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Merged
axlbonnet merged 8 commits into from
Nov 7, 2025
Merged

Release 1.2 #19

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7ed24f3
target next release : 1.2 (#14)
axlbonnet Sep 29, 2025
2f21714
typo in snapshot version
axlbonnet Sep 29, 2025
8f802da
modif pom et exit code
gwen-creatis Oct 22, 2025
28591cf
modif pom et exit code
gwen-creatis Oct 22, 2025
4bbe0f9
Merge pull request #16 from gwen-creatis/rest-error-new
axlbonnet Oct 22, 2025
329d803
correct killed job finalization
axlbonnet Oct 22, 2025
0dc6ae4
Merge pull request #17 from axlbonnet/correctExitStatus
axlbonnet Oct 22, 2025
4f4eb3c
[noci] prepare release 1.2 (#18)
axlbonnet Nov 7, 2025
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4 changes: 2 additions & 2 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@

<groupId>fr.insalyon.creatis</groupId>
<artifactId>gasw-batch-plugin</artifactId>
<version>1.1</version>
<version>1.2</version>
<packaging>jar</packaging>

<name>GASW-Batch-Plugin</name>
Expand All @@ -14,7 +14,7 @@
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>21</maven.compiler.source>
<maven.compiler.target>21</maven.compiler.target>
<gasw-version>4.2</gasw-version>
<gasw-version>4.3</gasw-version>
</properties>

<licenses>
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1 change: 1 addition & 0 deletions src/main/java/fr/insalyon/creatis/gasw/executor/batch/BatchMonitor.java
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Expand Up @@ -17,19 +17,19 @@
import lombok.extern.slf4j.Slf4j;

@Slf4j
final public class BatchMonitor extends GaswMonitor {

@Getter
@Setter
private BatchManager manager;
@Setter
private boolean stop = false;

public BatchMonitor() {
super();
}

private boolean notRunningJob(GaswStatus s) {

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Parameter 's' is not assigned and could be declared final 

Reports method and constructor parameters that can be made final because they are never reassigned within the body of the method.

This rule ignores unused parameters so as not to overlap with the rule {% rule java/bestpractices/UnusedFormalParameter %}.
It will also ignore the parameters of abstract methods.

MethodArgumentCouldBeFinal (Priority: 3, Ruleset: Code Style)
https://docs.pmd-code.org/snapshot/pmd_rules_java_codestyle.html#methodargumentcouldbefinal
return s != GaswStatus.RUNNING
&& s != GaswStatus.QUEUED
&& s != GaswStatus.UNDEFINED
Expand All @@ -37,7 +37,7 @@
}

@Override
public void run() {

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The method 'run()' has a cyclomatic complexity of 10. 

The complexity of methods directly affects maintenance costs and readability. Concentrating too much decisional logic
in a single method makes its behaviour hard to read and change.

Cyclomatic complexity assesses the complexity of a method by counting the number of decision points in a method,
plus one for the method entry. Decision points are places where the control flow jumps to another place in the
program. As such, they include all control flow statements, such as `if`, `while`, `for`, and `case`. For more
details on the calculation, see the documentation {% jdoc java::lang.java.metrics.JavaMetrics#CYCLO %}.

Generally, numbers ranging from 1-4 denote low complexity, 5-7 denote moderate complexity, 8-10 denote
high complexity, and 11+ is very high complexity. By default, this rule reports methods with a complexity >= 10.
Additionally, classes with many methods of moderate complexity get reported as well once the total of their
methods' complexities reaches 80, even if none of the methods was directly reported.

Reported methods should be broken down into several smaller methods. Reported classes should probably be broken down
into subcomponents.

CyclomaticComplexity (Priority: 3, Ruleset: Design)
https://docs.pmd-code.org/snapshot/pmd_rules_java_design.html#cyclomaticcomplexity

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The method 'run()' has a cognitive complexity of 22, current threshold is 15 

Methods that are highly complex are difficult to read and more costly to maintain. If you include too much decisional
logic within a single method, you make its behavior hard to understand and more difficult to modify.

Cognitive complexity is a measure of how difficult it is for humans to read and understand a method. Code that contains
a break in the control flow is more complex, whereas the use of language shorthands doesn't increase the level of
complexity. Nested control flows can make a method more difficult to understand, with each additional nesting of the
control flow leading to an increase in cognitive complexity.

Information about Cognitive complexity can be found in the original paper here:
<https://www.sonarsource.com/docs/CognitiveComplexity.pdf>

By default, this rule reports methods with a complexity of 15 or more. Reported methods should be broken down into less
complex components.

CognitiveComplexity (Priority: 3, Ruleset: Design)
https://docs.pmd-code.org/snapshot/pmd_rules_java_design.html#cognitivecomplexity
while ( ! stop) {
verifySignaledJobs();
try {
Expand All @@ -55,7 +55,7 @@
}

jobDAO.update(daoJob);
new BatchOutputParser(job).start();

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Avoid instantiating new objects inside loops 

New objects created within loops should be checked to see if they can created outside them and reused.

AvoidInstantiatingObjectsInLoops (Priority: 3, Ruleset: Performance)
https://docs.pmd-code.org/snapshot/pmd_rules_java_performance.html#avoidinstantiatingobjectsinloops

} else if (status == GaswStatus.RUNNING) {
updateJob(daoJob, status);
Expand All @@ -74,7 +74,7 @@
}

@Override
public synchronized void add(final String jobID, final String symbolicName, final String fileName, final String parameters) throws GaswException {

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Rather than using a lot of String arguments, consider using a container object for those values. 

When you write a public method, you should be thinking in terms of an API. If your method is public, it means other class
will use it, therefore, you want (or need) to offer a comprehensive and evolutive API. If you pass a lot of information
as a simple series of Strings, you may think of using an Object to represent all those information. You'll get a simpler
API (such as doWork(Workload workload), rather than a tedious series of Strings) and more importantly, if you need at some
point to pass extra data, you'll be able to do so by simply modifying or extending Workload without any modification to
your API.

UseObjectForClearerAPI (Priority: 3, Ruleset: Design)
https://docs.pmd-code.org/snapshot/pmd_rules_java_design.html#useobjectforclearerapi
final Job job = new Job(jobID, GaswConfiguration.getInstance().getSimulationID(),
GaswStatus.QUEUED, symbolicName, fileName, parameters,
Constants.EXECUTOR_NAME);
Expand All @@ -84,7 +84,7 @@
log.info("Adding job: {}", jobID);
}

public synchronized void stopMonitor(boolean force) throws InterruptedException {

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Parameter 'force' is not assigned and could be declared final 

Reports method and constructor parameters that can be made final because they are never reassigned within the body of the method.

This rule ignores unused parameters so as not to overlap with the rule {% rule java/bestpractices/UnusedFormalParameter %}.
It will also ignore the parameters of abstract methods.

MethodArgumentCouldBeFinal (Priority: 3, Ruleset: Code Style)
https://docs.pmd-code.org/snapshot/pmd_rules_java_codestyle.html#methodargumentcouldbefinal
if (force) {
interrupt();
} else {
Expand All @@ -98,7 +98,7 @@

// kill jobs that are still running (context of soft-kill)
try {
for (Job job : jobDAO.getActiveJobs()) {

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Local variable 'job' could be declared final 

A local variable assigned only once can be declared final.

LocalVariableCouldBeFinal (Priority: 3, Ruleset: Code Style)
https://docs.pmd-code.org/snapshot/pmd_rules_java_codestyle.html#localvariablecouldbefinal
kill(job);
}
} catch (DAOException e) {
Expand All @@ -122,7 +122,7 @@
}

@Override
protected void kill(Job job) {

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Parameter 'job' is not assigned and could be declared final 

Reports method and constructor parameters that can be made final because they are never reassigned within the body of the method.

This rule ignores unused parameters so as not to overlap with the rule {% rule java/bestpractices/UnusedFormalParameter %}.
It will also ignore the parameters of abstract methods.

MethodArgumentCouldBeFinal (Priority: 3, Ruleset: Code Style)
https://docs.pmd-code.org/snapshot/pmd_rules_java_codestyle.html#methodargumentcouldbefinal
final BatchJob batchJob = manager.getJob(job.getId());

if (batchJob != null) {
Expand All @@ -133,6 +133,7 @@
log.info("Job {} successfully killed!", job.getId());

updateJob(job, GaswStatus.DELETED);
new BatchOutputParser(batchJob).start();

} catch (GaswException e) {
log.warn("Failed to kill job {}", job.getId());
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22 changes: 2 additions & 20 deletions src/main/java/fr/insalyon/creatis/gasw/executor/batch/BatchOutputParser.java
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Expand Up @@ -34,28 +34,10 @@ public GaswOutput getGaswOutput() throws GaswException {
if (job.getStatus() != GaswStatus.DELETED) {
exitCode = parseStdOut(stdOut);
exitCode = parseStdErr(stdErr, exitCode);

switch (exitCode) {
case 0:
gaswExitCode = GaswExitCode.SUCCESS;
break;
case 1:
gaswExitCode = GaswExitCode.ERROR_READ_GRID;
break;
case 2:
gaswExitCode = GaswExitCode.ERROR_WRITE_GRID;
break;
case 6:
gaswExitCode = GaswExitCode.EXECUTION_FAILED;
break;
case 7:
gaswExitCode = GaswExitCode.ERROR_WRITE_LOCAL;
break;
default:
gaswExitCode = GaswExitCode.UNDEFINED;
}
gaswExitCode = GaswExitCode.fromExitCode(exitCode);
} else {
gaswExitCode = GaswExitCode.EXECUTION_CANCELED;
parseNonStdOut(GaswExitCode.EXECUTION_CANCELED.getExitCode());
}

return new GaswOutput(job.getId(), gaswExitCode, "", uploadedResults,
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