inou/scrape_mychart/import.go

package main

import (
	"database/sql"
	"encoding/json"
	"fmt"
	"os"
	"path/filepath"

	_ "github.com/mattn/go-sqlite3"
)

const sophiaPatientID = 1

type Response struct {
	OrderName string   `json:"orderName"`
	Key       string   `json:"key"`
	Results   []Result `json:"results"`
}

type Result struct {
	OrderMetadata    OrderMeta   `json:"orderMetadata"`
	ResultComponents []Component `json:"resultComponents"`
	IsAbnormal       bool        `json:"isAbnormal"`
}

type OrderMeta struct {
	OrderProviderName           string   `json:"orderProviderName"`
	AuthorizingProviderName     string   `json:"authorizingProviderName"`
	PrioritizedInstantISO       string   `json:"prioritizedInstantISO"`
	CollectionTimestampsDisplay string   `json:"collectionTimestampsDisplay"`
	ResultStatus                string   `json:"resultStatus"`
	ResultType                  string   `json:"resultType"`
	ResultingLab                Lab      `json:"resultingLab"`
	AssociatedDiagnoses         []string `json:"associatedDiagnoses"`
	SpecimensDisplay            string   `json:"specimensDisplay"`
}

type Lab struct {
	Name       string   `json:"name"`
	Address    []string `json:"address"`
	CliaNumber string   `json:"cliaNumber"`
}

type Component struct {
	ComponentInfo       CompInfo       `json:"componentInfo"`
	ComponentResultInfo CompResultInfo `json:"componentResultInfo"`
	ComponentComments   CompComments   `json:"componentComments"`
}

type CompInfo struct {
	Name       string `json:"name"`
	CommonName string `json:"commonName"`
	Units      string `json:"units"`
}

type CompResultInfo struct {
	Value          string   `json:"value"`
	NumericValue   *float64 `json:"numericValue,omitempty"`
	ReferenceRange RefRange `json:"referenceRange"`
	AbnormalFlag   string   `json:"abnormalFlagCategoryValue"`
}

type RefRange struct {
	Low                     *float64 `json:"low,omitempty"`
	High                    *float64 `json:"high,omitempty"`
	FormattedReferenceRange string   `json:"formattedReferenceRange"`
}

type CompComments struct {
	HasContent      bool   `json:"hasContent"`
	ContentAsString string `json:"contentAsString"`
}

func main() {
	dbPath := "labs.db"
	if len(os.Args) > 1 {
		dbPath = os.Args[1]
	}
	
	db, err := sql.Open("sqlite3", dbPath)
	if err != nil {
		fmt.Printf("Failed to open %s: %v\n", dbPath, err)
		os.Exit(1)
	}
	defer db.Close()

	files, _ := filepath.Glob("output/*.json")
	fmt.Printf("Processing %d files\n", len(files))

	labCount, skipCount, testCount := 0, 0, 0

	for _, f := range files {
		data, _ := os.ReadFile(f)
		var resp Response
		if err := json.Unmarshal(data, &resp); err != nil {
			continue
		}
		if len(resp.Results) == 0 {
			continue
		}

		r := resp.Results[0]
		if r.OrderMetadata.ResultType != "LAB" {
			skipCount++
			continue
		}

		provider := r.OrderMetadata.OrderProviderName
		if provider == "" {
			provider = r.OrderMetadata.AuthorizingProviderName
		}

		labAddr := ""
		if len(r.OrderMetadata.ResultingLab.Address) > 0 {
			for i, a := range r.OrderMetadata.ResultingLab.Address {
				if i > 0 {
					labAddr += ", "
				}
				labAddr += a
			}
		}

		diagnoses := ""
		for i, d := range r.OrderMetadata.AssociatedDiagnoses {
			if i > 0 {
				diagnoses += "; "
			}
			diagnoses += d
		}

		isAbnormal := 0
		if r.IsAbnormal {
			isAbnormal = 1
		}

		res, err := db.Exec(`INSERT OR IGNORE INTO lab_orders 
			(patient_id, order_name, order_key, collection_date, provider, lab_name, lab_address, lab_clia, specimen, status, is_abnormal, diagnoses)
			VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)`,
			sophiaPatientID, resp.OrderName, resp.Key, r.OrderMetadata.PrioritizedInstantISO, provider,
			r.OrderMetadata.ResultingLab.Name, labAddr, r.OrderMetadata.ResultingLab.CliaNumber,
			r.OrderMetadata.SpecimensDisplay, r.OrderMetadata.ResultStatus, isAbnormal, diagnoses)

		if err != nil {
			fmt.Printf("err %s: %v\n", f, err)
			continue
		}

		rowsAffected, _ := res.RowsAffected()
		var orderID int64
		if rowsAffected == 0 {
			// Already exists, get existing ID
			row := db.QueryRow(`SELECT id FROM lab_orders WHERE order_key = ?`, resp.Key)
			if err := row.Scan(&orderID); err != nil {
				fmt.Printf("err getting existing order %s: %v\n", f, err)
				continue
			}
		} else {
			orderID, _ = res.LastInsertId()
			labCount++
		}

		for _, c := range r.ResultComponents {
			var numVal, refLow, refHigh *float64
			if c.ComponentResultInfo.NumericValue != nil {
				numVal = c.ComponentResultInfo.NumericValue
			}
			if c.ComponentResultInfo.ReferenceRange.Low != nil {
				refLow = c.ComponentResultInfo.ReferenceRange.Low
			}
			if c.ComponentResultInfo.ReferenceRange.High != nil {
				refHigh = c.ComponentResultInfo.ReferenceRange.High
			}

			comments := ""
			if c.ComponentComments.HasContent {
				comments = c.ComponentComments.ContentAsString
			}

			db.Exec(`INSERT INTO lab_tests 
				(order_id, name, common_name, value, numeric_value, units, ref_low, ref_high, ref_range_display, abnormal_flag, comments)
				VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)`,
				orderID, c.ComponentInfo.Name, c.ComponentInfo.CommonName,
				c.ComponentResultInfo.Value, numVal, c.ComponentInfo.Units,
				refLow, refHigh, c.ComponentResultInfo.ReferenceRange.FormattedReferenceRange,
				c.ComponentResultInfo.AbnormalFlag, comments)
			testCount++
		}
	}

	fmt.Printf("Done: %d lab orders, %d tests (%d non-lab skipped)\n", labCount, testCount, skipCount)
}