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Add helper method to build platform independent file paths
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-This uses FilenameUtils.concat for underlying path concatenation
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@Chris0296
Chris0296 committed Oct 6, 2023
1 parent bd9ac88 commit d0704c0
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Showing 27 changed files with 117 additions and 57 deletions.
17 changes: 11 additions & 6 deletions tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/DTProcessor.java
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Expand Up @@ -33,6 +33,7 @@
import org.hl7.fhir.r4.model.UsageContext;
import org.opencds.cqf.tooling.Operation;
import org.opencds.cqf.tooling.terminology.SpreadsheetHelper;
import org.opencds.cqf.tooling.utilities.IOUtils;

import ca.uhn.fhir.context.FhirContext;

Expand Down Expand Up @@ -608,7 +609,7 @@ private void writeLibraryHeader(StringBuilder cql, Library library) {

private void writeLibraries(String outputPath) {
if (libraries != null && libraries.size() > 0) {
String outputFilePath = outputPath + File.separator + "input" + File.separator + "resources" + File.separator + "library";
String outputFilePath = IOUtils.concatFilePath(outputPath, "input", "resources", "library");
ensurePath(outputFilePath);

for (Library library : libraries.values()) {
Expand All @@ -620,8 +621,9 @@ private void writeLibraries(String outputPath) {
private void writeLibraryCQL(String outputPath) {
if (libraryCQL != null && libraryCQL.size() > 0) {
for (Map.Entry<String, StringBuilder> entry : libraryCQL.entrySet()) {
String outputDirectoryPath = outputPath + File.separator + "input" + File.separator + "cql";
String outputFilePath = outputDirectoryPath + File.separator + entry.getKey() + ".cql";
String outputDirectoryPath = IOUtils.concatFilePath(outputPath, "input", "cql");
String outputFilePath = IOUtils.concatFilePath(outputDirectoryPath,
entry.getKey() + ".cql");
ensurePath(outputDirectoryPath);

try (FileOutputStream writer = new FileOutputStream(outputFilePath)) {
Expand All @@ -639,7 +641,8 @@ private void writeLibraryCQL(String outputPath) {
private void writePlanDefinitions(String outputPath) {
if (planDefinitions != null && planDefinitions.size() > 0) {
for (PlanDefinition planDefinition : planDefinitions.values()) {
String outputFilePath = outputPath + File.separator + "input" + File.separator + "resources" + File.separator + "plandefinition";
String outputFilePath = IOUtils.concatFilePath(outputPath,
"input", "resources", "plandefinition");
ensurePath(outputFilePath);
writeResource(outputFilePath, planDefinition);
}
Expand All @@ -648,7 +651,8 @@ private void writePlanDefinitions(String outputPath) {

/* Write Methods */
public void writeResource(String path, Resource resource) {
String outputFilePath = path + File.separator + resource.getResourceType().toString().toLowerCase() + "-" + resource.getIdElement().getIdPart() + "." + encoding;
String outputFilePath = IOUtils.concatFilePath(path,
resource.getResourceType().toString().toLowerCase() + "-" + resource.getIdElement().getIdPart() + "." + encoding);
try (FileOutputStream writer = new FileOutputStream(outputFilePath)) {
writer.write(
encoding.equals("json")
Expand Down Expand Up @@ -681,7 +685,8 @@ private String buildPlanDefinitionIndex() {
}

public void writePlanDefinitionIndex(String outputPath) {
String outputFilePath = outputPath + File.separator + "input" + File.separator + "pagecontent"+ File.separator + "PlanDefinitionIndex.md";
String outputFilePath = IOUtils.concatFilePath(outputPath,
"input", "pagecontent", "PlanDefinitionIndex.md");
ensurePath(outputFilePath);

try (FileOutputStream writer = new FileOutputStream(outputFilePath)) {
Expand Down
13 changes: 9 additions & 4 deletions tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/Processor.java
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Expand Up @@ -40,6 +40,7 @@
import org.hl7.fhir.r4.model.ValueSet;
import org.opencds.cqf.tooling.Operation;
import org.opencds.cqf.tooling.terminology.SpreadsheetHelper;
import org.opencds.cqf.tooling.utilities.IOUtils;

import ca.uhn.fhir.context.FhirContext;

Expand Down Expand Up @@ -2574,7 +2575,8 @@ public void processExamples() {

/* Write Methods */
public void writeResource(String path, Resource resource) {
String outputFilePath = path + "/" + resource.getResourceType().toString().toLowerCase() + "-" + resource.getIdElement().getIdPart() + "." + encoding;
String outputFilePath = IOUtils.concatFilePath(path,
resource.getResourceType().toString().toLowerCase() + "-" + resource.getIdElement().getIdPart() + "." + encoding);
try (FileOutputStream writer = new FileOutputStream(outputFilePath)) {
writer.write(
encoding.equals("json")
Expand Down Expand Up @@ -2976,7 +2978,8 @@ public void writeConcepts(String scope, String scopePath) {
}

ensureCqlPath(scopePath);
try (FileOutputStream writer = new FileOutputStream(getCqlPath(scopePath) + "/" + scope + "Concepts.cql")) {
try (FileOutputStream writer = new FileOutputStream(
IOUtils.concatFilePath(getCqlPath(scopePath),scope + "Concepts.cql"))) {
writer.write(sb.toString().getBytes());
writer.flush();
}
Expand Down Expand Up @@ -3420,7 +3423,8 @@ public void writeDataElements(String scope, String scopePath, String context) {
}

ensureCqlPath(scopePath);
try (FileOutputStream writer = new FileOutputStream(getCqlPath(scopePath) + "/" + scope + (context.equals("Encounter") ? "Contact" : "") + "DataElements.cql")) {
try (FileOutputStream writer = new FileOutputStream(IOUtils.concatFilePath(getCqlPath(scopePath),
scope + (context.equals("Encounter") ? "Contact" : "") + "DataElements.cql"))) {
writer.write(sb.toString().getBytes());
writer.flush();
}
Expand All @@ -3429,7 +3433,8 @@ public void writeDataElements(String scope, String scopePath, String context) {
throw new IllegalArgumentException("Error writing concepts library source");
}

try (FileOutputStream writer = new FileOutputStream(getCqlPath(scopePath) + "/" + scope + "DataElementsByActivity.md")) {
try (FileOutputStream writer = new FileOutputStream(
IOUtils.concatFilePath(getCqlPath(scopePath), scope + "DataElementsByActivity.md"))) {
writer.write(activityIndex.toString().getBytes());
writer.flush();
}
Expand Down
5 changes: 3 additions & 2 deletions tooling/src/main/java/org/opencds/cqf/tooling/common/BaseCqfmSoftwareSystemHelper.java
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Expand Up @@ -3,12 +3,12 @@
import org.opencds.cqf.tooling.utilities.IOUtils;
import org.opencds.cqf.tooling.utilities.LogUtils;

import java.io.File;
import java.io.IOException;
import java.util.Objects;


public abstract class BaseCqfmSoftwareSystemHelper {
public static final String separator = System.getProperty("file.separator");
private String rootDir;
protected String getRootDir() {
return this.rootDir;
Expand All @@ -18,7 +18,8 @@ protected String getRootDir() {
private static String cqfToolingDeviceName = "cqf-tooling";
// private static String cqfToolingDeviceReferenceID = "#" + cqfToolingDeviceName;
private static String cqfmSoftwareSystemExtensionUrl = "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem";
protected static String devicePath = separator + "input" + separator + "resources" + separator + "device";
protected static String devicePath = IOUtils.concatFilePath(File.separator,
"input", "resources", "device");

protected String getCqfToolingDeviceName() { return cqfToolingDeviceName; }
// protected String getCqfToolingDeviceReferenceID() { return cqfToolingDeviceReferenceID; }
Expand Down
2 changes: 1 addition & 1 deletion ...main/java/org/opencds/cqf/tooling/common/JarEnabledCustomThymeleafNarrativeGenerator.java
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Expand Up @@ -72,7 +72,7 @@ static String loadResourceAlsoFromJar(String name) throws IOException {
String cpName = name.substring("classpath:".length());
try (InputStream resource = Thread.currentThread().getContextClassLoader().getResourceAsStream(cpName)) {
if (resource == null) {
try (InputStream resource2 =Thread.currentThread().getContextClassLoader().getResourceAsStream("/" + cpName)) {
try (InputStream resource2 =Thread.currentThread().getContextClassLoader().getResourceAsStream(File.separator + cpName)) {
if (resource2 == null) {
throw new IOException("Can not find '" + cpName + "' on classpath");
}
Expand Down
7 changes: 5 additions & 2 deletions tooling/src/main/java/org/opencds/cqf/tooling/cql_generation/drool/DroolCqlGenerator.java
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Expand Up @@ -24,6 +24,7 @@
import org.opencds.cqf.tooling.cql_generation.drool.visitor.DroolToElmVisitor.CQLTYPES;
import org.opencds.cqf.tooling.cql_generation.drool.visitor.ElmToCqlVisitor;
import org.opencds.cqf.tooling.cql_generation.drool.visitor.Visitor;
import org.opencds.cqf.tooling.utilities.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

Expand Down Expand Up @@ -115,7 +116,8 @@ private void writeCql(ElmContext context, File outpuDirectory) {
VersionedIdentifier vi = new VersionedIdentifier();
vi.setId(getIdFromSource(cql));
vi.setVersion(getVersionFromSource(cql));
File outputFile = new File(outpuDirectory.getAbsolutePath() + "/" + vi.getId() + "-" + vi.getVersion() + ".cql");
File outputFile = new File(IOUtils.concatFilePath(outpuDirectory.getAbsolutePath(),
vi.getId() + "-" + vi.getVersion() + ".cql"));
IOUtil.writeToFile(outputFile, cql);
} else {
throw new IllegalArgumentException("Output directory is not a directory: " + outpuDirectory.getAbsolutePath());
Expand All @@ -130,7 +132,8 @@ private void writeElm(ElmContext context, VmrToModelElmBuilder modelBuilder, Fil
try {
String elm = serializer.convertToXml(modelBuilder.of.createLibrary(entry.getValue()), serializer.getJaxbContext());
if (outpuDirectory.isDirectory()) {
File outputFile = new File(outpuDirectory.getAbsolutePath() + "/" + entry.getKey() + ".xml");
File outputFile = new File(IOUtils.concatFilePath(outpuDirectory.getAbsolutePath(),
entry.getKey() + ".xml"));
IOUtil.writeToFile(outputFile, elm);
} else {
throw new IllegalArgumentException("Output directory is not a directory: " + outpuDirectory.getAbsolutePath());
Expand Down
4 changes: 2 additions & 2 deletions ...g/src/main/java/org/opencds/cqf/tooling/cql_generation/drool/visitor/HtmlFileVisitor.java
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Expand Up @@ -19,6 +19,7 @@
import org.cdsframework.dto.OpenCdsConceptDTO;
import org.opencds.cqf.tooling.cql_generation.IOUtil;
import org.opencds.cqf.tooling.cql_generation.context.ElmContext;
import org.opencds.cqf.tooling.utilities.IOUtils;

/**
* Generates html files from an RCKMS Drool Object graph.
Expand Down Expand Up @@ -114,8 +115,7 @@ public void visit(ConditionDTO conditionDTO) {
@Override
public ElmContext visit(List<ConditionDTO> rootNode) {
htmlStrings.entrySet().stream().forEach(entry -> {
// Dont like this concat
String filePath = outputDirectoryPath.concat("/" + entry.getKey() + ".html");
String filePath = IOUtils.concatFilePath(outputDirectoryPath, entry.getKey() + ".html");
File file = new File(filePath);
String content = "<html><head><title>" + entry.getKey() + "</title></head><body><p>" + entry.getValue()
+ "</p></body></html>";
Expand Down
1 change: 0 additions & 1 deletion tooling/src/main/java/org/opencds/cqf/tooling/dateroller/DataDateRollerOperation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,6 @@

public class DataDateRollerOperation extends Operation {
private FhirContext fhirContext;
public static final String separator = System.getProperty("file.separator");
public String fhirVersion;
private IOUtils.Encoding fileEncoding;
private Logger logger = LoggerFactory.getLogger(this.getClass());
Expand Down
9 changes: 6 additions & 3 deletions tooling/src/main/java/org/opencds/cqf/tooling/fhir/api/FileFhirDal.java
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Expand Up @@ -12,6 +12,7 @@
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.opencds.cqf.tooling.parameter.FileFhirPlatformParameters;
import org.opencds.cqf.tooling.utilities.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

Expand Down Expand Up @@ -46,7 +47,7 @@ public void create(IBaseResource resource){
if (resourceTypeDefined(resource)){

//ensure resource type directory exists
String typePath = this.resourceDir + "/" + resource.getIdElement().getResourceType();
String typePath = IOUtils.concatFilePath(this.resourceDir, resource.getIdElement().getResourceType());
String path = getPath(resource);

File typeDir = new File(typePath);
Expand Down Expand Up @@ -129,11 +130,13 @@ private void writeResource(String path, IBaseResource resource){
}

private String getPath(IBaseResource resource){
return this.resourceDir + "/" + resource.getIdElement().getResourceType() + "/" + resource.getIdElement().getIdPart() + "." + this.encoding.toString();
return IOUtils.concatFilePath(this.resourceDir, resource.getIdElement().getResourceType(),
resource.getIdElement().getIdPart() + "." + this.encoding.toString());
}

private String getPath(IIdType id){
return this.resourceDir + "/" + id.getResourceType() + "/" + id.getIdPart() + "." + this.encoding.toString();
return IOUtils.concatFilePath(this.resourceDir, id.getResourceType(),
id.getIdPart() + "." + this.encoding.toString());
}

private boolean resourceTypeDefined(IBaseResource resource){
Expand Down
12 changes: 8 additions & 4 deletions tooling/src/main/java/org/opencds/cqf/tooling/modelinfo/StructureDefinitionToModelInfo.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@
import org.opencds.cqf.tooling.modelinfo.quick.QuickModelInfoBuilder;
import org.opencds.cqf.tooling.modelinfo.uscore.USCoreClassInfoBuilder;
import org.opencds.cqf.tooling.modelinfo.uscore.USCoreModelInfoBuilder;
import org.opencds.cqf.tooling.utilities.IOUtils;

import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBElement;
Expand Down Expand Up @@ -162,7 +163,8 @@ public void execute(String[] args) {
Map<String, TypeInfo> typeInfos = ciBuilder.build();
ciBuilder.afterBuild();

String fhirHelpersPath = this.getOutputPath() + "/" + modelName + "Helpers-" + modelVersion + ".cql";
String fhirHelpersPath = IOUtils.concatFilePath(this.getOutputPath(),
modelName + "Helpers-" + modelVersion + ".cql");
miBuilder = new FHIRModelInfoBuilder(modelVersion, typeInfos, atlas, fhirHelpersPath);
mi = miBuilder.build();
}
Expand All @@ -173,7 +175,8 @@ else if (modelName.equals("USCore")) {
Map<String, TypeInfo> typeInfos = ciBuilder.build();
ciBuilder.afterBuild();

String helpersPath = this.getOutputPath() + "/" + modelName + "Helpers-" + modelVersion + ".cql";
String helpersPath = IOUtils.concatFilePath(this.getOutputPath(),
modelName + "Helpers-" + modelVersion + ".cql");
miBuilder = new USCoreModelInfoBuilder(modelVersion, typeInfos, atlas, helpersPath);
mi = miBuilder.build();
}
Expand All @@ -184,7 +187,8 @@ else if (modelName.equals("QICore")) {
Map<String, TypeInfo> typeInfos = ciBuilder.build();
ciBuilder.afterBuild();

String helpersPath = this.getOutputPath() + "/" + modelName + "Helpers-" + modelVersion + ".cql";
String helpersPath = IOUtils.concatFilePath(this.getOutputPath(),
modelName + "Helpers-" + modelVersion + ".cql");
miBuilder = new QICoreModelInfoBuilder(modelVersion, typeInfos, atlas, helpersPath);
mi = miBuilder.build();
}
Expand Down Expand Up @@ -235,7 +239,7 @@ else if (modelName.equals("QUICK")) {
}

private void writeOutput(String fileName, String content) throws IOException {
try (FileOutputStream writer = new FileOutputStream(getOutputPath() + "/" + fileName)) {
try (FileOutputStream writer = new FileOutputStream(IOUtils.concatFilePath(getOutputPath(), fileName))) {
writer.write(content.getBytes());
writer.flush();
}
Expand Down
3 changes: 2 additions & 1 deletion tooling/src/main/java/org/opencds/cqf/tooling/operation/BundleResources.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@

import org.hl7.fhir.instance.model.api.IBaseResource;
import org.opencds.cqf.tooling.Operation;
import org.opencds.cqf.tooling.utilities.IOUtils;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
Expand Down Expand Up @@ -192,7 +193,7 @@ else if (resource.getPath().endsWith(".json")) {
public void output(IBaseResource resource, FhirContext context) {
String fileNameBase = getOutputPath() + getOutputPath().substring(getOutputPath().lastIndexOf(File.separator));
if (bundleId != null && !bundleId.isEmpty()) {
fileNameBase = getOutputPath() + File.separator + bundleId;
fileNameBase = IOUtils.concatFilePath(getOutputPath(), bundleId);
}

try (FileOutputStream writer = new FileOutputStream(fileNameBase + "-bundle." + encoding)) {
Expand Down
5 changes: 4 additions & 1 deletion tooling/src/main/java/org/opencds/cqf/tooling/operation/BundleToResources.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@

import org.hl7.fhir.instance.model.api.IBaseResource;
import org.opencds.cqf.tooling.Operation;
import org.opencds.cqf.tooling.utilities.IOUtils;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
Expand Down Expand Up @@ -163,7 +164,9 @@ else if (resource.getPath().endsWith(".json")) {

// Output
public void output(IBaseResource resource, FhirContext context) {
try (FileOutputStream writer = new FileOutputStream(getOutputPath() + "/" + resource.getIdElement().getResourceType() + "-" + resource.getIdElement().getIdPart() + "." + encoding)) {
try (FileOutputStream writer = new FileOutputStream(
IOUtils.concatFilePath(getOutputPath(),
resource.getIdElement().getResourceType() + "-" + resource.getIdElement().getIdPart() + "." + encoding))) {
writer.write(
encoding.equals("json")
? context.newJsonParser().setPrettyPrint(true).encodeResourceToString(resource).getBytes()
Expand Down
7 changes: 4 additions & 3 deletions tooling/src/main/java/org/opencds/cqf/tooling/operation/IgBundler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.opencds.cqf.tooling.Operation;
import org.opencds.cqf.tooling.utilities.IOUtils;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
Expand Down Expand Up @@ -157,12 +158,12 @@ private void setResourcePaths(final JsonObject igControl) {
if (resources.isJsonArray()) {
for (final JsonElement path : resources.getAsJsonArray()) {
if (path.isJsonPrimitive()) {
resourcePaths.add(pathToIg + "/" + path.getAsString());
resourcePaths.add(IOUtils.concatFilePath(pathToIg, path.getAsString()));
outputBundles.put(path.getAsString(), null);
}
}
} else {
resourcePaths.add(pathToIg + "/" + resources.getAsString());
resourcePaths.add(IOUtils.concatFilePath(pathToIg, resources.getAsString()));
}
}
}
Expand Down Expand Up @@ -247,7 +248,7 @@ private void addArtifactToBundle(final Path path, final Bundle bundle) {
private void outputBundles() {
for (final Map.Entry<String, IBaseResource> set : outputBundles.entrySet()) {
try (FileOutputStream writer = new FileOutputStream(
getOutputPath() + "/" + set.getKey() + "." + encoding)) {
IOUtils.concatFilePath(getOutputPath(), set.getKey() + "." + encoding))) {
writer.write(encoding.equals("json")
? jsonParser.setPrettyPrint(true).encodeResourceToString(set.getValue()).getBytes()
: xmlParser.setPrettyPrint(true).encodeResourceToString(set.getValue()).getBytes());
Expand Down
4 changes: 3 additions & 1 deletion tooling/src/main/java/org/opencds/cqf/tooling/operation/ProfilesToSpreadsheet.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import org.opencds.cqf.tooling.acceleratorkit.StructureDefinitionBindingObject;
import org.opencds.cqf.tooling.acceleratorkit.StructureDefinitionElementBindingVisitor;
import org.opencds.cqf.tooling.terminology.SpreadsheetCreatorHelper;
import org.opencds.cqf.tooling.utilities.IOUtils;
import org.opencds.cqf.tooling.utilities.ModelCanonicalAtlasCreator;


Expand Down Expand Up @@ -83,7 +84,8 @@ private void createOutput(List<StructureDefinitionBindingObject> bindingObjects)
bindingObjects.forEach((bindingObject) -> {
addBindingObjectRowDataToCurrentSheet(firstSheet, rowCount.getAndAccumulate(1, ibo), bindingObject);
});
SpreadsheetCreatorHelper.writeSpreadSheet(workBook, getOutputPath() + separator + modelName + modelVersion + ".xlsx");
SpreadsheetCreatorHelper.writeSpreadSheet(workBook,
IOUtils.concatFilePath(getOutputPath(), modelName + modelVersion + ".xlsx"));
}

private List<String> createHeaderNameList() {
Expand Down
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