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How to monitor and audit InteLIS

Find who changed a record, check that data and analyzer results are moving, and read how the lab is performing. Most pages sit under ADMIN → Monitoring. Instrument Activity, Lab Performance Indicators and Sample Referral Network sit under ADMIN → Reports.

Before starting

  • An account whose role holds the Monitoring pages needed. The built-in Admin role sees them all
  • On the Roles page, Lab Performance Indicators, Instrument Activity and Sample Referral Network are granted under Reports, not under Monitoring
Which pages appear
Installation Pages
Standalone or LIS Every page except Lab Sync Status and API Dashboard
STS Every page
Cloud For users without the built-in Admin role: User Activity Log, Audit Trail and Log File Viewer only

Page Usage appears only for the built-in Admin role, and for roles given the Page Usage privilege on the Roles page. No other role holds it by default.

Which page answers which question

Question Page
Who changed this sample, and to what? Audit Trail
What did this user do, and when did they sign in? User Activity Log
Which pages do users open, and for how long? Page Usage
Did data reach the STS? API History on a LIS. Lab Sync Status on the STS
Where did the STS requests come from, and did results go back? API Dashboard
Is this analyzer still sending? Instrument Activity
How many tests ran on each instrument and assay? Instrument Activity
How long is the lab taking, and how often do tests fail? Lab Performance Indicators
Where are samples lost between request and result? Source of Requests
What does InteLIS hold behind a result? Test Results Metadata
Which facilities send samples to which lab? Sample Referral Network
What errors has the system logged? Log File Viewer

Find who changed a sample

  1. Go to ADMIN → Monitoring → Audit Trail.
  2. Set Test Type.
  3. Enter the Sample ID or Remote Sample ID.
  4. Select Submit.

  5. Read the Table View: one row per revision, with the user who saved it and when. Open Changes Only to see each changed field with its Old Value and New Value.

    Other views
    View Shows
    Timeline View Each revision as an entry on a timeline
    Compare Versions Two chosen revisions side by side
    Export To CSV The history as a file, to send to support or an auditor
    If the page says the sample does not belong to the lab

    On a cloud instance, the Audit Trail opens only samples of the user's own lab.

  6. For TB, COVID-19 and Custom Tests, read Tests History below the sample's history: one row per change to one of the sample's tests, each change marked against that test's previous revision. The history starts from the update that added this section.

See what a user did

  1. Go to ADMIN → Monitoring → User Activity Log.
  2. Under Show, pick All, Actions or Logins.
  3. Set Date Range and User.
  4. Read the entries. Each carries the user, the action, the IP address and the browser.
  5. To follow one sign-in from start to end, select Filter by this session on one of its entries.

The User Activity Log records what users did. To see the old and new values of a sample, use the Audit Trail.

See which pages are used

  1. Go to ADMIN → Monitoring → Page Usage.
  2. Set Date Range. Set User to narrow it to one person.
  3. Read the cards: Users, Sessions, Pages Used, Page Opens and Time on Pages.
  4. Read Most Used Pages and Most Active Users.
  5. Under By User and Page, select a session to show only that session, then select Open in Activity Log in the filter above the cards.

Time counts only while the page is the tab in front of the user. It is not the length of the sign-in.

Page Usage is empty

Recording is switched by Track Page Usage in General configuration. It is on by default.

Check that data reached the STS

Choose the installation, then follow its steps from top to bottom.

  1. Go to ADMIN → Monitoring → API History.
  2. Set Date Range. Set Test Type to narrow it to one module.

  3. Read the most recent rows:

    Column Means
    Transaction ID The identifier of one sync
    Number of Records Synced How many records the sync carried
    Sync Type Which direction and which kind of data moved
    URL The server the sync went to
    Synced On When it ran

  4. Check for a recent row with a non-zero Number of Records Synced.

A lab whose data is missing nationally has no recent row, or rows carrying zero records.

  1. Go to ADMIN → Monitoring → Lab Sync Status.
  2. Set Province/State, District/County or Lab Name to narrow the list, and select Search.

  3. Read the lab's row. Its colour follows its most recent activity:

    Status Means
    Active Synced within 2 weeks
    Falling behind Synced 2 to 4 weeks ago
    Stopped Synced before, but not for 4 weeks or more
    Never synced Registered, never brought up

  4. Compare Last Results Sync from Lab and Last Requests Sync from STS. A gap in the first means results are sitting on the lab machine. A gap in the second means the lab does not see new requests.

  5. To see which facilities are behind, select the lab's row. Lab Sync Details opens in a new tab with Requests Sent to Lab and Results Received from Lab per facility.

To send a command to a lab from this page, see Remote command plane.

API Dashboard

ADMIN → Monitoring → API Dashboard follows requests that arrived from an EMR or another system through the API. It shows how many were received at the lab, tested and answered, and flags possible duplicate patients. Set the filters and select Refresh Dashboard.

Check that an analyzer is still sending

  1. Go to ADMIN → Reports → Instrument Activity.
  2. Open Interface Tool Events.
  3. Read Events (last 7 days), Failures (last 7 days) and Last event.
  4. Set Instrument to the analyzer, and select Search.
  5. Read the most recent Occurred On. A failed event carries a Failure Code. To keep the list, select Export to Excel.
  6. If nothing recent appears, open the testing lab's Interface Tool Connections and read Last Seen. See Interface Tool connections.

A stale Last Seen means the Interface Tool is not reaching InteLIS.

Count tests by instrument and assay

Use these figures to account for reagents by platform and to compare failure rates between instruments and assays.

  1. Go to ADMIN → Reports → Instrument Activity.
  2. Open Tests by Instrument. The tab appears when Viral Load or EID is active.
  3. Set Test, Tested On and Lab. Lab appears only when the instance has testing labs.
  4. Select Search.
  5. Read By Instrument Type for the totals of each make, and By Lab, Instrument and Assay for each instrument. When the analyzer reports its serial number, it follows the instrument's name, so two machines with the same name show as two rows.
  6. To narrow By Lab, Instrument and Assay, pick a value in the dropdown above a column. Select a column heading to sort by it. Total adds up the rows left showing.
  7. To see the samples behind a count, select the number under Samples, Valid First Time, Valid After Re-test or Still Failed. The list opens below the table, with the batch code, test date, result, number of runs, analyzer run ID and analyzer message of each sample.
  8. Read Failure Messages by Instrument for what the analyzer said about each failed run, most frequent first. A failure the analyzer gave no message for shows Not recorded.

  9. To keep the figures, select Export to Excel. The file downloads when it is ready. Progress shows in the Exports menu.

    What each column counts
    Column Counts
    Tests Run Every result and every recorded failure, on the date of the test
    Failed or Invalid Tests with the status Failed
    Samples Each sample once, under its latest run in the range
    Valid First Time Samples whose latest run is valid and that never failed
    Valid After Re-test Samples whose latest run is valid after an earlier failed run, in the range or before it
    Still Failed Samples whose latest run in the range failed: waiting for a re-test, or failed again

    A sample tested on two instruments, or failed in the range and re-tested after it, counts once, under its latest run in the range. So the sample columns add up across the rows and Total is the number of samples.

    The export also has Valid Results (Tests Run that did not fail), Failed Runs Re-tested (failed runs that a re-test replaced, each one also in Tests Run), the instrument's model and serial number, and a Failure Messages sheet.

    Cancelled and rejected samples are not counted. For the same test, range and lab, Tests Run matches Failures in Lab Performance Indicators.

    If the assay shows Not recorded

    The assay is recorded for results that arrive from the Interface Tool or from GeneXpert and Abbott m2000 result files, starting with the update that added this tab. Earlier results, results entered by hand and other result file formats show Not recorded.

    Where InteLIS reads the Interface Tool database directly, earlier Interface Tool results are filled in once, in the background, after the update that reads the analyzer's message. They then reach the central server with the next results sync.

    For Abbott m2000, Alinity m and GeneXpert results from the Interface Tool, the reagent lot number is recorded with the result too, with its expiry date when the analyzer sends one.

    From the same message, each Interface Tool result also keeps the instrument's model and serial number, the analyzer's run ID, its message about the run (for example the error behind a failed test) and the readings sent with the result, such as cycle thresholds. The Viral Load and EID exports carry them, with the reagent lot.

    If the instrument shows Not recorded

    The result was entered by hand without a testing platform.

Read the lab performance report

  1. Go to ADMIN → Reports → Lab Performance Indicators.
  2. Set Test, Date Range, View By and Lab. Lab appears only when the instance has testing labs.
  3. Select Apply.

  4. Open the tab needed. Overview appears when Test is All Tests (Overview). The other tabs appear when one test is chosen.

    Tab Shows
    Overview Samples registered and tested, results available and awaiting a result
    Turnaround Time Average days between collection, lab receipt, testing and release
    Testing Volume Results by entry mode: Manual Entry, Analyzer Interface, File Import. Older results show as Unclassified
    Failures Failed tests, the failure rate and the re-test rate
    Rejections Rejected samples, the rejection rate and the top reasons
    Repeat Patients Patients tested more than once, and result changes

  5. To keep a copy, select Export.

How are these numbers calculated? on the page explains each figure. A sample tested twice counts as two tests, so a retest does not hide a failure.

Find where samples are lost

  1. Go to ADMIN → Monitoring → Source of Requests.
  2. Set Date Range and Test Type. The page shows nothing until both are set.
  3. Narrow it with Province/State, Name of the Clinic, Name of the Testing Lab or Source of Request if needed.
  4. Select Search.
  5. Compare the counts along each row: No. of Samples Requested, Acknowledged, Received at Testing Lab, Tested and Results Returned. The count that drops shows where samples stop.

Read the record behind a result

  1. Go to ADMIN → Monitoring → Test Results Metadata.
  2. Set Test Type.
  3. Set Sample Test Date, or enter a Sample ID/Batch Code.
  4. Select Search.
  5. Read the row. It holds the collection, receipt and test dates, the result and its status, who tested it and on which instrument, whether it was entered by hand, rejection details, any change with its reason, and a link to the imported file.
  6. To send it to support, select Export To Excel.

See the referral network

  1. Go to ADMIN → Reports → Sample Referral Network.
  2. Set Date Range and Test Type.
  3. Set Date Based On: Sample Collection Date, Sample Registration Date or Sample Tested Date. Counting by tested date matches a lab's own testing figures.
  4. Select Search.
  5. Select a lab or facility on the map to show only its links. The table Referrals by Lab and Test Type lists every link.

A facility without latitude and longitude is left off the map and still counted in the table. To add coordinates, see Facilities and testing labs.

Read the log files

  1. Go to ADMIN → Monitoring → Log File Viewer.
  2. Set Date and Log Type: System Error Logs or PHP Error Logs.
  3. Filter by level, or search the text.
  4. If the error is not in that day's log, check Days with errors matching this search. It lists each day of the last 90 that logged a matching error. Select a day to open its log with the same search.
  5. Select Export Log File and send the file to support with the request.

The log records faults, not user actions.

Confirm it worked

Task Check
Traced a change The Audit Trail names the field, the old value, the new value and the user
Confirmed a sync API History or Lab Sync Status shows a recent sync carrying records
Confirmed an analyzer is live Instrument Activity holds a recent Interface Tool event, and Last Seen is recent
Found a missing sample Source of Requests shows the stage where the count drops