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Classes


Namespace LABKEY.Pipeline

Pipeline static class that allows programmatic manipulation of the data pipeline.
Defined in: Pipeline.js.

Namespace Summary
Constructor Attributes Constructor Name and Description
 
Method Summary
Method Attributes Method Name and Description
<static>  
LABKEY.Pipeline.getFileStatus(config)
Gets the status of analysis using a particular protocol for a particular pipeline.
<static>  
LABKEY.Pipeline.getPipelineContainer(config)
Gets the container in which the pipeline for this container is defined.
<static>  
LABKEY.Pipeline.getProtocols(config)
Gets the protocols that have been saved for a particular pipeline.
<static>  
LABKEY.Pipeline.startAnalysis(config)
Starts analysis of a set of files using a particular protocol definition with a particular pipeline.
Namespace Detail
LABKEY.Pipeline
Method Detail
<static> LABKEY.Pipeline.getFileStatus(config)
Gets the status of analysis using a particular protocol for a particular pipeline.
Parameters:
{Object} config
A configuration object with the following properties.
{String} config.taskId
Identifier for the pipeline.
{String} config.path
relative path from the folder's pipeline root
{String[]} config.files
names of the file within the subdirectory described by the path property
{String} config.protocolName
name of the analysis protocol
{String} config.containerPath Optional
The container in which to make the request (defaults to current container)
{Function} config.success
The function to call with the resulting information. This function will be passed two arguments, a list of file status objects (described below) and the name of the action that would be performed on the files if the user initiated processing ('Retry' or 'Analyze', for example).
  • name: name of the file, a String.
  • status: status of the file, a String
{Function} config.failure Optional
A function to call if an error occurs. This function will receive one parameter of type object with the following properties:
  • exception: The exception message.
{Object} config.scope Optional
The scope to use when calling the callbacks (defaults to this).

<static> LABKEY.Pipeline.getPipelineContainer(config)
Gets the container in which the pipeline for this container is defined. This may be the container in which the request was made, or a parent container if the pipeline was defined there.
Parameters:
{Object} config
A configuration object with the following properties.
{Function} config.success
The function to call with the resulting information. This function will be passed a single parameter of type object, which will have the following properties:
  • containerPath: the container path in which the pipeline is defined. If no pipeline has been defined in this container hierarchy, the value of this property will be null.
  • webDavURL: the WebDavURL for the pipeline root.
{Function} config.failure Optional
A function to call if an error occurs. This function will receive one parameter of type object with the following properties:
  • exception: The exception message.
{String} config.containerPath Optional
The container in which to make the request (defaults to current container)
{Object} config.scope Optional
The scope to use when calling the callbacks (defaults to this).

<static> LABKEY.Pipeline.getProtocols(config)
Gets the protocols that have been saved for a particular pipeline.
Parameters:
{Object} config
A configuration object with the following properties.
{String} config.taskId
Identifier for the pipeline.
{String} config.path
relative path from the folder's pipeline root
{Boolean} config.includeWorkbooks
If true, protocols from workbooks under the selected container will also be included
{String} config.containerPath Optional
The container in which to make the request (defaults to current container)
{Function} config.success
The function to call with the resulting information. This function will be passed a list of protocol objects, which will have the following properties:
  • name: name of the saved protocol.
  • description: description of the saved protocol, if provided.
  • xmlParameters: bioml representation of the parameters defined by this protocol.
  • jsonParameters: JSON representation of the parameters defined by this protocol.
  • containerPath: The container path where this protocol was saved
{Function} config.failure Optional
A function to call if an error occurs. This function will receive one parameter of type object with the following properties:
  • exception: The exception message.
{Object} config.scope Optional
The scope to use when calling the callbacks (defaults to this).

<static> LABKEY.Pipeline.startAnalysis(config)
Starts analysis of a set of files using a particular protocol definition with a particular pipeline.
Parameters:
{Object} config
A configuration object with the following properties.
{String} config.taskId
Identifier for the pipeline.
{String} config.path
relative path from the folder's pipeline root
{String[]} config.files
names of the file within the subdirectory described by the path property
{Integer[]} config.fileIds
data IDs of files be to used as inputs for this pipeline. these correspond to the rowIds from the table ext.data. they do not need to be located within the file path provided. the user does need read access to the container associated with each file.
{String} config.protocolName
name of the analysis protocol
{String} config.protocolDescription Optional
description of the analysis protocol
{String} config.pipelineDescription Optional
description displayed in the pipeline
{String|Element} config.xmlParameters Optional
XML representation of the protocol description. Not allowed if a protocol with the same name has already been saved. If no protocol with the same name exists, either this property or jsonParameters must be specified.
{String|Object} config.jsonParameters Optional
JSON representation of the protocol description. Not allowed if a protocol with the same name has already been saved. If no protocol with the same name exists, either this property or xmlParameters must be specified.
{String} config.saveProtocol Optional
if no protocol with this name already exists, whether or not to save this protocol definition for future use. Defaults to true.
{String} config.containerPath Optional
The container in which to make the request (defaults to current container)
{Function} config.success
A function to call if this operation is successful.
{Function} config.failure Optional
A function to call if an error occurs. This function will receive one parameter of type object with the following properties:
  • exception: The exception message.
{Object} config.scope Optional
The scope to use when calling the callbacks (defaults to this).

Documentation generated by JsDoc Toolkit 2.3.2 on Thu Jun 11 2020 17:30:56 GMT-0000 (UTC)