Failed whilst adding the schema information in pre.xsd

[MaxiReglisse]

In order to ensure data permanence, i am used to sharing data between containers and docker host. With version 3.10.3, I was sharing in particular /config, and the docker composition was working fine.

but with version 4.0.1 and 4.0.2, I encounter an error when I share /catalog-data ...

Exception message if any is /catalogue-data/resources/xml/schemas/iso19115-3.2018/schema/standards.iso.org/19135/-2/pre/1.0/pre.xsd, Error=Raised exception while starting the application. 
Fix the error and restart., Handler=org.fao.geonet.Geonetwork, Exception=OperationAbortedEx : Failed whilst adding the schema information. 
Exception message if any is /catalogue-data/resources/xml/schemas/iso19115-3.2018/schema/standards.iso.org/19135/-2/pre/1.0/pre.xsd,    Stack=OperationAbortedEx : 
Failed whilst adding the schema information. Exception message if any is /catalogue-data/resources/xml/schemas/iso19115-3.2018/schema/standards.iso.org/19135/-2/pre/1.0/pre.xsd

below is an extract from my docker-compose.yml:

geonetwork:
  image: geonetwork:4.0.2
...
 volumes:
  - /home/docker/docker-geonetwork/4.0.2/catalogue-data:/catalogue-data
    # - geonetwork:/catalogue-data

The file pre.xsd does exist in the local folder, and it is fully read / write accessible.

$ pwd
/home/docker/docker-geonetwork/4.0.2
$ ls -l catalogue-data/resources/xml/schemas/iso19115-3.2018/schema/standards.iso.org/19135/-2/pre/1.0/pre.xsd
-rw-r--r-- 1 docker users 386 août  17 08:41 catalogue-data/resources/xml/schemas/iso19115-3.2018/schema/standards.iso.org/19135/-2/pre/1.0/pre.xsd

any help would be appreciated.

Ernest.

[MaxiReglisse]

problem solved, or at least workaround: just assign the share folder to user 999:999, which is the user of the geonetwork container which provides the jetty service (replacing tomcat).

[MaxiReglisse]

999 is used by systemd-coredump in Debian... would it be possible to consider a solution like that proposed by Unify? Unifi user fixed at UID=999

[MaxiReglisse]

Following Bdruemen's suggestion, jenkins-docker-uid-from-volume/Dockerfile I tried to change the uid and gid of user jenkins ...

I added the following lines in the Dockerfile of GeoNetwork, so that you can use docker user (1001,100) instead of user jetty (999,999).

USER root

RUN useradd -rm -d /home/docker -s /bin/bash -g users -u 1001 docker

# gosu installation
ADD https://github.com/tianon/gosu/releases/download/1.5/gosu-amd64 /usr/local/bin/gosu

# Change the group of the jetty user to users
# usermod -u 1001 jetty # does not work...
RUN chmod 755 /usr/local/bin/gosu
RUN usermod -g 100 jetty
RUN chown -R docker:users /var/lib/jetty /catalogue-data /tmp /usr/local/jetty

# tini installation
RUN apt-get update && apt-get install -y tini && apt-get clean && rm -rf /var/lib/apt/lists/*

COPY ./docker-entrypoint.sh /geonetwork-entrypoint.sh

ENTRYPOINT gosu docker /usr/bin/tini -- /geonetwork-entrypoint.sh

CMD ["java","-jar","/usr/local/jetty/start.jar"]

VOLUME [ "${DATA_DIR}" ]

it deserves to work!

docker:~/docker-geonetwork/4.0.1 $ docker exec -it 401_geonetwork_1 grep docker /etc/passwd
docker:x:1001:100::/home/docker:/bin/bash

docker:~/docker-geonetwork/4.0.1 (mshe) $ docker exec -it 401_geonetwork_1 ls -l
total 36
drwxr-xr-x 2 docker users 4096 Jan  7 16:50 jcs_caching
-rw-r--r-- 1 docker users 2945 Jan  7 16:49 jetty.start
drwxr-xr-x 1 docker users 4096 Dec 22 14:13 lib
drwxr-xr-x 2 docker users 4096 Jan  7 16:50 logs
drwxr-xr-x 1 docker users 4096 Dec 22 14:13 resources
drwxr-xr-x 3 docker users 4096 Jan  7 16:50 src
drwxr-xr-x 1 docker users 4096 Dec 22 14:13 start.d
drwxr-xr-x 1 docker users 4096 Jan  7 16:44 webapps

docker:~/docker-geonetwork/4.0.1 (mshe) $ ls -ltr catalogue-data/
total 4
drwxr-xr-x 6 docker users 4096 janv.  7 17:50 resources/

But this generates the following warnings

[WARN  tini (8)] Tini is not running as PID 1 and isn't registered as a child subreaper.
Zombie processes will not be re-parented to Tini, so zombie reaping won't work.
To fix the problem, use the -s option or set the environment variable TINI_SUBREAPER to register Tini as a child subreaper, or run Tini as PID 1.
********************************************************************
WARNING: User is docker
     The user should be (re)set to 'jetty' in the Dockerfile
********************************************************************

What do you think?

Another solution would have been to use fixuid but i couldn't ...

Thanks in advance.

[kikislater]

changing rights to jetty user and group works, so a chown in entrypoint is more appropriated IMO