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Revert "close the dispatcher in the main method after running the las…
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…t check"

This reverts commit a51a9a3.
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@jeanetteclark
jeanetteclark committed Oct 13, 2023
1 parent acf0062 commit cc42268
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Showing 2 changed files with 46 additions and 74 deletions.
116 changes: 43 additions & 73 deletions src/main/java/edu/ucsb/nceas/mdqengine/MDQEngine.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
package edu.ucsb.nceas.mdqengine;

import edu.ucsb.nceas.mdqengine.dispatch.Dispatcher;
import edu.ucsb.nceas.mdqengine.dispatch.MDQCache;
import edu.ucsb.nceas.mdqengine.exception.MetadigException;
import edu.ucsb.nceas.mdqengine.model.*;
Expand Down Expand Up @@ -35,10 +34,9 @@
import java.util.concurrent.Future;

public class MDQEngine {

// private static final String RESOLVE_PREFIX =
// getConfiguration().getString("D1Client.CN_URL") + "/v2/resolve/";


//private static final String RESOLVE_PREFIX = getConfiguration().getString("D1Client.CN_URL") + "/v2/resolve/";

/**
* Default store uses the in-memory implementation
*/
Expand All @@ -47,17 +45,15 @@ public class MDQEngine {

protected Log log = LogFactory.getLog(this.getClass());
private static String metadigDataDir = null;

public MDQEngine() throws MetadigException, IOException, ConfigurationException {
store = new InMemoryStore();
// store = new MNStore();
MDQconfig cfg = new MDQconfig();
//store = new MNStore();
MDQconfig cfg = new MDQconfig ();
metadigDataDir = cfg.getString("metadig.data.dir");
MDQCache.initialize(null);
}

private Dispatcher dispatcher;

/**
* Executes the given suite for a given object
* @param suite
Expand Down Expand Up @@ -102,11 +98,8 @@ public Run runSuite(Suite suite, InputStream input, Map<String, Object> params,
run.setTimestamp(Calendar.getInstance().getTime());
List<Result> results = new ArrayList<Result>();

List<Check> check_list = suite.getCheck();
int lastIndex = check_list.size() - 1;
// run the checks in the suite to get results
for (int i = 0; i < check_list.size(); i++) {
Check check = check_list.get(i);
for (Check check: suite.getCheck()) {
// is this a reference to existing check?
if (check.getCode() == null && check.getId() != null) {
// then load it
Expand All @@ -130,18 +123,8 @@ public Run runSuite(Suite suite, InputStream input, Map<String, Object> params,
if(origCheck.getLevel() != null) check.setLevel(origCheck.getLevel());
if(origCheck.getType() != null) check.setType(origCheck.getType());
}
dispatcher = Dispatcher.getDispatcher(check.getEnvironment());
Result result = xml.runCheck(check, dispatcher);
Result result = xml.runCheck(check);
results.add(result);
// if its the last check, need to make sure to shut down the dispatcher
if (i == lastIndex){
try {
dispatcher.close();
dispatcher = null;
} catch (Exception e){
log.error("THE CLOSE EXCEPTION" + e);
}
}
}
run.setResult(results);

Expand All @@ -153,12 +136,11 @@ public Run runSuite(Suite suite, InputStream input, Map<String, Object> params,
return run;

}

/**
* Executes the given check for a given object
*
* @param check
* @param input the InputStream for the object to QC
* @param input the InputStream for the object to QC
* @param params optional additional parameters to make available for the check
* @return the Run results for this execution
* @throws MalformedURLException
Expand All @@ -168,53 +150,51 @@ public Run runSuite(Suite suite, InputStream input, Map<String, Object> params,
* @throws XPathExpressionException
* @throws ScriptException
*/
public Run runCheck(Check check, InputStream input, Map<String, Object> params, SystemMetadata sysMeta)
throws MalformedURLException, IOException, SAXException,
public Run runCheck(Check check, InputStream input, Map<String, Object> params, SystemMetadata sysMeta)
throws MalformedURLException, IOException, SAXException,
ParserConfigurationException, XPathExpressionException, ScriptException {


String content = IOUtils.toString(input, "UTF-8");
String metadataContent = content;

XMLDialect xml = new XMLDialect(IOUtils.toInputStream(metadataContent, "UTF-8"));
xml.setParams(params);
xml.setSystemMetadata(sysMeta);
Path tempDir = Files.createTempDirectory("mdq_run");
xml.setDirectory(tempDir.toFile().getAbsolutePath());

// make a run to capture results
Run run = new Run();
run.setId(UUID.randomUUID().toString());
run.setTimestamp(Calendar.getInstance().getTime());
List<Result> results = new ArrayList<Result>();

// run the check to get results
Result result = xml.runCheck(check, dispatcher);
Result result = xml.runCheck(check);
results.add(result);
run.setResult(results);

log.trace("Run results: " + JsonMarshaller.toJson(run));

// clean up
tempDir.toFile().delete();

return run;

}

/**
* To enable checks-by-id-reference, set the store so that checks can be
* retrieved

/**
* To enable checks-by-id-reference, set the store so that checks can be retrieved
* if not specified inline
*
* @param store The storage implementation to use for retrieving existing checks
*/
public void setStore(MDQStore store) {
this.store = store;
}

/**
* Run a suite on a given metadata document. Prints Run XML results.
*
* @param args first is the suite file path, second is the metadata file path
*
*/
Expand All @@ -226,32 +206,27 @@ public static void main(String args[]) {
try {
engine = new MDQEngine();
String xml = IOUtils.toString(new FileInputStream(args[0]), "UTF-8");
Suite suite = (Suite) XmlMarshaller.fromXml(xml, Suite.class);
Suite suite = (Suite) XmlMarshaller.fromXml(xml , Suite.class);
InputStream input = new FileInputStream(args[1]);
InputStream sysmetaInputStream = null;
SystemMetadata sysmeta = null;
Object tmpSysmeta = null;

// Read in the system metadata XML file if it is provided. Suites can be run
// without it.
// The SystemMetadata can be either version 1 or 2. The current type marshaller
// cannot handle version 1,
// so we have to convert v1 to v2 (seems like the marshalling call should do
// this for us).
// THe drawback to this approach is that it will be necessary to test for
// sysmeta v3 when it is released.
if (args.length >= 3) {
Class smClasses[] = { org.dataone.service.types.v2.SystemMetadata.class,
org.dataone.service.types.v1.SystemMetadata.class };
for (Class thisClass : smClasses) {
// Read in the system metadata XML file if it is provided. Suites can be run without it.
// The SystemMetadata can be either version 1 or 2. The current type marshaller cannot handle version 1,
// so we have to convert v1 to v2 (seems like the marshalling call should do this for us).
// THe drawback to this approach is that it will be necessary to test for sysmeta v3 when it is released.
if(args.length >= 3) {
Class smClasses[] = {org.dataone.service.types.v2.SystemMetadata.class, org.dataone.service.types.v1.SystemMetadata.class};
for (Class thisClass: smClasses) {
sysmetaInputStream = new FileInputStream(args[2]);
try {
tmpSysmeta = TypeMarshaller.unmarshalTypeFromStream(thisClass, sysmetaInputStream);
// Didn't get an error so proceed to convert to sysmeta v2, if needed.
break;
} catch (ClassCastException cce) {
cce.printStackTrace();
continue;
continue;
} catch (InstantiationException | IllegalAccessException | IOException | MarshallingException fis) {
fis.printStackTrace();
continue;
Expand All @@ -273,27 +248,23 @@ public static void main(String args[]) {
run.setRunStatus("SUCCESS");

// Add DataONE sysmeta, if it was provided.
if (sysmeta != null) {
if(sysmeta != null) {
SysmetaModel smm = new SysmetaModel();
// These sysmeta fields are always provided
smm.setOriginMemberNode(sysmeta.getOriginMemberNode().getValue());
smm.setRightsHolder(sysmeta.getRightsHolder().getValue());
smm.setDateUploaded(sysmeta.getDateUploaded());
smm.setFormatId(sysmeta.getFormatId().getValue());
// These fields aren't required.
if (sysmeta.getObsoletes() != null)
smm.setObsoletes(sysmeta.getObsoletes().getValue());
if (sysmeta.getObsoletedBy() != null)
smm.setObsoletedBy(sysmeta.getObsoletedBy().getValue());
if (sysmeta.getSeriesId() != null)
smm.setSeriesId(sysmeta.getSeriesId().getValue());
if (sysmeta.getObsoletes() != null) smm.setObsoletes(sysmeta.getObsoletes().getValue());
if (sysmeta.getObsoletedBy() != null) smm.setObsoletedBy(sysmeta.getObsoletedBy().getValue());
if (sysmeta.getSeriesId() != null) smm.setSeriesId(sysmeta.getSeriesId().getValue());

// Now make the call to DataONE to get the group information for this
// rightsHolder.
// Now make the call to DataONE to get the group information for this rightsHolder.
// Only wait for a certain amount of time before we will give up.
ExecutorService executorService = Executors.newSingleThreadExecutor();
ExecutorService executorService = Executors.newSingleThreadExecutor();

// Provide the rightsHolder to the DataONE group lookup.
// Provide the rightsHolder to the DataONE group lookup.
GroupLookupCheck glc = new GroupLookupCheck();
glc.setRightsHolder(sysmeta.getRightsHolder().getValue());
Future<List<String>> future = executorService.submit(glc);
Expand All @@ -307,13 +278,12 @@ public static void main(String args[]) {
}
// Sleep for 1 second

if (groups != null)
break;
System.out.println("Waiting 1 second for groups");
if(groups != null) break;
System.out.println("Waiting 1 second for groups");
Thread.sleep(1000);
}

if (groups != null) {
if(groups != null) {
System.out.println("Setting groups");
smm.setGroups(groups);
} else {
Expand Down
4 changes: 3 additions & 1 deletion src/main/java/edu/ucsb/nceas/mdqengine/processor/XMLDialect.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,8 @@ public class XMLDialect {

private String directory;

private Dispatcher dispatcher;

public static Log log = LogFactory.getLog(XMLDialect.class);

public XMLDialect(InputStream input) throws SAXException, IOException, ParserConfigurationException {
Expand Down Expand Up @@ -116,7 +118,7 @@ public void mergeNamespaces(List<Namespace> namespaces) {
}
}

public Result runCheck(Check check, Dispatcher dispatcher) throws XPathExpressionException {
public Result runCheck(Check check) throws XPathExpressionException {

Result result = null;

Expand Down

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