MethodAtlasApp.java

package org.egothor.methodatlas;

import java.io.FilterOutputStream;

import java.io.IOException;

import java.io.OutputStream;

import java.io.OutputStreamWriter;

import java.io.PrintWriter;

import java.nio.charset.StandardCharsets;

import java.nio.file.Path;

import org.egothor.methodatlas.ai.ManualConsumeEngine;

import org.egothor.methodatlas.ai.AiSuggestionEngine;

import org.egothor.methodatlas.api.TestDiscoveryConfig;

import org.egothor.methodatlas.command.AiRuntimeBuilder;

import org.egothor.methodatlas.command.ApplyTagsCommand;

import org.egothor.methodatlas.emit.ClassificationOverride;

import org.egothor.methodatlas.emit.OutputMode;

import org.egothor.methodatlas.command.ApplyTagsFromCsvCommand;

import org.egothor.methodatlas.command.DiffCommand;

import org.egothor.methodatlas.command.GitHubAnnotationsCommand;

import org.egothor.methodatlas.command.JsonCommand;

import org.egothor.methodatlas.command.ManualPrepareCommand;

import org.egothor.methodatlas.command.OverrideLoader;

import org.egothor.methodatlas.command.PluginLoader;

import org.egothor.methodatlas.command.SarifCommand;

import org.egothor.methodatlas.command.ScanCommand;

import org.egothor.methodatlas.command.ScanOrchestrator;

/**

 * Command-line application for scanning Java test sources, extracting JUnit

 * test metadata, and optionally enriching the emitted results with AI-generated

 * security tagging suggestions.

 *

 * <p>

 * The application traverses one or more directory roots, parses matching source

 * files using JavaParser, identifies supported JUnit Jupiter test methods, and

 * emits one output record per discovered test method. File selection matches

 * source files whose names end with the configured suffix (default:

 * {@code Test.java}).

 * </p>

 *

 * <h2>Source-Derived Metadata</h2>

 *

 * <p>

 * For each discovered test method, the application reports:

 * </p>

 * <ul>

 * <li>fully qualified class name</li>

 * <li>method name</li>

 * <li>inclusive line count of the method declaration</li>

 * <li>JUnit {@code @Tag} values declared on the method</li>

 * </ul>

 *

 * <h2>AI Enrichment</h2>

 *

 * <p>

 * When AI support is enabled, the application submits each discovered test

 * class to an {@link org.egothor.methodatlas.ai.AiSuggestionEngine} and merges

 * the returned method-level suggestions into the emitted output.

 * </p>

 *

 * <h2>Manual AI Workflow</h2>

 *

 * <p>

 * Operators who cannot access an AI API directly can use the two-phase manual

 * workflow:

 * </p>

 * <ol>

 * <li><b>Prepare phase</b> ({@code -manual-prepare}): the application scans

 * test sources and writes one work file per class to the specified directory.

 * Each work file contains operator instructions and the full AI prompt (with

 * class source embedded). No CSV output is produced in this phase.</li>

 * <li><b>Consume phase</b> ({@code -manual-consume}): the application reads

 * operator-saved AI response files ({@code <stem>.response.txt}) from the

 * response directory and produces the final enriched CSV. Classes whose

 * response file is absent receive empty AI columns.</li>

 * </ol>

 *

 * <h2>Supported Command-Line Options</h2>

 *

 * <ul>

 * <li>{@code -config <path>} — loads default values from a YAML configuration

 * file; command-line flags override YAML values</li>

 * <li>{@code -plain} — emits plain text output instead of CSV</li>

 * <li>{@code -sarif} — emits SARIF 2.1.0 JSON output</li>

 * <li>{@code -json} — emits a flat JSON array; each element carries the same

 * fields as CSV with {@code tags} and {@code ai_tags} as arrays and numeric

 * values as JSON numbers</li>

 * <li>{@code -ai} — enables AI-based enrichment</li>

 * <li>{@code -ai-provider <provider>} — selects the AI provider</li>

 * <li>{@code -ai-model <model>} — selects the provider-specific model</li>

 * <li>{@code -ai-base-url <url>} — overrides the provider base URL</li>

 * <li>{@code -ai-api-key <key>} — supplies the AI API key directly</li>

 * <li>{@code -ai-api-key-env <name>} — resolves the AI API key from an

 * environment variable</li>

 * <li>{@code -ai-taxonomy <path>} — loads taxonomy text from an external

 * file</li>

 * <li>{@code -ai-taxonomy-mode <mode>} — selects the built-in taxonomy

 * variant</li>

 * <li>{@code -ai-max-class-chars <count>} — limits class source size submitted

 * to AI</li>

 * <li>{@code -ai-timeout-sec <seconds>} — sets the AI request timeout</li>

 * <li>{@code -ai-max-retries <count>} — sets the retry limit for AI

 * operations</li>

 * <li>{@code -ai-confidence} — requests a confidence score for each AI

 * security classification; adds an {@code ai_confidence} column to the

 * output</li>

 * <li>{@code -min-confidence <threshold>} — silently drops methods whose AI

 * confidence score is below {@code threshold} (range {@code 0.0–1.0}); only

 * effective when {@code -ai-confidence} is also enabled</li>

 * <li>{@code -ai-cache <path>} — loads a previous scan CSV produced with

 * {@code -content-hash -ai} as an AI result cache; classes whose

 * {@code content_hash} matches a cache entry are classified without an API

 * call; changed and new classes are classified normally</li>

 * <li>{@code -file-suffix <suffix>} — matches source files by name suffix

 * (default: {@code Test.java}); may be repeated to match multiple patterns,

 * e.g. {@code -file-suffix Test.java -file-suffix IT.java}; the first

 * occurrence replaces the default</li>

 * <li>{@code -test-annotation <name>} — recognises methods annotated with

 * {@code name} as test methods; may be repeated; the first occurrence replaces

 * the JVM provider's default set (JUnit 5 {@code Test}, {@code ParameterizedTest},

 * {@code RepeatedTest}, {@code TestFactory}, {@code TestTemplate})</li>

 * <li>{@code -emit-metadata} — emits {@code # key: value} comment lines

 * before the header row describing the tool version, scan timestamp, and

 * taxonomy configuration</li>

 * <li>{@code -apply-tags} — instead of emitting a report, writes

 * AI-generated {@code @DisplayName} and {@code @Tag} annotations back to

 * the scanned source files; requires AI enrichment to be enabled</li>

 * <li>{@code -content-hash} — includes a SHA-256 fingerprint of each class

 * source as a {@code content_hash} column in CSV/plain output and as a SARIF

 * property; useful for detecting which classes changed between scans</li>

 * <li>{@code -security-only} — suppresses non-security methods from the output;

 * only methods whose AI classification (or override) has

 * {@code securityRelevant=true} are emitted; requires AI enrichment or a

 * classification override file to have any effect</li>

 * <li>{@code -manual-prepare <workdir> <responsedir>} — runs the manual AI

 * prepare phase, writing work files to {@code workdir} and empty response stubs

 * to {@code responsedir}; the two paths may be identical</li>

 * <li>{@code -manual-consume <workdir> <responsedir>} — runs the manual AI

 * consume phase, reading response files from {@code responsedir} and emitting

 * the final enriched CSV</li>

 * <li>{@code -diff <before.csv> <after.csv>} — compares two MethodAtlas scan

 * outputs and emits a delta report showing added, removed, and modified test

 * methods; all other flags are ignored when {@code -diff} is present</li>

 * <li>{@code -apply-tags-from-csv <path>} — instead of emitting a report,

 * applies the annotation decisions recorded in the reviewed CSV back to the

 * source files; the CSV is treated as a complete desired-state specification:

 * every test method's {@code @Tag} set and {@code @DisplayName} are driven

 * entirely by the corresponding CSV row</li>

 * <li>{@code -mismatch-limit <n>} — when used with {@code -apply-tags-from-csv},

 * aborts without modifying any source file if the number of mismatches between

 * the CSV and the current source tree reaches or exceeds {@code n}; {@code -1}

 * (the default) logs mismatches as warnings and proceeds</li>

 * <li>{@code -emit-source-root} — adds a {@code source_root} column to CSV

 * output and a {@code SRCROOT=} token to plain-text output, identifying which

 * scan root each record originated from; essential in multi-root or monorepo

 * projects where the same fully qualified class name can appear under different

 * source trees (e.g. {@code module-a/src/test/java/} and

 * {@code module-b/src/test/java/}); has no effect on SARIF or GitHub Annotations

 * output</li>

 * </ul>

 *

 * <p>

 * Any remaining non-option arguments are interpreted as root paths to scan. If

 * no scan path is supplied, the current working directory is scanned.

 * </p>

 *

 * @see org.egothor.methodatlas.ai.AiSuggestionEngine

 * @see org.egothor.methodatlas.api.SourcePatcher

 * @see org.egothor.methodatlas.emit.OutputEmitter

 * @see org.egothor.methodatlas.emit.SarifEmitter

 * @see org.egothor.methodatlas.command.Command

 * @see #main(String[])

 */

public final class MethodAtlasApp {

    private static final String FLAG_DIFF = "-diff";

    /**

     * Prevents instantiation of this utility class.

     */

    private MethodAtlasApp() {

    }

    /**

     * Program entry point.

     *

     * <p>

     * Delegates all work to {@link #run(String[], PrintWriter)}. Exits with a

     * non-zero status code if any source file could not be processed.

     * </p>

     *

     * @param args command-line arguments

     * @throws IOException              if traversal of a configured file tree fails

     * @throws IllegalArgumentException if an option is unknown, if a required

     *                                  option value is missing, or if an option

     *                                  value cannot be parsed

     * @throws IllegalStateException    if AI support is enabled but the AI engine

     *                                  cannot be created successfully

     */

    public static void main(String[] args) throws IOException {

        // Wrap System.out in a guarded stream whose close() only flushes.

        // This lets try-with-resources manage the PrintWriter (satisfying

        // SpotBugs CloseResource and PMD UseTryWithResources) without

        // permanently closing System.out (satisfying Error Prone's

        // ClosingStandardOutputStreams check).

        OutputStream guarded = new FilterOutputStream(System.out) {

            @Override

            public void close() throws IOException {

                flush(); // flush but do NOT close System.out

            }

        };

        try (PrintWriter out = new PrintWriter(new OutputStreamWriter(guarded, StandardCharsets.UTF_8), true)) {

            int exitCode = run(args, out);

            if (exitCode != 0) {

                System.exit(exitCode);

            }

        }

    }

    /**

     * Executes a full application run by routing to the appropriate

     * {@link org.egothor.methodatlas.command.Command} implementation.

     *

     * <p>

     * This method is the primary entry point for programmatic and test use. It

     * parses arguments, identifies the requested operating mode, constructs the

     * matching command object, and delegates execution to it.

     * </p>

     *

     * @param args command-line arguments

     * @param out  writer that receives all emitted output

     * @return {@code 0} if all files were processed successfully, {@code 1} if

     *         any file produced a parse or processing error

     * @throws IOException              if traversal of a configured file tree fails

     * @throws IllegalArgumentException if an option is unknown, if a required

     *                                  option value is missing, or if an option

     *                                  value cannot be parsed

     * @throws IllegalStateException    if AI support is enabled but the AI engine

     *                                  cannot be created successfully

     */

    @SuppressWarnings("PMD.AvoidInstantiatingObjectsInLoops") // DiffCommand is created inside the loop but returned immediately

    /* default */ static int run(String[] args, PrintWriter out) throws IOException {

        // -diff is handled before full argument parsing; all other flags are ignored.

        for (int i = 0; i < args.length; i++) {

            if (FLAG_DIFF.equals(args[i])) {

                if (i + 2 >= args.length) {

                    throw new IllegalArgumentException(

                            "-diff requires two arguments: -diff <before.csv> <after.csv>");

                }

                return new DiffCommand(Path.of(args[i + 1]), Path.of(args[i + 2])).execute(out);

            }

        }

        CliConfig cliConfig = CliArgs.parse(args);

        // Establish the run identity once and place it in the thread-local

        // context so the JUL formatter (Item 20) can prepend the correlation

        // id to every log record emitted during this invocation. clear() in

        // the finally block keeps the thread-local from outliving the run

        // when MethodAtlas is invoked programmatically (the standard CLI

        // exits the JVM anyway).

        String version = MethodAtlasApp.class.getPackage().getImplementationVersion();

        ScanRun scanRun = ScanRun.create(version, cliConfig.toString());

        ScanRunContext.set(scanRun);

        try {

            return runWithScanRun(out, cliConfig);

        } finally {

            ScanRunContext.clear();

        }

    }

    private static int runWithScanRun(PrintWriter out, CliConfig cliConfig) throws IOException {

        AiRuntimeBuilder aiRuntimeBuilder = new AiRuntimeBuilder();

        ClassificationOverride override = new OverrideLoader().load(cliConfig.overrideFile());

        AiResultCache aiCache = aiRuntimeBuilder.buildCache(cliConfig.aiCacheFile());

        TestDiscoveryConfig discoveryConfig =

                new TestDiscoveryConfig(cliConfig.fileSuffixes(), cliConfig.testMarkers(), cliConfig.properties());

        // One PluginLoader + one ScanOrchestrator are shared by every command in

        // this run; both are stateless and the providers they resolve are owned

        // (and closed) by the command that requested them.

        PluginLoader pluginLoader = new PluginLoader();

        ScanOrchestrator scanOrchestrator = new ScanOrchestrator(pluginLoader);

        // Manual prepare phase: write AI prompt work files; no CSV output.

        if (cliConfig.manualMode() instanceof ManualMode.Prepare prepare) {

            return new ManualPrepareCommand(prepare, cliConfig, discoveryConfig, pluginLoader).execute(out);

        }

        // Determine AI engine: manual consume reads from files; normal mode calls APIs.

        AiSuggestionEngine aiEngine;

        if (cliConfig.manualMode() instanceof ManualMode.Consume consume) {

            aiEngine = new ManualConsumeEngine(consume.responseDir());

        } else {

            aiEngine = aiRuntimeBuilder.buildEngine(cliConfig.aiOptions());

        }

        // Apply-tags-from-csv mode: apply reviewed CSV decisions to source files.

        if (cliConfig.applyTagsFromCsvFile() != null) {

            return new ApplyTagsFromCsvCommand(cliConfig, discoveryConfig, pluginLoader).execute(out);

        }

        // Apply-tags mode: annotate source files; no report emitted.

        if (cliConfig.applyTags()) {

            return new ApplyTagsCommand(cliConfig, discoveryConfig, aiEngine, override, aiCache,

                    pluginLoader, scanOrchestrator).execute(out);

        }

        // SARIF mode: buffer all records; write JSON once after the scan completes.

        if (cliConfig.outputMode() == OutputMode.SARIF) {

            return new SarifCommand(cliConfig, discoveryConfig, aiEngine, override, aiCache,

                    scanOrchestrator).execute(out);

        }

        // JSON mode: buffer all records; write flat JSON array after scan completes.

        if (cliConfig.outputMode() == OutputMode.JSON) {

            return new JsonCommand(cliConfig, discoveryConfig, aiEngine, override, aiCache,

                    pluginLoader, scanOrchestrator).execute(out);

        }

        // GitHub Annotations mode: emit ::notice/::warning workflow commands.

        if (cliConfig.outputMode() == OutputMode.GITHUB_ANNOTATIONS) {

            return new GitHubAnnotationsCommand(cliConfig, discoveryConfig, aiEngine, override, aiCache,

                    scanOrchestrator).execute(out);

        }

        // CSV / PLAIN mode: emit incrementally (default).

        return new ScanCommand(cliConfig, discoveryConfig, aiEngine, override, aiCache,

                pluginLoader, scanOrchestrator).execute(out);

    }

}

Active mutators

• CONDITIONALS_BOUNDARY
• EMPTY_RETURNS
• EXPERIMENTAL_SWITCH
• FALSE_RETURNS
• INCREMENTS
• INVERT_NEGS
• MATH
• NULL_RETURNS
• PRIMITIVE_RETURNS
• REMOVE_CONDITIONALS_EQUAL_ELSE
• REMOVE_CONDITIONALS_EQUAL_IF
• REMOVE_CONDITIONALS_ORDER_ELSE
• REMOVE_CONDITIONALS_ORDER_IF
• TRUE_RETURNS
• VOID_METHOD_CALLS

Tests examined

• org.egothor.methodatlas.MethodAtlasAppSarifTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppSarifTest]/[method:sarifMode_toolDriverNameIsMethodAtlas(java.nio.file.Path)] (15 ms)
• org.egothor.methodatlas.MethodAtlasAppSarifTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppSarifTest]/[method:sarifMode_outputIsNotCsvHeader(java.nio.file.Path)] (16 ms)
• org.egothor.methodatlas.MethodAtlasAppSarifTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppSarifTest]/[method:sarifMode_emitsValidSarifDocument(java.nio.file.Path)] (17 ms)
• org.egothor.methodatlas.MethodAtlasAppSarifTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppSarifTest]/[method:configFile_overridesOutputMode_toSarif(java.nio.file.Path)] (25 ms)
• org.egothor.methodatlas.MethodAtlasAppSarifTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppSarifTest]/[method:cliFlag_overridesConfigFileOutputMode(java.nio.file.Path)] (28 ms)
• org.egothor.methodatlas.MethodAtlasAppSarifTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppSarifTest]/[method:sarifMode_allMethodsUseLevelNone_whenAiDisabled(java.nio.file.Path)] (16 ms)
• org.egothor.methodatlas.MethodAtlasAppSarifTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppSarifTest]/[method:sarifMode_resultHasPhysicalAndLogicalLocation(java.nio.file.Path)] (26 ms)
• org.egothor.methodatlas.MethodAtlasAppSarifTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppSarifTest]/[method:sarifMode_emitsOneResultPerTestMethod(java.nio.file.Path)] (38 ms)
• org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:sarifMode_contentHashPresentAndValid_whenEnabled(java.nio.file.Path)] (36 ms)
• org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:sarifMode_contentHashAbsent_byDefault(java.nio.file.Path)] (44 ms)
• org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:sarifMode_methodsInSameClass_shareIdenticalHashInSarif(java.nio.file.Path)] (106 ms)
• org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:manualPrepare_unparseableFile_returnsExitCode1(java.nio.file.Path)] (6 ms)
• org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:manualPrepare_classWithNoTestMethods_writesNoWorkFiles(java.nio.file.Path)] (12 ms)
• org.egothor.methodatlas.MethodAtlasAppManualTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppManualTest]/[method:manualPrepare_returnsZeroExitCodeOnSuccess(java.nio.file.Path)] (12 ms)
• org.egothor.methodatlas.MethodAtlasAppManualTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppManualTest]/[method:manualPrepare_producesNoCSVOutput(java.nio.file.Path)] (13 ms)
• org.egothor.methodatlas.MethodAtlasAppManualTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppManualTest]/[method:manualPrepare_createsWorkFilesForAllDiscoveredTestClasses(java.nio.file.Path)] (18 ms)
• org.egothor.methodatlas.MethodAtlasAppManualTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppManualTest]/[method:manualPrepare_workFileContainsOperatorInstructionsAndPrompt(java.nio.file.Path)] (36 ms)
• org.egothor.methodatlas.DeltaReportTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.DeltaReportTest]/[method:app_diffFlag_producesReport(java.nio.file.Path)] (6 ms)
• org.egothor.methodatlas.MethodAtlasAppTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppTest]/[method:testAnnotation_customAnnotationIsRecognised(java.nio.file.Path)] (15 ms)
• org.egothor.methodatlas.MethodAtlasAppTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppTest]/[method:emitMetadata_prependsCommentLinesBeforeHeader(java.nio.file.Path)] (29 ms)
• org.egothor.methodatlas.MethodAtlasAppTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppTest]/[method:plainMode_detectsMethodsLocAndTags(java.nio.file.Path)] (42 ms)
• org.egothor.methodatlas.MethodAtlasAppTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppTest]/[method:csvMode_detectsMethodsLocAndTags(java.nio.file.Path)] (39 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_emptyCsvReturnsZero(java.nio.file.Path)] (15 ms)
• org.egothor.methodatlas.GitHubAnnotationsEmitterTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.GitHubAnnotationsEmitterTest]/[method:app_githubAnnotationsMode_emptyDirectoryProducesNoOutput(java.nio.file.Path)] (4 ms)
• org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:emitMetadata_aiEnabled_emitsBuiltinDefaultTaxonomy(java.nio.file.Path)] (3 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_mismatchLimitReturnsOne(java.nio.file.Path)] (6 ms)
• org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:emitMetadata_aiEnabled_optimizedMode_emitsBuiltinOptimized(java.nio.file.Path)] (3 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_mismatchLimitAborts(java.nio.file.Path)] (11 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_methodInSourceNotInCsvCountedAsMismatch(java.nio.file.Path)] (11 ms)
• org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:csvMode_unparseableFile_returnsExitCode1(java.nio.file.Path)] (11 ms)
• org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:emitMetadata_aiEnabled_taxonomyFile_emitsFilePath(java.nio.file.Path)] (6 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_addsDisplayNameImportWhenDisplayNameSet(java.nio.file.Path)] (12 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsUnsupportedLanguageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsUnsupportedLanguageTest]/[method:applyTagsFromCsv_goRowsAreReportedAsMismatchAndFileSkipped(java.nio.file.Path)] (10 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_noChangesWhenAlreadyMatchesCsv(java.nio.file.Path)] (14 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_setsDisplayNameFromCsv(java.nio.file.Path)] (15 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_removesDisplayNameWhenCsvEmpty(java.nio.file.Path)] (16 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_addsTagImportWhenTagsAdded(java.nio.file.Path)] (17 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsUnsupportedLanguageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsUnsupportedLanguageTest]/[method:applyTags_javaOnly_noSkipCountInSummary(java.nio.file.Path)] (8 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsTest]/[method:applyTags_exitCode0WhenNoErrors(java.nio.file.Path)] (9 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_returnsZeroOnSuccess(java.nio.file.Path)] (26 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsTest]/[method:applyTags_summaryLineAlwaysEmitted(java.nio.file.Path)] (9 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_mismatchBelowLimitProceeds(java.nio.file.Path)] (17 ms)
• org.egothor.methodatlas.MethodAtlasAppScanCoverageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppScanCoverageTest]/[method:csvMode_noPackageDeclaration_usesSimpleClassNameAsFqcn(java.nio.file.Path)] (7 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_oldCsvWithoutDisplayNameColumn_leavesDisplayNameUntouched(java.nio.file.Path)] (21 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_removesTagsNotInCsv(java.nio.file.Path)] (20 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsTest]/[method:applyTags_noAi_noFilesModified(java.nio.file.Path)] (13 ms)
• org.egothor.methodatlas.MethodAtlasAppSarifTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppSarifTest]/[method:configFile_overridesOutputMode_toPlain(java.nio.file.Path)] (11 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_addsMissingTags(java.nio.file.Path)] (25 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_summarisesChangesInOutput(java.nio.file.Path)] (25 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsTest]/[method:applyTags_noImportsAddedWhenNothingAnnotated(java.nio.file.Path)] (10 ms)
• org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:plainMode_hashTokenPresent_whenEnabled(java.nio.file.Path)] (11 ms)
• org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:csvMode_headerExcludesContentHashColumn_byDefault(java.nio.file.Path)] (14 ms)
• org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:csvMode_headerIncludesContentHashColumn_whenEnabled(java.nio.file.Path)] (12 ms)
• org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:csvMode_methodsInSameClass_shareIdenticalHash(java.nio.file.Path)] (9 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsTest]/[method:applyTags_nonSecurityMethod_notAnnotated(java.nio.file.Path)] (15 ms)
• org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:plainMode_noHashToken_byDefault(java.nio.file.Path)] (21 ms)
• org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:csvMode_distinctClasses_produceDifferentHashes(java.nio.file.Path)] (13 ms)
• org.egothor.methodatlas.MethodAtlasAppJsonTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppJsonTest]/[method:jsonMode_producesValidArray(java.nio.file.Path)] (23 ms)
• org.egothor.methodatlas.MethodAtlasAppJsonTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppJsonTest]/[method:minConfidence_noEffectWithoutAiConfidence(java.nio.file.Path)] (24 ms)
• org.egothor.methodatlas.MethodAtlasAppJsonTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppJsonTest]/[method:jsonMode_noAi_omitsAiFields(java.nio.file.Path)] (25 ms)
• org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:cliFlagOverridesYamlConfig_enablesHash(java.nio.file.Path)] (22 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsTest]/[method:applyTags_existingAnnotationsNotDuplicated(java.nio.file.Path)] (14 ms)
• org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:yamlConfig_contentHashTrue_enablesHashColumn(java.nio.file.Path)] (26 ms)
• org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:yamlConfig_contentHashFalse_noHashColumn(java.nio.file.Path)] (31 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsTest]/[method:applyTags_withAi_annotatesSecurityRelevantMethod(java.nio.file.Path)] (17 ms)
• org.egothor.methodatlas.MethodAtlasAppManualTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppManualTest]/[method:manualConsume_emitsEmptyAiColumnsForClassesWithoutResponseFile(java.nio.file.Path)] (27 ms)
• org.egothor.methodatlas.MethodAtlasAppJsonTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppJsonTest]/[method:jsonMode_recordsHaveRequiredFields(java.nio.file.Path)] (38 ms)
• org.egothor.methodatlas.MethodAtlasAppContentHashTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppContentHashTest]/[method:csvMode_contentHashIs64CharLowercaseHex_whenEnabled(java.nio.file.Path)] (34 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsTest]/[method:applyTags_summaryCountsMatchAnnotationsAdded(java.nio.file.Path)] (22 ms)
• org.egothor.methodatlas.MethodAtlasAppManualTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppManualTest]/[method:manualConsume_mixesEnrichedAndEmptyRowsForPartialResponses(java.nio.file.Path)] (20 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsTest]/[method:applyTags_addsDisplayNameImport(java.nio.file.Path)] (30 ms)
• org.egothor.methodatlas.MethodAtlasAppJsonTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppJsonTest]/[method:minConfidence_filtersLowConfidenceMethods(java.nio.file.Path)] (29 ms)
• org.egothor.methodatlas.MethodAtlasAppJsonTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppJsonTest]/[method:jsonMode_withAiAndConfidence_confidenceIsNumber(java.nio.file.Path)] (34 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsTest]/[method:applyTags_addsTagImport(java.nio.file.Path)] (29 ms)
• org.egothor.methodatlas.MethodAtlasAppManualTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppManualTest]/[method:manualConsume_emitsEnrichedCsvForClassesWithResponseFiles(java.nio.file.Path)] (39 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsUnsupportedLanguageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsUnsupportedLanguageTest]/[method:applyTags_mixedJavaAndGo_javaPatchedAndGoSkipped(java.nio.file.Path)] (13 ms)
• org.egothor.methodatlas.MethodAtlasAppAiTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppAiTest]/[method:aiCache_miss_engineCalledForUnknownHash(java.nio.file.Path)] (17 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsFromCsvTest]/[method:applyTagsFromCsv_noLimitWarnsAndProceeds(java.nio.file.Path)] (81 ms)
• org.egothor.methodatlas.MethodAtlasAppJsonTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppJsonTest]/[method:jsonMode_withAi_aiTagsIsArray(java.nio.file.Path)] (67 ms)
• org.egothor.methodatlas.MethodAtlasAppAiTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppAiTest]/[method:plainMode_aiFailureForOneClass_continuesScanningAndFallsBackForThatClass(java.nio.file.Path)] (72 ms)
• org.egothor.methodatlas.MethodAtlasAppAiTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppAiTest]/[method:csvMode_oversizedClass_skipsAiLookup_andLeavesAiColumnsEmpty(java.nio.file.Path)] (85 ms)
• org.egothor.methodatlas.MethodAtlasAppAiTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppAiTest]/[method:csvMode_aiEnabled_withRealisticFixtures_emitsMergedAiSuggestions(java.nio.file.Path)] (84 ms)
• org.egothor.methodatlas.MethodAtlasAppApplyTagsUnsupportedLanguageTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppApplyTagsUnsupportedLanguageTest]/[method:applyTags_goOnly_skippedWithDiagnosticAndExit0(java.nio.file.Path)] (161 ms)
• org.egothor.methodatlas.GitHubAnnotationsEmitterTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.GitHubAnnotationsEmitterTest]/[method:app_githubAnnotationsMode_emitsAnnotationsForSecurityMethods(java.nio.file.Path)] (349 ms)
• org.egothor.methodatlas.MethodAtlasAppAiTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppAiTest]/[method:aiCache_hit_engineNotCalledForUnchangedClass(java.nio.file.Path)] (754 ms)
• org.egothor.methodatlas.MethodAtlasAppSarifTest.[engine:junit-jupiter]/[class:org.egothor.methodatlas.MethodAtlasAppSarifTest]/[method:configFile_overridesFileSuffixes(java.nio.file.Path)] (899 ms)