:mod:`bin.referencelinker`
==========================

.. py:module:: bin.referencelinker

.. autoapi-nested-parse::

   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
---------------

.. data:: __author__
   :annotation: = Martin Paul Eve

   

.. data:: __email__
   :annotation: = martin@martineve.com

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


.. py:class:: ReplaceObject(global_variables, paragraph, reference_to_link)

   Bases: :class:`debug.Debuggable`

   
   .. method:: link(self)




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

   Bases: :class:`debug.Debuggable`

   
   .. method:: replace_in_text(self, element, link_text)



   
   .. method:: replace_in_tail(self, element, link_text)



   
   .. method:: replace_in_text_and_update_others(self, object_list, link_text)



   
   .. method:: link(self, object_list=None)




.. py:class:: ReferenceLinker(global_variables)

   Bases: :class:`debug.Debuggable`

   
   .. method:: process_ibid_authors(self, ref_items)



   
   .. method:: clean_ref_items(self, tree, ref_items, manipulate)



   
   .. method:: run(self, interactive)



   
   .. method:: search_references(self, search_term, ref_items, manipulate, input_block)



   
   .. method:: link_items(self, source_id, dest_id, manipulate=None, tree=None)



   
   .. method:: handle_search(self, manipulate, opts, p, prompt, ref_items)



   
   .. method:: cleanup(self)



   
   .. method:: extract_contents(self, p)



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



   
   .. method:: run_prompt(self)



   
   .. method:: prune(self)




.. function:: main()