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/
uoa-validator-engine2
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- Fix Logging System not working; Move to Logback and integrate all logs which were printed with "System.out". 

- Update dependencies.
- Code polishing.
This commit is contained in:
Lampros Smyrnaios 2023-07-10 14:38:06 +03:00
parent 1ece17e0a7
commit fd99f536d3
19 changed files with 300 additions and 237 deletions
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86
pom.xml
View File

@ -13,38 +13,8 @@
<!-- <timestamp>${maven.build.timestamp}</timestamp>-->
<!-- <maven.build.timestamp.format>E MMM dd HH:mm:ss z yyyy</maven.build.timestamp.format>-->
<!-- </properties>-->
<dependencies>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.11.0</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>31.1-jre</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>2.20.0</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>2.20.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.spockframework</groupId>
<artifactId>spock-core</artifactId>
<version>1.3-groovy-2.5</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
@ -60,11 +30,61 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>3.3.2</version>
<version>3.4.0</version>
<configuration>
<failOnMissingWebXml>false</failOnMissingWebXml>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.13.0</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>32.1.1-jre</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.spockframework</groupId>
<artifactId>spock-core</artifactId>
<version>1.3-groovy-2.5</version>
<scope>test</scope>
</dependency>
<!-- logback versions 1.4.X require Java-11 -->
<!-- logback versions 1.3.X require Java-8, but id this project is added as Dependency in Spring Boot, then Spring Boot throws an error, since it does not yet support logback 1.3.x -->
<!-- https://mvnrepository.com/artifact/ch.qos.logback/logback-core -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>1.2.12</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.36</version>
</dependency>
<!-- https://mvnrepository.com/artifact/ch.qos.logback/logback-classic -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.2.12</version>
</dependency>
</dependencies>
</project>

10
src/main/java/eu/dnetlib/validator2/engine/Helper.java
View File

@ -4,6 +4,7 @@ import eu.dnetlib.validator2.validation.guideline.Builders;
import eu.dnetlib.validator2.validation.guideline.Builders.ElementSpecBuilder;
import eu.dnetlib.validator2.validation.guideline.Cardinality;
import eu.dnetlib.validator2.validation.guideline.RequirementLevel;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
@ -24,6 +25,9 @@ import java.util.zip.ZipInputStream;
public class Helper {
private static final org.slf4j.Logger logger = LoggerFactory.getLogger(Helper.class);
private static final String EMPTY = "";
public static boolean isEmpty(String s) {
@ -116,15 +120,15 @@ public class Helper {
int len = nodes.getLength();
for (int i = 0; i < len; i++) {
Node node = nodes.item(i);
// System.out.println("Getting node: " + node);
//logger.debug("Getting node: " + node);
T t = nodeReader.apply(node);
// System.out.println("Read node value: " + t);
//logger.debug("Read node value: " + t);
if (predicate.test(t)) {
filtered.add(node);
}
}
}
// System.out.println(filtered.size() + " nodes matched the predicate");
//logger.debug(filtered.size() + " nodes matched the predicate");
return new ListOfNodes(filtered);
}

23
src/main/java/eu/dnetlib/validator2/engine/Reporter.java
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@ -1,7 +1,12 @@
package eu.dnetlib.validator2.engine;
import org.slf4j.LoggerFactory;
public class Reporter<T, R extends Rule<T>> {
private static final org.slf4j.Logger logger = LoggerFactory.getLogger(Reporter.class);
private final RuleDiagnostics<T, R> diagnostics;
public Reporter(RuleDiagnostics<T, R> diagnostics) {
@ -11,30 +16,24 @@ public class Reporter<T, R extends Rule<T>> {
public void reportSuccessFor(R rule, T t) {
try {
diagnostics.success(rule, t);
}
catch(Throwable throwable) {
System.err.println("Failed to report success of applying " + rule + " to value: " + t);
throwable.printStackTrace();
} catch (Throwable throwable) {
logger.error("Failed to report success of applying " + rule + " to value: " + t, throwable);
}
}
public void reportFailureFor(R rule, T t) {
try {
diagnostics.failure(rule, t);
}
catch(Throwable throwable) {
System.err.println("Failed to report failure of applying " + rule + " to value: " + t);
throwable.printStackTrace();
} catch (Throwable throwable) {
logger.error("Failed to report failure of applying " + rule + " to value: " + t, throwable);
}
}
public void reportErrorFor(R rule, T t, Throwable throwable) {
try {
diagnostics.error(rule, t, throwable);
}
catch(Throwable throwable1) {
System.err.println("Failed to report error of applying " + rule + " to value: " + t);
throwable1.printStackTrace();
} catch (Throwable throwable1) {
logger.error("Failed to report error of applying " + rule + " to value: " + t, throwable);
}
}
}

5
src/main/java/eu/dnetlib/validator2/engine/builtins/SimpleRule.java
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@ -3,14 +3,13 @@ package eu.dnetlib.validator2.engine.builtins;
import eu.dnetlib.validator2.engine.Rule;
import eu.dnetlib.validator2.engine.RuleContext;
import eu.dnetlib.validator2.engine.RuleEvaluationException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.function.Predicate;
public class SimpleRule<T, C extends RuleContext> implements Rule<T> {
private static final Logger logger = LogManager.getLogger();
private static final org.slf4j.Logger logger = LoggerFactory.getLogger(SimpleRule.class);
private final C context;
private final Predicate<T> predicate;

5
src/main/java/eu/dnetlib/validator2/engine/builtins/XMLRule.java
View File

@ -3,8 +3,7 @@ package eu.dnetlib.validator2.engine.builtins;
import eu.dnetlib.validator2.engine.Rule;
import eu.dnetlib.validator2.engine.RuleEvaluationException;
import eu.dnetlib.validator2.engine.contexts.XMLContext;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.NodeList;
@ -16,7 +15,7 @@ import java.util.function.Predicate;
*/
public class XMLRule<C extends XMLContext> implements Rule<Document> {
private static final Logger logger = LogManager.getLogger();
private static final org.slf4j.Logger logger = LoggerFactory.getLogger(XMLRule.class);
private final C context;
public final Predicate<NodeList> predicate;

4
src/main/java/eu/dnetlib/validator2/engine/builtins/XMLValidURLRule.java
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@ -10,9 +10,7 @@ import java.util.function.Predicate;
public class XMLValidURLRule extends XMLRule<XMLContext> {
protected XMLValidURLRule(XMLContext context) {
super(context, (NodeList nodes) -> {
return context.getNodeListActionProperty().test(nodes, (Predicate<String>) Helper.URLResolver::resolve);
});
super(context, (NodeList nodes) -> context.getNodeListActionProperty().test(nodes, (Predicate<String>) Helper.URLResolver::resolve));
}
public static Builder builder() {

5
src/main/java/eu/dnetlib/validator2/engine/builtins/XPathExpressionHelper.java
View File

@ -4,8 +4,7 @@ import com.google.common.cache.CacheBuilder;
import com.google.common.cache.CacheLoader;
import com.google.common.cache.LoadingCache;
import eu.dnetlib.validator2.engine.RuleEvaluationException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
@ -17,7 +16,7 @@ import java.util.concurrent.ExecutionException;
public class XPathExpressionHelper {
private static final Logger logger = LogManager.getLogger();
private static final org.slf4j.Logger logger = LoggerFactory.getLogger(XPathExpressionHelper.class);
// XPath expression compilation
private static final XPath XPATH = XPathFactory.newInstance().newXPath();

7
src/main/java/eu/dnetlib/validator2/engine/contexts/CardinalityContext.java
View File

@ -2,11 +2,16 @@ package eu.dnetlib.validator2.engine.contexts;
import eu.dnetlib.validator2.engine.Helper;
import eu.dnetlib.validator2.engine.RuleContext;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.function.Predicate;
public interface CardinalityContext extends RuleContext {
Logger logger = LoggerFactory.getLogger(CardinalityContext.class);
String GREATER_THAN_PROPERTY_NAME = "gt";
String LESS_THAN_PROPERTY_NAME = "lt";
String UPPER_BOUND_PROPERTY_NAME = LESS_THAN_PROPERTY_NAME;
@ -20,7 +25,7 @@ public interface CardinalityContext extends RuleContext {
BooleanRuleProperty getIsInclusiveProperty();
default Predicate<Integer> cardinalityPredicate() {
// System.out.println("Evaluating cardinality " + getIdProperty().getValue());
logger.debug("Evaluating cardinality " + getIdProperty().getValue());
long min = getLowerBoundProperty().getLongValue();
long max = getUpperBoundProperty().getLongValue();

11
src/main/java/eu/dnetlib/validator2/validation/guideline/ElementSpecCompiler.java
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@ -9,8 +9,8 @@ import eu.dnetlib.validator2.engine.builtins.StandardXMLContext;
import eu.dnetlib.validator2.engine.builtins.XMLRule;
import eu.dnetlib.validator2.engine.builtins.XPathExpressionHelper;
import eu.dnetlib.validator2.engine.contexts.XMLContext;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
@ -25,7 +25,7 @@ import java.util.stream.Stream;
class ElementSpecCompiler {
private static final Logger logger = LogManager.getLogger();
private static final org.slf4j.Logger logger = LoggerFactory.getLogger(ElementSpecCompiler.class);
private static final String[] EMPTY = new String[]{};
@ -288,6 +288,9 @@ class ElementSpecCompiler {
private static class ElementStruct {
private static final Logger logger = LoggerFactory.getLogger(ElementStruct.class);
Supplier<GuidelineEvaluation> runtimeInfo;
final ElementSpec spec;
final String[] parentElementNames;
@ -334,7 +337,7 @@ class ElementSpecCompiler {
if (spec.position().xpath != null) {
xpath = "(" + xpath + ")[" + spec.position().xpath + "]";
}
// System.out.println(xpath);
logger.debug(xpath);
return xpathWithText(xpath, withText);
}

15
src/main/java/eu/dnetlib/validator2/validation/guideline/GuidelineEvaluation.java
View File

@ -2,6 +2,8 @@ package eu.dnetlib.validator2.validation.guideline;
import eu.dnetlib.validator2.engine.*;
import eu.dnetlib.validator2.engine.builtins.StandardRuleDiagnostics;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.NodeList;
@ -12,6 +14,9 @@ import java.util.Map;
class GuidelineEvaluation {
private static final Logger logger = LoggerFactory.getLogger(GuidelineEvaluation.class);
// TODO: Report all rule diagnostics to System out/err (we should remove this or allow clients to disable it)
private static final RuleDiagnostics<Document, Rule<Document>> OUT = Helper.Diagnostics.systemOut();
private static final RuleDiagnostics<Document, Rule<Document>> ERR = Helper.Diagnostics.systemErr();
@ -40,7 +45,7 @@ class GuidelineEvaluation {
rules.add(result.rootNodeRule);
rules.addAll(result.nodeRules);
// System.out.println("Evaluating " + rules);
logger.debug("Evaluating " + rules);
for (SyntheticRule<Document> rule: rules) {
@ -58,7 +63,7 @@ class GuidelineEvaluation {
// Report the non-applicability of a rule as a warning
// The check for both status and non-applicable requirement level is redundant
// (non-applicable rules always succeed), yet it is more clear hopefully.
// System.out.println("Warn for non-applicable: " + rule);
logger.warn("Non-applicable: " + rule);
warnings.add(synthesizeFailureMessage(rule));
}
else if (status == Status.FAILURE) {
@ -70,7 +75,7 @@ class GuidelineEvaluation {
// This is the root rule failing!
// Fail fast here, too (don't waste resources to evaluate other rules).
// We will "enable" it, if it is requested.
// System.out.println("Fail fast for root failure: " + rule);
logger.error("Fail fast for root failure: " + rule);
errors.add(synthesizeFailureMessage(rule));
return StandardResult.forFailure(warnings, errors);
}
@ -79,7 +84,7 @@ class GuidelineEvaluation {
// (a) is non-mandatory or
// (b) it was successful.
// Thus, here we need only to warn and not to err, allowing the evaluation loop to proceed.
// System.out.println("Warn for mandatory failure: " + rule);
logger.warn("Mandatory failure: " + rule);
warnings.add(synthesizeFailureMessage(rule));
}
}
@ -87,7 +92,7 @@ class GuidelineEvaluation {
// This is a warning: a non-mandatory rule has failed.
// Note that MA rules are treated as non-mandatory.
// We let the evaluation loop proceed.
// System.out.println("Warn for optional/recommended failure: " + rule);
logger.warn("Optional/Recommended failure: " + rule);
warnings.add(synthesizeFailureMessage(rule));
}
}

5
src/main/java/eu/dnetlib/validator2/validation/guideline/SyntheticGuideline.java
View File

@ -4,13 +4,12 @@ import eu.dnetlib.validator2.engine.Helper;
import eu.dnetlib.validator2.engine.Rule;
import eu.dnetlib.validator2.engine.RuleContext;
import eu.dnetlib.validator2.engine.RuleEvaluationException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
public final class SyntheticGuideline extends AbstractGuideline<Document> {
private static final Logger logger = LogManager.getLogger();
private static final org.slf4j.Logger logger = LoggerFactory.getLogger(SyntheticGuideline.class);
private CompilationResult compilationResult;
private static final ThreadLocal<GuidelineEvaluation> evaluation = new ThreadLocal<>();

7
src/main/java/eu/dnetlib/validator2/validation/guideline/openaire/AbstractOpenAireProfile.java
View File

@ -10,6 +10,8 @@ import eu.dnetlib.validator2.validation.StandardValidationResult;
import eu.dnetlib.validator2.validation.XMLApplicationProfile;
import eu.dnetlib.validator2.validation.guideline.ElementSpec;
import eu.dnetlib.validator2.validation.guideline.Guideline;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
@ -19,6 +21,9 @@ import java.util.Map;
public abstract class AbstractOpenAireProfile implements XMLApplicationProfile {
private static final Logger logger = LoggerFactory.getLogger(AbstractOpenAireProfile.class);
private final String name;
public AbstractOpenAireProfile(String name) {
@ -42,7 +47,7 @@ public abstract class AbstractOpenAireProfile implements XMLApplicationProfile {
results.put(guideline.getName(), result);
score += (result.status() == Status.SUCCESS ? result.score() : 0);
// System.out.println("Score after " + guideline.getName() + " = " + score);
logger.debug("Score after " + guideline.getName() + " = " + score);
}
double percentScore = (score / maxScore) * 100;

197
src/main/java/eu/dnetlib/validator2/validation/guideline/openaire/FAIR_Data_GuidelinesProfile.java
View File

@ -5,6 +5,8 @@ package eu.dnetlib.validator2.validation.guideline.openaire;
import eu.dnetlib.validator2.engine.Status;
import eu.dnetlib.validator2.validation.XMLApplicationProfile;
import eu.dnetlib.validator2.validation.guideline.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import java.util.*;
@ -15,6 +17,8 @@ import static eu.dnetlib.validator2.validation.guideline.Cardinality.ONE_TO_N;
public final class FAIR_Data_GuidelinesProfile extends AbstractOpenAireProfile {
private static final Logger logger = LoggerFactory.getLogger(FAIR_Data_GuidelinesProfile.class);
private static final String[] TITLE_TYPES = {
"AlternativeTitle", "Subtitle", "TranslatedTitle", "Other"
};
@ -291,82 +295,86 @@ public final class FAIR_Data_GuidelinesProfile extends AbstractOpenAireProfile {
//// TODO this goes to FAIRProfile
//class MetadataCompleteness extends AbstractGuideline<Document> {
//
// public MetadataCompleteness() {
// super("MetadataCompleteness", 40);
// }
//
// @Override
// public Result validate(String id, Document t) {
// DataArchiveGuidelinesV2Profile profile = new DataArchiveGuidelinesV2Profile();
//
// // <></>ODO: iterate over results and build one Guideline.Result
// try {
//// System.out.println("Processing MetadataCompleteness...");
// XMLApplicationProfile.ValidationResult res = profile.validate(id, t);
// Map<String, Result> results = res.results();
// int MaxScoreMetadataCompleteness = (int) ((res.score()*getWeight())/100);
//
//// System.out.println("Max score DataValidator(%): " + res.score());
//// System.out.println("Weight FAIRG: " + getWeight());
//// System.out.println("Max score MetadataCompleteness: " + MaxScoreMetadataCompleteness);
//// System.out.println("\n\n\n\n");
//
//// for (Map.Entry entry : results.entrySet()) {
//// System.out.println(entry.getKey() + " = " + entry.getValue());
//// }
//// System.out.println(score);
// return getResult(MaxScoreMetadataCompleteness);
//
//// System.out.println(tempp.status() + " - " + tempp.score());
//// String printout = results.entrySet().stream().
//// map(entry -> entry.getValue() + ": " + entry.getKey()).collect(Collectors.joining("\n"));
//// System.out.println(printout);
//
//// System.out.println("\n\n\n\n");
// } catch (Exception e) {
// System.out.println(e.getMessage());
// System.out.println(e);
// e.printStackTrace();
// }
//
// return null;
// }
//
// private static Result getResult(int score) {
// String aa;
// aa = (score > 0) ? "SUCCESS" : "FAILURE";
// return new Result() {
// @Override
// public int score() {
// return score;
// }
//
// @Override
// public Status status() {
//// return null;
// return Status.valueOf(aa);
// }
//
// @Override
// public Iterable<String> warnings() { return null; }
//
// @Override
// public Iterable<String> errors() {
// return null;
// }
//
// @Override
// public String internalError() {
// return null;
// }
// };
// }
//}
/*class MetadataCompleteness extends AbstractGuideline<Document> {
private static final Logger logger = LoggerFactory.getLogger(MetadataCompleteness.class);
public MetadataCompleteness() {
super("MetadataCompleteness", 40);
}
@Override
public Result validate(String id, Document t) {
DataArchiveGuidelinesV2Profile profile = new DataArchiveGuidelinesV2Profile();
// <></>ODO: iterate over results and build one Guideline.Result
try {
// System.out.println("Processing MetadataCompleteness...");
XMLApplicationProfile.ValidationResult res = profile.validate(id, t);
Map<String, Result> results = res.results();
int MaxScoreMetadataCompleteness = (int) ((res.score()*getWeight())/100);
logger.debug("Max score DataValidator(%): " + res.score());
logger.debug("Weight FAIRG: " + getWeight());
logger.debug("Max score MetadataCompleteness: " + MaxScoreMetadataCompleteness);
logger.debug("\n\n\n\n");
if ( logger.isDebugEnabled() ) {
for ( Map.Entry entry : results.entrySet() ) {
logger.debug(entry.getKey() + " = " + entry.getValue());
}
}
logger.debug(results.entrySet().stream().
map(entry -> entry.getValue() + ": " + entry.getKey()).collect(Collectors.joining("\n")));
return getResult(MaxScoreMetadataCompleteness);
} catch (Exception e) {
System.out.println(e.getMessage());
System.out.println(e);
e.printStackTrace();
}
return null;
}
private static Result getResult(int score) {
String aa;
aa = (score > 0) ? "SUCCESS" : "FAILURE";
return new Result() {
@Override
public int score() {
return score;
}
@Override
public Status status() {
// return null;
return Status.valueOf(aa);
}
@Override
public Iterable<String> warnings() { return null; }
@Override
public Iterable<String> errors() {
return null;
}
@Override
public String internalError() {
return null;
}
};
}
}*/
class F2_01M_SPEC extends AbstractGuideline<Document> {
private static final Logger logger = LoggerFactory.getLogger(F2_01M_SPEC.class);
public F2_01M_SPEC() {
super("Rich metadata is provided to allow discovery", 2*6);
}
@ -382,9 +390,9 @@ class F2_01M_SPEC extends AbstractGuideline<Document> {
// Get actual score and not (%) to incorporate to FAIR score
final int MaxScoreF2_01M_SPEC = (int) ((res_F.score()*getWeight())/100);
// System.out.println("Max score DataValidator(%): " + res_F.score());
// System.out.println("Weight FAIRG: " + getWeight());
// System.out.println("Max score F2_01M_SPEC: " + MaxScoreF2_01M_SPEC);
logger.debug("Max score DataValidator(%): " + res_F.score());
logger.debug("Weight FAIRG: " + getWeight());
logger.debug("Max score F2_01M_SPEC: " + MaxScoreF2_01M_SPEC);
List<String> warnings2 = new ArrayList<>();
List<String> errors2 = new ArrayList<>();
@ -400,8 +408,8 @@ class F2_01M_SPEC extends AbstractGuideline<Document> {
if (entry.getValue().toString().contains("SUCCESS")) {
score += 2;
}
// System.out.println(res_F.results().get(entry.getKey()).warnings().getClass());
// System.out.println(warnings2.getClass());
logger.debug(String.valueOf(res_F.results().get(entry.getKey()).warnings().getClass()));
logger.debug(String.valueOf(warnings2.getClass()));
}
@ -410,9 +418,7 @@ class F2_01M_SPEC extends AbstractGuideline<Document> {
return new StandardResult(ress.score(), ress.status(), (List<String>) ress.warnings(), (List<String>) ress.errors(), ress.internalError());
} catch (Exception e) {
System.out.println(e.getMessage());
System.out.println(e);
e.printStackTrace();
logger.error("", e);
return null;
}
}
@ -451,6 +457,9 @@ class F2_01M_SPEC extends AbstractGuideline<Document> {
class F3_01M_SPEC extends AbstractGuideline<Document> {
private static final Logger logger = LoggerFactory.getLogger(F3_01M_SPEC.class);
public F3_01M_SPEC() { super("Metadata includes the identifier for the data", 2*2); }
@Override
@ -488,9 +497,7 @@ class F3_01M_SPEC extends AbstractGuideline<Document> {
return new StandardResult(ress.score(), ress.status(), (List<String>) ress.warnings(), (List<String>) ress.errors(), ress.internalError());
} catch (Exception e) {
System.out.println(e.getMessage());
System.out.println(e);
e.printStackTrace();
logger.error("", e);
return null;
}
}
@ -527,6 +534,8 @@ class F3_01M_SPEC extends AbstractGuideline<Document> {
class I2_01M_SPEC extends AbstractGuideline<Document> {
private static final Logger logger = LoggerFactory.getLogger(I2_01M_SPEC.class);
public I2_01M_SPEC() { super("Metadata uses FAIR-compliant vocabularies", 5*2); }
@Override
@ -535,7 +544,7 @@ class I2_01M_SPEC extends AbstractGuideline<Document> {
// TODO: iterate over results and build one Guideline.Result
try {
// System.out.println("\nMetadata uses FAIR-compliant vocabularies");
logger.debug("\nMetadata uses FAIR-compliant vocabularies");
XMLApplicationProfile.ValidationResult res_F = profile.validate(id, t);
Map<String, Result> results = res_F.results();
// int MaxScoreI2_01M_SPEC = (int) ((res_F.score()*getWeight())/100);
@ -564,9 +573,7 @@ class I2_01M_SPEC extends AbstractGuideline<Document> {
return new StandardResult(ress.score(), ress.status(), (List<String>) ress.warnings(), (List<String>) ress.errors(), ress.internalError());
} catch (Exception e) {
System.out.println(e.getMessage());
System.out.println(e);
e.printStackTrace();
logger.error("", e);
}
return null;
}
@ -604,6 +611,9 @@ class I2_01M_SPEC extends AbstractGuideline<Document> {
class R1_01M_SPEC extends AbstractGuideline<Document> {
private static final Logger logger = LoggerFactory.getLogger(R1_01M_SPEC.class);
public R1_01M_SPEC() { super("Plurality of accurate and relevant attributes are provided to allow reuse", 3*4); }
@Override
@ -637,9 +647,7 @@ class R1_01M_SPEC extends AbstractGuideline<Document> {
return new StandardResult(ress.score(), ress.status(), (List<String>) ress.warnings(), (List<String>) ress.errors(), ress.internalError());
} catch (Exception e) {
System.out.println(e.getMessage());
System.out.println(e);
e.printStackTrace();
logger.error("", e);
}
return null;
}
@ -677,6 +685,9 @@ class R1_01M_SPEC extends AbstractGuideline<Document> {
class R1_2_01M_SPEC extends AbstractGuideline<Document> {
private static final Logger logger = LoggerFactory.getLogger(R1_2_01M_SPEC.class);
public R1_2_01M_SPEC() { super("Metadata includes provenance information according to a cross-community language", 2*5); }
@Override
@ -711,9 +722,7 @@ class R1_2_01M_SPEC extends AbstractGuideline<Document> {
return new StandardResult(ress.score(), ress.status(), (List<String>) ress.warnings(), (List<String>) ress.errors(), ress.internalError());
} catch (Exception e) {
System.out.println(e.getMessage());
System.out.println(e);
e.printStackTrace();
logger.error("", e);
}
return null;
}

5
src/main/java/eu/dnetlib/validator2/validation/utils/ISOLangCodes.java
View File

@ -4,6 +4,7 @@ package eu.dnetlib.validator2.validation.utils;
import org.apache.commons.io.IOUtils;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
@ -20,10 +21,10 @@ public class ISOLangCodes {
private static void loadLangCodes() {
try (InputStream in = MediaTypes.class.getClassLoader().getResourceAsStream("iso639XLangCodes.csv")) {
//TODO:Remove the regex
List<String> l = Arrays.asList(IOUtils.toString(in, "UTF-8").split("\\s*,\\s*"));
List<String> l = Arrays.asList(IOUtils.toString(in, StandardCharsets.UTF_8).split("\\s*,\\s*"));
langs = new HashSet<>(l);
}
catch (Exception e) {}
catch (Exception e) {} // We may get an NPE.
}

16
src/test/java/eu/dnetlib/validator2/engine/Test.java
View File

@ -4,6 +4,7 @@ import eu.dnetlib.validator2.validation.XMLApplicationProfile;
import eu.dnetlib.validator2.validation.guideline.Guideline;
import eu.dnetlib.validator2.validation.guideline.openaire.LiteratureGuidelinesV3Profile;
import groovy.xml.DOMBuilder;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import java.io.FileReader;
@ -13,6 +14,9 @@ import java.util.stream.Collectors;
public class Test {
private static final org.slf4j.Logger logger = LoggerFactory.getLogger(Test.class);
private static final String[] FILES = new String[] {
// "src/test/resources/openaireguidelinesV3/dia.library.tuc.gr/Record_21811.xml",
// "src/test/resources/openaireguidelinesV3/cris.vtt.fi/01.xml",
@ -23,28 +27,26 @@ public class Test {
public static void main(String[] args) {
// String xmlFile = args[0];
LiteratureGuidelinesV3Profile profile = new LiteratureGuidelinesV3Profile();
System.out.println("Max score: " + profile.maxScore());
logger.info("Max score: " + profile.maxScore());
Map<String, Double> scorePerDoc = new LinkedHashMap<>();
for (String file: FILES) {
try {
System.out.println("Processing \"" + file + "\"");
logger.info("Processing \"" + file + "\"");
Document doc = DOMBuilder.parse(new FileReader(file), false, true, true);
XMLApplicationProfile.ValidationResult result = profile.validate(file, doc);
scorePerDoc.put(file, result.score());
Map<String, Guideline.Result> results = result.results();
for (Map.Entry entry : results.entrySet()) {
System.out.println(entry.getKey() + " = " + entry.getValue());
logger.info(entry.getKey() + " = " + entry.getValue());
}
}
catch(Exception e) {
System.out.println(e.getMessage());
System.out.println(e);
e.printStackTrace();
logger.error("", e);
}
}
String printout = scorePerDoc.entrySet().stream().
map(entry -> entry.getValue() + ": " + entry.getKey()).collect(Collectors.joining("\n"));
System.out.println(printout);
logger.info(printout);
}
}

37
src/test/java/eu/dnetlib/validator2/engine/Test_FAIR.java
View File

@ -1,24 +1,23 @@
package eu.dnetlib.validator2.engine;
//import com.google.gson.Gson;
import eu.dnetlib.validator2.validation.XMLApplicationProfile;
import eu.dnetlib.validator2.validation.guideline.Guideline;
import eu.dnetlib.validator2.validation.guideline.StandardResult;
import eu.dnetlib.validator2.validation.guideline.openaire.FAIR_Data_GuidelinesProfile;
import groovy.xml.DOMBuilder;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import java.io.FileReader;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.OptionalDouble;
import java.util.StringJoiner;
import java.util.function.ToDoubleFunction;
import java.util.stream.Collectors;
import java.util.stream.DoubleStream;
public class Test_FAIR {
private static final org.slf4j.Logger logger = LoggerFactory.getLogger(Test_FAIR.class);
private static final String[] FILES = new String[]{
"src/test/resources/openaireguidelinesV3/dia.library.tuc.gr/Record_21811.xml",
"src/test/resources/openaireguidelinesV3/cris.vtt.fi/03.xml",
@ -32,27 +31,25 @@ public class Test_FAIR {
public static void main(String[] args) {
// String xmlFile = args[0];
FAIR_Data_GuidelinesProfile profile = new FAIR_Data_GuidelinesProfile();
System.out.println("Max score: " + profile.maxScore());
logger.info("Max score: " + profile.maxScore());
Map<String, Double> scorePerDoc = new LinkedHashMap<>();
int i = 1;
for (String file : FILES) {
try {
System.out.println("Processing \"" + file + "\"");
logger.info("Processing \"" + file + "\"");
Document doc = DOMBuilder.parse(new FileReader(file), false, true, true);
XMLApplicationProfile.ValidationResult result = profile.validate(file, doc);
scorePerDoc.put(file, result.score());
Map<String, Guideline.Result> results = result.results();
// for (Map.Entry entry : results.entrySet()) {
// System.out.println(entry.getKey() + " = " + entry.getValue());
// }
if ( logger.isDebugEnabled() ) {
for ( Map.Entry entry : results.entrySet() ) {
logger.debug(entry.getKey() + " = " + entry.getValue());
}
}
} catch (Exception e) {
System.out.println(e.getMessage());
System.out.println(e);
e.printStackTrace();
logger.error("", e);
}
// System.out.println("\n\n\n\n");
}
// Individual scores
@ -60,13 +57,11 @@ public class Test_FAIR {
map(entry -> entry.getValue() + ": " + entry.getKey()).collect(Collectors.joining("\n"));
// Average Score
double FinalScore = scorePerDoc.entrySet().stream().mapToDouble(entry -> entry.getValue()).average().getAsDouble();
System.out.println(printout);
System.out.println("\nValidation Score: "+FinalScore);
// TotalScore.forEach(System.out::println);
OptionalDouble optionalFinalScore = scorePerDoc.values().stream().mapToDouble(aDouble -> aDouble).average();
double finalScore = (optionalFinalScore.isPresent() ? optionalFinalScore.getAsDouble() : -1 );
logger.info(printout);
logger.info("\nValidation Score: " + finalScore);
}
}

33
src/test/java/eu/dnetlib/validator2/engine/Test_v4.java
View File

@ -2,17 +2,23 @@ package eu.dnetlib.validator2.engine;
import eu.dnetlib.validator2.validation.XMLApplicationProfile;
import eu.dnetlib.validator2.validation.guideline.Guideline;
import eu.dnetlib.validator2.validation.guideline.openaire.AbstractOpenAireProfile;
import eu.dnetlib.validator2.validation.guideline.openaire.LiteratureGuidelinesV4Profile;
import groovy.xml.DOMBuilder;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import java.io.FileReader;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.OptionalDouble;
import java.util.stream.Collectors;
public class Test_v4 {
private static final org.slf4j.Logger logger = LoggerFactory.getLogger(Test_v4.class);
private static final String[] FILES = new String[] {
"src/test/resources/openaireguidelinesV4/v4_literature_all_invalid_guidelines_record.xml",
// "src/test/resources/openaireguidelinesV4/v4_literature_all_guidelines_record.xml",
@ -22,41 +28,40 @@ public class Test_v4 {
public static void main(String[] args) {
// String xmlFile = args[0];
LiteratureGuidelinesV4Profile profile = new LiteratureGuidelinesV4Profile();
System.out.println("Max score: " + profile.maxScore());
AbstractOpenAireProfile profile = new LiteratureGuidelinesV4Profile();
logger.info("Max score: " + profile.maxScore());
Map<String, Double> scorePerDoc = new LinkedHashMap<>();
for (String file: FILES) {
try {
System.out.println("Processing \"" + file + "\"");
logger.info("Processing \"" + file + "\"");
Document doc = DOMBuilder.parse(new FileReader(file), false, true, true);
XMLApplicationProfile.ValidationResult result = profile.validate(file, doc);
scorePerDoc.put(file, result.score());
Map<String, Guideline.Result> results = result.results();
for (Map.Entry entry : results.entrySet()) {
if (entry.getKey().toString().contains("Date")) {
System.out.println(results.get(entry.getKey()).warnings().toString());
System.out.println(results.get(entry.getKey()).errors().toString());
System.out.println(entry.getKey() + " = " + entry.getValue());
System.out.println("\n");
logger.info("Warnings: " + results.get(entry.getKey()).warnings().toString());
logger.info("Errors: " + results.get(entry.getKey()).errors().toString());
logger.info("Result: " + entry.getKey() + " = " + entry.getValue() + "\n");
}
// System.out.println(entry.getKey() + " = " + entry.getValue());
logger.debug(entry.getKey() + " = " + entry.getValue());
}
}
catch(Exception e) {
System.out.println(e.getMessage());
System.out.println(e);
logger.error(e.getMessage());
e.printStackTrace();
}
}
// Individual scores
String printout = scorePerDoc.entrySet().stream().
map(entry -> entry.getValue() + ": " + entry.getKey()).collect(Collectors.joining("\n"));
// Average Score
double FinalScore = scorePerDoc.entrySet().stream().mapToDouble(entry -> entry.getValue()).average().getAsDouble();
System.out.println(printout);
System.out.println("\nValidation Score: "+FinalScore);
OptionalDouble optionalFinalScore = scorePerDoc.values().stream().mapToDouble(aDouble -> aDouble).average();
double finalScore = (optionalFinalScore.isPresent() ? optionalFinalScore.getAsDouble() : -1 );
logger.info(printout);
logger.info("\nValidation Score: " + finalScore);
}
}

25
src/test/resources/log4j2.properties
View File

@ -1,25 +0,0 @@
status = error
dest = err
name = PropertiesConfig
property.filename = target/validator_testing.log
appender.rolling.type = RollingFile
appender.rolling.name = RollingFile
appender.rolling.fileName = ${filename}
appender.rolling.filePattern = target/validator_testing -%d{MM-dd-yy-HH-mm-ss}-%i.log.gz
appender.rolling.layout.type = PatternLayout
appender.rolling.layout.pattern = %d %p %C{1.} [%t] %m%n
appender.rolling.policies.type = Policies
appender.rolling.policies.time.type = TimeBasedTriggeringPolicy
appender.rolling.policies.time.interval = 2
appender.rolling.policies.time.modulate = true
appender.rolling.policies.size.type = SizeBasedTriggeringPolicy
appender.rolling.policies.size.size=100MB
appender.rolling.strategy.type = DefaultRolloverStrategy
appender.rolling.strategy.max = 5
logger.rolling.name = eu.dnetlib.validator2
logger.rolling.additivity = false
logger.rolling.appenderRef.rolling.ref = RollingFile

41
src/test/resources/logback.xml Normal file
View File

@ -0,0 +1,41 @@
<configuration debug="false">
<shutdownHook class="ch.qos.logback.core.hook.DelayingShutdownHook"/> <!-- Default delay: 0ms (zero) -->
<!-- <Appenders>-->
<appender name="RollingFile" class="ch.qos.logback.core.rolling.RollingFileAppender">
<file>logs/ValidationEngine.log</file>
<rollingPolicy class="ch.qos.logback.core.rolling.FixedWindowRollingPolicy">
<fileNamePattern>logs/ValidationEngine.%i.log.zip</fileNamePattern>
<minIndex>1</minIndex>
<maxIndex>20</maxIndex>
</rollingPolicy>
<triggeringPolicy class="ch.qos.logback.core.rolling.SizeBasedTriggeringPolicy">
<maxFileSize>50MB</maxFileSize> <!-- Lower the size to check the "RollingFileAppender" during tests. -->
</triggeringPolicy>
<encoder>
<charset>UTF-8</charset>
<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS z} [%thread] %-5level %logger{36}.%M\(@%line\) - %msg%n</pattern>
</encoder>
</appender>
<appender name="Console" class="ch.qos.logback.core.ConsoleAppender">
<encoder>
<charset>UTF-8</charset>
<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS z} [%thread] %highlight(%-5level) %cyan(%logger{36}.%M\(@%line\)) - %msg%n</pattern>
</encoder>
</appender>
<!-- </Appenders>-->
<!-- <Loggers>-->
<root level="debug">
<appender-ref ref="Console" />
</root>
<logger name="eu.dnetlib.validator2" level="trace"/>
<!-- </Loggers>-->
</configuration>