From f7c4f6a32ec01c3421f72b18ca2919f60d8e3f84 Mon Sep 17 00:00:00 2001
From: mlongobardo-gituname <mlongobardo>
Date: Wed, 25 Sep 2024 12:40:24 +0200
Subject: [PATCH] first improvements

---
 Dockerfile     | 77 ++++++++++++++++++++++++++++++++++++--------------
 pyproject.toml | 33 +++++++++++++++++++---
 2 files changed, 85 insertions(+), 25 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 6bf865c..610128c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,21 +1,56 @@
-FROM ubuntu:20.04
-
-SHELL ["/bin/bash", "-c"]
-ENV BASH_ENV=~/.bashrc                                          \
-    MAMBA_ROOT_PREFIX=/opt/conda                                \
-    PATH=$PATH:/opt/conda/envs/env_cwl_wrapper/bin
-
-# Install basic commands and mamba
-RUN apt-get update                                                                                                          && \
-    apt-get install -y ca-certificates wget bash bzip2 gcc linux-libc-dev libc6-dev curl                                    && \
-    wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba --strip-components=1 && \
-    ./micromamba shell init -s bash -p ~/micromamba                                                                         && \
-    apt-get clean autoremove --yes                                                                                          && \
-    rm -rf /var/lib/{apt,dpkg,cache,log}                                                                                    && \
-    cp ./micromamba /usr/bin
-
-COPY . /tmp
-
-RUN micromamba create -f /tmp/environment.yml                                                                               && \
-    cd /tmp                                                                                                                 && \
-    /opt/conda/envs/env_cwl_wrapper/bin/python setup.py install
+# Stage 1: Build stage
+FROM rockylinux:9.3-minimal AS build
+
+# Install necessary build tools
+RUN microdnf install -y curl tar
+
+# Download the hatch tar.gz file from GitHub
+RUN curl -L https://github.com/pypa/hatch/releases/latest/download/hatch-x86_64-unknown-linux-gnu.tar.gz -o /tmp/hatch-x86_64-unknown-linux-gnu.tar.gz
+
+# Extract the hatch binary
+RUN tar -xzf /tmp/hatch-x86_64-unknown-linux-gnu.tar.gz -C /tmp/
+
+# Stage 2: Final stage
+FROM rockylinux:9.3-minimal
+
+# Install runtime dependencies
+RUN microdnf install -y --nodocs nodejs && \
+    microdnf clean all
+
+# Set up a default user and home directory
+ENV HOME=/home/wrapper
+
+# Create a user with UID 1001, group root, and a home directory
+RUN useradd -u 1001 -r -g 0 -m -d ${HOME} -s /sbin/nologin \
+        -c "Default CWL Wrapper User" wrapper && \
+    mkdir -p /app && \
+    mkdir -p /prod && \
+    chown -R 1001:0 /app && \
+    chmod g+rwx ${HOME} /app
+
+# Copy the hatch binary from the build stage
+COPY --from=build /tmp/hatch /usr/bin/hatch
+
+# Ensure the hatch binary is executable
+RUN chmod +x /usr/bin/hatch
+
+# Switch to the non-root user
+USER wrapper
+
+# Copy the application files into the /app directory
+COPY --chown=1001:0 . /tmp
+WORKDIR /tmp
+
+# Set up virtual environment paths
+ENV VIRTUAL_ENV=/app/envs/wrapper
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+
+# Prune any existing environments and create a new production environment
+RUN cd /tmp && hatch env prune && \
+    hatch env create prod && \
+    rm -fr /tmp/* /tmp/.git /tmp/.pytest_cache
+
+WORKDIR /app
+
+# Set the default command to run when the container starts
+CMD ["cwl-wrapper"]
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 5738b3c..5adccfd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,14 +5,28 @@ build-backend = "hatchling.build"
 [project]
 name = "cwl-wrapper"
 dynamic = ["version"]
-description = "xxx"
+description = "CWL wrapper to add stage-in and stage-out to a base app package"
 readme = "README.md"
 license = "Apache-2.0"
-keywords = [
-    "keyword_1",
-    "keyword_2",
+keywords = []
+
+#To add other authors 
+authors = [
+{ name = "Fabrice Brito", email = "fabrice.brito@terradue.com"
+}
+] 
+
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Environment :: Console",
+  "Intended Audience :: Developers",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: Implementation :: PyPy"
 ]
 
+[tool.hatch.envs.prod]
+path = "/app/envs/wrapper"
+
 [project.scripts]
 cwl-wrapper = "cwl_wrapper.app:main"
 
@@ -29,6 +43,11 @@ include = [
     "/src",
 ]
 
+[project.urls]
+Documentation = "https://github.com/EOEPCA/cwl-wrapper#readme"
+Issues = "https://github.com/EOEPCA/cwl-wrapper/issues"
+Source = "https://github.com/EOEPCA/cwl-wrapper"
+
 [tool.hatch.envs.default]
 dependencies = [
     "click",
@@ -52,9 +71,15 @@ dependencies = [
     "loguru"
 ]
 
+#[tool.hatch.envs.test.env-vars]
+#RETRY_ATTEMPTS="0"
+
 [tool.hatch.envs.test.scripts]
 test = "hatch run nose2"
 testv = "hatch run nose2 --verbose"
 
+#it needs coverage in dependencies section
+#cov = ["coverage run --source=src -m nose2", "coverage report"]
+
 [[tool.hatch.envs.test.matrix]]
 python = ["3.8", "3.9", "3.10", "3.11", "3.12"]
\ No newline at end of file