Add 'docker/' from commit '1866be264483901ef1d372732ad95af787cdcd19'

git-subtree-dir: docker
git-subtree-mainline: b24e487
git-subtree-split: 1866be2

docker/.gitattributes

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+# source: https://docs.github.com/en/get-started/getting-started-with-git/configuring-git-to-handle-line-endings
+# Set the default behavior, in case people don't have core.autocrlf set.
+# * binary
+
+# Explicitly declare text files you want to always be normalized and converted
+# to native line endings on checkout.
+#*.c text
+#*.h text
+
+# Declare files that will always have CRLF line endings on checkout.
+#*.sln text eol=crlf
+
+# Denote all files that are truly binary and should not be modified.
+#*.png binary
+#*.jpg binary

docker/README.md

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+# iBridges-Integration-tests
+Dockerised integration tests of iBridges with iRODS
+
+## Docker images
+- iCAT database
+- iRODS server, version 4.3.0
+- Client: icommands, python-irodsclient and intgration tests
+
+## Usage
+1. Clone iBridges
+
+   ```sh
+   git clone --branch develop https://github.com/UtrechtUniversity/iBridges.git
+   ```
+
+Execute the following commands in the root ibridges directory:
+
+2. `docker-compose build`
+3. `docker-compose up`
+
+To recreate the images:
+
+1. `docker-compose rm -f`
+2. `docker-compose up --force-recreate --build --no-deps`
+
+Clean up
+
+1. `docker image prune`
+2. `docker container prune`
+
+Enter the irods-client
+1. Bring the images up
+2. `docker ps`
+3. `docker exec -it <IMAGE> /bin/bash`
+
+## Example output:
+
+```
+irods-client-1            | ============================= test session starts ==============================
+irods-client-1            | platform linux -- Python 3.10.12, pytest-8.0.0, pluggy-1.4.0
+irods-client-1            | rootdir: /ibridges/integration_test
+irods-client-1            | collected 14 items
+irods-client-1            | 
+irods-client-1            | test_meta.py ..                                                          [ 28%]
+irods-client-1            | test_permissions.py ..                                                   [ 42%]
+irods-client-1            | test_resources.py .                                                      [ 50%]
+irods-client-1            | test_rules.py .                                                          [ 57%]
+irods-client-1            | test_session.py .x                                                       [ 71%]
+irods-client-1            | test_ticket.py ....                                                      [100%]
+irods-client-1            | 
+irods-client-1            | ======================== 13 passed, 1 xfailed in 3.22s =========================
+```

docker/irods_catalog/Dockerfile

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+FROM postgres:10
+
+COPY init-user-db.sh /docker-entrypoint-initdb.d/init-user-db.sh

docker/irods_catalog/init-user-db.sh

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+#!/bin/bash
+
+# Adapted from "Initialization script" in documentation for official Postgres dockerhub:
+#   https://hub.docker.com/_/postgres/
+set -e
+
+psql -v ON_ERROR_STOP=1 --username "$POSTGRES_USER" --dbname "$POSTGRES_DB" <<-EOSQL
+    CREATE DATABASE "ICAT";
+    CREATE USER irods WITH PASSWORD 'testpassword';
+    GRANT ALL PRIVILEGES ON DATABASE "ICAT" to irods;
+EOSQL

docker/irods_catalog_provider/Dockerfile

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+FROM ubuntu:22.04
+ARG os_name=jammy
+
+ENV DEBIAN_FRONTEND=noninteractive
+ARG ubuntu_name=focal
+
+RUN apt-get update
+RUN apt-get install -y lsb-release gnupg wget sudo
+RUN apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/*
+
+# IRODS SERVER PACKAGES
+RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -
+RUN sudo rm -rf /etc/apt/sources.list.d/renci-irods.list
+RUN sudo echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" |sudo tee /etc/apt/sources.list.d/renci-irods.list
+
+RUN apt-get update
+RUN apt-get install -y python3 unixodbc
+RUN apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/*
+
+ARG irods_version=4.3.2
+ARG irods_package_version_suffix=-0~${os_name}
+ARG irods_package_version=${irods_version}${irods_package_version_suffix}
+#ARG irods_resource_plugin_version=${irods_version}.0${irods_package_version_suffix}
+
+RUN apt-get update && \
+    apt-get install -y irods-database-plugin-postgres=$irods_package_version
+RUN apt-get install irods-server=$irods_package_version
+RUN apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/*
+
+COPY setup-${irods_version}.input /
+RUN mv /setup-${irods_version}.input /irods_setup.input
+
+WORKDIR /
+COPY entrypoint.sh .
+RUN chmod u+x ./entrypoint.sh
+ENTRYPOINT ["./entrypoint.sh"]

docker/irods_catalog_provider/entrypoint.sh

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+#! /bin/bash -e
+
+catalog_db_hostname=irods-catalog
+
+echo "Waiting for iRODS catalog database to be ready"
+
+until pg_isready -h ${catalog_db_hostname} -d ICAT -U irods -q
+do
+    sleep 1
+done
+
+echo "iRODS catalog database is ready"
+
+setup_input_file=/irods_setup.input
+
+if [ -e "${setup_input_file}" ]; then
+    echo "Running iRODS setup"
+    python3 /var/lib/irods/scripts/setup_irods.py < "${setup_input_file}"
+    rm /irods_setup.input
+fi
+
+mkdir /var/lib/irods/Vault1
+chown irods:irods /var/lib/irods/Vault1
+
+#echo "Starting server"
+#su irods -c 'bash -c ./irodsctl start'
+#su irods -c 'iadmin mkresc resc2 unixfilesystem `hostname`:/var/lib/irods/Vault1'
+#echo "Stop server"
+#su irods -c 'bash -c ./irodsctl stop'
+
+echo "Creating resource"
+cd /var/lib/irods
+su irods -c 'bash -c "./irodsctl start"'
+su irods -c 'iadmin mkresc resc2 unixfilesystem `hostname`:/var/lib/irods/Vault1'
+su irods -c 'bash -c "./irodsctl stop"'
+
+echo "Starting server"
+cd /usr/sbin
+su irods -c 'bash -c "./irodsServer -u"'

docker/irods_catalog_provider/setup-4.3.1.input

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+
+
+
+
+irods-catalog
+5432
+ICAT
+irods
+y
+testpassword
+
+y
+demoResc
+
+tempZone
+1247
+20000
+20199
+1248
+
+rods
+y
+TEMPORARY_ZONE_KEY
+32_byte_server_negotiation_key__
+32_byte_server_control_plane_key
+rods
+
+

docker/irods_catalog_provider/setup-4.3.2.input

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+
+
+
+
+irods-catalog
+5432
+ICAT
+irods
+y
+testpassword
+
+y
+demoResc
+
+tempZone
+1247
+20000
+20199
+1248
+
+rods
+y
+TEMPORARY_ZONE_KEY
+32_byte_server_negotiation_key__
+32_byte_server_control_plane_key
+rods
+
+

docker/irods_client/Dockerfile

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+FROM ubuntu:22.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get install -y \
+        apt-transport-https \
+        gnupg \
+        wget \
+	lsb-release \
+    && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/*
+
+RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | apt-key add - && \
+    echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" | tee /etc/apt/sources.list.d/renci-irods.list
+
+# ARG icommands_version=4.3.0
+# ARG icommands_package_version_suffix=-1~focal
+# ARG icommands_package_version=${icommands_version}${icommands_package_version_suffix}
+
+RUN apt-get update && \
+    apt-get install -y \
+        netcat \
+	irods-runtime \
+	irods-icommands \
+    && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/*
+
+RUN mkdir -p /root/.irods
+COPY docker/irods_client/environments/plain-irods/irods_environment.json /root/.irods
+COPY docker/irods_client/environments/plain-irods/irods_environment_testuser.json /root/.irods
+
+RUN mkdir -p /tmp
+ADD docker/irods_client/testdata /tmp/testdata/
+
+# install python 3
+RUN apt-get update && \
+    apt-get upgrade -y
+RUN apt-get install -y python3 git 
+	# python3-pip \
+	# git
+
+# Work around for a bug in Ubuntu 22.04: https://github.com/pypa/setuptools/issues/3269#ref-issue-1217398136
+RUN wget https://bootstrap.pypa.io/get-pip.py
+RUN python3 get-pip.py
+RUN mkdir -p /ibridges/integration_test
+ADD ibridges /ibridges/ibridges
+ADD docker/irods_client/tests ibridges/integration_test
+ADD docker/irods_client/environments/plain-irods ibridges/integration_test/environment
+ADD .git /ibridges/.git
+COPY pyproject.toml /ibridges
+RUN /usr/local/bin/pip3 install /ibridges
+RUN /usr/local/bin/pip3 install pytest tomli
+
+WORKDIR /
+COPY docker/irods_client/entrypoint.sh .
+RUN chmod u+x ./entrypoint.sh
+ENTRYPOINT bash -c "./entrypoint.sh"

docker/irods_client/entrypoint.sh

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+#! /bin/bash -e
+
+echo "waiting for iRODS to be ready"
+
+irods_catalog_provider_hostname=irods-catalog-provider
+until nc -z ${irods_catalog_provider_hostname} 1247
+do
+    sleep 10
+done
+
+# After setting up iRODS, the server will respond on port 1247. However, the server process is
+# stopped after some preliminary tests are completed. The irods-catalog-provider service will
+# start the server manually again, but this will take a few seconds. Sleep here to ensure that
+# next time the server responds is not the temporary uptime provided during setup.
+sleep 3
+
+until nc -z ${irods_catalog_provider_hostname} 1247
+do
+    sleep 1
+done
+
+echo "iRODS is ready"
+
+# pre-authenticate the user so the iCommands are ready to use
+echo 'rods' | iinit
+echo 'Authenticated as rods'
+
+# wait until second resource is created
+ilsresc | grep 'resc2' &> /dev/null
+while [ $? != 0 ];
+do
+    echo "Sleep"
+    sleep 1
+done
+
+# create second user
+iadmin mkuser testuser rodsuser
+iadmin moduser testuser password testuser
+echo 'testuser created'
+echo $(iadmin lu testuser)
+
+cd /ibridges/integration_test
+pytest .
+
+result=$?
+if [[ -z "$CI" ]]; then
+    /bin/bash
+else
+    exit $result
+fi

docker/irods_client/environments/plain-irods/config.toml

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+password = "rods"
+server_version = "4.3.2"
+can_write_pam_pass = false
+has_cached_pw = true
+resources = ["demoResc", "resc2"]
+free_resources = [false, false, false]
+env_path = "/root/.irods/irods_environment.json"
+test_user = "testuser"
+test_user_pw = "testuser"
+test_user_env_path = "/root/.irods/irods_environment_testuser.json"
+ticket_date_only = true

docker/irods_client/environments/plain-irods/irods_environment.json

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+{
+"irods_host": "irods-catalog-provider",
+"irods_port": 1247,
+"irods_user_name": "rods",
+"irods_default_resource": "demoResc",
+"irods_home": "/tempZone/home/rods",
+"irods_zone_name": "tempZone"
+}

docker/irods_client/environments/plain-irods/irods_environment_testuser.json

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+{
+"irods_host": "irods-catalog-provider",
+"irods_port": 1247,
+"irods_user_name": "testuser",
+"irods_default_resource": "demoResc",
+"irods_home": "/tempZone/home/testuser",
+"irods_zone_name": "tempZone"
+}

docker/irods_client/environments/yoda/config.toml

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+password = "test"
+server_version = "4.2.12"
+can_write_pam_pass = false
+create_session_from_cached_pw = false
+resources = ["demoResc", "dev001", "dev001_1", "dev001_2", "dev001_p1", "dev001_p2", "dev002", "dev002_1", "dev002_p1", "dev003", "dev003_1", "dev003_p1", "irodsResc", "irodsRescRepl", "irodsRescReplS3"]
+free_resources = [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false]
+test_user = "researcher"
+test_user_pw = "test"
+ticket_date_only = true

docker/irods_client/environments/yoda/irods_environment.json

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+{
+"irods_host": "provider.yoda",
+"irods_port": 8247,
+"irods_user_name": "technicaladmin",
+"irods_password": "test",
+"irods_home": "/tempZone/home/rods",
+"irods_cwd": "/tempZone/home/rods",
+"irods_zone_name": "tempZone",
+"irods_client_server_negotiation": "request_server_negotiation",
+"irods_client_server_policy": "CS_NEG_REQUIRE",
+"irods_default_hash_scheme": "SHA256",
+"irods_default_resource": "irodsResc",
+"irods_encryption_algorithm": "AES-256-CBC",
+"irods_encryption_key_size": 32,
+"irods_encryption_num_hash_rounds": 16,
+"irods_encryption_salt_size": 8,
+"irods_ssl_verify_server": "none"
+}