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load dependency Packages, and load content from URL correctly

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This commit is contained in:
Grahame Grieve 2019-11-11 14:20:52 +11:00
parent 13da3db00d
commit 52b80cf71c
4 changed files with 531 additions and 496 deletions
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7
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/VersionUtilities.java
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@ -118,4 +118,11 @@ public class VersionUtilities {
return v1.substring(0, 3).equals(v2.substring(0, 3));
}
public static boolean isCorePackage(String s) {
if (s.contains("#")) {
s = s.substring(0, s.indexOf("#"));
}
return Utilities.existsInList(s, "hl7.fhir.core","hl7.fhir.r2.core", "hl7.fhir.r2b.core", "hl7.fhir.r3.core", "hl7.fhir.r4.core");
}
}

13
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/NpmPackage.java vendored
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@ -71,7 +71,7 @@ import com.google.gson.JsonObject;
* @author Grahame Grieve
*
*/
public class NpmPackage {
public class NpmPackage {
private String path;
private List<String> folders = new ArrayList<String>();
@ -544,4 +544,15 @@ import com.google.gson.JsonObject;
private String tail(String s) {
return s.substring(s.lastIndexOf("/")+1);
}
public List<String> dependencies() {
List<String> res = new ArrayList<>();
if (npm.has("dependencies")) {
for (Entry<String, JsonElement> e : npm.getAsJsonObject("dependencies").entrySet()) {
res.add(e.getKey()+"#"+e.getValue().getAsString());
}
}
return res;
}
}

35
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java
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@ -149,6 +149,7 @@ import org.hl7.fhir.r5.utils.ValidationProfileSet;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.cache.NpmPackage;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
@ -310,6 +311,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
private PackageCacheManager pcm;
private PrintWriter mapLog;
private boolean debug;
private Set<String> loadedIgs = new HashSet<>();
private class AsteriskFilter implements FilenameFilter {
String dir;
@ -403,7 +405,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
}
private void loadDefinitions(String src, boolean recursive) throws Exception {
Map<String, byte[]> source = loadIgSource(src, recursive);
Map<String, byte[]> source = loadIgSource(src, recursive, true);
if (version == null)
version = getVersionFromPack(source);
context = SimpleWorkerContext.fromDefinitions(source, loaderForVersion());
@ -478,7 +480,9 @@ public class ValidationEngine implements IValidatorResourceFetcher {
return TextFile.fileToBytes(src);
}
private Map<String, byte[]> loadIgSource(String src, boolean recursive) throws Exception {
/** explore should be true if we're trying to load an -ig parameter, and false if we're loading source **/
private Map<String, byte[]> loadIgSource(String src, boolean recursive, boolean explore) throws Exception {
// 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 package id for an ig - this will be loaded into the cache
@ -494,7 +498,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
if (!Utilities.noString(pid))
return fetchByPackage(pid+(v == null ? "" : "#"+v));
else
return fetchFromUrl(src+(v == null ? "" : "|"+v));
return fetchFromUrl(src+(v == null ? "" : "|"+v), explore);
}
File f = new File(src);
@ -526,7 +530,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
}
private Map<String, byte[]> fetchFromUrl(String src) throws Exception {
private Map<String, byte[]> fetchFromUrl(String src, boolean explore) throws Exception {
if (src.endsWith(".tgz"))
return loadPackage(fetchFromUrlSpecific(src, false), src);
if (src.endsWith(".pack"))
@ -534,7 +538,9 @@ public class ValidationEngine implements IValidatorResourceFetcher {
if (src.endsWith("igpack.zip"))
return readZip(fetchFromUrlSpecific(src, false));
InputStream stream = fetchFromUrlSpecific(Utilities.pathURL(src, "package.tgz"), true);
InputStream stream = null;
if (explore) {
stream = fetchFromUrlSpecific(Utilities.pathURL(src, "package.tgz"), true);
if (stream != null)
return loadPackage(stream, Utilities.pathURL(src, "package.tgz"));
// todo: these options are deprecated - remove once all IGs have been rebuilt post R4 technical correction
@ -546,6 +552,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
return readZip(stream);
stream = fetchFromUrlSpecific(Utilities.pathURL(src, "validator.pack"), true);
//// -----
}
// ok, having tried all that... now we'll just try to access it directly
byte[] cnt;
@ -612,11 +619,21 @@ public class ValidationEngine implements IValidatorResourceFetcher {
}
private Map<String, byte[]> loadPackage(InputStream stream, String name) throws FileNotFoundException, IOException {
private Map<String, byte[]> loadPackage(InputStream stream, String name) throws Exception {
return loadPackage(NpmPackage.fromPackage(stream));
}
public Map<String, byte[]> loadPackage(NpmPackage pi) throws IOException {
public Map<String, byte[]> loadPackage(NpmPackage pi) throws Exception {
loadedIgs.add(pi.name()+"#"+pi.version());
for (String s : pi.dependencies()) {
if (!loadedIgs.contains(s)) {
if (!VersionUtilities.isCorePackage(s)) {
System.out.println("+ .. load IG from "+s);
fetchByPackage(s);
}
}
}
Map<String, byte[]> res = new HashMap<String, byte[]>();
for (String s : pi.listResources("CodeSystem", "ConceptMap", "ImplementationGuide", "CapabilityStatement", "Conformance", "StructureMap", "ValueSet", "StructureDefinition")) {
res.put(s, TextFile.streamToBytes(pi.load("package", s)));
@ -772,7 +789,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
public void loadIg(String src, boolean recursive) throws IOException, FHIRException, Exception {
String canonical = null;
Map<String, byte[]> source = loadIgSource(src, recursive);
Map<String, byte[]> source = loadIgSource(src, recursive, true);
String version = Constants.VERSION;
if (this.version != null)
version = this.version;
@ -893,7 +910,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
}
public Content loadContent(String source, String opName) throws Exception {
Map<String, byte[]> s = loadIgSource(source, false);
Map<String, byte[]> s = loadIgSource(source, false, false);
Content res = new Content();
if (s.size() != 1)
throw new Exception("Unable to find resource " + source + " to "+opName);