Merge pull request #28 from Imaging-Plaza/feat/open-pulse-ontology-v2.0.0

Feat/open pulse ontology v2.0.0

Author: caviri

.devcontainer/.env.example

@@ -0,0 +1,18 @@
+# Copy to `.devcontainer/.env` for docker-compose variable substitution.
+# Compose reads this file from the `.devcontainer/` directory (not repo-root `.env` for these keys).
+#
+# Host port mappings (optional):
+# SSH_PORT=2220
+# APP_PORT=1234
+# DEV_PORT=8888
+#
+# DNS inside the container (optional; defaults are 1.1.1.1 + 8.8.8.8 in docker-compose.yml).
+# Use your corporate resolvers if public DNS is blocked:
+# DEVCONTAINER_DNS_1=10.0.0.1
+# DEVCONTAINER_DNS_2=10.0.0.2
+#
+# Selenium (standalone Firefox service in docker-compose.yml). Override URL if you use an external grid:
+# SELENIUM_REMOTE_URL=http://selenium-standalone-firefox:4444
+# Host ports if 4444 / 7900 are already in use:
+# SELENIUM_GRID_PORT=4445
+# SELENIUM_VNC_PORT=7901

.devcontainer/Dockerfile

@@ -1,10 +1,8 @@
 FROM ghcr.io/astral-sh/uv:python3.12-bookworm
 
-# Set locale to avoid warnings
 ENV LC_ALL=C.UTF-8
 ENV LANG=C.UTF-8
 
-# Install just and other system dependencies
 RUN apt-get update && apt-get install -y \
     sudo \
     curl \
@@ -13,16 +11,11 @@ RUN apt-get update && apt-get install -y \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
-# Crear usuario no-root con UID/GID que suele usar VS Code (1000:1000).
-# TOOD: Take this user out of sudoers if you want to use this in fully agents mode.
 RUN useradd -ms /bin/bash -u 1000 vscode \
-    && apt-get update && apt-get install -y sudo \
+    && apt-get update \
+    && apt-get install -y sudo \
     && echo "vscode ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
 
-# Gemini CLI
-# Please login outside of the container and copy your credentials to ~/.gemini/...
-RUN curl -fsSL https://deb.nodesource.com/setup_24.x | sudo -E bash - && sudo apt-get install -y nodejs
-RUN npm install -g @google/gemini-cli
 
 RUN mkdir -p /app/data \
     && chown -R 1000:1000 /app/data \

.devcontainer/devcontainer.json

@@ -1,16 +1,18 @@
 {
   "name": "git-metadata-extractor-dev",
-  "build": {
-    "dockerfile": "Dockerfile"
+  "dockerComposeFile": "docker-compose.yml",
+  "service": "devcontainer",
+  "workspaceFolder": "/workspaces/project",
+  "containerEnv": {
+    "UV_CACHE_DIR": "/workspaces/project/.uv-cache"
+  },
+  "overrideCommand": false,
+  "features": {
+    "ghcr.io/devcontainers/features/sshd:1": {
+      "version": "latest"
+    }
   },
-  "runArgs": [
-    "--env-file",
-    "${localWorkspaceFolder}/.env",
-    "--network",
-    "dev"
-  ],
   "remoteUser": "vscode",
-  "workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
   "customizations": {
     "vscode": {
       "settings": {
@@ -26,8 +28,6 @@
       ]
     }
   },
-  "forwardPorts": [
-    1234
-  ],
-  "postCreateCommand": "rm -rf .venv && uv venv && uv pip install -e .[dev] && echo '. $PWD/.venv/bin/activate' >> /home/vscode/.bashrc"
-}
+  "postCreateCommand": "mkdir -p .uv-cache && rm -rf .venv && uv venv && uv pip install -e .[dev] && echo '. $PWD/.venv/bin/activate' >> /home/vscode/.bashrc",
+  "postStartCommand": "bash .devcontainer/set-vscode-password.sh"
+}

.devcontainer/docker-compose.yml

@@ -0,0 +1,61 @@
+# Dev container stack. Compose publishes ports on the host (more reliable than
+# devcontainer forwardPorts in some setups). Interpolation vars (SSH_PORT, etc.)
+# can be set in `.devcontainer/.env` (see `.devcontainer/.env.example`).
+#
+# Internal SSH: devcontainers `sshd` feature listens on 2222, not 22 — map host:2222.
+#
+# Explicit DNS: containers on external networks (e.g. `dev`) sometimes get no working resolver
+# and `uv pip` fails with "dns error" / "failed to lookup address information".
+# Override in `.devcontainer/.env`: DEVCONTAINER_DNS_1 / DEVCONTAINER_DNS_2.
+services:
+  devcontainer:
+    build:
+      context: ..
+      dockerfile: .devcontainer/Dockerfile
+    dns:
+      - "${DEVCONTAINER_DNS_1:-1.1.1.1}"
+      - "${DEVCONTAINER_DNS_2:-8.8.8.8}"
+    env_file:
+      - ../.env
+    environment:
+      # Avoid ~/.cache/uv (often root-owned after sshd/common-utils); workspace is bind-mounted as vscode.
+      UV_CACHE_DIR: /workspaces/project/.uv-cache
+      SELENIUM_REMOTE_URL: ${SELENIUM_REMOTE_URL:-http://gme-selenium-firefox:4444}
+    ports:
+      - "${SSH_PORT:-2222}:2222"
+      - "${APP_PORT:-1234}:1234"
+      - "${DEV_PORT:-8888}:8888"
+    volumes:
+      - ..:/workspaces/project:cached
+    command: sleep infinity
+    networks:
+      - dev
+  gme-qdrant:
+    image: qdrant/qdrant:latest
+    container_name: gme-qdrant
+    ports:
+      - "6333:6333"
+      - "6334:6334"
+    volumes:
+      - ../data/qdrant/storage:/qdrant/storage
+    restart: unless-stopped
+    networks:
+      - dev
+  # README "Option B": multi-session standalone Firefox (ORCID, Selenium-backed tools).
+  gme-selenium-firefox:
+    image: selenium/standalone-firefox
+    container_name: gme-selenium-firefox
+    ports:
+      - "${SELENIUM_GRID_PORT:-4444}:4444"
+      - "${SELENIUM_VNC_PORT:-7900}:7900"
+    shm_size: "2g"
+    environment:
+      SE_NODE_MAX_SESSIONS: "5"
+      SE_NODE_SESSION_TIMEOUT: "300"
+    restart: unless-stopped
+    networks:
+      - dev
+
+networks:
+  dev:
+    external: true

.devcontainer/set-vscode-password.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+# Apply VSCODE_PASSWORD to user vscode at container start (not baked into the image).
+# Set VSCODE_PASSWORD in .env (this repo loads it via devcontainer runArgs --env-file).
+set -euo pipefail
+if [[ -z "${VSCODE_PASSWORD:-}" ]]; then
+  exit 0
+fi
+printf 'vscode:%s\n' "$VSCODE_PASSWORD" | sudo chpasswd