When I import the sample measures (v2.3) and sample patient data from Project Cypress into a popHealth instance using health-data-standards (3.2.7) and try to run a QRDA Cat3 export against the sample data it dies on the following line:

https://github.com/projectcypress/health-data-standards/blob/master/templates/cat3/_performance_rate.cat3.erb#L10

with an error indicating that I'm calling id on nil, which in this case means my aggregate_count.numerator object is nil.

In my sample instance I slightly modified this line for debugging to output aggregate_count.numerator every time this code is called and it indicates that the numerator is always nil.

Any idea why? Is it most likely something in the data, in the date range, in the patient data, or could this line of code be pulling the wrong object or was it perhaps built against a previous version of the QRDA Cat3 specification?

Hi, QRDA-1 Cypress given Patient data missing Procedures. Please check attached xml, it should give procedures data but its not. See entry

<entry>
  <procedure classCode="PROC" moodCode="EVN" negationInd="true">
    <!--  Procedure performed template -->
    <templateId root="2.16.840.1.113883.10.20.24.3.64" extension="2016-02-01"/>
    <!-- Procedure Activity Procedure-->
    <templateId root="2.16.840.1.113883.10.20.22.4.14" extension="2014-06-09"/>
    <id root="1.3.6.1.4.1.115" extension="598b6d12636239085b3738ef"/>
    <code nullFlavor="NA" sdtc:valueSet="2.16.840.1.113883.3.600.1.462"/>
    <text>Procedure, Performed: Current Medications Documented Snmd</text>
    <statusCode code="completed"/>
    <effectiveTime>
      <low value="20150301160000"/>
      <high value="20150301160000"/>
    </effectiveTime>
    
    <entryRelationship typeCode="RSON">
  <observation classCode="OBS" moodCode="EVN">
    <templateId root="2.16.840.1.113883.10.20.24.3.88" extension="2014-12-01"/>
    <id root="1.3.6.1.4.1.115" extension="E02C3F9B677C6C8A53AAF5360E113086"/>
    <code code="77301-0" codeSystem="2.16.840.1.113883.6.1" displayName="reason" codeSystemName="LOINC"/>
    <statusCode code="completed"/>
      <effectiveTime>
        <low value="20150301160000"/>
      </effectiveTime>
    <value xsi:type="CD" code="183932001" codeSystem="2.16.840.1.113883.6.96" sdtc:valueSet="2.16.840.1.113883.3.600.1.1502"/>
  </observation>
</entryRelationship>


  </procedure>
</entry>

46_Ricky_Graham.txt

Any help would be appreciated, thanks

In the HL7 spec regarding the assignedAuthoringDevice element, there's no mention of a manufacturerModelName element, but both the template that generates this, and the Cypress 2.4.0 schema expect it to show up before the softwareName element if it's going to be there.

Assuming that we're trying to get health-data-standards to match the Cypress schema, since that's the certification tool?

https://github.com/projectcypress/health-data-standards/blob/548eefb22a606282f2e362646c5ae1e2aae133a6/lib/health-data-standards/models/provider.rb#L6

RubyGems.org doesn't report a license for your gem. This is because it is not specified in the gemspec of your last release.

via e.g.

spec.license = 'MIT'
# or
spec.licenses = ['MIT', 'GPL-2']

Including a license in your gemspec is an easy way for rubygems.org and other tools to check how your gem is licensed. As you can imagine, scanning your repository for a LICENSE file or parsing the README, and then attempting to identify the license or licenses is much more difficult and more error prone. So, even for projects that already specify a license, including a license in your gemspec is a good practice. See, for example, how rubygems.org uses the gemspec to display the rails gem license.

There is even a License Finder gem to help companies/individuals ensure all gems they use meet their licensing needs. This tool depends on license information being available in the gemspec. This is an important enough issue that even Bundler now generates gems with a default 'MIT' license.

I hope you'll consider specifying a license in your gemspec. If not, please just close the issue with a nice message. In either case, I'll follow up. Thanks for your time!

Appendix:

If you need help choosing a license (sorry, I haven't checked your readme or looked for a license file), GitHub has created a license picker tool. Code without a license specified defaults to 'All rights reserved'-- denying others all rights to use of the code.
Here's a list of the license names I've found and their frequencies

p.s. In case you're wondering how I found you and why I made this issue, it's because I'm collecting stats on gems (I was originally looking for download data) and decided to collect license metadata,too, and make issues for gemspecs not specifying a license as a public service :). See the previous link or my blog post about this project for more information.

I'm interested in using popHealth to create location-level QRDA-III documents. It seems like when popHealth calls into health-data-standards after doing a location-level aggregation, it passes a null providers array. So one way of handling this is to change this branch in _providers.cat3.erb:

 <% if providers.empty? -%>
    <!-- No provider data found in the patient record
         putting in a fake provider -->
      ...

I can submit a pull request with this change, but I wanted to get feedback from others on the project about whether this is the right path. Is this the right thing to do? Should I pass in a location variable or modify the providers array somehow? Just have a default in the config file and not actually pass stuff between popHealth and hds? Other ideas?

We have been tracking the mongoid5 branch and I was curious if there was a place to track what the plans are for this branch?

It appears to be being updated actively, but is also behind master.

Thanks for any clarification.

Hi ,

Would like to know if hqmf1.xml is retired in health-data-standards version 3.6.1?
My code is referring to template Ids for data_criterias mentioned in hqmf1.xml of version 2.4.0.
Should I be replacing all my old templateIds of all data_criteria to refer to hqmf2.xml's templateIds from 3.6.1 version?

Found this gem when trying to investigate CDA parsing options outside of pure nokogiri. This gem seems very useful but there seems to be no documentation or examples anywhere on how to use it. Producing some documentation would be helpful.

Trying to bundle install into Rails 4.2 app, but there are many conflicts. Is there a branch that supports this Rails version?

Is there interest in a setting to use the CMS implementation guide? My guess is that most people using this library want to use it for Medicare reporting purposes.

Hi guys,

You also use a few xsd file from Health Level 7 which are listed under the BSD 3 clause license; could you please give a proper citation for those files?
https://www.w3.org/2005/05/25-schema/HL7.html
http://www.hl7.org/implement/standards/product_brief.cfm?product_id=214

Thanks

The code here defaults to a file that does not exist on the new demo server.

bundle_version = ENV["version"] || "latest"

https://github.com/projectcypress/health-data-standards/blob/04efeebbc9b99d6d8d7a917ff85f1a4ba225fed6/lib/health-data-standards/tasks/bundle.rake#L48

This is a 404 now.

https://cypressdemo.healthit.gov/measure_bundles/bundle-latest.zip

On the previous demo server this behavior worked as expected.

I am not sure what the expected behavior should be. The file should exist or the version should be required?

When trying to upload a file in popHealth with an encounter section but no dischargeDispositionCode, I get this error:

It seems to be coming from this line in health-data-standards:

encounter.discharge_disposition = extract_code(parent_element, "./sdtc:dischargeDispositionCode")

Encounters MAY contain [0..1] dischargeDispositionCodes, so the lack of a dischargeDispositionCode shouldn't be a fatal error.

Is this class even viable anymore (in version 3.7.0)?

I have imported patients and Cat3 export functions as expected but Cat1 export fails to produce any entries in Patient Data section.

I traced the problem to the measure class having no data_criteria. So I rewrote the all_data_criteria function to return the data_criteria from the hqmf_document and got results (after fixing several errors in related .erb files)

Now I am finding various other issues with missing / incorrect entry exports.
I am beginning to think that this is a dead class and I am wasting my time.

Is this the case?

Looking for guidance on how to use this project to convert generate/export a QRDA1 from a CCDA. It seems like it's possible from the README, but I couldn't find any documentation on how to do so.

Measure NQF_ID: 0004

Cypress error: Element '{urn:hl7-org:v3}id': This element is not expected. Expected is one of ( {urn:hl7-org:v3}realmCode, {urn:hl7-org:v3}typeId, {urn:hl7-org:v3}templateId, {urn:hl7-org:v3}representedCustodianOrganization ).

Proposed change: It appears that https://github.com/projectcypress/health-data-standards/blob/develop/templates/cat3/show.cat3.erb#L44 outputs an extra id element that is simply incorrect and should be removed

Supporting references:

• https://github.com/projectcypress/cypress/blob/develop/resources/schema/qrda/infrastructure/cda/POCD_MT000040_SDTC.xsd#L99
• page 33 / Quality Reporting Document Architecture – Category III, DSTU Release 1

Risk Category Assessments can have result values. For example, a depression screen can have a result of negative depression finding, coded in SNOMED. The importer should extract these result values.

The custodian organization section now requires an element named "representedCustodianOrganization" instead of "representedOrganization"

Cypress:

https://github.com/projectcypress/cypress/blob/master/resources/schematron/qrda/qrda_cat_3/QRDA_Category_III.sch#L80

QRDA 3:

3.1.6 Custodian
i. This assignedCustodian SHALL contain exactly one [1..1] representedCustodianOrganization (CONF:17215).

Hello, sorry if this question is too basic, but does this software implement any portion of the 2015 CEHRT, or does it actually relate to that in any way?

population.population_count('OBSERV') provides only one argument to a method with arity: 2

https://github.com/projectcypress/health-data-standards/blob/master/templates/cat3/_continuous_variable_value.cat3.erb#L8

Hello,

I would like to use the hqmf-generator.
Can you give me an example of how to use it?

I have seen that there are several .erb documents, for every part of the document, like population criteria.erb, data criteria.erb etc.

My question is what kind of parameters should I give to generate an hqmf.xml file?
In the ErbContext, I have seen that there is initialization of some vars, but I can not figure out what kind of parameters I should give to produce a HQMF file.

Thank you in advance

Since it checks the result of Nokogiri::XML::Node#xpath with .nil?, but #xpath never returns nil, only a blank array. This test should instead check for .blank?

I get the following messages when parsing a HQMF R1 file, for example CMS60v2.xml (from USHIK/CMS):

• Codes not passed in, cannot backfill properties like gender
• no code set to back fill: Clinical Trial Participant
• no code set to back fill: Clinical Trial Participant
• no code set to back fill: Clinical Trial Participant
• no code set to back fill: birth date
• no code set to back fill: birth date
• no code set to back fill: Clinical Trial Participant
• no code set to back fill: Clinical Trial Participant
• (0164)codes are nil!!!!!!!!!!!

I have traced these messages back to https://github.com/projectcypress/health-data-standards/blob/7896e22444f8ff51f5c5dbca4c12cb5be7c03e11/lib/hqmf-parser/converter/pass1/document_converter.rb and https://github.com/projectcypress/health-data-standards/blob/7896e22444f8ff51f5c5dbca4c12cb5be7c03e11/lib/hqmf-parser/parser.rb

Are "codes" another name for value sets/concepts? Is there an example of how to parse HQMF R1 with this library while providing "codes"?

Thanks in advance!

I'm trying to run the Cat 1 export test test/unit/export/cat_1_test.rb and I'm getting test failures.

$ ruby test/unit/export/cat_1_test.rb
Started with run options --seed 12363

Cat1Test
  test_record_target_export                                       PASS (0.64s)
  test_payer_information                                          PASS (0.64s)
  test_unique_data_criteria                                       PASS (0.70s)
  test_reporting_parameters_section_export                        PASS (0.62s)
Testing Cat I for Barry Berry
Testing Cat I for Mary Berry
  test_schematron_r2_validation                                   FAIL (6.39s)
Minitest::Assertion:         Invalid Cat I for Mary Berry (with header).
        --- expected
        +++ actual
        @@ -1 +1 @@
        -[]
        +[#<ValidationError:0xXXXXXX @location="/*[local-name()='ClinicalDocument' and namespace-uri()='urn:hl7-org:v3']/*[local-name()='component' and namespace-uri()='urn:hl7-org:v3']/*[local-name()='structuredBody' and namespace-uri()='urn:hl7-org:v3']/*[local-name()='component' and namespace-uri()='urn:hl7-org:v3'][3]/*[local-name()='section' and namespace-uri()='urn:hl7-org:v3']", @message="SHALL contain at least one [1..*] entry (CONF:14567).", @validator="QRDA Cat 1 Validator", @file_name="cat1_good.xml">]
        test/unit/export/cat_1_test.rb:78:in `block in test_schematron_r2_validation'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/mongoid-4.0.0/lib/mongoid/contextual/mongo.rb:648:in `yield_document'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/mongoid-4.0.0/lib/mongoid/contextual/mongo.rb:123:in `block in each'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/moped-2.0.7/lib/moped/cursor.rb:29:in `block in each'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/moped-2.0.7/lib/moped/cursor.rb:29:in `each'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/moped-2.0.7/lib/moped/cursor.rb:29:in `each'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/moped-2.0.7/lib/moped/query.rb:78:in `each'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/mongoid-4.0.0/lib/mongoid/contextual/mongo.rb:122:in `each'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/mongoid-4.0.0/lib/mongoid/contextual.rb:20:in `each'
        test/unit/export/cat_1_test.rb:67:in `test_schematron_r2_validation'

  test_entries_for_data_criteria                                  FAIL (0.72s)
Minitest::Assertion:         Expected: 1
          Actual: 0
        test/unit/export/cat_1_test.rb:105:in `test_entries_for_data_criteria'

  test_patient_data_section_export                                FAIL (0.67s)
Minitest::Assertion:         med_dispensed is nil
        test/unit/export/cat_1_test.rb:95:in `test_patient_data_section_export'

Testing Cat I for Barry Berry
Testing Cat I for Mary Berry
  test_schematron_validation                                      FAIL (7.30s)
Minitest::Assertion:         Invalid Cat I for Mary Berry (with header).
        --- expected
        +++ actual
        @@ -1 +1 @@
        -[]
        +[#<ValidationError:0xXXXXXX @location="/*[local-name()='ClinicalDocument' and namespace-uri()='urn:hl7-org:v3']/*[local-name()='component' and namespace-uri()='urn:hl7-org:v3']/*[local-name()='structuredBody' and namespace-uri()='urn:hl7-org:v3']/*[local-name()='component' and namespace-uri()='urn:hl7-org:v3'][3]/*[local-name()='section' and namespace-uri()='urn:hl7-org:v3']", @message="SHALL contain at least one [1..*] entry (CONF:14567).", @validator="QRDA Cat 1 R3 Validator", @file_name="cat1_good.xml">]
        test/unit/export/cat_1_test.rb:60:in `block in test_schematron_validation'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/mongoid-4.0.0/lib/mongoid/contextual/mongo.rb:648:in `yield_document'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/mongoid-4.0.0/lib/mongoid/contextual/mongo.rb:123:in `block in each'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/moped-2.0.7/lib/moped/cursor.rb:29:in `block in each'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/moped-2.0.7/lib/moped/cursor.rb:29:in `each'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/moped-2.0.7/lib/moped/cursor.rb:29:in `each'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/moped-2.0.7/lib/moped/query.rb:78:in `each'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/mongoid-4.0.0/lib/mongoid/contextual/mongo.rb:122:in `each'
        /Users/pairing/.rbenv/versions/2.2.1/lib/ruby/gems/2.2.0/gems/mongoid-4.0.0/lib/mongoid/contextual.rb:20:in `each'
        test/unit/export/cat_1_test.rb:49:in `test_schematron_validation'

Testing Cat I for Barry Berry
Testing Cat I for Mary Berry
Testing Cat I for Rosa Vasquez
  test_schema_validation                                          PASS (0.87s)
  test_handling_expired_patients                                  PASS (0.67s)
  test_cda_header_export                                          PASS (0.63s)
  test_measure_section_export                                     PASS (0.58s)

Finished in 20.44585s
12 tests, 28 assertions, 4 failures, 0 errors, 0 skips

I'm using Ruby 2.2.1 and mongo 3.4.4.

We don't specify the version of rubyzip we are using in our gemspec. Our code currently works with rubyzip 0.9.9, but breaks on versions greater than 1.0.0. We should upgrade to the latest version of rubyzip and specify a version number.

The attribute is currently 'type'

https://github.com/projectcypress/health-data-standards/blob/develop/templates/cat3/_continuous_variable_value.cat3.erb#L1

but should be 'typeCode'

Cypress:

https://github.com/projectcypress/cypress/blob/master/resources/schematron/qrda/qrda_cat_3/QRDA_Category_III.sch#L546

QRDA 3:
5.4 Measure Data
14. MAY contain zero or more [0..*] entryRelationship (CONF:18143) such that it
a. SHALL contain exactly one [1..1] @typecode="COMP" (CodeSystem: HL7ActRelationshipType 2.16.840.1.113883.5.1002 STATIC) (CONF:18148).

As discussed in the pophealth-dev group: https://groups.google.com/d/topic/pophealth-dev/mFRAwB3lsm4/discussion

Record#dedup_section! de-dups sections based on the Entry#cda_identifier or Entry#id and ignores content. This causes failures in various measures, including:

CMS163v2/0064
CMS182v3/0075
CMS167v2/0088
CMS64v3/CholesterolScreeningRisk

Hi,
In medication_import, Hash value is called as method at https://github.com/projectcypress/health-data-standards/blob/mongoid5/lib/health-data-standards/import/cda/medication_importer.rb#L42 for medication.allowed_administrations. Shouldn't it be extract_scalar(entry_element, "./cda:repeatNumber")['value'] as getting following exception

NoMethodError - undefined method `value' for {"unit"=>nil, "value"=>1}:Hash

Thanks

The C32 template has the ClinicalDocument's ID hard-coded:
https://github.com/projectcypress/health-data-standards/blob/master/templates/show.c32.erb#L9

  <id root="2.16.840.1.113883.3.72" extension="HITSP_C32v2.5_Rev6_16Sections_Entries_MinimalErrors" assigningAuthorityName="NIST Healthcare Project"/>

Looks like this line was cut/pasted from a NIST validation example -- but this ID should uniquely identify a CDA document...

In patient_importer.rb:
generate_importer(Cat1::ProcedureImporter, nil, '2.16.840.1.113883.3.560.1.129'), #comm from provider to provider

If I look at the spec, the code should be ...1.29 not ...1.129. There's an extra 1 in there.1.129is thenegation: trueversion ofcommunication_from_provider_to_provideraccording to thehqmf_template_oid_map`.

I think anyway :) If I'm wrong, please let me know why. FWIW, I had to edit my records documents in my DB to be 1.29 instead of 1.129 to pass Measure 0089 QRDA Cat I Test in Cypress.

Hello -

More of a question than an issue.

Some of the new EH measures released in May (EX: "EH_CMS190v4_NQF0372_VTE2/CMS190v4.xml") include excerpt entries that use sequenceNumber - no "subsetCode" entry.

The HQMF 2.x parser seems to want to have a type for these (https://github.com/projectcypress/health-data-standards/blob/7d49e1dd92815dd77b375a918b515c829a3a5a04/lib/hqmf-parser/2.0/types.rb#L183) "@type = attr_val('./cda:subsetCode/@code')"

In reading more of the documentation, there's a note that says "This representation aligns with the HQMF specification and does not require a subset operator."

The Data Criteria parser seems to attempt to create subset_operators for each "excerpt entry"
https://github.com/projectcypress/health-data-standards/blob/7d49e1dd92815dd77b375a918b515c829a3a5a04/lib/hqmf-parser/2.0/data_criteria.rb#L274

In the event that this is a sequence entry and does not contain a subsetCode, should we avoid creating a subset entry? Should the xpath in the data criteria parser only include entries that contain a subsetCode node?

Thank you,
Eric

I have an issue with a patient that should meet numerator for measure CMS69

The patient has a Medication, Order: Below Normal Medications with Reason Underweight. (CAT1 file)

        <!-- ================= Medication Order template ================= -->
        <substanceAdministration classCode="SBADM" moodCode="RQO">
          <templateId extension="2014-06-09" root="2.16.840.1.113883.10.20.22.4.42"/>
          <!-- Medication, Order template -->
          <templateId extension="2016-02-01" root="2.16.840.1.113883.10.20.24.3.47"/>
          <id extension="Get Well Clinic-1-1372-2400-DF" root="2.16.840.1.113883.3.1452.3"/>
          <text>SIG information not entered</text>
          <statusCode code="completed"/>
          <effectiveTime xsi:type="IVL_TS">
            <low value="20170510235959"/>
            <high nullFlavor="UNK"/>
          </effectiveTime>
          <routeCode/>
          <doseQuantity nullFlavor="NA"/>
          <consumable>
            <manufacturedProduct classCode="MANU">
              <!-- Medication Information (consolidation) template -->
              <templateId extension="2014-06-09" root="2.16.840.1.113883.10.20.22.4.23"/>
              <id root="ba86866c-73ff-40cf-841d-26cfe8747a8f"/>
              <manufacturedMaterial>
                <code code="860221" codeSystem="2.16.840.1.113883.6.88" codeSystemName="RxNorm" sdtc:valueSet="2.16.840.1.113883.3.600.1.1499" xsi:type="CE">
                  <originalText>SIG information not entered</originalText>
                </code>
              </manufacturedMaterial>
            </manufacturedProduct>
          </consumable>
          <author>
            <templateId root="2.16.840.1.113883.10.20.22.4.119"/>
            <time value="20170510235959"/>
            <assignedAuthor>
              <id root="3fd83a53-d600-4fb6-99c6-60939e63e91e"/>
            </assignedAuthor>
          </author>
          <!-- ================= Reason template ================= -->
          <entryRelationship typeCode="RSON">
            <observation classCode="OBS" moodCode="EVN">
              <templateId extension="2014-12-01" root="2.16.840.1.113883.10.20.24.3.88"/>
              <id extension="7368fe92-7891-4b76-b65e-524c9ed59668" root="2.16.840.1.113883.3.1452.1011"/>
              <code code="77301-0" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="reason"/>
              <statusCode code="completed"/>
              <effectiveTime>
                <low value="20170510235959"/>
              </effectiveTime>
              <value code="248342006" codeSystem="2.16.840.1.113883.6.96" sdtc:valueSet="2.16.840.1.113883.3.600.2388" xsi:type="CD"/>
            </observation>
          </entryRelationship>
        </substanceAdministration>
      </entry>
      <entry>

I reviewed the class medication_importer.rb (health-data-standards/lib/health-data-standards/import/cda/medication_importer.rb) the method in charge of to extract the reason or negation is implemented the following way:

    def extract_reason_or_negation(parent_element, medication)
      negation_indicator = parent_element['negationInd']
      if negation_indicator.nil? && parent_element.parent.name == "entryRelationship"
        super(parent_element.parent.parent, medication, parent_element)
      elsif negation_indicator.eql?('true')
        super(parent_element, medication)
      end
    end

In my scenario the medication order doesn't have a negationInd=true and the parent_element.parent.name != "entryRelationship", when the method receives the medication order entry the method doesn't extract the reason.

I think, the issue could be solved if the method is changed of the following way:

    def extract_reason_or_negation(parent_element, medication)
      negation_indicator = parent_element['negationInd']
      if negation_indicator.nil? && parent_element.parent.name == "entryRelationship"
        super(parent_element.parent.parent, medication, parent_element)
      else
        super(parent_element, medication)
      end
    end

Please let me know if this is an issue or there is something wrong in my medication order entry.

Thanks in advance.

I recently noticed that when importing sections that have a scalar unit (such as the dosage for a medication) that the value is being converted to an integer.

It looks like the culprit is the to_i on line 193 of lib/health-data-standards/import/cda/section_importer.rb.

{'unit' => scalar_element['unit'], 'value' => scalar_element['value'].to_i}

Will it break anything if we change this to to_f instead?

PatientImporter#get_demographics blows up at line 130 when the C32 file being parsed doesn't have a "ClinicalDocument > recordTarget > patientRole > patient" element:

NoMethodError: undefined method `at_xpath' for nil:NilClass
    /Users/pelargir/.rvm/gems/ruby-2.0.0-p0/gems/health-data-standards-3.1.1/lib/health-data-standards/import/c32/patient_importer.rb:130:in `get_demographics'
    /Users/pelargir/.rvm/gems/ruby-2.0.0-p0/gems/health-data-standards-3.1.1/lib/health-data-standards/import/c32/patient_importer.rb:86:in `parse_c32'

This should instead be handled gracefully without throwing an exception.

I see that pophealth/hqmf-parser has not been worked on as recently as the relevant files in this project.

Accordingly, if HQMF R1/R2 parsing is needed, should this repository be used rather than pophealth/hqmf-parser?

Thank you!

This gem defines dozens of models (most of them subclasses of Entry) but fails to namespace them within the HealthDataStandards. This means that my own application's Procedure, Provider, etc. classes get stepped on as soon as I import the gem.

+1 for properly namespacing these models.

In this particular file -> https://github.com/projectcypress/health-data-standards/blob/master/lib/hqmf-parser/2.0/field_value_helper.rb

I noticed that the file field_value_helper has the following method, using XPATH looking for typeCode="REFV"... should the XPATH be changed to typeCode="REFR"? I didn't notice that particular type code in the HQMF for the 2016 reporting year measures.

def self.parse_observation_fields(entry, fields) 
      parse_dset_cd(entry.at_xpath('./cda:methodCode', HQMF2::Document::NAMESPACES), 'METHOD', fields) 
      parse_dset_cd(entry.at_xpath('./cda:targetSiteCode', HQMF2::Document::NAMESPACES), 
                    'ANATOMICAL_LOCATION_SITE', fields) 
      parse_cd(entry.at_xpath("./cda:participation[@typeCode='SBJ']/cda:role[@classCode='PRS']/cda:code", 
                              HQMF2::Document::NAMESPACES), 
               'RELATIONSHIP', fields) 
      parse_pq(entry.at_xpath("./cda:outboundRelationship[@typeCode='REFV']/cda:observationCriteria/cda:value/cda:high", 
                              HQMF2::Document::NAMESPACES), 
               'REFERENCE_RANGE_HIGH', fields) 
      parse_pq(entry.at_xpath("./cda:outboundRelationship[@typeCode='REFV']/cda:observationCriteria/cda:value/cda:low", 
                              HQMF2::Document::NAMESPACES), 
               'REFERENCE_RANGE_LOW', fields) 
    end

Hi, tried importing patient but Encounters are not parsing. Following is the xml file used

33_Nancy_Manning.txt

Hi, using to extract information from QRDA, CAT-1, able to extract Patient without MongoDB but when extracting provider_performances, its giving up error

Problem:
  No configuration could be found for a session named 'default'.
Summary:
  When attempting to create the new session, Mongoid could not find a session configuration for the name: 'default'. This is necessary in order to know the host, port, and options needed to connect.
Resolution:
  Double check your mongoid.yml to make sure under the sessions key that a configuration exists for 'default'. If you have set the configuration programatically, ensure that 'default' exists in the configuration hash.

using snippet from bulk_record_importer.rb and used CDA::ProviderImporter.instance.extract_providers for extraction.

Any help would be appreciated, thanks

I'm wondering what the LOE/suggested course of implementing the following feature/output: I have a need to take a HQMF document, parse it, and, for each data element, see where in the population_criteria it exists (IPP, DENEX, NUMER, DENEXCEP, etc.). I know many data elements get used several times per measure.

Any guidance is much appreciated!

Thanks,

Mark

When generating QRDA Cat I, the value set for the overall encounter is passed in to the code_display method for transfer from and transfer to. This causes problems on CQMs like CMS188 because the transfer value sets do not overlap with the encounter value set. This causes the code_display method to null flavor the code even if it is not part of the encounter value set.

https://github.com/projectcypress/health-data-standards/blob/10dac4c594216493e7fb014a61b061061caff985/templates/cat3/_organization.cat3.erb#L1

In our instance, the cat3 template header somehow always outputs a representedOrganization tag, although by all review of the code, setting a local variable on the partial should change the tag to representedCustodianOrganization.

See: projectcypress@10dac4c#diff-dac787bbb748f453b53a9a5b3abde5edL1

Using popHealth with 3.6.1 of the HDS gem from rubygems. When I try to upload the following HQMF definition using the UI:
BP_Test_v4_3_eMeasure.txt

It is failing to be recognized as a valid v2 HQMF document (V2Parser::valid? is returning false). There is a commit that addresses this, however it does not appear to be applied in the version pulled down from rubygems. I did "gem unpack" and confirmed the relevant change does not exist in lib/hqmf-parser/parser.rb.

If I change the popHealth Gemfile to pull from the master github branch of the HDS library, the error goes away. This is a reasonable workaround to proceed with. I just wanted to raise this to confirm others have seen something similar, and to see if HDS may need to be updated in rubygems.

Please add Ruby 2.4 support.

This gem does not build with Ruby 2.4, due to out of date dependencies, and the deprecation of Fixnum and Bignum within Ruby 2.4.

Hi,
From which branch gem is being published on https://rubygems.org as master is stalled and most of the activity is on bonnie-gemfile-update, master_bonnie, activesupport and update_nokogiri.

Thanks

In Cypress health-data-standards-1bb2d48cf24f (mongoid) at least, file path /lib/health-data-standards/import/cda/provider_importer.rb the provider NPI is extracted but not the provider TIN.

2016 C4 filter applications that use the health-data-standards library require the provider TIN.
It is possibly a one-line addition to extract_provider_data in HealthDataStandards::Import::CDA::ProviderImporter.

I'm not a Ruby-experienced, but I will try the change locally and report.