Tetra Chromeleon Agent Release Notes (v2.x and Below)

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📘
NOTE
To upgrade the Tetra Chromeleon Agent, see Common Tetra Agent Upgrade and Installation Information and Tetra Chromeleon Agent Installation and Configuration (Version 2.x). As newer versions of Agents are released, their release notes will appear in the Tetra Agent and Tetra Data Release Notes topic.

The following are the Tetra Chromeleon Agent release notes for versions 2.x and earlier.

v2.1.2

Release date: 15 March 2024 (Last updated: 26 April 2024)

What's New

TetraScience has released its next version of the Tetra Chromeleon Agent, version 2.1.2. This release focuses on enhancements, including adding the ability to render Chromeleon Sequence Report Templates in RAW files, automatically detecting changes to regenerate injections, and more. It also introduces a patch for the out of memory issue discovered in v2.1.1 (Issue #3587).

Here are the details for what's new in Tetra Chromeleon Agent v2.1.2.

Prerequisites

The following Tetra Data components are required for Tetra Chromeleon Agent v2.1.2:

Protocol: chromeleon-raw-to-ids v4.0.1
Task Script: chromeleon-raw-to-ids v7.0.1
Intermediate Data Schema (IDS): thermofisher-chromeleon v6.0.1

⚠️
IMPORTANT
This release introduces breaking changes to the Agent’s RAW JSON schema. Starting with RAW JSON schema v3.0, data points are now recorded in Apache Parquet format. The Agent’s RAW JSON is also now contained in a zip file. Any pipelines, protocols, or task scripts that rely on the RAW JSON data directly from the Agent will not be compatible with the latest version and must be updated.

New Functionality

New Functionality includes features not previously available in the Tetra Data Platform (TDP) or Tetra Chromeleon Agent. These features may or may not affect Intended Use for GxP validation purposes.

Tetra Chromeleon Agent New Functionality

There is no new functionality for the Tetra Chromeleon Agent in this release.

Tetra Data New Functionality

The following fields were added to the chromeleon-raw-to-ids protocol:
- methods[*]
- runs[*]
- results[*].chromatogram
- results[*].peaks[*]
- runs[*].sequence.electronic_signature
The chromeleon-raw-to-ids protocol now supports results[*] for non-standard components.
The chromeleon-raw-to-idsIDS now includes is_error fields to indicate when there is an error thrown by the Chromeleon software development kit (SDK).
Added chromatography peak and methods components to the IDS

Enhancements

Enhancements are modifications to existing functionality that improve performance or usability, but don't alter the function or intended use of the system.

Tetra Chromeleon Agent Enhancements

A new Optimized Sequence Scan setting was added to the Injection Service settings. When the Optimized Sequence Scan setting is set to Yes (the default value), the Agent uses the Sequence audit trail to detect changes in Sequences. If set to No, the Agent scans Injections for every Sequence, regardless of changes in each scan iteration.
The Agent's RAW JSON schema has been updated to version v3.0.
Chromeleon Sequence Report Templates are now rendered and included in the RAW file. For each signal in the injection, the Report Template is rendered and included under the Signal.ReportTemplateData property.
The Agent now detects changes and regenerate injections in the following circumstances:
- If any chromatograms on any of the signals associated with an injection are updated
- If the processing method associated with an injection is updated or a different processing method is used
- If the status of the electronic signature associated with the sequence changes, all injections associated with the sequence are now regenerated
To improve scanning efficiency, the Agent now only scans sequences that have changed between scans.
The Agent now includes a build version that provides a more detailed version for troubleshooting. This version is visible on a new About tab in the Agent Management Console. The About tab also includes a button to copy the version (and some system information) to the clipboard for troubleshooting purposes.
The Agent now logs when a Data Vault is enabled or disabled.
If the Agent can't connect during configuration, the Agent Management Console now provides more details on the connection issue. You can select the “Not Connected - click for details” link to view additional information (for example, to see if the connection error was caused by an expired token).

Tetra Data Enhancements

Foreign key/ primary key (FK/PK) relationships are now included in the thermofisher-chromeleon IDS.

Bug Fixes

Optimized Sequence Scan setting has been disabled due to inability to efficiently query the audit trail for Sequences.
Chromeleon SDK objects are released proactively in order to reduce memory pressure during generation.
The summary page loads even on a large number of Total Scanned Injections (Issue #3587).
Injections that are updated to the Finished status after the last update time for the Sequence are now properly detected by the Agent (Issue #3099).
Chromeleon data generated by using IDS v6.0.0 was not indexed into Elasticsearch correctly because of an incorrect mapping, and not increasing the limit on the number of nested fields needed for indexing. This issue is fixed in IDS thermofisher-chromeleon v6.0.1, protocol chromeleon-raw-to-ids v4.0.1, and task script chromeleon-raw-to-ids v7.0.1.
Tetra Chromeleon Agent processes are now consistently stopped correctly when stopping the service.
Data Vaults that aren't accessible by the Chromeleon User the Agent is running under will now display an error row in the Scan Error Summary indicating No Access.
If a Data Vault is inaccessible during a scan attempt, the Agent now generates a single error message only.
Some injections would cause the Agent to run out of memory during generation because of the number of data points. The Agent now writes the data points in signal objects to a separate file in Parquet format and references that separate file in the RAW JSON. The RAW JSON and separate files are then compressed and uploaded as a single archive to the TDP.
The Scan Access Rate metric reported by the Chromeleon Agent was erroneously always reporting 0, which triggered a warning on the TDP Health Monitoring page. The calculation for this metric has been updated to (1 - [Sequence scan error count]) / Total sequence count, where Sequence scan error count is the number of unique sequences with errors in all enabled Data Vaults and Total sequence count is the number of sequences scanned by the Agent in all enabled Data Vaults.
If an injection is modified and scanned multiple times, the Agent no longer double counts them in the Scanned count on the Summary tab.

Deprecated Features

There are no new deprecated features in this release. For more information about TDP deprecations, see Tetra Product Deprecation Notices.

Known and Possible Issues

Report Templates using Report Templates 2.0 do not render correctly using the Chromeleon SDK. This issue is under investigation with the vendor.
Report Templates with pages which require a Component context do not render correctly when using the Chromeleon SDK. This issue is under investigation with the vendor.
Renaming a Report Template that is set as the Default Report Template for a Sequence in Chromeleon will not correctly update the Sequence with the new Report Template name. It will also cause any associated injections to be generated with an empty Report Template. To regenerate these injections after changing the name of a Report Template, you must select the Report Template as the Default Report Template for the Sequence again.
Because of a lack of the sample sequence and injections for testing, the formula used by the following Report Variables is not verified:
- Injection
  - ChemicalFormulaAndAdductMassesSingleLineListUsingInjectionAdducts
  - ChemicalFormulaAndAdductMassesMultiLineListUsingInjectionAdducts
  - ChemicalFormulaAndAdductsSingleLine
  - ChemicalFormulaAndAdductsMultiLine
  - LevelCheck
- Chromatogram
  - MsSignalExtractParameters
    - EvaluationType
- Peak Result
  - AmountDeviationAbsoluteInAmountUnits
  - AmountDeviationRelativeInPercentageOfTheExpectedAmount
  - KValueForDeadTimeStoredInProcessingMethod
  - RelativeAmountForCorrespondingInternalStandardComponent
  - RelativeAmountForCorrespondingReferenceComponent
  - RelativeAreaForCorrespondingInternalStandardComponent
  - RelativeAreaForCorrespondingReferenceComponent
  - RelativeCeAreaForCorrespondingInternalStandardComponent
  - RelativeCeAreaForCorrespondingReferenceComponent
  - RelativeHeightForCorrespondingInternalStandardComponent
  - RelativeHeightForCorrespondingReferenceComponent
  - RelativeRetentionTime
  - ResolutionWithEPFormulaAndPreviousIndentifiedPeak
  - ResolutionWithEPFormulaAndCorrespondingReferenceComponent
  - ResolutionWithEPFormulaAndCorrespondingInternalStandardComponment
  - ResolutionWithUSPFormulaAndPreviousIndentifiedPeak
  - ResolutionWithUSPFormulaAndCorrespondingReferenceComponent
  - ResolutionWithUSPFormulaAndCorrespondingInternalStandardComponment
  - ResolutionWithStatisticalMomentFormulaAndPreviousIndentifiedPeak
  - ResolutionWithStatisticalMomentFormulaAndCorrespondingReferenceComponent
  - ResolutionWithStatisticalMomentFormulaAndCorrespondingInternalStandardComponment
  - RetentionIndexLinear
  - RetentionIndexLogarithmic
- Peak Purity
  - InternalStandardChromatogramChannelName
  - InternalStandardChromatogramDetector
  - InternalStandardPeakName
  - InternalStandardPeakNumber
  - ReferenceMsSpectrumMatch
  - Hit Spectrum
- Peak Fluorescence Spectrum
  - ScanValue2ndGreatestRelativeMaximum
  - ScanValue3rdGreatestRelativeMaximum
  - ScanValue4thGreatestRelativeMaximum
  - ScanValue5thGreatestRelativeMaximum
- Peak Composite
  - IsotopicDotProduct
- Peak Tentative Identification
  - Amount
  - InternalStandardName
    LibraryName
  - Match
  - Name
  - Probability
  - ReverseMatch
- Processing Method
  - BlankRunInjectionName
  - LastFixedCalibrationUpdateOperator
  - LastFixedCalibrationUpdateTime
- Processing Method Component
  - RetentionIndex
- Processing Method Component Detection Parameters
  - BaseLineNoiseStartTime
  - BaseLineNoiseEndTime
  - LockedBaseline
  - MaxAreaReject
  - MaxHeightReject
  - MinBaselineScans
  - PeakShoulderThreshold
  - PeakSliceValue
  - RiderThreshold
  - FrontRidersToMainPeak
  - Sensitivity
  - ValleyToValley
  - VoidVolumeTreatment
- Processing Method Peak Group
  - CurrentInjectionAmount
  - MinAmount
  - MaxAmount
- Processing Method Ms Settings
  - AbsoluteThreshold
  - FixedBaselineCorrectionRangeMaxFor1stFixedRange
  - FixedBaselineCorrectionRangeMaxFor2ndFixedRange
  - FixedBaselineCorrectionRangeMinFor1stFixedRange
  - FixedBaselineCorrectionRangeMinFor2ndFixedRange
- Processing Method Test Case
  - NumberOfFailActions
  - NumberOfPassActions

Security

Dependencies with known vulnerabilities have been updated.

Upgrade Considerations

If an Agent is upgraded, the Agent may require certain database objects to be updated. The user will be prompted for the upgrade of the database (a separate Database updates required prompt will be displayed) when the Agent Management Console or service is started after the Agent is upgraded. The user can choose to either update or exit. Since it is undesirable for the Agent to run with an outdated database, the only options are to either perform the updates, or not perform the updates and close the application. If the user chooses to Close and Exit, they will be prompted again the next time the application is started. If the user selects Update, a progress dialog appears that displays the number of updates that need to be applied along with a progress bar for the current update. Depending on the size of the database, the update may take several minutes to complete.

v2.1.1

Release date: 22 January 2024 (Last updated: 26 April 2024)

🚧
IMPORTANT
Tetra Chromeleon Agent v2.1.1 is now deprecated because of a known issue and customers should not install or upgrade to this version. Customers should upgrade to the latest Agent version instead.

v2.1.0

Release date: 7 December 2023 (Last updated: 26 April 2024)

🚧
IMPORTANT
Tetra Chromeleon Agent v2.1.0 is now deprecated because of a known issue and customers should not install or upgrade to this version. Customers should upgrade to the latest Agent version instead.

v2.0.3

Release date: 3 August 2023

What's New

TetraScience has released its next version of the Tetra Chromeleon Agent, version 2.0.3. This release focuses on enhancements, including adding the ability to configure scan and generation batch size settings.

Prerequisites

The following Tetra Data components are required for the Tetra Chromeleon Agent v2.0.3 release:

Protocol chromeleon-raw-to-ids v3.0.0.

New Functionality

New Functionality includes features not previously available in the Tetra Data Platform (TDP) or Tetra Chromeleon Agent. These features may or may not affect "intended use" for GxP validation purposes.

There is no new functionality in this release.

Enhancements

Enhancements are modifications to existing functionality that improve performance or usability, but don't alter the function or intended use of the system.

Sequence Scan Batch Size and Injection Generation Batch Size settings can now be configured in the Agent Management Console. Customers can use these settings along with the existing Processing Interval setting to optimize scan and generation performance. Customers can also use these settings to manage the number of audits in Chromeleon that are recorded when the Agent connects to it for scan and generation. The default setting for Sequence Scan Batch Size is 25. The default setting for Injection Generation Batch Size is 50.
On the Data Vault tab of the Agent Management Console, the data vault list now displays the Data Vault Server in the tree view within the Server Name column. Customers can use this view to activate or turn off a Data Vault Server. Activating a Data Vault Server allows customers to select one or more data vaults in that server. Turning off a server makes it so that no data vaults in that server can be selected in the Agent, and so that the data vault server will not be accessed during scan. The Agent will scan all of the selected data vaults in the tree and log errors only if any of the data vaults have access errors.

Bug Fixes

There are no customer reported bugs fixed in this release.

Deprecated Features

There are no new deprecated features in this release. For more information about TDP deprecations, see Tetra Product Deprecation Notices.

Known and Possible Issues

There are no known issues in this release.

Upgrade Considerations

To upgrade the Agent, see Tetra Chromeleon Agent Installation and Configuration (Version 2.x). To upgrade the protocol, see Edit a Pipeline.

v2.0.2

RELEASE DATE: 3 November 2022

Enhancements

The following are enhancements for this release.

AG-2537 - Added “Decode Injection URL” toggle to Agent management console. When this is Yes, the injection path in the platform will not contain the URL encoding characters. Default value is No. To know more about how this feature impacts the data on TDP, please read here.
AG-2558/AG-2577 - Added support for running/loading .NET libraries at runtime which have been built in a lower version than the .NET runtime Agent uses. If there is still a .NET System.IO.FileLoadException runtime exception, the injection will not be extracted and error will be surfaced.

Bug Fixes

The bug fixes for this release appear below.

AG-2491 - Typo “Detrail” fixed to “Detail” in Agent summary screen.
AG-2565 - Following report variables are now extracted in RAW JSON:
- Number of Peaks in Peak Category
- Group Evaluation in Peak Group category
- Matrix Correction in Processing Method category
- Blank Run Subtraction in Processing Method category
- Use Amount Ratio for Var. ISTD Processing Method category
- Amount Ratio Confirmation channel in Composite Scoring - Processing Method category

Minor Functionality Changes

There are no minor functionality changes in this release.

Known Issues

Certain Report Variables may return error. This may be because the Agent does not have enough context to generate the Report Variable value through the SDK. For a complete list of such Report Variables please click here. Tetra is actively working with the vendor to resolve the errors and remediate the issue in a future release.

v2.0.1

RELEASE DATE: 21 September 2022

Enhancements

The following are enhancements for this release.

AG-2357 - To improve the Tetra Chromeleon Agent’s efficiency, failed injections are retried 2 additional times, in its own batch, at the end of the current Data Vault generation and in the next generation of Data Vault. If the maximum retry limit of 3 is reached and the injection still has errors, it will not get considered for further generation jobs.
AG-2358 - The Ignore Recycle Bin option has been added to the Tetra Chromeleon Agent Management Console screen. You can now determine if you want to exclude the generation of the Sequence and Injections stored in Data Vault’s Deleted Item folder. (Internally, Chromeleon refers to it as Recycle Bin.)

Bug Fixes

The bug fixes for this release appear below.

AG-2386 - For GxP compliance, Infinity or NaN is output as null in Chromatogram Data Points. In other places, they will be output as Negative Infinity or Positive Infinity or NaN respectively.
AG-2319 - Agent will retry failed database operation in case database transaction-related errors occur, such as the database is locked. The Agent logs every retry attempt. Since the Agent retries up to 5 times, only the message "Failed the operation in 5 times" message means a real operation failure.

v2.0.0

RELEASE DATE: 7/14/2022 (Updated 8/4/2022)

Enhancements

The following features and functionality have been added to the software for this release.

AG-1260 - A busy indicator now appears while the Chromeleon user account is being verified.
AG-1286 - User-deleted files during scans no longer cause unrecoverable errors.
AG-1723 - The culture/regional handling for dates and numbers has been improved. Context for the cultural and regional values are in the RAW JSON file.
AG-1899 - The TDP can push data to Chromeleon to create Sequences. This command will work when connecting through GDC and L7 Proxy.
AG-1965 - Password and role fields on the UI are now wider.
AG-1968/AG-1934 - Logging has been improved; more details have been added. Also, logs can now be over 1 MB in size.
AG-1992 - We've updated the logic to render report variables in RAW JSON with full object context.

"CreationTime": {
	"IsError":false,
	"IsNumeric":false,
	"IsString":false,
	"IsTime":true,
	"IsBoolean":false,
	"NumericValue":null,
	"StringValue":null,
	"TimeValue":"2022-05-12T10:21:53.0000000-04:00",
	"BooleanValue":null,
	"Value":"5/12/2022 4:21:53 PM +02:00"
}

AG-1993 - Scan errors are now available on the Management Console's Summary Page.
AG-2006 - Datapoint and Peak data (if available) is now shown; issues resolved by AG-2038, which changed the way it processes errors to better manage memory usage. The agent recovers from any out of memory errors and continues to process the injection(s) in a separate batch.
AG-2045 - We've updated the logic to render custom fields in RAW JSON so that they follow the same serialization logic as report variables.

{
        "FieldDefinitionContext": "Injection",
        "Name": "Column SN.",
        "Description": "",
        "Key": "Column SN.",
        "Value": null,
        "Value_Data_Type": "string",
        "Number_Value": null,
        "String_Value": "001290,01827143",
        "Boolean_Value": null,
        "Time_Value": null
}

{
        "FieldDefinitionContext": "Injection",
        "Name": "Column SN.",
        "Description": "",
        "Data": {
          "IsBoolean": false,
          "IsError": false,
          "IsNumeric": false,
          "IsString": true
          "IsTime": false,
          "BooleanValue": null,
          "NumericValue": null,
          "StringValue": "",
          "TimeValue": null;
          "Value": ""
        }   
}

AG-2044 - The following report variables are now part of the RAW file that is uploaded to the TDP:
- Chromatogram Category
- Sequence Category
- Injection Category
AG-2134 - Addressed additional memory issues. Note that the agent recovers from any out of memory errors and continues to process the injection(s) in a separate batch.

Bug Fixes

Here are the bug fixes made for this version of the agent software:

AG-1703/AG-1936 - Domain and local Chromeleon users are now set in the same way in the UI. The "Chromeleon LDAP User" yes/no setting has been removed from the UI.
AG-1972 - The file name now appears in the log when the SetValue Errors are thrown.

Bug Fixes from 1.3.0 were also included.

AG-1909/AG-1923 - If the Tetra Chromeleon Agent cannot access remote data vaults due to a network or user permission issue, this information now appears in the logs. If the Agent cannot access a data vault, scanning for the rest of the data vaults still continues.
AG-2000 - The Tetra Chromeleon Agent won’t upload empty injection object due to an access permission error; instead the Agent will mark the injection as a generation error.
AG-2007 - If the Tetra Chromeleon Agent scans a data vault and there is no access permission for a file, the Agent logs an error message.

Deprecated Features

There are no deprecated features for this release.

Minor Functionality Changes

AG-1703 - Users authenticated and authorized using LDAP is now handled differently. There is no longer "Chromeleon LDAP User" yes/no setting. Agent Group User is the service account that runs the Tetra Chromeleon Agent while Chromeleon user/password/role used in Service Settings is used to access Chromeleon (when User Mode is enabled in Chromeleon).

v1.3.0

RELEASE DATE: 6/6/2022 (Internal Release Only)

Enhancements

No new features and functionality have been added to the software for this release.

Bug Fixes

Here are the bug fixes made for this version of the agent software:

AG-1909/AG-1923 - If the Tetra Chromeleon Agent cannot access remote data vaults due to a network or user permission issue, this information now appears in the logs. If the Agent cannot access a data vault, scanning for the rest of the data vaults still continues.
AG-2000 - The Tetra Chromeleon Agent won’t upload empty injection object due to an access permission error; instead the Agent will mark the injection as a generation error.
AG-2007 - If the Tetra Chromeleon Agent scans a data vault and there is no access permission for a file, the Agent logs an error message.

Deprecated Features

There are no deprecated features for this version of the software.

Minor Functionality Changes

There are no minor functionality changes for this version of the software.

v1.2.0

RELEASE DATE: 27 December 2021

Enhancements (New Features and Functionality)

The Tetra Chromeleon Agent has been upgraded to receive a TDP command. Only one command can be accepted, which SequenceCreation. Note that the Tetra Chromeleon Agent can only receive this command if the Queue is manually enabled in both the TDP and the Tetra Chromeleon Agent.
FileId has been added in the Chromeleon Agent log files. This makes it consistent with the other Agent log files.
The Tetra Chromeleon Agent now has new sections: Windows Scheduled Task, Run Time, Enable Queue, and Agent Configuration Advanced Settings. These sections were added for consistency with other Tetra Agents. The authorization section was also updated. New documentation is also available.

Bug Fixes

AG-1214 - Connection status is missing
The status next to the Connection URL field always shows whether the Tetra Chromeleon Agent is connected or not.
AG-1251 - Chromeleon Agent failure when used with longer Folder Length
The Tetra Chromeleon Agent now supports folder path lengths that are longer than 256 characters.

Minor Functionality Changes

The Tetra Chromeleon Agent can no longer start until the TDP connection is established and the user account configuration is completed.

v1.1.0

RELEASE DATE: 7 Sep 2021

Enhancements (New Features and Functionality)

The Chromeleon Agent installer was modified to use the same installation mechanism as other Tetra Agents.

v1.0.1

RELEASE Date: 8 Dec 2020

Enhancements (New Features and Functionality)

Support Chromeleon 7.2.5

v1.0.0

RELEASE DATE: 6 Dec 2020

Main Functionality

Fetch Injection data from Chromeleon
The injection data is serialized as JSON format and uploaded to TDP for harmonization

Updated 7 months ago

📘NOTE

v2.1.2

What's New

Prerequisites

⚠️IMPORTANT

New Functionality

Tetra Chromeleon Agent New Functionality

Tetra Data New Functionality

Enhancements

Tetra Chromeleon Agent Enhancements

Tetra Data Enhancements

Bug Fixes

Deprecated Features

Known and Possible Issues

Security

Upgrade Considerations

v2.1.1

🚧IMPORTANT

v2.1.0

🚧IMPORTANT

v2.0.3

What's New

Prerequisites

New Functionality

Enhancements

Bug Fixes

Deprecated Features

Known and Possible Issues

Upgrade Considerations

v2.0.2

Enhancements

Bug Fixes

Minor Functionality Changes

Known Issues

v2.0.1

Enhancements

Bug Fixes

v2.0.0

Enhancements

Bug Fixes

Deprecated Features

Minor Functionality Changes

v1.3.0

Enhancements

Bug Fixes

Deprecated Features

Minor Functionality Changes

v1.2.0

Enhancements (New Features and Functionality)

Bug Fixes

Minor Functionality Changes

v1.1.0

Enhancements (New Features and Functionality)

v1.0.1

Enhancements (New Features and Functionality)

v1.0.0

Main Functionality

📘
NOTE

⚠️
IMPORTANT

🚧
IMPORTANT

🚧
IMPORTANT