Re-structure app to more generic architecture.

.readthedocs.yml

@@ -7,7 +7,7 @@ version:            2
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration:    fhe_collector/docs/source/conf.py
+  configuration:    app/docs/source/conf.py
 
 # Optionally build your docs in additional formats such as PDF and ePub
 formats:            all

app/api/__init__.py

@@ -0,0 +1,107 @@
+# !/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""API functions."""
+from flask import render_template
+from flask import request
+from flask import jsonify
+from flask import Blueprint
+
+api = Blueprint("api", __name__)
+
+
+@api.route("/")
+def homepage():
+    return jsonify({"status": "on", "api_version": "1.0"})
+
+
+@api.route("/add_data", methods=["POST", "GET"])
+def add_data():
+    """Add data via an API endpoint to the database.
+
+    Required: doi
+    Optional: url, date
+    """
+    response_status = "error"
+    url_type_list = [
+        "ojs",
+        "doi_new",
+        "doi_old",
+        "doi_new_landingpage",
+        "unpaywall",
+        "pubmed",
+        "pubmedcentral",
+    ]
+
+    json_data = request.get_json()
+    token = json_data["token"]
+
+    if request.method == "POST":
+        try:
+            if "X-API-Key" in request.headers:
+                if app.config["API_TOKEN"] == request.headers["X-API-Key"]:
+                    if request.headers["Content-Type"] == "application/json":
+                        json_data = request.get_json()
+                        if isinstance(json_data, list):
+                            is_data_valid = True
+                            for entry in data:
+                                # Validate entry
+                                if "doi" in entry:
+                                    if not isinstance(entry["doi"], str):
+                                        response = "DOI {} is no string.".format(
+                                            entry["doi"]
+                                        )
+                                        is_data_valid = False
+                                    if "url" in entry:
+                                        if not isinstance(entry["url"], str):
+                                            response = "URL {} is no string.".format(
+                                                entry["url"]
+                                            )
+                                            is_data_valid = False
+                                    else:
+                                        print("URL is missing")
+                                        is_data_valid = False
+                                    if "url_type" in entry:
+                                        if not isinstance(entry["url_type"], str):
+                                            response = "URL type {} is no string.".format(
+                                                entry["url_type"]
+                                            )
+                                            is_data_valid = False
+                                        if entry["url_type"] not in url_type_list:
+                                            response = "URL type {} is not one of the allowed types.".format(
+                                                entry["url_type"]
+                                            )
+                                            is_data_valid = False
+                                        else:
+                                            response = "URL type is missing."
+                                            is_data_valid = False
+                                    if "date" in entry:
+                                        if not isinstance(entry["date"], str):
+                                            response = "Date {} is no string.".format(
+                                                entry["date"]
+                                            )
+                                            is_data_valid = False
+                                    else:
+                                        response = "Date is missing."
+                                        is_data_valid = False
+                                else:
+                                    is_data_valid = False
+                                    response = "DOI is missing in {}.".format(entry)
+                            if is_data_valid:
+                                resp_func = import_dois_from_api(data)
+                                if resp_func:
+                                    response = resp_func
+                                    response_status = "ok"
+                                else:
+                                    response = "Error: JSON from API could not be stored in database."
+                        else:
+                            response = "No list of data in JSON."
+                    else:
+                        response = "No JSON delivered."
+                else:
+                    response = "Authentication token not right."
+            else:
+                response = "Authentication token not passed."
+        except:
+            response = "Undefined error."
+
+        return jsonify({"status": response_status, "content": response})

app/main/__init__.py

@@ -0,0 +1,9 @@
+# !/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""main functions."""
+
+from flask import Blueprint
+
+main = Blueprint("main", __name__)
+
+from . import views, errors

app/main/errors.py

@@ -0,0 +1,13 @@
+from flask import render_template
+from . import main
+
+
+@main.app_errorhandler(404)
+def not_found_error(error):
+    return render_template("404.html"), 404
+
+
+@main.app_errorhandler(500)
+def internal_error(error):
+    db.session.rollback()
+    return render_template("500.html"), 500

app/main/views.py

@@ -0,0 +1,27 @@
+from flask import render_template, current_app
+from flask_sqlalchemy import get_debug_queries
+from . import main
+
+
+@main.after_app_request
+def after_request(response):
+    for query in get_debug_queries():
+        if query.duration >= current_app.config["FLASKY_SLOW_DB_QUERY_TIME"]:
+            current_app.logger.warning(
+                "Slow query: %s\nParameters: %s\nDuration: %fs\nContext: %s\n"
+                % (query.statement, query.parameters, query.duration, query.context)
+            )
+    return response
+
+
+@main.route("/")
+@main.route("/index")
+def index():
+    """Homepage."""
+    return render_template("index.html", title="Home")
+
+
+@main.route("/api")
+def api():
+    """Api page."""
+    return render_template("api.html", title="API")

fhe.py

@@ -0,0 +1,19 @@
+from flask_migrate import Migrate, upgrade
+from app import create_app, db
+from app.models import Url, Doi
+import os
+from dotenv import load_dotenv
+
+
+dotenv_path = os.path.join(os.path.dirname(__file__), ".env")
+if os.path.exists(dotenv_path):
+    load_dotenv(dotenv_path)
+
+
+app = create_app(os.getenv("FLASK_CONFIG") or "default")
+migrate = Migrate(app, db)
+
+
+@app.shell_context_processor
+def make_shell_context():
+    return {"db": db, "Doi": Doi, "Url": Url}