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switch to plain mongo image #91

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fa2b90c
switch to plain mongo image
nr23730 Aug 12, 2024
571cf84
address review comments: add init.sh script origin
nr23730 Aug 12, 2024
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18 changes: 9 additions & 9 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,14 +1,15 @@
# This base image starts up mongo
# This version needs to correspond with the helm chart version
ARG MONGODBVERSION=4.0.12
FROM bitnami/mongodb:${MONGODBVERSION} as build
FROM docker.io/mongo:${MONGODBVERSION} as build

# Use .dockerignore file to ignore unwanted files
# These files are used by import_mongo.sh to initialize mongo
# Creating directories as root
# Set user back to the one in base image
USER root
RUN mkdir -p /data
RUN mkdir -p /seed && chmod 777 /seed
COPY data/ /data/

ARG ARG_REF_ENSEMBL_VERSION
Expand All @@ -17,15 +18,14 @@ ARG SPECIES=homo_sapiens
ARG MUTATIONASSESSOR=false

# Import data into mongodb
COPY scripts/import_mongo.sh /docker-entrypoint-initdb.d/
RUN /setup.sh
COPY scripts/import_mongo.sh /docker-entrypoint-initdb.d/import_mongo.sh
COPY scripts/init.sh /init.sh
RUN /init.sh mongod

FROM bitnami/mongodb:${MONGODBVERSION}
COPY --from=build /bitnami/mongodb /bitnami/seed
COPY /scripts/startup.sh /startup.sh
RUN ls -la /data/db

USER root
RUN chown -R 1001 /bitnami/seed
USER 1001
FROM docker.io/mongo:${MONGODBVERSION}
COPY --from=build /seed /seed
COPY /scripts/startup.sh /startup.sh

CMD [ "/startup.sh" ]
354 changes: 354 additions & 0 deletions scripts/init.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,354 @@
#!/bin/bash
set -Eeuo pipefail
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if [ "${1:0:1}" = '-' ]; then
set -- mongod "$@"
fi

originalArgOne="$1"

# allow the container to be started with `--user`
# all mongo* commands should be dropped to the correct user
if [[ "$originalArgOne" == mongo* ]] && [ "$(id -u)" = '0' ]; then
if [ "$originalArgOne" = 'mongod' ]; then
find /data/configdb /data/db \! -user mongodb -exec chown mongodb '{}' +
fi

# make sure we can write to stdout and stderr as "mongodb"
# (for our "initdb" code later; see "--logpath" below)
chown --dereference mongodb "/proc/$$/fd/1" "/proc/$$/fd/2" || :
# ignore errors thanks to https://github.com/docker-library/mongo/issues/149

exec gosu mongodb "$BASH_SOURCE" "$@"
fi

# you should use numactl to start your mongod instances, including the config servers, mongos instances, and any clients.
# https://docs.mongodb.com/manual/administration/production-notes/#configuring-numa-on-linux
if [[ "$originalArgOne" == mongo* ]]; then
numa='numactl --interleave=all'
if $numa true &> /dev/null; then
set -- $numa "$@"
fi
fi

# usage: file_env VAR [DEFAULT]
# ie: file_env 'XYZ_DB_PASSWORD' 'example'
# (will allow for "$XYZ_DB_PASSWORD_FILE" to fill in the value of
# "$XYZ_DB_PASSWORD" from a file, especially for Docker's secrets feature)
file_env() {
local var="$1"
local fileVar="${var}_FILE"
local def="${2:-}"
if [ "${!var:-}" ] && [ "${!fileVar:-}" ]; then
echo >&2 "error: both $var and $fileVar are set (but are exclusive)"
exit 1
fi
local val="$def"
if [ "${!var:-}" ]; then
val="${!var}"
elif [ "${!fileVar:-}" ]; then
val="$(< "${!fileVar}")"
fi
export "$var"="$val"
unset "$fileVar"
}

# see https://github.com/docker-library/mongo/issues/147 (mongod is picky about duplicated arguments)
_mongod_hack_have_arg() {
local checkArg="$1"; shift
local arg
for arg; do
case "$arg" in
"$checkArg"|"$checkArg"=*)
return 0
;;
esac
done
return 1
}
# _mongod_hack_get_arg_val '--some-arg' "$@"
_mongod_hack_get_arg_val() {
local checkArg="$1"; shift
while [ "$#" -gt 0 ]; do
local arg="$1"; shift
case "$arg" in
"$checkArg")
echo "$1"
return 0
;;
"$checkArg"=*)
echo "${arg#$checkArg=}"
return 0
;;
esac
done
return 1
}
declare -a mongodHackedArgs
# _mongod_hack_ensure_arg '--some-arg' "$@"
# set -- "${mongodHackedArgs[@]}"
_mongod_hack_ensure_arg() {
local ensureArg="$1"; shift
mongodHackedArgs=( "$@" )
if ! _mongod_hack_have_arg "$ensureArg" "$@"; then
mongodHackedArgs+=( "$ensureArg" )
fi
}
# _mongod_hack_ensure_no_arg '--some-unwanted-arg' "$@"
# set -- "${mongodHackedArgs[@]}"
_mongod_hack_ensure_no_arg() {
local ensureNoArg="$1"; shift
mongodHackedArgs=()
while [ "$#" -gt 0 ]; do
local arg="$1"; shift
if [ "$arg" = "$ensureNoArg" ]; then
continue
fi
mongodHackedArgs+=( "$arg" )
done
}
# _mongod_hack_ensure_no_arg '--some-unwanted-arg' "$@"
# set -- "${mongodHackedArgs[@]}"
_mongod_hack_ensure_no_arg_val() {
local ensureNoArg="$1"; shift
mongodHackedArgs=()
while [ "$#" -gt 0 ]; do
local arg="$1"; shift
case "$arg" in
"$ensureNoArg")
shift # also skip the value
continue
;;
"$ensureNoArg"=*)
# value is already included
continue
;;
esac
mongodHackedArgs+=( "$arg" )
done
}
# _mongod_hack_ensure_arg_val '--some-arg' 'some-val' "$@"
# set -- "${mongodHackedArgs[@]}"
_mongod_hack_ensure_arg_val() {
local ensureArg="$1"; shift
local ensureVal="$1"; shift
_mongod_hack_ensure_no_arg_val "$ensureArg" "$@"
mongodHackedArgs+=( "$ensureArg" "$ensureVal" )
}

# _js_escape 'some "string" value'
_js_escape() {
jq --null-input --arg 'str' "$1" '$str'
}

jsonConfigFile="${TMPDIR:-/tmp}/docker-entrypoint-config.json"
tempConfigFile="${TMPDIR:-/tmp}/docker-entrypoint-temp-config.json"
_parse_config() {
if [ -s "$tempConfigFile" ]; then
return 0
fi

local configPath
if configPath="$(_mongod_hack_get_arg_val --config "$@")"; then
# if --config is specified, parse it into a JSON file so we can remove a few problematic keys (especially SSL-related keys)
# see https://docs.mongodb.com/manual/reference/configuration-options/
mongo --norc --nodb --quiet --eval "load('/js-yaml.js'); printjson(jsyaml.load(cat($(_js_escape "$configPath"))))" > "$jsonConfigFile"
jq 'del(.systemLog, .processManagement, .net, .security)' "$jsonConfigFile" > "$tempConfigFile"
return 0
fi

return 1
}
dbPath=
_dbPath() {
if [ -n "$dbPath" ]; then
echo "$dbPath"
return
fi

if ! dbPath="$(_mongod_hack_get_arg_val --dbpath "$@")"; then
if _parse_config "$@"; then
dbPath="$(jq -r '.storage.dbPath // empty' "$jsonConfigFile")"
fi
fi

if [ -z "$dbPath" ]; then
if _mongod_hack_have_arg --configsvr "$@" || {
_parse_config "$@" \
&& clusterRole="$(jq -r '.sharding.clusterRole // empty' "$jsonConfigFile")" \
&& [ "$clusterRole" = 'configsvr' ]
}; then
# if running as config server, then the default dbpath is /data/configdb
# https://docs.mongodb.com/manual/reference/program/mongod/#cmdoption-mongod-configsvr
dbPath=/data/configdb
fi
fi

: "${dbPath:=/data/db}"

echo "$dbPath"
}

if [ "$originalArgOne" = 'mongod' ]; then
file_env 'MONGO_INITDB_ROOT_USERNAME'
file_env 'MONGO_INITDB_ROOT_PASSWORD'
# pre-check a few factors to see if it's even worth bothering with initdb
shouldPerformInitdb=
if [ "$MONGO_INITDB_ROOT_USERNAME" ] && [ "$MONGO_INITDB_ROOT_PASSWORD" ]; then
# if we have a username/password, let's set "--auth"
_mongod_hack_ensure_arg '--auth' "$@"
set -- "${mongodHackedArgs[@]}"
shouldPerformInitdb='true'
elif [ "$MONGO_INITDB_ROOT_USERNAME" ] || [ "$MONGO_INITDB_ROOT_PASSWORD" ]; then
cat >&2 <<-'EOF'

error: missing 'MONGO_INITDB_ROOT_USERNAME' or 'MONGO_INITDB_ROOT_PASSWORD'
both must be specified for a user to be created

EOF
exit 1
fi

if [ -z "$shouldPerformInitdb" ]; then
# if we've got any /docker-entrypoint-initdb.d/* files to parse later, we should initdb
for f in /docker-entrypoint-initdb.d/*; do
case "$f" in
*.sh|*.js) # this should match the set of files we check for below
shouldPerformInitdb="$f"
break
;;
esac
done
fi

# check for a few known paths (to determine whether we've already initialized and should thus skip our initdb scripts)
if [ -n "$shouldPerformInitdb" ]; then
dbPath="$(_dbPath "$@")"
for path in \
"$dbPath/WiredTiger" \
"$dbPath/journal" \
"$dbPath/local.0" \
"$dbPath/storage.bson" \
; do
if [ -e "$path" ]; then
shouldPerformInitdb=
break
fi
done
fi

if [ -n "$shouldPerformInitdb" ]; then
mongodHackedArgs=( "$@" )
if _parse_config "$@"; then
_mongod_hack_ensure_arg_val --config "$tempConfigFile" "${mongodHackedArgs[@]}"
fi
_mongod_hack_ensure_arg_val --bind_ip 127.0.0.1 "${mongodHackedArgs[@]}"
_mongod_hack_ensure_arg_val --port 27017 "${mongodHackedArgs[@]}"
_mongod_hack_ensure_no_arg --bind_ip_all "${mongodHackedArgs[@]}"

# remove "--auth" and "--replSet" for our initial startup (see https://docs.mongodb.com/manual/tutorial/enable-authentication/#start-mongodb-without-access-control)
# https://github.com/docker-library/mongo/issues/211
_mongod_hack_ensure_no_arg --auth "${mongodHackedArgs[@]}"
if [ "$MONGO_INITDB_ROOT_USERNAME" ] && [ "$MONGO_INITDB_ROOT_PASSWORD" ]; then
_mongod_hack_ensure_no_arg_val --replSet "${mongodHackedArgs[@]}"
fi

sslMode="$(_mongod_hack_have_arg '--sslPEMKeyFile' "$@" && echo 'allowSSL' || echo 'disabled')" # "BadValue: need sslPEMKeyFile when SSL is enabled" vs "BadValue: need to enable SSL via the sslMode flag when using SSL configuration parameters"
_mongod_hack_ensure_arg_val --sslMode "$sslMode" "${mongodHackedArgs[@]}"

if stat "/proc/$$/fd/1" > /dev/null && [ -w "/proc/$$/fd/1" ]; then
# https://github.com/mongodb/mongo/blob/38c0eb538d0fd390c6cb9ce9ae9894153f6e8ef5/src/mongo/db/initialize_server_global_state.cpp#L237-L251
# https://github.com/docker-library/mongo/issues/164#issuecomment-293965668
_mongod_hack_ensure_arg_val --logpath "/proc/$$/fd/1" "${mongodHackedArgs[@]}"
else
initdbLogPath="$(_dbPath "$@")/docker-initdb.log"
echo >&2 "warning: initdb logs cannot write to '/proc/$$/fd/1', so they are in '$initdbLogPath' instead"
_mongod_hack_ensure_arg_val --logpath "$initdbLogPath" "${mongodHackedArgs[@]}"
fi
_mongod_hack_ensure_arg --logappend "${mongodHackedArgs[@]}"

pidfile="${TMPDIR:-/tmp}/docker-entrypoint-temp-mongod.pid"
rm -f "$pidfile"
_mongod_hack_ensure_arg_val --pidfilepath "$pidfile" "${mongodHackedArgs[@]}"

"${mongodHackedArgs[@]}" --fork

mongo=( mongo --host 127.0.0.1 --port 27017 --quiet )

# check to see that our "mongod" actually did start up (catches "--help", "--version", MongoDB 3.2 being silly, slow prealloc, etc)
# https://jira.mongodb.org/browse/SERVER-16292
tries=30
while true; do
if ! { [ -s "$pidfile" ] && ps "$(< "$pidfile")" &> /dev/null; }; then
# bail ASAP if "mongod" isn't even running
echo >&2
echo >&2 "error: $originalArgOne does not appear to have stayed running -- perhaps it had an error?"
echo >&2
exit 1
fi
if "${mongo[@]}" 'admin' --eval 'quit(0)' &> /dev/null; then
# success!
break
fi
(( tries-- ))
if [ "$tries" -le 0 ]; then
echo >&2
echo >&2 "error: $originalArgOne does not appear to have accepted connections quickly enough -- perhaps it had an error?"
echo >&2
exit 1
fi
sleep 1
done

if [ "$MONGO_INITDB_ROOT_USERNAME" ] && [ "$MONGO_INITDB_ROOT_PASSWORD" ]; then
rootAuthDatabase='admin'

"${mongo[@]}" "$rootAuthDatabase" <<-EOJS
db.createUser({
user: $(_js_escape "$MONGO_INITDB_ROOT_USERNAME"),
pwd: $(_js_escape "$MONGO_INITDB_ROOT_PASSWORD"),
roles: [ { role: 'root', db: $(_js_escape "$rootAuthDatabase") } ]
})
EOJS
fi

export MONGO_INITDB_DATABASE="${MONGO_INITDB_DATABASE:-test}"

echo
for f in /docker-entrypoint-initdb.d/*; do
case "$f" in
*.sh) echo "$0: running $f"; . "$f" ;;
*.js) echo "$0: running $f"; "${mongo[@]}" "$MONGO_INITDB_DATABASE" "$f"; echo ;;
*) echo "$0: ignoring $f" ;;
esac
echo
done

"${mongodHackedArgs[@]}" --shutdown
rm -f "$pidfile"

echo
echo 'MongoDB init process complete; ready for start up.'
echo
fi

# MongoDB 3.6+ defaults to localhost-only binding
if mongod --help 2>&1 | grep -q -- --bind_ip_all; then # TODO remove this conditional when 3.4 is no longer supported
haveBindIp=
if _mongod_hack_have_arg --bind_ip "$@" || _mongod_hack_have_arg --bind_ip_all "$@"; then
haveBindIp=1
elif _parse_config "$@" && jq --exit-status '.net.bindIp // .net.bindIpAll' "$jsonConfigFile" > /dev/null; then
haveBindIp=1
fi
if [ -z "$haveBindIp" ]; then
# so if no "--bind_ip" is specified, let's add "--bind_ip_all"
set -- "$@" --bind_ip_all
fi
fi

unset "${!MONGO_INITDB_@}"
fi

rm -f "$jsonConfigFile" "$tempConfigFile"

cp -r /data/db/ /seed
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