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
  • Setting Up Access to the Files
  • Configuring the LIMS Server
  • Example: Mapping a Remote HTTP URI
  • Posting Information to the LIMS Referencing Files on the Remote Filestore

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  1. API and Database
  2. API Portal
  3. Tips and Tricks

Remote HTTP Filestore Setup

PreviousCreating Notifications When Files are Added via LabLinkNextCookbook

Last updated 10 months ago

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${baseName}.dirServer-side configuration allows for configuration of multiple filestores to be associated to entities (samples, projects, processes/steps, and so on) in BaseSpace Clarity LIMS.

This feature allows for linking to large data files on a different server, eliminating the need to move large files on the Clarity LIMS filestore. Large files can include results, images, and searches, and so on.

For example, sequencing instruments typically produce large result files. Attaching these files to the Sequencing step in Clarity LIMS results in the following drawbacks.

  • Involves transferring the files to the Clarity LIMS filestore. The larger the file, the slower the transfer speed.

  • Requires a large amount of space as runs build up.

An alternative solution is to set up a remote filestore to be used as the results directory from which Clarity LIMS accesses the files directly.

To do this setup, three steps are required:

  1. Set up HTTP, HTTPS, FTP, or SFTP access to the files and folders you wish to share.

  2. Configure the Clarity LIMS server to recognize the URI of a file on the remote filestore.

  3. POST information to Clarity LIMS, via the REST API, to reference the file from a Clarity LIMS entity (project, sample, process/step, result file, and so on).

Setting Up Access to the Files

BaseSpace Clarity LIMS can operate with many different forms of file servers – HTTP, HTTPS, FTP, and SFTP access are all supported.

It is your responsibility to set up this access. For HTTP, you may be interested in or for HTTP file serving.

Configuring the LIMS Server

Properties Required for Tracking a New Remote Filestore

To track a new remote filestore, Clarity LIMS requires four database properties: directory, host, port, and scheme.

The four properties share a base name, but have different suffixes attached (dir, host, port, scheme). These suffixes are summarized in the following table.

  • The base name can be anything. Clarity LIMS finds any base names that end in .scheme and uses that base name to find the other information.

  • If necessary, add the last three properties listed in the table (with the .domain, .user, and .password suffixes) to specify a domain, username, and password to be used when accessing files.

Property Name
Usage
Example Value
Required
Description

Directory

${baseName}.dir

/limsdata

True

The highest level directory in which it is valid to access files. Files outside this directory are not attached.

Hostname/IP

${baseName}.host

YourHTTPHost

True

The hostname or IP address to use when accessing the files.

Port

${baseName}.port

80

True

The port to use when accessing the files.

Scheme

${baseName}.scheme

http

True

The scheme of the URI used to access the files. Examples are HTTP, HTTPS, FTP, and SFTP.

Domain

${baseName}.domain

YourAuthDomain

False

The domain to use when authenticating access to the files.

Username

${baseName}.user

fileUser

False

The username to use when authenticating access to the files.

Password

${baseName}.password

filePassword

False

The password to use when authenticating access to the files.

It is highly recommended that you encrypt your password. See the following section for details.

  • Clarity LIMS v5 and later—For the property changes to take effect, Tomcat must be restarted.

Working with the Database Properties

Use the omxprops-ConfigTool.jar to create, update, and retrieve values of the database properties. This tool is found at the following location: /opt/gls/clarity/tools/propertytool

To create a property, use the following examples:

java -jar omxprops-ConfigTool.jar addPropertyType <baseName><suffix> /<value> <description>

NOTE: These properties may not be global properties. Do not use the -g property here.

To get the value of an existing property:

java -jar omxprops-ConfigTool.jar get <baseName><suffix>

To update the value of an existing property:

java -jar omxprops-ConfigTool.jar set -y <baseName><suffix> <newValue>

To encrypt a password:

java -jar omxprops-ConfigTool.jar encryptPassword <password>

NOTE: To set a property to the encrypted result, set the value as ENC().

Example: Mapping a Remote HTTP URI

In this case, the base name for the properties is http-lims-files.

Steps

  1. As the glsjboss user, access the omxprops property tool in /opt/gls/clarity/tools/propertytool.

  2. Add the following dir, host, port, and scheme properties to the server from the command line:

java -jar omxprops-ConfigTool.jar addPropertyType http-lims-files.dir '/limsdata' 'Alternate filestore server dir'

java -jar omxprops-ConfigTool.jar addPropertyType http-lims-files.host 'YourHTTPHost' 'Alternate filestore host'

java -jar omxprops-ConfigTool.jar addPropertyType http-lims-files.port '80' 'Alternate filestore port'

java -jar omxprops-ConfigTool.jar addPropertyType http-lims-files.scheme 'http' 'Alternate filestore server type'

In the example above, the <http-lims-files.dir> parameter value is /limsdata. Any file in http://<YourHTTPHost/limsdata/ is available to be referenced by BaseSpace Clarity LIMS.

For all files on the web server to be available, use the / parameter value, for example:

java -jar omxprops-ConfigTool.jar addPropertyType -y http-lims-files.dir / Alternate filestore server dir

Posting Information to the LIMS Referencing Files on the Remote Filestore

After the filestore properties are added to Clarity LIMS (and JBoss/Tomcat has been restarted, as applicable), you can attach the files to Clarity LIMS.

To attach the files to Clarity LIMS:

  • POST to http://hostname/api/v2/files, with the content-location tag pointing to the remote filestore.

An example XML POST is provided, using the filestore created in the previous example:

<file:file xmlns:file="http://genologics.com/ri/file">

<content-location>http://YourHTTPHost:80/limsdata/LegacyFile.RAW</content-location>

<attached-to>http://hostname/api/v2/artifacts/92-148</attached-to>

<original-location>http://YourHTTPHost:80/limsdata/LegacyFile.RAW</original-location>

<is-published>false</is-published>

</file:file>

Results

  • The file is now downloadable directly from Clarity LIMS.

  • Any entity that can have a file attached to it may be referenced in the parameter.

For more information on working with files, see Work with Files.

The following example maps a remote HTTP URI:

httpd
HFS
http://YourHTTPHost:80/limsdata/LegacyFile.RAW