A python library/command-line tool to extract the DOI or other identifiers of a scientific paper from a pdf file.
Project description
pdf2doi
pdf2doi is a Python library/command-line tool to automatically extract the DOI or other identifiers (e.g. arXiv ID) starting from the .pdf file of a publication
(or from a folder containing several .pdf files), and to retrieve bibliographic information.
It exploits several methods (see below for detailed description) to find a valid identifier of a pdf file, and it validates any result
via web queries to public archives (e.g. http://dx.doi.org).
The validation process also returns raw bibtex infos, which can be used for further processing, such as generating BibTeX entries (pdf2bib) or
automatically renaming pdf files (pdf-renamer).
pdf2doi can be used either from command line, or inside your python script or, only for Windows, directly from the right-click context menu of a pdf file or a folder.
Latest stable version
The latest stable version of pdf2doi is the 1.4. See here for the full change log.
[v1.4] - 2022-11-02
Main improvements (see also merge from https://github.com/MicheleCotrufo/pdf2doi/pull/20)
- Check for server error status codes when validating on dx.doi.org as 504 errors can occur
- When performing google searches, it looks for DOIs also in the URLs.
- Support any URL with a matching DOI and the doi keyword in the URL.
- Attempt to strip extensions from filenames doi10.111/1111.pdf will fail to locate the doi as 10.111/1111.pdf is a valid, if uncommon DOI.
- "Standardise" DOIs to handle loose matches e.g. case variations, or trailing punctuation.
Minor code changes (see also merge from https://github.com/MicheleCotrufo/pdf2doi/pull/20)
- Moved regex patterns to patterns.py + add pytest tests for common DOI patterns
- Update to use logger.exception which provides tracebacks on errors.
- Moved code to add the '/identifier' tag to a general function add_metadata() in finders.py
Installation
Use the package manager pip to install pdf2doi.
pip install pdf2doi==1.4.post1
Under Windows, after installation it is also possible to add shortcuts to the right-click context menu.
Used by
Here is a list of applications/repositories that make use of pdf2doi. If you use pdf2doi in your application and you wish to add it to this list, send me a message.
Table of Contents
- Installation
- Description
- Usage
- Installing the shortcuts in the right-click context menu of Windows -Contributing
- License
- Acknowledgment
- Donating
Description
Automatically associating a DOI or other identifiers (e.g. arXiv ID) to a pdf file can be either a very easy or a very difficult (sometimes nearly impossible) task, depending on how much care was placed in crafting the file. In the simplest case (which typically works with most recent publications) it is enough to look into the file metadata. For older publications, the identifier is often found within the pdf text and it can be extracted with the help of regular expressions. In the unluckiest cases, the only method left is to google some details of the publication (e.g. the title or parts of the text) and hope that a valid identifier is contained in one of the first results.
pdf2doi applies sequentially all these methods (starting from the simplest ones) until a valid identifier is found and validated.
Specifically, for a given .pdf file it will, in order,
-
Look into the metadata of the .pdf file (extracted via the library PyPDF2) and check if any of them contains a string that matches the pattern of a DOI or an arXiv ID. Priority is given to metadata which contain the word 'doi' in their label.
-
Check if the name of the pdf file contains any sub-string that matches the pattern of a DOI or an arXiv ID.
-
Scan the text inside the .pdf file, and check for any string that matches the pattern of a DOI or an arXiv ID. The text is extracted with the libraries PyPDF2 and textract.
-
Try to find possible titles of the publication. In the current version, possible titles are identified via the library pdftitle, and by the file name. For each possible title a google search is performed and the plain text of the first results is scanned for valid identifiers.
-
As a last desperate attempt, the first N=1000 characters of the pdf text are used as a query for a google search. The plain text of the first results is scanned for valid identifiers.
Any time that a potential identifier is found, it is also validated by performing a query to a relevant website (e.g., http://dx.doi.org for DOIs and http://export.arxiv.org for arxiv IDs). This validation process also returns raw BibTeX info when the identifier is valid.
When a valid identifier is found with any method different than the first one, the identifier is also stored inside the metadata of the pdf file. In this way, future lookups of this same file will be able to extract the identifier with the first method, speeding up the search (This feature can be disabled by the user, in case edits to the pdf file are not desired).
The library is far from being perfect. Often, especially for old publications, none of the currently implemented methods will work. Other times the wrong DOI might be extracted: this can happen, for example,
if the DOI of another paper is present in the pdf text and it appears before the correct DOI. A quick and dirty solution to this problem is to look up the identifier manually and then add it to the metadata
of the file, with the methods shown here (from python console) or here (from command line).
In this way, pdf2doi will always retrieve the correct DOI when analyzing this same file in the future, which can be useful when pdf2doi is used to automatize
bibliographic procedures for a large number of files (e.g. via pdf2bib or
pdf-renamer).
Currently, only the format of arXiv identifiers in use after 1 April 2007 is supported.
Usage
pdf2doi can be used either as a stand-alone application invoked from the command line, or by importing it in your python project or, only for Windows, directly from the right-click context menu of a pdf file or a folder.
Command line usage
pdf2doi can be invoked directly from the command line, without having to open a python console.
The simplest command-line invokation is
$ pdf2doi 'path/to/target'
where target is either a valid pdf file or a directory containing pdf files. Adding the optional command '-v' increases the output verbosity,
documenting all steps.
For example, when targeting the folder examples we get the following output
$ pdf2doi ".\examples" -v
[pdf2doi]: Looking for pdf files in the folder .\examples...
[pdf2doi]: Found 4 pdf files.
[pdf2doi]: ................
[pdf2doi]: Trying to retrieve a DOI/identifier for the file: .-s2.0-0021999186900938-main.pdf
[pdf2doi]: Method #1: Looking for a valid identifier in the document infos...
[pdf2doi]: Could not find a valid identifier in the document info.
[pdf2doi]: Method #2: Looking for a valid identifier in the file name...
[pdf2doi]: Could not find a valid identifier in the file name.
[pdf2doi]: Method #3: Looking for a valid identifier in the document text...
[pdf2doi]: Extracting text with the library PyPdf...
[pdf2doi]: Text extracted succesfully. Looking for an identifier in the text...
[pdf2doi]: Could not find a valid identifier in the document text extracted by PyPdf.
[pdf2doi]: Extracting text with the library textract...
[pdf2doi]: Text extracted succesfully. Looking for an identifier in the text...
[pdf2doi]: Could not find a valid identifier in the document text extracted by textract.
[pdf2doi]: Could not find a valid identifier in the document text.
[pdf2doi]: Method #4: Looking for possible publication titles...
[pdf2doi]: Found 2 possible title(s).
[pdf2doi]: Trying possible title #1
[pdf2doi]: Performing google search with key "An Efficient Numerical Evaluation of the Greenâs Function for the Helmholtz Operator on Periodic Str ...[query too long, the remaining part is suppressed in the logging]"
[pdf2doi]: and looking at the first 6 results...
[pdf2doi]: Looking for a valid identifier in the search result #1 : https://www.sciencedirect.com/science/article/pii/0021999186900938
[pdf2doi]: Validating the possible DOI 10.1016/0021-9991(86)90093-8 via a query to dx.doi.org...
[pdf2doi]: The DOI 10.1016/0021-9991(86)90093-8 is validated by dx.doi.org.
[pdf2doi]: A valid DOI was found with this google search.
[pdf2doi]: Trying to write the identifier '10.1016/0021-9991(86)90093-8' into the metadata of the file '.\examples-s2.0-0021999186900938-main.pdf'...
[pdf2doi]: The identifier '10.1016/0021-9991(86)90093-8' was added succesfully to the metadata of the file '.\examples-s2.0-0021999186900938-main.pdf' with key '/identifier'...
[pdf2doi]: 10.1016/0021-9991(86)90093-8
[pdf2doi]: ................
[pdf2doi]: Trying to retrieve a DOI/identifier for the file: .\examples\chaumet_JAP_07.pdf
[pdf2doi]: Method #1: Looking for a valid identifier in the document infos...
[pdf2doi]: Could not find a valid identifier in the document info.
[pdf2doi]: Method #2: Looking for a valid identifier in the file name...
[pdf2doi]: Could not find a valid identifier in the file name.
[pdf2doi]: Method #3: Looking for a valid identifier in the document text...
[pdf2doi]: Extracting text with the library PyPdf...
[pdf2doi]: Text extracted succesfully. Looking for an identifier in the text...
[pdf2doi]: Validating the possible DOI 10.1063/1.2409490I.INTRODUCTION via a query to dx.doi.org...
[pdf2doi]: The DOI 10.1063/1.2409490I.INTRODUCTION is not valid according to dx.doi.org.
[pdf2doi]: Validating the possible DOI 10.1063/1.2409490I.INTRODUCTION via a query to dx.doi.org...
[pdf2doi]: The DOI 10.1063/1.2409490I.INTRODUCTION is not valid according to dx.doi.org.
[pdf2doi]: Validating the possible DOI 10.1063/1.2409490 via a query to dx.doi.org...
[pdf2doi]: The DOI 10.1063/1.2409490 is validated by dx.doi.org.
[pdf2doi]: A valid DOI was found in the document text.
[pdf2doi]: Trying to write the identifier '10.1063/1.2409490' into the metadata of the file '.\examples\chaumet_JAP_07.pdf'...
[pdf2doi]: The identifier '10.1063/1.2409490' was added succesfully to the metadata of the file '.\examples\chaumet_JAP_07.pdf' with key '/identifier'...
[pdf2doi]: 10.1063/1.2409490
[pdf2doi]: ................
[pdf2doi]: Trying to retrieve a DOI/identifier for the file: .\examples\PhysRevLett.116.061102.pdf
[pdf2doi]: Method #1: Looking for a valid identifier in the document infos...
[pdf2doi]: Could not find a valid identifier in the document info.
[pdf2doi]: Method #2: Looking for a valid identifier in the file name...
[pdf2doi]: Could not find a valid identifier in the file name.
[pdf2doi]: Method #3: Looking for a valid identifier in the document text...
[pdf2doi]: Extracting text with the library PyPdf...
[pdf2doi]: Text extracted succesfully. Looking for an identifier in the text...
[pdf2doi]: Validating the possible DOI 10.1103/PhysRevLett.116.061102 via a query to dx.doi.org...
[pdf2doi]: The DOI 10.1103/PhysRevLett.116.061102 is validated by dx.doi.org.
[pdf2doi]: A valid DOI was found in the document text.
[pdf2doi]: Trying to write the identifier '10.1103/PhysRevLett.116.061102' into the metadata of the file '.\examples\PhysRevLett.116.061102.pdf'...
[pdf2doi]: The identifier '10.1103/PhysRevLett.116.061102' was added succesfully to the metadata of the file '.\examples\PhysRevLett.116.061102.pdf' with key '/identifier'...
[pdf2doi]: 10.1103/PhysRevLett.116.061102
[pdf2doi]: ................
[pdf2doi]: Trying to retrieve a DOI/identifier for the file: .\examples\s41586-019-1666-5.pdf
[pdf2doi]: Method #1: Looking for a valid identifier in the document infos...
[pdf2doi]: Validating the possible DOI 10.1038/s41586-019-1666-5 via a query to dx.doi.org...
[pdf2doi]: The DOI 10.1038/s41586-019-1666-5 is validated by dx.doi.org.
[pdf2doi]: A valid DOI was found in the document info labelled '/doi'.
[pdf2doi]: 10.1038/s41586-019-1666-5
[pdf2doi]: ................
DOI 10.1016/0021-9991(86)90093-8 .\examples-s2.0-0021999186900938-main.pdf
DOI 10.1063/1.2409490 .\examples\chaumet_JAP_07.pdf
DOI 10.1103/PhysRevLett.116.061102 .\examples\PhysRevLett.116.061102.pdf
DOI 10.1038/s41586-019-1666-5 .\examples\s41586-019-1666-5.pdf
Every line which begins with [pdf2doi] is omitted when the optional command '-v' is absent.
In the final output, the first column specifies the kind of identifier (currently either 'DOI' or 'arxiv'), the second column contains the found DOI/identifier, and the third column contains the file path.
A list of all optional arguments can be generated by pdf2doi --h
$ pdf2doi --h
usage: pdf2doi [-h] [-v] [-nws] [-nwv] [-nostore] [-id IDENTIFIER] [-google GOOGLE_RESULTS] [-s FILENAME_IDENTIFIERS] [-clip] [-install--right--click] [-uninstall--right--click] [path [path ...]]
Retrieves the DOI or other identifiers (e.g. arXiv) from pdf files of a publications.
positional arguments:
path Relative path of the target pdf file or of the targe folder.
optional arguments:
-h, --help show this help message and exit
-v, --verbose Increase verbosity. By default (i.e. when not using -v), only a table with the found identifiers will be printed as output.
-nws, --no_web_search
Disable any method to find identifiers which requires internet searches (e.g. queries to google).
-nwv, --no_web_validation
Disable the online validation of identifiers (e.g., via queries to http://dx.doi.org/).
-nostore, --no_store_identifier_metadata
By default, anytime an identifier is found it is added to the metadata of the pdf file (if not present yet). By using this additional option, the identifier is not stored in the file metadata.
-id IDENTIFIER Stores the string IDENTIFIER in the metadata of the target pdf file, with key '/identifier'. Note: when this argument is passed, all other arguments (except for the path to the pdf file) are ignored.
-google GOOGLE_RESULTS
Set how many results should be considered when doing a google search for the DOI (default=6).
-s FILENAME_IDENTIFIERS, --save_identifiers_file FILENAME_IDENTIFIERS
Save all the identifiers found in the target folder in a text file inside the same folder with name specified by FILENAME_IDENTIFIERS. This option is only available when a folder is targeted.
-clip, --save_doi_clipboard
Store all found DOI/identifiers into the clipboard.
-install--right--click
Add a shortcut to pdf2doi in the right-click context menu of Windows. You can copy the identifier and/or bibtex entry of a pdf file (or all pdf files in a folder) into the clipboard by just right clicking on it!
NOTE: this feature is only available on Windows.
-uninstall--right--click
Uninstall the right-click context menu functionalities. NOTE: this feature is only available on Windows.
Manually associate the correct identifier to a file from command line
Sometimes it is not possible to retrieve a DOI/identifier automatically, or maybe the one that is retrieved is not the correct one. In these (hopefully rare) occasions
it is possible to manually add the correct DOI/identifier to the pdf metadata, by using the -id argument,
$ pdf2doi "path o\pdf" -id "doi1234"
This creates a new metadata in the pdf file with label '/identifier' and containing the string doi1234. Future lookups of this same file via pdf2doi (in particular when used by other tools such as pdf2bib or
pdf-renamer) will then return the correct identifier and BibTeX infos.
Usage inside a python script
pdf2doi can also be used as a library within a python script. The function pdf2doi.pdf2doi is the main point of entry. The function looks for the identifier of a pdf file by applying all the available methods.
The first input argument must be a valid path (either absolute or relative) to a pdf file or to a folder containing pdf files.
The same optional arguments available in the command line operation are now available via the methods set and get of the object pdf2doi.config
For example, we can scan the folder examples while soppressing output verbosity by,
>>> import pdf2doi
>>> pdf2doi.config.set('verbose',False)
>>> results = pdf2doi.pdf2doi('.\examples')
A full list of the library settings can be printed by the method pdf2doi.config.print()
>>> import pdf2doi
>>> pdf2doi.config.print()
verbose : False (bool)
separator : \ (str)
method_dxdoiorg : application/citeproc+json (str)
webvalidation : True (bool)
websearch : True (bool)
numb_results_google_search : 6 (int)
N_characters_in_pdf : 1000 (int)
save_identifier_metadata : True (bool)
The output of the function pdf2doi is a list of dictionaries (or just a single dictionary if a single file was targeted). Each dictionary has the following keys
result['identifier'] = DOI or other identifier (or None if nothing is found)
result['identifier_type'] = string specifying the type of identifier (e.g. 'doi' or 'arxiv')
result['validation_info'] = Additional info on the paper. If config.get('webvalidation') = True, then result['validation_info']
will typically contain raw bibtex data for this paper. Otherwise it will just contain True
result['path'] = path of the pdf file
result['method'] = method used to find the identifier
For example, the DOIs/identifiers of each file can be printed by
>>> for result in results:
>>> print(result['identifier'])
10.1016/0021-9991(86)90093-8
10.1063/1.2409490
10.1103/PhysRevLett.116.061102
10.1038/s41586-019-1666-5
By default, everytime that a valid DOI/identifier is found, it is stored in the metadata of the pdf file. In this way, subsequent lookups of the same folder/file will be much faster. This behaviour can be removed (e.g. if the user does not want or cannot edit the files) by setting save_identifier_metadata to False, via
>>> pdf2doi.config.set('save_identifier_metadata',False)
Manually associate the correct identifier to a file
Similarly to what described above, it is possible to associate a (manually found)
identifier to a pdf file also from within python, by using the function pdf2doi.add_found_identifier_to_metadata:
>>> import pdf2doi
>>> pdf2doi.add_found_identifier_to_metadata(path_to_pdf_file, identifier)
this creates a new metadata in the pdf file with label '/identifier' and containing the string identifier.
Installing the shortcuts in the right-click context menu of Windows
This functionality is only available on Windows (and so far it has been tested only on Windows 10). It adds additional commands to the context menu of Windows which appears when right-clicking on a pdf file or on a folder.
The different menu commands allow to copy the paper(s) identifier(s) into the system clipboard, or also to manually set the identifier of a pdf file (see also here).
To install this functionality, first install pdf2doi via pip (as described above), then open a command prompt with administrator rights and execute
$ pdf2doi -install--right--click
To remove it, simply run (again from a terminal with administrator rights)
$ pdf2doi -uninstall--right--click
If it is not possible to run this command from a terminal with administrator rights, the batch files here can be alternatively used (see readme.MD file in the same folder for instructions), although it is still required to have admnistrator rights.
NOTE: when multiple pdf files are selected, and the right-click context menu commands are used, pdf2doi will be called separately for each file, and thus
only the info of the last file will be stored in the clipboard. In order to copy the info of multiple files it is necessary to save them in a folder and right-click on the folder.
Contributing
Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.
Acknowledgment
I am thankful to my friend and colleague Yarden Mazor for leading the beta-testing efforts for this project.
Donating
If you find this library useful (or amazing!), please consider making donations on my behalf to organizations that advocate for and promote free dissemination of science, such as
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