htslib-1.14/test/hfile.c

/*  test/hfile.c -- Test cases for low-level input/output streams.

    Copyright (C) 2013-2014, 2016, 2018 Genome Research Ltd.

    Author: John Marshall <jm18@sanger.ac.uk>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.  */

#include <config.h>

#include <stdarg.h>
#include <stdio.h>
#include <stdlib.h>
#include <errno.h>

#include <sys/stat.h>

#include "../htslib/hfile.h"
#include "../htslib/hts_defs.h"
#include "../htslib/kstring.h"

void HTS_NORETURN fail(const char *format, ...)
{
    int err = errno;
    va_list args;
    va_start(args, format);
    vfprintf(stderr, format, args);
    va_end(args);
    if (err != 0) fprintf(stderr, ": %s", strerror(err));
    fprintf(stderr, "\n");
    exit(EXIT_FAILURE);
}

void check_offset(hFILE *f, off_t off, const char *message)
{
    off_t ret = htell(f);
    if (ret < 0) fail("htell(%s)", message);
    if (ret == off) return;

    fprintf(stderr, "%s offset incorrect: expected %ld but got %ld\n",
            message, (long)off, (long)ret);
    exit(EXIT_FAILURE);
}

char *slurp(const char *filename)
{
    char *text;
    struct stat sbuf;
    size_t filesize;
    FILE *f = fopen(filename, "rb");
    if (f == NULL) fail("fopen(\"%s\", \"rb\")", filename);
    if (fstat(fileno(f), &sbuf) != 0) fail("fstat(\"%s\")", filename);
    filesize = sbuf.st_size;

    text = (char *) malloc(filesize + 1);
    if (text == NULL) fail("malloc(text)");

    if (fread(text, 1, filesize, f) != filesize) fail("fread");
    fclose(f);

    text[filesize] = '\0';
    return text;
}

hFILE *fin = NULL;
hFILE *fout = NULL;

void reopen(const char *infname, const char *outfname)
{
    if (fin) { if (hclose(fin) != 0) fail("hclose(input)"); }
    if (fout) { if (hclose(fout) != 0) fail("hclose(output)"); }

    fin = hopen(infname, "r");
    if (fin == NULL) fail("hopen(\"%s\")", infname);

    fout = hopen(outfname, "w");
    if (fout == NULL) fail("hopen(\"%s\")", outfname);
}

int main(void)
{
    static const int size[] = { 1, 13, 403, 999, 30000 };

    char buffer[40000];
    char *original;
    int c, i;
    ssize_t n;
    off_t off;

    reopen("vcf.c", "test/hfile1.tmp");
    while ((c = hgetc(fin)) != EOF) {
        if (hputc(c, fout) == EOF) fail("hputc");
    }
    if (herrno(fin)) { errno = herrno(fin); fail("hgetc"); }

    reopen("test/hfile1.tmp", "test/hfile2.tmp");
    if (hpeek(fin, buffer, 50) < 0) fail("hpeek");
    while ((n = hread(fin, buffer, 17)) > 0) {
        if (hwrite(fout, buffer, n) != n) fail("hwrite");
    }
    if (n < 0) fail("hread");

    reopen("test/hfile2.tmp", "test/hfile3.tmp");
    while ((n = hread(fin, buffer, sizeof buffer)) > 0) {
        if (hwrite(fout, buffer, n) != n) fail("hwrite");
        if (hpeek(fin, buffer, 700) < 0) fail("hpeek");
    }
    if (n < 0) fail("hread");

    reopen("test/hfile3.tmp", "test/hfile4.tmp");
    i = 0;
    off = 0;
    while ((n = hread(fin, buffer, size[i++ % 5])) > 0) {
        off += n;
        buffer[n] = '\0';
        check_offset(fin, off, "pre-peek");
        if (hputs(buffer, fout) == EOF) fail("hputs");
        if ((n = hpeek(fin, buffer, size[(i+3) % 5])) < 0) fail("hpeek");
        check_offset(fin, off, "post-peek");
    }
    if (n < 0) fail("hread");

    reopen("test/hfile4.tmp", "test/hfile5.tmp");
    while (hgets(buffer, 80, fin) != NULL) {
        size_t l = strlen(buffer);
        if (l > 79) fail("hgets read %zu bytes, should be < 80", l);
        if (hwrite(fout, buffer, l) != l) fail("hwrite");
    }
    if (herrno(fin)) fail("hgets");

    reopen("test/hfile5.tmp", "test/hfile6.tmp");
    n = hread(fin, buffer, 200);
    if (n < 0) fail("hread");
    else if (n != 200) fail("hread only got %d", (int)n);
    if (hwrite(fout, buffer, 1000) != 1000) fail("hwrite");
    check_offset(fin, 200, "input/first200");
    check_offset(fout, 1000, "output/first200");

    if (hseek(fin, 800, SEEK_CUR) < 0) fail("hseek/cur");
    check_offset(fin, 1000, "input/seek");
    for (off = 1000; (n = hread(fin, buffer, sizeof buffer)) > 0; off += n)
        if (hwrite(fout, buffer, n) != n) fail("hwrite");
    if (n < 0) fail("hread");
    check_offset(fin, off, "input/eof");
    check_offset(fout, off, "output/eof");

    if (hseek(fin, 200, SEEK_SET) < 0) fail("hseek/set");
    if (hseek(fout, 200, SEEK_SET) < 0) fail("hseek(output)");
    check_offset(fin, 200, "input/backto200");
    check_offset(fout, 200, "output/backto200");
    n = hread(fin, buffer, 800);
    if (n < 0) fail("hread");
    else if (n != 800) fail("hread only got %d", (int)n);
    if (hwrite(fout, buffer, 800) != 800) fail("hwrite");
    check_offset(fin, 1000, "input/wrote800");
    check_offset(fout, 1000, "output/wrote800");

    if (hflush(fout) == EOF) fail("hflush");

    original = slurp("vcf.c");
    for (i = 1; i <= 6; i++) {
        char *text;
        sprintf(buffer, "test/hfile%d.tmp", i);
        text = slurp(buffer);
        if (strcmp(original, text) != 0) {
            fprintf(stderr, "%s differs from vcf.c\n", buffer);
            free(text);
            free(original);
            return EXIT_FAILURE;
        }
        free(text);
    }
    free(original);

    if (hclose(fin) != 0) fail("hclose(input)");
    if (hclose(fout) != 0) fail("hclose(output)");

    fout = hopen("test/hfile_chars.tmp", "w");
    if (fout == NULL) fail("hopen(\"test/hfile_chars.tmp\")");
    for (i = 0; i < 256; i++)
        if (hputc(i, fout) != i) fail("chars: hputc (%d)", i);
    if (hclose(fout) != 0) fail("hclose(test/hfile_chars.tmp)");

    fin = hopen("test/hfile_chars.tmp", "r");
    if (fin == NULL) fail("hopen(\"test/hfile_chars.tmp\") for reading");
    for (i = 0; i < 256; i++)
        if ((c = hgetc(fin)) != i)
            fail("chars: hgetc (%d = 0x%x) returned %d = 0x%x", i, i, c, c);
    if ((c = hgetc(fin)) != EOF) fail("chars: hgetc (EOF) returned %d", c);
    if (hclose(fin) != 0) fail("hclose(test/hfile_chars.tmp) for reading");

    fin = hopen("preload:test/hfile_chars.tmp", "r");
    if (fin == NULL) fail("preloading \"test/hfile_chars.tmp\" for reading");
    for (i = 0; i < 256; i++)
        if ((c = hgetc(fin)) != i)
            fail("preloading chars: hgetc (%d = 0x%x) returned %d = 0x%x", i, i, c, c);
    if ((c = hgetc(fin)) != EOF) fail("preloading chars: hgetc (EOF) returned %d", c);
    if (hclose(fin) != 0) fail("preloading hclose(test/hfile_chars.tmp) for reading");

    char* test_string = strdup("Test string");
    fin = hopen("mem:", "r:", test_string, 12);
    if (fin == NULL) fail("hopen(\"mem:\", \"r:\", ...)");
    if (hread(fin, buffer, 12) != 12)
        fail("hopen('mem:', 'r') failed read");
    if(strcmp(buffer, test_string) != 0)
        fail("hopen('mem:', 'r') missread '%s' != '%s'", buffer, test_string);
    char* internal_buf;
    size_t interval_buf_len;
    if((internal_buf = hfile_mem_get_buffer(fin, &interval_buf_len)) == NULL){
        fail("hopen('mem:', 'r') failed to get internal buffer");
    }
    if (hclose(fin) != 0) fail("hclose mem for reading");

    test_string = strdup("Test string");
    fin = hopen("mem:", "wr:", test_string, 12);
    if (fin == NULL) fail("hopen(\"mem:\", \"w:\", ...)");
    if (hseek(fin, -1, SEEK_END) < 0)
        fail("hopen('mem:', 'wr') failed seek");
    if (hwrite(fin, " extra", 7) != 7)
        fail("hopen('mem:', 'wr') failed write");
    if (hseek(fin, 0, SEEK_SET) < 0)
        fail("hopen('mem:', 'wr') failed seek");
    if (hread(fin, buffer, 18) != 18)
        fail("hopen('mem:', 'wr') failed read");
    if (strcmp(buffer, "Test string extra") != 0)
        fail("hopen('mem:', 'wr') misswrote '%s' != '%s'", buffer, "Test string extra");
    if((internal_buf = hfile_mem_steal_buffer(fin, &interval_buf_len)) == NULL){
        fail("hopen('mem:', 'wr') failed to get internal buffer");
    }
    free(internal_buf);
    if (hclose(fin) != 0) fail("hclose mem for writing");

    fin = hopen("data:,hello, world!%0A", "r");
    if (fin == NULL) fail("hopen(\"data:...\")");
    n = hread(fin, buffer, 300);
    if (n < 0) fail("hread");
    buffer[n] = '\0';
    if (strcmp(buffer, "hello, world!\x0A") != 0) fail("hread result");
    if (hclose(fin) != 0) fail("hclose(\"data:...\")");

    fin = hopen("test/emptyfile", "r");
    if (fin == NULL) fail("hopen(\"test/emptyfile\") for reading");
    if (hread(fin, buffer, 100) != 0) fail("test/emptyfile is non-empty");
    if (hclose(fin) != 0) fail("hclose(\"test/emptyfile\") for reading");

    fin = hopen("data:,", "r");
    if (fin == NULL) fail("hopen(\"data:\") for reading");
    if (hread(fin, buffer, 100) != 0) fail("empty data: URL is non-empty");
    if (hclose(fin) != 0) fail("hclose(\"data:\") for reading");

    fin = hopen("data:;base64,"
// Wikipedia's example quote from Thomas Hobbes' Leviathan
"TWFuIGlzIGRpc3Rpbmd1aXNoZWQsIG5vdCBvbmx5IGJ5IGhpcyByZWFzb24sIGJ1dCBieSB0aGlz"
"IHNpbmd1bGFyIHBhc3Npb24gZnJvbSBvdGhlciBhbmltYWxzLCB3aGljaCBpcyBhIGx1c3Qgb2Yg"
"dGhlIG1pbmQsIHRoYXQgYnkgYSBwZXJzZXZlcmFuY2Ugb2YgZGVsaWdodCBpbiB0aGUgY29udGlu"
"dWVkIGFuZCBpbmRlZmF0aWdhYmxlIGdlbmVyYXRpb24gb2Yga25vd2xlZGdlLCBleGNlZWRzIHRo"
"ZSBzaG9ydCB2ZWhlbWVuY2Ugb2YgYW55IGNhcm5hbCBwbGVhc3VyZS4=", "r");
    if (fin == NULL) fail("hopen(\"data:;base64,...\")");
    n = hread(fin, buffer, 300);
    if (n < 0) fail("hread for base64");
    buffer[n] = '\0';
    if (strcmp(buffer, "Man is distinguished, not only by his reason, but by "
"this singular passion from other animals, which is a lust of the mind, that "
"by a perseverance of delight in the continued and indefatigable generation "
"of knowledge, exceeds the short vehemence of any carnal pleasure.") != 0)
        fail("hread result for base64");
    if (hclose(fin) != 0) fail("hclose(\"data:;base64,...\")");

    kstring_t kstr = { 0, 0, NULL };

    if (strcmp(haddextension(&kstr, "foo/bar.bam", 0, ".bai"),
               "foo/bar.bam.bai") != 0) fail("haddextension foo/bar.bam[.bai]");
    if (strcmp(haddextension(&kstr, "foo/bar.bam", 1, ".bai"),
               "foo/bar.bai") != 0) fail("haddextension foo/bar[.bai]");
    if (strcmp(haddextension(&kstr, "foo.bar/baz", 1, ".bai"),
               "foo.bar/baz.bai") != 0) fail("haddextension foo.bar/baz[.bai]");
    if (strcmp(haddextension(&kstr, "foo#bar.bam", 0, ".bai"),
               "foo#bar.bam.bai") != 0) fail("haddextension foo#bar.bam[.bai]");
    if (strcmp(haddextension(&kstr, ".bam", 1, ".bai"),
               ".bai") != 0) fail("haddextension [.bai]");
    if (strcmp(haddextension(&kstr, "foo", 1, ".csi"),
               "foo.csi") != 0) fail("haddextension foo[.csi]");

    if (strcmp(haddextension(&kstr, "http://host/bar.cram?a&b&c", 0, ".crai"),
               "http://host/bar.cram.crai?a&b&c") != 0)
        fail("haddextension http://host/bar.cram[.crai]?a&b&c");

    if (strcmp(haddextension(&kstr, "http://host/bar.cram#frag", 1, ".crai"),
               "http://host/bar.crai#frag") != 0)
        fail("haddextension http://host/bar[.crai]#frag");

    free(ks_release(&kstr));

    return EXIT_SUCCESS;
}