Metadata-Version: 2.1
Name: pubmed-mapper
Version: 0.0.1
Summary: PubMed Mapper: A Python library that map PubMed XML to Python object
Home-page: https://github.com/soultoolman/pubmed-mapper
Author: soultoolman
Author-email: soultooman@gmail.com
License: MIT
Description: 
        # pubmed-mapper: A Python Library that map PubMed XML to Python object
        
        ## UML
        
        # todo: add UML here.
        
        ## installation
        
        ```shell
        pip install pubmed-mapper
        ```
        
        ## usage
        
        ### use as API
        
        ```python
        from lxml import etree
        from pubmed_mapper import Article
        
        
        infile = 'xxx.xml'
        with open(infile) as fp:
            root = etree.parse(fp)
        
        
        articles = []
        for pubmed_article_element in root.xpath('/PubmedArticleSet/PubmedArticle'):
            article =  Article.parse_element(pubmed_article_element)
            articles.append(article)
        ```
        
        ### use as command line software
        
        #### parse single PubMed XML file
        
        ```
        pubmed-mapper file -i data/pubmed21n0001.xml -o output/pubmed21n0001.jl
        ```
        
        #### parse a directory who contains multiple PubMed XML files
        
        ```
        pubmed-mapper directory -i data/ -o output/pubmed-mapper.jl
        ```
        
        #### FAQs
        
        ##### 1. What is pubmed-mapper.log generated by pubmed-mapper?
        
        pubmed-mapper.log is the default log file generate by pubmed-mapper,
        you can change the file by using *--log-file* options:
        
        ```
        pubmed-mapper --log-file my-custom.log file -i data/pubmed21n0001.xml -o output/pubmed21n0001.jl
        ```
        
        You can go to this log file to find out more parsing details.
        
        ##### 2. I want log detail message in my log file?
        
        Using *--log-level* can log more detail message:
        
        ```
        pubmed-mapper --log-file my-custom.log --log-level DEBUG file -i data/pubmed21n0001.xml -o output/pubmed21n0001.jl
        ```
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6.0
Description-Content-Type: text/markdown
