Tuesday, April 6, 2010

BBL to BIB with BibDesk

BibDesk manages my bibliography, just like iTunes manages my music. I have a single iTunes library, and I also have only a single master bibliography. However, when writing a paper, I want to create a new bib file with only the publications cited in the paper. BibTeX nicely creates a bibliographic reference file (*.bbl), but I want a bibliography file (*.bib) in order to be able to open the paper related publications with BibDesk. So, what I needed was a tool to convert the bbl file into a bib file. Fortunately, I found everything for that on my machine: AppleScript, grep, sed and, of course, BibDesk. I wrote a small script which simply creates a new bib file using a source bib file and a selected bbl file. Simply install the script listed below to your script folder (~/Library/Scripts) and name it "Create BIB from BBL.scpt" . Open your master bib file with BibDesk, then select a bbl file and activate the script(from the script menu in the menu bar). It will automatically create a new bib file in the folder of the bbl file, with the same name as the original bbl file (but with the extension bib).
-- Creates a new bib-file from an bbl-file using BibDesk -- (C) 2010 Jens von Pilgrim -- Version: 1.1, 20100615 tell application "Finder" set selectedItems to the selection end tell if ((count of selectedItems) = 0) then display dialog "Please select at least one bbl file" buttons {"OK"} return end if -- retrieve master bib file set sourceDoc to "" tell application "BibDesk" if (count of documents) = 0 then display dialog "Please open the source bibliography with BibDesk" buttons {"OK"} return end if if (count of documents) > 1 then set listOfNames to {} as list repeat with doc in documents set listOfNames to listOfNames & name of doc end repeat set selected to (choose from list listOfNames) as string repeat with i from 1 to the count of documents set doc to (item i of documents) set strDocName to name of doc as string if (strDocName is equal to selected) then set sourceDoc to document i log "source doc set" end if end repeat if sourceDoc is equal to "" then return end if else set sourceDoc to document 1 end if end tell -- log "copy items from master bib file" -- convert all selected bbl files repeat with theItem in selectedItems set theFile to theItem as alias set posixpath to POSIX path of theFile if (offset of ".bbl" in posixpath) > 0 then set destPosixpath to (my rename(posixpath, "bbl", "bib")) set destFile to POSIX file destPosixpath tell application "Finder" if (exists destFile) then set rep to display dialog "File " & destFile & " already exists. Overwrite?" buttons {"Yes", "No"} set skip to (button returned of rep = "No") else set skip to false end if end tell if (not skip) then -- log "examine bbl file " & quoted form of posixpath -- actually, this is the most important line: set allCites to do shell script "grep -E \"\\\\\\\\bibitem[:space:]*(\\[[^]]*\\])?[:space:]*{([^}]*)}\" " & (quoted form of posixpath) & " | sed -E \"s/\\\\\\\\bibitem[:space:]*(\\[[^]]*\\])?[:space:]*{([^}]*)}/\\2/\"" set numberOfItems to length of paragraphs of allCites if numberOfItems = 0 then display dialog "No bibitems found in " & posixpath & ", maybe the file does not contain any bibitems or the search pattern does not recognize your file format." buttons {"Too bad."} else set numberOfMissedItems to 0 set missedItems to "" tell application "BibDesk" set destDoc to make new document repeat with cite in paragraphs of allCites set bibs to search sourceDoc for cite set bFound to false repeat with bib in bibs set strFoundKey to cite key of bib as string set strCite to cite as string if strFoundKey is equal to strCite then -- log strCite & " found, add to new bib" set newBib to make new publication at end of publications of destDoc duplicate bib to newBib set bFound to true end if end repeat if not bFound then set numberOfMissedItems to numberOfMissedItems + 1 if (numberOfMissedItems > 1) then set missedItems to missedItems & ", " end if set missedItems to missedItems & cite end if end repeat save destDoc in destFile end tell if numberOfMissedItems > 0 then display dialog "Did not found " & numberOfMissedItems & " out of " & numberOfItems & " items: " & missedItems & "." buttons {"Uups"} end if end if end if else display dialog "Can only extract bib entries from BBL file, was " & posixpath end if end repeat -- this sub-routine just comes up with the new name on rename(item_name, item_ext, new_extension) set the trimmed_name to text 1 thru -((length of item_ext) + 2) of the item_name set target_name to (the trimmed_name & "." & new_extension) as string return the target_name end rename
If you don't have BibDesk, you might want to have a look at Michael Zhang's Perl Script. Instead of parsing the bbl file, Zhang's script parses the latex source. I prefer parsing the bbl file, as sometimes I use a whole bunch of latex sources, and BibTeX is quite good in gathering all citations into a single bbl file. You may also want to read the comments to Zhang's post for other solutions. If you don't have a master bib file, you may look at http://www.tex.ac.uk/cgi-bin/texfaq2html?label=makebib. There's a perl scrip provided reconstructing a bib file from a bbl file only. Update 2010-06-15: I updated the script as some BBL files were not recognized. If the script doesn't work, you may have a look at your BBL file. At the moment, the script searches for bibitems like "\bibitem{key}" or "\bibitem[abbr]{key}".

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