/********************************************************************** * cbf_write -- write files * * * * Version 0.7.6 14 July 2006 * * * * Paul Ellis and * * Herbert J. Bernstein (yaya@bernstein-plus-sons.com) * * * * (C) Copyright 2006 Herbert J. Bernstein * * * **********************************************************************/ /********************************************************************** * * * YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL * * * * ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS * * OF THE LGPL * * * **********************************************************************/ /*************************** GPL NOTICES ****************************** * * * This program is free software; you can redistribute it and/or * * modify it under the terms of the GNU General Public License as * * published by the Free Software Foundation; either version 2 of * * (the License, or (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program; if not, write to the Free Software * * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA * * 02111-1307 USA * * * **********************************************************************/ /************************* LGPL NOTICES ******************************* * * * This library is free software; you can redistribute it and/or * * modify it under the terms of the GNU Lesser General Public * * License as published by the Free Software Foundation; either * * version 2.1 of the License, or (at your option) any later version. * * * * This library is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * * Lesser General Public License for more details. * * * * You should have received a copy of the GNU Lesser General Public * * License along with this library; if not, write to the Free * * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, * * MA 02110-1301 USA * * * **********************************************************************/ /********************************************************************** * * * Stanford University Notices * * for the CBFlib software package that incorporates SLAC software * * on which copyright is disclaimed * * * * This software * * ------------- * * The term Ôthis softwareÕ, as used in these Notices, refers to * * those portions of the software package CBFlib that were created by * * employees of the Stanford Linear Accelerator Center, Stanford * * University. * * * * Stanford disclaimer of copyright * * -------------------------------- * * Stanford University, owner of the copyright, hereby disclaims its * * copyright and all other rights in this software. Hence, anyone * * may freely use it for any purpose without restriction. * * * * Acknowledgement of sponsorship * * ------------------------------ * * This software was produced by the Stanford Linear Accelerator * * Center, Stanford University, under Contract DE-AC03-76SFO0515 with * * the Department of Energy. * * * * Government disclaimer of liability * * ---------------------------------- * * Neither the United States nor the United States Department of * * Energy, nor any of their employees, makes any warranty, express or * * implied, or assumes any legal liability or responsibility for the * * accuracy, completeness, or usefulness of any data, apparatus, * * product, or process disclosed, or represents that its use would * * not infringe privately owned rights. * * * * Stanford disclaimer of liability * * -------------------------------- * * Stanford University makes no representations or warranties, * * express or implied, nor assumes any liability for the use of this * * software. * * * * Maintenance of notices * * ---------------------- * * In the interest of clarity regarding the origin and status of this * * software, this and all the preceding Stanford University notices * * are to remain affixed to any copy or derivative of this software * * made or distributed by the recipient and are to be affixed to any * * copy of software made or distributed by the recipient that * * contains a copy or derivative of this software. * * * * Based on SLAC Software Notices, Set 4 * * OTT.002a, 2004 FEB 03 * **********************************************************************/ /********************************************************************** * 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_ascii.h" #include "cbf_binary.h" #include "cbf_compress.h" #include "cbf_file.h" #include "cbf_tree.h" #include "cbf_write.h" #include "cbf_write_binary.h" #include "cbf_read_mime.h" #include "cbf_string.h" #include "cbf_ws.h" #include #include #include #include int cbf_value_type (char *value); static char wordtok[5] = "word"; static char texttok[5] = "text"; static char dblqtok[5] = "dblq"; static char sglqtok[5] = "sglq"; static char nulltok[5] = "null"; static char tsqstok[5] = "tsqs"; static char tdqstok[5] = "tdqs"; static char prnstok[5] = "prns"; static char brcstok[5] = "brcs"; static char bktstok[5] = "bkts"; /* Get the value type of an ascii string */ int cbf_get_value_type(const char *value, const char **value_type) { /* Prepare an empty return */ *value_type = NULL; /* Is the value missing? */ if (!value) return 0; /* Is the value valid? */ if ((*value & '\200') != '\200') return CBF_ARGUMENT; /* Has the value already been checked? */ if ((value [0] & '\300') != '\300') { cbf_failnez(cbf_value_type((char *)value)) } if (*value == CBF_TOKEN_WORD) { *value_type = wordtok; return 0; } if (*value == CBF_TOKEN_SQSTRING) { *value_type = sglqtok; return 0; } if (*value == CBF_TOKEN_DQSTRING) { *value_type = dblqtok; return 0; } if (*value == CBF_TOKEN_SCSTRING) { *value_type = texttok; return 0; } if (*value == CBF_TOKEN_BKTSTRING) { *value_type = bktstok; return 0; } if (*value == CBF_TOKEN_BRCSTRING) { *value_type = brcstok; return 0; } if (*value == CBF_TOKEN_PRNSTRING) { *value_type = prnstok; return 0; } if (*value == CBF_TOKEN_TDQSTRING) { *value_type = tdqstok; return 0; } if (*value == CBF_TOKEN_TSQSTRING) { *value_type = tsqstok; return 0; } if (*value == CBF_TOKEN_NULL) { *value_type = nulltok; return 0; } return CBF_ARGUMENT; } /* Set the value type of an ascii string */ int cbf_set_value_type(cbf_handle handle,char *value, const char *value_type) { char *cptr; /* Is the value type missing? */ if (!value) return CBF_ARGUMENT; /* Is the value valid? */ if ((*value & '\200') != '\200') return CBF_ARGUMENT; /* Has the value already been checked? */ if ((value [0] & '\300') != '\300') { cbf_failnez(cbf_value_type(value)) } if (strcmp(value_type,wordtok) == 0) { if ( strcmp(&value[1],".") == 0 || strcmp(&value[1],"?") == 0 || *value == CBF_TOKEN_WORD ) { *value = CBF_TOKEN_WORD; return 0; } return CBF_ARGUMENT; } if (strcmp(value_type,nulltok) == 0) { if ( strcmp(&value[1],".") == 0 || strcmp(&value[1],"?") == 0) { *value = CBF_TOKEN_NULL; return 0; } return CBF_ARGUMENT; } if (strcmp(value_type,sglqtok) == 0) { if(strstr(&value[1],"' ") || strstr(&value[1],"'\t") || strstr(&value[1],"\n")) { return CBF_ARGUMENT; } *value = CBF_TOKEN_SQSTRING; return 0; } if (strcmp(value_type,dblqtok) == 0 ) { if(strstr(&value[1],"\" ") || strstr(&value[1],"\"\t") || strstr(&value[1],"\n")) { return CBF_ARGUMENT; } *value = CBF_TOKEN_DQSTRING; return 0; } if (strcmp(value_type,texttok) == 0 ) { cptr = &value[1]; while (*cptr && (cptr=strstr(cptr,"\n;")) ) { if (isspace(cptr[2])) { cbf_log(handle,"text field contains terminator, will be folded on output",CBF_LOGWARNING); break; } if (*cptr) cptr++; } *value = CBF_TOKEN_SCSTRING; return 0; } if (strcmp(value_type,tsqstok) == 0 ) { cptr = &value[1]; while (*cptr && (cptr=strstr(cptr,"'''")) ) { if (isspace(cptr[2])) { cbf_log(handle, "triple singled-quoted field contains terminator, will be folded on output",CBF_LOGWARNING); break; } if (*cptr) cptr++; } *value = CBF_TOKEN_TSQSTRING; return 0; } if (strcmp(value_type,tdqstok) == 0 ) { cptr = &value[1]; while (*cptr && (cptr=strstr(cptr,"\"\"\"")) ) { if (isspace(cptr[3])) { cbf_log(handle, "triple double-quoted field contains terminator, will be folded on output",CBF_LOGWARNING); break; } if (*cptr) cptr++; } *value = CBF_TOKEN_TDQSTRING; return 0; } if (strcmp(value_type,prnstok) == 0 ) { *value = CBF_TOKEN_PRNSTRING; return 0; } if (strcmp(value_type,brcstok) == 0 ) { *value = CBF_TOKEN_BRCSTRING; return 0; } if (strcmp(value_type,bktstok) == 0 ) { *value = CBF_TOKEN_BKTSTRING; return 0; } return CBF_ARGUMENT; } /* Check the value type */ int cbf_value_type (char *value) { int test [6], C, count; /* Is the value missing? */ if (!value) return 0; /* Is the value valid? */ if ((*value & '\200') != '\200') return CBF_ARGUMENT; /* Has the value already been checked? */ if ((value [0] & '\300') == '\300') return 0; /* Properties */ memset (test, 0, sizeof (test)); for (count = 1; value [count]; count++) { C = toupper (value [count]); test [0] |= isspace (C); test [1] |= C == '\n'; test [2] |= C == '\''; test [3] |= C == '"'; if (count <= 5) { test [4] |= C != " DATA_" [count]; test [5] |= C != " LOOP_" [count]; if (count <= 1) test [0] |= C == '_' || C == '\'' || C == '"' || C == '#'; } } if (count <= 5) test[4]=test[5]=1; test [0] |= strcmp (&value [1], "?") == 0; test [0] |= strcmp (&value [1], ".") == 0; /* Simple word? */ if (!test [0] && test [4] && test [5]) *value = CBF_TOKEN_WORD; else /* Single line? */ if (!test [1] && (!test [2] || !test [3])) { if (!test [2]) *value = CBF_TOKEN_SQSTRING; else *value = CBF_TOKEN_DQSTRING; } else /* Multiple lines */ *value = CBF_TOKEN_SCSTRING; /* Success */ return 0; } /* Write a datablock name to a file */ static int cbf_write_datablockname (const cbf_node *datablock, cbf_file *file) { /* Does the node exist? */ if (!datablock) return CBF_ARGUMENT; /* Write the name */ if (datablock->name) { cbf_failnez (cbf_write_string (file, "\ndata_")) cbf_failnez (cbf_write_string (file, datablock->name)) cbf_failnez (cbf_write_character (file, '\n')) } else if (datablock->children) cbf_failnez (cbf_write_string (file, "\ndata_\n")) /* Success */ return 0; } /* Write a save frame name to a file */ static int cbf_write_saveframename (const cbf_node *saveframe, cbf_file *file) { /* Does the node exist? */ if (!saveframe) return CBF_ARGUMENT; /* Write the name */ if (saveframe->name) { cbf_failnez (cbf_write_string (file, "\nsave_")) cbf_failnez (cbf_write_string (file, saveframe->name)) cbf_failnez (cbf_write_character (file, '\n')) } else if (saveframe->children) cbf_failnez (cbf_write_string (file, "\nsave_(none)\n")) /* Success */ return 0; } /* Compose an item name from a category and column */ int cbf_compose_itemname (cbf_handle handle, const cbf_node *column, char * itemname, size_t limit) { cbf_node *category; char column_fill[1] = "\0"; char * tempcat; char * tempcol; int ipos; itemname[0] = itemname[limit] = '\0'; /* Get the category */ cbf_failnez (cbf_find_parent (&category, column, CBF_CATEGORY)) /* Check that the name is valid */ if (!category->name && !column->name) { strncpy (itemname, "_(null)", limit ); return CBF_ARGUMENT; } /* construct the item name */ if (column->name) { tempcol = (char *)column->name; } else { tempcol = column_fill; } if (!category->name || !(category->name[0]) || !cbf_cistrcmp("(none)",category->name) || tempcol[0]=='_') { strncpy(itemname,tempcol,limit); if (strlen(tempcol) > limit) return CBF_ARGUMENT; } else { if(!category->name) return CBF_ARGUMENT; itemname[0] = '_'; cbf_failnez( cbf_require_category_root(handle,category->name,(const char **)&tempcat)) strncpy(itemname+1,tempcat,limit-1); if (strlen(tempcat) > 72 || strlen(tempcat) > limit-1) return CBF_ARGUMENT; ipos = strlen(itemname); if ( ipos < (ssize_t)limit ) itemname[ipos++] = '.'; if ( limit-ipos > 0) strncpy(itemname+ipos,tempcol,limit-ipos); if (strlen(tempcol)+ipos+2 > 75 || strlen(tempcol)+ipos+2 > limit) return CBF_ARGUMENT; } return 0; } /* Write an item name to a file */ static int cbf_write_itemname (cbf_handle handle, const cbf_node *column, cbf_file *file) { char itemname[81]; char buffer[255]; char * temptag; /* Compose the tag and get the root alias */ if ( cbf_compose_itemname (handle, column, itemname, (size_t )80)) { strcpy (itemname+77,"..."); sprintf (buffer, "output line %u(%u) column name too long or invalid\n converted to \"%s\"", 1+file->line, 1+file->column, itemname); cbf_log(handle,buffer,CBF_LOGWARNING|CBF_LOGCURRENTLOC); } cbf_failnez( cbf_require_tag_root(handle,(const char *)itemname,(const char **)&temptag)) /* Write the tag name */ cbf_failnez (cbf_write_string (file, temptag)) /* Success */ return 0; } /* Write a value to a file */ static int cbf_write_value (cbf_handle handle, cbf_node *column, unsigned int row, cbf_file *file, int isbuffer) { const char *text; /* Check the arguments */ if (!column) return CBF_ARGUMENT; if (row >= column->children) return CBF_NOTFOUND; /* Get the value */ cbf_failnez (cbf_get_columnrow (&text, column, row)) /* Missing value? */ if (!text) return cbf_write_ascii (handle, text, file); /* Plain ASCII? */ cbf_failnez (cbf_value_type ((char *) text)) if (*text == CBF_TOKEN_WORD || *text == CBF_TOKEN_SQSTRING || *text == CBF_TOKEN_DQSTRING || *text == CBF_TOKEN_SCSTRING || *text == CBF_TOKEN_TSQSTRING || *text == CBF_TOKEN_TDQSTRING || *text == CBF_TOKEN_PRNSTRING || *text == CBF_TOKEN_BKTSTRING || *text == CBF_TOKEN_BRCSTRING || *text == CBF_TOKEN_NULL) return cbf_write_ascii (handle, text, file); /* Plain binary? */ if (*text == CBF_TOKEN_BIN || *text == CBF_TOKEN_TMP_BIN) return cbf_write_binary (column, row, file, isbuffer); /* Undecoded MIME? */ if (*text == CBF_TOKEN_MIME_BIN) { /* Convert the value to a normal binary section */ cbf_failnez (cbf_mime_temp (column, row)) return cbf_write_binary (column, row, file, isbuffer); } /* Fail */ return CBF_ARGUMENT; } /* Write a category to a file */ static int cbf_write_category (cbf_handle handle, const cbf_node *category, cbf_file *file, int isbuffer) { unsigned int count, first, last=0, column, columns, row, maxrows, matrixcount; int loop, matrix, len; const char * column_name; /* Check the arguments */ if (!category) return CBF_ARGUMENT; /* Print out columns of the same length in loops unless the number of rows is 1 */ maxrows = 0; matrix = 0; for (first = 0, loop = 1; first < category->children; first = last) { columns = 1; if (category->child [first] && category->child [first]->children > maxrows) maxrows = category->child [first]->children; if (category->child [first]) { for (last = first + 1; last < category->children; last++) if (category->child [last]) { if (category->child [last]->children != category->child [first]->children) { if (category->child [last]->children > maxrows) maxrows = category->child [last]->children; break; } columns++; } /* check for a matrix */ matrix = 0; matrixcount = 0; for (count = first ; count < last; count++) { column_name = (category->child [count])->name; if (column_name) { len = strlen(column_name); if ((len > 0 && column_name[len-1]==']') || (len > 4 && !cbf_cistrncmp("]_esd",(char *)column_name+len-5,5))) { matrixcount++; if (matrixcount > ((last-first+1)>>1)+1) { matrix = 1; break; } } } } /* Make a loop? */ if ( matrix || (maxrows > 1 && (columns > 1 || category->child [first]->children > 1))) { cbf_failnez (cbf_write_string (file, "\nloop_\n")) loop = 1; } else { cbf_failnez (cbf_write_character (file, '\n')) loop = 0; } /* Write the items for a loop */ if (loop) for (count = first; count < last; count++) { cbf_failnez (cbf_write_itemname (handle, category->child [count], file)) cbf_failnez (cbf_write_character (file, '\n')) } /* Write the values */ for (row = 0; row < category->child [first]->children; row++) { unsigned int xcol; for (column = first; column < last; column++) { if (!loop) { cbf_failnez (cbf_write_itemname (handle, category->child [column], file)) } if (matrix) { column_name = (category->child [column])->name; if (column_name) { len = strlen(column_name); if ((len > 2 && !cbf_cistrncmp("[1]",(char *)column_name+len-3,3)) || (len > 6 && !cbf_cistrncmp("[1]_esd",(char *)column_name+len-7,7))) { cbf_failnez (cbf_write_character (file, '\n')) } } } cbf_failnez (cbf_write_value (handle, category->child [column], row, file, isbuffer)) if (!loop) { cbf_failnez (cbf_write_character (file, '\n')) } } cbf_failnez (cbf_get_filecoordinates (file, NULL, &xcol)) if (xcol) cbf_failnez (cbf_write_character (file, '\n')) } } } /* Success */ return 0; } /* Write a node to a file */ int cbf_write_node (cbf_handle handle, const cbf_node *node, cbf_file *file, int isbuffer) { unsigned int count; /* Follow any links */ node = cbf_get_link (node); /* Does the node exist? */ if (!node) return CBF_ARGUMENT; /* Write any appropriate white space prologue */ cbf_failnez(cbf_write_ws_prologue(node, file, isbuffer)) /* Node type */ switch (node->type) { /* For the root, suppress automatic comments if whitespace handling has been specified */ case CBF_ROOT: if ( (file->write_headers & CBF_PARSE_WS) == 0 ) { cbf_failnez (cbf_write_string (file, "###" CBF_DIC_VERSION "\n")) if (file->write_encoding & ENC_NONE) { cbf_failnez (cbf_write_string (file, "# CBF file written by " CBF_API_VERSION "\n")) } else { cbf_failnez (cbf_write_string (file, "# CIF file written by " CBF_API_VERSION "\n")) } } break; case CBF_DATABLOCK: cbf_failnez (cbf_write_datablockname (node, file)) break; case CBF_CATEGORY: cbf_failnez (cbf_write_category (handle, node, file, isbuffer)) break; case CBF_SAVEFRAME: cbf_failnez (cbf_write_saveframename (node, file)) break; default: return CBF_ARGUMENT; } /* Write any appropriate white space emlogue */ cbf_failnez(cbf_write_ws_emlogue(node, file, isbuffer)) /* Write the children */ if (node->type == CBF_ROOT || node->type == CBF_DATABLOCK || node->type == CBF_SAVEFRAME) for (count = 0; count < node->children; count++) cbf_failnez (cbf_write_node (handle, node->child [count], file, isbuffer)) if (node->type == CBF_SAVEFRAME ) cbf_failnez (cbf_write_string (file, "\nsave_\n")) /* Write any appropriate white space epilogue */ if ( (file->write_headers & CBF_PARSE_WS) != 0 ) { cbf_failnez(cbf_write_ws_epilogue(node, file, isbuffer)) } /* Flush the buffers */ return cbf_flush_characters (file); } #ifdef __cplusplus } #endif