mahis_his_emr_api_lab 1.2.0

data/lib/lab/engine.rb

@@ -0,0 +1,15 @@
+if Rails.env == 'test'
+  require 'rswag/ui'
+  require 'rswag/api'
+end
+
+module Lab
+  class Engine < ::Rails::Engine
+    isolate_namespace Lab
+    config.generators.api_only = true
+
+    config.generators do |g|
+      g.test_framework :rspec
+    end
+  end
+end

data/lib/lab/version.rb

@@ -0,0 +1,5 @@
+# frozen_string_literal: true
+
+module Lab
+  VERSION = '1.2.0'
+end

data/lib/logger_multiplexor.rb

@@ -0,0 +1,38 @@
+# frozen_string_literal: true
+
+##
+# Log to multiple streams.
+#
+# The 'logger' module does not provide a logger that can log
+# to multiple streams at once hence this hack. This class
+# bundles multiple loggers so that they can be treated as
+# one.
+#
+# Example:
+#   >>> logger = LoggerMultiplexor.new(STDOUT, 'development.log')
+#   >>> logger.info('Hello') # Logs 'Hello' to both streams
+class LoggerMultiplexor
+  def initialize(*loggers)
+    @loggers = loggers.map do |stream|
+      if stream.is_a?(Logger) || stream.is_a?(LoggerMultiplexor)
+        stream
+      else
+        Logger.new(stream)
+      end
+    end
+  end
+
+  def method_missing(method_name, *args)
+    if respond_to_missing?(method_name)
+      @loggers.each { |logger| logger.send(method_name, *args) }
+    else
+      super
+    end
+  end
+
+  def respond_to_missing?(method_name)
+    @loggers.all? do |logger|
+      logger.respond_to?(method_name)
+    end
+  end
+end

data/lib/tasks/lab_tasks.rake

@@ -0,0 +1,25 @@
+desc 'Generate openapi/swagger documentation template in engine'
+task :swag, ['app:rswag:specs:swaggerize'] do
+  source = 'spec/dummy/swagger/v1/swagger.yaml'
+  destination = 'lib/generators/lab/install/templates/swagger.yaml'
+
+  FileUtils.copy(source, destination)
+end
+
+namespace :lab do
+  desc 'Install Lab engine into container application'
+  task :install do
+    sh 'rails generate lab:install'
+    sh 'rake lab:install:migrations'
+  end
+
+  desc 'Uninstall Lab engine from container application'
+  task :uninstall do
+    sh 'rails destroy lab:install'
+  end
+
+  desc 'Load Lab metadata into database'
+  task :load_metadata do
+    sh "rails r #{__dir__}/loaders/metadata_loader.rb"
+  end
+end

data/lib/tasks/loaders/data/reasons-for-test.csv

@@ -0,0 +1,7 @@
+"reason_name"
+"Routine"
+"Repeat / Missing"
+"Targeted"
+"Confirmatory"
+"Stat"
+"Other"

data/lib/tasks/loaders/data/test-measures.csv

@@ -0,0 +1,225 @@
+"test_name","measure_name"
+"TB Microscopic Exam","tb"
+"GeneXpert","MTB"
+"GeneXpert","RIF Resistance"
+"Gram Stain","Gram"
+"Gram Stain","Clue cells"
+"Gram Stain","Other organism seen"
+"Culture & Sensitivity","Culture"
+"Cell Count","WBC"
+"Cell Count","RBC"
+"India Ink","India ink"
+"Differential","Polymorphs"
+"Differential","Lymphocytes"
+"Differential","Diff remarks"
+"ZN Stain","ZN"
+"Wet prep","wet prep"
+"Wet prep","Other organism seen"
+"TB Tests","Macro exam"
+"TB Tests","Smear microscopy result"
+"TB Tests","Gene Xpert MTB"
+"TB Tests","Gene Xpert RIF Resistance"
+"TB Tests","HIV Status"
+"TB Tests","Reason For Testing"
+"TB Tests","Indication for GeneXpert Test"
+"Urine Macroscopy","Colour"
+"Urine Macroscopy","Appearance"
+"Urine Microscopy","WBC"
+"Urine Microscopy","RBC"
+"Urine Microscopy","Epithelial cells"
+"Urine Microscopy","Casts"
+"Urine Microscopy","Crystals"
+"Urine Microscopy","Parasites"
+"Urine Microscopy","Yeast cells"
+"Urine Chemistries","pH"
+"Urine Chemistries","Blood"
+"Urine Chemistries","Urobilinogen"
+"Urine Chemistries","Bilirubin"
+"Urine Chemistries","Protein"
+"Urine Chemistries","Nitrate"
+"Urine Chemistries","Ketones"
+"Urine Chemistries","Glucose"
+"Urine Chemistries","Specific gravity"
+"Urine Chemistries","Leucocytes"
+"Stool Analysis","Macroscopy"
+"Stool Analysis","Consistency"
+"Stool Analysis","Microscopy"
+"Malaria Screening","Blood film"
+"Malaria Screening","Malaria Species"
+"Malaria Screening","MRDT"
+"Blood Parasites Screen","Blood film"
+"Semen Analysis","Progressive motility"
+"Semen Analysis","Non-progressive motility"
+"Semen Analysis","Immotility"
+"Semen Analysis","Appearance"
+"Semen Analysis","Liquifaction time"
+"Semen Analysis","volume"
+"Semen Analysis","pH"
+"Semen Analysis","Sperm count"
+"Semen Analysis","Sperm morphology"
+"HVS analysis","Macroscopy"
+"HVS analysis","WBC"
+"HVS analysis","Epithelial cells"
+"HVS analysis","Parasites/Bacteria"
+"HVS analysis","Spermatozoa"
+"Syphilis Test","RPR"
+"Syphilis Test","VDRL"
+"Syphilis Test","TPHA"
+"Hepatitis B Test","Hepatitis B"
+"Hepatitis C Test","Hepatitis C"
+"Rheumatoid Factor Test","Rheumatoid Factor"
+"CrAg","CrAg"
+"Cryptococcus Antigen Test","CrAg"
+"Anti Streptolysis O","ASO"
+"C-reactive protein","CRP"
+"Measles","Measles IgM ELISA-Behring enzygnost"
+"Rubella","Rubella IgM ELISA-Behring enzynost"
+"CD4","CD4 Count"
+"CD4","CD4 %"
+"CD4","Lymphocyte Count"
+"CD4","CD8 Count"
+"CD4","CD3 Count"
+"ABO Blood Grouping","Grouping"
+"Cross-match","Pack No."
+"Cross-match","Pack ABO Group"
+"Cross-match","Product Type"
+"Cross-match","Expiry Date"
+"Cross-match","Volume"
+"Cross-match","Cross-match Method"
+"Transfusion Outcome","Outcome"
+"Liver Function Tests","ALT/GPT"
+"Liver Function Tests","AST/GOT"
+"Liver Function Tests","Alkaline Phosphate(ALP)"
+"Liver Function Tests","GGT/r-GT"
+"Liver Function Tests","Bilirubin Direct(BID)"
+"Liver Function Tests","Bilirubin Total(BIT))"
+"Liver Function Tests","Albumin(ALB)"
+"Liver Function Tests","Total Protein(PRO)"
+"Renal Function Test","Urea"
+"Renal Function Test","Creatinine"
+"Lipogram","Triglycerides(TG)"
+"Lipogram","Cholestero l(CHOL)"
+"Lipogram","HDL Direct (HDL-C)"
+"Lipogram","LDL Direct (LDL-C)"
+"FBC","WBC"
+"FBC","RBC"
+"FBC","HGB"
+"FBC","HCT"
+"FBC","MCV"
+"FBC","MCH"
+"FBC","MCHC"
+"FBC","PLT"
+"FBC","RDW-SD"
+"FBC","RDW-CV"
+"FBC","PDW"
+"FBC","MPV"
+"FBC","PCT"
+"FBC","NEUT%"
+"FBC","LYMPH%"
+"FBC","MONO%"
+"FBC","EO%"
+"FBC","BASO%"
+"FBC","NEUT#"
+"FBC","LYMPH#"
+"FBC","MONO#"
+"FBC","EO#"
+"FBC","BASO#"
+"FBC","Mid#"
+"FBC","Gran#"
+"FBC","Mid%"
+"FBC","Gran%"
+"FBC","EOS%"
+"FBC","P-LCC"
+"FBC","P-LCR"
+"Electrolytes","K"
+"Electrolytes","Na"
+"Electrolytes","Cl"
+"Enzymes","a-AMYLASE-H"
+"Enzymes","ALT-H"
+"Enzymes","AST-H"
+"Enzymes","ALP-H"
+"Enzymes","TP-H"
+"Enzymes","TC-H"
+"Enzymes","UREA-H"
+"Enzymes","GLU-O-H"
+"Enzymes","TBIL-DSA-H"
+"Enzymes","DBIL-DSA-H"
+"Enzymes","UA-H"
+"Enzymes","TG-H"
+"Enzymes","ALB-H"
+"Glucose","Glucose"
+"Prothrombin Time","PT"
+"APTT","APTT"
+"INR","INR"
+"ESR","ESR"
+"Sickling Test","Sickling Screen"
+"Pregnancy Test","Pregnancy Test"
+"Manual Differential & Cell Morphology","Nucleated Red Cells"
+"Manual Differential & Cell Morphology","Neutrophils"
+"Manual Differential & Cell Morphology","Lymphocytes"
+"Manual Differential & Cell Morphology","Monocytes"
+"Manual Differential & Cell Morphology","Eosinophils"
+"Manual Differential & Cell Morphology","Basophils"
+"Manual Differential & Cell Morphology","Promyelocytes"
+"Manual Differential & Cell Morphology","Myelocytes"
+"Manual Differential & Cell Morphology","Metamyelocytes"
+"Manual Differential & Cell Morphology","Band/Staff Forms"
+"Manual Differential & Cell Morphology","Blasts"
+"Manual Differential & Cell Morphology","Other"
+"Manual Differential & Cell Morphology","RBC Comments"
+"Manual Differential & Cell Morphology","WBC Comments"
+"Manual Differential & Cell Morphology","Platelet Comments"
+"Manual Differential & Cell Morphology","Interpretative Comments"
+"Manual Differential & Cell Morphology","Attempted/ Differential Diagnosis"
+"Manual Differential & Cell Morphology","Further Tests"
+"Pancreatic Function Test","Amylase"
+"Pancreatic Function Test","Lipase"
+"Direct Coombs Test","Direct Coombs Test"
+"Calcium","Ca"
+"Phosphorus","P"
+"Magnesium","Mg"
+"Creatinine Kinase","CK"
+"Uric Acid","UA"
+"ESBL Test","ESBL"
+"ESBL Test","Cefotaxime"
+"ESBL Test","Cefotaxime + Clavulanate"
+"ESBL Test","Ceftazidime"
+"ESBL Test","Ceftazidime + Clavulanate"
+"ESBL Test","Cefepime"
+"ESBL Test","Cefepime + clavulanate"
+"APTT Ratio","APTT Ratio"
+"Fibronogen","Fibronogen"
+"50:50 Normal Plasma","50:50 Normal Plasma"
+"50:50 Mix FVIII Deficient","50:50 Mix FVIII Deficient"
+"50:50 Mix F-IX Deficient","50:50 Mix F-IX Deficient"
+"Factor VIII Assay","Factor VIII Assay"
+"Factor IX Assay","Factor IX Assay"
+"TT","TT"
+"Coagulation Assay","PT"
+"Coagulation Assay","INR"
+"Coagulation Assay","APTT"
+"Coagulation Assay","APTT Ratio"
+"Coagulation Assay","TT"
+"Coagulation Assay","Fibronogen"
+"Coagulation Assay","50:50 Mix Normal Plasma"
+"Coagulation Assay","50:50 Mix FVIII Deficient"
+"Coagulation Assay","50:50 Mix F-IX Deficient"
+"Coagulation Assay","Factor IX Assay"
+"Coagulation Assay","Factor VIII Assay"
+"Cardiac Function Tests","Creatine Kinase MB(CKMB)"
+"Cardiac Function Tests","Creatine Kinase(CKN)"
+"Cardiac Function Tests","Lactatedehydrogenase(LDH)"
+"Minerals","Calcium (CA)"
+"Minerals","Phosphorus (PHOS)"
+"Minerals","Magnesium (MGXB)"
+"BioMarkers","C-reactive Protein (CRP)"
+"BioMarkers","Rheumatoid Factor (RF)"
+"BioMarkers","Antistreptolysin O (ASO)"
+"Iron Studies","Iron"
+"Iron Studies","UIBC"
+"HbA1c","HbA1c"
+"Microalbumin","MAL"
+"Microprotein","MPR"
+"Von Willebrand Factor","Von Willebrand (Antigen)"
+"Von Willebrand Factor","Von Willebrand (Activity)"
+"Viral Load","Viral Load"

data/lib/tasks/loaders/data/tests.csv

@@ -0,0 +1,161 @@
+specimen_name,test_name,created_at
+Sputum,"TB Microscopic Exam","2019-11-19 14:05:31"
+Sputum,GeneXpert,"2019-11-19 14:05:31"
+Sputum,"Gram Stain","2019-11-19 14:05:31"
+Sputum,"Culture & Sensitivity","2019-11-19 14:05:31"
+Sputum,Differential,"2019-11-19 14:05:31"
+Sputum,"TB Tests","2019-11-19 14:05:31"
+CSF,"Gram Stain","2019-11-19 14:05:31"
+CSF,"Culture & Sensitivity","2019-11-19 14:05:31"
+CSF,"Cell Count","2019-11-19 14:05:31"
+CSF,"India Ink","2019-11-19 14:05:31"
+CSF,Differential,"2019-11-19 14:05:31"
+CSF,"ZN Stain","2019-11-19 14:05:31"
+CSF,"TB Tests","2019-11-19 14:05:31"
+CSF,"ESBL Test","2019-11-19 14:05:31"
+CSF,CrAg,"2019-11-19 14:05:31"
+Blood,"Gram Stain","2019-11-19 14:05:31"
+Blood,"Culture & Sensitivity","2019-11-19 14:05:31"
+Blood,"Malaria Screening","2019-11-19 14:05:31"
+Blood,"Blood Parasites Screen","2019-11-19 14:05:31"
+Blood,"Syphilis Test","2019-11-19 14:05:31"
+Blood,"Hepatitis B Test","2019-11-19 14:05:31"
+Blood,"Hepatitis C Test","2019-11-19 14:05:31"
+Blood,"Rheumatoid Factor Test","2019-11-19 14:05:31"
+Blood,"Cryptococcus Antigen Test","2019-11-19 14:05:31"
+Blood,"Anti Streptolysis O","2019-11-19 14:05:31"
+Blood,"C-reactive protein","2019-11-19 14:05:31"
+Blood,Measles,"2019-11-19 14:05:31"
+Blood,Rubella,"2019-11-19 14:05:31"
+Blood,CD4,"2019-11-19 14:05:31"
+Blood,"ABO Blood Grouping","2019-11-19 14:05:31"
+Blood,Cross-match,"2019-11-19 14:05:31"
+Blood,"Transfusion Outcome","2019-11-19 14:05:31"
+Blood,"Liver Function Tests","2019-11-19 14:05:31"
+Blood,"Renal Function Test","2019-11-19 14:05:31"
+Blood,Lipogram,"2019-11-19 14:05:31"
+Blood,FBC,"2019-11-19 14:05:31"
+Blood,"FBS","2021-04-11 00:00:00"
+Blood,Electrolytes,"2019-11-19 14:05:31"
+Blood,Enzymes,"2019-11-19 14:05:31"
+Blood,Glucose,"2019-11-19 14:05:31"
+Blood,"Prothrombin Time","2019-11-19 14:05:31"
+Blood,APTT,"2019-11-19 14:05:31"
+Blood,INR,"2019-11-19 14:05:31"
+Blood,ESR,"2019-11-19 14:05:31"
+Blood,"D/Coombs","2021-04-11 00:00:00"
+Blood,"creat","2021-04-11 00:00:00"
+Blood,"Widal","2021-04-11 00:00:00"
+Blood,"AAFB (3rd)","2021-04-11 00:00:00"
+Blood,"Urine micro","2021-04-11 00:00:00"
+Blood,"AAFB (1st)","2021-04-11 00:00:00"
+Blood,ASOT,"2021-04-11 00:00:00"
+Blood,"Blood C/S","2021-04-11 00:00:00"
+Blood,"Cryptococcal Ag","2021-04-11 00:00:00"
+Blood,"I/Ink","2021-04-11 00:00:00"
+Blood,"Prot& Sugar","2021-04-11 00:00:00"
+Blood,C_S,"2021-04-11 00:00:00"
+Blood,hep,"2021-04-11 00:00:00"
+Blood,"Cryptococcal Antigen","2021-04-11 00:00:00"
+Blood,Resistance,"2021-04-11 00:00:00"
+Blood,Sickle,"2021-04-11 00:00:00"
+Blood,"Sickling Test","2019-11-19 14:05:31"
+Blood,"Manual Differential & Cell Morphology","2019-11-19 14:05:31"
+Blood,"Pancreatic Function Test","2019-11-19 14:05:31"
+Blood,"Direct Coombs Test","2019-11-19 14:05:31"
+Blood,Calcium,"2019-11-19 14:05:31"
+Blood,Phosphorus,"2019-11-19 14:05:31"
+Blood,Magnesium,"2019-11-19 14:05:31"
+Blood,"Creatinine Kinase","2019-11-19 14:05:31"
+Blood,"Uric Acid","2019-11-19 14:05:31"
+Blood,"ESBL Test","2019-11-19 14:05:31"
+Blood,"APTT Ratio","2019-11-19 14:05:31"
+Blood,Fibronogen,"2019-11-19 14:05:31"
+Blood,"50:50 Normal Plasma","2019-11-19 14:05:31"
+Blood,"50:50 Mix FVIII Deficient","2019-11-19 14:05:31"
+Blood,"50:50 Mix F-IX Deficient","2019-11-19 14:05:31"
+Blood,"Factor VIII Assay","2019-11-19 14:05:31"
+Blood,"Factor IX Assay","2019-11-19 14:05:31"
+Blood,TT,"2019-11-19 14:05:31"
+Blood,"Coagulation Assay","2019-11-19 14:05:31"
+Blood,"Cardiac Function Tests","2019-11-19 14:05:31"
+Blood,Minerals,"2019-11-19 14:05:31"
+Blood,BioMarkers,"2019-11-19 14:05:31"
+Blood,"Iron Studies","2019-11-19 14:05:31"
+Blood,HbA1c,"2019-11-19 14:05:31"
+Blood,Microalbumin,"2019-11-19 14:05:31"
+Blood,Microprotein,"2019-11-19 14:05:31"
+Blood,"Von Willebrand Factor","2019-11-19 14:05:31"
+Blood,"Viral Load","2019-11-19 14:05:31"
+Blood,"Urine Lam","2019-11-19 14:05:31"
+Blood,"Protein and Sugar","2021-04-16"
+Blood,"White cell count","2021-04-16"
+Blood,Urea,"2019-11-19 14:05:31"
+Blood,Creatinine,"2019-11-19 14:05:31"
+Blood,ALT,"2019-11-19 14:05:31"
+Blood,AST,"2019-11-19 14:05:31"
+"Pleural Fluid","Gram Stain","2019-11-19 14:05:31"
+"Pleural Fluid","Culture & Sensitivity","2019-11-19 14:05:31"
+"Pleural Fluid","Cell Count","2019-11-19 14:05:31"
+"Pleural Fluid",Differential,"2019-11-19 14:05:31"
+"Pleural Fluid","ZN Stain","2019-11-19 14:05:31"
+"Pleural Fluid","TB Tests","2019-11-19 14:05:31"
+"Pleural Fluid","ESBL Test","2019-11-19 14:05:31"
+"Ascitic Fluid","Gram Stain","2019-11-19 14:05:31"
+"Ascitic Fluid","Culture & Sensitivity","2019-11-19 14:05:31"
+"Ascitic Fluid","Cell Count","2019-11-19 14:05:31"
+"Ascitic Fluid",Differential,"2019-11-19 14:05:31"
+"Ascitic Fluid","ZN Stain","2019-11-19 14:05:31"
+"Ascitic Fluid","TB Tests","2019-11-19 14:05:31"
+"Ascitic Fluid","ESBL Test","2019-11-19 14:05:31"
+"Pericardial Fluid","Gram Stain","2019-11-19 14:05:31"
+"Pericardial Fluid","Culture & Sensitivity","2019-11-19 14:05:31"
+"Pericardial Fluid","Cell Count","2019-11-19 14:05:31"
+"Pericardial Fluid",Differential,"2019-11-19 14:05:31"
+"Pericardial Fluid","ZN Stain","2019-11-19 14:05:31"
+"Pericardial Fluid","TB Tests","2019-11-19 14:05:31"
+"Pericardial Fluid","ESBL Test","2019-11-19 14:05:31"
+"Peritoneal Fluid","Gram Stain","2019-11-19 14:05:31"
+"Peritoneal Fluid","Culture & Sensitivity","2019-11-19 14:05:31"
+"Peritoneal Fluid","Cell Count","2019-11-19 14:05:31"
+"Peritoneal Fluid",Differential,"2019-11-19 14:05:31"
+"Peritoneal Fluid","ZN Stain","2019-11-19 14:05:31"
+"Peritoneal Fluid","TB Tests","2019-11-19 14:05:31"
+"Peritoneal Fluid","ESBL Test","2019-11-19 14:05:31"
+HVS,"Gram Stain","2019-11-19 14:05:31"
+HVS,"Culture & Sensitivity","2019-11-19 14:05:31"
+HVS,"Wet prep","2019-11-19 14:05:31"
+HVS,"HVS analysis","2019-11-19 14:05:31"
+HVS,"ESBL Test","2019-11-19 14:05:31"
+Swabs,"Gram Stain","2019-11-19 14:05:31"
+Swabs,"Culture & Sensitivity","2019-11-19 14:05:31"
+Swabs,"Wet prep","2019-11-19 14:05:31"
+Swabs,"ESBL Test","2019-11-19 14:05:31"
+Pus,"Gram Stain","2019-11-19 14:05:31"
+Pus,"Culture & Sensitivity","2019-11-19 14:05:31"
+Pus,"TB Tests","2019-11-19 14:05:31"
+Pus,"ESBL Test","2019-11-19 14:05:31"
+Stool,"Gram Stain","2019-11-19 14:05:31"
+Stool,"Culture & Sensitivity","2019-11-19 14:05:31"
+Stool,"Stool Analysis","2019-11-19 14:05:31"
+Urine,"Gram Stain","2019-11-19 14:05:31"
+Urine,"Culture & Sensitivity","2019-11-19 14:05:31"
+Urine,"Urine Macroscopy","2019-11-19 14:05:31"
+Urine,"Urine Microscopy","2019-11-19 14:05:31"
+Urine,"Urine Chemistries","2019-11-19 14:05:31"
+Urine,"Pregnancy Test","2019-11-19 14:05:31"
+Urine,"ESBL Test","2019-11-19 14:05:31"
+Urine,"Urine Lam","2019-11-19 14:05:31"
+Urine,"Urine Dipstick","2019-11-19 14:05:31"
+Other,"Gram Stain","2019-11-19 14:05:31"
+Other,"Culture & Sensitivity","2019-11-19 14:05:31"
+Other,"Cell Count","2019-11-19 14:05:31"
+Other,"ZN Stain","2019-11-19 14:05:31"
+Swab,"Culture & Sensitivity","2019-11-19 14:05:31"
+Swab,"Semen Analysis","2019-11-19 14:05:31"
+Plasma,"Gram Stain","2019-11-19 14:05:31"
+Plasma,"Culture & Sensitivity","2019-11-19 14:05:31"
+Plasma,"Cell Count","2019-11-19 14:05:31"
+Plasma,"ZN Stain","2019-11-19 14:05:31"
+"DBS (Free drop to DBS card)","Viral Load","2019-11-19 14:05:31"
+"DBS (Using capillary tube)","Viral Load","2019-11-19 14:05:31"

data/lib/tasks/loaders/loader_mixin.rb

@@ -0,0 +1,53 @@
+# frozen_string_literal: true
+
+module Lab
+  module Loaders
+    module LoaderMixin
+      def self.included(_mod)
+        User.current = User.find_by_username('admin') || User.first
+        Location.current = Location.find_by_name('Registration') || Location.first
+      end
+
+      CONCEPT_DATATYPE_CODED = 2
+      CONCEPT_CLASS_TEST = 1
+
+      def find_or_create_concept(name, is_set: false)
+        # Filter out concept_names with voided concepts
+        concept = ConceptName.joins(:concept).find_by_name(name)
+        return concept if concept
+
+        ConceptName.create!(
+          concept: Concept.create!(
+            short_name: name,
+            datatype_id: CONCEPT_DATATYPE_CODED,
+            class_id: CONCEPT_CLASS_TEST,
+            is_set: is_set,
+            uuid: SecureRandom.uuid,
+            creator: User.current.user_id,
+            date_created: Time.now
+          ),
+          name: name,
+          locale: 'en',
+          concept_name_type: 'FULLY_SPECIED',
+          uuid: SecureRandom.uuid,
+          creator: User.current.user_id,
+          date_created: Time.now
+        )
+      end
+
+      def add_concept_to_set(set_concept_id:, concept_id:)
+        set = ConceptSet.find_by(concept_set: set_concept_id, concept_id: concept_id)
+        return set if set
+
+        ConceptSet.create!(concept_set: set_concept_id,
+                           concept_id: concept_id,
+                           creator: User.current.user_id,
+                           date_created: Time.now)
+      end
+
+      def data_path(filename)
+        "#{__dir__}/data/#{filename}"
+      end
+    end
+  end
+end

data/lib/tasks/loaders/metadata_loader.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+require_relative 'reasons_for_test_loader'
+require_relative 'specimens_loader'
+require_relative 'test_result_indicators_loader'
+
+module Lab
+  module Loaders
+    module MetadataLoader
+      def self.load
+        unless Program.where(name: 'Laboratory program').exists?
+          Program.create(name: 'Laboratory program',
+                         description: 'Manage Lab information',
+                         creator: 1,
+                         uuid: SecureRandom.uuid)
+        end
+
+        SpecimensLoader.load
+        TestResultIndicatorsLoader.load
+        ReasonsForTestLoader.load
+      end
+    end
+  end
+end
+
+Lab::Loaders::MetadataLoader.load

data/lib/tasks/loaders/reasons_for_test_loader.rb

@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+
+require_relative './loader_mixin'
+
+module Lab
+  module Loaders
+    module ReasonsForTestLoader
+      class << self
+        include LoaderMixin
+
+        def load
+          CSV.open(data_path('reasons-for-test.csv'), headers: :first_row) do |csv|
+            csv.each do |row|
+              puts "Adding reason for test: #{row['reason_name']}"
+              add_concept_to_set(set_concept_id: find_or_create_concept(Lab::Metadata::REASON_FOR_TEST_CONCEPT_NAME).concept_id,
+                                 concept_id: find_or_create_concept(row['reason_name']).concept_id)
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/tasks/loaders/specimens_loader.rb

@@ -0,0 +1,65 @@
+# frozen_string_literal: true
+
+require 'csv'
+require_relative './loader_mixin'
+
+module Lab
+  module Loaders
+    ##
+    # Load specimens and their tests into the database
+    module SpecimensLoader
+      class << self
+        include LoaderMixin
+      
+        def load
+          puts "------- Loading tests and specimens ---------"
+          CSV.open(data_path('tests.csv'), headers: :first_row) do |csv|
+            csv.each_with_object({}) do |row, test_types|
+              specimen_name = row['specimen_name']
+              test_name = row['test_name']
+
+              ActiveRecord::Base.transaction do
+                test_type = test_types[test_name] || create_test_type(test_name)
+                create_specimen_type(specimen_name, test_type)
+
+                test_types[test_name] ||= test_type
+              end
+
+              puts "Created test #{test_name} <--< #{specimen_name}"
+            rescue StandardError => e
+              puts "Error: #{test_name}: #{e}"
+            end
+          end
+        end
+
+        def test_type_concept_id
+          find_or_create_concept(Lab::Metadata::TEST_TYPE_CONCEPT_NAME).concept_id
+        end
+
+        def specimen_type_concept_id
+          find_or_create_concept(Lab::Metadata::SPECIMEN_TYPE_CONCEPT_NAME).concept_id
+        end
+
+
+        def create_test_type(name)
+          concept_id = find_or_create_concept(name, is_set: true).concept_id
+
+          add_concept_to_set(set_concept_id: test_type_concept_id, concept_id: concept_id)
+        rescue StandardError => e
+          raise "Failed to create test type `#{name}`: #{e}"
+        end
+
+        def create_specimen_type(name, test_type)
+          concept_id = find_or_create_concept(name).concept_id
+
+          [
+            add_concept_to_set(set_concept_id: specimen_type_concept_id, concept_id: concept_id),
+            add_concept_to_set(set_concept_id: test_type.concept_id, concept_id: concept_id)
+          ]
+        rescue StandardError => e
+          raise "Failed to create specimen type `#{name}`: #{e}"
+        end
+      end
+    end
+  end
+end