Update base Docker image to Debian Bookworm

.github/workflows/test-with-docker.yml

@@ -17,6 +17,6 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: pull base image
-      run: docker pull pombase/canto-base:v17
+      run: docker pull pombase/canto-base:v18
     - name: run make test inside a Docker container
       run: ./etc/docker-run-tests.sh

.travis.yml

@@ -4,7 +4,7 @@ services:
   - docker
 
 before_install:
-  - docker pull pombase/canto-base:v15
+  - docker pull pombase/canto-base:v18
 
 # this runs "make test" inside a Docker container
 script: ./etc/docker-run-tests.sh

Dockerfile

@@ -1,4 +1,4 @@
-FROM pombase/canto-base:v15
+FROM pombase/canto-base:v18
 MAINTAINER Kim Rutherford <[email protected]>
 
 COPY . canto/

etc/Dockerfile-base

@@ -1,6 +1,6 @@
-# build with: docker build --squash -f etc/Dockerfile-base -t=pombase/canto-base:v15 .
+# build with: docker build --squash -f etc/Dockerfile-base -t=pombase/canto-base:v18 .
 
-FROM bitnami/minideb:stretch
+FROM bitnami/minideb:bookworm
 MAINTAINER Kim Rutherford <[email protected]>
 
 RUN apt-get update && apt-get upgrade -y && apt-get install -y apt-utils
@@ -12,7 +12,16 @@ RUN apt-get install -y ntpdate sqlite3 make tar gzip whiptail gcc g++ wget \
 
 RUN apt-get update; \
   apt-get install -y libcatalyst-perl libcatalyst-modules-perl \
-    libserver-starter-perl starman \
+    libserver-starter-perl starman liblwp-protocol-https-perl \
+    libnet-ssleay-perl libnet-https-any-perl \
+    libbio-chado-schema-perl libcarp-always-perl libdata-rmap-perl \
+    libdbd-sqlite3-perl libdbix-class-perl \
+    libextutils-makemaker-dist-zilla-develop-perl \
+    libiterator-simple-perl libjson-any-perl liblist-compare-perl \
+    libmoosex-traits-perl libmouse-perl libplack-middleware-debug-perl \
+    libplack-middleware-expires-perl libstring-similarity-perl \
+    libtest-more-utf8-perl libtext-csv-encoded-perl \
+    libtext-multimarkdown-perl libtext-trim-perl libutf8-all-perl \
     libmodule-install-perl libcatalyst-devel-perl liblocal-lib-perl \
     apt-transport-https ca-certificates && \
    apt-get clean
@@ -25,7 +34,7 @@ RUN echo installing lib lucene && (cd /tmp/; \
   dpkg -i libclucene0ldbl_0.9.21b-2+b1_amd64.deb libclucene-dev_0.9.21b-2+b1_amd64.deb && \
   rm libclucene0ldbl_0.9.21b-2+b1_amd64.deb libclucene-dev_0.9.21b-2+b1_amd64.deb)
 
-RUN apt-get -y install openjdk-8-jre-headless
+RUN apt-get -y install openjdk-17-jre-headless
 
 RUN mkdir /tmp/canto
 COPY . /tmp/canto/
@@ -34,7 +43,7 @@ RUN patch /usr/include/CLucene/store/FSDirectory.h < /tmp/canto/etc/clucene_comp
 
 RUN cpanm Lucene
 
-RUN (cd /tmp/canto; perl Makefile.PL && make installdeps_notest); rm -rf /tmp/canto
+RUN (cd /tmp/canto; export PERL_MM_USE_DEFAULT=1; perl Makefile.PL && make installdeps_notest); rm -rf /tmp/canto
 
 RUN rm -rf /root/.local /root/.cpan*
 

etc/docker-run-tests.sh

@@ -1,4 +1,4 @@
 #!/bin/sh -
 
 docker run --rm --net="host" --mount type=bind,source=$(pwd)/,target=/canto -w=/canto \
-    pombase/canto-base:v17 /bin/bash -c "cd /canto && perl Makefile.PL && make test"
+    pombase/canto-base:v18 /bin/bash -c "cd /canto && perl Makefile.PL && make test"

script/canto_docker

@@ -55,7 +55,7 @@ then
     DOCKER_COMMAND="podman"
 fi
 
-CANTO_DOCKER_RUN_ARGS="$EXTRA_ARGS --rm $INTERACTIVE_ARGS --mount type=bind,source=$(pwd)/logs,target=/logs --mount type=bind,source=$(pwd)/data,target=/data --mount type=bind,source=$(pwd)/import_export,target=/import_export --mount type=bind,source=$(pwd)/canto,target=/canto -w=/canto docker.io/pombase/canto-base:v15"
+CANTO_DOCKER_RUN_ARGS="$EXTRA_ARGS --rm $INTERACTIVE_ARGS --mount type=bind,source=$(pwd)/logs,target=/logs --mount type=bind,source=$(pwd)/data,target=/data --mount type=bind,source=$(pwd)/import_export,target=/import_export --mount type=bind,source=$(pwd)/canto,target=/canto -w=/canto docker.io/pombase/canto-base:v18"
 
 cd canto
 

script/canto_start_docker

@@ -76,7 +76,7 @@ then
     fi
 fi
 
-CANTO_DOCKER_RUN_ARGS="$EXTRA_ARGS -i $TTY_OPT --rm $DEBUG --mount type=bind,source=$(pwd)/logs,target=/logs  --mount type=bind,source=$(pwd)/data,target=/data --mount type=bind,source=$(pwd)/import_export,target=/import_export --mount type=bind,source=$(pwd)/canto,target=/canto -w=/canto pombase/canto-base:v15"
+CANTO_DOCKER_RUN_ARGS="$EXTRA_ARGS -i $TTY_OPT --rm $DEBUG --mount type=bind,source=$(pwd)/logs,target=/logs  --mount type=bind,source=$(pwd)/data,target=/data --mount type=bind,source=$(pwd)/import_export,target=/import_export --mount type=bind,source=$(pwd)/canto,target=/canto -w=/canto pombase/canto-base:v18"
 
 cd canto