Minimal updates

assets/mimic_iv/split_mimic.go

@@ -0,0 +1,90 @@
+package main
+
+import (
+	"bufio"
+	"fmt"
+	"log"
+	"os"
+	"path/filepath"
+	"strings"
+)
+
+// SplitNDJSON splits a large NDJSON file into smaller chunks
+func SplitNDJSON(inputFile string, outputDir string, linesPerFile int) error {
+	// Open the input NDJSON file
+	file, err := os.Open(inputFile)
+	if err != nil {
+		return fmt.Errorf("failed to open input file: %v", err)
+	}
+	defer file.Close()
+
+	// Create the output directory if it doesn't exist
+	if err := os.MkdirAll(outputDir, 0755); err != nil {
+		return fmt.Errorf("failed to create output directory: %v", err)
+	}
+
+	// Extract the base name of the input file (without extension)
+	baseFileName := strings.TrimSuffix(filepath.Base(inputFile), filepath.Ext(inputFile))
+
+	// Initialize reader
+	scanner := bufio.NewScanner(file)
+
+	// Variables to track the current chunk
+	var currentFile *os.File
+	var currentLineCount int
+	var fileIndex int
+
+	for scanner.Scan() {
+		// If starting a new chunk, create a new file
+		if currentLineCount == 0 {
+			outputFile := filepath.Join(outputDir, fmt.Sprintf("%s_%d.ndjson", baseFileName, fileIndex))
+			currentFile, err = os.Create(outputFile)
+			if err != nil {
+				return fmt.Errorf("failed to create output file: %v", err)
+			}
+			defer currentFile.Close()
+			log.Printf("Created new chunk: %s", outputFile)
+		}
+
+		// Write the current line to the file
+		_, err := currentFile.WriteString(scanner.Text() + "\n")
+		if err != nil {
+			return fmt.Errorf("failed to write to output file: %v", err)
+		}
+
+		// Increment the line count
+		currentLineCount++
+
+		// If we reach the limit, close the current file and start a new one
+		if currentLineCount >= linesPerFile {
+			currentFile.Close()
+			currentLineCount = 0
+			fileIndex++
+		}
+	}
+
+	if scanner.Err() != nil {
+		return fmt.Errorf("error reading file: %v", scanner.Err())
+	}
+
+	// Close the last file if it's still open
+	if currentFile != nil {
+		currentFile.Close()
+	}
+
+	return nil
+}
+
+func main() {
+	// Input file, output directory, and lines per file
+	inputFile := "ObservationChartevents.ndjson"
+	outputDir := "./"
+	linesPerFile := 20000 // Adjust based on your needs
+
+	err := SplitNDJSON(inputFile, outputDir, linesPerFile)
+	if err != nil {
+		log.Fatalf("Error splitting NDJSON file: %v", err)
+	}
+
+	log.Println("NDJSON file split successfully!")
+}

build/build_android.sh

@@ -17,4 +17,8 @@ if [ $? -ne 0 ]; then
     echo "Android build failed!"
     exit 1
 fi
+mv pocketfhir.aar ../fhir_ant/android/app/libs/pocketfhir.aar
+rm pocketfhir-sources.jar
+
 echo "PocketFHIR Android build completed successfully."
+

go.mod

@@ -8,6 +8,7 @@ require (
 	github.com/google/fhir/go v0.7.4
 	github.com/labstack/echo/v5 v5.0.0-20230722203903-ec5b858dab61
 	github.com/pocketbase/pocketbase v0.22.15
+	golang.org/x/net v0.31.0
 	google.golang.org/protobuf v1.34.2
 )
 
@@ -80,7 +81,6 @@ require (
 	golang.org/x/image v0.22.0 // indirect
 	golang.org/x/mobile v0.0.0-20241108191957-fa514ef75a0f // indirect
 	golang.org/x/mod v0.22.0 // indirect
-	golang.org/x/net v0.31.0 // indirect
 	golang.org/x/oauth2 v0.21.0 // indirect
 	golang.org/x/sync v0.9.0 // indirect
 	golang.org/x/sys v0.27.0 // indirect

main.go

@@ -4,6 +4,10 @@ import "github.com/fhir-fli/pocketfhir/pocketfhir"
 
 func main() {
 	// Use the string wrapper for local development
-	dataDir := "."
-	pocketfhir.RunServer(dataDir)
+	dataDir := "./assets"
+	hostname := "127.0.0.1"
+	port := "8080" // Changed from 443 to 8080 to avoid permission issues
+	getApiLogs := false
+
+	pocketfhir.RunServer(dataDir, hostname, port, getApiLogs)
 }

pocketfhir/initial_collections.go

@@ -24,13 +24,13 @@ func initializeCollections(app *pocketbase.PocketBase) error {
 		// Step 2: Check if FHIR spec has been initialized
 		if !isFhirSpecInitialized(app) {
 			// Load the FHIR spec into the database
-			if err := loadFhirSpecOnce(app); err != nil {
-				log.Printf("Failed to load FHIR spec: %v", err)
-				return err
-			}
+			// if err := loadFhirSpecOnce(app); err != nil {
+			// 	log.Printf("Failed to load FHIR spec: %v", err)
+			// 	return err
+			// }
 
 			// Set the FHIR spec as initialized
-			setFhirSpecInitialized(app)
+			// setFhirSpecInitialized(app)
 		} else {
 			log.Println("FHIR spec already initialized.")
 		}

pocketfhir/load_spec.go

@@ -215,3 +215,39 @@ func loadNDJSONFile(app *pocketbase.PocketBase, filePath string) error {
 
 	return nil
 }
+
+// Check if the FHIR spec is already initialized
+func isFhirSpecInitialized(app *pocketbase.PocketBase) bool {
+	metadataCollection, err := app.Dao().FindCollectionByNameOrId("metadata")
+	if err != nil {
+		log.Printf("Metadata collection not found: %v", err)
+		return false
+	}
+
+	// Check for a record indicating FHIR spec initialization
+	record, err := app.Dao().FindFirstRecordByData(metadataCollection.Id, "fhirSpecInitialized", true)
+	if err != nil || record == nil {
+		return false
+	}
+
+	return true
+}
+
+// Mark the FHIR spec as initialized in the "metadata" collection
+func setFhirSpecInitialized(app *pocketbase.PocketBase) {
+	metadataCollection, err := app.Dao().FindCollectionByNameOrId("metadata")
+	if err != nil {
+		log.Printf("Metadata collection not found: %v", err)
+		return
+	}
+
+	// Create a new record in the metadata collection
+	record := models.NewRecord(metadataCollection)
+	record.Set("fhirSpecInitialized", true)
+
+	if err := app.Dao().SaveRecord(record); err != nil {
+		log.Printf("Failed to save metadata record: %v", err)
+	} else {
+		log.Println("FHIR spec initialization marked as complete.")
+	}
+}