def get_agr_title(self):
"""Convert chars and sub/superscript tags in FlyBase title for AGR export."""
# First determine if there's any title and/or volumetitle.
if self.title is not None and self.volumetitle is not None:
title_to_use = self.title + ' ' + self.volumetitle
elif self.title is not None:
title_to_use = self.title
else:
# Special exception for compendia: use pub.miniref if pub.title is null.
if self.pub_type == 'compendium':
title_to_use = self.miniref
else:
self.processing_warnings.append('No pub.title available.')
title_to_use = 'No title available.'
# Once title to use had been chosen, convert problematic characters.
title_to_use = sub_sup_sgml_to_html(title_to_use)
try:
title_to_use = sgml_to_unicode(title_to_use)
except KeyError:
self.processing_warnings.append(
'Atypical sgml character(s) in title.')
self.agr_title = title_to_use
return
def get_agr_citation(self):
"""Convert chars and sub/superscript tags in FlyBase miniref for AGR export."""
if self.miniref is None:
self.processing_warnings.append('No pub.miniref available.')
self.agr_citation = 'No citation available.'
else:
converted_miniref = sgml_to_unicode(self.miniref)
self.agr_citation = sub_sup_sgml_to_html(converted_miniref)
return
def convert_fullname_synonyms(self):
"""Convert all FB script designations in fullname synonyms to proper html."""
if self.fullname_synonym_list is None:
log.warning(
'Feature {} has no fullname_synonym_list to convert.'.format(
self.uniquename))
return
else:
self.fullname_synonym_list = [
sub_sup_sgml_to_html(i) for i in self.fullname_synonym_list
]
return
def get_agr_abstract(self):
"""Convert chars and sub/superscript tags in FlyBase abstract for AGR export."""
if self.pubmed_abstract != []:
if len(self.pubmed_abstract) > 1:
self.processing_warnings.append(
'Pub has many abstracts ({}). Using the first one.')
abstract_to_use = sub_sup_sgml_to_html(self.pubmed_abstract[0])
try:
abstract_to_use = sgml_to_unicode(abstract_to_use)
except KeyError:
self.processing_warnings.append(
'Atypical sgml character(s) in abstract.')
self.agr_abstract = abstract_to_use
return
def get_agr_title(self):
"""Convert chars and sub/superscript tags in FlyBase title for AGR export."""
# First determine if there's any title and/or volumetitle.
if self.title is None:
self.processing_warnings.append('No pub.title available.')
title_to_use = 'No title available.'
elif self.volumetitle is None:
title_to_use = self.title
else:
title_to_use = self.title + ' ' + self.volumetitle
# Next convert, handling odd chars that will raise error in "sgml_to_unicode" function.
title_to_use = sub_sup_sgml_to_html(title_to_use)
try:
title_to_use = sgml_to_unicode(title_to_use)
except KeyError:
self.processing_warnings.append(
'Atypical sgml character(s) in title.')
self.agr_title = title_to_use
return
def make_description(self):
"""Concatenate "nature_lesion" strings into a description."""
if self.molecular_info is None:
log.warning(
'Allele {} missing "molecular_info" info for description.'.
format(self.uniquename))
self.description = None
elif self.aminoacid_rep is None:
log.warning(
'Allele {} missing "aminoacid_rep" info for description.'.
format(self.uniquename))
self.description = None
elif self.nucleotide_sub is None:
log.warning(
'Allele {} missing "nucleotide_sub" info for description.'.
format(self.uniquename))
self.description = None
else:
nature_lesion_list = []
nature_lesion_list.extend(self.molecular_info)
nature_lesion_list.extend(self.aminoacid_rep)
nature_lesion_list.extend(self.nucleotide_sub)
if len(nature_lesion_list) > 0:
nature_lesion = ' '.join(nature_lesion_list)
nature_lesion = nature_lesion.replace('@', '')
nature_lesion = sub_sup_to_sgml(
nature_lesion) # Convert brackets into FB sub/superscript.
nature_lesion = sub_sup_sgml_to_html(
nature_lesion) # Convert FB sub/superscript to html.
nature_lesion = sgml_to_unicode(
nature_lesion) # Convert FB "&.gr;" Greeks to unicode.
self.description = nature_lesion
else:
log.debug(
'Allele {} has no nature_lesion to report for description'.
format(self.uniquename))
self.description = None
return
def get_agr_symbol(self):
"""Convert FB symbol_sgml to AGR format (proper html sub/superscripts."""
self.agr_symbol = self.symbol_sgml
self.agr_symbol = sub_sup_sgml_to_html(self.symbol_sgml)
return
