def test_normalize_name():
from clldutils.misc import normalize_name
assert normalize_name('class') == 'class_'
assert normalize_name('a-name') == 'a_name'
assert normalize_name('a näme') == 'a_name'
assert normalize_name('Name') == 'Name'
assert normalize_name('') == '_'
assert normalize_name('1') == '_1'
def test():
if not data_path().exists():
return # pragma: no cover
# load bibtex
bib = Database.from_file(data_path('references', 'references.bib'))
assert bib
cls = {
cl.name: read_tsv(cl, unique=None)
for cl in conceptlists() if not cl.stem.startswith('.')}
read_tsv(data_path('concepticon.tsv'))
concepticon = read_tsv(data_path('concepticon.tsv'), unique='GLOSS')
for i, cs in concepticon:
for attr in ['SEMANTICFIELD', 'ONTOLOGICAL_CATEGORY']:
valid = getattr(data, attr)
value = cs[attr]
if value and value not in valid: # pragma: no cover
error('invalid %s: %s' % (attr, value), data_path('concepticon.tsv'), i)
# We collect all cite keys used to refer to references.
all_refs = set()
for source in concept_set_meta():
specs = load(source.parent.joinpath(source.stem + '.tsv-metadata.json'))
tsv = read_tsv(source, unique='CONCEPTICON_ID')
cnames = [var['name'] for var in specs['tableSchema']['columns']]
if not [n for n in cnames if n in list(tsv[0][1])]: # pragma: no cover
error('column names in {0} but not in json-specs'.format(source.stem), 'name')
for i, line in tsv:
if len(line) != len(cnames): # pragma: no cover
error('meta data {0} contains irregular number of columns in line {1}'
.format(source.stem, i), 'name')
if 'dc:references' in specs:
all_refs.add(specs['dc:references'])
# Make sure only records in the BibTeX file references.bib are referenced by
# concept lists.
clmd = data_path('conceptlists.tsv')
clids = {}
visited1, visited2 = set(), set()
tags = getattr(data, 'CL_TYPES')
for i, cl in read_tsv(clmd):
clids[cl['ID']] = cl
for ref in split_ids(cl['REFS']):
if ref not in bib.keymap and ref not in visited1: # pragma: no cover
error('unknown bibtex record "%s" referenced' % ref, clmd, i)
visited1.add(ref)
else: # pragma: no cover
# we fail when author/editor, or year, or title/booktitle are missing
if 'Title' not in bib[ref] \
and 'Booktitle' not in bib[ref] \
and ref not in visited2:
error('missing bibtex title in record "%s"' % ref, clmd, i)
visited2.add(ref)
if 'Author' not in bib[ref] and 'Editor' not in bib[ref]:
error('missing bibtex author/editor in record "%s"' % ref, clmd, i)
visited2.add(ref)
if 'Year' not in bib[ref]:
error('missing bibtex year in record "%s"' % ref, clmd, i)
visited2.add(ref)
all_refs.add(ref)
for tag in split_ids(cl['TAGS']):
if tag not in tags: # pragma: no cover
error('invalid cl type: %s' % tag, clmd, i)
for i, ref in enumerate(bib.keymap):
if ref not in all_refs: # pragma: no cover
error('bibtex record %s is in the references but not referenced in the data.'
% ref, clmd, i)
#
# make also sure that all sources are accompanied as pdf, but only write a
# warning if this is not the case
#
pdfs = [f.stem for f in data_path('sources').glob('*.pdf')]
no_pdf_for_source = set()
for i, cl in read_tsv(clmd):
for ref in split_ids(cl['PDF']):
if ref not in pdfs: # pragma: no cover
no_pdf_for_source.add(ref)
if no_pdf_for_source: # pragma: no cover
warning(
'\n'.join(no_pdf_for_source),
'no pdf found for {0} sources'.format(len(no_pdf_for_source)))
ref_cols = {
'CONCEPTICON_ID': set(cs[1]['ID'] for cs in concepticon),
'CONCEPTICON_GLOSS': set(cs[1]['GLOSS'] for cs in concepticon),
}
for name, concepts in cls.items():
try:
cl = clids[name.replace('.tsv', '')]
except KeyError: # pragma: no cover
error('unkown record {0} referenced'.format(name), '', '')
cl = {}
missing = []
for i, (line, concept) in enumerate(concepts):
if i == 0: # pragma: no cover
cols = list(concept.keys())
try:
namedtuple('nt', [normalize_name(n) for n in cols])
except ValueError as e:
error('%s' % e, name, line)
for lg in split(cl.get('SOURCE_LANGUAGE', '')):
if lg.upper() not in cols:
error('missing source language col %s' % lg.upper(), name, '')
for lg in split(cl.get('SOURCE_LANGUAGE', '')):
if not concept.get(lg.upper()): # pragma: no cover
error('missing source language translation %s' % lg.upper(), name, line)
if not NUMBER_PATTERN.match(concept['NUMBER']): # pragma: no cover
error('invalid concept NUMBER %(NUMBER)s' % concept, name, line)
for col, values in ref_cols.items():
if col not in concept:
if col not in missing: # pragma: no cover
error('missing column %s' % col, name)
missing.append(col)
elif concept[col] and concept[col] not in values: # pragma: no cover
error('invalid value for %s: %s' % (col, concept[col]), name, line)
if not SUCCESS: # pragma: no cover
raise ValueError('integrity checks failed!')
def test():
conceptlists = {
cl.name: read_tsv(cl, unique=None)
for cl in PKG_PATH.joinpath('conceptlists').glob('*.tsv')
if not cl.stem.startswith('.')
}
read_tsv(data_path('concepticon.tsv'))
concepticon = read_tsv(data_path('concepticon.tsv'), unique='GLOSS')
for i, cs in concepticon:
for attr in ['SEMANTICFIELD', 'ONTOLOGICAL_CATEGORY']:
valid = getattr(data, attr)
value = cs[attr]
if value and value not in valid:
error('invalid %s: %s' % (attr, value),
data_path('concepticon.tsv'), i)
for source in read_metadata(data_path('concept_set_meta')):
specs = json.loads(
open(data_path('concept_set_meta',
source + '.tsv-metadata.json')).read())
tsv = read_tsv(data_path('concept_set_meta', source + '.tsv'),
unique='CONCEPTICON_ID')
cnames = [var['name'] for var in specs['tableSchema']['columns']]
if not [n for n in cnames if n in list(tsv[0][1])]:
error('column names in {0} do not json-specs'.format(source),
'name')
for i, line in tsv:
if len(line) != len(cnames):
error(
'meta data {0} contains irregular number of columns in line {1}'
.format(source, i), 'name')
refs = set()
with io.open(data_path('references', 'references.bib'),
encoding='utf8') as fp:
for line in fp:
match = BIB_ID_PATTERN.match(line.strip())
if match:
refs.add(match.group('id'))
#
# Make sure only records in the BibTeX file references.bib are referenced by
# concept lists.
clmd = data_path('conceptlists.tsv')
clids = {}
visited = []
tags = getattr(data, 'CL_TYPES')
for i, cl in read_tsv(clmd):
clids[cl['ID']] = cl
for ref in split_ids(cl['REFS']):
if ref not in refs and ref not in visited:
error('unknown bibtex record "%s" referenced' % ref, clmd, i)
visited += [ref]
for tag in split_ids(cl['TAGS']):
if tag not in tags:
error('invalid cl type: %s' % tag, clmd, i)
#
# make also sure that all sources are accompanied as pdf, but only write a
# warning if this is not the case
#
pdfs = read_sources(data_path('sources'))
no_pdf_for_source = []
for i, cl in read_tsv(clmd):
for ref in split_ids(cl['PDF']):
if ref not in pdfs:
no_pdf_for_source += [ref]
if no_pdf_for_source:
warning('\n'.join(no_pdf_for_source),
'no pdf found for {0} sources'.format(len(no_pdf_for_source)))
ref_cols = {
'CONCEPTICON_ID': set(cs[1]['ID'] for cs in concepticon),
'CONCEPTICON_GLOSS': set(cs[1]['GLOSS'] for cs in concepticon),
}
for name, concepts in conceptlists.items():
try:
cl = clids[name.replace('.tsv', '')]
except KeyError:
error('unkown record {0} referenced'.format(name), '', '')
cl = {}
missing = []
for i, (line, concept) in enumerate(concepts):
if i == 0:
cols = list(concept.keys())
try:
namedtuple('nt', [normalize_name(n) for n in cols])
except ValueError as e:
error('%s' % e, name, line)
for lg in split(cl.get('SOURCE_LANGUAGE', [])):
if lg.upper() not in cols:
error('missing source language col %s' % lg.upper(),
name, '')
if not NUMBER_PATTERN.match(concept['NUMBER']):
error('invalid concept NUMBER %(NUMBER)s' % concept, name,
line)
for col, values in ref_cols.items():
if col not in concept:
if col not in missing:
error('missing column %s' % col, name)
missing.append(col)
elif concept[col] and concept[col] not in values:
error('invalid value for %s: %s' % (col, concept[col]),
name, line)
if not SUCCESS:
raise ValueError('integrity checks failed!')
def item(self, row):
d = UnicodeDictReader.item(self, row)
for name in self.fieldnames:
d.setdefault(name, None)
return self.cls(
**{normalize_name(k): v for k, v in d.items() if k in self.fieldnames})
def test():
conceptlists = {
cl.name: read_tsv(cl, unique=None)
for cl in PKG_PATH.joinpath('conceptlists').glob('*.tsv')
if not cl.stem.startswith('.')}
read_tsv(data_path('concepticon.tsv'))
concepticon = read_tsv(data_path('concepticon.tsv'), unique='GLOSS')
for i, cs in concepticon:
for attr in ['SEMANTICFIELD', 'ONTOLOGICAL_CATEGORY']:
valid = getattr(data, attr)
value = cs[attr]
if value and value not in valid:
error('invalid %s: %s' % (attr, value), data_path('concepticon.tsv'), i)
refs = set()
with io.open(data_path('references', 'references.bib'), encoding='utf8') as fp:
for line in fp:
match = BIB_ID_PATTERN.match(line.strip())
if match:
refs.add(match.group('id'))
#
# Make sure only records in the BibTeX file references.bib are referenced by
# concept lists.
clmd = data_path('conceptlists.tsv')
clids = {}
visited = []
tags = getattr(data, 'CL_TYPES')
for i, cl in read_tsv(clmd):
clids[cl['ID']] = cl
for ref in split_ids(cl['REFS']):
if ref not in refs and ref not in visited:
error('unknown bibtex record "%s" referenced' % ref, clmd, i)
visited += [ref]
for tag in split_ids(cl['TAGS']):
if tag not in tags:
error('invalid cl type: %s' % tag, clmd, i)
#
# make also sure that all sources are accompanied as pdf, but only write a
# warning if this is not the case
#
pdfs = read_sources(data_path('sources'))
no_pdf_for_source = []
for i, cl in read_tsv(clmd):
for ref in split_ids(cl['PDF']):
if ref not in pdfs:
no_pdf_for_source += [ref]
if no_pdf_for_source:
warning(
'\n'.join(no_pdf_for_source),
'no pdf found for {0} sources'.format(len(no_pdf_for_source)))
ref_cols = {
'CONCEPTICON_ID': set(cs[1]['ID'] for cs in concepticon),
'CONCEPTICON_GLOSS': set(cs[1]['GLOSS'] for cs in concepticon),
}
for name, concepts in conceptlists.items():
try:
cl = clids[name.replace('.tsv', '')]
except KeyError:
error('unkown record {0} referenced'.format(name), '', '')
cl = {}
missing = []
for i, (line, concept) in enumerate(concepts):
if i == 0:
cols = list(concept.keys())
try:
namedtuple('nt', [normalize_name(n) for n in cols])
except ValueError as e:
error('%s' % e, name, line)
for lg in split(cl.get('SOURCE_LANGUAGE', [])):
if lg.upper() not in cols:
error('missing source language col %s' % lg.upper(), name, '')
if not NUMBER_PATTERN.match(concept['NUMBER']):
error('invalid concept NUMBER %(NUMBER)s' % concept, name, line)
for col, values in ref_cols.items():
if col not in concept:
if col not in missing:
error('missing column %s' % col, name)
missing.append(col)
elif concept[col] and concept[col] not in values:
error('invalid value for %s: %s' % (col, concept[col]), name, line)
if not SUCCESS:
raise ValueError('integrity checks failed!')
