ADSIngestParser

ADSIngestParser is a library used to parse publisher-provided files, in well-structured XML or other formats, into our own data model, defined by the ingest_data_model. The output is a dictionary.

Example usage, with the arXiv parser:

from adsingestp.parsers import arxiv

with open("infile.xml", "rb") as fp:
    input_data = fp.read()

parser = arxiv.ArxivParser()
parsed = parser.parse(input_data)

Installation

Install this via pip (or your favourite package manager):

pip install adsingestp

Development

Install locally into virtualenv

virtualenv .venv
source .venv/bin/activate
pip install -e .

Parser structure

Parsers for each source file format should be in their own file. The parser itself is object-oriented, and the class name should take the format <Format>Parser (e.g. ArxivParser). XML parsers should inherit BaseBeautifulSoupParser. All parser classes should ultimately inherit IngestBase (BaseBeautifulSoupParser inherits this base class). All parsers will parse the source file into an intermediate dictionary format, outlined in IngestBase.format. The intermediate dictionary format must then be converted to the final ingest_data_model format via

output = self.format(<intermediate_dictionary>, format=...)

This final formatting into the ingest_data_model format is done separately from the parsing in order to simplify any updates that may need to happen if/when the upstream ingest_data_model is changed.

Publisher-specific parsers are discouraged unless the publisher uses a proprietary data format. If a proprietary format is based on a generic format (e.g. DublinCore / OAI-PMH), then the generic parser should be written first, with a publisher-specific parser inheriting from the generic class.

Required methods:

• __init__: initialize the intermediate dictionary and other needed structures
• parse: the primary external method. The primary input is the text of the source file (the source file must be read in prior to calling the parse method; no I/O is included in this library). The output is a dictionary in the ingest_data_model format

Other sub-functions may be included as needed, to enhance code readability. Prepend an underscore (_) to internal sub-function names.

XML parsers

Parsers that handle XML source files should use BeautifulSoup to handle initial parsing. To do so, the parser should inherit BaseBeautifulSoupParser, then call the bsstrtodict method on the input text:

d = self.bsstrtodict(text, parser="lxml-xml")

The BS parser is generally lxml-xml, but this can be changed as needed.

Author name parsing

Many of the parsers utilize the utils.AuthorNames.parse method to parse a single raw author name string into a structured name dictionary. Use this method for author name parsing unless something more comprehensive is required.

Unittests

Unittests must be included for each new parsers, with a minimum of 2 example source files per parser. Preferably, at least one of these source files should be of a more complex structure. Unittest coverage should be 80% or higher for each parser. If more example source files are needed, check with the curation team.

If a parser fails to properly parse any legitimate metadata file having that format, it is likely that there are features included in the format schema that weren't captured in our parser. The parser must be modified to properly parse the file, and the metadata file must be added to the unittest suite.

We are restricted from making some content publicly available in some cases, so parser authors should check with curators to ensure we are not violating publisher rights by making content available on Github. When such cases occur, the metadata file should be kept largely intact to the extent possible, with impermissible data redacted in such a way that the replacement text still provides a sufficient parsing test. When possible, parser authors should use content with open-access licensing for test cases.

Unittest output files should be in .json format and contain the parsed metadata in the ingest data model format. The file effectively contains a Python dictionary, though some small edits must be made to conform to the .json file standard (e.g. a Boolean is capitalized in Python but lower case in .json: True vs. true). In addition, please pretty print the input and output data before copying it into the relevant files, to make the diff work correctly. There are a few different methods for doing this; here are a few options:

• pprint: adjust the width as needed to keep from introducing extraneous line breaks

import pprint
pprint.pprint(output, width=2000)

• json.dumps:

json.dumps(output, indent=2)

Documentation

documentation

Maintained by

Mugdha, Matt