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Add in-memory I/O using hFILE fixed buffers #590

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80bb84f
Add in-memory I/O
ThomasHickman Sep 11, 2017
58fb979
Add better error handling in hpreload_fd
ThomasHickman Sep 12, 2017
29a6789
Add create_hfile_mem
ThomasHickman Sep 12, 2017
5cd9e07
Move mem backend code to the correct section
ThomasHickman Sep 12, 2017
3972015
Fix issues with mem hfile
ThomasHickman Sep 12, 2017
3d11377
Free hFILE buffer when erroring
ThomasHickman Sep 13, 2017
3656732
Stop freeing hfile mem buffers in hclose
ThomasHickman Sep 22, 2017
fde4dcf
Fixes to PR#590.
jkbonfield Dec 7, 2017
5fa67e9
Create preload scheme
ThomasHickman Dec 12, 2017
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95 changes: 93 additions & 2 deletions hfile.c
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Original file line number Diff line number Diff line change
Expand Up @@ -404,7 +404,7 @@ off_t hseek(hFILE *fp, off_t offset, int whence)
{
off_t curpos, pos;

if (writebuffer_is_nonempty(fp)) {
if (writebuffer_is_nonempty(fp) && fp->mobile) {
int ret = flush_buffer(fp);
if (ret < 0) return ret;
}
Expand Down Expand Up @@ -615,6 +615,47 @@ static hFILE *hopen_fd(const char *filename, const char *mode)
return NULL;
}

static hFILE *hpreload_fd(const char *filename, const char *mode)
{
if(!strchr(mode, 'r'))
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@valeriuo valeriuo Sep 12, 2017

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You should check mode value. If NULL, strchr will seg fault.

{
return NULL;
}

hFILE_fd *fp = NULL;
FILE *file = fopen(filename, mode);
if (!file) goto error;

fseek(file, 0, SEEK_END);
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@jkbonfield jkbonfield Sep 11, 2017

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You need to check the return value of fseek, incase someone has given a non-seekable stream to this function. (Eg /dev/stdin)

int len = ftell(file);
fseek(file, 0, SEEK_SET);

char* buffer = malloc(len);
if(buffer == NULL)
{
errno = ENOMEM;
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@jkbonfield jkbonfield Sep 11, 2017

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Manually setting errno isn't recommended. Malloc will do this itself, as would the fread below. Indeed we're obscuring the fread return as it may have other more meaningful errno values.

goto error;
}
if(fread(buffer, 1, len, file) != len)
{
errno = EIO;
goto error;
}

fp = (hFILE_fd *) hfile_init_fixed(sizeof (hFILE_fd), mode, buffer, len, len);
if (fp == NULL) goto error;

fp->fd = fileno(file);
fp->is_socket = 0;
fp->base.backend = &fd_backend;
return &fp->base;

error:
if (file) { int save = errno; (void) fclose(file); errno = save; }
hfile_destroy((hFILE *) fp);
return NULL;
}

hFILE *hdopen(int fd, const char *mode)
{
hFILE_fd *fp = (hFILE_fd*) hfile_init(sizeof (hFILE_fd), mode, blksize(fd));
Expand Down Expand Up @@ -821,6 +862,41 @@ static int init_add_plugin(void *obj, int (*init)(struct hFILE_plugin *),
return 0;
}

hFILE *hopenv_mem(const char *filename, const char *mode, va_list args)
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@jkbonfield jkbonfield Sep 11, 2017

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I'm wondering if the existing hopen_mem, which is strictly URL based rather than generic memory based, should be reimplemented in terms of the generic hopenv_mem.

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@ThomasHickman ThomasHickman Sep 12, 2017

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Looks like a good idea, though in hopenv_mem there isn't (and I don't think it would be a good idea to) a way to specify a different buffer size from the length of the buffer that is filled - this is needed in hopen_mem. I think it would be a good to create a function create_hfile_mem, which would do the functionality in common with both functions (which I have implemented below)

{
char* buffer = va_arg(args, char*);
size_t sz = va_arg(args, size_t);
va_end(args);

hFILE_mem *fp = (hFILE_mem *) hfile_init_fixed(sizeof(hFILE_mem), mode, buffer, sz, sz);

fp->base.backend = &mem_backend;

return &fp->base;
}

int hfile_mem_get_buffer(hFILE *file, char **buffer, size_t *length){
if(file->backend != &mem_backend) {
errno = EINVAL;
return -1;
}

*buffer = file->buffer;
*length = file->buffer - file->limit;

return 0;
}

int hfile_plugin_init_mem(struct hFILE_plugin *self)
{
// mem files are declared remote so they work with a tabix index
static const struct hFILE_scheme_handler handler =
{NULL, hfile_always_remote, "mem", 2000 + 50, hopenv_mem};
self->name = "mem";
hfile_add_scheme_handler("mem", &handler);
return 0;
}

static void load_hfile_plugins()
{
static const struct hFILE_scheme_handler
Expand All @@ -833,6 +909,7 @@ static void load_hfile_plugins()
hfile_add_scheme_handler("data", &data);
hfile_add_scheme_handler("file", &file);
init_add_plugin(NULL, hfile_plugin_init_net, "knetfile");
init_add_plugin(NULL, hfile_plugin_init_mem, "mem");

#ifdef ENABLE_PLUGINS
struct hts_path_itr path;
Expand Down Expand Up @@ -879,11 +956,25 @@ static hFILE *hopen_unknown_scheme(const char *fname, const char *mode)
return fp;
}

static hFILE *hopenv_unknown_scheme(const char *fname, const char *mode, va_list args)
{
char* method_type = va_arg(args, char*);
va_end(args);
if(!strcmp(method_type, "preload")){
errno = EPROTONOSUPPORT;
return NULL;
}

hFILE *fp = hpreload_fd(fname, mode);
if (fp == NULL && errno == ENOENT) errno = EPROTONOSUPPORT;
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@jkbonfield jkbonfield Dec 6, 2017

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I'm unsure why this line exists. hpreload_fd can return NULL/ENOENT for valid reasons, and ENOENT is suitable then I think.

return fp;
}

/* Returns the appropriate handler, or NULL if the string isn't an URL. */
static const struct hFILE_scheme_handler *find_scheme_handler(const char *s)
{
static const struct hFILE_scheme_handler unknown_scheme =
{ hopen_unknown_scheme, hfile_always_local, "built-in", 0 };
{ hopen_unknown_scheme, hfile_always_local, "built-in", 2000 + 50, hopenv_unknown_scheme };

char scheme[12];
int i;
Expand Down
17 changes: 15 additions & 2 deletions htslib/hfile.h
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Original file line number Diff line number Diff line change
Expand Up @@ -202,7 +202,7 @@ hread(hFILE *fp, void *buffer, size_t nbytes)
if (n > nbytes) n = nbytes;
memcpy(buffer, fp->begin, n);
fp->begin += n;
return (n == nbytes)? (ssize_t) n : hread2(fp, buffer, nbytes, n);
return (n == nbytes || !fp->mobile)? (ssize_t) n : hread2(fp, buffer, nbytes, n);
}

/// Write a character to the stream
Expand Down Expand Up @@ -239,7 +239,15 @@ static inline ssize_t HTS_RESULT_USED
hwrite(hFILE *fp, const void *buffer, size_t nbytes)
{
extern ssize_t hwrite2(hFILE *, const void *, size_t, size_t);

extern int hfile_set_blksize(hFILE *fp, size_t bufsiz);

if(!fp->mobile){
if (fp->limit - fp->begin < nbytes){
hfile_set_blksize(fp, fp->limit - fp->buffer + nbytes);
fp->end = fp->limit;
}
}

size_t n = fp->limit - fp->begin;
if (n > nbytes) n = nbytes;
memcpy(fp->begin, buffer, n);
Expand All @@ -254,6 +262,11 @@ This includes low-level flushing such as via `fdatasync(2)`.
*/
int hflush(hFILE *fp) HTS_RESULT_USED;

/// For hfile_mem: get the internal buffer and it's size from a hfile
/** @return 0 if successful, or -1 if an error occurred
*/
int hfile_mem_get_buffer(hFILE *file, char **buffer, size_t *length);

#ifdef __cplusplus
}
#endif
Expand Down
32 changes: 32 additions & 0 deletions test/hfile.c
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Expand Up @@ -202,6 +202,38 @@ int main(void)
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("test/hfile_chars.tmp", "r:", "preload");
if (fin == NULL) fail("preloading hopen(\"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);
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, strdup(" 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 (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);
Expand Down