/* tomedlin.c * =========================================================================== * * 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. * * =========================================================================== * * File Name: tomedlin.c * * Author: Jonathan Kans * * Version Creation Date: 10/15/91 * * $Revision: 6.8 $ * * File Description: conversion to medlars format * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * $Log: tomedlin.c,v $ * Revision 6.8 2001/10/29 20:37:06 kans * MakeAuthorString for structured authors * * Revision 6.7 2001/10/22 13:37:12 kans * break up huge author list * * Revision 6.6 2001/10/15 12:24:05 kans * MedlineEntryToDataFile breaks up long mesh, substance, and xref lists * * Revision 6.5 1999/10/26 20:17:04 kans * allocate separate string for abstract since some may be very long * * Revision 6.4 1999/10/01 17:20:08 kans * fixed stack overflow found by DV * * Revision 6.3 1999/03/11 23:32:08 kans * sprintf casts * * Revision 6.2 1998/06/12 20:05:50 kans * fixed unix compiler warnings * * Revision 6.1 1997/12/02 17:42:29 kans * added cast in sprintf * * Revision 6.0 1997/08/25 18:07:55 madden * Revision changed to 6.0 * * Revision 5.16 1997/06/19 18:39:27 vakatov * [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization * * Revision 5.15 1997/04/14 18:02:31 grisha * set MedlarsEntryToDataFile() to be external * * Revision 5.14 1997/04/11 16:24:13 levitsky * *** empty log message *** * * Revision 5.13 1997/04/11 15:58:58 levitsky * New functions for support tomedlars added * * Revision 5.12 1997/04/10 18:16:06 levitsky * New version of MEDLARS output * * Revision 5.11 1997/04/08 19:35:43 levitsky * *** empty log message *** * * Revision 5.10 1997/04/08 17:30:46 levitsky * fixed break error * * Revision 5.9 1997/04/07 21:34:40 levitsky * Added SO field for medlars report * * Revision 5.8 1997/03/19 18:06:23 kans * fixed use of mep->pub_type * * Revision 5.7 1997/03/19 16:53:08 levitsky * publication type added to output * * Revision 5.6 1997/02/20 21:25:17 kans * added MedlineEntryToAbsFile and MedlarsEntryToAbsFile * * Revision 5.5 1997/02/19 15:09:22 levitsky * pmid added to output * * Revision 5.4 1997/02/12 21:30:02 grisha * add code to support MEDLARS report generation * for MedlarsEntry * * Revision 5.3 1997/01/27 16:15:39 grisha * Fix bugs with SO field generation * * Revision 5.2 1996/08/27 23:10:43 kans * protect prefixes (e.g., van, el, den) with initials that can be * mistaken for suffixes (e.g., I). this won't protect against * names with the Van incorrectly entered at the end. * * Revision 5.1 1996/05/31 21:04:12 kans * check for individual suffixes before stripping * * Revision 5.0 1996/05/28 13:23:23 ostell * Set to revision 5.0 * * Revision 4.2 1996/01/23 20:59:15 kans * now allows iso-jta as well as ml-jta * * Revision 4.1 1995/12/27 17:50:11 kans * changed StringAppend to StrngAppend to avoid conflict with future ncbistr.h * * Revision 4.0 1995/07/26 13:49:01 ostell * force revision to 4.0 * * Revision 2.5 1995/05/15 21:46:05 ostell * added Log line * * * * ========================================================================== */ #include #include #include #ifdef VAR_ARGS #include #else #include #endif #ifdef COMP_MPW #pragma segment CdrSegD #endif #define BUFSIZE 8192 static CharPtr buffer; static CharPtr pos; /* ----- Function Prototypes ----- */ static void ClearString PROTO((void)); static void AddString PROTO((CharPtr string)); static CharPtr CleanAuthorString PROTO((CharPtr auth)); static CharPtr CDECL StrngAppend VPROTO((CharPtr first, ...)); /* ----- Function Bodies ----- */ static void ClearString (void) { pos = buffer; *pos = '\0'; } static void AddString (CharPtr string) { pos = StringMove (pos, string); *pos = '\0'; } static ColData table [2] = {{0, 6, 0, 'l', TRUE, TRUE, FALSE}, {0, 72, 0, 'l', TRUE, TRUE, TRUE}}; static Char *months[13] = {"", "Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"}; NLM_EXTERN Boolean MedlineEntryToDataFile (MedlineEntryPtr mep, FILE *fp) { CharPtr abstract; AffilPtr affil; AuthListPtr authors = NULL; CitArtPtr cit; CitJourPtr citjour; Int2 count; DatePtr date = NULL; ValNodePtr gene; Int2 i; ImprintPtr imp = NULL; CharPtr issue = NULL; size_t len; MedlineMeshPtr mesh; ValNodePtr names; CharPtr p; CharPtr pages = NULL; ParData para; CharPtr ptr; ValNodePtr qual; Boolean rsult; Char str [32]; MedlineRnPtr substance; ValNodePtr title; CharPtr tmp; CharPtr volume = NULL; ValNodePtr xref; CharPtr lpTemp; CharPtr lpMedAbbr = NULL; CharPtr lpMedCode = NULL; CharPtr lpIssn = NULL; rsult = TRUE; buffer = MemNew (BUFSIZE); if (buffer != NULL) { para.openSpace = FALSE; ClearString (); AddString ("UI -\t"); sprintf (str, "%ld", (long) mep->uid); AddString (str); AddString ("\n"); rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); if ( mep->pmid > 0 ) { ClearString (); AddString ("PM -\t"); sprintf (str, "%ld", (long) mep->pmid); AddString (str); AddString ("\n"); rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); } if ( mep->pub_type != NULL ) { ClearString (); AddString ("PT -\t"); AddString ((CharPtr) mep->pub_type->data.ptrvalue); AddString ("\n"); rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); } cit = mep->cit; if (cit != NULL) { authors = cit->authors; if (authors != NULL && (authors->choice == 2 || authors->choice == 3)) { names = authors->names; count = 0; while (names != NULL) { if (count >= 20) { rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); count = 0; } AddString ("AU -\t"); AddString (names->data.ptrvalue); AddString ("\n"); names = names->next; count++; } } rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); title = cit->title; count = 0; while (title != NULL) { if (count >= 20) { rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); count = 0; } if (title->choice == 1) { AddString ("TI -\t"); AddString (title->data.ptrvalue); AddString ("\n"); } title = title->next; count++; } rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); } mesh = mep->mesh; count = 0; while (mesh != NULL) { if (count >= 20) { rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); count = 0; } AddString ("MH -\t"); if (mesh->mp) { AddString ("*"); } AddString (mesh->term); qual = mesh->qual; while (qual != NULL) { AddString ("/"); if (qual->choice != 0) { AddString ("*"); } p = (CharPtr) qual->data.ptrvalue; while (*p != '\0') { *p = TO_UPPER (*p); p++; } AddString (qual->data.ptrvalue); qual = qual->next; } AddString ("\n"); mesh = mesh->next; count++; } rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); substance = mep->substance; count = 0; while (substance != NULL) { if (count >= 20) { rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); count = 0; } AddString ("RN -\t"); switch (substance->type) { case 0: AddString ("0 ("); AddString (substance->name); AddString (")"); break; case 1: AddString (substance->cit); AddString (" ("); AddString (substance->name); AddString (")"); break; case 2: AddString ("EC "); AddString (substance->cit); AddString (" ("); AddString (substance->name); AddString (")"); break; default: break; } AddString ("\n"); substance = substance->next; count++; } rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); gene = mep->gene; while (gene != NULL) { AddString ("GS -\t"); AddString (gene->data.ptrvalue); AddString ("\n"); gene = gene->next; } xref = mep->xref; count = 0; while (xref != NULL) { if (count >= 20) { rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); count = 0; } AddString ("SI -\t"); switch (xref->choice) { case 1: AddString ("DDBJ/"); break; case 2: AddString ("CARBBANK/"); break; case 3: AddString ("EMBL/"); break; case 4: AddString ("HDB/"); break; case 5: AddString ("GENBANK/"); break; case 6: AddString ("HGML/"); break; case 7: AddString ("MIM/"); break; case 8: AddString ("MSD/"); break; case 9: AddString ("PDB/"); break; case 10: AddString ("PIR/"); break; case 11: AddString ("PRFSEQDB/"); break; case 12: AddString ("PSD/"); break; case 13: AddString ("SWISSPROT/"); break; default: AddString ("?/"); break; } AddString (xref->data.ptrvalue); AddString ("\n"); xref = xref->next; count++; } rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); citjour = cit->fromptr; if (citjour != NULL) { imp = citjour->imp; if (imp != NULL) { date = imp->date; if (date != NULL) { switch (date->data [0]) { case 0: AddString ("DP -\t"); StringNCpy (str, date->str, sizeof (str) - 1); AddString (str); AddString ("\n"); break; case 1: AddString ("DP -\t"); sprintf (str, "%d", date->data [1] + 1900); AddString (str); AddString (" "); i = date->data [2]; if (i >= 0 && i <= 11) { AddString (months [i]); } if (date->data [3] > 0) { AddString (" "); sprintf (str, "%d", date->data [3]); AddString (str); } AddString ("\n"); default: break; } } } title = citjour->title; while (title != NULL) { if ( title->choice == Cit_title_jta ) { lpTemp = "JC -\t"; lpMedCode = title->data.ptrvalue; } else if ( title->choice == Cit_title_ml_jta ) { lpTemp = "TA -\t"; lpMedAbbr = title->data.ptrvalue; } else if ( title->choice == Cit_title_issn ) { lpTemp = "IS -\t"; lpIssn = title->data.ptrvalue; } else { title = title->next; continue; } AddString (lpTemp); AddString (title->data.ptrvalue); AddString ("\n"); title = title->next; } if (imp != NULL) { pages = imp->pages; if (pages != NULL) { AddString ("PG -\t"); AddString (pages); AddString ("\n"); } issue = imp->issue; if (issue != NULL) { AddString ("IP -\t"); AddString (issue); AddString ("\n"); } volume = imp->volume; if (volume != NULL) { AddString ("VI -\t"); AddString (volume); AddString ("\n"); } } } rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); abstract = mep->abstract; if (abstract != NULL) { len = StringLen (abstract); tmp = (CharPtr) MemNew (sizeof (Char) * (len + 10)); ptr = StringMove (tmp, "AB -\t"); ptr = StringMove (ptr, abstract); ptr = StringMove (ptr, "\n"); rsult = (Boolean) (SendTextToFile (fp, tmp, ¶, table) && rsult); MemFree (tmp); } ClearString (); if (cit != NULL && authors != NULL) { affil = authors->affil; if (affil != NULL && affil->choice == 1) { AddString ("AD -\t"); AddString (affil->affil); AddString ("\n"); } } if (citjour != NULL && imp != NULL) { AddString ("SO -\t"); if ( lpMedAbbr != NULL ) { AddString(lpMedAbbr); } else if ( lpIssn != NULL ) { AddString(lpIssn); } else if ( lpMedCode != NULL ) { AddString(lpMedCode); } AddString (" "); if (date != NULL) { switch (date->data [0]) { case 0: StringNCpy (str, date->str, sizeof (str) - 1); AddString (str); AddString (";"); break; case 1: sprintf (str, "%d", date->data [1] + 1900); AddString (str); AddString (" "); i = date->data [2]; if (i >= 0 && i <= 11) { AddString (months [i]); } if (date->data [3] > 0) { AddString (" "); sprintf (str, "%d", date->data [3]); AddString (str); } AddString (";"); default: break; } } if (volume != NULL) { AddString (volume); } if (issue != NULL) { AddString ("("); AddString (issue); AddString (")"); } if (pages != NULL) { AddString (":"); AddString (pages); } AddString ("\n"); } rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, table) && rsult); ClearString (); buffer = MemFree (buffer); } return rsult; } #ifdef VAR_ARGS static CharPtr CDECL StrngAppend (first, va_alist) CharPtr first; va_dcl #else static CharPtr CDECL StrngAppend (CharPtr first, ...) #endif { va_list args; Uint2 len; CharPtr rsult; CharPtr str; #ifdef VAR_ARGS va_start (args); #else va_start (args, first); #endif len = (Uint2) StringLen (first); str = va_arg (args, CharPtr); while (str != NULL) { len += StringLen (str); str = va_arg (args, CharPtr); } va_end(args); #ifdef VAR_ARGS va_start (args); #else va_start (args, first); #endif rsult = MemNew (len + 1); StringCpy (rsult, first); str = va_arg (args, CharPtr); while (str != NULL) { StringCat (rsult, str); str = va_arg (args, CharPtr); } va_end(args); return rsult; } static CharPtr suffixes [] = {"Jr", "Sr", "I", "II", "III", "IV", "V", "VI", "1st", "2nd", "3rd", "4th", "5th", "6th", "1d", "2d", "3d", NULL}; static CharPtr prefixes [] = {"van ", "ten ", "ter ", "Mac ", "Mc ", "el ", "al ", "Ben ", "ben ", "Bar ", "den ", NULL}; static CharPtr CleanAuthorString (CharPtr auth) { Char ch; CharPtr first; Int2 i; CharPtr last; Uint4 len; CharPtr p; CharPtr per; CharPtr ps; CharPtr str; if (StringLen (auth) > 0) { if (StringCmp (auth, "et al") == 0) { str = StringSave ("..."); } else { p = NULL; first = NULL; last = StringSave (auth); ps = StringRChr (last, ' '); if (ps != NULL && ps != StringChr (last, ' ')) { i = 0; while (prefixes [i] != NULL) { len = StringLen (prefixes [i]); if (len > 0 && StringNCmp (last, prefixes [i], len) == 0) { last [len - 1] = '_'; } i++; } ps = StringRChr (last, ' '); } if (ps != NULL && ps != StringChr (last, ' ')) { per = StringChr (ps, '.'); if (per != NULL) { *per = '\0'; } i = 0; while (suffixes [i] != NULL) { if (StringCmp (ps + 1, suffixes [i]) == 0) { *ps = '\0'; } i++; } /* p = ps + 1; while (*p != '\0') { if (! IS_UPPER(*p)) { *ps = '\0'; p = ps; } else { p++; } } */ } ps = StringRChr (last, ' '); if (ps != NULL) { p = ps + 1; *ps = '\0'; } if (p != NULL) { len = StringLen (p); first = MemNew (3 * (size_t) len + 1); i = 0; while (*p != '\0') { first [i] = *p; i++; first [i] = '.'; i++; first [i] = ' '; i++; p++; } } ps = last; ch = *ps; while (ch != '\0') { if (ch == '_') { *ps = ' '; } ps++; ch = *ps; } if (first != NULL) { str = StrngAppend (first, (CharPtr) last, (CharPtr) NULL); last = MemFree (last); first = MemFree (first); } else { str = last; } } } else { str = StringSave (""); } return str; } static CharPtr MakeAuthorString ( CharPtr name, CharPtr initials, CharPtr suffix ) { Char ch; size_t len; CharPtr ptr; CharPtr str; CharPtr tmp; if (name == NULL) return NULL; len = StringLen (name) + StringLen (initials) * 3 + StringLen (suffix); str = MemNew (sizeof (Char) * (len + 4)); if (str == NULL) return NULL; tmp = str; ptr = initials; if (! StringHasNoText (initials)) { ch = *ptr; while (ch != '\0') { if (ch == '-') { *tmp = '-'; tmp++; } else if (ch != '.') { *tmp = ch; tmp++; *tmp = '.'; tmp++; *tmp = ' '; tmp++; } ptr++; ch = *ptr; } *tmp = '\0'; } tmp = StringMove (tmp, name); if (! StringHasNoText (suffix)) { tmp = StringMove (tmp, " "); tmp = StringMove (tmp, suffix); } return str; } NLM_EXTERN MedlinePtr ParseMedline (MedlineEntryPtr mep) { AffilPtr affil; AuthorPtr ap; AuthListPtr authors; CharPtr chptr; CitArtPtr cit; CitJourPtr citjour; CharPtr curr; DatePtr date; ValNodePtr gene; ImprintPtr imp; CharPtr last; MedlineMeshPtr mesh; MedlinePtr mPtr = NULL; ValNodePtr names; NameStdPtr nsp; PersonIdPtr pid; ValNodePtr qual; Char str [32]; MedlineRnPtr substance; ValNodePtr title; buffer = MemNew (BUFSIZE); if (buffer != NULL) { ClearString (); mPtr = MemNew (sizeof (MedlineData)); if (mPtr != NULL && mep != NULL) { sprintf (str, "%1ld", (long) mep->uid); mPtr->uid = StringSave (str); cit = mep->cit; if (cit != NULL) { if (cit->from == 1) { citjour = (CitJourPtr) cit->fromptr; if (citjour != NULL) { title = citjour->title; while (title != NULL) { if (title->choice == 6 || title->choice == 5) { AddString (title->data.ptrvalue); AddString (" "); mPtr->journal = StringSave (buffer); ClearString (); } title = title->next; } imp = citjour->imp; if (imp != NULL) { date = imp->date; if (date != NULL) { switch (date->data [0]) { case 0: StringNCpy (str, date->str, sizeof (str) - 1); chptr = StringChr (str, ' '); if (chptr != NULL) { *chptr = '\0'; } mPtr->year = StringSave (str); break; case 1: sprintf (str, "%0d", (Int2) (date->data [1] + 1900)); mPtr->year = StringSave (str); default: break; } } mPtr->volume = StringSave (imp->volume); mPtr->pages = StringSave (imp->pages); } } } title = cit->title; while (title != NULL) { switch (title->choice) { case 1: mPtr->title = StringSave ((CharPtr) title->data.ptrvalue); break; case 2: break; case 3: mPtr->transl = StringSave ((CharPtr) title->data.ptrvalue); break; default: break; } title = title->next; } authors = cit->authors; if (authors != NULL) { if (authors->choice == 1 || authors->choice == 2 || authors->choice == 3) { names = authors->names; while (names != NULL) { last = mPtr->authors; curr = NULL; if (authors->choice == 1) { ap = (AuthorPtr) names->data.ptrvalue; if (ap != NULL) { pid = ap->name; if (pid != NULL) { if (pid->choice == 2) { nsp = (NameStdPtr) pid->data; if (nsp != NULL) { if (! StringHasNoText (nsp->names [0])) { curr = MakeAuthorString (nsp->names [0], nsp->names [4], nsp->names [5]); } else if (! StringHasNoText (nsp->names [3])) { curr = MakeAuthorString (nsp->names [3], NULL, NULL); } } } else if (pid->choice == 3 || pid->choice == 4) { curr = MakeAuthorString ((CharPtr) pid->data, NULL, NULL); } } } } else if (authors->choice == 2 || authors->choice == 3) { curr = CleanAuthorString ((CharPtr) names->data.ptrvalue); } if (last != NULL) { if (names->next != NULL) { mPtr->authors = StrngAppend (last, (CharPtr) ", ", (CharPtr) curr, (CharPtr) NULL); } else { mPtr->authors = StrngAppend (last, (CharPtr) " & ", (CharPtr) curr, (CharPtr) NULL); } last = MemFree (last); curr = MemFree (curr); } else { mPtr->authors = curr; } names = names->next; } } affil = authors->affil; if (affil != NULL) { if (affil->choice == 1) { mPtr->affil = StringSave (affil->affil); } } } } mPtr->abstract = StringSave (mep->abstract); mesh = mep->mesh; while (mesh != NULL) { if (mesh->mp) { StringNCpy (str, "*", sizeof (str)); } else { StringNCpy (str, "", sizeof (str)); } last = mPtr->mesh; if (last != NULL) { mPtr->mesh = StrngAppend (last, (CharPtr) "\n ", (CharPtr) str, (CharPtr) mesh->term, (CharPtr) NULL); last = MemFree (last); } else { mPtr->mesh = StrngAppend ((CharPtr) " ", (CharPtr) str, (CharPtr) mesh->term, (CharPtr) NULL); } qual = mesh->qual; while (qual != NULL) { if (qual->choice != 0) { StringNCpy (str, "*", sizeof (str)); } else { StringNCpy (str, "", sizeof (str)); } last = mPtr->mesh; mPtr->mesh = StrngAppend (last, (CharPtr) "/", (CharPtr) str, (CharPtr) qual->data.ptrvalue, (CharPtr) NULL); last = MemFree (last); qual = qual->next; } mesh = mesh->next; } if (mPtr->mesh != NULL) { last = mPtr->mesh; mPtr->mesh = StrngAppend (last, (CharPtr) "\n", (CharPtr) NULL); last = MemFree (last); } gene = mep->gene; if (gene != NULL) { ClearString (); while (gene != NULL) { AddString (" "); AddString (gene->data.ptrvalue); AddString ("\n"); gene = gene->next; } mPtr->gene = StringSave (buffer); } substance = mep->substance; if (substance != NULL) { ClearString (); while (substance != NULL) { AddString (" "); switch (substance->type) { case 0: AddString (substance->name); break; case 1: AddString (substance->name); AddString (" ("); AddString ("CAS "); AddString (substance->cit); AddString (")"); break; case 2: AddString (substance->name); AddString (" ("); AddString ("EC "); AddString (substance->cit); AddString (")"); break; default: break; } AddString ("\n"); substance = substance->next; } mPtr->substance = StringSave (buffer); } } ClearString (); buffer = MemFree (buffer); } return mPtr; } NLM_EXTERN MedlinePtr FreeMedline (MedlinePtr mPtr) { if (mPtr != NULL) { mPtr->journal = MemFree (mPtr->journal); mPtr->volume = MemFree (mPtr->volume); mPtr->pages = MemFree (mPtr->pages); mPtr->year = MemFree (mPtr->year); mPtr->title = MemFree (mPtr->title); mPtr->transl = MemFree (mPtr->transl); mPtr->authors = MemFree (mPtr->authors); mPtr->affil = MemFree (mPtr->affil); mPtr->abstract = MemFree (mPtr->abstract); mPtr->mesh = MemFree (mPtr->mesh); mPtr->gene = MemFree (mPtr->gene); mPtr->substance = MemFree (mPtr->substance); mPtr->uid = MemFree (mPtr->uid); mPtr = MemFree (mPtr); } return NULL; } static ColData colFmt [3] = {{0, 0, 0, 'l', TRUE, TRUE, FALSE}, {0, 0, 0, 'l', TRUE, TRUE, FALSE}, {0, 0, 0, 'l', TRUE, TRUE, TRUE}}; static ColData mshFmt [1] = {{0, 80, 0, 'l', FALSE, FALSE, TRUE}}; static Boolean MedlineEntryToDocOrAbsFile (MedlineEntryPtr mep, FILE *fp, Boolean showMesh) { size_t len; MedlinePtr mPtr; ParData para; CharPtr ptr; Boolean rsult; CharPtr tmp; rsult = TRUE; if (fp != NULL && mep != NULL) { mPtr = ParseMedline (mep); if (mPtr != NULL) { buffer = MemNew (BUFSIZE); if (buffer != NULL) { para.openSpace = FALSE; ClearString (); AddString (mPtr->journal); AddString ("\t"); AddString (mPtr->volume); AddString (":\t"); AddString (mPtr->pages); AddString (" ("); AddString (mPtr->year); AddString (")"); AddString (" ["); AddString (mPtr->uid); AddString ("]"); AddString ("\n"); rsult = (Boolean) (SendTextToFile (fp, buffer, ¶, colFmt) && rsult); ClearString (); AddString (mPtr->title); AddString ("\n"); rsult = (Boolean) (SendTextToFile (fp, buffer, NULL, NULL) && rsult); ClearString (); if (mPtr->transl != NULL) { AddString ("["); AddString (mPtr->transl); AddString ("]\n"); rsult = (Boolean) (SendTextToFile (fp, buffer, NULL, NULL) && rsult); ClearString (); } AddString (mPtr->authors); AddString ("\n"); rsult = (Boolean) (SendTextToFile (fp, buffer, NULL, NULL) && rsult); ClearString (); if (mPtr->affil != NULL) { AddString (mPtr->affil); AddString ("\n"); rsult = (Boolean) (SendTextToFile (fp, buffer, NULL, NULL) && rsult); ClearString (); } if (mPtr->abstract != NULL) { len = StringLen (mPtr->abstract); tmp = (CharPtr) MemNew (sizeof (Char) * (len + 10)); ptr = StringMove (tmp, mPtr->abstract); ptr = StringMove (ptr, "\n"); rsult = (Boolean) (SendTextToFile (fp, tmp, NULL, NULL) && rsult); MemFree (tmp); } if (showMesh) { if (mPtr->mesh != NULL) { rsult = (Boolean) (SendTextToFile (fp, "MeSH Terms:\n", NULL, NULL) && rsult); rsult = (Boolean) (SendTextToFile (fp, mPtr->mesh, ¶, mshFmt) && rsult); } if (mPtr->gene != NULL) { rsult = (Boolean) (SendTextToFile (fp, "Gene Symbols:\n", NULL, NULL) && rsult); rsult = (Boolean) (SendTextToFile (fp, mPtr->gene, ¶, mshFmt) && rsult); } if (mPtr->substance != NULL) { rsult = (Boolean) (SendTextToFile (fp, "Substances:\n", NULL, NULL) && rsult); rsult = (Boolean) (SendTextToFile (fp, mPtr->substance, ¶, mshFmt) && rsult); } } buffer = MemFree (buffer); } mPtr = FreeMedline (mPtr); } } return rsult; } NLM_EXTERN Boolean MedlineEntryToDocFile (MedlineEntryPtr mep, FILE *fp) { return MedlineEntryToDocOrAbsFile (mep, fp, TRUE); } NLM_EXTERN Boolean MedlineEntryToAbsFile (MedlineEntryPtr mep, FILE *fp) { return MedlineEntryToDocOrAbsFile (mep, fp, FALSE); } #define IBM_MEDLINE_DIVSS '$' #define IBM_MEDLINE_DIVSV '&' #define IBM_MEDLINE_DIVEV '#' #define SIZE_OF_ARRAY(x) (sizeof(x)/sizeof(x[0])) typedef struct { char cSubHead[4]; char* pFullName; } SSubheadAbbr; static SSubheadAbbr theSubHead [] = { { "VE", "veterinary" }, { "UR", "urine" }, { "UT", "utilization" }, { "UY", "Uruguay" }, { "UL", "ultrastructure" }, { "US", "ultrasonography" }, { "TD", "trends" }, { "TR", "transplantation" }, { "TM", "transmission" }, { "TO", "toxicity" }, { "TH", "therapy" }, { "TU", "therapeutic use" }, { "SU", "surgery" }, { "SD", "supply & distribution" }, { "SN", "statistics & numerical data" }, { "ST", "standards" }, { "SE", "secretion" }, { "SC", "secondary" }, { "RH", "rehabilitation" }, { "RT", "radiotherapy" }, { "RI", "radionuclide imaging" }, { "RA", "radiography" }, { "RE", "radiation effects" }, { "PX", "psychology" }, { "PC", "prevention & control" }, { "PO", "poisoning" }, { "PP", "physiopathology" }, { "PH", "physiology" }, { "PD", "pharmacology" }, { "PK", "pharmacokinetics" }, { "PA", "pathology" }, { "PY", "pathogenicity" }, { "PS", "parasitology" }, { "OG", "organization & administration" }, { "NU", "nursing" }, { "NP", "Nepal" }, { "MO", "mortality" }, { "MI", "microbiology" }, { "MT", "methods" }, { "ME", "metabolism" }, { "MA", "manpower" }, { "LJ", "legislation & jurisprudence" }, { "IP", "isolation & purification" }, { "IS", "instrumentation" }, { "IR", "innervation" }, { "IN", "injuries" }, { "PR", "in pregnancy" }, { "OA", "in old age" }, { "MY", "in middle age" }, { "IC", "in infancy & childhood" }, { "AU", "in adulthood" }, { "AO", "in adolescence" }, { "IM", "immunology" }, { "IL", "Illinois" }, { "HI", "history" }, { "GD", "growth & development" }, { "GE", "genetics" }, { "ET", "etiology" }, { "EH", "ethnology" }, { "EP", "epidemiolgy" }, { "EN", "enzymology" }, { "EM", "embryology" }, { "ED", "education" }, { "EC", "economics" }, { "DT", "drug therapy" }, { "DE", "drug effects" }, { "DH", "diet therapy" }, { "DU", "diagnostic use" }, { "DI", "diagnosis" }, { "DF", "deficiency" }, { "CI", "chemically induced" }, { "CY", "cytology" }, { "CT", "contraindications" }, { "CN", "congenital" }, { "CO", "complications" }, { "CL", "classification" }, { "CH", "chemistry" }, { "CL", "chemistry induced" }, { "CS", "chemical synthesis" }, { "CD", "Chad" }, { "CF", "cerebrospinal fluid" }, { "BS", "blood supply" }, { "BL", "blood" }, { "BI", "biosynthesis" }, { "BT", "Bhutan" }, { "AI", "antagonists & inhibitors" }, { "AH", "anatomy & histology" }, { "AN", "analysis" }, { "AA", "analogs & derivatives" }, { "AE", "adverse effects" }, { "AD", "administration & dosage" }, { "AB", "abnormalities" }, { "AG", "AG" }, { "VI", "VI" } }; /****************************************************************************/ /*.doc GetTopicSubHead (internal) */ /*+ This function search subhead using subhead abbreviation. Return pointer to founded subhead or original subhead abbreviation if subhead not found. -*/ /****************************************************************************/ static char* /*FCN*/GetTopicSubHead ( char* lpSubHead ){ register int i; /* fast index */ for ( i = 0; i < SIZE_OF_ARRAY(theSubHead); i++ ) { if ( StringICmp (lpSubHead, theSubHead[i].cSubHead) == 0 ) { return theSubHead[i].pFullName; /* return full name */ } } return lpSubHead; /* return original subhead */ } /* GetTopicSubHead() */ /****************************************************************************/ /*.doc TranslateMesh (internal) */ /*+ This function translate MeSH string to standart printable form -*/ /****************************************************************************/ static void /*FCN*/TranslateMesh ( char* lpOut, char* lpRecord ){ register char* lpTemp; /* Temporary pointer */ char* lpMainTerm; /* Main termin */ int iDescClass; /* Descriptor Class */ char cInputType; /* Input type */ /* extract Mesh Term from Mesh record */ if ( (lpTemp = strchr (lpRecord, IBM_MEDLINE_DIVSS)) != NULL ) { *lpTemp = '\0'; /* set EOS for Mesh Term */ lpTemp++; /* lpTemp set to next character after $ */ } else { strcpy(lpOut,lpRecord); return; } lpMainTerm = lpRecord; strcpy(lpOut,lpMainTerm); /* Skip descriptor class. A number that designates to what class the MeSH heading belongs as follows: 1 - an INDEX MEDICUS major descriptor 2 - a citation type major descriptor, e.g., ENGLISH ABSTRACT 3 - a check tag major descriptor, e.g., HUMAN 4 - a geographic major descriptor, e.g., FRANCE 5 - a non-MeSH major descriptor, e.g., PATIENT CARE MANAGEMENT (NON MESH) 6 - a withdrawn major descriptor */ if ( isdigit((int)(*lpTemp)) ) { lpRecord = lpTemp; lpTemp++; iDescClass = atoi (lpRecord); iDescClass = iDescClass; /* Do not use descriptor class */ } /* Skip next subelement. Value is I or M. 'I' means an indexer input the Heading. 'M' means it was attached throwgh computer mapping */ if ( *lpTemp == IBM_MEDLINE_DIVSS && (*(lpTemp+1) == 'I' || *(lpTemp+1) == 'M') ) { lpTemp++; /* skip IBM_MEDLINE_DIVSS */ cInputType = *lpTemp++; cInputType = cInputType; } /* Qualifier List. A list of two-letter subheading (qualifier) abbreviations, separated by slashes if there is more than one value. Each subheading abbreviation may have an * (central concept indicator) preceding it. This subelement may consist of a single *, which indicates the MeSH heading alone is a central concept of the article. */ if ( *lpTemp == IBM_MEDLINE_DIVSS ) { int bIsCentralConcept; char cSubHead[3]; lpTemp++; /* skip IBM_MEDLINE_DIVSS */ cSubHead[2] = '\0'; /* set EOL */ /* read tokens from qualifier list */ while ( (cSubHead[0]=*lpTemp++) != '\0' ) { bIsCentralConcept = 0; if ( cSubHead[0] == '*' ) { /* is central concept mark? */ cSubHead[0] = *lpTemp++; if ( cSubHead[0] == '/' ) { strcpy(lpOut,"*"); strcat(lpOut,lpMainTerm); continue; } if ( cSubHead[0] == '\0' || cSubHead[0] == IBM_MEDLINE_DIVEV || cSubHead[0] == IBM_MEDLINE_DIVSV ) { strcpy(lpOut,"*"); strcat(lpOut,lpMainTerm); break; } bIsCentralConcept = 1; } if ( (cSubHead[1] = *lpTemp++) == '\0' ) { /* Special case for mii.d80.back66.rf, it has a bad data in MeSH heading for entry 68324942 */ break; } strcat(lpOut,"/"); if ( bIsCentralConcept == 1 ) { strcat(lpOut,"*"); } strcat(lpOut,GetTopicSubHead(cSubHead)); if ( *lpTemp == '/' ) { lpTemp++; } else if ( *lpTemp == IBM_MEDLINE_DIVEV || *lpTemp == IBM_MEDLINE_DIVSV ) { /* ignore Sort version and Entry version */ break; } } } return; } /* TranslateMesh() */ /***********************************************************************/ /*.doc MedlarsEntryToDataFile (external) */ /*+ Function send MEDLARS entry to I/O stream -*/ /***********************************************************************/ NLM_EXTERN Boolean /*FCN*/MedlarsEntryToDataFile ( MedlarsEntryPtr mep, FILE *fp ){ ParData thePara; CharPtr lpBuffer; MedlarsRecordPtr pRecord; Boolean bResult = TRUE; char buf[BUFSIZE]; int i, exist; char* ptr; #define MAX_ELHILL 24 int ElhillOrder[MAX_ELHILL] = { /* UI */ MEDLINE_UI, /* AU */ MEDLINE_AU, /* TI */ MEDLINE_TI, /* LA */ MEDLINE_LA, /* MH */ MEDLINE_MH, /* RN */ MEDLINE_RN, /* PT */ MEDLINE_PT, /* ID */ MEDLINE_ID, /* DA */ MEDLINE_DA, /* DP */ MEDLINE_DP, /* IS */ MEDLINE_IS, /* TA */ MEDLINE_TA, /* PG */ MEDLINE_PG, /* SB */ MEDLINE_SB, /* CY */ MEDLINE_CY, /* IP */ MEDLINE_IP, /* VI */ MEDLINE_VI, /* JC */ MEDLINE_JC, /* AA */ MEDLINE_AA, /* EM */ MEDLINE_EM, /* AB */ MEDLINE_AB, /* AD */ MEDLINE_AD, /* RF */ MEDLINE_RF, /* RO */ MEDLINE_RO }; char* TA=""; char* DP=""; char* VI=""; char* IP=""; char* PG=""; if ( mep == NULL || fp == NULL ) { return FALSE; } MemSet (&thePara, 0, sizeof(thePara)); if ( (lpBuffer=MemNew(BUFSIZE)) == NULL ) return FALSE; /* First run to print known Elhill codes */ for( i = 0; i < MAX_ELHILL; i++ ) { for ( pRecord = mep->recs; pRecord != NULL; pRecord = pRecord->next ) { if( pRecord->code != ElhillOrder[i] ) continue; if ( pRecord->abbr != NULL ) { /* This record has record type abbreviation */ sprintf( lpBuffer, "%-4s-\t", pRecord->abbr ); } else { /* This record has no record type abbreviation, use number */ sprintf ( lpBuffer, "%-4d-\t", pRecord->code ); } if ( MEDLINE_TA == pRecord->code ) TA = pRecord->data; /* TA - name of journal */ if ( MEDLINE_DP == pRecord->code ) DP = pRecord->data; /* DP - date of publication */ if ( MEDLINE_VI == pRecord->code ) VI = pRecord->data; /* VI - volume number */ if ( MEDLINE_IP == pRecord->code ) IP = pRecord->data; /* IP - issue number */ if ( MEDLINE_PG == pRecord->code ) PG = pRecord->data; /* PG - page numbers */ switch( pRecord->code ) { case MEDLINE_MH: TranslateMesh( buf, pRecord->data); StringCat(lpBuffer,buf); break; case MEDLINE_RO: strncpy( buf, pRecord->data, BUFSIZE-1 ); for ( ptr = buf; *ptr; ptr++ ) if( '$' == *ptr ) *ptr = ':'; StringCat( lpBuffer, buf ); break; case MEDLINE_ID: strncpy( buf, pRecord->data, BUFSIZE-1 ); for ( ptr = buf; *ptr; ptr++ ) if( '$' == *ptr ) *ptr = '/'; StringCat( lpBuffer, buf ); break; default: StringCat(lpBuffer,pRecord->data); break; } StringCat(lpBuffer,"\n"); if ( SendTextToFile (fp, lpBuffer, &thePara, table) != TRUE ) { MemFree(lpBuffer); return FALSE; } } } /* Second run to print unknown Elhill codes */ for ( pRecord = mep->recs; pRecord != NULL; pRecord = pRecord->next ) { exist = 0; for( i = 0; i < MAX_ELHILL; i++ ) { if( pRecord->code == ElhillOrder[i] ) { exist = 1; break; } } if( exist ) continue; if ( pRecord->abbr != NULL ) { /* This record has record type abbreviation */ sprintf ( lpBuffer, "%-4s-\t", pRecord->abbr ); } else { /* This record has no record type abbreviation, use number */ sprintf ( lpBuffer, "%-4d-\t", pRecord->code ); } StringCat(lpBuffer,pRecord->data); StringCat(lpBuffer,"\n"); if ( SendTextToFile (fp, lpBuffer, &thePara, table) != TRUE ) { MemFree(lpBuffer); return FALSE; } } /* Generate SO field */ strcpy( lpBuffer,"SO -\t"); strcat( lpBuffer, TA ); strcat( lpBuffer," " ); strcat( lpBuffer, DP ); strcat( lpBuffer,";" ); strcat( lpBuffer, VI ); if ( *IP != '\0' ) { strcat( lpBuffer,"("); strcat( lpBuffer, IP ); strcat( lpBuffer,")" ); } strcat( lpBuffer, ":" ); strcat( lpBuffer, PG ); strcat(lpBuffer,"\n"); if ( SendTextToFile (fp, lpBuffer, &thePara, table) != TRUE ) bResult = FALSE; MemFree(lpBuffer); return bResult; } /* MedlarsEntryToDataFile() */ /***********************************************************************/ /*.doc MedlarsEntryToDocFile (external) */ /*+ Function send MEDLARS entry to I/O stream -*/ /***********************************************************************/ NLM_EXTERN Boolean /*FCN*/MedlarsEntryToDocFile ( MedlarsEntryPtr mep, FILE *fp ){ if ( mep == NULL || fp == NULL ) { return FALSE; } return TRUE; } /* MedlarsEntryToDocFile() */ /***********************************************************************/ /*.doc MedlarsEntryToAbsFile (external) */ /*+ Function send MEDLARS entry to I/O stream -*/ /***********************************************************************/ NLM_EXTERN Boolean /*FCN*/MedlarsEntryToAbsFile ( MedlarsEntryPtr mep, FILE *fp ){ if ( mep == NULL || fp == NULL ) { return FALSE; } return TRUE; } /* MedlarsEntryToAbsFile() */