Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Resubmitting the PR #81

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Empty file modified _gencontinuous.sh
100644 → 100755
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Still not sure why this is cleared out?

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@brynrhodes - I think we saw this with Sara's PR as well. Not sure if this is just a weird GitHub comparison artifact when PR-ing from a fork? When I click View File under the ellipsis, here's what I see as the file contents:

#!/bin/bash
./_genonce.sh -watch

Empty file.
398 changes: 212 additions & 186 deletions input-cache/schemas/R5/fhir-single.xsd

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion input/cql/QICoreCommonExample.cql
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ codesystem "ConditionVerificationStatusCodes": 'http://terminology.hl7.org/CodeS
codesystem "AllergyIntoleranceClinicalStatusCodes": 'http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical'
codesystem "AllergyIntoleranceVerificationStatusCodes": 'http://terminology.hl7.org/CodeSystem/allergyintolerance-verification'
codesystem "ObservationCategoryCodes": 'http://terminology.hl7.org/CodeSystem/observation-category'
codesystem "USCoreObservationCategoryExtensionCodes": 'http://hl7.org/fhir/us/core/CodeSystem/us-core-observation-category'
codesystem "USCoreObservationCategoryExtensionCodes": 'http://terminology.hl7.org/CodeSystem/observation-category'
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This isn't right, this is specifically pointing to the USCoreObservationCategoryCodes, needs to keep the fhir/us/core CodeSystem reference

codesystem "ConditionCategory": 'http://terminology.hl7.org/CodeSystem/condition-category'
codesystem "USCoreConditionCategoryExtensionCodes": 'http://hl7.org/fhir/us/core/CodeSystem/condition-category'

Expand Down
10 changes: 7 additions & 3 deletions input/ignoreWarnings.txt
Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
== Suppressed Messages ==

# Add warning and/or information messages here after you've confirmed that they aren't really a problem
# instructions for ignoreWarnings.txt https://confluence.hl7.org/pages/viewpage.action?pageId=66938614#ImplementationGuideParameters-ManagingWarningsandHints
# (And include comments like this justifying why)
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Need to keep these instructional messages, this is a template IG that is supposed to provide documentation on how to build a content IG, this is an important part of that

# The expression language text/cql-identifier is not supported, so can't be validated
# Constraint failed: cqm-4: 'Group population criteria SHOULD be simple expression names found within the primary library for the measure. The criteria SHOULD NOT include a namespace.' (defined in http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/measure-cqfm)
# Constraint failed: cmp-2: 'Scoring must be specified at the root, or on each group'





22 changes: 16 additions & 6 deletions input/mycontentig.xml
Original file line number Diff line number Diff line change
Expand Up @@ -2,22 +2,22 @@
<!-- Start by finding all references to "mycontentig" and updating to appropriate text for your IG, including changing realm -->
<ImplementationGuide xmlns="http://hl7.org/fhir" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://hl7.org/fhir ../input-cache/schemas/R5/fhir-single.xsd">
<id value="example.fhir.uv.mycontentig"/>
<!-- <extension url="http://hl7.org/fhir/tools/StructureDefinition/igpublisher-spreadsheet">
<valueString value="resources-spreadsheet.xml"/>
</extension>-->
<url value="http://somewhere.org/fhir/uv/mycontentig/ImplementationGuide/example.fhir.uv.mycontentig"/>
<extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
<valueCode value="cqi"/>
</extension>
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Don't add this extension here, this isn't a CQI WG IG

<url value="http://hl7.org/fhir/uv/mycontentig/ImplementationGuide/example.fhir.uv.mycontentig"/>
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Don't change the URL here, this isn't an HL7 IG, it's a sample content IG, the "somewhere.org" URL is important, it's providing an example for what people should do

<!-- This version will propagate to all artifacts unless the "propagate-version" extension is overridden -->
<version value="0.4.1"/>
<name value="YourComputableMyContentIGNameHere"/>
<title value="Your User Friendly Name for MyContentIG Here"/>
<status value="draft"/>
<experimental value="false"/>
<publisher value="HL7 International - [Some] Work Group"/>
<publisher value="HL7 International / Clinical Quality Information"/>
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Don't change this value, this is example content illustrating what people should do

<contact>
<telecom>
<!-- Or whatever URL and/or email address(es) are appropriate -->
<system value="url"/>
<value value="http://hl7.org/Special/committees/[something]"/>
<value value="http://www.hl7.org/Special/committees/cqi"/>
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Don't change this value, this is an example IG

</telecom>
</contact>
<description value="A brief description of what MyContentIG is about (probably the same text as in your readme)"/>
Expand Down Expand Up @@ -58,6 +58,16 @@
<packageId value="hl7.fhir.us.cqfmeasures"/>
<version value="3.0.0"/>
</dependsOn>
<dependsOn id="crmi">
<uri value="http://hl7.org/fhir/uv/crmi/ImplementationGuide/hl7.fhir.uv.crmi"/>
<packageId value="hl7.fhir.uv.crmi"/>
<version value="1.0.0-snapshot"/>
</dependsOn>
<dependsOn id="qicore">
<uri value="http://hl7.org/fhir/us/qicore/ImplementationGuide/hl7.fhir.us.qicore"/>
<packageId value="hl7.fhir.us.qicore"/>
<version value="6.0.0"/>
</dependsOn>
<definition>
<!-- You don't need to define any groupings. The IGPublisher will define them for you. You only need to do so if your IG is 'special' and it's
inappropriate to use the defaults. Feel free to provide feedback about the defaults... -->
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -663,7 +663,17 @@
"dataRequirement": [ {
"type": "Patient",
"profile": [ "http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-patient" ],
"mustSupport": [ "url", "extension" ]
"mustSupport": [ "url", "extension" ],
"codeFilter": [ {
"path": "url"
} ]
}, {
"type": "Patient",
"profile": [ "http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-patient" ],
"mustSupport": [ "url", "extension" ],
"codeFilter": [ {
"path": "url"
} ]
}, {
"type": "Encounter",
"profile": [ "http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-encounter" ],
Expand All @@ -679,6 +689,8 @@
"codeFilter": [ {
"path": "type",
"valueSet": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1111.143"
}, {
"path": "status.value"
} ]
}, {
"type": "Encounter",
Expand All @@ -687,6 +699,11 @@
"codeFilter": [ {
"path": "type",
"valueSet": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.117.1.7.1.292"
}, {
"path": "status.value"
} ],
"dateFilter": [ {
"path": "period"
} ]
}, {
"type": "Condition",
Expand Down Expand Up @@ -758,36 +775,12 @@
} ]
} ]
} ],
"extension": [ {
"id": "supplementalDataGuidance",
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-supplementalDataGuidance",
"extension": [ {
"url": "guidance",
"valueString": "Patient's Ethnicity:\nHispanic or Latino\nNot Hispanic or Latino\n Patient's Payer:\nCategories of types of health care payer entities as defined by the US Public Health Data Consortium SOP code system\n Patient's Race:\nNative Hawaiian or Other Pacific Islander\nAsian\nAmerican Indian or Alaska Native\nOther Race\nWhite\nBlack or African American\n Patient's Sex:\nGender identity restricted to only Male and Female used in administrative situations requiring a restriction to these two categories.\n"
}, {
"url": "usage",
"valueCodeableConcept": {
"coding": [ {
"system": "http://terminology.hl7.org/CodeSystem/measure-data-usage",
"code": "supplemental-data",
"display": "Supplemental Data"
} ],
"text": "Supplemental Data Guidance"
}
} ]
}, {
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem",
"valueReference": {
"reference": "Device/cqf-tooling"
}
}, {
"id": "effective-data-requirements",
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-effectiveDataRequirements",
"valueReference": {
"reference": "#effective-data-requirements"
}
} ],
"url": "http://somewhere.org/fhir/uv/mycontentig/Measure/DischargedonAntithromboticTherapyFHIRExample",
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-effectiveDataRequirements",
"valueCanonical" : "#effective-data-requirements"
}],
"url": "http://hl7.org/fhir/uv/mycontentig/Measure/DischargedonAntithromboticTherapyFHIR",
"identifier": [ {
"use": "usual",
"type": {
Expand Down Expand Up @@ -832,9 +825,10 @@
"display": "CMS"
}
} ],
"name": "DischargedonAntithromboticTherapyFHIRExample",
"title": "Discharged on Antithrombotic Therapy FHIR Example",
"status": "draft",
"version": "0.8.000",
"name": "DischargedonAntithromboticTherapyFHIR",
"title": "Discharged on Antithrombotic TherapyFHIR",
"status": "active",
"experimental": false,
"date": "2024-05-06T01:40:05+00:00",
"publisher": "The Joint Commission",
Expand Down Expand Up @@ -879,7 +873,7 @@
"rationale": "The effectiveness of antithrombotic agents in reducing stroke mortality, stroke-related morbidity and recurrence rates has been studied in several large clinical trials. While the use of these agents for patients with acute ischemic stroke and transient ischemic attacks continues to be the subject of study, substantial evidence is available from completed studies. Data at this time suggest that antithrombotic therapy should be prescribed at discharge following acute ischemic stroke to reduce stroke mortality and morbidity as long as no contraindications exist.\n\nor patients with a stroke due to a cardioembolic source (e.g. atrial fibrillation, mechanical heart valve), warfarin is recommended unless contraindicated. In recent years, novel oral anticoagulant agents (NOACs) have been developed and approved by the U.S. Food and Drug Administration (FDA) for stroke prevention, and may be considered as an alternative to warfarin for select patients. Anticoagulation therapy is not generally recommended for secondary stroke prevention in patients presumed to have a non-cardioembolic stroke.\nAnticoagulants at doses to prevent venous thromboembolism are insufficient antithrombotic therapy to prevent recurrent ischemic stroke or transient ischemic attack (TIA).",
"clinicalRecommendationStatement": "Clinical trial results suggest that antithrombotic therapy should be prescribed at discharge following acute ischemic stroke to reduce stroke mortality and morbidity as long as no contraindications exist",
"group": [ {
"id": "64403d17d4d7050edabb0562",
"id": "group-64403d17d4d7050edabb0562",
"extension": [ {
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-scoring",
"valueCodeableConcept": {
Expand Down Expand Up @@ -912,8 +906,7 @@
} ]
},
"description": "Inpatient hospitalizations for patients age 18 and older, discharged from inpatient care (non-elective admissions) with a principal diagnosis of ischemic or hemorrhagic stroke and a length of stay less than or equal to 120 days that ends during the measurement period",
"criteria": {
"language": "text/cql-identifier",
"criteria": {"language": "text/cql-identifier",
"expression": "Initial Population"
}
}, {
Expand All @@ -926,8 +919,7 @@
} ]
},
"description": "Inpatient hospitalizations for patients with a principal diagnosis of Ischemic stroke",
"criteria": {
"language": "text/cql-identifier",
"criteria": {"language": "text/cql-identifier",
"expression": "Denominator"
}
}, {
Expand Down Expand Up @@ -982,7 +974,8 @@
} ]
},
"criteria": {
"language": "text/cql-identifier"
"language": "text/cql-identifier",
"expression": "Numerator"
}
} ]
} ],
Expand Down
24 changes: 14 additions & 10 deletions input/resources/measure/Measure-HIVViralSuppressionFHIRExample.json
Original file line number Diff line number Diff line change
Expand Up @@ -391,7 +391,7 @@
"reference": "#effective-data-requirements"
}
} ],
"url": "http://somewhere.org/fhir/uv/mycontentig/Measure/HIVViralSuppressionFHIRExample",
"url": "http://hl7.org/fhir/uv/mycontentig/Measure/HIVViralSuppressionFHIR",
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Don't change the URL here

"identifier": [ {
"use": "usual",
"type": {
Expand Down Expand Up @@ -440,16 +440,17 @@
"display": "CMS"
}
} ],
"name": "HIVViralSuppressionFHIRExample",
"title": "HIV Viral Suppression FHIR Example",
"status": "draft",
"version": "0.0.001",
"name": "HIVViralSuppressionFHIR",
"title": "HIV Viral SuppressionFHIR",
"status": "active",
"experimental": false,
"date": "2024-05-06T01:40:05+00:00",
"publisher": "Health Resources & Services Administration",
"contact": [ {
"telecom": [ {
"system": "url",
"value": " https://www.hrsa.gov/"
"value": "https://www.hrsa.gov/"
} ]
} ],
"description": "Percentage of patients, regardless of age, diagnosed with HIV prior to or during the first 90 days of the measurement period, with an eligible encounter in the first 240 days of the measurement period, whose last HIV viral load test result was less than 200 copies/mL during the measurement period",
Expand Down Expand Up @@ -479,15 +480,15 @@
"name": "Health Resources & Services Administration",
"telecom": [ {
"system": "url",
"value": " https://www.hrsa.gov/"
"value": "https://www.hrsa.gov/"
} ]
} ],
"library": [ "http://somewhere.org/fhir/uv/mycontentig/Library/HIVViralSuppressionFHIRExample" ],
"disclaimer": "These performance measures are not clinical guidelines and do not establish a standard of medical care, and have not been tested for all potential applications.\n\nTHE MEASURES AND SPECIFICATIONS ARE PROVIDED \"AS IS\" WITHOUT WARRANTY OF ANY KIND.\n\nDue to technical limitations, registered trademarks are indicated by (R) or [R] and unregistered trademarks are indicated by (TM) or [TM].",
"rationale": "HIV is a communicable infection that leads to a progressive disease with a long asymptomatic period. Approximately 40,000 persons in the United States are newly infected with HIV each year (Centers for Disease Control and Prevention, 2021, p. 51). Without treatment, most persons develop acquired immunodeficiency syndrome (AIDS) within 10 years of HIV infection.\n\nHIV viral suppression is a long-standing priority outcome among the HIV community in the United States and around the world. The National HIV/AIDS Strategy for the United States from 2022-2025, developed by the White House Office of National AIDS Policy with input from the HIV community across the United States, prioritizes increasing HIV viral suppression rates to 95% (The White House, 2020). The DHHS Panel on Antiretroviral Guidelines for Adults and Adolescents defines viral suppression as a viral load below the lower limits of detection in its guidelines on virologic failure, and it defines viral suppression as a viral load of less than 200 copies/mL as part of its guidelines for the use of antiretroviral therapy to prevent HIV transmission (Panel on Antiretroviral Guidelines for Adults and Adolescents, 2022).\n\nAntiretroviral therapy (ART) delays the progression to AIDS and increases the length of survival. ART reduces HIV-associated morbidity and mortality by maximally inhibiting HIV replication to achieve viral suppression (Hogg et al., 2001; Lundgern et al., 2015). ART has also been shown to reduce transmission of HIV (Rodger et al., 2019). Studies show disparities in rates of viral suppression by race and ethnicity among MSM and among women, with Black and Hispanic or Latino/a study participants having lower rates of viral suppression than White participants (Buchacz et al., 2020; Buchacz et al., 2018; Geter et al., 2018). This measure will help providers direct their attention and quality improvement efforts towards improving HIV viral suppression rates.",
"clinicalRecommendationStatement": "Adult guidelines:\n\"The primary goal of antiretroviral therapy (ART) is to prevent HIV-associated morbidity and mortality. This goal is accomplished by using effective ART to achieve and maintain a plasma HIV-1 RNA (viral load) below the quantification limits of commercially available assays. Durable viral suppression improves immune function and overall quality of life, lowers the risk of both AIDS-defining and non-AIDS–defining complications, and allows persons with HIV to live a lifespan approaching that of persons without HIV\" (Panel on Antiretroviral Guidelines for Adults and Adolescents, 2022, p. E-1).\n\n\"ART is recommended for all individuals with HIV to reduce the morbidity and mortality associated with HIV infection and to prevent HIV transmission to sexual partners and infants (AI). ART should be initiated as soon as possible after HIV diagnosis (AI)\" (Panel on Antiretroviral Guidelines for Adults and Adolescents, 2022, p. E-2).\n\n\"The guidelines and the AIDS Clinical Trials Group (ACTG) now define virologic failure as a confirmed viral load >200 copies/mL- a threshold that eliminates most cases of apparent viremia caused by viral load blips or assay variability\" (Panel on Antiretroviral Guidelines for Adults and Adolescents, 2022, p. C-6).\n\n\"Individuals who are adherent to their ARV regimen and do not harbor resistance mutations to the component drugs can generally achieve suppression 8 to 24 weeks after ART initiation; rarely, in some patients it may take longer\" (Panel on Antiretroviral Guidelines for Adults and Adolescents, 2022, p. C-6).\n\nPediatric guidelines: \n\"Based on accumulated experience with currently available assays, the current definition of virologic suppression is a plasma viral load below the detection limit of the assay used (generally <20 to 75 copies/mL)\" (Panel on Antiretroviral Therapy and Medical Management of Children Living with HIV, 2022, p. D-5).\n\n\"Temporary viral load elevations (\"blips\") that are between the level of detection and 200 copies/mL to 500 copies/mL are often detected in adults and children who are on ART; these temporary elevations do not represent virologic failure, as long as the values have returned to below the level of detection when testing is repeated\" (Panel on Antiretroviral Therapy and Medical Management of Children Living with HIV, 2022, p. D-5).",
"group": [ {
"id": "64873a03be23a058642d5816",
"id": "group-64873a03be23a058642d5816",
"extension": [ {
"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-scoring",
"valueCodeableConcept": {
Expand Down Expand Up @@ -548,7 +549,8 @@
} ]
},
"criteria": {
"language": "text/cql-identifier"
"language": "text/cql-identifier",
"expression": "Numerator"
}
}, {
"id": "E492BC05-FD48-4459-8574-5CF67CC14C66",
Expand All @@ -574,7 +576,8 @@
} ]
},
"criteria": {
"language": "text/cql-identifier"
"language": "text/cql-identifier",
"expression": "Numerator"
}
}, {
"id": "4e8d7586-8625-42d1-9cff-c02d3d4b87f3",
Expand All @@ -586,7 +589,8 @@
} ]
},
"criteria": {
"language": "text/cql-identifier"
"language": "text/cql-identifier",
"expression": "Numerator"
}
} ]
} ]
Expand Down
Loading