Capturing Data using On-line Data Capture Sessions
Related Topics
Overview
The On-line application collects data from instruments or a data file issued from a specific instrument, for example, an XRF analytical instrument, and decodes the data strings to extract sample name and other sample details (if required), and the analytical results for a multiple number of analytes. VBScript can be used to automatically perform quality control and product assessments.
The data being collected by this On-line module may be either weights of samples to be analysed, raw (weight and/or volume corrected) results, or final (weight or volume corrected) results.
Data capture can be set up to automatically capture and store, or to manually step through samples.
This process is pertinent to laboratory supervisors and operators who interact with instruments to upload analytical results.
Process
On-line data capture sessions are managed using the On-line application.
Where the LIMS configured to automatically load and execute a custom form on application start up, then the form displays, otherwise the main screen of the On-line module displays. Automatically loaded forms are typically used to trigger automatic data collection from an instrument.
Where the main screen displays, an empty instrument run list displays on the form to which you add samples by finding the first sample scheme, then adding the rest of the samples in the job scheme or the rest of the sample's schemes, or by adding different sample schemes, or by adding a pre-configured run list, or by creating a dynamic run-list for an instrument scheme.
Setting up the Instrument Run List
Add samples to the instrument run list
Where a sample links to a product and the product contains scheme analyte limits, when samples are analysed and one of those scheme analytes receives a result, then the result is assessed against the product's scheme analyte limits, resulting in the sample either passing or failing the product limits. Any sample scheme analyte with a result above the upper action limit is marked to be checked. Also, if the scheme is included in the product's rules, then the associated VBScript for the product rule's scheme runs.
Assigning Products to Samples in the Instrument Run List
Assign a product to a sample in the instrument run list
Registering Samples via the Instrument Run List
New samples or rereads can be registered using an existing sample in the instrument run list.
Register a sample using an instrument run list sample
Register a reread sample using an instrument run list sample
Saving an Instrument Run List
Once an instrument run list is built, it can be saved to a RUN file, typically for upload to the instrument.
Each line in a RUN file has the following format: [Job],[Scheme],[CUID],[Type],[Ident],[Product]
Save an instrument run list to a file
Selecting the Instrument, Data Mode, and Weight-to-volume Correction Mode
Before data can be captured, the instrument must be selected. The On-line application can be operated without being attached to an instrument (or data file). In this case, the pseudo instrument code (none) is selected. This is the default instrument upon module start up.
The data being collected may be either sample weights and volumes, raw results (weight and/or volume uncorrected), or final results (weight or volume corrected). The default data mode is Final, however, the instrument format file can override this.
When raw or final results are collected, weight-to-volume correction can be applied. The default weight-to-volume correction mode is Off, however, the instrument format fIle can override this.
Once an instrument is selected, the instrument format file (IFF) associated with the instrument is used to decode instrument transmission. The IFF name is displayed as the title of the child window within the On-line window. The red square on the status line indicates the initial state that no data is currently being collected.
Select the instrument, data mode, weight-to-volume correction mode for data capture
Once the instrument is selected, and the instrument is ready for transmission, start data capture, usually by pressing a specific button or sending the instrument a specific string using a pre-defined key on the keyboard, or by starting the data load from a file.
Start data capture from an instrument data capture session
After the instrument is started, it is interacted with to transmit results to CCLAS. The IFF is configured to manage:
- Manual capture is required for instruments that cannot create data files because incoming data must be associated with a CUID scheme analyte. After a result is stored for a sample, the IFF is typically configured to automatically advance the cursor to the next sample in the instrument run list, and to jump over cells that already have a locked status (for example, NA, IS, LNR).
- Automatic capture is required for instruments that can create data files which contain enough information to determine the CUID scheme analyte, otherwise the next sample in the instrument run list receives the results.
If the incoming data contains enough details to define the sample ([CUID and scheme] or [sample ident, job and scheme]), then the On-line module knows where to put the data. However, if these details cannot be decoded from the incoming data, they must be defined prior to collecting data.
Capture a result from an instrument into a sample scheme
Once data transmissions are finalised, the instrument must be stopped to release the communication channel.
Stop data capture from an instrument data capture session
After a record is received by the On-line application, it is decoded. If the decoded sample is not registered in CCLAS, then the IFF file may contain logic to determine the outcome.
The IFF may be configured to automatically append new samples that are decoded from the instrument data string to the instrument run list.
Rereads can be used to calculate the result of the unknown, and the unknown result submitted to quality control testing and/or product limit checking. VBScript can be used to automatically perform quality control and product checks.
Sometimes the type of data in the on-line grid means that the data is not displayed properly. Change the format of the on-line grid to display the data correctly.
Format a cell in the On-line grid
Matching Results with Samples in the Instrument Run List and Managing Unregistered Samples
Where the sample data decoded from an instrument transmission contains enough information for the IFF to determine the job, sample, scheme and analyte, then the IFF also determines whether the sample is already registered in CCLAS, and goes on to set whether registration is permitted where it is required. This may be overridden by the user. When another instrument is selected for the data capture session, then the auto append mode is reset to Never.
Where registration is required and permitted, then the sample is appended to the instrument run list.
Manage results for unregistered samples
Where only the data, and optionally the analyte, is decoded from the instrument string, then the job, scheme and sample details are taken from the current sample in the instrument run list, with sequential progression through the list of samples. When results are captured for a QC sample, where the sample type and sample ident are used to find the next QC sample, but there are multiple QC samples with the same type and ident, the on-line data capture session may be configured to advance to the next non-analysed QC sample to receive the result.
Managing Results from the Instrument String
Where a cell in the On-line grid contains a formula, it can be cleared, if required.
Clear a cell formula in the On-line grid
The best result, or a minimum, maximum or average of selected rereads can be used to determine the result of the unknown sample.
| Formula | Description |
|---|---|
|
Average |
Calculates the average value for the selected cells. |
|
Count |
Calculates the average value for the selected cells. |
|
CountIf |
calculates the number of rereads in the selected cells, but only if a cell contains a value >= 0. |
|
Min |
Calculates the non-zero minimum value for the selected cells. |
|
Max |
Calculates the non-zero maximum value for the selected cells. |
|
Sum |
Calculates the sum of values in the selected cells. |
|
SumIf |
Calculates the sum of values in the following cells, only if all values are non-zero. |
Calculate an instrument run list sample results from reread samples
Formula Evaluations
Where formulas are set up on CUID scheme analytes, the cell's value is evaluated if all dependencies are available.
Formula cells are calculated automatically as data is entered.
Logical and error values are usually the result of a formula, although entering these values can be useful for testing formulas. The logical values that can be entered are TRUE and FALSE. The error values that can be entered are #N/A, #VALUE!, #REF!, #NULL!, #DIV/0!, #NUM!, and #NAME?.
Assessing Results
A CUID scheme analyte's status indicates the quality and state of the result.
Initially, when a sample is registered into CCLAS, a blank status is given to each profiled analyte.
Results are assessed against quality control limits where the sample is a blank, standard or spike QC sample, and against detection limits, upper scheme limits and product limits where the sample is an unknown sample.
System Assessment of Detection Limits
CUID scheme analyte's status indicates the quality and state of the result. Initially, when a sample is registered into CCLAS, a blank status is given to each profiled analyte.
Detection limit and upper scheme limits are assessed for unknown samples.
- Where a result is more than the upper limit for the scheme-analyte. then the result is given a CHK status indicating a check is required.
- Where the LIMS is configured to assess results against the lower detection limit and a result is less than the detection limit for the scheme-analyte, then the result is given a CHK status indicating a check is required.
- Where a cell contains a CHK status, then the cell is highlighted accordingly.
System Assessment of Quality Control Limits
Quality control samples are checked against their expected limits. If an analytical result for a quality control sample falls outside of the quality control limits, warning flags are displayed. If the results are out of specification, and where:
- Where the result is above the critical upper limit, then the result is given a QFH status indicating a Quality Failure - High.
- Where the result is below the critical lower limit, then the result is given a QFL status indicating a Quality Failure - Low.
- Where the result is above the upper warning limit, then the result is given a QWH status indicating a Quality Warning - High.
- Where the result is below the lower warning limit, then the result is given a QWL status indicating a Quality Warning - Low.
System Assessment of Product Limits
If a sample links to a product, then it can undergo a product check, that is, the results are assessed against the scheme analyte limits defined in the product, and product rules are run for the scheme.
The LIMS may be configured to have results automatically assessed against product limits as results are captured. Product assessment can also be manually requested.
Display the minimum and maximum product limits each analyte specified in the product to see the expected range of result.
Display product limits for a sample in the instrument run list
Where the LIMS is configured with a product rule script for the scheme, then product limit checking includes running the script to perform custom logic.
Check sample results against product limits for a sample in the instrument run list
Product rules are applied to schemes or scheme-analytes, such that, as data is entered, the data is only accepted where the rule passes.
Note: The scheme and analyte referred to in the rule does not have to be the same scheme and analyte of the current column.Column.Row. $Column$Row can be used to refer to a particular cell. If the Column.Row format is used in a validation rule, this is added as an item in the list of defined names.
Examples:
Rule: BAL1.WEIGHT1 < 20
Text: Initial weight should be less than 20.
Rule: WEIGHT2 > WEIGHT1
Text: Weight should be greater than the initial weight.
Rule: G.1 < 20
Text: Initial weight should be less than 20.
Rule: $G$1 < 20
Text: Initial weight should be less than 20.
The IFF may have automatic product checking turned off. This can be toggled on to perform automatic product checking as results are captured, or toggled off, as required.
Toggle automatic product checking on results
Result Validation
Once results are entered and are within the range of the scheme, that is, there are no detection limit failures, then the next step is result validation.
Result validation may be undertaken by the analyst, but more often by the supervisor, section head, or sometimes in a small laboratory, by the laboratory head.
Initially, when a sample is registered into CCLAS, a blank status is given to each profiled analyte.
For each analyte, with a numeric data type, that had data entered into it during the sample analysis session, if the analyte's result does not require a check due to exceeded detection limits, and analyte's Status Active flag is:
-
Enabled, then the analyte's Status for the sample is set to NVL (Not Validated), If the result is subsequently validated, then the analyte's Status is set to VAL (Validated), and upon saving of the validated result, the analyte's Status is set to CPL (Completed).
-
Disabled, then the analyte's Status for the sample is set to CPL (Completed) immediately.
Note that results are not reportable until the analyte's Status is CPL (Completed).
Refer to the Validating Results process.
Saving Results
If a result is manually entered, then the sample is colour highlighted until it is saved.
When the result entry is completed for the data capture session, save the data.
Each result entered or captured in final results mode is stored as the CUID scheme analyte's Final value and where the system is configured to do so, the CUID scheme analyte's Formatted value is calculated.
All changes to status flags, user notes, limit status, or any other field in the PROFJOB_CUID_SCHEME_ANALYTE table are audited.
Where the system is configured to do so, then the job status is updated after results are saved.
Ending a Data Capture Session
You can log out of a data capture session but keep the Pool Control and Security Manager running. This allows you to log back in to the data entry session without having to re-establish the connection. This method of logging in to CCLAS is used when the CCLAS Menu is not used to run CCLAS applications, and another user has logged out of the current session, but left the On-line application running.
Log out from a data capture session
Log back in to a data capture session
Managing Data Capture Sessions
Multiple on-line data capture sessions can be opened at a time so that data can be captured from multiple instruments simultaneously, but only works with instruments that write data to a file (for example, an XRF analysis instrument) where human intervention is not required. Each data capture session has its own instrument run list.
