create project iatlas-api based on iatlas-data

apps/iatlas/api/.dockerignore

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+**/*.md
+.gitignore
+.git/
+Dockerfile
+no_commit/
+scripts/

apps/iatlas/api/.gitignore

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+# git
+# used by git-log to rewrite usernames
+.mailmap
+git-genui.config.json
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# Generated files
+.DS_Store
+
+# Visual Studio Code
+.vscode
+*.code-workspace
+
+# VIM
+*.swp
+*.swo
+
+docker/
+no_commit/
+scripts/__pycache__

apps/iatlas/api/.python-version

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+3.10.13

apps/iatlas/api/Dockerfile

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+FROM python:3.10.13
+
+# RUN apt-get -y update && apt-get -y install \
+#     wget && \
+#     # Install the GPG key for the Postgres repo
+#     wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add - && \
+#     # Add the repo
+#     echo "deb http://apt.postgresql.org/pub/repos/apt/ bookworm-pgdg main" | tee /etc/apt/sources.list.d/pgdg.list && \
+#     apt-get -y update && \
+#     # Install the Postgres 12 client
+#     apt-get -y install postgresql-client-12
+
+# COPY requirements.txt requirements.txt
+COPY src/ /src
+
+# RUN pip3 install -r requirements.txt
+
+WORKDIR /
+COPY docker-entrypoint.sh ./
+RUN chmod +x docker-entrypoint.sh
+
+ENTRYPOINT ["/docker-entrypoint.sh"]
+
+# Set up the iAtlas database
+# CMD python /src/build_database.py

apps/iatlas/api/docker-entrypoint.sh

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+#!/usr/bin/env bash
+set -e
+
+if [ "$1" = 'python' ]; then
+    cd ${APP_DIR}
+    exec gosu www-data "$@"
+fi
+
+exec "$@"

apps/iatlas/api/poetry.toml

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+[virtualenvs]
+in-project = true
+create = true

apps/iatlas/api/prepare-python.sh

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+#!/usr/bin/env bash
+
+PYTHON_VERSION="3.10.13"
+
+pyenv install --skip-existing $PYTHON_VERSION
+
+# Initializing pyenv again solves an issue encountered by GitHub action where the version of Python
+# installed above is not detected.
+eval "$(pyenv init -)"
+
+pyenv local $PYTHON_VERSION
+poetry env use $PYTHON_VERSION
+poetry install
+# poetry install --with prod,dev

apps/iatlas/api/project.json

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+{
+  "name": "iatlas-api",
+  "$schema": "../../../node_modules/nx/schemas/project-schema.json",
+  "sourceRoot": "apps/iatlas/api/scripts",
+  "projectType": "application",
+  "targets": {
+    "create-config": {
+      "executor": "nx:run-commands",
+      "options": {
+        "command": "cp -n .env.example .env",
+        "cwd": "{projectRoot}"
+      }
+    },
+    "prepare": {
+      "executor": "nx:run-commands",
+      "options": {
+        "command": "./prepare-python.sh",
+        "cwd": "{projectRoot}"
+      }
+    },
+    "serve": {
+      "executor": "nx:run-commands",
+      "options": {
+        "command": "docker compose up",
+        "cwd": "apps/iatlas/api"
+      },
+      "dependsOn": []
+    },
+    "serve-detach": {
+      "executor": "nx:run-commands",
+      "options": {
+        "command": "docker/iatlas/serve-detach.sh {projectName}"
+      }
+    },
+    "build-image": {
+      "executor": "@nx-tools/nx-container:build",
+      "options": {
+        "context": "apps/iatlas/api",
+        "metadata": {
+          "images": ["ghcr.io/sage-bionetworks/{projectName}"],
+          "tags": ["type=edge,branch=main", "type=raw,value=local", "type=sha"]
+        },
+        "push": false
+      }
+    },
+    "publish-image": {
+      "executor": "@nx-tools/nx-container:build",
+      "options": {
+        "context": "apps/iatlas/api",
+        "metadata": {
+          "images": ["ghcr.io/sage-bionetworks/{projectName}"],
+          "tags": ["type=edge,branch=main", "type=sha"]
+        },
+        "push": true
+      },
+      "dependsOn": ["build-image"]
+    },
+    "scan-image": {
+      "executor": "nx:run-commands",
+      "options": {
+        "command": "trivy image ghcr.io/sage-bionetworks/{projectName}:local --quiet",
+        "color": true
+      }
+    }
+  },
+  "tags": ["type:app", "scope:backend", "language:python"],
+  "implicitDependencies": []
+}

apps/iatlas/api/pyproject.toml

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+[tool.poetry]
+name = "iatlas-api"
+version = "0.1.0"
+description = ""
+authors = ["andrewelamb <[email protected]>"]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = "3.10.13"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"