cqm-models 2.0.0 → 3.0.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 453a6d2a2d21dbbccbf15183693d0961004c6d2dc5d6e29cef52dbdeec81d0c9
-  data.tar.gz: 0c8a483ca5cc294cb67c98790010e3eb1821a40a4a4f613cdf143bc5d1443122
+  metadata.gz: 83362482babb18d63be92649ba769910dfa5690ba3c6f0c8207021d7c3a3f9d4
+  data.tar.gz: 04c04fec5017ee07a5cc013e03f2183bf9a41bf17cc886e14be594fb2be7c89e
 SHA512:
-  metadata.gz: 4c7776a8b071aea930ea925c36b8074b5bcf25ab30e9ca208020dfb94d6d9c77540e5a437b0b82331ea27949ead287842f36fad20ee94ee5a0b055e60a108a1b
-  data.tar.gz: 63eca8a60d51e17c611c85408fc5446670b70b410c74829a5d95af3c4ab3937ea3a4db8736c502f8603d794ee328da5a82f79d402ca5ef31491d90f1f2509ff0
+  metadata.gz: 74534970a1ebfb588c06911618313011e2f728e88d7b991680968952d4f659866fc4d989201542fbf94faeaf5462e3af6ff36fcf657e8f1acf9cc93bf8954b6e
+  data.tar.gz: cbcd07691bbc4b2ea05b678645eb127bacaa3b66bb226864e6f9120295b44bdf029c1bcd6ecefc6a1f9e647f54291b7c4e8692b4a44201a5fbbab753ea642219

data/.eslintrc.json

@@ -2,7 +2,7 @@
   "extends": "airbnb-base",
   "rules": {
     "max-len": ["error", {"code": 200, "ignoreComments": true}],
-    "no-unused-vars": ["error", { "varsIgnorePattern": "IdSchema|DataElementSchema|ComponentSchema|FacilityLocationSchema|Code|Quantity|Interval|Integer|Array|Float|Time|Number|Date|Mixed|Any" }],
+    "no-unused-vars": ["error", { "varsIgnorePattern": "EntitySchema|Identifier|IdentifierSchema|DataElementSchema|ComponentSchema|FacilityLocationSchema|Code|Quantity|Interval|Integer|Array|Float|Time|Number|Date|Mixed|Any" }],
     "camelcase": "off",
     "comma-dangle": ["error", {
       "arrays": "always-multiline",

data/.github/workflows/gitleaks_github_actions.yml

@@ -0,0 +1,28 @@
+name: Github Secrets Scanner
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    env:
+      REPO: https://github.com/projecttacoma/cqm-models
+      REMOTE_EXCLUDES_URL: https://raw.githubusercontent.com/casey-erdmann/bmat-gitleaks-automation/master/cqm-models/gitleaks.toml
+      GITLEAKS_VERSION: v3.0.3
+    steps:
+    - name: Execute Gitleaks
+      run: |
+        wget ${REMOTE_EXCLUDES_URL} -O gitleaks.toml
+        wget https://github.com/zricethezav/gitleaks/releases/download/${GITLEAKS_VERSION}/gitleaks-linux-amd64 -O gitleaks
+        chmod +x gitleaks
+        echo ${GITHUB_SHA}
+        echo "gitleaks --repo=${REPO} -v --pretty --redact --commit=${GITHUB_SHA} --config=gitleaks.toml"
+        ./gitleaks --repo=${REPO} -v --pretty --redact --commit=${GITHUB_SHA} --config=gitleaks.toml
+    - name: Slack notification
+      if: failure()
+      env:
+        SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }}
+      uses: Ilshidur/action-slack@master
+      with:
+        args: 'Potential Secrets found in: https://github.com/{{ GITHUB_REPOSITORY }}/commit/{{ GITHUB_SHA }}. Link to build with full gitleaks output: https://github.com/{{ GITHUB_REPOSITORY }}/commit/{{ GITHUB_SHA }}/checks'

data/.travis.yml

@@ -9,7 +9,7 @@ matrix:
       before_install:
         - "find /home/travis/.rvm/rubies -wholename '*default/bundler-*.gemspec' -delete"
         - rvm @global do gem uninstall bundler -a -x -I || true
-        - gem install bundler -v "< 2.0"
+        - gem install bundler -v "2.1.4"
       script:
         - bundle exec rake
         - bundle exec rubocop
@@ -23,7 +23,7 @@ matrix:
       before_install:
         - "find /home/travis/.rvm/rubies -wholename '*default/bundler-*.gemspec' -delete"
         - rvm @global do gem uninstall bundler -a -x -I || true
-        - gem install bundler -v "< 2.0"
+        - gem install bundler -v "2.1.4"
       script:
         - bundle exec rake
         - bundle exec rubocop

data/README.md

@@ -17,7 +17,7 @@ See the top of the `lib/generate_models.rb` script for RubyGem requirements.
 
 To use, execute the following:
 ```
-ruby lib/generate_models.rb modelinfo/qdm-modelinfo-5.4.xml data/oids_qdm_5.4.json
+ruby lib/generate_models.rb modelinfo/qdm-modelinfo-5.5.xml data/oids_qdm_5.5.json
 ```
 
 The first parameter is the file path to the modelinfo file you wish to generate from. The second parameter is the OID map file. You must include both.
@@ -36,17 +36,17 @@ The QDM patient generator script can be used to create CQMPatients that have a Q
 
 To generate a set of patients using the most recent model-info file, each of which has a single data element in addition to the 5 PatientCharactaristic types execute the following:
 ```
-QDM::PatientGeneration.generate_exhastive_data_element_patients()
+QDM::PatientGeneration.generate_exhaustive_data_element_patients()
 ```
 
 To generate a single patient that has every data element from a specific model-info file execute the following:
 ```
-QDM::PatientGeneration.generate_exhastive_data_element_patients(false, 'qdm-modelinfo-5.3.xml')
+QDM::PatientGeneration.generate_exhaustive_data_element_patients(false, 'qdm-modelinfo-5.3.xml')
 ```
 
 ## Running the tests
 
-### To run frontend Jasmine tests 
+### To run frontend Jasmine tests
 
 ```
 yarn test
@@ -61,15 +61,18 @@ bundle exec rake
 
 ## Versioning
 
-Starting with version **1.1.1.0** released on 5/22/2019, cqm-models versioning has the format **W.X.Y.Z**, where:
+Starting with version **2.0.0** released on 6/20/2019, cqm-models versioning has the format **X.Y.Z**, where:
 
-* **W** maps to a version of QDM. See the table below to see the existing mapping to QDM versions.
+* **X** maps to a version of QDM. See the table below to see the existing mapping to QDM versions.
 
-  | W | QDM version |
+  | X | QDM version |
   | --- | --- |
-  | 1 | 5.4 |
+  | 2 | 5.4 |
+  | 3 | 5.5 |
 
-* **X.Y.Z** uses [SemVer](http://semver.org/) for versioning. **X.Y.Z** starts at 0.0.0 when **W** is incremented.
+* **Y** indicates major changes (incompatible API changes)
+
+* **Z** indicates minor changes (added functionality in a backwards-compatible manner) and patch changes (backwards-compatible bug fixes)
 
 For the versions available, see [tags on this repository](https://github.com/projecttacoma/cqm-models/tags).
 

data/app/assets/javascripts/AdverseEvent.js

@@ -1,14 +1,17 @@
 const mongoose = require('mongoose/browser');
 
-const { IdSchema } = require('./Id');
+const { IdentifierSchema } = require('./attributes/Identifier');
 const { DataElementSchema } = require('./basetypes/DataElement');
 const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
+const QDMDate = require('./basetypes/QDMDate');
 const Any = require('./basetypes/Any');
+const AnyEntity = require('./basetypes/AnyEntity');
 const { ComponentSchema } = require('./attributes/Component');
 const { FacilityLocationSchema } = require('./attributes/FacilityLocation');
+const { EntitySchema } = require('./attributes/Entity');
 
 
 const [Number, String] = [
@@ -18,14 +21,15 @@ const [Number, String] = [
 
 const AdverseEventSchema = DataElementSchema({
   authorDatetime: DateTime,
-  relevantPeriod: Interval,
+  relevantDatetime: DateTime,
   severity: Code,
   facilityLocation: FacilityLocationSchema,
   type: Code,
+  recorder: AnyEntity,
   qdmTitle: { type: String, default: 'Adverse Event' },
   hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.4.120' },
   qdmCategory: { type: String, default: 'adverse_event' },
-  qdmVersion: { type: String, default: '5.4' },
+  qdmVersion: { type: String, default: '5.5' },
   _type: { type: String, default: 'QDM::AdverseEvent' },
 
 });
@@ -37,4 +41,6 @@ class AdverseEvent extends mongoose.Document {
     this._type = 'QDM::AdverseEvent';
   }
 }
+
 module.exports.AdverseEvent = AdverseEvent;
+

data/app/assets/javascripts/AllDataElements.js

@@ -1,5 +1,17 @@
-module.exports.Id = require('./Id.js').Id;
-module.exports.IdSchema = require('./Id.js').IdSchema;
+module.exports.Identifier = require('./attributes/Identifier.js').Identifier;
+module.exports.IdentifierSchema = require('./attributes/Identifier.js').IdentifierSchema;
+module.exports.Entity = require('./attributes/Entity.js').Entity;
+module.exports.EntitySchema = require('./attributes/Entity.js').EntitySchema;
+module.exports.PatientEntity = require('./attributes/PatientEntity.js').PatientEntity;
+module.exports.PatientEntitySchema = require('./attributes/PatientEntity.js').PatientEntitySchema;
+module.exports.CarePartner = require('./attributes/CarePartner.js').CarePartner;
+module.exports.CarePartnerSchema = require('./attributes/CarePartner.js').CarePartnerSchema;
+module.exports.RelatedPerson = require('./RelatedPerson.js').RelatedPerson;
+module.exports.RelatedPersonSchema = require('./RelatedPerson.js').RelatedPersonSchema;
+module.exports.Practitioner = require('./attributes/Practitioner.js').Practitioner;
+module.exports.PractitionerSchema = require('./attributes/Practitioner.js').PractitionerSchema;
+module.exports.Organization = require('./attributes/Organization.js').Organization;
+module.exports.OrganizationSchema = require('./attributes/Organization.js').OrganizationSchema;
 module.exports.PhysicalExamOrder = require('./PhysicalExamOrder.js').PhysicalExamOrder;
 module.exports.PhysicalExamOrderSchema = require('./PhysicalExamOrder.js').PhysicalExamOrderSchema;
 module.exports.Participation = require('./Participation.js').Participation;
@@ -42,8 +54,10 @@ module.exports.FamilyHistory = require('./FamilyHistory.js').FamilyHistory;
 module.exports.FamilyHistorySchema = require('./FamilyHistory.js').FamilyHistorySchema;
 module.exports.Component = require('./attributes/Component.js').Component;
 module.exports.ComponentSchema = require('./attributes/Component.js').ComponentSchema;
-module.exports.ResultComponent = require('./ResultComponent.js').ResultComponent;
-module.exports.ResultComponentSchema = require('./ResultComponent.js').ResultComponentSchema;
+module.exports.DiagnosisComponent = require('./attributes/DiagnosisComponent.js').DiagnosisComponent;
+module.exports.DiagnosisComponentSchema = require('./attributes/DiagnosisComponent.js').DiagnosisComponentSchema;
+module.exports.ResultComponent = require('./attributes/ResultComponent.js').ResultComponent;
+module.exports.ResultComponentSchema = require('./attributes/ResultComponent.js').ResultComponentSchema;
 module.exports.FacilityLocation = require('./attributes/FacilityLocation.js').FacilityLocation;
 module.exports.FacilityLocationSchema = require('./attributes/FacilityLocation.js').FacilityLocationSchema;
 module.exports.MedicationActive = require('./MedicationActive.js').MedicationActive;
@@ -74,8 +88,6 @@ module.exports.ProcedurePerformed = require('./ProcedurePerformed.js').Procedure
 module.exports.ProcedurePerformedSchema = require('./ProcedurePerformed.js').ProcedurePerformedSchema;
 module.exports.AllergyIntolerance = require('./AllergyIntolerance.js').AllergyIntolerance;
 module.exports.AllergyIntoleranceSchema = require('./AllergyIntolerance.js').AllergyIntoleranceSchema;
-module.exports.ProviderCharacteristic = require('./ProviderCharacteristic.js').ProviderCharacteristic;
-module.exports.ProviderCharacteristicSchema = require('./ProviderCharacteristic.js').ProviderCharacteristicSchema;
 module.exports.PhysicalExamRecommended = require('./PhysicalExamRecommended.js').PhysicalExamRecommended;
 module.exports.PhysicalExamRecommendedSchema = require('./PhysicalExamRecommended.js').PhysicalExamRecommendedSchema;
 module.exports.PatientCharacteristicBirthdate = require('./PatientCharacteristicBirthdate.js').PatientCharacteristicBirthdate;

data/app/assets/javascripts/AllergyIntolerance.js

@@ -1,14 +1,17 @@
 const mongoose = require('mongoose/browser');
 
-const { IdSchema } = require('./Id');
+const { IdentifierSchema } = require('./attributes/Identifier');
 const { DataElementSchema } = require('./basetypes/DataElement');
 const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
+const QDMDate = require('./basetypes/QDMDate');
 const Any = require('./basetypes/Any');
+const AnyEntity = require('./basetypes/AnyEntity');
 const { ComponentSchema } = require('./attributes/Component');
 const { FacilityLocationSchema } = require('./attributes/FacilityLocation');
+const { EntitySchema } = require('./attributes/Entity');
 
 
 const [Number, String] = [
@@ -21,11 +24,12 @@ const AllergyIntoleranceSchema = DataElementSchema({
   prevalencePeriod: Interval,
   type: Code,
   severity: Code,
+  recorder: AnyEntity,
   qdmTitle: { type: String, default: 'Allergy/Intolerance' },
   hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.4.119' },
   qdmCategory: { type: String, default: 'allergy' },
   qdmStatus: { type: String, default: 'intolerance' },
-  qdmVersion: { type: String, default: '5.4' },
+  qdmVersion: { type: String, default: '5.5' },
   _type: { type: String, default: 'QDM::AllergyIntolerance' },
 
 });
@@ -37,4 +41,6 @@ class AllergyIntolerance extends mongoose.Document {
     this._type = 'QDM::AllergyIntolerance';
   }
 }
+
 module.exports.AllergyIntolerance = AllergyIntolerance;
+

data/app/assets/javascripts/AssessmentOrder.js

@@ -1,14 +1,17 @@
 const mongoose = require('mongoose/browser');
 
-const { IdSchema } = require('./Id');
+const { IdentifierSchema } = require('./attributes/Identifier');
 const { DataElementSchema } = require('./basetypes/DataElement');
 const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
+const QDMDate = require('./basetypes/QDMDate');
 const Any = require('./basetypes/Any');
+const AnyEntity = require('./basetypes/AnyEntity');
 const { ComponentSchema } = require('./attributes/Component');
 const { FacilityLocationSchema } = require('./attributes/FacilityLocation');
+const { EntitySchema } = require('./attributes/Entity');
 
 
 const [Number, String] = [
@@ -20,11 +23,12 @@ const AssessmentOrderSchema = DataElementSchema({
   authorDatetime: DateTime,
   negationRationale: Code,
   reason: Code,
+  requester: AnyEntity,
   qdmTitle: { type: String, default: 'Assessment, Order' },
   hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.4.131' },
   qdmCategory: { type: String, default: 'assessment' },
   qdmStatus: { type: String, default: 'order' },
-  qdmVersion: { type: String, default: '5.4' },
+  qdmVersion: { type: String, default: '5.5' },
   _type: { type: String, default: 'QDM::AssessmentOrder' },
 
 });
@@ -36,4 +40,6 @@ class AssessmentOrder extends mongoose.Document {
     this._type = 'QDM::AssessmentOrder';
   }
 }
+
 module.exports.AssessmentOrder = AssessmentOrder;
+

data/app/assets/javascripts/AssessmentPerformed.js

@@ -1,14 +1,17 @@
 const mongoose = require('mongoose/browser');
 
-const { IdSchema } = require('./Id');
+const { IdentifierSchema } = require('./attributes/Identifier');
 const { DataElementSchema } = require('./basetypes/DataElement');
 const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
+const QDMDate = require('./basetypes/QDMDate');
 const Any = require('./basetypes/Any');
+const AnyEntity = require('./basetypes/AnyEntity');
 const { ComponentSchema } = require('./attributes/Component');
 const { FacilityLocationSchema } = require('./attributes/FacilityLocation');
+const { EntitySchema } = require('./attributes/Entity');
 
 
 const [Number, String] = [
@@ -18,17 +21,20 @@ const [Number, String] = [
 
 const AssessmentPerformedSchema = DataElementSchema({
   authorDatetime: DateTime,
+  relevantDatetime: DateTime,
+  relevantPeriod: Interval,
   negationRationale: Code,
   reason: Code,
   method: Code,
   result: Any,
   components: [ComponentSchema],
-  relatedTo: [IdSchema],
+  relatedTo: [String],
+  performer: AnyEntity,
   qdmTitle: { type: String, default: 'Assessment, Performed' },
   hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.4.117' },
   qdmCategory: { type: String, default: 'assessment' },
   qdmStatus: { type: String, default: 'performed' },
-  qdmVersion: { type: String, default: '5.4' },
+  qdmVersion: { type: String, default: '5.5' },
   _type: { type: String, default: 'QDM::AssessmentPerformed' },
 
 });
@@ -40,4 +46,6 @@ class AssessmentPerformed extends mongoose.Document {
     this._type = 'QDM::AssessmentPerformed';
   }
 }
+
 module.exports.AssessmentPerformed = AssessmentPerformed;
+

data/app/assets/javascripts/AssessmentRecommended.js

@@ -1,14 +1,17 @@
 const mongoose = require('mongoose/browser');
 
-const { IdSchema } = require('./Id');
+const { IdentifierSchema } = require('./attributes/Identifier');
 const { DataElementSchema } = require('./basetypes/DataElement');
 const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
+const QDMDate = require('./basetypes/QDMDate');
 const Any = require('./basetypes/Any');
+const AnyEntity = require('./basetypes/AnyEntity');
 const { ComponentSchema } = require('./attributes/Component');
 const { FacilityLocationSchema } = require('./attributes/FacilityLocation');
+const { EntitySchema } = require('./attributes/Entity');
 
 
 const [Number, String] = [
@@ -20,11 +23,12 @@ const AssessmentRecommendedSchema = DataElementSchema({
   authorDatetime: DateTime,
   negationRationale: Code,
   reason: Code,
+  requester: AnyEntity,
   qdmTitle: { type: String, default: 'Assessment, Recommended' },
   hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.4.118' },
   qdmCategory: { type: String, default: 'assessment' },
   qdmStatus: { type: String, default: 'recommended' },
-  qdmVersion: { type: String, default: '5.4' },
+  qdmVersion: { type: String, default: '5.5' },
   _type: { type: String, default: 'QDM::AssessmentRecommended' },
 
 });
@@ -36,4 +40,6 @@ class AssessmentRecommended extends mongoose.Document {
     this._type = 'QDM::AssessmentRecommended';
   }
 }
+
 module.exports.AssessmentRecommended = AssessmentRecommended;
+

data/app/assets/javascripts/CareGoal.js

@@ -1,14 +1,17 @@
 const mongoose = require('mongoose/browser');
 
-const { IdSchema } = require('./Id');
+const { IdentifierSchema } = require('./attributes/Identifier');
 const { DataElementSchema } = require('./basetypes/DataElement');
 const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
+const QDMDate = require('./basetypes/QDMDate');
 const Any = require('./basetypes/Any');
+const AnyEntity = require('./basetypes/AnyEntity');
 const { ComponentSchema } = require('./attributes/Component');
 const { FacilityLocationSchema } = require('./attributes/FacilityLocation');
+const { EntitySchema } = require('./attributes/Entity');
 
 
 const [Number, String] = [
@@ -17,13 +20,15 @@ const [Number, String] = [
 ];
 
 const CareGoalSchema = DataElementSchema({
+  statusDate: QDMDate,
   relevantPeriod: Interval,
-  relatedTo: [IdSchema],
+  relatedTo: [String],
   targetOutcome: Any,
+  performer: AnyEntity,
   qdmTitle: { type: String, default: 'Care Goal' },
   hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.4.7' },
   qdmCategory: { type: String, default: 'care_goal' },
-  qdmVersion: { type: String, default: '5.4' },
+  qdmVersion: { type: String, default: '5.5' },
   _type: { type: String, default: 'QDM::CareGoal' },
 
 });
@@ -35,4 +40,6 @@ class CareGoal extends mongoose.Document {
     this._type = 'QDM::CareGoal';
   }
 }
+
 module.exports.CareGoal = CareGoal;
+

data/app/assets/javascripts/CommunicationPerformed.js

@@ -1,14 +1,17 @@
 const mongoose = require('mongoose/browser');
 
-const { IdSchema } = require('./Id');
+const { IdentifierSchema } = require('./attributes/Identifier');
 const { DataElementSchema } = require('./basetypes/DataElement');
 const Code = require('./basetypes/Code');
 const Interval = require('./basetypes/Interval');
 const Quantity = require('./basetypes/Quantity');
 const DateTime = require('./basetypes/DateTime');
+const QDMDate = require('./basetypes/QDMDate');
 const Any = require('./basetypes/Any');
+const AnyEntity = require('./basetypes/AnyEntity');
 const { ComponentSchema } = require('./attributes/Component');
 const { FacilityLocationSchema } = require('./attributes/FacilityLocation');
+const { EntitySchema } = require('./attributes/Entity');
 
 
 const [Number, String] = [
@@ -20,16 +23,17 @@ const CommunicationPerformedSchema = DataElementSchema({
   authorDatetime: DateTime,
   category: Code,
   medium: Code,
-  sender: Code,
-  recipient: Code,
-  relatedTo: [IdSchema],
-  relevantPeriod: Interval,
+  sender: AnyEntity,
+  recipient: AnyEntity,
+  relatedTo: [String],
+  sentDatetime: DateTime,
+  receivedDatetime: DateTime,
   negationRationale: Code,
   qdmTitle: { type: String, default: 'Communication, Performed' },
   hqmfOid: { type: String, default: '2.16.840.1.113883.10.20.28.4.132' },
   qdmCategory: { type: String, default: 'communication' },
   qdmStatus: { type: String, default: 'performed' },
-  qdmVersion: { type: String, default: '5.4' },
+  qdmVersion: { type: String, default: '5.5' },
   _type: { type: String, default: 'QDM::CommunicationPerformed' },
 
 });
@@ -41,4 +45,6 @@ class CommunicationPerformed extends mongoose.Document {
     this._type = 'QDM::CommunicationPerformed';
   }
 }
+
 module.exports.CommunicationPerformed = CommunicationPerformed;
+