/********************************************************************** * cbf_read_mime -- read MIME-encoded binary sections * * * * Version 0.7.4 12 January 2004 * * * * Paul Ellis (ellis@ssrl.slac.stanford.edu) and * * Herbert J. Bernstein (yaya@bernstein-plus-sons.com) * **********************************************************************/ /********************************************************************** * NOTICE * * Creative endeavors depend on the lively exchange of ideas. There * * are laws and customs which establish rights and responsibilities * * for authors and the users of what authors create. This notice * * is not intended to prevent you from using the software and * * documents in this package, but to ensure that there are no * * misunderstandings about terms and conditions of such use. * * * * Please read the following notice carefully. If you do not * * understand any portion of this notice, please seek appropriate * * professional legal advice before making use of the software and * * documents included in this software package. In addition to * * whatever other steps you may be obliged to take to respect the * * intellectual property rights of the various parties involved, if * * you do make use of the software and documents in this package, * * please give credit where credit is due by citing this package, * * its authors and the URL or other source from which you obtained * * it, or equivalent primary references in the literature with the * * same authors. * * * * Some of the software and documents included within this software * * package are the intellectual property of various parties, and * * placement in this package does not in any way imply that any * * such rights have in any way been waived or diminished. * * * * With respect to any software or documents for which a copyright * * exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT. * * * * Even though the authors of the various documents and software * * found here have made a good faith effort to ensure that the * * documents are correct and that the software performs according * * to its documentation, and we would greatly appreciate hearing of * * any problems you may encounter, the programs and documents any * * files created by the programs are provided **AS IS** without any * * warranty as to correctness, merchantability or fitness for any * * particular or general use. * * * * THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF * * PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE * * PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS * * OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE * * PROGRAMS OR DOCUMENTS. * **********************************************************************/ /********************************************************************** * * * The IUCr Policy * * for the Protection and the Promotion of the STAR File and * * CIF Standards for Exchanging and Archiving Electronic Data * * * * Overview * * * * The Crystallographic Information File (CIF)[1] is a standard for * * information interchange promulgated by the International Union of * * Crystallography (IUCr). CIF (Hall, Allen & Brown, 1991) is the * * recommended method for submitting publications to Acta * * Crystallographica Section C and reports of crystal structure * * determinations to other sections of Acta Crystallographica * * and many other journals. The syntax of a CIF is a subset of the * * more general STAR File[2] format. The CIF and STAR File approaches * * are used increasingly in the structural sciences for data exchange * * and archiving, and are having a significant influence on these * * activities in other fields. * * * * Statement of intent * * * * The IUCr's interest in the STAR File is as a general data * * interchange standard for science, and its interest in the CIF, * * a conformant derivative of the STAR File, is as a concise data * * exchange and archival standard for crystallography and structural * * science. * * * * Protection of the standards * * * * To protect the STAR File and the CIF as standards for * * interchanging and archiving electronic data, the IUCr, on behalf * * of the scientific community, * * * * * holds the copyrights on the standards themselves, * * * * * owns the associated trademarks and service marks, and * * * * * holds a patent on the STAR File. * * * * These intellectual property rights relate solely to the * * interchange formats, not to the data contained therein, nor to * * the software used in the generation, access or manipulation of * * the data. * * * * Promotion of the standards * * * * The sole requirement that the IUCr, in its protective role, * * imposes on software purporting to process STAR File or CIF data * * is that the following conditions be met prior to sale or * * distribution. * * * * * Software claiming to read files written to either the STAR * * File or the CIF standard must be able to extract the pertinent * * data from a file conformant to the STAR File syntax, or the CIF * * syntax, respectively. * * * * * Software claiming to write files in either the STAR File, or * * the CIF, standard must produce files that are conformant to the * * STAR File syntax, or the CIF syntax, respectively. * * * * * Software claiming to read definitions from a specific data * * dictionary approved by the IUCr must be able to extract any * * pertinent definition which is conformant to the dictionary * * definition language (DDL)[3] associated with that dictionary. * * * * The IUCr, through its Committee on CIF Standards, will assist * * any developer to verify that software meets these conformance * * conditions. * * * * Glossary of terms * * * * [1] CIF: is a data file conformant to the file syntax defined * * at http://www.iucr.org/iucr-top/cif/spec/index.html * * * * [2] STAR File: is a data file conformant to the file syntax * * defined at http://www.iucr.org/iucr-top/cif/spec/star/index.html * * * * [3] DDL: is a language used in a data dictionary to define data * * items in terms of "attributes". Dictionaries currently approved * * by the IUCr, and the DDL versions used to construct these * * dictionaries, are listed at * * http://www.iucr.org/iucr-top/cif/spec/ddl/index.html * * * * Last modified: 30 September 2000 * * * * IUCr Policy Copyright (C) 2000 International Union of * * Crystallography * **********************************************************************/ /********************************************************************** * The following notice applies to some portions of this software * * which were derived in part from the routine decode.c in mpack * * * * (C) Copyright 1993,1994 by Carnegie Mellon University * * All Rights Reserved. * * * * Permission to use, copy, modify, distribute, and sell this * * softwareand its documentation for any purpose is hereby granted * * without fee, provided that the above copyright notice appear in * * all copies and that both that copyright notice and this permission * * notice appear in supporting documentation, and that the name of * * Carnegie Mellon University not be used in advertising or publicity * * pertaining to distribution of the software without specific, * * written prior permission. Carnegie Mellon University makes no * * representations about the suitability of this software for any * * purpose. It is provided "as is" without express or implied * * warranty. * * * * CARNEGIE MELLON UNIVERSITY DISCLAIMS ALL WARRANTIES WITH REGARD TO * * THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY * * AND FITNESS, IN NO EVENT SHALL CARNEGIE MELLON UNIVERSITY BE * * LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY * * DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, * * WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS * * ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR * * PERFORMANCE OF THIS SOFTWARE. * **********************************************************************/ #ifdef __cplusplus extern "C" { #endif #include "cbf.h" #include "cbf_file.h" #include "cbf_context.h" #include "cbf_binary.h" #include "cbf_codes.h" #include "cbf_read_mime.h" #include "cbf_string.h" #include #include /* Convert a MIME-encoded binary section to a temporary binary section */ int cbf_mime_temp (cbf_node *column, unsigned int row) { cbf_file *file; cbf_file *temp_file; long start, temp_start; size_t size; int id, bits, sign, type, checked_digest; unsigned int compression; char old_digest [25], *new_digest, digest [25]; /* Check the value */ if (!cbf_is_mimebinary (column, row)) return CBF_ASCII; /* Parse it */ size = 0; cbf_failnez (cbf_get_bintext (column, row, &type, &id, &file, &start, &size, &checked_digest, old_digest, &bits, &sign, &compression)) /* Position the file at the start of the mime section */ cbf_failnez (cbf_set_fileposition (file, start, SEEK_SET)) /* Get the temporary file */ cbf_failnez (cbf_open_temporary (column->context, &temp_file)) /* Move to the end of the temporary file */ cbf_onfailnez (cbf_set_fileposition (temp_file, 0, SEEK_END), cbf_delete_fileconnection (&temp_file)) /* Get the starting location */ cbf_onfailnez (cbf_get_fileposition (temp_file, &temp_start), cbf_delete_fileconnection (&temp_file)) /* Calculate a new digest if necessary */ if (cbf_is_base64digest (old_digest) && (file->read_headers & MSG_DIGEST) && !checked_digest) new_digest = digest; else new_digest = NULL; /* Decode the binary data to the temporary file */ cbf_onfailnez (cbf_read_mime (file, temp_file, NULL, NULL, old_digest, new_digest), cbf_delete_fileconnection (&temp_file)) /* Check the digest */ if (new_digest) if (strcmp (old_digest, new_digest) == 0) checked_digest = 1; else return CBF_FORMAT | cbf_delete_fileconnection (&temp_file); /* Replace the connection */ cbf_onfailnez (cbf_set_bintext (column, row, CBF_TOKEN_TMP_BIN, id, temp_file, temp_start, size, checked_digest, old_digest, bits, sign, compression), cbf_delete_fileconnection (&temp_file)) /* Success */ return 0; } /* Convert a MIME-encoded binary section to a normal binary section */ int cbf_read_mime (cbf_file *infile, cbf_file *outfile, size_t *size, long *id, char *old_digest, char *new_digest) { int encoding; size_t file_size; unsigned int compression; /* Read the header */ encoding = 0; file_size = 0; cbf_failnez (cbf_parse_mimeheader (infile, &encoding, &file_size, id, old_digest, &compression, NULL, NULL)) if (file_size <= 0) return CBF_FORMAT; /* Discard any bits in the buffers */ cbf_failnez (cbf_reset_bits (outfile)) /* Decode the binary data */ switch (encoding) { case ENC_QP: cbf_failnez (cbf_fromqp (infile, outfile, file_size, NULL, new_digest)) break; case ENC_BASE64: cbf_failnez (cbf_frombase64 (infile, outfile, file_size, NULL, new_digest)) break; case ENC_BASE8: case ENC_BASE10: case ENC_BASE16: cbf_failnez (cbf_frombasex (infile, outfile, file_size, NULL, new_digest)) break; default: return CBF_FORMAT; } /* Flush the buffers */ cbf_failnez (cbf_flush_bits (outfile)) /* Size (excluding the encoding) */ if (size) *size = file_size; /* Success */ return 0; } /* Is the line blank? */ int cbf_is_blank (const char *line) { if (line) for (; *line; line++) if (!isspace (*line)) return 0; return 1; } /* Find non-blank length of a line */ int cbf_nblen (const char *line, size_t *nblen) { register char *myline; register size_t mylen; *nblen = mylen = 0; if (!(myline = (char *)line)) return 1; for (; *myline; myline++) if (!isspace (*myline)) mylen = myline-(char *)line+1; *nblen = mylen; return 0; } /* Skip whitespace and comments */ int cbf_skip_whitespace (cbf_file *file, const char **line, const char **curpoint, int *freshline) { static const char end = '\0'; const char *c; int comment_level; /* Repeating the end of a line? */ if (*freshline) { *curpoint = &end; return 0; } c = *curpoint; comment_level = 0; while (isspace (*c) || *c == '(' || *c == '\0') if (*c == '\0') { cbf_failnez (cbf_read_line (file, line)) c = *line; if (cbf_is_blank (c) || (*c != ' ' && *c != '\t')) { *freshline = 1; *curpoint = &end; return 0; } } else if (*c == '(') { c++; comment_level++; while (comment_level) { switch (*c) { case '\0': cbf_failnez (cbf_read_line (file, line)) c = *line; if (cbf_is_blank (c) || (*c != ' ' && *c != '\t')) { *freshline = 1; *curpoint = &end; return 0; } break; case '\\': c++; break; case '(': comment_level++; break; case ')': comment_level--; break; } c++; } } else c++; *freshline = 0; *curpoint = c; /* Success */ return 0; } /* Parse the MIME header looking for values of type: Content-Type: Content-Transfer-Encoding: X-Binary-Size: X-Binary-ID: X-Binary-Element-Type: Content-MD5: */ int cbf_parse_mimeheader (cbf_file *file, int *encoding, size_t *size, long *id, char *digest, unsigned int *compression, int *bits, int *sign) { static const char *value [] = { "Content-Type:", /* State 0 */ "Content-Transfer-Encoding:", /* State 1 */ "X-Binary-Size:", /* State 2 */ "X-Binary-ID:", /* State 3 */ "X-Binary-Element-Type:", /* State 4 */ "Content-MD5:" /* State 5 */ }; const char *line, *c; int state, continuation, item, line_count, fresh_line, quote, text_bits, count, failure=0; size_t nblen; /* Defaults */ if (encoding) *encoding = 0; if (size) *size = 0; if (id) *id = 0; if (digest) *digest = '\0'; if (compression) *compression = CBF_NONE; if (bits) *bits = 0; if (sign) *sign = -1; /* Read the file line by line */ state = -1; line_count = 0; fresh_line = 0; nblen = 1; while (nblen) { if (!fresh_line) cbf_failnez (cbf_read_line (file, &line)) cbf_nblen (line, &nblen); fresh_line = 0; line_count++; /* Check for premature terminations */ if ( (line[0] == ';') || ( cbf_cistrncmp(line,"--CIF-BINARY-FORMAT-SECTION--",29) == 0 ) ) return CBF_FORMAT; /* Check for a header continuation line */ continuation = line [0] == ' ' || line [0] == '\t'; /* Check for a new item */ if (continuation) item = 0; else { for (c = line; *c != ':' && *c > 32 && *c < 127; c++); item = c != line && *c == ':'; } /* Check for the end of the header */ if (line_count > 1 && cbf_is_blank (line)) return 0; /* Check for valid header-ness of line */ if (!item && (line_count == 1 || !continuation)) return CBF_FORMAT; /* Look for the entries we are interested in */ c = line; if (item) for (state = 5; state > -1; state--) if (cbf_cistrncmp (line, value [state], strlen (value [state])) == 0) { c = line + strlen (value [state]); break; } /* Skip past comments and whitespace */ cbf_failnez (cbf_skip_whitespace (file, &line, &c, &fresh_line)) /* Get the value */ switch (state) { case 0: /* Content */ if (cbf_cistrncmp (c, "application/", 12) != 0 && cbf_cistrncmp (c, "image/", 6) != 0 && cbf_cistrncmp (c, "text/", 5) != 0 && cbf_cistrncmp (c, "audio/", 6) != 0 && cbf_cistrncmp (c, "video/", 6) != 0) return CBF_FORMAT; while (*c) { /* Skip to the end of the section (a semicolon) */ while (*c) if (*c == '\"') { c++; while (*c) if (*c == '\"') { c++; break; } else { if (*c == '\\') c++; if (*c) c++; } } else if (*c == '(') cbf_failnez (cbf_skip_whitespace (file, &line, &c, &fresh_line)) else if (*c == ';') { c++; break; } else c++; /* We are at the end of the section or the end of the item */ cbf_failnez (cbf_skip_whitespace (file, &line, &c, &fresh_line)) if (cbf_cistrncmp (c, "conversions", 11) == 0) { c += 11; cbf_failnez (cbf_skip_whitespace (file, &line, &c, &fresh_line)) if (*c == '=') { c++; cbf_failnez (cbf_skip_whitespace (file, &line, &c, &fresh_line)) if (compression) { quote = 0; if (*c == '\"') quote = 1; *compression = CBF_NONE; if (cbf_cistrncmp (c + quote, "x-cbf_packed", 12) == 0) *compression = CBF_PACKED; if (cbf_cistrncmp (c + quote, "x-cbf_canonical", 15) == 0) *compression = CBF_CANONICAL; if (cbf_cistrncmp (c + quote, "x-cbf_byte_offset", 17) == 0) *compression = CBF_BYTE_OFFSET; if (cbf_cistrncmp (c + quote, "x-cbf_predictor", 15) == 0) *compression = CBF_PREDICTOR; } } } } state = -1; break; case 1: /* Binary encoding */ if (encoding) { failure = 1; quote = 0; if (*c == '\"') quote = 1; if (cbf_cistrncmp (c+quote, "Quoted-Printable", 16) == 0) if (isspace (c [16]) || c [16] == '(' || (quote && c [16] == '\"')) { failure = 0; *encoding = ENC_QP; } if (cbf_cistrncmp (c+quote, "Base64", 6) == 0) if (isspace (c [6]) || c [6] == '(' || (quote && c [16] == '\"')) { failure = 0; *encoding = ENC_BASE64; } if (cbf_cistrncmp (c+quote, "X-Base8", 7) == 0) if (isspace (c [7]) || c [7] == '(' || (quote && c [16] == '\"')) { failure = 0; *encoding = ENC_BASE8; } if (cbf_cistrncmp (c+quote, "X-Base10", 8) == 0) if (isspace (c [8]) || c [8] == '(' || (quote && c [16] == '\"')) { failure = 0; *encoding = ENC_BASE10; } if (cbf_cistrncmp (c+quote, "X-Base16", 8) == 0) if (isspace (c [8]) || c [8] == '(' || (quote && c [16] == '\"')) { failure = 0; *encoding = ENC_BASE16; } if (cbf_cistrncmp (c+quote, "7bit", 4) == 0 || cbf_cistrncmp (c+quote, "8bit", 4) == 0) if (isspace (c [4]) || c [4] == '(' || (quote && c [16] == '\"')) { failure = 0; *encoding = ENC_NONE; } if (cbf_cistrncmp (c+quote, "Binary", 6) == 0) if (isspace (c [6]) || c [6] == '(' || (quote && c [16] == '\"')) { failure = 0; *encoding = ENC_NONE; } } if (failure) return CBF_FORMAT; break; case 2: /* Binary size */ if (size) *size = atol (c); break; case 3: /* Binary ID */ if (id) *id = atol (c); break; case 4: /* Binary element type (signed/unsigned ?-bit integer) */ failure = 3; while (*c) { quote = 0; cbf_failnez (cbf_skip_whitespace (file, &line, &c, &fresh_line)) if (*c == '\"') { if (quote) break; c++; quote++; } if (failure == 3) { if (cbf_cistrncmp (c, "signed", 6) == 0) { c += 6; if (sign) *sign = 1; failure --; } if (cbf_cistrncmp (c, "unsigned", 8) == 0) { c += 8; if (sign) *sign = 0; failure --; } } if (failure == 2) { count = 0; sscanf (c, "%d-%n", &text_bits, &count); if (cbf_cistrncmp (c+count, "bit", 3 ) == 0) if (count && text_bits > 0 && text_bits <= 64) { c += count; if (bits) *bits = text_bits; failure --; } } if (failure == 1) { if (cbf_cistrncmp (c, "integer", 7 ) == 0) failure--; } if (*c) c++; } if (failure) return CBF_FORMAT; break; case 5: /* Message digest */ if (digest) { strncpy (digest, c, 24); digest [24] = '\0'; } break; } } /* Success */ return 0; } #ifdef __cplusplus } #endif