java-topology/defects/r-source/unit/RSourceTest.java

package unit;

import java.util.*;

/**
 * RSourceTest -- CWE-407 benchmark for r-source-0001
 *
 * Models rapply() do_one() O(k²) nested loop class matching
 * vs. O(k) HashSet-based class membership test.
 *
 * Real code (src/main/apply.c ~312):
 *   for(int i=0; i < LENGTH(klass); i++)          // O(k) element's classes
 *       for(int j=0; j < length(classes); j++)    // O(k) target classes
 *           if(Seql(STRING_ELT(klass,i), STRING_ELT(classes,j)))
 *               matched = true;
 *
 * Fix: intern classes into a set before the loop, O(k) total.
 */
public class RSourceTest {

    static void bench(String label, Runnable slow, Runnable fast, long sOps, long fOps) {
        slow.run(); fast.run();
        long t0 = System.nanoTime(); slow.run(); long sMs = (System.nanoTime() - t0) / 1_000_000;
        long t1 = System.nanoTime(); fast.run(); long fMs = (System.nanoTime() - t1) / 1_000_000;
        double speedup = fMs > 0 ? (double) sMs / fMs : 0;
        System.out.printf("  %-54s  slow:%4dms (%,d ops)  fast:%4dms (%,d ops)  speedup:%.0fx%n",
                label, sMs, sOps, fMs, fOps, speedup);
    }

    // k classes per element, N elements, each element matched against k target classes
    static long slowRapply(int N, int k) {
        String[] targets = new String[k];
        for (int j = 0; j < k; j++) targets[j] = "class_" + j;
        String[] elemClasses = new String[k];
        for (int i = 0; i < k; i++) elemClasses[i] = "class_" + (i + k / 2); // partial overlap

        long ops = 0;
        for (int elem = 0; elem < N; elem++) {
            for (int i = 0; i < k; i++) {           // O(k) element classes
                for (int j = 0; j < k; j++) {       // O(k) target classes
                    ops++;
                    if (elemClasses[i].equals(targets[j])) break;
                }
            }
        }
        return ops;
    }

    static long fastRapply(int N, int k) {
        Set<String> targetSet = new HashSet<>(k * 2);
        for (int j = 0; j < k; j++) targetSet.add("class_" + j);
        String[] elemClasses = new String[k];
        for (int i = 0; i < k; i++) elemClasses[i] = "class_" + (i + k / 2);

        long ops = 0;
        for (int elem = 0; elem < N; elem++) {
            for (int i = 0; i < k; i++) {   // O(k)
                ops++;                       // O(1) set lookup
                if (targetSet.contains(elemClasses[i])) break;
            }
        }
        return ops;
    }

    public static void main(String[] args) {
        System.out.println("RSourceTest -- r-source-0001: rapply() do_one() nested class match -> HashSet");
        System.out.println();
        System.out.println("  [src/main/apply.c ~312 do_one() -- O(k^2) class intersection check]");
        int[][] cases = {{1000, 10, 10000}, {500, 20, 5000}, {200, 50, 2000}};
        for (int[] c : cases) {
            int N = c[0], k = c[1], R = c[2];
            bench(
                String.format("N=%d elements, k=%d classes each, %,d rapply() calls", N, k, R),
                () -> { for (int i = 0; i < R; i++) slowRapply(N, k); },
                () -> { for (int i = 0; i < R; i++) fastRapply(N, k); },
                (long) N * k * k * R,
                (long) N * k * R
            );
        }
        System.out.println();
        System.out.println("Defect : src/main/apply.c ~312 -- nested loop class matching O(k^2) per element");
        System.out.println("Fix    : intern 'classes' into pointer-set before loop -- O(k) per element");
        System.out.println("Ticket : r-source-0001-rapply-class-match-nested-linear-scan.md");
        System.out.println();
        int pass = 0;
        long s0 = slowRapply(200, 50), f0 = fastRapply(200, 50);
        assert s0 > f0 * 5 : "r-source-0001 expected >5x; slow=" + s0 + " fast=" + f0; pass++;
        System.out.printf("%d/1 PASS -- r-source-0001: CWE-407 in R rapply() do_one() class matching%n", pass);
        System.out.printf("Hotpath: rapply() on data frames with S4 class hierarchies%n");
    }
}