dispatching on resolver response status inside submit is a major design flaw

[tgbugs]

Passing the tuples around across function boundaries makes it extremely hard to understand what is going on and what the logic of the code actually is. Each step in the pipeline should be responsible for interpreting its own data.

scibot/scibot/submit.py

Lines 61 to 129 in dd3942e

	if status_code < 300:
	root = etree.fromstring(xml)
	if duplicate:
	# just mark the duplicate so that it will anchor in the client
	# but don't add the RRID: tag and don't include the resolver metadata
	r = h.create_annotation_with_target_using_only_text_quote(url=target_uri,
	document=document,
	prefix=prefix,
	exact=exact_for_hypothesis,
	suffix=suffix,
	text='',
	tags=new_tags,
	extra=extra,)
	elif root.findall('error'):
	s = 'Resolver lookup failed.'
	s += '<hr><p><a href="%s">resolver lookup</a></p>' % resolver_uri
	r = h.create_annotation_with_target_using_only_text_quote(url=target_uri,
	document=document,
	prefix=prefix,
	exact=exact_for_hypothesis,
	suffix=suffix,
	text=s,
	tags=new_tags + ['RRIDCUR:Unresolved'],
	extra=extra,)
	log.error(f'rrid unresolved {exact}')
	else:
	s = ''
	title = root.findall('title')[0].text
	s += f'Title: {title}\n'
	data_elements = root.findall('data')[0]
	data_elements = [(e.find('name').text, e.find('value').text) for e in data_elements] # these shouldn't duplicate
	citation = [(n, v) for n, v in data_elements if n == 'Proper Citation']
	rrid = [rrid_from_citation(c) for _, c in citation] if citation else [exact]
	name = [(n, v) for n, v in data_elements if n == 'Name']
	data_elements = citation + name + sorted([(n, v) for n, v in
	data_elements if (n != 'Proper Citation' or
	n != 'Name') and v is not None])
	for name, value in data_elements:
	if ((name == 'Reference' or name == 'Mentioned In Literature')
	and value is not None and value.startswith('<a class')):
	if len(value) > 500:
	continue # nif-0000-30467 fix keep those pubmed links short!
	s += '<p>%s: %s</p>' % (name, value)
	s += '<hr><p><a href="%s">resolver lookup</a></p>' % resolver_uri
	r = h.create_annotation_with_target_using_only_text_quote(url=target_uri,
	document=document,
	prefix=prefix,
	exact=exact_for_hypothesis,
	suffix=suffix,
	text=s,
	tags=new_tags + rrid,
	extra=extra,)
	elif status_code >= 500:
	s = 'Resolver lookup failed due to server error.'
	s += '<hr><p><a href="%s">resolver lookup</a></p>' % resolver_uri
	else:
	s = 'Resolver lookup failed.'
	s += '<hr><p><a href="%s">resolver lookup</a></p>' % resolver_uri
	r = h.create_annotation_with_target_using_only_text_quote(url=target_uri,
	document=document,
	prefix=prefix,
	exact=exact_for_hypothesis,
	suffix=suffix,
	text=s,
	tags=new_tags + ['RRIDCUR:Unresolved'],
	extra=extra,)