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CRDCDH-1839 #555

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CRDCDH-1839 #555

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6d99bed
move configuration to MongoDB
knockknockyoo Nov 13, 2024
2fec35f
update submission config
knockknockyoo Nov 14, 2024
dadbe4c
Merge remote-tracking branch 'origin/3.2.0' into CRDCDH-1839
knockknockyoo Nov 14, 2024
9e3111b
Replaced notify days conf
knockknockyoo Nov 14, 2024
fc83ba3
merge the current config
knockknockyoo Nov 14, 2024
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40 changes: 19 additions & 21 deletions app.js
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Original file line number Diff line number Diff line change
Expand Up @@ -4,23 +4,23 @@ const {join} = require("path");
const cors = require('cors');
const logger = require('morgan');
const createError = require('http-errors');
const config = require('./config');
const configuration = require('./config');
const cronJob = require("node-cron");
const createSession = require("./crdc-datahub-database-drivers/session-middleware");
const statusRouter = require("./routers/status-endpoints-router");
const graphqlRouter = require("./routers/graphql-router");
const {MongoDBCollection} = require("./crdc-datahub-database-drivers/mongodb-collection");
const {DATABASE_NAME, APPLICATION_COLLECTION, USER_COLLECTION, LOG_COLLECTION, APPROVED_STUDIES_COLLECTION,
ORGANIZATION_COLLECTION, SUBMISSIONS_COLLECTION, BATCH_COLLECTION, DATA_RECORDS_COLLECTION, VALIDATION_COLLECTION,
CONFIGURATION_COLLECTION, DATA_RECORDS_ARCHIVE_COLLECTION
DATA_RECORDS_ARCHIVE_COLLECTION, QC_RESULTS_COLLECTION
} = require("./crdc-datahub-database-drivers/database-constants");
const {Application} = require("./services/application");
const {Submission} = require("./services/submission");
const {DataRecordService} = require("./services/data-record-service");
const {S3Service} = require("./crdc-datahub-database-drivers/services/s3-service");
const {MongoQueries} = require("./crdc-datahub-database-drivers/mongo-queries");
const {DatabaseConnector} = require("./crdc-datahub-database-drivers/database-connector");
const {getCurrentTime, subtractDaysFromNow} = require("./crdc-datahub-database-drivers/utility/time-utility");
const {getCurrentTime} = require("./crdc-datahub-database-drivers/utility/time-utility");
const {EmailService} = require("./services/email");
const {NotifyUser} = require("./services/notify-user");
const {User} = require("./crdc-datahub-database-drivers/services/user");
Expand All @@ -32,10 +32,9 @@ const {LOGIN, REACTIVATE_USER} = require("./crdc-datahub-database-drivers/consta
const {BatchService} = require("./services/batch-service");
const {AWSService} = require("./services/aws-request");
const {UtilityService} = require("./services/utility");
const authenticationMiddleware = require("./middleware/authentication-middleware");
const {ConfigurationService} = require("./services/configurationService");
const {QcResultService} = require("./services/qc-result-service");
// print environment variables to log
console.info(config);
console.info(configuration);

// create logs folder if it does not already exist
const LOGS_FOLDER = 'logs';
Expand All @@ -56,7 +55,7 @@ app.use(express.static(join(__dirname, 'public')));
app.use("/", statusRouter);

// create session
app.use(createSession(config.session_secret, config.session_timeout, config.mongo_db_connection_string));
app.use(createSession(configuration.session_secret, configuration.session_timeout, configuration.mongo_db_connection_string));

// // authentication middleware
// app.use(async (req, res, next) => {
Expand All @@ -70,22 +69,18 @@ app.use(createSession(config.session_secret, config.session_timeout, config.mong

// add graphql endpoint
app.use("/api/graphql", graphqlRouter);
const INACTIVE_SUBMISSION_DAYS = "Inactive_Submission_Notify_Days";
cronJob.schedule(config.schedule_job, async () => {
const dbConnector = new DatabaseConnector(config.mongo_db_connection_string);
const dbService = new MongoQueries(config.mongo_db_connection_string, DATABASE_NAME);
const emailService = new EmailService(config.email_transport, config.emails_enabled);
const notificationsService = new NotifyUser(emailService);
cronJob.schedule(configuration.schedule_job, async () => {
const dbConnector = new DatabaseConnector(configuration.mongo_db_connection_string);
const dbService = new MongoQueries(configuration.mongo_db_connection_string, DATABASE_NAME);
dbConnector.connect().then( async () => {
const config = await configuration.updateConfig(dbConnector);
const emailService = new EmailService(config.email_transport, config.emails_enabled);
const notificationsService = new NotifyUser(emailService, config.committee_emails);
const applicationCollection = new MongoDBCollection(dbConnector.client, DATABASE_NAME, APPLICATION_COLLECTION);
const userCollection = new MongoDBCollection(dbConnector.client, DATABASE_NAME, USER_COLLECTION);

const configurationCollection = new MongoDBCollection(dbConnector.client, DATABASE_NAME, CONFIGURATION_COLLECTION);
const configurationService = new ConfigurationService(configurationCollection)
const inactiveSubmissionConf = await configurationService.findByType(INACTIVE_SUBMISSION_DAYS);
const inactiveSubmissionsTimeout = Array.isArray(inactiveSubmissionConf?.timeout) && inactiveSubmissionConf?.timeout?.length > 0 ? inactiveSubmissionConf?.timeout : [7, 30, 60];
const emailParams = {url: config.emails_url, officialEmail: config.official_email, inactiveDays: config.inactive_application_days, remindDay: config.remind_application_days,
submissionSystemPortal: config.submission_system_portal, submissionHelpdesk: config.submission_helpdesk, remindSubmissionDay: inactiveSubmissionsTimeout,
submissionSystemPortal: config.submission_system_portal, submissionHelpdesk: config.submission_helpdesk, remindSubmissionDay: config.inactiveSubmissionNotifyDays,
finalRemindSubmissionDay: config.inactive_submission_days || 120};
const logCollection = new MongoDBCollection(dbConnector.client, DATABASE_NAME, LOG_COLLECTION);
const approvedStudiesCollection = new MongoDBCollection(dbConnector.client, DATABASE_NAME, APPROVED_STUDIES_COLLECTION);
Expand All @@ -94,16 +89,19 @@ cronJob.schedule(config.schedule_job, async () => {
const organizationCollection = new MongoDBCollection(dbConnector.client, DATABASE_NAME, ORGANIZATION_COLLECTION);
const organizationService = new Organization(organizationCollection);
const submissionCollection = new MongoDBCollection(dbConnector.client, DATABASE_NAME, SUBMISSIONS_COLLECTION);
const userService = new User(userCollection, logCollection, organizationCollection, notificationsService, submissionCollection, applicationCollection, config.official_email, config.tier);
const userService = new User(userCollection, logCollection, organizationCollection, notificationsService, submissionCollection, applicationCollection, config.official_email, config.tier, config.inactive_user_days);

const s3Service = new S3Service();
const batchCollection = new MongoDBCollection(dbConnector.client, DATABASE_NAME, BATCH_COLLECTION);
const awsService = new AWSService(submissionCollection, userService);
const awsService = new AWSService(submissionCollection, userService, config.role_arn, config.presign_expiration);
const batchService = new BatchService(s3Service, batchCollection, config.sqs_loader_queue, awsService);

const qcResultCollection = new MongoDBCollection(dbConnector.client, DATABASE_NAME, QC_RESULTS_COLLECTION);
const qcResultsService = new QcResultService(qcResultCollection, submissionCollection);

const dataRecordCollection = new MongoDBCollection(dbConnector.client, DATABASE_NAME, DATA_RECORDS_COLLECTION);
const dataRecordArchiveCollection = new MongoDBCollection(dbConnector.client, DATABASE_NAME, DATA_RECORDS_ARCHIVE_COLLECTION);
const dataRecordService = new DataRecordService(dataRecordCollection, dataRecordArchiveCollection, config.file_queue, config.metadata_queue, awsService);
const dataRecordService = new DataRecordService(dataRecordCollection, dataRecordArchiveCollection, config.file_queue, config.metadata_queue, awsService, s3Service, qcResultsService, config.export_queue);

const utilityService = new UtilityService();
const dataModelInfo = await utilityService.fetchJsonFromUrl(config.model_url);
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