add: add combined cgm tracing view generator class #29

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

@@ -0,0 +1,88 @@
+import { DB } from "https://deno.land/x/sqlite/mod.ts";
+
+// Path to your existing SQLite database
+const dbFilePath = "resource-surveillance.sqlite.db";
+
+// Open the existing database
+const db = new DB(dbFilePath);
+console.log(`Opened database: ${dbFilePath}`);
+
+// Create error log table if it doesn't exist
+db.execute(`
+  CREATE TABLE IF NOT EXISTS error_log (
+    errorLogId INTEGER PRIMARY KEY AUTOINCREMENT,
+    datetime TEXT DEFAULT (datetime('now')),
+    error_message TEXT
+  );
+`);
+
+console.log("Error log table created or already exists.");
+
+// Get the list of participant IDs from the view
+const participants = db.query("SELECT DISTINCT patient_id FROM drh_participant_file_names;");
+
+// Array to hold table names for the combined view
+const tableNames: string[] = [];
+
+for (const [patient_id_raw] of participants) {
+  // Cast patient_id_raw to a string type
+  const patient_id: string = patient_id_raw as string; 
+
+  console.log(`Processing participant: ${patient_id}`);
+
+  // Get the file names associated with the participant
+  const [file_names_row] = db.query("SELECT file_names FROM drh_participant_file_names WHERE patient_id = ?", [patient_id]);
+  if (!file_names_row) {
+    console.log(`No file names found for participant ${patient_id}.`);
+    continue;
+  }
+
+  const file_names = file_names_row[0];
+  console.log(`File names for participant ${patient_id}: ${file_names}`);
+
+  if (file_names) {
+    // Construct table names
+    const participantTableNames = file_names.split(', ').map(fileName => `uniform_resource_${fileName}`);
+    tableNames.push(...participantTableNames); // Add participant's tables to the main array
+  } else {
+    console.log(`No file names found for participant ${patient_id}.`);
+  }
+}
+
+// Create the combined view for all participants
+if (tableNames.length > 0) {
+  const combinedUnionAllQuery = tableNames.map(tableName =>
+    `SELECT 
+       '${tableName}' as participant_id, 
+       strftime('%Y-%m-%d %H:%M:%S', date_time) as Date_Time, 
+       CAST(CGM_Value as REAL) as CGM_Value 
+     FROM ${tableName}`
+  ).join(' UNION ALL ');
+
+  const createCombinedViewSql = `CREATE VIEW IF NOT EXISTS combined_cgm_tracing AS ${combinedUnionAllQuery};`;
+
+  console.log(`Creating combined view with SQL:\n${createCombinedViewSql}`);
+
+  try {
+    db.execute(createCombinedViewSql);
+    console.log("Combined view 'combined_cgm_tracing' created successfully.");
+  } catch (error) {
+    console.error("Error creating combined view 'combined_cgm_tracing':", error);
+    const sqlQuery = "INSERT INTO error_log (error_message) VALUES (?);";
+    const params = JSON.stringify({ message: error.message });
+
+    // Combine into a single string
+    const combinedString = `${sqlQuery} Params: ${params}`;
+
+    console.log(combinedString);
+
+    // Insert error log as JSON
+    db.execute(combinedString);
+  }
+} else {
+  console.log("No participant tables found, so the combined view will not be created.");
+}
+
+// Close the database connection
+db.close();
+console.log(`Closed database: ${dbFilePath}`);

lib/service/diabetes-research-hub/package.sql.ts

@@ -303,15 +303,15 @@ export class DRHSqlPages extends spn.TypicalSqlPageNotebook {
     SELECT
       'These are scientific professionals and medical experts who design and conduct studies related to diabetes management and treatment. Their expertise ranges from clinical research to data analysis, and they are crucial in interpreting results and guiding future research directions.Principal investigators lead the research projects, overseeing the study design, implementation, and data collection. They ensure the research adheres to ethical standards and provides valuable insights into diabetes management.' as contents;
     SELECT 'table' as component, 1 as search, 1 as sort, 1 as hover, 1 as striped_rows;
-    SELECT * from drh_investigator_data;
+    SELECT * from drh_investigator;
 
     SELECT
       'text' as component,
       'Institution' as title;
     SELECT
       'The researchers and investigators are associated with various institutions, including universities, research institutes, and hospitals. These institutions provide the necessary resources, facilities, and support for conducting high-quality research. Each institution brings its unique strengths and expertise to the collaborative research efforts.' as contents;
     SELECT 'table' as component, 1 as search, 1 as sort, 1 as hover, 1 as striped_rows;
-    SELECT * from drh_institution_data;
+    SELECT * from drh_institution;
 
 
     SELECT
@@ -320,7 +320,7 @@ export class DRHSqlPages extends spn.TypicalSqlPageNotebook {
     SELECT
       'Within these institutions, specialized labs are equipped with state-of-the-art technology to conduct diabetes research. These labs focus on different aspects of diabetes studies, such as glucose monitoring, metabolic analysis, and data processing. They play a critical role in executing experiments, analyzing samples, and generating data that drive research conclusions.' as contents;
     SELECT 'table' as component, 1 as search, 1 as sort, 1 as hover, 1 as striped_rows;
-    SELECT * from drh_lab_data;
+    SELECT * from drh_lab;
 
 
 
@@ -334,7 +334,7 @@ export class DRHSqlPages extends spn.TypicalSqlPageNotebook {
     siblingOrder: 5,
   })
   "drh/study-related-data/index.sql"() {
-    const viewName = `drh_participant_data`;
+    const viewName = `drh_participant`;
     const pagination = this.pagination({ tableOrViewName: viewName });
     return this.SQL`
   ${this.activePageTitle()}
@@ -357,7 +357,7 @@ export class DRHSqlPages extends spn.TypicalSqlPageNotebook {
   ' as contents_md;
 
   SELECT 'table' as component, 1 as search, 1 as sort, 1 as hover, 1 as striped_rows;
-  SELECT * from drh_study_data;
+  SELECT * from drh_study;
 
 
       SELECT
@@ -378,7 +378,7 @@ Research sites are locations where the studies are conducted. They include clini
       ' as contents_md;
 
       SELECT 'table' as component, 1 as search, 1 as sort, 1 as hover, 1 as striped_rows;
-      SELECT * from drh_site_data;
+      SELECT * from drh_site;
 
 
 
@@ -391,7 +391,7 @@ Research sites are locations where the studies are conducted. They include clini
     siblingOrder: 6,
   })
   "drh/uniform-resource-participant.sql"() {
-    const viewName = `drh_participant_data`;
+    const viewName = `drh_participant`;
     const pagination = this.pagination({ tableOrViewName: viewName });
     return this.SQL`
     ${this.activePageTitle()}
@@ -441,7 +441,7 @@ This section contains information about the authors involved in study publicatio
       ' as contents_md;
 
   SELECT 'table' as component, 1 as search, 1 as sort, 1 as hover, 1 as striped_rows;
-  SELECT * from drh_author_data;
+  SELECT * from drh_author;
   SELECT
   'text' as component,
   '
@@ -461,7 +461,7 @@ This section provides information about the publications resulting from a study.
   ' as contents_md;
 
   SELECT 'table' as component, 1 as search, 1 as sort, 1 as hover, 1 as striped_rows;
-  SELECT * from drh_publication_data;
+  SELECT * from drh_publication;
 
 
       `;
@@ -694,43 +694,43 @@ select
       'MRN: ' || participant_id || '' AS title,
       ' ' AS description
   FROM
-      drh_participant_data
+      drh_participant
   WHERE participant_id = $participant_id;
 
   SELECT
       'Study: ' || study_arm || '' AS title,
       ' ' AS description
   FROM
-      drh_participant_data
+      drh_participant
   WHERE participant_id = $participant_id;
 
   
   SELECT
       'Age: '|| age || ' Years' AS title,
       ' ' AS description
   FROM
-      drh_participant_data
+      drh_participant
   WHERE participant_id = $participant_id;
 
   SELECT
       'hba1c: ' || baseline_hba1c || '' AS title,
       ' ' AS description
   FROM
-      drh_participant_data
+      drh_participant
   WHERE participant_id = $participant_id;
 
   SELECT
       'BMI: '|| bmi || '' AS title,
       ' ' AS description
   FROM
-      drh_participant_data
+      drh_participant
   WHERE participant_id = $participant_id;
 
   SELECT
       'Diabetes Type: '|| diabetes_type || ''  AS title,
       ' ' AS description
   FROM
-      drh_participant_data
+      drh_participant
   WHERE participant_id = $participant_id;
 
   SELECT
@@ -766,7 +766,7 @@ select
     siblingOrder: 12,
   })
   "drh/study-participant-dashboard/index.sql"() {
-    const viewName = `drh_participant_data`;
+    const viewName = `drh_participant`;
     const pagination = this.pagination({ tableOrViewName: viewName });
     return this.SQL`
   ${this.activePageTitle()}
@@ -987,7 +987,7 @@ SELECT
     siblingOrder: 19,
   })
   "drh/participant-related-data/index.sql"() {
-    const viewName = `drh_participant_data`;
+    const viewName = `drh_participant`;
     const pagination = this.pagination({ tableOrViewName: viewName });
     return this.SQL`
   ${this.activePageTitle()}

lib/service/diabetes-research-hub/stateless.sql

@@ -1,6 +1,6 @@
--- Drop and recreate the device_data view
-DROP VIEW IF EXISTS drh_device_data;
-CREATE VIEW drh_device_data AS
+-- Drop and recreate the device view
+DROP VIEW IF EXISTS drh_device;
+CREATE VIEW drh_device AS
 SELECT device_id, name, created_at
 FROM device d;
 
@@ -64,9 +64,9 @@ SELECT
     input_text, exec_error_text, output_text, output_nature, narrative_md
 FROM orchestration_session_exec;
 
--- Drop and recreate the study_data view
-DROP VIEW IF EXISTS drh_study_data;
-CREATE VIEW drh_study_data AS
+-- Drop and recreate the study view
+DROP VIEW IF EXISTS drh_study;
+CREATE VIEW drh_study AS
 SELECT
     study_id, study_name, start_date, end_date, treatment_modalities,
     funding_source, nct_number, study_description
@@ -82,54 +82,54 @@ SELECT
     data_end_date, study_id
 FROM uniform_resource_cgm_file_metadata;
 
--- Drop and recreate the author_data view
-DROP VIEW IF EXISTS drh_author_data;
-CREATE VIEW drh_author_data AS
+-- Drop and recreate the author view
+DROP VIEW IF EXISTS drh_author;
+CREATE VIEW drh_author AS
 SELECT
     author_id, name, email, investigator_id, study_id
 FROM uniform_resource_author;
 
--- Drop and recreate the institution_data view
-DROP VIEW IF EXISTS drh_institution_data;
-CREATE VIEW drh_institution_data AS
+-- Drop and recreate the institution view
+DROP VIEW IF EXISTS drh_institution;
+CREATE VIEW drh_institution AS
 SELECT
     institution_id, institution_name, city, state, country
 FROM uniform_resource_institution;
 
--- Drop and recreate the investigator_data view
-DROP VIEW IF EXISTS drh_investigator_data;
-CREATE VIEW drh_investigator_data AS
+-- Drop and recreate the investigator view
+DROP VIEW IF EXISTS drh_investigator;
+CREATE VIEW drh_investigator AS
 SELECT
     investigator_id, investigator_name, email, institution_id, study_id
 FROM uniform_resource_investigator;
 
--- Drop and recreate the lab_data view
-DROP VIEW IF EXISTS drh_lab_data;
-CREATE VIEW drh_lab_data AS
+-- Drop and recreate the lab view
+DROP VIEW IF EXISTS drh_lab;
+CREATE VIEW drh_lab AS
 SELECT
     lab_id, lab_name, lab_pi, institution_id, study_id
 FROM uniform_resource_lab;
 
--- Drop and recreate the participant_data view
-DROP VIEW IF EXISTS drh_participant_data;
-CREATE VIEW drh_participant_data AS
+-- Drop and recreate the participant view
+DROP VIEW IF EXISTS drh_participant;
+CREATE VIEW drh_participant AS
 SELECT
     participant_id, study_id, site_id, diagnosis_icd, med_rxnorm,
     treatment_modality, gender, race_ethnicity, age, bmi, baseline_hba1c,
     diabetes_type, study_arm
 FROM uniform_resource_participant;
 
--- Drop and recreate the publication_data view
-DROP VIEW IF EXISTS drh_publication_data;
-CREATE VIEW drh_publication_data AS
+-- Drop and recreate the publication view
+DROP VIEW IF EXISTS drh_publication;
+CREATE VIEW drh_publication AS
 SELECT
     publication_id, publication_title, digital_object_identifier,
     publication_site, study_id
 FROM uniform_resource_publication;
 
--- Drop and recreate the site_data view
-DROP VIEW IF EXISTS drh_site_data;
-CREATE VIEW drh_site_data AS
+-- Drop and recreate the site view
+DROP VIEW IF EXISTS drh_site;
+CREATE VIEW drh_site AS
 SELECT
     study_id, site_id, site_name, site_type
 FROM uniform_resource_site;
@@ -268,8 +268,8 @@ LEFT JOIN uniform_resource_investigator i ON s.study_id = i.study_id
 GROUP BY s.study_id, s.study_name, s.study_description, s.start_date, s.end_date, s.nct_number;
 
 
-DROP TABLE IF EXISTS raw_cgm_data_lst_cached;
-CREATE TABLE raw_cgm_data_lst_cached AS 
+DROP TABLE IF EXISTS raw_cgm_lst_cached;
+CREATE TABLE raw_cgm_lst_cached AS 
   SELECT * FROM drh_raw_cgm_table_lst;
 
 DROP VIEW IF EXISTS drh_study_files_table_info;