Initial commit

Author: adamjgnoel

mendeleyBibFix.c

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+/*
+ * mendeleyBibFix - correct formatting of bib-files that are automatically
+ * 	generated by Mendeley Desktop
+ *
+ * NOTE: Mendeley Desktop is copyright 2009-2013 by Mendeley Ltd.
+ * This software is not provided by Mendeley and the author has no affiliation
+ * with their company.
+ *
+ * Documentation:
+ * This is a simple function intended to correct bib-files that are
+ * automatically generated by Mendeley Desktop. I have found it to work
+ * for bib-files generated with the IEEE citation style, but it should
+ * work for other styles as well. It makes the following corrections:
+ * 		- changes double braces around titles to single braces
+ * 		- removes escaping of { and } (will only matter if you checked
+ * 			"Escape LaTeX special characters" in the "Bibtex" Options tab)
+ * 		- removes URL for any entry that is not specified as an exception
+ *			(read the comment block after start of main function to read
+ *			how to change the exceptions)
+ * 		- removes braces around months
+ *
+ * It should work correctly for files generated by Mendeley Desktop v1.16.1.
+ *
+ * A number of fixes are hard-coded, i.e., it expects to know where the braces are.
+ * So this code runs very fast (bib files with hundreds of entries are fixed in a
+ * small fraction of a second) but may not be "future-proof"
+ *
+ * You will need to compile this code to run it. A compiled version for windows is
+ * included on the release page of Github. If you are going to compile it yourself with gcc,
+ * then you will need the -std=c99 option
+ *
+ * Call syntax (windows):
+ * 		mendeleyBibFix.exe [OUTPUT_FILENAME] [INPUT_FILENAME]
+ *
+ * Both arguments are optional. If there is only one argument, then it is assumed to be
+ * the output filename. The default input filename is "library.bib", and the default
+ * output filename is "library_fixed.bib"
+ *
+ * Copyright 2016 Adam Noel. All rights reserved.
+ * Distributed under the New BSD license. See LICENSE.txt for license details.
+ *
+ * Created June 15, 2016
+ * Current version v1.0 (2016-06-15)
+ *
+ * Revision history:
+ *
+ * Revision v1.0
+ * - File created
+ *
+ *
+*/
+
+#include <stdio.h>
+#include <stdlib.h> // for exit(), malloc
+#include <string.h> // for strcpy()
+#include <stdbool.h> // for C++ bool naming, requires C99
+#include <time.h> // For time record keeping
+
+#define BIB_TYPE_MAX 25
+
+// Function declarations
+char * stringAllocate(long stringLength);
+char * stringWrite(char * src);
+unsigned long findEndOfLine(char * str, unsigned long startInd);
+
+//
+// MAIN
+//
+int main(int argc, char *argv[])
+{
+	// MODIFY THIS BLOCK TO ADD/REMOVE BIB ENTRY TYPES THAT
+	// SHOULD HAVE A URL DISPLAYED. BY DEFAULT, ALL URLS
+	// ARE REMOVED FROM THE BIB-FILE.
+	// TO ADD AN EXCEPTION:
+	//	1)	INCREMENT NUM_URL_EXCEPTIONS
+	//  2) 	APPEND THE NEW EXCEPTION TO THE LAST INDEX OF
+	// 		URL_EXCEPTION_TYPES (WRITE WITHOUT THE '@' PREFIX).
+	// TO REMOVE AN EXCEPTION:
+	// 	1)	DECREMENT NUM_URL_EXCEPTIONS
+	// 	2) 	REMOVE EXCEPTION STRING WRITTEN TO URL_EXCEPTION_TYPES
+	// 	3) 	CORRECT INDICES OF REMAINING EXCEPTIONS SO THAT THEY
+	// 		GO FROM 0 TO (NUM_URL_EXCEPTIONS-1)
+	// NOTE: MENDELEY EXPORTS A "WEB PAGE" ENTRY AS "misc"
+	const int NUM_URL_EXCEPTIONS = 2;
+	const char *URL_EXCEPTION_TYPES[NUM_URL_EXCEPTIONS];
+	URL_EXCEPTION_TYPES[0] = "misc";
+	URL_EXCEPTION_TYPES[1] = "unpublished";
+	// END OF USER-MODIFIED BLOCK
+	
+	int curException;
+	bool bUrlException;
+	char bibType[BIB_TYPE_MAX];
+	
+	char INPUT_DEFAULT[] = "library.bib";
+	char OUTPUT_DEFAULT[] = "library_fixed.bib";
+
+	char * inputName;
+	char * outputName;
+	
+	FILE * inputFile;
+	FILE * outputFile;
+	
+	unsigned long fileLength;
+	unsigned long temp; // Garbage variable for discarded file content length
+	char * inputContent;
+	char * outputContent;
+	
+	unsigned long curInputInd, curInputAnchorInd;
+	char curInputChar;
+	unsigned long curEntryInd;
+	char curEntryChar;
+	
+	unsigned long numEntry = 0;
+	char * curBibEntry;
+	char * curBibFixed;
+	unsigned long curBibInd, curBibLength, indEOL;
+	
+	
+	// Timer variables
+	clock_t startTime, endTime;
+	
+	// Read in output filename if defined
+	if(argc > 2)
+	{
+		inputName = stringWrite(argv[2]);
+	} else
+	{
+		inputName = stringWrite(INPUT_DEFAULT);
+	}
+	
+	// Read in input filename if defined
+	if(argc > 1)
+	{
+		outputName = stringWrite(argv[1]);
+	} else
+	{
+		outputName = stringWrite(OUTPUT_DEFAULT);
+	}
+	
+	// Open input file
+	inputFile = fopen(inputName, "r");
+	if(inputFile == NULL)
+	{
+		fprintf(stderr,"ERROR: Input file \"%s\" not found.\n",inputName);
+		exit(EXIT_FAILURE);
+	}
+	printf("Successfully opened input file at \"%s\".\n", inputName);
+	
+	// Read in contents of input file
+	fseek(inputFile, 0, SEEK_END);
+	fileLength = ftell(inputFile);
+	fseek(inputFile,0,SEEK_SET);
+	inputContent = malloc(fileLength + 1);
+	outputContent = malloc(fileLength + 1); // Output will be no longer than input
+	if(inputContent == NULL
+		|| outputContent == NULL)
+	{
+		fprintf(stderr,"ERROR: Memory could not be allocated to store the input file contents.\n");
+		exit(EXIT_FAILURE);
+	}
+	temp = fread(inputContent,1,fileLength,inputFile);
+	fclose(inputFile);
+	printf("Successfully read and closed input file.\n");
+	
+	//
+	// Scan and fix bib entries
+	//
+	numEntry = 0;
+	startTime = clock();
+	curInputInd = 0;
+	curInputAnchorInd = 0;
+	outputContent[0] = '\0'; // Initialize output string as empty
+	while(true)
+	{
+		// Find start of next entry
+		while(inputContent[curInputInd] != '@')
+		{
+			if(inputContent[curInputInd] == '\0')
+				break; // Reached EOF. No more entries to scan
+			else
+				curInputInd++;
+		}
+		
+		if(inputContent[curInputInd] == '\0')
+			break;
+	
+		curInputAnchorInd = curInputInd++;
+		
+		// Find end of entry
+		while(true)
+		{
+			if((inputContent[curInputInd] == '}'
+				&& inputContent[curInputInd-1] == '\n')
+				|| inputContent[curInputInd] == '\0')
+				break; // Reached end of current entry (or EOF)
+			else
+				curInputInd++;
+			
+		}
+		
+		if(inputContent[curInputInd] == '\0')
+			break;
+		
+		// Current entry goes from inputContent[curInputAnchorInd]
+		// to inputContent[curInputInd]+1
+		curBibLength = curInputInd-curInputAnchorInd+2;
+		curBibEntry = malloc((curBibLength + 1)*sizeof(char));
+		if(curBibEntry == NULL)
+		{
+			fprintf(stderr,"ERROR: Memory could not be allocated to copy bib entry %u.\n", numEntry);
+			exit(EXIT_FAILURE);
+		}
+		for(curBibInd = 0; curBibInd < curBibLength; curBibInd++)
+		{
+			curBibEntry[curBibInd] = inputContent[curInputAnchorInd+curBibInd];
+		}
+		curBibEntry[curBibInd] = '\0';
+		
+		// curBibEntry is now a valid substring of the original input file
+		// Apply fixes as necessary
+		curBibInd = 1; // We know first character is '@'
+		
+		// Check URL exception types
+		bUrlException = false;
+		while(curBibEntry[curBibInd] != '{'
+			&& curBibInd < BIB_TYPE_MAX)
+		{
+			bibType[curBibInd-1] = curBibEntry[curBibInd];
+			curBibInd++;
+		}
+		bibType[curBibInd-1] = '\0';
+		
+		for(curException = 0; curException < NUM_URL_EXCEPTIONS; curException++)
+		{
+			if(!strcmp(bibType,URL_EXCEPTION_TYPES[curException]))
+			{
+				bUrlException = true; // Current type of entry needs to keep URL
+				break;
+			}
+		}
+		
+		// Scan Remainder of entry
+		while(curBibEntry[curBibInd] != '\0')
+		{
+			if(curBibEntry[curBibInd] == '\n')
+			{
+				// We're at the start of a line in the current bib entry
+				// Scan ahead to see if its an entry that we need to fix
+				if(!strncmp(&curBibEntry[curBibInd+1], "month =",7))
+				{	// Next line lists month. Format should be mmm
+					// and not {mmm}
+					if(curBibEntry[curBibInd+9] == '{'
+						&& curBibEntry[curBibInd+13] == '}')
+					{
+						curBibEntry[curBibInd+9] = curBibEntry[curBibInd+10];
+						curBibEntry[curBibInd+10] = curBibEntry[curBibInd+11];
+						curBibEntry[curBibInd+11] = curBibEntry[curBibInd+12];
+						// Delete offsets 12 and 13
+						memmove(&curBibEntry[curBibInd+12], &curBibEntry[curBibInd+14],
+							curBibLength - curBibInd-13);
+						curBibLength -= 2;
+					}
+				} else if(!strncmp(&curBibEntry[curBibInd+1], "title =",7))
+				{ 	// Title is supposed to be surrounded by 1 set of braces and not 2
+					// Remove extra set of curly braces
+					indEOL = findEndOfLine(curBibEntry, curBibInd+1);
+					// Shift title over extra opening curly brace
+					memmove(&curBibEntry[curBibInd+10], &curBibEntry[curBibInd+11],
+						indEOL - curBibInd-13);
+					// Shift remaining text over extra closing curly brace
+					memmove(&curBibEntry[indEOL-3], &curBibEntry[indEOL-1],
+						curBibLength - indEOL + 2);
+					curBibLength -= 2;
+				} else if(!bUrlException
+					&& !strncmp(&curBibEntry[curBibInd+1], "url =",5))
+				{	// Entry has a URL but it should be removed. Erase the whole line
+					indEOL = findEndOfLine(curBibEntry, curBibInd+1);
+					memmove(&curBibEntry[curBibInd+1], &curBibEntry[indEOL+1],
+						curBibLength - indEOL + 1);
+					curBibLength -= indEOL - curBibInd;
+				}
+			} else if(!strncmp(&curBibEntry[curBibInd], "{\\{}",4))
+			{ 	// We have an incorrectly formatted opening curly brace
+				// Remove 3 characters of memory
+				memmove(&curBibEntry[curBibInd+1], &curBibEntry[curBibInd+4],
+					curBibLength - curBibInd-2);
+				curBibLength -= 3;
+			} else if(!strncmp(&curBibEntry[curBibInd], "{\\}}",4))
+			{ 	// We have an incorrectly formatted closing curly brace
+				// Remove 3 characters of memory
+				curBibEntry[curBibInd] = '}';
+				memmove(&curBibEntry[curBibInd+1], &curBibEntry[curBibInd+4],
+					curBibLength - curBibInd-2);
+				curBibLength -= 3;
+			}
+			
+			curBibInd++;
+		}
+		
+		// Write fixed entry to output string
+		strcat(outputContent, curBibEntry);
+			
+		numEntry++;
+	}
+	
+	endTime = clock();
+	printf("Entry fixing took %f seconds\n", (double) (endTime-startTime)/CLOCKS_PER_SEC);
+	
+	// Write output string to output file
+	if((outputFile = fopen(outputName, "w")) == NULL)
+	{
+		fprintf(stderr,"ERROR: Cannot create output file \"%s\".\n",outputName);
+		exit(EXIT_FAILURE);
+	}
+	printf("Successfully created output file at \"%s\".\n", outputName);
+	
+	fprintf(outputFile, "%s", outputContent);
+	fclose(outputFile);
+	printf("Successfully wrote and closed output file with %u entries.\n", numEntry);
+	
+	// Cleanup
+	free(inputContent);
+	free(inputName);
+	free(outputName);
+	free(curBibEntry);
+	free(curBibFixed);
+	
+	return 0;
+}
+
+// Allocate memory for a string
+char * stringAllocate(long stringLength)
+{
+	char * string = malloc(stringLength+1);
+	if(string == NULL)
+	{
+		fprintf(stderr,"ERROR: Memory could not be allocated for string copy.\n");
+		exit(EXIT_FAILURE);
+	}
+	
+	return string;
+}
+
+// Copy string (with memory allocation)
+char * stringWrite(char * src)
+{
+	char * string = stringAllocate(strlen(src));
+	strcpy(string, src);
+	
+	return string;
+}
+
+// Find next end of line in current string
+unsigned long findEndOfLine(char * str, unsigned long startInd)
+{
+	unsigned long curInd = startInd;
+	while(str[curInd] != '\n')
+		curInd++;
+	
+	return curInd;
+}