Clarity LIMS
Illumina Connected Software
Clarity LIMS Software
Clarity LIMS Software
  • Announcements
  • 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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On this page
  • Compatibility
  • Isolate System Components
  • Start with the Script
  • Validate AI Node/Automation Worker
  • Review Automated Informatics Log File

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  1. API and Database
  2. API Portal
  3. Automation

Troubleshooting Automation

Compatibility

Clarity LIMS v4 and later

Automation is powerful and simple in design. However, its applications can quickly become complex. We recommend you keep your scripts simple. When troubleshooting, the best practice is to isolate the issue to determine the source. The Automated Informatics (AI)/automation worker log file, automatedinformatics.log, is useful for isolating system components and diagnosing problems.

Isolate System Components

Isolate the behavior of each component in the system. In particular, determine if the following components can be ruled out as causing of the problem:

  • The script or program—Running the custom logic, REST calls, and file handling.

  • The AI nodes/automation workers—Calling the command line and invoking the script or program.

  • The network—Providing reliable and timely TCP/IP packet transfers.

  • The client—Completing the process/step and notifying the server.

  • The server—Responding to client notifications and dispatching to AI nodes/automation workers.

Start with the Script

The script provides many options for troubleshooting. For example, increase logging to rule out unexpected behavior.

  • Printing to stderr in the script writes a line to the Error Handling automatedinformatics.log file. This file is a great source of information.

  • The records in the log file allow for emulating the command-line call for unit testing the script, and calling it manually on the command-line prompt (see Review Automated Informatics Log File).

  • Validate AI Node/Automation Worker helps verify the automation program on the AI node/automation worker. If the script and the AI node/automation worker are functioning, review the log file entries for any warning (WARN) or error (ERR) lines near the time-stamp of the process completion event sent from the client.

  • If the issue is related to the client or server software, contact the Illumina Support team, providing:

    • The automatedinformatics.log file

    • The server log

    • The results of the isolation tests (in the previous section).

Validate AI Node/Automation Worker

Use the following steps to test and verify the setup.

Test and Verify Setup on a Windows AI Node/Automation Worker

  1. Create a process/step that generates a result file.

  2. Configure an automation on the process/step. Associate it with the channel on which the AI node/automation worker is configured to communicate.

  3. Add the following command line string.

    cmd /c "C:\ai\ai.bat {outputFile0}"

  4. On the AI node/automation worker machine, create an ai folder in C:\ so the system has an C:\ai path. Create a new file named ai.bat.

  5. Edit the ai.bat file and add the following line:

    echo Data for Output File LIMS ID %1 > %1.txt

  6. Run the process/step created on an existing attached result file.

    • The step passes the LIMS ID of its output file placeholder to the script.

    • The script creates a file in the working directory.

    • When the script exits, this file transfers to the LIMS and associated with the step. The file contains a single line of text that includes the LIMS ID of the output file for easy verification.

Test and Verify Setup on a Linux AI Node/Automation Worker

  1. Create a process/step that generates a result file

  2. Configure an automation on the process/step. Associate it with the channel on which the AI node/automation worker is configured to communicate.

  3. Add the following command line string:

    bash -c "echo Automation Test > {outputFile0}.txt"

  4. Run the process/step created on an existing attached result file.

    • The step passes the LIMS ID of its output file placeholder to the script.

    • The script creates a file in the working directory with a file name that contains this LIMS ID.

    • When the script exits, this file transfers to the LIMS and associated with the step. The file contains the text "Automation Test". When open, the file opens in the default program associated with *.txt files.

With automation, the command-line information is important. The actual values sent on the command line are recorded in the AI log file as the AI node/automation worker receives them. Copy the parameters/tokens from the log and use them on the command line to troubleshoot. If scripting in Groovy, the cli class handles command-line tokens well. See the example *.groovy files used with automation and the utility class section in Work with EPP/Automation and Files.

Review Automated Informatics Log File

AI nodes/automation workers are installed using the Automated Informatics (Automation Worker for LIMS v5 and later) software package.

In the installation directory:

  1. Find the /log directory, which contains an automatedinformatics.log file.

  2. Use this file to locate log lines near the time of the process/step completion event.

    • Locate the log line containing the parameter/token command string, and manually run and test the script.

    • Locate the working directory to review temporary files created.

Step 1: Locate log lines near time of the process completion event

This step can indicate if the cause of the error lies with a network or other issue external to the computer running the AI node / automation worker.

  • If no records are found, use the Validate AI Node/Automation Worker procedure to confirm that logging is functional.

Step 2: Locate log line containing parameter/token command string to manually run/test script

Running the script manually forms a unit test. The script is run on the command line, without being invoked by automation.

To locate the line containing the command-line string, search for the Command string, or externalprogram.runExternalProgram.

An example is shown in the following abridged log file section. Copy the line to a text file and modify it for script testing.

2014-02-28 21:24:48,688 INFO ... definitions.behaviour.automatedinformatics.plugins.externalprogram.runExternalProham as ...

2014-02-28 21:24:49,323 INFO ... (ExternalProgramBehaviour.java:133)... Command string: bash -c "~/scripts/HelloWorld.sh http://###.###.###.###/api/v2/processes/A30-MXX-110228-24-2320 > 92-2869.txt"

Step 3: Locate working directory to review temporary files created

Used when temporary files are left by the script, this automation script removes the temporary working directory, unless there was an error. In case of an error, the directory provides clues to the root cause of the error.

To locate the working directory, search for "Working directory:" in the log file.

An example is shown in the following abridged log file section. Use the recorded directory to list and review temporary files.

2014-02-28 21:24:49,324 INFO ... Working directory: /home/gls/GenoLogicsAutomatedInformatics/temp/runExternalProgram-28022014-432350866632555775.A30-MXX-110228-24-2320

2014-02-28 21:24:49,324 INFO ... Retrieved files. Executing command.

As of BaseSpace Clarity LIMS v5.0, several terms have been deprecated:

  • Automation replaces External Program Integration Plug-in (EPP). In LIMS v4.x and earlier, the Operations Interface still uses the term EPP.

  • Automation worker/AW node replaces AI node.

  • Token replaces Parameter.

  • Step replaces Process in the web interface.

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Last updated 10 months ago

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