From 2d81bc9dc0b38317dc4058c6a97222515f417e93 Mon Sep 17 00:00:00 2001 From: JP Date: Thu, 25 Jan 2024 15:42:15 -0700 Subject: [PATCH] Add a CQL export option to the StripGeneratedContent operation (#511) * Add CQL export to StripContent operation * More cleanup / refactoring of the strip content processor * Add suppression for errorneous warning * Cleanup and a test * Fix coment * Fix parameter name * Further clean-up * Swap to utility functions --- .vscode/settings.json | 3 + .../StripGeneratedContentOperation.java | 539 +----------------- .../stripcontent/BaseContentStripper.java | 201 +++++++ .../stripcontent/ContentStripper.java | 8 + .../stripcontent/ContentStripperDstu3.java | 11 + .../stripcontent/ContentStripperOptions.java | 62 ++ .../stripcontent/ContentStripperR4.java | 11 + .../stripcontent/ContentStripperR5.java | 12 + .../stripcontent/StripContentExecutor.java | 82 +++ .../stripcontent/StripContentParams.java | 45 ++ .../StripGeneratedContentOperationTest.java | 52 +- .../LibraryBreastCancerScreeningFHIR.json | 4 - 12 files changed, 479 insertions(+), 551 deletions(-) create mode 100644 tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/BaseContentStripper.java create mode 100644 tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripper.java create mode 100644 tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperDstu3.java create mode 100644 tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperOptions.java create mode 100644 tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperR4.java create mode 100644 tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperR5.java create mode 100644 tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/StripContentExecutor.java create mode 100644 tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/StripContentParams.java diff --git a/.vscode/settings.json b/.vscode/settings.json index 5ab17bf37..3f86936a0 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -8,11 +8,14 @@ "conceptmap", "Cqfm", "cqloptions", + "DEPENDSON", + "Dstu", "Fhir", "opencds", "pagecontent", "plandefinition", "qicore", + "stripcontent", "testng" ], "java.compile.nullAnalysis.mode": "automatic", diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/operation/StripGeneratedContentOperation.java b/tooling/src/main/java/org/opencds/cqf/tooling/operation/StripGeneratedContentOperation.java index 4939a2895..8ac2b52e6 100644 --- a/tooling/src/main/java/org/opencds/cqf/tooling/operation/StripGeneratedContentOperation.java +++ b/tooling/src/main/java/org/opencds/cqf/tooling/operation/StripGeneratedContentOperation.java @@ -1,39 +1,13 @@ package org.opencds.cqf.tooling.operation; -import java.io.BufferedWriter; -import java.io.File; -import java.io.FileNotFoundException; -import java.io.FileReader; -import java.io.FileWriter; -import java.io.IOException; -import java.util.Collection; -import java.util.Collections; -import java.util.List; -import java.util.stream.Collectors; - -import org.apache.commons.io.FileUtils; -import org.apache.commons.lang3.StringUtils; -import org.hl7.fhir.instance.model.api.IBaseResource; -import org.hl7.fhir.r4.model.Attachment; -import org.hl7.fhir.r4.model.Extension; -import org.hl7.fhir.r4.model.Library; -import org.hl7.fhir.r4.model.Measure; -import org.hl7.fhir.r4.model.Narrative; -import org.hl7.fhir.r4.model.PlanDefinition; -import org.hl7.fhir.r4.model.Questionnaire; -import org.hl7.fhir.r4.model.RelatedArtifact; import org.opencds.cqf.tooling.Operation; - -import ca.uhn.fhir.context.FhirContext; +import org.opencds.cqf.tooling.operations.stripcontent.StripContentParams; +import org.opencds.cqf.tooling.operations.stripcontent.StripContentExecutor; public class StripGeneratedContentOperation extends Operation { - - private String pathToResource; - private FhirContext context; - String version; - @Override public void execute(String[] args) { + var params = new StripContentParams(); for (String arg : args) { if (arg.equals("-StripGeneratedContent")) continue; String[] flagAndValue = arg.split("="); @@ -46,513 +20,24 @@ public void execute(String[] args) { switch (flag.replace("-", "").toLowerCase()) { case "outputpath": case "op": - setOutputPath(value); + params.outputDirectory(value); break; case "pathtores": case "ptr": - pathToResource = value; + params.inputDirectory(value); break; case "version": case "v": - version = value; + params.fhirVersion(value); break; - default: - throw new IllegalArgumentException("Unknown flag: " + flag); - } - } - this.context = contextForVersion(version); - File res = validateDirectory(pathToResource); - var files = getListOfActionableFiles(res); - - for(File file : files) { - parseAndStripResource(file); - } - - } - - private File validateDirectory(String pathToDir) { - if (pathToDir == null) { - throw new IllegalArgumentException("The path to the directory is required"); - } - - File bundleDirectory = new File(pathToDir); - if (!bundleDirectory.isDirectory()) { - throw new IllegalArgumentException("The path supplied is not a directory"); - } - return bundleDirectory; - } - private Collection getListOfActionableFiles(File file) { - return FileUtils.listFiles(file, new String[] { "json", "xml"}, true); - } - - private FhirContext contextForVersion(String version) { - if (StringUtils.isEmpty(version)) { - return FhirContext.forR4Cached(); - } else { - switch (version.toLowerCase()) { - case "dstu3": - return FhirContext.forDstu3Cached(); - case "r4": - return FhirContext.forR4Cached(); - case "r5": - return FhirContext.forR5Cached(); + case "cql": + params.cqlExportDirectory(value); + break; default: - throw new IllegalArgumentException("Unknown fhir version: " + version); - } - } - } - - private void parseAndStripResource(File file) { - IBaseResource theResource = null; - try { - if (file.getName().endsWith(".json")) { - theResource = context.newJsonParser().parseResource(new FileReader(file)); - } else if(file.getName().endsWith(".xml")){ - theResource = context.newXmlParser().parseResource(new FileReader(file)); - } - - if (theResource == null) { - throw new RuntimeException(String.format("failed to parse resource for file: %s", file.toString())); - } - - stripResource(file.getPath().substring(pathToResource.length()), theResource); - } catch (FileNotFoundException e) { - e.printStackTrace(); - throw new RuntimeException(e.getMessage()); - } - catch (Exception e) { - e.printStackTrace(); - String message = String.format("'%s' will not be included in the resource because the following error occurred: '%s'", file.getName(), e.getMessage()); - System.out.println(message); - } - } - - private void stripResource(String fileName, IBaseResource resource) { - switch(context.getVersion().getVersion().name().toLowerCase()) { - case "dstu3": - if(resource.getIdElement().getResourceType().equals("Library")) { - org.hl7.fhir.dstu3.model.Library library = (org.hl7.fhir.dstu3.model.Library) resource; - stripLibraryAndWrite(fileName, library); - } else if (resource.getIdElement().getResourceType().equals("Measure")) { - org.hl7.fhir.dstu3.model.Measure measure = (org.hl7.fhir.dstu3.model.Measure) resource; - stripMeasureAndWrite(fileName, measure); - } else if (resource.getIdElement().getResourceType().equals("PlanDefinition")) { - org.hl7.fhir.dstu3.model.PlanDefinition planDefinition = (org.hl7.fhir.dstu3.model.PlanDefinition) resource; - stripPlanDefinitionAndWrite(fileName, planDefinition); - } else if (resource.getIdElement().getResourceType().equals("Questionnaire")) { - org.hl7.fhir.dstu3.model.Questionnaire questionnaire = (org.hl7.fhir.dstu3.model.Questionnaire) resource; - stripQuestionnaireAndWrite(fileName, questionnaire); - } else if (resource instanceof org.hl7.fhir.dstu3.model.DomainResource) { - stripResourceAndWrite(fileName, (org.hl7.fhir.dstu3.model.DomainResource)resource); - } - break; - case "r4": - if(resource.getIdElement().getResourceType().equals("Library")) { - Library library = (Library) resource; - stripLibraryAndWrite(fileName, library); - } else if (resource.getIdElement().getResourceType().equals("Measure")) { - Measure measure = (Measure) resource; - stripMeasureAndWrite(fileName, measure); - } else if (resource.getIdElement().getResourceType().equals("PlanDefinition")) { - PlanDefinition planDefinition = (PlanDefinition) resource; - stripPlanDefinitionAndWrite(fileName, planDefinition); - } else if (resource.getIdElement().getResourceType().equals("Questionnaire")) { - Questionnaire questionnaire = (Questionnaire) resource; - stripQuestionnaireAndWrite(fileName, questionnaire); - } else if (resource instanceof org.hl7.fhir.r4.model.DomainResource) { - stripResourceAndWrite(fileName, (org.hl7.fhir.r4.model.DomainResource)resource); - } - break; - case "r5": - if(resource.getIdElement().getResourceType().equals("Library")) { - org.hl7.fhir.r5.model.Library library = (org.hl7.fhir.r5.model.Library) resource; - stripLibraryAndWrite(fileName, library); - } else if (resource.getIdElement().getResourceType().equals("Measure")) { - org.hl7.fhir.r5.model.Measure measure = (org.hl7.fhir.r5.model.Measure) resource; - stripMeasureAndWrite(fileName, measure); - } else if (resource.getIdElement().getResourceType().equals("PlanDefinition")) { - org.hl7.fhir.r5.model.PlanDefinition planDefinition = (org.hl7.fhir.r5.model.PlanDefinition) resource; - stripPlanDefinitionAndWrite(fileName, planDefinition); - } else if (resource.getIdElement().getResourceType().equals("Questionnaire")) { - org.hl7.fhir.r5.model.Questionnaire questionnaire = (org.hl7.fhir.r5.model.Questionnaire) resource; - stripQuestionnaireAndWrite(fileName, questionnaire); - } else if (resource instanceof org.hl7.fhir.r5.model.DomainResource) { - stripResourceAndWrite(fileName, (org.hl7.fhir.r5.model.DomainResource)resource); - } - break; - - } - - } - - private void stripResourceAndWrite(String fileName, org.hl7.fhir.dstu3.model.DomainResource resource) { - resource.setText(null); - writeFile(fileName, resource); - } - - private void stripResourceAndWrite(String fileName, org.hl7.fhir.r4.model.DomainResource resource) { - resource.setText(null); - writeFile(fileName, resource); - } - - private void stripResourceAndWrite(String fileName, org.hl7.fhir.r5.model.DomainResource resource) { - resource.setText(null); - writeFile(fileName, resource); - } - - private void stripLibraryAndWrite(String fileName, Library library) { - if(library.hasText()) { - library.setText(new Narrative()); - } - if(library.hasParameter()) { - library.setParameter(Collections.emptyList()); - } - if(library.hasDataRequirement()) { - library.setDataRequirement(Collections.emptyList()); - } - if (library.hasRelatedArtifact()) { - List list = library.getRelatedArtifact() - .stream() - .filter(relatedArtifact -> (relatedArtifact.hasType() && - relatedArtifact.getType() != RelatedArtifact.RelatedArtifactType.DEPENDSON)) - .collect(Collectors.toList()); - library.setRelatedArtifact(list); - } - - if(library.hasExtension()) { - List list = library.getExtension() - .stream() - .filter(extension -> - !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode"))) - .collect(Collectors.toList()); - library.setExtension(list); - } - if(library.hasContent()) { - List attachments = - library.getContent() - .stream() - .filter(attachment -> - !(attachment.getContentType().equalsIgnoreCase("application/elm+xml")) - && !(attachment.getContentType().equalsIgnoreCase("application/elm+json")) - && !(attachment.getContentType().equalsIgnoreCase("text/cql") && - (StringUtils.isEmpty(attachment.getUrl()) && attachment.getData() != null))) - .collect(Collectors.toList()); - library.setContent(attachments); - } - writeFile(fileName, library); - - } - - private void stripMeasureAndWrite(String fileName, Measure measure) { - if(measure.hasText()) { - measure.setText(new Narrative()); - } - if(measure.hasExtension()) { - List list = measure.getExtension() - .stream() - .filter(extension -> - !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-logicDefinition")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode"))) - .collect(Collectors.toList()); - measure.setExtension(list); - } - - if(measure.hasRelatedArtifact()) { - measure.setRelatedArtifact(Collections.emptyList()); - } - writeFile(fileName, measure); - } - - private void stripPlanDefinitionAndWrite(String fileName, PlanDefinition planDefinition) { - if(planDefinition.hasText()) { - planDefinition.setText(new Narrative()); - } - - if(planDefinition.hasRelatedArtifact()) { - planDefinition.setRelatedArtifact(Collections.emptyList()); - } - - if(planDefinition.hasExtension()) { - List list = planDefinition.getExtension() - .stream() - .filter(extension -> - !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode"))) - .collect(Collectors.toList()); - planDefinition.setExtension(list); - } - writeFile(fileName, planDefinition); - } - - private void stripQuestionnaireAndWrite(String fileName, Questionnaire questionnaire) { - if(questionnaire.hasText()) { - questionnaire.setText(new Narrative()); - } - - - if(questionnaire.hasExtension()) { - List list = questionnaire.getExtension() - .stream() - .filter(extension -> - !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode"))) - .collect(Collectors.toList()); - questionnaire.setExtension(list); - } - writeFile(fileName, questionnaire); - } - - private void stripLibraryAndWrite(String fileName, org.hl7.fhir.dstu3.model.Library library) { - if(library.hasText()) { - library.setText(new org.hl7.fhir.dstu3.model.Narrative()); - } - if(library.hasParameter()) { - library.setParameter(Collections.emptyList()); - } - if(library.hasDataRequirement()) { - library.setDataRequirement(Collections.emptyList()); - } - if (library.hasRelatedArtifact()) { - List list = library.getRelatedArtifact() - .stream() - .filter(relatedArtifact -> (relatedArtifact.hasType() && - !(relatedArtifact.getType()== org.hl7.fhir.dstu3.model.RelatedArtifact.RelatedArtifactType.DEPENDSON))) - .collect(Collectors.toList()); - library.setRelatedArtifact(list); - } - - if(library.hasExtension()) { - List list = library.getExtension() - .stream() - .filter(extension -> - !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode"))) - .collect(Collectors.toList()); - library.setExtension(list); - } - if(library.hasContent()) { - List attachments = - library.getContent() - .stream() - .filter(attachment -> - !(attachment.getContentType().equalsIgnoreCase("application/elm+xml")) - && !(attachment.getContentType().equalsIgnoreCase("application/elm+json"))) - .collect(Collectors.toList()); - library.setContent(attachments); - } - writeFile(fileName, library); - - } - - private void stripMeasureAndWrite(String fileName, org.hl7.fhir.dstu3.model.Measure measure) { - if(measure.hasText()) { - measure.setText(new org.hl7.fhir.dstu3.model.Narrative()); - } - if(measure.hasExtension()) { - List list = measure.getExtension() - .stream() - .filter(extension -> - !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-logicDefinition")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode"))) - .collect(Collectors.toList()); - measure.setExtension(list); - } - - if(measure.hasRelatedArtifact()) { - measure.setRelatedArtifact(Collections.emptyList()); - } - writeFile(fileName, measure); - } - - private void stripPlanDefinitionAndWrite(String fileName, org.hl7.fhir.dstu3.model.PlanDefinition planDefinition) { - if(planDefinition.hasText()) { - planDefinition.setText(new org.hl7.fhir.dstu3.model.Narrative()); - } - - if(planDefinition.hasRelatedArtifact()) { - planDefinition.setRelatedArtifact(Collections.emptyList()); - } - - if(planDefinition.hasExtension()) { - List list = planDefinition.getExtension() - .stream() - .filter(extension -> - !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode"))) - .collect(Collectors.toList()); - planDefinition.setExtension(list); - } - writeFile(fileName, planDefinition); - } - - private void stripQuestionnaireAndWrite(String fileName, org.hl7.fhir.dstu3.model.Questionnaire questionnaire) { - if(questionnaire.hasText()) { - questionnaire.setText(new org.hl7.fhir.dstu3.model.Narrative()); - } - - - if(questionnaire.hasExtension()) { - List list = questionnaire.getExtension() - .stream() - .filter(extension -> - !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode"))) - .collect(Collectors.toList()); - questionnaire.setExtension(list); - } - writeFile(fileName, questionnaire); - } - - private void stripLibraryAndWrite(String fileName, org.hl7.fhir.r5.model.Library library) { - if(library.hasText()) { - library.setText(new org.hl7.fhir.r5.model.Narrative()); - } - if(library.hasParameter()) { - library.setParameter(Collections.emptyList()); - } - if(library.hasDataRequirement()) { - library.setDataRequirement(Collections.emptyList()); - } - if (library.hasRelatedArtifact()) { - List list = library.getRelatedArtifact() - .stream() - .filter(relatedArtifact -> (relatedArtifact.hasType() && - !(relatedArtifact.getType() == org.hl7.fhir.r5.model.RelatedArtifact.RelatedArtifactType.DEPENDSON))) - .collect(Collectors.toList()); - library.setRelatedArtifact(list); - } - - if(library.hasExtension()) { - List list = library.getExtension() - .stream() - .filter(extension -> - !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode"))) - .collect(Collectors.toList()); - library.setExtension(list); - } - if(library.hasContent()) { - List attachments = - library.getContent() - .stream() - .filter(attachment -> - !(attachment.getContentType().equalsIgnoreCase("application/elm+xml")) - && !(attachment.getContentType().equalsIgnoreCase("application/elm+json"))) - .collect(Collectors.toList()); - library.setContent(attachments); - } - writeFile(fileName, library); - - } - - private void stripMeasureAndWrite(String fileName, org.hl7.fhir.r5.model.Measure measure) { - if(measure.hasText()) { - measure.setText(new org.hl7.fhir.r5.model.Narrative()); - } - if(measure.hasExtension()) { - List list = measure.getExtension() - .stream() - .filter(extension -> - !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-logicDefinition")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode"))) - .collect(Collectors.toList()); - measure.setExtension(list); - } - - if(measure.hasRelatedArtifact()) { - measure.setRelatedArtifact(Collections.emptyList()); - } - writeFile(fileName, measure); - } - - private void stripPlanDefinitionAndWrite(String fileName, org.hl7.fhir.r5.model.PlanDefinition planDefinition) { - if(planDefinition.hasText()) { - planDefinition.setText(new org.hl7.fhir.r5.model.Narrative()); - } - - if(planDefinition.hasRelatedArtifact()) { - planDefinition.setRelatedArtifact(Collections.emptyList()); - } - - if(planDefinition.hasExtension()) { - List list = planDefinition.getExtension() - .stream() - .filter(extension -> - !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode"))) - .collect(Collectors.toList()); - planDefinition.setExtension(list); - } - writeFile(fileName, planDefinition); - } - - private void stripQuestionnaireAndWrite(String fileName, org.hl7.fhir.r5.model.Questionnaire questionnaire) { - if(questionnaire.hasText()) { - questionnaire.setText(new org.hl7.fhir.r5.model.Narrative()); - } - - - if(questionnaire.hasExtension()) { - List list = questionnaire.getExtension() - .stream() - .filter(extension -> - !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement")) - && !(extension.hasUrl() && extension.getUrl().equals("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode"))) - .collect(Collectors.toList()); - questionnaire.setExtension(list); - } - writeFile(fileName, questionnaire); - } - - - private void writeFile(String fileName, IBaseResource resource) { - String output = ""; - if (fileName.endsWith(".json")) { - output = context.newJsonParser().setPrettyPrint(true).encodeResourceToString(resource); - } else if (fileName.endsWith(".xml")) { - output = context.newXmlParser().setPrettyPrint(true).encodeResourceToString(resource); - } - BufferedWriter writer; - String outFileName = String.format("%s%s", getOutputPath(), fileName); - try { - File f = new File(outFileName); - if (!f.getParentFile().exists()) { - f.getParentFile().mkdirs(); - } - if (!f.exists()) { - f.createNewFile(); + throw new IllegalArgumentException("Unknown flag: " + flag); } - writer = new BufferedWriter(new FileWriter(outFileName)); - writer.write(output); - writer.flush(); - writer.close(); - } catch (IOException e) { - throw new RuntimeException(e); } + + new StripContentExecutor(params).execute(); } } diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/BaseContentStripper.java b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/BaseContentStripper.java new file mode 100644 index 000000000..09689924f --- /dev/null +++ b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/BaseContentStripper.java @@ -0,0 +1,201 @@ +package org.opencds.cqf.tooling.operations.stripcontent; + +import static com.google.common.base.Preconditions.checkNotNull; + +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileReader; +import java.io.FileWriter; +import java.io.IOException; +import java.util.List; +import java.util.Set; + +import static org.opencds.cqf.tooling.utilities.converters.ResourceAndTypeConverter.convertFromR5Resource; +import static org.opencds.cqf.tooling.utilities.converters.ResourceAndTypeConverter.convertToR5Resource; + +import org.hl7.fhir.instance.model.api.IAnyResource; +import org.hl7.fhir.instance.model.api.IBaseResource; +import org.hl7.fhir.r5.model.Attachment; +import org.hl7.fhir.r5.model.DomainResource; +import org.hl7.fhir.r5.model.Extension; +import org.hl7.fhir.r5.model.Library; +import org.hl7.fhir.r5.model.Measure; +import org.hl7.fhir.r5.model.Parameters; +import org.hl7.fhir.r5.model.PlanDefinition; +import org.hl7.fhir.r5.model.Questionnaire; +import org.hl7.fhir.r5.model.RelatedArtifact; +import org.hl7.fhir.r5.model.Resource; + +import ca.uhn.fhir.context.FhirContext; +import ca.uhn.fhir.parser.DataFormatException; +import ca.uhn.fhir.parser.IParser; + +/** + * This class is used to strip autogenerated content from FHIR resources. This includes narrative, + * extensions added by the tooling, related artifacts that are auto detected from the CQL, + * contained resources added by the tooling, and ELM generated from the CQL. + * + * This class converts the resource to its R5 equivalent, strips the content, and then converts + * back to the original FHIR version. + * + * The T parameter is used to specify the version of the Resource base class to use for the operation + * and conversions. + */ +abstract class BaseContentStripper implements ContentStripper { + protected abstract FhirContext context(); + + public void stripFile(File inputFile, File outputFile, ContentStripperOptions options) { + var resource = parseResource(inputFile); + + var upgraded = convertToR5Resource(context(), resource); + stripResource(upgraded, outputFile, options); + + @SuppressWarnings("unchecked") + var downgraded = (T) convertFromR5Resource(context(), upgraded); + writeResource(outputFile, downgraded); + } + + protected void writeContent(File f, String content) { + if (!f.getParentFile().exists()) { + f.getParentFile().mkdirs(); + } + + try (var writer = new BufferedWriter(new FileWriter(f))) { + writer.write(content); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + + protected IParser parserForFile(File file) { + if (file.getName().endsWith(".json")) { + return context().newJsonParser(); + } else if (file.getName().endsWith(".xml")) { + return context().newXmlParser(); + } else { + throw new IllegalArgumentException(String.format("unsupported file type: %s", file.getName())); + } + } + + protected IBaseResource parseResource(File file) { + var parser = parserForFile(file); + try (var reader = new FileReader(file)) { + return parser.parseResource(reader); + } + catch (IOException | DataFormatException e) { + throw new RuntimeException(String.format("Error parsing file %s", file.getName()), e); + } + } + + protected void writeResource(File file, IBaseResource resource) { + var parser = parserForFile(file).setPrettyPrint(true); + var output = parser.encodeResourceToString(resource); + writeContent(file, output); + } + + // Output file is required because the CQL export functionality requires knowledge of the library + // file location to correctly set the Library.content.url property. + private Resource stripResource(IBaseResource resource, File outputFile, ContentStripperOptions options) { + switch (resource.fhirType()) { + case "Library": + return stripLibrary((Library) resource, outputFile, options); + case "Measure": + return stripMeasure((Measure) resource, options); + case "PlanDefinition": + return stripPlanDefinition((PlanDefinition) resource, options); + case "Questionnaire": + return stripQuestionnaire((Questionnaire) resource, options); + default: + return stripResource((DomainResource) resource, options); + } + } + + private boolean isCqlOptionsParameters(Resource resource) { + if (!(resource instanceof Parameters)) { + return false; + } + + var parameters = (Parameters) resource; + return "options".equals(parameters.getId()); + } + + private void filterContained(List contained) { + contained.removeIf(this::isCqlOptionsParameters); + } + + private void filterExtensions(List extensions, Set strippedExtensions) { + extensions.removeIf(x -> strippedExtensions.contains(x.getUrl())); + } + + private void filterContent(List attachments, Set strippedContentTypes) { + attachments.removeIf(x -> strippedContentTypes.contains(x.getContentType())); + } + + private void filterRelatedArtifacts(List artifacts) { + artifacts.removeIf(x -> RelatedArtifact.RelatedArtifactType.DEPENDSON.equals(x.getType())); + } + + // Strip library includes functionality to export the cql file, + // so it requires knowledge of the target directory for the Library. + private Library stripLibrary(Library library, File libraryFile, ContentStripperOptions options) { + stripResource(library, options); + library.setParameter(null); + library.setDataRequirement(null); + filterRelatedArtifacts(library.getRelatedArtifact()); + filterContent(library.getContent(), options.strippedContentTypes()); + exportCql(library.getContent(), library.getName(), libraryFile, options.cqlExportDirectory()); + return library; + } + + private Measure stripMeasure(Measure measure, ContentStripperOptions options) { + stripResource(measure, options); + filterRelatedArtifacts(measure.getRelatedArtifact()); + return measure; + } + + private PlanDefinition stripPlanDefinition(PlanDefinition planDefinition, ContentStripperOptions options) { + stripResource(planDefinition, options); + filterRelatedArtifacts(planDefinition.getRelatedArtifact()); + return planDefinition; + } + + private Questionnaire stripQuestionnaire(Questionnaire questionnaire, ContentStripperOptions options) { + stripResource(questionnaire, options); + filterRelatedArtifacts(questionnaire.getRelatedArtifact()); + return questionnaire; + } + + private DomainResource stripResource(DomainResource resource, ContentStripperOptions options) { + resource.setText(null); + filterExtensions(resource.getExtension(), options.strippedExtensionUrls()); + filterContained(resource.getContained()); + return resource; + } + + private void exportCql(Attachment content, String libraryName, File libraryFile, File cqlExportDirectory) { + checkNotNull(libraryName, "libraryName must be provided"); + if (content.getData() == null || cqlExportDirectory == null) { + return; + } + + // CQL content is encoded as base64, so we need to decode it + // to get back to the original CQL. + var base64 = content.getDataElement().getValueAsString(); + var cql = new String(java.util.Base64.getDecoder().decode(base64)); + + var cqlFileName = libraryName + ".cql"; + var cqlFile = cqlExportDirectory.toPath().resolve(cqlFileName).toFile(); + + content.setUrl(libraryFile.toPath().relativize(cqlFile.toPath()).toString()); + content.setDataElement(null); + writeContent(cqlFile, cql); + } + + private void exportCql(List content, String libraryName, File libraryOutputFile, File cqlExportDirectory) { + for (Attachment attachment : content) { + if (ContentStripperOptions.CQL_CONTENT_TYPE.equals(attachment.getContentType())) { + exportCql(attachment, libraryName, libraryOutputFile, cqlExportDirectory); + } + } + } +} diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripper.java b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripper.java new file mode 100644 index 000000000..9db8b6e31 --- /dev/null +++ b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripper.java @@ -0,0 +1,8 @@ +package org.opencds.cqf.tooling.operations.stripcontent; + +import java.io.File; + +// Intentionally package-private. This is a package-internal API for ContentStripper +interface ContentStripper { + void stripFile(File inputPath, File outputPath, ContentStripperOptions options); +} \ No newline at end of file diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperDstu3.java b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperDstu3.java new file mode 100644 index 000000000..c2ae95c02 --- /dev/null +++ b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperDstu3.java @@ -0,0 +1,11 @@ +package org.opencds.cqf.tooling.operations.stripcontent; + +import org.hl7.fhir.dstu3.model.Resource; +import ca.uhn.fhir.context.FhirContext; + +class ContentStripperDstu3 extends BaseContentStripper { + @Override + protected FhirContext context() { + return FhirContext.forDstu3Cached(); + } +} \ No newline at end of file diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperOptions.java b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperOptions.java new file mode 100644 index 000000000..08ffcd559 --- /dev/null +++ b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperOptions.java @@ -0,0 +1,62 @@ +package org.opencds.cqf.tooling.operations.stripcontent; + +import java.io.File; +import java.util.Arrays; +import java.util.HashSet; +import java.util.Set; + +// Intentionally package-private. This is a package-internal API for ContentStripper +class ContentStripperOptions { + static final String CQL_CONTENT_TYPE = "text/cql"; + static final String ELM_JSON_CONTENT_TYPE = "application/elm+json"; + static final String ELM_XML_CONTENT_TYPE = "application/elm+xml"; + + static final Set DEFAULT_STRIPPED_CONTENT_TYPES = new HashSet<>( + Arrays.asList(ELM_JSON_CONTENT_TYPE, ELM_XML_CONTENT_TYPE)); + + static final Set DEFAULT_STRIPPED_EXTENSION_URLS = new HashSet<>( + Arrays.asList("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter", + "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement", + "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-logicDefinition", + "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem", + "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode", + "http://hl7.org/fhir/StructureDefinition/cqf-cqlOptions")); + + private ContentStripperOptions() { + // Intentionally empty, forces use of the static factory + } + + public static ContentStripperOptions defaultOptions() { + return new ContentStripperOptions(); + } + + private File cqlExportDirectory; + public File cqlExportDirectory() { + return cqlExportDirectory; + } + public ContentStripperOptions cqlExportDirectory(File cqlExportDirectory) { + this.cqlExportDirectory = cqlExportDirectory; + return this; + } + + private Set strippedContentTypes = DEFAULT_STRIPPED_CONTENT_TYPES; + public Set strippedContentTypes() { + return this.strippedContentTypes; + } + + public ContentStripperOptions strippedContentTypes(Set strippedContentTypes) { + this.strippedContentTypes = strippedContentTypes; + return this; + } + + private Set strippedExtensionUrls = DEFAULT_STRIPPED_EXTENSION_URLS; + public Set strippedExtensionUrls() { + return this.strippedExtensionUrls; + } + + public ContentStripperOptions strippedExtensionUrls(Set strippedExtensionUrls) { + this.strippedExtensionUrls = strippedExtensionUrls; + return this; + } + +} \ No newline at end of file diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperR4.java b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperR4.java new file mode 100644 index 000000000..5cbcda706 --- /dev/null +++ b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperR4.java @@ -0,0 +1,11 @@ +package org.opencds.cqf.tooling.operations.stripcontent; + +import org.hl7.fhir.r4.model.Resource; +import ca.uhn.fhir.context.FhirContext; + +class ContentStripperR4 extends BaseContentStripper { + @Override + protected FhirContext context() { + return FhirContext.forR4Cached(); + } +} \ No newline at end of file diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperR5.java b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperR5.java new file mode 100644 index 000000000..d2e94c312 --- /dev/null +++ b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperR5.java @@ -0,0 +1,12 @@ +package org.opencds.cqf.tooling.operations.stripcontent; + +import org.hl7.fhir.r5.model.Resource; + +import ca.uhn.fhir.context.FhirContext; + +class ContentStripperR5 extends BaseContentStripper { + @Override + protected FhirContext context() { + return FhirContext.forR5Cached(); + } +} \ No newline at end of file diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/StripContentExecutor.java b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/StripContentExecutor.java new file mode 100644 index 000000000..656aefdc7 --- /dev/null +++ b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/StripContentExecutor.java @@ -0,0 +1,82 @@ +package org.opencds.cqf.tooling.operations.stripcontent; + +import java.io.File; +import java.util.Collection; + +import org.apache.commons.io.FileUtils; + +import static com.google.common.base.Preconditions.checkNotNull; +import static com.google.common.base.Preconditions.checkArgument; +import ca.uhn.fhir.context.FhirVersionEnum; + +/** + * This class executes the StripContent command line operation. It picks the correct version + * of a ContentStripper based on the FHIR version specified in the command line arguments. It then + * iterates over all the files in the input directory and runs the stripFile method on each file. + */ +public class StripContentExecutor { + + private FhirVersionEnum versionEnum; + private File inputDirectory; + private File outputDirectory; + private String cqlExportDirectory; + + public StripContentExecutor(StripContentParams params) { + checkNotNull(params, "params must be provided"); + checkArgument(params.inputDirectory() != null, "inputDirectory must be provided"); + checkArgument(params.outputDirectory() != null, "outputDirectory must be provided"); + this.versionEnum = versionForString(params.fhirVersion()); + this.inputDirectory = validateDirectory(params.inputDirectory()); + this.outputDirectory = new File(params.outputDirectory()); + this.cqlExportDirectory = params.cqlExportDirectory(); + } + + public void execute() { + var files = listResourceFiles(inputDirectory); + var contentStripper = createContentStripper(); + var options = createContentStripperOptions(); + for (File file : files) { + // Keep the same filename, but change the directory to the output directory + var outputFile = outputDirectory.toPath().resolve(file.getName()).toFile(); + contentStripper.stripFile(file, outputFile, options); + } + } + + private ContentStripperOptions createContentStripperOptions() { + var cqlExportFile = this.cqlExportDirectory != null ? new File(this.cqlExportDirectory) : null; + return ContentStripperOptions.defaultOptions().cqlExportDirectory(cqlExportFile); + } + + private ContentStripper createContentStripper() { + switch (versionEnum) { + case DSTU3: + return new ContentStripperDstu3(); + case R4: + return new ContentStripperR4(); + case R5: + return new ContentStripperR5(); + default: + throw new IllegalArgumentException("Unsupported FHIR version"); + } + } + + private File validateDirectory(String pathToDir) { + checkNotNull(pathToDir, "The path to the directory is required"); + File directory = new File(pathToDir); + if (!directory.isDirectory()) { + throw new IllegalArgumentException("The path supplied is not a directory"); + } + return directory; + } + + private Collection listResourceFiles(File file) { + return FileUtils.listFiles(file, new String[] { "json", "xml"}, true); + } + + private FhirVersionEnum versionForString(String version) { + if (version == null) { + return FhirVersionEnum.R4; + } + return FhirVersionEnum.forVersionString(version.toUpperCase()); + } +} diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/StripContentParams.java b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/StripContentParams.java new file mode 100644 index 000000000..8f734aa79 --- /dev/null +++ b/tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/StripContentParams.java @@ -0,0 +1,45 @@ +package org.opencds.cqf.tooling.operations.stripcontent; + +public class StripContentParams { + + private String inputDirectory; + private String outputDirectory; + private String fhirVersion; + private String cqlExportDirectory; + + public String inputDirectory() { + return inputDirectory; + } + + public StripContentParams inputDirectory(String inputDirectory) { + this.inputDirectory = inputDirectory; + return this; + } + + public String outputDirectory() { + return outputDirectory; + } + + public StripContentParams outputDirectory(String outputDirectory) { + this.outputDirectory = outputDirectory; + return this; + } + + public String fhirVersion() { + return fhirVersion; + } + + public StripContentParams fhirVersion(String fhirVersion) { + this.fhirVersion = fhirVersion; + return this; + } + + public String cqlExportDirectory() { + return cqlExportDirectory; + } + + public StripContentParams cqlExportDirectory(String cqlExportDirectory) { + this.cqlExportDirectory = cqlExportDirectory; + return this; + } +} diff --git a/tooling/src/test/java/org/opencds/cqf/tooling/operation/StripGeneratedContentOperationTest.java b/tooling/src/test/java/org/opencds/cqf/tooling/operation/StripGeneratedContentOperationTest.java index 41a320824..8cb3f4079 100644 --- a/tooling/src/test/java/org/opencds/cqf/tooling/operation/StripGeneratedContentOperationTest.java +++ b/tooling/src/test/java/org/opencds/cqf/tooling/operation/StripGeneratedContentOperationTest.java @@ -1,6 +1,7 @@ package org.opencds.cqf.tooling.operation; import ca.uhn.fhir.context.FhirContext; + import org.hl7.fhir.r4.model.Library; import org.opencds.cqf.tooling.Operation; import org.testng.annotations.Test; @@ -13,23 +14,20 @@ import java.io.FileReader; import java.net.URISyntaxException; import java.nio.file.Path; -import java.nio.file.Paths; public class StripGeneratedContentOperationTest { - private static final String separator = System.getProperty("file.separator"); @Test public void test_strip_generated_content() throws URISyntaxException, FileNotFoundException { String dataInputPath = "strip-resources"; String operation = "StripGeneratedContent"; - String inputFilePath = StripGeneratedContentOperationTest.class.getResource(dataInputPath).toURI().getPath(); - String outputPath = "target/test-output/strip-generated-content"; + var inputFilePath = Path.of(StripGeneratedContentOperationTest.class.getResource(dataInputPath).toURI()); + var outputPath = Path.of("target", "test-output", "strip-generated-content"); String version = "r4"; - Library libraryBeforeStrip = (Library)FhirContext.forR4Cached().newJsonParser().parseResource( - new FileReader(inputFilePath+"/LibraryBreastCancerScreeningFHIR.json")); + new FileReader(inputFilePath + "/LibraryBreastCancerScreeningFHIR.json")); - assertEquals(libraryBeforeStrip.getContent().size(), 4); + assertEquals(libraryBeforeStrip.getContent().size(), 3); assertTrue(libraryBeforeStrip.hasText()); assertTrue(libraryBeforeStrip.hasParameter()); assertTrue(libraryBeforeStrip.hasDataRequirement()); @@ -39,30 +37,44 @@ public void test_strip_generated_content() throws URISyntaxException, FileNotFou Operation stripGeneratedContentOperation = new StripGeneratedContentOperation(); stripGeneratedContentOperation.execute(args); - Library libraryAfterStrip = null; - if (separator.equalsIgnoreCase("/")) { + File jsonFile = outputPath.resolve("LibraryBreastCancerScreeningFHIR.json").toFile(); - Path path = Paths.get(getClass().getProtectionDomain().getCodeSource().getLocation().getPath() + - "/../test-output/strip-generated-content"); - libraryAfterStrip = (Library)FhirContext.forR4Cached().newJsonParser().parseResource( - new FileReader(path + "/LibraryBreastCancerScreeningFHIR.json")); + var libraryAfterStrip = (Library) FhirContext.forR4Cached().newJsonParser().parseResource(new FileReader(jsonFile)); - }else{ + assertEquals(libraryAfterStrip.getContent().size(), 1); + // Cql should not be stripped or exported + assertTrue(libraryAfterStrip.getContent().get(0).hasData()); + assertFalse(libraryAfterStrip.hasText()); + assertFalse(libraryAfterStrip.hasParameter()); + assertFalse(libraryAfterStrip.hasDataRequirement()); + assertEquals(libraryAfterStrip.getRelatedArtifact().size(), 1); - File classLocation = new File(getClass().getProtectionDomain().getCodeSource().getLocation().toURI()); - File parentDir = classLocation.getParentFile(); // Get the parent directory of the class location - File outputDir = new File(parentDir, "test-output/"); - File jsonFile = new File(outputDir, "strip-generated-contentLibraryBreastCancerScreeningFHIR.json"); + } - libraryAfterStrip = (Library) FhirContext.forR4Cached().newJsonParser().parseResource(new FileReader(jsonFile)); - } + @Test + void exportsCql() throws URISyntaxException, FileNotFoundException { + String dataInputPath = "strip-resources"; + String operation = "StripGeneratedContent"; + var inputFilePath = Path.of(StripGeneratedContentOperationTest.class.getResource(dataInputPath).toURI()); + var outputPath = Path.of("target", "test-output", "strip-generated-content-cql"); + + String[] args = { "-" + operation, "-ptr=" + inputFilePath, "-op=" + outputPath, "-cql=" + outputPath + File.separator + "cql"}; + Operation stripGeneratedContentOperation = new StripGeneratedContentOperation(); + stripGeneratedContentOperation.execute(args); + File jsonFile = outputPath.resolve("LibraryBreastCancerScreeningFHIR.json").toFile(); + var libraryAfterStrip = (Library) FhirContext.forR4Cached().newJsonParser().parseResource(new FileReader(jsonFile)); assertEquals(libraryAfterStrip.getContent().size(), 1); + // Cql should be exported + assertFalse(libraryAfterStrip.getContent().get(0).hasData()); + assertTrue(libraryAfterStrip.getContent().get(0).hasUrl()); assertFalse(libraryAfterStrip.hasText()); assertFalse(libraryAfterStrip.hasParameter()); assertFalse(libraryAfterStrip.hasDataRequirement()); assertEquals(libraryAfterStrip.getRelatedArtifact().size(), 1); + File cqlFile = outputPath.resolve("cql").resolve("BreastCancerScreeningFHIR.cql").toFile(); + assertTrue(cqlFile.exists()); } } diff --git a/tooling/src/test/resources/org/opencds/cqf/tooling/operation/strip-resources/LibraryBreastCancerScreeningFHIR.json b/tooling/src/test/resources/org/opencds/cqf/tooling/operation/strip-resources/LibraryBreastCancerScreeningFHIR.json index df9b50f34..f52e1f9d7 100644 --- a/tooling/src/test/resources/org/opencds/cqf/tooling/operation/strip-resources/LibraryBreastCancerScreeningFHIR.json +++ b/tooling/src/test/resources/org/opencds/cqf/tooling/operation/strip-resources/LibraryBreastCancerScreeningFHIR.json @@ -752,10 +752,6 @@ } ], "content": [ - { - "contentType": "text/cql", - "url": "someData" - }, { "contentType": "text/cql", "data": "library BreastCancerScreeningFHIR version '2.0.003'

using FHIR version '4.0.1'

include FHIRHelpers version '4.0.001' called FHIRHelpers
include SupplementalDataElementsFHIR4 version '2.0.000' called SDE
include MATGlobalCommonFunctionsFHIR4 version '6.0.000' called Global
include AdultOutpatientEncountersFHIR4 version '2.0.000' called AdultOutpatientEncounters
include HospiceFHIR4 version '2.0.000' called Hospice
include AdvancedIllnessandFrailtyExclusionECQMFHIR4 version '5.12.000' called Frailty

codesystem "LOINC": 'http://loinc.org'
codesystem "SNOMEDCT": 'http://snomed.info/sct'

valueset "Bilateral Mastectomy": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1005'
valueset "Ethnicity": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.837'
valueset "Female": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.560.100.2'
valueset "History of bilateral mastectomy": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1068'
valueset "Left": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.122.12.1036'
valueset "Mammography": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.108.12.1018'
valueset "ONC Administrative Sex": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1'
valueset "Payer": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.3591'
valueset "Race": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.114222.4.11.836'
valueset "Right": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.122.12.1035'
valueset "Status Post Left Mastectomy": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1069'
valueset "Status Post Right Mastectomy": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1070'
valueset "Unilateral Mastectomy Left": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1133'
valueset "Unilateral Mastectomy Right": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1134'
valueset "Unilateral Mastectomy, Unspecified Laterality": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1071'

code "Birth date": '21112-8' from "LOINC" display 'Birth date'
code "Left (qualifier value)": '7771000' from "SNOMEDCT" display 'Left (qualifier value)'
code "Right (qualifier value)": '24028007' from "SNOMEDCT" display 'Right (qualifier value)'

parameter "Measurement Period" Interval<DateTime>
  default Interval[@2019-01-01T00:00:00.0, @2020-01-01T00:00:00.0)

context Patient

define "SDE Ethnicity":
  SDE."SDE Ethnicity"

define "SDE Payer":
  SDE."SDE Payer"

define "SDE Race":
  SDE."SDE Race"

define "SDE Sex":
  SDE."SDE Sex"

define "Initial Population":
  Patient.gender = 'female'
  			and AgeInYearsAt(start of "Measurement Period") between 51 and 74
  			and exists AdultOutpatientEncounters."Qualifying Encounters"

define "Denominator":
  "Initial Population"

define "Right Mastectomy Diagnosis":
  (
  				( [Condition: "Status Post Right Mastectomy"]
            //where C.clinicalStatus ~ ToConcept(Global."active") not nneeded for exclusion
          )
  				union (
  						[Condition: "Unilateral Mastectomy, Unspecified Laterality"] UnilateralMastectomyDiagnosis
  								where UnilateralMastectomyDiagnosis.bodySite in "Right"
                //    and UnilateralMastectomyDiagnosis.clinicalStatus ~ ToConcept(Global."active") not needed for exclusion
  				)
  		) RightMastectomy
  				where Global."Normalize Interval"(RightMastectomy.onset) starts on or before end of "Measurement Period"

define "Right Mastectomy Procedure":
  [Procedure: "Unilateral Mastectomy Right"] UnilateralMastectomyRightPerformed
           		where Global."Normalize Interval"(UnilateralMastectomyRightPerformed.performed) ends on or before end of "Measurement Period"
                  and UnilateralMastectomyRightPerformed.status = 'completed'

define "Left Mastectomy Procedure":
  [Procedure: "Unilateral Mastectomy Left"] UnilateralMastectomyLeftPerformed
              where Global."Normalize Interval"(UnilateralMastectomyLeftPerformed.performed) ends on or before end of "Measurement Period"
                 and UnilateralMastectomyLeftPerformed.status = 'completed'

define "Left Mastectomy":
  (
  		    ( [Condition: "Status Post Left Mastectomy"]
          //  where C.clinicalStatus ~ ToConcept(Global."active") not needed for exclusion
          )
  				union (
  						[Condition: "Unilateral Mastectomy, Unspecified Laterality"] UnilateralMastectomyDiagnosis
  								where UnilateralMastectomyDiagnosis.bodySite in "Left"
                  //  and UnilateralMastectomyDiagnosis.clinicalStatus ~ ToConcept(Global."active") not needed for exclusion
  				)
  		) LeftMastectomy
  				where Global."Normalize Interval"(LeftMastectomy.onset) starts on or before end of "Measurement Period"

define "Bilateral Mastectomy Diagnosis":
  [Condition: "History of bilateral mastectomy"] BilateralMastectomyHistory
  				where Global."Normalize Interval"(BilateralMastectomyHistory.onset) starts on or before end of "Measurement Period"
      //      and BilateralMastectomyHistory.clinicalStatus ~ ToConcept(Global."active") not needed because it is an exclusion

define "Bilateral Mastectomy Procedure":
  [Procedure: "Bilateral Mastectomy"] BilateralMastectomyPerformed
  				where Global."Normalize Interval"(BilateralMastectomyPerformed.performed) ends on or before end of "Measurement Period"
  						and BilateralMastectomyPerformed.status = 'completed'

define "Numerator":
  exists (
  				[DiagnosticReport: "Mammography"] Mammogram
  						where ( Global."Normalize Interval"(Mammogram.effective) ends 27 months or less on or before end of "Measurement Period" )
  								and Mammogram.status in { 'final', 'amended', 'corrected', 'appended' }
  		)

define "Denominator Exclusion":
  Hospice."Has Hospice"
  				or (( exists "Right Mastectomy Diagnosis"
  				or exists "Right Mastectomy Procedure")
            and (exists "Left Mastectomy" or exists "Left Mastectomy Procedure"))
  				or exists "Bilateral Mastectomy Diagnosis"
  				or exists "Bilateral Mastectomy Procedure"
          or Frailty."Advanced Illness and Frailty Exclusion Not Including Over Age 80"
          or (AgeInYearsAt(start of "Measurement Period") >= 65
            and Frailty."Long Term Care Periods Longer Than 90 Consecutive Days")
"