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Updating the test paths

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This commit is contained in:
mvaradi 2018-10-12 17:53:13 +01:00
parent 8abd4ec9f8
commit adf22847de
3 changed files with 113 additions and 33 deletions
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41
data/test_data.json
View file

@ -7,42 +7,38 @@
"pdb_id": "2gs6", "pdb_id": "2gs6",
"chains": [ "chains": [
{ {
"additional_chain_annotations": {},
"residues": [ "residues": [
{ {
"additional_residue_annotations": {}, "pdb_res_label": "811",
"pdb_res_label": 811,
"aa_type": "HIS", "aa_type": "HIS",
"site_data": [ "site_data": [
{ {
"confidence_score": 1, "confidence_score": 1,
"site_id_ref": 811, "site_id_ref": 1,
"confidence_classification": "high", "confidence_classification": "high",
"raw_score": 1 "raw_score": 1
} }
] ]
}, },
{ {
"additional_residue_annotations": {}, "pdb_res_label": "812",
"pdb_res_label": 812,
"aa_type": "ARG", "aa_type": "ARG",
"site_data": [ "site_data": [
{ {
"confidence_score": 1, "confidence_score": 1,
"site_id_ref": 812, "site_id_ref": 2,
"confidence_classification": "high", "confidence_classification": "high",
"raw_score": 1 "raw_score": 1
} }
] ]
}, },
{ {
"additional_residue_annotations": {}, "pdb_res_label": "813",
"pdb_res_label": 813,
"aa_type": "ASP", "aa_type": "ASP",
"site_data": [ "site_data": [
{ {
"confidence_score": 1, "confidence_score": 1,
"site_id_ref": 813, "site_id_ref": 2,
"confidence_classification": "high", "confidence_classification": "high",
"raw_score": 1 "raw_score": 1
} }
@ -54,31 +50,18 @@
], ],
"sites": [ "sites": [
{ {
"additional_site_annotations": {}, "site_id": 1,
"source_release_date": "06/20/2006", "label": "HRD motif"
"site_id": 811,
"label": "HRD motif",
"source_accession": "2gs6",
"source_database": "pdb"
}, },
{ {
"additional_site_annotations": {}, "site_id": 2,
"source_release_date": "06/20/2006", "label": "HRD motif"
"site_id": 812,
"label": "HRD motif",
"source_accession": "2gs6",
"source_database": "pdb"
}, },
{ {
"additional_site_annotations": {}, "site_id": 3,
"source_release_date": "06/20/2006", "label": "HRD motif"
"site_id": 813,
"label": "HRD motif",
"source_accession": "2gs6",
"source_database": "pdb"
} }
], ],
"additional_entry_annotations": {},
"evidence_code_ontology": [ "evidence_code_ontology": [
{ {
"eco_term": "computational combinatorial evidence", "eco_term": "computational combinatorial evidence",

88
data/test_data_invalid.json Normal file
View file

@ -0,0 +1,88 @@
{
"data_resource": "ProKinO",
"resource_version": "2.0",
"software_version": "2.0",
"resource_entry_url": "http://vulcan.cs.uga.edu/prokino/",
"release_date": "10/02/2017",
"pdb_id": "2gs6",
"chains": [
{
"additional_chain_annotations": {},
"residues": [
{
"additional_residue_annotations": {},
"pdb_res_label": 811,
"aa_type": "HIS",
"site_data": [
{
"confidence_score": 1,
"site_id_ref": 811,
"confidence_classification": "high",
"raw_score": 1
}
]
},
{
"additional_residue_annotations": {},
"pdb_res_label": 812,
"aa_type": "ARG",
"site_data": [
{
"confidence_score": 1,
"site_id_ref": 812,
"confidence_classification": "high",
"raw_score": 1
}
]
},
{
"additional_residue_annotations": {},
"pdb_res_label": 813,
"aa_type": "ASP",
"site_data": [
{
"confidence_score": 1,
"site_id_ref": 813,
"confidence_classification": "high",
"raw_score": 1
}
]
}
],
"chain_label": "A"
}
],
"sites": [
{
"additional_site_annotations": {},
"source_release_date": "06/20/2006",
"site_id": 811,
"label": "HRD motif",
"source_accession": "2gs6",
"source_database": "pdb"
},
{
"additional_site_annotations": {},
"source_release_date": "06/20/2006",
"site_id": 812,
"label": "HRD motif",
"source_accession": "2gs6",
"source_database": "pdb"
},
{
"additional_site_annotations": {},
"source_release_date": "06/20/2006",
"site_id": 813,
"label": "HRD motif",
"source_accession": "2gs6",
"source_database": "pdb"
}
],
"additional_entry_annotations": {},
"evidence_code_ontology": [
{
"eco_term": "computational combinatorial evidence",
"eco_code": "ECO_0000246"
}
]
}

17
tests/test_validator.py
View file

@ -28,15 +28,14 @@ class TestValidator(unittest.TestCase):
def test_json_parser(self): def test_json_parser(self):
validator = Validator("resource_name") validator = Validator("resource_name")
data = validator.parse_json("../data/test_data.json") data = validator.parse_json("data/test_data.json")
self.assertIsNotNone(data) self.assertIsNotNone(data)
validator.parse_json("../data/test_data_malformed.json") validator.parse_json("data/test_data_malformed.json")
self.assertIn("JSON error", validator.error_log) self.assertIn("JSON error", validator.error_log)
def test_basic_checks(self): def test_basic_checks(self):
validator = Validator("test") validator = Validator("test")
validator.json_data = {"data_resource": "test", "pdb_id": "1abc"} validator.json_data = {"data_resource": "test", "pdb_id": "1abc"}
print(validator.json_data)
self.assertTrue(validator.basic_checks()) self.assertTrue(validator.basic_checks())
validator.json_data = {"data_resource": "test"} validator.json_data = {"data_resource": "test"}
self.assertFalse(validator.basic_checks()) self.assertFalse(validator.basic_checks())
@ -61,4 +60,14 @@ class TestValidator(unittest.TestCase):
def test_invalid_pdb_id(self): def test_invalid_pdb_id(self):
validator = Validator("test") validator = Validator("test")
validator.json_data = {"data_resource": "test", "pdb_id": "invalid"} validator.json_data = {"data_resource": "test", "pdb_id": "invalid"}
self.assertFalse(validator.test_pdb_id()) self.assertFalse(validator.test_pdb_id())
def test_json_validation(self):
validator = Validator("ProKinO")
validator.load_json("data/test_data.json")
validator.load_schema("data/funpdbe_schema.json")
validation = validator.validate_against_schema()
self.assertTrue(validation)
validator.load_json("data/test_data_invalid.json")
validation = validator.validate_against_schema()
self.assertFalse(validation)