This file is indexed.

/usr/include/ncbi-vdb/kfs/impl.h is in libncbi-vdb-dev 2.8.1+dfsg-2.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
/*===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
*  Government have not placed any restriction on its use or reproduction.
*
*  Although all reasonable efforts have been taken to ensure the accuracy
*  and reliability of the software and data, the NLM and the U.S.
*  Government do not and cannot warrant the performance or results that
*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
*  purpose.
*
*  Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/

#ifndef _h_kfs_impl_
#define _h_kfs_impl_

#ifndef _h_kfs_extern_
#include <kfs/extern.h>
#endif

#ifndef _h_kfs_file_impl_
#include <kfs/file-impl.h>
#endif

#ifndef _h_kfs_directory_
#include <kfs/directory.h>
#endif

#ifndef _h_kfs_arrayfile_
#include <kfs/arrayfile.h>
#endif

#ifndef _h_klib_namelist_
#include <klib/namelist.h>
#endif

#if KFILE_VERS != 1 && KDIRECTORY_VERS != 1
#error "include <kfs/file-impl.h> and <kfs/directory-impl.h> separately"
#endif

#ifdef __cplusplus
extern "C" {
#endif


/*--------------------------------------------------------------------------
 * forwards
 */
struct KPath;
struct KBufFile;
struct KSysDir_v1;
struct KSysDir_v2;
typedef union KDirectory_vt KDirectory_vt;

#if KDIRECTORY_VERS == 1
#define KSysDir KSysDir_v1
#elif KDIRECTORY_VERS == 2
#define KSysDir KSysDir_v2
#endif


/*--------------------------------------------------------------------------
 * KDirectory
 *  a virtual directory
 */
struct KDirectory_v1
{
    const KDirectory_vt *vt;
    KRefcount refcount;
    uint8_t read_only;
    uint8_t align [ 3 ];
};

struct KDirectory_v2
{
    const KDirectory_vt *vt;
    KRefcount refcount;
    uint8_t read_only;
    uint8_t align [ 3 ];
};

#ifndef KDIR_IMPL
#define KDIR_IMPL struct KDirectory
#endif

#if KDIRECTORY_VERS == 1
#define KDIRECTORY_V1_IMPL KDIR_IMPL
#define KDIRECTORY_V2_IMPL struct KDirectory_v2
#elif KDIRECTORY_VERS == 2
#define KDIRECTORY_V1_IMPL struct KDirectory_v1
#define KDIRECTORY_V2_IMPL KDIR_IMPL
#else
#error unknown KDirectory version
#endif


typedef struct KDirectory_vt_v1 KDirectory_vt_v1;
struct KDirectory_vt_v1
{
    /* version == 1.x */
    uint32_t maj;
    uint32_t min;

    /* start minor version == 0 */
    rc_t ( CC * destroy ) ( KDIR_IMPL *self );
    rc_t ( CC * list_dir ) ( const KDIR_IMPL *self, struct KNamelist **list,
         bool ( CC * f ) ( const KDirectory *dir, const char *name, void *data ),
         void *data, const char *path, va_list args );
    rc_t ( CC * visit ) ( const KDIR_IMPL *self, bool recur,
        rc_t ( CC * f ) ( const KDirectory*, uint32_t, const char*, void* ),
        void *data, const char *path, va_list args );
    rc_t ( CC * visit_update ) ( KDIR_IMPL *self, bool recur,
        rc_t ( CC * f ) ( KDirectory*, uint32_t, const char*, void* ),
        void *data, const char *path, va_list args );
    uint32_t ( CC * path_type ) ( const KDIR_IMPL *self, const char *path, va_list args );
    rc_t ( CC * resolve_path ) ( const KDIR_IMPL *self, bool absolute,
        char *resolved, size_t rsize, const char *path, va_list args );
    rc_t ( CC * resolve_alias ) ( const KDIR_IMPL *self, bool absolute,
        char *resolved, size_t rsize, const char *alias, va_list args );
    rc_t ( CC * rename ) ( KDIR_IMPL *self, bool force, const char *from, const char *to );
    rc_t ( CC * remove ) ( KDIR_IMPL *self, bool force, const char *path, va_list args );
    rc_t ( CC * clear_dir ) ( KDIR_IMPL *self, bool force, const char *path, va_list args );
    rc_t ( CC * access ) ( const KDIR_IMPL *self,
        uint32_t *access, const char *path, va_list args );
    rc_t ( CC * set_access ) ( KDIR_IMPL *self, bool recur,
        uint32_t access, uint32_t mask, const char *path, va_list args );
    rc_t ( CC * create_alias ) ( KDIR_IMPL *self, uint32_t access,
        KCreateMode mode, const char *targ, const char *alias );
    rc_t ( CC * open_file_read ) ( const KDIR_IMPL *self,
        const KFile **f, const char *path, va_list args );
    rc_t ( CC * open_file_write ) ( KDIR_IMPL *self,
        KFile **f, bool update, const char *path, va_list args );
    rc_t ( CC * create_file ) ( KDIR_IMPL *self, KFile **f, bool update,
        uint32_t access, KCreateMode mode, const char *path, va_list args );
    rc_t ( CC * file_size ) ( const KDIR_IMPL *self,
        uint64_t *size, const char *path, va_list args );
    rc_t ( CC * set_size ) ( KDIR_IMPL *self,
        uint64_t size, const char *path, va_list args );
    rc_t ( CC * open_dir_read ) ( const KDIR_IMPL *self,
        const KDirectory **sub, bool chroot, const char *path, va_list args );
    rc_t ( CC * open_dir_update ) ( KDIR_IMPL *self,
        KDirectory **sub, bool chroot, const char *path, va_list args );
    rc_t ( CC * create_dir ) ( KDIR_IMPL *self, uint32_t access,
        KCreateMode mode, const char *path, va_list args );

    /* optional destructor method - leave NULL if not needed */
    rc_t ( CC * destroy_file ) ( KDIR_IMPL *self, KFile *f );
    /* end minor version == 0 */

    /* start minor version == 1 */
    rc_t ( CC * date ) ( const KDIR_IMPL *self,
        KTime_t * date, const char *path, va_list args );
    rc_t ( CC * setdate ) ( KDIR_IMPL * self, bool recur,
        KTime_t date, const char *path, va_list args );
    struct KSysDir_v1* ( CC * get_sysdir ) ( const KDIR_IMPL *self );
    /* end minor version == 1 */

    /* start minor version == 2 */
    rc_t ( CC * file_locator ) ( const KDIR_IMPL *self,
        uint64_t *locator, const char *path, va_list args );
    /* end minor version == 2 */

    /* start minor version == 3 */
    rc_t ( CC * file_phys_size ) ( const KDIR_IMPL *self,
        uint64_t *phys_size, const char *path, va_list args );
    rc_t ( CC * file_contiguous ) ( const KDIR_IMPL *self,
        bool *contiguous, const char *path, va_list args );
    /* end minor version == 3 */

    /* ANY NEW ENTRIES MUST BE REFLECTED IN libs/kfs/directory.c
       BY BOTH THE CORRESPONDING MESSAGE DISPATCH FUNCTION(s) AND
       VTABLE VALIDITY CHECKS IN KDirectoryInit */
};

typedef struct KDirectory_vt_v2 KDirectory_vt_v2;
struct KDirectory_vt_v2
{
    /* version == 2.x */
    uint32_t maj;
    uint32_t min;

    /* start minor version == 0 */
    void ( CC * destroy ) ( KDIRECTORY_V2_IMPL *self, ctx_t ctx );
    void ( CC * visit ) ( const KDIRECTORY_V2_IMPL *self, ctx_t ctx, bool recur,
        bool ( CC * f ) ( const KDirectory_v2 *dir, uint32_t type, const char *name, void *data ),
        void *data, struct KPath const *path );
    struct KPath * ( CC * resolve_path ) ( const KDIRECTORY_V2_IMPL *self, ctx_t ctx, bool absolute,
        struct KPath const *path );
    void ( CC * rename ) ( KDIRECTORY_V2_IMPL *self, ctx_t ctx, bool force, struct KPath const *from, struct KPath const *to );
    void ( CC * remove ) ( KDIRECTORY_V2_IMPL *self, ctx_t ctx, bool force, struct KPath const *path );
    void ( CC * clear_dir ) ( KDIRECTORY_V2_IMPL *self, ctx_t ctx, bool force, struct KPath const *path );
    void ( CC * create_alias ) ( KDIRECTORY_V2_IMPL *self, ctx_t ctx, uint32_t access,
        KCreateMode mode, struct KPath const *targ, struct KPath const *alias );
    struct KFile_v2 * ( CC * create_file ) ( KDIRECTORY_V2_IMPL *self, ctx_t ctx, bool update,
        uint32_t access, KCreateMode mode, struct KPath const *path );
    void ( CC * create_dir ) ( KDIRECTORY_V2_IMPL *self, ctx_t ctx, uint32_t access,
        KCreateMode mode, struct KPath const *path );

    /* ANY NEW ENTRIES MUST BE REFLECTED IN libs/kfs/directory.c
       BY BOTH THE CORRESPONDING MESSAGE DISPATCH FUNCTION(s) AND
       VTABLE VALIDITY CHECKS IN KDirectoryInit */
};

union KDirectory_vt
{
    KDirectory_vt_v1 v1;
    KDirectory_vt_v2 v2;
};

/* Init
 *  initialize a newly allocated directory object
 */
KFS_EXTERN rc_t CC KDirectoryInit_v1 ( KDirectory_v1 *self, const KDirectory_vt *vt, 
    const char * class_name, const char * path, bool update );

/* DestroyFile
 *  does whatever is necessary with an unreferenced file
 */
KFS_EXTERN rc_t CC KDirectoryDestroyFile_v1 ( const KDirectory_v1 *self, KFile_v1 *f );
KFS_EXTERN void CC KDirectoryDestroyFile_v2 ( const KDirectory_v2 *self, ctx_t ctx, KFile_v2 *f );

/* GetSysDir
 *  returns an underlying system file object
 */
KFS_EXTERN struct KSysDir_v1* CC KDirectoryGetSysDir_v1 ( const KDirectory_v1 *self );
KFS_EXTERN struct KSysDir_v2* CC KDirectoryGetSysDir_v2 ( const KDirectory_v2 *self, ctx_t ctx );


/* RealPath
 *  exposes functionality of system directory
 */
KFS_EXTERN rc_t CC KSysDirRealPath_v1 ( struct KSysDir_v1 const *self,
    char *real, size_t bsize, const char *path, ... );
KFS_EXTERN rc_t CC KSysDirVRealPath ( struct KSysDir_v1 const *self,
    char *real, size_t bsize, const char *path, va_list args );

#define KDirectoryInit NAME_VERS ( KDirectoryInit, KFILE_VERS )
#define KDirectoryDestoryFile NAME_VERS ( KDirectoryDestoryFile, KFILE_VERS )
#define KDirectoryGetSysDir NAME_VERS ( KDirectoryGetSysDir, KFILE_VERS )
#define KSysDirRealPath NAME_VERS ( KSysDirRealPath, KFILE_VERS )


/*--------------------------------------------------------------------------
 * KArrayFile
 *  an array-file is created from a KFile
 */
typedef union  KArrayFile_vt KArrayFile_vt;
struct KArrayFile
{
    const KArrayFile_vt *vt;
    KRefcount refcount;
    uint8_t read_enabled;
    uint8_t write_enabled;
    uint8_t align [ 2 ];
};

#ifndef KARRAYFILE_IMPL
#define KARRAYFILE_IMPL KArrayFile
#endif

typedef struct KArrayFile_vt_v1 KArrayFile_vt_v1;
struct KArrayFile_vt_v1
{
    /* version number */
    uint32_t maj, min;

    /* start minor version == 0 */
    rc_t ( CC * destroy ) ( KARRAYFILE_IMPL *self );
    rc_t ( CC * dimensionality ) ( const KARRAYFILE_IMPL *self, uint8_t *dim );
    rc_t ( CC * set_dimensionality ) ( KARRAYFILE_IMPL *self, uint8_t dim );
    rc_t ( CC * dim_extents ) ( const KARRAYFILE_IMPL *self, uint8_t dim, uint64_t *extents );
    rc_t ( CC * set_dim_extents ) ( KARRAYFILE_IMPL *self, uint8_t dim, uint64_t *extents );
    rc_t ( CC * element_size ) ( const KARRAYFILE_IMPL *self, uint64_t *elem_bits );
    rc_t ( CC * read ) ( const KARRAYFILE_IMPL *self, uint8_t dim,
        const uint64_t *pos, void *buffer, const uint64_t *elem_count,
        uint64_t *num_read );
    rc_t ( CC * write ) ( KARRAYFILE_IMPL *self, uint8_t dim,
        const uint64_t *pos, const void *buffer, const uint64_t *elem_count,
        uint64_t *num_writ );
    rc_t ( CC * get_meta ) ( const KARRAYFILE_IMPL *self, const char *key, 
                             const KNamelist **list );

    rc_t ( CC * read_v ) ( const KARRAYFILE_IMPL *self, uint8_t dim,
        const uint64_t * pos, char * buffer, const uint64_t buffer_size,
        uint64_t * num_read );

    /* end minor version == 0 */
};

union KArrayFile_vt
{
    KArrayFile_vt_v1 v1;
};

/* Init
 *  initialize a newly allocated array-file object
 */
KFS_EXTERN rc_t CC KArrayFileInit ( KArrayFile *self, const KArrayFile_vt *vt, 
    bool read_enabled, bool write_enabled );


#ifdef __cplusplus
}
#endif

#endif /* _h_kfs_impl_ */