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New Concerns (from Chege)

  1. To modify the current registration dash board to use a bar code scanner and also be able to pool urgent samples differently.COMPLETED
  2. The system has been occasionally assigning the same accessioning Identifier to two different patients.COMPLETED
  3. The system changes patients clients after registration.COMPLETED
  4. Flocytometry are not supposed to report in decimal points but the system assigning decimal points even though the facs calibur don't report that.COMPLETED
  5. The LIS system has a default time as 01-01-1900,This is affecting the results going to Amrs.(suggest to pick the current age or time) COMPLETED
  6. After every importation of the master to Busia lab,all the equipment mapping are distorted and all the Doc's list refresh.COMPLETED
  7. Modify the HL7 interface for one to able to search through the different queues and also be able to link the different queues for various reports as may be required.COMPLETED
  8. To interface the following equipment with Lis CAPCTM,ABBORT both in molecular,FACS CALIBUR in flocytometry,BACTEC MGIT 960 in TB lab and COULTER ACT 5DIFF AL in hematology.COMPLETED

New Concerns (from Jeremy, Paul and Burke)





23 Feb 2012

HL7, datatype

Now that we receive non-numeric values for numeric concepts as ST OBX segments, we have over 3,300 observations in AMRS from May 2011 until now where the value is stored in the value_text column instead of value_numeric (because the value is not numeric). This is a drawback of our ORU^R01 processor, not validating concepts against OBX datatypes, but we need to work this out with PCS as well.

PCS clearly has requirements for acceptable values for each lab result. We need to see all of those requirements so we know what to expect when processing the HL7s, and we also need to decide on a better way to communicate that a lab result is invalid. Right now, PCS appends an NTE segment with a reason (if given), but most of the time there is nothing but an automated response of invalid entry. If the data entry is by hand, can it not be enforced in the PCS application to enter it right or provide some explanation for an invalid result?

On our end, we should modify the PCS Lab Interface Module to validate OBX datatypes against referenced concepts, and throw the HL7 to the error queue if it fails.


23 Feb 2012


The Module was recently released and is taking the place of the existing REST Module. This will mean a new form of communication for looking up patients and providers from the PCS interface. It would be great to have PCS integrate the new REST schema so we can retire the outdated REST Module and go with the new one.


Previous Pending Issues (in order by priority)









Sending null result for OBX when not all tests from lab set are ordered:

  • OpenMRS issue TRUNK-136 corrected HL7 queue hangups due to these null entries and is considered complete
  • When a test from a lab set is not ordered, LIMS will send ^^99DCT for that particular test.
  • Cornelious emailed Sandeep on such issue on March 15, 2010 and followed up on March 22, 2010 and March 24, 2010.
  • As of April 19, 2010, there is no reply from PCS.
  • Sandeep replied on April 26, 2010 that he will work on it after returning to India in first week of May.
  • Example of the message:

    OBR|1|||87^Syphilis TPHA^99PCS
    OBX|1|CWE|1032^Syphilis TPHA^99DCT||^^99DCT|||||||||201003111600|||||201003111423
    OBX|2|CWE|1031^Syphilis TPHA in Titre^99DCT||1314^01:08^99DCT|||||||||201003111600|||||201003111417

    On April 29, 2010, we find out another lab set which also experiences the same problem which LIMS sends null value for one of the OBX to AMRS.  Example of the message:

    OBR|1|||66^Urine Analysis (10 parameter)^99PCS
    OBX|1|NM|2339^URINE Protein^99DCT||+|^mg/dL|Below 20 mg/dl|||||20090220||201004271408|||||201004271529
    OBR|2|||68^CBC (FHG)^99PCS
    OBX|1|NM|21^HGB^99DCT||13.5|^g/dL|10.4 - 15.7|||||20090220||201004271408|||||201004271440
    OBX|2|NM|679^RBC^99DCT||4.65|^10\S\6cells/uL|3.5 - 5.2|||||20090220||201004271408|||||201004271440
    OBX|3|NM|1015^HCT^99DCT||40.8|^%|36.10 - 50.30|||||20090220||201004271408|||||201004271440
    OBX|4|NM|851^MCV^99DCT||87.7|^fL|76.0 - 96.0|||||20090220||201004271408|||||201004271440
    OBX|5|NM|1018^MCH^99DCT||29|^pg|26.00 - 34.00|||||20090220||201004271408|||||201004271440
    OBX|6|NM|1017^MCHC^99DCT||33.1|^g/dL|33.00 - 37.00|||||20090220||201004271408|||||201004271440
    OBX|7|NM|1016^RDW^99DCT||13|^%|10.00 - 20.00|||||20090220||201004271408|||||201004271440
    OBX|8|NM|729^PLT^99DCT||236|^103cells/uL|146.0 - 419.0|||||20090220||201004271408|||||201004271440
    OBX|9|NM|1022^Neutrophils^99DCT||81.4|^%|34.00 - 67.00|||||20090220||201004271408|||||201004271440
    OBX|10|NM|1024^Eosinophils^99DCT||3.7|^%|0.0 - 5.0|||||20090220||201004271408|||||201004271440
    OBX|11|NM|1025^Basophils^99DCT||0.7|^%|0.0 - 2.0|||||20090220||201004271408|||||201004271440
    OBX|12|NM|678^WBC Count^99DCT||9.5|^10\S\3cells/uL|3.3 - 8.2|||||20090220||201004271408|||||201004271440
    OBX|13|NM|1021^Lymphocytes^99DCT||6.8|^%|25.00 - 50.00|||||20090220||201004271408|||||201004271440
    OBX|14|NM|1023^Monocytes^99DCT||7.4|^%|2.00 - 11.00|||||20090220||201004271408|||||201004271440
    OBX|15|NM|1307^MPV^99DCT||5|^%|7.40 - 10.40|||||20090220||201004271408|||||201004271440
    OBX|16|NM|1308^PCT^99DCT||0.12|^%|0.200 - 0.500|||||20090220||201004271408|||||201004271440
    OBX|17|NM|1309^PDW^99DCT||17.5|^%|8.00 - 18.00|||||20090220||201004271408|||||201004271440
    OBX|18|NM|952^Abs. Lympho^99DCT||0.6|^10\S\3/uL|1.5 - 4.0|||||20090220||201004271408|||||201004271440
    OBX|19|NM|1330^Abs. Neutrophils^99DCT||7.7|^10\S\3/uL|1.00 - 5.00|||||20090220||201004271408|||||201004271440
    OBX|20|NM|1331^Abs. Mono^99DCT||0.7|^10\S\3/uL|0.20 - 0.80|||||20090220||201004271408|||||201004271440
    OBX|21|NM|1332^Abs Eosinophiles^99DCT||0.4|^10\S\3/uL|0.05 - 0.77|||||20090220||201004271408|||||201004271440
    OBX|22|NM|1333^Abs. Basophiles^99DCT||0.1|^10\S\3/uL|0.02 - 0.1|||||20090220||201004271408|||||201004271440
    OBX|23|NM|1334^Abs. ATL^99DCT|||^10\S\3/uL|0.0 - 2.0|||||20090220||201004271408|||||201004281611

    (Issue still pending)

Tests separated . COMPLETED




How to handle results that come through to Amrs as dashes(-).This happens when either the target is out of range or indeterminate.  





After a sample is processed, we expect it to have some required fields like AMPATH ID or Study ID, test ordered, doctor who requested, clinic and person who accessioned the sample.

  • PCSHL7_Administrator in HL7 machine dashboard, go to PATIENT IDENTIFIER NOT DEFINED from dropdown box.
  • On May 26th, 2010, we find not all required information (such as AMAPTH ID or Study ID, Test Ordered and Registered User) are stored/shown.(still pending)





possibility of parsing comments made in Lims into Amrs.





Occasional changes in various result units


Completed Issues (in order by priority)








Busia, AMRS, RestModule

How will the rest module in Busia handle patients demographics before sychronization

Sol: We have implemented REST API module in Busia.
Now, during order registration , user type the AMRSID in Lab system and it will get verified by AMRS server and patient demographic is added/updated in Lab system.
One which are not verified by AMRS server through REST API  there in busia, will be verified in Eldoret after get imported through PCSHL7AMRScheck window services.





The import/export feature in lims has a problem hence making it difficult to upload data from Busia.

  • It hasn't been working since March 2010.
  • Sandeep is informed on May 3rd, 2010 that this is the top priority he should work on.
  • Sandeep starts checking on this on May 24th, 2010.

    Sol: HL7 Table (I_Table_R01) that creating problem is exempt from export/import. 
    Data in this table will be generated once data is imported in Eldoret from busia to generate HL7 mesaages.





Incoprate check digit algorithm in Busia pcs interface.

Sol: Implemented. User will get a prompt to enter correct ID. Note: System will prompt only, it will not restrict the registration as its delay the lab processing.
So, User must note down such patient and update to correct identifier once its avaliable from clinic
Also, HL7 messages generated for correct identifier invalid identifier will be list in HL7 "Invalid identifier" queue





Most transactions from busia have no providers numbers hence messages have been sent to patient identifier not defined queue.Seems the doctors list is refreshing despite i updating it manully at Busia in March.

Sol: Doctor list updated





AMRS not defined queue in HL7:

  • When new patients got their lab done and their records are not in AMRS, their lab test results are put in "AMRS not defined queue in HL7. Once those patients' records in AMRS, there is no mechanism in LIMS to re-check the AMRS not defined queue and send their lab results to AMRS.
  • Cornelious informed Sandeep on Jan 18, 2010.
  • Lagat informed Vishal the same issue.
  • Cornelious followed up with Sandeep on March 30, 2010.
  • As of April 19th, 2010, there is no reply from PCS.
  • Sandeep replied on April 26, 2010 that he will work on it after returning to India in first week of May(The manual process to re-check the queue was fixed but the auto part it still pending)

    Sol: PCSHL7AMRSCheck service is updated and started to do auto verifying of Patient identifier in every 5 hrs





The I_Table_R01 table has  an error after importation from Busia.

Sol: HL7 Table (I_Table_R01) that creating problem is exempt from export/import. 
Data in this table will be generated once data is imported in Eldoret from busia to generate HL7 mesaages.





The current dll file for the barcode printer is for a different label size which has caused the printer not  to print barcode labels.

  • Sandeep replied on April 26, 2010 that he will work on it after returning to India in first week of May.(Issue still pending)
  • Chat with James and Cornelius on June 30,2010** Barcode printer - need a Barcode S/w to generate the script again
    • check on internet to get the Bartender s/w for barcode model
    • install the s/w on the computer where barcode printer is connected
    • design the Barcode again as per Label size and test it by printing
    • Once it completed there is option in S/w to generate the script for the same
    • Sol: Printer Cabel has a problem, is replaced. Barcode is printing now





Doctors list refreshing.Some doctors that were previously added into the Lims are currently not available during accessioning.When we try to add them again it gives an error.
Jer will modify REST module to include multiple roles (Clinical Officer, Clinician, Consultant Physician, Medical Officer) for doctors.

DOCTOR API is implemented at reception to fetch Doctor information using AMRS userid





Scrip  to generate  HL7 messages from Busia  after importation.This is after stopping the importation of 'I_Table_R01' table which  has a problem.





How to handle the comments made regarding a sample in LIMS and how to parse the same to Amrs.





Capability to send ACTG results to AMRS:

  • Cornelious emailed Sandeep on Jan 28, 2010.
  • As of April 19, 2010, there is no reply from PCS.
  • Sandeep replied on April 26, 2010 that he will work on it after returning to India in first week of May.(Issue not yet resolved)

    Sol: System updated





Cornelious has identified on May 6th, 2010 that when a patient doesn't have a preferred identifier checked in AMRS, LIMS will only pull the Kenyan National ID . This causes LIMS results not sent to AMRS.
 (still pending)

Sol: Script Updated.
Problem was we are considering only one or none  attribute for "Identifier List" node. If Node has more that one attribute we consider as preferred identifier. But since we are getting "Voided" also as a attribute so system assume it as preferred one. Script is updated.





After importing data from Busia the clinic change to HCT.





Need to be able to use Pcslabinterfacemodule when calling the rest module.





Cobas machine in Busia is not porting results, ? com port damaged.

  • Require 2 modular adapters (DB 9 F to RJ45)                                        





The default DOB in lims is 01-01-1900 but after the patient's demographics  are pulled from Arms the DOB does not change.





Added new hematology machine-Done


LIMS Issues which have been resolved:

  1. Fixed on May 26th, 2010.

Details of the issue:  Improper concept mapping in LIMS on Urine protein was found on May 3rd, 2010.

OBR\|1\|\|\|66^Urine Analysis (10 parameter)^99PCS
OBX\|1\|NM\|2339^URINE Protein^99DCT\|\|+\|^mg/dL\|Below 20 mg/dl\|\|\|\|\|20090220\|\|201004291547\|\|\|\|\|201004291635

  2. The HL7 machine is slow, could be the cause of messages ovestaying in the IN QUEUE in LIMS?


  1. Burke Mamlin, Cornelius Chege and Ada Yeung is it possible to provide updates by editting this page on what has been completed so far for LIMS ? Thanks.

    1. Thanks for following up on this, Boniface Wabuti.  Cornelius Chege is the best person to provide updates on this page.  

  2. Cornelius Chege now that the LIMS developer is here, is it about that time that you help follow on this itesm ? We have issues 5,14,18,17 and 20 pending. No sure if that is the right channle to follow, but can we meet to dicsuss this ?