mahis_emr_api_lab 1.2.0
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- checksums.yaml +7 -0
- data/MIT-LICENSE +20 -0
- data/README.md +71 -0
- data/Rakefile +32 -0
- data/app/controllers/lab/application_controller.rb +6 -0
- data/app/controllers/lab/labels_controller.rb +17 -0
- data/app/controllers/lab/orders_controller.rb +78 -0
- data/app/controllers/lab/reasons_for_test_controller.rb +9 -0
- data/app/controllers/lab/results_controller.rb +20 -0
- data/app/controllers/lab/specimen_types_controller.rb +15 -0
- data/app/controllers/lab/test_result_indicators_controller.rb +9 -0
- data/app/controllers/lab/test_types_controller.rb +15 -0
- data/app/controllers/lab/tests_controller.rb +25 -0
- data/app/controllers/lab/users_controller.rb +32 -0
- data/app/jobs/lab/application_job.rb +4 -0
- data/app/jobs/lab/push_order_job.rb +12 -0
- data/app/jobs/lab/update_patient_orders_job.rb +32 -0
- data/app/jobs/lab/void_order_job.rb +17 -0
- data/app/mailers/lab/application_mailer.rb +6 -0
- data/app/models/lab/application_record.rb +5 -0
- data/app/models/lab/lab_accession_number_counter.rb +13 -0
- data/app/models/lab/lab_acknowledgement.rb +6 -0
- data/app/models/lab/lab_encounter.rb +7 -0
- data/app/models/lab/lab_order.rb +58 -0
- data/app/models/lab/lab_result.rb +31 -0
- data/app/models/lab/lab_test.rb +19 -0
- data/app/models/lab/lims_failed_import.rb +4 -0
- data/app/models/lab/lims_order_mapping.rb +10 -0
- data/app/models/lab/order_extension.rb +14 -0
- data/app/serializers/lab/lab_order_serializer.rb +56 -0
- data/app/serializers/lab/result_serializer.rb +36 -0
- data/app/serializers/lab/test_serializer.rb +52 -0
- data/app/services/lab/accession_number_service.rb +77 -0
- data/app/services/lab/acknowledgement_service.rb +47 -0
- data/app/services/lab/concepts_service.rb +82 -0
- data/app/services/lab/json_web_token_service.rb +20 -0
- data/app/services/lab/labelling_service/order_label.rb +106 -0
- data/app/services/lab/lims/acknowledgement_serializer.rb +29 -0
- data/app/services/lab/lims/acknowledgement_worker.rb +37 -0
- data/app/services/lab/lims/api/blackhole_api.rb +21 -0
- data/app/services/lab/lims/api/couchdb_api.rb +53 -0
- data/app/services/lab/lims/api/mysql_api.rb +316 -0
- data/app/services/lab/lims/api/rest_api.rb +434 -0
- data/app/services/lab/lims/api/ws_api.rb +121 -0
- data/app/services/lab/lims/api_factory.rb +19 -0
- data/app/services/lab/lims/config.rb +105 -0
- data/app/services/lab/lims/exceptions.rb +11 -0
- data/app/services/lab/lims/migrator.rb +216 -0
- data/app/services/lab/lims/order_dto.rb +105 -0
- data/app/services/lab/lims/order_serializer.rb +251 -0
- data/app/services/lab/lims/pull_worker.rb +314 -0
- data/app/services/lab/lims/push_worker.rb +152 -0
- data/app/services/lab/lims/utils.rb +91 -0
- data/app/services/lab/lims/worker.rb +94 -0
- data/app/services/lab/metadata.rb +26 -0
- data/app/services/lab/notification_service.rb +72 -0
- data/app/services/lab/orders_search_service.rb +72 -0
- data/app/services/lab/orders_service.rb +330 -0
- data/app/services/lab/results_service.rb +166 -0
- data/app/services/lab/tests_service.rb +105 -0
- data/app/services/lab/user_service.rb +62 -0
- data/config/routes.rb +28 -0
- data/db/migrate/20210126092910_create_lab_lab_accession_number_counters.rb +12 -0
- data/db/migrate/20210310115457_create_lab_lims_order_mappings.rb +15 -0
- data/db/migrate/20210323080140_change_lims_id_to_string_in_lims_order_mapping.rb +15 -0
- data/db/migrate/20210326195504_add_order_revision_to_lims_order_mapping.rb +5 -0
- data/db/migrate/20210407071728_create_lab_lims_failed_imports.rb +19 -0
- data/db/migrate/20210610095024_fix_numeric_results_value_type.rb +20 -0
- data/db/migrate/20210807111531_add_default_to_lims_order_mapping.rb +7 -0
- data/lib/auto12epl.rb +201 -0
- data/lib/couch_bum/couch_bum.rb +92 -0
- data/lib/generators/lab/install/USAGE +9 -0
- data/lib/generators/lab/install/install_generator.rb +19 -0
- data/lib/generators/lab/install/templates/rswag-ui-lab.rb +5 -0
- data/lib/generators/lab/install/templates/start_worker.rb +32 -0
- data/lib/generators/lab/install/templates/swagger.yaml +714 -0
- data/lib/lab/engine.rb +13 -0
- data/lib/lab/version.rb +5 -0
- data/lib/logger_multiplexor.rb +38 -0
- data/lib/mahis_emr_api_lab.rb +6 -0
- data/lib/tasks/lab_tasks.rake +25 -0
- data/lib/tasks/loaders/data/reasons-for-test.csv +7 -0
- data/lib/tasks/loaders/data/test-measures.csv +225 -0
- data/lib/tasks/loaders/data/tests.csv +161 -0
- data/lib/tasks/loaders/loader_mixin.rb +53 -0
- data/lib/tasks/loaders/metadata_loader.rb +26 -0
- data/lib/tasks/loaders/reasons_for_test_loader.rb +23 -0
- data/lib/tasks/loaders/specimens_loader.rb +65 -0
- data/lib/tasks/loaders/test_result_indicators_loader.rb +54 -0
- metadata +331 -0
data/lib/lab/version.rb
ADDED
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# frozen_string_literal: true
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##
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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
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# to multiple streams at once hence this hack. This class
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# bundles multiple loggers so that they can be treated as
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# 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
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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)
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end
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end
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end
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def method_missing(method_name, *args)
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if respond_to_missing?(method_name)
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@loggers.each { |logger| logger.send(method_name, *args) }
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else
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super
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end
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end
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def respond_to_missing?(method_name)
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@loggers.all? do |logger|
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logger.respond_to?(method_name)
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end
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end
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end
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desc 'Generate openapi/swagger documentation template in engine'
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task :swag, ['app:rswag:specs:swaggerize'] do
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source = 'spec/dummy/swagger/v1/swagger.yaml'
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destination = 'lib/generators/lab/install/templates/swagger.yaml'
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FileUtils.copy(source, destination)
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end
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namespace :lab do
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desc 'Install Lab engine into container application'
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task :install do
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sh 'rails generate lab:install'
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sh 'rake lab:install:migrations'
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end
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desc 'Uninstall Lab engine from container application'
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task :uninstall do
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sh 'rails destroy lab:install'
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end
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desc 'Load Lab metadata into database'
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task :load_metadata do
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sh "rails r #{__dir__}/loaders/metadata_loader.rb"
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end
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end
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"test_name","measure_name"
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"TB Microscopic Exam","tb"
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"GeneXpert","MTB"
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"GeneXpert","RIF Resistance"
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"Gram Stain","Gram"
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"Gram Stain","Clue cells"
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"Gram Stain","Other organism seen"
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"Culture & Sensitivity","Culture"
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"Cell Count","WBC"
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"Cell Count","RBC"
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"India Ink","India ink"
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"Differential","Polymorphs"
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"Differential","Lymphocytes"
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"Differential","Diff remarks"
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"ZN Stain","ZN"
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"Wet prep","wet prep"
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"Wet prep","Other organism seen"
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"TB Tests","Macro exam"
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"TB Tests","Smear microscopy result"
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"TB Tests","Gene Xpert MTB"
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"TB Tests","Gene Xpert RIF Resistance"
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"TB Tests","HIV Status"
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"TB Tests","Reason For Testing"
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"TB Tests","Indication for GeneXpert Test"
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"Urine Macroscopy","Colour"
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"Urine Macroscopy","Appearance"
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"Urine Microscopy","WBC"
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"Urine Microscopy","RBC"
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"Urine Microscopy","Epithelial cells"
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"Urine Microscopy","Casts"
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"Urine Microscopy","Crystals"
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"Urine Microscopy","Parasites"
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"Urine Microscopy","Yeast cells"
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"Urine Chemistries","pH"
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"Urine Chemistries","Blood"
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"Urine Chemistries","Urobilinogen"
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"Urine Chemistries","Bilirubin"
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"Urine Chemistries","Protein"
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"Urine Chemistries","Nitrate"
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"Urine Chemistries","Ketones"
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"Urine Chemistries","Glucose"
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"Urine Chemistries","Specific gravity"
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"Urine Chemistries","Leucocytes"
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"Stool Analysis","Macroscopy"
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"Stool Analysis","Consistency"
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"Stool Analysis","Microscopy"
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"Malaria Screening","Blood film"
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"Malaria Screening","Malaria Species"
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"Malaria Screening","MRDT"
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"Blood Parasites Screen","Blood film"
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"Semen Analysis","Progressive motility"
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"Semen Analysis","Non-progressive motility"
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"Semen Analysis","Immotility"
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"Semen Analysis","Appearance"
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"Semen Analysis","Liquifaction time"
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"Semen Analysis","volume"
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"Semen Analysis","pH"
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"Semen Analysis","Sperm count"
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"Semen Analysis","Sperm morphology"
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"HVS analysis","Macroscopy"
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"HVS analysis","WBC"
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"HVS analysis","Epithelial cells"
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"HVS analysis","Parasites/Bacteria"
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"HVS analysis","Spermatozoa"
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"Syphilis Test","RPR"
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"Syphilis Test","VDRL"
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"Syphilis Test","TPHA"
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"Hepatitis B Test","Hepatitis B"
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"Hepatitis C Test","Hepatitis C"
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"Rheumatoid Factor Test","Rheumatoid Factor"
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"CrAg","CrAg"
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"Cryptococcus Antigen Test","CrAg"
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"Anti Streptolysis O","ASO"
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"C-reactive protein","CRP"
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"Measles","Measles IgM ELISA-Behring enzygnost"
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"Rubella","Rubella IgM ELISA-Behring enzynost"
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"CD4","CD4 Count"
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"CD4","CD4 %"
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"CD4","Lymphocyte Count"
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"CD4","CD8 Count"
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"CD4","CD3 Count"
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"ABO Blood Grouping","Grouping"
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"Cross-match","Pack No."
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"Cross-match","Pack ABO Group"
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"Cross-match","Product Type"
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"Cross-match","Expiry Date"
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"Cross-match","Volume"
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"Cross-match","Cross-match Method"
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"Transfusion Outcome","Outcome"
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"Liver Function Tests","ALT/GPT"
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"Liver Function Tests","AST/GOT"
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"Liver Function Tests","Alkaline Phosphate(ALP)"
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"Liver Function Tests","GGT/r-GT"
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"Liver Function Tests","Bilirubin Direct(BID)"
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"Liver Function Tests","Bilirubin Total(BIT))"
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"Liver Function Tests","Albumin(ALB)"
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"Liver Function Tests","Total Protein(PRO)"
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"Renal Function Test","Urea"
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"Renal Function Test","Creatinine"
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"Lipogram","Triglycerides(TG)"
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"Lipogram","Cholestero l(CHOL)"
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"Lipogram","HDL Direct (HDL-C)"
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"Lipogram","LDL Direct (LDL-C)"
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"FBC","WBC"
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"FBC","RBC"
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"FBC","HGB"
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"FBC","HCT"
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"FBC","MCV"
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"FBC","MCH"
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"FBC","MCHC"
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"FBC","PLT"
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"FBC","RDW-SD"
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"FBC","RDW-CV"
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"FBC","PDW"
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115
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"FBC","MPV"
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"FBC","PCT"
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"FBC","NEUT%"
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"FBC","LYMPH%"
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"FBC","MONO%"
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120
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"FBC","EO%"
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121
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"FBC","BASO%"
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"FBC","NEUT#"
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"FBC","LYMPH#"
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"FBC","MONO#"
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"FBC","EO#"
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126
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"FBC","BASO#"
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"FBC","Mid#"
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128
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"FBC","Gran#"
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129
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"FBC","Mid%"
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"FBC","Gran%"
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"FBC","EOS%"
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"FBC","P-LCC"
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133
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"FBC","P-LCR"
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134
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"Electrolytes","K"
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135
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"Electrolytes","Na"
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136
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"Electrolytes","Cl"
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137
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"Enzymes","a-AMYLASE-H"
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138
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"Enzymes","ALT-H"
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139
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"Enzymes","AST-H"
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"Enzymes","ALP-H"
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141
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"Enzymes","TP-H"
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"Enzymes","TC-H"
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143
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"Enzymes","UREA-H"
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144
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"Enzymes","GLU-O-H"
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145
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"Enzymes","TBIL-DSA-H"
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146
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"Enzymes","DBIL-DSA-H"
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147
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"Enzymes","UA-H"
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148
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"Enzymes","TG-H"
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149
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"Enzymes","ALB-H"
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150
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"Glucose","Glucose"
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151
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"Prothrombin Time","PT"
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152
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"APTT","APTT"
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153
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"INR","INR"
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154
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"ESR","ESR"
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155
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"Sickling Test","Sickling Screen"
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156
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"Pregnancy Test","Pregnancy Test"
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157
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"Manual Differential & Cell Morphology","Nucleated Red Cells"
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158
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"Manual Differential & Cell Morphology","Neutrophils"
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159
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"Manual Differential & Cell Morphology","Lymphocytes"
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160
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"Manual Differential & Cell Morphology","Monocytes"
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161
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"Manual Differential & Cell Morphology","Eosinophils"
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162
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"Manual Differential & Cell Morphology","Basophils"
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163
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"Manual Differential & Cell Morphology","Promyelocytes"
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164
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"Manual Differential & Cell Morphology","Myelocytes"
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165
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"Manual Differential & Cell Morphology","Metamyelocytes"
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166
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"Manual Differential & Cell Morphology","Band/Staff Forms"
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167
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"Manual Differential & Cell Morphology","Blasts"
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168
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"Manual Differential & Cell Morphology","Other"
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169
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"Manual Differential & Cell Morphology","RBC Comments"
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170
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"Manual Differential & Cell Morphology","WBC Comments"
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171
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"Manual Differential & Cell Morphology","Platelet Comments"
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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"
|
|
@@ -0,0 +1,161 @@
|
|
|
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"
|
|
@@ -0,0 +1,53 @@
|
|
|
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
|
|
@@ -0,0 +1,26 @@
|
|
|
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
|
|
@@ -0,0 +1,23 @@
|
|
|
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
|
|
@@ -0,0 +1,65 @@
|
|
|
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
|