From ae27a5c9996f34487ee0f2669104b30dee263189 Mon Sep 17 00:00:00 2001
From: Navan Chauhan <navanchauhan@gmail.com>
Date: Mon, 24 Aug 2020 16:02:32 +0530
Subject: [PATCH] added pubmed search

---
 README.md                 |  3 +++
 app/forms.py              |  5 +++-
 app/templates/search.html | 50 +++++++++++++++++++++++++++++++++++++++
 app/views.py              | 27 +++++++++++++++++++--
 requirements.txt          |  9 +++++++
 5 files changed, 91 insertions(+), 3 deletions(-)
 create mode 100644 app/templates/search.html

diff --git a/README.md b/README.md
index 231bbec..232e35e 100644
--- a/README.md
+++ b/README.md
@@ -5,6 +5,9 @@
 [![DeepSource](https://static.deepsource.io/deepsource-badge-dark-mini.svg)](https://deepsource.io/gh/navanchauhan/Curie-Web/?ref=repository-badge) 
 
 
+**Do Not Forget To Change DB Host configuration!**
+
+
 
 ```
 export PATH=$PATH:/home/pi/Desktop/Curie-Web/app/src/scripts
diff --git a/app/forms.py b/app/forms.py
index 44dadfc..975b3ad 100644
--- a/app/forms.py
+++ b/app/forms.py
@@ -36,4 +36,7 @@ class statusForm(FlaskForm):
 
 class generateSMILES(FlaskForm):
     n = IntegerField('Number of Molecules to Generate',default=1,validators=[DataRequired()])
-    #modelSelection = SelectField('Model',choices=[("alpha","Alpha"),("beta","Beta")])
\ No newline at end of file
+    #modelSelection = SelectField('Model',choices=[("alpha","Alpha"),("beta","Beta")])
+
+class PyMedSearch(FlaskForm):
+    query = StringField('Search Query for PubMed',default="Covid-19",validators=[DataRequired()])
\ No newline at end of file
diff --git a/app/templates/search.html b/app/templates/search.html
new file mode 100644
index 0000000..1faf151
--- /dev/null
+++ b/app/templates/search.html
@@ -0,0 +1,50 @@
+{% extends 'base.html' %}
+
+{% block main %}
+    <h1>Curie Search</h1>
+    <p>Search PubMed articles.</p>
+    <form action="{{ url_for('pubmed') }}" method="post" enctype="multipart/form-data">
+        {% include 'flash_messages.html' %}
+        {{ form.csrf_token }}
+        <div class="form-row">
+                {{ form.query.label }}
+                {{ form.query(class="form-control")}}
+        </div>
+        <!--<div class="form-row">
+            {\{ form.modelSelection.label }}
+            {\{ form.modelSelection(class="form-control")}}
+        </div>-->
+        <br>
+        <div class="form-row">
+            <button type="submit" class="btn btn-primary">Search</button>
+        </div>
+    </form>
+
+    {% if result %}
+        <h3>Search Results</h3>
+        {% for x in range(result|length) %}
+        <!--<i>{\{result}}</i>-->
+        <!--<p>{{result[x]}}</p>-->
+        <div class="card mb-3">
+            <div class="row no-gutters">
+                <div class="col-md-4 text-white bg-dark">
+                    <div class="card-body">
+                    <p class="card-text"><b>DOI: </b><a href="https://doi.org/{{result[x]['doi']}}">{{result[x]['doi']}}</a></p>
+                    <p class="card-text"><b>PubMed ID: </b><a href="https://pubmed.ncbi.nlm.nih.gov/{{result[x]['pubmed_id']}}">{{result[x]['pubmed_id']}}</a></p>
+                    <p class="card-text"><b>Download: </b><a href="https://sci-hub.tw/{{result[x]['doi']}}">Sci-Hub</a></p>
+                    <p class="card-text"><b>Journal: </b>{{result[x]['journal']}}</p>
+                </div>
+            </div>
+              <div class="col-md-8">
+                <div class="card-body">
+                  <h5 class="card-title">{{result[x]["title"]}}</h5>
+                  <p class="card-text"><b>Abstract: </b>{{result[x]["abstract"]}}</p>
+                  <p class="card-text"><small class="text-muted">Published on {{result[x]['publication_date']}}</small></p>
+                </div>
+              </div>
+            </div>
+          </div>
+        {% endfor %}
+    {% endif %}
+
+{% endblock %}
\ No newline at end of file
diff --git a/app/views.py b/app/views.py
index 0f544b1..89b0374 100644
--- a/app/views.py
+++ b/app/views.py
@@ -9,10 +9,13 @@ from flask import render_template, request, flash
 from werkzeug.utils import secure_filename
 from random import choice, shuffle
 from string import digits, ascii_lowercase
+from pymed import PubMed
+from datetime import datetime
+import json
 
 # Note: that when using Flask-WTF we need to import the Form Class that we created
 # in forms.py
-from .forms import MyForm, curieForm, statusForm, generateSMILES
+from .forms import MyForm, curieForm, statusForm, generateSMILES, PyMedSearch
 
 def gen_word(N, min_N_dig, min_N_low):
     choose_from = [digits]*min_N_dig + [ascii_lowercase]*min_N_low
@@ -47,6 +50,26 @@ def visualise():
     """Render visualisation page."""
     return render_template('visualise.html')    
 
+@app.route('/Search',methods=['GET','POST'])
+def pubmed():
+    """Query PubMed"""
+    form = PyMedSearch()
+    pubmed = PubMed(tool="Curie", email="navanchauhan@gmail.com")
+
+    if request.method == 'POST' and form.validate_on_submit():
+        q = form.query.data
+        print(form)
+        print(pubmed)
+        results = pubmed.query(q,max_results=100) 
+        search = []
+        for x in results:
+            search.append(x.toDict())
+
+        return render_template('search.html',result=search,form=form)
+    
+    flash_errors(form)
+    return render_template('search.html',form=form)
+
 @app.route('/Status',methods=['GET','POST'])
 def status():
     taskStatusForm = statusForm()
@@ -110,7 +133,7 @@ def wtform():
         flash_errors(myform)
     return render_template('wtform.html', form=myform)
 
-tfWorking = -1
+tfWorking = 0
 
 if tfWorking == -1:
     try:
diff --git a/requirements.txt b/requirements.txt
index d031e0e..8fb62fd 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -16,3 +16,12 @@ uvicorn
 tensorflow-cpu==2.2.0
 bunch
 tqdm
+prettytable
+gradio 
+git+https://github.com/bp-kelley/descriptastorus 
+pandas_flavor 
+subword_nmt 
+wget 
+lifelines 
+scikit-plot
+pymed
\ No newline at end of file