summaryrefslogtreecommitdiff
path: root/support/texlab/crates/bibutils_sys/src/medin.c
diff options
context:
space:
mode:
Diffstat (limited to 'support/texlab/crates/bibutils_sys/src/medin.c')
-rw-r--r--support/texlab/crates/bibutils_sys/src/medin.c645
1 files changed, 0 insertions, 645 deletions
diff --git a/support/texlab/crates/bibutils_sys/src/medin.c b/support/texlab/crates/bibutils_sys/src/medin.c
deleted file mode 100644
index 5bc39cfc33..0000000000
--- a/support/texlab/crates/bibutils_sys/src/medin.c
+++ /dev/null
@@ -1,645 +0,0 @@
-/*
- * medin.c
- *
- * Copyright (c) Chris Putnam 2004-2019
- *
- * Source code released under the GPL version 2
- *
- */
-#include <stdio.h>
-#include <stdlib.h>
-#include "is_ws.h"
-#include "str.h"
-#include "str_conv.h"
-#include "fields.h"
-#include "xml.h"
-#include "xml_encoding.h"
-#include "iso639_2.h"
-#include "bibutils.h"
-#include "bibformats.h"
-
-static int medin_readf( FILE *fp, char *buf, int bufsize, int *bufpos, str *line, str *reference, int *fcharset );
-static int medin_processf( fields *medin, const char *data, const char *filename, long nref, param *p );
-
-
-/*****************************************************
- PUBLIC: void medin_initparams()
-*****************************************************/
-int
-medin_initparams( param *pm, const char *progname )
-{
- pm->readformat = BIBL_MEDLINEIN;
- pm->charsetin = BIBL_CHARSET_UNICODE;
- pm->charsetin_src = BIBL_SRC_DEFAULT;
- pm->latexin = 0;
- pm->xmlin = 1;
- pm->utf8in = 1;
- pm->nosplittitle = 0;
- pm->verbose = 0;
- pm->addcount = 0;
- pm->output_raw = BIBL_RAW_WITHMAKEREFID |
- BIBL_RAW_WITHCHARCONVERT;
-
- pm->readf = medin_readf;
- pm->processf = medin_processf;
- pm->cleanf = NULL;
- pm->typef = NULL;
- pm->convertf = NULL;
- pm->all = NULL;
- pm->nall = 0;
-
- slist_init( &(pm->asis) );
- slist_init( &(pm->corps) );
-
- if ( !progname ) pm->progname = NULL;
- else {
- pm->progname = strdup( progname );
- if ( !pm->progname ) return BIBL_ERR_MEMERR;
- }
-
- return BIBL_OK;
-}
-
-/*****************************************************
- PUBLIC: int medin_readf()
-*****************************************************/
-
-/*
- * The only difference between MEDLINE and PUBMED in format is
- * that the entire library is wrapped in <MedlineCitationSet>
- * or <PubmedArticle> tags...
- */
-static char *wrapper[] = { "PubmedArticle", "MedlineCitation" };
-static int nwrapper = sizeof( wrapper ) / sizeof( wrapper[0] );
-
-static char *
-medin_findstartwrapper( char *buf, int *ntype )
-{
- char *startptr=NULL;
- int i;
- for ( i=0; i<nwrapper && startptr==NULL; ++i ) {
- startptr = xml_find_start( buf, wrapper[ i ] );
- if ( startptr && *ntype==-1 ) *ntype = i;
- }
- return startptr;
-}
-
-static char *
-medin_findendwrapper( char *buf, int ntype )
-{
- char *endptr = xml_find_end( buf, wrapper[ ntype ] );
- return endptr;
-}
-
-static int
-medin_readf( FILE *fp, char *buf, int bufsize, int *bufpos, str *line, str *reference, int *fcharset )
-{
- str tmp;
- char *startptr = NULL, *endptr;
- int haveref = 0, inref = 0, file_charset = CHARSET_UNKNOWN, m, type = -1;
- str_init( &tmp );
- while ( !haveref && str_fget( fp, buf, bufsize, bufpos, line ) ) {
- if ( line->data ) {
- m = xml_getencoding( line );
- if ( m!=CHARSET_UNKNOWN ) file_charset = m;
- }
- if ( line->data ) {
- startptr = medin_findstartwrapper( line->data, &type );
- }
- if ( startptr || inref ) {
- if ( inref ) str_strcat( &tmp, line );
- else {
- str_strcatc( &tmp, startptr );
- inref = 1;
- }
- endptr = medin_findendwrapper( str_cstr( &tmp ), type );
- if ( endptr ) {
- str_segcpy( reference, str_cstr( &tmp ), endptr );
- haveref = 1;
- }
- }
- }
- str_free( &tmp );
- *fcharset = file_charset;
- return haveref;
-}
-
-/*****************************************************
- PUBLIC: int medin_processf()
-*****************************************************/
-
-typedef struct xml_convert {
- char *in; /* The input tag */
- char *a, *aval; /* The attribute="attribute_value" pair, if nec. */
- char *out; /* The output tag */
- int level;
-} xml_convert;
-
-static int
-medin_doconvert( xml *node, fields *info, xml_convert *c, int nc, int *found )
-{
- int i, fstatus;
- char *d;
- *found = 0;
- if ( !xml_has_value( node ) ) return BIBL_OK;
- d = xml_value_cstr( node );
- for ( i=0; i<nc && *found==0; ++i ) {
- if ( c[i].a==NULL ) {
- if ( xml_tag_matches( node, c[i].in ) ) {
- *found = 1;
- fstatus = fields_add( info, c[i].out, d, c[i].level );
- if ( fstatus!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- }
- } else {
- if ( xml_tag_has_attribute( node, c[i].in, c[i].a, c[i].aval ) ) {
- *found = 1;
- fstatus = fields_add( info, c[i].out, d, c[i].level );
- if ( fstatus!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- }
- }
-
- }
- return BIBL_OK;
-}
-
-/* <ArticleTitle>Mechanism and.....</ArticleTitle>
- */
-static int
-medin_articletitle( xml *node, fields *info )
-{
- int fstatus, status = BIBL_OK;
- if ( xml_has_value( node ) ) {
- fstatus = fields_add( info, "TITLE", xml_value_cstr( node ), 0 );
- if ( fstatus!=FIELDS_OK ) status = BIBL_ERR_MEMERR;
- }
- return status;
-}
-
-/* <MedlineDate>2003 Jan-Feb</MedlineDate> */
-static int
-medin_medlinedate( fields *info, const char *p, int level )
-{
- int fstatus;
- str tmp;
-
- str_init( &tmp );
-
- p = str_cpytodelim( &tmp, skip_ws( p ), " \t\n\r", 0 );
- if ( str_memerr( &tmp ) ) return BIBL_ERR_MEMERR;
-
- if ( str_has_value( &tmp ) ) {
- fstatus = fields_add( info, "PARTDATE:YEAR", str_cstr( &tmp ), level );
- if ( fstatus!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- }
-
- p = str_cpytodelim( &tmp, skip_ws( p ), " \t\n\r", 0 );
- if ( str_memerr( &tmp ) ) return BIBL_ERR_MEMERR;
-
- if ( str_has_value( &tmp ) ) {
- str_findreplace( &tmp, "-", "/" );
- fstatus = fields_add( info, "PARTDATE:MONTH", str_cstr( &tmp ), level );
- if ( fstatus!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- }
-
- (void) str_cpytodelim( &tmp, skip_ws( p ), " \t\n\r", 0 );
- if ( str_memerr( &tmp ) ) return BIBL_ERR_MEMERR;
-
- if ( str_has_value( &tmp ) ) {
- fstatus = fields_add( info, "PARTDATE:DAY", str_cstr( &tmp ), level );
- if ( fstatus!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- }
-
- str_free( &tmp );
-
- return BIBL_OK;
-}
-
-/* <Langauge>eng</Language>
- */
-static int
-medin_language( xml *node, fields *info, int level )
-{
- char *code, *language;
- int fstatus;
- code = xml_value_cstr( node );
- if ( !code ) return BIBL_OK;
- language = iso639_2_from_code( code );
- if ( language )
- fstatus = fields_add( info, "LANGUAGE", language, level );
- else
- fstatus = fields_add( info, "LANGUAGE", code, level );
- if ( fstatus==FIELDS_OK ) return BIBL_OK;
- else return BIBL_ERR_MEMERR;
-}
-
-/* <Journal>
- * <ISSN>0027-8424</ISSN>
- * <JournalIssue PrintYN="Y">
- * <Volume>100</Volume>
- * <Issue>21</Issue>
- * <PubDate>
- * <Year>2003</Year>
- * <Month>Oct</Month>
- * <Day>14</Day>
- * </PubDate>
- * </Journal Issue>
- * </Journal>
- *
- * or....
- *
- * <Journal>
- * <ISSN IssnType="Print">0735-0414</ISSN>
- * <JournalIssue CitedMedium="Print">
- * <Volume>38</Volume>
- * <Issue>1</Issue>
- * <PubDate>
- * <MedlineDate>2003 Jan-Feb</MedlineDate>
- * </PubDate>
- * </JournalIssue>
- * <Title>Alcohol and alcoholism (Oxford, Oxfordshire) </Title>
- * <ISOAbbreviation>Alcohol Alcohol.</ISOAbbreviation>
- * </Journal>
- */
-static int
-medin_journal1( xml *node, fields *info )
-{
- xml_convert c[] = {
- { "Title", NULL, NULL, "TITLE", 1 },
- { "ISOAbbreviation", NULL, NULL, "SHORTTITLE", 1 },
- { "ISSN", NULL, NULL, "ISSN", 1 },
- { "Volume", NULL, NULL, "VOLUME", 1 },
- { "Issue", NULL, NULL, "ISSUE", 1 },
- { "Year", NULL, NULL, "PARTDATE:YEAR", 1 },
- { "Month", NULL, NULL, "PARTDATE:MONTH", 1 },
- { "Day", NULL, NULL, "PARTDATE:DAY", 1 },
- };
- int nc = sizeof( c ) / sizeof( c[0] ), status, found;
- if ( xml_has_value( node ) ) {
- status = medin_doconvert( node, info, c, nc, &found );
- if ( status!=BIBL_OK ) return status;
- if ( !found ) {
- if ( xml_tag_matches( node, "MedlineDate" ) ) {
- status = medin_medlinedate( info, xml_value_cstr( node ), 1 );
- if ( status!=BIBL_OK ) return status;
- }
- if ( xml_tag_matches( node, "Language" ) ) {
- status = medin_language( node, info, 1 );
- if ( status!=BIBL_OK ) return status;
- }
- }
- }
- if ( node->down ) {
- status = medin_journal1( node->down, info );
- if ( status!=BIBL_OK ) return status;
- }
- if ( node->next ) {
- status = medin_journal1( node->next, info );
- if ( status!=BIBL_OK ) return status;
- }
- return BIBL_OK;
-}
-
-/* <Pagination>
- * <MedlinePgn>12111-6</MedlinePgn>
- * </Pagination>
- */
-static int
-medin_pagination( xml *node, fields *info )
-{
- int i, fstatus, status;
- str sp, ep;
- const char *p, *pp;
- if ( xml_tag_matches( node, "MedlinePgn" ) && node->value.len ) {
- strs_init( &sp, &ep, NULL );
- p = str_cpytodelim( &sp, xml_value_cstr( node ), "-", 1 );
- if ( str_memerr( &sp ) ) return BIBL_ERR_MEMERR;
- if ( str_has_value( &sp ) ) {
- fstatus = fields_add( info, "PAGES:START", str_cstr( &sp ), 1 );
- if ( fstatus!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- }
- (void) str_cpytodelim( &ep, p, "", 0 );
- if ( str_memerr( &ep ) ) return BIBL_ERR_MEMERR;
- if ( str_has_value( &ep ) ) {
- if ( sp.len > ep.len ) {
- for ( i=sp.len-ep.len; i<sp.len; ++i )
- sp.data[i] = ep.data[i-sp.len+ep.len];
- pp = sp.data;
- } else pp = ep.data;
- fstatus = fields_add( info, "PAGES:STOP", pp, 1 );
- if ( fstatus!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- }
- strs_free( &sp, &ep, NULL );
- }
- if ( node->down ) {
- status = medin_pagination( node->down, info );
- if ( status!=BIBL_OK ) return status;
- }
- if ( node->next ) {
- status = medin_pagination( node->next, info );
- if ( status!=BIBL_OK ) return status;
- }
- return BIBL_OK;
-}
-
-/* <Abstract>
- * <AbstractText>ljwejrelr</AbstractText>
- * </Abstract>
- */
-static int
-medin_abstract( xml *node, fields *info )
-{
- int fstatus;
- if ( xml_tag_matches_has_value( node, "AbstractText" ) ) {
- fstatus = fields_add( info, "ABSTRACT", xml_value_cstr( node ), 0 );
- if ( fstatus!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- } else if ( node->next ) return medin_abstract( node->next, info );
- return BIBL_OK;
-}
-
-/* <AuthorList CompleteYN="Y">
- * <Author>
- * <LastName>Barondeau</LastName>
- * <ForeName>David P</ForeName>
- * ( or <FirstName>David P</FirstName> )
- * <Initials>DP</Initials>
- * </Author>
- * <Author>
- * <CollectiveName>Organization</CollectiveName>
- * </Author>
- * </AuthorList>
- */
-static int
-medin_author( xml *node, str *name )
-{
- char *p;
- if ( xml_tag_matches( node, "LastName" ) ) {
- if ( str_has_value( name ) ) {
- str_prepend( name, "|" );
- str_prepend( name, xml_value_cstr( node ) );
- }
- else str_strcat( name, xml_value( node ) );
- } else if ( xml_tag_matches( node, "ForeName" ) ||
- xml_tag_matches( node, "FirstName" ) ) {
- p = xml_value_cstr( node );
- while ( p && *p ) {
- if ( str_has_value( name ) ) str_addchar( name, '|' );
- while ( *p==' ' ) p++;
- while ( *p && *p!=' ' ) str_addchar( name, *p++ );
- }
- } else if ( xml_tag_matches( node, "Initials" ) && !strchr( name->data, '|' )) {
- p = xml_value_cstr( node );
- while ( p && *p ) {
- if ( str_has_value( name ) ) str_addchar( name, '|' );
- if ( !is_ws(*p) ) str_addchar( name, *p++ );
- }
- }
- if ( node->next ) medin_author( node->next, name );
- return BIBL_OK;
-}
-
-static int
-medin_corpauthor( xml *node, str *name )
-{
- if ( xml_tag_matches( node, "CollectiveName" ) ) {
- str_strcpy( name, xml_value( node ) );
- } else if ( node->next ) medin_corpauthor( node->next, name );
- return BIBL_OK;
-}
-
-static int
-medin_authorlist( xml *node, fields *info )
-{
- int fstatus, status;
- str name;
- char *tag;
- str_init( &name );
- node = node->down;
- while ( node ) {
- if ( xml_tag_matches( node, "Author" ) && node->down ) {
- status = medin_author( node->down, &name );
- tag = "AUTHOR";
- if ( str_is_empty( &name ) ) {
- status = medin_corpauthor( node->down, &name );
- tag = "AUTHOR:CORP";
- }
- if ( str_memerr( &name ) || status!=BIBL_OK ) return BIBL_ERR_MEMERR;
- if ( str_has_value( &name ) ) {
- fstatus = fields_add(info,tag,name.data,0);
- if ( fstatus!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- }
- str_empty( &name );
- }
- node = node->next;
- }
- str_free( &name );
- return BIBL_OK;
-}
-
-/* <PublicationTypeList>
- * <PublicationType>Journal Article</PublicationType>
- * </PublicationTypeList>
- */
-
-/* <MedlineJournalInfo>
- * <Country>United States</Country>
- * <MedlineTA>Proc Natl Acad Sci U S A</MedlineTA>
- * <NlmUniqueID>7507876</NlmUniqueID>
- * </MedlineJournalInfo>
- */
-
-static int
-medin_journal2( xml *node, fields *info )
-{
- int fstatus, status = BIBL_OK;
- if ( xml_tag_matches_has_value( node, "MedlineTA" ) && fields_find( info, "TITLE", LEVEL_HOST )==FIELDS_NOTFOUND ) {
- fstatus = fields_add( info, "TITLE", xml_value_cstr( node ), 1 );
- if ( fstatus!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- }
- if ( node->down ) {
- status = medin_journal2( node->down, info );
- if ( status!=BIBL_OK ) return status;
- }
- if ( node->next ) status = medin_journal2( node->next, info );
- return status;
-}
-
-/*
-<MeshHeadingList>
-<MeshHeading>
-<DescriptorName MajorTopicYN="N">Biophysics</DescriptorName>
-</MeshHeading>
-<MeshHeading>
-<DescriptorName MajorTopicYN="N">Crystallography, X-Ray</DescriptorName>
-</MeshHeading>
-</MeshHeadingList>
-*/
-static int
-medin_meshheading( xml *node, fields *info )
-{
- int fstatus, status = BIBL_OK;
- if ( xml_tag_matches_has_value( node, "DescriptorName" ) ) {
- fstatus = fields_add( info, "KEYWORD", xml_value_cstr( node ), 0 );
- if ( fstatus!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- }
- if ( node->next ) status = medin_meshheading( node->next, info );
- return status;
-}
-
-static int
-medin_meshheadinglist( xml *node, fields *info )
-{
- int status = BIBL_OK;
- if ( xml_tag_matches( node, "MeshHeading" ) && node->down ) {
- status = medin_meshheading( node->down, info );
- if ( status!=BIBL_OK ) return status;
- }
- if ( node->next ) status = medin_meshheadinglist( node->next, info );
- return status;
-}
-
-/* <PubmedData>
- * ....
- * <ArticleIdList>
- * <ArticleId IdType="pubmed">14523232</ArticleId>
- * <ArticleId IdType="doi">10.1073/pnas.2133463100</ArticleId>
- * <ArticleId IdType="pii">2133463100</ArticleId>
- * <ArticleId IdType="pmc">PMC4833866</ArticleId>
- * </ArticleIdList>
- * </PubmedData>
- *
- * I think "pii" is "Publisher Item Identifier"
- */
-static int
-medin_pubmeddata( xml *node, fields *info )
-{
- xml_convert c[] = {
- { "ArticleId", "IdType", "doi", "DOI", 0 },
- { "ArticleId", "IdType", "pubmed", "PMID", 0 },
- { "ArticleId", "IdType", "medline", "MEDLINE", 0 },
- { "ArticleId", "IdType", "pmc", "PMC", 0 },
- { "ArticleId", "IdType", "pii", "PII", 0 },
- };
- int nc = sizeof( c ) / sizeof( c[0] ), found, status;
- status = medin_doconvert( node, info, c, nc, &found );
- if ( status!=BIBL_OK ) return status;
- if ( node->next ) {
- status = medin_pubmeddata( node->next, info );
- if ( status!=BIBL_OK ) return status;
- }
- if ( node->down ) {
- status = medin_pubmeddata( node->down, info );
- if ( status!=BIBL_OK ) return status;
- }
- return BIBL_OK;
-}
-
-static int
-medin_article( xml *node, fields *info )
-{
- int fstatus, status = BIBL_OK;
- if ( xml_tag_matches( node, "Journal" ) )
- status = medin_journal1( node, info );
- else if ( xml_tag_matches( node, "ArticleTitle" ) )
- status = medin_articletitle( node, info );
- else if ( xml_tag_matches( node, "Pagination" ) && node->down )
- status = medin_pagination( node->down, info );
- else if ( xml_tag_matches( node, "Abstract" ) && node->down )
- status = medin_abstract( node->down, info );
- else if ( xml_tag_matches( node, "AuthorList" ) )
- status = medin_authorlist( node, info );
- else if ( xml_tag_matches( node, "Language" ) )
- status = medin_language( node, info, 0 );
- else if ( xml_tag_matches( node, "Affiliation" ) ) {
- fstatus = fields_add( info, "ADDRESS", xml_value_cstr( node ), 0 );
- if ( fstatus!=FIELDS_OK ) status = BIBL_ERR_MEMERR;
- }
- if ( status!=BIBL_OK ) return status;
- if ( node->next ) status = medin_article( node->next, info );
- return status;
-}
-
-static int
-medin_medlinecitation( xml *node, fields *info )
-{
- int fstatus, status = BIBL_OK;
- if ( xml_tag_matches_has_value( node, "PMID" ) ) {
- fstatus = fields_add( info, "PMID", xml_value_cstr( node ), 0 );
- if ( fstatus!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- }
- if ( node->down ) {
- if ( xml_tag_matches( node, "Article" ) ) {
- status = medin_article( node->down, info );
- } else if ( xml_tag_matches( node, "MedlineJournalInfo" ) ) {
- status = medin_journal2( node->down, info );
- } else if ( xml_tag_matches( node, "MeshHeadingList" ) )
- status = medin_meshheadinglist( node->down, info );
- if ( status!=BIBL_OK ) return status;
- }
- if ( node->next ) status = medin_medlinecitation( node->next, info );
- return status;
-}
-
-static int
-medin_pubmedarticle( xml *node, fields *info )
-{
- int status = BIBL_OK;
- if ( node->down ) {
- if ( xml_tag_matches( node, "MedlineCitation" ) )
- status = medin_medlinecitation( node->down, info );
- else if ( xml_tag_matches( node, "PubmedData" ) )
- status = medin_pubmeddata( node->down, info );
- if ( status!=BIBL_OK ) return status;
- }
- if ( node->next ) status = medin_pubmedarticle( node->next, info );
- return status;
-}
-
-static int
-medin_assembleref( xml *node, fields *info )
-{
- int status = BIBL_OK;
- if ( node->down ) {
- if ( xml_tag_matches( node, "PubmedArticle" ) )
- status = medin_pubmedarticle( node->down, info );
- else if ( xml_tag_matches( node, "MedlineCitation" ) )
- status = medin_medlinecitation( node->down, info );
- else
- status = medin_assembleref( node->down, info );
- }
- if ( status!=BIBL_OK ) return status;
-
- if ( node->next ) {
- status = medin_assembleref( node->next, info );
- if ( status!=BIBL_OK ) return status;
- }
-
- /* assume everything is a journal article */
- if ( fields_num( info ) ) {
- status = fields_add( info, "RESOURCE", "text", 0 );
- if ( status!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- status = fields_add( info, "ISSUANCE", "continuing", 1 );
- if ( status!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- status = fields_add( info, "GENRE:MARC", "periodical", 1 );
- if ( status!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- status = fields_add( info, "GENRE:BIBUTILS", "academic journal", 1 );
- if ( status!=FIELDS_OK ) return BIBL_ERR_MEMERR;
- status = BIBL_OK;
- }
-
- return status;
-}
-
-static int
-medin_processf( fields *medin, const char *data, const char *filename, long nref, param *p )
-{
- int status;
- xml top;
-
- xml_init( &top );
- xml_parse( data, &top );
- status = medin_assembleref( &top, medin );
- xml_free( &top );
-
- if ( status==BIBL_OK ) return 1;
- return 0;
-}