cb2Bib: Configuring cb2Bib
- Journal Abbreviation List File
This file contains a list of journal names equivalences: a capital-letter acronym,
standard abbreviated form, and full name of the journal. If an input journal name
is recognized, cb2Bib will use the standard abbreviated form for the
journal bibkey. If your usual journal were not within the distributed,
default abbreviations.txt, you could edit this file, or point to a
personalized abbreviation file. Note: Changes in the abbreviation file only
take place after reestarting cb2Bib.
- Regular Expression List File
The cb2Bib distribution includes the file regexps.txt with a few set
of rules for reference extraction. This includes most of the scientific literature.
Extracting from email alerts or publisher abstract pages is a volatile
task. Information does not follow a standardized structure. Extraction pattern may
then change as often as the web design needs to. Besides, such extraction from the
clipboard is system dependent, in a way that produces different formatting of the
text copies on different systems. You can use your personalized
regexps.txt file, for testing, debugging -regular expressions are
reloaded each time the automatic recognition engine executes-, and fullfiling your
particular extraction needs.
- Bookmarks and Network Query Info File
The cb2Bib distribution includes the file netqinf.txt that contains
bookmarks data, and server related information for bibliographic querying. Note
that the cb2Bib treats bibliographic queries as generalized net bookmarks. This
allows accessing almost any online bibliographic resource. Check this file for
implementations details and customization.
- Browser Cascading Style Sheet (CSS)
This file contains the style sheet to configure the appearance of the bibliographic
references when viewed in browser mode. The cb2Bib distribution includes the
references.css file as a CSS example.
- Search In Files Cache Directory
Directory containing internal data for Search In Files functionality. If an
existing directory is selected the cb2Bib will write all internal data on it. If
otherwise, cache data will be written on the same directory from where BibTeX are
searched. It might be, therefore, convenient to group all this files in a separate
directory that does not need to be backup, and that can easily be deleted whenever
desired.
- Rename and Copy/Move article files to Directory
If selected, each file 'drag and dropped' onto the cb2Bib main window is renamed to
citeID.pdf (or citeID.ps, citeID.dvi, etc.) and moved to the pointed
storage directory. If unselected, the file URL is written to the file
bibkeyword, without any renaming or moving of the file. The actual copy/move action
is scheduled and performed once the reference is accepted, e.g., once it is
saved.
- Copy or Move article files
Choose whether copy or move Network Files 'dropped' onto the cb2Bib main window.
See also Use External Network Client.
- Set Article Files Directory Relative to current BibTeX file
Directory
If checked, the article file is copied/moved to the current BibTeX file directory.
Only the filename, instead of the fullpath filename, is written to the BibTeX
entry. File retrieving from within the cb2Bib browser will be relative to the
BibTeX file absolute location. Use this option if you plan to store in a same
directory the BibTeX and article files. This option is appropriate for storing
bibliographic collections in removal devices.
- Font Selector
Selects the main window and editor font family and size.
- Context Colors
Doubleclick on context color items to select syntax highlighter font color. Besides
syntax highlighting, and to ease manual bibliographic extractions, cb2Bib has the
following coloring convention. 'cb2Bib unrelevant text' colors non-word, non-digit,
and cb2Bib's internal tags. 'cb2Bib relevant text' refers to the reference's year.
'cb2Bib highly relevant' attempts to guess text sectioning, highlighting
'abstract', 'introduction', and 'keywords'.
- Replace/Remove from input stream
If checked, input stream is preprocessed by performing a customizable set of string
substitutions/removals. This option is mainly intended to remove image HTML
alt tags. Although not visible, alt tags reach the
clipboard when selecting and copying text. Author lists embellished with email
icons may therefore contain alt strings that would interfere with the
author names processing. In addition, this option is also appropriate to help
translating special characters to Unicode and LaTeX. Use it carefully, as to avoid
unwanted or unsuspected substitutions. See also Extracting Data from the Clipboard.
- External Clipboard Preparsing Command
Preparses input stream through an external, user-defined tool. Use the box bellow
to specify its name and path. cb2Bib executes the command tool_name
tmp_inputfile tmp_outputfile. You might consider a wrapper shell script to
fullfill this particular syntax requirement. Two examples, isi2bib and
ris2bib are provided. To test them, make sure the BibUtils Package is available on your machine. Otherwise, modify these
scripts according to your needs. See also Additional, Keyboard Functionality, Extracting Data from the Clipboard, and the
examples ISI Reference
Format and RIS Reference
Format.
- Perform always, as part of an automatic extraction
Performs preparsing each time the recognition engine is invoked. Caution:
cb2Bib, when not in disconnected mode, starts the recognition engine each time the
clipboard changes. Thus, it might send arbitrary data to the external parsing tool.
The tool might not be prepared to handle 'any data' and might fall into a
sort of 'infinite loop'. cb2Bib kills the external tool after a reasonable
waiting. But, if the tool is called through a wrapper script, killing the script
will not end the tool itself. Therefore, check this box only when needed. If
you write your own preparser, design it as to write no data to output file whenever
it can not process an input properly. When the preparser produces no data, the
cb2Bib sends instead the input stream to the recognition engine. In this way,
preparsing and normal cb2Bib functioning will work harmoniously.
- Do not show log output
If unchecked, the external process messages, and the input and output streams are
shown in a log window. Showing output logs is usefull for debugging purposes.
- Use External Network Client
cb2Bib manages local and network files in an equivalent manner. Network file
retrieving, however, requires sometimes password and/or cookies administration.
Opening and browsing retrieved files requires also desktop specific commands. The
KDE desktop incorporates kfmclient utility. A command kfmclient
(copy|move|exec) orig [dest] permits copying, moving or opening files,
taking care of redirections, cookies or user browsing preferences. By checking this
box, cb2Bib will use the specified file manger client. External file managers
should be used whenever redirections or cookies are an issue. Note: Internal
Network file manager has been found to 'freeze' on some Windows platforms. Switch
to an appropriate external manager if experiencing problems.
- Perform Network Queries after automatic reference extractions
Network queries can be used to complete a partial reference extraction. For
instance, provided a reference 'J. Name, 25, 103' and an appropriate pattern to
extract it, cb2Bib will attempt to complete the reference automatically. Currently,
it should work out-of-the-box for PubMed, PNAS, and ACS publications. See also the
file netqinf.txt.
- Download PDF article if available
If checked, cb2Bib downloads article PDF files to the directory specified in
Rename and Copy/Move dropped PDF article files to Directory. See also the
file netqinf.txt for details. Download is scheduled and performed once
the reference is accepted, e.g., once it is saved.
- Keep Query temporary files (Debug Only)
cb2Bib may use up to three temporary files to perform a network query. If this box
is checked, the temporary files are not deleted. This facilitates the customization
of the information file netqinf.txt.
- Author and Editor Name Format
Sets Authors and Editor names in abbreviated or full form, if the latter is
available.
- Journal Name Format
Sets output journal names in abbreviated or full form. Note that this feature only
works if journal names are found in the Journal Abbreviation List
File.
- CiteID Pattern
Specifies the pattern for formating cite's ID. Pattern editing and predefined
placeholders popup menu are available upon mouse rightclicks. Placeholders will be
substituted by the actual cite field values. See Predefined cite ID placeholders for
descriptions.
- Convert entry strings to LaTeX
If checked, cb2Bib converts special, Unicode characters to LaTeX commands. Most
BibTeX import filters do not process LaTeX escaped characters. Keeping this box
unchecked can thus be appropriate when using cb2Bib-BibTeX as a temporary media to
transfer references to non BibTeX reference managers and formats.
- Set 'title' in double braces
If checked, it writes extra braces in title. This will keep capitalization as is,
when processed by BibTeX.
- Postprocess 'month'
If checked, cb2Bib elaborates the 'month' string on a BibTeX fashion. E.g., 'April
1' becomes '"1~" # apr'.
- Try Heuristic Guess if recognition fails
If checked, and the automatic recognition fails, cb2Bib tries to catch some of the
fields of the reference through an heuristic set of rules. See Field Recognition Rules.
- Page Number Separator
Sets separator, e.g., ' - ' or ' -- '. Spaces count.
- External BibTeX Postprocessing
Use this box to select a preferred BibTeX postprocessing external tool. The name of
the executable, the command arguments and the output file extension are required
fields. Arguments, any number, are passed to the executable. For the sake of
generality, it is required to specify the %finput and
%foutput placeholders. The first one is later substituted by the
current BibTeX filename. The second one is substituted by the current filename with
the specified output extension. Caution: Be careful if using the same file
extension for input and output, e.g., using bib because you want to
use a beautifier or a sorting script. The cb2Bib has no control on external disk
modifications. Moreover, if the script fails, the input data might be lost. See
also Additional, Keyboard
Functionality.
- To plain text converter
Selects the external some_format_to_text tool that cb2Bib uses to
convert sets of files prior to reference extraction. cb2Bib executes the line
command converter [options] inputfile tmp_output.txt, where
[options] are user defined arguments. As a default, cb2Bib launches
pdftotext, a PDF to text utility found in many platforms. Default
arguments are -f 1 -l 1 to extract only the first page when used
within PDFImport, and -raw, to convert all the document, when used
within Search in Files. Appropriate for PDFImport could also be a document metadata
extractor. Often metadata contains structured information regarding document
authors, title, and source.
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