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_duplicate_column_type(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
res = epidb.create_column_type_simple("name2", "description", "string", self.admin_key)
self.assertSuccess(res)
res = epidb.create_column_type_simple("name2", "description", "integer", self.admin_key)
self.assertFailure(res)
def test_basic_column_types(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
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)
def test_remove_column(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
res, u1 = epidb.add_user("user1", "*****@*****.**", "test", self.admin_key)
self.assertSuccess(res, u1)
user_key = u1[1]
s, user_tmp = epidb.modify_user_admin(u1[0], "permission_level", "INCLUDE_COLLECTION_TERMS", self.admin_key)
self.assertSuccess(s)
res, c = epidb.create_column_type_simple("GENE_ID_ENTREZ", "rebimboca da parafuseta", "string", user_key)
self.assertSuccess(res, c)
res = epidb.remove(c, user_key)
self.assertSuccess(res)
res, s = epidb.search("GENE_ID_ENTREZ", None, user_key)
self.assertSuccess(res, s)
self.assertEqual(len(s), 0)
res, s = epidb.search("rebimboca", None, user_key)
self.assertSuccess(res, s)
self.assertEqual(len(s), 0)
res, s = epidb.search("parafuseta", None, user_key)
self.assertSuccess(res, s)
self.assertEqual(len(s), 0)
def test_chromosome_explicit(self):
# regression test: chromosome was put in the first column no matter
# what the format string specified
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
self.insert_experiment(epidb, "hg19_chr1_1")
(s, m) = epidb.create_column_type_simple("foobar", "", "string",
self.admin_key)
self.assertSuccess(s, m)
full_experiment_regions = helpers.get_result("full_experiment_regions")
res, qid = epidb.select_regions("hg19_chr1_1", "hg19", None, None,
None, None, None, None, None,
self.admin_key)
self.assertSuccess(res, qid)
fmt = "foobar,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK"
res, req = epidb.get_regions(qid, fmt, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertNotEqual(regions, full_experiment_regions)
fmt = "START,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK"
res, req = epidb.get_regions(qid, fmt, self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertNotEqual(regions, full_experiment_regions)
# leave out chromosome entirely
regions_wo_chr = helpers.get_result("full_experiment_regions_wo_chr")
# Creating another column, named NAME, that in the experiment is name.
# This column should return empty.
(s, m) = epidb.create_column_type_simple("COISA", "", "string",
self.admin_key)
self.assertSuccess(s, m)
fmt = "START,END,COISA,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK"
res, req = epidb.get_regions(qid, fmt, self.admin_key)
regions = self.get_regions_request(req)
self.assertSuccess(res, regions)
self.assertEqual(regions, regions_wo_chr)
def test_no_ignore_if(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, 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'")
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_wig_clone_calculated(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
res, _id = epidb.add_experiment(
"test_exp1", "hg19", "Methylation", sample_id, "tech1", "ENCODE",
"desc1", "", "wig",
{"__local_file__": "../tests/data/wig/scores1.wig"},
self.admin_key)
self.assertSuccess(res, id)
(s, m) = epidb.create_column_type_simple("METHYLATION_LEVEL", "",
"double", self.admin_key)
self.assertSuccess(s, m)
res = epidb.create_column_type_calculated(
"METHYLATION_LEVEL_SQRT", "Square root of the methylation level",
"return math.sqrt(value_of('VALUE'))", self.admin_key)
self.assertSuccess(res)
(s, clone_id) = epidb.clone_dataset(
_id, "New Wig File", "", "", "", "", "",
"CHROMOSOME,START,END,METHYLATION_LEVEL_SQRT", None,
self.admin_key)
self.assertFailure(s, clone_id)
self.assertEqual(
clone_id,
"The column 'METHYLATION_LEVEL_SQRT' (type: calculated) is incompatible with the original column 'VALUE' (type: double)"
)
(s, clone_id) = epidb.clone_dataset(
_id, "New Wig File", "", "", "", "", "",
"CHROMOSOME,START,END,METHYLATION_LEVEL", None, self.admin_key)
self.assertSuccess(s, clone_id)
(status, wig_data) = epidb.select_regions('New Wig File', "hg19", None,
None, None, None, None, None,
None, self.admin_key)
(s, req) = epidb.get_regions(
wig_data,
"CHROMOSOME,START,END,METHYLATION_LEVEL,METHYLATION_LEVEL_SQRT",
self.admin_key)
rs = self.get_regions_request(req)
self.assertEqual(rs.split("\n")[0].split("\t")[3], "8.1235")
self.assertEqual(rs.split("\n")[0].split("\t")[4], "2.850168")
self.assertEqual(rs.split("\n")[6].split("\t")[3], "30.0000")
self.assertEqual(rs.split("\n")[6].split("\t")[4], "5.477226")
def test_better_names(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, 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)
self.assertEqual(clone_id, "a4")
def test_wig_clone(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
res, _id = epidb.add_experiment(
"test_exp1", "hg19", "Methylation", sample_id, "tech1", "ENCODE",
"desc1", "", "wig",
{"__local_file__": "../tests/data/wig/scores1.wig"},
self.admin_key)
self.assertSuccess(res, id)
(s, m) = epidb.create_column_type_simple("METHYLATION_LEVEL", "",
"double", self.admin_key)
self.assertSuccess(s, m)
(s, clone_id) = epidb.clone_dataset(
_id, "New Wig File", "", "", "", "", "",
"CHROMOSOME,START,END,METHYLATION_LEVEL", None, self.admin_key)
self.assertSuccess(s, clone_id)
(status, wig_data) = epidb.select_regions('test_exp1', "hg19", None,
None, None, None, None, None,
None, self.admin_key)
(s, req) = epidb.get_regions(wig_data, "CHROMOSOME,START,END,VALUE",
self.admin_key)
rs = self.get_regions_request(req)
(status, wig_data) = epidb.select_regions('New Wig File', "hg19", None,
None, None, None, None, None,
None, self.admin_key)
(s,
req2) = epidb.get_regions(wig_data,
"CHROMOSOME,START,END,METHYLATION_LEVEL",
self.admin_key)
rs2 = self.get_regions_request(req2)
self.assertEqual(rs.split("\n")[0].split("\t")[3], "8.1235")
self.assertEqual(rs, rs2)
def test_invalid_column(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
aid1 = self.insert_annotation(epidb, "Cpg Islands")
(s, msg) = epidb.clone_dataset(aid1, "New CpG Islands", "", "", "", "",
"",
"CHROMOSOME,START,END,INVALID_COLUMN",
{"new": "true"}, self.admin_key)
self.assertEqual(
msg, "125000:Column name 'INVALID_COLUMN' does not exist.")
(s, m) = epidb.create_column_type_simple("NICE_COLUMN", "", "string",
self.admin_key)
self.assertSuccess(s, m)
(s, msg) = epidb.clone_dataset(aid1, "New CpG Islands", "", "", "", "",
"", "NICE_COLUMN,START,END,VALUE",
{"new": "true"}, self.admin_key)
self.assertEqual(
msg,
'Column CHROMOSOME can not be renamed. Columns CHROMOSOME,START, and END are immutable.'
)
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)
def test_invalid_format_size(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, 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)
s, info = epidb.info(clone_id, self.admin_key)
info[0]['upload_info']['upload_end'] = '0'
info[0]['upload_info']['upload_start'] = '0'
info[0]['upload_info']['total_size'] = '0'
info[0]['upload_info']['client_address'] = '0'
self.assertEqual(
info[0], {
'description':
'CpG islands are associated ... (all fields)',
'format':
'CHROMOSOME,START,END,CPG_ISLAND_NAME,LENGTH,NUM_CPG,NUM_GC,PER_CPG,PER_CG,OBS_EXP',
'extra_metadata': {
'new': 'true'
},
'upload_info': {
'total_size': '0',
'content_format': 'peaks',
'done': 'true',
'user': '******',
'upload_end': '0',
'upload_start': '0',
'client_address': '0'
},
'genome':
'hg19',
'_id':
'a4',
'type':
'annotation',
'columns': [{
'name': 'CHROMOSOME',
'column_type': 'string'
}, {
'name': 'START',
'column_type': 'integer'
}, {
'name': 'END',
'column_type': 'integer'
}, {
'name': 'CPG_ISLAND_NAME',
'column_type': 'string'
}, {
'name': 'LENGTH',
'column_type': 'integer'
}, {
'name': 'NUM_CPG',
'column_type': 'integer'
}, {
'name': 'NUM_GC',
'column_type': 'integer'
}, {
'name': 'PER_CPG',
'column_type': 'double'
}, {
'name': 'PER_CG',
'column_type': 'double'
}, {
'name': 'OBS_EXP',
'column_type': 'double'
}],
'name':
'New CpG Islands'
})
