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fix so recursive loading is only by request

This commit is contained in:
Grahame Grieve 2019-08-18 18:15:18 +10:00
parent 539eee9266
commit 6d611afd48
5 changed files with 23 additions and 17 deletions
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2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/NativeHostServices.java
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@ -164,7 +164,7 @@ public class NativeHostServices {
* @throws Exception * @throws Exception
*/ */
public void load(String pack) throws Exception { public void load(String pack) throws Exception {
validator.loadIg(pack); validator.loadIg(pack, false);
} }
/** /**

23
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java
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@ -292,7 +292,7 @@ public class ValidationEngine {
} }
public void loadInitialDefinitions(String src) throws Exception { public void loadInitialDefinitions(String src) throws Exception {
loadDefinitions(src); loadDefinitions(src, false);
} }
public void setTerminologyServer(String src, String log, FhirPublication version) throws Exception { public void setTerminologyServer(String src, String log, FhirPublication version) throws Exception {
@ -329,7 +329,7 @@ public class ValidationEngine {
} }
public ValidationEngine(String src) throws Exception { public ValidationEngine(String src) throws Exception {
loadDefinitions(src); loadDefinitions(src, false);
pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION); pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
} }
@ -341,8 +341,8 @@ public class ValidationEngine {
this.language = language; this.language = language;
} }
private void loadDefinitions(String src) throws Exception { private void loadDefinitions(String src, boolean recursive) throws Exception {
Map<String, byte[]> source = loadIgSource(src); Map<String, byte[]> source = loadIgSource(src, recursive);
if (version == null) if (version == null)
version = getVersionFromPack(source); version = getVersionFromPack(source);
context = SimpleWorkerContext.fromDefinitions(source, loaderForVersion()); context = SimpleWorkerContext.fromDefinitions(source, loaderForVersion());
@ -417,7 +417,7 @@ public class ValidationEngine {
return TextFile.fileToBytes(src); return TextFile.fileToBytes(src);
} }
private Map<String, byte[]> loadIgSource(String src) throws Exception { private Map<String, byte[]> loadIgSource(String src, boolean recursive) throws Exception {
// src can be one of the following: // src can be one of the following:
// - a canonical url for an ig - this will be converted to a package id and loaded into the cache // - a canonical url for an ig - this will be converted to a package id and loaded into the cache
// - a package id for an ig - this will be loaded into the cache // - a package id for an ig - this will be loaded into the cache
@ -445,7 +445,7 @@ public class ValidationEngine {
if (f.isDirectory() && new File(Utilities.path(src, "validator.pack")).exists()) if (f.isDirectory() && new File(Utilities.path(src, "validator.pack")).exists())
return readZip(new FileInputStream(Utilities.path(src, "validator.pack"))); return readZip(new FileInputStream(Utilities.path(src, "validator.pack")));
if (f.isDirectory()) if (f.isDirectory())
return scanDirectory(f); return scanDirectory(f, recursive);
if (src.endsWith(".tgz")) if (src.endsWith(".tgz"))
return loadPackage(new FileInputStream(src), src); return loadPackage(new FileInputStream(src), src);
if (src.endsWith(".pack")) if (src.endsWith(".pack"))
@ -505,11 +505,12 @@ public class ValidationEngine {
} }
} }
private Map<String, byte[]> scanDirectory(File f) throws FileNotFoundException, IOException { private Map<String, byte[]> scanDirectory(File f, boolean recursive) throws FileNotFoundException, IOException {
Map<String, byte[]> res = new HashMap<>(); Map<String, byte[]> res = new HashMap<>();
for (File ff : f.listFiles()) { for (File ff : f.listFiles()) {
if (ff.isDirectory()){ if (ff.isDirectory()){
res.putAll(scanDirectory(ff)); if (recursive)
res.putAll(scanDirectory(ff, true));
} }
else if (!isIgnoreFile(ff)) { else if (!isIgnoreFile(ff)) {
FhirFormat fmt = checkIsResource(ff.getAbsolutePath()); FhirFormat fmt = checkIsResource(ff.getAbsolutePath());
@ -685,9 +686,9 @@ public class ValidationEngine {
context.cacheResource(r); context.cacheResource(r);
} }
public void loadIg(String src) throws IOException, FHIRException, Exception { public void loadIg(String src, boolean recursive) throws IOException, FHIRException, Exception {
String canonical = null; String canonical = null;
Map<String, byte[]> source = loadIgSource(src); Map<String, byte[]> source = loadIgSource(src, recursive);
String version = Constants.VERSION; String version = Constants.VERSION;
if (this.version != null) if (this.version != null)
version = this.version; version = this.version;
@ -808,7 +809,7 @@ public class ValidationEngine {
} }
public Content loadContent(String source, String opName) throws Exception { public Content loadContent(String source, String opName) throws Exception {
Map<String, byte[]> s = loadIgSource(source); Map<String, byte[]> s = loadIgSource(source, false);
Content res = new Content(); Content res = new Content();
if (s.size() != 1) if (s.size() != 1)
throw new Exception("Unable to find resource " + source + " to "+opName); throw new Exception("Unable to find resource " + source + " to "+opName);

9
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/Validator.java
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@ -163,6 +163,8 @@ public class Validator {
System.out.println(" Default: results are sent to the std out."); System.out.println(" Default: results are sent to the std out.");
System.out.println("-debug"); System.out.println("-debug");
System.out.println(" Produce additional information about the loading/validation process"); System.out.println(" Produce additional information about the loading/validation process");
System.out.println("-recurse");
System.out.println(" Look in subfolders when -ig refers to a folder");
System.out.println("-native: use schema for validation as well"); System.out.println("-native: use schema for validation as well");
System.out.println(" * XML: w3c schema+schematron"); System.out.println(" * XML: w3c schema+schematron");
System.out.println(" * JSON: json.schema"); System.out.println(" * JSON: json.schema");
@ -228,7 +230,7 @@ public class Validator {
String s = args[++i]; String s = args[++i];
if (!s.startsWith("hl7.fhir.core-")) { if (!s.startsWith("hl7.fhir.core-")) {
System.out.println("Load Package: "+s); System.out.println("Load Package: "+s);
validator.loadIg(s); validator.loadIg(s, true);
} }
} }
} }
@ -268,6 +270,7 @@ public class Validator {
boolean doNative = false; boolean doNative = false;
boolean anyExtensionsAllowed = true; boolean anyExtensionsAllowed = true;
boolean hintAboutNonMustSupport = false; boolean hintAboutNonMustSupport = false;
boolean recursive = false;
List<String> profiles = new ArrayList<String>(); List<String> profiles = new ArrayList<String>();
EngineMode mode = EngineMode.VALIDATION; EngineMode mode = EngineMode.VALIDATION;
String output = null; String output = null;
@ -323,6 +326,8 @@ public class Validator {
doNative = true; doNative = true;
else if (args[i].equals("-debug")) else if (args[i].equals("-debug"))
doDebug = true; doDebug = true;
else if (args[i].equals("-recurse"))
recursive = true;
else if (args[i].equals("-strictExtensions")) else if (args[i].equals("-strictExtensions"))
anyExtensionsAllowed = false; anyExtensionsAllowed = false;
else if (args[i].equals("-hintAboutNonMustSupport")) else if (args[i].equals("-hintAboutNonMustSupport"))
@ -390,7 +395,7 @@ public class Validator {
validator.setVersion(sv); validator.setVersion(sv);
for (String src : igs) { for (String src : igs) {
System.out.println("+ .. load IG from "+src); System.out.println("+ .. load IG from "+src);
validator.loadIg(src); validator.loadIg(src, recursive);
} }
validator.setQuestionnaires(questionnaires); validator.setQuestionnaires(questionnaires);
validator.setNative(doNative); validator.setNative(doNative);

4
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ProfileComparisonTests.java
View File

@ -22,8 +22,8 @@ public class ProfileComparisonTests {
if (!TestUtilities.silent) if (!TestUtilities.silent)
System.out.println("Compare US Patient Core with AU Patient Base"); System.out.println("Compare US Patient Core with AU Patient Base");
ValidationEngine ve = new ValidationEngine("hl7.fhir.core#3.0.1", DEF_TX, null, FhirPublication.R4); ValidationEngine ve = new ValidationEngine("hl7.fhir.core#3.0.1", DEF_TX, null, FhirPublication.R4);
ve.loadIg("hl7.fhir.us.core#1.0.1"); ve.loadIg("hl7.fhir.us.core#1.0.1", false);
ve.loadIg("hl7.fhir.au.base#dev"); ve.loadIg("hl7.fhir.au.base#dev", false);
String left = "http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"; String left = "http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient";

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationEngineTests.java
View File

@ -159,7 +159,7 @@ public class ValidationEngineTests {
ValidationEngine ve = new ValidationEngine("hl7.fhir.core#3.0.1", DEF_TX, null, FhirPublication.STU3); ValidationEngine ve = new ValidationEngine("hl7.fhir.core#3.0.1", DEF_TX, null, FhirPublication.STU3);
if (!TestUtilities.silent) if (!TestUtilities.silent)
System.out.println(" .. load USCore"); System.out.println(" .. load USCore");
ve.loadIg("hl7.fhir.us.core#1.0.1"); ve.loadIg("hl7.fhir.us.core#1.0.1", false);
List<String> profiles = new ArrayList<>(); List<String> profiles = new ArrayList<>();
profiles.add("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"); profiles.add("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient");
OperationOutcome op = ve.validate(TestUtilities.resourceNameToFile("validation-examples", "patient301.xml"), profiles); OperationOutcome op = ve.validate(TestUtilities.resourceNameToFile("validation-examples", "patient301.xml"), profiles);