def get_data_links(self, request):
"Return the links data."
get_url = request.application.get_url
links = []
if configuration.PARENT_URL:
link = dict(href=configuration.PARENT_URL,
title=configuration.PARENT_TITLE or 'Parent page')
if configuration.PARENT_LOGO:
link['image'] = configuration.PARENT_LOGO
links.append(link)
links.append(dict(title='Most recent',
href=get_url()))
links.append(dict(title='Search',
href=get_url('search')))
if self.is_login_admin():
links.append(dict(title='Administration: Edit PI list',
href=get_url('pilist')))
links.append(dict(title='Administration: Add publication',
href=get_url('publication')))
links.append(dict(title='Administration:PubMed import',
href=get_url('pubmed', 'import')))
links.append(dict(title='Administration:PubMed fetched',
href=get_url('pubmed', 'fetched')))
years = self.get_years()
for year in reversed(sorted(years.keys())):
links.append(dict(title="Year (all PIs): %s" % year,
href=get_url('year', str(year)),
count=years[year]))
try:
doc = self.db['pilist']
except couchdb.http.ResourceNotFound:
pass
else:
pis = doc['pis']
pis.sort(lambda i, j: cmp(i['name'].lower(), j['name'].lower()))
for pi in pis:
name = pi['name']
key = to_ascii(name).lower().replace(' ', '_')
links.append(dict(title="Principal Investigator: %s" % name,
href=get_url('author', key)))
## for item in self.db.view('publication/tags', group=True):
## links.append(dict(title="Tags: %s" % item.key,
## href=get_url('tag', item.key)))
links.append(dict(title='Recently modified',
href=get_url('modified')))
links.append(dict(title='Incomplete info',
href=get_url('incomplete')))
links.append(dict(title='Journals',
href=get_url('journals')))
return links
def normalize_publication(self, publication, get_url):
"""Normalize the contents of the publication:
Change key '_id' to 'iui' and '_rev' to 'rev'.
Remove the '_attachments' entry.
Add the 'href' entry.
Add the 'alt_href' entry, if slug defined.
Add 'href' to each author."""
publication['iui'] = publication.pop('_id')
publication['rev'] = publication.pop('_rev')
publication['href'] = get_url(publication['iui'])
slug = publication.get('slug')
if slug:
publication['alt_href'] = get_url(slug)
publication.pop('_attachments', None)
for author in publication['authors']:
name = get_author_name(author)
name = to_ascii(name.replace(' ', '_')).lower()
author['href'] = get_url('author', name)
return publication
def load_pilist(db):
"Load the PI list, if not already done."
if db.get('pilist'): return
# Get the list from a CSV file
doc = dict(_id='pilist',
pis=[])
pis = doc['pis']
try:
infile = open('data/pilist.csv')
except IOError:
pass
else:
reader = csv.reader(infile)
for record in reader:
name = record[0].strip()
if not name: continue
affiliations = [a.strip() for a in record[1:] if a.strip()]
pis.append(dict(name=name,
normalized_name=to_ascii(name),
affiliation=', '.join(affiliations)))
with MetadataSaver(db, doc):
pass
