Merge pull request #1 from qresp-code-development/qresp-1.1

Qresp 1.1

.gitignore

@@ -5,3 +5,5 @@ web/flask_session/
 flask_session/
 web/dist/
 web/project/__pycache__/
+web/build/
+web/qresp.egg-info/

.travis.yml

@@ -1,13 +1,50 @@
 language: python
-python:
-  - "3.3"
-  - "3.4"
-  - "3.5"
-  - "3.6"
-# command to install dependencies
+matrix:
+    include:
+        - os: linux
+          python: 3.4
+          env: TOXENV=py34
+        - os: linux
+          python: 3.5
+          env: TOXENV=py35
+        - os: linux
+          python: 3.6
+          env: TOXENV=py36
+        - os: osx
+          env: PYTHON=3.4.4
+          language: generic
+
+before_install: |
+  if [ "$TRAVIS_OS_NAME" == "osx" ]; then
+    brew update
+    # Per the `pyenv homebrew recommendations <https://github.com/yyuu/pyenv/wiki#suggested-build-environment>`_.
+    brew install openssl readline
+    # See https://docs.travis-ci.com/user/osx-ci-environment/#A-note-on-upgrading-packages.
+    # I didn't do this above because it works and I'm lazy.
+    brew outdated pyenv || brew upgrade pyenv
+    # virtualenv doesn't work without pyenv knowledge. venv in Python 3.3
+    # doesn't provide Pip by default. So, use `pyenv-virtualenv <https://github.com/yyuu/pyenv-virtualenv/blob/master/README.md>`_.
+    brew install pyenv-virtualenv
+    pyenv install $PYTHON
+    # I would expect something like ``pyenv init; pyenv local $PYTHON`` or
+    # ``pyenv shell $PYTHON`` would work, but ``pyenv init`` doesn't seem to
+    # modify the Bash environment. ??? So, I hand-set the variables instead.
+    export PYENV_VERSION=$PYTHON
+    export PATH="/Users/travis/.pyenv/shims:${PATH}"
+    pyenv-virtualenv venv
+    source venv/bin/activate
+    # A manual check that the correct version of Python is running.
+    pip install --upgrade setuptools
+    python --version
+  fi
+
 install:
   - cd web
+  - pip install -r requirements.txt
   - python setup.py install
 # command to run tests
-#script:
-#  - pytest
+script:
+  - nose2 --with-coverage -v
+
+after_success:
+  - coveralls

README.md

@@ -1,3 +1,5 @@
+[![Build Status](https://travis-ci.org/qresp-code-development/qresp.svg?branch=master)](https://travis-ci.org/qresp-code-development/qresp)
+[![Coverage Status](https://coveralls.io/repos/github/qresp-code-development/qresp/badge.svg?branch=master)](https://coveralls.io/github/qresp-code-development/qresp?branch=master)
 # Qresp
 [Qresp](http://qresp.org) software repository. 
 

docker-compose.override.yml

@@ -16,4 +16,4 @@ services:
       - MAIL_PWD=<administrators password>
     volumes:
       - ./web/:/usr/src/app/web
-    command: flask run --host=0.0.0.0 --port 8080
+    command: python run.py --host=0.0.0.0 --port 8080

docker-compose.yml.services

@@ -0,0 +1,45 @@
+version: '2'
+
+services:
+  web:
+    restart: always
+    build: ./web
+    expose:
+      - 8080
+    ports:
+      - "8080:8080"
+    volumes:
+      - ./web/:/usr/src/app/web
+    environment:
+      - KEY=<insert key>
+      - GOOGLE_CLIENT_ID=<insert google client id>
+      - GOOGLE_CLIENT_SECRET=<insert google client secret>
+      - REDIRECT_URI=<insert redirect uri>
+      - MAIL_ADDR=<administrators mail address>
+      - MAIL_PWD=<administrators password>
+    command: python run.py --host=0.0.0.0 --port 8080
+
+  nginx:
+    restart: always
+    build: ./nginx
+    ports:
+      - "8001:8001"
+    volumes:
+      - /www/static
+      - ./papercollection:/usr/src/files
+    volumes_from:
+      - web
+    depends_on:
+      - web
+
+  mongodb:
+    image: mongo:latest
+    container_name: "mongodb"
+    environment:
+      - MONGO_DATA_DIR=/usr/data/db
+      - MONGO_LOG_DIR=/dev/null
+    volumes:
+      - ./data/db:/usr/data/db
+    ports:
+      - 27017:27017
+    command: mongod --smallfiles --logpath=/dev/null # --quiet

web/MANIFEST.in

@@ -1,2 +1,3 @@
 recursive-include project/templates *
-recursive-include project/static *
+recursive-include project/static *
+include project/swagger.yml

web/project/__init__.py

@@ -4,6 +4,7 @@
 from flask_session import Session
 from flask_wtf import CSRFProtect
 from flask_sitemap import Sitemap
+import connexion
 
 GOOGLE_CLIENT_ID = os.environ.get("GOOGLE_CLIENT_ID")
 GOOGLE_CLIENT_SECRET = os.environ.get("GOOGLE_CLIENT_SECRET")
@@ -21,9 +22,14 @@
 MONGODB_PASSWORD = os.environ.get("MONGODB_PASSWORD")
 MONGODB_DB = os.environ.get("MONGODB_DB")
 
+# Create the application instance
+connexionapp = connexion.App(__name__, specification_dir='./')
 
-app = Flask(__name__)
+# Read the swagger.yml file to configure the endpoints
+connexionapp.add_api('swagger.yml')
+app = connexionapp.app
 app.secret_key = '\\\xfcS\x1e\x8f\xfb]6\x1e.\xa8\xb3\xe1x\xc8\x8e\xc1\xeb5^x\x81\xcc\xd5'
+
 csrf = CSRFProtect(app)
 SESSION_TYPE = 'filesystem'
 app.config.from_object(__name__)

web/project/__main__.py

@@ -2,6 +2,16 @@
 # For desktop version running from command line
 
 from flask import Flask
-app = Flask(__name__,template_folder='project/templates')
+import connexion
+# Create the application instance
+connexionapp = connexion.App(__name__, specification_dir='./')
+
+# Read the swagger.yml file to configure the endpoints
+connexionapp.add_api('swagger.yml')
+app = connexionapp.app
 from .routes import main
-main()
+import sys
+port = 80
+if len(sys.argv)>1:
+    port = sys.argv[1]
+main(port)

web/project/api.py

@@ -0,0 +1,122 @@
+from .paperdao import *
+
+#edit swagger.yml file for method changes
+
+def search(searchWord=None,paperTitle=None,doi=None,tags=None,collectionList=None,authorsList=None,publicationList=None):
+    """
+    This function responds to a request for /api/search
+    with the complete lists of papers
+
+    :return:        list of papers
+    """
+    allpaperslist = []
+    try:
+        dao = PaperDAO()
+        if collectionList:
+            collectionList = collectionList.split(",")
+        if authorsList:
+            authorsList = authorsList.split(",")
+        if publicationList:
+            publicationList = publicationList.split(",")
+        allpaperslist = dao.getAllFilteredSearchObjects(searchWord=searchWord,paperTitle=paperTitle,doi=doi,
+                                                        tags=tags,collectionList=collectionList,
+                                                        authorsList=authorsList,publicationList=publicationList)
+    except Exception as e:
+        print("Exception in search", e)
+    return allpaperslist
+
+def collections():
+    """
+    This function responds to a request for /api/collections
+    with the complete lists of c
+
+    :return:        list of collections
+    """
+    allcollectionlist = []
+    try:
+        dao = PaperDAO()
+        allcollectionlist = dao.getCollectionList()
+    except Exception as e:
+        print("Exception in ", e)
+    return list(allcollectionlist)
+
+def authors():
+    """
+    This function responds to a request for /api/authors
+    with the complete lists of authors
+
+    :return:        list of authors
+    """
+    allauthorlist = []
+    try:
+        dao = PaperDAO()
+        allauthorlist = dao.getAuthorList()
+    except Exception as e:
+        print("Exception in ", e)
+    return list(allauthorlist)
+
+def publications():
+    """
+    This function responds to a request for /api/publications
+    with the complete lists of publications
+
+    :return:        list of publications
+    """
+    allpublist = []
+    try:
+        dao = PaperDAO()
+        allpublist = dao.getPublicationList()
+    except Exception as e:
+        print("Exception in ", e)
+    return list(allpublist)
+
+def paper(id):
+    """
+    This function responds to a request for /api/paper/{id}
+    with the details of paper given id
+
+    :return:        paper details object
+    """
+    paperdetail = None
+    try:
+        dao = PaperDAO()
+        paperdetail = dao.getPaperDetails(id)
+    except Exception as e:
+        msg = "Exception in paper api " + str(e)
+        print("Exception in paper api ", e)
+        return e, 400
+    return paperdetail
+
+def workflow(id):
+    """
+    This function responds to a request for /api/workflow/{id}
+    with the workflow given id
+
+    :return:        workflow object
+    """
+    workflowdetail = None
+    try:
+        dao = PaperDAO()
+        workflowdetail = dao.getWorkflowDetails(id)
+    except Exception as e:
+        msg = "Exception in workflow api " + str(e)
+        print("Exception in workflow api ", e)
+        return msg,400
+    return workflowdetail
+
+def chart(id,cid):
+    """
+    This function responds to a request for /api/paper/{id}/chart/{cid}
+    with the chart given id
+
+    :return:        chart object
+    """
+    chartworkflowdetail = None
+    try:
+        dao = PaperDAO()
+        chartworkflowdetail = dao.getWorkflowForChartDetails(id, cid)
+    except Exception as e:
+        msg = "Exception in chart api " + str(e)
+        print("Exception in chart api ", e)
+        return msg,400
+    return chartworkflowdetail

web/project/db.py

@@ -1,7 +1,7 @@
 from flask_mongoengine import MongoEngine
 from pymongo import errors
-
-from project import app
+from project import connexionapp
+app = connexionapp.app
 
 class MongoDBConnection():
     """Class representing connection to Mongo database

web/project/models.py

@@ -307,6 +307,12 @@ def year(self):
     def year(self, val):
         self.__year = val
 
+    def __hash__(self):
+        return hash(self.__title)
+
+    def __eq__(self, other):
+        return self.__title == other.__title
+
 
 class PaperDetails(object):
     def __init__(self):