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#377 - added PlanDefinition refresh processing and plugged into IGRef…
…resh operation ... updated tests ... pretty print by default in IOUtils
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52 changes: 52 additions & 0 deletions
52
tooling/src/main/java/org/opencds/cqf/tooling/parameter/RefreshPlanDefinitionParameters.java
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| package org.opencds.cqf.tooling.parameter; | ||
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| import ca.uhn.fhir.context.FhirContext; | ||
| import org.opencds.cqf.tooling.processor.IProcessorContext; | ||
| import org.opencds.cqf.tooling.utilities.IOUtils; | ||
|
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| public class RefreshPlanDefinitionParameters { | ||
| /* | ||
| The ig ini file | ||
| */ | ||
| public String ini; | ||
|
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| /* | ||
| The canonical base URL of the ig | ||
| */ | ||
| public String igCanonicalBase; | ||
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| /* | ||
| The path to CQL library content | ||
| */ | ||
| public String cqlContentPath; | ||
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| /* | ||
| The fhirContext for the current process | ||
| */ | ||
| public FhirContext fhirContext; | ||
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| /* | ||
| The target encoding for the output | ||
| */ | ||
| public IOUtils.Encoding encoding; | ||
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| /* | ||
| Whether or not version is included in the name | ||
| */ | ||
| public Boolean versioned; | ||
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| /* | ||
| The path to the measure resource(s) | ||
| */ | ||
| public String planDefinitionPath; | ||
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| /* | ||
| An initialized processor context that can provide the IG context directly | ||
| */ | ||
| public IProcessorContext parentContext; | ||
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| /* | ||
| Directory target for writing output | ||
| */ | ||
| public String planDefinitionOutputDirectory; | ||
| } |
359 changes: 359 additions & 0 deletions
359
tooling/src/main/java/org/opencds/cqf/tooling/plandefinition/PlanDefinitionProcessor.java
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82 changes: 82 additions & 0 deletions
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.../src/main/java/org/opencds/cqf/tooling/plandefinition/PlanDefinitionRefreshProcessor.java
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| package org.opencds.cqf.tooling.plandefinition; | ||
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| import org.cqframework.cql.cql2elm.CqlTranslatorOptions; | ||
| import org.cqframework.cql.cql2elm.LibraryManager; | ||
| import org.cqframework.cql.cql2elm.model.CompiledLibrary; | ||
| import org.cqframework.cql.elm.requirements.fhir.DataRequirementsProcessor; | ||
| import org.hl7.fhir.r5.model.*; | ||
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|
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| import java.util.Date; | ||
| import java.util.HashSet; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
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| public class PlanDefinitionRefreshProcessor { | ||
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| public PlanDefinition refreshPlanDefinition(PlanDefinition planToUse, LibraryManager libraryManager, | ||
| CompiledLibrary compiledLibrary, CqlTranslatorOptions options) { | ||
| planToUse.setDate(new Date()); | ||
| Set<String> expressions = new HashSet<>(); | ||
| if (planToUse.hasAction()) { | ||
| getExpressions(planToUse.getAction(), expressions); | ||
| } | ||
| DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor(); | ||
| Library moduleDefinitionLibrary = dqReqTrans.gatherDataRequirements(libraryManager, compiledLibrary, | ||
| options, expressions, true); | ||
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| planToUse.getExtension().removeAll(planToUse.getExtensionsByUrl( | ||
| "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter")); | ||
| planToUse.getExtension().removeAll(planToUse.getExtensionsByUrl( | ||
| "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement")); | ||
| planToUse.getExtension().removeAll(planToUse.getExtensionsByUrl( | ||
| "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode")); | ||
| planToUse.getExtension().removeAll(planToUse.getExtensionsByUrl( | ||
| "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-logicDefinition")); | ||
| planToUse.getExtension().removeAll(planToUse.getExtensionsByUrl( | ||
| "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-effectiveDataRequirements")); | ||
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| for (Extension extension : moduleDefinitionLibrary.getExtension()) { | ||
| if (extension.hasUrl() | ||
| && extension.getUrl().equals( | ||
| "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode")) { | ||
| continue; | ||
| } | ||
| planToUse.addExtension(extension); | ||
| } | ||
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| planToUse.getContained().removeIf(resource -> resource.getId().equalsIgnoreCase("effective-data-requirements")); | ||
| // planToUse.addContained(moduleDefinitionLibrary.setId("effective-data-requirements")); | ||
| // planToUse.addExtension().setUrl("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-effectiveDataRequirements").setValue(new Reference("#effective-data-requirements")).setId("effective-data-requirements"); | ||
| return planToUse; | ||
| } | ||
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| private void getExpressions(List<PlanDefinition.PlanDefinitionActionComponent> actions, Set<String> expressions) { | ||
| for (PlanDefinition.PlanDefinitionActionComponent action : actions) { | ||
| if (action.hasCondition()) { | ||
| for (PlanDefinition.PlanDefinitionActionConditionComponent condition : action.getCondition()) { | ||
| if (condition.hasKind() && condition.getKind() == Enumerations.ActionConditionKind.APPLICABILITY | ||
| && condition.hasExpression() && isExpressionIdentifier(condition.getExpression())) { | ||
| expressions.add(condition.getExpression().getExpression()); | ||
| } | ||
| } | ||
| } | ||
| if (action.hasDynamicValue()) { | ||
| for (PlanDefinition.PlanDefinitionActionDynamicValueComponent dynamicValue : action.getDynamicValue()) { | ||
| if (dynamicValue.hasExpression() && isExpressionIdentifier(dynamicValue.getExpression())) { | ||
| expressions.add(dynamicValue.getExpression().getExpression()); | ||
| } | ||
| } | ||
| } | ||
| if (action.hasAction()) { | ||
| getExpressions(action.getAction(), expressions); | ||
| } | ||
| } | ||
| } | ||
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| private boolean isExpressionIdentifier(Expression expression) { | ||
| return expression.hasLanguage() && expression.hasExpression() | ||
| && (expression.getLanguage().equalsIgnoreCase("text/cql.identifier") | ||
| || expression.getLanguage().equalsIgnoreCase("text/cql")); | ||
| } | ||
|
|
||
| } |
153 changes: 153 additions & 0 deletions
153
...ng/src/main/java/org/opencds/cqf/tooling/plandefinition/r4/R4PlanDefinitionProcessor.java
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|---|---|---|
| @@ -0,0 +1,153 @@ | ||
| package org.opencds.cqf.tooling.plandefinition.r4; | ||
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| import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50; | ||
| import org.hl7.fhir.convertors.conv40_50.VersionConvertor_40_50; | ||
| import org.hl7.fhir.r4.formats.FormatUtilities; | ||
| import org.opencds.cqf.tooling.common.r4.CqfmSoftwareSystemHelper; | ||
| import org.opencds.cqf.tooling.library.LibraryProcessor; | ||
| import org.opencds.cqf.tooling.parameter.RefreshPlanDefinitionParameters; | ||
| import org.opencds.cqf.tooling.plandefinition.PlanDefinitionProcessor; | ||
| import org.opencds.cqf.tooling.processor.CDSHooksProcessor; | ||
| import org.opencds.cqf.tooling.utilities.IOUtils; | ||
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| import java.io.File; | ||
| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.Objects; | ||
|
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| public class R4PlanDefinitionProcessor extends PlanDefinitionProcessor { | ||
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| private static CqfmSoftwareSystemHelper cqfmHelper; | ||
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| public R4PlanDefinitionProcessor(LibraryProcessor libraryProcessor, CDSHooksProcessor cdsHooksProcessor) { | ||
| super(libraryProcessor, cdsHooksProcessor); | ||
| } | ||
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| private String getPlanDefinitionPath(String planDefinitionPath) { | ||
| File f = new File(planDefinitionPath); | ||
| if (!f.exists() && f.getParentFile().isDirectory() && f.getParentFile().exists()) { | ||
| return f.getParentFile().toString(); | ||
| } | ||
| return planDefinitionPath; | ||
| } | ||
| /* | ||
| Refresh all PlanDefinition resources in the given planDefinitionPath | ||
| If the path is not specified, or is not a known directory, process | ||
| all known PlanDefinition resources overriding any currently existing files. | ||
| */ | ||
| protected List<String> refreshPlanDefinitions(String planDefinitionPath, IOUtils.Encoding encoding) { | ||
| return refreshPlanDefinitions(planDefinitionPath, null, encoding); | ||
| } | ||
|
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| /* | ||
| Refresh all PlanDefinition resources in the given planDefinitionPath | ||
| If the path is not specified, or is not a known directory, process | ||
| all known PlanDefinition resources | ||
| */ | ||
| protected List<String> refreshPlanDefinitions(String planDefinitionPath, String planDefinitionOutputDirectory, IOUtils.Encoding encoding) { | ||
| File file = planDefinitionPath != null ? new File(planDefinitionPath) : null; | ||
| Map<String, String> fileMap = new HashMap<>(); | ||
| List<org.hl7.fhir.r5.model.PlanDefinition> planDefinitions = new ArrayList<>(); | ||
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| if (file == null || !file.exists()) { | ||
| for (String path : IOUtils.getPlanDefinitionPaths(this.fhirContext)) { | ||
| loadPlanDefinition(fileMap, planDefinitions, new File(path)); | ||
| } | ||
| } | ||
| else if (file.isDirectory()) { | ||
| for (File libraryFile : Objects.requireNonNull(file.listFiles())) { | ||
| if(IOUtils.isXMLOrJson(planDefinitionPath, libraryFile.getName())) { | ||
| loadPlanDefinition(fileMap, planDefinitions, libraryFile); | ||
| } | ||
| } | ||
| } | ||
| else { | ||
| loadPlanDefinition(fileMap, planDefinitions, file); | ||
| } | ||
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| List<String> refreshedPlanDefinitionNames = new ArrayList<>(); | ||
| List<org.hl7.fhir.r5.model.PlanDefinition> refreshedPlanDefinitions = super.refreshGeneratedContent(planDefinitions); | ||
| VersionConvertor_40_50 versionConvertor = new VersionConvertor_40_50(new BaseAdvisor_40_50()); | ||
| for (org.hl7.fhir.r5.model.PlanDefinition refreshedPlanDefinition : refreshedPlanDefinitions) { | ||
| org.hl7.fhir.r4.model.PlanDefinition planDefinition = (org.hl7.fhir.r4.model.PlanDefinition) versionConvertor.convertResource(refreshedPlanDefinition); | ||
| if (planDefinition.hasIdentifier() && !planDefinition.getIdentifier().isEmpty()) { | ||
| this.getIdentifiers().addAll(planDefinition.getIdentifier()); | ||
| } | ||
| String filePath; | ||
| IOUtils.Encoding fileEncoding; | ||
| if (fileMap.containsKey(refreshedPlanDefinition.getId())) | ||
| { | ||
| filePath = fileMap.get(refreshedPlanDefinition.getId()); | ||
| fileEncoding = IOUtils.getEncoding(filePath); | ||
| } else { | ||
| filePath = getPlanDefinitionPath(planDefinitionPath); | ||
| fileEncoding = encoding; | ||
| } | ||
| cqfmHelper.ensureCQFToolingExtensionAndDevice(planDefinition, fhirContext); | ||
| // Issue 96 | ||
| // Passing the includeVersion here to handle not using the version number in the filename | ||
| if (new File(filePath).exists()) { | ||
| // TODO: This prevents mangled names from being output | ||
| // It would be nice for the tooling to generate library shells, we have enough information to, | ||
| // but the tooling gets confused about the ID and the filename and what gets written is garbage | ||
| String outputPath = filePath; | ||
| if (planDefinitionOutputDirectory != null) { | ||
| File planDefinitionDirectory = new File(planDefinitionOutputDirectory); | ||
| if (!planDefinitionDirectory.exists()) { | ||
| //TODO: add logger and log non existant directory for writing | ||
| } else { | ||
| outputPath = planDefinitionDirectory.getAbsolutePath(); | ||
| } | ||
| } | ||
| IOUtils.writeResource(planDefinition, outputPath, fileEncoding, fhirContext, this.versioned); | ||
| String refreshedPlanDefinitionName; | ||
| if (this.versioned && refreshedPlanDefinition.getVersion() != null) { | ||
| refreshedPlanDefinitionName = refreshedPlanDefinition.getName() + "-" + refreshedPlanDefinition.getVersion(); | ||
| } else { | ||
| refreshedPlanDefinitionName = refreshedPlanDefinition.getName(); | ||
| } | ||
| refreshedPlanDefinitionNames.add(refreshedPlanDefinitionName); | ||
| } | ||
| } | ||
|
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| return refreshedPlanDefinitionNames; | ||
| } | ||
|
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| private void loadPlanDefinition(Map<String, String> fileMap, List<org.hl7.fhir.r5.model.PlanDefinition> planDefinitions, File planDefinitionFile) { | ||
| try { | ||
| org.hl7.fhir.r4.model.Resource resource = FormatUtilities.loadFile(planDefinitionFile.getAbsolutePath()); | ||
| VersionConvertor_40_50 versionConvertor = new VersionConvertor_40_50(new BaseAdvisor_40_50()); | ||
| org.hl7.fhir.r5.model.PlanDefinition planDefinition = (org.hl7.fhir.r5.model.PlanDefinition) versionConvertor.convertResource(resource); | ||
| fileMap.put(planDefinition.getId(), planDefinitionFile.getAbsolutePath()); | ||
| planDefinitions.add(planDefinition); | ||
| } catch (Exception ex) { | ||
| logMessage(String.format("Error reading PlanDefinition: %s. Error: %s", planDefinitionFile.getAbsolutePath(), ex.getMessage())); | ||
| } | ||
| } | ||
|
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| @Override | ||
| public List<String> refreshPlanDefinitionContent(RefreshPlanDefinitionParameters params) { | ||
| if (params.parentContext != null) { | ||
| initialize(params.parentContext); | ||
| } | ||
| else { | ||
| initializeFromIni(params.ini); | ||
| } | ||
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| String planDefinitionPath = params.planDefinitionPath; | ||
| String planDefinitionOutputDirectory = params.planDefinitionOutputDirectory; | ||
| fhirContext = params.fhirContext; | ||
| IOUtils.Encoding encoding = params.encoding; | ||
| versioned = params.versioned; | ||
|
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| cqfmHelper = new CqfmSoftwareSystemHelper(rootDir); | ||
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| if (planDefinitionOutputDirectory != null) { | ||
| return refreshPlanDefinitions(planDefinitionPath, planDefinitionOutputDirectory, encoding); | ||
| } else { | ||
| return refreshPlanDefinitions(planDefinitionPath, encoding); | ||
| } | ||
| } | ||
| } |
11 changes: 11 additions & 0 deletions
11
...rc/main/java/org/opencds/cqf/tooling/plandefinition/stu3/STU3PlanDefinitionProcessor.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| package org.opencds.cqf.tooling.plandefinition.stu3; | ||
|
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| import org.opencds.cqf.tooling.library.LibraryProcessor; | ||
| import org.opencds.cqf.tooling.plandefinition.PlanDefinitionProcessor; | ||
| import org.opencds.cqf.tooling.processor.CDSHooksProcessor; | ||
|
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| public class STU3PlanDefinitionProcessor extends PlanDefinitionProcessor { | ||
| public STU3PlanDefinitionProcessor(LibraryProcessor libraryProcessor, CDSHooksProcessor cdsHooksProcessor) { | ||
| super(libraryProcessor, cdsHooksProcessor); | ||
| } | ||
| } |
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