Merge branch 'in-mem-io' into ref

hfile.c

@@ -150,11 +150,12 @@ hFILE *hfile_init_wrapper(size_t struct_size, hFILE* wrapper)
 
     return &fp->base;
 }
+static const struct hFILE_backend mem_backend;
 
 void hfile_destroy(hFILE *fp)
 {
     int save = errno;
-    if (fp) free(fp->buffer);
+    if (fp && fp->backend != &mem_backend) free(fp->buffer);
     free(fp);
     errno = save;
 }
@@ -663,7 +664,7 @@ static hFILE *hopen_fd(const char *filename, const char *mode)
 
 static hFILE *hpreload_fd(const char *filename, const char *mode)
 {
-    if(!strchr(mode, 'r'))
+    if(mode == NULL || !strchr(mode, 'r'))
     {
         return NULL;
     }
@@ -672,21 +673,13 @@ static hFILE *hpreload_fd(const char *filename, const char *mode)
     FILE *file = fopen(filename, mode);
     if (!file) goto error;
 
-    fseek(file, 0, SEEK_END);
+    if(fseek(file, 0, SEEK_END) != 0) goto error;
     int len = ftell(file);
     fseek(file, 0, SEEK_SET);
 
     char* buffer = malloc(len);
-    if(buffer == NULL)
-    {
-        errno = ENOMEM;
-        goto error;
-    }
-    if(fread(buffer, 1, len, file) != len)
-    {
-        errno = EIO;
-        goto error;
-    }
+    if(buffer == NULL) goto error;
+    if(fread(buffer, 1, len, file) != len) goto error;
 
     fp = (hFILE_fd *) hfile_init_fixed(sizeof (hFILE_fd), mode, buffer, len, len);
     if (fp == NULL) goto error;
@@ -798,6 +791,16 @@ static int cmp_prefix(const char *key, const char *s)
     return 0;
 }
 
+static hFILE *create_hfile_mem(char* buffer, const char* mode, size_t buf_filled, size_t buf_size)
+{
+    hFILE_mem *fp = (hFILE_mem *) hfile_init_fixed(sizeof(hFILE_mem), mode, buffer, buf_filled, buf_size);
+    if (fp == NULL)
+        return NULL;
+
+    fp->base.backend = &mem_backend;
+    return &fp->base;
+}
+
 static hFILE *hopen_mem(const char *url, const char *mode)
 {
     size_t length, size;
@@ -821,13 +824,52 @@ static hFILE *hopen_mem(const char *url, const char *mode)
         if (buffer == NULL) return NULL;
         hts_decode_percent(buffer, &length, data);
     }
+    hFILE* hf;
 
-    hFILE_mem *fp = (hFILE_mem *)
-        hfile_init_fixed(sizeof (hFILE_mem), mode, buffer, length, size);
-    if (fp == NULL) { free(buffer); return NULL; }
+    if(!(hf = create_hfile_mem(buffer, mode, length, size))){
+        free(buffer);
+        return NULL;
+    }
 
-    fp->base.backend = &mem_backend;
-    return &fp->base;
+    return hf;
+}
+
+hFILE *hopenv_mem(const char *filename, const char *mode, va_list args)
+{
+    char* buffer = va_arg(args, char*);
+    size_t sz = va_arg(args, size_t);
+    va_end(args);
+
+    hFILE* hf;
+
+    if(!(hf = create_hfile_mem(buffer, mode, sz, sz))){
+        free(buffer);
+        return NULL;
+    }
+
+    return hf;
+}
+
+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;
 }
 
 
@@ -908,44 +950,6 @@ 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)
-{
-    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->is_hFILE_wrapper)
-        file = ((hFILE_wrapper*)file)->wrapper;
-
-    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

test/hfile.c

@@ -217,7 +217,13 @@ int main(void)
         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(hfile_mem_get_buffer(fin, &internal_buf, &interval_buf_len) != 0){
+        fail("hopen('mem:', 'r') failed to get internal buffer");
+    }
     if (hclose(fin) != 0) fail("hclose mem for reading");
+    free(internal_buf);
 
     test_string = strdup("Test string");
     fin = hopen("mem:", "wr:", test_string, 12);
@@ -232,7 +238,11 @@ int main(void)
         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(hfile_mem_get_buffer(fin, &internal_buf, &interval_buf_len) != 0){
+        fail("hopen('mem:', 'wr') failed to get internal buffer");
+    }
     if (hclose(fin) != 0) fail("hclose mem for writing");
+    free(internal_buf);
 
     fin = hopen("data:,hello, world!%0A", "r");
     if (fin == NULL) fail("hopen(\"data:...\")");