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2026 04 gg vsac fix #197

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Merged
grahamegrieve merged 2 commits into from
Apr 7, 2026
Merged

2026 04 gg vsac fix #197

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73c9417
fix bug handling excluded concepts using a filter
grahamegrieve Apr 7, 2026
e65201f
VSAC upgrade to pick up more changes
grahamegrieve Apr 7, 2026
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250 changes: 150 additions & 100 deletions tx/vs/vs-database.js
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Original file line number Diff line number Diff line change
Expand Up @@ -37,23 +37,32 @@ class ValueSetDatabase {
if (!hasCol) {
migrations.push(new Promise((res, rej) => {
db.run(
"ALTER TABLE valuesets ADD COLUMN date_first_seen INTEGER DEFAULT 0",
[],
(err) => err ? rej(err) : res()
"ALTER TABLE valuesets ADD COLUMN date_first_seen INTEGER DEFAULT 0",
[],
(err) => err ? rej(err) : res()
);
}));
}
// Ensure vsac_runs table exists
migrations.push(new Promise((res, rej) => {
db.run(`
CREATE TABLE IF NOT EXISTS vsac_runs (
id INTEGER PRIMARY KEY AUTOINCREMENT,
started_at INTEGER NOT NULL,
finished_at INTEGER,
status TEXT NOT NULL DEFAULT 'running',
error_message TEXT,
total_fetched INTEGER,
total_new INTEGER
id INTEGER PRIMARY KEY AUTOINCREMENT,
started_at INTEGER NOT NULL,
finished_at INTEGER,
status TEXT NOT NULL DEFAULT 'running',
error_message TEXT,
total_fetched INTEGER,
total_new INTEGER
)
`, [], (err) => err ? rej(err) : res());
}));
// Ensure vsac_settings table exists (for _lastUpdated tracking etc.)
migrations.push(new Promise((res, rej) => {
db.run(`
CREATE TABLE IF NOT EXISTS vsac_settings (
key TEXT PRIMARY KEY,
value TEXT
)
`, [], (err) => err ? rej(err) : res());
}));
Expand Down Expand Up @@ -170,69 +179,77 @@ class ValueSetDatabase {
db.serialize(() => {
// Main value sets table
db.run(`
CREATE TABLE valuesets (
id TEXT PRIMARY KEY,
url TEXT,
version TEXT,
date TEXT,
description TEXT,
effectivePeriod_start TEXT,
effectivePeriod_end TEXT,
expansion_identifier TEXT,
name TEXT,
publisher TEXT,
status TEXT,
title TEXT,
content TEXT NOT NULL,
last_seen INTEGER DEFAULT (strftime('%s', 'now')),
date_first_seen INTEGER DEFAULT (strftime('%s', 'now'))
)
CREATE TABLE valuesets (
id TEXT PRIMARY KEY,
url TEXT,
version TEXT,
date TEXT,
description TEXT,
effectivePeriod_start TEXT,
effectivePeriod_end TEXT,
expansion_identifier TEXT,
name TEXT,
publisher TEXT,
status TEXT,
title TEXT,
content TEXT NOT NULL,
last_seen INTEGER DEFAULT (strftime('%s', 'now')),
date_first_seen INTEGER DEFAULT (strftime('%s', 'now'))
)
`);

// Identifiers table (0..* Identifier)
db.run(`
CREATE TABLE valueset_identifiers (
valueset_id TEXT,
system TEXT,
value TEXT,
use_code TEXT,
type_system TEXT,
type_code TEXT,
FOREIGN KEY (valueset_id) REFERENCES valuesets(url)
)
CREATE TABLE valueset_identifiers (
valueset_id TEXT,
system TEXT,
value TEXT,
use_code TEXT,
type_system TEXT,
type_code TEXT,
FOREIGN KEY (valueset_id) REFERENCES valuesets(url)
)
`);

// Jurisdictions table (0..* CodeableConcept with 0..* Coding)
db.run(`
CREATE TABLE valueset_jurisdictions (
valueset_id TEXT,
system TEXT,
code TEXT,
display TEXT,
FOREIGN KEY (valueset_id) REFERENCES valuesets(url)
)
CREATE TABLE valueset_jurisdictions (
valueset_id TEXT,
system TEXT,
code TEXT,
display TEXT,
FOREIGN KEY (valueset_id) REFERENCES valuesets(url)
)
`);

// Systems table (from compose.include[].system)
db.run(`
CREATE TABLE valueset_systems (
valueset_id TEXT,
system TEXT,
version TEXT,
FOREIGN KEY (valueset_id) REFERENCES valuesets(url)
)
CREATE TABLE valueset_systems (
valueset_id TEXT,
system TEXT,
version TEXT,
FOREIGN KEY (valueset_id) REFERENCES valuesets(url)
)
`);

// Run tracking table
db.run(`
CREATE TABLE vsac_runs (
id INTEGER PRIMARY KEY AUTOINCREMENT,
started_at INTEGER NOT NULL,
finished_at INTEGER,
status TEXT NOT NULL DEFAULT 'running',
error_message TEXT,
total_fetched INTEGER,
total_new INTEGER
CREATE TABLE vsac_runs (
id INTEGER PRIMARY KEY AUTOINCREMENT,
started_at INTEGER NOT NULL,
finished_at INTEGER,
status TEXT NOT NULL DEFAULT 'running',
error_message TEXT,
total_fetched INTEGER,
total_new INTEGER
)
`);

// Settings table (key-value store for _lastUpdated tracking etc.)
db.run(`
CREATE TABLE IF NOT EXISTS vsac_settings (
key TEXT PRIMARY KEY,
value TEXT
)
`);

Expand Down Expand Up @@ -271,9 +288,9 @@ class ValueSetDatabase {
const db = await this._getWriteConnection();
return new Promise((resolve, reject) => {
db.run(
`INSERT INTO vsac_runs (started_at, status) VALUES (strftime('%s','now'), 'running')`,
[],
function(err) { err ? reject(err) : resolve(this.lastID); }
`INSERT INTO vsac_runs (started_at, status) VALUES (strftime('%s','now'), 'running')`,
[],
function(err) { err ? reject(err) : resolve(this.lastID); }
);
});
}
Expand All @@ -289,10 +306,10 @@ class ValueSetDatabase {
const db = await this._getWriteConnection();
return new Promise((resolve, reject) => {
db.run(
`UPDATE vsac_runs SET finished_at = strftime('%s','now'), status = 'ok',
total_fetched = ?, total_new = ? WHERE id = ?`,
[totalFetched, totalNew, id],
err => err ? reject(err) : resolve()
`UPDATE vsac_runs SET finished_at = strftime('%s','now'), status = 'ok',
total_fetched = ?, total_new = ? WHERE id = ?`,
[totalFetched, totalNew, id],
err => err ? reject(err) : resolve()
);
});
}
Expand All @@ -307,10 +324,43 @@ class ValueSetDatabase {
const db = await this._getWriteConnection();
return new Promise((resolve, reject) => {
db.run(
`UPDATE vsac_runs SET finished_at = strftime('%s','now'), status = 'error',
error_message = ? WHERE id = ?`,
[errorMessage, id],
err => err ? reject(err) : resolve()
`UPDATE vsac_runs SET finished_at = strftime('%s','now'), status = 'error',
error_message = ? WHERE id = ?`,
[errorMessage, id],
err => err ? reject(err) : resolve()
);
});
}

/**
* Get a setting value from the vsac_settings table
* @param {string} key - The setting key
* @returns {Promise<string|null>} The setting value, or null if not found
*/
async getSetting(key) {
const db = await this._getReadConnection();
return new Promise((resolve, reject) => {
db.get('SELECT value FROM vsac_settings WHERE key = ?', [key], (err, row) => {
if (err) reject(err);
else resolve(row ? row.value : null);
});
});
}

/**
* Set a setting value in the vsac_settings table
* @param {string} key - The setting key
* @param {string} value - The setting value
* @returns {Promise<void>}
*/
async setSetting(key, value) {
const db = await this._getWriteConnection();
return new Promise((resolve, reject) => {
db.run(
`INSERT INTO vsac_settings (key, value) VALUES (?, ?)
ON CONFLICT(key) DO UPDATE SET value = excluded.value`,
[key, value],
err => err ? reject(err) : resolve()
);
});
}
Expand Down Expand Up @@ -353,24 +403,24 @@ class ValueSetDatabase {
const expansionId = valueSet.expansion?.identifier || null;

db.run(`
INSERT INTO valuesets (
id, url, version, date, description, effectivePeriod_start, effectivePeriod_end,
expansion_identifier, name, publisher, status, title, content, last_seen, date_first_seen
) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, strftime('%s', 'now'), strftime('%s', 'now'))
ON CONFLICT(id) DO UPDATE SET
url=excluded.url,
version=excluded.version,
date=excluded.date,
description=excluded.description,
effectivePeriod_start=excluded.effectivePeriod_start,
effectivePeriod_end=excluded.effectivePeriod_end,
expansion_identifier=excluded.expansion_identifier,
name=excluded.name,
publisher=excluded.publisher,
status=excluded.status,
title=excluded.title,
content=excluded.content,
last_seen=strftime('%s', 'now')
INSERT INTO valuesets (
id, url, version, date, description, effectivePeriod_start, effectivePeriod_end,
expansion_identifier, name, publisher, status, title, content, last_seen, date_first_seen
) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, strftime('%s', 'now'), strftime('%s', 'now'))
ON CONFLICT(id) DO UPDATE SET
url=excluded.url,
version=excluded.version,
date=excluded.date,
description=excluded.description,
effectivePeriod_start=excluded.effectivePeriod_start,
effectivePeriod_end=excluded.effectivePeriod_end,
expansion_identifier=excluded.expansion_identifier,
name=excluded.name,
publisher=excluded.publisher,
status=excluded.status,
title=excluded.title,
content=excluded.content,
last_seen=strftime('%s', 'now')
`, [
valueSet.id,
valueSet.url,
Expand Down Expand Up @@ -414,10 +464,10 @@ class ValueSetDatabase {

return new Promise((resolve, reject) => {
db.run(`
update valuesets
set last_seen = strftime('%s', 'now')
where url = ?
and version = ?
update valuesets
set last_seen = strftime('%s', 'now')
where url = ?
and version = ?
`, [
valueSet.url,
valueSet.version
Expand Down Expand Up @@ -466,9 +516,9 @@ class ValueSetDatabase {
const typeCode = id.type?.coding?.[0]?.code || null;

db.run(`
INSERT INTO valueset_identifiers (
valueset_id, system, value, use_code, type_system, type_code
) VALUES (?, ?, ?, ?, ?, ?)
INSERT INTO valueset_identifiers (
valueset_id, system, value, use_code, type_system, type_code
) VALUES (?, ?, ?, ?, ?, ?)
`, [
valueSet.id,
id.system || null,
Expand All @@ -490,9 +540,9 @@ class ValueSetDatabase {
for (const coding of jurisdiction.coding) {
pendingOperations++;
db.run(`
INSERT INTO valueset_jurisdictions (
valueset_id, system, code, display
) VALUES (?, ?, ?, ?)
INSERT INTO valueset_jurisdictions (
valueset_id, system, code, display
) VALUES (?, ?, ?, ?)
`, [
valueSet.id,
coding.system || null,
Expand All @@ -514,7 +564,7 @@ class ValueSetDatabase {
pendingOperations++;

db.run(`
INSERT INTO valueset_systems (valueset_id, system, version) VALUES (?, ?, ?)
INSERT INTO valueset_systems (valueset_id, system, version) VALUES (?, ?, ?)
`, [valueSet.id, include.system, include.version], function(err) {
if (err) {
operationError(new Error(`Failed to insert system: ${err.message}`));
Expand Down Expand Up @@ -598,12 +648,12 @@ class ValueSetDatabase {
async search(spaceId, map, searchParams, elements = null) {
// Check if we can optimize by selecting only indexed columns
const canOptimize = elements && elements.length > 0 &&
elements.every(e => INDEXED_COLUMNS.includes(e));
elements.every(e => INDEXED_COLUMNS.includes(e));

// Always include 'id' in the columns to select when optimizing
const columnsToSelect = canOptimize
? (elements.includes('id') ? elements : ['id', ...elements])
: null;
? (elements.includes('id') ? elements : ['id', ...elements])
: null;

const db = await this._getReadConnection();

Expand Down
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