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Merged
YvanOceanops merged 2 commits into from
Apr 22, 2026
Merged

V3.0.1 #46

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61c3df7
fix wrong java api version for deprecated R03 table read
Apr 22, 2026
459edbe
deactivate log file
Apr 22, 2026
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114 changes: 113 additions & 1 deletion file_checker_exec/.settings/org.eclipse.jdt.core.prefs
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@@ -1,10 +1,122 @@
eclipse.preferences.version=1
org.eclipse.jdt.core.builder.annotationPath.allLocations=disabled
org.eclipse.jdt.core.compiler.annotation.inheritNullAnnotations=disabled
org.eclipse.jdt.core.compiler.annotation.missingNonNullByDefaultAnnotation=ignore
org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jdt.annotation.NonNull
org.eclipse.jdt.core.compiler.annotation.nonnull.secondary=
org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annotation.NonNullByDefault
org.eclipse.jdt.core.compiler.annotation.nonnullbydefault.secondary=
org.eclipse.jdt.core.compiler.annotation.notowning=org.eclipse.jdt.annotation.NotOwning
org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nullable
org.eclipse.jdt.core.compiler.annotation.nullable.secondary=
org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled
org.eclipse.jdt.core.compiler.annotation.owning=org.eclipse.jdt.annotation.Owning
org.eclipse.jdt.core.compiler.annotation.resourceanalysis=disabled
org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.APILeak=warning
org.eclipse.jdt.core.compiler.problem.annotatedTypeArgumentToUnannotated=info
org.eclipse.jdt.core.compiler.problem.annotationSuperInterface=warning
org.eclipse.jdt.core.compiler.problem.autoboxing=ignore
org.eclipse.jdt.core.compiler.problem.comparingIdentical=warning
org.eclipse.jdt.core.compiler.problem.deadCode=warning
org.eclipse.jdt.core.compiler.problem.deprecation=warning
org.eclipse.jdt.core.compiler.problem.deprecationInDeprecatedCode=disabled
org.eclipse.jdt.core.compiler.problem.deprecationWhenOverridingDeprecatedMethod=disabled
org.eclipse.jdt.core.compiler.problem.discouragedReference=warning
org.eclipse.jdt.core.compiler.problem.emptyStatement=ignore
org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
org.eclipse.jdt.core.compiler.problem.explicitlyClosedAutoCloseable=ignore
org.eclipse.jdt.core.compiler.problem.fallthroughCase=ignore
org.eclipse.jdt.core.compiler.problem.fatalOptionalError=disabled
org.eclipse.jdt.core.compiler.problem.fieldHiding=ignore
org.eclipse.jdt.core.compiler.problem.finalParameterBound=warning
org.eclipse.jdt.core.compiler.problem.finallyBlockNotCompletingNormally=warning
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.problem.hiddenCatchBlock=warning
org.eclipse.jdt.core.compiler.problem.includeNullInfoFromAsserts=disabled
org.eclipse.jdt.core.compiler.problem.incompatibleNonInheritedInterfaceMethod=warning
org.eclipse.jdt.core.compiler.problem.incompatibleOwningContract=warning
org.eclipse.jdt.core.compiler.problem.incompleteEnumSwitch=warning
org.eclipse.jdt.core.compiler.problem.indirectStaticAccess=ignore
org.eclipse.jdt.core.compiler.problem.insufficientResourceAnalysis=warning
org.eclipse.jdt.core.compiler.problem.localVariableHiding=ignore
org.eclipse.jdt.core.compiler.problem.methodWithConstructorName=warning
org.eclipse.jdt.core.compiler.problem.missingDefaultCase=ignore
org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=ignore
org.eclipse.jdt.core.compiler.problem.missingEnumCaseDespiteDefault=disabled
org.eclipse.jdt.core.compiler.problem.missingHashCodeMethod=ignore
org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotation=ignore
org.eclipse.jdt.core.compiler.problem.missingOverrideAnnotationForInterfaceMethodImplementation=enabled
org.eclipse.jdt.core.compiler.problem.missingSerialVersion=warning
org.eclipse.jdt.core.compiler.problem.missingSynchronizedOnInheritedMethod=ignore
org.eclipse.jdt.core.compiler.problem.noEffectAssignment=warning
org.eclipse.jdt.core.compiler.problem.noImplicitStringConversion=warning
org.eclipse.jdt.core.compiler.problem.nonExternalizedStringLiteral=ignore
org.eclipse.jdt.core.compiler.problem.nonnullParameterAnnotationDropped=warning
org.eclipse.jdt.core.compiler.problem.nonnullTypeVariableFromLegacyInvocation=warning
org.eclipse.jdt.core.compiler.problem.nullAnnotationInferenceConflict=error
org.eclipse.jdt.core.compiler.problem.nullReference=warning
org.eclipse.jdt.core.compiler.problem.nullSpecViolation=error
org.eclipse.jdt.core.compiler.problem.nullUncheckedConversion=warning
org.eclipse.jdt.core.compiler.problem.overridingPackageDefaultMethod=warning
org.eclipse.jdt.core.compiler.problem.parameterAssignment=ignore
org.eclipse.jdt.core.compiler.problem.pessimisticNullAnalysisForFreeTypeVariables=warning
org.eclipse.jdt.core.compiler.problem.possibleAccidentalBooleanAssignment=ignore
org.eclipse.jdt.core.compiler.problem.potentialNullReference=ignore
org.eclipse.jdt.core.compiler.problem.potentiallyUnclosedCloseable=ignore
org.eclipse.jdt.core.compiler.problem.rawTypeReference=warning
org.eclipse.jdt.core.compiler.problem.redundantNullAnnotation=warning
org.eclipse.jdt.core.compiler.problem.redundantNullCheck=ignore
org.eclipse.jdt.core.compiler.problem.redundantSpecificationOfTypeArguments=ignore
org.eclipse.jdt.core.compiler.problem.redundantSuperinterface=ignore
org.eclipse.jdt.core.compiler.problem.reportMethodCanBePotentiallyStatic=ignore
org.eclipse.jdt.core.compiler.problem.reportMethodCanBeStatic=ignore
org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.problem.specialParameterHidingField=disabled
org.eclipse.jdt.core.compiler.problem.staticAccessReceiver=warning
org.eclipse.jdt.core.compiler.problem.suppressOptionalErrors=disabled
org.eclipse.jdt.core.compiler.problem.suppressWarnings=enabled
org.eclipse.jdt.core.compiler.problem.suppressWarningsNotFullyAnalysed=info
org.eclipse.jdt.core.compiler.problem.syntacticNullAnalysisForFields=disabled
org.eclipse.jdt.core.compiler.problem.syntheticAccessEmulation=ignore
org.eclipse.jdt.core.compiler.problem.terminalDeprecation=warning
org.eclipse.jdt.core.compiler.problem.typeParameterHiding=warning
org.eclipse.jdt.core.compiler.problem.unavoidableGenericTypeProblems=enabled
org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=ignore
org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
org.eclipse.jdt.core.compiler.problem.unlikelyCollectionMethodArgumentType=warning
org.eclipse.jdt.core.compiler.problem.unlikelyCollectionMethodArgumentTypeStrict=disabled
org.eclipse.jdt.core.compiler.problem.unlikelyEqualsArgumentType=info
org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=ignore
org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
org.eclipse.jdt.core.compiler.problem.unstableAutoModuleName=warning
org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownException=ignore
org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionExemptExceptionAndThrowable=enabled
org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionIncludeDocCommentReference=enabled
org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionWhenOverriding=disabled
org.eclipse.jdt.core.compiler.problem.unusedExceptionParameter=ignore
org.eclipse.jdt.core.compiler.problem.unusedImport=warning
org.eclipse.jdt.core.compiler.problem.unusedLabel=warning
org.eclipse.jdt.core.compiler.problem.unusedLocal=warning
org.eclipse.jdt.core.compiler.problem.unusedObjectAllocation=ignore
org.eclipse.jdt.core.compiler.problem.unusedParameter=ignore
org.eclipse.jdt.core.compiler.problem.unusedParameterIncludeDocCommentReference=enabled
org.eclipse.jdt.core.compiler.problem.unusedParameterWhenImplementingAbstract=disabled
org.eclipse.jdt.core.compiler.problem.unusedParameterWhenOverridingConcrete=disabled
org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
org.eclipse.jdt.core.compiler.problem.unusedTypeParameter=ignore
org.eclipse.jdt.core.compiler.problem.unusedWarningToken=warning
org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
org.eclipse.jdt.core.compiler.release=enabled
org.eclipse.jdt.core.compiler.source=1.8
org.eclipse.jdt.core.formatter.align_arrows_in_switch_on_columns=false
org.eclipse.jdt.core.formatter.align_assignment_statements_on_columns=false
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11 changes: 10 additions & 1 deletion file_checker_exec/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>fr.ifremer</groupId>
<artifactId>file_checker_exec</artifactId>
<version>3.0.0</version>
<version>3.0.1</version>

<name>Argo NetCDF file format checker</name>

Expand Down Expand Up @@ -161,6 +161,15 @@
</testResource>
</testResources>
<plugins>
<!-- Enforce Java 8 API compatibility -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.13.0</version>
<configuration>
<release>8</release>
</configuration>
</plugin>
<!--Rename the log4j2 xml production file-->
<plugin>
<groupId>com.coderplus.maven.plugins</groupId>
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12 changes: 7 additions & 5 deletions file_checker_exec/src/main/java/fr/coriolis/checker/specs/ArgoFileSpecification.java
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Expand Up @@ -2372,7 +2372,7 @@ private void addParamEntries(List<R03DeprecatedEntry> entries, String paramName,
String oldValue, String status, String message, String version) {

// Always: base + ADJUSTED
List<String> names = new ArrayList<>(List.of(paramName, paramName + "_ADJUSTED"));
List<String> names = new ArrayList<>(Arrays.asList(paramName, paramName + "_ADJUSTED"));

// ADJUSTED_ERROR — excluded for min/max/name attributes
boolean excludeFromAdjustedError = attributeKey.equals("valid_min") || attributeKey.equals("valid_max")
Expand All @@ -2385,7 +2385,7 @@ private void addParamEntries(List<R03DeprecatedEntry> entries, String paramName,

// STD & MED family — units and fillValue share the same oldValue
if (attributeKey.equals("units") || attributeKey.equals("fillValue")) {
names.addAll(List.of(paramName + "_STD", paramName + "_MED", paramName + "_STD_ADJUSTED",
names.addAll(Arrays.asList(paramName + "_STD", paramName + "_MED", paramName + "_STD_ADJUSTED",
paramName + "_MED_ADJUSTED", paramName + "_STD_ADJUSTED_ERROR", paramName + "_MED_ADJUSTED_ERROR"));
}

Expand All @@ -2399,9 +2399,11 @@ private void addParamEntries(List<R03DeprecatedEntry> entries, String paramName,

// long_name — STD/MED variants get a prefixed oldValue
if (attributeKey.equals("long_name")) {
Map<String, String> longNameVariants = Map.of(paramName + "_STD", "Standard deviation of " + oldValue,
paramName + "_MED", "Median value of " + oldValue, paramName + "_STD_ADJUSTED",
"Standard deviation of " + oldValue, paramName + "_MED_ADJUSTED", "Median value of " + oldValue);
Map<String, String> longNameVariants = new HashMap<>();
longNameVariants.put(paramName + "_STD", "Standard deviation of " + oldValue);
longNameVariants.put(paramName + "_MED", "Median value of " + oldValue);
longNameVariants.put(paramName + "_STD_ADJUSTED", "Standard deviation of " + oldValue);
longNameVariants.put(paramName + "_MED_ADJUSTED", "Median value of " + oldValue);
longNameVariants.forEach((name, derivedValue) -> entries
.add(new R03DeprecatedEntry(name, attributeKey, derivedValue, status, message)));
}
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3 changes: 0 additions & 3 deletions file_checker_exec/src/main/java/fr/coriolis/checker/tables/ArgoNVSReferenceTable.java
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Expand Up @@ -127,9 +127,6 @@ public static void initializeFromInternet(String baseUrl) {
} catch (IOException e) {
stderr.println("Table file not found on NVS : " + tableUrl + " (" + e.getMessage() + ")");
break;
} catch (InterruptedException e) {
stderr.println("Error while retrieving table on NVS : " + tableUrl + " (" + e.getMessage() + ")");
break;
}
}

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52 changes: 27 additions & 25 deletions file_checker_exec/src/main/java/fr/coriolis/checker/utils/NetUtils.java
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Expand Up @@ -2,35 +2,37 @@

import java.io.IOException;
import java.io.InputStream;
import java.net.URI;
import java.net.http.HttpClient;
import java.net.http.HttpRequest;
import java.net.http.HttpResponse;
import java.net.http.HttpResponse.BodyHandlers;
import java.time.Duration;
import java.net.HttpURLConnection;
import java.net.URL;

public final class NetUtils {
private static final HttpClient httpClient = HttpClient.newBuilder().followRedirects(HttpClient.Redirect.NORMAL)
.build(); // need to automatically follow redirection

public static InputStream openInputStream(String url) throws IOException, InterruptedException {

// create request
HttpRequest req = HttpRequest.newBuilder(URI.create(url)).timeout(Duration.ofSeconds(15))
.header("Accept", "application/ld+json").GET().build();

// send request :
HttpResponse<InputStream> res = httpClient.send(req, BodyHandlers.ofInputStream());

// client error response
if (res.statusCode() >= 400) {
// close stream if serveur send one
try (InputStream body = res.body()) {
/* ensure release */ }
throw new IOException("HTTP " + res.statusCode() + " for " + url);
private static final int TIMEOUT_MS = 15_000;

public static InputStream openInputStream(String url) throws IOException {

HttpURLConnection conn = (HttpURLConnection) new URL(url).openConnection();
conn.setInstanceFollowRedirects(true); // follow redirects
conn.setConnectTimeout(TIMEOUT_MS);
conn.setReadTimeout(TIMEOUT_MS);
conn.setRequestProperty("Accept", "application/ld+json");
conn.setRequestMethod("GET");
conn.connect();

int status = conn.getResponseCode();

// client/server error response
if (status >= 400) {
try (InputStream err = conn.getErrorStream()) {
if (err != null) {
byte[] buf = new byte[1024];
while (err.read(buf) != -1) {
/* drain */ }
}
}
throw new IOException("HTTP " + status + " for " + url);
}

return res.body();
return conn.getInputStream();
}

}
4 changes: 2 additions & 2 deletions file_checker_exec/src/main/resources/log4j2-prod.xml
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Expand Up @@ -28,11 +28,11 @@
<Loggers>
<Logger name="ArgoFileSpecification" level="warn" additivity="false">
<AppenderRef ref="Console"/>
<AppenderRef ref="File"/>
<AppenderRef ref="File" level="off"/>
</Logger>
<Logger name="ValidateSubmit" level="warn" additivity="false">
<AppenderRef ref="Console"/>
<AppenderRef ref="File"/>
<AppenderRef ref="File" level="off"/>
</Logger>
<Root level="off" />

Expand Down
7 changes: 4 additions & 3 deletions file_checker_exec/src/test/java/fr/coriolis/checker/e2etests/TestsUtils.java
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Expand Up @@ -51,12 +51,13 @@ private static String executeJarAndGetResult(String fileName, String dac, String
assertThat(TestsUtils.outputDir).exists().isDirectory().as("output directory should exist");

// ACT
List<String> command = new ArrayList<>(List.of("java", "-jar", TestsUtils.jarPath));
if (options != null && !options.isBlank()) {
List<String> command = new ArrayList<>(Arrays.asList("java", "-jar", TestsUtils.jarPath));
if (options != null && !options.trim().isEmpty()) {
// split eventual multiple options
command.addAll(Arrays.asList(options.split("\\s+")));
}
command.addAll(List.of(dac, TestsUtils.SPEC_DIR_PATH, TestsUtils.OUTPUT_DIR_PATH, inputDirPath, fileName));
command.addAll(
Arrays.asList(dac, TestsUtils.SPEC_DIR_PATH, TestsUtils.OUTPUT_DIR_PATH, inputDirPath, fileName));
ProcessBuilder builder = new ProcessBuilder(command);
builder.redirectErrorStream(true);
Process process = builder.start();
Expand Down
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