update: automation script modification to execute combind view and la…

…test metrics #29

lib/service/diabetes-research-hub/combined-cgm-tracing-generator.ts

@@ -4,7 +4,7 @@ import { DB } from "https://deno.land/x/sqlite/mod.ts";
 export function createCombinedCGMView(dbFilePath: string): void {
   // Open the existing database
   const db = new DB(dbFilePath);
-  console.log(`Opened database: ${dbFilePath}`);
+  //console.log(`Opened database: ${dbFilePath}`);
 
   // Create error log table if it doesn't exist
   db.execute(`
@@ -14,7 +14,7 @@ export function createCombinedCGMView(dbFilePath: string): void {
       error_message TEXT
     );
   `);
-  console.log("Error log table created or already exists.");
+  //console.log("Error log table created or already exists.");
 
   // Drop the view if it exists and create it
   try {
@@ -29,7 +29,7 @@ export function createCombinedCGMView(dbFilePath: string): void {
       GROUP BY
         patient_id;
     `);
-    console.log("View 'drh_participant_file_names' created successfully.");
+    //console.log("View 'drh_participant_file_names' created successfully.");
   } catch (error) {
     console.error("Error creating view 'drh_participant_file_names':", error);
     const sqlQuery = "INSERT INTO error_log (error_message) VALUES (?);";
@@ -80,11 +80,11 @@ export function createCombinedCGMView(dbFilePath: string): void {
   }
 
   db.close();
-  console.log(`Closed database: ${dbFilePath}`);
+  //console.log(`Closed database: ${dbFilePath}`);
 }
 
 // If the script is being run directly, execute the function
 if (import.meta.main) {
-  const dbFilePath = "resource-surveillance.sqlite.db"; // You can modify this path as needed
+  const dbFilePath = "resource-surveillance.sqlite.db"; 
   createCombinedCGMView(dbFilePath);
 }

lib/service/diabetes-research-hub/drhctl.ts

@@ -3,6 +3,7 @@
 import * as colors from "https://deno.land/std@0.224.0/fmt/colors.ts";
 import { DB } from "https://deno.land/x/sqlite@v3.6.0/mod.ts";
 import * as drhux from "./package.sql.ts";
+import { createCombinedCGMView } from "./combined-cgm-tracing-generator.ts";
 import {
   FlexibleTextSupplierSync,
   spawnedResult,
@@ -13,10 +14,13 @@ import {
 // Detect platform-specific command format
 const isWindows = Deno.build.os === "windows";
 const toolCmd = isWindows ? ".\\surveilr" : "surveilr";
+const dbFilePath = "resource-surveillance.sqlite.db"; // Path to your SQLite DB
 
 const RSC_BASE_URL =
   "https://raw.githubusercontent.com/surveilr/www.surveilr.com/main/lib/service/diabetes-research-hub";
 
+const UX_URL ="https://www.surveilr.com/lib/service/diabetes-research-hub"
+
 // Helper function to fetch SQL content
 async function fetchSqlContent(url: string): Promise<string> {
   try {
@@ -87,30 +91,28 @@ async function checkAndDeleteFile(filePath: string) {
   }
 }
 
-// Function to fetch UX SQL content
-async function fetchUxSqlContent(): Promise<string> {
-  try {
-    const uxSQLContent = await drhux.drhSQL();
-    return uxSQLContent.join("\n");
-  } catch (error) {
-    console.error(
-      colors.red("Error fetching UX SQL content:"),
-      error.message,
-    );
-    Deno.exit(1);
-  }
-}
+// Function to check for table existence and create combined view
+async function checkAndCreateCombinedView() {  
+  const db = new DB(dbFilePath);
 
-// Function to execute SQL commands directly on SQLite database
-function executeSqlCommands(sqlCommands: string) {
   try {
-    const db = new DB(dbFilePath);
-    db.execute(sqlCommands); // Execute the SQL commands
-    db.close();
-    console.log(colors.green("UX SQL executed successfully."));
+    // Check if the specific table exists
+    const tableName = 'uniform_resource_cgm_file_metadata'; // Change to your required table name
+    const tableExists = db.query(`SELECT name FROM sqlite_master WHERE type='table' AND name='${tableName}';`).length > 0;
+
+
+    if (tableExists) {
+        console.log(colors.green("Required table exists. Proceeding to create the combined view."));
+        await createCombinedCGMView(dbFilePath); // Call the function to create the combined view
+
+    } else {
+      console.error(colors.red("The required table does not exist. Cannot create the combined view."));
+    }
   } catch (error) {
-    console.error(colors.red("Error executing SQL commands:"), error.message);
-    Deno.exit(1);
+    console.error(colors.red("Error in checkAndCreateCombinedView:"), error.message);
+  } finally {
+    // Close the database connection
+    db.close();
   }
 }
 
@@ -125,28 +127,33 @@ if (Deno.args.length === 0) {
 // Store the folder name in a variable
 const folderName = Deno.args[0];
 
-// Path to the SQLite database file
-const dbFilePath = "./resource-surveillance.sqlite.db";
+
+// Path to the SQLite database journal
+const dbjournalfile = "./resource-surveillance.sqlite.db-journal";
 
 // Define synchronous suppliers
 const deidentificationSQLSupplier: FlexibleTextSupplierSync = () =>
   deidentificationSQL;
 const vvSQLSupplier: FlexibleTextSupplierSync = () => vvSQL;
-//const uxSQLSupplier: FlexibleTextSupplierSync = () => uxSQL;
+const uxSQLSupplier: FlexibleTextSupplierSync = () => uxSQL;
 
 let deidentificationSQL: string;
 let vvSQL: string;
 let uxSQL: string;
 
+
+
 try {
   // Fetch SQL content for DeIdentification, Verification & Validation, and UX orchestration
   deidentificationSQL = await fetchSqlContent(
     `${RSC_BASE_URL}/de-identification/drh-deidentification.sql`,
   );
   vvSQL = await fetchSqlContent(
     `${RSC_BASE_URL}/verfication-validation/orchestrate-drh-vv.sql`,
+  );  
+  uxSQL = await fetchSqlContent(
+    `${UX_URL}/package.sql`,
   );
-  uxSQL = await fetchUxSqlContent(); // Fetch UX SQL content
 } catch (error) {
   console.error(
     colors.red(
@@ -171,6 +178,7 @@ try {
   Deno.exit(1);
 }
 
+
 try {
   await executeCommand([toolCmd, "orchestrate", "transform-csv"]);
   console.log(
@@ -181,6 +189,18 @@ try {
   Deno.exit(1);
 }
 
+// Check and delete the file if it exists
+await checkAndDeleteFile(dbjournalfile);
+
+try {
+  console.log(colors.dim(`Generate combined views: ${folderName}...`));
+  checkAndCreateCombinedView(); 
+  console.log(colors.green("View generation completed successfully."));
+} catch (error) {
+  console.error(colors.red("Error during View generation:"), error.message);
+  Deno.exit(1);
+}
+
 
 try {
   console.log(colors.dim(`Performing DeIdentification: ${folderName}...`));
@@ -213,8 +233,8 @@ try {
 }
 
 try {
-  console.log(colors.dim(`Performing UX orchestration: ${folderName}...`));
-  executeSqlCommands(uxSQL); // Execute UX SQL commands
+  console.log(colors.dim(`Performing UX orchestration: ${folderName}...`));  
+  await executeCommand([toolCmd, "shell"], uxSQLSupplier);
   console.log(colors.green("UX orchestration completed successfully."));
 } catch (error) {
   console.error(colors.red("Error during UX orchestration:"), error.message);