/usr/lib/ncbi/schema/built-in.vschema is in sra-toolkit 2.1.7a-1ubuntu2.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 | /*===========================================================================
*
* 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.
*
* ===========================================================================
*
*/
/*==========================================================================
* VDB built-in functions, formats and types
*/
version 1;
/*--------------------------------------------------------------------------
* types
*/
// Row id range consist of row_id_start and row_id_stop
typedef I64 vdb:row_id_range [ 2 ];
/*--------------------------------------------------------------------------
* typesets
*/
typeset integer_set { I8, U8, I16, U16, I32, U32, I64, U64 };
typeset float_set { F32, F64 };
typeset numeric_set { integer_set, float_set };
typeset text_set { utf8, utf16, utf32, ascii };
typeset transpose_set { B8, B16, B32, B64 };
/*--------------------------------------------------------------------------
* formats
*/
fmtdef merged_fmt;
fmtdef transposed_fmt;
/*--------------------------------------------------------------------------
* constants
*/
const U8 ALIGN_LEFT = 0;
const U8 ALIGN_RIGHT = 1;
/*--------------------------------------------------------------------------
* functions
*/
/* cast
* performs a "C++ reinterpret_cast" style cast
* rewrites input as required to produce output
*
* legal operations include numeric_set -> numeric_set,
* numeric <-> character, etc.
*/
function
any cast #1.0 ( any in )
= vdb:cast;
/* bit_or
* performs a bitwise operation 'OR' for every byte in A and B
* A and B are not neccesarily have the same size
* the resulting row will have the size of B while OR operation is done for portion of A overlapping B
* For different sizes of A and B 'align' parameter provides what edge of A and B are alligned
* possible values ALIGN_LEFT, ALIGN_RIGHT
*
*/
function < type T >
T bit_or #1 < U8 align > ( T A, T B )
= vdb:bit_or;
/* trim
* performs trimming of value val from column A
* align provides left- or right- trimming
*/
function < type T >
T trim #1 < U8 align, T val > ( T A )
= vdb:trim;
/* redimension
* performs a change of dimension without changing bit pattern
*/
function
any redimension #1.0 ( any in )
= vdb:redimension;
/* row_id
* returns the row id of a request
*/
function
I64 row_id #1.0 ()
= vdb:row_id;
/* row_len
* returns the number of elements in a row
*
* "in" [ DATA ] - column supplying row. if row does not exist
* in column, the resultant length is 0.
*/
function
U32 row_len #1.0 ( any in )
= vdb:row_len;
/* fixed_row_len
* returns non-zero if the entire page
* has a uniform row-length, zero otherwise
*
* "in" [ DATA ] - column to query
*/
function
U32 fixed_row_len #1.0 ( any in )
= vdb:fixed_row_len;
/* compare
* evaluates src [ i ] == cmp [ i ]
* causes writing exception if unequal.
*
* For whole types, equality is bitwise equal
* for floating point types see below.
*
* "T" [ TYPE ] - base element type to be processed
*
* "sig_bits" [ OPTIONAL CONST >= 1 ] - for floating point types, ignored
* otherwise, the number of significant binary digits in the mantissas to
* compare such that |x - y| <= 1, for corresponding numbers x (in a) and
* y (in b) both scaled according to sig_bits and their common magnitude.
* "sig_bits" may be an array, if so "sel" is required (see below).
*
* "src" [ DATA ] - standard input data derived from source
*
* "cmp" [ DATA ] - feedback data after being written and re-read
*
*/
validate function < type T >
void compare #1.0 < * U32 sig_bits > ( T src, T cmp )
= vdb:compare;
validate function < type T >
void no_compare #1.0 ( T src, T cmp )
= vdb:no_compare;
/* compare2f
* evaluates src [ i ] == cmp [ i ]
* causes writing exception if unequal.
*
* "T" [ TYPE ] - base element type to be processed
*
* "sig_bits" [ CONST >= 1 ] - for floating point types, ignored otherwise,
* array containing the number of significant binary digits in the mantissas
* to compare such that |x - y| <= 1, for corresponding numbers x (in a) and
* y (in b) both scaled according to sig_bits and their common magnitude.
*
* "src" [ DATA ] - standard input data derived from source
*
* "cmp" [ DATA ] - feedback data after being written and re-read
*
* "sel" [ DATA ] - data to select which element of "sig_bits" to
* use for the comparison. The valid values of "sel" are
* [0 .. length sig_bits).
*
validate function < type T >
void compare2f #1.0 < U32 sig_bits > ( float_set src, float_set cmp, T sel )
= vdb:compare2f;
*/
/* range_validate
* passes input through if all values fall between lower and
* upper bounds, INCLUSIVE
*
* "T" [ TYPE ] - type to be validated
*
* "lower" [ CONST ] and "upper" [ CONST ] - inclusive
* bounds on input values
*
* "in" [ DATA ] - data to be validated
*/
function < type T >
T range_validate #1.0 < T lower, T upper > ( T in )
= vdb:range_validate;
/* select
* return first non-null input for id
* inputs are taken from first to last
*
* "T" [ TYPE ] - data type of selection
*
* "first" [ DATA ] - first of N inputs
*
* "second" [ DATA ] - second of N inputs
* all other inputs are optional and must
* be compatible with type "T"
*/
function < type T >
T select #1.0 ( T first, T second, ... )
= vdb:select;
/* transpose
* transpose a page of unformatted data
*
* for example - convert a simple page of values,
* where vertical scale is row id and horizontal element index:
*
* 1 2 3
* +---+---+---+
* 1 | a | b | c |
* +---+---+---+
* 2 | d | e | f |
* +---+---+---+
* 3 | g | h | i |
* +---+---+---+
* 4 | j | k | l |
* +---+---+---+
*
* into:
*
* 1 2 3 4
* +---+---+---+---+
* 1 | a | d | g | j |
* +---+---+---+---+
* 2 | b | e | h | k |
* +---+---+---+---+
* 3 | c | f | i | l |
* +---+---+---+---+
*
* variable row-lengths are supported. The output blob is
* formatted, meaning that the result can no longer be addressed
* as a matrix, but the transposition has be applied to data.
*
* "in" [ DATA ] - unformatted data to be transposed
*/
function
transposed_fmt transpose #1 ( transpose_set in )
= vdb:transpose;
/* detranspose
* pardoning the awful name, apply a transposition on the result
* of "transpose" to produce the original blob. "transpose"
* itself cannot be reused because of its signature.
*/
function
transpose_set detranspose #1 ( transposed_fmt in )
= vdb:detranspose;
/* merge
* merges all input blobs of any format/type into a single blob
*/
function
merged_fmt merge #1.0 ( any in, ... )
= vdb:merge;
/* split
* extracts a single blob from a merged blob by index
*
* "idx" [ CONST ] - blob index
*/
function
any split #1.0 < U32 idx > ( merged_fmt in )
= vdb:split;
/* meta:read
* reads table metadata node as a row
* meta:value
* reads metadata node as single value,
* performing size conversion if necessary,
* e.g. I8 TO I64, I32 TO I16
*
* "T" [ TYPE ] - cast data type of metadata node
*
* "node" [ CONST ] - path to metadata node
*/
function < type T >
T meta:read #1.0 < ascii node, * bool deterministic > ();
function < type T >
T meta:value #1.0 < ascii node, * bool deterministic > ();
/* meta:write
* writes row data to table metadata node
*
* "T" [ TYPE ] - cast data type of metadata node
*
* "node" [ CONST ] - path to metadata node
*
* "in" [ DATA ] - source of row data
*/
function < type T >
T meta:write #1.0 < ascii node > ( T in );
/* meta:attr:read
* reads table metadata attribute as a row
*
* "node" [ CONST ] - path to metadata node
*
* "attr" [ CONST ] - attribute name on node
*/
function
ascii meta:attr:read #1.0 < ascii node, ascii attr, * bool deterministic > ();
/* meta:attr:write
* write row data as table metadata attribute
*
* "node" [ CONST ] - path to metadata node
*
* "attr" [ CONST ] - attribute name on node
*/
function
ascii meta:attr:write #1.0 < ascii node, ascii attr > ( ascii in );
/* parameter:read
* reads named cursor parameter text
*
* "name" [ CONST ] - parameter name
*/
function
utf8 parameter:read #1.0 < ascii name, * bool deterministic > ();
/* environment:read
* reads named environment variable text
*
* "name" [ CONST ] - environment variable name
*/
function
utf8 environment:read #1.0 < ascii name > ();
/* idx:text:project
* perform a reverse lookup in an index
* if key not found then use substitute
*
* "index_name" [ CONST ] - name of text index
*
* "substitute" [ DATA, OPTIONAL ] - source
* of values to substitute for values not
* found in the index.
*/
function utf8 idx:text:project #1.0 < ascii index_name > ( * utf8 substitute );
/* idx:text:insert
*/
function utf8 idx:text:insert #1.0 < ascii index_name > ( utf8 key );
/* vdb:row_id_range
*/
function vdb:row_id_range idx:text:lookup #1 < ascii index_name , ascii query_by_name > ();
|