Publishing Files and Progress

The lab carrying out the processing/assaying of the samples can publish the following, and make them available to collaborators:

• Files that are attached to steps and derived samples.

  Examples include the following use cases:

  • Publishing an image of an electropherogram for a sample that failed Bioanalyzer QC.

  • Publishing small files such as AB1 files that result from Capillary Electrophoresis sequencing.

    NOTE: It is not recommended to publish large NGS or microarray derived data (such as FASTQ or VCF files) through LabLink. Although technically possible, BaseSpace Sequence Hub works much better for these large files.

• Custom fields that are defined and populated on samples in Clarity LIMS. For example, a field that tracks the progress of the samples.

Publish a File

The only way to publish a file is by using the Clarity LIMS API. To publish documents to LabLink, run a custom script in Clarity LIMS at the end of a step.

For example, at the end of a Bioanalyzer QC step, if individual electropherogram images are available, they may be published and made available immediately in LabLink. See the API & Database documentation for an example script that publishes files to LabLink.

Files published to LabLink are available under the Results and Documents tab of a LabLink project, in the Sample Results and Documents section.

The Sample Results and Documents section of the page has three elements for each row:

• Document Name—The name of the file that has been stored in Clarity LIMS and published.

• Sample Name—The name of the sample associated with the published file.

• Download Link—Select this link to download a copy of the file from LabLink.

For example, if all samples in a project participate in a step, publishing a file associated with that step causes the file to also be associated with all samples in that step.

Publishing a step-level file may have undesired consequences. Imagine a single step that was run on samples from two separate LabLink projects. If that step includes a step-level file that is published, it is available to both LabLink projects.

Depending on the contents of the file, publishing might lead to one collaborator seeing sample data that relates to another collaborator.

NOTE: Only publish step-level files if they are associated with samples in a single LabLink project.

Publishing Progress

The lab can publish custom fields that are defined and populated on samples in Clarity LIMS. Collaborators in LabLink can then see these custom fields.

This functionality depends on how Clarity LIMS is configured. For example, assume that the sample-level custom field called Progress should be visible in Clarity LIMS.

1. Define the Progress custom field in Clarity LIMS, including field type, field options, and additional options.

2. Make the Progress custom field visible in LabLink.

   1. Navigate to the Custom Fields screen from the Configuration menu.

   2. Select the Progress checkbox for the field to be visible in LabLink.

3. When samples are first submitted to LabLink, the Progress field is empty.

4. When the lab receives the samples, they may set the Progress field to have the Awaiting QC value for all samples in the project.

5. When the samples have completed the QC steps, the lab may update the Progress field with different values depending on the success or failure of QC.

6. As the samples move through the workflow, lab technicians update the Progress field as required. These updates provide the collaborator with insight into what is happening in the lab, on a per-sample basis. You can configure a script that automatically updates the Progress field, eliminating the need for manual updates by lab technicians. For example, configure the following automation command line that uses Clarity LIMS Lab Logic Toolkit to update the Progress field.

   bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-
   
   extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression - t
   
   true -h false -exp '\
   
   submittedSample.::Progress:: = ::Awaiting QC::; \
   
   ' -log {compoundOutputFileLuid0}"

If the value of the Progress field is long, it may be truncated in LabLink. However, the full value can be obtained by hovering the mouse over the truncated value.

NOTE: Widening the browser window may show more of the field, but truncation may still occur.