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PostgreSQL migration: now both SQLite3 and PostgreSQL 15 databases ar…
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…e supported by server and DAO layer.
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@vmdocua
vmdocua committed Sep 6, 2023
1 parent 9bfb304 commit 14b0587
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735 changes: 735 additions & 0 deletions db/db_dev_postgres15.sql
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175 changes: 175 additions & 0 deletions db/db_dev_sqlite3.sql
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PRAGMA foreign_keys=OFF;
BEGIN TRANSACTION;
CREATE TABLE IF NOT EXISTS "sec_user_role" (
"id" INTEGER NOT NULL UNIQUE,
"user_id" INTEGER NOT NULL,
"role_id" INTEGER NOT NULL,
PRIMARY KEY("id" AUTOINCREMENT),
UNIQUE("user_id","role_id")
);
INSERT INTO sec_user_role VALUES(1,4,1);
INSERT INTO sec_user_role VALUES(2,1,2);
INSERT INTO sec_user_role VALUES(3,2,3);
INSERT INTO sec_user_role VALUES(4,3,4);
INSERT INTO sec_user_role VALUES(5,5,4);
INSERT INTO sec_user_role VALUES(6,5,2);
INSERT INTO sec_user_role VALUES(7,5,3);
INSERT INTO sec_user_role VALUES(8,6,5);
INSERT INTO sec_user_role VALUES(9,1,1);
INSERT INTO sec_user_role VALUES(10,5,5);
CREATE TABLE IF NOT EXISTS "message_category" (
"id" INTEGER NOT NULL UNIQUE,
"category" VARCHAR(45),
PRIMARY KEY("id" AUTOINCREMENT)
);
INSERT INTO message_category VALUES(1,'Feedback');
CREATE TABLE IF NOT EXISTS "data_provider" (
"id" INTEGER NOT NULL UNIQUE,
"provider" VARCHAR(15) NOT NULL UNIQUE,
PRIMARY KEY("id" AUTOINCREMENT)
);
INSERT INTO data_provider VALUES(1,'ReproIn');
INSERT INTO data_provider VALUES(2,'ReproStim');
INSERT INTO data_provider VALUES(3,'ReproEvents');
INSERT INTO data_provider VALUES(4,'PACS');
INSERT INTO data_provider VALUES(5,'Noisseur');
INSERT INTO data_provider VALUES(6,'DICOM/QA');
INSERT INTO data_provider VALUES(7,'MRI');
CREATE TABLE IF NOT EXISTS "study_status" (
"id" INTEGER NOT NULL UNIQUE,
"status" VARCHAR(45),
PRIMARY KEY("id" AUTOINCREMENT)
);
INSERT INTO study_status VALUES(100,'New');
INSERT INTO study_status VALUES(101,'Collecting MRI Data');
INSERT INTO study_status VALUES(190,'Completed');
INSERT INTO study_status VALUES(191,'Failed');
INSERT INTO study_status VALUES(200,'Entering Participant Data');
INSERT INTO study_status VALUES(300,'Designing Sequences');
CREATE TABLE IF NOT EXISTS "todo_study_session" (
"id" INTEGER NOT NULL UNIQUE,
PRIMARY KEY("id" AUTOINCREMENT)
);
CREATE TABLE IF NOT EXISTS "todo_study_screen" (
"id" INTEGER NOT NULL UNIQUE,
PRIMARY KEY("id" AUTOINCREMENT)
);
CREATE TABLE IF NOT EXISTS "message_level" (
"id" INTEGER NOT NULL UNIQUE,
"level" VARCHAR(8),
PRIMARY KEY("id")
);
INSERT INTO message_level VALUES(1,'INFO');
INSERT INTO message_level VALUES(2,'WARNING');
INSERT INTO message_level VALUES(3,'ERROR');
CREATE TABLE IF NOT EXISTS "device" (
"id" INTEGER NOT NULL UNIQUE,
"kind" VARCHAR(15),
"description" VARCHAR(128),
PRIMARY KEY("id" AUTOINCREMENT)
);
INSERT INTO device VALUES(1,'MRI','DBIC 3T Siemens Prisma MRI');
CREATE TABLE IF NOT EXISTS "sec_user_device" (
"id" INTEGER NOT NULL UNIQUE,
"user_id" INTEGER NOT NULL,
"device_id" INTEGER NOT NULL,
UNIQUE("user_id","device_id"),
PRIMARY KEY("id" AUTOINCREMENT)
);
INSERT INTO sec_user_device VALUES(1,1,1);
INSERT INTO sec_user_device VALUES(2,2,1);
INSERT INTO sec_user_device VALUES(3,3,1);
INSERT INTO sec_user_device VALUES(4,4,1);
INSERT INTO sec_user_device VALUES(5,5,1);
INSERT INTO sec_user_device VALUES(6,6,1);
CREATE TABLE IF NOT EXISTS "user" (
"id" INTEGER NOT NULL UNIQUE,
"username" VARCHAR(15) NOT NULL UNIQUE,
"is_active" CHAR(1) DEFAULT 'N',
"is_system" CHAR(1) NOT NULL DEFAULT 'N',
"first_name" VARCHAR(45),
"last_name" VARCHAR(45),
"email" VARCHAR(128) UNIQUE,
"phone" VARCHAR(16),
"description" VARCHAR(128),
"password" VARCHAR(45),
"password_changed_on" TIMESTAMP,
"last_login" TIMESTAMP,
PRIMARY KEY("id" AUTOINCREMENT),
UNIQUE("email")
);
INSERT INTO user VALUES(1,'user1','Y','N','John','Smith','[email protected]','321',NULL,'$2b$12$ShaYDykDo9yJe0sLxBCMqe0f4OhUXD9iZf4FYFhQIwNTt9/WNBkfq',NULL,NULL);
INSERT INTO user VALUES(2,'user2','Y','N','Dave','Cooper','[email protected]','231',NULL,'$2b$12$ShaYDykDo9yJe0sLxBCMqe0f4OhUXD9iZf4FYFhQIwNTt9/WNBkfq',NULL,NULL);
INSERT INTO user VALUES(3,'user3','Y','N','Lucy','Nelson','[email protected]','111',NULL,'$2b$12$ShaYDykDo9yJe0sLxBCMqe0f4OhUXD9iZf4FYFhQIwNTt9/WNBkfq',NULL,NULL);
INSERT INTO user VALUES(4,'admin','Y','N','Admin','Admin','[email protected]',NULL,'Administrator','$2b$12$ShaYDykDo9yJe0sLxBCMqe0f4OhUXD9iZf4FYFhQIwNTt9/WNBkfq',NULL,NULL);
INSERT INTO user VALUES(5,'poweruser','Y','N','Power','User','[email protected]',NULL,'Power user','$2b$12$ShaYDykDo9yJe0sLxBCMqe0f4OhUXD9iZf4FYFhQIwNTt9/WNBkfq',NULL,NULL);
INSERT INTO user VALUES(6,'noisseur','Y','Y','noisseur','noisseur','',NULL,'System con/noisseur user','$2b$12$ShaYDykDo9yJe0sLxBCMqe0f4OhUXD9iZf4FYFhQIwNTt9/WNBkfq',NULL,NULL);
INSERT INTO user VALUES(7,'reprostim','Y','Y','reprostim','reprostim',NULL,NULL,replace('ReproStim Screen Capture\n','\n',char(10)),'$2b$12$ShaYDykDo9yJe0sLxBCMqe0f4OhUXD9iZf4FYFhQIwNTt9/WNBkfq',NULL,NULL);
INSERT INTO user VALUES(8,'reproevt','Y','Y','reproevt','reproevt',NULL,NULL,replace('ReproEvents Capture\n','\n',char(10)),'$2b$12$ShaYDykDo9yJe0sLxBCMqe0f4OhUXD9iZf4FYFhQIwNTt9/WNBkfq',NULL,NULL);
INSERT INTO user VALUES(9,'dicomqa','Y','Y','dicomqa','dicomqa',NULL,NULL,'DICOMS/QA','$2b$12$ShaYDykDo9yJe0sLxBCMqe0f4OhUXD9iZf4FYFhQIwNTt9/WNBkfq',NULL,NULL);
CREATE TABLE IF NOT EXISTS "role" (
"id" INTEGER NOT NULL UNIQUE,
"rolename" VARCHAR(45) NOT NULL,
"description" VARCHAR(128),
UNIQUE("rolename"),
PRIMARY KEY("id" AUTOINCREMENT)
);
INSERT INTO role VALUES(1,'admin','Administrator');
INSERT INTO role VALUES(2,'data_collector','Data Collector');
INSERT INTO role VALUES(3,'mri_operator','MRI Operator');
INSERT INTO role VALUES(4,'participant','Participant');
INSERT INTO role VALUES(5,'sys_data_entry','System Data Entry');
INSERT INTO role VALUES(6,'tester','Automatic System Tester');
CREATE TABLE IF NOT EXISTS "study_data" (
"id" INTEGER NOT NULL UNIQUE,
"name" VARCHAR(128),
"device_id" INTEGER,
"status_id" INTEGER,
"start_ts" TIMESTAMP,
"end_ts" TIMESTAMP,
"info" JSON,
PRIMARY KEY("id" AUTOINCREMENT)
);
INSERT INTO study_data VALUES(1,'Halchenko/Horea/1020_animal_mri',1,101,'2023-06-07 10:41:25',NULL,replace('{\n "data_collector": ["user1", "poweruser"],\n "mri_operator": ["user2"],\n "participant": ["user3"]\n}','\n',char(10)));
CREATE TABLE IF NOT EXISTS "message_log" (
"id" INTEGER NOT NULL UNIQUE,
"level_id" INTEGER,
"category_id" INTEGER,
"device_id" INTEGER,
"provider_id" INTEGER,
"study_id" INTEGER,
"study_name" VARCHAR(128),
"is_visible" INTEGER NOT NULL DEFAULT 'Y',
"visible_updated_on" TIMESTAMP,
"visible_updated_by" VARCHAR(15),
"description" VARCHAR(255),
"payload" JSON,
"event_on" TIMESTAMP,
"registered_on" TIMESTAMP,
"recorded_on" TIMESTAMP,
"recorded_by" VARCHAR(15),
PRIMARY KEY("id" AUTOINCREMENT)
);
INSERT INTO message_log VALUES(1,1,1,1,2,NULL,NULL,'Y',NULL,NULL,'stimuli display dis-connected',NULL,'2023-06-07 10:49:31','2023-06-07 10:50:01','2023-06-07 10:50:31','reprostim');
INSERT INTO message_log VALUES(2,1,1,1,2,NULL,NULL,'Y',NULL,NULL,replace('stimuli display connected(1024x768, …)\n','\n',char(10)),NULL,'2023-06-07 10:50:22','2023-06-07 10:51:02','2023-06-07 10:51:22','reprostim');
INSERT INTO message_log VALUES(3,3,1,1,5,1,'Halchenko/Horea/1020_animal_mri','Y',NULL,NULL,replace('subject “John” is not conformant, must match [0-9]{6} regular expression. [link to screen with highlight]\n','\n',char(10)),NULL,'2023-06-07 10:51:44','2023-06-07 10:52:04','2023-06-07 10:52:44','noisseur');
INSERT INTO message_log VALUES(4,1,1,1,5,1,'Halchenko/Horea/1020_animal_mri','Y',NULL,NULL,'proceeded with compliant data on study Halchenko/Horea/1020_animal_mri',NULL,'2023-06-07 10:54:17','2023-06-07 10:55:07','2023-06-07 10:55:17','noisseur');
INSERT INTO message_log VALUES(5,1,1,1,3,NULL,NULL,'Y',NULL,NULL,'MRI trigger event received',NULL,'2023-06-07 10:55:45','2023-06-07 10:56:05','2023-06-07 10:56:45','reproevt');
INSERT INTO message_log VALUES(6,3,1,1,6,NULL,NULL,'Y',NULL,NULL,'MRI data lacks rear head coils data [link to PACS recording to review]',NULL,'2023-06-07 10:58:01','2023-06-07 10:59:00','2023-06-07 10:59:01','dicomqa');
DELETE FROM sqlite_sequence;
INSERT INTO sqlite_sequence VALUES('sec_user_role',10);
INSERT INTO sqlite_sequence VALUES('message_category',1);
INSERT INTO sqlite_sequence VALUES('data_provider',7);
INSERT INTO sqlite_sequence VALUES('study_status',300);
INSERT INTO sqlite_sequence VALUES('todo_study_session',0);
INSERT INTO sqlite_sequence VALUES('todo_study_screen',0);
INSERT INTO sqlite_sequence VALUES('device',1);
INSERT INTO sqlite_sequence VALUES('sec_user_device',6);
INSERT INTO sqlite_sequence VALUES('user',9);
INSERT INTO sqlite_sequence VALUES('role',6);
INSERT INTO sqlite_sequence VALUES('study_data',1);
INSERT INTO sqlite_sequence VALUES('message_log',6);
CREATE INDEX "idx_user_name" ON "user" (
"username"
);
COMMIT;
4 changes: 4 additions & 0 deletions docs/install.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -55,3 +55,7 @@ poetry run srv
1) Generate TOKEN_SECRET_KEY:

openssl rand -hex 32

[PostgreSQL on MacOS]

export PATH=/Library/PostgreSQL/15/bin:$PATH
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