# Deploying genecup

# Hosting

The source repo has moved to

=> https://git.genenetwork.org/genecup/

If you have ssh access you can push to the repo with

=> yourname@git.genenetwork.org:/home/git/public/genecup

# Deploy on tux02

On Tux02 as shepherd user I can build:

```
./guix/bin/guix build -L ~/services/genecup/guix-past/modules -L ~/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native -c 24 -M 8
```

To run genecup in a container we have a trick to include the source code by cd'ing into the built version

```
export EDIRECT_PUBMED_MASTER=/export2/PubMed
export TMPDIR=/export/ratspub/tmp
export NLTK_DATA=/export2/PubMed/nltk_data

# This version for the genecup guix profile which includes guix-bioinformatics, using genecup-channels.scm.
# shepherd@tux02:~/services/genecup$ ./guix/bin/guix build -L ~/services/genecup/guix-past/modules -L ~/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native -c 24 -M 8

cd /home/shepherd/services/genecup
cd $(/home/shepherd/services/genecup/guix/bin/guix build -L /home/shepherd/services/genecup/guix-past/modules -L /home/shepherd/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native -c 4)

/home/shepherd/services/genecup/guix/bin/guix shell -C -N --expose=/etc/ssl/certs --expose=$EDIRECT_PUBMED_MASTER --share=$TMPDIR -L /home/shepherd/services/genecup/guix-past/modules -L /home/shepherd/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native coreutils-minimal -- env TMPDIR=$TMPDIR EDIRECT_PUBMED_MASTER=$EDIRECT_PUBMED_MASTER NLTK_DATA=$NLTK_DATA ./server.py
```

That means you can also develop software running in a container with the last command by switching into a repo:

```
cd $repo
run last command using guix shell
```

The only problem, at this point, is that python is not in the path.

The alternative is to use a guix shell, as described in the README.md

=> https://git.genenetwork.org/genecup/tree/README.md

and port forward:

```
ssh -L 4200:127.0.0.1:4200 -f -N server
curl localhost:4200
```

# Troubleshooting

## Moving the PubMed dir

After moving the PubMed dir GeneCup stopped displaying part of the connections. This can be reproduced by running the standard example on the home page - the result should look like the image on the right of the home page.

After fixing the paths and restarting the service there still was no result.

Genecup is currently managed by the shepherd as user shepherd. Stop the service as that user:

```
shepherd@tux02:~$ herd stop genecup
guile: warning: failed to install locale
Service genecup has been stopped.
```

Now the servic looks stopped, but it is still running and you need to kill by hand:

```
shepherd@tux02:~$ ps xau|grep genecup
shepherd  89524  0.0  0.0  12780   944 pts/42   S+   00:32   0:00 grep genecup
shepherd 129334  0.0  0.7 42620944 2089640 ?    Sl   Mar05  66:30 /gnu/store/1w5v338qk5m8khcazwclprs3znqp6f7f-python-3.10.7/bin/python3 /gnu/store/a6z0mmj6iq6grwynfvkzd0xbbr4zdm0l-genecup-latest-with-tensorflow-native-HEAD-of-master-branch/.server.py-real
shepherd@tux02:~$ kill -9 129334
shepherd@tux02:~$ ps xau|grep genecup
shepherd  89747  0.0  0.0  12780   944 pts/42   S+   00:32   0:00 grep genecup
shepherd@tux02:~$
```

The log file lives in

```
shepherd@tux02:~/logs$ tail -f genecup.log
```

and we were getting errors on a reload and I had to fix

```
shepherd@tux02:~/shepherd-services$ grep export run_genecup.sh
export EDIRECT_PUBMED_MASTER=/export3/PubMed
export TMPDIR=/export/ratspub/tmp
export NLTK_DATA=/export3/PubMed/nltk_data
```

See

=> https://git.genenetwork.org/gn-shepherd-services/commit/?id=cd4512634ce1407b14b0842b0ef6a9cd35e6d46c

The symlink from /export2 is not honoured by the guix container. Now the service works.

Note we have deprecation warnings that need to be addressed in the future:

```
2025-04-22 00:40:07 /home/shepherd/services/genecup/guix-past/modules/past/packages/python.scm:740:19: warning: 'texlive-union' is deprecated,
 use 'texlive-updmap.cfg' instead
2025-04-22 00:40:07 guix build: warning: 'texlive-latex-base' is deprecated, use 'texlive-latex-bin' instead
2025-04-22 00:40:15 updating checkout of 'https://git.genenetwork.org/genecup'...
/gnu/store/9lbn1l04y0xciasv6zzigqrrk1bzz543-tensorflow-native-1.9.0/lib/python3.10/site-packages/tensorflow/python/framewo
rk/dtypes.py:526: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
2025-04-22 00:40:38   _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
2025-04-22 00:40:38 /gnu/store/9lbn1l04y0xciasv6zzigqrrk1bzz543-tensorflow-native-1.9.0/lib/python3.10/site-packages/tensorflow/python/framewo
rk/dtypes.py:527: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
2025-04-22 00:40:38   _np_qint32 = np.dtype([("qint32", np.int32, 1)])
2025-04-22 00:40:38 /gnu/store/9lbn1l04y0xciasv6zzigqrrk1bzz543-tensorflow-native-1.9.0/lib/python3.10/site-packages/tensorflow/python/framewo
rk/dtypes.py:532: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
2025-04-22 00:40:38   np_resource = np.dtype([("resource", np.ubyte, 1)])
2025-04-22 00:40:39 /gnu/store/7sam0mr9kxrd4p7g1hlz9wrwag67a6x6-python-flask-sqlalchemy-2.5.1/lib/python3.10/site-packages/flask_sqlalchemy/__
init__.py:872: FSADeprecationWarning: SQLALCHEMY_TRACK_MODIFICATIONS adds significant overhead and will be disabled by default in the future. Set it to True or False to suppress this warning.
```