From d7c98fc23989ded1b7e19eda9b73a70d79956d4c Mon Sep 17 00:00:00 2001 From: NishaSharma14 Date: Mon, 11 Sep 2023 11:29:12 +0200 Subject: [PATCH 1/5] fix: allow multiple domains in traefik host rule --- ops/docker-compose-dev.yml | 4 ++-- ops/docker-compose-prod.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/ops/docker-compose-dev.yml b/ops/docker-compose-dev.yml index 2c16e0a..cd2104d 100644 --- a/ops/docker-compose-dev.yml +++ b/ops/docker-compose-dev.yml @@ -22,7 +22,7 @@ services: pull_policy: always labels: - "traefik.enable=true" - - "traefik.http.routers.web.rule=Host(`dev.api.naturalproducts.net`)" + - "traefik.http.routers.web.rule=Host(`dev.api.naturalproducts.net`, `nfdi4chem-oss1-vm11.ianchm.uni-jena.de`)" - "traefik.http.routers.web.entrypoints=web" - "traefik.http.services.web.loadbalancer.server.port=80" healthcheck: @@ -64,4 +64,4 @@ volumes: postgres_data: networks: default: - name: cm_fastapi \ No newline at end of file + name: cm_fastapi diff --git a/ops/docker-compose-prod.yml b/ops/docker-compose-prod.yml index 67b8c26..08392a0 100644 --- a/ops/docker-compose-prod.yml +++ b/ops/docker-compose-prod.yml @@ -22,7 +22,7 @@ services: pull_policy: always labels: - "traefik.enable=true" - - "traefik.http.routers.web.rule=Host(`api.naturalproducts.net`)" + - "traefik.http.routers.web.rule=Host(`dev.api.naturalproducts.net`, `nfdi4chem-oss1-vm11.ianchm.uni-jena.de`)" - "traefik.http.routers.web.entrypoints=web" - "traefik.http.services.web.loadbalancer.server.port=80" healthcheck: From 31e7481f26f30935e9f19f815e345e31b37261e3 Mon Sep 17 00:00:00 2001 From: NishaSharma14 Date: Mon, 11 Sep 2023 12:46:50 +0200 Subject: [PATCH 2/5] refactor: revert docker-compose changes --- ops/docker-compose-dev.yml | 2 +- ops/docker-compose-prod.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ops/docker-compose-dev.yml b/ops/docker-compose-dev.yml index cd2104d..752fe72 100644 --- a/ops/docker-compose-dev.yml +++ b/ops/docker-compose-dev.yml @@ -22,7 +22,7 @@ services: pull_policy: always labels: - "traefik.enable=true" - - "traefik.http.routers.web.rule=Host(`dev.api.naturalproducts.net`, `nfdi4chem-oss1-vm11.ianchm.uni-jena.de`)" + - "traefik.http.routers.web.rule=Host(`dev.api.naturalproducts.net`)" - "traefik.http.routers.web.entrypoints=web" - "traefik.http.services.web.loadbalancer.server.port=80" healthcheck: diff --git a/ops/docker-compose-prod.yml b/ops/docker-compose-prod.yml index 08392a0..f56e481 100644 --- a/ops/docker-compose-prod.yml +++ b/ops/docker-compose-prod.yml @@ -22,7 +22,7 @@ services: pull_policy: always labels: - "traefik.enable=true" - - "traefik.http.routers.web.rule=Host(`dev.api.naturalproducts.net`, `nfdi4chem-oss1-vm11.ianchm.uni-jena.de`)" + - "traefik.http.routers.web.rule=Host(`dev.api.naturalproducts.net`)" - "traefik.http.routers.web.entrypoints=web" - "traefik.http.services.web.loadbalancer.server.port=80" healthcheck: From a7104c60fb76f3e942a662fe37d41375bf84f14e Mon Sep 17 00:00:00 2001 From: NishaSharma14 Date: Mon, 11 Sep 2023 12:47:50 +0200 Subject: [PATCH 3/5] revert: update prod domain --- ops/docker-compose-prod.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ops/docker-compose-prod.yml b/ops/docker-compose-prod.yml index f56e481..67b8c26 100644 --- a/ops/docker-compose-prod.yml +++ b/ops/docker-compose-prod.yml @@ -22,7 +22,7 @@ services: pull_policy: always labels: - "traefik.enable=true" - - "traefik.http.routers.web.rule=Host(`dev.api.naturalproducts.net`)" + - "traefik.http.routers.web.rule=Host(`api.naturalproducts.net`)" - "traefik.http.routers.web.entrypoints=web" - "traefik.http.services.web.loadbalancer.server.port=80" healthcheck: From 6070580a3b46ed5234d54381998cc529e0aeb0f3 Mon Sep 17 00:00:00 2001 From: NishaSharma14 Date: Mon, 8 Jan 2024 16:15:11 +0100 Subject: [PATCH 4/5] BREAKING CHANGE: upgrade versions of RDKIT, CDK and OB. --- Dockerfile | 8 ++++---- app/modules/toolkits/cdk_wrapper.py | 2 +- docs/versions.md | 6 +++--- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/Dockerfile b/Dockerfile index 8b7f71f..64c9902 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,8 +1,8 @@ FROM continuumio/miniconda3 AS cheminf-python-ms ENV PYTHON_VERSION=3.10 -ENV RDKIT_VERSION=2023.03.1 -ENV OPENBABEL_VERSION=v3.1 +ENV RDKIT_VERSION=2023.09.4 +ENV OPENBABEL_VERSION=v3.1.1 # Install runtime dependencies RUN apt-get update && \ @@ -17,7 +17,7 @@ RUN chmod +x surge RUN mv surge /usr/bin RUN conda install -c conda-forge python>=PYTHON_VERSION -#RUN conda install -c conda-forge rdkit==RDKIT_VERSION +RUN conda install -c conda-forge rdkit==RDKIT_VERSION RUN conda install -c conda-forge openbabel>=OPENBABEL_VERSION RUN python3 -m pip install -U pip @@ -32,7 +32,7 @@ RUN pip3 install --upgrade setuptools pip RUN pip3 install --no-cache-dir -r /code/requirements.txt RUN python3 -m pip uninstall -y imantics RUN pip3 install imantics==0.1.12 -RUN pip3 install rdkit +#RUN pip3 install rdkit RUN pip3 install --no-deps decimer-segmentation==1.1.3 RUN pip3 install --no-deps decimer==2.3.0 RUN pip3 install --no-deps STOUT-pypi>=2.0.5 diff --git a/app/modules/toolkits/cdk_wrapper.py b/app/modules/toolkits/cdk_wrapper.py index dc64de6..1d5daa7 100644 --- a/app/modules/toolkits/cdk_wrapper.py +++ b/app/modules/toolkits/cdk_wrapper.py @@ -23,7 +23,7 @@ ) jvmPath = "Define/path/or/set/JAVA_HOME/variable/properly" if not isJVMStarted(): - cdk_path = "https://github.com/cdk/cdk/releases/download/cdk-2.8/cdk-2.8.jar" + cdk_path = "https://github.com/cdk/cdk/releases/download/cdk-2.9/cdk-2.9.jar" sru_path = "https://github.com/JonasSchaub/SugarRemoval/releases/download/v1.3.2/SugarRemovalUtility-jar-with-dependencies.jar" centres_path = ( "https://github.com/SiMolecule/centres/releases/download/1.0/centres.jar" diff --git a/docs/versions.md b/docs/versions.md index 5be00e8..d0e18d3 100644 --- a/docs/versions.md +++ b/docs/versions.md @@ -19,9 +19,9 @@ The Cheminformatics Microservice, framework is developed using Python and [FastA | Toolkits | Version | |-------------|-------------| -| RDKit 1 | 2023.03.1 | -| CDK 2 | 2.8.0 | -| Open Babel 3 | 3.1.0 | +| RDKit 1 | 2023.09.4 | +| CDK 2 | 2.9.0 | +| Open Babel 3 | 3.1.1 | **External Tools Versions** From d162ae4272b0e856e3a0cabb955c1aa3919b2529 Mon Sep 17 00:00:00 2001 From: Kohulan Rajan Date: Mon, 8 Jan 2024 16:22:29 +0100 Subject: [PATCH 5/5] fix: update version 2.8->2.9 cdk_wrapper.py --- app/modules/toolkits/cdk_wrapper.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/modules/toolkits/cdk_wrapper.py b/app/modules/toolkits/cdk_wrapper.py index 1d5daa7..6b1ff81 100644 --- a/app/modules/toolkits/cdk_wrapper.py +++ b/app/modules/toolkits/cdk_wrapper.py @@ -30,7 +30,7 @@ ) opsin_path = "https://github.com/dan2097/opsin/releases/download/2.8.0/opsin-cli-2.8.0-jar-with-dependencies.jar" - cdkjar_path = str(pystow.join("STOUT-V2")) + "/cdk-2.8.jar" + cdkjar_path = str(pystow.join("STOUT-V2")) + "/cdk-2.9.jar" srujar_path = ( str(pystow.join("STOUT-V2")) + "/SugarRemovalUtility-jar-with-dependencies.jar" )