def test_list_column_types(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
res = epidb.create_column_type_simple("name", "description", "string", self.admin_key)
self.assertSuccess(res)
res = epidb.create_column_type_simple("string_column", "description", "string", self.admin_key)
self.assertSuccess(res)
res = epidb.create_column_type_simple("integer_column", "description", "integer", self.admin_key)
self.assertSuccess(res)
res = epidb.create_column_type_simple("double_column", "description", "double", self.admin_key)
self.assertSuccess(res)
res = epidb.create_column_type_range("score", "description", 0.0, 1.0, self.admin_key)
self.assertSuccess(res)
strand = ["+", "-"]
res = epidb.create_column_type_category("STRAND", "description", strand, self.admin_key)
self.assertSuccess(res)
res, column_types = epidb.list_column_types(self.admin_key)
self.assertSuccess(res, column_types)
self.assertEqual(column_types[0][1], "column type name: 'CHROMOSOME' type: 'string'")
self.assertEqual(column_types[1][1], "column type name: 'START' type: 'integer'")
self.assertEqual(column_types[2][1], "column type name: 'END' type: 'integer'")
self.assertEqual(column_types[3][1], "column type name: 'VALUE' type: 'double'")
self.assertEqual(column_types[4][1], "column type name: 'GTF_SCORE' type: 'string'")
self.assertEqual(column_types[5][1], "column type name: 'FEATURE' type: 'string'")
self.assertEqual(column_types[6][1], "column type name: 'SOURCE' type: 'string'")
self.assertEqual(column_types[7][1], "column type name: 'FRAME' type: 'string'")
self.assertEqual(column_types[8][1], "column type name: 'GTF_ATTRIBUTES' type: 'string'")
self.assertEqual(column_types[9][1], "column type name: 'TRACKING_ID' type: 'string'")
def test_category_fail(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
format = ",".join([
"CHROMOSOME",
"START",
"END",
"NAME",
"SCORE",
"STRAND_X",
"SIGNAL_VALUE",
"P_VALUE",
"Q_VALUE",
"PEAK"
])
res = epidb.create_column_type_category("STRAND_X", "strand of the region", ["X", "-"], self.admin_key)
self.assertSuccess(res)
regions_data = helpers.load_bed("hg19_chr1_1")
res, msg = epidb.add_experiment("test_exp_fail2", "hg19", "Methylation", sample_id, "tech1", "ENCODE",
"desc1", regions_data, format, None, self.admin_key)
self.assertFailure(res, msg)
self.assertTrue("STRAND_X" in msg)
def init_base(self, epidb=None):
if not epidb:
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
for genome in data.GENOMES:
self.insert_genome(epidb, genome)
for bsource in data.BIOSOURCES:
self.insert_biosource(epidb, bsource)
for tech in data.TECHNIQUES:
self.insert_technique(epidb, tech)
for epimark in data.EPIGENETIC_MARKS:
self.insert_epigenetic_mark(epidb, epimark)
for project in data.PROJECTS:
self.insert_project(epidb, project)
for sample in data.SAMPLES:
self.insert_samples(epidb, sample)
for column in data.COLUMNS:
self.insert_column(epidb, column)
res, cid = epidb.create_column_type_category("STRAND", "Region strand: +, -, .", ["+", "-", "."], self.admin_key)
self.assertSuccess(res, cid)
def test_column_complex_types(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
res = epidb.create_column_type_range("score", "description", 0.0, 1.0, self.admin_key)
self.assertSuccess(res)
strand = ["+", "-"]
res = epidb.create_column_type_category("STRAND", "description", strand, self.admin_key)
self.assertSuccess(res)
def test_empty_no_permission_column_type(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
res, cid = epidb.create_column_type_category("PLUS_MINUS_DOT",
"Region strand: +, -, .",
["+", "-", "."],
self.admin_key)
s, (u_id, u_key) = epidb.add_user("user", "email", "institution",
self.admin_key)
self.assertSuccess(s)
s = epidb.modify_user_admin(u_id, "permission_level", "NONE",
self.admin_key)
self.assertSuccess(s)
info = epidb.info(cid, u_key)
self.assertEqual(info, [
'error',
'100100:Insufficient permission. Permission LIST_COLLECTIONS is required.'
])
info_e1 = epidb.info("e1", u_key)
self.assertEqual(info_e1, [
'error',
'100100:Insufficient permission. Permission LIST_COLLECTIONS is required.'
])
info_e2 = epidb.info("me", u_key)
self.assertEqual(info_e2, [
'okay',
[{
'name': 'user',
'institution': 'institution',
'id': 'u3',
'permission_level': 'NONE',
'type': 'user',
'email': 'email'
}]
])
def test_column_types_search(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
res = epidb.create_column_type_simple("name", "description", "string", self.admin_key)
self.assertSuccess(res)
res = epidb.create_column_type_simple("string_column", "description", "string", self.admin_key)
self.assertSuccess(res)
res = epidb.create_column_type_simple("integer_column", "description", "integer", self.admin_key)
self.assertSuccess(res)
res = epidb.create_column_type_simple("double_column", "description", "double", self.admin_key)
self.assertSuccess(res)
res = epidb.create_column_type_range("score", "description", 0.0, 1.0, self.admin_key)
self.assertSuccess(res)
strand = ["+", "-"]
res = epidb.create_column_type_category("STRAND", "description", strand, self.admin_key)
self.assertSuccess(res)
(s, ss) = epidb.search("string_column", "column_types", self.admin_key)
(s, info) = epidb.info(ss[0][0], self.admin_key)
self.assertEqual(info[0], {'_id': 'ct31', 'description': 'description', 'type': 'column_type', 'name': 'string_column', 'column_type': 'string'})
(s, ss) = epidb.search("integer_column", "column_types", self.admin_key)
(s, info) = epidb.info(ss[0][0], self.admin_key)
self.assertEqual(info[0], {'_id': 'ct32', 'column_type': 'integer', 'description': 'description', 'type': 'column_type', 'name': 'integer_column'})
(s, ss) = epidb.search("double_column", "column_types", self.admin_key)
(s, info) = epidb.info(ss[0][0], self.admin_key)
self.assertEqual(info[0], {'_id': 'ct33', 'column_type': 'double', 'description': 'description', 'type': 'column_type', 'name': 'double_column'})
(s, ss) = epidb.search("score", "column_types", self.admin_key)
(s, info) = epidb.info(ss[0][0], self.admin_key)
self.assertEqual(info[0], {'_id': 'ct34','type': 'column_type', 'description': 'description', 'maximum': '1', 'minimum': '0', 'name': 'score', 'column_type': 'range'})
(s, ss) = epidb.search("STRAND", "column_types", self.admin_key)
(s, info) = epidb.info(ss[0][0], self.admin_key)
self.assertEqual(info[0], {'_id': 'ct35', 'type': 'column_type', 'description': 'description', 'name': 'STRAND', 'column_type': 'category', 'items': '+,-'})
def test_invalid_format_types(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
aid1 = self.insert_annotation(epidb, "Cpg Islands All Fields")
(s, m) = epidb.create_column_type_simple("CPG_ISLAND_NAME", "",
"string", self.admin_key)
self.assertSuccess(s, m)
(s, m) = epidb.create_column_type_simple("NUM_CPG_S", "", "string",
self.admin_key)
self.assertSuccess(s, m)
(s, m) = epidb.create_column_type_simple("NUM_GC_S", "", "string",
self.admin_key)
self.assertSuccess(s, m)
(s, m) = epidb.create_column_type_simple("PER_CG_S", "", "string",
self.admin_key)
self.assertSuccess(s, m)
(s, m) = epidb.create_column_type_simple("OBS_EXP_S", "", "string",
self.admin_key)
self.assertSuccess(s, m)
(s, m) = epidb.create_column_type_simple("PER_CPG_S", "", "string",
self.admin_key)
self.assertSuccess(s, m)
(s, m) = epidb.create_column_type_simple("LENGTH_S", "", "string",
self.admin_key)
self.assertSuccess(s, m)
(s, clone_id) = epidb.clone_dataset(
aid1, "New CpG Islands", "", "", "", "", "",
"CHROMOSOME,START,END,CPG_ISLAND_NAME,LENGTH_S,NUM_CPG_S,NUM_GC_S,PER_CPG_S,PER_CG_S,OBS_EXP_S",
{"new": "true"}, self.admin_key)
self.assertFailure(s, clone_id)
self.assertEqual(
clone_id,
"The column 'LENGTH_S' (type: string) is incompatible with the original column 'LENGTH' (type: integer)"
)
# --
(s, m) = epidb.create_column_type_simple("OBS_EXP_INT", "", "integer",
self.admin_key)
self.assertSuccess(s, m)
(s, clone_id) = epidb.clone_dataset(
aid1, "New CpG Islands", "", "", "", "", "",
"CHROMOSOME,START,END,CPG_ISLAND_NAME,LENGTH,NUM_CPG,NUM_GC,PER_CPG,PER_CG,OBS_EXP_INT",
{"new": "true"}, self.admin_key)
self.assertFailure(s, clone_id)
self.assertEqual(
clone_id,
"The column 'OBS_EXP_INT' (type: integer) is incompatible with the original column 'OBS_EXP' (type: double)"
)
# --
(s, m) = epidb.create_column_type_range("OBS_EXP_RANGE", "", -1.0, 1.0,
self.admin_key)
self.assertSuccess(s, m)
(s, clone_id) = epidb.clone_dataset(
aid1, "New CpG Islands", "", "", "", "", "",
"CHROMOSOME,START,END,CPG_ISLAND_NAME,LENGTH,NUM_CPG,NUM_GC,PER_CPG,PER_CG,OBS_EXP_RANGE",
{"new": "true"}, self.admin_key)
self.assertFailure(s, clone_id)
self.assertEqual(
clone_id,
"The column 'OBS_EXP_RANGE' (type: range) is incompatible with the original column 'OBS_EXP' (type: double)"
)
# --
(s, m) = epidb.create_column_type_category("OBS_EXP_CATEGORY", "",
["+", "-"], self.admin_key)
self.assertSuccess(s, m)
(s, clone_id) = epidb.clone_dataset(
aid1, "New CpG Islands", "", "", "", "", "",
"CHROMOSOME,START,END,CPG_ISLAND_NAME,LENGTH,NUM_CPG,NUM_GC,PER_CPG,PER_CG,OBS_EXP_CATEGORY",
{"new": "true"}, self.admin_key)
self.assertFailure(s, clone_id)
self.assertEqual(
clone_id,
"The column 'OBS_EXP_CATEGORY' (type: category) is incompatible with the original column 'OBS_EXP' (type: double)"
)
# --
(s, clone_id) = epidb.clone_dataset(
aid1, "New CpG Islands", "", "", "", "", "",
"CHROMOSOME,START,END,CPG_ISLAND_NAME,LENGTH,NUM_CPG,NUM_GC,PER_CPG,PER_CG,OBS_EXP",
{"new": "true"}, self.admin_key)
self.assertSuccess(s, clone_id)
