Fix various issues with installation of CamCHILDMine

.env

@@ -0,0 +1,12 @@
+DOCKER_UID=1000
+DOCKER_GID=1000
+MINE_NAME=biotestmine
+MINE_REPO_URL=
+IM_DATA_DIR=DATA_DIR
+BUILDER_MEM_OPTS=:"-Xmx2g -Xms1g"
+SOLR_MEM_OPTS=:"-Xmx2g -Xms1g"
+TOMCAT_MEM_OPTS=:"-Xmx1g -Xms500m"
+IM_REPO_URL=
+IM_REPO_BRANCH=
+TOMCAT_HOST_PORT=9999
+TOMCAT_PORT=8080

.github/workflows/biotestmine.yml

@@ -0,0 +1,63 @@
+---
+# yamllint disable rule:line-length
+name: Biotestmine
+# yamllint disable-line rule:truthy
+on:
+    push:
+        paths:
+            - '.env'
+            - '.github/workflows/biotestmine.yml'
+            - 'intermine_builder/**'
+            - 'local.docker-compose.yml'
+            - 'mkdatadirs.sh'
+            - 'postgres/**'
+            - 'solr/**'
+            - 'tomcat/**'
+
+jobs:
+    biotestmine:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Install prerequisites
+              run: |
+                  set -euo pipefail
+                  sudo apt -y install wait-for-it
+            - name: Make data dirs
+              run: |
+                  set -euo pipefail
+                  cd ${GITHUB_WORKSPACE}
+                  ./mkdatadirs.sh
+                  mkdir ./data/mine/biotestmine
+            - name: Up
+              run: |
+                  set -euo pipefail
+                  cd ${GITHUB_WORKSPACE}
+                  # Use run to trap any build errors early
+                  # DOCKER_UID=$(id -u) DOCKER_GID=$(id -g) docker compose -f local.docker-compose.yml run --rm intermine_builder
+                  DOCKER_UID=$(id -u) DOCKER_GID=$(id -g) docker compose -f local.docker-compose.yml up -d
+            - name: Wait
+              run: |
+                  set -euo pipefail
+                  cd ${GITHUB_WORKSPACE}
+                  # Wait for builder to finish and return exit code
+                  DOCKER_UID=$(id -u) DOCKER_GID=$(id -g) docker compose -f local.docker-compose.yml wait intermine_builder
+                  # Wait 15 minutes
+                  wait-for-it localhost:9999 --timeout=900
+
+            - name: Check webapp
+              run: |
+                  set -euo pipefail
+                  curl -I -L --retry 10 --fail --insecure "http://localhost:9999/biotestmine/"
+
+            - name: Dump Docker logs
+              if: failure()
+              run: |
+                  set -euo pipefail
+                  cd ${GITHUB_WORKSPACE}
+                  sleep 120
+                  DOCKER_UID=$(id -u) DOCKER_GID=$(id -g) docker compose -f local.docker-compose.yml logs intermine_builder
+                  DOCKER_UID=$(id -u) DOCKER_GID=$(id -g) docker compose -f local.docker-compose.yml logs postgres
+                  DOCKER_UID=$(id -u) DOCKER_GID=$(id -g) docker compose -f local.docker-compose.yml logs solr
+                  DOCKER_UID=$(id -u) DOCKER_GID=$(id -g) docker compose -f local.docker-compose.yml logs tomcat

.gitignore

@@ -1,2 +1,7 @@
-.env
 /data
+
+# Emacs backup
+*~
+
+# Silver searcher
+.ignore

dockerhub.docker-compose.yml

@@ -1,4 +1,3 @@
-version: "3"
 services:
   intermine_builder:
     container_name: intermine_builder
@@ -19,7 +18,7 @@ services:
       - MEM_OPTS=${MEM_OPTS:-"-Xmx2g -Xms1g"}
       - IM_REPO_URL=${IM_REPO_URL:-}
       - IM_REPO_BRANCH=${IM_REPO_BRANCH:-}
-    depends_on: 
+    depends_on:
       - postgres
       - solr
       - tomcat

intermine_builder/intermine_builder.Dockerfile

@@ -1,12 +1,24 @@
 FROM alpine:3.12.5
 LABEL maintainer="Ank"
 
+# -----------------------------------------------------------------------------
+# Permissions
+# -----------------------------------------------------------------------------
+# https://vsupalov.com/docker-shared-permissions/
+
+ARG USER_ID
+ARG GROUP_ID
+
+RUN addgroup --gid $GROUP_ID intermine
+RUN adduser -D -g '' -u $USER_ID -G intermine intermine
+
 ENV JAVA_HOME="/usr/lib/jvm/default-jvm"
 
 RUN apk add --no-cache openjdk8 openjdk8-jre && \
     ln -sf "${JAVA_HOME}/bin/"* "/usr/bin/"
 
-RUN apk add --no-cache git \
+RUN apk add --no-cache bash \
+                       git \
                        maven \
                        postgresql-client \
                        perl \
@@ -58,9 +70,6 @@ RUN cpanm --force Ouch \
                 #  Digest::MD5 \
                 #  Log::Handler
 
-RUN mkdir /home/intermine && mkdir /home/intermine/intermine
-RUN chmod -R 777 /home/intermine
-
 ENV MEM_OPTS="-Xmx1g -Xms500m"
 ENV GRADLE_OPTS="-server ${MEM_OPTS} -XX:+UseParallelGC -XX:SoftRefLRUPolicyMSPerMB=1 -XX:MaxHeapFreeRatio=99 -Dorg.gradle.daemon=false -Duser.home=/home/intermine"
 ENV HOME="/home/intermine"
@@ -73,8 +82,16 @@ ENV TOMCAT_PWD="tomcat"
 ENV TOMCAT_PORT=8080
 ENV PGPORT=5432
 
+RUN mkdir /home/intermine/intermine
 COPY ./build.sh /home/intermine
-RUN chmod a+rx /home/intermine/build.sh
+RUN chown -R intermine:intermine /home/intermine
+RUN chmod u+x /home/intermine/build.sh
+
+COPY ./wait-for-it/wait-for-it.sh /usr/local/bin/wait-for-it
+RUN chmod +x /usr/local/bin/wait-for-it
+
 WORKDIR /home/intermine/intermine
 
+USER intermine
+
 CMD ["/bin/sh","/home/intermine/build.sh"]

intermine_builder/wait-for-it/LICENSE

@@ -0,0 +1,20 @@
+The MIT License (MIT)
+Copyright (c) 2016 Giles Hall
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

intermine_builder/wait-for-it/wait-for-it.sh

@@ -0,0 +1,182 @@
+#!/usr/bin/env bash
+# Use this script to test if a given TCP host/port are available
+
+WAITFORIT_cmdname=${0##*/}
+
+echoerr() { if [[ $WAITFORIT_QUIET -ne 1 ]]; then echo "$@" 1>&2; fi }
+
+usage()
+{
+    cat << USAGE >&2
+Usage:
+    $WAITFORIT_cmdname host:port [-s] [-t timeout] [-- command args]
+    -h HOST | --host=HOST       Host or IP under test
+    -p PORT | --port=PORT       TCP port under test
+                                Alternatively, you specify the host and port as host:port
+    -s | --strict               Only execute subcommand if the test succeeds
+    -q | --quiet                Don't output any status messages
+    -t TIMEOUT | --timeout=TIMEOUT
+                                Timeout in seconds, zero for no timeout
+    -- COMMAND ARGS             Execute command with args after the test finishes
+USAGE
+    exit 1
+}
+
+wait_for()
+{
+    if [[ $WAITFORIT_TIMEOUT -gt 0 ]]; then
+        echoerr "$WAITFORIT_cmdname: waiting $WAITFORIT_TIMEOUT seconds for $WAITFORIT_HOST:$WAITFORIT_PORT"
+    else
+        echoerr "$WAITFORIT_cmdname: waiting for $WAITFORIT_HOST:$WAITFORIT_PORT without a timeout"
+    fi
+    WAITFORIT_start_ts=$(date +%s)
+    while :
+    do
+        if [[ $WAITFORIT_ISBUSY -eq 1 ]]; then
+            nc -z $WAITFORIT_HOST $WAITFORIT_PORT
+            WAITFORIT_result=$?
+        else
+            (echo -n > /dev/tcp/$WAITFORIT_HOST/$WAITFORIT_PORT) >/dev/null 2>&1
+            WAITFORIT_result=$?
+        fi
+        if [[ $WAITFORIT_result -eq 0 ]]; then
+            WAITFORIT_end_ts=$(date +%s)
+            echoerr "$WAITFORIT_cmdname: $WAITFORIT_HOST:$WAITFORIT_PORT is available after $((WAITFORIT_end_ts - WAITFORIT_start_ts)) seconds"
+            break
+        fi
+        sleep 1
+    done
+    return $WAITFORIT_result
+}
+
+wait_for_wrapper()
+{
+    # In order to support SIGINT during timeout: http://unix.stackexchange.com/a/57692
+    if [[ $WAITFORIT_QUIET -eq 1 ]]; then
+        timeout $WAITFORIT_BUSYTIMEFLAG $WAITFORIT_TIMEOUT $0 --quiet --child --host=$WAITFORIT_HOST --port=$WAITFORIT_PORT --timeout=$WAITFORIT_TIMEOUT &
+    else
+        timeout $WAITFORIT_BUSYTIMEFLAG $WAITFORIT_TIMEOUT $0 --child --host=$WAITFORIT_HOST --port=$WAITFORIT_PORT --timeout=$WAITFORIT_TIMEOUT &
+    fi
+    WAITFORIT_PID=$!
+    trap "kill -INT -$WAITFORIT_PID" INT
+    wait $WAITFORIT_PID
+    WAITFORIT_RESULT=$?
+    if [[ $WAITFORIT_RESULT -ne 0 ]]; then
+        echoerr "$WAITFORIT_cmdname: timeout occurred after waiting $WAITFORIT_TIMEOUT seconds for $WAITFORIT_HOST:$WAITFORIT_PORT"
+    fi
+    return $WAITFORIT_RESULT
+}
+
+# process arguments
+while [[ $# -gt 0 ]]
+do
+    case "$1" in
+        *:* )
+        WAITFORIT_hostport=(${1//:/ })
+        WAITFORIT_HOST=${WAITFORIT_hostport[0]}
+        WAITFORIT_PORT=${WAITFORIT_hostport[1]}
+        shift 1
+        ;;
+        --child)
+        WAITFORIT_CHILD=1
+        shift 1
+        ;;
+        -q | --quiet)
+        WAITFORIT_QUIET=1
+        shift 1
+        ;;
+        -s | --strict)
+        WAITFORIT_STRICT=1
+        shift 1
+        ;;
+        -h)
+        WAITFORIT_HOST="$2"
+        if [[ $WAITFORIT_HOST == "" ]]; then break; fi
+        shift 2
+        ;;
+        --host=*)
+        WAITFORIT_HOST="${1#*=}"
+        shift 1
+        ;;
+        -p)
+        WAITFORIT_PORT="$2"
+        if [[ $WAITFORIT_PORT == "" ]]; then break; fi
+        shift 2
+        ;;
+        --port=*)
+        WAITFORIT_PORT="${1#*=}"
+        shift 1
+        ;;
+        -t)
+        WAITFORIT_TIMEOUT="$2"
+        if [[ $WAITFORIT_TIMEOUT == "" ]]; then break; fi
+        shift 2
+        ;;
+        --timeout=*)
+        WAITFORIT_TIMEOUT="${1#*=}"
+        shift 1
+        ;;
+        --)
+        shift
+        WAITFORIT_CLI=("$@")
+        break
+        ;;
+        --help)
+        usage
+        ;;
+        *)
+        echoerr "Unknown argument: $1"
+        usage
+        ;;
+    esac
+done
+
+if [[ "$WAITFORIT_HOST" == "" || "$WAITFORIT_PORT" == "" ]]; then
+    echoerr "Error: you need to provide a host and port to test."
+    usage
+fi
+
+WAITFORIT_TIMEOUT=${WAITFORIT_TIMEOUT:-15}
+WAITFORIT_STRICT=${WAITFORIT_STRICT:-0}
+WAITFORIT_CHILD=${WAITFORIT_CHILD:-0}
+WAITFORIT_QUIET=${WAITFORIT_QUIET:-0}
+
+# Check to see if timeout is from busybox?
+WAITFORIT_TIMEOUT_PATH=$(type -p timeout)
+WAITFORIT_TIMEOUT_PATH=$(realpath $WAITFORIT_TIMEOUT_PATH 2>/dev/null || readlink -f $WAITFORIT_TIMEOUT_PATH)
+
+WAITFORIT_BUSYTIMEFLAG=""
+if [[ $WAITFORIT_TIMEOUT_PATH =~ "busybox" ]]; then
+    WAITFORIT_ISBUSY=1
+    # Check if busybox timeout uses -t flag
+    # (recent Alpine versions don't support -t anymore)
+    if timeout &>/dev/stdout | grep -q -e '-t '; then
+        WAITFORIT_BUSYTIMEFLAG="-t"
+    fi
+else
+    WAITFORIT_ISBUSY=0
+fi
+
+if [[ $WAITFORIT_CHILD -gt 0 ]]; then
+    wait_for
+    WAITFORIT_RESULT=$?
+    exit $WAITFORIT_RESULT
+else
+    if [[ $WAITFORIT_TIMEOUT -gt 0 ]]; then
+        wait_for_wrapper
+        WAITFORIT_RESULT=$?
+    else
+        wait_for
+        WAITFORIT_RESULT=$?
+    fi
+fi
+
+if [[ $WAITFORIT_CLI != "" ]]; then
+    if [[ $WAITFORIT_RESULT -ne 0 && $WAITFORIT_STRICT -eq 1 ]]; then
+        echoerr "$WAITFORIT_cmdname: strict mode, refusing to execute subprocess"
+        exit $WAITFORIT_RESULT
+    fi
+    exec "${WAITFORIT_CLI[@]}"
+else
+    exit $WAITFORIT_RESULT
+fi