Migration/bu isciii deployment standard

.bu-isciii-deployment/state.json

@@ -0,0 +1,63 @@
+{
+  "config": {
+    "ADDONS": {
+      "apache": {
+        "CONFIG_SERVICE": "iskylims"
+      },
+      "samba": {
+        "CONFIG_SERVICE": "iskylims",
+        "MODES": [
+          "test"
+        ]
+      }
+    },
+    "APP_NAME": "iSkyLIMS",
+    "APP_SLUG": "iskylims",
+    "DEFAULT_BRANCH": "main",
+    "DESCRIPTION": "Laboratory information management system for wet-lab and dry-lab sequencing workflows.",
+    "PYTHON_VERSION": "3.11",
+    "REPOSITORY_URL": "https://github.com/BU-ISCIII/iSkyLIMS.git",
+    "SERVICES": {
+      "iskylims": {
+        "BUILD_CONTEXT": ".",
+        "DOCKERFILE": "Dockerfile",
+        "IMAGE": "iskylims:local",
+        "INSTALL_CONF": "conf/docker_production_settings.txt",
+        "PROFILE": "django",
+        "PROJECT_MODULE": "iskylims",
+        "TEST_INSTALL_CONF": "conf/docker_test_settings.txt"
+      }
+    },
+    "TIMEZONE": "Europe/Madrid"
+  },
+  "files": {
+    ".dockerignore": "bd9c115511d6b9dae318e4b6a85ddb282e60a46fd89c6cdecccdc20c668eb0e9",
+    ".gitignore": "de487336ed72efd6601b985eda1c83754d6ee33b1cb4ce9f8973411caae833ed",
+    "Dockerfile": "95d77c59cec771592957755e699c19401f70e631eb42bd6a9ac73c2024786de1",
+    "LEAME.md": "9c7353110884db0a9e48b92d35c3ed8813b83e331d5ae2ab75a70f2878bd4811",
+    "README.md": "f8808b6ee80aa7a942dd505463f155b2314bd70f948d74ce6e3f9fad938d8c22",
+    "conf/INSTALL_SETTINGS.md": "f5b1437a0e13a803ff020b5cb3aa1476b6876c169b23e6bcfc3e5042224af636",
+    "conf/apache/00-logs.conf": "3c2ab4e693e528d2cad37c0c5bb0bc4511803a7f206b339182de192d4e398092",
+    "conf/apache/01-reverse-proxy.conf": "1c93e81d44ef88091c4ec7872d9220128813ba5111908ea70b22996182ffd5be",
+    "conf/apache/02-server-status.conf": "c3b5d26f9b551083faf0d85b188bfa9c577ff0bd3b805f0ec104fe4f7d5101cb",
+    "conf/apache/apache_production_settings.txt": "169c2d22d4933090003875da7359c49926b9dd4be0838a7875744723c9cf771a",
+    "conf/apache/apache_test_settings.txt": "8092b49e5b3950a9e6ef64f6fc9d004d51e487cfdd4c17c71bcfa3469494e0b6",
+    "conf/docker_production_settings.txt": "51182733d5cd3b12d826cd085a804e310c9a89bced71d7396cbef59df2801c82",
+    "conf/docker_test_settings.txt": "c1d910b42629559304ee6a750d6f37a5ed322ca9efa7a9cfffd373de7a75cae6",
+    "conf/samba/samba_production_settings.txt": "f19da30ab0890a79254e22c571629b34de2d37ad9c12449607158bff9a9188a1",
+    "conf/samba/samba_test_settings.txt": "c383b88d43de8d65886cdd2b45bf9f27d91f5f3fe290f8f82378578fbeeff0b2",
+    "conf/template_settings.py": "af539ad10729a371e0c735c121e6e62dfece96afce77fb86e3a0820df2e9dd2f",
+    "container_install.sh": "82500f1e800e1a5dbd3429b14f1c3bae7f3554f988408b5f7939478afde45abd",
+    "deployment_health/README.md": "3d7c4295938708813369deeac9edc0eb8fe2153c77d03f9138febf3aed715aa5",
+    "deployment_health/__init__.py": "bedcff132309f8970b1ca72fcea20c7cb38bb727d48f82d96dbf7104922abda0",
+    "deployment_health/urls.py": "8d274b44d326f26d71b05021a34969c742478efbe47691aadd8c3a90ba16f340",
+    "deployment_health/views.py": "d19cc3e8fef8519bae2b7fbdc25d17f6ae7df02479aa8890f4b4d250bb07f2e4",
+    "docker-compose.prod.yml": "3408e0e424a06587f61e9e04d46e4225bdfab473206bd28a1f18d2d014b2d9dc",
+    "docker-compose.test.yml": "a56a89a26ae8e30627e401405e273d99cfeb24b8e508f24204882d57ba79f51d",
+    "install.sh": "6cedd3a990de21bf2343b75d8f93dd37420c1b358a1529b5e50892cf6df1526c",
+    "scripts/container_start.sh": "8d6e24f848d0562c17f323bbcf8d49e89a247648895bc209c4eb79bc9c8adf12",
+    "scripts/smoke_test.sh": "24aabe5c89c2ede2d373d282f1c3d17ed4a19f3c8e73b07a148e8472869bf17f"
+  },
+  "source": "BU-ISCIII deployment standards",
+  "standard_version": "0.1.0"
+}

.dockerignore

@@ -1,53 +1,34 @@
-# Keep .git: install/build diagnostics use git metadata inside the image.
+# Production installation settings are passed through a build secret. Exclude
+# all local settings and allow only committed, non-sensitive templates/tests.
+install_settings.txt
+conf/*settings*.txt
+!conf/docker_test_settings.txt
+!conf/template_install_settings.txt
+!conf/template_settings.txt
+.tmp_docker_install_conf_*.txt
+.env
+.env.*
+!.env.example
+.env.prod.file
+# Runtime-rendered add-on bind sources are not image build inputs.
+deployment/apache/*.conf
+deployment/settings/
 
-# Local Python environments and caches
 .venv/
 venv/
-env/
-ENV/
 virtualenv/
+node_modules/
+.npm/
+.next/
+.vite/
 __pycache__/
 *.py[cod]
 .pytest_cache/
-.mypy_cache/
-.hypothesis/
-.coverage
-.coverage.*
-htmlcov/
-.tox/
-
-# Local editor and OS files
 .vscode/
 .idea/
-.DS_Store
-*.swp
-*.swo
-
-# Local runtime/generated deployment files
-.env
-.env.*
-!.env.example
-.env.prod.file
-install_settings.txt
-wetlab/logging_config.ini
 logs/
 tmp/
 documents/
-outputs/
-catboost_info/
-
-# Build, package, and generated archives
 build/
 dist/
 *.egg-info/
-.eggs/
-*.egg
-*.log
-*.gz
-*.zip
-*.tar
-*.tgz
-
-# Generated Django/runtime files at repo root
-/manage.py
-/static/

.gitignore

@@ -1,124 +1,21 @@
-## Custom
-*.xml
-*.bin
-*.gz
-*_BAK
-tmp/
-logs/
-/static/
-install_settings.txt
+# Local deployment configuration and generated synchronization candidates
+.env
+.env.*.file
+conf/production_settings.txt
+# Legacy/application-specific production settings must remain local.
 my_prod_settings*.txt
-wetlab/logging_config.ini
-#--- updates introduced for iSkyLIMS in submodules packaging ---
-virtualenv/
-iSkyLIMS/
-*iskylims/
-documents/
-manage.py
-logs/
-logs
-.vscode/
-
+*.bu-isciii-update
+# Final add-on bind sources are regenerated from repository-owned conf files.
+deployment/apache/*.conf
+deployment/settings/
 
-# Byte-compiled / optimized / DLL files
+# Python and runtime artifacts
 __pycache__/
 *.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
-# dotenv
-.env
-.env.prod.file
-
-# virtualenv
-.venv
-venv/
-ENV/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
+.venv/
+virtualenv/
+node_modules/
+.next/
+.npm/
+logs/
+documents/