Merge pull request #29 from qresp-code-development/develop

New Release, v2.0.0

.dockerignore

@@ -0,0 +1,6 @@
+__pycache__
+.pytest_cache
+.vscode
+.next
+flask_session
+node_modules

.gitignore

@@ -12,22 +12,20 @@ web/qresp.egg-info/
 web/project/config_test.ini 
 web/project/tests/__pycache__/
 
+Ignore Temp Files
+PREVIEW_*
+PUBLISH_*
 
 # VsCode
 .vscode/
 
 # Python
 __pycache__
 
-# Dev
-run_flask.sh
+# Pytest
+.pytest_cache
 
-
-=======
-# Python
-__pycache__
-
-# Dev Envs
-.vscode/
-run_flask.sh
-TexSamples/
+# Certificate Files
+*.certs
+*.crt
+*.key

.travis.yml

@@ -1,15 +1,15 @@
 language: python
 matrix:
-    include:
-        - os: linux
-          python: 3.5
-          env: TOXENV=py35
-        - os: linux
-          python: 3.6
-          env: TOXENV=py36
-        - os: linux
-          python: 3.7
-          env: TOXENV=py37
+  include:
+    - os: linux
+      python: 3.5
+      env: TOXENV=py35
+    - os: linux
+      python: 3.6
+      env: TOXENV=py36
+    - os: linux
+      python: 3.7
+      env: TOXENV=py37
 
 before_install: |
   if [ "$TRAVIS_OS_NAME" == "osx" ]; then
@@ -36,12 +36,12 @@ before_install: |
   fi
 
 install:
-  - cd web
+  - cd backend
   - pip install -r requirements.txt
   - python setup.py install
 # command to run tests
 script:
   - nose2 --with-coverage -v
 
 after_success:
-  - coveralls
+  - coveralls

AUTHORS.md

@@ -1,6 +1,6 @@
 This file lists the authors of the Qresp software as well as the known contributors.
 
-# Project Leads 
+# Project Leads
 
 - Marco Govoni (Argonne National Laboratory and University of Chicago)
 - Giulia Galli (University of Chicago and Argonne National Laboratory)
@@ -10,12 +10,13 @@ This file lists the authors of the Qresp software as well as the known contribut
 The current list of developers, in alphabetical order:
 
 - Marco Govoni (Argonne National Laboratory and University of Chicago)
-- Aditya Tanikanti (University of Chicago)
+- Sushant Bansal (University of Chicago)
 
 # Former Developers
 
 The former list of developers, in alphabetical order:
 
+- Aditya Tanikanti (2017-2019)
 - Milson Munakami (2017-2018)
 
 # Contributors

CHANGELOG.md

@@ -1,21 +1,31 @@
-Change Log
-==========
+# Change Log
 
-v1.2.2 (2020/09/25)
--------------------
+## v2.0.0 (2020/10/19)
+
+Major Update
+
+- Added new frontend service, using NextJS(React)
+    - Improved UI using Material UI
+    - Updated outdated packages
+    - Reduced external dependencies
+    - Fixed search by tags 
+    - And added various small quality of life improvements for users
+
+- Added new API routes, to publish and verify humans
+- Updated schema from v1.1 to v1.2, added new License field. 
+
+## v1.2.2 (2020/09/25)
 
 - Fixed bug impacting workflow hover info cards.
 - Updated File server parser to make compatible with new file server.
 
-v1.2.1 (2020/05/26)
--------------------
+## v1.2.1 (2020/05/26)
 
 - Fixed bug causing edit workflow functionality to break.
 - Fixed bugs breaking DOI minting.
 - Fixed python's package version incompatibilities causing build to break.
 
-v1.2.0 (2019/09/20)
--------------------
+## v1.2.0 (2019/09/20)
 
 - Updated Curator UI
 - Added Preview Functionality
@@ -26,8 +36,7 @@ v1.2.0 (2019/09/20)
 - Removed ssh connection and added Zenodo & HTTP connection
 - New unit tests
 
-v1.1.0 (2019/01/25)
--------------------
+## v1.1.0 (2019/01/25)
 
 - Fixed bugs related to port number
 - Fixed bugs related to DOI minting and search functionality
@@ -36,7 +45,6 @@ v1.1.0 (2019/01/25)
 - Added unit test cases
 - Added CI(Travis)
 
-v1.0.0 (2018/12/18)
--------------------
+## v1.0.0 (2018/12/18)
 
 - Initial Qresp release

backend/Dockerfile

@@ -0,0 +1,24 @@
+FROM python:3.6-alpine
+
+# Add to dump logs to file without buffering
+ENV PYTHONUNBUFFERED 1
+
+# install ca-certificates so that HTTPS works consistently
+# the other runtime dependencies for Python are installed later
+RUN apk add --no-cache ca-certificates
+
+# Create the working directory (and set it as the working directory)
+RUN mkdir -p /home/flask/app/web
+WORKDIR /home/flask/app/web
+
+# Install the package dependencies 
+RUN apk add --no-cache curl pkgconfig openssl-dev libffi-dev musl-dev make gcc libxslt-dev
+RUN pip install lxml
+
+
+COPY requirements.txt /home/flask/app/web
+RUN pip install --no-cache-dir -r requirements.txt
+
+# Copy the source code into the container
+COPY . /home/flask/app/web
+COPY project/static  /usr/src/app/web/project/static

backend/Dockerfile.dev

@@ -0,0 +1,24 @@
+FROM python:3.6-alpine
+
+# Add to dump logs to file without buffering
+ENV PYTHONUNBUFFERED 1
+
+# install ca-certificates so that HTTPS works consistently
+# the other runtime dependencies for Python are installed later
+RUN apk add --no-cache ca-certificates
+
+# Create the working directory (and set it as the working directory)
+RUN mkdir -p /home/flask/app/web
+WORKDIR /home/flask/app/web
+
+# Install the package dependencies 
+RUN apk add --no-cache curl pkgconfig openssl-dev libffi-dev musl-dev make gcc libxslt-dev
+RUN pip install lxml
+
+
+COPY requirements.txt /home/flask/app/web
+RUN pip install --no-cache-dir -r requirements.txt
+
+# Copy the source code into the container
+COPY . /home/flask/app/web
+COPY project/static  /usr/src/app/web/project/static

backend/dev_docs/Publish.md

@@ -0,0 +1,31 @@
+# Publish
+
+## How was it done
+
+In upto release 1.2.2, there was a strong dependence on Google services because that was the authentication/verification method.
+
+Basically, on publish we would ask the user to login using a google account and if successful we publish.
+
+## How it's done currently
+
+Now, we generate a publish link and send it to the user's email. And when the user clicks on that link in the mailm, it redirects to Qresp and the paper is published.
+
+## Why ?
+
+No Google dependence anymore, more fluent. We maintain most of the routes, people with their university emails can curate and publish.
+
+## Technically
+
+Let's talk about exaclt what'll happen when the user clicks the publish button
+
+### Flow
+
+1. On click, the data comes in a json format as defined in the schema at the route `/api/publish`. We store that data temporarily in the publish folder on disk (This needs to be database in the future, really).
+2. We process the data and send back a verify(or the actual) publish link to the curator via email.
+3. If there are any errors the user is provided with the error and no email is sent.
+
+4. The user clicks on the link in the url in the email and is redirected to the GUI of the instance. The link would be like `instance/publish/{id}`, the frontend then takes in the id, calls the api at `/api/verify/{id}`. This is where we nmotify the user that paper is successfully published or if there was error.
+
+## Contributing
+
+Always welcome, thanks. Suggestions, pull requests welcome. If you find a bug please, open on issue on Github.