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_clone_annotatation(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
aid1 = self.insert_annotation(epidb, "Cpg Islands")
(s, id_clone_no_columns) = epidb.clone_dataset(aid1, "New CpG Islands",
"", "", "", "", "", "",
{"new": "true"},
self.admin_key)
self.assertSuccess(s, id_clone_no_columns)
(s, info) = epidb.info(id_clone_no_columns, 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], {
'format':
'CHROMOSOME,START,END',
'extra_metadata': {
'new': 'true'
},
'upload_info': {
'client_address': '0',
'total_size': '0',
'content_format': 'peaks',
'upload_start': '0',
'upload_end': '0',
'done': 'true',
'user': '******'
},
'name':
'New CpG Islands',
'genome':
'hg19',
'_id':
'a4',
'type':
'annotation',
'columns': [{
'name': 'CHROMOSOME',
'column_type': 'string'
}, {
'name': 'START',
'column_type': 'integer'
}, {
'name': 'END',
'column_type': 'integer'
}],
'description':
'CpG islands are associated ...'
})
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_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 removeest_remove_experiment(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
eid1 = self.insert_experiment(epidb, "hg18_chr1_1")
(s, q) = epidb.select_regions("hg18_chr1_1", "hg18", None, None, None,
None, None, None, None, self.admin_key)
self.assertSuccess(s, q)
(s, regions) = epidb.get_regions(q, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(s, regions)
(s, id_clone_plus) = epidb.clone_dataset(
eid1, "novo experimen", "getting only the default values", "", {
"new data": "true",
"cool": "a lot"
}, user[1])
self.assertSuccess(s, id_clone_plus)
res, user = epidb.add_user("user1", "*****@*****.**", "test",
self.admin_key)
self.assertSuccess(res, user)
res = epidb.remove(eid1, user[1])
self.assertFailure(res)
(s, id_removed) = epidb.remove(eid1, self.admin_key)
self.assertSuccess(s, id_removed)
self.assertEqual(id_removed, eid1)
(s, q2) = epidb.select_regions("novo experimen", "hg18", None, None,
None, None, None, None, None,
self.admin_key)
self.assertSuccess(s, q)
(s, regions2) = epidb.get_regions(q2, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(s, regions)
(s, id_removed) = epidb.remove(id_clone_plus, user[1])
self.assertSuccess(s, id_removed)
self.assertEqual(id_removed, id_clone_plus)
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_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'
})
def test_clone_experiment(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
eid1 = self.insert_experiment(epidb, "hg18_chr1_1")
(s, info_original) = epidb.info(eid1, self.admin_key)
info_original[0]['upload_info']['upload_end'] = '0'
info_original[0]['upload_info']['upload_start'] = '0'
info_original[0]['upload_info']['client_address'] = '0'
info_original[0]['upload_info']['total_size'] = '0'
self.assertEqual(
info_original[0], {
'description':
'desc1',
'data_type':
'peaks',
'format':
'CHROMOSOME,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK',
'sample_info': {
'biosource_name': 'K562',
'karyotype': 'cancer',
'sex': 'F'
},
'technique':
'tech1',
'upload_info': {
'total_size': '0',
'done': 'true',
'user': '******',
'upload_end': '0',
'upload_start': '0',
'client_address': '0'
},
'project':
'ENCODE',
'genome':
'hg18',
'sample_id':
's1',
'epigenetic_mark':
'Methylation',
'_id':
'e1',
'type':
'experiment',
'columns': [{
'name': 'CHROMOSOME',
'column_type': 'string'
}, {
'name': 'START',
'column_type': 'integer'
}, {
'name': 'END',
'column_type': 'integer'
}, {
'name': 'NAME',
'column_type': 'string'
}, {
'name': 'SCORE',
'column_type': 'double'
}, {
'name': 'STRAND',
'column_type': 'category',
'items': '+,-,.',
}, {
'name': 'SIGNAL_VALUE',
'column_type': 'double'
}, {
'name': 'P_VALUE',
'column_type': 'double'
}, {
'name': 'Q_VALUE',
'column_type': 'double'
}, {
'name': 'PEAK',
'column_type': 'integer'
}],
'name':
'hg18_chr1_1'
})
(s, id_clone_plus) = epidb.clone_dataset(
eid1, "new experiment clone", "", "", "", "",
"getting only the default values", "", {
"new data": "true",
"cool": "a lot"
}, self.admin_key)
self.assertSuccess(s, id_clone_plus)
(s, info_clone_plus) = epidb.info(id_clone_plus, self.admin_key)
info_clone_plus[0]['upload_info']['upload_start'] = '0'
info_clone_plus[0]['upload_info']['upload_end'] = '0'
info_clone_plus[0]['upload_info']['total_size'] = '0'
info_clone_plus[0]['upload_info']['client_address'] = '0'
self.assertEqual(
info_clone_plus[0], {
'description':
'getting only the default values',
'data_type':
'peaks',
'format':
'CHROMOSOME,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK',
'extra_metadata': {
'new data': 'true',
'cool': 'a lot'
},
'sample_info': {
'biosource_name': 'K562',
'karyotype': 'cancer',
'sex': 'F'
},
'technique':
'tech1',
'upload_info': {
'total_size': '0',
'done': 'true',
'user': '******',
'upload_end': '0',
'upload_start': '0',
'client_address': '0'
},
'project':
'ENCODE',
'genome':
'hg18',
'sample_id':
's1',
'epigenetic_mark':
'Methylation',
'_id':
'e2',
'type':
'experiment',
'columns': [{
'name': 'CHROMOSOME',
'column_type': 'string'
}, {
'name': 'START',
'column_type': 'integer'
}, {
'name': 'END',
'column_type': 'integer'
}, {
'name': 'NAME',
'column_type': 'string'
}, {
'name': 'SCORE',
'column_type': 'double'
}, {
'name': 'STRAND',
'column_type': 'category',
'items': '+,-,.',
}, {
'name': 'SIGNAL_VALUE',
'column_type': 'double'
}, {
'name': 'P_VALUE',
'column_type': 'double'
}, {
'name': 'Q_VALUE',
'column_type': 'double'
}, {
'name': 'PEAK',
'column_type': 'integer'
}],
'name':
'new experiment clone'
})
(s, _id_clone_same) = epidb.clone_dataset(
eid1, "clone of new experiment", "", "", "", "", "",
"CHROMOSOME,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK",
{}, self.admin_key)
self.assertSuccess(s, _id_clone_same)
(s, info_clone) = epidb.info(_id_clone_same, self.admin_key)
self.assertSuccess(s, info_clone)
info_clone[0]['upload_info']['upload_start'] = '0'
info_clone[0]['upload_info']['upload_end'] = '0'
info_clone[0]['upload_info']['total_size'] = '0'
info_clone[0]['upload_info']['client_address'] = '0'
self.assertEqual(
info_clone[0], {
'data_type':
'peaks',
'description':
'desc1',
'format':
'CHROMOSOME,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE,PEAK',
'sample_info': {
'biosource_name': 'K562',
'karyotype': 'cancer',
'sex': 'F'
},
'technique':
'tech1',
'upload_info': {
'total_size': '0',
'done': 'true',
'user': '******',
'upload_end': '0',
'upload_start': '0',
'client_address': '0'
},
'project':
'ENCODE',
'genome':
'hg18',
'sample_id':
's1',
'epigenetic_mark':
'Methylation',
'_id':
'e3',
'type':
'experiment',
'columns': [{
'name': 'CHROMOSOME',
'column_type': 'string'
}, {
'name': 'START',
'column_type': 'integer'
}, {
'name': 'END',
'column_type': 'integer'
}, {
'name': 'NAME',
'column_type': 'string'
}, {
'name': 'SCORE',
'column_type': 'double'
}, {
'name': 'STRAND',
'column_type': 'category',
'items': '+,-,.',
'name': 'STRAND'
}, {
'name': 'SIGNAL_VALUE',
'column_type': 'double'
}, {
'name': 'P_VALUE',
'column_type': 'double'
}, {
'name': 'Q_VALUE',
'column_type': 'double'
}, {
'name': 'PEAK',
'column_type': 'integer'
}],
'name':
'clone of new experiment'
})
