Assure UTC time stored in MySQL by using an aware object

README.md

@@ -48,7 +48,7 @@ cd docker
 ./docker-development.sh [check|config|build|start|stop|down]
 ```
 
-## Docker build for deployment on TEST/STAGE/PROD
+## Docker build for deployment on PROD
 
 ```
 cd hubmap-docker
@@ -57,13 +57,6 @@ cd hubmap-docker
 
 ## Development process
 
-### To release via TEST infrastructure
-- Make new feature or bug fix branches from `main` branch (the default branch)
-- Make PRs to `main`
-- As a codeowner, Zhou (github username `yuanzhou`) is automatically assigned as a reviewer to each PR. When all other reviewers have approved, he will approve as well, merge to TEST infrastructure, and redeploy the TEST instance.
-- Developer or someone on the team who is familiar with the change will test/qa the change
-- When any current changes in the `main` have been approved after test/qa on TEST, Zhou will release to PROD using the same docker image that has been tested on TEST infrastructure.
-
 ### To work on features in the development environment before ready for testing and releasing
 - Make new feature branches off the `main` branch
 - Make PRs to `dev-integrate`
@@ -73,4 +66,4 @@ cd hubmap-docker
 
 ### Updating API Documentation
 
-The documentation for the API calls is hosted on SmartAPI. Modifying the `uuid-api-spec.yaml` file and commititng the changes to github should update the API shown on SmartAPI.  SmartAPI allows users to register API documents. The documentation is associated with this github account: [email protected]. 
+The documentation for the API calls is hosted on SmartAPI. Modifying the `uuid-api-spec.yaml` file and committing the changes to GitHub should update the API shown on SmartAPI.  SmartAPI allows users to register API documents. The documentation is associated with this GitHub account: [email protected]. 

sql/README.md

@@ -48,3 +48,11 @@ Click "Next".  Examine the generated SQL script to assure it is independent of t
 
 Click "Cancel" to abandon the rest of the "forward engineer" process.
 
+## Create as database in which DDL script will execute
+A database should be created on the server to receive the DDL commands generated by "forward engineer."
+
+Ways of creating the database vary by platform (e.g. MySQL Workbench, dBeaver, mysql AKA the command line client.) The essential command to run is:
+````
+CREATE DATABASE `hm_kbkbkb_uuid`
+````
+Note the backquotes of this command.  Also decide whether you want to start with a customized name, and how you will manage that if the database will eventually become Dev, Stage, or Prod.

sql/uuid-api.sql

@@ -14,7 +14,7 @@ SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='ONLY_FULL_GROUP_BY,STRICT_TRANS_TABLES,N
 CREATE TABLE IF NOT EXISTS `uuids` (
   `UUID` CHAR(32) NOT NULL,
   `ENTITY_TYPE` VARCHAR(20) NOT NULL,
-  `TIME_GENERATED` TIMESTAMP NOT NULL,
+  `TIME_GENERATED` TIMESTAMP NOT NULL DEFAULT now(),
   `USER_ID` VARCHAR(50) NOT NULL,
   `USER_EMAIL` VARCHAR(50) NULL DEFAULT NULL,
   PRIMARY KEY (`UUID`))
@@ -77,6 +77,7 @@ CREATE TABLE IF NOT EXISTS `files` (
   `PATH` MEDIUMTEXT NULL DEFAULT NULL,
   `CHECKSUM` VARCHAR(50) NULL DEFAULT NULL,
   `SIZE` BIGINT NULL DEFAULT NULL,
+  `LAST_MODIFIED` TIMESTAMP NOT NULL DEFAULT now() ON UPDATE now(),
   PRIMARY KEY (`UUID`),
   CONSTRAINT `files_ibfk_1`
     FOREIGN KEY (`UUID`)

src/uuid_worker.py

@@ -1,3 +1,4 @@
+from datetime import datetime, timezone
 import logging
 
 import mysql.connector.errors
@@ -611,7 +612,9 @@ def newUUIDs(self, parentIDs, entityType, userId, userEmail, nIds, organ_code=No
         # if entityType == 'DONOR':
         gen_base_ids = entityType in ID_ENTITY_TYPES
         returnIds = []
-        now = time.strftime('%Y-%m-%d %H:%M:%S')
+        # See admonition at https://docs.python.org/3/library/datetime.html#datetime.datetime.utcnow to
+        # retrieve a non-naive UTC time.
+        awareUTCTimeNow = datetime.now(timezone.utc)
         store_file_info = False
         if entityType == 'FILE':
             store_file_info = True
@@ -673,7 +676,7 @@ def newUUIDs(self, parentIDs, entityType, userId, userEmail, nIds, organ_code=No
                     #     insRow = (insUuid, ins_app_base_id, entityType, now, userId, userEmail)
 
                     # Only set the attributes tuple of committing attributes to the table besides the UUID
-                    insertVals.append((insUuid, entityType, now, userId, userEmail))
+                    insertVals.append((insUuid, entityType, awareUTCTimeNow, userId, userEmail))
                     if insert_attributes_for_uuid:
                         insertAttribVals.append((insUuid, ins_app_base_id, submission_ids[n] if gen_submission_ids else None))