Address Stefans changes

Author: Anna-Rehm

Images/qiita/Dockerfile

@@ -1,14 +1,17 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 
 ARG MINIFORGE_VERSION=24.1.2-0
 
 ENV CONDA_DIR=/opt/conda
 ENV PATH=${CONDA_DIR}/bin:${PATH}
 
 RUN apt-get -y update
-RUN apt-get -y install \
+RUN apt-get -y --fix-missing install \
 	git \
-	wget
+	wget \
+	libpq-dev \
+	python3-dev \
+	gcc
 RUN apt-get -y install build-essential
 # install miniforge3 for "conda"
 # see https://github.com/conda-forge/miniforge-images/blob/master/ubuntu/Dockerfile
@@ -31,36 +34,32 @@ RUN pip install \
 	sphinx-bootstrap-theme \
 	nose-timer \
 	Click \
-	coverage
+	coverage \
+	psycopg2-binary
 
-#Clone the Qiita Repo
-#RUN git clone -b master https://github.com/qiita-spots/qiita.git
+#cClone the Qiita Repo
+# RUN git clone -b master https://github.com/qiita-spots/qiita.git
 RUN git clone -b auth_oidc https://github.com/jlab/qiita.git
 
-#We need to install necessary dependencies
-#as well as some extra dependencies for psycopg2 to work
+# We need to install necessary dependencies
+# as well as some extra dependencies for psycopg2 to work
 RUN git clone https://github.com/psycopg/psycopg2.git
-RUN apt-get -y update
-RUN apt-get -y install libpq-dev python3-dev gcc
-RUN pg_config --version
 RUN export PATH=/usr/lib/postgresql/14.11/bin/:$PATH
-RUN pip install psycopg2-binary
 RUN pip install -e psycopg2/.
 
-#Install pip packaages for Qiita
-RUN pip install -e qiita/. --no-binary redbiom
-RUN pip install "Jinja2<3.1"
+# Install pip packaages for Qiita
+RUN pip install -e qiita --no-binary redbiom
 
 
-#Copy modified config file to the container
+# Copy modified config file to the container
 COPY config_qiita_oidc.cfg .
-RUN chmod 777 config_qiita_oidc.cfg
+RUN chmod 755 config_qiita_oidc.cfg
 
-#Copy Bash Script to run Qiita to the container
+# Copy Bash Script to run Qiita to the container
 COPY start_qiita.sh .
-RUN chmod 777 start_qiita.sh
+RUN chmod 755 start_qiita.sh
 
-#I will leave this ENTRYPOINT here as a comment in case debugging
-#is necessary
-#ENTRYPOINT ["/bin/bash"]
+# I will leave this ENTRYPOINT here as a comment in case debugging
+# is necessary
+# SHELL ["/bin/bash"]
 ENTRYPOINT ["conda", "run", "-n", "qiita", "./start_qiita.sh"]

Images/qiita/start_qiita.sh

@@ -1,13 +1,17 @@
 #!/bin/bash
 
-#first we start the redis server
+# first we start the redis server
 redis-server --daemonize yes --port 7777
 redis-server --daemonize yes --port 6379
 
-export QIITA_CONFIG_FP="./config_qiita_oidc.cfg"
+export QIITA_CONFIG_FP="/config_qiita_oidc.cfg"
 
-#building the database without ontologies
-qiita-env make --no-load-ontologies
+conda list
 
-#starting the webserver without building the docs
-qiita pet webserver --no-build-docs start
+# building the database without ontologies
+qiita-env make --no-load-ontologies #|| true
+
+# starting the webserver without building the docs
+qiita pet webserver --no-build-docs start
+
+# supervisord -c ./qiita/qiita_pet/supervisor_example.conf

README.md

@@ -1,4 +1,6 @@
 **IMPORTANT: Have docker installed!**
+**THIS VERSION CURRENTLY ONLY WORKS WITH DOCKER, NOT WITH PODMAN**
+**FOR TESTING ON LOCAL MACHINES**
 
 ### Hopefully "foolproof" instructions:
 1. Clone repository
@@ -16,7 +18,7 @@
 2. Run `docker compose up keycloak_web keycloakdb`
 3. Open `http://localhost:8080`, login admin pw admin
 4. Configure Qiita as a service, create a user
-5. Edit `config_qiita_oidc.cfg` to fit your local Keycloak configuration, comment out necessary oidc configuration part.
+5. Edit `config_qiita_oidc.cfg` to fit your local Keycloak configuration, remove # from necessary oidc block.
 6. Open a new terminal, move into Image Folder `cd Images/qiita`
 7. Build docker image `docker build . -f qiita/Dockerfile -t qiita`
 8. Move to folder containing compose file `cd ../..`

compose.yaml

@@ -10,8 +10,6 @@ services:
     environment:
       - POSTGRES_DB=postgres
       - POSTGRES_USER=postgres
-      - POSTGRES_DB_NAME=postgres
-      - POSTGRES_DB_USER=postgres
     volumes:
       - './environments/qiita-db-init.sh:/docker-entrypoint-initdb.d/qiita-db-init.sh'
       - 'postgres-data:/var/lib/postgresql/data'
@@ -20,22 +18,26 @@ services:
 
   qiita:
       image: qiita:latest 
-      command: ['./start_qiita.sh'] #executes bash script inside the container
+      command: ['./start_qiita.sh'] # executes bash script inside the container
+      # entrypoint: /bin/bash
       stdin_open: true
       tty: true
       network_mode: host
       ports:
-        - "21174:21174"  #wihtout nginx
+        - "21174:21174"  # wihtout nginx
       restart: no
       depends_on:
         - qiita-db
       env_file:
         - './environments/qiita.env'
       environment:
         - QIITA_ROOTCA_CERT=/qiita/qiita_core/support_files/ci_rootca.crt
-        - QIITA_CONFIG_FP=./config_qiita_oidc.cfg
+        - QIITA_CONFIG_FP=/config_qiita_oidc.cfg
+      volumes:
+          - qiita-data:/qiita
 
-  keycloak_web: #from https://stackoverflow.com/questions/78071458/keycloak-docker-compose
+
+  keycloak_web: # from https://stackoverflow.com/questions/78071458/keycloak-docker-compose
     image: quay.io/keycloak/keycloak:24.0.2
     container_name: keycloak_web
     environment:
@@ -45,7 +47,7 @@ services:
       KC_DB_PASSWORD: password
 
       KC_HOSTNAME: localhost
-      KC_HOSTNAME_PORT: 8080
+      KC_HOSTNAME_PORT: 9999
       KC_HOSTNAME_STRICT: false
       KC_HOSTNAME_STRICT_HTTPS: false
 
@@ -58,7 +60,7 @@ services:
     depends_on:
       - keycloakdb
     ports:
-      - 8080:8080
+      - 9999:8080
 
   keycloakdb:
     image: postgres:15
@@ -68,9 +70,24 @@ services:
       POSTGRES_DB: keycloak
       POSTGRES_USER: keycloak
       POSTGRES_PASSWORD: password
+  
+  # nginx:
+  #   image: nginx_qiita:latest
+  #   ports:
+  #     - "8080:8080"
+  #   command: ['./start_nginx.sh']
+    # command: /bin/bash
+    # entrypoint: /bin/bash
+  #   stdin_open: true
+  #   tty: true
+  #   restart: no
+    # volumes:
+    #   - qiita:/qiita/
 
 volumes:
   postgres-data:
     name: qiita-postgres-data
   keycloak-postgres-data:
-    name: keycloak-postgres-data
+    name: keycloak-postgres-data
+  qiita-data:
+    name: qiita-data

environments/qiita-db-init.sh

@@ -4,5 +4,5 @@ set -e
 set -u
 
 psql -v ON_ERROR_STOP=1 --username "$POSTGRES_USER" "$POSTGRES_DB" <<-EOSQL
-      ALTER DATABASE "$POSTGRES_DB_NAME" OWNER TO "$POSTGRES_USER"
+      ALTER DATABASE "$POSTGRES_DB" OWNER TO "$POSTGRES_USER"
 EOSQL