Skip to content

hide workflows to NOT filter commands for artifact processing #10

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
sjanssen2 merged 1 commit into from
May 8, 2025
Merged

hide workflows to NOT filter commands for artifact processing #10

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions Images/qiita/qiita.dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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"]
6 changes: 6 additions & 0 deletions Images/qiita/start_qiita-initDB.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
2 changes: 1 addition & 1 deletion Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down