idmtools-test 0.0.0.dev0__py3-none-any.whl → 0.0.2__py3-none-any.whl

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Files changed (141) hide show
  1. idmtools_test/__init__.py +16 -8
  2. idmtools_test/inputs/__init__.py +0 -0
  3. idmtools_test/inputs/assets/collections/1/a.txt +0 -0
  4. idmtools_test/inputs/assets/collections/1/b.txt +0 -0
  5. idmtools_test/inputs/assets/collections/2/c.txt +0 -0
  6. idmtools_test/inputs/assets/collections/d.txt +0 -0
  7. idmtools_test/inputs/builder/sweeps.csv +6 -0
  8. idmtools_test/inputs/builder/sweeps.yaml +8 -0
  9. idmtools_test/inputs/compsplatform/__init__.py +0 -0
  10. idmtools_test/inputs/compsplatform/failing_model.py +5 -0
  11. idmtools_test/inputs/compsplatform/mixed_model.py +10 -0
  12. idmtools_test/inputs/compsplatform/working_model.py +5 -0
  13. idmtools_test/inputs/configuration/idmtools_test.ini +71 -0
  14. idmtools_test/inputs/custom/Eradication.exe +0 -0
  15. idmtools_test/inputs/custom/Local_Migration.bin +0 -0
  16. idmtools_test/inputs/custom/Local_Migration.bin.json +12 -0
  17. idmtools_test/inputs/custom/Regional_Migration.bin +0 -0
  18. idmtools_test/inputs/custom/Regional_Migration.bin.json +12 -0
  19. idmtools_test/inputs/custom/Zambia_30arcsec_air_temperature_daily.bin +0 -0
  20. idmtools_test/inputs/custom/Zambia_30arcsec_air_temperature_daily.bin.json +26 -0
  21. idmtools_test/inputs/custom/Zambia_30arcsec_rainfall_daily.bin +0 -0
  22. idmtools_test/inputs/custom/Zambia_30arcsec_rainfall_daily.bin.json +26 -0
  23. idmtools_test/inputs/custom/Zambia_30arcsec_relative_humidity_daily.bin +0 -0
  24. idmtools_test/inputs/custom/Zambia_30arcsec_relative_humidity_daily.bin.json +26 -0
  25. idmtools_test/inputs/custom/campaign.json +95384 -0
  26. idmtools_test/inputs/custom/config.json +943 -0
  27. idmtools_test/inputs/custom/custom_reports.json +163 -0
  28. idmtools_test/inputs/custom/demo.json +1258 -0
  29. idmtools_test/inputs/custom/emodules_map.json +9 -0
  30. idmtools_test/inputs/custom/reporter_plugins/libReportMalariaFiltered.dll +0 -0
  31. idmtools_test/inputs/custom/reporter_plugins/libSpatialReportMalariaFiltered.dll +0 -0
  32. idmtools_test/inputs/custom/reporter_plugins/libreporteventcounter.dll +0 -0
  33. idmtools_test/inputs/duplicated_model/exe/Eradication +0 -0
  34. idmtools_test/inputs/duplicated_model/f1 +0 -0
  35. idmtools_test/inputs/emod/Eradication.exe +0 -0
  36. idmtools_test/inputs/emod_files/campaign.json +21 -0
  37. idmtools_test/inputs/emod_files/config.json +125 -0
  38. idmtools_test/inputs/emod_files/demographics.json +81 -0
  39. idmtools_test/inputs/fakemodels/AnotherOne +0 -0
  40. idmtools_test/inputs/fakemodels/Eradication +0 -0
  41. idmtools_test/inputs/fakemodels/Eradication-2.11.custom.exe +0 -0
  42. idmtools_test/inputs/fakemodels/Eradication.exe +0 -0
  43. idmtools_test/inputs/files/campaign.json +21 -0
  44. idmtools_test/inputs/files/config.json +119 -0
  45. idmtools_test/inputs/files/demographics.json +82 -0
  46. idmtools_test/inputs/files/hello.txt +1 -0
  47. idmtools_test/inputs/id_files/slurm.example_python_experiment.id +1 -0
  48. idmtools_test/inputs/malaria_brazil_central_west_spatial/Assets/Brazil_Central_West_Brazil_Central_West_2.5arcmin_air_temperature_daily.bin +0 -0
  49. idmtools_test/inputs/malaria_brazil_central_west_spatial/Assets/Brazil_Central_West_Brazil_Central_West_2.5arcmin_air_temperature_daily.bin.json +26 -0
  50. idmtools_test/inputs/malaria_brazil_central_west_spatial/Assets/Brazil_Central_West_Brazil_Central_West_2.5arcmin_demographics.json +559 -0
  51. idmtools_test/inputs/malaria_brazil_central_west_spatial/Assets/Brazil_Central_West_Brazil_Central_West_2.5arcmin_rainfall_daily.bin +0 -0
  52. idmtools_test/inputs/malaria_brazil_central_west_spatial/Assets/Brazil_Central_West_Brazil_Central_West_2.5arcmin_rainfall_daily.bin.json +26 -0
  53. idmtools_test/inputs/malaria_brazil_central_west_spatial/Assets/Brazil_Central_West_Brazil_Central_West_2.5arcmin_relative_humidity_daily.bin +0 -0
  54. idmtools_test/inputs/malaria_brazil_central_west_spatial/Assets/Brazil_Central_West_Brazil_Central_West_2.5arcmin_relative_humidity_daily.bin.json +26 -0
  55. idmtools_test/inputs/malaria_brazil_central_west_spatial/Assets/Eradication +0 -0
  56. idmtools_test/inputs/malaria_brazil_central_west_spatial/Assets/Eradication.exe +0 -0
  57. idmtools_test/inputs/malaria_brazil_central_west_spatial/campaign.json +4 -0
  58. idmtools_test/inputs/malaria_brazil_central_west_spatial/config.json +667 -0
  59. idmtools_test/inputs/malaria_brazil_central_west_spatial/malaria_brazil_central_west_spatial-ERA5Input_demo.csv +37 -0
  60. idmtools_test/inputs/python/Assets/MyExternalLibrary/__init__.py +0 -0
  61. idmtools_test/inputs/python/Assets/MyExternalLibrary/functions.py +15 -0
  62. idmtools_test/inputs/python/Assets/MyLib/functions.py +2 -0
  63. idmtools_test/inputs/python/Assets/MyLib/temp.py +271 -0
  64. idmtools_test/inputs/python/Assets/__init__.py +0 -0
  65. idmtools_test/inputs/python/__init__.py +0 -0
  66. idmtools_test/inputs/python/folder_dup_file/__init__.py +0 -0
  67. idmtools_test/inputs/python/folder_dup_file/model1.py +19 -0
  68. idmtools_test/inputs/python/hello_world.py +1 -0
  69. idmtools_test/inputs/python/model.py +26 -0
  70. idmtools_test/inputs/python/model1.py +20 -0
  71. idmtools_test/inputs/python/model3.py +21 -0
  72. idmtools_test/inputs/python/newmodel2.py +20 -0
  73. idmtools_test/inputs/python/output_generator/generate.py +39 -0
  74. idmtools_test/inputs/python/realpath_verify.py +6 -0
  75. idmtools_test/inputs/python/ye_seir_model/Assets/MyExternalLibrary/Python36/dtk_generic_intrahost.pyd +0 -0
  76. idmtools_test/inputs/python/ye_seir_model/Assets/MyExternalLibrary/Python36/dtk_nodedemog.pyd +0 -0
  77. idmtools_test/inputs/python/ye_seir_model/Assets/MyExternalLibrary/Python37/dtk_generic_intrahost.pyd +0 -0
  78. idmtools_test/inputs/python/ye_seir_model/Assets/MyExternalLibrary/Python37/dtk_nodedemog.pyd +0 -0
  79. idmtools_test/inputs/python/ye_seir_model/Assets/SEIR_model.py +252 -0
  80. idmtools_test/inputs/python/ye_seir_model/Assets/SEIR_model_slurm.py +242 -0
  81. idmtools_test/inputs/python/ye_seir_model/Assets/config_sim.py +48 -0
  82. idmtools_test/inputs/python/ye_seir_model/Assets/custom_csv_analyzer.py +133 -0
  83. idmtools_test/inputs/python/ye_seir_model/Assets/python.sh +4 -0
  84. idmtools_test/inputs/python/ye_seir_model/Assets/requirements.txt +4 -0
  85. idmtools_test/inputs/python/ye_seir_model/Assets/templates/config.json +68 -0
  86. idmtools_test/inputs/python/ye_seir_model/Assets/templates/demographics_template.json +44 -0
  87. idmtools_test/inputs/python/ye_seir_model/__init__.py +0 -0
  88. idmtools_test/inputs/python_experiments/__init__.py +0 -0
  89. idmtools_test/inputs/python_experiments/model.py +10 -0
  90. idmtools_test/inputs/r/model1.R +1 -0
  91. idmtools_test/inputs/r/ncov_analysis/individual_dynamics_estimates/estimate_incubation_period.R +89 -0
  92. idmtools_test/inputs/regression/107/Assets/__init__.py +0 -0
  93. idmtools_test/inputs/regression/107/Assets/model.py +1 -0
  94. idmtools_test/inputs/regression/107/__init__.py +0 -0
  95. idmtools_test/inputs/regression/125/Assets/__init__.py +0 -0
  96. idmtools_test/inputs/regression/125/Assets/model.py +1 -0
  97. idmtools_test/inputs/regression/125/Assets2/__init__.py +0 -0
  98. idmtools_test/inputs/regression/125/Assets2/dir1/__init__.py +0 -0
  99. idmtools_test/inputs/regression/125/Assets2/dir1/model.py +1 -0
  100. idmtools_test/inputs/regression/125/Assets2/dir2/__init__.py +0 -0
  101. idmtools_test/inputs/regression/125/Assets2/dir2/model.py +1 -0
  102. idmtools_test/inputs/regression/125/__init__.py +0 -0
  103. idmtools_test/inputs/regression/__init__.py +0 -0
  104. idmtools_test/inputs/scheduling/hpc/WorkOrder.json +7 -0
  105. idmtools_test/inputs/scheduling/slurm/WorkOrder.json +11 -0
  106. idmtools_test/inputs/scheduling/slurm/WorkOrder1.json +11 -0
  107. idmtools_test/inputs/scheduling/slurm/WorkOrder2.json +13 -0
  108. idmtools_test/inputs/scheduling/slurm/commandline_model.py +22 -0
  109. idmtools_test/inputs/serialization/Eradication.exe +0 -0
  110. idmtools_test/inputs/serialization/single_node_demographics.json +82 -0
  111. idmtools_test/inputs/singularity/alpine_simple/Singularity.def +28 -0
  112. idmtools_test/inputs/singularity/alpine_simple/run_model.py +41 -0
  113. idmtools_test/inputs/singularity/alpine_template/Singularity.jinja +22 -0
  114. idmtools_test/test_precreate_hooks.py +25 -0
  115. idmtools_test/utils/__init__.py +0 -0
  116. idmtools_test/utils/cli.py +41 -0
  117. idmtools_test/utils/common_experiments.py +79 -0
  118. idmtools_test/utils/comps.py +152 -0
  119. idmtools_test/utils/decorators.py +208 -0
  120. idmtools_test/utils/execute_operations/__init__.py +0 -0
  121. idmtools_test/utils/execute_operations/experiment_operations.py +237 -0
  122. idmtools_test/utils/execute_operations/simulate_operations.py +368 -0
  123. idmtools_test/utils/itest_with_persistence.py +25 -0
  124. idmtools_test/utils/operations/__init__.py +0 -0
  125. idmtools_test/utils/operations/experiment_operations.py +64 -0
  126. idmtools_test/utils/operations/simulation_operations.py +114 -0
  127. idmtools_test/utils/shared_functions.py +25 -0
  128. idmtools_test/utils/test_asset.py +89 -0
  129. idmtools_test/utils/test_asset_collection.py +223 -0
  130. idmtools_test/utils/test_execute_platform.py +137 -0
  131. idmtools_test/utils/test_platform.py +94 -0
  132. idmtools_test/utils/test_task.py +69 -0
  133. idmtools_test/utils/utils.py +146 -0
  134. idmtools_test-0.0.2.dist-info/METADATA +48 -0
  135. idmtools_test-0.0.2.dist-info/RECORD +139 -0
  136. idmtools_test-0.0.2.dist-info/entry_points.txt +9 -0
  137. idmtools_test-0.0.2.dist-info/licenses/LICENSE.TXT +3 -0
  138. idmtools_test-0.0.0.dev0.dist-info/METADATA +0 -41
  139. idmtools_test-0.0.0.dev0.dist-info/RECORD +0 -5
  140. {idmtools_test-0.0.0.dev0.dist-info → idmtools_test-0.0.2.dist-info}/WHEEL +0 -0
  141. {idmtools_test-0.0.0.dev0.dist-info → idmtools_test-0.0.2.dist-info}/top_level.txt +0 -0
idmtools_test/inputs/custom/config.json ADDED
@@ -0,0 +1,943 @@
1
+ {
2
+ "parameters": {
3
+ "Acquisition_Blocking_Immunity_Decay_Rate": 0.01,
4
+ "Acquisition_Blocking_Immunity_Duration_Before_Decay": 90,
5
+ "Age_Dependent_Biting_Risk_Type": "SURFACE_AREA_DEPENDENT",
6
+ "Age_Initialization_Distribution_Type": "DISTRIBUTION_SIMPLE",
7
+ "Air_Migration_Filename": "",
8
+ "Air_Migration_Roundtrip_Duration": 0,
9
+ "Air_Migration_Roundtrip_Probability": 0,
10
+ "Air_Temperature_Filename": "Zambia_30arcsec_air_temperature_daily.bin",
11
+ "Air_Temperature_Offset": 0,
12
+ "Air_Temperature_Variance": 2,
13
+ "Anemia_Mortality_Inverse_Width": 150,
14
+ "Anemia_Mortality_Threshold": 1,
15
+ "Anemia_Severe_Inverse_Width": 100,
16
+ "Anemia_Severe_Threshold": 5,
17
+ "Animal_Reservoir_Type": "NO_ZOONOSIS",
18
+ "Antibody_CSP_Decay_Days": 90,
19
+ "Antibody_CSP_Killing_Inverse_Width": 1.5,
20
+ "Antibody_CSP_Killing_Threshold": 20,
21
+ "Antibody_Capacity_Growth_Rate": 0.09,
22
+ "Antibody_IRBC_Kill_Rate": 1.596,
23
+ "Antibody_Memory_Level": 0.34,
24
+ "Antibody_Stimulation_C50": 30,
25
+ "Antigen_Switch_Rate": 7.645570124964182e-10,
26
+ "Base_Air_Temperature": 27,
27
+ "Base_Gametocyte_Fraction_Male": 0.2,
28
+ "Base_Gametocyte_Mosquito_Survival_Rate": 0.002011099,
29
+ "Base_Gametocyte_Production_Rate": 0.06150582,
30
+ "Base_Incubation_Period": 7,
31
+ "Base_Individual_Sample_Rate": 1,
32
+ "Base_Infectious_Period": 180,
33
+ "Base_Infectivity": 1,
34
+ "Base_Land_Temperature": 27,
35
+ "Base_Mortality": 0,
36
+ "Base_Population_Scale_Factor": 1,
37
+ "Base_Rainfall": 10.0,
38
+ "Base_Relative_Humidity": 0.75,
39
+ "Base_Sporozoite_Survival_Fraction": 0.25,
40
+ "Birth_Rate_Dependence": "FIXED_BIRTH_RATE",
41
+ "Birth_Rate_Time_Dependence": "NONE",
42
+ "Campaign_Filename": "campaign.json",
43
+ "Climate_Model": "CLIMATE_BY_DATA",
44
+ "Climate_Update_Resolution": "CLIMATE_UPDATE_DAY",
45
+ "Clinical_Fever_Threshold_High": 1.5,
46
+ "Clinical_Fever_Threshold_Low": 0.5,
47
+ "Config_Name": "",
48
+ "Custom_Reports_Filename": "custom_reports.json",
49
+ "Cytokine_Gametocyte_Inactivation": 0.01667,
50
+ "Death_Rate_Dependence": "NONDISEASE_MORTALITY_BY_AGE_AND_GENDER",
51
+ "Default_Geography_Initial_Node_Population": 100,
52
+ "Default_Geography_Torus_Size": 10,
53
+ "Demographics_Filenames": [
54
+ "demo.json"
55
+ ],
56
+ "Disable_IP_Whitelist": 1,
57
+ "Egg_Hatch_Delay_Distribution": "NO_DELAY",
58
+ "Egg_Hatch_Density_Dependence": "NO_DENSITY_DEPENDENCE",
59
+ "Egg_Saturation_At_Oviposition": "SATURATION_AT_OVIPOSITION",
60
+ "Enable_Aging": 1,
61
+ "Enable_Air_Migration": 0,
62
+ "Enable_Birth": 1,
63
+ "Enable_Climate_Stochasticity": 0,
64
+ "Enable_Default_Reporting": 1,
65
+ "Enable_Demographics_Birth": 1,
66
+ "Enable_Demographics_Builtin": 0,
67
+ "Enable_Demographics_Gender": 1,
68
+ "Enable_Demographics_Initial": 1,
69
+ "Enable_Demographics_Other": 1,
70
+ "Enable_Demographics_Reporting": 0,
71
+ "Enable_Demographics_Risk": 0,
72
+ "Enable_Disease_Mortality": 0,
73
+ "Enable_Drought_Egg_Hatch_Delay": 0,
74
+ "Enable_Egg_Mortality": 0,
75
+ "Enable_Family_Migration": 0,
76
+ "Enable_Heterogeneous_Intranode_Transmission": 0,
77
+ "Enable_Immune_Decay": 1,
78
+ "Enable_Immunity": 1,
79
+ "Enable_Immunity_Distribution": 0,
80
+ "Enable_Immunity_Initialization_Distribution": 0,
81
+ "Enable_Initial_Prevalence": 1,
82
+ "Enable_Interventions": 1,
83
+ "Enable_Local_Migration": 1,
84
+ "Enable_Log_Throttling": 1,
85
+ "Enable_Maternal_Antibodies_Transmission": 1,
86
+ "Enable_Maternal_Infection_Transmission": 0,
87
+ "Enable_Maternal_Protection": 0,
88
+ "Enable_Maternal_Transmission": 0,
89
+ "Enable_Migration_Heterogeneity": 0,
90
+ "Enable_Natural_Mortality": 1,
91
+ "Enable_Nondisease_Mortality": 1,
92
+ "Enable_Property_Output": 0,
93
+ "Enable_Rainfall_Stochasticity": 1,
94
+ "Enable_Regional_Migration": 1,
95
+ "Enable_Sea_Demographics_Modifiers": 0,
96
+ "Enable_Sea_Family_Migration": 0,
97
+ "Enable_Sea_Migration": 0,
98
+ "Enable_Sexual_Combination": 0,
99
+ "Enable_Skipping": 0,
100
+ "Enable_Spatial_Output": 0,
101
+ "Enable_Superinfection": 1,
102
+ "Enable_Susceptibility_Scaling": 0,
103
+ "Enable_Temperature_Dependent_Egg_Hatching": 0,
104
+ "Enable_Temperature_Dependent_Feeding_Cycle": 0,
105
+ "Enable_Timestep_Channel_In_Report": 0,
106
+ "Enable_Vector_Aging": 0,
107
+ "Enable_Vector_Migration": 0,
108
+ "Enable_Vector_Migration_Human": 0,
109
+ "Enable_Vector_Migration_Local": 0,
110
+ "Enable_Vector_Migration_Regional": 0,
111
+ "Enable_Vector_Migration_Wind": 0,
112
+ "Enable_Vector_Mortality": 1,
113
+ "Enable_Vector_Species_Report": 1,
114
+ "Enable_Vital_Dynamics": 1,
115
+ "Erythropoiesis_Anemia_Effect": 3.5,
116
+ "Falciparum_MSP_Variants": 32,
117
+ "Falciparum_Nonspecific_Types": 76,
118
+ "Falciparum_PfEMP1_Variants": 1070,
119
+ "Family_Migration_Filename": "",
120
+ "Family_Migration_Roundtrip_Duration": 1.0,
121
+ "Fever_Detection_Threshold": 1,
122
+ "Fever_IRBC_Kill_Rate": 1.4,
123
+ "Fever_Mortality_Inverse_Width": 1000,
124
+ "Fever_Mortality_Threshold": 10,
125
+ "Fever_Severe_Inverse_Width": 30.323,
126
+ "Fever_Severe_Threshold": 3.8719,
127
+ "Gametocyte_Smear_Sensitivity": 0.1,
128
+ "Gametocyte_Stage_Survival_Rate": 0.588569307,
129
+ "Genome_Markers": [],
130
+ "Geography": "",
131
+ "HEG_Fecundity_Limiting": 0.0,
132
+ "HEG_Homing_Rate": 0.0,
133
+ "HEG_Model": "OFF",
134
+ "Human_Feeding_Mortality": 0.1,
135
+ "Immunity_Acquisition_Factor": 1,
136
+ "Immunity_Initialization_Distribution_Type": "DISTRIBUTION_OFF",
137
+ "Immunity_Mortality_Factor": 1,
138
+ "Immunity_Transmission_Factor": 1,
139
+ "Incubation_Period_Distribution": "FIXED_DURATION",
140
+ "Individual_Sampling_Type": "TRACK_ALL",
141
+ "Infection_Updates_Per_Timestep": 8,
142
+ "Infectious_Period_Distribution": "EXPONENTIAL_DURATION",
143
+ "Infectivity_Scale_Type": "CONSTANT_INFECTIVITY",
144
+ "Innate_Immune_Variation_Type": "NONE",
145
+ "Land_Temperature_Filename": "Zambia_30arcsec_air_temperature_daily.bin",
146
+ "Land_Temperature_Offset": 0,
147
+ "Land_Temperature_Variance": 2,
148
+ "Larval_Density_Dependence": "UNIFORM_WHEN_OVERPOPULATION",
149
+ "Listed_Events": [
150
+ "TestedPositive_47811",
151
+ "TestedNegative_76286",
152
+ "Received_Campaign_Drugs",
153
+ "TestedPositive_33839",
154
+ "TestedNegative_60576",
155
+ "TestedPositive_83798",
156
+ "TestedPositive_36525",
157
+ "Received_RCD_Drugs",
158
+ "TestedNegative_97232",
159
+ "TestedNegative_15428",
160
+ "TestedNegative_3352",
161
+ "TestedNegative_25411",
162
+ "TestedNegative_72899",
163
+ "TestedNegative_14048",
164
+ "TestedPositive_28006",
165
+ "TestedNegative_44207",
166
+ "TestedPositive_7881",
167
+ "TestedNegative_59380",
168
+ "TestedPositive_1946",
169
+ "TestedNegative_66395",
170
+ "TestedPositive_36424",
171
+ "TestedNegative_13474",
172
+ "TestedPositive_92478",
173
+ "TestedPositive_20095",
174
+ "TestedPositive_5227",
175
+ "TestedNegative_58574",
176
+ "TestedNegative_53042",
177
+ "TestedNegative_44962",
178
+ "TestedPositive_60909",
179
+ "TestedNegative_49062",
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+ "TestedNegative_72353",
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+ "TestedNegative_78805",
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+ "TestedPositive_81576",
183
+ "TestedPositive_43531",
184
+ "Received_IRS",
185
+ "TestedPositive_86245",
186
+ "TestedNegative_77400",
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+ "TestedNegative_80599",
188
+ "TestedPositive_63686",
189
+ "TestedPositive_20091",
190
+ "TestedPositive_93494",
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+ "TestedPositive_56297",
192
+ "TestedNegative_3813",
193
+ "TestedNegative_47153",
194
+ "TestedPositive_81632",
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+ "TestedNegative_82631",
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+ "TestedNegative_8337",
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+ "TestedPositive_70915",
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+ "TestedPositive_93855",
199
+ "TestedPositive_92926",
200
+ "TestedPositive_78965",
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+ "TestedNegative_41736",
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+ "TestedNegative_28401",
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+ "TestedNegative_58325",
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+ "TestedNegative_23389",
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+ "TestedPositive_19963",
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+ "TestedNegative_91820",
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+ "TestedPositive_74617",
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+ "TestedNegative_46595",
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+ "TestedNegative_28866",
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+ "TestedPositive_30913",
211
+ "TestedPositive_28809",
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+ "TestedNegative_56634",
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+ "TestedNegative_58753",
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+ "TestedPositive_57698",
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+ "Diagnostic_Survey_0",
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