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natharisa wants to merge 14 commits into dev from global-translations

.gitignore

-Original file line number
+Diff line change
@@ Expand Up / @@ -12,5 +12,4 @@ src/api_service/experiments/venv @@
     docker-compose.yml
     src/secretkey.txt
     docker-compose.mauri_dev.yml
-    venv
-    .DS_Store
+    venv

Dockerfile

            
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                      Diff line number
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    @@ -1,64 +1,47 @@
  
    FROM python:3.12-slim-bookworm

    # Docker Files Vars

    ARG LISTEN_PORT=8000

    ARG LISTEN_IP="0.0.0.0"

    ARG LISTEN_PORT 8000

    ARG LISTEN_IP "0.0.0.0"

    # Default values for deploying with multiomix image

    ENV LISTEN_PORT=$LISTEN_PORT

    ENV LISTEN_IP=$LISTEN_IP

    ENV DJANGO_SETTINGS_MODULE="multiomics_intermediate.settings_prod"

    ENV RESULT_DATAFRAME_LIMIT_ROWS=500

    ENV TABLE_PAGE_SIZE=10

    ENV LISTEN_PORT $LISTEN_PORT

    ENV LISTEN_IP $LISTEN_IP

    ENV DJANGO_SETTINGS_MODULE "multiomics_intermediate.settings_prod"

    ENV RESULT_DATAFRAME_LIMIT_ROWS 500

    ENV TABLE_PAGE_SIZE 10

    # Modulector connection parameters

    ENV MODULECTOR_HOST="127.0.0.1"

    ENV MODULECTOR_PORT="8001"

    ENV MODULECTOR_HOST "127.0.0.1"

    ENV MODULECTOR_PORT "8001"

    # BioAPI connection parameters

    ENV BIOAPI_HOST="127.0.0.1"

    ENV BIOAPI_PORT="8002"

    ENV BIOAPI_HOST "127.0.0.1"

    ENV BIOAPI_PORT "8002"

    # PostgreSQL DB connection parameters

    ENV POSTGRES_USERNAME="multiomics"

    ENV POSTGRES_PASSWORD="multiomics"

    ENV POSTGRES_HOST="db"

    ENV POSTGRES_PORT=5432

    ENV POSTGRES_DB="multiomics"

    ENV POSTGRES_USERNAME "multiomics"

    ENV POSTGRES_PASSWORD "multiomics"

    ENV POSTGRES_HOST "db"

    ENV POSTGRES_PORT 5432

    ENV POSTGRES_DB "multiomics"

    # Mongo DB connection parameters

    ENV MONGO_USERNAME="multiomics"

    ENV MONGO_PASSWORD="multiomics"

    ENV MONGO_HOST="mongo"

    ENV MONGO_PORT=27017

    ENV MONGO_DB="multiomics"

    ENV MONGO_USERNAME "multiomics"

    ENV MONGO_PASSWORD "multiomics"

    ENV MONGO_HOST "mongo"

    ENV MONGO_PORT 27017

    ENV MONGO_DB "multiomics"

    # Redis

    ENV REDIS_HOST="redis"

    ENV REDIS_PORT=6379

    ENV REDIS_HOST "redis"

    ENV REDIS_PORT 6379

    # Installs system dependencies and Node.js

    RUN apt-get update && apt-get install -y python3-pip curl libcurl4-openssl-dev libssl-dev libxml2-dev \

        && curl -fsSL https://deb.nodesource.com/setup_20.x | bash - && apt-get install -y nodejs && mkdir /config \

        && mkdir /src

    # Install R 4.4.2 from CRAN (Debian bookworm) and system dependencies

    RUN set -eux; \

      echo "deb http://deb.debian.org/debian sid main" > /etc/apt/sources.list.d/debian-unstable.list; \

      printf 'APT::Default-Release "%s";\n' "bookworm" > /etc/apt/apt.conf.d/00default-release; \

      echo 'APT::Install-Recommends "false";' > /etc/apt/apt.conf.d/90no-recommends; \

      printf 'Package: *\nPin: release a=unstable\nPin-Priority: 50\n' > /etc/apt/preferences.d/99pin-unstable; \

      apt-get update; \

      apt-get install -y --no-install-recommends \

        ca-certificates curl gnupg build-essential gfortran libblas-dev liblapack-dev git \

        libssl-dev libcurl4-openssl-dev libxml2-dev; \

      apt-get install -y \

        r-base=4.2.2.20221110-2 r-base-dev=4.2.2.20221110-2 r-recommended=4.2.2.20221110-2; \

      rm -rf /var/lib/apt/lists/*

    # Install Bioconductor limma (stats and base come with R)

    RUN R -q -e 'options(repos=c(CRAN="https://cloud.r-project.org")); install.packages("BiocManager"); BiocManager::install(version="3.16", ask=FALSE); BiocManager::install("limma", ask=FALSE, update=FALSE)'

    # Installs Python dependencies and compiles the frontend

    ADD config/requirements.txt /config/

    WORKDIR /src

    @@ -75,3 +58,4 @@ HEALTHCHECK --interval=5m --timeout=30s CMD ["/bin/bash", "-c", "/src/tools/chec
  
    ENTRYPOINT ["/bin/bash", "-c", "/src/entrypoint.sh"]

    EXPOSE $LISTEN_PORT

Dockerfile-celery

            
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    @@ -1,64 +1,47 @@
  
    FROM python:3.12-slim-bookworm

    # Docker Files Vars

    ARG LISTEN_PORT=8000

    ARG LISTEN_IP="0.0.0.0"

    ARG LISTEN_PORT 8000

    ARG LISTEN_IP "0.0.0.0"

    # Default values for deploying with multiomix image

    ENV LISTEN_PORT=$LISTEN_PORT

    ENV LISTEN_IP=$LISTEN_IP

    ENV DJANGO_SETTINGS_MODULE="multiomics_intermediate.settings_prod"

    ENV RESULT_DATAFRAME_LIMIT_ROWS=500

    ENV TABLE_PAGE_SIZE=10

    ENV LISTEN_PORT $LISTEN_PORT

    ENV LISTEN_IP $LISTEN_IP

    ENV DJANGO_SETTINGS_MODULE "multiomics_intermediate.settings_prod"

    ENV RESULT_DATAFRAME_LIMIT_ROWS 500

    ENV TABLE_PAGE_SIZE 10

    # Modulector connection parameters

    ENV MODULECTOR_HOST="127.0.0.1"

    ENV MODULECTOR_PORT="8001"

    ENV MODULECTOR_HOST "127.0.0.1"

    ENV MODULECTOR_PORT "8001"

    # BioAPI connection parameters

    ENV BIOAPI_HOST="127.0.0.1"

    ENV BIOAPI_PORT="8002"

    ENV BIOAPI_HOST "127.0.0.1"

    ENV BIOAPI_PORT "8002"

    # PostgreSQL DB connection parameters

    ENV POSTGRES_USERNAME="multiomics"

    ENV POSTGRES_PASSWORD="multiomics"

    ENV POSTGRES_HOST="db"

    ENV POSTGRES_PORT=5432

    ENV POSTGRES_DB="multiomics"

    ENV POSTGRES_USERNAME "multiomics"

    ENV POSTGRES_PASSWORD "multiomics"

    ENV POSTGRES_HOST "db"

    ENV POSTGRES_PORT 5432

    ENV POSTGRES_DB "multiomics"

    # Mongo DB connection parameters

    ENV MONGO_USERNAME="multiomics"

    ENV MONGO_PASSWORD="multiomics"

    ENV MONGO_HOST="mongo"

    ENV MONGO_PORT=27017

    ENV MONGO_DB="multiomics"

    ENV MONGO_USERNAME "multiomics"

    ENV MONGO_PASSWORD "multiomics"

    ENV MONGO_HOST "mongo"

    ENV MONGO_PORT 27017

    ENV MONGO_DB "multiomics"

    # Redis

    ENV REDIS_HOST="redis"

    ENV REDIS_PORT=6379

    ENV REDIS_HOST "redis"

    ENV REDIS_PORT 6379

    # Installs system dependencies

    RUN apt-get update && apt-get install -y python3-pip curl libcurl4-openssl-dev libssl-dev libxml2-dev \

        && mkdir /config \

        && mkdir /src

    # Install R 4.4.2 from CRAN (Debian bookworm) and system dependencies

    RUN set -eux; \

      echo "deb http://deb.debian.org/debian sid main" > /etc/apt/sources.list.d/debian-unstable.list; \

      printf 'APT::Default-Release "%s";\n' "bookworm" > /etc/apt/apt.conf.d/00default-release; \

      echo 'APT::Install-Recommends "false";' > /etc/apt/apt.conf.d/90no-recommends; \

      printf 'Package: *\nPin: release a=unstable\nPin-Priority: 50\n' > /etc/apt/preferences.d/99pin-unstable; \

      apt-get update; \

      apt-get install -y --no-install-recommends \

        ca-certificates curl gnupg build-essential gfortran libblas-dev liblapack-dev git \

        libssl-dev libcurl4-openssl-dev libxml2-dev; \

      apt-get install -y \

        r-base=4.2.2.20221110-2 r-base-dev=4.2.2.20221110-2 r-recommended=4.2.2.20221110-2; \

      rm -rf /var/lib/apt/lists/*

    # Install Bioconductor limma (stats and base come with R)

    RUN R -q -e 'options(repos=c(CRAN="https://cloud.r-project.org")); install.packages("BiocManager"); BiocManager::install(version="3.16", ask=FALSE); BiocManager::install("limma", ask=FALSE, update=FALSE)'

    # Installs Python dependencies

    ADD config/requirements_celery.txt /config/requirements.txt

    RUN pip install --upgrade pip && pip3 install -r /config/requirements.txt

README.md

-Original file line number
+Diff line change
@@ -1,4 +1,4 @@
-    <img style="float: right" src="src/frontend/static/frontend/img/logo-readme.png" alt="Multiomix logo">
+    <img align="right" src="src/frontend/static/frontend/img/logo-readme.png" alt="Multiomix logo">
     # Multiomix
@@ Expand All @@
     - Node JS >= `20.x` (tested version: `20.x`)
     - [Modulector][modulector] `2.2.0`
     - [BioAPI][bioapi] `1.2.1`
-    - R `4.4.2` (required for `differential-expression`)
     ## Installation
@@ Expand Down Expand Up @@
 . `python3 -m celery -A multiomics_intermediate worker -l info -Q stats`
 . `python3 -m celery -A multiomics_intermediate worker -l info -Q inference`
 . `python3 -m celery -A multiomics_intermediate worker -l info -Q sync_datasets`
-. `python3 -m celery -A multiomics_intermediate worker -l info -Q differential_expression`
 . If you want to check Task in the GUI you can run [Flower](https://flower.readthedocs.io/en/latest/index.html) `python3 -m celery -A multiomics_intermediate flower`
         **NOTE:** maybe in Windows is needed to add `--pool=solo` to the previous commands. Example: `python3 -m celery -A multiomics_intermediate worker -l info -Q correlation_analysis --concurrency 1 --pool=solo`
@@ Expand Down @@

config/requirements.txt

-Original file line number
+Diff line change
@@ Expand Up / @@ -28,5 +28,3 @@ scipy==1.13.0 @@
     statsmodels==0.14.2
     xlrd==2.0.1
     openpyxl==3.1.5
-    rpy2==3.6.1
-    urllib3==2.5.0

config/requirements_celery.txt

-Original file line number
+Diff line change
@@ Expand Up / @@ -25,5 +25,3 @@ scipy==1.13.0 @@
     statsmodels==0.14.2
     xlrd==2.0.1
     openpyxl==3.1.5
-    rpy2==3.6.1
-    urllib3==2.5.0

docker-compose_dist.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -233,21 +233,6 @@ services: @@
                 # REDIS_HOST: 'redis'
                 # REDIS_PORT: 6379
-        # Celery worker for differential expression
-        differential-expression-worker:
-            image: omicsdatascience/multiomix:5.6.0-celery
-            restart: 'always'
-            depends_on:
-                - db
-                - mongo
-            volumes:
-                - media_data:/src/media
-            environment:
-                <<: *common-variables
-                QUEUE_NAME: 'differential_expression'  # This MUST NOT be changed
-                CONCURRENCY: 2
-                # PostgreSQL, Mongo y Redis usan los valores por defecto del resto de servicios
         # Django backend service
         multiomix:
             image: omicsdatascience/multiomix:5.6.0
@@ Expand Down Expand Up / @@ -305,7 +290,6 @@ services: @@
                 - stats-worker
                 - inference-worker
                 - sync-datasets-worker
-                - differential-expression-worker
     volumes:
         mongo_data:
@@ Expand Down @@

src/api_service/migrations/0062_alter_experiment_clinical_source_and_more.py

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