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Merged
merged 1 commit into from
Jun 1, 2020
Merged

Add tree sequence metadata and schema to low-level python #644

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162 changes: 114 additions & 48 deletions python/_tskitmodule.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1786,6 +1786,24 @@ parse_table_collection_dict(tsk_table_collection_t *tables, PyObject *tables_dic
return ret;
}

static const char *
parse_metadata_schema_arg(PyObject *arg, Py_ssize_t* metadata_schema_length)
{
const char *ret = NULL;
if (arg == NULL) {
PyErr_Format(
PyExc_AttributeError,
"Cannot del metadata_schema, set to empty string (\"\") to clear.");
goto out;
}
ret = PyUnicode_AsUTF8AndSize(arg, metadata_schema_length);
if (ret == NULL) {
goto out;
}
out:
return ret;
}

static int
write_table_arrays(tsk_table_collection_t *tables, PyObject *dict)
{
Expand Down Expand Up @@ -2519,16 +2537,10 @@ IndividualTable_set_metadata_schema(IndividualTable *self, PyObject *arg, void *
const char *metadata_schema;
Py_ssize_t metadata_schema_length;

if (arg == NULL) {
PyErr_Format(
PyExc_AttributeError,
"Cannot del metadata_schema, set to empty string (\"\") to clear.");
goto out;
}
if (IndividualTable_check_state(self) != 0) {
goto out;
}
metadata_schema = PyUnicode_AsUTF8AndSize(arg, &metadata_schema_length);
metadata_schema = parse_metadata_schema_arg(arg, &metadata_schema_length);
if (metadata_schema == NULL) {
goto out;
}
Expand Down Expand Up @@ -2995,16 +3007,10 @@ NodeTable_set_metadata_schema(NodeTable *self, PyObject *arg, void *closure)
const char *metadata_schema;
Py_ssize_t metadata_schema_length;

if (arg == NULL) {
PyErr_Format(
PyExc_AttributeError,
"Cannot del metadata_schema, set to empty string (\"\") to clear.");
goto out;
}
if (NodeTable_check_state(self) != 0) {
goto out;
}
metadata_schema = PyUnicode_AsUTF8AndSize(arg, &metadata_schema_length);
metadata_schema = parse_metadata_schema_arg(arg, &metadata_schema_length);
if (metadata_schema == NULL) {
goto out;
}
Expand Down Expand Up @@ -3488,15 +3494,10 @@ EdgeTable_set_metadata_schema(EdgeTable *self, PyObject *arg, void *closure)
const char *metadata_schema;
Py_ssize_t metadata_schema_length;

if (arg == NULL) {
PyErr_Format(PyExc_AttributeError,
"Cannot del metadata_schema, set to empty string (\"\") to clear.");
goto out;
}
if (EdgeTable_check_state(self) != 0) {
goto out;
}
metadata_schema = PyUnicode_AsUTF8AndSize(arg, &metadata_schema_length);
metadata_schema = parse_metadata_schema_arg(arg, &metadata_schema_length);
if (metadata_schema == NULL) {
goto out;
}
Expand Down Expand Up @@ -3989,16 +3990,10 @@ MigrationTable_set_metadata_schema(MigrationTable *self, PyObject *arg, void *cl
const char *metadata_schema;
Py_ssize_t metadata_schema_length;

if (arg == NULL) {
PyErr_Format(
PyExc_AttributeError,
"Cannot del metadata_schema, set to empty string (\"\") to clear.");
goto out;
}
if (MigrationTable_check_state(self) != 0) {
goto out;
}
metadata_schema = PyUnicode_AsUTF8AndSize(arg, &metadata_schema_length);
metadata_schema = parse_metadata_schema_arg(arg, &metadata_schema_length);
if (metadata_schema == NULL) {
goto out;
}
Expand Down Expand Up @@ -4453,16 +4448,10 @@ SiteTable_set_metadata_schema(SiteTable *self, PyObject *arg, void *closure)
const char *metadata_schema;
Py_ssize_t metadata_schema_length;

if (arg == NULL) {
PyErr_Format(
PyExc_AttributeError,
"Cannot del metadata_schema, set to empty string (\"\") to clear.");
goto out;
}
if (SiteTable_check_state(self) != 0) {
goto out;
}
metadata_schema = PyUnicode_AsUTF8AndSize(arg, &metadata_schema_length);
metadata_schema = parse_metadata_schema_arg(arg, &metadata_schema_length);
if (metadata_schema == NULL) {
goto out;
}
Expand Down Expand Up @@ -4956,16 +4945,10 @@ MutationTable_set_metadata_schema(MutationTable *self, PyObject *arg, void *clos
const char *metadata_schema;
Py_ssize_t metadata_schema_length;

if (arg == NULL) {
PyErr_Format(
PyExc_AttributeError,
"Cannot del metadata_schema, set to empty string (\"\") to clear.");
goto out;
}
if (MutationTable_check_state(self) != 0) {
goto out;
}
metadata_schema = PyUnicode_AsUTF8AndSize(arg, &metadata_schema_length);
metadata_schema = parse_metadata_schema_arg(arg, &metadata_schema_length);
if (metadata_schema == NULL) {
goto out;
}
Expand Down Expand Up @@ -5375,16 +5358,10 @@ PopulationTable_set_metadata_schema(PopulationTable *self, PyObject *arg, void *
const char *metadata_schema;
Py_ssize_t metadata_schema_length;

if (arg == NULL) {
PyErr_Format(
PyExc_AttributeError,
"Cannot del metadata_schema, set to empty string (\"\") to clear.");
goto out;
}
if (PopulationTable_check_state(self) != 0) {
goto out;
}
metadata_schema = PyUnicode_AsUTF8AndSize(arg, &metadata_schema_length);
metadata_schema = parse_metadata_schema_arg(arg, &metadata_schema_length);
if (metadata_schema == NULL) {
goto out;
}
Expand Down Expand Up @@ -6083,6 +6060,71 @@ TableCollection_get_file_uuid(TableCollection *self, void *closure)
return Py_BuildValue("s", self->tables->file_uuid);
}

static PyObject *
TableCollection_get_metadata(TableCollection *self, void *closure)
{
return PyBytes_FromStringAndSize(self->tables->metadata, self->tables->metadata_length);
}

static int
TableCollection_set_metadata(TableCollection *self, PyObject *arg, void *closure)
{
int ret = -1;
int err;
char *metadata;
Py_ssize_t metadata_length;

if (arg == NULL) {
PyErr_Format(
PyExc_AttributeError,
"Cannot del metadata, set to empty string (b\"\") to clear.");
goto out;
}
err = PyBytes_AsStringAndSize(arg, &metadata, &metadata_length);
if (err != 0) {
goto out;
}
err = tsk_table_collection_set_metadata(
self->tables, metadata, metadata_length);
if (err != 0) {
handle_library_error(err);
goto out;
}
ret = 0;
out:
return ret;
}

static PyObject *
TableCollection_get_metadata_schema(TableCollection *self, void *closure)
{
return make_Py_Unicode_FromStringAndLength(
self->tables->metadata_schema, self->tables->metadata_schema_length);
}

static int
TableCollection_set_metadata_schema(TableCollection *self, PyObject *arg, void *closure)
{
int ret = -1;
int err;
const char *metadata_schema;
Py_ssize_t metadata_schema_length;

metadata_schema = parse_metadata_schema_arg(arg, &metadata_schema_length);
if (metadata_schema == NULL) {
goto out;
}
err = tsk_table_collection_set_metadata_schema(
self->tables, metadata_schema, metadata_schema_length);
if (err != 0) {
handle_library_error(err);
goto out;
}
ret = 0;
out:
return ret;
}

static PyObject *
TableCollection_simplify(TableCollection *self, PyObject *args, PyObject *kwds)
{
Expand Down Expand Up @@ -6340,6 +6382,12 @@ static PyGetSetDef TableCollection_getsetters[] = {
(setter) TableCollection_set_sequence_length, "The sequence length."},
{"file_uuid", (getter) TableCollection_get_file_uuid, NULL,
"The UUID of the corresponding file."},
{"metadata",
(getter) TableCollection_get_metadata,
(setter) TableCollection_set_metadata, "The metadata."},
{"metadata_schema",
(getter) TableCollection_get_metadata_schema,
(setter) TableCollection_set_metadata_schema, "The metadata schema."},
{NULL} /* Sentinel */
};

Expand Down Expand Up @@ -6680,6 +6728,20 @@ TreeSequence_get_site(TreeSequence *self, PyObject *args)
return ret;
}

static PyObject *
TreeSequence_get_metadata(TreeSequence * self) {
return PyBytes_FromStringAndSize(
self->tree_sequence->tables->metadata,
self->tree_sequence->tables->metadata_length);
}

static PyObject *
TreeSequence_get_metadata_schema(TreeSequence * self) {
return make_Py_Unicode_FromStringAndLength(
self->tree_sequence->tables->metadata_schema,
self->tree_sequence->tables->metadata_schema_length);
}

static PyObject *
TreeSequence_get_table_metadata_schemas(TreeSequence *self) {
PyObject *ret = NULL;
Expand Down Expand Up @@ -8173,6 +8235,10 @@ static PyMethodDef TreeSequence_methods[] = {
METH_NOARGS, "Returns the tree breakpoints as a numpy array." },
{"get_file_uuid", (PyCFunction) TreeSequence_get_file_uuid,
METH_NOARGS, "Returns the UUID of the underlying file, if present." },
{"get_metadata", (PyCFunction) TreeSequence_get_metadata, METH_NOARGS,
"Returns the metadata for the tree sequence"},
{"get_metadata_schema", (PyCFunction) TreeSequence_get_metadata_schema, METH_NOARGS,
"Returns the metadata schema for the tree sequence metadata"},
{"get_num_sites", (PyCFunction) TreeSequence_get_num_sites,
METH_NOARGS, "Returns the number of sites" },
{"get_num_mutations", (PyCFunction) TreeSequence_get_num_mutations, METH_NOARGS,
Expand Down
54 changes: 54 additions & 0 deletions python/tests/test_lowlevel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -197,6 +197,38 @@ def test_set_sequence_length(self):
tables.sequence_length = value
self.assertEqual(tables.sequence_length, value)

def test_set_metadata_errors(self):
tables = _tskit.TableCollection(1)
with self.assertRaises(AttributeError):
del tables.metadata
for bad_value in ["bytes only", 59, 43.4, None, []]:
with self.assertRaises(TypeError):
tables.metadata = bad_value

def test_set_metadata(self):
tables = _tskit.TableCollection(1)
self.assertEqual(tables.metadata, b"")
for value in [b"foo", b"", "💩".encode(), b"null char \0 in string"]:
tables.metadata = value
tables.metadata_schema = "Test we have two separate fields"
self.assertEqual(tables.metadata, value)

def test_set_metadata_schema_errors(self):
tables = _tskit.TableCollection(1)
with self.assertRaises(AttributeError):
del tables.metadata_schema
for bad_value in [59, 43.4, None, []]:
with self.assertRaises(TypeError):
tables.metadata_schema = bad_value

def test_set_metadata_schema(self):
tables = _tskit.TableCollection(1)
self.assertEqual(tables.metadata_schema, "")
for value in ["foo", "", "💩", "null char \0 in string"]:
tables.metadata_schema = value
tables.metadata = b"Test we have two separate fields"
self.assertEqual(tables.metadata_schema, value)

def test_simplify_bad_args(self):
ts = msprime.simulate(10, random_seed=1)
tc = ts.tables.ll_tables
Expand Down Expand Up @@ -478,6 +510,28 @@ def test_metadata_schemas(self):
for table_name in self.metadata_tables:
self.assertEqual(getattr(schemas, table_name), "")

def test_metadata(self):
tables = _tskit.TableCollection(1)
ts = _tskit.TreeSequence()
ts.load_tables(tables)
self.assertEqual(ts.get_metadata(), b"")
for value in [b"foo", b"", "💩".encode(), b"null char \0 in string"]:
tables.metadata = value
ts = _tskit.TreeSequence()
ts.load_tables(tables)
self.assertEqual(ts.get_metadata(), value)

def test_metadata_schema(self):
tables = _tskit.TableCollection(1)
ts = _tskit.TreeSequence()
ts.load_tables(tables)
self.assertEqual(ts.get_metadata_schema(), "")
for value in ["foo", "", "💩", "null char \0 in string"]:
tables.metadata_schema = value
ts = _tskit.TreeSequence()
ts.load_tables(tables)
self.assertEqual(ts.get_metadata_schema(), value)

def test_kc_distance_errors(self):
ts1 = self.get_example_tree_sequence(10)
self.assertRaises(TypeError, ts1.get_kc_distance)
Expand Down