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Clarity LIMS Software
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Clarity LIMS Software
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  • Clarity LIMS
    • Clarity & LabLink
  • API and Database
    • API Portal
      • REST
        • REST General Concepts
        • REST Web Services
        • HTTP Response Codes and Errors
        • XML UTF-8 Character Encoding
        • Requesting API Version Information
        • Viewing Paginated List Resources
        • Filtering List Resources
        • Working with User-Defined Fields (UDF) and Types (UDT)
        • Traversing a Genealogy
        • Working with Batch Resources
      • Getting Started with API
        • Understanding API Terminology (LIMS v5 and later)
        • API-Based URIs (LIMS v4 and later)
        • Development Prerequisites
        • Structure of REST Resources
        • The Life Cycle of a Sample: Stages Versus Steps
        • Integrating Scripts
      • Automation
        • Automation Triggers and Command Line Calls
        • Automation Execution Environment
        • Supported Command Line Interpreters
        • Automation Channels
        • Error Handling
        • Automation Tokens
          • Derived Sample Automation Tokens
          • Step Automation Tokens
          • Project Automation Tokens
        • Automation Testing
        • Troubleshooting Automation
      • Tips and Tricks
        • Accessing Step UDFs from a different Step
        • Obfuscating Sensitive Data in Scripts
        • Integrating Clarity LIMS with Upstream Sample Accessioning Systems
        • Creating Samples and Projects via the API
        • Displaying Files From an Earlier Step
        • Transitioning Output Artifacts into the Next Step
        • Determining the Workflow(s) to Which a Sample is Assigned
        • Standardizing Sample Naming via the API
        • Copying UDF Values from Source to Destination
        • Updating Preset Value of a Step UDF through API
        • Automating BCL Conversion
        • Finding QC Flags in Aggregate QC (Library Validation) via REST API
        • Setting the Value of a QC Flag on an Artifact
        • Creating Notifications When Files are Added via LabLink
        • Remote HTTP Filestore Setup
      • Cookbook
        • Get Started with the Cookbook
          • Tips and Troubleshooting
          • Obtain and Use the REST API Utility Classes
        • Work with EPP/Automation and Files
          • Automation Trigger Configuration
          • Process Execution with EPP/Automation Support
        • Work with Submitted Samples
          • Adding Samples to the System
          • Renaming Samples
          • Assigning Samples to Workflows
          • Updating Sample Information
          • Show the Relationship Between Samples and Analyte Artifacts (Derived Samples)
        • Work with Containers
          • Add an Empty Container to the System
          • Find the Contents of a Well Location in a Container
          • Filter Containers by Name
        • Work with Derived Sample Automations
          • Remove Samples from Workflows
          • Requeue Samples
          • Rearray Samples
        • Work with Process/Step Outputs
          • Update UDF/Custom Field Values for a Derived Sample Output
          • Rename Derived Samples Using the API
          • Find the Container Location of a Derived Sample
          • Traverse a Pooled and Demultiplexed Sample History/Genealogy
          • View the Inputs and Outputs of a Process/Step
        • Work with Projects and Accounts
          • Remove Information from a Project
          • Add a New Project to the System with UDF/Custom Field Value
          • Get a Project Name
          • Find an Account Registered in the System
          • Update Contact (User and Client) Information
        • Work with Multiplexing
          • Find the Index Sequence for a Reagent Label
          • Demultiplexing
          • Pool Samples with Reagent Labels
          • Apply Reagent Labels with REST
          • Apply Reagent Labels When Samples are Imported
          • Apply Reagent Labels by Adding Reagents to Samples
        • Working with User Defined Fields/Custom Fields
          • About UDFs/Custom Fields and UDTs
          • Performing Post-Step Calculations with Custom Fields/UDFs
        • Work with Processes/Steps
          • Filter Processes by Date and Type
          • Find Terminal Processes/Steps
          • Run a Process/Step
          • Update UDF/Custom Field Information for a Process/Step
          • Work with the Steps Pooling Endpoint
        • Work with Batch Resources
          • Introduction to Batch Resources
          • Update UDF/Custom Field Information with Batch Operations
          • Retrieve Multiple Entities with a Single API Interaction
          • Select the Optimal Batch Size
        • Work with Files
          • Attach a File with REST and Python
          • Attach Files Located Outside the Default File Storage Repository
          • Attach a File to a File Placeholder with REST
        • Work with Controls
          • Automated Removal of Controls from a Workflow
      • Application Examples
        • Python API Library (glsapiutil.py) Location
        • Scripts That Help Automate Steps
          • Route Artifacts Based Off a Template File
          • Invoking bcl2fastq from BCL Conversion and Demultiplexing Step
          • Email Notifications
          • Finishing the Current Step and Starting the Next
          • Adding Downstream Samples to Additional Workflows
          • Advancing/Completing a Protocol Step via the API
          • Setting a Default Next Action
          • Automatic Placement of Samples Based on Input Plate Map (Multiple Plates)
          • Automatic Placement of Samples Based on Input Plate Map
          • Publishing Files to LabLink
          • Automatic Pooling Based on a Sample UDF/Custom Field
          • Completing a Step Programmatically
          • Automatic Sample Placement into Existing Containers
          • Routing Output Artifacts to Specific Workflows/Stages
          • Creating Multiple Containers / Types for Placement
          • Starting a Protocol Step via the API
          • Setting Quality Control Flags
          • Applying Indexing Patterns to Containers Automatically
          • Assignment of Sample Next Steps Based On a UDF
          • Parsing Metadata into UDFs (BCL Conversion and Demultiplexing)
        • Scripts That Validate Step Contents
          • Validating Process/Step Level UDFs
          • Checking That Containers Are Named Appropriately
          • Checking for Index Clashes Based on Index Sequence
          • Validating Illumina TruSeq Index Adapter Combinations
        • Scripts Triggered Outside of Workflows/Steps
          • Repurposing a Process to Upload Indexes
          • Adding Users in Bulk
          • Moving Reagent Kits & Lots to New Clarity LIMS Server
          • Programatically Importing the Sample Submission Excel File
          • Generating an MS Excel Sample Submission Spreadsheet
          • Assigning Samples to New Workflows
        • Miscellaneous Scripts
          • Illumina LIMS Integration
          • Generating a Hierarchical Sample History
          • Protocol-based Permissions
          • Self-Incremental Counters
          • Generic CSV Parser Template (Python)
          • Renaming Samples to Add an Internal ID
          • Creating Custom Sample Sheets
          • Copying Output UDFs to Submitted Samples
          • Parsing Sequencing Meta-Data into Clarity LIMS
          • Submit to a Compute Cluster via PBS
          • Downloading a File and PDF Image Extraction
        • Resources and References
          • Understanding LIMS ID Prefixes
          • Container States
          • Useful Tools
          • Unsupported Artifact Types
          • Unsupported Process Types
          • Suggested Reading
          • API Training Videos
  • Illumina Preset Protocols
    • IPP v2.10
      • Release Notes
      • Installation and User Configuration
      • Manual Upgrade
    • IPP v2.9
      • Release Notes
      • Installation and User Configuration
    • IPP v2.8
      • Release Notes
      • Installation and User Configuration
      • Manual Upgrade
    • IPP v2.7
      • Release Notes
      • Installation and User Configuration
    • IPP v2.6
      • Release Notes
      • Installation and User Configuration
      • Manual Upgrade
  • Sample Prep
    • QC and Sample Prep
      • DNA Initial QC 5.1.2
      • RNA Initial QC 5.1.2
      • Library Validation QC 5.1.2
  • Library Prep
    • AmpliSeq for Illumina
      • BRCA Panel
        • Library Preparation v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Cancer HotSpot Panel v2
        • Library Preparation v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Childhood Cancer Panel
        • DNA Library Prep v1.1
        • RNA Library Prep v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Comprehensive Cancer Panel
        • Library Preparation v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Comprehensive Panel v3
        • DNA Library Prep v1.1
        • RNA Library Prep v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Custom DNA Panel
        • Library Preparation v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Focus Panel
        • DNA Library Prep v1.1
        • RNA Library Prep v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Immune Repertoire Panel
        • RNA Library Prep v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Immune Response Panel
        • RNA Library Prep v1.1
        • Equalizer v1.1
        • Standard v1.1
      • Myeloid Panel
        • DNA Library Prep v1.1
        • RNA Library Prep v1.1
        • Equalizer v1.1
        • Standard v1.1
      • TCR beta-SR Panel
        • DNA Library Prep v1.1
        • RNA Library Prep v1.1
      • Transcriptome Human Gene Expression Panel
        • RNA Library Prep v1.1
        • Equalizer v1.1
        • Standard v1.1
    • Library Prep Validation
    • Nextera
      • Nextera Mate Pair v1.0
      • Nextera Rapid Capture Custom Enrichment v2.0
      • Nextera XT v2.0
    • Targeted Enrichment
      • Illumina DNA Prep with Enrichment (S) Tagmentation v1.2
      • Illumina RNA Prep with Enrichment (L) Tagmentation v1.1
    • TruSeq
      • TruSeq ChIP-Seq v1.0
      • TruSeq Custom Amplicon v1.0
      • TruSeq DNA Exome v2.0
      • TruSeq DNA PCR-Free v2.0
      • TruSeq Methyl Capture EPIC v2.0
      • TruSeq Nano DNA v1.0
      • TruSeq RNA Access v2.0
      • TruSeq RNA Exome v1.0
      • TruSeq Small RNA v1.0
      • TruSeq Stranded mRNA v2.0
    • TruSight
      • TruSight Oncology 500 ctDNA v1.1
      • TruSight Oncology 500 HT v1.1
      • TruSight Oncology 500 v1.1
      • TruSight Tumor 170 v2.0
    • Other DNA Protocols
      • Illumina DNA PCR-Free Library Prep Manual v1.1
      • Illumina DNA Prep (M) Tagmentation v1.0
    • Other RNA Protocols
      • Illumina Stranded mRNA Prep Ligation 1.1
      • Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus v1.1
  • iLASS & Infinium Arrays
    • iLASS
      • iLASS Infinium Genotyping v1.1
        • iLASS Infinium Batch DNA v1.1
        • iLASS Infinium Genotyping Assay v1.1
        • iLASS Infinium Genotyping with PGx Assay v1.1
      • iLASS Infinium Genotyping v1.0
        • iLASS Infinium Genotyping Assay v1.0
        • iLASS Infinium Genotyping with PGx Assay v1.0
    • Infinium Arrays
      • Infinium HD Methylation Assay Manual v1.2
      • Infinium HTS Assay Manual v1.2
      • Infinium LCG Assay Manual v1.2
      • Infinium XT Assay Manual v1.2
      • GenomeStudio v1.0
  • Applications
    • IGA
      • IGA v2.1
        • IGA Library Prep Automated v2.1
        • IGA NovaSeq Sequencing v2.1
    • Viral Pathogen Protocols
      • CDC COVID-19 RT-PCR
        • Sort Specimens to Extraction v1.1
        • Qiagen QIAamp DSP Viral RNA Mini Kit v1.1
        • Qiagen EZ1 Advanced XL v1.1
        • Roche MagNA Pure LC v1.1
        • Roche MagNA Pure Compact v1.1
        • Roche MagNA Pure 96 v1.1
        • bioMerieux NucliSENS easyMAG Instrument v1.1
        • bioMerieux EMAG Instrument v1.1
        • Real-Time RT-PCR Prep v1.1
      • Illumina COVIDSeq v1.6
      • Respiratory Virus Panel v1.0
  • Instruments & Integrations
    • Compatibility
    • Integration Properties
      • Integration Properties Details
    • Clarity LIMS Product Analytics
      • Supported Workflows
      • Workflow Customization
      • Clarity LIMS Product Analytics v1.4.0
        • Configuration
      • Clarity LIMS Product Analytics v1.3.1
        • Configuration
      • Clarity LIMS Product Analytics v1.3.0
        • Configuration
      • Clarity LIMS Product Analytics v1.2.0
        • Configuration
    • Illumina Run Manager
      • Illumina Run Manager v1.0.0
        • Installation and User Interaction
    • iScan
      • iScan System
      • iScan v1.2.0
        • Release Notes
        • BeadChip Accessioning, Imaging, and Analysis
      • iScan v1.1.0
        • Release Notes
        • BeadChip Accessioning, Imaging, and Analysis
      • iScan System v1.0
    • iSeq 100 Run Setup v1.0
    • MiniSeq v1.0
    • MiSeq
      • MiSeq v8.3.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
      • MiSeq v8.2.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
        • Manual Upgrade
    • MiSeq i100 (On-Prem)
      • MiSeq i100 On-Prem v1.0.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • MiSeq i100 (Hosted)
      • MiSeq i100 v1.0.0
        • Release Notes
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • MiSeqDx
      • MiSeqDx Sample Sheet Generation (v1.11.0 and later)
      • MiSeqDx v1.11.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
      • MiSeqDx v1.10.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
        • Sample Sheet Generation
        • Manual Upgrade
    • Next Generation Sequencing Package
      • Release Notes
        • NGS Extensions v5.25.0
        • NGS Extensions v5.24.0
        • NGS Extensions v5.23.0
      • Accession Kit Lots
      • Auto-Placement of Reagent Indexes
      • Compute Replicate Average
      • Copy UDFs
      • Initialize Artifact UDFs
      • Label Non-Labeled Outputs
      • Linear Regression Calculation
      • Normalization Buffer Volumes
      • Process Summary Report
      • Routing Script
      • Set UDF
      • Validate Complete Plate
      • Validate Sample Count
      • Validate Unique Indexes
    • NextSeq 500/550
      • NextSeq 500/550 v2.5.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
        • Manual Upgrade
      • NextSeq 500/550 v2.4.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
      • NextSeq 500/550 v2.3.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • NextSeq 1000/2000 (Hosted)
      • NextSeq 1000/2000 v2.5.1
        • Release Notes
      • NextSeq 1000/2000 v2.5.0
        • Release Notes
        • Configuration
        • User Interaction, Validation and Troubleshooting
        • Manual Upgrade
      • NextSeq 1000/2000 v2.4.0
        • Release Notes
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • NextSeq 1000/2000 (On-Prem)
      • NextSeq 1000/2000 On-Prem v1.0.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • NovaSeq 6000 (API-based)
      • NovaSeq 6000 API-based v3.7.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
      • NovaSeq 6000 API-based v3.6.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
        • Manual Upgrade
    • NovaSeq 6000 (File-based)
      • NovaSeq 6000 File-based v2.6.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
      • NovaSeq 6000 File-based v2.5.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • NovaSeq 6000Dx (API-based)
      • NovaSeq 6000Dx API-based v1.3.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
      • NovaSeq 6000Dx API-based v1.2.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • NovaSeq X Series (Hosted)
      • NovaSeq X Series v1.3.0
        • Release Notes
        • Configuration
        • Manual Upgrade
      • NovaSeq X Series v1.2.1
        • Release Notes
      • NovaSeq X Series v1.2.0
        • Release Notes
        • Configuration
        • User Interaction, Validation and Troubleshooting
        • Manual Upgrade
      • NovaSeq X Series v1.1.0
        • Release Notes
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • NovaSeq X Series (On-Prem)
      • NovaSeq X Series On-Prem v1.0.0
        • Release Notes
        • Installation
        • Configuration
        • User Interaction, Validation and Troubleshooting
    • References
      • Configure Multiple Identical netPathPrefixSearch Values
      • Configure Support for Samples Having Duplicate Names with Different Indexes
      • Illumina Instrument Sample Sheets
      • Terminology
  • Integration Toolkits
    • Lab Instrument Toolkit
      • Template File Generator
        • Creating Template Files
        • Template File Contents
        • Template File Generator Troubleshooting
      • Add Blank Lines
      • Convert CSV to Excel
      • Parse CSV
      • Name Matching XML Parser
      • Sample Placement Helper
    • Lab Logic Toolkit
      • Working with Lab Logic Toolkit
        • Data Collection Entities
        • Failing a Script
        • Mapping Field Types
        • Non-UDF/Custom Field Properties
        • Setting QC Flags
        • Setting Next Actions
        • Specifying Custom Fields
        • Working with Submitted Samples
        • Working with Containers
      • Lab Logic Toolkit Script Examples
        • Comparing Stop/Start Dates and Times with LLTK
      • Lab Logic Toolkit FAQ
  • Known Issues
    • Integration
      • Sample Sheet Generation Issue and CLPA Issues When Samples Have Been Assigned QC Flag Prior to Entering Steps
  • Security Bulletin
    • Investigation of OpenSSH vulnerability with Clarity LIMS
  • Resources
    • Third Party Software Information
  • Others
    • Revision History
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  • Non-production Scripting Sandbox Server
  • Cookbook Examples for Learning the API on Nonproduction Servers
  • Related resources

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  1. API and Database
  2. API Portal
  3. Application Examples
  4. Resources and References

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Last updated 10 months ago

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To help with learning, BaseSpace Clarity LIMS documentation includes:

  • An introduction to the API architecture (see REST General Concepts).

  • Details of the methods and interfaces (see REST API documentation and Automation).

  • Example code (see Cookbook).

However, there is more to the Clarity LIMS Rapid Scripting™ API package than these resources.

Details on tools, training, and best practices are covered in the following sections and in Development Prerequisites.

Non-production Scripting Sandbox Server

Nonproduction server licenses and training are essential. A nonproduction scripting sandbox server is set up with Groovy, BaseSpace Clarity LIMS, and automation ready to be used with the scripts provided in the Cookbook and with the .

  • Have the nonproduction servers set up before learning to script (see Development Prerequisites).

  • All the examples in the Cookbook are intended to be used with the nonproduction scripting sandbox server. This server has all the software packaged up to start scripting with the API.

  • The Cookbook examples do not explain how to configure the servers for process configuration. Server installation and server-side configuration instructions are covered during implementation, as part of the installation and training services.

  • For more information and to understand the importance of a dedicated scripting server, see Development Prerequisites.

Cookbook Examples for Learning the API on Nonproduction Servers

The nonproduction server license and the Cookbook examples are not for production use. It is not practical to integrate actual instruments to this server permanently, but it does provide a great way to learn to script.

The nonproduction scripting sandbox server provides a safe place to learn the API, using the Cookbook example scripts as a guide. The typical installation includes the Clarity LIMS software, the Automation Informatics node (referred to as the automation worker in Clarity LIMS v5), and Groovy.

Installation and Administration Training

IInstallation and administration training enables IT administrators to support multiple script writers with multiple nonproduction servers for development and testing. Administrators learn about server-side tools and procedures, such as the backup and restore procedure. This procedure moves scripts between systems.

  • The production and nonproduction server installation training is provided to IT administrators at the start of each implementation or when the Rapid Scripting API package is purchased.

  • Automation Worker (AW) node training is also included. This component can be installed on multiple computers using the Automation Worker software package.

  • Explore other training, consulting, and issue management services available from Illumina in case the packaged services are exceeded.

Contact Illumina if you need additional training or support for installing and maintaining servers and AW nodes.

API Training and Consulting

The script training includes instructor-led, hands-on sessions and the training included on this site.

Instructors start from a basic Hello World script kicked off from within Clarity LIMS using automation, then progress to more in-depth concepts.

Also provided in the package is on-demand consulting. For quality service, all requests are handled via the Support team. However, expert script writers are available in technical services to consult by email, phone, or web-based sessions.

Script Deployment

Illumina recommends placing scripts in sub-directories starting from a common root, namely /opt/gls/clarity/customextensions/.

This makes moving scripts between development, test, and production systems much easier and less error-prone. This directory is assumed by the backup and restore process.

Use a directory structure beneath this root to expand your deployed scripts over time. This customextensions folder is reserved exclusively for your custom scripts.

At Illumina, this practice is called deploying on the rails. The following directories illustrate how this method is used to deploy multiple instrument integrations.

/opt/gls/clarity/extensions/
/opt/gls/clarity/extensions/Illumina/HiSeq/v1.1
/opt/gls/clarity/extensions/ABI/SOLiD/v1.0
/opt/gls/clarity/customextensions/'YourRootDirectory'
- root dir for all automation scripts
- Integration from Illumina, do not modify
- Another integration for Illumina
- Scripts created by you

Putting all the scripts into a common root directory also allows multiple teams to work on the implementation independently. For example, when Illumina provides custom integrations and you are scripting at the same time. The backup and restore process allows you to transfer all files in the root directory between systems. It is important to not place server-specific settings, such as IP addresses or login details, in these directories.

To learn more about the backup and restore process, talk to the IT Administrator (who attended the installation and administration training) and refer to the Clarity LIMS Installation Procedure documentation (accessible from the Installation section of the Clarity LIMS documentation).

Groovy

The Cookbook how-to examples and the nonproduction server use scripts written in Groovy, a Java-based scripting language.

You can use other languages with the API. However, Groovy is easy to understand. Groovy scripts look similar to pseudocode.

In addition, Groovy is particularly suited to real scripting because it handles and manipulates the major inputs, outputs, and interfaces within Clarity LIMS well.

Related resources

  • Development Prerequisites

  • Integrating Scripts

  • Suggested Reading

Clarity LIMS API Application Examples