From c34a733720d69f30dc97702039dd6ce72956f559 Mon Sep 17 00:00:00 2001
From: Martin Weise <martin.weise@tuwien.ac.at>
Date: Tue, 22 Nov 2022 17:51:51 +0100
Subject: [PATCH] Progress on fixing int to bigint and references
---
fda-authentication-service/Dockerfile | 4 +--
fda-authentication-service/pom.xml | 5 ++++
fda-container-service/Dockerfile | 4 +--
fda-database-service/Dockerfile | 4 +--
fda-identifier-service/Dockerfile | 4 +--
fda-metadata-db/Dockerfile | 12 ++++++--
fda-metadata-db/setup-schema.sql | 43 +++++++++++++--------------
fda-metadata-db/setup-user.sh | 5 ++++
fda-metadata-service/Dockerfile | 4 +--
fda-metadata-service/pom.xml | 6 ++++
fda-query-service/Dockerfile | 4 +--
fda-table-service/Dockerfile | 4 +--
12 files changed, 60 insertions(+), 39 deletions(-)
create mode 100644 fda-metadata-db/setup-user.sh
diff --git a/fda-authentication-service/Dockerfile b/fda-authentication-service/Dockerfile
index 42dece92fa..3011726fb1 100644
--- a/fda-authentication-service/Dockerfile
+++ b/fda-authentication-service/Dockerfile
@@ -22,8 +22,8 @@ RUN mvn -q clean package -DskipTests
FROM openjdk:11-jre-slim as runtime
ENV METADATA_DB=fda
-ENV METADATA_USERNAME=postgres
-ENV METADATA_PASSWORD=postgres
+ENV METADATA_USERNAME=dbrepo
+ENV METADATA_PASSWORD=dbrepo
ENV BROKER_USERNAME=fda
ENV BROKER_PASSWORD=fda
ENV WEBSITE=http://example.com
diff --git a/fda-authentication-service/pom.xml b/fda-authentication-service/pom.xml
index 2d96e04186..4fd2e72422 100644
--- a/fda-authentication-service/pom.xml
+++ b/fda-authentication-service/pom.xml
@@ -117,6 +117,11 @@
<artifactId>h2</artifactId>
<scope>runtime</scope>
</dependency>
+ <dependency>
+ <groupId>org.mariadb.jdbc</groupId>
+ <artifactId>mariadb-java-client</artifactId>
+ <version>${mariadb.version}</version>
+ </dependency>
<!-- IDE -->
<dependency>
<groupId>org.projectlombok</groupId>
diff --git a/fda-container-service/Dockerfile b/fda-container-service/Dockerfile
index 3bea5887a3..9fbaa3dc94 100644
--- a/fda-container-service/Dockerfile
+++ b/fda-container-service/Dockerfile
@@ -22,8 +22,8 @@ RUN mvn -q clean package -DskipTests > /dev/null
FROM openjdk:11-jre-slim as runtime
ENV METADATA_DB=fda
-ENV METADATA_USERNAME=postgres
-ENV METADATA_PASSWORD=postgres
+ENV METADATA_USERNAME=dbrepo
+ENV METADATA_PASSWORD=dbrepo
ENV BROKER_USERNAME=fda
ENV BROKER_PASSWORD=fda
ENV SHARED_FILESYSTEM=/tmp
diff --git a/fda-database-service/Dockerfile b/fda-database-service/Dockerfile
index a6f4b9a8f9..4da92d5f6a 100644
--- a/fda-database-service/Dockerfile
+++ b/fda-database-service/Dockerfile
@@ -22,8 +22,8 @@ RUN mvn -q clean package -DskipTests > /dev/null
FROM openjdk:11-jre-slim as runtime
ENV METADATA_DB=fda
-ENV METADATA_USERNAME=postgres
-ENV METADATA_PASSWORD=postgres
+ENV METADATA_USERNAME=dbrepo
+ENV METADATA_PASSWORD=dbrepo
ENV BROKER_USERNAME=fda
ENV BROKER_PASSWORD=fda
ENV SEARCH_ENDPOINT=search-service
diff --git a/fda-identifier-service/Dockerfile b/fda-identifier-service/Dockerfile
index 3db7b8b6f7..7a05fc2856 100644
--- a/fda-identifier-service/Dockerfile
+++ b/fda-identifier-service/Dockerfile
@@ -23,8 +23,8 @@ RUN mvn -q clean package -DskipTests > /dev/null
FROM openjdk:11-jre-slim as runtime
ENV METADATA_DB=fda
-ENV METADATA_USERNAME=postgres
-ENV METADATA_PASSWORD=postgres
+ENV METADATA_USERNAME=dbrepo
+ENV METADATA_PASSWORD=dbrepo
ENV GATEWAY_ENDPOINT=http://gateway-service:9095
ENV WEBSITE=http://localhost:3000
ENV LOG_LEVEL=debug
diff --git a/fda-metadata-db/Dockerfile b/fda-metadata-db/Dockerfile
index 5cb120f95a..bc6ee91576 100644
--- a/fda-metadata-db/Dockerfile
+++ b/fda-metadata-db/Dockerfile
@@ -18,14 +18,20 @@ RUN mvn -q clean package -DskipTests > /dev/null
RUN mvn -q clean install > /dev/null
###### SECOND STAGE ######
-FROM postgres:14-alpine as runtime
+FROM mariadb:10.5 as runtime
+ENV METADATA_DB=fda
ENV METADATA_USERNAME=dbrepo
ENV METADATA_PASSWORD=dbrepo
+ENV MARIADB_DATABASE="${METADATA_DB}"
+ENV MARIADB_ROOT_PASSWORD="${METADATA_PASSWORD}"
+ENV MARIADB_USERNAME="${METADATA_USERNAME}"
+ENV MARIADB_PASSWORD="${METADATA_PASSWORD}"
# Scripts are copied to /docker-entrypoint-initdb.d/ in docker-compose from analyze service
-HEALTHCHECK --interval=10s --timeout=5s --retries=12 CMD pg_isready
+HEALTHCHECK --interval=10s --timeout=5s --retries=12 CMD mysqladmin ping --user="$METADATA_USERNAME" --password="$METADATA_PASSWORD" --silent
-COPY ./setup-schema.sql /docker-entrypoint-initdb.d/
+COPY ./setup-schema.sql /docker-entrypoint-initdb.d/1.sql
+COPY ./setup-user.sh /docker-entrypoint-initdb.d/2.sh
COPY --from=build /root/.m2/repository/at/tuwien /root/.m2/repository/at/tuwien
\ No newline at end of file
diff --git a/fda-metadata-db/setup-schema.sql b/fda-metadata-db/setup-schema.sql
index 1e18e92dc3..fd2dd014a2 100644
--- a/fda-metadata-db/setup-schema.sql
+++ b/fda-metadata-db/setup-schema.sql
@@ -126,6 +126,13 @@ CREATE SEQUENCE mdb_tokens_seq
NO MAXVALUE
CACHE 1;
+CREATE SEQUENCE mdb_concepts_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+
CREATE TABLE IF NOT EXISTS mdb_users
(
UserID bigint not null DEFAULT nextval(mdb_user_seq),
@@ -306,7 +313,7 @@ CREATE TABLE IF NOT EXISTS mdb_tables
tDescription TEXT,
NumCols INTEGER,
NumRows INTEGER,
- separator CHAR(1),
+ `separator` CHAR(1),
quote CHAR(1),
element_null VARCHAR(50),
skip_lines BIGINT,
@@ -404,21 +411,22 @@ CREATE TABLE IF NOT EXISTS mdb_COLUMNS_cat
CREATE TABLE IF NOT EXISTS mdb_concepts
(
+ id bigint not null default nextval(mdb_concepts_seq),
URI TEXT,
name TEXT,
created timestamp NOT NULL DEFAULT NOW(),
created_by bigint,
FOREIGN KEY (created_by) REFERENCES mdb_users (UserID),
- PRIMARY KEY (URI)
+ PRIMARY KEY (id)
);
CREATE TABLE IF NOT EXISTS mdb_columns_concepts
(
- cDBID bigint NOT NULL,
- tID bigint NOT NULL,
- cID bigint NOT NULL,
- URI TEXT REFERENCES mdb_concepts (URI),
- created timestamp NOT NULL DEFAULT NOW(),
+ cDBID bigint NOT NULL,
+ tID bigint NOT NULL,
+ cID bigint NOT NULL,
+ concept_id bigint REFERENCES mdb_concepts (id), /* mysql does not allow text primary keys */
+ created timestamp NOT NULL DEFAULT NOW(),
FOREIGN KEY (cDBID, tID, cID) REFERENCES mdb_COLUMNS (cDBID, tID, ID),
PRIMARY KEY (cDBID, tID, cID)
);
@@ -509,21 +517,12 @@ CREATE TABLE IF NOT EXISTS mdb_creators
FOREIGN KEY (pid) REFERENCES mdb_identifiers (id)
);
-CREATE TABLE IF NOT EXISTS mdb_views_databases
-(
- mdb_view_id bigint,
- databases_id bigint REFERENCES mdb_databases (id),
- created timestamp NOT NULL DEFAULT NOW(),
- FOREIGN KEY (mdb_view_id, databases_id) REFERENCES mdb_VIEW (id, vdbid),
- PRIMARY KEY (mdb_view_id, databases_id)
-);
-
CREATE TABLE IF NOT EXISTS mdb_feed
(
fDBID bigint,
fID bigint,
- fUserId INTEGER REFERENCES mdb_users (UserID),
- fDataID INTEGER REFERENCES mdb_data (ID),
+ fUserId bigint REFERENCES mdb_users (UserID),
+ fDataID bigint REFERENCES mdb_data (ID),
created timestamp NOT NULL DEFAULT NOW(),
FOREIGN KEY (fDBID, fID) REFERENCES mdb_tables (tDBID, ID),
PRIMARY KEY (fDBID, fID, fUserId, fDataID)
@@ -531,7 +530,7 @@ CREATE TABLE IF NOT EXISTS mdb_feed
CREATE TABLE IF NOT EXISTS mdb_update
(
- uUserID INTEGER REFERENCES mdb_users (UserID),
+ uUserID bigint REFERENCES mdb_users (UserID),
uDBID bigint REFERENCES mdb_databases (id),
created timestamp NOT NULL DEFAULT NOW(),
PRIMARY KEY (uUserID, uDBID)
@@ -539,7 +538,7 @@ CREATE TABLE IF NOT EXISTS mdb_update
CREATE TABLE IF NOT EXISTS mdb_access
(
- aUserID INTEGER REFERENCES mdb_users (UserID),
+ aUserID bigint REFERENCES mdb_users (UserID),
aDBID bigint REFERENCES mdb_databases (id),
attime TIMESTAMP,
download BOOLEAN,
@@ -551,14 +550,14 @@ CREATE TABLE IF NOT EXISTS mdb_have_access
(
hUserID bigint REFERENCES mdb_users (UserID),
hDBID bigint REFERENCES mdb_databases (id),
- hType ENUM('R', 'W'),
+ hType ENUM ('R', 'W'),
created timestamp NOT NULL DEFAULT NOW(),
PRIMARY KEY (hUserID, hDBID)
);
CREATE TABLE IF NOT EXISTS mdb_owns
(
- oUserID INTEGER REFERENCES mdb_users (UserID),
+ oUserID bigint REFERENCES mdb_users (UserID),
oDBID bigint REFERENCES mdb_databases (ID),
created timestamp NOT NULL DEFAULT NOW(),
PRIMARY KEY (oUserID, oDBID)
diff --git a/fda-metadata-db/setup-user.sh b/fda-metadata-db/setup-user.sh
new file mode 100644
index 0000000000..63c5e77afe
--- /dev/null
+++ b/fda-metadata-db/setup-user.sh
@@ -0,0 +1,5 @@
+#!/bin/sh
+mysql --user="root" --password="${METADATA_PASSWORD}" --database="${METADATA_DB}" << EOF
+CREATE USER '${MARIADB_USERNAME}' IDENTIFIED BY '${MARIADB_PASSWORD}';
+GRANT ALL PRIVILEGES ON '${METADATA_DB}' TO '${MARIADB_USERNAME}';
+EOF
\ No newline at end of file
diff --git a/fda-metadata-service/Dockerfile b/fda-metadata-service/Dockerfile
index a727f81379..9b486066e9 100644
--- a/fda-metadata-service/Dockerfile
+++ b/fda-metadata-service/Dockerfile
@@ -22,8 +22,8 @@ RUN mvn -q clean package -DskipTests > /dev/null
FROM openjdk:11-jre-slim as runtime
ENV METADATA_DB=fda
-ENV METADATA_USERNAME=postgres
-ENV METADATA_PASSWORD=postgres
+ENV METADATA_USERNAME=dbrepo
+ENV METADATA_PASSWORD=dbrepo
ENV GATEWAY_ENDPOINT=http://gateway-service:9095
ENV PID_BASE="https://example.com/pid/"
ENV REPOSITORY_NAME="Example Repository"
diff --git a/fda-metadata-service/pom.xml b/fda-metadata-service/pom.xml
index d54686f8c3..43a00dab90 100644
--- a/fda-metadata-service/pom.xml
+++ b/fda-metadata-service/pom.xml
@@ -60,6 +60,12 @@
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-actuator</artifactId>
</dependency>
+ <!-- Datasource -->
+ <dependency>
+ <groupId>org.mariadb.jdbc</groupId>
+ <artifactId>mariadb-java-client</artifactId>
+ <version>${mariadb.version}</version>
+ </dependency>
<!-- Monitoring -->
<dependency>
<groupId>io.micrometer</groupId>
diff --git a/fda-query-service/Dockerfile b/fda-query-service/Dockerfile
index b2dac0fa18..dab9e245a7 100644
--- a/fda-query-service/Dockerfile
+++ b/fda-query-service/Dockerfile
@@ -23,8 +23,8 @@ RUN mvn -q clean package -DskipTests > /dev/null
FROM openjdk:11-jre-slim as runtime
ENV METADATA_DB=fda
-ENV METADATA_USERNAME=postgres
-ENV METADATA_PASSWORD=postgres
+ENV METADATA_USERNAME=dbrepo
+ENV METADATA_PASSWORD=dbrepo
ENV BROKER_USERNAME=fda
ENV BROKER_PASSWORD=fda
ENV GATEWAY_ENDPOINT=http://gateway-service:9095
diff --git a/fda-table-service/Dockerfile b/fda-table-service/Dockerfile
index e0849c308f..837ca53a56 100644
--- a/fda-table-service/Dockerfile
+++ b/fda-table-service/Dockerfile
@@ -24,8 +24,8 @@ FROM openjdk:11-jre-slim as runtime
ENV multipart.location=/tmp
ENV METADATA_DB=fda
-ENV METADATA_USERNAME=postgres
-ENV METADATA_PASSWORD=postgres
+ENV METADATA_USERNAME=dbrepo
+ENV METADATA_PASSWORD=dbrepo
ENV BROKER_USERNAME=fda
ENV BROKER_PASSWORD=fda
ENV SEARCH_ENDPOINT=search-service
--
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