From 3b34ddcb247b3a62d674c85f150f4c263e2b45b4 Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Wed, 9 Jan 2019 00:07:54 -0600
Subject: [PATCH 01/15] Added Swagger API support and moved API to logic to API
 files. Also added few inital unit tests

---
 .gitignore                                    |   2 +
 .travis.yml                                   |   4 +-
 web/project/__init__.py                       |  10 +-
 web/project/__main__.py                       |  15 +-
 web/project/api.py                            |  62 +++
 web/project/db.py                             |   4 +-
 web/project/models.py                         |   6 +
 web/project/paperdao.py                       |  10 +-
 web/project/routes.py                         |  97 ++--
 .../static/javascript/modules/search.js       |   4 +-
 web/project/swagger.yml                       | 150 +++++-
 web/project/templates/qrespexplorer.html      |  10 +-
 web/project/tests/__init__.py                 |   0
 .../tests/__pycache__/__init__.cpython-36.pyc | Bin 0 -> 149 bytes
 .../__pycache__/test_paperDAO.cpython-36.pyc  | Bin 0 -> 2022 bytes
 .../__pycache__/test_routes.cpython-36.pyc    | Bin 0 -> 914 bytes
 web/project/tests/data.json                   | 508 ++++++++++++++++++
 web/project/tests/test_paperDAO.py            |  72 +++
 web/project/tests/test_routes.py              |  24 +
 web/project/util.py                           |  34 ++
 web/project/views.py                          |   4 +
 web/requirements.txt                          |   6 +-
 web/run.py                                    |   6 +-
 web/setup.py                                  |   6 +-
 24 files changed, 930 insertions(+), 104 deletions(-)
 create mode 100644 web/project/api.py
 create mode 100644 web/project/tests/__init__.py
 create mode 100644 web/project/tests/__pycache__/__init__.cpython-36.pyc
 create mode 100644 web/project/tests/__pycache__/test_paperDAO.cpython-36.pyc
 create mode 100644 web/project/tests/__pycache__/test_routes.cpython-36.pyc
 create mode 100644 web/project/tests/data.json
 create mode 100644 web/project/tests/test_paperDAO.py
 create mode 100644 web/project/tests/test_routes.py

diff --git a/.gitignore b/.gitignore
index 3d637e3b..0ef78f98 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,5 @@ web/flask_session/
 flask_session/
 web/dist/
 web/project/__pycache__/
+web/build/
+web/qresp.egg-info/
diff --git a/.travis.yml b/.travis.yml
index 65f88949..1ffd9fdd 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,5 +9,5 @@ install:
   - cd web
   - python setup.py install
 # command to run tests
-#script:
-#  - pytest
+script:
+  - nose2
diff --git a/web/project/__init__.py b/web/project/__init__.py
index f0cfc4d7..753b89c6 100644
--- a/web/project/__init__.py
+++ b/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")
@@ -22,7 +23,13 @@
 MONGODB_DB = os.environ.get("MONGODB_DB")
 
 
-app = Flask(__name__)
+#app = Flask(__name__)
+# 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
 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'
@@ -47,5 +54,4 @@
 Session(app)
 ext = Sitemap(app)
 
-
 from project import routes
diff --git a/web/project/__main__.py b/web/project/__main__.py
index e0c7c7c3..859efd5a 100644
--- a/web/project/__main__.py
+++ b/web/project/__main__.py
@@ -2,6 +2,17 @@
 # For desktop version running from command line
 
 from flask import Flask
-app = Flask(__name__,template_folder='project/templates')
+import connexion
+#app = Flask(__name__)
+# Create the application instance
+connexionapp = connexion.App(__name__, specification_dir='./',template_folder='project/templates')
+
+# Read the swagger.yml file to configure the endpoints
+connexionapp.add_api('swagger.yml')
+app = connexionapp.app
 from .routes import main
-main()
\ No newline at end of file
+import sys
+port = 80
+if len(sys.argv)>1:
+    port = sys.argv[1]
+main(port)
\ No newline at end of file
diff --git a/web/project/api.py b/web/project/api.py
new file mode 100644
index 00000000..6bd87612
--- /dev/null
+++ b/web/project/api.py
@@ -0,0 +1,62 @@
+from .paperdao import *
+def search(searchWord=None,paperTitle=None,doi=None,tags=None,collectionList=[],authorsList=[],publicationList=[]):
+    """
+    This function responds to a request for /api/search
+    with the complete lists of papers
+
+    :return:        list of papers
+    """
+    allpaperslist = []
+    try:
+        dao = PaperDAO()
+        allpaperslist = dao.getAllFilteredSearchObjects(searchWord=searchWord,paperTitle=paperTitle,doi=doi,
+                                                        tags=tags,collectionList=collectionList,
+                                                        authorsList=authorsList,publicationList=publicationList)
+    except Exception as e:
+        print("Exception in ", 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)
\ No newline at end of file
diff --git a/web/project/db.py b/web/project/db.py
index 36bb1a19..60ffc938 100644
--- a/web/project/db.py
+++ b/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
diff --git a/web/project/models.py b/web/project/models.py
index 934cc4eb..5a1516b4 100644
--- a/web/project/models.py
+++ b/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):
diff --git a/web/project/paperdao.py b/web/project/paperdao.py
index dca03198..0c54aa88 100644
--- a/web/project/paperdao.py
+++ b/web/project/paperdao.py
@@ -40,8 +40,8 @@ def getAllPapers(self):
         allPapers = [paper.to_json() for paper in Paper.objects()]
         return allPapers
 
-    def getAllFilteredSearchObjects(self, searchWord, paperTitle, doi, tags, collectionList, authorsList,
-                                    publicationList):
+    def getAllFilteredSearchObjects(self, searchWord=None, paperTitle=None, doi=None, tags=None, collectionList=[], authorsList=[],
+                                    publicationList=[]):
         """
         Produces papers after filtering with word
         :param searchWord:
@@ -58,13 +58,13 @@ def getAllFilteredSearchObjects(self, searchWord, paperTitle, doi, tags, collect
             allFilteredSearchObjects = self.__filtersearchedPaper(filteredPaper)
         else:
             searchquery = Q()
-            if paperTitle.strip():
+            if paperTitle and paperTitle.strip():
                 searchTitleQuery = Q(reference__title__icontains=paperTitle)
                 searchquery = searchquery & searchTitleQuery
-            if doi.strip():
+            if doi and doi.strip():
                 searchdoiquery = Q(reference__DOI__icontains=doi)
                 searchquery = searchquery & searchdoiquery
-            if tags.strip():
+            if tags and tags.strip():
                 searchtagquery = Q(tags__icontains=tags)
                 searchquery = searchquery & searchtagquery
             if len(collectionList) > 0:
diff --git a/web/project/routes.py b/web/project/routes.py
index bb38b807..cc07d913 100644
--- a/web/project/routes.py
+++ b/web/project/routes.py
@@ -7,7 +7,6 @@
 import schedule
 from flask import render_template, request, flash, redirect, url_for, jsonify, session,send_file
 from project import csrf
-from project import app
 from project import ext
 import smtplib
 
@@ -16,7 +15,7 @@
 from .paperdao import *
 from .util import *
 from .views import *
-
+from project import app
 qresp_config = {}
 ftp_dict = {}
 
@@ -50,15 +49,6 @@ def closeConnection():
 
 
 
-@app.errorhandler(InvalidUsage)
-def handle_invalid_usage(error):
-    """ Returns error code
-    """
-    response = jsonify(error.to_dict())
-    response.status_code = error.status_code
-    return response
-
-
 @app.before_request
 def make_session_permanent():
     """ makes session values last for a day
@@ -72,31 +62,8 @@ def make_session_permanent():
 def index():
     """ Fetches the homepage
     """
-    dbAdmin = MongoDBConnection.getDB()
     return render_template('index.html')
 
-@ext.register_generator
-def index():
-    # Not needed if you set SITEMAP_INCLUDE_RULES_WITHOUT_PARAMS=True
-    yield 'index', {}
-    yield 'qrespexplorer', {}
-    yield 'paperdetails', {'paperid': '594186a91bd40fd4f2ce1aa0'}, {}
-    yield 'paperdetails', {'paperid': '5bb12835096ace7a9d8eb97d'}, {}
-    yield 'paperdetails', {'paperid': '5b3441242986382db00fab92'}, {}
-    yield 'paperdetails', {'paperid': '5b33a02629863800f82e297c'}, {}
-    yield 'paperdetails', {'paperid': '5b339eb029863800f82e297b'}, {}
-    yield 'paperdetails', {'paperid': '5b0ef8381f87c63760acb909'}, {}
-    yield 'paperdetails', {'paperid': '5a5e4e933a2c122ca8e9cd92'}, {}
-    yield 'paperdetails', {'paperid': '5ad8df0650cefd3974d05a83'}, {}
-    yield 'paperdetails', {'paperid': '5a5e437e3a2c122ca8e9cd75'}, {}
-    yield 'paperdetails', {'paperid': '5950fbfc1bd40f6cb67fb939'}, {}
-    yield 'paperdetails', {'paperid': '5992072a7590617df5a88a85'}, {}
-    yield 'paperdetails', {'paperid': '5983afce759061384c1aae48'}, {}
-    yield 'paperdetails', {'paperid': '594c507f1bd40f5ebf185fde'}, {}
-    yield 'paperdetails', {'paperid': '594c50671bd40f5e9b5c043b'}, {}
-    yield 'paperdetails', {'paperid': '594c504a1bd40f5e7819a0aa'}, {}
-
-
 @app.route('/downloads/<file>')
 def downloadfile(file=None):
     if file:
@@ -109,14 +76,6 @@ def downloadfile(file=None):
             return jsonify(msg),400
 
 
-
-@app.route('/qrespexplorer')
-def qrespexplorer():
-    """ Fetches the explorer homepage
-    """
-    serverslist = Servers()
-    return render_template('qrespexplorer.html', serverslist=serverslist.getServersList())
-
 @app.route('/qrespcurator')
 def qrespcurator():
     """ Fetches the curator homepage
@@ -759,6 +718,25 @@ def acknowledgement():
 
 ########################################EXPLORER#############################################################################
 
+@csrf.exempt
+@app.route('/qrespexplorer',methods=['GET','POST'])
+def qrespexplorer():
+    """ Fetches the explorer homepage
+    """
+    dao = PaperDAO()
+    dao.getDB()
+    form = QrespServerForm()
+    serverslist = Servers()
+    form.serverList = [qrespserver['qresp_server_url'] for qrespserver in
+                           serverslist.getServersList()]
+    form.serverList.append('http://localhost')
+    if request.method == 'POST':
+        if request.form.get('serversList'):
+            session["selectedserver"] = request.form.get('serversList')
+        else:
+            session['selectedserver'] = form.serverList
+        return redirect(url_for('search'))
+    return render_template('qrespexplorer.html', form=form)
 
 @csrf.exempt
 @app.route('/verifyPasscode',methods=['POST'])
@@ -815,19 +793,21 @@ def search():
     """  This method helps in filtering paper content
     :return: template: search.html
     """
+    allpaperslist = []
     try:
-        dao = PaperDAO()
-        allpaperslist = dao.getAllFilteredSearchObjects("", "", "", "", "", "", "")
-        if not allpaperslist:
-            allpaperslist = []
-        return render_template('search.html',
-                               collectionlist=dao.getCollectionList(), authorslist=dao.getAuthorList(),
-                               publicationlist=dao.getPublicationList(), allPapersSize=len(dao.getAllSearchObjects()),
-                               allpaperslist = allpaperslist)
+        selectedserver = session.get("selectedserver")
+        fetchdata = FetchDataFromAPI(selectedserver)
+        allpaperslist = fetchdata.fetchOutput('/api/search')
+        collectionlist = fetchdata.fetchOutput('/api/collections')
+        authorslist = fetchdata.fetchOutput('/api/authors')
+        publicationlist = fetchdata.fetchOutput('/api/publications')
+        allPapersSize = len(allpaperslist)
     except Exception as e:
         print(e)
         flash('Error in search. ' + str(e))
-        return render_template('search.html',allpaperslist=[])
+        return render_template('search.html', allpaperslist=allpaperslist)
+    return render_template('search.html',allpaperslist=allpaperslist,collectionlist=collectionlist,authorslist=authorslist,
+                           publicationlist=publicationlist,allPapersSize=allPapersSize)
 
 
 # Fetches search word options after selecting server
@@ -846,8 +826,12 @@ def searchWord():
         collectionList = json.loads(request.args.get('collectionList'))
         authorsList = json.loads(request.args.get('authorsList'))
         publicationList = json.loads(request.args.get('publicationList'))
-        allpaperslist = dao.getAllFilteredSearchObjects(searchWord, paperTitle, doi, tags, collectionList, authorsList,
-                                                        publicationList)
+        selectedserver = session.get("selectedserver")
+        fetchdata = FetchDataFromAPI(selectedserver)
+        url = '/api/search' + "?searchWord=" + searchWord
+        # url = '/api/search'+"?searchWord="+searchWord+"&paperTitle="+paperTitle+"&doi="+doi+"&tags="+tags+"&collectionList="+",".join(collectionList) + \
+        #       "&authorsList="+",".join(authorsList)+"&publicationList="+",".join(publicationList)
+        allpaperslist = fetchdata.fetchOutput(url)
         return jsonify(allpaperslist=allpaperslist)
     except Exception as e:
         print(e)
@@ -897,6 +881,9 @@ def chartworkflow():
 @csrf.exempt
 @app.route('/getDescriptor', methods=['POST','GET'])
 def getDescriptor():
+    """
+    Inserts and fetches the metadata into Papers collections
+    """
     try:
         data = request.get_json()
         paper = data.get("metadata")
@@ -927,7 +914,7 @@ def mint():
     """
     return render_template('mint.html')
 
-def main():
+def main(port):
     app.secret_key = '\xfd{H\xe5<\x95\xf9\xe3\x96.5\xd1\x01O<!\xd5\xa2\xa0\x9fR"\xa1\xa8'
     CORS(app)
-    app.run(port=80, debug=False)
\ No newline at end of file
+    app.run(port=port, debug=False)
\ No newline at end of file
diff --git a/web/project/static/javascript/modules/search.js b/web/project/static/javascript/modules/search.js
index 1c60a4f2..55a4c424 100644
--- a/web/project/static/javascript/modules/search.js
+++ b/web/project/static/javascript/modules/search.js
@@ -127,13 +127,13 @@ function buildTable(allPapers) {
                     var downloads = "<li><a href='" + row["_Search__downloadPath"] + "' title='Download' target='_blank'><img src='static/images/download-icon.png' alt='download'></a></li>";
                     var notebookPath = row["_Search__notebookPath"];
                     var notebookFile = row["_Search__notebookFile"];
-                    if (notebookPath !== "") {
+                    if (notebookPath !==undefined  && notebookPath !== "") {
                         if (notebookPath.indexOf('notebooks') < 0) {
                             notebookPath = notebookPath.replace(/^(https?:\/\/)?(www\.)?/, '');
                             notebookPath = "http://nbviewer.jupyter.org/url/" + notebookPath;
                         }
                     }
-                    if (notebookFile !== undefined || notebookFile !== null || notebookFile !== "") {
+                    if (notebookFile !== undefined && notebookFile !== null && notebookFile !== "") {
                         notebookPath = notebookPath + "/" + notebookFile;
                     }
                     var notebooks = "<li><a href='" + notebookPath + "' title='Jupyter Notebook' target='_blank'> <img src='static/images/jupyter.png' alt='jupyter'></a></li>";
diff --git a/web/project/swagger.yml b/web/project/swagger.yml
index 7c97dc4d..a5983efb 100644
--- a/web/project/swagger.yml
+++ b/web/project/swagger.yml
@@ -1,7 +1,7 @@
 swagger: "2.0"
 info:
-  description: This is the swagger file that goes with our server code
-  version: "1.0.0"
+  description: This is the swagger file that provides the API to fetch data from Qresp server
+  version: "1.0"
   title: Swagger REST Article
 consumes:
   - "application/json"
@@ -10,25 +10,127 @@ produces:
 
 basePath: "/api"
 
-## Paths supported by the server application
-#paths:
-#  /people:
-#    get:
-#      operationId: "people.read"
-#      tags:
-#        - "People"
-#      summary: "The people data structure supported by the server application"
-#      description: "Read the list of people"
-#      responses:
-#        200:
-#          description: "Successful read people list operation"
-#          schema:
-#            type: "array"
-#            items:
-#              properties:
-#                fname:
-#                  type: "string"
-#                lname:
-#                  type: "string"
-#                timestamp:
-#                  type: "string"
\ No newline at end of file
+# Paths supported by the server application
+paths:
+  /search:
+    get:
+      operationId: "project.api.search"
+      tags:
+        - "Papers"
+      summary: "Fetches all papers"
+      description: "Read the list of papers"
+      parameters:
+        - in: query
+          name: searchWord
+          type: string
+          required: false
+          description: Filter paper results based on search word
+        - in: query
+          name: paperTitle
+          type: string
+          required: false
+          description: Filter paper results based on paper title
+        - in: query
+          name: doi
+          type: string
+          required: false
+          description: Filter paper results based on paper doi
+        - in: query
+          name: tags
+          type: string
+          required: false
+          description: Filter paper results based on paper tags
+        - in: query
+          name: collectionList
+          type: array
+          required: false
+          description: Filter paper results based on collection
+        - in: query
+          name: authorsList
+          type: array
+          required: false
+          description: Filter paper results based on authors
+        - in: query
+          name: publicationList
+          required: false
+          type: array
+          description: Filter paper results based on publication
+      responses:
+        200:
+          description: "Successful read papers list operation"
+          schema:
+            type: "array"
+            items:
+              properties:
+                _Search__abstract:
+                  type: "string"
+                _Search__authors:
+                  type: "string"
+                _Search__collections:
+                  type: "array"
+                _Search__doi:
+                  type: "string"
+                _Search__downloadPath:
+                  type: "string"
+                _Search__fileServerPath:
+                  type: "string"
+                _Search__folderAbsolutePath:
+                  type: "string"
+                _Search__id":
+                  type: "string"
+                _Search__notebookFile:
+                  type: "string"
+                _Search__notebookPath:
+                  type: "string"
+                _Search__publication:
+                  type: "string"
+                _Search__serverPath:
+                  type: "string"
+                _Search__tags:
+                  type: "array"
+                _Search__title:
+                  type: "string"
+                _Search__year:
+                  type: "integer"
+  /collections:
+    get:
+      operationId: "project.api.collections"
+      tags:
+        - "Collections"
+      summary: "Fetches all collections"
+      description: "Read the list of collections"
+      responses:
+        200:
+          description: "Successful read collections list operation"
+          schema:
+            type: "array"
+            items:
+                type: "string"
+  /authors:
+    get:
+      operationId: "project.api.authors"
+      tags:
+        - "Authors"
+      summary: "Fetches all authors"
+      description: "Read the list of authors"
+      responses:
+        200:
+          description: "Successful read authors list operation"
+          schema:
+            type: "array"
+            items:
+                type: "string"
+  /publications:
+    get:
+      operationId: "project.api.publications"
+      tags:
+        - "Publications"
+      summary: "Fetches all publications"
+      description: "Read the list of publications"
+      responses:
+        200:
+          description: "Successful read publications list operation"
+          schema:
+            type: "array"
+            items:
+                type: "string"
\ No newline at end of file
diff --git a/web/project/templates/qrespexplorer.html b/web/project/templates/qrespexplorer.html
index 67d205c2..06dcff0a 100644
--- a/web/project/templates/qrespexplorer.html
+++ b/web/project/templates/qrespexplorer.html
@@ -5,11 +5,11 @@
      <div class="card">
         <div class="card-body">
             <h2 data-toggle="tooltip" class="card-title" style="text-align: center;"> Select Qresp node to search </h2>
-                    <form action="{{ url_for('search') }}" method="post" class="text-center">
-                        <select name="serversList" id="serversList" class="selectpicker show-tick form-control"
-                                data-width="auto" data-actions-box="true" multiple data-live-search="true">
-                            {% for server in serverslist %}
-                                <option value="{{ server.qresp_server_url }}">{{ server.qresp_server_url }}</option>
+                    <form method="post" class="text-center">
+                        <select name="serversList" id="serversList" multiple="multiple" class="selectpicker show-tick form-control"
+                                data-width="80%" data-actions-box="true" multiple data-live-search="true">
+                            {% for server in form.serverList %}
+                                <option value="{{ server }}">{{ server }}</option>
                             {% endfor %}
                         </select>
                         <input type="submit" id="btnSearch"
diff --git a/web/project/tests/__init__.py b/web/project/tests/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/web/project/tests/__pycache__/__init__.cpython-36.pyc b/web/project/tests/__pycache__/__init__.cpython-36.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..a487519c40812ca491e14b70d00cbda4c359eeab
GIT binary patch
literal 149
zcmXr!<>fL8(~V&Og2x~N1{i@12OutH0TL+;!3>&=ek&P@K*9*(my@$qOlWaxQE^OS
zN@j^kOh9FFMq*KJKv8~HYH~?&Okh!JaY0OZYEn!AL@1^twHPQKAD@|*SrQ+wS5SG2
T!zMRBr8Fni4rF#Q5HkP()SV^d

literal 0
HcmV?d00001

diff --git a/web/project/tests/__pycache__/test_paperDAO.cpython-36.pyc b/web/project/tests/__pycache__/test_paperDAO.cpython-36.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..eacd236120d589fb5ed816e08d348a7f1957184f
GIT binary patch
literal 2022
zcmbtV&2Jnv6u0MlHyfHnp}p`iQlT&@By9mzDhRdRNWH)|rKzY!D~%>=Z!(kFnZfoF
zy4sw!M+$!j|B|nq_!l_wo_8}@!g8ude)c>+zmMO0w!c_kZ@>BVt9}#^@+Vnp4$L1y
zmn9HJ7%fPQqg9X*jVZ;sU08?nH9NMAj1xO%bYqt}%zaH_&;0wb&pqxZ-V?$+=D#M)
z=X7Sr0dKM3)Dk%-d3#1cD}7F))?Z+g^dhQ*LoQV}l^o`DXMk*M7IX^zDRhaRG6LIZ
z?++4L+DXN+)ZXbCjsjN=`TI%tLH~v1LiSUZsW1BnuLdWn7#)Zz=L04C&jgos|BN5?
z>p82hz_>ItsneQ^{YOuC>sQ(V&83f~(GNleU`HC?kcIq*(B)@9IEg7EvBfB}01%tm
z%z+W$VIGVw^H~6+$663WTX!(zgN3;PMv2XZ-iF?VE~h{g$tk1CV%Cg;M$n1+nE%G7
zMA^BMyM}r|{n?xosMd_mK>nPn_I!0pS%941H_k1!mUpJOYX1nSeMWvDFNs<olBxY0
zJ$I%~{*FnIjR~6Uw8KSv&Xo+ub;wec9zmu;RfPy#BQSY)RF%ios2ZF;*xM_rL0X(t
zQfc?z{X2K>_u^}2nU}{|$#J804cOZ1Rgtd)lr7T{*G^ptrGqh~(EJB=D&<)vnD*F_
z;j{-;Q9v%Us?=^Kr7R{bbZa-4RT*8=o8O}&`;WU-Szd@8bG83i+gYi!RY@?CsuLXu
zo)%{2<W*K`52OZXO#3Wb*iMpRR`4XzPF3?#J7_^WMU^t`n&fFmra$w@g^?G-xRWFp
zIl2a$=uo#zkm#LQgLGcjsldw8uH@=Py^h)5211+;b>IuAN8h8{blYmv$<}hE?3xWt
zz1Xk^yQ!BDCW_3+Ii1p+!e~uNZYdkHJ;S4nht8VZX;OxYWta`av?#($P-Vz}$(AzP
ziyR$Xl&anYkh)C*z5_wsh756`4#gPKR{$rn#Z7QV+bpg0CTPD@j>}h3xQ_LZ{73Km
zph9{;h~ohylbinnV)dT4Lgv#e$P6nH*5jihn`cxu%YcaZ1Owaxrw=YA5DgK*g4hAF
zKtbGwdAtQEEa_SW!;OoOu4w!i_Ale`(MlYyY<epoZZ(mjDH$RVSR<yGSHRE#7#<ac
zsS)`<0JIPQyziDS>-izryokF|@%fdAKUf)YBi_RcBuVgcfK%5_l2OIR=Gek{{ArvP
z^A&Lm)C$xs_K@5~(mWjV8J<ef0@8sl@x~8mun|BrTr@LEGdSGQ8r)H3rqFkR4?(=K
zcu#gslu-HN2C#LjxfaET@NZrb9pKxNmGE$(EpZP89aOx^A02!%59nKbCggP>0qwwv
OSbP>-7uLqt0sRMpL<aHz

literal 0
HcmV?d00001

diff --git a/web/project/tests/__pycache__/test_routes.cpython-36.pyc b/web/project/tests/__pycache__/test_routes.cpython-36.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..4da16b65961ef54a54fe1d180ac4adb69964c90b
GIT binary patch
literal 914
zcmZuvJ#X7E5GAP(v$hjB$<(#zq9q;LEJYC%b%Sh1+B%CMfM7)?wJS>sNyA9sPR`Py
zKcxSpzkyrPDSshT?<6~QfC|v*jz_-t_)af(cDld6A7w|3kUwPW2_b(AuYCtW5k(7<
zwqKf3s9C{gK^jnUN>rf2TcScur{O9{BOR;gD>KJXcUFYL*-s>i?*NC466yn4*EtrO
z2dG=B=a6WE@F`PNv0IV`EqEHLNX1Y`ssmu$cRyBhr^nhlo6|KAei3U3uib^<$ds<g
zk_ZqEr|2kQ1~>SggM%V3Cc1Q>D73n`_(@C*z5A2l>+IZWV>78H?p1bnoqv&Lc4n%n
z&YjIZ7;Wopp+9GJyObfAZK5!!${yC&KC;@K*L{?Nl!V?4{z*P;nvaB|_(nJyzn0qw
zN~noosma^WfzorQrFma1$^ldxii0hRP5*%fWgvLN@(hwCnSw!Rv<iN(Zxm{_q*IvY
ziow*-vS@TqUyKu)4lb&qs20L#H8JSJ-7i2$!q(5=Qaj(17Ho4TS94kTo^{gAt;j2-
z!F9ZW=jdEj!X`9&>n^*^IA(HEidtUk1L#^*O6Y*zJbiR07~8|XQ4)JDL@8%l2;UWA
zR;hV`d0z-r(RK_+wkH_St1a?I2D)hi2v}JRJmw(}nl;34_yqiOtg@cZ%ZWp|zOx>G
n>i{3a+EBvX5X$U9@FAZ3AD!oKTB*l4b=yTw%2}W7?{WGU1$)#8

literal 0
HcmV?d00001

diff --git a/web/project/tests/data.json b/web/project/tests/data.json
new file mode 100644
index 00000000..2ffe18b2
--- /dev/null
+++ b/web/project/tests/data.json
@@ -0,0 +1,508 @@
+{
+   "PIs":[
+      {
+         "firstName":"Giulia",
+         "lastName":"Galli"
+      }
+   ],
+   "charts":[
+      {
+         "caption":" Experimental PE spectrum of a 1 M solution of NaCl and molecular orbitals of a single water molecule corresponding to specific bands in the spectrum. The background due to secondary electrons has been subtracted following ref 11. The sharp peak at 12.6 eV arises from ionization of the 1b1 orbital of gas-phase water.",
+         "files":[
+            "charts/figure1/winter_exp.txt"
+         ],
+         "id":"c0",
+         "imageFile":"charts/figure1/fig1.png",
+         "kind":"figure",
+         "notebookFile":"charts/figure1/plot.ipynb",
+         "number":"1",
+         "properties":[
+            "electron binding energy",
+            "photo-electron spectrum"
+         ]
+      },
+      {
+         "caption":"PE spectra of a 1 M aqueous NaCl solution computed with density functional approximations compared to the experimental spectrum of Figure 1. The gray area under the spectral features of sodium (2p) and chloride (3p) is the DOS projected on the maximally localized Wannier functions centered on the ionic sites. Theoretical spectra were aligned to the vacuum level (see text and Table SI).",
+         "files":[
+            "charts/figure2/winter_exp.txt",
+            "charts/figure2/pdos_pbe.txt",
+            "charts/figure2/pdos_pbe0.txt",
+            "charts/figure2/pdos_rsh.txt",
+            "charts/figure2/pdos_sc.txt"
+         ],
+         "id":"c1",
+         "imageFile":"charts/figure2/fig2.png",
+         "kind":"figure",
+         "notebookFile":"charts/figure2/plot.ipynb",
+         "number":"2",
+         "properties":[
+            "density of states",
+            "photo-electron spectrum"
+         ]
+      },
+      {
+         "caption":"PE spectra of a 1 M aqueous NaCl solution computed using the G0W0 approximation starting from different sets of eigenfunctions and eigenvalues. Each theoretical spectrum is from a single snapshot representative of the entire trajectory. The spectra were aligned to the vacuum level (see text and SI). The gray area is projected DOS on Na and Cl atoms defined in Figure 2 caption.",
+         "files":[
+            "charts/figure3/winter_exp.txt",
+            "charts/figure3/pdos_pbe_GW.txt",
+            "charts/figure3/pdos_pbe0_GW.txt",
+            "charts/figure3/pdos_rsh_GW.txt",
+            "charts/figure3/pdos_sc_GW.txt"
+         ],
+         "id":"c2",
+         "imageFile":"charts/figure3/fig3.png",
+         "kind":"figure",
+         "notebookFile":"charts/figure3/plot.ipynb",
+         "number":"3",
+         "properties":[
+            "density of states",
+            "photo-electron spectrum"
+         ]
+      },
+      {
+         "caption":"Experimental (black) and theoretical (blue) PE spectra of a 1 M aqueous solution of NaCl. Theoretical spectrum was computed using G0W0/sc-hybrid line widths and experimental photoionization cross sections as explained in the SI. Both spectra were normalized to the 1b1 peak of water. The gray area is projected DOS on Na and Cl atoms (see Figure 2 caption).",
+         "files":[
+            "charts/figure4/winter_exp.txt",
+            "charts/figure4/pdos_GW_Banna_115eV+Yeh_ions_200eV.txt",
+            "charts/figure4/pdos_pbe0_GW.txt",
+            "charts/figure4/pdos_rsh_GW.txt",
+            "charts/figure4/pdos_sc_GW.txt"
+         ],
+         "id":"c3",
+         "imageFile":"charts/figure4/fig4.png",
+         "kind":"figure",
+         "notebookFile":"charts/figure4/plot.ipynb",
+         "number":"4",
+         "properties":[
+            "density of states",
+            "photo-electron spectrum"
+         ]
+      },
+      {
+         "caption":"Electron BE in PE Spectra of a 1 M NaCl Solution Computed Using DFT and Many-Body Perturbation Theory at the G0W0 Level",
+         "files":[
+            "charts/table1/dos.ods"
+         ],
+         "id":"c4",
+         "imageFile":"charts/table1/table1.png",
+         "kind":"table",
+         "notebookFile":"charts/table1/plot.ipynb",
+         "number":"1",
+         "properties":[
+            "electron binding energy",
+            "photo-electron spectrum"
+         ]
+      }
+   ],
+   "collections":[
+      "MICCoM"
+   ],
+   "datasets":[
+      {
+         "files":[
+            "charts/figure1"
+         ],
+         "id":"d0",
+         "readme":"Processed experimental spectrum from Winters and Siedel and orbital image files -- processing of experimental data unknown"
+      },
+      {
+         "files":[
+            "data/input"
+         ],
+         "id":"d1",
+         "readme":"Example input files for dft pw.x calculations, MLWF calculations and WEST G0W0 calculations."
+      },
+      {
+         "files":[
+            "data/s10"
+         ],
+         "id":"d2",
+         "readme":"electronic structure outputs at various levels of theory (pbe, pbe0, rsh, sc-hybrid, G0W0@pbe, G0W0@pbe0, G0W0@rsh, G0W0@sc-hybrid) along with MLWF outputs at the same levels of theory. Each subfolder geometry in the s10 subfolder contains a geometry obtained as a snapshot sxxxx from a PBE0 MD trajectory of 1M salt water."
+      },
+      {
+         "files":[
+            "data/s15"
+         ],
+         "id":"d3",
+         "readme":"electronic structure outputs at various levels of theory (pbe, pbe0, rsh, sc-hybrid, G0W0@pbe, G0W0@pbe0, G0W0@rsh, G0W0@sc-hybrid) along with MLWF outputs at the same levels of theory. Each subfolder geometry in the s15 subfolder contains a geometry obtained as a snapshot sxxxx from a PBE0 MD trajectory of 1M salt water."
+      }
+   ],
+   "heads":[
+      {
+         "URLs":[
+            ""
+         ],
+         "id":"h0",
+         "readme":"Experimental setup info"
+      },
+      {
+         "URLs":[
+            "http://www.quantum-simulation.org/reference/nacl/index.htm"
+         ],
+         "id":"h1",
+         "readme":"NACL2016 dataset: NVT s10 simulation data"
+      },
+      {
+         "URLs":[
+            "http://www.quantum-simulation.org/reference/nacl/index.htm"
+         ],
+         "id":"h2",
+         "readme":"NACL2016 dataset: NVT s15 simulation data"
+      }
+   ],
+   "info":{
+      "downloadPath":"https://www.globus.org/app/transfer?origin_id=72277ed4-1ad3-11e7-bbe1-22000b9a448b&origin_path=jacs.6b00225",
+      "fileServerPath":"http://notebook.rcc.uchicago.edu/files/jacs.6b00225",
+      "folderAbsolutePath":"/cds/gagalli/DATA_COLLECTIONS/public/jacs.6b00225",
+      "insertedBy":{
+         "firstName":"Jonathan",
+         "lastName":"Skone",
+         "middleName":"H."
+      },
+      "isPublic":true,
+      "notebookFile":"Main.ipynb",
+      "notebookPath":"http://notebook.rcc.uchicago.edu/notebooks/jacs.6b00225",
+      "serverPath":"midway.rcc.uchicago.edu",
+      "timeStamp":"2017-06-22 18:19:02"
+   },
+   "reference":{
+      "DOI":"10.1021/jacs.6b00225",
+      "authors":[
+         {
+            "firstName":"Alex",
+            "lastName":"Gaiduk"
+         },
+         {
+            "firstName":"Marco",
+            "lastName":"Govoni"
+         },
+         {
+            "firstName":"Robert",
+            "lastName":"Siedel"
+         },
+         {
+            "firstName":"Jonathan",
+            "lastName":"Skone",
+            "middleName":"H."
+         },
+         {
+            "firstName":"Bernd",
+            "lastName":"Winter"
+         },
+         {
+            "firstName":"Giulia",
+            "lastName":"Galli"
+         }
+      ],
+      "journal":{
+         "abbrevName":"JACS Comm.",
+         "fullName":"Journal of the American Chemical Society"
+      },
+      "kind":"article",
+      "page":"6912",
+      "publishedAbstract":"We present a combined computational and experimental study of the photoelectron spectrum of a simple aqueous solution of NaCl. Measurements were conducted on microjets, and first-principles calculations were performed using hybrid functionals and many-body perturbation theory at the G0W0 level, starting with wave functions computed in ab initio molecular dynamics simulations. We show excellent agreement between theory and experiments for the positions of both the solute and solvent excitation energies on an absolute energy scale and for peak intensities. The best comparison was obtained using wave functions obtained with dielectric-dependent self-consistent and range-separated hybrid functionals. Our computational protocol opens the way to accurate, predictive calculations of the electronic properties of electrolytes, of interest to a variety of energy problems.",
+      "publishedDate":"2016-04-22 00:00:00",
+      "receivedDate":"2016-01-08 00:00:00",
+      "title":"Photoelectron spectra of aqueous solutions from first principle",
+      "volume":"138",
+      "year":2016
+   },
+   "scripts":[
+      {
+         "files":[
+            "charts/figure1/pes.plt"
+         ],
+         "id":"s0",
+         "readme":"gnuplot script to generate experimental PES plot of water overlayed with the orbitals for each DOS peak"
+      },
+      {
+         "files":[
+            "scripts/coords.sh"
+         ],
+         "id":"s1",
+         "readme":"extract atomic coordinates from Qbox output files"
+      },
+      {
+         "files":[
+            "scripts/mksam.sh"
+         ],
+         "id":"s2",
+         "readme":"make sample"
+      },
+      {
+         "files":[
+            "scripts/pdos.sh"
+         ],
+         "id":"s3",
+         "readme":"evaluate projected-density of states from wannier localized orbitals"
+      },
+      {
+         "files":[
+            "scripts/average.sh"
+         ],
+         "id":"s4",
+         "readme":"compute average of some quantity"
+      },
+      {
+         "files":[
+            "scripts/pdos-GW.sh"
+         ],
+         "id":"s5",
+         "readme":"projected density of states for GW calculations"
+      },
+      {
+         "files":[
+            "scripts/pdos+intensities.sh"
+         ],
+         "id":"s6",
+         "readme":"evaluate the projected density of states intensities"
+      },
+      {
+         "files":[
+            "scripts/detmax.sh"
+         ],
+         "id":"s7",
+         "readme":"determine maximum peak location"
+      },
+      {
+         "files":[
+            "charts/figure2/dft.plt"
+         ],
+         "id":"s8",
+         "readme":"gnuplot script to plot the experimental PES of salt water overlayed with theoretical DOS evaluated at several DFT levels of theory"
+      },
+      {
+         "files":[
+            "charts/figure3/gw.plt"
+         ],
+         "id":"s9",
+         "readme":"gnuplot script to plot the experimental PES of salt water overlayed with theoretical DOS evaluated at GW@dft level of theory where dft is several dft levels of theory"
+      },
+      {
+         "files":[
+            "charts/figure4/sc_intensity_Banna_115eV.plt"
+         ],
+         "id":"s10",
+         "readme":"gnuplot script to plot the experimental PES of salt water overlayed with theoretical DOS evaluated at GW@sc-hybrid level of theory"
+      }
+   ],
+   "tags":[
+      "DFT",
+      "MBPT",
+      "GW",
+      "PES",
+      "photo electron spectra",
+      "band edges",
+      "density of states",
+      "water",
+      "FPMD",
+      "Qbox",
+      "WEST"
+   ],
+   "tools":[
+      {
+         "URLs":[
+            "https://www.helmholtz-berlin.de/pubbin/igama_output?modus=einzel&sprache=en&gid=1648&typoid"
+         ],
+         "facilityName":"Helmholtz-Zentrum Berlin",
+         "id":"t0",
+         "kind":"experiment",
+         "measurement":"soft X-ray Photoemission"
+      },
+      {
+         "URLs":[
+            "http://www.quantum-espresso.org/"
+         ],
+         "id":"t1",
+         "kind":"software",
+         "packageName":"Quantum-Espresso",
+         "programName":"pw.x",
+         "version":"5.2"
+      },
+      {
+         "URLs":[
+            "http://www.west-code.org"
+         ],
+         "id":"t2",
+         "kind":"software",
+         "packageName":"West",
+         "programName":"wstat.x",
+         "version":"2.0.0"
+      },
+      {
+         "URLs":[
+            "http://www.west-code.org"
+         ],
+         "id":"t3",
+         "kind":"software",
+         "packageName":"West",
+         "programName":"wfreq.x",
+         "version":"2.0.0"
+      }
+   ],
+   "workflow":{
+      "edges":[
+         [
+            "s4",
+            "s6"
+         ],
+         [
+            "s4",
+            "s9"
+         ],
+         [
+            "s4",
+            "s8"
+         ],
+         [
+            "s4",
+            "s7"
+         ],
+         [
+            "s9",
+            "c2"
+         ],
+         [
+            "d3",
+            "s5"
+         ],
+         [
+            "d3",
+            "s3"
+         ],
+         [
+            "s5",
+            "s4"
+         ],
+         [
+            "s2",
+            "d1"
+         ],
+         [
+            "t3",
+            "d2"
+         ],
+         [
+            "t3",
+            "d3"
+         ],
+         [
+            "s0",
+            "c0"
+         ],
+         [
+            "h1",
+            "s1"
+         ],
+         [
+            "s6",
+            "s10"
+         ],
+         [
+            "s8",
+            "c1"
+         ],
+         [
+            "s3",
+            "s4"
+         ],
+         [
+            "d2",
+            "s5"
+         ],
+         [
+            "d2",
+            "s3"
+         ],
+         [
+            "h0",
+            "t0"
+         ],
+         [
+            "s1",
+            "s2"
+         ],
+         [
+            "d0",
+            "s10"
+         ],
+         [
+            "d0",
+            "s9"
+         ],
+         [
+            "d0",
+            "s0"
+         ],
+         [
+            "d0",
+            "s8"
+         ],
+         [
+            "t1",
+            "d2"
+         ],
+         [
+            "t1",
+            "t2"
+         ],
+         [
+            "t1",
+            "d3"
+         ],
+         [
+            "s7",
+            "c4"
+         ],
+         [
+            "d1",
+            "t1"
+         ],
+         [
+            "s10",
+            "c3"
+         ],
+         [
+            "h2",
+            "s1"
+         ],
+         [
+            "t0",
+            "d0"
+         ],
+         [
+            "t2",
+            "t3"
+         ]
+      ],
+      "nodes":[
+         "s4",
+         "s9",
+         "d3",
+         "s5",
+         "s2",
+         "t3",
+         "s0",
+         "h1",
+         "s6",
+         "s8",
+         "s3",
+         "d2",
+         "h0",
+         "c4",
+         "s1",
+         "d0",
+         "c1",
+         "t1",
+         "s7",
+         "c0",
+         "d1",
+         "c2",
+         "s10",
+         "h2",
+         "t0",
+         "c3",
+         "t2"
+      ]
+   }
+}
\ No newline at end of file
diff --git a/web/project/tests/test_paperDAO.py b/web/project/tests/test_paperDAO.py
new file mode 100644
index 00000000..f7b0ac5f
--- /dev/null
+++ b/web/project/tests/test_paperDAO.py
@@ -0,0 +1,72 @@
+import unittest
+from unittest import TestCase
+from project.paperdao import *
+import os
+import mongomock
+import json
+def warn(*args, **kwargs):
+    pass
+import warnings
+warnings.warn = warn
+
+class TestPaperDAO(TestCase):
+    def setUp(self):
+        """
+        Sets up database to test
+        """
+        MongoDBConnection.getDB(hostname='mongomock://localhost', port=int('27017'),
+                                          username=None, password=None,
+                                          dbname='mongoenginetest', collection='paper',
+                                          isssl='No')
+        __location__ = os.path.realpath(
+            os.path.join(os.getcwd(), os.path.dirname(__file__)))
+        with open(os.path.join(__location__, 'data.json')) as f:
+            paperdata = json.load(f)
+        #paperdata = json.loads(paperdata)
+        paper = Paper(**paperdata)
+        paper.save()
+
+    def test_getCollectionList(self):
+        """
+        Tests if all collections exist
+        """
+        dao = PaperDAO()
+        allcollectionlist = dao.getCollectionList()
+        self.assertTrue(list(allcollectionlist))
+
+    def test_getPublicationList(self):
+        """
+        Tests for publications
+        """
+        dao = PaperDAO()
+        allpublicationlist = dao.getPublicationList()
+        self.assertTrue(list(allpublicationlist))
+
+    def test_getAllPapers(self):
+        """
+        Tests for all papers
+        """
+        dao = PaperDAO()
+        allpapers = dao.getAllPapers()
+        self.assertTrue(list(allpapers))
+
+    # def test_getAllFilteredSearchObjects(self):
+    #     self.fail()
+    #
+    # def test_getAllSearchObjects(self):
+    #     self.fail()
+    #
+    # def test_insertIntoPapers(self):
+    #     self.fail()
+    #
+    # def test_getPaperDetails(self):
+    #     self.fail()
+    #
+    # def test_getWorkflowDetails(self):
+    #     self.fail()
+    #
+    # def test_getWorkflowForChartDetails(self):
+    #     self.fail()
+
+if __name__ == "__main__":
+    unittest.main()
\ No newline at end of file
diff --git a/web/project/tests/test_routes.py b/web/project/tests/test_routes.py
new file mode 100644
index 00000000..2877aa63
--- /dev/null
+++ b/web/project/tests/test_routes.py
@@ -0,0 +1,24 @@
+import os
+import unittest
+
+from project import app
+
+class RouteTests(unittest.TestCase):
+    ############################
+    #### setup and teardown ####
+    ############################
+
+    # executed prior to each test
+    def setUp(self):
+        self.app = app.test_client()
+
+    # executed after each test
+    def tearDown(self):
+        pass
+
+    def test_main_page(self):
+        response = self.app.get('/', follow_redirects=True)
+        self.assertEqual(response.status_code, 200)
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/web/project/util.py b/web/project/util.py
index c202fc28..dce5b495 100644
--- a/web/project/util.py
+++ b/web/project/util.py
@@ -6,6 +6,7 @@
 import requests
 from jsonschema import Draft4Validator
 from requests_oauthlib import OAuth2Session
+import itertools
 
 
 from .views import ReferenceForm, ChartForm, DatasetForm, ToolForm, ScriptForm, HeadForm
@@ -400,6 +401,39 @@ def sendDescriptorToServer(self,data):
         response = requests.post(url, data=json.dumps(payload), headers=headers, verify=False)
         return response
 
+class FetchDataFromAPI():
+    """ Fetches data for search,paper details and chart details for explorer
+    """
+    def __init__(self,servernames):
+        if servernames and len(servernames)>0:
+            self.__servernames = servernames
+        else:
+            serverslist = Servers()
+            serverList = [qrespserver['qresp_server_url'] for qrespserver in
+                               serverslist.getServersList()]
+            serverList.append('http://localhost')
+            serverList.append('http://localhost')
+            self.__servernames = serverList
+
+    def fetchOutput(self,apiname):
+        """ Fetches output to server
+        :return: object: sends descriptor to server
+        """
+        outDict = {}
+        for snames in self.__servernames:
+            url = snames + apiname
+            print("url>",url)
+            headers = {'Application': 'qresp', 'Accept': 'application/json', 'Content-Type': 'application/json'}
+            response = requests.get(url,headers=headers, verify=False)
+            if response.status_code == 200:
+                if "search" in apiname:
+                    outDict.update({eachsearchObj['_Search__title']:eachsearchObj for eachsearchObj in response.json()})
+                else:
+                    outDict.update({eachsearchObj:eachsearchObj for eachsearchObj in response.json()})
+        output = list(outDict.values())
+        return output
+
+
 class GoogleAuth():
     """ Authorization for google.
     """
diff --git a/web/project/views.py b/web/project/views.py
index ef7e2580..fdc173b1 100644
--- a/web/project/views.py
+++ b/web/project/views.py
@@ -48,6 +48,10 @@ class ConfigForm(Form):
     downloadPath = StringField('Download Path',description='The Globus service allows to download the paper content using gridFTP.')
     fileServerPath = StringField('File Server Path', description='If a HTTP service is running on the server, a URL may be associated to the paper content. This URL is only required by Qresp | Exploration to view images & download files using a web browser.')
 
+class QrespServerForm(Form):
+    serverList = FieldList(StringField(description='Select the Address of the Database. Qresp automatically inserts the metadata file in the database'))
+
+
 class NameForm(Form):
     firstName = StringField(validators=[validators.DataRequired()],description='e.g. John',render_kw={"placeholder": "Enter first name"})
     middleName = StringField(description='e.g. L.',render_kw={"placeholder": "Enter middle name"})
diff --git a/web/requirements.txt b/web/requirements.txt
index e7e9c80d..31d7a5a8 100644
--- a/web/requirements.txt
+++ b/web/requirements.txt
@@ -22,4 +22,8 @@ Werkzeug==0.14.1
 WTForms==2.2.1
 schedule
 flask-sitemap
-requests_oauthlib
\ No newline at end of file
+requests_oauthlib
+mongomock
+connexion
+coverage
+nose2
\ No newline at end of file
diff --git a/web/run.py b/web/run.py
index 40913e57..a5b9fff3 100644
--- a/web/run.py
+++ b/web/run.py
@@ -1,11 +1,11 @@
 # run.py
 from flask_cors import CORS
 
-from project import app
-
+from project import connexionapp
+app = connexionapp.app
 CORS(app)
 
 #app.run()
 if __name__ == "__main__":
-    app.run(port=80,debug=True)
+    connexionapp.run(port=80,debug=True)
 
diff --git a/web/setup.py b/web/setup.py
index 23db8d21..e03d0305 100644
--- a/web/setup.py
+++ b/web/setup.py
@@ -35,7 +35,11 @@
         'schedule',
         'wtforms',
         'flask-sitemap',
-        'requests_oauthlib'
+        'requests_oauthlib',
+        'mongomock',
+        'connexion',
+        'coverage',
+        'nose2'
       ],
     include_package_data=True
 )

From aba57d8a284d1c85c932b989795fcc3c1425a6af Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Wed, 9 Jan 2019 12:11:10 -0600
Subject: [PATCH 02/15] Updated swagger API tests

---
 web/MANIFEST.in                    |  3 ++-
 web/project/__main__.py            |  3 +--
 web/project/routes.py              |  8 +++-----
 web/project/swagger.yml            |  6 +++---
 web/project/tests/test_paperDAO.py |  1 -
 web/project/tests/test_routes.py   |  4 ++++
 web/project/util.py                | 18 +++++++++++++-----
 7 files changed, 26 insertions(+), 17 deletions(-)

diff --git a/web/MANIFEST.in b/web/MANIFEST.in
index eeb65b00..628a7319 100644
--- a/web/MANIFEST.in
+++ b/web/MANIFEST.in
@@ -1,2 +1,3 @@
 recursive-include project/templates *
-recursive-include project/static *
\ No newline at end of file
+recursive-include project/static *
+include project/swagger.yml
diff --git a/web/project/__main__.py b/web/project/__main__.py
index 859efd5a..9ec8bb4f 100644
--- a/web/project/__main__.py
+++ b/web/project/__main__.py
@@ -3,9 +3,8 @@
 
 from flask import Flask
 import connexion
-#app = Flask(__name__)
 # Create the application instance
-connexionapp = connexion.App(__name__, specification_dir='./',template_folder='project/templates')
+connexionapp = connexion.App(__name__, specification_dir='./')
 
 # Read the swagger.yml file to configure the endpoints
 connexionapp.add_api('swagger.yml')
diff --git a/web/project/routes.py b/web/project/routes.py
index cc07d913..9d560dee 100644
--- a/web/project/routes.py
+++ b/web/project/routes.py
@@ -19,9 +19,6 @@
 qresp_config = {}
 ftp_dict = {}
 
-
-
-
 class InvalidUsage(Exception):
     """ Invalid page
     """
@@ -62,6 +59,8 @@ def make_session_permanent():
 def index():
     """ Fetches the homepage
     """
+    #TO BE DELETED
+    SetLocalHost(str(request.host_url).strip("/"))
     return render_template('index.html')
 
 @app.route('/downloads/<file>')
@@ -729,7 +728,6 @@ def qrespexplorer():
     serverslist = Servers()
     form.serverList = [qrespserver['qresp_server_url'] for qrespserver in
                            serverslist.getServersList()]
-    form.serverList.append('http://localhost')
     if request.method == 'POST':
         if request.form.get('serversList'):
             session["selectedserver"] = request.form.get('serversList')
@@ -764,11 +762,11 @@ def admin():
             dbAdmin = MongoDBConnection.getDB(hostname=form.hostname.data, port=int(form.port.data),
                                         username=form.username.data, password=form.password.data,
                                         dbname=form.dbname.data, collection=form.collection.data, isssl=form.isSSL.data)
-            paperCollectionlist = Paper.objects.get_unique_values('collections')
         except Exception as e:
             flash('Could not connect to server, \n ' + str(e))
             raise InvalidUsage('Could not connect to server, \n ' + str(e), status_code=410)
         flash('Connected')
+        SetLocalHost(str(request.host_url).strip("/"))
         return redirect(url_for('qrespexplorer'))
     return render_template('admin.html', form=form,verifyform =verifyform )
 
diff --git a/web/project/swagger.yml b/web/project/swagger.yml
index a5983efb..4db13a1b 100644
--- a/web/project/swagger.yml
+++ b/web/project/swagger.yml
@@ -98,7 +98,7 @@ paths:
       tags:
         - "Collections"
       summary: "Fetches all collections"
-      description: "Read the list of collections"
+      description: "Fetches collections from all Papers"
       responses:
         200:
           description: "Successful read collections list operation"
@@ -112,7 +112,7 @@ paths:
       tags:
         - "Authors"
       summary: "Fetches all authors"
-      description: "Read the list of authors"
+      description: "Fetches authors from papers"
       responses:
         200:
           description: "Successful read authors list operation"
@@ -126,7 +126,7 @@ paths:
       tags:
         - "Publications"
       summary: "Fetches all publications"
-      description: "Read the list of publications"
+      description: "Fetches publications from all papers"
       responses:
         200:
           description: "Successful read publications list operation"
diff --git a/web/project/tests/test_paperDAO.py b/web/project/tests/test_paperDAO.py
index f7b0ac5f..f204803d 100644
--- a/web/project/tests/test_paperDAO.py
+++ b/web/project/tests/test_paperDAO.py
@@ -22,7 +22,6 @@ def setUp(self):
             os.path.join(os.getcwd(), os.path.dirname(__file__)))
         with open(os.path.join(__location__, 'data.json')) as f:
             paperdata = json.load(f)
-        #paperdata = json.loads(paperdata)
         paper = Paper(**paperdata)
         paper.save()
 
diff --git a/web/project/tests/test_routes.py b/web/project/tests/test_routes.py
index 2877aa63..c0e08f65 100644
--- a/web/project/tests/test_routes.py
+++ b/web/project/tests/test_routes.py
@@ -20,5 +20,9 @@ def test_main_page(self):
         response = self.app.get('/', follow_redirects=True)
         self.assertEqual(response.status_code, 200)
 
+    def test_main_page(self):
+        response = self.app.get('/', follow_redirects=True)
+        self.assertEqual(response.status_code, 200)
+
 if __name__ == "__main__":
     unittest.main()
diff --git a/web/project/util.py b/web/project/util.py
index dce5b495..5192413a 100644
--- a/web/project/util.py
+++ b/web/project/util.py
@@ -12,6 +12,7 @@
 from .views import ReferenceForm, ChartForm, DatasetForm, ToolForm, ScriptForm, HeadForm
 
 
+LOCALHOST = None
 
 
 
@@ -406,14 +407,16 @@ class FetchDataFromAPI():
     """
     def __init__(self,servernames):
         if servernames and len(servernames)>0:
-            self.__servernames = servernames
+            serverList = servernames
         else:
             serverslist = Servers()
             serverList = [qrespserver['qresp_server_url'] for qrespserver in
                                serverslist.getServersList()]
-            serverList.append('http://localhost')
-            serverList.append('http://localhost')
-            self.__servernames = serverList
+        global LOCALHOST
+        print(LOCALHOST)
+        if LOCALHOST:
+            serverList.append(LOCALHOST)
+        self.__servernames = serverList
 
     def fetchOutput(self,apiname):
         """ Fetches output to server
@@ -453,4 +456,9 @@ def getGoogleAuth(self,state=None,token=None):
                 state=state,
                 redirect_uri=self.redirecturi)
         oauth = OAuth2Session(self.clientid,redirect_uri=self.redirecturi,scope=self.scope)
-        return oauth
\ No newline at end of file
+        return oauth
+
+class SetLocalHost:
+    def __init__(self,localhost):
+        global LOCALHOST
+        LOCALHOST = localhost
\ No newline at end of file

From 79fea1028084530f8ca1dc99362dd7963239044c Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Wed, 9 Jan 2019 13:40:38 -0600
Subject: [PATCH 03/15] Updated Travis

---
 web/project/__init__.py            | 11 +++++------
 web/project/tests/test_paperDAO.py | 26 +++++++++++++++++---------
 2 files changed, 22 insertions(+), 15 deletions(-)

diff --git a/web/project/__init__.py b/web/project/__init__.py
index 753b89c6..b843c590 100644
--- a/web/project/__init__.py
+++ b/web/project/__init__.py
@@ -45,12 +45,11 @@
 os.environ['OAUTHLIB_INSECURE_TRANSPORT'] = '1'
 app.config['MAIL_ADDR'] = MAIL_ADDR
 app.config['MAIL_PWD'] = MAIL_PWD
-app.config['MONGODB_HOST'] = MONGODB_HOST
-app.config['MONGODB_PORT'] = MONGODB_PORT
-app.config['MONGODB_USERNAME'] = MONGODB_USERNAME
-app.config['MONGODB_PASSWORD'] = MONGODB_PASSWORD
-app.config['MONGODB_DB'] = MONGODB_DB
-
+app.config['MONGODB_HOST'] = 'paperstack.uchicago.edu'
+app.config['MONGODB_PORT'] = 27017
+app.config['MONGODB_USERNAME'] = 'qresp_user_explorer'
+app.config['MONGODB_PASSWORD'] = 'qresp_pwd'
+app.config['MONGODB_DB'] = 'explorer'
 Session(app)
 ext = Sitemap(app)
 
diff --git a/web/project/tests/test_paperDAO.py b/web/project/tests/test_paperDAO.py
index f204803d..6e5e096b 100644
--- a/web/project/tests/test_paperDAO.py
+++ b/web/project/tests/test_paperDAO.py
@@ -49,15 +49,23 @@ def test_getAllPapers(self):
         allpapers = dao.getAllPapers()
         self.assertTrue(list(allpapers))
 
-    # def test_getAllFilteredSearchObjects(self):
-    #     self.fail()
-    #
-    # def test_getAllSearchObjects(self):
-    #     self.fail()
-    #
-    # def test_insertIntoPapers(self):
-    #     self.fail()
-    #
+    def test_getAllFilteredSearchObjects(self):
+        """
+        Tests for all search Objects
+        """
+        dao = PaperDAO()
+        allSearchObjects = dao.getAllFilteredSearchObjects()
+        self.assertTrue(list(allSearchObjects))
+
+    def test_getFilteredPaperObjects(self):
+        """
+        Tests for all search Objects with name
+        """
+        dao = PaperDAO()
+        allSearchObjects = dao.getAllFilteredSearchObjects(authorsList=['Marco Govoni'])
+        print(allSearchObjects)
+        self.assertTrue(list(allSearchObjects))
+
     # def test_getPaperDetails(self):
     #     self.fail()
     #

From 044a5022ae914bf417861eaa7eb352fcb598b173 Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Wed, 9 Jan 2019 13:57:21 -0600
Subject: [PATCH 04/15] Updated setup for travis

---
 web/setup.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/web/setup.py b/web/setup.py
index e03d0305..4c041458 100644
--- a/web/setup.py
+++ b/web/setup.py
@@ -26,7 +26,6 @@
         'mongoengine',
         'cryptography',
         'jinja2',
-        'requests',
         'pyOpenSSL',
         'werkzeug',
         'itsdangerous',

From 371d248122e34c4eff11e028245f7cbe8d329c49 Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Wed, 9 Jan 2019 14:06:09 -0600
Subject: [PATCH 05/15] Updated setup for travis

---
 .travis.yml          | 1 +
 web/requirements.txt | 1 +
 2 files changed, 2 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 1ffd9fdd..3b267d95 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,6 +7,7 @@ python:
 # command to install dependencies
 install:
   - cd web
+  - pip install -r requirements.txt
   - python setup.py install
 # command to run tests
 script:
diff --git a/web/requirements.txt b/web/requirements.txt
index 31d7a5a8..fe657a5e 100644
--- a/web/requirements.txt
+++ b/web/requirements.txt
@@ -1,3 +1,4 @@
+setuptools
 Flask==1.0.2
 Flask-API==1.0
 Flask-Cors==3.0.6

From 7e22acd510d566009a19687cef2923aa0bcaa307 Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Wed, 9 Jan 2019 14:12:55 -0600
Subject: [PATCH 06/15] Updated travis and setup file

---
 .travis.yml  | 1 -
 web/setup.py | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 3b267d95..0f604c96 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,6 +1,5 @@
 language: python
 python:
-  - "3.3"
   - "3.4"
   - "3.5"
   - "3.6"
diff --git a/web/setup.py b/web/setup.py
index 4c041458..041e8dad 100644
--- a/web/setup.py
+++ b/web/setup.py
@@ -11,7 +11,7 @@
     author='Aditya Tanikanti, Marco Govoni',
     author_email='datadev@lists.uchicago.edu',
     description='Qresp "Curation and Exploration of Reproducible Scientific Papers" is a Python application that facilitates the organization, annotation and exploration of data presented in scientific papers. ',
-    python_requires='>=3.0',
+    python_requires='>=3.4',
     packages=find_packages(),
     install_requires=[
         'flask_api',

From 697f9ff2b782ac851e2743836852ce126e357288 Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Fri, 11 Jan 2019 09:33:06 -0600
Subject: [PATCH 07/15] Fixes for API and added more tests

---
 web/project/api.py                            | 63 ++++++++++++++++-
 web/project/paperdao.py                       | 58 ++++++++++++----
 web/project/routes.py                         | 63 +++++++++++++----
 .../static/javascript/modules/curate.js       | 24 +++++--
 .../static/javascript/modules/paperdetails.js | 12 ++--
 web/project/swagger.yml                       | 69 ++++++++++++++++---
 web/project/templates/curate.html             |  2 +-
 web/project/templates/mint.html               | 40 ++++-------
 web/project/templates/project.html            |  2 +-
 web/project/templates/publish.html            |  2 +-
 web/project/templates/qrespcurator.html       |  2 +-
 web/project/tests/test_paperDAO.py            | 52 +++++++++++++-
 web/project/util.py                           | 16 +++--
 web/project/views.py                          |  2 +-
 web/requirements.txt                          |  2 +-
 web/setup.py                                  |  2 +-
 16 files changed, 322 insertions(+), 89 deletions(-)

diff --git a/web/project/api.py b/web/project/api.py
index 6bd87612..225e7be4 100644
--- a/web/project/api.py
+++ b/web/project/api.py
@@ -1,5 +1,5 @@
 from .paperdao import *
-def search(searchWord=None,paperTitle=None,doi=None,tags=None,collectionList=[],authorsList=[],publicationList=[]):
+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
@@ -9,11 +9,17 @@ def search(searchWord=None,paperTitle=None,doi=None,tags=None,collectionList=[],
     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 ", e)
+        print("Exception in search", e)
     return allpaperslist
 
 def collections():
@@ -59,4 +65,55 @@ def publications():
         allpublist = dao.getPublicationList()
     except Exception as e:
         print("Exception in ", e)
-    return list(allpublist)
\ No newline at end of file
+    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, 500
+    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,500
+    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,500
+    return chartworkflowdetail
\ No newline at end of file
diff --git a/web/project/paperdao.py b/web/project/paperdao.py
index 0c54aa88..e7fa7710 100644
--- a/web/project/paperdao.py
+++ b/web/project/paperdao.py
@@ -53,29 +53,55 @@ def getAllFilteredSearchObjects(self, searchWord=None, paperTitle=None, doi=None
             searchRegWord = re.compile(regSearch, re.IGNORECASE)
             filteredPaper = Paper.objects.filter(
                 Q(reference__title=searchRegWord) | Q(reference__publishedAbstract=searchRegWord) |
-                Q(tags=searchRegWord) | Q(collections=searchRegWord) | Q(reference__authors__firstName=searchWord) |
-                Q(reference__authors__lastName=searchWord))
+                Q(tags__in=[searchRegWord]) | Q(collections__in=[searchRegWord]) | Q(reference__authors__firstName__in=[searchRegWord]) |
+                Q(reference__authors__lastName__in=[searchRegWord]))
             allFilteredSearchObjects = self.__filtersearchedPaper(filteredPaper)
         else:
             searchquery = Q()
             if paperTitle and paperTitle.strip():
-                searchTitleQuery = Q(reference__title__icontains=paperTitle)
+                regSearch = '.*' + paperTitle + '.*'
+                searchRegWord = re.compile(regSearch, re.IGNORECASE)
+                searchTitleQuery = Q(reference__title=searchRegWord)
                 searchquery = searchquery & searchTitleQuery
             if doi and doi.strip():
-                searchdoiquery = Q(reference__DOI__icontains=doi)
+                regSearch = '.*' + doi + '.*'
+                searchRegWord = re.compile(regSearch, re.IGNORECASE)
+                searchdoiquery = Q(reference__DOI=searchRegWord)
                 searchquery = searchquery & searchdoiquery
-            if tags and tags.strip():
-                searchtagquery = Q(tags__icontains=tags)
+            if tags and len(tags)>0:
+                newtagList = []
+                for item in tags:
+                    regSearch = '.*' + item + '.*'
+                    searchRegWord = re.compile(regSearch, re.IGNORECASE)
+                    newtagList.append(searchRegWord)
+                searchtagquery = Q(tags__in=newtagList)
                 searchquery = searchquery & searchtagquery
-            if len(collectionList) > 0:
-                searchcollectionquery = Q(collections__in=collectionList)
+            if collectionList and len(collectionList) > 0:
+                newcollectionList = []
+                for item in collectionList:
+                    regSearch = '.*' + item + '.*'
+                    searchRegWord = re.compile(regSearch, re.IGNORECASE)
+                    newcollectionList.append(searchRegWord)
+                searchcollectionquery = Q(collections__in=newcollectionList)
                 searchquery = searchquery & searchcollectionquery
-            if len(authorsList) > 0:
-                lastnamelist = [name.split(" ")[1] for name in authorsList]
-                searchauthorquery = Q(reference__authors__lastName__in=lastnamelist)
-                searchquery = searchquery & searchauthorquery
-            if len(publicationList) > 0:
-                searchpubquery = Q(reference__journal__fullName__in=publicationList)
+            if authorsList and len(authorsList) > 0:
+                namelist = [name.split(" ") for name in authorsList]
+                newnamelist = []
+                for sublist in namelist:
+                    for item in sublist:
+                        regSearch = '.*' + item + '.*'
+                        searchRegWord = re.compile(regSearch, re.IGNORECASE)
+                        newnamelist.append(searchRegWord)
+                searchlastauthorquery = Q(reference__authors__lastName__in=newnamelist)
+                searchfirstauthorquery = Q(reference__authors__firstName__in=newnamelist)
+                searchquery = searchquery & (searchlastauthorquery | searchfirstauthorquery)
+            if publicationList and len(publicationList) > 0:
+                newpubList = []
+                for item in publicationList:
+                    regSearch = '.*' + item + '.*'
+                    searchRegWord = re.compile(regSearch, re.IGNORECASE)
+                    newpubList.append(searchRegWord)
+                searchpubquery = Q(reference__journal__fullName__in=newpubList)
                 searchquery = searchquery & searchpubquery
             if searchquery:
                 filteredPaper = Paper.objects.filter(searchquery)
@@ -100,6 +126,10 @@ def insertIntoPapers(self,paperdata):
         paper.save()
         return str(paper.id)
 
+    def insertDOI(self,id,doi):
+        """ Inserts into collection"""
+        paper = Paper.objects(id=id).update(info__doi=doi)
+        return paper
 
 
     def __filtersearchedPaper(self, filteredPaper):
diff --git a/web/project/routes.py b/web/project/routes.py
index 9d560dee..4b949ce2 100644
--- a/web/project/routes.py
+++ b/web/project/routes.py
@@ -81,6 +81,13 @@ def qrespcurator():
     """
     return render_template('qrespcurator.html')
 
+@app.route('/startfromscratch')
+def startfromscratch():
+    """ clears session
+    """
+    session.clear()
+    return redirect(url_for('details'))
+
 @csrf.exempt
 @app.route('/uploadFile',methods=['POST','GET'])
 def uploadFile():
@@ -145,6 +152,7 @@ def uploadFile():
         infoform = InfoForm(**paperform.data)
         infoform.tags.data = ", ".join(paperform.tags.data)
         infoform.collections.data = ", ".join(paperform.collections.data)
+        infoform.notebookFile.data = paperform.info.notebookFile.data
         session["info"] = infoform.data
         session["PIs"] = [form.data for form in infoform.PIs.entries]
         session["tags"] = [form for form in paperform.tags.data]
@@ -217,15 +225,22 @@ def setproject():
             absPath = pathDetails['folderAbsolutePath']
             ftpclient = session.get("sftpclient")
             ftp = ftp_dict[ftpclient]
-            dtree = Dtree(ftp, absPath.rsplit("/", 1)[0], session)
+            if "/" in absPath:
+                dtree = Dtree(ftp, absPath.rsplit("/", 1)[0], session)
+            else:
+                dtree = Dtree(ftp, absPath, session)
             dtree.openFileToReadConfig("qresp.ini")
             services = dtree.fetchServices()
             isConfig = dtree.checkIsConfigFile()
             session["folderAbsolutePath"] = absPath
-            session["ProjectName"] = absPath.rsplit("/",1)[1]
+            if "/" in absPath:
+                session["ProjectName"] = absPath.rsplit("/",1)[1]
+            else:
+                session["ProjectName"] = absPath
             return jsonify(folderAbsolutePath=absPath,isConfigFile=isConfig,services=services)
     except Exception as e:
-        flash("Could not connect to server. Plase try again!" + str(e))
+        print(e)
+        flash("Could not connect to server. Plase try again! " + str(e))
         return jsonify(folderAbsolutePath=absPath, isConfigFile=isConfig, services=services)
 
 
@@ -301,7 +316,7 @@ def info():
         session["PIs"] = [form.data for form in infoform.PIs.entries]
         session["tags"] = infoform.tags.data.split(",")
         session["collections"] = infoform.collections.data.split(",")
-        session["notebookFile"] = infoform.mainnotebookfile.data
+        session["notebookFile"] = infoform.notebookFile.data
         msg = "Info Saved"
         return jsonify(data=msg)
     return jsonify(data=infoform.errors)
@@ -826,9 +841,8 @@ def searchWord():
         publicationList = json.loads(request.args.get('publicationList'))
         selectedserver = session.get("selectedserver")
         fetchdata = FetchDataFromAPI(selectedserver)
-        url = '/api/search' + "?searchWord=" + searchWord
-        # url = '/api/search'+"?searchWord="+searchWord+"&paperTitle="+paperTitle+"&doi="+doi+"&tags="+tags+"&collectionList="+",".join(collectionList) + \
-        #       "&authorsList="+",".join(authorsList)+"&publicationList="+",".join(publicationList)
+        url = '/api/search'+"?searchWord="+searchWord+"&paperTitle="+paperTitle+"&doi="+doi+"&tags="+tags+"&collectionList="+",".join(collectionList) + \
+              "&authorsList="+",".join(authorsList)+"&publicationList="+",".join(publicationList)
         allpaperslist = fetchdata.fetchOutput(url)
         return jsonify(allpaperslist=allpaperslist)
     except Exception as e:
@@ -844,9 +858,12 @@ def paperdetails(paperid):
     :return: template: paperdetails.html
     """
     try:
-        dao = PaperDAO()
-        paperdetail = dao.getPaperDetails(paperid)
-        workflowdetail = dao.getWorkflowDetails(paperid)
+        selectedserver = session.get("selectedserver")
+        fetchdata = FetchDataFromAPI(selectedserver)
+        url = '/api/paper/'+paperid
+        paperdetail = fetchdata.fetchOutput(url)
+        url = '/api/workflow/'+paperid
+        workflowdetail = fetchdata.fetchOutput(url)
         return render_template('paperdetails.html', paperdetail=paperdetail, workflowdetail=workflowdetail)
     except Exception as e:
         print(e)
@@ -870,7 +887,10 @@ def chartworkflow():
         paperid = str(paperid).strip()
         chartid = request.args.get('chartid', 0, type=str)
         chartid = str(chartid).strip()
-        chartworkflowdetail = dao.getWorkflowForChartDetails(paperid, chartid)
+        selectedserver = session.get("selectedserver")
+        fetchdata = FetchDataFromAPI(selectedserver)
+        url = '/api/paper/' + paperid + '/chart/' + chartid
+        chartworkflowdetail = fetchdata.fetchOutput(url)
         return jsonify(chartworkflowdetail=chartworkflowdetail)
     except Exception as e:
         print(e)
@@ -906,12 +926,31 @@ def getDescriptor():
         return jsonify(content),400
     return jsonify(content),200
 
-@app.route('/mint')
+@app.route('/mint', methods=['POST','GET'])
 def mint():
     """ Fetches the mint page
     """
     return render_template('mint.html')
 
+@app.route('/insertDOI', methods=['POST','GET'])
+def insertDOI():
+    """ Inserts DOI to database
+    """
+    try:
+        paperid = request.args.get('paperId', 0, type=str)
+        paperid = str(paperid).strip()
+        doi = request.args.get('doi', 0, type=str)
+        doi = str(doi).strip()
+        dao = PaperDAO()
+        if paperid and doi:
+            dao.insertDOI(paperid,doi)
+    except Exception as e:
+        print(e)
+        content = {'Failed': 'Could Not Insert'}
+        return jsonify(content), 500
+    content = {'Success': 'Inserted'}
+    return jsonify(content), 200
+
 def main(port):
     app.secret_key = '\xfd{H\xe5<\x95\xf9\xe3\x96.5\xd1\x01O<!\xd5\xa2\xa0\x9fR"\xa1\xa8'
     CORS(app)
diff --git a/web/project/static/javascript/modules/curate.js b/web/project/static/javascript/modules/curate.js
index ba471bb7..5570cf0e 100644
--- a/web/project/static/javascript/modules/curate.js
+++ b/web/project/static/javascript/modules/curate.js
@@ -121,7 +121,7 @@ $('input[type=text]').bind("keyup focusin", function () {
 });
 
 //copy from tree
-$('form[name="info"] #mainnotebookfile').bind("keyup focusin", function () {
+$('form[name="info"] #notebookFile').bind("keyup focusin", function () {
 	$('#tree').removeClass('disabledtree');
 	var values = []
 	$("#tree").fancytree("getTree").visit(function (node) {
@@ -131,7 +131,7 @@ $('form[name="info"] #mainnotebookfile').bind("keyup focusin", function () {
 				var path = keypath.substring(keypath.indexOf(projectName) + projectName.length + 1);
 				values.push(path);
 				var copiedcontent = values.slice();
-				$('form[name="info"] #mainnotebookfile').val(copiedcontent);
+				$('form[name="info"] #notebookFile').val(copiedcontent);
 			}
 		}
 	});
@@ -623,11 +623,21 @@ function fillValues(obj,type) {
             $("div[data-toggle=author-fieldset-toggle]").each(function() {
                 var $this = $(this);
                  if(value.firstName) {
-                    $this.find("button[data-toggle=fieldset-add-row-author]").trigger('click');
-                    // $this.find("button[data-toggle=fieldset-remove-row-authors]").trigger('click');
-                     $('#authors-' + index + '-firstName').val(value.firstName);
-                    $('#authors-' + index + '-middleName').val(value.middleName);
-                    $('#authors-' + index + '-lastName').val(value.lastName);
+                     // $this.find("button[data-toggle=fieldset-remove-row-authors]").trigger('click');
+                     if($('#authors-' + index + '-firstName').length) {
+                         $('#authors-' + index + '-firstName').val(value.firstName);
+                         $('#authors-' + index + '-middleName').val(value.middleName);
+                         $('#authors-' + index + '-lastName').val(value.lastName);
+                     }else{
+                        $this.find("button[data-toggle=fieldset-add-row-author]").trigger('click');
+                         var oldrow = $this.find("#authorTable tr:last");
+                         var row = oldrow.clone(true, true);
+                         var elem_id = row.find(":input")[0].id;
+                         var elem_num = parseInt(elem_id.replace(/.*-(\d{1,4})-.*/m, '$1'));
+                         $('#authors-' + elem_num + '-firstName').val(value.firstName);
+                         $('#authors-' + elem_num + '-middleName').val(value.middleName);
+                         $('#authors-' + elem_num + '-lastName').val(value.lastName);
+                     }
                 }
             });
         });
diff --git a/web/project/static/javascript/modules/paperdetails.js b/web/project/static/javascript/modules/paperdetails.js
index aafcc156..013610ba 100644
--- a/web/project/static/javascript/modules/paperdetails.js
+++ b/web/project/static/javascript/modules/paperdetails.js
@@ -2,7 +2,6 @@ var bindModal = function (info) {
     $('#myModalLabel').html(info[0]);
     $('#myModalLabel').css('position', 'absolute');
     $('#myModalBody').html(info[1]);
-
     $('#modalInfo').modal('show');
 };
 
@@ -116,15 +115,18 @@ $(function () {
 
 //Builds first half of page i.e. paper details
 function buildPaperInfo(paperDetails) {
+    //id
+    localStorage.setItem("paperId", paperDetails._PaperDetails__id);
+    //link
+    var currenturl = window.location.href;
+    localStorage.setItem("link",currenturl);
+
     //title
     $("#lblTitle").html(paperDetails._PaperDetails__title);
+    localStorage.setItem("title", paperDetails._PaperDetails__title);
 
     //authors
     var authors = "by " + paperDetails._PaperDetails__authors ;
-    // $.each(paperDetails._PaperDetails__authors, function (i, item) {
-    //     authors += item.firstName + " " + item.lastName + ", ";
-    // });
-    // authors = authors.replace(/,\s*$/, "");
     $("#lblAuthor").html(authors);
 
     //cite
diff --git a/web/project/swagger.yml b/web/project/swagger.yml
index 4db13a1b..e4d44829 100644
--- a/web/project/swagger.yml
+++ b/web/project/swagger.yml
@@ -42,19 +42,19 @@ paths:
           description: Filter paper results based on paper tags
         - in: query
           name: collectionList
-          type: array
+          type: string
           required: false
-          description: Filter paper results based on collection
+          description: Filter paper results based on collection. Seperate by comma for multiple values
         - in: query
           name: authorsList
-          type: array
+          type: string
           required: false
-          description: Filter paper results based on authors
+          description: Filter paper results based on authors. Seperate by comma for multiple values
         - in: query
           name: publicationList
           required: false
-          type: array
-          description: Filter paper results based on publication
+          type: string
+          description: Filter paper results based on publication. Seperate by comma for multiple values
       responses:
         200:
           description: "Successful read papers list operation"
@@ -129,8 +129,61 @@ paths:
       description: "Fetches publications from all papers"
       responses:
         200:
-          description: "Successful read publications list operation"
+          description: "Successful read paper publications operation"
           schema:
             type: "array"
             items:
-                type: "string"
\ No newline at end of file
+                type: "string"
+  /paper/{id}:
+    get:
+      operationId: "project.api.paper"
+      tags:
+        - "Paper details"
+      summary: "Fetches details of paper given id"
+      description: "Fetches paper details given id"
+      parameters:
+        - in: path
+          name: id
+          type: string
+          required: true
+          description: Paper Id
+      responses:
+        200:
+          description: "Successful read paper details "
+  /workflow/{id}:
+    get:
+      operationId: "project.api.workflow"
+      tags:
+        - "Workflow details"
+      summary: "Fetches workflow of paper given id"
+      description: "Fetches workflow of paper given id"
+      parameters:
+        - in: path
+          name: id
+          type: string
+          required: true
+          description: Paper Id
+      responses:
+        200:
+          description: "Successful read workflow details of paper"
+  /paper/{id}/chart/{cid}:
+    get:
+      operationId: "project.api.chart"
+      tags:
+        - "Chart details"
+      summary: "Fetches chart of paper given id of paper and chart"
+      description: "Fetches chart of paper given id"
+      parameters:
+        - in: path
+          name: id
+          type: string
+          required: true
+          description: Paper Id
+        - in: path
+          name: cid
+          type: string
+          required: true
+          description: Chart Id
+      responses:
+        200:
+          description: "Successful read workflow details of paper"
\ No newline at end of file
diff --git a/web/project/templates/curate.html b/web/project/templates/curate.html
index 8b7a5ffb..1d29456c 100644
--- a/web/project/templates/curate.html
+++ b/web/project/templates/curate.html
@@ -64,7 +64,7 @@ <h3 class="card-title" data-toggle="tooltip" data-placement="left" title="This s
                                     <tbody>
                                     {{ render_field_curate(infoform.collections) }}
                                     {{ render_field_curate(infoform.tags) }}
-                                    {{ render_field_curate(infoform.mainnotebookfile) }}
+                                    {{ render_field_curate(infoform.notebookFile) }}
                                     <tr style="padding-bottom: 1rem;">
                                         <td style="padding-bottom: 1rem;">
                                             <input type="submit" id="btnInfoSave"
diff --git a/web/project/templates/mint.html b/web/project/templates/mint.html
index 481cf3ab..95975cc2 100644
--- a/web/project/templates/mint.html
+++ b/web/project/templates/mint.html
@@ -169,32 +169,20 @@ <h3 data-toggle="tooltip" class="card-title" style="text-align: center;"> Mint D
     }
 
    function insertDOI(link,doi){
-       $.ajax({
-            type : "POST",
-            url : "REST/papers/insertDOI",
-            dataType : "json",
-            data : JSON.stringify({
-                    paperId : paperId,
-                    doi : doi
-            })
-        }).done(function(response) {
-            if (response) {
-                var redirect = link;
-                window.location.replace(redirect);
-
-                return false;
-            } else {
-              alert("An error occurred.");
-            }
-        }).fail(
-                function(jqXHR, textStatus,
-                                errorThrown) {
-                        alert(jqXHR.responseText.message + ': ' + errorThrown);
-                        //window.location.href = "search.jsp";
-                }).always(function() {
-        //alert("Complete!");
-        });
-    }
+        $.getJSON('/insertDOI', {
+               paperId : paperId,
+                doi : doi
+            }, function (data) {
+                if (data) {
+                    var redirect = link;
+                    window.location.replace(redirect);
+
+                    return false;
+                } else {
+                  alert("An error occurred.");
+                }
+            });
+   }
 
 
 
diff --git a/web/project/templates/project.html b/web/project/templates/project.html
index 8e579678..a5076bc8 100644
--- a/web/project/templates/project.html
+++ b/web/project/templates/project.html
@@ -58,7 +58,7 @@ <h3 data-toggle="tooltip" title="This step identifies whether services are runni
 							</tbody>
 						</table>
 						<div class="col-md-12">
-							<input type="button" style="font-weight: bold;height: 50px;" class="btn btn-theme-colored btn-lg m-0" title="Continue to Step 6." id ="Save" value="Continue" onclick="saveProjectPath('POST');"/>
+							<input type="button" style="font-weight: bold;height: 50px;" class="btn btn-theme-colored btn-lg m-0" title="Continue to Step 5." id ="Save" value="Continue" onclick="saveProjectPath('POST');"/>
                         </div>
 					</form>
 				</div>
diff --git a/web/project/templates/publish.html b/web/project/templates/publish.html
index 888b7058..6e082bc7 100644
--- a/web/project/templates/publish.html
+++ b/web/project/templates/publish.html
@@ -19,7 +19,7 @@ <h3 data-toggle="tooltip" title="This step defines the location of the remote da
                             <input type="button" id="btnSkip"
                                    value="Skip"
                                    class="btn btn-theme-colored btn-lg m-0"
-                                   style="font-weight: bold; height: 50px;" onclick="window.href='/acknowledgement'">
+                                   style="font-weight: bold; height: 50px;" onclick="window.location='/acknowledgement';">
                             <a id="downloadLink" title='Download the meta data'><i class='fa fa-download' style='font-size:23px; color: #800000; margin-left: 10px;'></i></a>
                         </span>
                     </form>
diff --git a/web/project/templates/qrespcurator.html b/web/project/templates/qrespcurator.html
index 2f0d0536..f363f3fb 100644
--- a/web/project/templates/qrespcurator.html
+++ b/web/project/templates/qrespcurator.html
@@ -22,7 +22,7 @@
                         <input type="button" id="btnExplorer"
                                name="general_search_button" value="Start from scratch"
                                class="btn btn-theme-colored btn-lg m-0" title="Start from scratch."
-                               style="font-weight: bold; height: 50px;" onclick="window.location='/details';" >
+                               style="font-weight: bold; height: 50px;" onclick="window.location='/startfromscratch';" >
                      <input type="button" id="btnCurator"
                             name="general_search_button" value="Resume"
                             class="btn btn-theme-colored btn-lg m-0" title="Continue with existing JSON file."
diff --git a/web/project/tests/test_paperDAO.py b/web/project/tests/test_paperDAO.py
index 6e5e096b..f14a9305 100644
--- a/web/project/tests/test_paperDAO.py
+++ b/web/project/tests/test_paperDAO.py
@@ -57,15 +57,61 @@ def test_getAllFilteredSearchObjects(self):
         allSearchObjects = dao.getAllFilteredSearchObjects()
         self.assertTrue(list(allSearchObjects))
 
-    def test_getFilteredPaperObjects(self):
+    def test_getFilteredPaperObjectsForAuthors(self):
         """
         Tests for all search Objects with name
         """
         dao = PaperDAO()
-        allSearchObjects = dao.getAllFilteredSearchObjects(authorsList=['Marco Govoni'])
-        print(allSearchObjects)
+        allSearchObjects = dao.getAllFilteredSearchObjects(authorsList=['marco'])
+        print(len(allSearchObjects))
         self.assertTrue(list(allSearchObjects))
 
+    def test_getFilteredPaperObjectsForSearchWord(self):
+        """
+        Tests for all search Objects with name
+        """
+        dao = PaperDAO()
+        allSearchObjects = dao.getAllFilteredSearchObjects(searchWord='photo')
+        print(len(allSearchObjects))
+        self.assertTrue(list(allSearchObjects))
+
+    def test_getFilteredPaperObjectsForTitle(self):
+        """
+        Tests for all search Objects with name
+        """
+        dao = PaperDAO()
+        allSearchObjects = dao.getAllFilteredSearchObjects(paperTitle='photo')
+        print(len(allSearchObjects))
+        self.assertTrue(list(allSearchObjects))
+
+    def test_getFilteredPaperObjectsForTags(self):
+        """
+        Tests for all search Objects with name
+        """
+        dao = PaperDAO()
+        allSearchObjects = dao.getAllFilteredSearchObjects(tags=['photo'])
+        print(len(allSearchObjects))
+        self.assertTrue(list(allSearchObjects))
+
+    def test_getFilteredPaperObjectsForCollections(self):
+        """
+        Tests for all search Objects with name
+        """
+        dao = PaperDAO()
+        allSearchObjects = dao.getAllFilteredSearchObjects(collectionList=['miccom'])
+        print(len(allSearchObjects))
+        self.assertTrue(list(allSearchObjects))
+
+    def test_insertDOI(self):
+        """
+        Tests for isertion of DOI
+        """
+        dao = PaperDAO()
+        allSearchObjects = dao.getAllFilteredSearchObjects()
+        paper = dao.insertDOI(allSearchObjects[0]['_Search__id'],'123')
+        self.assertEquals(1, paper)
+
+
     # def test_getPaperDetails(self):
     #     self.fail()
     #
diff --git a/web/project/util.py b/web/project/util.py
index 5192413a..d235b15a 100644
--- a/web/project/util.py
+++ b/web/project/util.py
@@ -170,7 +170,10 @@ def fetchForTree(self):
             if "qresp.ini" in file:
                 self.openFileToReadConfig("qresp.ini")
             dataFile.title = file
-            parent = self.__path.split("/")
+            if "/" in self.__path:
+                parent = self.__path.split("/")
+            else:
+                parent = self.__path
             parentName = parent[len(parent) - 1]
             dataFile.key = self.__path + "/" + file
             dataFile.id = file
@@ -406,6 +409,7 @@ class FetchDataFromAPI():
     """ Fetches data for search,paper details and chart details for explorer
     """
     def __init__(self,servernames):
+        serverList = []
         if servernames and len(servernames)>0:
             serverList = servernames
         else:
@@ -413,7 +417,6 @@ def __init__(self,servernames):
             serverList = [qrespserver['qresp_server_url'] for qrespserver in
                                serverslist.getServersList()]
         global LOCALHOST
-        print(LOCALHOST)
         if LOCALHOST:
             serverList.append(LOCALHOST)
         self.__servernames = serverList
@@ -423,17 +426,22 @@ def fetchOutput(self,apiname):
         :return: object: sends descriptor to server
         """
         outDict = {}
+        output = None
+        self.__servernames = list(set(self.__servernames))
         for snames in self.__servernames:
             url = snames + apiname
             print("url>",url)
             headers = {'Application': 'qresp', 'Accept': 'application/json', 'Content-Type': 'application/json'}
             response = requests.get(url,headers=headers, verify=False)
             if response.status_code == 200:
-                if "search" in apiname:
+                if "paper" or "workflow" in apiname:
+                    output = response.json()
+                elif "search" in apiname:
                     outDict.update({eachsearchObj['_Search__title']:eachsearchObj for eachsearchObj in response.json()})
+                    output = list(outDict.values())
                 else:
                     outDict.update({eachsearchObj:eachsearchObj for eachsearchObj in response.json()})
-        output = list(outDict.values())
+                    output = list(outDict.values())
         return output
 
 
diff --git a/web/project/views.py b/web/project/views.py
index fdc173b1..863d509d 100644
--- a/web/project/views.py
+++ b/web/project/views.py
@@ -89,7 +89,7 @@ class InfoForm(Form):
     PIs = FieldList(FormField(NameForm), label='Principal Investigator(s)', description='Enter PI(s)', min_entries=1, validators=[validators.DataRequired()])
     collections = StringField(label='PaperStack',validators = [validators.DataRequired("Please enter keywords")], description='Enter name(s) defining group of papers (e.g. according to source of fundings)',render_kw={"placeholder": "Enter collection to which project belongs"})
     tags = StringField(label='Keywords',validators = [validators.DataRequired("Please enter keywords")], description='Enter Keyword(s) (e.g: DFT, organic materials, charge transfer): they facilitate paper searches using Qresp | Explorer',render_kw={"placeholder": "Enter tags for the project"})
-    mainnotebookfile = StringField('Main Notebook File', description='Enter name of a notebook file, this file may serve as a table of contents and may contain links to all datasets, charts, scripts, tools and documentation. Use the Paper Content widget (on the left) to fill this field',render_kw={"placeholder": "Enter main notebook filename"})
+    notebookFile = StringField('Main Notebook File', description='Enter name of a notebook file, this file may serve as a table of contents and may contain links to all datasets, charts, scripts, tools and documentation. Use the Paper Content widget (on the left) to fill this field',render_kw={"placeholder": "Enter main notebook filename"})
     doi = StringField('DOI',description='DOI minted by Qresp',render_kw={'readonly': True})
 
 class ExtraForm(Form):
diff --git a/web/requirements.txt b/web/requirements.txt
index fe657a5e..9d88081c 100644
--- a/web/requirements.txt
+++ b/web/requirements.txt
@@ -25,6 +25,6 @@ schedule
 flask-sitemap
 requests_oauthlib
 mongomock
-connexion
+connexion[swagger-ui]
 coverage
 nose2
\ No newline at end of file
diff --git a/web/setup.py b/web/setup.py
index 041e8dad..88c3e53c 100644
--- a/web/setup.py
+++ b/web/setup.py
@@ -36,7 +36,7 @@
         'flask-sitemap',
         'requests_oauthlib',
         'mongomock',
-        'connexion',
+        'connexion[swagger-ui]',
         'coverage',
         'nose2'
       ],

From c834411b5883ad070066c87ea0a3bdfc4a6925bd Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Fri, 11 Jan 2019 14:25:41 -0600
Subject: [PATCH 08/15] Added more tests and OS checks with travis

---
 .travis.yml                                    |   5 +++++
 README.md                                      |   2 ++
 web/project/api.py                             |   3 +++
 .../tests/__pycache__/__init__.cpython-36.pyc  | Bin 149 -> 0 bytes
 .../__pycache__/test_paperDAO.cpython-36.pyc   | Bin 2022 -> 0 bytes
 .../__pycache__/test_routes.cpython-36.pyc     | Bin 914 -> 0 bytes
 web/project/tests/test_paperDAO.py             |  17 ++++++++++-------
 7 files changed, 20 insertions(+), 7 deletions(-)
 delete mode 100644 web/project/tests/__pycache__/__init__.cpython-36.pyc
 delete mode 100644 web/project/tests/__pycache__/test_paperDAO.cpython-36.pyc
 delete mode 100644 web/project/tests/__pycache__/test_routes.cpython-36.pyc

diff --git a/.travis.yml b/.travis.yml
index 0f604c96..9d9d6faa 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,6 +4,11 @@ python:
   - "3.5"
   - "3.6"
 # command to install dependencies
+os:
+  - linux
+  - osx
+  - windows
+
 install:
   - cd web
   - pip install -r requirements.txt
diff --git a/README.md b/README.md
index 5b236c94..65a1cfe0 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,5 @@
+[![Build Status](https://travis-ci.com/atanikan/Qresp.svg?branch=qresp-1.1)](https://travis-ci.com/atanikan/Qresp)
+
 # Qresp
 [Qresp](http://qresp.org) software repository. 
 
diff --git a/web/project/api.py b/web/project/api.py
index 225e7be4..e40968ea 100644
--- a/web/project/api.py
+++ b/web/project/api.py
@@ -1,4 +1,7 @@
 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
diff --git a/web/project/tests/__pycache__/__init__.cpython-36.pyc b/web/project/tests/__pycache__/__init__.cpython-36.pyc
deleted file mode 100644
index a487519c40812ca491e14b70d00cbda4c359eeab..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 149
zcmXr!<>fL8(~V&Og2x~N1{i@12OutH0TL+;!3>&=ek&P@K*9*(my@$qOlWaxQE^OS
zN@j^kOh9FFMq*KJKv8~HYH~?&Okh!JaY0OZYEn!AL@1^twHPQKAD@|*SrQ+wS5SG2
T!zMRBr8Fni4rF#Q5HkP()SV^d

diff --git a/web/project/tests/__pycache__/test_paperDAO.cpython-36.pyc b/web/project/tests/__pycache__/test_paperDAO.cpython-36.pyc
deleted file mode 100644
index eacd236120d589fb5ed816e08d348a7f1957184f..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 2022
zcmbtV&2Jnv6u0MlHyfHnp}p`iQlT&@By9mzDhRdRNWH)|rKzY!D~%>=Z!(kFnZfoF
zy4sw!M+$!j|B|nq_!l_wo_8}@!g8ude)c>+zmMO0w!c_kZ@>BVt9}#^@+Vnp4$L1y
zmn9HJ7%fPQqg9X*jVZ;sU08?nH9NMAj1xO%bYqt}%zaH_&;0wb&pqxZ-V?$+=D#M)
z=X7Sr0dKM3)Dk%-d3#1cD}7F))?Z+g^dhQ*LoQV}l^o`DXMk*M7IX^zDRhaRG6LIZ
z?++4L+DXN+)ZXbCjsjN=`TI%tLH~v1LiSUZsW1BnuLdWn7#)Zz=L04C&jgos|BN5?
z>p82hz_>ItsneQ^{YOuC>sQ(V&83f~(GNleU`HC?kcIq*(B)@9IEg7EvBfB}01%tm
z%z+W$VIGVw^H~6+$663WTX!(zgN3;PMv2XZ-iF?VE~h{g$tk1CV%Cg;M$n1+nE%G7
zMA^BMyM}r|{n?xosMd_mK>nPn_I!0pS%941H_k1!mUpJOYX1nSeMWvDFNs<olBxY0
zJ$I%~{*FnIjR~6Uw8KSv&Xo+ub;wec9zmu;RfPy#BQSY)RF%ios2ZF;*xM_rL0X(t
zQfc?z{X2K>_u^}2nU}{|$#J804cOZ1Rgtd)lr7T{*G^ptrGqh~(EJB=D&<)vnD*F_
z;j{-;Q9v%Us?=^Kr7R{bbZa-4RT*8=o8O}&`;WU-Szd@8bG83i+gYi!RY@?CsuLXu
zo)%{2<W*K`52OZXO#3Wb*iMpRR`4XzPF3?#J7_^WMU^t`n&fFmra$w@g^?G-xRWFp
zIl2a$=uo#zkm#LQgLGcjsldw8uH@=Py^h)5211+;b>IuAN8h8{blYmv$<}hE?3xWt
zz1Xk^yQ!BDCW_3+Ii1p+!e~uNZYdkHJ;S4nht8VZX;OxYWta`av?#($P-Vz}$(AzP
ziyR$Xl&anYkh)C*z5_wsh756`4#gPKR{$rn#Z7QV+bpg0CTPD@j>}h3xQ_LZ{73Km
zph9{;h~ohylbinnV)dT4Lgv#e$P6nH*5jihn`cxu%YcaZ1Owaxrw=YA5DgK*g4hAF
zKtbGwdAtQEEa_SW!;OoOu4w!i_Ale`(MlYyY<epoZZ(mjDH$RVSR<yGSHRE#7#<ac
zsS)`<0JIPQyziDS>-izryokF|@%fdAKUf)YBi_RcBuVgcfK%5_l2OIR=Gek{{ArvP
z^A&Lm)C$xs_K@5~(mWjV8J<ef0@8sl@x~8mun|BrTr@LEGdSGQ8r)H3rqFkR4?(=K
zcu#gslu-HN2C#LjxfaET@NZrb9pKxNmGE$(EpZP89aOx^A02!%59nKbCggP>0qwwv
OSbP>-7uLqt0sRMpL<aHz

diff --git a/web/project/tests/__pycache__/test_routes.cpython-36.pyc b/web/project/tests/__pycache__/test_routes.cpython-36.pyc
deleted file mode 100644
index 4da16b65961ef54a54fe1d180ac4adb69964c90b..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 914
zcmZuvJ#X7E5GAP(v$hjB$<(#zq9q;LEJYC%b%Sh1+B%CMfM7)?wJS>sNyA9sPR`Py
zKcxSpzkyrPDSshT?<6~QfC|v*jz_-t_)af(cDld6A7w|3kUwPW2_b(AuYCtW5k(7<
zwqKf3s9C{gK^jnUN>rf2TcScur{O9{BOR;gD>KJXcUFYL*-s>i?*NC466yn4*EtrO
z2dG=B=a6WE@F`PNv0IV`EqEHLNX1Y`ssmu$cRyBhr^nhlo6|KAei3U3uib^<$ds<g
zk_ZqEr|2kQ1~>SggM%V3Cc1Q>D73n`_(@C*z5A2l>+IZWV>78H?p1bnoqv&Lc4n%n
z&YjIZ7;Wopp+9GJyObfAZK5!!${yC&KC;@K*L{?Nl!V?4{z*P;nvaB|_(nJyzn0qw
zN~noosma^WfzorQrFma1$^ldxii0hRP5*%fWgvLN@(hwCnSw!Rv<iN(Zxm{_q*IvY
ziow*-vS@TqUyKu)4lb&qs20L#H8JSJ-7i2$!q(5=Qaj(17Ho4TS94kTo^{gAt;j2-
z!F9ZW=jdEj!X`9&>n^*^IA(HEidtUk1L#^*O6Y*zJbiR07~8|XQ4)JDL@8%l2;UWA
zR;hV`d0z-r(RK_+wkH_St1a?I2D)hi2v}JRJmw(}nl;34_yqiOtg@cZ%ZWp|zOx>G
n>i{3a+EBvX5X$U9@FAZ3AD!oKTB*l4b=yTw%2}W7?{WGU1$)#8

diff --git a/web/project/tests/test_paperDAO.py b/web/project/tests/test_paperDAO.py
index f14a9305..b57b458d 100644
--- a/web/project/tests/test_paperDAO.py
+++ b/web/project/tests/test_paperDAO.py
@@ -1,15 +1,13 @@
 import unittest
-from unittest import TestCase
 from project.paperdao import *
 import os
-import mongomock
 import json
 def warn(*args, **kwargs):
     pass
 import warnings
 warnings.warn = warn
 
-class TestPaperDAO(TestCase):
+class TestPaperDAO(unittest.TestCase):
     def setUp(self):
         """
         Sets up database to test
@@ -25,6 +23,14 @@ def setUp(self):
         paper = Paper(**paperdata)
         paper.save()
 
+    def tearDown(self):
+        """
+        Sets up database to test
+        """
+        paper = Paper()
+        paper.drop_collection()
+
+
     def test_getCollectionList(self):
         """
         Tests if all collections exist
@@ -63,7 +69,6 @@ def test_getFilteredPaperObjectsForAuthors(self):
         """
         dao = PaperDAO()
         allSearchObjects = dao.getAllFilteredSearchObjects(authorsList=['marco'])
-        print(len(allSearchObjects))
         self.assertTrue(list(allSearchObjects))
 
     def test_getFilteredPaperObjectsForSearchWord(self):
@@ -72,7 +77,6 @@ def test_getFilteredPaperObjectsForSearchWord(self):
         """
         dao = PaperDAO()
         allSearchObjects = dao.getAllFilteredSearchObjects(searchWord='photo')
-        print(len(allSearchObjects))
         self.assertTrue(list(allSearchObjects))
 
     def test_getFilteredPaperObjectsForTitle(self):
@@ -90,7 +94,6 @@ def test_getFilteredPaperObjectsForTags(self):
         """
         dao = PaperDAO()
         allSearchObjects = dao.getAllFilteredSearchObjects(tags=['photo'])
-        print(len(allSearchObjects))
         self.assertTrue(list(allSearchObjects))
 
     def test_getFilteredPaperObjectsForCollections(self):
@@ -99,7 +102,6 @@ def test_getFilteredPaperObjectsForCollections(self):
         """
         dao = PaperDAO()
         allSearchObjects = dao.getAllFilteredSearchObjects(collectionList=['miccom'])
-        print(len(allSearchObjects))
         self.assertTrue(list(allSearchObjects))
 
     def test_insertDOI(self):
@@ -109,6 +111,7 @@ def test_insertDOI(self):
         dao = PaperDAO()
         allSearchObjects = dao.getAllFilteredSearchObjects()
         paper = dao.insertDOI(allSearchObjects[0]['_Search__id'],'123')
+        print(dao.getAllPapers())
         self.assertEquals(1, paper)
 
 

From 56999481ddc2dab3a16658a3b76964205d9fd90f Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Wed, 16 Jan 2019 13:58:03 -0600
Subject: [PATCH 09/15] Updates for coverall

---
 .travis.yml                        | 6 ++++--
 README.md                          | 3 ++-
 web/project/tests/test_paperDAO.py | 1 -
 web/requirements.txt               | 3 ++-
 4 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 9d9d6faa..a4a49447 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,6 @@ python:
 os:
   - linux
   - osx
-  - windows
 
 install:
   - cd web
@@ -15,4 +14,7 @@ install:
   - python setup.py install
 # command to run tests
 script:
-  - nose2
+  - nose2 -v
+
+after_success:
+  - coveralls
\ No newline at end of file
diff --git a/README.md b/README.md
index 65a1cfe0..3f5cb6c6 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,5 @@
-[![Build Status](https://travis-ci.com/atanikan/Qresp.svg?branch=qresp-1.1)](https://travis-ci.com/atanikan/Qresp)
+[![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=qresp-1.1)
 
 # Qresp
 [Qresp](http://qresp.org) software repository. 
diff --git a/web/project/tests/test_paperDAO.py b/web/project/tests/test_paperDAO.py
index b57b458d..e56e24ee 100644
--- a/web/project/tests/test_paperDAO.py
+++ b/web/project/tests/test_paperDAO.py
@@ -111,7 +111,6 @@ def test_insertDOI(self):
         dao = PaperDAO()
         allSearchObjects = dao.getAllFilteredSearchObjects()
         paper = dao.insertDOI(allSearchObjects[0]['_Search__id'],'123')
-        print(dao.getAllPapers())
         self.assertEquals(1, paper)
 
 
diff --git a/web/requirements.txt b/web/requirements.txt
index 9d88081c..2a896d94 100644
--- a/web/requirements.txt
+++ b/web/requirements.txt
@@ -27,4 +27,5 @@ requests_oauthlib
 mongomock
 connexion[swagger-ui]
 coverage
-nose2
\ No newline at end of file
+nose2
+python-coveralls
\ No newline at end of file

From 2152d9e6aa6758b885de102129a2656daee83dcd Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Wed, 16 Jan 2019 14:14:25 -0600
Subject: [PATCH 10/15] Updates for coverall

---
 .travis.yml | 36 ++++++++++++++++++++++++++++--------
 README.md   |  4 ++--
 2 files changed, 30 insertions(+), 10 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index a4a49447..45adebac 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,12 +1,32 @@
 language: python
-python:
-  - "3.4"
-  - "3.5"
-  - "3.6"
+#python:
+#  - "3.4"
+#  - "3.5"
+#  - "3.6"
 # command to install dependencies
-os:
-  - linux
-  - osx
+#os:
+#  - linux
+#  - osx
+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
+          python: 3.4
+          env: TOXENV=py34
+        - os: osx
+          python: 3.5
+          env: TOXENV=py35
+        - os: osx
+          python: 3.6
+          env: TOXENV=py36
 
 install:
   - cd web
@@ -14,7 +34,7 @@ install:
   - python setup.py install
 # command to run tests
 script:
-  - nose2 -v
+  - nose2 --with-coverage -v
 
 after_success:
   - coveralls
\ No newline at end of file
diff --git a/README.md b/README.md
index 3f5cb6c6..7edce470 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 [![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=qresp-1.1)
-
+[![Coverage Status](https://coveralls.io/repos/github/qresp-code-development/qresp/badge.svg?branch=qresp-1.1)](https://coveralls.io/github/qresp-code-development/qresp?branch=qresp-1.1)
+[![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. 
 

From 493b22057b4c38d6b16871a28a0749bec60db8de Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Wed, 16 Jan 2019 14:24:22 -0600
Subject: [PATCH 11/15] Updates for coverall

---
 .travis.yml | 34 +++++++++++++++++++++++++++-------
 1 file changed, 27 insertions(+), 7 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 45adebac..128a47f7 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -19,14 +19,34 @@ matrix:
           python: 3.6
           env: TOXENV=py36
         - os: osx
-          python: 3.4
-          env: TOXENV=py34
-        - os: osx
-          python: 3.5
-          env: TOXENV=py35
+          env: PYTHON=3.4.4
+          language: generic
         - os: osx
-          python: 3.6
-          env: TOXENV=py36
+          language: generic
+          env: PYTHON=3.5.1
+
+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.
+    python --version
+  fi
 
 install:
   - cd web

From 7b034097602c772ddcfa288547db659e258373a0 Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Wed, 16 Jan 2019 14:33:36 -0600
Subject: [PATCH 12/15] Updates for coverall with Readme and travis for OSX

---
 README.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/README.md b/README.md
index 7edce470..fddcc6f3 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,4 @@
 [![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=qresp-1.1)](https://coveralls.io/github/qresp-code-development/qresp?branch=qresp-1.1)
 [![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. 

From 3d86af609f32a60388dc40aa1a23902ee719d6d9 Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Wed, 23 Jan 2019 19:35:52 -0600
Subject: [PATCH 13/15] Added support for coverall

---
 .travis.yml                 | 9 +--------
 docker-compose.override.yml | 2 +-
 2 files changed, 2 insertions(+), 9 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 128a47f7..bcf4edc0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,12 +1,4 @@
 language: python
-#python:
-#  - "3.4"
-#  - "3.5"
-#  - "3.6"
-# command to install dependencies
-#os:
-#  - linux
-#  - osx
 matrix:
     include:
         - os: linux
@@ -45,6 +37,7 @@ before_install: |
     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
 
diff --git a/docker-compose.override.yml b/docker-compose.override.yml
index 891190b0..eca42112 100644
--- a/docker-compose.override.yml
+++ b/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

From c7badf9ca1b7e210ef8fb1579abebb5a5fb61a22 Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Thu, 24 Jan 2019 11:46:28 -0600
Subject: [PATCH 14/15] Added more unit tests and corrections based on unit
 tests

---
 .travis.yml                        |   3 -
 web/project/__init__.py            |  15 ++--
 web/project/api.py                 |   6 +-
 web/project/routes.py              | 120 ++++++++++++++++-------------
 web/project/tests/test_paperDAO.py |  45 ++++++++---
 web/project/tests/test_routes.py   |  86 ++++++++++++++++++---
 web/project/util.py                |   4 +-
 web/run.py                         |   2 +-
 8 files changed, 191 insertions(+), 90 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index bcf4edc0..56e36c69 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -13,9 +13,6 @@ matrix:
         - os: osx
           env: PYTHON=3.4.4
           language: generic
-        - os: osx
-          language: generic
-          env: PYTHON=3.5.1
 
 before_install: |
   if [ "$TRAVIS_OS_NAME" == "osx" ]; then
diff --git a/web/project/__init__.py b/web/project/__init__.py
index b843c590..d65b3197 100644
--- a/web/project/__init__.py
+++ b/web/project/__init__.py
@@ -22,8 +22,6 @@
 MONGODB_PASSWORD = os.environ.get("MONGODB_PASSWORD")
 MONGODB_DB = os.environ.get("MONGODB_DB")
 
-
-#app = Flask(__name__)
 # Create the application instance
 connexionapp = connexion.App(__name__, specification_dir='./')
 
@@ -31,6 +29,7 @@
 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__)
@@ -45,12 +44,14 @@
 os.environ['OAUTHLIB_INSECURE_TRANSPORT'] = '1'
 app.config['MAIL_ADDR'] = MAIL_ADDR
 app.config['MAIL_PWD'] = MAIL_PWD
-app.config['MONGODB_HOST'] = 'paperstack.uchicago.edu'
-app.config['MONGODB_PORT'] = 27017
-app.config['MONGODB_USERNAME'] = 'qresp_user_explorer'
-app.config['MONGODB_PASSWORD'] = 'qresp_pwd'
-app.config['MONGODB_DB'] = 'explorer'
+app.config['MONGODB_HOST'] = MONGODB_HOST
+app.config['MONGODB_PORT'] = MONGODB_PORT
+app.config['MONGODB_USERNAME'] = MONGODB_USERNAME
+app.config['MONGODB_PASSWORD'] = MONGODB_PASSWORD
+app.config['MONGODB_DB'] = MONGODB_DB
+
 Session(app)
 ext = Sitemap(app)
 
+
 from project import routes
diff --git a/web/project/api.py b/web/project/api.py
index e40968ea..12b6a5bf 100644
--- a/web/project/api.py
+++ b/web/project/api.py
@@ -84,7 +84,7 @@ def paper(id):
     except Exception as e:
         msg = "Exception in paper api " + str(e)
         print("Exception in paper api ", e)
-        return e, 500
+        return e, 400
     return paperdetail
 
 def workflow(id):
@@ -101,7 +101,7 @@ def workflow(id):
     except Exception as e:
         msg = "Exception in workflow api " + str(e)
         print("Exception in workflow api ", e)
-        return msg,500
+        return msg,400
     return workflowdetail
 
 def chart(id,cid):
@@ -118,5 +118,5 @@ def chart(id,cid):
     except Exception as e:
         msg = "Exception in chart api " + str(e)
         print("Exception in chart api ", e)
-        return msg,500
+        return msg,400
     return chartworkflowdetail
\ No newline at end of file
diff --git a/web/project/routes.py b/web/project/routes.py
index 4b949ce2..37f0314a 100644
--- a/web/project/routes.py
+++ b/web/project/routes.py
@@ -12,7 +12,7 @@
 
 from flask_cors import CORS
 
-from .paperdao import *
+from .paperdao import PaperDAO,MongoDBConnection
 from .util import *
 from .views import *
 from project import app
@@ -60,7 +60,7 @@ def index():
     """ Fetches the homepage
     """
     #TO BE DELETED
-    SetLocalHost(str(request.host_url).strip("/"))
+    #SetLocalHost(str(request.host_url).strip("/"))
     return render_template('index.html')
 
 @app.route('/downloads/<file>')
@@ -158,11 +158,12 @@ def uploadFile():
         session["tags"] = [form for form in paperform.tags.data]
         session["collections"] = [form for form in paperform.collections.data]
         session["workflow"] = paperform.workflow.data
-        return jsonify(out="Processed text")
-    except:
-        return jsonify(error="Could not process json file")
-
+        return jsonify(out="Processed text"), 200
+    except Exception as e:
+        print(e)
+        return jsonify(error=str(e)), 400
 
+@csrf.exempt
 @app.route('/details', methods=['POST', 'GET'])
 def details():
     """ This method helps in storing the details of the person using the curator.
@@ -193,12 +194,12 @@ def server():
             return redirect(url_for('project'))
         except Exception as e:
             flash("Could not connect to server. Plase try again!"+str(e))
-            render_template('server.html', form=form)
-    return render_template('server.html', form=form)
+            render_template('server.html', form=form), 400
+    return render_template('server.html', form=form), 200
 
 
 @csrf.exempt
-@app.route('/project', methods=['POST', 'GET'])
+@app.route('/project', methods=['GET'])
 def project():
     """ This method helps in populating the project form.
     """
@@ -237,11 +238,11 @@ def setproject():
                 session["ProjectName"] = absPath.rsplit("/",1)[1]
             else:
                 session["ProjectName"] = absPath
-            return jsonify(folderAbsolutePath=absPath,isConfigFile=isConfig,services=services)
+            return jsonify(folderAbsolutePath=absPath,isConfigFile=isConfig,services=services), 200
     except Exception as e:
         print(e)
         flash("Could not connect to server. Plase try again! " + str(e))
-        return jsonify(folderAbsolutePath=absPath, isConfigFile=isConfig, services=services)
+        return jsonify(folderAbsolutePath=absPath, isConfigFile=isConfig, services=services), 401
 
 
 @csrf.exempt
@@ -252,19 +253,20 @@ def getTreeInfo():
     pathDetails = request.get_json()
     listObjects = []
     services = []
-    ftpclient = session.get("sftpclient")
-    ftp = ftp_dict[ftpclient]
-    if 'folderAbsolutePath' in pathDetails:
-        content_path = pathDetails['folderAbsolutePath']
-    else:
-        content_path = session.get("folderAbsolutePath")
     try:
+        ftpclient = session.get("sftpclient")
+        ftp = ftp_dict[ftpclient]
+        if 'folderAbsolutePath' in pathDetails:
+            content_path = pathDetails['folderAbsolutePath']
+        else:
+            content_path = session.get("folderAbsolutePath")
         dtree = Dtree(ftp,content_path,session)
         listObjects = dtree.fetchForTree()
         services = dtree.fetchServices()
     except Exception as e:
+        jsonify({'errors':str(e)}), 400
         print(e)
-    return jsonify({'listObjects': listObjects, 'services': services})
+    return jsonify({'listObjects': listObjects, 'services': services}), 200
 
 @app.route('/curate', methods=['POST', 'GET'])
 def curate():
@@ -318,8 +320,8 @@ def info():
         session["collections"] = infoform.collections.data.split(",")
         session["notebookFile"] = infoform.notebookFile.data
         msg = "Info Saved"
-        return jsonify(data=msg)
-    return jsonify(data=infoform.errors)
+        return jsonify(data=msg), 200
+    return jsonify(data=infoform.errors), 400
 
 @csrf.exempt
 @app.route('/charts', methods=['POST', 'GET'])
@@ -343,8 +345,8 @@ def charts():
                 chartList = [item for item in chartList if item['saveas'] not in chartform.saveas.data]
                 chartList.append(chartform.data)
                 session["charts"] = deepcopy(chartList)
-        return jsonify(chartList = chartList)
-    return jsonify(data=chartform.errors)
+        return jsonify(chartList = chartList), 200
+    return jsonify(data=chartform.errors), 200
 
 @csrf.exempt
 @app.route('/tools', methods=['POST', 'GET'])
@@ -368,8 +370,8 @@ def tools():
                 toolList = [item for item in toolList if item['saveas'] not in toolform.saveas.data]
                 toolList.append(toolform.data)
                 session["tools"] = deepcopy(toolList)
-        return jsonify(toolList = toolList)
-    return jsonify(errors=toolform.errors)
+        return jsonify(toolList = toolList), 200
+    return jsonify(errors=toolform.errors), 200
 
 @csrf.exempt
 @app.route('/datasets', methods=['POST', 'GET'])
@@ -393,8 +395,8 @@ def datasets():
                 datasetList = [item for item in datasetList if item['saveas'] not in datasetform.saveas.data]
                 datasetList.append(datasetform.data)
                 session["datasets"] = deepcopy(datasetList)
-        return jsonify(datasetList = datasetList)
-    return jsonify(data=datasetform.errors)
+        return jsonify(datasetList = datasetList), 200
+    return jsonify(data=datasetform.errors), 200
 
 @csrf.exempt
 @app.route('/scripts', methods=['POST', 'GET'])
@@ -418,8 +420,8 @@ def scripts():
                 scriptList = [item for item in scriptList if item['saveas'] not in scriptform.saveas.data]
                 scriptList.append(scriptform.data)
                 session["scripts"] = deepcopy(scriptList)
-        return jsonify(scriptList = scriptList)
-    return jsonify(data=scriptform.errors)
+        return jsonify(scriptList = scriptList), 200
+    return jsonify(data=scriptform.errors), 200
 
 @csrf.exempt
 @app.route('/reference', methods=['POST', 'GET'])
@@ -430,8 +432,8 @@ def reference():
     if request.method == 'POST' and referenceform.validate():
         session["reference"] = referenceform.data
         msg = "Reference Saved"
-        return jsonify(data=msg)
-    return jsonify(data=referenceform.errors)
+        return jsonify(data=msg), 200
+    return jsonify(data=referenceform.errors), 200
 
 @csrf.exempt
 @app.route('/fetchReferenceDOI', methods=['POST', 'GET'])
@@ -444,8 +446,8 @@ def fetchReferenceDOI():
         refdata = fetchDOI.fetchFromDOI()
     except Exception as e:
         print(e)
-        return jsonify(errors="Recheck your DOI")
-    return jsonify(fetchDOI=refdata.data)
+        return jsonify(errors="Recheck your DOI"), 400
+    return jsonify(fetchDOI=refdata.data), 200
 
 @csrf.exempt
 @app.route('/documentation', methods=['POST', 'GET'])
@@ -456,8 +458,8 @@ def documentation():
     if request.method == 'POST' and docform.validate():
         session["documentation"] = docform.data
         msg = "Documentation Saved"
-        return jsonify(data=msg)
-    return jsonify(data=docform.errors)
+        return jsonify(data=msg), 200
+    return jsonify(data=docform.errors), 200
 
 @csrf.exempt
 @app.route('/workflow', methods=['POST', 'GET'])
@@ -559,10 +561,9 @@ def workflow():
         session["workflow"] = workflowinfo.data
     except Exception as e:
         print(e)
-    return jsonify({'workflow': workflow.__dict__})
+    return jsonify({'workflow': workflow.__dict__}), 200
 
 
-# Fetches list of qresp servers for the explorer
 @csrf.exempt
 @app.route('/publish', methods=['POST', 'GET'])
 def publish():
@@ -720,7 +721,7 @@ def download():
     with open("papers/"+projectName+"/"+"data.json", "w") as outfile:
         json.dump(paperdata, outfile, default=lambda o: o.__dict__, separators=(',', ':'), sort_keys=True, indent=3)
     session["paper"] = paperdata
-    return jsonify(paper=paperdata)
+    return jsonify(paper=paperdata), 200
 
 
 @csrf.exempt
@@ -737,15 +738,13 @@ def acknowledgement():
 def qrespexplorer():
     """ Fetches the explorer homepage
     """
-    dao = PaperDAO()
-    dao.getDB()
     form = QrespServerForm()
     serverslist = Servers()
     form.serverList = [qrespserver['qresp_server_url'] for qrespserver in
                            serverslist.getServersList()]
     if request.method == 'POST':
-        if request.form.get('serversList'):
-            session["selectedserver"] = request.form.get('serversList')
+        if request.form.getlist('serversList'):
+            session["selectedserver"] = request.form.getlist('serversList')
         else:
             session['selectedserver'] = form.serverList
         return redirect(url_for('search'))
@@ -760,8 +759,8 @@ def verifypasscode():
     confirmpasscode = app.config['passkey']
     if request.method == 'POST' and form.validate():
         if confirmpasscode == form.passcode.data:
-            return jsonify(msg="success")
-    return jsonify(msg="failed")
+            return jsonify(msg="success"),200
+    return jsonify(msg="failed"),401
 
 # Fetches list of qresp admin
 @csrf.exempt
@@ -807,14 +806,23 @@ def search():
     :return: template: search.html
     """
     allpaperslist = []
+    collectionlist = []
+    authorslist = []
+    publicationlist = []
+    allPapersSize = 0
     try:
         selectedserver = session.get("selectedserver")
         fetchdata = FetchDataFromAPI(selectedserver)
-        allpaperslist = fetchdata.fetchOutput('/api/search')
-        collectionlist = fetchdata.fetchOutput('/api/collections')
-        authorslist = fetchdata.fetchOutput('/api/authors')
-        publicationlist = fetchdata.fetchOutput('/api/publications')
-        allPapersSize = len(allpaperslist)
+        fetchallpaperslist = fetchdata.fetchOutput('/api/search')
+        fetchcollectionlist = fetchdata.fetchOutput('/api/collections')
+        fetchauthorslist = fetchdata.fetchOutput('/api/authors')
+        fetchpublicationlist = fetchdata.fetchOutput('/api/publications')
+        if fetchallpaperslist and len(fetchallpaperslist)>0:
+            allpaperslist = fetchallpaperslist
+            collectionlist = fetchcollectionlist
+            authorslist = fetchauthorslist
+            publicationlist = fetchpublicationlist
+            allPapersSize = len(allpaperslist)
     except Exception as e:
         print(e)
         flash('Error in search. ' + str(e))
@@ -830,6 +838,7 @@ def searchWord():
     """  filtering paper content
     :return: object: allpaperlist
     """
+    allpaperslist = []
     try:
         dao = PaperDAO()
         searchWord = request.args.get('searchWord', type=str)
@@ -844,10 +853,11 @@ def searchWord():
         url = '/api/search'+"?searchWord="+searchWord+"&paperTitle="+paperTitle+"&doi="+doi+"&tags="+tags+"&collectionList="+",".join(collectionList) + \
               "&authorsList="+",".join(authorsList)+"&publicationList="+",".join(publicationList)
         allpaperslist = fetchdata.fetchOutput(url)
-        return jsonify(allpaperslist=allpaperslist)
+        return jsonify(allpaperslist=allpaperslist), 200
     except Exception as e:
         print(e)
         flash('Error in search. ' + str(e))
+        return jsonify(allpaperslist=allpaperslist), 400
 
 
 # Fetches details of chart based on user click
@@ -857,6 +867,8 @@ def paperdetails(paperid):
     """  fetching papers details content
     :return: template: paperdetails.html
     """
+    paperdetail = []
+    workflowdetail = []
     try:
         selectedserver = session.get("selectedserver")
         fetchdata = FetchDataFromAPI(selectedserver)
@@ -868,8 +880,6 @@ def paperdetails(paperid):
     except Exception as e:
         print(e)
         flash('Error in paperdetails. ' + str(e))
-        paperdetail = []
-        workflowdetail = []
         return render_template('paperdetails.html', paperdetail=paperdetail, workflowdetail=workflowdetail)
 
 
@@ -881,6 +891,7 @@ def chartworkflow():
     """  Fetching chart workflow content
     :return: object: chartworkflow
     """
+    chartworkflowdetail = []
     try:
         dao = PaperDAO()
         paperid = request.args.get('paperid', 0, type=str)
@@ -891,10 +902,11 @@ def chartworkflow():
         fetchdata = FetchDataFromAPI(selectedserver)
         url = '/api/paper/' + paperid + '/chart/' + chartid
         chartworkflowdetail = fetchdata.fetchOutput(url)
-        return jsonify(chartworkflowdetail=chartworkflowdetail)
+        return jsonify(chartworkflowdetail=chartworkflowdetail), 200
     except Exception as e:
         print(e)
-        flash('Error in paperdetails. ' + str(e))
+        flash('Error in chartdetails. ' + str(e))
+        return jsonify(chartworkflowdetail=chartworkflowdetail), 400
 
 @csrf.exempt
 @app.route('/getDescriptor', methods=['POST','GET'])
@@ -947,7 +959,7 @@ def insertDOI():
     except Exception as e:
         print(e)
         content = {'Failed': 'Could Not Insert'}
-        return jsonify(content), 500
+        return jsonify(content), 400
     content = {'Success': 'Inserted'}
     return jsonify(content), 200
 
diff --git a/web/project/tests/test_paperDAO.py b/web/project/tests/test_paperDAO.py
index e56e24ee..8ef9ce81 100644
--- a/web/project/tests/test_paperDAO.py
+++ b/web/project/tests/test_paperDAO.py
@@ -1,5 +1,5 @@
 import unittest
-from project.paperdao import *
+from project.paperdao import PaperDAO,MongoDBConnection,Paper
 import os
 import json
 def warn(*args, **kwargs):
@@ -85,7 +85,6 @@ def test_getFilteredPaperObjectsForTitle(self):
         """
         dao = PaperDAO()
         allSearchObjects = dao.getAllFilteredSearchObjects(paperTitle='photo')
-        print(len(allSearchObjects))
         self.assertTrue(list(allSearchObjects))
 
     def test_getFilteredPaperObjectsForTags(self):
@@ -106,7 +105,7 @@ def test_getFilteredPaperObjectsForCollections(self):
 
     def test_insertDOI(self):
         """
-        Tests for isertion of DOI
+        Tests for insertion of DOI
         """
         dao = PaperDAO()
         allSearchObjects = dao.getAllFilteredSearchObjects()
@@ -114,14 +113,38 @@ def test_insertDOI(self):
         self.assertEquals(1, paper)
 
 
-    # def test_getPaperDetails(self):
-    #     self.fail()
-    #
-    # def test_getWorkflowDetails(self):
-    #     self.fail()
-    #
-    # def test_getWorkflowForChartDetails(self):
-    #     self.fail()
+    def test_getPaperDetails(self):
+        """
+        Tests Paper details given paper id
+        """
+        dao = PaperDAO()
+        allSearchObjects = dao.getAllFilteredSearchObjects()
+        paperDetails = dao.getPaperDetails(allSearchObjects[0]['_Search__id'])
+        self.assertEquals(allSearchObjects[0]['_Search__id'], paperDetails['_PaperDetails__id'])
+
+
+    def test_getWorkflowDetails(self):
+        """
+        Tests workflow details given paper id
+        """
+        dao = PaperDAO()
+        allSearchObjects = dao.getAllFilteredSearchObjects()
+        workflowdetails = dao.getWorkflowDetails(allSearchObjects[0]['_Search__id'])
+        self.assertEquals(workflowdetails['paperTitle'],allSearchObjects[0]['_Search__title'])
+
+
+
+    def test_getWorkflowForChartDetails(self):
+        """
+        Tests workflow details given chart id and paper id
+        :return:
+        """
+        dao = PaperDAO()
+        allSearchObjects = dao.getAllFilteredSearchObjects()
+        paperDetails = dao.getPaperDetails(allSearchObjects[0]['_Search__id'])
+        chartid = paperDetails['_PaperDetails__charts'][0].id
+        workflowchartdetails = dao.getWorkflowForChartDetails(paperDetails['_PaperDetails__id'],chartid)
+        self.assertEquals(workflowchartdetails['paperTitle'],allSearchObjects[0]['_Search__title'])
 
 if __name__ == "__main__":
     unittest.main()
\ No newline at end of file
diff --git a/web/project/tests/test_routes.py b/web/project/tests/test_routes.py
index c0e08f65..7f86f909 100644
--- a/web/project/tests/test_routes.py
+++ b/web/project/tests/test_routes.py
@@ -1,7 +1,10 @@
 import os
 import unittest
-
+import json
 from project import app
+from project.views import *
+from flask import Flask, request, jsonify
+
 
 class RouteTests(unittest.TestCase):
     ############################
@@ -10,19 +13,84 @@ class RouteTests(unittest.TestCase):
 
     # executed prior to each test
     def setUp(self):
-        self.app = app.test_client()
+
+        self.app = self.create_app()
+        self.client = app.test_client()
+        self.ctx = self.app.test_request_context()
+        self.ctx.push()
+
+        self.pagenames = ['/','qrespcurator','startfromscratch','details','server','project','curate','workflow','publish',
+                          'acknowledgement','qrespexplorer','admin','search',
+                          'searchWord?searchWord=&paperTitle=&tags=&doi=&collectionList=[]&authorsList=[]&publicationList=[]',
+                          'paperdetails/5941869f1bd40fd44db0024a','chartworkflow?paperid=5941869f1bd40fd44db0024a&chartid=c0']
+
+        postpagedicts = {'details':{'firstName':'John','middleName':'L','lastName':'Doe'},
+                         'server':{'serverName':'testServer','username':'testuser','password':'testpassword','isDUOAuth':'No'},
+                         'charts':{'caption':'cc','number':'1','files':'a,b','imageFile':'a.png','properties':'1,2','saveas':'c0'},
+                         'tools':{'packageName':'West','version':'v0','facilityName':'Xray','measurement':'xray','saveas':'t0'},
+                         'datasets':{'files':'a,b','readme':'readdata','saveas':'d0'},
+                         'scripts':{'files':'a,b','readme':'readdata','saveas':'s0'},
+                         'reference':{'DOI':'doi/10.123','title':'Test','page':'1','publishedAbstract':'Abs','volume':'1','year':2019},
+                         'fetchReferenceDOI':{},
+                         'documentation':{'readme':'read'},
+                         'publish':{},
+                         'download':{}}
+
+        nameform = NameForm()
+        nameform.firstName.data = 'John'
+        nameform.middleName.data = 'L.'
+        nameform.lastName.data = 'Doe'
+        detailsform = DetailsForm(**postpagedicts['details'])
+        serverform = ServerForm(**postpagedicts['server'])
+        chartform = ChartForm(**postpagedicts['charts'])
+        chartform.extraFields.entries = []
+        toolform = ToolForm(**postpagedicts['tools'])
+        toolform.extraFields.entries = []
+        datasetform = DatasetForm(**postpagedicts['datasets'])
+        datasetform.extraFields.entries = []
+        scriptform = ScriptForm(**postpagedicts['scripts'])
+        scriptform.extraFields.entries = []
+        referenceform = ReferenceForm(**postpagedicts['reference'])
+        referenceform.authors.entries = []
+        referenceform.journal.abbrevName.data = 'JAbbr'
+        referenceform.journal.fullName.data = 'JFull'
+        documentationform = DocumentationForm(**postpagedicts['documentation'])
+        self.postPageForms = {'details':detailsform,'server':serverform,'charts':chartform,'tools':toolform,
+                              'datasets':datasetform,'scripts':scriptform,'fetchReferenceDOI':{'doi':'10.1021/nl903868w'},
+                              'documentation':documentationform,'workflow':[['to','do'],['to','do']],
+                              'publish':{},'download':{}}
 
     # executed after each test
+    def create_app(self):
+        app = Flask(__name__)
+        app.secret_key = "secret"
+        return app
+
     def tearDown(self):
-        pass
+        self.ctx.pop()
+
+    def request(self,*args, **kwargs):
+        return self.app.test_request_context(*args, **kwargs)
+
+    def test_getMethods(self):
+        for pagename in self.pagenames:
+            response = self.client.get(pagename, follow_redirects=True)
+            self.assertEquals(response.status_code,200)
+
+
+    def test_postMethods(self):
+        for pagename in self.postPageForms.keys():
+            form = self.postPageForms[pagename]
+            if 'fetchReferenceDOI' in pagename or 'workflow' in pagename or 'publish' in pagename or 'download' in pagename:
+                response = self.client.post(pagename, data=json.dumps(form), content_type='application/json')
+            else:
+                response = self.client.post(pagename,data=form.data)
+            if 'details' in pagename:
+                self.assertEqual(response.status_code, 302)
+            else:
+                self.assertEqual(response.status_code, 200)
 
-    def test_main_page(self):
-        response = self.app.get('/', follow_redirects=True)
-        self.assertEqual(response.status_code, 200)
 
-    def test_main_page(self):
-        response = self.app.get('/', follow_redirects=True)
-        self.assertEqual(response.status_code, 200)
 
 if __name__ == "__main__":
     unittest.main()
diff --git a/web/project/util.py b/web/project/util.py
index d235b15a..cbb2f4bf 100644
--- a/web/project/util.py
+++ b/web/project/util.py
@@ -409,7 +409,8 @@ class FetchDataFromAPI():
     """ Fetches data for search,paper details and chart details for explorer
     """
     def __init__(self,servernames):
-        serverList = []
+        if isinstance(servernames,str):
+            servernames = [servernames]
         if servernames and len(servernames)>0:
             serverList = servernames
         else:
@@ -430,7 +431,6 @@ def fetchOutput(self,apiname):
         self.__servernames = list(set(self.__servernames))
         for snames in self.__servernames:
             url = snames + apiname
-            print("url>",url)
             headers = {'Application': 'qresp', 'Accept': 'application/json', 'Content-Type': 'application/json'}
             response = requests.get(url,headers=headers, verify=False)
             if response.status_code == 200:
diff --git a/web/run.py b/web/run.py
index a5b9fff3..32ac3525 100644
--- a/web/run.py
+++ b/web/run.py
@@ -7,5 +7,5 @@
 
 #app.run()
 if __name__ == "__main__":
-    connexionapp.run(port=80,debug=True)
+    connexionapp.run(host='0.0.0.0',port=80,debug=True)
 

From 2ecdb7c64f4fd3c09b3d1d38a377eb4f5e3a7bcd Mon Sep 17 00:00:00 2001
From: atanikan <aditya.tanikanti@gmail.com>
Date: Fri, 25 Jan 2019 10:07:14 -0600
Subject: [PATCH 15/15] Added new docker compose for services

---
 docker-compose.yml.services | 45 +++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 docker-compose.yml.services

diff --git a/docker-compose.yml.services b/docker-compose.yml.services
new file mode 100644
index 00000000..ae62d4bf
--- /dev/null
+++ b/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