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org.opencds.cqf.tooling.library.LibraryProcessor Maven / Gradle / Ivy
package org.opencds.cqf.tooling.library;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.regex.Pattern;
import com.google.common.base.Strings;
import org.apache.commons.io.FilenameUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Attachment;
import org.hl7.fhir.r5.model.Library;
import org.hl7.fhir.r5.model.RelatedArtifact;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.opencds.cqf.tooling.library.r4.R4LibraryProcessor;
import org.opencds.cqf.tooling.library.stu3.STU3LibraryProcessor;
import org.opencds.cqf.tooling.parameter.RefreshLibraryParameters;
import org.opencds.cqf.tooling.processor.*;
import org.opencds.cqf.tooling.utilities.IOUtils;
import org.opencds.cqf.tooling.utilities.IOUtils.Encoding;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.opencds.cqf.tooling.utilities.LogUtils;
import org.opencds.cqf.tooling.utilities.ResourceUtils;
import ca.uhn.fhir.context.FhirContext;
public class LibraryProcessor extends BaseProcessor {
private Logger logger = LoggerFactory.getLogger(this.getClass());
public static final String ResourcePrefix = "library-";
public static String getId(String baseId) {
return ResourcePrefix + baseId;
}
private static Pattern pattern;
private static Pattern getPattern() {
if(pattern == null) {
String regex = "^[a-zA-Z]+[a-zA-Z0-9_\\-\\.]*";
pattern = Pattern.compile(regex);
}
return pattern;
}
public static void validateIdAlphaNumeric(String id) {
if(!getPattern().matcher(id).find()) {
throw new RuntimeException("The library id format is invalid.");
}
}
public List refreshIgLibraryContent(BaseProcessor parentContext, Encoding outputEncoding, Boolean versioned, FhirContext fhirContext, Boolean shouldApplySoftwareSystemStamp) {
return refreshIgLibraryContent(parentContext, outputEncoding, null, null, versioned, fhirContext, shouldApplySoftwareSystemStamp);
}
public List refreshIgLibraryContent(BaseProcessor parentContext, Encoding outputEncoding, String libraryOutputDirectory, Boolean versioned, FhirContext fhirContext, Boolean shouldApplySoftwareSystemStamp) {
return refreshIgLibraryContent(parentContext, outputEncoding, null, libraryOutputDirectory, versioned, fhirContext, shouldApplySoftwareSystemStamp);
}
public List refreshIgLibraryContent(BaseProcessor parentContext, Encoding outputEncoding, String libraryPath, String libraryOutputDirectory, Boolean versioned, FhirContext fhirContext, Boolean shouldApplySoftwareSystemStamp) {
System.out.println("Refreshing libraries...");
// ArrayList refreshedLibraryNames = new ArrayList();
LibraryProcessor libraryProcessor;
switch (fhirContext.getVersion().getVersion()) {
case DSTU3:
libraryProcessor = new STU3LibraryProcessor();
break;
case R4:
libraryProcessor = new R4LibraryProcessor();
break;
default:
throw new IllegalArgumentException(
"Unknown fhir version: " + fhirContext.getVersion().getVersion().getFhirVersionString());
}
if (libraryPath == null) {
libraryPath = FilenameUtils.concat(parentContext.getRootDir(), IGProcessor.libraryPathElement);
}
else if (!Utilities.isAbsoluteFileName(libraryPath)) {
libraryPath = FilenameUtils.concat(parentContext.getRootDir(), libraryPath);
}
RefreshLibraryParameters params = new RefreshLibraryParameters();
if (Strings.isNullOrEmpty(libraryOutputDirectory)) {
logger.info("No output directory found for libraries. Any existing libraries will be overwritten.");
} else {
params.libraryOutputDirectory = libraryOutputDirectory;
}
params.libraryPath = libraryPath;
params.parentContext = parentContext;
params.fhirContext = fhirContext;
params.encoding = outputEncoding;
params.versioned = versioned;
params.shouldApplySoftwareSystemStamp = shouldApplySoftwareSystemStamp;
return libraryProcessor.refreshLibraryContent(params);
}
public Boolean bundleLibraryDependencies(String path, FhirContext fhirContext, Map resources,
Encoding encoding, boolean versioned) {
String fileName = FilenameUtils.getName(path);
boolean prefixed = fileName.toLowerCase().startsWith("library-");
Boolean shouldPersist = true;
try {
Map dependencies = ResourceUtils.getDepLibraryResources(path, fhirContext, encoding, versioned, logger);
// String currentResourceID = IOUtils.getTypeQualifiedResourceId(path, fhirContext);
for (IBaseResource resource : dependencies.values()) {
resources.putIfAbsent(resource.getIdElement().getIdPart(), resource);
// NOTE: Assuming dependency library will be in directory of dependent.
String dependencyPath = IOUtils.getResourceFileName(IOUtils.getResourceDirectory(path), resource, encoding, fhirContext, versioned, prefixed);
bundleLibraryDependencies(dependencyPath, fhirContext, resources, encoding, versioned);
}
} catch (Exception e) {
shouldPersist = false;
LogUtils.putException(path, e);
}
return shouldPersist;
}
protected boolean versioned;
/*
Refreshes generated content in the given library.
The name element of the library resource is used to find the cql file (filename = .cql)
The CqlProcessor is used to get the CqlSourceFileInformation
Sets
* cqlContent
* elmXmlContent
* elmJsonContent
* dataRequirements
* relatedArtifacts
* parameters
Does not set publisher-level information (id, name, url, version, publisher, contact, jurisdiction)
Does not generate narrative
*/
protected Library refreshGeneratedContent(Library sourceLibrary) {
String libraryName = sourceLibrary.getName();
if (versioned) {
libraryName += "-" + sourceLibrary.getVersion();
}
String fileName = libraryName + ".cql";
Attachment attachment = null;
try {
attachment = loadFile(fileName);
} catch (IOException e) {
logMessage(String.format("Error loading CQL source for library %s", libraryName));
e.printStackTrace();
}
if (attachment != null) {
sourceLibrary.getContent().clear();
sourceLibrary.getContent().add(attachment);
setLibraryType(sourceLibrary);
CqlProcessor.CqlSourceFileInformation info = getCqlProcessor().getFileInformation(attachment.getUrl());
attachment.setUrlElement(null);
if (info != null) {
//f.getErrors().addAll(info.getErrors());
if (info.getElm() != null) {
sourceLibrary.addContent().setContentType("application/elm+xml").setData(info.getElm());
}
if (info.getJsonElm() != null) {
sourceLibrary.addContent().setContentType("application/elm+json").setData(info.getJsonElm());
}
sourceLibrary.getDataRequirement().clear();
sourceLibrary.getDataRequirement().addAll(info.getDataRequirements());
sourceLibrary.getRelatedArtifact().removeIf(n -> n.getType() == RelatedArtifact.RelatedArtifactType.DEPENDSON);
sourceLibrary.getRelatedArtifact().addAll(info.getRelatedArtifacts());
sourceLibrary.getParameter().clear();
sourceLibrary.getParameter().addAll(info.getParameters());
} else {
logMessage(String.format("No cql info found for ", fileName));
//f.getErrors().add(new ValidationMessage(ValidationMessage.Source.Publisher, ValidationMessage.IssueType.NOTFOUND, "Library", "No cql info found for "+f.getName(), ValidationMessage.IssueSeverity.ERROR));
}
}
return sourceLibrary;
}
protected List refreshGeneratedContent(List sourceLibraries) {
return internalRefreshGeneratedContent(sourceLibraries);
}
public List refreshGeneratedContent(String cqlDirectoryPath, String fhirVersion) {
List result = new ArrayList();
File input = new File(cqlDirectoryPath);
if (input.exists() && input.isDirectory()) {
result.add(input.getAbsolutePath());
}
setBinaryPaths(result);
List libraries = new ArrayList();
return internalRefreshGeneratedContent(libraries);
}
private void setLibraryType(Library library) {
library.setType(new CodeableConcept().addCoding(
new Coding().setCode("logic-library")
.setSystem("http://terminology.hl7.org/CodeSystem/library-type")));
}
private List internalRefreshGeneratedContent(List sourceLibraries) {
getCqlProcessor().execute();
// For each CQL file, ensure that there is a Library resource with a matching name and version
for (CqlProcessor.CqlSourceFileInformation fileInfo : getCqlProcessor().getAllFileInformation()) {
if (fileInfo.getIdentifier() != null && fileInfo.getIdentifier().getId() != null && !fileInfo.getIdentifier().getId().equals("")) {
Library existingLibrary = null;
for (Library sourceLibrary : sourceLibraries) {
if (fileInfo.getIdentifier().getId().equals(sourceLibrary.getName())
&& (fileInfo.getIdentifier().getVersion() == null || fileInfo.getIdentifier().getVersion().equals(sourceLibrary.getVersion()))
) {
existingLibrary = sourceLibrary;
break;
}
}
if (existingLibrary == null) {
Library newLibrary = new Library();
newLibrary.setName(fileInfo.getIdentifier().getId());
newLibrary.setVersion(fileInfo.getIdentifier().getVersion());
newLibrary.setUrl(String.format("%s/Library/%s", (newLibrary.getName().equals("FHIRHelpers") ? "http://hl7.org/fhir" : canonicalBase), fileInfo.getIdentifier().getId()));
newLibrary.setId(newLibrary.getName() + (versioned ? "-" + newLibrary.getVersion() : ""));
setLibraryType(newLibrary);
validateIdAlphaNumeric(newLibrary.getId());
List attachments = new ArrayList();
Attachment attachment = new Attachment();
attachment.setContentType("application/elm+xml");
attachment.setData(fileInfo.getElm());
attachments.add(attachment);
newLibrary.setContent(attachments);
sourceLibraries.add(newLibrary);
}
}
}
List resources = new ArrayList();
for (Library library : sourceLibraries) {
resources.add(refreshGeneratedContent(library));
}
return resources;
}
private Attachment loadFile(String fn) throws IOException {
for (String dir : getBinaryPaths()) {
File f = new File(Utilities.path(dir, fn));
if (f.exists()) {
Attachment att = new Attachment();
att.setContentType("text/cql");
att.setData(TextFile.fileToBytes(f));
att.setUrl(f.getAbsolutePath());
return att;
}
}
return null;
}
public List refreshLibraryContent(RefreshLibraryParameters params) {
return new ArrayList();
}
}
