Troubleshooting Config Slicer

If there is an API version mismatch, Config Slicer will log a message at the beginning of an import:

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API version mismatch - package: v2,r20 - server: v2,r21. This may result in some differences between configuration in package and on server.

Generally, this message is not a cause for concern.

However, if there are warnings about configuration differences during the import, changes that have been made to the API in between the package version and the server version may be responsible.

In addition, if the package being imported is from v4.x, a log message may appear at the beginning of an import:

Detected package is from a pre-5.0 Clarity system. The package will be upgraded to match new configuration requirements.

In this case, the package is upgraded and the resulting configuration is output to a folder in the same location as the package being imported. This upgraded configuration package is the v5.x representation of the v4.x configuration and can be used directly to troubleshoot error occurring on import. The updated packaged can also be imported directly.

Config Slicer Version Updates

The following changes have been included in the latest release of Config Slicer (v 3.0.51):

General changes:

• The entity summary is now shown after the individual differences have written to the log file, as opposed to before these differences.

• Support was dropped for the following process type attributes which are no longer used:

  • SupportsExternalProgram,

  • ShowInExplorer,

  • ShowInButtonBar,

  • OpenPostProcess,

  • IconConstant

• Support was dropped for the show-in-tables property on Custom Fields (UDFs) because it is no longer used.

• There is now support for the new Clarity LIMS 5.0 distinction between Protocol Step names and Master Step (ProcessType) names.

• It is now possible to slice in and out all the new Master Step settings added in Clarity 5.0, including:

  • Default Process Template

  • Instrument Types

  • Container Types

  • Reagent Kits

  • Reagent Types

  • Control Types

  • Sample Fields

  • Queue Fields

  • Ice Bucket Fields

  • Step Fields

  • Step Properties

• When importing/validating a slice from 4.x into 5.x, if the package contains any Master Steps (process types) or Protocols, it is upgraded to be compatible with the new configuration available in 5.x. This process is automatic, and the updated package is written out to the directory containing the package being imported or the directory that log file is being written to. If errors occur while importing, this updated package can be manipulated directly and imported to fix them.

Note: If upgrading the package fails, import/validation will fail. In general, this will reflect a mistake in the configuration package being imported.

Changes in support of slicing from 4.x to 5.0:

The following changes were specifically added to support slicing between Clarity LIMS 4.x and BaseSpace Clarity LIMS 5.0. All of these changes will be saved into a new configuration package that will be written to the same location as the package being sliced:

• Backwards compatibility for Protocol Step setup configuration.

• Support for updates of parent entities after both the parent and child entities have been imported.

  • This change is required for updating the defaultProcessTemplate and step-fields step properties on Master Steps. Both require that the Master Step (ProcessType), ProcessTemplate, and Master Step Custom Fields (ProcessType UDFs) exist before they can be set on the Master Step.

• Support for setting the qcProtocolStep flag on Master Steps, allowing the correct Master Step type to be displayed in the Lab Work Configuration UI. The setting is propagated up from the Protocol Step to the Master Step.

After slicing, it is recommended to examine the configuration closely for any QC Protocol Steps that previously shared a Master Step with nonQC Protocol Steps. This setting may not transfer as expected and there is potential for misconfigured Protocol Steps. In particular, if the Master Step produces measurements, and even just one child step of a Master Step has qcProtocolStep=true, then the Master Step will get qcProtocolStep=true set on it. Thus, all other steps that use that Master Step have qcProtocolStep=true, whether or not it was set before.

• Support for setting the default container on Steps and Master Steps in such a way that all behaviour is maintained from 4.2

  • If every child step of a Master Step has the default container that was defined as a permitted container on the master (through the 'OutputContainerType' process-type-attribute) then the default will be added as a permitted container on the master step

  • If any child does not have the default container from the Master Step, then the default is removed from the Master and each child that had the container is updated so that the default is the first permitted container (and hence default)

• Extra containers and any step properties that are no longer valid on a step will be migrated to new properties or removed.

• Step-setup file configuration has been moved to the Master Step and it not possible to have a different set of step-setup files on a step than are specified on the Master. The master step owns the list of files. Both the search-result-file-index attribute on each file element and the message element for each file are defined by the Master and must be duplicated on every step. When moving a 4.x configuration with step-setup files to a 5.x configuration, the following events will occur:

  • The set of all the step-setup files found on all the child steps in the slice are added to to the Master Step and each child step.

  • If more than one step in the slice defines step-setup files for the same search-result-file-index, then all the messages for that search-result-file-index will be concatenated by newlines.

  • The enabled attribute will be set to true for the step-setup on all child steps.

  • The locked attribute will be set to false for the step-setup on all child steps.

  • In the case of importAndOverwrite, the step-setup of any existing child steps for an overwritten master step will be included.

• Upon validation after import, the following differences have been reconciled:

  • UDFs that differ by STYLE only

  • missing defaultProcessTemplate

  • missing attemptAutoPlacement

  • missing autoAttachFiles

  • missing qcWithPlacement