From 316618080882547389f63892ed29df9c03205def Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 7 Mar 2025 17:34:29 +0100 Subject: [PATCH] hide workflows to NOT filter commands for artifact processing --- Images/qiita/qiita.dockerfile | 2 ++ Images/qiita/start_qiita-initDB.sh | 6 ++++++ Makefile | 2 +- 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/Images/qiita/qiita.dockerfile b/Images/qiita/qiita.dockerfile index 22287a3..b185724 100644 --- a/Images/qiita/qiita.dockerfile +++ b/Images/qiita/qiita.dockerfile @@ -75,4 +75,6 @@ RUN rm -rf /qiita/qiita_core/support_files # hide default configurations from github sources RUN rm -f /qiita/qiita_pet/nginx_example.conf /qiita/qiita_pet/supervisor_example.conf /qiita/qiita_pet/support_files/config_portal.cfg +COPY drop_workflows.py /drop_workflows.py + # CMD ["conda", "run", "-n", "qiita"] diff --git a/Images/qiita/start_qiita-initDB.sh b/Images/qiita/start_qiita-initDB.sh index 62aeaf2..6c9f45b 100644 --- a/Images/qiita/start_qiita-initDB.sh +++ b/Images/qiita/start_qiita-initDB.sh @@ -8,3 +8,9 @@ ENV_NAME=qiita source $CONDA_DIR/etc/profile.d/conda.sh; conda activate $CONDA_DIR/envs/$ENV_NAME; cd /qiita; qiita-env make --no-load-ontologies 2> .env-make.err || true # To avoid confusing the user, STDERR is written into a file and only reported if it does not contain the text that we expect to see if it just reports the existing DB grep 'already present on the system. You can drop it by running' .env-make.err > /dev/null || cat .env-make.err + + +# currently, commands with which you can process artifacts are limited to those that are present in available "recommended workflows". +# As they are not properly set up in the test database, we e.g. cannot run "deblur" on demux or trimmed existing artifacts (it's different in workflows in construction) +# As long as we don't have a nice mechanism to carry over recommended workflow, we better remove them altogether +source $CONDA_DIR/etc/profile.d/conda.sh; conda activate $CONDA_DIR/envs/$ENV_NAME; python /drop_workflows.py diff --git a/Makefile b/Makefile index d6b0bd5..2e73dc5 100644 --- a/Makefile +++ b/Makefile @@ -84,7 +84,7 @@ plugin: Images/qtp-biom/trigger.py Certificates/ chmod a+rw ./logs/nginx_access.log ./logs/nginx_error.log touch .built_image_nginx -.built_image_qiita: Images/qiita/qiita.dockerfile Images/qiita/config_qiita_oidc.cfg Images/qiita/start_qiita.sh Images/qiita/start_qiita-initDB.sh Images/qiita/supervisor_foreground.conf Images/qiita/start_plugin.py Images/qiita/config_portal.cfg +.built_image_qiita: Images/qiita/qiita.dockerfile Images/qiita/config_qiita_oidc.cfg Images/qiita/start_qiita.sh Images/qiita/start_qiita-initDB.sh Images/qiita/supervisor_foreground.conf Images/qiita/start_plugin.py Images/qiita/config_portal.cfg Images/qiita/drop_workflows.py test -d src/qiita || git clone -b auth_oidc https://github.com/jlab/qiita.git src/qiita # remove configuration and certificate files from upstream qiita repo rm -rf src/qiita/qiita_core/support_files