Parse URLs for DOIs, PubMed identifiers, PMC identifiers, arXiv identifiers, etc.

Charles Tapley Hoyt

Last update: Feb 12, 2022

Related tags

General Utilities citation-url

Overview

citation-url

Parse URLs for DOIs, PubMed identifiers, PMC identifiers, arXiv identifiers, etc.

This module has a single parse() function that takes in a URL and gives back a CURIE pair (with None as the first entry if it could not parse)

>> citation_url.parse("http://www.ncbi.nlm.nih.gov/pubmed/34739845") ('pubmed', '34739845') >>> citation_url.parse("https://example.com/true-garbage") (None, 'https://example.com/true-garbage')">

>>> import citation_url
>>> citation_url.parse("https://joss.theoj.org/papers/10.21105/joss.01708")
('doi', '10.21105/joss.01708')
>>> citation_url.parse("http://www.ncbi.nlm.nih.gov/pubmed/34739845")
('pubmed', '34739845')
>>> citation_url.parse("https://example.com/true-garbage")
(None, 'https://example.com/true-garbage')

🚀 Installation

The most recent release can be installed from PyPI with:

$ pip install citation_url

The most recent code and data can be installed directly from GitHub with:

$ pip install git+https://github.com/cthoyt/citation-url.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instrutions

The final section of the README is for if you want to get involved by making a code contribution.

Development Installation

To install in development mode, use the following:

$ git clone git+https://github.com/cthoyt/citation-url.git
$ cd citation-url
$ pip install -e .

🥼 Testing

After cloning the repository and installing tox with pip install tox, the unit tests in the tests/ folder can be run reproducibly with:

$ tox

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📖 Building the Documentation

$ tox -e docs

📦 Making a Release

After installing the package in development mode and installing tox with pip install tox, the commands for making a new release are contained within the finish environment in tox.ini. Run the following from the shell:

$ tox -e finish

This script does the following:

Uses Bump2Version to switch the version number in the setup.cfg and src/citation_url/version.py to not have the -dev suffix
Packages the code in both a tar archive and a wheel
Uploads to PyPI using twine. Be sure to have a .pypirc file configured to avoid the need for manual input at this step
Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use tox -e bumpversion minor after.

MeSH2Matrix - A set of Python codes for the generation of biomedical ontologies from the MeSH keywords of the PubMed scholarly publications

A set of Python codes for the generation of biomedical ontologies from the MeSH keywords of the PubMed scholarly publications

6 Nov 30, 2022

Empirical Study of Transformers for Source Code & A Simple Approach for Handling Out-of-Vocabulary Identifiers in Deep Learning for Source Code

Transformers for variable misuse, function naming and code completion tasks The official PyTorch implementation of: Empirical Study of Transformers fo

56 Nov 15, 2022

Simple DDL Parser to parse SQL (HQL, TSQL, AWS Redshift, Snowflake and other dialects) ddl files to json/python dict with full information about columns: types, defaults, primary keys, etc.

Simple DDL Parser Build with ply (lex & yacc in python). A lot of samples in 'tests/. Is it Stable? Yes, library already has about 5000+ usage per day

95 Jan 5, 2023

Python based Web Scraper which can discover javascript files and parse them for juicy information (API keys, IP's, Hidden Paths etc)

Python based Web Scraper which can discover javascript files and parse them for juicy information (API keys, IP's, Hidden Paths etc).

6 Aug 26, 2022

🗃 Open source self-hosted web archiving. Takes URLs/browser history/bookmarks/Pocket/Pinboard/etc., saves HTML, JS, PDFs, media, and more...

14.8k Jan 5, 2023

This python script extracts all the video URLs from any youtube channel. Then it extracts all the information like the name of the youtube channel, published date, likes, dislikes, comments, views, etc for all the videos in that channel.

youtube-channel-video-url-extractor This python script extracts all the video URLs from any youtube channel. Then it extracts all the information like

6 Feb 25, 2022

We have implemented shaDow-GNN as a general and powerful pipeline for graph representation learning. For more details, please find our paper titled Deep Graph Neural Networks with Shallow Subgraph Samplers, available on arXiv (https//arxiv.org/abs/2012.01380).

Deep GNN, Shallow Sampling Hanqing Zeng, Muhan Zhang, Yinglong Xia, Ajitesh Srivastava, Andrey Malevich, Rajgopal Kannan, Viktor Prasanna, Long Jin, R

117 Dec 20, 2022

arxiv-sanity, but very lite, simply providing the core value proposition of the ability to tag arxiv papers of interest and have the program recommend similar papers.

671 Dec 31, 2022

Listing arxiv - Personalized list of today's articles from ArXiv

Personalized list of today's articles from ArXiv Print and/or send to your gmail

5 Jun 17, 2022

Arxiv harvester - Poor man's simple harvester for arXiv resources

Poor man's simple harvester for arXiv resources This modest Python script takes

5 Oct 18, 2022

This tool extracts Credit card numbers, NTLM(DCE-RPC, HTTP, SQL, LDAP, etc), Kerberos (AS-REQ Pre-Auth etype 23), HTTP Basic, SNMP, POP, SMTP, FTP, IMAP, etc from a pcap file or from a live interface.

1.6k Jan 1, 2023

Parse feeds in Python

1.5k Dec 30, 2022

A python module to parse the Open Graph Protocol

OpenGraph is a module of python for parsing the Open Graph Protocol, you can read more about the specification at http://ogp.me/ Installation $ pip in

213 Nov 12, 2022

Parse human-readable date/time strings

parsedatetime Parse human-readable date/time strings. Python 2.6 or greater is required for parsedatetime version 1.0 or greater. While we still test

651 Dec 23, 2022

Parse 11.000 free proxies!

Proxy Machine Description I did this project in order to boost views with the teleboost ✈️ in my Telegram channel. You can use it not only for boostin

77 Jan 8, 2023

Parse Robinhood 1099 Tax Document from PDF into CSV

Robinhood 1099 Parser This project converts Robinhood Securities 1099 tax document from PDF to CSV file. This tool will be helpful for those who need

52 Jun 10, 2022

Release of SPLASH: Dataset for semantic parse correction with natural language feedback in the context of text-to-SQL parsing

SPLASH: Semantic Parsing with Language Assistance from Humans SPLASH is dataset for the task of semantic parse correction with natural language feedba

Microsoft Research - Language and Information Technologies (MSR LIT)

35 Oct 31, 2022

Aggrokatz is an aggressor plugin extension for Cobalt Strike which enables pypykatz to interface with the beacons remotely and allows it to parse LSASS dump files and registry hive files to extract credentials and other secrets stored without downloading the file and without uploading any suspicious code to the beacon.

aggrokatz What is this aggrokatz is an Aggressor plugin extension for CobaltStrike which enables pypykatz to interface with the beacons remotely. The

148 Dec 9, 2022

Using context-free grammar formalism to parse English sentences to determine their structure to help computer to better understand the meaning of the sentence.

Sentance Parser Executing the Program Make sure Python 3.6+ is installed. Install requirements $ pip install requirements.txt Run the program:

12 Sep 28, 2022

Parse URLs for DOIs, PubMed identifiers, PMC identifiers, arXiv identifiers, etc.

Related tags

Overview

citation-url

🚀 Installation

👐 Contributing

👋 Attribution

⚖️ License

🍪 Cookiecutter

🛠️ For Developers

Development Installation

🥼 Testing

📖 Building the Documentation

📦 Making a Release

You might also like...

MeSH2Matrix - A set of Python codes for the generation of biomedical ontologies from the MeSH keywords of the PubMed scholarly publications

Empirical Study of Transformers for Source Code & A Simple Approach for Handling Out-of-Vocabulary Identifiers in Deep Learning for Source Code

Simple DDL Parser to parse SQL (HQL, TSQL, AWS Redshift, Snowflake and other dialects) ddl files to json/python dict with full information about columns: types, defaults, primary keys, etc.

Python based Web Scraper which can discover javascript files and parse them for juicy information (API keys, IP's, Hidden Paths etc)

🗃 Open source self-hosted web archiving. Takes URLs/browser history/bookmarks/Pocket/Pinboard/etc., saves HTML, JS, PDFs, media, and more...

This python script extracts all the video URLs from any youtube channel. Then it extracts all the information like the name of the youtube channel, published date, likes, dislikes, comments, views, etc for all the videos in that channel.

We have implemented shaDow-GNN as a general and powerful pipeline for graph representation learning. For more details, please find our paper titled Deep Graph Neural Networks with Shallow Subgraph Samplers, available on arXiv (https//arxiv.org/abs/2012.01380).

arxiv-sanity, but very lite, simply providing the core value proposition of the ability to tag arxiv papers of interest and have the program recommend similar papers.

Listing arxiv - Personalized list of today's articles from ArXiv

Arxiv harvester - Poor man's simple harvester for arXiv resources

This tool extracts Credit card numbers, NTLM(DCE-RPC, HTTP, SQL, LDAP, etc), Kerberos (AS-REQ Pre-Auth etype 23), HTTP Basic, SNMP, POP, SMTP, FTP, IMAP, etc from a pcap file or from a live interface.

Parse feeds in Python

A python module to parse the Open Graph Protocol

Parse human-readable date/time strings

Parse 11.000 free proxies!

Parse Robinhood 1099 Tax Document from PDF into CSV

Release of SPLASH: Dataset for semantic parse correction with natural language feedback in the context of text-to-SQL parsing

Using context-free grammar formalism to parse English sentences to determine their structure to help computer to better understand the meaning of the sentence.

Releases(v0.1.0)

v0.1.0(Feb 12, 2022)

Owner

Charles Tapley Hoyt

Small Python script to parse endlessh's output and print some neat statistics

jfc is an utility to make reviewing ArXiv papers for your Journal Club easier.

Auto-generate /etc/hosts for HackTheBox machines

A library from RCTI+ to handle RabbitMQ tasks (connect, send, receive, etc) in Python.

PubMed Mapper: A Python library that map PubMed XML to Python object

Simple Python Script to Parse Apache Log, Get all Unique IPs and Urls visited by that IP

Easily turn large sets of image urls to an image dataset. Can download, resize and package 100M urls in 20h on one machine.

Fast pattern fetcher, Takes a URLs list and outputs the URLs which contains the parameters according to the specified pattern.

Snscrape-jsonl-urls-extractor - Extracts urls from jsonl produced by snscrape

PyMed is a Python library that provides access to PubMed.