Adding Samples to the System

You can add samples to the system using API (v2 r21 and later). This example assumes that you have sample information in a file that is difficult to convert into a format suitable for importing into Clarity LIMS. The aim is to add the samples, and all associated data, into Clarity LIMS without having to translate the file manually. You can use the REST API to add the samples.

Prerequisites

Follow the instructions provided in the following examples:

• Add a New Project to the System with UDF/Custom Field Value

• Add an Empty Container to the System

Code example

To add a sample in Clarity LIMS, you must assign it to a project and place it into a container. This example assumes that you are adding a new project and container for the samples being created.

Step 1. Create a New Project

As shown in Add a New Project to the System with UDF/Custom Field Value, you define a project by using StreamingMarkupBuilder. StreamingMarkupBuilder is a built-in Groovy data structure designed to build XML structures. This structure creates the XML that is used in a POST to the projects resource:

def builder = new StreamingMarkupBuilder()
builder.encoding = "UTF-8"
String openDate = new SimpleDateFormat("yyyy-MM-dd").format(new Date())
 
// Create a new project using the Markup Builder
def projectDoc = builder.bind {
    mkp.xmlDeclaration()
    mkp.declareNamespace(prj: 'http://genologics.com/ri/project')
    'prj:project' {
        'name'("${projectName}")
        'open-date'("${openDate}")
        'researcher'(uri:researcherURI)
    }
}
// Post the new project to the API
createdProjectNode = GLSRestApiUtils.xmlStringToNode(projectDoc.toString())
createdProjectNode = GLSRestApiUtils.httpPOST(createdProjectNode, "${projectListURI}", username, password)
println GLSRestApiUtils.nodeToXmlString(createdProjectNode)

If the POST to projects is successful, the following XML is returned:

<prj:project xmlns:prj="http://genologics.com/ri/project" uri="http://yourIPaddress/api/v2/projects/EXA2248" limsid="EXA2248">
  <name>Cookbook Project POST 8.1</name>
  <open-date>2010-09-14</open-date>
  <researcher uri="http://yourIPaddress/api/v2/researchers/1"/>
</prj:project>

Step 2. Create a New Container

As shown in the Add an Empty Container to the System example, you can add a container by using StreamingMarkupBuilder to create the XML for a new container. This creates the XML that is used in a POST to the containers resource:

// Determine the URI of the containers list
containersListURI = "http://${hostname}/api/v2/containers"
// Create a new container using the Markup Builder
def containerDoc = builder.bind {
    mkp.xmlDeclaration()
    mkp.declareNamespace(con: 'http://genologics.com/ri/container')
    mkp.declareNamespace(udf: 'http://genologics.com/ri/userdefined')
    'con:container' {
        'name'("${containerName}")
        'type'(uri:"http://${hostname}/api/v2/containertypes/1", name:"96 well plate")
    }
}
// Post the new container to the API
createdContainerNode = GLSRestApiUtils.xmlStringToNode(containerDoc.toString())
println GLSRestApiUtils.nodeToXmlString(createdContainerNode)
createdContainerNode = GLSRestApiUtils.httpPOST(createdContainerNode, containersListURI, username, password)
println GLSRestApiUtils.nodeToXmlString(createdContainerNode)

If the POST to containers is successful, the following XML is returned:

/** NOTE: if the system has unique container name constraints enabled, change this
value every time script runs*/
<con:container xmlns:con="http://genologics.com/ri/container" uri="http://yourIPaddress/api/v2/containers/27-4075" limsid="27-4075">
  <name>Example 8.1 container</name>
  <type uri="http://yourIPaddress/api/v2/containertypes/1" name="96 well plate"/>
</con:container>

Step 3. Create a New Sample

Now that you have the project and container, you can use StreamingMarkupBuilder to create the sample. The XML created to add the sample uses the URIs for the project and container that were created in the previous steps.

// Determine the samples list URI
sampleListURI = "http://${hostname}/api/v2/samples"
// Create a sample using the Markup Builder
def sampleDoc = builder.bind {
  mkp.xmlDeclaration()
  mkp.declareNamespace(smp: 'http://genologics.com/ri/sample')
  'smp:samplecreation' {
    'name'("${sampleName}")
    'project'(uri:"${createdProjectNode.'@uri'}")
    'location' {
        'container'(limsid:"${createdContainerNode.'@limsid'}", uri:"${createdContainerNode.'@uri'}")
        'value'('A:1')
    }
  }
}
// Post the sample to the API
createdSampleNode = GLSRestApiUtils.xmlStringToNode(sampleDoc.toString())
createdSampleNode = GLSRestApiUtils.httpPOST(createdSampleNode, "${sampleListURI}", username, password)
println GLSRestApiUtils.nodeToXmlString(createdSampleNode)

This POST to the samples resource creates a sample in Clarity LIMS, adding it to the project and container specified in the POST.

Expected Output and Results

In Clarity LIMS Projects and Samples dashboard, open the project to find the new sample in its container.

Attachments

PostSample.groovy:

PostSample.groovy

4KB

Open