Update main#12
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updated Dockerfile and pyproject.toml
added new dependencies
adjustment to work with new pymongo version
Dockerfile update
skip parsing disgenet
Dockerfile update
JohannesKersting
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Aug 25, 2025
Bumps [setuptools](https://github.com/pypa/setuptools) from 69.5.1 to 70.0.0. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v69.5.1...v70.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
JohannesKersting
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that referenced
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Aug 25, 2025
* made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * added additional launch flags for development * adding additional development options; fixed numpy version * merge dev branch into master (#10) (#11) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * updated disgenet path to import from file; fixing issues with uniprot formatting * Bump setuptools from 69.5.1 to 70.0.0 (#12) Bumps [setuptools](https://github.com/pypa/setuptools) from 69.5.1 to 70.0.0. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v69.5.1...v70.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * small security patch by removing dev dependencies from docker image * merge dev branch into master (#10) (#13) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
JohannesKersting
pushed a commit
that referenced
this pull request
Aug 25, 2025
* made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * added additional launch flags for development * adding additional development options; fixed numpy version * merge dev branch into master (#10) (#11) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * updated disgenet path to import from file; fixing issues with uniprot formatting * Bump setuptools from 69.5.1 to 70.0.0 (#12) Bumps [setuptools](https://github.com/pypa/setuptools) from 69.5.1 to 70.0.0. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v69.5.1...v70.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * small security patch by removing dev dependencies from docker image * merge dev branch into master (#10) (#13) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * small sec update * created neo4j docker image with apoc plugin * updated databases; using neo4j with apoc --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
JohannesKersting
pushed a commit
that referenced
this pull request
Aug 25, 2025
* made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * added additional launch flags for development * adding additional development options; fixed numpy version * merge dev branch into master (#10) (#11) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * updated disgenet path to import from file; fixing issues with uniprot formatting * Bump setuptools from 69.5.1 to 70.0.0 (#12) Bumps [setuptools](https://github.com/pypa/setuptools) from 69.5.1 to 70.0.0. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v69.5.1...v70.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * small security patch by removing dev dependencies from docker image * merge dev branch into master (#10) (#13) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * small sec update * created neo4j docker image with apoc plugin * updated databases; using neo4j with apoc --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
JohannesKersting
pushed a commit
that referenced
this pull request
Aug 25, 2025
* Many updates regardung security and interoperability (#15) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * added additional launch flags for development * adding additional development options; fixed numpy version * merge dev branch into master (#10) (#11) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * updated disgenet path to import from file; fixing issues with uniprot formatting * Bump setuptools from 69.5.1 to 70.0.0 (#12) Bumps [setuptools](https://github.com/pypa/setuptools) from 69.5.1 to 70.0.0. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v69.5.1...v70.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * small security patch by removing dev dependencies from docker image * merge dev branch into master (#10) (#13) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * small sec update * created neo4j docker image with apoc plugin * updated databases; using neo4j with apoc --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update docker-compose.yml (#16) * Merge with dev (#17) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * added additional launch flags for development * adding additional development options; fixed numpy version * merge dev branch into master (#10) (#11) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * updated disgenet path to import from file; fixing issues with uniprot formatting * Bump setuptools from 69.5.1 to 70.0.0 (#12) Bumps [setuptools](https://github.com/pypa/setuptools) from 69.5.1 to 70.0.0. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v69.5.1...v70.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * small security patch by removing dev dependencies from docker image * merge dev branch into master (#10) (#13) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * small sec update * created neo4j docker image with apoc plugin * updated databases; using neo4j with apoc --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
JohannesKersting
pushed a commit
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Aug 25, 2025
* made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * added additional launch flags for development * adding additional development options; fixed numpy version * merge dev branch into master (#10) (#11) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * updated disgenet path to import from file; fixing issues with uniprot formatting * Bump setuptools from 69.5.1 to 70.0.0 (#12) Bumps [setuptools](https://github.com/pypa/setuptools) from 69.5.1 to 70.0.0. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v69.5.1...v70.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * small security patch by removing dev dependencies from docker image * merge dev branch into master (#10) (#13) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * small sec update * created neo4j docker image with apoc plugin * updated databases; using neo4j with apoc * Master (#18) * Many updates regardung security and interoperability (#15) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * added additional launch flags for development * adding additional development options; fixed numpy version * merge dev branch into master (#10) (#11) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * updated disgenet path to import from file; fixing issues with uniprot formatting * Bump setuptools from 69.5.1 to 70.0.0 (#12) Bumps [setuptools](https://github.com/pypa/setuptools) from 69.5.1 to 70.0.0. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v69.5.1...v70.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * small security patch by removing dev dependencies from docker image * merge dev branch into master (#10) (#13) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * small sec update * created neo4j docker image with apoc plugin * updated databases; using neo4j with apoc --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update docker-compose.yml (#16) * Merge with dev (#17) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * added additional launch flags for development * adding additional development options; fixed numpy version * merge dev branch into master (#10) (#11) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * updated disgenet path to import from file; fixing issues with uniprot formatting * Bump setuptools from 69.5.1 to 70.0.0 (#12) Bumps [setuptools](https://github.com/pypa/setuptools) from 69.5.1 to 70.0.0. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v69.5.1...v70.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * small security patch by removing dev dependencies from docker image * merge dev branch into master (#10) (#13) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- * Master (#9) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- * Disease network fixes (#8) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script * Master (#7) * made dev mongo express port variable to circumvent port in use issues (#3) * Small fixes and improvements (#6) * made dev mongo express port variable to circumvent port in use issues * added build to launch script * Add Download Flag & is_reviewed (#5) * add changes from old repository: add comments, add chembl downloader, add is_reviewed param to protein node * add Download parameter in docker-compose.dev.yml * clean up for pull request - revert path & download Setting * clean up for pull request - revert path & download Setting --------- * Update docker-compose.dev.yml fixed typo in env variable * Update docker-compose.yml added env var to prod docker-compose.yaml * fixed repotrial importer * removed static file download from Download OFF build script --------- --------- --------- --------- * added additional launch flags for development * adding additional development options; fixed numpy version --------- Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> * small sec update * created neo4j docker image with apoc plugin * updated databases; using neo4j with apoc --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: ahoewi <112104849+ahoewi@users.noreply.github.com> Co-authored-by: hoel <public.hoelzlwimmer@tum.de> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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