def from_metadata(cls, fname):
fname = pathlib.Path(fname)
if fname.is_dir():
name = '{0}{1}'.format(cls.__name__, MD_SUFFIX)
tablegroup = TableGroup.from_file(pkg_path('modules', name))
# adapt the path of the metadata file such that paths to tables are resolved
# correctly:
tablegroup._fname = fname.joinpath(name)
else:
tablegroup = TableGroup.from_file(fname)
comps = collections.Counter()
for table in tablegroup.tables:
try:
dt = Dataset.get_tabletype(table)
if dt:
comps.update([dt])
except ValueError:
pass
if comps and comps.most_common(1)[0][1] > 1:
raise ValueError('{0}: duplicate components!'.format(fname))
for mod in get_modules():
if mod.match(tablegroup):
return mod.cls(tablegroup)
return cls(tablegroup)
def from_metadata(cls, fname):
fname = Path(fname)
if fname.is_dir():
name = '{0}{1}'.format(cls.__name__, MD_SUFFIX)
tablegroup = TableGroup.from_file(pkg_path('modules', name))
# adapt the path of the metadata file such that paths to tables are resolved
# correctly:
tablegroup._fname = fname.joinpath(name)
else:
tablegroup = TableGroup.from_file(fname)
for mod in get_modules():
if mod.match(tablegroup):
return mod.cls(tablegroup)
return cls(tablegroup)
def iteraliases(name, table_name=None):
for table in TableGroup.from_file(data_path(name, 'metadata.json')).tables:
if table_name is None or table.local_name == table_name:
for row in table:
if row:
for alias in row['alias']:
yield char(alias), char(row['char'])
def metadata(self):
md = self.path.parent.joinpath(self.path.name + '-metadata.json')
if not md.exists():
ddir = self._api.data_path() if hasattr(self._api, 'data_path') \
else REPOS_PATH.joinpath('concepticondata')
if self.local:
md = ddir.joinpath('conceptlists', 'local-metadata.json')
if not md.exists():
md = ddir.joinpath('conceptlists', 'default-metadata.json')
tg = TableGroup.from_file(md)
if isinstance(self._api, Path):
tg._fname = self._api.parent.joinpath(self._api.name + '-metadata.json')
tg.tables[0].url = Link('{0}.tsv'.format(self.id))
return tg.tables[0]
def from_metadata(cls, fname):
fname = Path(fname)
if fname.is_dir():
name = '{0}{1}'.format(cls.__name__, MD_SUFFIX)
tablegroup = TableGroup.from_file(pkg_path('modules', name))
# adapt the path of the metadata file such that paths to tables are resolved
# correctly:
tablegroup._fname = fname.joinpath(name)
else:
tablegroup = TableGroup.from_file(fname)
comps = Counter()
for table in tablegroup.tables:
try:
comps.update([Dataset.get_tabletype(table)])
except ValueError:
pass
if comps and comps.most_common(1)[0][1] > 1:
raise ValueError('{0}: duplicate components!'.format(fname))
for mod in get_modules():
if mod.match(tablegroup):
return mod.cls(tablegroup)
return cls(tablegroup)
def get_modules():
global _modules
if not _modules:
ds = sys.modules[__name__]
for p in pkg_path('modules').glob('*{0}'.format(MD_SUFFIX)):
tg = TableGroup.from_file(p)
mod = Module(
tg.common_props['dc:conformsTo'],
tg.tables[0].url.string if tg.tables else None)
mod.cls = getattr(ds, mod.id)
_modules.append(mod)
# prefer Wordlist over ParallelText (forms.csv)
_modules = sorted(
_modules,
key=lambda m: (m.cls in (Wordlist, ParallelText), m.cls is ParallelText))
return _modules
def get_modules():
global _modules
if not _modules:
ds = sys.modules[__name__]
for p in pkg_path('modules').glob('*{0}'.format(MD_SUFFIX)):
tg = TableGroup.from_file(p)
mod = Module(
tg.common_props['dc:conformsTo'],
tg.tables[0].url.string if tg.tables else None)
mod.cls = getattr(ds, mod.id)
_modules.append(mod)
# prefer Wordlist over ParallelText (forms.csv)
_modules = sorted(
_modules,
key=lambda m: (m.cls in (Wordlist, ParallelText), m.cls is ParallelText))
return _modules
def tg(self):
md = self.path.parent.joinpath(self.path.name + MD_SUFFIX)
if not md.exists():
if hasattr(self._api, 'repos'):
ddir = self._api.path('concepticondata')
if self.local:
md = ddir.joinpath('conceptlists', 'local' + MD_SUFFIX)
if not md.exists():
md = ddir.joinpath('conceptlists', 'default' + MD_SUFFIX)
else:
md = Path(__file__).parent / 'conceptlist-metadata.json'
tg = TableGroup.from_file(md)
if isinstance(self._api, Path):
tg._fname = self._api.parent.joinpath(self._api.name + MD_SUFFIX)
tg.tables[0].url = Link('{0}.tsv'.format(self.id))
return tg
def validate(self, log=None, validators=None):
validators = validators or []
validators.extend(VALIDATORS)
success = True
default_tg = TableGroup.from_file(
pkg_path('modules', '{0}{1}'.format(self.module, MD_SUFFIX)))
for default_table in default_tg.tables:
dtable_uri = default_table.common_props['dc:conformsTo']
try:
table = self[dtable_uri]
except KeyError:
log_or_raise('{0} requires {1}'.format(self.module, dtable_uri), log=log)
success = False
table = None
if table:
default_cols = {
c.propertyUrl.uri for c in default_table.tableSchema.columns
if c.required or c.common_props.get('dc:isRequiredBy')}
cols = {
c.propertyUrl.uri for c in table.tableSchema.columns
if c.propertyUrl}
table_uri = table.common_props['dc:conformsTo']
for col in default_cols - cols:
log_or_raise('{0} requires column {1}'.format(table_uri, col), log=log)
success = False
for table in self.tables:
type_uri = table.common_props.get('dc:conformsTo')
if type_uri:
try:
TERMS.is_cldf_uri(type_uri)
except ValueError:
success = False
log_or_raise('invalid CLDF URI: {0}'.format(type_uri), log=log)
# FIXME: check whether table.common_props['dc:conformsTo'] is in validators!
validators_ = []
for col in table.tableSchema.columns:
if col.propertyUrl:
col_uri = col.propertyUrl.uri
try:
TERMS.is_cldf_uri(col_uri)
except ValueError:
success = False
log_or_raise('invalid CLDF URI: {0}'.format(col_uri), log=log)
for table_, col_, v_ in validators:
if (not table_ or table is self.get(table_)) and col is self.get((table, col_)):
validators_.append((col, v_))
fname = Path(table.url.resolve(table._parent.base))
if fname.exists():
for fname, lineno, row in table.iterdicts(log=log, with_metadata=True):
for col, validate in validators_:
try:
validate(self, table, col, row)
except ValueError as e:
log_or_raise(
'{0}:{1}:{2} {3}'.format(fname.name, lineno, col.name, e),
log=log)
success = False
if not table.check_primary_key(log=log):
success = False
if not self.tablegroup.check_referential_integrity(log=log):
success = False
return success
def validate(self, log=None, validators=None):
validators = validators or []
validators.extend(VALIDATORS)
success = True
default_tg = TableGroup.from_file(
pkg_path('modules', '{0}{1}'.format(self.module, MD_SUFFIX)))
for default_table in default_tg.tables:
dtable_uri = default_table.common_props['dc:conformsTo']
try:
table = self[dtable_uri]
except KeyError:
log_or_raise('{0} requires {1}'.format(self.module, dtable_uri), log=log)
success = False
table = None
if table:
default_cols = {
c.propertyUrl.uri for c in default_table.tableSchema.columns
if c.required or c.common_props.get('dc:isRequiredBy')}
cols = {
c.propertyUrl.uri for c in table.tableSchema.columns
if c.propertyUrl}
table_uri = table.common_props['dc:conformsTo']
for col in default_cols - cols:
log_or_raise('{0} requires column {1}'.format(table_uri, col), log=log)
success = False
for table in self.tables:
type_uri = table.common_props.get('dc:conformsTo')
if type_uri:
try:
TERMS.is_cldf_uri(type_uri)
except ValueError:
success = False
log_or_raise('invalid CLDF URI: {0}'.format(type_uri), log=log)
# FIXME: check whether table.common_props['dc:conformsTo'] is in validators!
validators_ = []
for col in table.tableSchema.columns:
if col.propertyUrl:
col_uri = col.propertyUrl.uri
try:
TERMS.is_cldf_uri(col_uri)
except ValueError:
success = False
log_or_raise('invalid CLDF URI: {0}'.format(col_uri), log=log)
for table_, col_, v_ in validators:
if (not table_ or table is self.get(table_)) and col is self.get((table, col_)):
validators_.append((col, v_))
fname = Path(table.url.resolve(table._parent.base))
if fname.exists():
for fname, lineno, row in table.iterdicts(log=log, with_metadata=True):
for col, validate in validators_:
try:
validate(self, table, col, row)
except ValueError as e:
log_or_raise(
'{0}:{1}:{2} {3}'.format(fname.name, lineno, col.name, e),
log=log)
success = False
if not table.check_primary_key(log=log):
success = False
else:
log_or_raise('{0} does not exist'.format(fname), log=log)
success = False
if not self.tablegroup.check_referential_integrity(log=log):
success = False
return success
from csvw.metadata import TableGroup
from lingpy import util
from lingpy.convert.html import template_path
# receive the template path from lingpy for splitstree
tpath = util.Path(template_path('splitstree.nex'))
if tpath.exists:
_template = util.read_text_file(tpath.as_posix())
else: # pragma: no cover
raise IOError("Unknown template %s" % template)
tbg = TableGroup.from_file('cldf/StructureDataset-metadata.json')
taxa = {t['ID']: (i, t['Name']) for i, t in
enumerate(tbg.tabledict['languages.csv'])}
params = {t['ID']: (i, t['Name']) for i, t in
enumerate(tbg.tabledict['parameters.csv'])}
matrix = [[0 for p in params] for t in taxa]
for row in tbg.tabledict['values.csv']:
tidx, tname = taxa[row['Language_ID']]
pidx, pname = params[row['Parameter_ID']]
if row['Value'] == '+':
matrix[tidx][pidx] = 1
alpha = 'abcdefghijklmnopqrstuvwxyz'
alpha += alpha.upper()
alpha += '0123456789'
matrix_string = ''
tax_list = sorted([t[1] for t in taxa.items()], key=lambda x: x[0])
for i, line in enumerate(matrix):
matrix_string += '{0:12}'.format(''.join([x for x in tax_list[i][1] if
def add_metadata(fname: Path, logger: cli.logging.Logger = cli.logger):
if fname.name != "forms.csv":
cli.Exit.CLI_ARGUMENT_ERROR(
"A metadata-free Wordlist must be in a file called 'forms.csv'.")
default_wordlist = TableGroup.from_file(
pycldf.util.pkg_path("modules", "Wordlist-metadata.json"))
default_wordlist._fname = fname.with_name("Wordlist-metadata.json")
ds = pycldf.Wordlist(default_wordlist)
# `from_data` checks that the reqired columns of the FormTable are present,
# but it does not consolidate the columns further.
colnames = next(iterrows(fname))
understood_colnames = {
c.name
for c in ds[ds.primary_table].tableSchema.columns if c.name in colnames
}
more_columns = {
c.propertyUrl.uri: c
for c in ds[ds.primary_table].tableSchema.columns
if c.name not in understood_colnames
}
logger.info(
"CLDF freely understood the columns %s in your forms.csv.",
sorted(understood_colnames),
)
# Consider the columns that were not understood.
columns_without_metadata = set(colnames) - understood_colnames
for column_name in columns_without_metadata:
column: Column
# Maybe they are known CLDF properties?
if column_name in pycldf.terms.TERMS:
column = pycldf.TERMS[column_name].to_column()
# Maybe they are CLDF default column names?
elif column_name in DEFAULT_NAME_COLUMNS:
column = DEFAULT_NAME_COLUMNS[column_name]
# Maybe they are columns that Lexedata knows to handle?
elif column_name in LEXEDATA_COLUMNS:
column = LEXEDATA_COLUMNS[column_name]
# Maybe they are columns inherited from LingPy?
elif column_name.upper() in LINGPY_COLUMNS:
column = LINGPY_COLUMNS[column_name.upper()]
# Maybe they are some name we have seen before?
elif column_name in OTHER_KNOWN_COLUMNS:
column = OTHER_KNOWN_COLUMNS[column_name]
else:
# TODO: Maybe they look like they have a specific type?
...
# Otherwise, they are probably just text to be kept.
column = Column(
datatype=Datatype(base="string"),
default="",
null=[""],
name=column_name,
)
column.name = column_name
ds[ds.primary_table].tableSchema.columns.append(column)
summary = column.propertyUrl or column.datatype
logger.info(f"Column {column_name} seems to be a {summary} column.")
if column.propertyUrl:
to_be_replaced = more_columns.pop(column.propertyUrl.uri, None)
if to_be_replaced is not None:
ds[ds.primary_table].tableSchema.columns.remove(to_be_replaced)
for column in more_columns.values():
logger.info(
f"Also added column {column.name}, as expected for a FormTable.")
ds[ds.primary_table].tableSchema.columns.sort(
key=lambda k: colnames.index(k.name) if k.name in colnames else 1e10)
# TODO: Once lexedata is properly published, we can give a better URL.
ds.properties["dc:contributor"] = [
"https://github.com/Anaphory/lexedata/blob/master/src/lexedata/edit/add_metadata.py"
]
return ds
try:
alignments = [
len(
split_segments(data[value]['Alignment'])[
data[value]['Cognate_Sets'].index(key)])
for value in values
]
if len(set(alignments)) != 1:
errors += [key]
except IndexError:
errors += [key]
return errors
if __name__ == '__main__':
tg = TableGroup.from_file('Wordlist-metadata.json')
problems = []
count = 1
wordlist = {}
for item in tg.tables[0]:
morphemes = validate_morphemes(item)
wordlist[item['ID']] = item
struc = validate_structure(item)
if not morphemes:
problems += [[
count, 'morphemes',
str(item['ID']), item['Language_Name'], item['Parameter_name'],
' '.join(item['Segments'])
]]
count += 1
if not struc:
def tablegroup(self):
return TableGroup.from_file(self.dir.joinpath(self.fname + '-metadata.json'))
def table(self):
return TableGroup.from_file(self.path).tabledict[self.id + '.tsv']
def from_cldf(path, to=Wordlist, concept='Name', concepticon='Concepticon_ID',
glottocode='Glottocode', language='Name'
):
"""
Load data from CLDF into a LingPy Wordlist object or similar.
Parameters
----------
path : str
The path to the metadata-file of your CLDF dataset.
to : ~lingpy.basic.wordlist.Wordlist
A ~lingpy.basic.wordlist.Wordlist object or one of the descendants
(LexStat, Alignmnent).
concept : str (default='gloss')
The name used for the basic gloss in the `parameters.csv` table.
glottocode : str (default='glottocode')
The default name for the column storing the Glottolog ID in the
`languages.csv` table.
language : str (default='name')
The default name for the language name in the `languages.csv` table.
concepticon : str (default='conceptset')
The default name for the concept set in the `paramters.csv` table.
Notes
-----
This function does not offer absolute flexibility regarding the data you
can input so far. However, it can regularly read CLDF-formatted data into
LingPy and thus allow you to use CLDF data in LingPy analyses.
"""
tbg = TableGroup.from_file(path)
forms = tbg.tabledict['forms.csv']
# obtain the dictionaries to convert ids to values
taxa = {t['ID']: (t[language], t[glottocode]) for t in
tbg.tabledict['languages.csv']}
concepts = {c['ID']: (c[concept], c[concepticon]) for c in
tbg.tabledict['parameters.csv']}
# create dictionary
D = {}
id2idx = {}
for i, row in enumerate(forms):
# check for numeric ID
if row['ID'].isdigit():
idx = int(row['ID'])
else:
idx = i+1
id2idx[row['ID']] = idx
doculect, glottocode = taxa[row['Language_ID']]
concept, concepticon_id = concepts[row['Parameter_ID']]
D[idx] = [doculect, glottocode, concept, concepticon_id] + [row.get(f,
'') or '' for f in ['form_in_source', 'Form', 'Segments',
'Comment', 'Source']]
# add the header
D[0] = ['doculect', 'glottocode', 'concept', 'concepticon_id', 'value',
'form', 'tokens', 'note', 'source']
# convert to wordlist (simplifies handling)
wordlist = to(D)
# add cognates if they are needed and provided
if 'cognates.csv' in tbg.tabledict:
cognates = {id2idx[row['Form_ID']]: (row['Cognateset_ID'],
row['Alignment']) for row in tbg.tabledict['cognates.csv']}
if cognates:
wordlist.add_entries('cogid', cognates, lambda x: x[0] or 0)
wordlist.add_entries('alignment', cognates, lambda x: x[1] or '')
return wordlist
def from_cldf(path, to=Wordlist, concept='Name', concepticon='Concepticon_ID',
glottocode='Glottocode', language='Name'
):
"""
Load data from CLDF into a LingPy Wordlist object or similar.
Parameters
----------
path : str
The path to the metadata-file of your CLDF dataset.
to : ~lingpy.basic.wordlist.Wordlist
A ~lingpy.basic.wordlist.Wordlist object or one of the descendants
(LexStat, Alignmnent).
concept : str (default='gloss')
The name used for the basic gloss in the `parameters.csv` table.
glottocode : str (default='glottocode')
The default name for the column storing the Glottolog ID in the
`languages.csv` table.
language : str (default='name')
The default name for the language name in the `languages.csv` table.
concepticon : str (default='conceptset')
The default name for the concept set in the `paramters.csv` table.
Notes
-----
This function does not offer absolute flexibility regarding the data you
can input so far. However, it can regularly read CLDF-formatted data into
LingPy and thus allow you to use CLDF data in LingPy analyses.
"""
tbg = TableGroup.from_file(path)
forms = tbg.tabledict['forms.csv']
# obtain the dictionaries to convert ids to values
taxa = {t['ID']: (t[language], t[glottocode]) for t in
tbg.tabledict['languages.csv']}
concepts = {c['ID']: (c[concept], c[concepticon]) for c in
tbg.tabledict['parameters.csv']}
# create dictionary
D = {}
id2idx = {}
for i, row in enumerate(forms):
# check for numeric ID
if row['ID'].isdigit():
idx = int(row['ID'])
else:
idx = i+1
id2idx[row['ID']] = idx
doculect, glottocode = taxa[row['Language_ID']]
concept, concepticon_id = concepts[row['Parameter_ID']]
D[idx] = [doculect, glottocode, concept, concepticon_id] + [row.get(f,
'') or '' for f in ['form_in_source', 'Form', 'Segments',
'Comment', 'Source']]
# add the header
D[0] = ['doculect', 'glottocode', 'concept', 'concepticon_id', 'value',
'form', 'tokens', 'note', 'source']
# convert to wordlist (simplifies handling)
wordlist = to(D)
# add cognates if they are needed and provided
if 'cognates.csv' in tbg.tabledict:
cognates = {id2idx[row['Form_ID']]: (row['Cognateset_ID'],
row['Alignment']) for row in tbg.tabledict['cognates.csv']}
if cognates:
wordlist.add_entries('cogid', cognates, lambda x: x[0] or 0)
wordlist.add_entries('alignment', cognates, lambda x: x[1] or '')
return wordlist