Reply/feature

.env_example

@@ -10,8 +10,7 @@ SENTRY_DSN=
 PAPERSWITHCODE_USER=
 PAPERSWITHCODE_PASS=
 DB_URI=
-DB_URI=
 TWITTER_FREQ_HOURS=
 PAPERS_WITH_CODE_FREQ_HOURS=
 ARXIV_FREQ_HOURS=
-FRONTEND_URL=
+FRONTEND_URL=

README.md

@@ -3,20 +3,80 @@
 Read, collaborate and talk about scientific papers.
 
 ## Getting started
-1. Install Postgres
-2. Install `pandoc` to support references extraction from here: https://pandoc.org/installing.html
-3. Install `pdftotext` to support acronyms extraction: `sudo apt-get install poppler-utils`
-4. Create your Python 3.7 virtual env
-5. Create `.env` file based on the `.env_example` and fill out the values
-6. Run `flask fetch-papers` to grab some papers (you can stop the function after fetching ~200 papers) 
-7. Run `flask run`
-8. See `SciHive.postman_collection.json` for some examples of queries
 
+### 1) Install Postgres
+
+```
+podman run --name postgresql -p 5432:5432 -d postgres:latest
+```
+
+### Install pgadmin (optional)
+
+Change the default settings.
+
+```
+podman run --name pgadmin -p 5050:80 -e "PGADMIN_DEFAULT_EMAIL=pgadmin4@pgadmin.org" -e "PGADMIN_DEFAULT_PASSWORD=admin" -d dpage/pgadmin4
+```
+
+### 2) Install Pandoc
+
+Pandoc is needed to support references extraction. Installation can be found here: https://pandoc.org/installing.html.
+
+#### Archlinux
+```
+sudo pacman -S pandoc
+```
+
+### 3) Install pdftotext
+
+`pdftotext` is needed to support acronyms extraction.
+
+#### Archlinux
+```
+sudo pacman -S poppler
+```
+
+#### Ubuntu
+```
+sudo apt-get install poppler-utils
+```
+
+### 4) Configure a virtualenv
+
+```
+mkvirtualenv scihive
+workon scihive
+
+pip install -r requirements.txt
+```
+
+### 5) Set the configuration variables in the .env
+
+Create `.env` file based on the `.env_example` and fill out the values
+
+
+### 6) Prepare the backend
+
+Run `flask fetch-arxiv` to grab some papers (you can stop the function after fetching ~200 papers) 
+
+### 7) Run the backend
+
+To start the backend
+```
+flask run
+```
+
+To visualize the routes
+```
+flask routes
+```
+
+### 8) See `SciHive.postman_collection.json` for some examples of queries
 
 ## Production
 - Repeat steps 2-5
 - Run `sh restart_server.sh`
 
-###Changelog
+### Changelog
 
-- May 31, 2019 - Acronym extraction and enrichment (from other papers)
+- May 31, 2019 - Acronym extraction and enrichment (from other papers)

requirements.txt

@@ -16,6 +16,8 @@ flask-caching
 
 schedule
 
+bson
+
 boto3
 Flask-RESTful
 Flask-JWT-Extended
@@ -44,4 +46,4 @@ pep8
 pylint-flask
 pylint-flask-sqlalchemy
 sqlalchemy-easy-profile
-itsdangerous==1.1.0
+itsdangerous==1.1.0

src/main.py

@@ -14,6 +14,7 @@
 from flask_caching import Cache
 from .routes.paper import app as paper_routes
 from .routes.comments import app as comments_routes
+from .routes.replies import app as replies_routes
 from .routes.paper_list import app as paper_list_routes
 from .routes.user import app as user_routes
 from .routes.groups import app as groups_routes
@@ -77,6 +78,7 @@ def before_send(event, hint):
 
 app.register_blueprint(paper_list_routes, url_prefix='/papers')
 app.register_blueprint(paper_routes, url_prefix='/paper')
+app.register_blueprint(replies_routes, url_prefix='/reply')
 app.register_blueprint(comments_routes, url_prefix='/paper')
 app.register_blueprint(user_routes, url_prefix='/user')
 app.register_blueprint(groups_routes, url_prefix='/groups')
@@ -108,7 +110,6 @@ def background_tasks():
 def hello_world():
     return 'Hello, World!'
 
-
 @app.cli.command("migrate-db")
 @click.option('--path', help='folder path')
 def migrate_db(path):

src/routes/replies.py

@@ -0,0 +1,55 @@
+import logging
+from datetime import datetime
+
+from flask import Blueprint
+from flask_jwt_extended import get_jwt_identity, jwt_required
+from flask_restful import (Api, Resource, abort, fields, inputs, marshal_with, reqparse)
+from sqlalchemy import or_
+from typing import Optional
+from src.new_backend.models import Collection, Comment, Paper, Reply, db, User
+from .user_utils import get_user
+
+app = Blueprint('replies', __name__)
+api = Api(app)
+logger = logging.getLogger(__name__)
+
+replies_fields = {
+    'id': fields.String,
+    'user': fields.String(attribute='user.username'),
+    'text': fields.String,
+    'createdAt': fields.DateTime(dt_format='rfc822', attribute='creation_date'),
+}
+
+EMPTY_FIELD_MSG = 'This field cannot be blank'
+
+class ReplyResource(Resource):
+    method_decorators = [jwt_required]
+
+    def _get_reply(self, reply_id):
+
+        reply = Reply.query.get_or_404(reply_id)
+
+        user = get_user()
+
+        if reply.user != user:
+            abort(403, message='unauthorized to modify the reply')
+
+        return reply
+
+
+    @marshal_with(replies_fields, envelope='reply')
+    def post(self, reply_id):
+
+        reply = self._get_reply(reply_id)
+
+        edit_reply_parser = reqparse.RequestParser()
+        edit_reply_parser.add_argument('text', help=EMPTY_FIELD_MSG, type=str, location='json', required=False)
+        data = edit_reply_parser.parse_args()
+        reply.text = data['text']
+
+        db.session.commit()
+
+        return reply
+
+
+api.add_resource(ReplyResource, "/<reply_id>")