👷‍♂️❄️ ↝ Merge pull request #3 from DeSci-md/actions

🌌👷‍♂️ ↝ Adding Docker, Flake & Actions config

.github/workflows/nodemon.yml

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+- name: Setup Node.js environment
+  uses: actions/[email protected]
+  with:
+    # Set always-auth in npmrc.
+    always-auth: # optional, default is false
+    # Version Spec of the version to use. Examples: 12.x, 10.15.1, >=10.15.0.
+    node-version: # optional
+    # File containing the version Spec of the version to use.  Examples: .nvmrc, .node-version, .tool-versions.
+    node-version-file: # optional
+    # Target architecture for Node to use. Examples: x86, x64. Will use system architecture by default.
+    architecture: # optional
+    # Set this option if you want the action to check for the latest available version that satisfies the version spec.
+    check-latest: # optional
+    # Optional registry to set up for auth. Will set the registry in a project level .npmrc and .yarnrc file, and set up auth to read in from env.NODE_AUTH_TOKEN.
+    registry-url: # optional
+    # Optional scope for authenticating against scoped registries. Will fall back to the repository owner when using the GitHub Packages registry (https://npm.pkg.github.com/).
+    scope: # optional
+    # Used to pull node distributions from node-versions. Since there's a default, this is typically not supplied by the user. When running this action on github.com, the default value is sufficient. When running on GHES, you can pass a personal access token for github.com if you are experiencing rate limiting.
+    token: # optional, default is ${{ github.server_url == 'https://github.com' && github.token || '' }}
+    # Used to specify a package manager for caching in the default directory. Supported values: npm, yarn, pnpm.
+    cache: # optional
+    # Used to specify the path to a dependency file: package-lock.json, yarn.lock, etc. Supports wildcards or a list of file names for caching multiple dependencies.
+    cache-dependency-path: # optional

.github/workflows/python-pipeline.yml

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+name: Python Container for Text Extraction
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "jira-plugin.workingProject": ""
+}

Ansible/habanero.py

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+"""
+Script for extracting machine readable text from a web publication/paper which
+needs to be downloaded
+Adapted from the process described by Wang et. al. 2022 10.1038/s41524-021-00687-2
+
+Crossref API info: https://api.crossref.org/swagger-ui/index.html
+
+habanero package info: https://pypi.org/project/habanero/
+"""
+import time  # for using time.sleep() if needing to pause data requests
+from habanero import Crossref
+from habanero import cn
+
+
+cr = Crossref()
+
+# Setting info for mailto for contact email and user-agent for description of use case
+# For attempts to get into the 'polite pool' for paper requests through the API
+cr.mailto = '[email protected]'
+cr.ua_string = 'Python script for retrieving paper info from query for research.'
+
+# query section, request results based on a search
+# cursor='*' alloy 'deep paging' (according to function documentation in crossref.py)
+# cursor_max sets the max number of records to retrieve, by default it's 20 I think
+# seems to do max results returned from deep paging in sets of 20, e.g. a request of 15 still gives 20
+n = 2  # multiple of 20 for deep paging
+request = cr.works(query = "Automated pipeline for superalloy data by text mining", cursor='*', cursor_max=n*20, progress_bar=True)  # test query searching for papers based on a string
+
+allowed_types = ['proceedings-article', 'book-chapter', 'dissertation', 'journal-article']  # specifying document types of parse
+# print the title and the type of item from the results
+for i in range(n):
+    for j in range(len(request[i]['message']['items'])):
+        if request[i]['message']['items'][j]['type'] not in allowed_types:  # skipping if not a type wanted
+            continue
+        title = request[i]['message']['items'][j]['title'][0]
+        type = request[i]['message']['items'][j]['type']
+        print(f'{title}, {type}')  # print the title and type of each results
+        time.sleep(0.25)  # sleep between prints so it's not too fast
+
+
+request_doi = cr.works(ids = '10.1038/s41524-021-00687-2')  # search for a specific paper using a DOI number
+print(request_doi['message']['title'][0])
+citation = cn.content_negotiation(ids = '10.1038/s41524-021-00687-2', format = 'text')  # get citation for the DOI
+print(citation)

DOCKERFILE

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+FROM python:3.9.16-bullseye
+
+ENV PROJECT_DIR /app
+
+WORKDIR /app
+RUN pip install pipenv
+
+# COPY requirements.txt requirements.txt
+# RUN pip install -r requirements.txt
+
+WORKDIR ${PROJECT_DIR}
+COPY Pipfile .
+# COPY Pipfile.lock .
+
+RUN pipenv install
+# RUN pipenv install --system
+# RUN pipenv install --system --deploy
+COPY . .
+
+# CMD ["python", "-m", "flask", "run", "--host=0.0.0.0"]
+CMD ["pipenv", "run", "flask", "run", "--host=0.0.0.0"]

Makefile

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+# Convenient shortcuts for local development
+
+build:
+	docker build --tag sytizen-server .
+
+# Default port 5000 is in use on Ventura Macs
+# 7355 chosen for TESS
+run:
+	docker compose up --build --detach
+
+logs:
+	docker compose logs --follow
+
+stop:
+	docker compose down

Pipfile

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+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+moralis = "*"
+flask = "*"
+flask_cors = "*"
+python-dotenv = "*"
+matplotlib = "*"
+lightkurve = "*"
+nbformat = "*"
+gunicorn = "*"
+sqlalchemy = "*"
+psycopg2-binary = "*"
+flask-sqlalchemy = "*"
+thirdweb-sdk = "*"
+
+[dev-packages]

README.md

@@ -29,4 +29,48 @@ pip install habanero
 ```
 
 # Web Interface/Client
-Current progress is being tracked by [signal-k/client](http://github.com/Signal-K/client/pull/19) and will be added as a git submodule once our generator & metadata smart contracts are completed
+Current progress is being tracked by [signal-k/client](http://github.com/Signal-K/client/pull/19) and will be added as a git submodule once our generator & metadata smart contracts are completed
+
+## Generative API
+### Containerisation for local development
+
+In root dir, `Dockerfile` runs the Flask Server in a container.
+
+The `docker-compose.yml` defines a cluster with the Server and a local PostgreSQL container
+
+For convenience, a Makefile supports the following simple operations:
+
+* `make build` builds an image from the current working copy
+* `make run` starts the cluster, rebuilding if necessary
+* `make logs` tails the logs for both containers
+* `make stop` stops and deletes the clusters
+
+For rapid iteration, I use:
+`make stop run logs`
+
+#### Prerequisites
+
+You will need to have a Docker environment available... Docker Desktop or an equivalent
+
+#### Previous Issues
+
+##### ThirdWeb
+
+The build step (`make build`) fails whilst running `pipenv install` during the build of the Docker image.
+
+`thirdweb-sdk` caused errors on `pipenv install`. The output was long and ugly; but a resolution has been found.
+The problem was the use of the `slim-` base image.  Switching from `p`ython:3.9.9-slim-bullseye` to `python:3.9.9-bullseye` avoided the problem.
+
+##### Ventura - Flask default port 5000
+
+Flask runs by default on port 5000.  However, on macos Ventura, there is a system service "Airplay Receiver" listening on this port.
+
+In this case, `localhost:5000` does not reach the Flask app, although `127.0.0.1:5000` does.
+
+The easiest solution is to turn off the Airplay Receiver service; an alternative is to run Flask on a different port... perhaps 7355 for TESS?
+
+#### Current Issue
+
+The server responds to `http://localhost:5000` with a classic "Hello World"
+
+Several of the blueprints in `app.py` are commented out since they have dependencies on ThirdWeb

Server/.flaskenv

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+FLASK_APP=app.py
+FLASK_DEBUG=1

Server/app.py

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+from flask import Flask, request, make_response, jsonify, Blueprint
+from datetime import datetime, timedelta
+
+"""# Jupyter interaction
+import io, os, sys, types # https://jupyter-notebook.readthedocs.io/en/stable/examples/Notebook/Importing%20Notebooks.html
+from IPython import get_ipython
+from nbformat import read
+from IPython.core.interactiveshell import Interactiveshell"""
+
+# Flask blueprints/routes
+from auth.moralisHandler import moralis_handler
+from contracts.planetDrop import planet_drop
+from database.connection import database_connection
+# from database.unity-integration import unity_database_connection
+# from ansible.tic_classify import tic_classify
+# from ansible.classify import lightkurve_handler
+
+app = Flask(__name__)
+app.register_blueprint(moralis_handler, url_prefix='/moralis-auth')
+app.register_blueprint(planet_drop, url_prefix='/planets')
+app.register_blueprint(database_connection, url_prefix='/database')
+# app.register_blueprint(unity-database_connection, url_prefix='/database-unity')
+# app.register_blueprint(tic_classify, url_prefix='/lightkurve')
+# app.register_blueprint(lightkurve__handler, url_prefix='/lightkurve-handle')
+
+@app.route('/')
+def index():
+    return "Hello World"

Server/database/connection.py

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+from flask import Blueprint, request
+from dotenv import load_dotenv
+import psycopg2
+import os
+
+database_connection = Blueprint('database_connection', __name__)
+
+load_dotenv()
+url = os.getenv("DATABASE_URL")
+print("DATABASE",url)
+connection = psycopg2.connect(dsn=url, user='postgres')
+
+# PostgreSQL queries
+CREATE_USERS_TABLE = (
+    'CREATE TABLE IF NOT EXISTS users (id SERIAL PRIMARY KEY, address TEXT);'
+)
+CREATE_PLANETS_TABLE = (
+    """CREATE TABLE IF NOT EXISTS planets (user_id INTEGER, temperature REAL, date TIMESTAMP, FOREIGN KEY(user_id) REFERENCES users(id) ON DELETE CASCADE);"""
+)
+INSERT_USER_RETURN_ID = 'INSERT INTO users (address) VALUES (%s) RETURNING id;'
+INSERT_PLANET = (
+    'INSERT INTO planets (user_id, temperature, date) VALUES (%s, %s, %s);'
+)
+
+# User Management
+@database_connection.post('/api/user')
+def addUser():
+    data = request.get_json()
+    address = data['address']
+
+    # Connect to the database
+    with connection:
+        with connection.cursor() as cursor:
+            cursor.execute(CREATE_USERS_TABLE)
+            cursor.execute(INSERT_USER_RETURN_ID, (address,))
+            user_id = cursor.fetchone()[0]
+
+    return {'id': user_id, 'message': f"User {address} created"}, 201

Server/database/retrieveData.cs

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+using System.Collections;
+using System.Collections.Generic;
+using UnityEngine;
+using UnityEngine.Networking;
+
+public class GetMe : MonoBehaviour {
+
+    public void GetData()
+    {
+        StartCoroutine(GetRequest("http://127.0.0.1:5000/unity-database_connection/list"));
+    }
+
+    IEnumerator GetRequest(string uri)
+    {
+        UnityWebRequest uwr = UnityWebRequest.Get(uri);
+        yield return uwr.SendWebRequest();
+
+        if (uwr.isNetworkError)
+        {
+            Debug.Log("Error While Sending: " + uwr.error);
+        }
+        else
+        {
+            Debug.Log("Received: " + uwr.downloadHandler.text);
+        }
+    }
+}

contracts/serverDropConnection.py

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+from flask import Blueprint, request
+from thirdweb import ThirdwebSDK
+
+planet_drop = Blueprint('planet_drop', __name__)
+
+# Get NFT balance for Planet Edition Drop (https://thirdweb.com/goerli/0xdf35Bb26d9AAD05EeC5183c6288f13c0136A7b43/code)
+@planet_drop.route('/balance')
+def get_balance():
+    # Planet Edition Drop Contract
+    network = "goerli"
+    sdk = ThirdwebSDK(network)
+    contract = sdk.get_edition_drop("0xdf35Bb26d9AAD05EeC5183c6288f13c0136A7b43")
+
+    address = "0xCdc5929e1158F7f0B320e3B942528E6998D8b25c"
+    token_id = 0
+    balance = contract.balance_of(address, token_id)
+
+    return str(balance)
+
+@planet_drop.route('/get_planet')
+def get_planet():
+    network = 'goerli'
+    sdk = ThirdwebSDK(network)
+
+    # Getting Planet (candidate nfts)
+    contract = sdk.get_contract("0x766215a318E2AD1EbdC4D92cF2A3b70CBedeac31")
+    tic55525572 = contract.call("uri", 0) # For token id 0, tic id 55525572
+    return str(tic55525572)
+
+@planet_drop.route('/mint_planet', methods=["GET", "POST"])
+def create_planet():
+    #Output from IPFS gateway: #{"name":"TIC 55525572","description":"Exoplanet candidate discovered by TIC ID. \n\nReferences: https://exoplanets.nasa.gov/exoplanet-catalog/7557/toi-813-b/\nhttps://exofop.ipac.caltech.edu/tess/target.php?id=55525572\n\nDeepnote Analysis: https://deepnote.com/workspace/star-sailors-49d2efda-376f-4329-9618-7f871ba16007/project/Star-Sailors-Light-Curve-Plot-b4c251b4-c11a-481e-8206-c29934eb75da/%2FMultisector%20Analysis.ipynb","image":"ipfs://Qma2q8RgX1X2ZVcfnJ7b9RJeKHzoTXahs2ezzqQP4f5yvT/0.png","external_url":"","background_color":"","attributes":[{"trait_type":"tic","value":"55525572"},{"trait_type":"mass_earth","value":"36.4"},{"trait_type":"type","value":"neptune-like"},{"trait_type":"orbital_period","value":"83.9"},{"trait_type":"eccentricity","value":"0.0"},{"trait_type":"detection_method","value":"transit"},{"trait_type":"orbital_radius","value":"0.423"},{"trait_type":"radius_jupiter","value":"0.599"},{"trait_type":"distance_earth","value":"858"}]}
+    # Multiple instances for the same ID will be created (as long as the traits are the same), one for each person, as each planet instance appeared differently and will be manipulated differently by users
+    # Creating a planet nft based on discovery
+    network = 'goerli'
+    sdk = ThirdwebSDK(network)
+    contract = sdk.get_contract("0x766215a318E2AD1EbdC4D92cF2A3b70CBedeac31")
+    #data = contract.call("lazyMint", _amount, _baseURIForTokens, _data) (POST data)
+    # Interaction flow -> https://www.notion.so/skinetics/Sample-Planets-Contract-4c3bdcbca4b9450382f9cc4e72e081f7
+
+"""
+# Flask/api routes
+@app.route('/planet')
+def planet():
+    return jsonify({'planet' : 'planet'})
+@app.post('/select_planet')
+def select_planet():
+    data = request.get_json()
+    planetId = data['planetId']
+    planetName = data['planetName']
+    planetTic = data['planetTic']
+    sector_data = lk.search_lightcurve(planetTic, author = 'SPOC', sector = 23)
+    #lc = sector_data.download()
+    #lc.plot()
+    return sector_data
+# Show planet data on frontend
+@app.post('/show_planet') # Can we do some calculation for nft revealing using this (i.e. mint nft after classification)
+def show_tic():
+    lc = sector_data.plot()
+    return lc
+@app.post('/mint-planet')
+def mint_planet():
+    data = request.get_json()
+    _receiver = data['profileAddress']
+    _tokenId = data['tokenId']
+    _quantity = 1
+    data = contract.call("claim", _receiver, _tokenId, _quantity)
+app.run(host='0.0.0.0', port=8080)
+"""