Merge pull request #14 from openhealthalgorithms/OHAS-4-who-lookup

Ohas 4 who lookup

actions/algorithm.go

@@ -6,6 +6,7 @@ import (
 	"fmt"
 	"log"
 	"net/http"
+	"os"
 	"path/filepath"
 	"strings"
 
@@ -24,13 +25,14 @@ import (
 )
 
 var (
-	dbFile = filepath.Join(tools.GetCurrentDirectory(), "logs.db")
-	sqlite *database.SqliteDb
+	dbFile          = filepath.Join(tools.GetCurrentDirectory(), "logs.db")
+	sqlite          *database.SqliteDb
+	currentSettings config.Settings
 )
 
 func load(c echo.Context) error {
 	var err error
-	currentSettings := c.Get("current_config").(config.Settings)
+	currentSettings = c.Get("current_config").(config.Settings)
 	dbFile = currentSettings.LogFile
 	sqlite, err = database.InitDb(dbFile)
 	if err != nil {
@@ -56,6 +58,27 @@ func AlgorithmHandler(c echo.Context) error {
 	if *o.Config.Algorithm != "hearts" {
 		return ErrorResponse(c, errors.New("algorithm not found"), 404)
 	}
+
+	if o.Config.RiskModelVersion == nil {
+		rmVersion := "who_ish_2007"
+		o.Config.RiskModelVersion = &rmVersion
+	}
+
+	if o.Config.LabBased == nil {
+		lab := false
+		o.Config.LabBased = &lab
+	}
+
+	colorChartPath := filepath.Join(currentSettings.ColorChart, *o.Config.RiskModel, *o.Config.RiskModelVersion, "charts.json")
+	if _, e := os.Stat(colorChartPath); e != nil {
+		return ErrorResponse(c, e, 400)
+	}
+
+	countriesPath := filepath.Join(currentSettings.ColorChart, *o.Config.RiskModel, *o.Config.RiskModelVersion, "countries.json")
+	if _, e := os.Stat(countriesPath); e != nil {
+		return ErrorResponse(c, e, 400)
+	}
+
 	guideFiles, err := tools.ParseGuidesFiles(c)
 	if err != nil {
 		return ErrorResponse(c, err, 500)
@@ -73,7 +96,7 @@ func AlgorithmHandler(c echo.Context) error {
 		GoalContent:      *glc,
 	}
 
-	hs, hg, hr, hd, hrs, err := hearts.Process(*o)
+	hs, hg, hr, hd, hrs, err := hearts.Process(*o, colorChartPath, countriesPath)
 	if err != nil {
 		return ErrorResponse(c, err, 500)
 	}
@@ -84,11 +107,17 @@ func AlgorithmHandler(c echo.Context) error {
 	output.Referrals = hr
 	output.Errors = make([]string, 0)
 	output.Errors = append(output.Errors, hrs...)
+	output.Meta.Debug = false
+	output.Meta.CarePlan = false
+	output.Meta.RiskModelVersion = *o.Config.RiskModelVersion
+	output.Meta.LabBased = *o.Config.LabBased
+
 	if o.Config.Debug != nil && *o.Config.Debug {
 		output.Debug = make(map[string]interface{})
 		for k, v := range hd {
 			output.Debug[k] = v
 		}
+		output.Meta.Debug = true
 	}
 
 	if o.Config.CarePlan != nil && *o.Config.CarePlan {
@@ -171,6 +200,7 @@ func AlgorithmHandler(c echo.Context) error {
 			CarePlanOutputActivities: outActivities,
 		}
 		output.CarePlan = &carePlan
+		output.Meta.CarePlan = true
 	}
 
 	tx, err := sqlite.DB.Begin()

algorithms/hearts.go

@@ -19,7 +19,7 @@ type Hearts struct {
 }
 
 // Process function
-func (h *Hearts) Process(o m.OHARequest) (*m.ORRAssessments, []m.ORRGoal, *m.ORRReferrals, map[string]interface{}, []string, error) {
+func (h *Hearts) Process(o m.OHARequest, colorChartPath, countriesPath string) (*m.ORRAssessments, []m.ORRGoal, *m.ORRReferrals, map[string]interface{}, []string, error) {
 	var err error
 	assessments := m.NewORRAssessments()
 	goals := make([]m.ORRGoal, 0)
@@ -404,9 +404,9 @@ func (h *Hearts) Process(o m.OHARequest) (*m.ORRAssessments, []m.ORRGoal, *m.ORR
 	}
 
 	// Blood Pressure
-	diab = false
-	if diabetes.Value == "diabetes" {
-		diab = true
+	diab = true
+	if diabetes.Code == "DM-NONE" || diabetes.Code == "DM-PRE-DIABETES" {
+		diab = false
 	}
 	bp, err := h.Guideline.Body.BloodPressure.Process(diab, sbp, dbp, age, medications)
 	if err != nil {
@@ -431,9 +431,9 @@ func (h *Hearts) Process(o m.OHARequest) (*m.ORRAssessments, []m.ORRGoal, *m.ORR
 		}
 	}
 
-	countries := tools.Countries()
+	countries := tools.Countries(countriesPath)
 	region := ""
-	if code, ok := countries[*o.Params.Demographics.BirthCountryCode]; ok {
+	if code, ok := countries.Countries[*o.Params.Demographics.BirthCountryCode]; ok {
 		if code.Region != "#N/A" {
 			region = code.Region
 		} else {
@@ -442,11 +442,24 @@ func (h *Hearts) Process(o m.OHARequest) (*m.ORRAssessments, []m.ORRGoal, *m.ORR
 
 			return assessments, goals, referrals, debug, errs, err
 		}
+	} else {
+		errr := errors.New("invalid country/region")
+		errs = append(errs, errr.Error())
+
+		return assessments, goals, referrals, debug, errs, err
 	}
 
 	// CVD
+	bmiValue, err := strconv.ParseFloat(bmi.Value, 64)
+	if err != nil {
+		errr := errors.New("invalid BMI value")
+		errs = append(errs, errr.Error())
+		return assessments, goals, referrals, debug, errs, err
+	}
+
 	cvdScore := ""
 	cvd, dbg, err := h.Guideline.Body.CVD.Guidelines.Process(
+		*o.Config.RiskModelVersion,
 		conditions,
 		age,
 		*h.Guideline.Body.CVD.PreProcessing,
@@ -459,10 +472,13 @@ func (h *Hearts) Process(o m.OHARequest) (*m.ORRAssessments, []m.ORRGoal, *m.ORR
 		diab,
 		cSm,
 		debugInputValue,
+		colorChartPath,
+		*o.Config.LabBased,
+		bmiValue,
 	)
 	if err == nil {
 		cvdScore = cvd.Value
-		res := GetResults(cvd, *h.GuidelineContent.Body.Contents)
+		res := GetResultWithVersion(cvd, *h.GuidelineContent.Body.Contents, *o.Config.RiskModelVersion)
 		assessments.CVD = &res
 		if res.Refer != nil && *res.Refer != "no" {
 			referral = referral || true
@@ -614,7 +630,7 @@ func (h *Hearts) Process(o m.OHARequest) (*m.ORRAssessments, []m.ORRGoal, *m.ORR
 	if assessments.Cholesterol != nil && assessments.Cholesterol.Components.TChol != nil {
 		lTChol = *assessments.Cholesterol.Components.TChol.Code
 	}
-	if assessments.CVD != nil {
+	if assessments.CVD != nil && assessments.CVD.Code != nil {
 		lCVD = *assessments.CVD.Code
 	}
 
@@ -648,3 +664,23 @@ func GetResults(response a.Response, contents a.Contents) m.ORRAssessment {
 
 	return assessment
 }
+
+// GetResultWithVersion from response
+func GetResultWithVersion(response a.Response, contents a.Contents, version string) m.ORRAssessment {
+	assessment := m.ORRAssessment{}
+
+	code := response.Code + "-" + strings.ToUpper(version)
+
+	if output, ok := contents[code]; ok {
+		assessment.Code = &response.Code
+		assessment.Value = &response.Value
+		assessment.Target = &response.Target
+
+		assessment.Eval = output.Eval
+		assessment.TFL = output.TFL
+		assessment.Message = output.Message
+		assessment.Refer = output.Refer
+	}
+
+	return assessment
+}

config/config.go

@@ -66,6 +66,7 @@ func configSettings(v *viper.Viper) Settings {
 	settings.CareplanConditionsFile = filepath.Join(v.GetString("directories.careplan_path"), v.GetString("files.careplan_file"))
 	settings.CareplanContentFile = filepath.Join(v.GetString("directories.careplan_path"), v.GetString("files.careplan_content_file"))
 	settings.LogFile = filepath.Join(v.GetString("directories.log_file_path"), v.GetString("files.log_file"))
+	settings.ColorChart = v.GetString("directories.guideline_path")
 
 	cloudEnable := v.GetBool("cloud.cloud_enable")
 	if cloudEnable {

config/types.go

@@ -10,6 +10,7 @@ type Settings struct {
 	CareplanConditionsFile string
 	CareplanContentFile    string
 	LogFile                string
+	ColorChart             string
 	CloudEnable            bool
 	CloudBucket            string
 	CloudConfigFile        string