update .omero, some test failing

.omero/.env

@@ -2,7 +2,7 @@
 ROOTPASS=omero
 # Other configuration properties
 POSTGRES_IMAGE=postgres
-POSTGRES_VERSION=10
+POSTGRES_VERSION=15
 POSTGRES_PASSWORD=postgres
 OMERO_SERVER_IMAGE=openmicroscopy/omero-server
 OMERO_SERVER_VERSION=5
@@ -13,4 +13,5 @@ OMERO_WEB_VERSION=5
 OMERO_WEB_PORT=
 
 # srv-compose.yml related values
-BUILD_IMAGE=adoptopenjdk:11-jdk-hotspot-bionic
+BUILD_IMAGE=eclipse-temurin:11-jdk-jammy
+OMERO_POLICY_BINARY_ACCESS=+read,+write,+image

.omero/cli-build

@@ -11,15 +11,7 @@ cd $TARGET
 GUESS=${PWD#*omero-cli-*}
 PLUGIN=${PLUGIN:-$GUESS}
 
-export JAVA_HOME=$(readlink -f /usr/bin/java | sed "s:/bin/java::")
-export JAVA_LD_LIBRARY_PATH="$JAVA_HOME/lib/:$JAVA_HOME/lib/server"
-export CONDA_BACKUP_JAVA_HOME=$JAVA_HOME
-export CONDA_BACKUP_JAVA_LD_LIBRARY_PATH=$JAVA_LD_LIBRARY_PATH
-
-source /tmp/miniconda/bin/activate
-conda init
-conda activate omero
-
 export OMERO_DIST=${OMERO_DIST:-/opt/omero/server/OMERO.server}
 omero $PLUGIN -h
+
 python setup.py test -t test -i ${OMERO_DIST}/etc/ice.config -vs

.omero/compose

@@ -5,8 +5,13 @@ dir=$(cd -P -- "$(dirname -- "$0")" && pwd -P)
 
 . ${dir}/utils
 PROJECT=${PROJECT:-$(get_project_name)}
+POLICY_BINARY_ACCESS=${POLICY_BINARY_ACCESS:-+read,+write,+image}
 # Note: for backwards compatibility, we're not yet
 # making use of COMPOSE_PROJECT_NAME
 
 cd $dir
+
+sed -i -e "/OMERO_POLICY_BINARY_ACCESS/d" .env
+echo "OMERO_POLICY_BINARY_ACCESS="$POLICY_BINARY_ACCESS >> .env
+
 exec docker compose -p ${PROJECT} "$@"

.omero/docker

@@ -21,6 +21,7 @@ export TARGET=/$(basename $PWD)
 export NOCLEAN=${NOCLEAN:-"false"}
 export LOGS=${LOGS:-"false"}
 export PLUGIN=${PLUGIN:-}
+export POLICY_BINARY_ACCESS=${POLICY_BINARY_ACCESS:-+read,+write,+image}
 
 if [ $# -eq 0 ]; then
     echo "docker [stage [stage [stage]]]"

.omero/docker-compose.yml

@@ -16,9 +16,8 @@ services:
       - CONFIG_omero_db_name=postgres
       - CONFIG_omero_db_pass=${POSTGRES_PASSWORD}
       - CONFIG_omero_upgrades_url=
+      - CONFIG_omero_policy_binary__access=${OMERO_POLICY_BINARY_ACCESS}
       - CONFIG_Ice_IPv6=0
-      - CONFIG_omero_policy_binary__access=+read,+write,+image,+plate
-      - JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF8
     ports:
       - "${OMERO_SERVER_TCP}4063"
       - "${OMERO_SERVER_SSL}4064"

.omero/omeroserver/Dockerfile

@@ -2,7 +2,7 @@ ARG OMEROSERVER_BASE_IMAGE=openmicroscopy/omero-server:latest
 FROM $OMEROSERVER_BASE_IMAGE
 
 USER root
-RUN yum install -y -q \
+RUN dnf install -y -q \
     git && \
-    rm -rf /var/cache/yum
+    dnf clean all
 USER omero-server

.omero/omeroweb/Dockerfile

@@ -2,8 +2,8 @@ ARG OMEROWEB_BASE_IMAGE=openmicroscopy/omero-web:latest
 FROM $OMEROWEB_BASE_IMAGE
 
 USER root
-RUN yum install -y -q \
+RUN dnf install -y -q \
     java-11-openjdk \
     git && \
-    rm -rf /var/cache/yum
+    dnf clean all
 USER omero-web

.omero/persist.sh

@@ -24,15 +24,15 @@ function backup_volume {
   volume_name=$1
   backup_destination=$2
   echo "Backup $volume_name to $backup_destination"
-  docker run --rm -v $volume_name:/data -v $backup_destination:/backup ubuntu tar -zcf /backup/$volume_name.tar /data
+  MSYS_NO_PATHCONV=1 docker run --rm -v $volume_name:/data -v $backup_destination:/backup ubuntu tar -zcf /backup/$volume_name.tar /data
 }
 
 function restore_volume {
   volume_name=$1
   backup_destination=$2
   echo "Restore $volume_name from $backup_destination"
-  docker run --rm -v $volume_name:/data ubuntu find /data -mindepth 1 -delete
-  docker run --rm -v $volume_name:/data -v $backup_destination:/backup ubuntu tar -xf /backup/$volume_name.tar -C .
+  MSYS_NO_PATHCONV=1 docker run --rm -v $volume_name:/data ubuntu find /data -mindepth 1 -delete
+  MSYS_NO_PATHCONV=1 docker run --rm -v $volume_name:/data -v $backup_destination:/backup ubuntu tar -xf /backup/$volume_name.tar -C .
 }
 
 function main {

.omero/py-check

@@ -6,10 +6,18 @@ set -u
 set -x
 
 TARGET=${TARGET:-..}
+
+git config --global --add safe.directory $TARGET
+
 cd $TARGET
 if [ -f .pre-commit-config.yaml ]; then
     pre-commit run -a
 else
     flake8 -v .
 fi
-rst-lint README.md
+# Check if there is an README.rst
+if [ -f README.rst ]; then
+    rst-lint README.rst
+else
+    rst-lint README.md
+fi

.omero/py-setup

@@ -8,21 +8,9 @@ set -x
 TARGET=${TARGET:-..}
 PLUGIN=${PLUGIN:-}
 
-export JAVA_HOME=$(readlink -f /usr/bin/java | sed "s:/bin/java::")
-export JAVA_LD_LIBRARY_PATH="$JAVA_HOME/lib/:$JAVA_HOME/lib/server"
-export CONDA_BACKUP_JAVA_HOME=$JAVA_HOME
-export CONDA_BACKUP_JAVA_LD_LIBRARY_PATH=$JAVA_LD_LIBRARY_PATH
-wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-sh Miniconda3-latest-Linux-x86_64.sh -b -p /tmp/miniconda
-source /tmp/miniconda/bin/activate
-conda init
-conda create -n omero python=3.8
-conda activate omero
-conda install -c conda-forge zeroc-ice=3.6.5
-conda install -c bioconda bftools
-
 cd $TARGET
 cd $(setup_dir)
-pip install .
+python setup.py sdist
+pip install -U dist/*.tar.gz
 python setup.py clean
 rm -rf dist *egg-info src/*egg-info

.omero/requirements.txt

@@ -1,12 +1,13 @@
-flake8<3.6.0
+flake8
+pyflakes
 pep8-naming
 pre-commit
-pycodestyle<2.4.0
+pycodestyle
 restructuredtext_lint
-pytest==3.3.2
-attrs==19.1.0
+pytest<5
+attrs
 restview
 mox
 # TODO: Apps only
-pytest-django==3.1.2
-pytest-runner==3.0.1
+pytest-django
+pytest-runner

test/integration/test_transfer.py

@@ -205,7 +205,7 @@ def test_pack_metadata_only(self, target_name, tmpdir):
         args = self.args + ["pack", target, "--binaries", "none", "--simple",
                             str(tmpdir)]
         with pytest.raises(ValueError):
-                self.cli.invoke(args, strict=True)
+            self.cli.invoke(args, strict=True)
         self.delete_all()
 
     @pytest.mark.parametrize('folder_name', TEST_FOLDERS)