def run(self):
"""
Handle Zotero in-line reference items
@return: a list of items handled
"""
tei_manipulator = TeiManipulate(self.gv)
object_list = tei_manipulator.get_object_list('//tei:ref[@rend="ref"]', ' ADDIN EN.CITE', u'zoterobiblio')
object_list += tei_manipulator.get_object_list('//tei:ref', ' ADDIN ZOTERO_ITEM CSL_CITATION', u'zoterobiblio')
tei_manipulator.drop_addin('//tei:ref[@rend="ref"]', ' ADDIN EN.CITE', 'EndNote',
'hi', 'reference_to_link', self, u'zoterobiblio', True)
tei_manipulator.drop_addin_json('//tei:ref', ' ADDIN ZOTERO_ITEM CSL_CITATION',
'hi', 'reference_to_link', self)
tei_manipulator.drop_addin_json('//tei:ref', ' ADDIN ZOTERO_ITEM',
'hi', 'reference_to_link', self)
# handle bibliography
self.handle_bibliography(tei_manipulator)
if len(object_list) > 0:
self.debug.print_debug(self, u'Stashed {0} references for bibliography parsing'.format(len(object_list)))
return object_list
def pre_clean(self):
self.extract_metadata_fields()
manipulate = TeiManipulate(self.gv)
tree = manipulate.load_dom_tree()
# get all elements in the body
section = tree.xpath('//tei:body//*', namespaces={'tei': 'http://www.tei-c.org/ns/1.0'})
items_to_match = ['{http://www.tei-c.org/ns/1.0}head', '{http://www.tei-c.org/ns/1.0}p',
'{http://www.tei-c.org/ns/1.0}cit']
count = 0
matched_authors = []
for item in section:
if count > 2:
break
if item.tag in items_to_match:
count += 1
text = self.get_stripped_text(item)
processed = False
for author in self.authors:
if not author in matched_authors:
has_all = True
for component in author:
if not component in text:
has_all = False
break
if has_all:
# found a metadata line
matched_authors.append(author)
count -= 1
item.getparent().remove(item)
self.debug.print_debug(self, u'Removed line "{0}" '
u'because it appears to be author metadata'.format(text))
processed = True
break
if not processed:
for metadata in self.metadata:
if metadata in text:
# found a metadata line
count -= 1
item.getparent().remove(item)
self.debug.print_debug(self, u'Removed line "{0}" '
u'because it appears to be duplicated metadata'.format(text))
manipulate.save_tree(tree)
def run(self):
"""
Handle Mendeley reference tags, replacing them with NLM-spec references
@return: a list of processed tags
"""
tei_manipulator = TeiManipulate(self.gv)
object_list = tei_manipulator.get_object_list('//tei:ref[@rend="ref"]', 'ADDIN CSL_CITATION', u'zoterobiblio')
tei_manipulator.drop_addin_json('//tei:ref', 'ADDIN CSL_CITATION',
'hi', 'reference_to_link', self)
self.handle_bibliography(tei_manipulator)
if len(object_list) > 0:
self.debug.print_debug(self, u'Stashed {0} references for bibliography parsing'.format(len(object_list)))
return object_list
def run(self):
"""
Handle all unknown types of addin, stripping them from the output
@return: a list of tags that were removed
"""
tei_manipulator = TeiManipulate(self.gv)
object_list = tei_manipulator.get_object_list('//*', ' ADDIN', u'addin')
drop = self.gv.setting('drop-unknown-addins')
tei_manipulator.drop_addin('//*', ' ADDIN', 'EndNote',
'hi', 'unknown_addin_text', self, u'addin',
drop == 'True')
if len(object_list) > 0:
self.debug.print_debug(self, u'Handled {0} unknown addin tags'.format(len(object_list)))
return object_list
def pre_cleanup(self):
manipulate = TeiManipulate(self.gv)
tree = manipulate.load_dom_tree()
# make sure that head elements are not encapsulated within any elements that will stop them from being
# correctly transformed by the XSL
allowed = ['{http://www.tei-c.org/ns/1.0}div', '{http://www.tei-c.org/ns/1.0}body']
head_elements = tree.xpath('//tei:div[tei:head]', namespaces={'tei': 'http://www.tei-c.org/ns/1.0'})
count = 0
for element in head_elements:
current = element
while current is not None:
current = current.getparent()
if current is not None:
if current.tag and current.tag not in allowed:
current.tag = 'REMOVE'
count += 1
elif current.tag and current.tag in allowed:
break
else:
break
if count > 0:
etree.strip_tags(tree, 'REMOVE')
manipulate.save_tree(tree)
self.debug.print_debug(self, u'Extracted {0} headings from inside invalid elements'.format(count))
# split any p tags with sub-tags hi rend="Indent" into new elements
biblio_elements = tree.xpath('//tei:p'
'[tei:hi[contains(@rend, "Indent") or contains(@rend, "Default Style") or '
'contains(@rend, "Text Body")]]',
namespaces={'tei': 'http://www.tei-c.org/ns/1.0'})
for parent in biblio_elements:
add_position = parent
for element in parent.xpath('tei:hi[contains(@rend, "Indent") or contains(@rend, "Default Style") or '
'contains(@rend, "Text Body")]',
namespaces={'tei': 'http://www.tei-c.org/ns/1.0'}):
new_p = etree.Element('p')
if 'rend' in parent.attrib:
new_p.attrib['rend'] = parent.attrib['rend']
add_position.addnext(new_p)
new_p.append(element)
add_position = new_p
manipulate.save_tree(tree)
self.debug.print_debug(self, u'Separated out p {0}'.format(manipulate.get_stripped_text(parent)))
def pre_cleanup(self):
manipulate = TeiManipulate(self.gv)
tree = manipulate.load_dom_tree()
# make sure that head elements are not encapsulated within any elements that will stop them from being
# correctly transformed by the XSL
allowed = [
'{http://www.tei-c.org/ns/1.0}div',
'{http://www.tei-c.org/ns/1.0}body'
]
head_elements = tree.xpath(
'//tei:div[tei:head]',
namespaces={'tei': 'http://www.tei-c.org/ns/1.0'})
count = 0
for element in head_elements:
current = element
while current is not None:
current = current.getparent()
if current is not None:
if current.tag and current.tag not in allowed:
current.tag = 'REMOVE'
count += 1
elif current.tag and current.tag in allowed:
break
else:
break
if count > 0:
etree.strip_tags(tree, 'REMOVE')
manipulate.save_tree(tree)
self.debug.print_debug(
self,
u'Extracted {0} headings from inside invalid elements'.format(
count))
# split any p tags with sub-tags hi rend="Indent" into new elements
biblio_elements = tree.xpath(
'//tei:p'
'[tei:hi[contains(@rend, "Indent") or contains(@rend, "Default Style") or '
'contains(@rend, "Text Body")]]',
namespaces={'tei': 'http://www.tei-c.org/ns/1.0'})
for parent in biblio_elements:
add_position = parent
for element in parent.xpath(
'tei:hi[contains(@rend, "Indent") or contains(@rend, "Default Style") or '
'contains(@rend, "Text Body")]',
namespaces={'tei': 'http://www.tei-c.org/ns/1.0'}):
new_p = etree.Element('p')
if 'rend' in parent.attrib:
new_p.attrib['rend'] = parent.attrib['rend']
add_position.addnext(new_p)
new_p.append(element)
add_position = new_p
manipulate.save_tree(tree)
self.debug.print_debug(
self, u'Separated out p {0}'.format(
manipulate.get_stripped_text(parent)))
def run_modules(self):
ag = int(self.gv.settings.args['--aggression'])
self.debug.print_debug(
self, u'Running at aggression level {0} {1}'.format(
ag, "[grrr!]" if ag == 10 else ""))
if ag > 10:
self.debug.print_debug(
self,
"WARNING: safety bail-out features are disabled at aggression level 11"
)
if self.args['bibscan']:
BibliographyDatabase(self.gv).scan()
else:
# check for stylesheets
self.gv.check_file_exists(self.gv.docx_style_sheet_dir)
# metadata file
gv.metadata_file = self.set_metadata_file()
self.gv.mk_dir(self.gv.output_folder_path)
if self.args['doc']:
# run doc to docx conversion
# then run docx to tei
UnoconvToDocx(self.gv).run('doc')
DocxToTei(self.gv).run(True, self.args['--proprietary'])
elif self.args['odt']:
# run odt to docx conversion
# then run docx to tei
UnoconvToDocx(self.gv).run('odt')
DocxToTei(self.gv).run(True, self.args['--proprietary'])
elif self.args['other']:
# run other unoconv-supported format to docx conversion
# then run docx to tei
UnoconvToDocx(self.gv).run('unoconv')
DocxToTei(self.gv).run(True, self.args['--proprietary'])
elif self.args['docx']:
# run docx to tei conversion
# includes hooks for proprietary transforms if enabled
DocxToTei(self.gv).run(True, self.args['--proprietary'])
elif self.args['docxextracted']:
self.debug.print_debug(self, u'Skipping docx extraction')
DocxToTei(self.gv).run(False, self.args['--proprietary'])
elif self.args['tei']:
self.debug.print_debug(
self, u'Skipping docx extraction; processing TEI file')
DocxToTei(self.gv).run(False,
self.args['--proprietary'],
tei=True)
if self.args['--puretei']:
self.debug.print_debug(self,
u'Exiting as TEI transform complete')
return
metadata = Metadata(self.gv)
metadata.pre_clean()
# run size classifier
# aggression 5
SizeClassifier(self.gv).run()
# run bibliographic addins handler
# aggression 4
found_bibliography = BibliographyAddins(self.gv).run()
# run list classifier
# aggression 4
ListClassifier(self.gv).run()
bibliography_classifier = BibliographyClassifier(self.gv)
if not found_bibliography:
# run bibliographic classifier
# aggression 4
bibliography_classifier.run()
# tei
# aggression 3
TeiManipulate(self.gv).run()
# run tei to nlm conversion
TeiToNlm(self.gv).run(not found_bibliography)
if self.gv.settings.args['--purenlm']:
self.debug.print_debug(self,
u'Exiting as NLM transform complete')
return
manipulate = NlmManipulate(self.gv)
if not self.gv.used_list_method:
manipulate.fuse_references()
# run reference linker
if not (self.args['--nolink']):
rl = ReferenceLinker(self.gv)
rl.run(self.args['--interactive'])
rl.cleanup()
# run table classifier
cc = CaptionClassifier(self.gv)
if int(self.args['--aggression']) > int(
self.gv.settings.get_setting(
'tablecaptions', self, domain='aggression')):
cc.run_tables()
if int(self.args['--aggression']) > int(
self.gv.settings.get_setting(
'graphiccaptions', self, domain='aggression')):
cc.run_graphics()
# run metadata merge
metadata.run()
if self.args['--interactive']:
bibliography_classifier.run_prompt(True)
# process any bibliography entries that are possible
BibliographyDatabase(self.gv).run()
# remove stranded titles and cleanup
manipulate.final_clean()
if self.args['--identifiers']:
IdGenerator(self.gv).run()
if self.args['--chain']:
# construct and run an XSLT chainer
XslChain(self.gv).run()
if self.args['--clean']:
ComplianceEnforcer(self.gv).run()
def pre_clean(self):
self.extract_metadata_fields()
manipulate = TeiManipulate(self.gv)
tree = manipulate.load_dom_tree()
# get all elements in the body
section = tree.xpath('//tei:body//*',
namespaces={'tei': 'http://www.tei-c.org/ns/1.0'})
items_to_match = [
'{http://www.tei-c.org/ns/1.0}head',
'{http://www.tei-c.org/ns/1.0}p',
'{http://www.tei-c.org/ns/1.0}cit'
]
count = 0
matched_authors = []
for item in section:
if count > 2:
break
if item.tag in items_to_match:
count += 1
text = self.get_stripped_text(item)
processed = False
for author in self.authors:
if not author in matched_authors:
has_all = True
for component in author:
if not component in text:
has_all = False
break
if has_all:
# found a metadata line
matched_authors.append(author)
count -= 1
item.getparent().remove(item)
self.debug.print_debug(
self, u'Removed line "{0}" '
u'because it appears to be author metadata'.
format(text))
processed = True
break
if not processed:
for metadata in self.metadata:
if metadata in text:
# found a metadata line
count -= 1
item.getparent().remove(item)
self.debug.print_debug(
self, u'Removed line "{0}" '
u'because it appears to be duplicated metadata'
.format(text))
manipulate.save_tree(tree)