build error docker rest VV 2.0

[AnotherSimon]

A bit late to the 2.0 party but I seem to be getting a build error using docker on version c034e95.

Followed the instructions at DOCKER.md (seemingly without errors) up to docker-compose up at which point I see the following error:

$ docker-compose up
Creating network "rest_variantvalidator_default" with the default driver
Creating volume "rest_variantvalidator_share" with local driver
Creating volume "rest_variantvalidator_seqdata" with local driver
Creating volume "rest_variantvalidator_logs" with local driver
Creating rest_variantvalidator_seqrepo_1 ... error
Creating rest_variantvalidator_vdb_1     ... 
Creating rest_variantvalidator_vvta_1    ... 
Creating rest_variantvalidator_vdb_1     ... done
Creating rest_variantvalidator_vvta_1    ... done
Creating rest_variantvalidator_restvv_1  ... error

ERROR: for rest_variantvalidator_restvv_1  Cannot start service restvv: error while mounting volume '/var/lib/docker/volumes/rest_variantvalidator_seqdata/_data': failed to mount local volume: mount /home/simon/variantvalidator_data/share/seqrepo:/var/lib/docker/volumes/rest_variantvalidator_seqdata/_data, flags: 0x1000: no such file or directory

ERROR: for seqrepo  Cannot create container for service seqrepo: failed to mount local volume: mount /home/simon/variantvalidator_data/share/seqrepo:/var/lib/docker/volumes/rest_variantvalidator_seqdata/_data, flags: 0x1000: no such file or directory

ERROR: for restvv  Cannot start service restvv: error while mounting volume '/var/lib/docker/volumes/rest_variantvalidator_seqdata/_data': failed to mount local volume: mount /home/simon/variantvalidator_data/share/seqrepo:/var/lib/docker/volumes/rest_variantvalidator_seqdata/_data, flags: 0x1000: no such file or directory
ERROR: Encountered errors while bringing up the project.

Is there supposed to be an underscore in the leaf paths on the docker containers? (like .../volumes/rest_variantvalidator_seqdata/_data)
I also noticed that there isn't any data in the folder ~/variantvalidator_data/share/ on the host system. I do believe there are some folders that should be created here but docker-compose build --no-cache does not seem to have done this.
This problem persists after issuing the command docker system prune -a --volumes.

[Peter-J-Freeman]

Hi @AnotherSimon

Let me check this out.

It looks like you created the folders on your local system? https://github.com/openvar/rest_variantValidator/blob/master/docs/DOCKER.md

• Create a directory for sharing resources between your computer and the container

$ mkdir ~/variantvalidator_data
$ mkdir ~/variantvalidator_data/share

i.e. a directory called share in your home directory

I will try spark up a new install on my machine now and see if debugging is needed

[Peter-J-Freeman]

I also noticed that there isn't any data in the folder ~/variantvalidator_data/share/ on the host system

OK, I get the following

$ ls ~/variantvalidator_data
share
$ ls ~/variantvalidator_data/share/
applications	ca-certificates	fonts		icons		jupyter		logs		man		seqrepo

Re-building now

[Peter-J-Freeman]

Hi @AnotherSimon
look at this error
ERROR: for rest_variantvalidator_restvv_1 Cannot start service restvv: error while mounting volume '/var/lib/docker/volumes/rest_variantvalidator_seqdata/_data': failed to mount local volume: mount /home/simon/variantvalidator_data/share/seqrepo:/var/lib/docker/volumes/rest_variantvalidator_seqdata/_data, flags: 0x1000: no such file or directory

please confirm you created the requested directories as above in this issue. I'm not seeing this error

[AnotherSimon]

There was one more issue I encountered when building the docker version on a different server. For vdb image to be built, I had to edit vdb_docker.df as follows:

FROM mysql:latest

ENV MYSQL_RANDOM_ROOT_PASSWORD yes

ENV MYSQL_DATABASE validator

ENV MYSQL_USER vvadmin

ENV MYSQL_PASSWORD var1ant

USER root

RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 467B942D3A79BD29

RUN apt-get update && apt-get install -y wget && rm -rf /var/lib/apt/lists/*

RUN wget --output-document=validator_2022_04.sql.gz https://www528.lamp.le.ac.uk/vvdata/validator/validator_2022_04.sql.gz -O /docker-entrypoint-initdb.d/validator_2022_04.sql.gz

Note that the line switching to user root may or may not be necessary. (it's a copy-pasta solution)

Not sure why this only happened on this particular server.

[Peter-J-Freeman]

Thanks for the update. Leave it with me. I'll get back to you.