Maintaining Samples

Overview

All types of jobs can contain samples. It is the samples that have the tests assigned for analysis.

Except for samples in laboratory batch jobs which are created by the CCBTCH—Job Batch application, the CCREGN—Job application can create samples in all types of jobs, including ad-hoc jobs and jobs created from a template or other registered job, and can create samples from a template or other registered sample.

Samples are scoped by the job.

Process

Once samples are added to a job, single or multiple samples within the context of a job can be searched and maintained using the CCREGN—Job application, or single samples outside the context of a job can be searched and maintained using the CCSAMP—Sample application.

Where required, samples can be deleted from the system. Any QC records associated with the sample job are maintained in the QC history repository.

Maintain samples

When the Samples tab is selected in the CCREGN—Job Detail screen, then the AUTO_RETRIEVE_ALL_JOB_SAMPLES application preference controls whether all samples are retrieved automatically from the server and displayed in the grid:

  • If enabled, then paging is turned off and all samples are retrieved and loaded in the grid. Enabling this preference is useful to retrieve all samples in the job from the server prior to performing multiple sample editing, otherwise only the first fifty samples are retrieved by default.

  • If disabled, then only the first fifty samples are retrieved by default, and more are retrieved as the grid is navigated, or Grid RetrieveGrid Retrieve All Records is selected to retrieve all samples in the job from the server.

Set the AUTO_RETRIEVE_ALL_JOB_SAMPLES application preference

Exporting Samples to a Report

From a Job

Samples in a job in the CCREGN—Job application can be exported to a report. Refer to Generating Grid Reports.

Available report templates are defined in the SEARCH_REPORT_CCREGNSAMP application preference.

From a Sample Search

Samples returned from a search in the CCSAMP—Sample application can be exported to a report. Refer to Generating Grid Reports.

Available report templates are defined in the SEARCH_REPORT_CCSAMP application preference.

Creating Samples

Refer to:

Updating Samples

Where it is important to consider samples within the context of their job, use the CCREGN—Job application to search for and maintain samples. This application allows for the update of samples one at a time, or in bulk using a multiple sample update.

Where it does not matter to consider samples within the context of their job, use the CCSAMP—Sample application to search for and maintain samples. This application only allows for the update of samples one at a time, however, the extensive search criteria often make it practical to use this application.

Updating Multiple Samples Updating a Single Sample
Within the context of a job Within the context of a job
-- Outside the context of a job

Updating multiple samples:

  • When samples require update to change some attribute or test, you often need to apply the same change to multiple samples. Multiple samples within a job can be selected and opened in multiple sample update, such that, the update is applied to all selected samples.

  • The multiple-sample update screen consists of tabs that are identical to the Primary Details tab, Notes tab, Tests tab, and Biofields tab of the single sample update screen, however, multiple sample update does not allow for the update of all child properties of a sample.

  • Sample scheme and sample scheme analyte details across multiple samples can only be updated within the sample test grid and not in the CCREGNSMPLSCH—Sample Scheme Detail and CCREGNSMPLSCHANA—Sample Scheme Analyte Detail screens.

  • Field content that is identical across samples display in a field, whereas if the field content is dissimilar across samples, the field is blank. Details can be entered in any enabled fields. Entering a value into any enabled field changes the value in all the samples. For example, if No. of Containers is updated, for each sample in the multiple update, where:

    • No. of Containers is greater than the number of as-registered portions on the sample, extra as-registered portions are created to match the number of containers on all samples in the multiple sample update.
    • No. of Containers is less than or equal to the number of as-registered portions on the sample, then no sample portions are deleted for any sample in the multiple sample update.

Updating laboratory batch jobs:

  • When a sample in a laboratory batch job is opened, if the sample's belongs to a registered job and not to the laboratory batch job, then the Tests and Specifications tabs are not visible. These tabs are only visible for samples created just in the laboratory batch job, that is, laboratory batch-owned QC samples.

Deleting Samples

A sample can be deleted if it is referenced in an invoice and the invoice's Invoice Status is Initial or Draft, in which case, when the sample is deleted then the job invoice sample is deleted.

A sample cannot be deleted if it is referenced in an invoice and the invoice's Invoice Status is Edited or beyond.

Sample deletion is controlled by the following preferences:

Restrictions on Deleting a Duplicate QC Sample

When you attempt to delete a sample, then the action does not proceed if:

Removing Links to Laboratory Batch Jobs

If a sample belongs to a job where the job's Job Type is Production or Internal, then any links to laboratory batch jobs should be removed before the sample is deleted. If this is not done, then any related laboratory batch sample cannot have results entered, leaving the laboratory batch job in a state where it can never be completed.

Links to laboratory batch jobs can either be removed one of the following ways:

  • Deleting the related sample in the laboratory batch job

    This removes the link from any sample scheme analytes in the production/internal jobs to the laboratory batch job.

    Warning: The consequence of this action is that the laboratory batch jobs are shrunk and the rack positions adjusted, meaning that any instrument run lists created previously may now be out of date.

  • Removing the links from the production/internal sample scheme analytes to the laboratory batch job and samples.

    When the link from any sample scheme analytes to the laboratory batch job and samples are removed, then the Workflow Status for each associated laboratory batch sample scheme analyte is set to Not Analysed, which cascades up to set the Workflow Status for each associated laboratory batch sample scheme to Not Analysed, and in turn, cascades up to set the Workflow Status for the associated laboratory batch sample to Not Analysed.

    This means that the de-linked laboratory batch samples do not leave the laboratory batch job in a state where it can never be completed.

Remove links from registered samples to laboratory batch samples

After doing this, deletion of the sample can proceed.

Upon Maintaining Samples

Upon sample deletion:

  • If the sample has a Primary Analytical Type of Unknown or Duplicate and it is in a job that has a Workflow Status of Registered, Not Started or Cancelled, then all related replicate and spike QC samples are deleted from all job invoices in the job, any job schemes that associated with the deleted samples are also removed from all job invoices in the job, and the sample schemes and sample scheme analytes are also deleted from any invoice that has an Invoice Status of Initial, Draft or Cancelled.

  • If the RETAIN_DUP_UPON_UNK_DELETION application preference is defined and selected, then any related duplicate QC samples are retained and the link to the deleted unknown sample is removed from the duplicate QC sample. Otherwise, if the preference is not defined, or is defined and is not selected, then any related duplicate QC samples are deleted also.

  • If the sample is in a laboratory batch job, then any reference to the laboratory batch sample in the related production sample scheme analytes is cleared.

  • Job invoice scheme and job invoice scheme analyte records are deleted, as required.

  • Any QC history records related to the deleted sample/s are retained but set to inactive, so they can still form part of the historical assessment of the laboratory's quality performance.

  • The event is audited. Refer to Reviewing Operational Data Audits.

Upon maintaining one or multiple samples:

Searched samples within the context of a job can be exported to a report. Available report templates are defined in the SEARCH_REPORT_CCREGNSAMP application preference. Searched samples outside the context of a job can be exported to a report. Available report templates are defined in the SEARCH_REPORT_CCSAMP application preference. Refer to Generating Grid Reports.

Job locks are not applied for samples opened in the CCSAMP—Sample application.

On sample update or deletion, various updates occur on the server, depending on the action. Refer to:

Sample Identification

Samples have three primary identifiers: Code, Sample Name and Client Sample Name.

A sample's Code and Sample Name should not be updated.

Depending upon the type of sample, when a sample is opened, the name and description fields that are displayed changes:

  • For a sample in a registered, laboratory batch or draft job—Client Sample Name and Description.
  • For a template sample in a template job—Client Sample Name/Syntax and Description. These fields usually contain unexpanded forms to later set the Client Sample Name and Description in a registered job.
  • For a stream sample in a schedule job—Production Client Sample Name Syntax Code and Production Description Syntax Code. These fields are used to later set the Client Sample Name and Description in a registered job,

QC Assessment Details

The QC Source specifies the point in the laboratory process at which the sample is created:

  • 0—Registration from the client,

  • 1—Post-registration and to the original job, for example, QC samples added to a production job via an Append or Overwrite QC process or QC sample maintenance of the production job,

  • 2—Pre-analysis in the laboratory batch job, for example, scheme QC added during laboratory batch creation or QC samples maintenance of the laboratory batch job.

This field is not shown by default during sample update but can be added to the screen, if required, using personalisation.

The Primary Analytical Type denotes the type of QC assessment the sample primarily undergoes, as requested by the client: Unknown, Duplicate, Replicate, Blank, Standard or Spike.

The Primary QC Type is a sub-classification of the Primary Analytical Type and allows for custom QC assessment after the core QC assessment. The Primary QC Type is selected from active QC types in scope, as configured in the CCQCTP—QC Type application. If a sample's Primary Analytical Type is Unknown, then the Primary QC Type is not required.

Typically samples that come from a client are unknown samples, however, sometimes the registration documentation may indicate that the sample is a duplicate QC sample. Also, replicate, blank, standard and spike QC samples typically do not come from the client so are generally created during sample preparation or analytical preparation and not during registration.

The Secondary Analytical Type denotes the type of QC assessment the sample undergoes after the primary assessment: N/A (not applicable), Duplicate, Replicate, Blank, Standard or Spike, and is set by the laboratory technician.

The Secondary QC Type is a sub-classification of the Secondary Analytical Type and allows for custom QC assessment after the core QC assessment. The Secondary QC Type is selected from active QC types in scope, as configured in the CCQCTP—QC Type application. If a sample's Secondary Analytical Type is N/A, then the Secondary QC Type is not required.

  • A sample with a Primary Analytical Type of Blank, Standard or Spike and a Secondary Analytical Type of Duplicate indicates the second of a pair of blank duplicate, standard duplicate or spike duplicate QC samples, respectively, such that, after standard assessment, the sample undergoes duplicate assessment.

  • A sample with a Primary Analytical Type of Blank, Standard or Spike and a Secondary Analytical Type of Replicate indicates the second of a pair of blank replicate, standard replicate or spike replicate QC samples, respectively, such that, after standard assessment, the sample undergoes replicate assessment.

An experienced sample preparation technician may notice that a sample presented from the client as an unknown sample is actually a blank or standard QC sample, for example. Setting a secondary analytical type allows the sample to undergo additional QC assessment.

Duplicate or Replicate Requirements

  • Where the Primary Analytical Type or Secondary Analytical Type is Duplicate or Replicate, then the Dup Original Sample Code, Dup Original Sample Name and Dup Original Client Sample Name are the sample code, sample name and client sample name of the duplicate or replicate original sample, the sample used to create the duplicate or replicate QC sample. However, primarily because this is a bulk sample group registration, and individual duplicate or replicate QC samples would link to their own original sample. This is typically done during sample preparation or analytical preparation using the CCQCSM—Sample Modification application.

Blank, Standard and Spike Requirements

  • Where the Primary Analytical Type or Secondary Analytical Type is Duplicate or Replicate, then the Standard Code and Standard Lot Code define which blank or standard material comprises the sample, and the current lot of the standard, respectively. The Standard Code is selected from active standards in scope, as configured in the CCSTND—Standard application. The Standard Lot Code is selected from active lots for the standard that have a Stock Level greater than zero and an Expiry that is after the current system date-time, as configured in the CCSTND—Standard application. Defaults to the standard's Current Standard Lot Code. Refer to Conditions for Allowing Standards as Spikes.

  • When the sample undergoes accuracy assessment, the results are assessed against the specification defined by the standard lot's Specification Code.

Sample Origin

The Sample Type Code classifies a sample, for example, ship hold sample, truck oil sample, shirt, or dog blood, and Sample Point Code classifies the type of sample taken from the field or production process, for example, powder, slurry. Sampling and delivery details can be entered for informational purposes. Samples within a scheduled job can be tied to a sample type and sample point.

The Sampling Started On and Sampled On is the date-time at which the collection of the sample in the field started and ended. Often, just Sampled On is recorded. Sampled By is the name of the person who or machine that performed the sampling.

For any sample scheme included in a laboratory batch job, if the registered sample scheme's Holding Time is set and the sample scheme does not have a precursor sample scheme, when the Sampled On or Received On date-time is updated on the registered sample, then the laboratory batch sample scheme's Expiry Date is calculated by the holding time engine.

  • Example: A production job contains S2Ana5 and S2Ana6, and S2Ana5 is the precursor sample scheme of S2Ana6. If S2Ana5 and S2Ana6 are included in the same laboratory batch job, then in the laboratory batch job, LB_S2_Ana5 is the precursor sample scheme of LB_S2_Ana6. In this case, an update to S2's Sampled Date would recalculate S2Ana5's Holding Time and LB_S2Ana5's Holding Time.

When a duplicate, replicate or spike sample is created during an append/overwrite QC process, or a sample is created by a sample copy or by creating a composite sample, or a laboratory batch sample is created during a batching process, then the related sample inherits the sampling details from the source sample.

Refer to Conditions for Calculating Expiry and Warning Dates and Using Sample Expiry.

Numbers of Containers Supplied for each Sample

Where the sample is associated with a production, internal or lab-scope template job, and the Portion tab is displayed for Maintaining Sample Portions during Registration, if the number of portions created for the sample is less than the sample's required Number of Containers on the Primary Details tab, then the missing portions are created for the sample, using the current logic to set portion field defaults.

Priority and Dates

A sample's Priority is used when selecting and sorting samples for laboratory batching,

If a sample's Priority or Received On date-time is updated by the user, then the sample's Required On, Possible On and Agreed On date-times immediately recalculates as:

  • Received On + Priority + any non-working days due to holidays.

Refer to Conditions for Calculating Job and Sample Required On Date.

If a sample's Priority or Received On date-time is cleared, then the sample's Required On, Possible On and Agreed On date-times are cleared automatically.

If the sample's Required On, Possible On or Agreed On date-time is updated by the user, then there is no effect on the sample's other dates, however, the following validations apply:

  • ReceivedDateTime < Required DateTime
  • ReceivedDateTime < PossibleDateTime
  • ReceivedDateTime < AgreedDateTime.

    Note: Priority and dates in the job are not impacted by sample dates, even when sample dates are updated.

Refer to:

Considering a Sample in Context of Job Scheme QC Placements

When Creating QC Samples using QC Masks, then the related sample schemes' QC masks are applied to add QC samples to the job scheme where the sample scheme's Include in Job QC is selected.

An append QC process can only be applied where the job's Workflow Status is Registered or Not Started, otherwise an overwrite QC process can only be applied. In an overwrite QC process, existing QC samples are deleted, and the sample schemes' Include in Job QC are all re-selected, then the same process as update QC runs.

For each job scheme included in the process, then:

  • The related sample schemes' QC masks are applied to add QC samples to the job scheme where the sample scheme's Include in Job QC is selected.

  • Once a sample scheme has been included in a update QC process, then the sample scheme's Include in Job QC is cleared by the system.

Auto-validate Sample

Where all sample schemes in a sample have their validated date stamped and the sample's Auto-validated is selected, during a cascade up the job tree by the cascade engine, then the sample's Workflow Status is Completed since all of its sample schemes have a Workflow Status of Completed, and the sample is validated automatically.

Where all sample schemes in a sample have their validated date stamped and the sample's Auto-validated is cleared, during a cascade up the job tree by the cascade engine, then the sample's Workflow Status is Completed since all of its sample schemes have a Workflow Status of Completed, and the sample remains unvalidated, such that, it requires manual validation.

When sample is validated, then the sample's Workflow Status remains at Completed, its Validated Date is stamped and Finalised By is set to the current user.

Sample inclusion in Paperwork or Labels

If a sample has Generate Paperwork selected, when a paperwork report request is created, then the report request sample's Reportable is selected, allowing the sample to appear in the job paperwork.

If a duplicate, replicate, blank, standard or spike QC sample has Generate Labels selected, when a labels report request is created, then the report request sample's Reportable is selected, allowing the sample to appear in the job labels. Unknown samples are always included in a labels report request.

Sample inclusion in Certificate Reports

Unknown samples are always included in certificate report requests, and the report request sample's Reportable is selected if the sample's Reportable is selected, and cleared otherwise.

However, a duplicate, replicate, blank, standard or spike QC sample is only included in a certificate report where the sample has Reportable selected, and the report request sample's Reportable is selected.

Sample inclusion in Invoices

An invoice contains fees payable by a client for work performed by the laboratory, raised from one or more job invoices, where one of the job invoices is marked as the invoice's primary job invoice.

An interactive mechanism is available to present system-determined line items for last-minute price adjustments, including the addition of any surcharges or discounts.

An invoice has a status and a life-cycle. and requires approval before it is transmitted to the client.

If a sample has Invoiceable selected, when invoices are drafted, then the sample is included as invoiceable in the invoice.

Sample inclusion in Job Costs

A job cost is the actual cost of analysis to the laboratory for the job. The pricing framework for internal costs is maintained in exactly the same manner as with client invoicing. A costing price catalogue group is created and associated with the laboratory and related price books contain price schedules for the costs. The price codes used for costing are the same as those assigned for client invoicing.

If a sample has Include in Costs selected, when job costs are generated, then the sample is included in costing calculations.

Sample Notes

Registration, analysis and report notes can be added to a sample for informational or reporting purposes.

Canned comments are available to quickly entered pre-canned text. When canned comments are accessed for a given note field, the canned comments are filtered by Canned Comment Type and Canned Comment Subtype.

  • The Canned Comment Type of GLOBAL, JOB, SAMPLE or SCHEME, and the Canned Comment Subtype of GLOBAL, REGISTRATION, RECEIPT, ANALYSIS, RELEASE, VALIDATION, REPORT or INVOICE.

or:

Sample Biofields

A sample biofield is a field added to a sample that is used to store additional information just for that sample. Each sample can have a different set of biofields from other samples in the system. Sample biofields can be used in search criteria and placed on reports. A biofield has a value and a flag to indicate its reportability.

A biofield is automatically added to a sample if the biofield is in scope, has a Use Scope of Sample and it is active, and either one of the following is true:

Biofield scope must also be satisfied:

  • Where the biofield has org-scope, then it must link to no line of business, or link to a line of business within the laboratory's lines of business.
  • Where an org-scope biofield is linked, optionally, to a line of business that is associated with the current laboratory, then the org-scope biofield is viewable by users within that laboratory. Otherwise, the biofield is hidden for use. This allows for a limited list of visible org-scope biofields for a laboratory, based on the analytical tests a laboratory is able to perform. Until a laboratory is linked to one or more lines of business, all org-scope biofields associated with a line of business are hidden to the laboratory's users. Refer to Limiting User Visibility of Biofields by Line of Business.

A biofield with a Biofield Type of List must have biofield values with matching descriptions to provide the user with a populated drop-down selection list of values.

Where the job is not a template job, when an interim sample is expanded, then any biofield on the interim sample is added to each registered sample, such that, each sample links to a separate biofield value.

When a sample is created from an existing sample, then job biofields are inherited from the source sample into the destination sample.

Refer to Maintaining Sample Biofields.

Tests

If tests are added to an interim sample, when the sample group is expanded, then the tests are added to all expanded samples.

Tests can also be added to a single sample or to multiple samples in a multiple sample update.

When a test is added to a sample, then the job scheme and job scheme analyte composite records are created or updated, to keep in sync with the related sample schemes and sample scheme analytes.

Refer to Maintaining Sample Tests.

Product and Specifications

A product is a substance that has a suite of grades, where each grade relates to a specific product specification. A product may be produced by a plant, or be any other substance with known specifications (for example, an environmental air sample).

A sample can be assessed against specifications associated with the product or against any other specification to set a sample scheme analyte specification's Specification Status which is an indication of the quality of the sample against expected limits.

The sample's primary product is used to set a sample scheme analyte's Specification Status which rolls into the sample scheme analyte's Composite QC Status.

Refer to Maintaining Sample Product and Specifications.

Portions

Where the sample is an unknown sample associated with a production, internal or lab-scope template job (lab-scope template jobs have been added to this list):

  • If the JOB_LEVEL_TRACKING application preference is false, the SAM_TRACK_REG_AT_SAMPLE_REG application preference is true and either a) the SAM_TRACK_REG_WHEN_JOB_COMPLETE application preference is false, or b) the SAM_TRACK_REG_WHEN_JOB_COMPLETE preference is true and the job’s Workflow Status is Completed, then the Portions tab is shown by default so that it can be accessed for maintaining sample portions during registration, and rows can be added, removed or updated in the grid and persisted upon submit. Also, if the number of portions persisted upon submit is less than the sample's required Number of Containers on the Primary Details tab, then the missing portions are created as as-received portions for the sample, using the current logic to set portion field defaults.

  • Otherwise the Portions tab is hidden by default.

Note: A sample portion must be associated with a location and locations can only have lab-scope, which is why they cannot be created for samples in org-scope template jobs.

When a sample portion is created:

  • Sample portion's Code is generated as a running sequence of three digits for the portion within the sample, '0' padded (that is, 001).
  • Sample portions received from a client, or sometimes created in the laboratory's sample preparation area, have a Portion Type of As Registered (enumeration 0).
  • The event is audited. Refer to Reviewing Operational Data Audits.

Refer to:

Linked Samples for Composite Samples

Where the sample is a composite sample, that is, it comprises material from multiple samples in the job, then the list of composite samples can be maintained.

Refer to Maintaining Composite Samples.

Opening the Worklist Dialog for a Sample in a Job

The worklist dialog allows a single sample to be opened for result review or update using the CCWKOPTRAN—Open Transposed Workbook application.

Open the worklist dialog for a sample

Approving Samples for Distribution

Template samples are approved for distribution, that is, so they are exportable from the central library on the master instance to remote instances.

Once the entities are available in the organisation on a remote instance, they can be imported into production organisations on that remote instance.

The LIMS manager schedules periodic import, to upload any changes to the test configuration.

The laboratory manager reviews the updated entities imported into the 'holding' organisation on their instance (that is, in the LIBMAN organisation), and then imports selected entities into their laboratory's master organisation (that is, the GLOBAL organisation).