python run_extraction.py /path/to/file.pdf [path/to/output/dir]

If a path to an output directory is not supplied, results will be put in the same directory as the pdf file.

• extraction framework python library (on python path (run python setup.py install --user from its root directory)
• defusedxml python library (run pip install defusedxml --user to install)
• requests python library (run pip install requests --user to install)

Grobid is used to extract header information from the PDF files. Grobid should be running as a service somwhere. (Run mvn jetty:run-war from grobid-service directory if not already running. See Grobid's Github project for more complete installation instructions.) The URL for Grobid can be configured in csxextract/config.py.

PDFBox is used to get a plain text representation of the PDF files. The PDFBox jar needs to be on the machine somewhere. The default expected location is ~/bin but this can be configured in csxextract/config.py.

The PDF Classifier .jar file is used to classify PDFs as academic or not. It should be on the local machine somewhere, as well as its associated acl file and training data file. The paths to these three files can be configured in csxextract/config.py. These files an be found in resources/classifier.

ParsCit is used to extract citation information from the PDF files. The path to it's citeExtract.pl script should be configured in csxextract/config.py. The default expected location is ~/bin/pars_cit/bin/citeExtract.pl.

Installation of ParsCit can be tricky. See its INSTALL doc for full instructions details. Also important is the Troubleshooting page which has answers for common problems.

A message like "Can't locate XML/Twig.pm in @INC (@INC contains: ...)" means that a Perl library is missing. Missing libraries can be installed with cpan.

Also note the question "When running citeExtract.pl I get some errors complaining about the wrong ELF class of the binaries. How can I fix this?" After Step 1 in the install instructions, the following commands should be run:

$ cp -Rf * ../../.libs 
$ cp crf_learn ../../.libs/lt-crf_learn
$ cp crf_test ../../.libs/lt-crf_test

Finally, the step marked as "optional" in the install instructions might actually be necessary when installing ParsCit.

pdffigures is used to extract figures and tables from PDF files along with related figure and table metadata. It should be installed as directed by the pdffigures Github page. The path to the pdffigures binary can be configured in csxextract/config.py

A Java jar is used to extract algorithms from PDFs. The required files can be found at resources/algextract/. Store the algo_extractor.jar file and the perl/ directory on your system where you wish. Then, in csxextract/config.py, set the ALGORITHM_JAR_PATH variable to the location of the algo_extractor.jar and the ALGORITHMS_PERL_PATH variable to the location of the perl/ directory.

Finally, make sure you have the Lingua::Stem Perl module installed. This can be installed with cpan.