his_emr_api_lab 1.1.21 → 1.1.22

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Files changed (81) hide show
  1. checksums.yaml +4 -4
  2. metadata +3 -82
  3. data/MIT-LICENSE +0 -20
  4. data/README.md +0 -71
  5. data/Rakefile +0 -32
  6. data/app/controllers/lab/application_controller.rb +0 -6
  7. data/app/controllers/lab/labels_controller.rb +0 -17
  8. data/app/controllers/lab/orders_controller.rb +0 -38
  9. data/app/controllers/lab/reasons_for_test_controller.rb +0 -9
  10. data/app/controllers/lab/results_controller.rb +0 -19
  11. data/app/controllers/lab/specimen_types_controller.rb +0 -15
  12. data/app/controllers/lab/test_result_indicators_controller.rb +0 -9
  13. data/app/controllers/lab/test_types_controller.rb +0 -15
  14. data/app/controllers/lab/tests_controller.rb +0 -26
  15. data/app/jobs/lab/application_job.rb +0 -4
  16. data/app/jobs/lab/push_order_job.rb +0 -12
  17. data/app/jobs/lab/update_patient_orders_job.rb +0 -32
  18. data/app/jobs/lab/void_order_job.rb +0 -17
  19. data/app/mailers/lab/application_mailer.rb +0 -6
  20. data/app/models/lab/application_record.rb +0 -5
  21. data/app/models/lab/lab_accession_number_counter.rb +0 -13
  22. data/app/models/lab/lab_encounter.rb +0 -7
  23. data/app/models/lab/lab_order.rb +0 -58
  24. data/app/models/lab/lab_result.rb +0 -31
  25. data/app/models/lab/lab_test.rb +0 -19
  26. data/app/models/lab/lims_failed_import.rb +0 -4
  27. data/app/models/lab/lims_order_mapping.rb +0 -10
  28. data/app/serializers/lab/lab_order_serializer.rb +0 -55
  29. data/app/serializers/lab/result_serializer.rb +0 -36
  30. data/app/serializers/lab/test_serializer.rb +0 -29
  31. data/app/services/lab/accession_number_service.rb +0 -77
  32. data/app/services/lab/concepts_service.rb +0 -82
  33. data/app/services/lab/labelling_service/order_label.rb +0 -106
  34. data/app/services/lab/lims/api/blackhole_api.rb +0 -21
  35. data/app/services/lab/lims/api/couchdb_api.rb +0 -53
  36. data/app/services/lab/lims/api/mysql_api.rb +0 -316
  37. data/app/services/lab/lims/api/rest_api.rb +0 -416
  38. data/app/services/lab/lims/api/ws_api.rb +0 -121
  39. data/app/services/lab/lims/api_factory.rb +0 -19
  40. data/app/services/lab/lims/config.rb +0 -100
  41. data/app/services/lab/lims/exceptions.rb +0 -11
  42. data/app/services/lab/lims/migrator.rb +0 -216
  43. data/app/services/lab/lims/order_dto.rb +0 -105
  44. data/app/services/lab/lims/order_serializer.rb +0 -244
  45. data/app/services/lab/lims/pull_worker.rb +0 -289
  46. data/app/services/lab/lims/push_worker.rb +0 -149
  47. data/app/services/lab/lims/utils.rb +0 -91
  48. data/app/services/lab/lims/worker.rb +0 -86
  49. data/app/services/lab/metadata.rb +0 -24
  50. data/app/services/lab/orders_search_service.rb +0 -66
  51. data/app/services/lab/orders_service.rb +0 -212
  52. data/app/services/lab/results_service.rb +0 -147
  53. data/app/services/lab/tests_service.rb +0 -93
  54. data/config/routes.rb +0 -17
  55. data/db/migrate/20210126092910_create_lab_lab_accession_number_counters.rb +0 -12
  56. data/db/migrate/20210310115457_create_lab_lims_order_mappings.rb +0 -15
  57. data/db/migrate/20210323080140_change_lims_id_to_string_in_lims_order_mapping.rb +0 -15
  58. data/db/migrate/20210326195504_add_order_revision_to_lims_order_mapping.rb +0 -5
  59. data/db/migrate/20210407071728_create_lab_lims_failed_imports.rb +0 -19
  60. data/db/migrate/20210610095024_fix_numeric_results_value_type.rb +0 -20
  61. data/db/migrate/20210807111531_add_default_to_lims_order_mapping.rb +0 -7
  62. data/lib/auto12epl.rb +0 -201
  63. data/lib/couch_bum/couch_bum.rb +0 -92
  64. data/lib/generators/lab/install/USAGE +0 -9
  65. data/lib/generators/lab/install/install_generator.rb +0 -19
  66. data/lib/generators/lab/install/templates/rswag-ui-lab.rb +0 -5
  67. data/lib/generators/lab/install/templates/start_worker.rb +0 -32
  68. data/lib/generators/lab/install/templates/swagger.yaml +0 -714
  69. data/lib/his_emr_api_lab.rb +0 -5
  70. data/lib/lab/engine.rb +0 -15
  71. data/lib/lab/version.rb +0 -5
  72. data/lib/logger_multiplexor.rb +0 -38
  73. data/lib/tasks/lab_tasks.rake +0 -25
  74. data/lib/tasks/loaders/data/reasons-for-test.csv +0 -7
  75. data/lib/tasks/loaders/data/test-measures.csv +0 -225
  76. data/lib/tasks/loaders/data/tests.csv +0 -161
  77. data/lib/tasks/loaders/loader_mixin.rb +0 -53
  78. data/lib/tasks/loaders/metadata_loader.rb +0 -26
  79. data/lib/tasks/loaders/reasons_for_test_loader.rb +0 -23
  80. data/lib/tasks/loaders/specimens_loader.rb +0 -65
  81. data/lib/tasks/loaders/test_result_indicators_loader.rb +0 -54
data/lib/lab/engine.rb DELETED
@@ -1,15 +0,0 @@
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- if Rails.env == 'test'
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- require 'rswag/ui'
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- require 'rswag/api'
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- end
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-
6
- module Lab
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- class Engine < ::Rails::Engine
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- isolate_namespace Lab
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- config.generators.api_only = true
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-
11
- config.generators do |g|
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- g.test_framework :rspec
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- end
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- end
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- end
data/lib/lab/version.rb DELETED
@@ -1,5 +0,0 @@
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- # frozen_string_literal: true
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-
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- module Lab
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- VERSION = '1.1.21'
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- end
data/lib/logger_multiplexor.rb DELETED
@@ -1,38 +0,0 @@
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- # frozen_string_literal: true
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-
3
- ##
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- # Log to multiple streams.
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- #
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- # The 'logger' module does not provide a logger that can log
7
- # to multiple streams at once hence this hack. This class
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- # bundles multiple loggers so that they can be treated as
9
- # one.
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- #
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- # Example:
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- # >>> logger = LoggerMultiplexor.new(STDOUT, 'development.log')
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- # >>> logger.info('Hello') # Logs 'Hello' to both streams
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- class LoggerMultiplexor
15
- def initialize(*loggers)
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- @loggers = loggers.map do |stream|
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- if stream.is_a?(Logger) || stream.is_a?(LoggerMultiplexor)
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- stream
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- else
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- Logger.new(stream)
21
- end
22
- end
23
- end
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-
25
- def method_missing(method_name, *args)
26
- if respond_to_missing?(method_name)
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- @loggers.each { |logger| logger.send(method_name, *args) }
28
- else
29
- super
30
- end
31
- end
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-
33
- def respond_to_missing?(method_name)
34
- @loggers.all? do |logger|
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- logger.respond_to?(method_name)
36
- end
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- end
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- end
data/lib/tasks/lab_tasks.rake DELETED
@@ -1,25 +0,0 @@
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- desc 'Generate openapi/swagger documentation template in engine'
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- task :swag, ['app:rswag:specs:swaggerize'] do
3
- source = 'spec/dummy/swagger/v1/swagger.yaml'
4
- destination = 'lib/generators/lab/install/templates/swagger.yaml'
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-
6
- FileUtils.copy(source, destination)
7
- end
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-
9
- namespace :lab do
10
- desc 'Install Lab engine into container application'
11
- task :install do
12
- sh 'rails generate lab:install'
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- sh 'rake lab:install:migrations'
14
- end
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-
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- desc 'Uninstall Lab engine from container application'
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- task :uninstall do
18
- sh 'rails destroy lab:install'
19
- end
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-
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- desc 'Load Lab metadata into database'
22
- task :load_metadata do
23
- sh "rails r #{__dir__}/loaders/metadata_loader.rb"
24
- end
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- end
data/lib/tasks/loaders/data/reasons-for-test.csv DELETED
@@ -1,7 +0,0 @@
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- "reason_name"
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- "Routine"
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- "Repeat / Missing"
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- "Targeted"
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- "Confirmatory"
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- "Stat"
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- "Other"
data/lib/tasks/loaders/data/test-measures.csv DELETED
@@ -1,225 +0,0 @@
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- "test_name","measure_name"
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- "TB Microscopic Exam","tb"
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- "GeneXpert","MTB"
4
- "GeneXpert","RIF Resistance"
5
- "Gram Stain","Gram"
6
- "Gram Stain","Clue cells"
7
- "Gram Stain","Other organism seen"
8
- "Culture & Sensitivity","Culture"
9
- "Cell Count","WBC"
10
- "Cell Count","RBC"
11
- "India Ink","India ink"
12
- "Differential","Polymorphs"
13
- "Differential","Lymphocytes"
14
- "Differential","Diff remarks"
15
- "ZN Stain","ZN"
16
- "Wet prep","wet prep"
17
- "Wet prep","Other organism seen"
18
- "TB Tests","Macro exam"
19
- "TB Tests","Smear microscopy result"
20
- "TB Tests","Gene Xpert MTB"
21
- "TB Tests","Gene Xpert RIF Resistance"
22
- "TB Tests","HIV Status"
23
- "TB Tests","Reason For Testing"
24
- "TB Tests","Indication for GeneXpert Test"
25
- "Urine Macroscopy","Colour"
26
- "Urine Macroscopy","Appearance"
27
- "Urine Microscopy","WBC"
28
- "Urine Microscopy","RBC"
29
- "Urine Microscopy","Epithelial cells"
30
- "Urine Microscopy","Casts"
31
- "Urine Microscopy","Crystals"
32
- "Urine Microscopy","Parasites"
33
- "Urine Microscopy","Yeast cells"
34
- "Urine Chemistries","pH"
35
- "Urine Chemistries","Blood"
36
- "Urine Chemistries","Urobilinogen"
37
- "Urine Chemistries","Bilirubin"
38
- "Urine Chemistries","Protein"
39
- "Urine Chemistries","Nitrate"
40
- "Urine Chemistries","Ketones"
41
- "Urine Chemistries","Glucose"
42
- "Urine Chemistries","Specific gravity"
43
- "Urine Chemistries","Leucocytes"
44
- "Stool Analysis","Macroscopy"
45
- "Stool Analysis","Consistency"
46
- "Stool Analysis","Microscopy"
47
- "Malaria Screening","Blood film"
48
- "Malaria Screening","Malaria Species"
49
- "Malaria Screening","MRDT"
50
- "Blood Parasites Screen","Blood film"
51
- "Semen Analysis","Progressive motility"
52
- "Semen Analysis","Non-progressive motility"
53
- "Semen Analysis","Immotility"
54
- "Semen Analysis","Appearance"
55
- "Semen Analysis","Liquifaction time"
56
- "Semen Analysis","volume"
57
- "Semen Analysis","pH"
58
- "Semen Analysis","Sperm count"
59
- "Semen Analysis","Sperm morphology"
60
- "HVS analysis","Macroscopy"
61
- "HVS analysis","WBC"
62
- "HVS analysis","Epithelial cells"
63
- "HVS analysis","Parasites/Bacteria"
64
- "HVS analysis","Spermatozoa"
65
- "Syphilis Test","RPR"
66
- "Syphilis Test","VDRL"
67
- "Syphilis Test","TPHA"
68
- "Hepatitis B Test","Hepatitis B"
69
- "Hepatitis C Test","Hepatitis C"
70
- "Rheumatoid Factor Test","Rheumatoid Factor"
71
- "CrAg","CrAg"
72
- "Cryptococcus Antigen Test","CrAg"
73
- "Anti Streptolysis O","ASO"
74
- "C-reactive protein","CRP"
75
- "Measles","Measles IgM ELISA-Behring enzygnost"
76
- "Rubella","Rubella IgM ELISA-Behring enzynost"
77
- "CD4","CD4 Count"
78
- "CD4","CD4 %"
79
- "CD4","Lymphocyte Count"
80
- "CD4","CD8 Count"
81
- "CD4","CD3 Count"
82
- "ABO Blood Grouping","Grouping"
83
- "Cross-match","Pack No."
84
- "Cross-match","Pack ABO Group"
85
- "Cross-match","Product Type"
86
- "Cross-match","Expiry Date"
87
- "Cross-match","Volume"
88
- "Cross-match","Cross-match Method"
89
- "Transfusion Outcome","Outcome"
90
- "Liver Function Tests","ALT/GPT"
91
- "Liver Function Tests","AST/GOT"
92
- "Liver Function Tests","Alkaline Phosphate(ALP)"
93
- "Liver Function Tests","GGT/r-GT"
94
- "Liver Function Tests","Bilirubin Direct(BID)"
95
- "Liver Function Tests","Bilirubin Total(BIT))"
96
- "Liver Function Tests","Albumin(ALB)"
97
- "Liver Function Tests","Total Protein(PRO)"
98
- "Renal Function Test","Urea"
99
- "Renal Function Test","Creatinine"
100
- "Lipogram","Triglycerides(TG)"
101
- "Lipogram","Cholestero l(CHOL)"
102
- "Lipogram","HDL Direct (HDL-C)"
103
- "Lipogram","LDL Direct (LDL-C)"
104
- "FBC","WBC"
105
- "FBC","RBC"
106
- "FBC","HGB"
107
- "FBC","HCT"
108
- "FBC","MCV"
109
- "FBC","MCH"
110
- "FBC","MCHC"
111
- "FBC","PLT"
112
- "FBC","RDW-SD"
113
- "FBC","RDW-CV"
114
- "FBC","PDW"
115
- "FBC","MPV"
116
- "FBC","PCT"
117
- "FBC","NEUT%"
118
- "FBC","LYMPH%"
119
- "FBC","MONO%"
120
- "FBC","EO%"
121
- "FBC","BASO%"
122
- "FBC","NEUT#"
123
- "FBC","LYMPH#"
124
- "FBC","MONO#"
125
- "FBC","EO#"
126
- "FBC","BASO#"
127
- "FBC","Mid#"
128
- "FBC","Gran#"
129
- "FBC","Mid%"
130
- "FBC","Gran%"
131
- "FBC","EOS%"
132
- "FBC","P-LCC"
133
- "FBC","P-LCR"
134
- "Electrolytes","K"
135
- "Electrolytes","Na"
136
- "Electrolytes","Cl"
137
- "Enzymes","a-AMYLASE-H"
138
- "Enzymes","ALT-H"
139
- "Enzymes","AST-H"
140
- "Enzymes","ALP-H"
141
- "Enzymes","TP-H"
142
- "Enzymes","TC-H"
143
- "Enzymes","UREA-H"
144
- "Enzymes","GLU-O-H"
145
- "Enzymes","TBIL-DSA-H"
146
- "Enzymes","DBIL-DSA-H"
147
- "Enzymes","UA-H"
148
- "Enzymes","TG-H"
149
- "Enzymes","ALB-H"
150
- "Glucose","Glucose"
151
- "Prothrombin Time","PT"
152
- "APTT","APTT"
153
- "INR","INR"
154
- "ESR","ESR"
155
- "Sickling Test","Sickling Screen"
156
- "Pregnancy Test","Pregnancy Test"
157
- "Manual Differential & Cell Morphology","Nucleated Red Cells"
158
- "Manual Differential & Cell Morphology","Neutrophils"
159
- "Manual Differential & Cell Morphology","Lymphocytes"
160
- "Manual Differential & Cell Morphology","Monocytes"
161
- "Manual Differential & Cell Morphology","Eosinophils"
162
- "Manual Differential & Cell Morphology","Basophils"
163
- "Manual Differential & Cell Morphology","Promyelocytes"
164
- "Manual Differential & Cell Morphology","Myelocytes"
165
- "Manual Differential & Cell Morphology","Metamyelocytes"
166
- "Manual Differential & Cell Morphology","Band/Staff Forms"
167
- "Manual Differential & Cell Morphology","Blasts"
168
- "Manual Differential & Cell Morphology","Other"
169
- "Manual Differential & Cell Morphology","RBC Comments"
170
- "Manual Differential & Cell Morphology","WBC Comments"
171
- "Manual Differential & Cell Morphology","Platelet Comments"
172
- "Manual Differential & Cell Morphology","Interpretative Comments"
173
- "Manual Differential & Cell Morphology","Attempted/ Differential Diagnosis"
174
- "Manual Differential & Cell Morphology","Further Tests"
175
- "Pancreatic Function Test","Amylase"
176
- "Pancreatic Function Test","Lipase"
177
- "Direct Coombs Test","Direct Coombs Test"
178
- "Calcium","Ca"
179
- "Phosphorus","P"
180
- "Magnesium","Mg"
181
- "Creatinine Kinase","CK"
182
- "Uric Acid","UA"
183
- "ESBL Test","ESBL"
184
- "ESBL Test","Cefotaxime"
185
- "ESBL Test","Cefotaxime + Clavulanate"
186
- "ESBL Test","Ceftazidime"
187
- "ESBL Test","Ceftazidime + Clavulanate"
188
- "ESBL Test","Cefepime"
189
- "ESBL Test","Cefepime + clavulanate"
190
- "APTT Ratio","APTT Ratio"
191
- "Fibronogen","Fibronogen"
192
- "50:50 Normal Plasma","50:50 Normal Plasma"
193
- "50:50 Mix FVIII Deficient","50:50 Mix FVIII Deficient"
194
- "50:50 Mix F-IX Deficient","50:50 Mix F-IX Deficient"
195
- "Factor VIII Assay","Factor VIII Assay"
196
- "Factor IX Assay","Factor IX Assay"
197
- "TT","TT"
198
- "Coagulation Assay","PT"
199
- "Coagulation Assay","INR"
200
- "Coagulation Assay","APTT"
201
- "Coagulation Assay","APTT Ratio"
202
- "Coagulation Assay","TT"
203
- "Coagulation Assay","Fibronogen"
204
- "Coagulation Assay","50:50 Mix Normal Plasma"
205
- "Coagulation Assay","50:50 Mix FVIII Deficient"
206
- "Coagulation Assay","50:50 Mix F-IX Deficient"
207
- "Coagulation Assay","Factor IX Assay"
208
- "Coagulation Assay","Factor VIII Assay"
209
- "Cardiac Function Tests","Creatine Kinase MB(CKMB)"
210
- "Cardiac Function Tests","Creatine Kinase(CKN)"
211
- "Cardiac Function Tests","Lactatedehydrogenase(LDH)"
212
- "Minerals","Calcium (CA)"
213
- "Minerals","Phosphorus (PHOS)"
214
- "Minerals","Magnesium (MGXB)"
215
- "BioMarkers","C-reactive Protein (CRP)"
216
- "BioMarkers","Rheumatoid Factor (RF)"
217
- "BioMarkers","Antistreptolysin O (ASO)"
218
- "Iron Studies","Iron"
219
- "Iron Studies","UIBC"
220
- "HbA1c","HbA1c"
221
- "Microalbumin","MAL"
222
- "Microprotein","MPR"
223
- "Von Willebrand Factor","Von Willebrand (Antigen)"
224
- "Von Willebrand Factor","Von Willebrand (Activity)"
225
- "Viral Load","Viral Load"
data/lib/tasks/loaders/data/tests.csv DELETED
@@ -1,161 +0,0 @@
1
- specimen_name,test_name,created_at
2
- Sputum,"TB Microscopic Exam","2019-11-19 14:05:31"
3
- Sputum,GeneXpert,"2019-11-19 14:05:31"
4
- Sputum,"Gram Stain","2019-11-19 14:05:31"
5
- Sputum,"Culture & Sensitivity","2019-11-19 14:05:31"
6
- Sputum,Differential,"2019-11-19 14:05:31"
7
- Sputum,"TB Tests","2019-11-19 14:05:31"
8
- CSF,"Gram Stain","2019-11-19 14:05:31"
9
- CSF,"Culture & Sensitivity","2019-11-19 14:05:31"
10
- CSF,"Cell Count","2019-11-19 14:05:31"
11
- CSF,"India Ink","2019-11-19 14:05:31"
12
- CSF,Differential,"2019-11-19 14:05:31"
13
- CSF,"ZN Stain","2019-11-19 14:05:31"
14
- CSF,"TB Tests","2019-11-19 14:05:31"
15
- CSF,"ESBL Test","2019-11-19 14:05:31"
16
- CSF,CrAg,"2019-11-19 14:05:31"
17
- Blood,"Gram Stain","2019-11-19 14:05:31"
18
- Blood,"Culture & Sensitivity","2019-11-19 14:05:31"
19
- Blood,"Malaria Screening","2019-11-19 14:05:31"
20
- Blood,"Blood Parasites Screen","2019-11-19 14:05:31"
21
- Blood,"Syphilis Test","2019-11-19 14:05:31"
22
- Blood,"Hepatitis B Test","2019-11-19 14:05:31"
23
- Blood,"Hepatitis C Test","2019-11-19 14:05:31"
24
- Blood,"Rheumatoid Factor Test","2019-11-19 14:05:31"
25
- Blood,"Cryptococcus Antigen Test","2019-11-19 14:05:31"
26
- Blood,"Anti Streptolysis O","2019-11-19 14:05:31"
27
- Blood,"C-reactive protein","2019-11-19 14:05:31"
28
- Blood,Measles,"2019-11-19 14:05:31"
29
- Blood,Rubella,"2019-11-19 14:05:31"
30
- Blood,CD4,"2019-11-19 14:05:31"
31
- Blood,"ABO Blood Grouping","2019-11-19 14:05:31"
32
- Blood,Cross-match,"2019-11-19 14:05:31"
33
- Blood,"Transfusion Outcome","2019-11-19 14:05:31"
34
- Blood,"Liver Function Tests","2019-11-19 14:05:31"
35
- Blood,"Renal Function Test","2019-11-19 14:05:31"
36
- Blood,Lipogram,"2019-11-19 14:05:31"
37
- Blood,FBC,"2019-11-19 14:05:31"
38
- Blood,"FBS","2021-04-11 00:00:00"
39
- Blood,Electrolytes,"2019-11-19 14:05:31"
40
- Blood,Enzymes,"2019-11-19 14:05:31"
41
- Blood,Glucose,"2019-11-19 14:05:31"
42
- Blood,"Prothrombin Time","2019-11-19 14:05:31"
43
- Blood,APTT,"2019-11-19 14:05:31"
44
- Blood,INR,"2019-11-19 14:05:31"
45
- Blood,ESR,"2019-11-19 14:05:31"
46
- Blood,"D/Coombs","2021-04-11 00:00:00"
47
- Blood,"creat","2021-04-11 00:00:00"
48
- Blood,"Widal","2021-04-11 00:00:00"
49
- Blood,"AAFB (3rd)","2021-04-11 00:00:00"
50
- Blood,"Urine micro","2021-04-11 00:00:00"
51
- Blood,"AAFB (1st)","2021-04-11 00:00:00"
52
- Blood,ASOT,"2021-04-11 00:00:00"
53
- Blood,"Blood C/S","2021-04-11 00:00:00"
54
- Blood,"Cryptococcal Ag","2021-04-11 00:00:00"
55
- Blood,"I/Ink","2021-04-11 00:00:00"
56
- Blood,"Prot& Sugar","2021-04-11 00:00:00"
57
- Blood,C_S,"2021-04-11 00:00:00"
58
- Blood,hep,"2021-04-11 00:00:00"
59
- Blood,"Cryptococcal Antigen","2021-04-11 00:00:00"
60
- Blood,Resistance,"2021-04-11 00:00:00"
61
- Blood,Sickle,"2021-04-11 00:00:00"
62
- Blood,"Sickling Test","2019-11-19 14:05:31"
63
- Blood,"Manual Differential & Cell Morphology","2019-11-19 14:05:31"
64
- Blood,"Pancreatic Function Test","2019-11-19 14:05:31"
65
- Blood,"Direct Coombs Test","2019-11-19 14:05:31"
66
- Blood,Calcium,"2019-11-19 14:05:31"
67
- Blood,Phosphorus,"2019-11-19 14:05:31"
68
- Blood,Magnesium,"2019-11-19 14:05:31"
69
- Blood,"Creatinine Kinase","2019-11-19 14:05:31"
70
- Blood,"Uric Acid","2019-11-19 14:05:31"
71
- Blood,"ESBL Test","2019-11-19 14:05:31"
72
- Blood,"APTT Ratio","2019-11-19 14:05:31"
73
- Blood,Fibronogen,"2019-11-19 14:05:31"
74
- Blood,"50:50 Normal Plasma","2019-11-19 14:05:31"
75
- Blood,"50:50 Mix FVIII Deficient","2019-11-19 14:05:31"
76
- Blood,"50:50 Mix F-IX Deficient","2019-11-19 14:05:31"
77
- Blood,"Factor VIII Assay","2019-11-19 14:05:31"
78
- Blood,"Factor IX Assay","2019-11-19 14:05:31"
79
- Blood,TT,"2019-11-19 14:05:31"
80
- Blood,"Coagulation Assay","2019-11-19 14:05:31"
81
- Blood,"Cardiac Function Tests","2019-11-19 14:05:31"
82
- Blood,Minerals,"2019-11-19 14:05:31"
83
- Blood,BioMarkers,"2019-11-19 14:05:31"
84
- Blood,"Iron Studies","2019-11-19 14:05:31"
85
- Blood,HbA1c,"2019-11-19 14:05:31"
86
- Blood,Microalbumin,"2019-11-19 14:05:31"
87
- Blood,Microprotein,"2019-11-19 14:05:31"
88
- Blood,"Von Willebrand Factor","2019-11-19 14:05:31"
89
- Blood,"Viral Load","2019-11-19 14:05:31"
90
- Blood,"Urine Lam","2019-11-19 14:05:31"
91
- Blood,"Protein and Sugar","2021-04-16"
92
- Blood,"White cell count","2021-04-16"
93
- Blood,Urea,"2019-11-19 14:05:31"
94
- Blood,Creatinine,"2019-11-19 14:05:31"
95
- Blood,ALT,"2019-11-19 14:05:31"
96
- Blood,AST,"2019-11-19 14:05:31"
97
- "Pleural Fluid","Gram Stain","2019-11-19 14:05:31"
98
- "Pleural Fluid","Culture & Sensitivity","2019-11-19 14:05:31"
99
- "Pleural Fluid","Cell Count","2019-11-19 14:05:31"
100
- "Pleural Fluid",Differential,"2019-11-19 14:05:31"
101
- "Pleural Fluid","ZN Stain","2019-11-19 14:05:31"
102
- "Pleural Fluid","TB Tests","2019-11-19 14:05:31"
103
- "Pleural Fluid","ESBL Test","2019-11-19 14:05:31"
104
- "Ascitic Fluid","Gram Stain","2019-11-19 14:05:31"
105
- "Ascitic Fluid","Culture & Sensitivity","2019-11-19 14:05:31"
106
- "Ascitic Fluid","Cell Count","2019-11-19 14:05:31"
107
- "Ascitic Fluid",Differential,"2019-11-19 14:05:31"
108
- "Ascitic Fluid","ZN Stain","2019-11-19 14:05:31"
109
- "Ascitic Fluid","TB Tests","2019-11-19 14:05:31"
110
- "Ascitic Fluid","ESBL Test","2019-11-19 14:05:31"
111
- "Pericardial Fluid","Gram Stain","2019-11-19 14:05:31"
112
- "Pericardial Fluid","Culture & Sensitivity","2019-11-19 14:05:31"
113
- "Pericardial Fluid","Cell Count","2019-11-19 14:05:31"
114
- "Pericardial Fluid",Differential,"2019-11-19 14:05:31"
115
- "Pericardial Fluid","ZN Stain","2019-11-19 14:05:31"
116
- "Pericardial Fluid","TB Tests","2019-11-19 14:05:31"
117
- "Pericardial Fluid","ESBL Test","2019-11-19 14:05:31"
118
- "Peritoneal Fluid","Gram Stain","2019-11-19 14:05:31"
119
- "Peritoneal Fluid","Culture & Sensitivity","2019-11-19 14:05:31"
120
- "Peritoneal Fluid","Cell Count","2019-11-19 14:05:31"
121
- "Peritoneal Fluid",Differential,"2019-11-19 14:05:31"
122
- "Peritoneal Fluid","ZN Stain","2019-11-19 14:05:31"
123
- "Peritoneal Fluid","TB Tests","2019-11-19 14:05:31"
124
- "Peritoneal Fluid","ESBL Test","2019-11-19 14:05:31"
125
- HVS,"Gram Stain","2019-11-19 14:05:31"
126
- HVS,"Culture & Sensitivity","2019-11-19 14:05:31"
127
- HVS,"Wet prep","2019-11-19 14:05:31"
128
- HVS,"HVS analysis","2019-11-19 14:05:31"
129
- HVS,"ESBL Test","2019-11-19 14:05:31"
130
- Swabs,"Gram Stain","2019-11-19 14:05:31"
131
- Swabs,"Culture & Sensitivity","2019-11-19 14:05:31"
132
- Swabs,"Wet prep","2019-11-19 14:05:31"
133
- Swabs,"ESBL Test","2019-11-19 14:05:31"
134
- Pus,"Gram Stain","2019-11-19 14:05:31"
135
- Pus,"Culture & Sensitivity","2019-11-19 14:05:31"
136
- Pus,"TB Tests","2019-11-19 14:05:31"
137
- Pus,"ESBL Test","2019-11-19 14:05:31"
138
- Stool,"Gram Stain","2019-11-19 14:05:31"
139
- Stool,"Culture & Sensitivity","2019-11-19 14:05:31"
140
- Stool,"Stool Analysis","2019-11-19 14:05:31"
141
- Urine,"Gram Stain","2019-11-19 14:05:31"
142
- Urine,"Culture & Sensitivity","2019-11-19 14:05:31"
143
- Urine,"Urine Macroscopy","2019-11-19 14:05:31"
144
- Urine,"Urine Microscopy","2019-11-19 14:05:31"
145
- Urine,"Urine Chemistries","2019-11-19 14:05:31"
146
- Urine,"Pregnancy Test","2019-11-19 14:05:31"
147
- Urine,"ESBL Test","2019-11-19 14:05:31"
148
- Urine,"Urine Lam","2019-11-19 14:05:31"
149
- Urine,"Urine Dipstick","2019-11-19 14:05:31"
150
- Other,"Gram Stain","2019-11-19 14:05:31"
151
- Other,"Culture & Sensitivity","2019-11-19 14:05:31"
152
- Other,"Cell Count","2019-11-19 14:05:31"
153
- Other,"ZN Stain","2019-11-19 14:05:31"
154
- Swab,"Culture & Sensitivity","2019-11-19 14:05:31"
155
- Swab,"Semen Analysis","2019-11-19 14:05:31"
156
- Plasma,"Gram Stain","2019-11-19 14:05:31"
157
- Plasma,"Culture & Sensitivity","2019-11-19 14:05:31"
158
- Plasma,"Cell Count","2019-11-19 14:05:31"
159
- Plasma,"ZN Stain","2019-11-19 14:05:31"
160
- "DBS (Free drop to DBS card)","Viral Load","2019-11-19 14:05:31"
161
- "DBS (Using capillary tube)","Viral Load","2019-11-19 14:05:31"
data/lib/tasks/loaders/loader_mixin.rb DELETED
@@ -1,53 +0,0 @@
1
- # frozen_string_literal: true
2
-
3
- module Lab
4
- module Loaders
5
- module LoaderMixin
6
- def self.included(_mod)
7
- User.current = User.find_by_username('admin') || User.first
8
- Location.current = Location.find_by_name('Registration') || Location.first
9
- end
10
-
11
- CONCEPT_DATATYPE_CODED = 2
12
- CONCEPT_CLASS_TEST = 1
13
-
14
- def find_or_create_concept(name, is_set: false)
15
- # Filter out concept_names with voided concepts
16
- concept = ConceptName.joins(:concept).find_by_name(name)
17
- return concept if concept
18
-
19
- ConceptName.create!(
20
- concept: Concept.create!(
21
- short_name: name,
22
- datatype_id: CONCEPT_DATATYPE_CODED,
23
- class_id: CONCEPT_CLASS_TEST,
24
- is_set: is_set,
25
- uuid: SecureRandom.uuid,
26
- creator: User.current.user_id,
27
- date_created: Time.now
28
- ),
29
- name: name,
30
- locale: 'en',
31
- concept_name_type: 'FULLY_SPECIED',
32
- uuid: SecureRandom.uuid,
33
- creator: User.current.user_id,
34
- date_created: Time.now
35
- )
36
- end
37
-
38
- def add_concept_to_set(set_concept_id:, concept_id:)
39
- set = ConceptSet.find_by(concept_set: set_concept_id, concept_id: concept_id)
40
- return set if set
41
-
42
- ConceptSet.create!(concept_set: set_concept_id,
43
- concept_id: concept_id,
44
- creator: User.current.user_id,
45
- date_created: Time.now)
46
- end
47
-
48
- def data_path(filename)
49
- "#{__dir__}/data/#{filename}"
50
- end
51
- end
52
- end
53
- end
data/lib/tasks/loaders/metadata_loader.rb DELETED
@@ -1,26 +0,0 @@
1
- # frozen_string_literal: true
2
-
3
- require_relative 'reasons_for_test_loader'
4
- require_relative 'specimens_loader'
5
- require_relative 'test_result_indicators_loader'
6
-
7
- module Lab
8
- module Loaders
9
- module MetadataLoader
10
- def self.load
11
- unless Program.where(name: 'Laboratory program').exists?
12
- Program.create(name: 'Laboratory program',
13
- description: 'Manage Lab information',
14
- creator: 1,
15
- uuid: SecureRandom.uuid)
16
- end
17
-
18
- SpecimensLoader.load
19
- TestResultIndicatorsLoader.load
20
- ReasonsForTestLoader.load
21
- end
22
- end
23
- end
24
- end
25
-
26
- Lab::Loaders::MetadataLoader.load
data/lib/tasks/loaders/reasons_for_test_loader.rb DELETED
@@ -1,23 +0,0 @@
1
- # frozen_string_literal: true
2
-
3
- require_relative './loader_mixin'
4
-
5
- module Lab
6
- module Loaders
7
- module ReasonsForTestLoader
8
- class << self
9
- include LoaderMixin
10
-
11
- def load
12
- CSV.open(data_path('reasons-for-test.csv'), headers: :first_row) do |csv|
13
- csv.each do |row|
14
- puts "Adding reason for test: #{row['reason_name']}"
15
- add_concept_to_set(set_concept_id: find_or_create_concept(Lab::Metadata::REASON_FOR_TEST_CONCEPT_NAME).concept_id,
16
- concept_id: find_or_create_concept(row['reason_name']).concept_id)
17
- end
18
- end
19
- end
20
- end
21
- end
22
- end
23
- end
data/lib/tasks/loaders/specimens_loader.rb DELETED
@@ -1,65 +0,0 @@
1
- # frozen_string_literal: true
2
-
3
- require 'csv'
4
- require_relative './loader_mixin'
5
-
6
- module Lab
7
- module Loaders
8
- ##
9
- # Load specimens and their tests into the database
10
- module SpecimensLoader
11
- class << self
12
- include LoaderMixin
13
-
14
- def load
15
- puts "------- Loading tests and specimens ---------"
16
- CSV.open(data_path('tests.csv'), headers: :first_row) do |csv|
17
- csv.each_with_object({}) do |row, test_types|
18
- specimen_name = row['specimen_name']
19
- test_name = row['test_name']
20
-
21
- ActiveRecord::Base.transaction do
22
- test_type = test_types[test_name] || create_test_type(test_name)
23
- create_specimen_type(specimen_name, test_type)
24
-
25
- test_types[test_name] ||= test_type
26
- end
27
-
28
- puts "Created test #{test_name} <--< #{specimen_name}"
29
- rescue StandardError => e
30
- puts "Error: #{test_name}: #{e}"
31
- end
32
- end
33
- end
34
-
35
- def test_type_concept_id
36
- find_or_create_concept(Lab::Metadata::TEST_TYPE_CONCEPT_NAME).concept_id
37
- end
38
-
39
- def specimen_type_concept_id
40
- find_or_create_concept(Lab::Metadata::SPECIMEN_TYPE_CONCEPT_NAME).concept_id
41
- end
42
-
43
-
44
- def create_test_type(name)
45
- concept_id = find_or_create_concept(name, is_set: true).concept_id
46
-
47
- add_concept_to_set(set_concept_id: test_type_concept_id, concept_id: concept_id)
48
- rescue StandardError => e
49
- raise "Failed to create test type `#{name}`: #{e}"
50
- end
51
-
52
- def create_specimen_type(name, test_type)
53
- concept_id = find_or_create_concept(name).concept_id
54
-
55
- [
56
- add_concept_to_set(set_concept_id: specimen_type_concept_id, concept_id: concept_id),
57
- add_concept_to_set(set_concept_id: test_type.concept_id, concept_id: concept_id)
58
- ]
59
- rescue StandardError => e
60
- raise "Failed to create specimen type `#{name}`: #{e}"
61
- end
62
- end
63
- end
64
- end
65
- end