance to run Java code to make decisions on things like the number and type of outputs for a ProtocolApplication based on any criteria they desire. This provides flexibility beyond just what is supported in the XAR schema for describing runs. They are passed an XMLBeans
representation of the XAR.
RunExpansionHandlers are registered by implementing the getRunExpansionHandlers() method on Module.org.labkey.api.exp.ExperimentRunFilter
ExperimentRunFilters let other modules drive what columns are available when viewing particular kinds of runs in the experiment run grids in the web interface. The filter narrows the list of runs based on the runs' protocol LSID.
Using the Query module, the ExperimentRunFilter can join in additional columns from other tables that may be related to the run. For example, for MS2 search runs, there is a row in the MS2Runs table that corresponds to a row in the exp.ExperimentRun table. The MS2 module provides ExperimentRunFilters that tell the Experiment module to use a particular virtual table, defined in the MS2 module, to display the MS2 search runs. This virtual table lets the user select columns for the type of mass spectrometer used, the name of the search engine, the type of quantitation run, and so forth. The virtual tables defined in the MS2 schema also specify the set of columns that should be visible by default, meaning that the user will automatically see some of files that were the inputs to the run, like the FASTA file and the mzXML file.
ExperimentRunFilters are registered by implementing the getExperimentRunFilters() method on Module.
Generating and Loading XARs
When a module does data analysis, typically performed in the context of a PipelineJob, it should generally describe the work that it has done in a XAR and then cause the Experiment module to load the XAR after the analysis is complete.
It can do this by creating a new ExperimentPipelineJob and inserting it into the queue, or by calling org.labkey.api.exp.ExperimentPipelineJob.loadExperiment(). The module will later get callbacks if it has registered the appropriate ExperimentDataHandlers or RunExpansionHandlers.
API for Creating Simple Protocols and Experiment Runs
LabKey provides an API for creating simple protocols and simple experiment runs that use those protocols. It is appropriate for runs that start with one or more data/material objects and output one or more data/material objects after performing a single logical step.
To create a simple protocol, call org.labkey.api.exp.ExperimentService.get().insertSimpleProtocol(). You must pass it a Protocol object that has already been configured with the appropriate properties. For example, set its description, name, container, and the number of input materials and data objects. The call will create the surrounding Protocols, ProtocolActions, and so forth, that are required for a full fledged Protocol.
To create a simple experiment run, call org.labkey.api.exp.ExperimentService.get().insertSimpleExperimentRun(). As with creating a simple Protocol, you must populate an ExperimentRun object with the relevant properties. The run must use a Protocol that was created with the insertSimpleProtocol() method. The run must have at least one input and one output. The call will create the ProtocolApplications, DataInputs, MaterialInputs, and so forth that are required for a full-fledged ExperimentRun.