Coverage for tests/conftest.py: 71%

1import os 

2import subprocess 

3from atexit import register 

4 

5import pytest 

6 

7from bbconf.bbagent import BedBaseAgent 

8 

9from .utils import BED_TEST_ID 

10 

11DB_CMD = """ 

12docker run --rm -it --name bedbase-test \ 

13 -e POSTGRES_USER=postgres \ 

14 -e POSTGRES_PASSWORD=docker\ 

15 -e POSTGRES_DB=bedbase \ 

16 -p 5432:5432 postgres 

17""" 

18 

19try: 

20 subprocess.check_output( 

21 "docker inspect bedbase-test --format '{{.State.Status}}'", shell=True 

22 ) 

23 SERVICE_UNAVAILABLE = False 

24except: 

25 register( 

26 print, f"Some tests require a test database. To initiate it, run:\n{DB_CMD}" 

27 ) 

28 SERVICE_UNAVAILABLE = True 

29 

30 

31TESTS_DIR = os.path.dirname(os.path.abspath(__file__)) 

32 

33CONFIG_PATH = os.path.join( 

34 TESTS_DIR, 

35 "config_test.yaml", 

36) 

37DATA_PATH = os.path.join( 

38 TESTS_DIR, 

39 "data", 

40) 

41 

42if not SERVICE_UNAVAILABLE: 

43 agent = BedBaseAgent(config=CONFIG_PATH) 

44 

45 

46def get_bbagent(): 

47 return agent 

48 

49 

50@pytest.fixture(scope="function") 

51def bbagent_obj(): 

52 yield agent 

53 

54 

55@pytest.fixture() 

56def example_bedset_plot(): 

57 return { 

58 "name": "chrombins", 

59 "description": "Regions distribution over chromosomes", 

60 "title": "Regions distribution over chromosomes", 

61 "path": "data/plots/bbad85f21962bb8d972444f7f9a3a932_chrombins.pdf", 

62 "path_thumbnail": "data/plots/bbad85f21962bb8d972444f7f9a3a932_chrombins.png", 

63 "bedset_id": BED_TEST_ID, 

64 } 

65 

66 

67@pytest.fixture() 

68def example_dict(): 

69 plots = { 

70 "chrombins": { 

71 "name": "Regions distribution over chromosomes", 

72 "path": "plots/bbad85f21962bb8d972444f7f9a3a932_chrombins.pdf", 

73 "path_thumbnail": "plots/bbad85f21962bb8d972444f7f9a3a932_chrombins.png", 

74 } 

75 } 

76 files = { 

77 "bedfile": { 

78 "name": "Bed file", 

79 "path": os.path.join( 

80 DATA_PATH, "files/bbad85f21962bb8d972444f7f9a3a932.bed.gz" 

81 ), 

82 "description": "Bed file with regions", 

83 } 

84 } 

85 classification = { 

86 "bed_format": "narrowpeak", 

87 "bed_type": "bed6+4", 

88 "genome_alias": "hg38", 

89 "genome_digest": "2230c535660fb4774114bfa966a62f823fdb6d21acf138d4", 

90 "name": "bbad85f21962bb8d972444f7f9a3a932", 

91 } 

92 

93 return dict( 

94 identifier="bbad85f21962bb8d972444f7f9a3a932", 

95 stats={ 

96 "number_of_regions": 1, 

97 "median_tss_dist": 2, 

98 "mean_region_width": 3, 

99 "exon_frequency": 4, 

100 "exon_percentage": 5, 

101 "intron_frequency": 6, 

102 "intron_percentage": 7, 

103 "intergenic_percentage": 8, 

104 "intergenic_frequency": 9, 

105 "promotercore_frequency": 10, 

106 "promotercore_percentage": 11, 

107 "fiveutr_frequency": 12, 

108 "fiveutr_percentage": 13, 

109 "threeutr_frequency": 14, 

110 "threeutr_percentage": 15, 

111 "promoterprox_frequency": 16, 

112 "promoterprox_percentage": 17, 

113 }, 

114 metadata={"sample_name": "sample_name_1"}, 

115 plots=plots, 

116 files=files, 

117 classification=classification, 

118 upload_qdrant=False, 

119 upload_pephub=False, 

120 upload_s3=True, 

121 local_path=DATA_PATH, 

122 overwrite=False, 

123 nofail=False, 

124 ) 

125 

126 

127@pytest.fixture 

128def load_test_data(): 

129 get_bbagent().config.db_engine() 

130 

131 

132@pytest.fixture() 

133def mocked_phc(mocker): 

134 mocker.patch( 

135 "pephubclient.modules.sample.PEPHubSample.get", 

136 return_value={"sample_name": BED_TEST_ID, "other_metadata": "other_metadata_1"}, 

137 )