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cnvtNbibToBib.c
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cnvtNbibToBib.c
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/*#########################################################
# Name: cnvtPubmedToBib
# Use:
# - Holds functions to convert .pubmed to .bib
# Dependencies:
# - "cStrFun.h"
# - "nbibToBibSettings.h"
# - "unac.h" or <unac.h> (-DLINKUNAC)
# o libiconv-1.9.1
# - <stdlib.h>
# - <stdio.h>
# o <string.h>
#########################################################*/
#include "cnvtNbibToBib.h"
/*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\
' SOF: Start Of Functions
' - fun-01 processPubMed:
' o Processes one section (one paper) of a .pubmed file
' - fun-02 pubmedSTToBib:
' o Outputs data in a pubmedStruct to a .bib file
' - fun-03 blankPubmedST:
' o Blanks a pubmedStruct structer to 0's and '\0'
' - fun-04 makeBibEntryName:
' o Build the citekey and file name.
' o Format: author1-year-pmid-pmidNumber.
' - fun-05 findPublicatonType:
' o Finds the bibtex publication type of a pubmed file.
' o This has only a limited number of entries
' - fun-06 getPubmedEntry:
' o Adds pubmed entry to a pubmedStruct structure
' - fun-07 getDPPubDate:
' o Extract year, month, and day from a pubmed DP entry
' - fun-08 moveToStartOfPubEntry:
' o Move to the start of pubmed entry & adjust length
' - fun-09 moveToStartPubEntryNoLen:
' o Move to the start of the pubmed entry only
' - fun-10 pubmedSTAddTag:
' o Add a tag to the tag list in a pubmedStruct tag list
' - fun-11 pubmedSTAddAbstract:
' o Add an abstract entry to pubmedStruct structure
' - fun-12 pubmedSTAddFullAuthor:
' o Add an full author name to the list of authors
' - fun-13 pubmedSTAddMesh:
' o Add an mesh term to a list of mesh terms
' - fun-14 pubmedSTAddKeyWord:
' o Add an key word to a list of key words
' - fun-15 pubmedSTAddArticleType:
' o Add an article type to a list of article types
' - fun-16 pubmedSTAddTitle:
' o Add an title to a pubmedStruct structure
' - fun-17 pubSTAddJournal:
' o Add an journal name to a pubmedStruct structure
' - fun-18 finishPubmedSTTag:
' o Removes the ", " off the end of a tags list
' - fun-19 finishPubmedSTKeyWords:
' o Removes the ", " off the end of a key words list
' - fun-20 finishPubmedSTMesh:
' o Removes the ", " off the end of a mesh list
' - fun-21 finishPubmedSTArticleType:
' o Removes the ", " off the end of an article type list
' - fun-22 finishPubmedSTAuthors:
' o Removes the " and " off the end of the author list
' - fun-23 pubmedSTSetPad:
' o Set the padding on a pubmedStruct variable
' - fun-24 pubmedSTSetBreak:
' o Set the line break values in a pubmedStruct
' - fun-25 blankPubOutST:
' o Sets a pubOut structure to default values
' - fun-26 pubmedLang:
' o Convert a pubmed language code to full language name
\~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*/
/*--------------------------------------------------------\
| Output:
| - Modifies:
| o pubmedST to hold extracted information
| o pubmedFILE to point next PubMed entry to convert
| - Returns:
| o 0 for EOF
| o 1 if succeded
| o 2 for blanlk line
| o 4 for an invalid file
| o 8 failed to make citekey
\--------------------------------------------------------*/
unsigned char processPubMed(
FILE *pubmedFILE, // pointer to pubmed file to process
struct pubmedStruct *pubmedST // holds data from file
){ /*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\
' Fun-01 TOC: Sec-01 Sub-01: processPubMed
' - Processes one section (one paper) of a .pubmed file
\~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*/
char hasEntriesBl = 0; // Mark if has entries
char *tmpCStr = 0;
char buffCStr[1024];
// No PubMed from ncbi has an entry is greater
// than 80 char per line. So this should be safe
// These are for keeping trakc of multi-line entries
char onAbstractBl = 0;
// Keep track if processing an abstract
// (can be multi-line)
char onJournalBl = 0; // For the journal entry
char onTitleBl = 0; // keep track of title lines
unsigned char errUC = 0; // Reports any errors
unsigned char retErrUC = 0; // Return value
unsigned long lenBuffUL = 0;
blankPubmedST(0, 0, 0, 0, pubmedST);
// Make sure all values are set to their defaults
// 0's are to avoid setting non-entry specific
// variables, like line wrapping.
if(pubmedFILE == 0) return 4; // Invalid file
while(fgets(buffCStr, 1024, pubmedFILE))
{ // While have pubmed entries to read
tmpCStr = buffCStr;
while(*tmpCStr == ' ' || *tmpCStr =='\t') ++tmpCStr;
// Check if done with the entry
if(*tmpCStr < 33)
{ // IF on a blank line (done with entry)
if(hasEntriesBl == 0) retErrUC = 2;
else retErrUC = 1;
break;
} // IF on a blank line (done with entry)
hasEntriesBl = 1;
lenBuffUL = (unsigned short) strlen(buffCStr);
getPubmedEntry(
buffCStr,
pubmedST,
lenBuffUL,
&onAbstractBl,
&onJournalBl,
&onTitleBl
); // Add the line to the pubmed structuer
} // While have pubmed entries to read
errUC = makeBibEntryName(pubmedST);
// Error in making the reference name
if(errUC != 0) return 8;
findPublicationType(pubmedST);
// Clean up the list endings
finshPubmedSTKeyWords(pubmedST);
finshPubmedSTMesh(pubmedST);
finshPubmedSTArticleType(pubmedST);
finshPubmedSTAuthors(pubmedST);
return retErrUC;
} // processPubMed
/*--------------------------------------------------------\
| Output: prints pubmedStruct to a bibtext file
\--------------------------------------------------------*/
void pubmedSTToBib(
struct pubmedStruct *pubST, // has .pubmed entries
struct pubOut *pubOutST, // tells entries to print
FILE *bibFILE // File to output data to
){ /*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\
' Fun-02 TOC: pubmedSTToBib
' - Outputs data in pubST to a bibtex file
' o fun-02 sec-01: Output format
' o fun-02 sec-02: Print out bibtex entry type and key
' o fun-02 sec-03: Print out the title
' o fun-02 sec-04: Print out the author list
' o fun-02 sec-05:jounral,year,month,volume,& issue
' o fun-02 sec-06: Check if printing the edition
' o fun-02 sec-07: Check which page count to print out
' o fun-02 sec-08:
' - doi,url,ISSN,PMID,PMCID,language & article type
' o fun-02 sec-09: Check if have a PMC id
' o fun-02 sec-10: Check if have a isbn number
' o fun-02 sec-11: Check if printing out the file name
' o fun-02 sec-12: Print out the tags
' o fun-02 sec-13: Check if printing wrapped key words
' o fun-02 sec-14: Check if printing wrapped mesh terms
' o fun-02 sec-15: out, notes, abstract, and ending }
\~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*/
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-01 Sub-01: Output format
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
/* Bibtex Format (... means text from variables)
Note:
- The Edition, ISBN, & PMC entries will only be printed when
they were extracted.
- The title,
@Article{author1-year-pmid-pmidNumber,
Author={...},
Title={...},
Journal={...},
Year={...},
Month={...},
Volume={...},
Number={...},
Edition{...},
doi={...},
url={https://dx.doi.org/...},
ISSN={...},
PMID={...},
PMC={...},
ISBN={...},
File={...},
Supplement={},
Tags={...},
Notes={
},
Abstract={
....
},
}
*/
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-02 Sub-01: Print bibtex entry type and key
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(pubOutST->citeKeyBl & 1)
fprintf(
bibFILE,
"@%s{%s,",
pubST->bibTypeCStr,
pubST->citeKeyCStr
);
else
fprintf(
bibFILE,
"@%s={,",
pubST->bibTypeCStr
);
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-03 Sub-01: Print out the title
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(pubST->wrapUS != 0 &&
pubST->lenTitleStrUL + 11 > pubST->wrapUS
)
fprintf(
bibFILE,
"%s Title={%s%s%s%s },",
pubST->lineBreakCStr,
pubST->lineBreakCStr,
pubST->padCStr,
pubST->titleCStr,
pubST->lineBreakCStr
); // need to break title into multiple lines
else
fprintf(
bibFILE,
"%s Title={%s},",
pubST->lineBreakCStr,
pubST->titleCStr
);
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-04 Sub-01: Print out the author list
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(pubST->wrapUS != 0 &&
pubST->lenAuthorsStrUL + 12 > pubST->wrapUS
)
fprintf(
bibFILE,
"%s Author={%s%s%s%s },",
pubST->lineBreakCStr,
pubST->lineBreakCStr,
pubST->padCStr,
pubST->authorsCStr,
pubST->lineBreakCStr
); //need to break author list into multiple lines
else
fprintf(
bibFILE,
"%s Author={%s},",
pubST->lineBreakCStr,
pubST->authorsCStr
);
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-05 Sub-01:jounral,year,month,volume,& issue
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(pubST->wrapUS != 0 &&
pubST->lenJournalStrUL + 13 > pubST->wrapUS
)
fprintf(
bibFILE,
"%s Journal={%s%s%s%s },",
pubST->lineBreakCStr,
pubST->lineBreakCStr,
pubST->padCStr,
pubST->journalCStr,
pubST->lineBreakCStr
); // Print out a multiline journal entry
else
fprintf(
bibFILE,
"%s Journal={%s},",
pubST->lineBreakCStr,
pubST->journalCStr
); // Printint the journal name (required)
if(pubOutST->abvJournalBl & 1)
fprintf(
bibFILE,
"%s AbrevJournal={%s},",
pubST->lineBreakCStr,
pubST->abrevJournalCStr
); // Printint the journal name (required)
if(pubOutST->journalIDBl & 1)
fprintf(
bibFILE,
"%s JournalId={%s},",
pubST->lineBreakCStr,
pubST->journalIdCStr
); // Printint the journal name
fprintf(
bibFILE,
"%s Year={%s},",
pubST->lineBreakCStr,
pubST->yearCStr
); // Printint the publication year (required bibtex)
if(pubOutST->monthBl & 1 && pubST->monthCStr[0] !='\0')
fprintf(
bibFILE,
"%s Month={%s},",
pubST->lineBreakCStr,
pubST->monthCStr
); // Printing the pulication month
if(pubOutST->dayBl & 1 && pubST->dayCStr[0] != '\0')
fprintf(
bibFILE,
"%s Day={%s},",
pubST->lineBreakCStr,
pubST->dayCStr
); // Printing the publication day
if(pubOutST->volBl & 1)
fprintf(
bibFILE,
"%s Volume={%s},",
pubST->lineBreakCStr,
pubST->volumeNumCStr
); // Printing the volume number
if(pubOutST->issueBl & 1)
fprintf(
bibFILE,
"%s Number={%s},",
pubST->lineBreakCStr,
pubST->issueCStr
); // Printing out the issue number
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-06 Sub-01: Check if printing the edition
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(pubST->editionCStr[0] != '\0' &&
pubOutST->editionBl & 1
)
fprintf(
bibFILE,
"%s Edition={%s},",
pubST->lineBreakCStr,
pubST->editionCStr
);
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-07 Sub-01: which page count to print out
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(pubOutST->pgBl & 1)
{ // If I am printing out a page number
if(pubST->pageNumCStr[0] != '\0')
fprintf(
bibFILE,
"%s Pages={%s},",
pubST->lineBreakCStr,
pubST->pageNumCStr
);
else
fprintf(
bibFILE,
"%s Pages={%s},",
pubST->lineBreakCStr,
pubST->electronicPageCStr
);
} // If I am printing out a page number
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-08 Sub-01:
^ - doi,url,ISSN,PMID,PMCID,language & article type
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(pubOutST->articleTypeBl & 1)
{ // If I am printing out the article type list
if(pubST->wrapUS != 0 &&
pubST->lenArticleTypeStrUL + 17 > pubST->wrapUS
)
fprintf(
bibFILE,
"%s ArticleType={%s%s%s%s },",
pubST->lineBreakCStr,
pubST->lineBreakCStr,
pubST->padCStr,
pubST->articleTypeCStr,
pubST->lineBreakCStr
);
else
fprintf(
bibFILE,
"%s ArticleType={%s},",
pubST->lineBreakCStr,
pubST->articleTypeCStr
);
} // If I am printing out the article type list
/*Check if printing out note with a line wrap*/
if(pubST->noteStr[0] != '\0' &&
pubST->wrapUS != 0 &&
pubST->lenNoteUC + 10 > pubST->wrapUS
){ /*If I am printing out the note for an ariticle*/
fprintf(
bibFILE,
"%s Note={%s%s%s},",
pubST->lineBreakCStr,
pubST->lineBreakCStr,
pubST->noteStr,
pubST->lineBreakCStr
); /*print out the note entry*/
} /*If I am printing out the note for an ariticle*/
/*Note with no linewrap*/
else if(pubST->noteStr[0] != '\0')
{ /*else if I am printing out the note for an ariticle*/
fprintf(
bibFILE,
"%s Note={%s},",
pubST->lineBreakCStr,
pubST->noteStr
); /*print out the note entry*/
} /*If I am printing out the note for an ariticle*/
if(pubOutST->doiBl & 1)
fprintf(
bibFILE,
"%s doi={%s},",
pubST->lineBreakCStr,
pubST->doiCStr
);
if(pubOutST->urlBl & 1)
fprintf(
bibFILE,
"%s url={https://dx.doi.org/%s},",
pubST->lineBreakCStr,
pubST->doiCStr
);
if(pubOutST->ppiBl & 1)
fprintf(
bibFILE,
"%s ppi={%s},",
pubST->lineBreakCStr,
pubST->ppiCStr
);
if(pubOutST->issnBl & 1)
fprintf(
bibFILE,
"%s ISSN={%s},",
pubST->lineBreakCStr,
pubST->issnCStr
);
if(pubOutST->pmidBl & 1)
if(pubST->pmidCStr[0] != '\0')
fprintf(
bibFILE,
"%s PMID={%s},",
pubST->lineBreakCStr,
pubST->pmidCStr
);
if(pubOutST->langBl & 1)
fprintf(
bibFILE,
"%s language={%s},",
pubST->lineBreakCStr,
pubST->langCStr
); // If printing out the publication language
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-09 Sub-01: Check if have a PMC id
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(pubST->pmcidCStr[0] != '\0' && pubOutST->pmcBl & 1)
fprintf(
bibFILE,
"%s PMC={%s},",
pubST->lineBreakCStr,
pubST->pmcidCStr
);
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-10 Sub-01: Check if have a isbn number
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(pubST->isbnCStr[0] != '\0' && pubOutST->isbnBl & 1)
fprintf(
bibFILE,
"%s ISBN={%s},",
pubST->lineBreakCStr,
pubST->isbnCStr
);
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-11 Sub-01: printing out the file name?
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(pubOutST->fileNameBl & 1)
fprintf(
bibFILE,
"%s File={%s},",
pubST->lineBreakCStr,
pubST->fileCStr
); // if printing out the file name
if(pubOutST->supBl & 1)
fprintf(
bibFILE,
"%s Supplement={},",
pubST->lineBreakCStr
); // Print out the supplement tag
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-12 Sub-01: Print out the tags
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(pubOutST->tagsBl & 1)
{ // If printing out the tags
if(pubST->wrapUS != 0 &&
pubST->lenTagsStrUL + 10 > pubST->wrapUS
)
fprintf(
bibFILE,
"%s Tags={%s%s%s%s },",
pubST->lineBreakCStr,
pubST->lineBreakCStr,
pubST->padCStr,
pubST->tagsCStr,
pubST->lineBreakCStr
);
else
fprintf(
bibFILE,
"%s Tags={%s},",
pubST->lineBreakCStr,
pubST->tagsCStr
);
} // If printing out the tags
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-13 Sub-01: printing wrapped key words?
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(pubOutST->keyWordsBl & 1)
{ // If printing out the key words
if(pubST->wrapUS != 0 &&
pubST->lenKeyWordsStrUL + 14 > pubST->wrapUS
)
fprintf(
bibFILE,
"%s Keywords={%s%s%s%s },",
pubST->lineBreakCStr,
pubST->lineBreakCStr,
pubST->padCStr,
pubST->keyWordsCStr,
pubST->lineBreakCStr
); // need to break the title into multiple lines
else
fprintf(
bibFILE,
"%s Keywords={%s},",
pubST->lineBreakCStr,
pubST->keyWordsCStr
);
} // If printing out the key words
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-14 Sub-01: printing wrapped mesh terms?
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(pubOutST->meshBl & 1)
{ // If printing out the mesh terms
if(pubST->wrapUS != 0 &&
pubST->lenMeshStrUL + 13 > pubST->wrapUS
)
fprintf(
bibFILE,
"%s Meshterms={%s%s%s%s },",
pubST->lineBreakCStr,
pubST->lineBreakCStr,
pubST->padCStr,
pubST->meshCStr,
pubST->lineBreakCStr
); // need to break the title into multiple lines
else
fprintf(
bibFILE,
"%s Meshterms={%s},",
pubST->lineBreakCStr,
pubST->meshCStr
);
} // If printing out the mesh terms
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
^ Fun-02 Sec-15 Sub-01: notes, abstract, and ending }
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(pubOutST->notesBl & 1)
fprintf(
bibFILE,
"%s NotesP={%s },",
pubST->lineBreakCStr,
pubST->lineBreakCStr
); // Print out the notes tag
if(pubOutST->abstractBl & 1)
{ // If printing out the abstract
if(pubST->wrapUS != 0 &&
pubST->lenAbstractStrUL + 16 > pubST->wrapUS
)
fprintf(
bibFILE,
"%s Abstract={%s%s%s%s },",
pubST->lineBreakCStr,
pubST->lineBreakCStr,
pubST->padCStr,
pubST->abstractCStr,
pubST->lineBreakCStr
);
else
fprintf(
bibFILE,
"%s Abstract={%s},",
pubST->lineBreakCStr,
pubST->abstractCStr
);
} // IF printing out the abstract
// Print out the closing statement
fprintf(
bibFILE,
"%s}%s",
pubST->lineBreakCStr,
pubST->lineBreakCStr
);
fflush(bibFILE);
return;
} // pubmedSTToBib
/*--------------------------------------------------------\
| Output: Sets all variables in pubmedST to defaults.
\--------------------------------------------------------*/
void blankPubmedST(
char blankTagsBl, // 1: wipe tags; 0: do not
char blankWrapBl, // 1: set line wrap to defaults
char blankBreakBl, //1:Set line break string to default
char blankPadBl, //1:Set padding to defaults (" ")
struct pubmedStruct *pubmedST // Structure to blank
){ /*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\
' Fun-03 TOC: Sec-1 Sub-1: blankPubmedST
' - Blanks a pubmedStruct structer to 0's and '\0'
\~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*/
// See if resting the line wrap settings
if(blankWrapBl & 1) pubmedST->wrapUS = defLineWrap;
if(blankBreakBl & 1)
{ /*If blanking the line break type*/
switch(defBreakType)
{ /*Switch: Check the default line break*/
case 0: /*Linux*/
pubmedSTSetBreak("\n", pubmedST);
break;
case 1: /*Windows*/
pubmedSTSetBreak("\r\n", pubmedST);
break;
default: /*Assume linux*/
pubmedSTSetBreak("\n", pubmedST);
break;
} /*Switch: Check the default line break*/
} /*If blanking the line break type*/
if(blankPadBl & 1) pubmedSTSetPad(" ", pubmedST);
// variables unique to the bibtex output
pubmedST->citeKeyCStr[0] = '\0';
pubmedST->lenCiteKeyStrUC = 0;
pubmedST->bibTypeCStr[0] = '\0';
pubmedST->lenBibTypeStrUC = 0;
pubmedST->fileCStr[0] = '\0'; // Location of pdf
pubmedST->lenFileStrUC = 0;
// Tags that the user might input
if(blankTagsBl & 1)
{ // If blanking the user supplied tags
pubmedST->tagsCStr[0] = '\0';
pubmedST->lenTagsStrUL = 0;
pubmedST->lenTagLineOnUS = pubmedST->lenPadUC;
} // If blanking the user supplied tags
// pubmed id variables
pubmedST->pmidCStr[0] = '\0';
pubmedST->lenPMIDStrUC = 0;
pubmedST->pmcidCStr[0] = '\0';
pubmedST->lenPMCIDStrUC = 0;
// Abstract variables
pubmedST->abstractCStr[0] = '\0';
pubmedST->lenAbstractStrUL = 0;
pubmedST->lenAbstractLineOnUS = pubmedST->lenPadUC;
// Setting wrap to a base values so that I have
// the correct counts for printing. Otherwise the
// first line would be off by LEN_PAD_UC.
// This would only happen for multiline entries
// publication date variables
pubmedST->yearCStr[0] = '\0';
pubmedST->lenYearStrUC = 0;
pubmedST->monthCStr[0] = '\0';
pubmedST->lenMonthStrUC = 0;
pubmedST->dayCStr[0] = '\0';
pubmedST->lenDayStrUC = 0;
// edition data variables
pubmedST->editionCStr[0] = '\0';
pubmedST->lenEditionStrUC = 0;
// list of author names
pubmedST->authorsCStr[0] = '\0';
pubmedST->lenAuthorsStrUL = 0;
pubmedST->lenAuthorsLineOnUS = pubmedST->lenPadUC;
// ISBN variables
pubmedST->isbnCStr[0] = '\0';
pubmedST->lenIsbnStrUC = '\0';
// ISSN variables
pubmedST->issnCStr[0] = '\0';
pubmedST->lenIssnStrUC = '\0';
pubmedST->printISSNBl = 0;
pubmedST->electronicISSNBl = 0;
pubmedST->linkISSNBl = 0;
// List of aritcle type variables
pubmedST->articleTypeCStr[0] = '\0';
pubmedST->lenArticleTypeStrUL = 0;
pubmedST->lenArticleTypeLineOnUS = pubmedST->lenPadUC;
// Note (for unpublished works)
pubmedST->noteStr[0] = '\0';
pubmedST->lenNoteUC = 0;
// journal abbreviation
pubmedST->abrevJournalCStr[0] = '\0';
pubmedST->lenAbrevJournalStrUC = 0;
// journal name (non-abbrevation) variables
pubmedST->journalCStr[0] = '\0';
pubmedST->lenJournalStrUL = 0;
pubmedST->lenJournalLineOnUS = pubmedST->lenPadUC;
// Journal ID
pubmedST->journalIdCStr[0] = '\0';
pubmedST->lenJournalIdStrUC = 0;
// Paper title variables
pubmedST->titleCStr[0] = '\0';
pubmedST->lenTitleStrUL = 0;
pubmedST->lenTitleLineOnUS = pubmedST->lenPadUC;
// paper language
pubmedST->langCStr[0] = '\0';
pubmedST->lenLangStrUC = 0;
// doi variables
pubmedST->doiCStr[0] = '\0';
pubmedST->lenDoiStrUC = 0;
// electronic page number
pubmedST->electronicPageCStr[0] = '\0';
pubmedST->lenEPgStrUC = 0;
// mesh term variables
pubmedST->meshCStr[0] = '\0';
pubmedST->lenMeshStrUL = 0;
pubmedST->lenMeshLineOnUS = pubmedST->lenPadUC;
// key word variables
pubmedST->keyWordsCStr[0] = '\0';
pubmedST->lenKeyWordsStrUL = 0;
pubmedST->lenKeyWordsLineOnUS = pubmedST->lenPadUC;
// page number (non-electronic) variables
pubmedST->pageNumCStr[0] = '\0';
pubmedST->lenPgStrUC = 0;
// volume number variablesk
pubmedST->volumeNumCStr[0] = '\0';
pubmedST->lenVolStrUC = 0;
return;
} // blankPubmedST
/*--------------------------------------------------------\
| Output:
| - Modifies:
| o pubmedST->citeKeyCStr to hold the citation key
| o pubmedST->fileCStr citation key with .pdf ending
\--------------------------------------------------------*/
unsigned char makeBibEntryName(
struct pubmedStruct *pubmedST
){ /*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\
' Fun-04 TOC: makeBibEntryName
' - Make name for the cite key/file name.
' Format is: author1-year-pmid-pmidNumber.
' o fun-04 sec-01: Remove accents from 1st authors name
' o fun-04 sec-02: Build the cite key
' o fun-04 sec-03: Get length of cite key & add to file
\~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*/
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
' Fun-04 Sec-01 Sub-01: Remove accents from 1st authors
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
char *nameCStr = 0;
size_t lenCnvtStrUL = 0; // Lenght of converted string
// here so the user can remove unac as a dependency
#ifndef NORMACCENT
int lenFirstNameI = 0;
int errI = 0;
nameCStr = pubmedST->authorsCStr;
// Find end of the last name
while(*nameCStr > 32)
{ // While have names to copy over
++nameCStr;
++lenFirstNameI;
if(*nameCStr == ',') break;
} // While have names to copy over
nameCStr = 0; // blank for unac
// https://www.nongnu.org/unac/unac-man3.en.html
errI =
unac_string(
"UTF-8", // Encoding of string
pubmedST->authorsCStr,// string of authors
lenFirstNameI, // length to convert
&nameCStr, // Holds normalized string
&lenCnvtStrUL
); // remove any accents from the authors names
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
' Fun-04 Sec-02 Sub-01: Build the cite key
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
if(errI != 0) return 2; // name normalization error
memcpy(
pubmedST->citeKeyCStr,
nameCStr,
lenCnvtStrUL
);
if(nameCStr != 0) free(nameCStr);
// Add in the spacer between first author and year
nameCStr = &pubmedST->citeKeyCStr[lenCnvtStrUL];
*nameCStr = '-';
++nameCStr;
#else // unac disablled
nameCStr = pubmedST->citeKeyCStr;
#endif
// Add in the year
memcpy(
nameCStr,
pubmedST->yearCStr,
pubmedST->lenYearStrUC
);
nameCStr += pubmedST->lenYearStrUC;
// Add in the pmid ending
memcpy(nameCStr, "-pmid-", 6);
nameCStr += 6;
memcpy(
nameCStr,
pubmedST->pmidCStr,
pubmedST->lenPMIDStrUC
);
// Make the name into a c-string
nameCStr += pubmedST->lenPMIDStrUC;
*nameCStr = '\0';
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\
' Fun-04 Sec-03 Sub-01: length of cite key & build file
\<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/
// Get the id length
pubmedST->lenCiteKeyStrUC =
lenCnvtStrUL
+ 1 // "-" between name and year
+ pubmedST->lenYearStrUC
+ 6 // "-pmid-"
+ pubmedST->lenPMIDStrUC;
// Make the file name and set its length
nameCStr =
cStrCpInvsDelm(
pubmedST->fileCStr,
pubmedST->citeKeyCStr
);
cStrCpInvsDelm(nameCStr, ".pdf");
pubmedST->lenFileStrUC = pubmedST->lenCiteKeyStrUC + 4;
return 0;
} // makeBibEntryName
/*--------------------------------------------------------\
| Output: Puts puclication type in pubmedST->bibTypeCStr.
| Note:
| - This is not comprehensive, but will work for now.
| o It would be more time efficent to hardcode in an if
| tree, but I do not want to commit the time.
| - Preprints are treated like an article
| - Their can be mutliple article types in a .pubmed file
\--------------------------------------------------------*/
void findPublicationType(
struct pubmedStruct *pubmedST
){ /*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\
' Fun-05 TOC: findPublicatonType
' - Finds the bibtex publication type of a pubmed file.
' - This has only a limited number of entries
\~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*/
if(
strstr(
pubmedST->articleTypeCStr,
"Unpublished Work"
) != 0
) { // If this has not been published yet
memcpy(pubmedST->bibTypeCStr, "Unpublished\0", 12);
pubmedST->lenBibTypeStrUC = 11;
memcpy(
pubmedST->noteStr,
"unpublished work on webpage at ",
32
);