/*
* medin.c
*
* Copyright (c) Chris Putnam 2004-2009
*
* Program and source code released under the GPL
*
*/
#include <stdio.h>
#include <stdlib.h>
#include "is_ws.h"
#include "newstr.h"
#include "newstr_conv.h"
#include "fields.h"
#include "xml.h"
#include "xml_encoding.h"
#include "medin.h"
/*
* The only difference between MEDLINE and PUBMED in format is
* that the entire library is wrapped in <MedlineCitationSet>
* or <PubmedArticle> tags...
*/
static char *wrapper[] = { "MedlineCitationSet", "PubmedArticle" };
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_findstart( buf, wrapper[ i ] );
if ( startptr ) *ntype = i;
}
return startptr;
}
static char *
medin_findendwrapper( char *buf, int ntype )
{
char *endptr = xml_findend( buf, wrapper[ ntype ] );
return endptr;
}
int
medin_readf( FILE *fp, char *buf, int bufsize, int *bufpos, newstr *line, newstr *reference, int *fcharset )
{
newstr tmp;
char *startptr = NULL, *endptr;
int haveref = 0, inref = 0, file_charset = CHARSET_UNKNOWN, m, type = 1;
newstr_init( &tmp );
while ( !haveref && newstr_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 ) newstr_strcat( &tmp, line->data );
else {
newstr_strcat( &tmp, startptr );
inref = 1;
}
endptr = medin_findendwrapper( tmp.data, type );
if ( endptr ) {
newstr_segcpy( reference, tmp.data, endptr );
haveref = 1;
}
}
}
newstr_free( &tmp );
*fcharset = file_charset;
return haveref;
}
static inline int
xml_hasdata( xml *node )
{
if ( node && node->value && node->value->data ) return 1;
return 0;
}
static inline char *
xml_data( xml *node )
{
return node->value->data;
}
static inline int
xml_tagwithdata( xml *node, char *tag )
{
if ( !xml_hasdata( node ) ) return 0;
return xml_tagexact( node, tag );
}
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 i, found = 0;
char *d;
if ( !xml_hasdata( node ) ) return 0;
d = xml_data( node );
for ( i=0; i<nc && found==0; ++i ) {
if ( c[i].a==NULL ) {
if ( xml_tagexact( node, c[i].in ) ) {
found = 1;
fields_add( info, c[i].out, d, c[i].level );
}
} else {
if ( xml_tag_attrib( node, c[i].in, c[i].a, c[i].aval)){
found = 1;
fields_add( info, c[i].out, d, c[i].level );
}
}
}
return found;
}
/* <ArticleTitle>Mechanism and.....</ArticleTitle>
*/
static void
medin_articletitle( xml *node, fields *info )
{
if ( xml_hasdata( node ) )
fields_add( info, "TITLE", xml_data( node ), 0 );
}
/* <MedlineDate>2003 Jan-Feb</MedlineDate> */
static void
medin_medlinedate( fields *info, char *string, int level )
{
newstr tmp;
char *p, *q;
newstr_init( &tmp );
/* extract year */
p = string;
q = skip_notws( string );
/* p = q = string;*/
/* while ( *q && !is_ws(*q) ) q++;*/
newstr_segcpy( &tmp, p, q );
fields_add( info, "PARTYEAR", tmp.data, level );
q = skip_ws( q );
/* extract month */
if ( q ) {
p = q;
newstr_empty( &tmp );
q = skip_notws( q );
/* while ( *q && !is_ws(*q) ) q++;*/
newstr_segcpy( &tmp, p, q );
newstr_findreplace( &tmp, "-", "/" );
fields_add( info, "PARTMONTH", tmp.data, level );
q = skip_ws( q );
}
/* extract day */
if ( q ) {
p = q;
newstr_empty( &tmp );
q = skip_notws( q );
/* while ( *q && !is_ws(*q) ) q++;*/
newstr_segcpy( &tmp, p, q );
fields_add( info, "PARTDAY", tmp.data, level );
}
newstr_free( &tmp );
}
/* <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 void
medin_journal1( xml *node, fields *info )
{
xml_convert c[] = {
{ "ISSN", NULL, NULL, "ISSN", 1 },
{ "Volume", NULL, NULL, "VOLUME", 1 },
{ "Issue", NULL, NULL, "ISSUE", 1 },
{ "Year", NULL, NULL, "PARTYEAR", 1 },
{ "Month", NULL, NULL, "PARTMONTH", 1 },
{ "Day", NULL, NULL, "PARTDAY", 1 },
{ "Language", NULL, NULL, "LANGUAGE", 1 },
};
int nc = sizeof( c ) / sizeof( c[0] );;
if ( xml_hasdata( node ) && !medin_doconvert( node, info, c, nc ) ) {
if ( xml_tagexact( node, "MedlineDate" ) )
medin_medlinedate( info, xml_data( node ), 1 );
}
if ( node->down ) medin_journal1( node->down, info );
if ( node->next ) medin_journal1( node->next, info );
}
/* <Pagination>
* <MedlinePgn>12111-6</MedlinePgn>
* </Pagination>
*/
static void
medin_pagination( xml *node, fields *info )
{
newstr sp, ep;
char *p;
int i;
if ( xml_tagexact( node, "MedlinePgn" ) && node->value ) {
newstrs_init( &sp, &ep, NULL );
p = xml_data( node );
while ( *p && *p!='-' )
newstr_addchar( &sp, *p++ );
if ( *p=='-' ) p++;
while ( *p )
newstr_addchar( &ep, *p++ );
if ( sp.len ) fields_add( info, "PAGESTART", sp.data, 1 );
if ( ep.len ) {
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];
fields_add( info, "PAGEEND", sp.data, 1 );
} else
fields_add( info, "PAGEEND", ep.data, 1 );
}
newstrs_free( &sp, &ep, NULL );
}
if ( node->down ) medin_pagination( node->down, info );
if ( node->next ) medin_pagination( node->next, info );
}
/* <Abstract>
* <AbstractText>ljwejrelr</AbstractText>
* </Abstract>
*/
static void
medin_abstract( xml *node, fields *info )
{
if ( xml_tagwithdata( node, "AbstractText" ) )
fields_add( info, "ABSTRACT", xml_data( node ), 0 );
else if ( node->next ) medin_abstract( node->next, info );
}
/* <AuthorList CompleteYN="Y">
* <Author>
* <LastName>Barondeau</LastName>
* <ForeName>David P</ForeName>
* ( or <FirstName>David P</FirstName> )
* <Initials>DP</Initials>
* </Author>
* </AuthorList>
*/
static void
medin_author( xml *node, newstr *name )
{
char *p;
if ( xml_tagexact( node, "LastName" ) ) {
if ( name->len ) {
newstr_prepend( name, "|" );
newstr_prepend( name, xml_data( node ) );
}
else newstr_strcat( name, xml_data( node ) );
} else if ( xml_tagexact( node, "ForeName" ) ||
xml_tagexact( node, "FirstName" ) ) {
p = xml_data( node );
while ( p && *p ) {
if ( name->len ) newstr_addchar( name, '|' );
while ( *p && *p==' ' ) p++;
while ( *p && *p!=' ' ) newstr_addchar( name, *p++ );
}
} else if ( xml_tagexact( node, "Initials" ) && !strchr( name->data, '|' )) {
p = xml_data( node );
while ( p && *p ) {
if ( name->len ) newstr_addchar( name, '|' );
if ( !is_ws(*p) ) newstr_addchar( name, *p++ );
}
}
if ( node->down ) medin_author( node->down, name );
if ( node->next ) medin_author( node->next, name );
}
static void
medin_authorlist( xml *node, fields *info )
{
newstr name;
newstr_init( &name );
node = node->down;
while ( node ) {
if ( xml_tagexact( node, "Author" ) && node->down ) {
medin_author( node->down, &name );
if ( name.len ) fields_add(info,"AUTHOR",name.data,0);
newstr_empty( &name );
}
node = node->next;
}
newstr_free( &name );
}
/* <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 void
medin_journal2( xml *node, fields *info )
{
if ( xml_tagwithdata( node, "MedlineTA" ) )
fields_add( info, "TITLE", xml_data( node ), 1 );
if ( node->down ) medin_journal2( node->down, info );
if ( node->next ) medin_journal2( node->next, info );
}
/*
<MeshHeadingList>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Biophysics</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Crystallography, X-Ray</DescriptorName>
</MeshHeading>
</MeshHeadingList>
*/
static void
medin_meshheading( xml *node, fields *info )
{
if ( xml_tagwithdata( node, "DescriptorName" ) )
fields_add( info, "KEYWORD", xml_data( node ), 0 );
if ( node->next ) medin_meshheading( node->next, info );
}
static void
medin_meshheadinglist( xml *node, fields *info )
{
if ( xml_tagexact( node, "MeshHeading" ) && node->down )
medin_meshheading( node->down, info );
if ( node->next ) medin_meshheadinglist( node->next, info );
}
/* <PubmedData>
* ....
* <ArticleIdList>
* <ArticleId IdType="pubmed">14523232</ArticleId>
* <ArticleId IdType="doi">10.1073/pnas.2133463100</ArticleId>
* <ArticleId IdType="pii">2133463100</ArticleId>
* <ArticleId IdType="medline">22922082</ArticleId>
* </ArticleIdList>
* </PubmedData>
*
* I think "pii" is "Publisher Item Identifier"
*/
static void
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", "pii", "PII", 0 },
};
int nc = sizeof( c ) / sizeof( c[0] );
medin_doconvert( node, info, c, nc );
if ( node->next ) medin_pubmeddata( node->next, info );
if ( node->down ) medin_pubmeddata( node->down, info );
}
static void
medin_article( xml *node, fields *info )
{
if ( xml_tagexact( node, "Journal" ) )
medin_journal1( node, info );
else if ( xml_tagexact( node, "ArticleTitle" ) )
medin_articletitle( node, info );
else if ( xml_tagexact( node, "Pagination" ) && node->down )
medin_pagination( node->down, info );
else if ( xml_tagexact( node, "Abstract" ) && node->down )
medin_abstract( node->down, info );
else if ( xml_tagexact( node, "AuthorList" ) )
medin_authorlist( node, info );
if ( node->next ) medin_article( node->next, info );
}
static void
medin_medlinecitation( xml *node, fields *info )
{
if ( node->down ) {
if ( xml_tagexact( node, "Article" ) )
medin_article( node->down, info );
else if ( xml_tagexact( node, "MedlineJournalInfo" ) )
medin_journal2( node->down, info );
else if ( xml_tagexact( node, "MeshHeadingList" ) )
medin_meshheadinglist( node->down, info );
}
if ( node->next ) medin_medlinecitation( node->next, info );
}
static void
medin_pubmedarticle( xml *node, fields *info )
{
if ( node->down ) {
if ( xml_tagexact( node, "MedlineCitation" ) )
medin_medlinecitation( node->down, info );
else if ( xml_tagexact( node, "PubmedData" ) )
medin_pubmeddata( node->down, info );
}
if ( node->next ) medin_pubmedarticle( node->next, info );
}
static void
medin_assembleref( xml *node, fields *info )
{
if ( xml_tagexact( node, "PubmedArticle" ) ||
xml_tagexact( node, "MedlineCitationSet" ) ) {
if ( node->down ) medin_pubmedarticle( node->down, info );
} else if ( node->down ) medin_assembleref( node->down, info );
if ( node->next ) medin_assembleref( node->next, info );
/* assume everything is a journal article */
if ( info->nfields ) {
fields_add( info, "RESOURCE", "text", 0 );
fields_add( info, "ISSUANCE", "continuing", 1 );
fields_add( info, "GENRE", "periodical", 1 );
fields_add( info, "GENRE", "academic journal", 1 );
}
}
int
medin_processf( fields *medin, char *data, char *filename, long nref )
{
xml top;
xml_init( &top );
xml_tree( data, &top );
medin_assembleref( &top, medin );
xml_free( &top );
return 1;
}
void
medin_convertf( fields *medin, fields *info, int reftype, int verbose,
variants *all, int nall )
{
int i;
for ( i=0; i<medin->nfields; ++i )
fields_add( info, medin->tag[i].data, medin->data[i].data,
medin->level[i] );
}