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Fix headless stdout flooding #645

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Fix headless stdout flooding #645

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9df4464
fix: add missing full local build deps
travisformayor Mar 25, 2026
17c876e
fix: update .gitignore for java sdkman
travisformayor Mar 25, 2026
e2d8b7a
fix: filter unread progress stdout noise in headless mode
travisformayor Mar 27, 2026
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ bin/iBioSim.jar
.settings/
**/.project
/.metadata/
.sdkmanrc

# intellij artefacts
out
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4 changes: 3 additions & 1 deletion analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java
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Expand Up @@ -876,9 +876,11 @@ public void run () {
String line = br.readLine ();
if (line == null) break;
if (name.equals("stdin")) {
boolean isProgress = false;
try {
if (line.contains("Time")) {
time = Double.parseDouble(line.substring(line.indexOf('=') + 1, line.length()));
isProgress = true;
if (oldTime > time) {
runNum++;
}
Expand All @@ -900,7 +902,7 @@ public void run () {
if (parent!=null) {
message.setInteger(prog);
parent.send(RequestType.REQUEST_PROGRESS, message);
Comment on lines 903 to 904
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Copilot AI Mar 27, 2026

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In the non-GUI path (parent == null), progress lines are now suppressed, but in the GUI path you still call parent.send(REQUEST_PROGRESS, ...) for every line read, even when the line wasn't parsed as a progress update (prog remains stale). This can create unnecessary IPC traffic and repeated identical progress events. Consider sending REQUEST_PROGRESS only when a progress update was successfully parsed (e.g., gate the send on isProgress).

Suggested change
message.setInteger(prog);
parent.send(RequestType.REQUEST_PROGRESS, message);
if (isProgress) {
message.setInteger(prog);
parent.send(RequestType.REQUEST_PROGRESS, message);
}

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} else{
} else if (!isProgress) {
System.out.println(line);
}
} else {
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23 changes: 22 additions & 1 deletion dataModels/pom.xml
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Expand Up @@ -24,7 +24,7 @@
<repository>
<id>osgeo</id>
<name>osgeo</name>
<url>http://download.osgeo.org/webdav/geotools/</url>
<url>https://download.osgeo.org/webdav/geotools/</url>
</repository>
<repository>
<id>alfresco</id>
Expand Down Expand Up @@ -82,6 +82,27 @@
<version>1.7-SNAPSHOT</version>
</dependency>

<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.5.3</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
<version>4.4.6</version>
</dependency>
<dependency>
Comment on lines +91 to +95
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Copilot AI Mar 27, 2026

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httpclient already brings in a compatible httpcore transitively. Declaring httpcore explicitly here is redundant unless you're intentionally overriding the transitive version; if you do need to pin it, it would help to add a brief comment explaining why. Otherwise consider removing the direct httpcore dependency to reduce version-locking and future maintenance overhead.

Suggested change
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
<version>4.4.6</version>
</dependency>
<dependency>

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<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.7</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>18.0</version>
Comment on lines +98 to +103
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Copilot AI Mar 27, 2026

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The newly added dependency versions (gson 2.7 and guava 18.0) are quite old and are commonly flagged by vulnerability scanners / have many fixes in newer releases. If there isn't a compatibility constraint forcing these versions, consider upgrading to more recent releases (or centralizing the versions in the parent POM) to reduce security and maintenance risk.

Suggested change
<version>2.7</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>18.0</version>
<version>2.10.1</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>32.1.3-jre</version>

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</dependency>

<dependency>
<groupId>net.sf.trove4j</groupId>
<artifactId>trove4j</artifactId>
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