Updated the deployment for maximum statement timeout

Signed-off-by: Martin Weise <martin.weise@tuwien.ac.at>

.docker/docker-compose.yml

@@ -7,23 +7,23 @@ x-resources-nano: &resources-nano
       cpus: '0.15'
       memory: 192M
 
-x-resources-nano-hm: &resources-nano-hm
+x-resources-micro: &resources-micro
   resources:
     reservations:
-      cpus: '0.1'
-      memory: 1024M
+      cpus: '0.25'
+      memory: 256M
     limits:
-      cpus: '0.5'
-      memory: 4096M
+      cpus: '0.375'
+      memory: 384M
 
-x-resources-micro: &resources-micro
+x-resources-nano-hm: &resources-micro-hm
   resources:
     reservations:
       cpus: '0.25'
       memory: 256M
     limits:
       cpus: '0.375'
-      memory: 384M
+      memory: 4096M
 
 x-resources-small: &resources-small
   resources:
@@ -72,7 +72,7 @@ services:
     restart: "no"
     container_name: dbrepo-metadata-db
     hostname: metadata-db
-    image: docker.io/mariadb:${MARIADB_VERSION}
+    image: docker.io/bitnami/mariadb:${MARIADB_VERSION}
     volumes:
       - metadata-db-data:/var/lib/mysql
       - ./config/1_setup-schema.sql:/docker-entrypoint-initdb.d/1_setup-schema.sql
@@ -81,12 +81,13 @@ services:
       - "3306:3306"
     environment:
       MARIADB_DATABASE: "${METADATA_DB:-dbrepo}"
+      MARIADB_EXTRA_FLAGS: "${METADATA_DB_EXTRA_FLAGS:---max_connections=155 --max-statement-time=60}"
       MARIADB_ROOT_PASSWORD: "${METADATA_DB_PASSWORD:-dbrepo}"
     healthcheck:
-      test: ./usr/local/bin/healthcheck.sh --connect --innodb_initialized
+      test: /opt/bitnami/scripts/mariadb/healthcheck.sh --connect --innodb_initialized
       <<: *healthcheck-params
     deploy:
-      <<: *resources-nano-hm
+      <<: *resources-micro-hm
     logging:
       driver: json-file
 
@@ -94,21 +95,22 @@ services:
     restart: "no"
     container_name: dbrepo-data-db
     hostname: data-db
-    image: docker.io/mariadb:${MARIADB_VERSION}
+    image: docker.io/bitnami/mariadb:${MARIADB_VERSION}
     volumes:
       - data-db-data:/var/lib/mysql
       - ./config/1_grant-user.sql:/docker-entrypoint-initdb.d/1_grant-user.sql
     ports:
       - "3307:3306"
     environment:
+      MARIADB_EXTRA_FLAGS: "${DATA_DB_EXTRA_FLAGS:---max_connections=155 --max-statement-time=60}"
       MARIADB_PASSWORD: "${READONLY_PASSWORD:-readonly}"
       MARIADB_ROOT_PASSWORD: "${DATA_DB_PASSWORD:-dbrepo}"
       MARIADB_USER: "${READONLY_USERNAME:-readonly}"
     healthcheck:
-      test: ./usr/local/bin/healthcheck.sh --connect --innodb_initialized
+      test: /opt/bitnami/scripts/mariadb/healthcheck.sh --connect --innodb_initialized
       <<: *healthcheck-params
     deploy:
-      <<: *resources-nano-hm
+      <<: *resources-micro-hm
     logging:
       driver: json-file
 
@@ -128,7 +130,7 @@ services:
       test: "psql -U ${AUTH_DB_USERNAME:-keycloak} -h 127.0.0.1 -p 5432 -d ${AUTH_DB_NAME:-keycloak} -c 'select version();'"
       <<: *healthcheck-params
     deploy:
-      <<: *resources-nano
+      <<: *resources-micro
     logging:
       driver: json-file
 
@@ -164,7 +166,7 @@ services:
       test: curl -fsS localhost:8080/realms/master
       <<: *healthcheck-params
     deploy:
-      <<: *resources-small
+      <<: *resources-medium
     depends_on:
       dbrepo-identity-service:
         condition: service_healthy

dbrepo-dashboard-service/Dockerfile

@@ -20,8 +20,8 @@ WORKDIR /app
 
 USER 1001
 
-COPY --chown=1001 ./ds-yml ./ds-yml
 COPY --chown=1001 ./app.py ./app.py
+COPY --chown=1001 ./ds-yml ./ds-yml
 
 # non-root port
 EXPOSE 8080

dbrepo-dashboard-service/init/Dockerfile → dbrepo-dashboard-service/init.Dockerfile

@@ -20,6 +20,6 @@ WORKDIR /app
 
 USER 1001
 
-COPY --chown=1001 ./app.py ./app.py
+COPY --chown=1001 ./init.py ./init.py
 
-ENTRYPOINT [ "python", "./app.py" ]
+ENTRYPOINT [ "python", "./init.py" ]

dbrepo-dashboard-service/init/.coveragerc

-[report]
-omit =
-    # omit tests
-    ./tests/*
-
-[html]
-directory = htmlcov
\ No newline at end of file

dbrepo-dashboard-service/init/Pipfile

-[[source]]
-url = "https://pypi.org/simple"
-verify_ssl = true
-name = "pypi"
-
-[packages]
-flasgger = "*"
-flask = "~=2.0"
-flask-cors = "~=4.0"
-flask-jwt-extended = "~=4.5"
-prometheus-flask-exporter = "*"
-python-dotenv = "~=1.0"
-pytest = "*"
-dbrepo = {path = "./lib/dbrepo-1.8.1.tar.gz"}
-gunicorn = "*"
-pydantic = "*"
-flask_httpauth = "*"
-grafana-client = "*"
-
-[dev-packages]
-coverage = "*"
-pytest = "*"
-testcontainers = "*"
-requests-mock = "*"
-grafana-client = "*"
-
-[requires]
-python_version = "3.11"

dbrepo-dashboard-service/init/tests/rsa/rs256.key

------BEGIN RSA PRIVATE KEY-----
-MIIEpAIBAAKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQABAoIBADNcMt6hAHub4JTAYS6Mra0EPRBO2XhWmACBrv3+8ETClXd5475KPLDewgRVtlmtbwU8G8awUXESQgPS9lfiqvQhPreA3cHlm6oP2WMKOEtakr2s8I+frsTBLCo0Ini9RaSzjoVVgS0zofyhASKi+T970MafSj5P3XNb8YBFdXgoYDiA7FXLH6a/+m7LScL+wGcFMAAeYESxZbMQLfH3v8L+4EcTraiwjLG17ZdlF3dpybMyUSse6ZQ/PdlyvBuzzLXhN6Ce2gd9ATfS+YWTzo7Yf+GU+ex5bIpVOfHqtuM/hyq7YGKENClsXwNZIAoFnvGCbvECAfgyapVrD30IfykCgYEA0rgsSZ82pxT40NxwgBD1g9lbNVBKXphRB/3S078qusUzJjT7AldEj4imGPhAbI7bI8gAeWJsp1XJWkjM8ktaVrh+NQl7p8e9OPh0pQF/5Bdg8ajbjXESpjnaU66pVYRQy/d+jNli/YRAHX5RUfsBl+6W4+WSVMGmKBiqJsur+ecCgYEAz1YVXClcmUnyZem5B+2E9noIzjF6ROE+jIb6rawM85P3Xd0lXtECQavtxw+Qk7I32qOwrxl1UpK2foVel3pazi+4OpMfmqtYGenRP1Zk1cZwrDo0cIemTDGjj3kJ8tYn12CGolFQpJZgK6OHzvG0tOxI5VZgjIViWNPe1PGWXtUCgYEAxXGNDe8BZs1f11S2lUlOw5yGug3hoYFXbAWJ5p7Ziuf8ZXB/QlJDC7se54a11wKEk6Jzz0lKRgE8CjzszJuOqnN0zn10QGIIC7nCklo1W6QMUmPGVWH994N976tZP6gbjQL6sT+AYcvpx7j0ubxYYeRNvnz+ACzzY964kGGHY0ECgYEAumlwPPNnMN7+VEjGNm2D7UMdJZ3wi3tkjF5ThdA5uMohTsAk+FG80KSu3RmOaGyEsUwY7+VYyYvlDm4E9PZqLBVVczyR3rMNPAcwPd0EPfvzk7WlLkOX7ct3fehaXH3VRlyfz9KCSeh1wOZ/lT1VtpD2nVOC7PSDzs92+kfXZZ0CgYAnrD1y4skgXkdwolZ3unn3EFyGm2d+X5aMTHwQPdWxqoNIAl/9wdghlzihwnPhhsxq1WzlxuC3V2IMrNPtRx70Mi+FbSmR5m4Xx5RptgMtMlwno+L40PzNJgMjHGjt0wcx3Vel8wuohDtnqMyS7P5nG1/TQx0Cyzwn7QOXlNpgbQ==
------END RSA PRIVATE KEY-----
\ No newline at end of file

dbrepo-dashboard-service/init/tests/rsa/rsa256.pkey

------BEGIN PUBLIC KEY-----
-MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB
------END PUBLIC KEY-----

dbrepo-data-service/services/src/main/java/at/ac/tuwien/ac/at/ifs/dbrepo/mapper/MariaDbMapper.java

@@ -194,12 +194,6 @@ public interface MariaDbMapper {
         return statement.toString();
     }
 
-    default String databaseViewSelectRawQuery() {
-        final String statement = "SELECT t.`TABLE_NAME`, t.`TABLE_TYPE`, t.`TABLE_ROWS`, t.`AVG_ROW_LENGTH`, t.`DATA_LENGTH`, t.`MAX_DATA_LENGTH`, COALESCE(t.`CREATE_TIME`, NOW()) as `CREATE_TIME`, t.`UPDATE_TIME`, v.`VIEW_DEFINITION` FROM information_schema.TABLES t LEFT JOIN information_schema.VIEWS v ON t.`TABLE_NAME` = v.`TABLE_NAME` WHERE t.`TABLE_SCHEMA` = ? AND t.`TABLE_TYPE` = 'VIEW' AND t.`TABLE_NAME` != 'qs_queries' AND t.`TABLE_NAME` = ?";
-        log.trace("mapped select view statement: {}", statement);
-        return statement;
-    }
-
     default String columnsCheckConstraintSelectRawQuery() {
         final String statement = "SELECT DISTINCT c.`CHECK_CLAUSE` FROM information_schema.COLUMNS k JOIN information_schema.CHECK_CONSTRAINTS c ON k.TABLE_NAME = c.TABLE_NAME WHERE k.TABLE_SCHEMA = ? AND k.TABLE_NAME = ?";
         log.trace("mapped select column constraint statement: {}", statement);

dbrepo-data-service/services/src/main/java/at/ac/tuwien/ac/at/ifs/dbrepo/service/impl/DatabaseServiceMariaDbImpl.java

@@ -135,6 +135,7 @@ public class DatabaseServiceMariaDbImpl extends DataConnector implements Databas
                 .databaseId(database.getId())
                 .columns(new LinkedList<>())
                 .build();
+        log.debug("creating view: {}.{}", database.getInternalName(), view.getInternalName());
         try {
             /* create view if not exists */
             final long start = System.currentTimeMillis();

dbrepo-search-service/Dockerfile

 FROM python:3.11-alpine3.21
 LABEL org.opencontainers.image.authors="martin.weise@tuwien.ac.at"
 
-RUN apk add --no-cache curl bash jq
-
-WORKDIR /home/alpine
+RUN apk add --no-cache \
+    curl \
+    bash \
+    jq
 
 COPY Pipfile Pipfile.lock ./
 
@@ -19,7 +20,7 @@ WORKDIR /app
 
 USER 1001
 
-COPY --chown=1001 ./init/friendly_names_overrides.json ./friendly_names_overrides.json
+COPY --chown=1001 ./friendly_names_overrides.json ./friendly_names_overrides.json
 COPY --chown=1001 ./os-yml ./os-yml
 COPY --chown=1001 ./app.py ./app.py
 

dbrepo-search-service/Pipfile

@@ -15,8 +15,6 @@ python-dotenv = "~=1.0"
 sqlalchemy-utils = "*"
 flask_httpauth = "*"
 jwt = "~=1.3"
-testcontainers-opensearch = "*"
-pytest = "*"
 rdflib = "*"
 grafana-client = "*"
 dbrepo = {path = "./lib/dbrepo-1.8.1.tar.gz"}
@@ -26,6 +24,8 @@ gunicorn = "*"
 coverage = "*"
 pytest = "*"
 requests-mock = "*"
+jwt = "~=1.3"
+testcontainers-opensearch = "*"
 
 [requires]
 python_version = "3.11"

dbrepo-search-service/init/Dockerfile → dbrepo-search-service/init.Dockerfile

@@ -20,7 +20,7 @@ WORKDIR /app
 
 USER 1001
 
-COPY --chown=1001 ./app.py ./app.py
 COPY --chown=1001 ./database.json ./database.json
+COPY --chown=1001 ./init.py ./init.py
 
-ENTRYPOINT [ "python", "./app.py" ]
+ENTRYPOINT [ "python", "./init.py" ]