/********************************************************************** * cbf_write_binary -- write 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 * **********************************************************************/ #ifdef __cplusplus extern "C" { #endif #include "cbf.h" #include "cbf_tree.h" #include "cbf_compress.h" #include "cbf_context.h" #include "cbf_binary.h" #include "cbf_codes.h" #include #include #include #include #include "cbf_write_binary.h" /* Write a binary value */ int cbf_write_binary (cbf_node *column, unsigned int row, cbf_file *file, int isbuffer) { cbf_file *infile; char digest [25], text [100]; long start; size_t size; unsigned int compression; int id, bits, sign, type, checked_digest, elsize; /* Check the arguments */ if (!file) return CBF_ARGUMENT; if (((file->write_encoding & ENC_QP) > 0) + ((file->write_encoding & ENC_BASE64) > 0) + ((file->write_encoding & ENC_BASE8) > 0) + ((file->write_encoding & ENC_BASE10) > 0) + ((file->write_encoding & ENC_BASE16) > 0) + ((file->write_encoding & ENC_NONE) > 0) != 1) return CBF_ARGUMENT; if (!cbf_is_binary (column, row)) return CBF_ARGUMENT; if (cbf_is_mimebinary (column, row)) return CBF_ARGUMENT; /* Parse the value */ cbf_failnez (cbf_get_bintext (column, row, &type, &id, &infile, &start, &size, &checked_digest, digest, &bits, &sign, &compression)) /* Position the file at the start of the binary section */ cbf_failnez (cbf_set_fileposition (infile, start, SEEK_SET)) /* Calculate the digest if necessary */ if (!cbf_is_base64digest (digest) && (file->write_headers & MSG_DIGEST)) { /* Discard any bits in the buffers */ cbf_failnez (cbf_reset_bits (infile)) /* Compute the message digest */ cbf_failnez (cbf_md5digest (infile, size, digest)) /* Go back to the start of the binary data */ cbf_failnez (cbf_set_fileposition (infile, start, SEEK_SET)) /* Update the entry */ checked_digest = 1; cbf_failnez (cbf_set_bintext (column, row, type, id, infile, start, size, checked_digest, digest, bits, sign, compression)) } /* Discard any bits in the buffers */ cbf_failnez (cbf_reset_bits (infile)) /* Do we need MIME headers? */ if (compression == CBF_NONE && (file->write_headers & MIME_NOHEADERS)) return CBF_ARGUMENT; /* Write the header */ cbf_failnez (cbf_write_string (file, "\n;\n")) /* MIME header? */ if (file->write_headers & MIME_HEADERS) { cbf_failnez (cbf_write_string (file, "--CIF-BINARY-FORMAT-SECTION--\n")) if (compression == CBF_NONE) cbf_failnez (cbf_write_string (file, "Content-Type: application/octet-stream\n")) else { cbf_failnez (cbf_write_string (file, "Content-Type: application/octet-stream;\n")) switch (compression) { case CBF_PACKED: cbf_failnez (cbf_write_string (file, " conversions=\"x-CBF_PACKED\"\n")) break; case CBF_CANONICAL: cbf_failnez (cbf_write_string (file, " conversions=\"x-CBF_CANONICAL\"\n")) break; case CBF_BYTE_OFFSET: cbf_failnez (cbf_write_string (file, " conversions=\"x-CBF_BYTE_OFFSET\"\n")) break; case CBF_PREDICTOR: cbf_failnez (cbf_write_string (file, " conversions=\"x-CBF_PREDICTOR\"\n")) break; default: cbf_failnez (cbf_write_string (file, " conversions=\"x-CBF_UNKNOWN\"\n")) } } if (file->write_encoding & ENC_QP) cbf_failnez (cbf_write_string (file, "Content-Transfer-Encoding: QUOTED-PRINTABLE\n")) else if (file->write_encoding & ENC_BASE64) cbf_failnez (cbf_write_string (file, "Content-Transfer-Encoding: BASE64\n")) else if (file->write_encoding & ENC_BASE8) cbf_failnez (cbf_write_string (file, "Content-Transfer-Encoding: X-BASE8\n")) else if (file->write_encoding & ENC_BASE10) cbf_failnez (cbf_write_string (file, "Content-Transfer-Encoding: X-BASE10\n")) else if (file->write_encoding & ENC_BASE16) cbf_failnez (cbf_write_string (file, "Content-Transfer-Encoding: X-BASE16\n")) else cbf_failnez (cbf_write_string (file, "Content-Transfer-Encoding: BINARY\n")) sprintf (text, "X-Binary-Size: %lu\n", (long)size); cbf_failnez (cbf_write_string (file, text)) sprintf (text, "X-Binary-ID: %d\n", id); cbf_failnez (cbf_write_string (file, text)) if (sign) sprintf (text, "X-Binary-Element-Type: \"signed %d-bit integer\"\n", bits); else sprintf (text, "X-Binary-Element-Type: \"unsigned %d-bit integer\"\n", bits); cbf_failnez (cbf_write_string (file, text)) /* Save the digest if we have one */ if (cbf_is_base64digest (digest)) { sprintf (text, "Content-MD5: %24s\n", digest); cbf_failnez (cbf_write_string (file, text)) } cbf_failnez (cbf_write_string (file, "\n")) } else /* Simple header */ cbf_failnez (cbf_write_string (file, "START OF BINARY SECTION\n")) /* Copy the binary section to the output file */ if (file->write_encoding & ENC_NONE) { /* Write the separators */ cbf_failnez (cbf_put_character (file, 12)) cbf_failnez (cbf_put_character (file, 26)) cbf_failnez (cbf_put_character (file, 4)) cbf_failnez (cbf_put_character (file, 213)) /* Flush any bits in the buffers */ cbf_failnez (cbf_flush_bits (file)) /* If no MIME header, write the necessary data here */ if ( !(file->write_headers & MIME_HEADERS) ) { /* Write the binary identifier (64 bits) */ cbf_failnez (cbf_put_integer (file, id, 1, 64)) /* Write the size of the binary section (64 bits) */ cbf_failnez (cbf_put_integer (file, size, 0, 64)) /* Write the compression type (64 bits) */ cbf_failnez (cbf_put_integer (file, compression, 0, 64)) } /* Get the current point in the new file */ cbf_failnez (cbf_get_fileposition (file, &start)) /* Copy the binary section to the output file */ cbf_failnez (cbf_copy_file (file, infile, size)) } else { /* Read the element size with no compression? */ if (compression == CBF_NONE) { elsize = (bits + 4) / 8; if (elsize < 1 || elsize == 5) elsize = 4; else if (elsize == 7) elsize = 6; else if (elsize > 8) elsize = 8; } else elsize = 4; /* Go back to the start of the binary data */ cbf_failnez (cbf_set_fileposition (infile, start, SEEK_SET)) /* Flush any bits in the buffers */ cbf_failnez (cbf_flush_bits (infile)) if (file->write_encoding & ENC_QP) cbf_failnez (cbf_toqp (infile, file, size)) else if (file->write_encoding & ENC_BASE64) cbf_failnez (cbf_tobase64 (infile, file, size)) else if (file->write_encoding & ENC_BASE8) cbf_failnez (cbf_tobasex (infile, file, size, elsize, 8)) else if (file->write_encoding & ENC_BASE10) cbf_failnez (cbf_tobasex (infile, file, size, elsize, 10)) else cbf_failnez (cbf_tobasex (infile, file, size, elsize, 16)) } /* Write the MIME footer */ if (file->write_headers & MIME_HEADERS) cbf_failnez (cbf_write_string (file, "\n--CIF-BINARY-FORMAT-SECTION----\n;\n")) else cbf_failnez (cbf_write_string (file, "\nEND OF BINARY SECTION\n;\n")) /* Flush the buffer */ cbf_failnez (cbf_flush_characters (file)) /* Replace a connection to a temporary file? */ if (start != 0 && isbuffer && type == CBF_TOKEN_TMP_BIN && (file->write_encoding & ENC_NONE)) cbf_failnez (cbf_set_bintext (column, row, CBF_TOKEN_BIN, id, file, start, size, checked_digest, digest, bits, sign, compression)) /* Success */ return 0; } #ifdef __cplusplus } #endif