problem with measurements

[Jignesh Patel]

We are trying to import 2019 measure but now system shows 2 measurements instead of 1. 
Is there a document to do proper clean up etc.

[pclvi...@gmail.com]

CMS53 measure is not part of the EH measure for 2020 reporting - https://ecqi.healthit.gov/eh-cah-ecqms?field_year_value=2.  I believe you are still seeing the measures from the 2018 bundle.

 

BTW, to use a new 2019 bundle, you should drop the pophealth-production database from the MongoDB first.  The installation of the new bundle will recreate the pophealth-production database with just the new bundle, i.e., 2019 bundle.

 

Peter

 

From: worldvista-pophealth-...@googlegroups.com <worldvista-pophealth-...@googlegroups.com> On Behalf Of Jignesh Patel
Sent: Tuesday, April 21, 2020 1:08 PM
To: WorldVistA popHealth Open Source Work Group <worldvista-pophealth-...@googlegroups.com>
Subject: [wv-pophealth-open-source-wg] problem with measurements

 

We are trying to import 2019 measure but now system shows 2 measurements instead of 1. 
Is there a document to do proper clean up etc.

 

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[Jignesh Patel]

ok following command. is not installing new bundle into mongodb other than just creating database, but if I install 2018 bundle it creates required collections in the database.

bundle exec rake pophealth:download_update_install version=2019 RAILS_ENV=production

(in /home/pophealth/popHealth)

W, [2020-04-21T18:52:36.540948 #398]  WARN -- : Overwriting existing field root in class CDAIdentifier.

W, [2020-04-21T18:52:36.541187 #398]  WARN -- : Overwriting existing field extension in class CDAIdentifier.

W, [2020-04-21T18:52:37.383916 #398]  WARN -- : Overwriting existing field measure_id in class QME::ManualExclusion.

W, [2020-04-21T18:52:37.384116 #398]  WARN -- : Overwriting existing field sub_id in class QME::ManualExclusion.

W, [2020-04-21T18:52:37.384231 #398]  WARN -- : Overwriting existing field medical_record_id in class QME::ManualExclusion.

W, [2020-04-21T18:52:38.183405 #398]  WARN -- : Overwriting existing field start_date in class ProviderPerformance.

W, [2020-04-21T18:52:38.184283 #398]  WARN -- : Overwriting existing field end_date in class ProviderPerformance.

W, [2020-04-21T18:52:38.239968 #398]  WARN -- : Overwriting existing field categories in class HealthDataStandards::SVS::ValueSet.

/home/pophealth/popHealth/lib/tasks/sharding.rake:4: warning: class variable access from toplevel

NLM Username?: XXXXXX

NLM Password?: 

Downloading and saving bundle-2019.zip to /home/pophealth/popHealth/bundles

Downloading Static Measure files

Modifying bundle bundle-2019.zip to support variable date ranges

bundle metadata unpacked...

Loading: Value Sets Complete          

Loading: Measures Complete          

Loading: Patients Complete          

Loading: Results Complete          

Bundle import Successful

In import_static_bundle

Bundle import Successful

Cleaning out records and caches

> show dbs

admin                 0.000GB

local                 0.000GB

pophealth-production  0.000GB

pophealth-test        0.000GB

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[Jignesh Patel]

Is there any heads up, for uploading 2019 bundle?

[pclvi...@gmail.com]

It is one of the items that needs to be developed for version 6.1.

 

Peter

[Jignesh Patel]

Peter

Is there any other way to update it.

[pclvi...@gmail.com]

I wish there is an easy way, but it hasn’t been the case since OSEHRA took over the product management of the popHealth.  Every year there has been changes, both the measures and the CAT1/CAT3 standards that required updates to the popHealth software.  For some years such as 2017, the changes are small and it didn’t take much new development; while for other years such as 2018, it was like replace everything due to the CQL update.

 

I think we just need to bite the bullet; either share the cost and pay someone to work on the development or share the load by splitting the development work amongst several organizations.

[Jignesh Patel]

If there is any guidance on fixing this issue. I will dig into it.

[Jignesh Patel]

seems there is no technical guidance :) or architecture flow.

We will have our development team start looking into this and see if we can make it work.

[l...@osehra.org]

Hi Jignesh,

 

Raj Naga and I created a technical document that describes what needs to be done for popHealth v6.1 – see attached.

 

However, we didn’t mention importing of the measure bundle.  The best way to update the section of the code that imports the 2019 bundle is to look at the similar code in Cypress v5.x code.  Update what is in popHealth with what is used in Cypress v5.x.

To view this discussion on the web visit https://groups.google.com/d/msgid/worldvista-pophealth-open-source-work-group/CAHTx_0yj8fXFqBFoT8AY4gTegqfLAhtxfqu%2BceWjuDy116rSgg%40mail.gmail.com.

[Jignesh Patel]

Peter,

I have tried multiple times to build cypress AMI in AWS services. I tried m5 and then later m3 instances, using 5.3 and 5.2  community versions of cypress to get this going.

But for some reason, the AMI is not let me access via root, even though port 22 is open to the world.

If I can't access to the system nothing much I can do. Let me know if there is  more information to know.

Reference:

https://github.com/projectcypress/cypress/wiki/Cypress-5-AMI-Install-Instructions

[pclvi...@gmail.com]

Hi Jignesh,

 

I’ve not used the cypress AMI in AWS service.  If you have to, you probably should post questions to the Cypress mailing group.  I’ve always used the VM images running on VirtualBox, and they seemed to work fine.

[Jignesh Patel]

Yup I made it work in my local box. We are analyzing further. But it wout be great if you share some insight of where to look for.

I will also join Cypress mailing list.

[l...@osehra.org]

Hi Jignesh,

 

See popHealth v6 pophealth.rake file for the code that download and installs the bundle - https://github.com/WorldVistA/popHealth/blob/97c23f80c9382079eec254ff8d259f9f3f43eac7/lib/tasks/pophealth.rake#L187

 

The import_bundle() method uses CqlBundle::CqlBundleImporter class to import the measures – see https://github.com/WorldVistA/popHealth/blob/97c23f80c9382079eec254ff8d259f9f3f43eac7/contrib/measure_dates.rb#L73

 

Cyress uses the same CqlBundle::CqlBundleImporter class to import measure – see https://github.com/projectcypress/cypress/blob/5030013dfc84baac0f8d0152adfb5f11493fc840/lib/cypress/cql_bundle_importer.rb#L3

 

You need to see what change has been made in the Cypress 5.0 for the 2019 bundle and update popHealth class accordingly.

To view this discussion on the web visit https://groups.google.com/d/msgid/worldvista-pophealth-open-source-work-group/CAHTx_0xQZkVaVgSsr26jUrzSYoQ5cpHg-M1-GoACSh8r6w7J2w%40mail.gmail.com.

[Jignesh Patel]

Peter

This level of detail certainly helps.

[Jignesh Patel]

While we made good progress in upgrading code we stuck at the following place

In cypress the files exist in the below location:

/opt/cypress/vendor/bundle/ruby/2.6.0/gems/mongoid-6.4.4/lib/mongoid/clients/sessions.rb

/opt/cypress/vendor/bundle/ruby/2.6.0/gems/mongoid-6.4.4/lib/mongoid/clients.rb

/opt/cypress/vendor/bundle/ruby/2.6.0/gems/mongoid-6.4.4/spec for all the rb files for client, sessions and mongo.

But sessions.rb is missing in pophealth and when it is added in the same location and checked other places too. But error stays:

~/.bundle/ruby/2.6.0/gems/mongoid-6.4.4/lib/mongoid/clients/sessions.rb

NameError: uninitialized constant Mongoid::Clients::Sessions

Just to let you know that we have updated ruby version as cypress 5 is using Ruby 2.6.3.

Let us know if there is any insight?

[Jignesh Patel]

We updated the existing pophealth as per new cypress version and we had following issue to run healthdatastandards:

[Jignesh Patel]

 we are able to import 2019 measurement bundle, the next work is to display in the pophealth GUI.

> show dbs
admin                 0.000GB
local                 0.000GB

pophealth-production  0.079GB

[l...@osehra.org]

Excellent.

 

Are you able to import CAT1 patient files?

 

Peter

 

From: Jignesh Patel <jignes...@gmail.com>
Sent: Tuesday, May 19, 2020 5:06 AM
To: petercyli <l...@osehra.org>
Cc: peter li <pclvi...@gmail.com>; WorldVistA popHealth Open Source Work Group <worldvista-pophealth-...@googlegroups.com>
Subject: Re: [wv-pophealth-open-source-wg] problem with measurements

 

 we are able to import 2019 measurement bundle, the next work is to display in the pophealth GUI.

 

> show dbs
admin                 0.000GB
local                 0.000GB
pophealth-production  0.079GB

 

On Thu, May 14, 2020 at 5:13 PM Jignesh Patel <jignes...@gmail.com> wrote:

We updated the existing pophealth as per new cypress version and we had following issue to run healthdatastandards:

 

 

 

 

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[Mahesh Dabi]

Hi

 

When I try to import QRDA1 file, it gives error. The error is quite generic.

Cannot call method 'lastIndexOf' of null

After long digging found that the Text of medication dispensed section has to have highlighted part. This is true for other sections as well where it expects text in certain format.

<text>ZITHROMAX 250 MG TABLET</text> Doesn't work

<text>Medication, Dispensed: ZITHROMAX 250 MG TABLET</text> Works after adding highlighted text

 Seems that we need to modify all the XML files prior to importing to append corresponding text. Do we have list of expected text which need to be added for each template?

Thanks

Mahesh

[pclvi...@gmail.com]

Hi Mahesh,

 

I have seen this type of errors in popHealth where the content of the <text>..</text> has to be prefixed with specific set of strings, i.e., “Medication, Dispensed:” , “Encounter, Performed:”, “Medication, Active:”, etc. 

 

It seemed that this is a bit restrictive since the prefix string is just the description of the template used for the entry.   As I remembered this may have to do with the conversion process of the HDS patient “records” object to the CQL “qdm_patient” object, where it is using the prefix string to map the source to the destination object.

 

Peter

 

From: worldvista-pophealth-...@googlegroups.com <worldvista-pophealth-...@googlegroups.com> On Behalf Of Mahesh Dabi
Sent: Monday, May 25, 2020 9:38 AM
To: WorldVistA popHealth Open Source Work Group <worldvista-pophealth-...@googlegroups.com>

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[pclvi...@gmail.com]

Yes. I’ve mentioned this issue to Raj Naga at the time when he was developing the popHealth v6.0.  I believe with all the other issues that he had to work on, he just didn’t get to it.

 

Not sure what’s impact of commenting out the “verify_description_validity” function.  Just make sure that after you commented out the function, you verify that all the entries in the CAT1 file are extracted and present in the qdm_patient collection.

 

Peter

 

From: Mahesh Dabi <mah...@secureit.co.in>
Sent: Tuesday, May 26, 2020 10:23 AM
To: pclvi...@gmail.com
Cc: WorldVistA popHealth Open Source Work Group <worldvista-pophealth-...@googlegroups.com>
Subject: Re: [wv-pophealth-open-source-wg] QRDA1 import issues

 

Hi Peter

 

This is bit crazy as log doesn't give any clue of which section got skipped, error is very generic. Is there way to add log just to identify which sections are failing? 

 

verify_description_validity is function in hds_record.rb I am trying to see if I can comment this function and get it working. I am not sure impact of this.

 

There are 2019 files for which we have to generate report. Any suggestions to get this going?

 

Thanks

Mahesh 

[pclvi...@gmail.com]

The suggested change was for improved logging instead of a generic error message, not a major design change.

 

Peter

 

From: Mahesh Dabi <mah...@secureit.co.in>
Sent: Tuesday, May 26, 2020 11:33 AM
To: pclvi...@gmail.com
Cc: WorldVistA popHealth Open Source Work Group <worldvista-pophealth-...@googlegroups.com>
Subject: Re: [wv-pophealth-open-source-wg] QRDA1 import issues

 

Ok. Let me try. Do you think any change which you suggested  Raj Naga ? Or it is big design change?

[Mahesh Dabi]

Yeah same here was trying to put log but not sure where to put it in bundle so that it will appear in delayed.log file.

Mahesh

To view this discussion on the web visit https://groups.google.com/d/msgid/worldvista-pophealth-open-source-work-group/00b301d63374%24dd7e4070%24987ac150%24%40gmail.com.

[Mahesh Dabi]

Hi Peter

This is bit crazy as log doesn't give any clue of which section got skipped, error is very generic. Is there way to add log just to identify which sections are failing? 

verify_description_validity is function in hds_record.rb I am trying to see if I can comment this function and get it working. I am not sure impact of this.

There are 2019 files for which we have to generate report. Any suggestions to get this going?

Thanks

Mahesh 

On Tue, May 26, 2020 at 7:12 PM <pclvi...@gmail.com> wrote:

[Mahesh Dabi]

Or else let me know where I can log so that Incan get list of sections giving problem.

Mahesh

On Tue, 26 May, 2020, 21:02 Mahesh Dabi, <mah...@secureit.co.in> wrote:

Ok. Let me try. Do you think any change which you suggested  Raj Naga ? Or it is big design change?

Mahesh 

On Tue, May 26, 2020 at 8:18 PM <pclvi...@gmail.com> wrote:

[Mahesh Dabi]

Ok. Let me try. Do you think any change which you suggested  Raj Naga ? Or it is big design change?

Mahesh 

On Tue, May 26, 2020 at 8:18 PM <pclvi...@gmail.com> wrote:

[Mike Stark]

A technique we used to resolve many issues was to start with the Cypress test file set for any given measure  -- if they loaded correctly then we simply adjusted our files to match (regardless of our reading of the standard).

To view this discussion on the web visit https://groups.google.com/d/msgid/worldvista-pophealth-open-source-work-group/CACiyMNasqt3S9fw%3DyuoWUfV_duxbQvKk74F99qmi-KCWcp6nvg%40mail.gmail.com.

[Mahesh Dabi]

Adding logging is also tricky. it throws error in ExecJS in ruby file. I am not sure whether ExecJs allows logging directly.

/home/ubuntu/.bundle/ruby/2.3.0/cqm-converter-9111d4d9d961/lib/cqm/converter/util.rb

    # Builds JavaScript to assist the HDS Record to QDM Patient conversion.
    def self.hds_to_qdm_js(js_dependencies, record, qdm_model_attrs)
      record_json = JSON.parse(record.to_json)
      # Bonnie changes start_date and end_date in the front end before calculation,
      # and this is what is expected by the cql_qdm_patientapi, so make that change
      # before generating the executable JavaScript.
      record_json = record_json.deep_transform_keys { |key| key.to_s == 'start_date' ? 'start_time' : key }
      record_json = record_json.deep_transform_keys { |key| key.to_s == 'end_date' ? 'end_time' : key }
      <<-JS
        window = {};
        #{js_dependencies};
        function PatientWrapper() {
        }
        PatientWrapper.prototype.get = function(attr) {
          const contents = #{record_json.to_json};
          return contents[attr];
        }
        cql = window.cql;
        patient = new CQL_QDM.CQLPatient(new PatientWrapper());

To view this discussion on the web visit https://groups.google.com/d/msgid/worldvista-pophealth-open-source-work-group/00b301d63374%24dd7e4070%24987ac150%24%40gmail.com.

[Mahesh Dabi]

Rather than changing QRDA1 files I changed the function in hds_record.rb (as I donot need descriptions to display properly in PopHealth) to import all the files. These are only templates used across all of my 6K files. We can put Case statement and pu as many templates as possible to get files imported.

    def verify_description(rec)
      Valid_Sections.each do |section|
        if !rec.send(section).blank?
          tmp = rec.send(section)  
          tmp.each do |t|
            #check we have description on the record
 #Delayed::Worker.logger.info("starting mahesh " + " $" + t['oid'].to_s.strip.bytes.count.to_s + " $" +  t['oid'])
          if t['oid'].strip ==  '2.16.840.1.113883.3.560.1.1001'
#Delayed::Worker.logger.info("Got in " + t['description'] + " $" + t['oid'])
t['description'] = 'Intervention, Performed: test'
          elsif t['oid'].strip == '2.16.840.1.113883.3.560.1.13'
#Delayed::Worker.logger.info("Got in " + t['description'] + " $" + t['oid'])
t['description'] = 'Medication, Active: test'
          elsif t['oid'].strip == '2.16.840.1.113883.3.560.1.14'
#Delayed::Worker.logger.info("Got in " + t['description'] + " $" + t['oid'])
t['description'] = 'Medication, Administered: test'
          elsif t['oid'].strip == '2.16.840.1.113883.3.560.1.17'
#Delayed::Worker.logger.info("Got in " + t['description'] + " $" + t['oid'])
t['description'] = 'Medication, Order: test'
          elsif t['oid'].strip == '2.16.840.1.113883.3.560.1.18'
#Delayed::Worker.logger.info("Got in " + t['description'] + " $" + t['oid'])
t['description'] = 'Physical Exam, Performed: test'
          elsif t['oid'].strip == '2.16.840.1.113883.3.560.1.2'
#Delayed::Worker.logger.info("Got in " + t['description'] + " $" + t['oid'])
t['description'] = 'Diagnosis: test'
         elsif t['oid'].strip == '2.16.840.1.113883.3.560.1.57'
#Delayed::Worker.logger.info("Got in " + t['description'] + " $" + t['oid'])
t['description'] = 'Physical Exam, Performed: test'
         elsif t['oid'].strip == '2.16.840.1.113883.3.560.1.64'
#Delayed::Worker.logger.info("Got in " + t['description'] + " $" + t['oid'])
t['description'] = 'Substance, Administered: test'
         elsif t['oid'].strip == "2.16.840.1.113883.3.560.1.79"
#Delayed::Worker.logger.info("Got in " + t['description'] + " $" + t['oid'])
t['description'] = 'Encounter, Performed: test'
         elsif t['oid'].strip == '2.16.840.1.113883.3.560.1.8'
#Delayed::Worker.logger.info("Got in " + t['description'] + " $" + t['oid'])
t['description'] = 'Medication, Dispensed: test'
else
          Delayed::Worker.logger.info("Doesn't match " + " $" + t['oid'])
end

       

   #Delayed::Worker.logger.info("description set again here" + t['description'])
            if t['description'] != nil && t['description'].length > 0
              #if description is present, check for colon and availablity from the list of acceptable classnames
     #Delayed::Worker.logger.info("start checking description validity of " + t['description'] + " $" + t['oid'])
              t['description'] = verify_description_validity(t['description'], t['oid'])
     #Delayed::Worker.logger.info("end checking description validity of " + t['description'] + " $" + t['oid'])
            elsif t['description'] == nil
     #Delayed::Worker.logger.info("start description null $" +  t['oid'])
              description= update_default_description(t['oid'])
     #Delayed::Worker.logger.info("end description null $" +  t['oid'])
              t['description'] = description
            else
              Delayed::Worker.logger.info(" description not in format $" +  t['oid'])
     puts "Description is not in the format expected"
            end
          end  
        end
      end
      rec
    end

On Tue, May 26, 2020 at 9:16 PM <pclvi...@gmail.com> wrote:

To view this discussion on the web visit https://groups.google.com/d/msgid/worldvista-pophealth-open-source-work-group/00b301d63374%24dd7e4070%24987ac150%24%40gmail.com.

[Mahesh Dabi]

Hi

Can anybody help to confirm whether it works now for importing the 2019 bundle? 

Thanks 

Mahesh

To view this discussion on the web visit https://groups.google.com/d/msgid/worldvista-pophealth-open-source-work-group/04a701d62dd6%2438c31a90%24aa494fb0%24%40osehra.org.

[pclvi...@gmail.com]

Hi Mahesh,

 

We are planning to release the popHealth v6.1 in the coming week.  The v6.1 will be able to import 2019 bundle.  I’ve ran through and passed all Cypress test measures for C2 and C3 criteria.

 

Peter

[Mahesh Dabi]

That's great news. Is there any RC candidate where I can help to test measures as well?

Thanks

Mahesh

To view this discussion on the web visit https://groups.google.com/d/msgid/worldvista-pophealth-open-source-work-group/00b701d6ca3c%24103d2720%2430b77560%24%40gmail.com.

[pclvi...@gmail.com]

Hi Mahesh,

 

Here is the installation guide - https://github.com/WorldVistA/popHealth/wiki/Installation-v6.1-%282020-Reporting-Period%29

 

Give a try.  Let me know if you have any issues.

 

Just a reminder, we are still fixing some issues related to the C4 criteria.

 

Thanks.

 

Peter

 

From: Mahesh Dabi <mah...@secureit.co.in>
Sent: Friday, December 4, 2020 9:33 AM
To: pclvi...@gmail.com

[Mahesh Dabi]

Hi Peter

Which Cypress are you using for test data? I am trying to generate some test cases in Cypress and test them. I am trying to use Cypress 6.0.1. It allows only.

Cypress bundle for the 2021 Reporting/Performance period (eCQM value sets as of May 7, 2020) 2020.0.4  

Thanks

Mahesh

To view this discussion on the web visit https://groups.google.com/d/msgid/worldvista-pophealth-open-source-work-group/00cf01d6ca4e%24d3b32080%247b196180%24%40gmail.com.

[pclvi...@gmail.com]

Cypress 5.4.1 for 2020 reporting.  The Cypress 6 is for next year.