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fix(env): read environment via System.getenv instead of forking a subprocess (#117) #118

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Merged
tkuhn merged 2 commits into from
Jun 1, 2026
Merged

fix(env): read environment via System.getenv instead of forking a subprocess (#117) #118

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4ded0e3
fix(env): read environment via System.getenv instead of forking a sub…
tkuhn Jun 1, 2026
7178e33
test(env): mock the getRawEnv seam instead of getProcEnvironment
tkuhn Jun 1, 2026
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11 changes: 7 additions & 4 deletions src/main/java/com/knowledgepixels/query/TripleStore.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
package com.knowledgepixels.query;

import org.apache.commons.exec.environment.EnvironmentUtils;
import org.apache.http.client.config.RequestConfig;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpUriRequest;
Expand Down Expand Up @@ -79,10 +78,14 @@ public static TripleStore get() {
}

private TripleStore() throws IOException {
Map<String, String> env = EnvironmentUtils.getProcEnvironment();
endpointBase = env.get("ENDPOINT_BASE");
// Read directly from the JVM's in-memory environment block rather than via
// Apache Commons Exec's EnvironmentUtils.getProcEnvironment(), which forks a
// subprocess and can throw under memory pressure / a restart storm — leaving
// the singleton uninitialised. Same fragile mechanism that caused issue #117
// on the per-nanopub hot path (see Utils.getEnvString); retired here too.
endpointBase = System.getenv("ENDPOINT_BASE");
log.info("Endpoint base: {}", endpointBase);
endpointType = env.get("ENDPOINT_TYPE");
endpointType = System.getenv("ENDPOINT_TYPE");

getRepository("empty"); // Make sure empty repo exists
}
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33 changes: 25 additions & 8 deletions src/main/java/com/knowledgepixels/query/Utils.java
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Expand Up @@ -9,7 +9,6 @@
import java.util.Map;
import java.util.Properties;

import org.apache.commons.exec.environment.EnvironmentUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.client.config.CookieSpecs;
import org.apache.http.client.config.RequestConfig;
Expand Down Expand Up @@ -165,17 +164,35 @@ public static List<Value> getObjectsForPattern(RepositoryConnection conn, IRI gr
* @return environment variable value
*/
public static String getEnvString(String envVarName, String defaultValue) {
try {
String s = EnvironmentUtils.getProcEnvironment().get(envVarName);
if (s != null && !s.isEmpty()) {
return s;
}
} catch (Exception ex) {
log.info("Could not get environment variable", ex);
String s = getRawEnv(envVarName);
if (s != null && !s.isEmpty()) {
return s;
}
return defaultValue;
}

/**
* Reads a single environment variable from the JVM's in-memory environment
* block. The previous implementation used Apache Commons Exec's
* {@code EnvironmentUtils.getProcEnvironment()}, which forks a subprocess
* ({@code env}/{@code sh}) and parses its stdout on every call. That is neither
* thread-safe nor robust under load, and since {@link #getEnvString} is on the
* per-nanopub hot path ({@link FeatureFlags#fullRepoEnabled()} and friends,
* called from the 4-thread loading pool) an intermittently mangled read made
* {@code fullRepoEnabled()} evaluate to {@code false} and silently skip the
* full-repo write for individual nanopubs — leaving {@code full} behind
* {@code meta} undetectably (issue #117).
*
* <p>Extracted as a package-private seam because {@link System} static methods
* cannot be mocked directly with Mockito; tests stub this instead.
*
* @param envVarName environment variable name
* @return the raw value, or {@code null} if unset
*/
static String getRawEnv(String envVarName) {
return System.getenv(envVarName);
}

/**
* Returns the system environment variable content as an integer for the given environment variable name.
*
Expand Down
36 changes: 14 additions & 22 deletions src/test/java/com/knowledgepixels/query/UtilsTest.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
package com.knowledgepixels.query;

import com.github.jsonldjava.shaded.com.google.common.hash.Hashing;
import org.apache.commons.exec.environment.EnvironmentUtils;
import org.apache.http.client.config.RequestConfig;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Value;
Expand All @@ -14,7 +13,6 @@
import org.mockito.Mockito;
import org.nanopub.vocabulary.NPA;

import java.io.IOException;
import java.lang.reflect.Field;
import java.nio.charset.StandardCharsets;
import java.util.HashMap;
Expand Down Expand Up @@ -128,24 +126,20 @@ void getObjectsForPattern() {
@Test
void getEnvString() {
final String defaultValue = "default";
final String mockValueString = "value";

Map<String, String> mockEnv = new HashMap<>();
String mockValueString = "value";
mockEnv.put("EXISTING_VAR", mockValueString);
mockEnv.put("EMPTY_VAR", "");
mockEnv.put("NULL_VAR", null);

try (MockedStatic<EnvironmentUtils> mockedEnvUtils = Mockito.mockStatic(EnvironmentUtils.class)) {
mockedEnvUtils.when(EnvironmentUtils::getProcEnvironment).thenReturn(mockEnv);
// getEnvString now reads the env via the Utils.getRawEnv seam (System.getenv
// cannot be mocked directly — see #117). CALLS_REAL_METHODS keeps getEnvString real.
try (MockedStatic<Utils> mockedUtils = Mockito.mockStatic(Utils.class, Mockito.CALLS_REAL_METHODS)) {
mockedUtils.when(() -> Utils.getRawEnv("EXISTING_VAR")).thenReturn(mockValueString);
mockedUtils.when(() -> Utils.getRawEnv("EMPTY_VAR")).thenReturn("");
mockedUtils.when(() -> Utils.getRawEnv("NULL_VAR")).thenReturn(null);
mockedUtils.when(() -> Utils.getRawEnv("NON_EXISTING_VAR")).thenReturn(null);

assertEquals(mockValueString, Utils.getEnvString("EXISTING_VAR", defaultValue));
assertEquals(defaultValue, Utils.getEnvString("NON_EXISTING_VAR", defaultValue));
assertEquals(defaultValue, Utils.getEnvString("EMPTY_VAR", defaultValue));
assertEquals(defaultValue, Utils.getEnvString("NULL_VAR", defaultValue));

mockedEnvUtils.when(EnvironmentUtils::getProcEnvironment).thenThrow(IOException.class);
assertEquals(defaultValue, Utils.getEnvString("EXISTING_VAR", defaultValue));

}
}

Expand All @@ -156,14 +150,12 @@ void getEnvInt() {
final int validInt = Integer.parseInt(validIntValue);
final String invalidIntValue = "not_an_int";

Map<String, String> mockEnv = new HashMap<>();
mockEnv.put("VALID_INT", validIntValue);
mockEnv.put("INVALID_INT", invalidIntValue);
mockEnv.put("EMPTY_VAR", "");
mockEnv.put("NULL_VAR", null);

try (MockedStatic<EnvironmentUtils> mockedEnvUtils = Mockito.mockStatic(EnvironmentUtils.class)) {
mockedEnvUtils.when(EnvironmentUtils::getProcEnvironment).thenReturn(mockEnv);
try (MockedStatic<Utils> mockedUtils = Mockito.mockStatic(Utils.class, Mockito.CALLS_REAL_METHODS)) {
mockedUtils.when(() -> Utils.getRawEnv("VALID_INT")).thenReturn(validIntValue);
mockedUtils.when(() -> Utils.getRawEnv("INVALID_INT")).thenReturn(invalidIntValue);
mockedUtils.when(() -> Utils.getRawEnv("EMPTY_VAR")).thenReturn("");
mockedUtils.when(() -> Utils.getRawEnv("NULL_VAR")).thenReturn(null);
mockedUtils.when(() -> Utils.getRawEnv("NON_EXISTING_VAR")).thenReturn(null);

assertEquals(validInt, Utils.getEnvInt("VALID_INT", defaultValue));
assertEquals(defaultValue, Utils.getEnvInt("NON_EXISTING_VAR", defaultValue));
Expand Down