def main(args):
#get_obsolete_refs(args)
with transaction.manager:
#match_obsolete_refs(args)
#
# TODO:
# - create bibtex file containing all refs to be removed!
# -
#
matched = args.data_file(args.version, 'obsolete_refs_matched.json')
if matched.exists():
with open(matched) as fp:
matched = json.load(fp)
else:
matched = {}
for id_, repl in matched.items():
if not repl:
continue
ref = Ref.get(id_, default=None)
if ref is None:
continue
Config.add_replacement(ref, repl, session=DBSession, model=Source)
DBSession.delete(ref)
def match_obsolete_refs(args):
with open(args.data_file(args.version, 'obsolete_refs.json')) as fp:
refs = json.load(fp)
matched = args.data_file(args.version, 'obsolete_refs_matched.json')
if matched.exists():
with open(matched) as fp:
matched = json.load(fp)
else:
matched = {}
#
# TODO: optionally re-evaluate known-unmatched refs!
#
count = 0
f, m = 0, 0
for id_ in refs:
if id_ in matched:
continue
count += 1
if count > 1000:
print '1000 obsolete refs processed!'
break
ref = Ref.get(id_)
found = False
if ref.description and len(ref.description) > 5:
for match in DBSession.query(Ref)\
.filter(not_(Source.id.in_(refs)))\
.filter(Source.description.contains(ref.description))\
.filter(or_(Source.author == ref.author, Source.year == ref.year))\
.limit(10):
print '++', ref.id, '->', match.id, '++', ref.author, '->', match.author, '++', ref.year, '->', match.year
matched[ref.id] = match.id
found = True
break
if not found and ref.name and len(ref.name) > 5:
for match in DBSession.query(Ref)\
.filter(not_(Source.id.in_(refs)))\
.filter(Source.name == ref.name)\
.limit(10):
try:
if match.description and ref.description and slug(match.description) == slug(ref.description):
print '++', ref.id, '->', match.id, '++', ref.description, '->', match.description
matched[ref.id] = match.id
found = True
break
except AssertionError:
continue
if not found:
m += 1
print '--', ref.id, ref.name, ref.description
matched[ref.id] = None
else:
f += 1
print f, 'found'
print m, 'missed'
with open(args.data_file(args.version, 'obsolete_refs_matched.json'), 'w') as fp:
json.dump(matched, fp)
def update(args):
author = 'ISO 639-3 Registration Authority'
pid = 'iso6393'
dtid = 'overview'
dt = Doctype.get(dtid)
provider = Provider.get(pid, default=None)
if provider is None:
provider = Provider(
id=pid,
abbr=pid,
name=author,
description="Change requests submitted to the ISO 639-3 registration authority.")
iid = max(int(DBSession.execute(
"select max(cast(id as integer)) from source").fetchone()[0]), 500000)
pk = int(DBSession.execute("select max(pk) from source").fetchone()[0])
for crno, affected in args.json['changerequests'].items():
year, serial = crno.split('-')
title = 'Change Request Number %s' % crno
ref = Ref.get(title, key='title', default=None)
if not ref:
iid += 1
pk += 1
ref = Ref(
pk=pk,
id=str(iid),
name='%s %s' % (author, year),
bibtex_type=EntryType.misc,
number=crno,
description=title,
year=year,
year_int=int(year),
title=title,
author=author,
address='Dallas',
publisher='SIL International',
url='http://www.sil.org/iso639-3/cr_files/%s.pdf' % crno,
doctypes_str=dtid,
providers_str=pid,
language_note=', '.join('%(Language Name)s [%(Affected Identifier)s]' % spec for spec in affected),
jsondata=dict(hhtype=dtid, src=pid))
ref.doctypes.append(dt)
ref.providers.append(provider)
for spec in affected:
lang = Languoid.get(spec['Affected Identifier'], key='hid', default=None)
if lang and lang not in ref.languages:
ref.languages.append(lang)
DBSession.add(ref)
transaction.commit()
transaction.begin()
matched = 0
near = 0
max_identifier_pk = DBSession.query(
Identifier.pk).order_by(desc(Identifier.pk)).first()[0]
families = []
for family in DBSession.query(Languoid)\
.filter(Languoid.level == LanguoidLevel.family)\
.filter(Language.active == True)\
.all():
isoleafs = set()
for row in DBSession.query(TreeClosureTable.child_pk, Languoid.hid)\
.filter(family.pk == TreeClosureTable.parent_pk)\
.filter(Languoid.pk == TreeClosureTable.child_pk)\
.filter(Languoid.hid != None)\
.filter(Languoid.level == LanguoidLevel.language)\
.filter(Languoid.status == LanguoidStatus.established)\
.all():
if len(row[1]) == 3:
isoleafs.add(row[1])
families.append((family, isoleafs))
families = sorted(families, key=lambda p: len(p[1]))
for mid, leafs in args.json['macrolanguages'].items():
leafs = set(leafs)
found = False
for family, isoleafs in families:
if leafs == isoleafs:
if mid not in [c.name for c in family.identifiers
if c.type == IdentifierType.iso.value]:
family.codes.append(Identifier(
id=str(max_identifier_pk + 1),
name=mid,
type=IdentifierType.iso.value))
max_identifier_pk += 1
matched += 1
found = True
break
elif leafs.issubset(isoleafs):
print '~~~', family.name, '-->', mid, 'distance:', len(leafs), len(isoleafs)
near += 1
found = True
break
if not found:
print '---', mid, leafs
print 'matched', matched, 'of', len(args.json['macrolanguages']), 'macrolangs'
print near
def main(args): # pragma: no cover
bib = Database.from_file(args.data_file(args.version, 'refs.bib'), encoding='utf8')
count = 0
skipped = 0
changes = {}
with transaction.manager:
update_providers(args)
DBSession.flush()
provider_map = get_map(Provider)
macroarea_map = get_map(Macroarea)
doctype_map = get_map(Doctype)
known_ids = set(r[0] for r in DBSession.query(Ref.pk))
languoid_map = {}
for l in DBSession.query(Languoid):
if l.hid:
languoid_map[l.hid] = l
languoid_map[l.id] = l
for i, rec in enumerate(bib):
if i and i % 1000 == 0:
print i, 'records done', count, 'changed'
if len(rec.keys()) < 6:
# not enough information!
skipped += 1
continue
changed = False
assert rec.get('glottolog_ref_id')
id_ = int(rec.get('glottolog_ref_id'))
if args.mode != 'update' and id_ in known_ids:
continue
ref = DBSession.query(Source).get(id_)
update = True if ref else False
kw = {
'pk': id_,
'bibtex_type': rec.genre,
'id': str(id_),
'jsondata': {'bibtexkey': rec.id},
}
for source, target in FIELD_MAP.items():
if target is None:
continue
value = rec.get(source)
if value:
value = unescape(value)
if target:
kw[target] = CONVERTER.get(source, lambda x: x)(value)
else:
kw['jsondata'][source] = value
if kw['jsondata'].get('hhtype'):
trigger = ca_trigger(kw['jsondata']['hhtype'])
if trigger:
kw['ca_doctype_trigger'], kw['jsondata']['hhtype'] = trigger
# try to extract numeric year, startpage, endpage, numberofpages, ...
if kw.get('year'):
# prefer years in brackets over the first 4-digit number.
match = PREF_YEAR_PATTERN.search(kw.get('year'))
if match:
kw['year_int'] = int(match.group('year'))
else:
match = YEAR_PATTERN.search(kw.get('year'))
if match:
kw['year_int'] = int(match.group('year'))
if kw.get('publisher'):
p = kw.get('publisher')
if ':' in p:
address, publisher = [s.strip() for s in kw['publisher'].split(':', 1)]
if not 'address' in kw or kw['address'] == address:
kw['address'], kw['publisher'] = address, publisher
if rec.get('numberofpages'):
try:
kw['pages_int'] = int(rec.get('numberofpages').strip())
except ValueError:
pass
if kw.get('pages'):
start, end, number = compute_pages(kw['pages'])
if start is not None:
kw['startpage_int'] = start
if end is not None:
kw['endpage_int'] = end
if number is not None and 'pages_int' not in kw:
kw['pages_int'] = number
if update:
for k in kw.keys():
if k == 'pk':
continue
v = getattr(ref, k)
if kw[k] != v:
if k == 'jsondata':
d = ref.jsondata or {}
d.update(**kw[k])
for s, t in FIELD_MAP.items():
if t is None and s in d:
del d[s]
ref.jsondata = d
else:
print k, '--', v
print k, '++', kw[k]
setattr(ref, k, kw[k])
changed = True
if ref.id in changes:
changes[ref.id][k] = ('%s' % v, '%s' % kw[k])
else:
changes[ref.id] = {k: ('%s' % v, '%s' % kw[k])}
else:
changed = True
ref = Ref(name='%s %s' % (kw.get('author', 'na'), kw.get('year', 'nd')), **kw)
ref.description = ref.title or ref.booktitle
ref.name = '%s %s' % (ref.author or 'n.a.', ref.year or 'n.d.')
def append(attr, obj):
if obj and obj not in attr:
attr.append(obj)
return True
a, r = update_relationship(
ref.macroareas,
[macroarea_map[name] for name in
set(filter(None, [s.strip() for s in kw['jsondata'].get('macro_area', '').split(',')]))])
changed = changed or a or r
for name in set(filter(None, [s.strip() for s in kw['jsondata'].get('src', '').split(',')])):
result = append(ref.providers, provider_map[slug(name)])
changed = changed or result
a, r = update_relationship(
ref.doctypes,
[doctype_map[m.group('name')] for m in
DOCTYPE_PATTERN.finditer(kw['jsondata'].get('hhtype', ''))])
changed = changed or a or r
if not update:
DBSession.add(ref)
if changed:
count += 1
ref.doctypes_str = ', '.join(o.id for o in ref.doctypes)
ref.providers_str = ', '.join(o.id for o in ref.providers)
print count, 'records updated or imported'
print skipped, 'records skipped because of lack of information'
DBSession.execute("update source set description = title where description is null and title is not null;")
DBSession.execute("update source set description = booktitle where description is null and booktitle is not null;")
for row in list(DBSession.execute(
"select pk, pages, pages_int, startpage_int from source where pages_int < 0")):
pk, pages, number, start = row
_start, _end, _number = compute_pages(pages)
if _number > 0 and _number != number:
DBSession.execute(
"update source set pages_int = %s, startpage_int = %s where pk = %s",
(_number, _start, pk))
DBSession.execute(
"update ref set endpage_int = %s where pk = %s",
(_end, pk))
return changes
def update(args):
author = 'ISO 639-3 Registration Authority'
pid = 'iso6393'
dtid = 'overview'
dt = Doctype.get(dtid)
provider = Provider.get(pid, default=None)
if provider is None:
provider = Provider(
id=pid,
abbr=pid,
name=author,
description=
"Change requests submitted to the ISO 639-3 registration authority."
)
iid = max(
int(
DBSession.execute(
"select max(cast(id as integer)) from source").fetchone()[0]),
500000)
pk = int(DBSession.execute("select max(pk) from source").fetchone()[0])
for crno, affected in args.json['changerequests'].items():
year, serial = crno.split('-')
title = 'Change Request Number %s' % crno
ref = Ref.get(title, key='title', default=None)
if not ref:
iid += 1
pk += 1
ref = Ref(pk=pk,
id=str(iid),
name='%s %s' % (author, year),
bibtex_type=EntryType.misc,
number=crno,
description=title,
year=year,
year_int=int(year),
title=title,
author=author,
address='Dallas',
publisher='SIL International',
url='http://www.sil.org/iso639-3/cr_files/%s.pdf' % crno,
language_note=', '.join(
'%(Language Name)s [%(Affected Identifier)s]' % spec
for spec in affected),
jsondata=dict(hhtype=dtid, src=pid))
ref.doctypes.append(dt)
ref.providers.append(provider)
for spec in affected:
lang = Languoid.get(spec['Affected Identifier'],
key='hid',
default=None)
if lang and lang not in ref.languages:
ref.languages.append(lang)
DBSession.add(ref)
transaction.commit()
transaction.begin()
matched = 0
near = 0
max_identifier_pk = DBSession.query(Identifier.pk).order_by(
desc(Identifier.pk)).first()[0]
families = []
for family in DBSession.query(Languoid)\
.filter(Languoid.level == LanguoidLevel.family)\
.filter(Language.active == True)\
.all():
isoleafs = set()
for row in DBSession.query(TreeClosureTable.child_pk, Languoid.hid)\
.filter(family.pk == TreeClosureTable.parent_pk)\
.filter(Languoid.pk == TreeClosureTable.child_pk)\
.filter(Languoid.hid != None)\
.filter(Languoid.level == LanguoidLevel.language)\
.filter(Languoid.status == LanguoidStatus.established)\
.all():
if len(row[1]) == 3:
isoleafs.add(row[1])
families.append((family, isoleafs))
families = sorted(families, key=lambda p: len(p[1]))
for mid, leafs in args.json['macrolanguages'].items():
leafs = set(leafs)
found = False
for family, isoleafs in families:
if leafs == isoleafs:
if mid not in [
c.name for c in family.identifiers
if c.type == IdentifierType.iso.value
]:
family.codes.append(
Identifier(id=str(max_identifier_pk + 1),
name=mid,
type=IdentifierType.iso.value))
max_identifier_pk += 1
matched += 1
found = True
break
elif leafs.issubset(isoleafs):
print '~~~', family.name, '-->', mid, 'distance:', len(
leafs), len(isoleafs)
near += 1
found = True
break
if not found:
print '---', mid, leafs
print 'matched', matched, 'of', len(
args.json['macrolanguages']), 'macrolangs'
print near
def main(bib, mode): # pragma: no cover
count = 0
skipped = 0
with transaction.manager:
provider_map = get_map(Provider)
macroarea_map = get_map(Macroarea)
doctype_map = get_map(Doctype)
known_ids = set(r[0] for r in DBSession.query(Ref.pk))
languoid_map = {}
for l in DBSession.query(Languoid):
if l.hid:
languoid_map[l.hid] = l
languoid_map[l.id] = l
for i, rec in enumerate(bib):
if len(rec.keys()) < 6:
skipped += 1
#print '---> skip', rec.id
#print rec
continue
changed = False
assert rec.get('glottolog_ref_id')
id_ = int(rec.get('glottolog_ref_id'))
if mode != 'update' and id_ in known_ids:
continue
ref = DBSession.query(Source).get(id_)
update = True if ref else False
kw = {
'pk': id_,
'bibtex_type': getattr(EntryType, rec.genre),
'id': str(id_),
'jsondata': {
'bibtexkey': rec.id
},
}
for source, target in FIELD_MAP.items():
value = rec.get(source)
if value:
value = unescape(value)
if target:
kw[target] = CONVERTER.get(source, lambda x: x)(value)
else:
kw['jsondata'][source] = value
# try to extract numeric year, startpage, endpage, numberofpages, ...
if rec.get('numberofpages'):
try:
kw['pages_int'] = int(rec.get('numberofpages').strip())
except ValueError:
pass
if kw.get('year'):
match = YEAR_PATTERN.search(kw.get('year'))
if match:
kw['year_int'] = int(match.group('year'))
if kw.get('publisher'):
p = kw.get('publisher')
if ':' in p:
address, publisher = [
s.strip() for s in kw['publisher'].split(':', 1)
]
if not 'address' in kw or kw['address'] == address:
kw['address'], kw['publisher'] = address, publisher
if kw.get('pages'):
pages = kw.get('pages')
match = ROMANPAGESPATTERNra.search(pages)
if not match:
match = ROMANPAGESPATTERNar.search(pages)
if match:
if 'pages_int' not in kw:
kw['pages_int'] = roman_to_int(match.group('roman')) \
+ int(match.group('arabic'))
else:
start = None
number = None
match = None
for match in PAGES_PATTERN.finditer(pages):
if start is None:
start = int(match.group('start'))
number = (number or 0) \
+ (int(match.group('end')) - int(match.group('start')) + 1)
if match:
kw['endpage_int'] = int(match.group('end'))
kw['startpage_int'] = start
kw.setdefault('pages_int', number)
else:
try:
kw['startpage_int'] = int(pages)
except ValueError:
pass
if update:
for k in kw.keys():
if k == 'pk':
continue
#if k == 'title':
# v = ref.title or ref.description
#else:
if 1:
v = getattr(ref, k)
if kw[k] != v:
#
# TODO!
#
setattr(ref, k, kw[k])
#if k not in ['jsondata', 'publisher']:
# print k, ref.pk
# print kw[k]
# print v
# print '--------------'
changed = True
if ref.title:
ref.description = ref.title
else:
changed = True
ref = Ref(**kw)
def append(attr, obj):
if obj and obj not in attr:
changed = True
#
# TODO!
#
attr.append(obj)
for name in set(
filter(None, [
s.strip() for s in kw['jsondata'].get(
'macro_area', '').split(',')
])):
append(ref.macroareas, macroarea_map[name])
for name in set(
filter(None, [
s.strip()
for s in kw['jsondata'].get('src', '').split(',')
])):
append(ref.providers, provider_map[slug(name)])
for m in DOCTYPE_PATTERN.finditer(kw['jsondata'].get('hhtype',
'')):
append(ref.doctypes, doctype_map[m.group('name')])
if len(kw['jsondata'].get('lgcode', '')) == 3:
kw['jsondata']['lgcode'] = '[%s]' % kw['jsondata']['lgcode']
for m in CODE_PATTERN.finditer(kw['jsondata'].get('lgcode', '')):
for code in set(m.group('code').split(',')):
if code not in languoid_map:
if code not in ['NOCODE_Payagua', 'emx']:
print '--> unknown code:', code.encode('utf8')
else:
append(ref.languages, languoid_map[code])
for glottocode in filter(
None, kw['jsondata'].get('alnumcodes', '').split(';')):
if glottocode not in languoid_map:
print '--> unknown glottocode:', glottocode.encode('utf8')
else:
append(ref.languages, languoid_map[glottocode])
if not update:
#pass
#
# TODO!
#
DBSession.add(ref)
if i % 100 == 0:
print i, 'records done'
if changed:
count += 1
print count, 'records updated or imported'
print skipped, 'records skipped because of lack of information'
def main(args): # pragma: no cover
stats = Counter(new=0, updated=0, skipped=0)
changes = {}
with transaction.manager:
update_providers(args)
DBSession.flush()
provider_map = get_map(Provider)
macroarea_map = get_map(Macroarea)
doctype_map = get_map(Doctype)
languoid_map = {}
for l in DBSession.query(Languoid):
if l.hid:
languoid_map[l.hid] = l
languoid_map[l.id] = l
for i, rec in enumerate(get_bib(args)):
if i and i % 1000 == 0:
print i, 'records done', stats['updated'] + stats['new'], 'changed'
if len(rec.keys()) < 6:
# not enough information!
stats.update(['skipped'])
continue
changed = False
assert rec.get('glottolog_ref_id')
id_ = int(rec.get('glottolog_ref_id'))
ref = DBSession.query(Source).get(id_)
update = True if ref else False
kw = {
'pk': id_,
'bibtex_type': rec.genre,
'id': str(id_),
'jsondata': {'bibtexkey': rec.id},
}
for source, target in FIELD_MAP.items():
if target is None:
continue
value = rec.get(source)
if value:
value = unescape(value)
if target:
kw[target] = CONVERTER.get(source, lambda x: x)(value)
else:
kw['jsondata'][source] = value
if kw['jsondata'].get('hhtype'):
trigger = ca_trigger(kw['jsondata']['hhtype'])
if trigger:
kw['ca_doctype_trigger'], kw['jsondata']['hhtype'] = trigger
# try to extract numeric year, startpage, endpage, numberofpages, ...
if kw.get('year'):
# prefer years in brackets over the first 4-digit number.
match = PREF_YEAR_PATTERN.search(kw.get('year'))
if match:
kw['year_int'] = int(match.group('year'))
else:
match = YEAR_PATTERN.search(kw.get('year'))
if match:
kw['year_int'] = int(match.group('year'))
if kw.get('publisher'):
p = kw.get('publisher')
if ':' in p:
address, publisher = [s.strip() for s in kw['publisher'].split(':', 1)]
if 'address' not in kw or kw['address'] == address:
kw['address'], kw['publisher'] = address, publisher
if rec.get('numberofpages'):
try:
kw['pages_int'] = int(rec.get('numberofpages').strip())
except ValueError:
pass
if kw.get('pages'):
start, end, number = compute_pages(kw['pages'])
if start is not None:
kw['startpage_int'] = start
if end is not None:
kw['endpage_int'] = end
if number is not None and 'pages_int' not in kw:
kw['pages_int'] = number
for k in kw.keys():
v = kw[k]
if isinstance(v, basestring):
v = v.strip() or None
kw[k] = v
if update:
for k in kw.keys():
if k == 'pk':
continue
v = getattr(ref, k)
if kw[k] != v:
if k == 'jsondata':
d = {k: v for k, v in ref.jsondata.items()
if k in NONREF_JSONDATA}
d.update(**kw[k])
ref.jsondata = d
else:
#print k, '--', v
#print k, '++', kw[k]
setattr(ref, k, kw[k])
changed = True
if ref.id in changes:
changes[ref.id][k] = ('%s' % v, '%s' % kw[k])
else:
changes[ref.id] = {k: ('%s' % v, '%s' % kw[k])}
else:
changed = True
ref = Ref(name='%s %s' % (kw.get('author', 'na'), kw.get('year', 'nd')), **kw)
ref.description = ref.title or ref.booktitle
originator = ref.author or ref.editor or 'Anonymous'
ref.name = '%s %s' % (originator, ref.year or 'n.d.')
a, r = update_relationship(
ref.macroareas,
[macroarea_map[name] for name in
set(filter(None, [s.strip() for s in kw['jsondata'].get('macro_area', '').split(',')]))])
changed = changed or a or r
src = [s.strip() for s in kw['jsondata'].get('src', '').split(',')]
prv = {provider_map[slug(s)] for s in src if s}
if set(ref.providers) != prv:
ref.providers = list(prv)
changed = True
a, r = update_relationship(
ref.doctypes,
[doctype_map[m.group('name')] for m in
DOCTYPE_PATTERN.finditer(kw['jsondata'].get('hhtype', ''))])
changed = changed or a or r
if not update:
stats.update(['new'])
DBSession.add(ref)
elif changed:
stats.update(['updated'])
args.log.info('%s' % stats)
DBSession.execute("update source set description = title where description is null and title is not null;")
DBSession.execute("update source set description = booktitle where description is null and booktitle is not null;")
for row in list(DBSession.execute(
"select pk, pages, pages_int, startpage_int from source where pages_int < 0")):
pk, pages, number, start = row
_start, _end, _number = compute_pages(pages)
if _number > 0 and _number != number:
DBSession.execute(
"update source set pages_int = %s, startpage_int = %s where pk = %s" %
(_number, _start, pk))
DBSession.execute(
"update ref set endpage_int = %s where pk = %s" %
(_end, pk))
jsondump(changes, args.data_dir.joinpath('references', 'changes.json'))