bin.referencelinker

referencelinker.py: a tool to link parenthetical references to ref-list elements in a JATS file

Usage:

referencelinker.py scan <input> [options] referencelinker.py link <input> <source_id> <dest_id> [options] referencelinker.py prune <input> [options]

Options:

-d, --debug

Enable debug output

--interactive

Prompt the user to assist in interactive tagging

-h, --help

Show this screen.

--nogit

Disable git debug filesystem (only of use with –debug)

-v, --version

Show version.

-z, --zotero

Enable Zotero integration for references.

Module Contents

bin.referencelinker.__author__ = Martin Paul Eve

bin.referencelinker.__email__ = martin@martineve.com

A class that looks for references to link in an NLM file and joins them to the corresponding reference entry

class bin.referencelinker.ReplaceObject(global_variables, paragraph, reference_to_link)

Bases: debug.Debuggable

link(self)

class bin.referencelinker.ReplaceStub(global_variables, paragraph, replace_text, tree, manipulate, link_text='TO_LINK', length_ignore=False)

Bases: debug.Debuggable

replace_in_text(self, element, link_text)

replace_in_tail(self, element, link_text)

replace_in_text_and_update_others(self, object_list, link_text)

link(self, object_list=None)

class bin.referencelinker.ReferenceLinker(global_variables)

Bases: debug.Debuggable

process_ibid_authors(self, ref_items)

clean_ref_items(self, tree, ref_items, manipulate)

run(self, interactive)

search_references(self, search_term, ref_items, manipulate, input_block)

link_items(self, source_id, dest_id, manipulate=None, tree=None)

handle_search(self, manipulate, opts, p, prompt, ref_items)

cleanup(self)

extract_contents(self, p)

handle_input(self, manipulate, opts, p, prompt, ref_items, sel, candidates=None, tree=None)

run_prompt(self)

prune(self)

bin.referencelinker.main()