| from pathlib import Path
|
| import sys
|
| _test_root=Path(__file__).resolve().parents[1]
|
| sys.path.insert(0,str(_test_root/'generator'))
|
| sys.path.insert(0,str(_test_root/'validator'))
|
| import copy
|
| import random
|
| import tempfile
|
| from pathlib import Path
|
| import unittest
|
| from jsonschema import Draft202012Validator
|
| import make
|
| import check
|
| from common import *
|
|
|
| class OracleTests(unittest.TestCase):
|
| def test_all_families_and_corrupt_labels(self):
|
| for kind in NAMES:
|
| for i,family in enumerate(FAMILIES[kind]):
|
| with self.subTest(kind=kind,family=family):
|
| for attempt in range(100):
|
| try:inp,out=make.MAKERS[kind](random.Random(12345+i+attempt*100),family);break
|
| except ValueError:continue
|
| check.CHECKS[kind](inp,out)
|
| bad=copy.deepcopy(out)
|
| if kind=='nav':bad['reachability_changed']=not bad['reachability_changed']
|
| elif kind=='coord':bad['optimal_makespan']=10000
|
| elif kind=='reads':bad['passed_filter']=not bad['passed_filter']
|
| elif kind=='align':bad['edit_distance']+=1
|
| else:bad['union_overlap_bases']+=1
|
| with self.assertRaises(ValueError):check.CHECKS[kind](inp,bad)
|
| def test_myers_against_exhaustive_small_cases(self):
|
| import itertools
|
| sequences=['']+[''.join(chars) for n in range(1,5) for chars in itertools.product('AC',repeat=n)]
|
| for a in sequences:
|
| for b in sequences:self.assertEqual(make.alignment(a,b)[0],check.myers(a,b))
|
| def test_interval_touching_and_coordinate_conversion(self):
|
| inp={'contigs':{'synthetic_A':100},'features':[{'contig':'synthetic_A','start':1,'end':10,'basis':'one_closed','strand':'+'},{'contig':'synthetic_A','start':10,'end':20,'basis':'zero_half_open','strand':'+'},{'contig':'synthetic_A','start':20,'end':30,'basis':'zero_half_open','strand':'-'}],
|
| 'query':{'contig':'synthetic_A','start':10,'end':20,'basis':'zero_half_open','strand':'+'},'same_strand':True}
|
| expected={'query_bed':[10,20],'matches':[{'feature_index':1,'overlap_bases':10}],'union_overlap_bases':10,'query_length':10}
|
| self.assertEqual(make.interval_label(inp),expected);check.intervals(inp,expected)
|
| def test_phred_and_threshold_boundaries(self):
|
| inp={'fastq':'@synthetic_read\nACGN\n+\n555#','policy':{'min_length':3,'max_n':0,'mean_q_min':20,'trim_q_min':10}}
|
| out=make.read_label(inp['fastq'],inp['policy']);self.assertEqual(out['trimmed_sequence'],'ACG');self.assertTrue(out['passed_filter']);check.reads(inp,out)
|
| def test_grid_symmetry_semantic_identity(self):
|
| inp,out=make.nav(random.Random(12),'gap_close');fp,group=semantic('nav',inp)
|
| grid,p,c=transforms(inp['grid'],[inp['start'],inp['goal'],inp['edit']],inp['costs'])[3]
|
| other={'grid':grid,'start':list(p[0]),'goal':list(p[1]),'edit':list(p[2]),'costs':c}
|
| self.assertEqual((fp,group),semantic('nav',other))
|
| def test_schema_rejects_wrong_label_types(self):
|
| inp,out=make.align(random.Random(3),'clustered_indels');fp,group=semantic('align',inp)
|
| row={'id':'ALIGN-0000000','index':0,'seed':1,'family':'clustered_indels','input':inp,'expected':out,'fingerprint':fp,'group_id':group,'split':split(group),'provenance':provenance('align')}
|
| Draft202012Validator(schema('align')).validate(row)
|
| row['expected']['within_threshold']=1
|
| with self.assertRaises(Exception):Draft202012Validator(schema('align')).validate(row)
|
| def test_resume_and_byte_reproduction(self):
|
| with tempfile.TemporaryDirectory() as tmp:
|
| out=Path(tmp)/'a';make.generate('reads',out,100,987)
|
| original=(out/'dataset.jsonl').read_bytes();make.generate('reads',out,100,987,resume=True)
|
| self.assertEqual(original,(out/'dataset.jsonl').read_bytes())
|
| second=Path(tmp)/'b';make.generate('reads',second,100,987)
|
| self.assertEqual(original,(second/'dataset.jsonl').read_bytes())
|
| with self.assertRaises(ValueError):make.generate('reads',out,100,988,resume=True)
|
| def test_resume_after_missing_final_file_and_partial_commit(self):
|
| with tempfile.TemporaryDirectory() as tmp:
|
| out=Path(tmp)/'run';make.generate('reads',out,1000,991)
|
| original=(out/'dataset.jsonl').read_bytes()
|
| (out/'dataset.jsonl').unlink();(out/'chunks/0000500.jsonl').unlink()
|
| make.generate('reads',out,1000,991,resume=True)
|
| self.assertEqual(original,(out/'dataset.jsonl').read_bytes())
|
| def test_missing_file_and_reject_preservation(self):
|
| with tempfile.TemporaryDirectory() as tmp:
|
| root=Path(tmp);report=check.validate('reads',root/'missing.jsonl',100,root/'report')
|
| self.assertEqual(report['status'],'FAIL');self.assertTrue((root/'report/rejected.jsonl').read_text())
|
| path=root/'broken.jsonl';path.write_text('{broken json}\n',encoding='utf-8')
|
| report=check.validate('reads',path,100,root/'report2');self.assertEqual(report['rejected'],1)
|
| self.assertIn('broken json',(root/'report2/rejected.jsonl').read_text())
|
| if __name__=='__main__':unittest.main()
|
|
|
