PyBibTextTools

• SpringerCsv2Bib
• GetAbstract
• BibFilesMerge

Libraries

You need install this (and others)

• pip install pybtex
• pip install pandas
• pip install argparse
• pip install unidecode

SpringerCsv2Bib

Convert Springer CSV file to Bibtext file

RUN

python e:/GitHub/PyBibTextTools/SpringerCsv2Bib.py -husage: SpringerCsv2Bib.py [-h] -c CSVFILENAME -b BIBFILENAME

optional arguments:
  -h, --help            show this help message and exit
  -c CSVFILENAME, --csvFileName CSVFILENAME
                        CSV file name
  -b BIBFILENAME, --bibFileName BIBFILENAME
                        BibText file name

Example:
python e:/GitHub/PyBibTextTools/SpringerCsv2Bib.py -c "e:\Google Drive\Doutorado\Revisão Sistematica\resultados pesquisas\Springer.csv" -b "E:\Google Drive\Doutorado\Revisão Sistematica\resultados pesquisas\Springer.bib"

File founded: e:\Google Drive\Doutorado\Revisão Sistematica\resultados pesquisas\Springer.csv
Processed 590
Removid without author 5
Total Final 585
Saved file E:\Google Drive\Doutorado\Revisão Sistematica\resultados pesquisas\Springer.bib

GetAbstract

This tools get abstract on digital library, its a Magver function, not official.

Obs 1: ACM need use limit parameter, because ACM blocks if you get many abstracts same time.

Obs 2: In my case, I use proxy, because I access in my house by proxy of my university.

RUN

python GetAbstract.py -h
usage: GetAbstract.py [-h] -d {springer,acm,ieee} -f BIBFILENAME
                      [--proxy PROXY] [-l LIMIT]

optional arguments:
  -h, --help            show this help message and exit
  -d {springer,acm,ieee}, --database {springer,acm,ieee}
                        select database
  -f BIBFILENAME, --bibFileName BIBFILENAME
                        Springer bibFile name
  --proxy PROXY         proxy, ex:
                        https://john:password123@palmas.pucrs.br:4001
  -l LIMIT, --limit LIMIT
                        abstract load limit

Example:

python GetAbstract.py -d acm -f "E:\Google Drive\Doutorado\Revisão Sistematica\resultados pesquisas\ACM.bib" -l 10 -p https://peter:mypass@palmas.pucrs.br:4001

or

python GetAbstract.py -d springer -f "E:\Google Drive\Doutorado\Revisão Sistematica\resultados pesquisas\Springer.bib"

Had Abstract 85
Url errors 0
Loaded Abstract 10
Total Entries 585
Limit to process 10
Processed 95
Left 490

BibFilesMerge

Merge BibText files and:

• remove duplicate entries
• in some cases merge information before removing duplicates
• remove entries that not have:
  • author or
  • title or
  • year or
  • journal name or conference name

This tool has been tested with digital library files:

• ACM Digital Library
• IEEE Xplore
• Scopus
• SpringerLink
• ScienceDirect - ElsevierWeb of Science
• Web of Science (thanks @dineiar for this)

RUN

python BibFilesMerge.py -h
usage: BibFilesMerge.py [-h] -p FOLDERPATH [-f [FILELIST [FILELIST ...]]]
                        [-o FILENAMEOUT] [-l]

optional arguments:
  -h, --help            show this help message and exit
  -p FOLDERPATH, --folderPath FOLDERPATH
                        Bib files folder path
  -f [FILELIST [FILELIST ...]], --fileList [FILELIST [FILELIST ...]]
                        bib file name list, e.g. -files IEEE.bib ACM.bib
                        science.bib Springer.bib
  -o FILENAMEOUT, --fileNameOut FILENAMEOUT
                        File name of merged file
  -l, --logProcess      List merged and final references to CSV files 
                        on FOLDERPATH

Example:

python BibFilesMerge.py -p "output_folder" -o MyFile.bib -f IEEE.bib ACM.bib science.bib Springer.bib scopus.bib -l

IEEE.bib 561
ACM.bib 773
science.bib 542
Springer.bib 585
scopus.bib 792

Total 3253
without Author 65
without Year 0
without Jornal or conference or booktitle 76
Duplicates 842 merged 833
Final 2270
without Abstract 746

The two CSV files created on output_folder by the -l switch are:

• BibFilesMerge_removed.csv, with columns cause, source, key, doi, author, year, title and publish
  • cause is one of: no author, no year, no journal, duplicate of next or duplicate of prev
• BibFilesMerge_final.csv, with columns key, doi, author, year, title, publish and abstract

Load Bib File Error

Sometimes errors occur while reading the bib file.
In this case, note at the end of the error line of the bib file.
Then edit the bib file and adjust the error.

Error, see the last line:

python BibFilesMerge.py -p "E:\Google Drive\Doutorado\Revisão Sistematica\resultados pesquisas" -f IEEE.bib ACM.bib science.bib Springer.bib -o "MyFile.bib"
-p  E:\Google Drive\Doutorado\Revisão Sistematica\resultados pesquisas
-o  MyFile.bib
-f  ['IEEE.bib', 'ACM.bib', 'science.bib', 'Springer.bib']
IEEE.bib
ACM.bib
science.bib
Traceback (most recent call last):
  File "BibFilesMerge.py", line 146, in <module>
    run(args["folderPath"], args["fileList"], args["fileNameOut"])
  File "BibFilesMerge.py", line 63, in run
    bibData = parse_file(os.path.join(folderPath,bibFileName))
  File "./pybtex\pybtex\database\__init__.py", line 865, in parse_file
    return parser.parse_file(file)
  File "./pybtex\pybtex\database\input\__init__.py", line 54, in parse_file
    self.parse_stream(f)
  File "./pybtex\pybtex\database\input\bibtex.py", line 410, in parse_stream
    return self.parse_string(text)
  File "./pybtex\pybtex\database\input\bibtex.py", line 397, in parse_string
    for entry in entry_iterator:
  File "./pybtex\pybtex\database\input\bibtex.py", line 191, in parse_bibliography
    self.handle_error(error)
  File "./pybtex\pybtex\database\input\bibtex.py", line 383, in handle_error
    report_error(error)
  File "./pybtex\pybtex\errors.py", line 78, in report_error
    raise exception
  File "./pybtex\pybtex\database\input\bibtex.py", line 189, in parse_bibliography
    yield tuple(self.parse_command())
  File "./pybtex\pybtex\database\input\bibtex.py", line 222, in parse_command
    self.handle_error(error)
  File "./pybtex\pybtex\database\input\bibtex.py", line 383, in handle_error
    report_error(error)
  File "./pybtex\pybtex\errors.py", line 78, in report_error
    raise exception
  File "./pybtex\pybtex\database\input\bibtex.py", line 220, in parse_command
    self.required([body_end])
  File "./pybtex\pybtex\scanner.py", line 120, in required
    raise TokenRequired(description, self)
pybtex.scanner.TokenRequired: syntax error in line 2264: '}' expected

Bib file Content in line 2264:

2264 note = "Special issue on Assistive Computer Vision and Robotics - "Assistive Solutions for Mobility, Communication and HMI" ",

you need fix to

2264 note = "Special issue on Assistive Computer Vision and Robotics - Assistive Solutions for Mobility, Communication and HMI",