ScanCommand.java

1 
package org.egothor.methodatlas.command;
2
3 
import java.io.IOException;
4 
import java.io.PrintWriter;
5 
import java.nio.file.Path;
6 
import java.nio.file.Paths;
7 
import java.time.Instant;
8 
import java.util.List;
9 
import java.util.logging.Level;
10 
import java.util.logging.Logger;
11
12 
import org.egothor.methodatlas.AiResultCache;
13 
import org.egothor.methodatlas.emit.ClassificationOverride;
14 
import org.egothor.methodatlas.CliConfig;
15 
import org.egothor.methodatlas.emit.OutputMode;
16 
import org.egothor.methodatlas.emit.TestMethodSink;
17 
import org.egothor.methodatlas.ai.AiSuggestionEngine;
18 
import org.egothor.methodatlas.api.TestDiscovery;
19 
import org.egothor.methodatlas.api.TestDiscoveryConfig;
20 
import org.egothor.methodatlas.emit.OutputEmitter;
21
22 
/**
23 
 * CLI command handler for the default CSV and {@code -plain} output modes.
24 
 *
25 
 * <p>
26 
 * Scans one or more source roots, optionally enriches the output with AI
27 
 * suggestions, and emits test-method records incrementally to the supplied
28 
 * writer. When {@link CliConfig#detectSecrets()} is enabled, deterministic
29 
 * credential detection runs after the scan and writes a dedicated secrets CSV
30 
 * (see {@link CredentialDetectionRunner}).
31 
 * </p>
32 
 *
33 
 * @see org.egothor.methodatlas.emit.OutputEmitter
34 
 * @see SarifCommand
35 
 * @see GitHubAnnotationsCommand
36 
 */
37 
public final class ScanCommand implements Command {
38
39 
    private static final Logger LOG = Logger.getLogger(ScanCommand.class.getName());
40
41 
    private final CliConfig cliConfig;
42 
    private final TestDiscoveryConfig discoveryConfig;
43 
    private final AiSuggestionEngine aiEngine;
44 
    private final ClassificationOverride override;
45 
    private final AiResultCache aiCache;
46 
    private final PluginLoader pluginLoader;
47 
    private final ScanOrchestrator scanOrchestrator;
48
49 
    /**
50 
     * Creates a new scan command.
51 
     *
52 
     * @param cliConfig         full parsed CLI configuration
53 
     * @param discoveryConfig   discovery configuration forwarded to providers
54 
     * @param aiEngine          AI engine providing suggestions; {@code null}
55 
     *                          when AI is disabled
56 
     * @param override          human classification overrides
57 
     * @param aiCache           AI result cache
58 
     * @param pluginLoader      loader used to resolve and close
59 
     *                          {@link TestDiscovery} providers
60 
     * @param scanOrchestrator  scan-and-emit orchestrator used to process
61 
     *                          each root with the configured per-record sink
62 
     */
63 
    public ScanCommand(CliConfig cliConfig, TestDiscoveryConfig discoveryConfig,
64 
            AiSuggestionEngine aiEngine, ClassificationOverride override,
65 
            AiResultCache aiCache, PluginLoader pluginLoader,
66 
            ScanOrchestrator scanOrchestrator) {
67 
        this.cliConfig = cliConfig;
68 
        this.discoveryConfig = discoveryConfig;
69 
        this.aiEngine = aiEngine;
70 
        this.override = override;
71 
        this.aiCache = aiCache;
72 
        this.pluginLoader = pluginLoader;
73 
        this.scanOrchestrator = scanOrchestrator;
74 
    }
75
76 
    /**
77 
     * Runs the scan and emits output incrementally.
78 
     *
79 
     * @param out writer that receives all emitted output
80 
     * @return {@code 0} if all files were processed successfully, {@code 1} if
81 
     *         any file produced a parse or processing error
82 
     * @throws IOException if traversing a file tree fails
83 
     */
84 
    @Override
85 
    @SuppressWarnings("PMD.NPathComplexity") // combinatorial expansion of optional CSV columns; inherent to the format
86 
    public int execute(PrintWriter out) throws IOException {
87 2 1. execute : removed conditional - replaced equality check with true → KILLED
2. execute : removed conditional - replaced equality check with false → KILLED
 
        boolean aiEnabled = aiEngine != null;
88 4 1. execute : removed conditional - replaced equality check with true → SURVIVED
2. execute : removed conditional - replaced equality check with true → KILLED
3. execute : removed conditional - replaced equality check with false → KILLED
4. execute : removed conditional - replaced equality check with false → KILLED
 
        boolean confidenceEnabled = aiEnabled && cliConfig.aiOptions().confidence();
89 
        boolean contentHashEnabled = cliConfig.contentHash();
90 2 1. execute : removed conditional - replaced equality check with false → SURVIVED
2. execute : removed conditional - replaced equality check with true → TIMED_OUT
 
        List<Path> roots = cliConfig.paths().isEmpty() ? List.of(Paths.get(".")) : cliConfig.paths();
91
92 
        OutputEmitter emitter = new OutputEmitter(out, aiEnabled, confidenceEnabled, contentHashEnabled,
93 
                cliConfig.driftDetect(), cliConfig.emitSourceRoot());
94
95 2 1. execute : removed conditional - replaced equality check with false → KILLED
2. execute : removed conditional - replaced equality check with true → KILLED
 
        if (cliConfig.emitMetadata()) {
96 
            String version = ScanCommand.class.getPackage().getImplementationVersion();
97 
            String taxonomyInfo = new AiRuntimeBuilder().resolveTaxonomyInfo(cliConfig.aiOptions(), aiEnabled);
98 3 1. execute : removed conditional - replaced equality check with false → SURVIVED
2. execute : removed conditional - replaced equality check with true → SURVIVED
3. execute : removed call to org/egothor/methodatlas/emit/OutputEmitter::emitMetadata → KILLED
 
            emitter.emitMetadata(version != null ? version : "dev", Instant.now().toString(), taxonomyInfo);
99 
        }
100
101 1 1. execute : removed call to org/egothor/methodatlas/emit/OutputEmitter::emitCsvHeader → KILLED
 
        emitter.emitCsvHeader(cliConfig.outputMode());
102
103 
        final OutputMode mode = cliConfig.outputMode();
104 
        final boolean emitSourceRoot = cliConfig.emitSourceRoot();
105
106 
        // Credential detection: prepare() decides whether to fold triage into the
107 
        // per-class classification call (so the class source is sent once) and, when
108 
        // folding, returns the context the scan threads through; finish() emits.
109 2 1. execute : removed conditional - replaced equality check with false → SURVIVED
2. execute : removed conditional - replaced equality check with true → KILLED
 
        CredentialDetectionRunner secretRunner = cliConfig.detectSecrets()
110 
                ? new CredentialDetectionRunner(cliConfig, discoveryConfig, pluginLoader, scanOrchestrator, aiEngine)
111 
                : null;
112 2 1. execute : removed conditional - replaced equality check with false → SURVIVED
2. execute : removed conditional - replaced equality check with true → KILLED
 
        CredentialTriageContext secretCtx = secretRunner != null ? secretRunner.prepare(roots) : null;
113
114 
        // Scan each root with its own sink so the source_root value can be captured
115 
        // per root. When emitSourceRoot is false, sourceRoot is null and the column
116 
        // is omitted from the output.
117 
        List<TestDiscovery> providers = pluginLoader.loadProviders(discoveryConfig);
118 
        boolean hadErrors = false;
119 
        try {
120 
            for (Path root : roots) {
121 2 1. execute : removed conditional - replaced equality check with false → SURVIVED
2. execute : removed conditional - replaced equality check with true → SURVIVED
 
                String sourceRoot = emitSourceRoot ? ContentHasher.filePrefix(List.of(root)) : null;
122 
                TestMethodSink rootSink = (fqcn, method, beginLine, loc, contentHash, tags, displayName, suggestion) ->
123 1 1. lambda$execute$0 : removed call to org/egothor/methodatlas/emit/OutputEmitter::emit → KILLED
 
                        emitter.emit(mode, fqcn, method, loc, contentHash, tags, displayName, suggestion, sourceRoot);
124 2 1. execute : removed conditional - replaced equality check with false → KILLED
2. execute : removed conditional - replaced equality check with true → KILLED
 
                if (scanOrchestrator.runDiscovery(root, providers, cliConfig.aiOptions(), aiEngine,
125 
                        scanOrchestrator.filterSink(rootSink, cliConfig.securityOnly(),
126 
                                cliConfig.minConfidence(), confidenceEnabled),
127 
                        cliConfig.contentHash(), override, aiCache, secretCtx)) {
128 
                    hadErrors = true;
129 
                }
130 
            }
131 
        } finally {
132 1 1. execute : removed call to org/egothor/methodatlas/command/PluginLoader::closeAll → SURVIVED
 
            pluginLoader.closeAll(providers);
133 
        }
134
135 
        // Surface any write error the streaming PrintWriter swallowed, so a
136 
        // truncated report (broken pipe, full disk) is never reported as success.
137 1 1. execute : removed call to org/egothor/methodatlas/emit/OutputEmitter::finish → SURVIVED
 
        emitter.finish();
138
139 
        if (aiCache.isActive() && LOG.isLoggable(Level.INFO)) {
140 
            LOG.log(Level.INFO, "AI cache: {0} hit(s), {1} miss(es)",
141 
                    new Object[] { aiCache.hits(), aiCache.misses() });
142 
        }
143
144 2 1. execute : removed conditional - replaced equality check with false → SURVIVED
2. execute : removed conditional - replaced equality check with true → KILLED
 
        if (secretRunner != null) {
145 1 1. execute : removed call to org/egothor/methodatlas/command/CredentialDetectionRunner::finish → NO_COVERAGE
 
            secretRunner.finish(roots, null);
146 
        }
147
148 2 1. execute : removed conditional - replaced equality check with true → KILLED
2. execute : removed conditional - replaced equality check with false → KILLED
 
        return hadErrors ? 1 : 0;
149 
    }
150 
}

Mutations

87

1.1
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:csvMode_headerIncludesContentHashColumn_whenEnabled(java.nio.file.Path)] removed conditional - replaced equality check with true → KILLED

2.2
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:emitMetadata_aiEnabled_emitsBuiltinDefaultTaxonomy(java.nio.file.Path)] removed conditional - replaced equality check with false → KILLED

88

1.1
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppManualTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppManualTest]/[method:manualConsume_emitsEmptyAiColumnsForClassesWithoutResponseFile(java.nio.file.Path)] removed conditional - replaced equality check with true → KILLED

2.2
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppJsonTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppJsonTest]/[method:minConfidence_filtersLowConfidenceMethods(java.nio.file.Path)] removed conditional - replaced equality check with false → KILLED

3.3
Location : execute
Killed by : none removed conditional - replaced equality check with true → SURVIVED Covering tests

4.4
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppJsonTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppJsonTest]/[method:minConfidence_filtersLowConfidenceMethods(java.nio.file.Path)] removed conditional - replaced equality check with false → KILLED

90

1.1
Location : execute
Killed by : none removed conditional - replaced equality check with true → TIMED_OUT

2.2
Location : execute
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

95

1.1
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:emitMetadata_aiEnabled_emitsBuiltinDefaultTaxonomy(java.nio.file.Path)] removed conditional - replaced equality check with false → KILLED

2.2
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:csvMode_noPackageDeclaration_usesSimpleClassNameAsFqcn(java.nio.file.Path)] removed conditional - replaced equality check with true → KILLED

98

1.1
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:emitMetadata_aiEnabled_emitsBuiltinDefaultTaxonomy(java.nio.file.Path)] removed call to org/egothor/methodatlas/emit/OutputEmitter::emitMetadata → KILLED

2.2
Location : execute
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

3.3
Location : execute
Killed by : none removed conditional - replaced equality check with true → SURVIVED Covering tests

101

1.1
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:csvMode_noPackageDeclaration_usesSimpleClassNameAsFqcn(java.nio.file.Path)] removed call to org/egothor/methodatlas/emit/OutputEmitter::emitCsvHeader → KILLED

109

1.1
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppAiTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppAiTest]/[method:plainMode_aiFailureForOneClass_continuesScanningAndFallsBackForThatClass(java.nio.file.Path)] removed conditional - replaced equality check with true → KILLED

2.2
Location : execute
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

112

1.1
Location : execute
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

2.2
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:csvMode_unparseableFile_returnsExitCode1(java.nio.file.Path)] removed conditional - replaced equality check with true → KILLED

121

1.1
Location : execute
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

2.2
Location : execute
Killed by : none removed conditional - replaced equality check with true → SURVIVED Covering tests

123

1.1
Location : lambda$execute$0
Killed by : org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:csvMode_noPackageDeclaration_usesSimpleClassNameAsFqcn(java.nio.file.Path)] removed call to org/egothor/methodatlas/emit/OutputEmitter::emit → KILLED

124

1.1
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:csvMode_unparseableFile_returnsExitCode1(java.nio.file.Path)] removed conditional - replaced equality check with false → KILLED

2.2
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppCoverageTest]/[method:emitCoverage_writesReportToCustomPath(java.nio.file.Path)] removed conditional - replaced equality check with true → KILLED

132

1.1
Location : execute
Killed by : none removed call to org/egothor/methodatlas/command/PluginLoader::closeAll → SURVIVED Covering tests

137

1.1
Location : execute
Killed by : none removed call to org/egothor/methodatlas/emit/OutputEmitter::finish → SURVIVED Covering tests

144

1.1
Location : execute
Killed by : none removed conditional - replaced equality check with false → SURVIVED Covering tests

2.2
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:csvMode_unparseableFile_returnsExitCode1(java.nio.file.Path)] removed conditional - replaced equality check with true → KILLED

145

1.1
Location : execute
Killed by : none removed call to org/egothor/methodatlas/command/CredentialDetectionRunner::finish → NO_COVERAGE

148

1.1
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppCoverageTest]/[method:emitCoverage_writesReportToCustomPath(java.nio.file.Path)] removed conditional - replaced equality check with true → KILLED

2.2
Location : execute
Killed by : org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:csvMode_unparseableFile_returnsExitCode1(java.nio.file.Path)] removed conditional - replaced equality check with false → KILLED

Active mutators

Tests examined


Report generated by PIT 1.22.1