Merge pull request #5 from Small-Bodies-Node/infrastructure-update-20…

…24.02

Infrastructure update 2024.02

LICENSE

@@ -0,0 +1,11 @@
+Copyright 2021-2024 SBN Survey Image Service Developers
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

_initial_setup.sh

@@ -1,57 +1,88 @@
-#!/usr/bin/env false
+#!/bin/bash
 
-### 0. Load vars defined in .env
-if [ ! -f $PWD/.env ]; then
-    echo -e "No .env file found.  Generate with '_sbnsis env' then edit."
-    return 1
+set -e
+
+reset_color="\033[00m"
+black="\033[30m"
+red="\033[31m"
+green="\033[32m"
+yellow="\033[33m"
+blue="\033[34m"
+magenta="\033[35m"
+cyan="\033[36m"
+white="\033[37m"
+
+if [[ -z $PYTHON ]]; then
+    PYTHON=python3
 fi
-source .env
 
-### 1. Message user
 clear
-echo -e """${GRE}
-=======================================
-Initializing Python Virtual Environment
-=======================================
-${WHI}"""
+echo -e """${green}
+==========================
+Python Virtual Environment
+==========================
+${reset_color}"""
 
 sleep 1
 
-### 2. Get rid of caches NOT in .venv
+### Get rid of caches NOT in .venv
+echo -e """${cyan}
+    Cleaning cached pyc files
+${reset_color}"""
 find . -type d ! -path './.venv/*' -name '__pycache__' -exec rm -rf {} +
 find . -type d ! -path './.venv/*' -name '.pytest_cache' -exec rm -rf {} +
 find . -type d ! -path './.venv/*' -name '.mypy_cache' -exec rm -rf {} +
 
-### 3. Check for existence of `.venv` dir
+### Check for existence of `.venv` dir
 if [[ ! -d $PWD/.venv ]]; then
-    echo -e """${BLU}
-    virtual Environment Not Found -- Creating '.venv'
-"""
-    $PYTHON_3_6_OR_HIGHER -m venv .venv --prompt=$APP_NAME
+    echo -e """${cyan}
+    Virtual environment not found -- Creating ".venv"
+${reset_color}"""
+    $PYTHON -m venv .venv --prompt=sbn-survey-image-service
+else
+    echo -e """${cyan}
+    Virtual environment found in ".venv"
+${reset_color}"""
 fi
 
-### 4. Activate VENV
+### Activate VENV
 source ./.venv/bin/activate
 
-### 5. Install package dependencies for project
+### Install package dependencies for project
+
+echo -e """${green}
+===========================
+Setup dependencies and code
+===========================
+${reset_color}"""
+
 pip install --upgrade -q -q -q pip setuptools wheel
-pip install -q -r requirements.vscode.txt
-pip install -q -r requirements.txt
-pip install -e .
+pip install -e .[recommended,dev]
 
 if [[ ! -e $VIRTUAL_ENV/bin/fitscut ]]; then
-    echo -e """${BLU}
-    installing fitscut
-${WHI}
+    echo -e """${cyan}
+    Installing fitscut
+${reset_color}
 """
     ./_install_fitscut
 fi
 
-### 6. Link git pre-commit-hook script
+### Link git pre-commit-hook script
 ln -fs $PWD/_precommit_hook $PWD/.git/hooks/pre-commit
 
+if [ ! -f $PWD/.env ]; then
+    echo -e """${red}
+To create a .env file:
+
+    source .venv/bin/activate
+    _sbnsis env
+
+Then edit .env
+${reset_color}"""
+fi
+
 ### 7. Final Message
-echo -e """${BLU}
+echo -e """${cyan}
     Done. Bon courage!
-${WHI}
-"""
+${reset_color}
+"""

_sbnsis

@@ -1,2 +1,3 @@
-#!/bin/bash
-./.venv/bin/python3 -m sbn_survey_image_service.scripts.sbnsis $*
+#!/usr/bin/env python3
+from sbn_survey_image_service.scripts.sbnsis import SBNSISService
+SBNSISService()

pyproject.toml

@@ -0,0 +1,47 @@
+[project]
+name = "sbn-survey-image-service"
+description = "Serves images and cutouts via REST API."
+readme = "readme.md"
+authors = [
+    { name = "Michael S. P. Kelley", email = "[email protected]" }
+]
+license = { text = "BSD 3-Clause License" }
+dependencies = [
+    "Flask>=3.0",
+    "Flask-Cors>=4.0",
+    "gunicorn>=21",
+    "connexion>=3.0",
+    "swagger-ui-bundle>1.0",
+    "astropy>=6.0",
+    "pds4_tools==1.3",
+    "SQLAlchemy>=2.0",
+    "python-dotenv>1.0",
+    "pytest-remotedata>=0.4",
+]
+dynamic = ["version"]
+
+[project.urls]
+homepage = "https://github.com/Small-Bodies-Node/sbn-survey-image-service"
+
+[build-system]
+requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]
+build-backend = 'setuptools.build_meta'
+
+[tool.setuptools_scm]
+
+[tool.setuptools]
+zip-safe = false
+
+[tool.setuptools.packages.find]
+
+[project.optional-dependencies]
+recommended = [
+    "psycopg2-binary>=2.8",
+]
+dev = [
+    "autopep8",
+    "mypy",
+    "pycodestyle",
+    "pytest>=7.0",
+    "pytest-cov>=3.0",
+]

readme.md

@@ -8,16 +8,14 @@ Live at the PDS [Small Bodies Node](https://sbnsurveys.astro.umd.edu/api/ui)
 
 The SBN Survey Image Service is a REST API that enables a user to retrieve archive images and cutouts thereof from the Planetary Data System's Small-Bodies Node (PDS SBN). For example, a user may request a full-frame image from the ATLAS survey archive, or a small cutout around their object of interest. The returned data may be in FITS, JPEG, or PNG formats. The service can also return the image's PDS label.
 
-The data model is partially compatible with the IVOA's [Simple Image Access protocol](https://www.ivoa.net/documents/SIA/), which is based on the [ObsCore Data Model](https://www.ivoa.net/documents/ObsCore/20111028/). However, this functionality is deprecated.
-
 ![SBN Survey Image Service workflow](docs/SBNSIS-workflow.png)
 
 ## Code Features
 
 - Uses [fitscut](https://github.com/spacetelescope/fitscut) for image cutouts and JPEG/PNG generation
 - Flask API layer
-- Connexion used to generate swagger interface
-- Gunicorn/Apache used for production deployment
+- OpenAPI spec with Connexion and Swagger
+- Gunicorn for production deployment
 - Backed by Postgresql or Sqlite3
 
 ## Development
@@ -33,7 +31,7 @@ The data model is partially compatible with the IVOA's [Simple Image Access prot
 
 This repo has code for:
 
-- Running a flask-connexion API
+- Running the API
 - Testing
 
 Most day-to-day tasks can be accomplished with the `_sbnsis` command.
@@ -53,11 +51,11 @@ The following steps are needed to set up the code base:
       cd sbn-survey-image-service
   ```
 
-- Create a new environment variable file and edit to suit your needs: `_sbnsis env`.
-- Initialize your installation with `source _initial_setup.sh`. This will:
+- Initialize your installation with `bash _initial_setup.sh`. This will:
   - Create and activate a python virtual environment.
-  - Install dependencies (e.g., `fitscut`) to the virtual env, if needed.
-  - Make available to your shell the variables `.env`.
+    - To use a specific Python interpreter, set the PYTHON environment variable: `PYTHON=/path/to/python3 bash _install_setup.sh`
+  - Install dependencies, including `fitscut`, to the virtual env.
+- Create a new environment variable file and edit to suit your needs: `_sbnsis env`.
 - Optionally test your set up:
   - Be aware that the testing suite will use the database parameters specified in the `.env` file.
     - The database user must have write permissions for testing.

sbn_survey_image_service/__init__.py

@@ -1,11 +1,19 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 """SBN Survey Image Service"""
 
+import os
+from importlib.metadata import version as _version, PackageNotFoundError
+
 # make cache directory set umask
 from . import exceptions
 from . import env
 from . import services
 from . import models
-import os
-os.system(f'mkdir -p {env.ENV.SBNSIS_CUTOUT_CACHE}')
-del os
+
+try:
+    __version__ = _version(__name__)
+except PackageNotFoundError:
+    pass
+
+os.system(f"mkdir -p {env.ENV.SBNSIS_CUTOUT_CACHE}")
+del os, PackageNotFoundError, _version

sbn_survey_image_service/api/openapi.yaml

@@ -15,7 +15,7 @@ paths:
       parameters:
         - name: id
           in: path
-          description: Unique image data product ID (PDS3) or logical identifier (PDS4)
+          description: Unique image data logical identifier (PDS4)
           example: urn:nasa:pds:gbo.ast.neat.survey:data_tricam:p20020222_obsdata_20020222120052c
           required: true
           allowEmptyValue: false