can request and display some data in json format

.gitignore

@@ -160,3 +160,9 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
+
+*bin/
+avenv
+lib64
+pyvenv.cfg
+*.swp

FormulariesMatching/FormulariesMatching/__init__.py

@@ -0,0 +1,50 @@
+from flask import (Flask,render_template)
+import os
+from .db_interface import get_connection_details, check_connection
+
+
+
+
+
+
+def create_app(test_config=None):
+    # create and configure the app
+    app = Flask(__name__, instance_relative_config=True)
+    app.config.from_mapping(
+        SECRET_KEY='6e674d6e41b733270fd01c6257b3a1b4769eb80f3f773cd0fe8eff25f350fc1f',
+        POSTGRES_DB="aact_db",
+        POSTGRES_USER="root",
+        POSTGRES_HOST="localhost",
+        POSTGRES_PORT=5432,
+        POSTGRES_PASSWORD="root",
+    )
+
+
+    # ensure the instance folder exists
+    try:
+        os.makedirs(app.instance_path)
+    except OSError:
+        pass
+
+    # a simple page that says hello
+    @app.route('/')
+    def hello():
+        return render_template("index.html")
+
+
+    @app.route('/debug')
+    def debug_info():
+        return {
+                "connection": get_connection_details(), 
+                }
+
+
+
+    from . import db_interface
+    #db_interface.check_connection(app)
+
+    from . import formularies_matching
+    app.register_blueprint(formularies_matching.bp)
+
+
+    return app

FormulariesMatching/FormulariesMatching/db_interface.py

@@ -0,0 +1,83 @@
+import psycopg as psyco
+from datetime import datetime
+from flask import current_app,g
+
+
+def get_db(**kwargs):
+
+    if "db" not in g:
+        g.db = psyco.connect(
+            dbname=current_app.config["POSTGRES_DB"]
+            ,user=current_app.config["POSTGRES_USER"]
+            ,host=current_app.config["POSTGRES_HOST"]
+            ,port=current_app.config["POSTGRES_PORT"]
+            ,password=current_app.config["POSTGRES_PASSWORD"]
+            ,**kwargs
+        )
+    return g.db
+
+def close_db(e=None):
+    db = g.pop('db', None)
+
+    if db is not None:
+        db.close()
+
+def get_connection_details():
+    return {    
+            "dbname":current_app.config["POSTGRES_DB"]
+            ,"user":current_app.config["POSTGRES_USER"]
+            ,"host":current_app.config["POSTGRES_HOST"]
+            ,"port":current_app.config["POSTGRES_PORT"]
+            ,"password":current_app.config["POSTGRES_PASSWORD"]
+        }
+
+def check_connection(app):
+    db = get_db()
+    with db.cursor() as curse:
+        curse.execute("select count(*) from \"DiseaseBurden\".trial_to_icd10")
+        curse.fetchall()
+        #just checking if everything is going to fail
+    return True
+
+
+
+def get_trial_summary(db_conn,nct_id):
+    sql_summary ="""
+select 
+    s.nct_id,
+    brief_title ,
+    official_title ,
+    bs.description as brief_description,
+    dd.description as detailed_description
+from ctgov.studies s 
+    left join ctgov.brief_summaries bs
+        on bs.nct_id = s.nct_id 
+    left join ctgov.detailed_descriptions dd 
+        on dd.nct_id = s.nct_id 
+where s.nct_id = %s
+;
+"""
+    sql_conditions="""
+--conditions mentioned
+select * from ctgov.conditions c 
+where c.nct_id = %s
+;
+"""
+    sql_keywords="""
+select nct_id ,downcase_name 
+from ctgov.keywords k 
+where k.nct_id = %s
+;
+"""
+    with db_conn.cursor() as curse:
+        curse.execute(sql_summary,[nct_id])
+        summary = curse.fetchall()
+
+        curse.execute(sql_keywords,[nct_id])
+        keywords = curse.fetchall()
+
+        curse.execute(sql_conditions,[nct_id])
+        conditions = curse.fetchall()
+
+    return {"summary":summary, "keywords":keywords, "conditions":conditions}
+

FormulariesMatching/FormulariesMatching/formularies_db.py.template

@@ -0,0 +1,25 @@
+import psycopg as psyco
+from datetime import datetime
+
+from flask import current_app, g
+
+
+
+
+def get_all_formulary_groups(db_conn):
+    '''
+    Get the list of active formulary groups
+    TODO: IMplement for the given formulary
+    '''
+    pass
+
+def get_formulary_groups_per_NCTID(db_conn, nct_id):
+    '''
+    Get the list of formulary groups associated with
+    the drugs found in a trial identified by NCTID
+    '''
+    pass
+
+
+def store_trial_to_formulary_group_matches():
+    pass

FormulariesMatching/FormulariesMatching/formularies_matching.py

@@ -0,0 +1,47 @@
+import functools
+from flask import (Blueprint, flash, g, redirect, render_template, request, session, url_for)
+from datetime import datetime
+
+from FormulariesMatching.db_interface import (
+        get_db,
+        get_connection_details,
+        get_trial_summary,
+        )
+
+
+
+#setup blueprint
+bp = Blueprint("formularies validation", __name__, url_prefix='/link/formularies')
+
+@bp.route("/", methods=['GET'])
+def get_remaining():
+    #get db connection
+    #db_conn = get_db()
+
+    #get required data
+    connection_valid = get_connection_details()
+
+    #return html
+    return connection_valid
+
+
+@bp.route("/<nct_id>", methods=['GET',"POST"])
+def match_trial_to_formulary_groups(nct_id):
+    #get db connection
+    db_conn = get_db()
+
+    if request.method == "GET":
+        pass
+        #get list of potential matches for each of the formularies
+        #get trial summary
+        summary = get_trial_summary(db_conn,nct_id)
+
+        #render template
+        return summary
+
+    elif request.method == "POST":
+        pass
+        #build array of data to insert
+
+    else:
+        pass

FormulariesMatching/FormulariesMatching/icd10_db.py

@@ -0,0 +1,175 @@
+import psycopg2 as psyco
+from psycopg2 import extras
+from datetime import datetime
+
+import click #used for cli commands. Not needed for what I am doing.
+from flask import current_app, g
+
+def get_db(**kwargs):
+
+    if "db" not in g:
+        g.db = psyco.connect(
+            dbname=current_app.config["POSTGRES_DB"]
+            ,user=current_app.config["POSTGRES_USER"]
+            ,host=current_app.config["POSTGRES_HOST"]
+            ,port=current_app.config["POSTGRES_PORT"]
+            ,password=current_app.config["POSTGRES_PASSWORD"]
+            ,**kwargs
+        )
+    return g.db
+
+def close_db(e=None):
+    db = g.pop('db', None)
+
+    if db is not None:
+        db.close()
+
+def check_initialization(app):
+    db = get_db()
+    with db.cursor() as curse:
+        curse.execute("select count(*) from \"DiseaseBurden\".trial_to_icd10")
+    curse.fetchall()
+    #just checking if everything is going to fail
+
+def init_database(app):
+    #check_initialization(app)
+    app.teardown_appcontext(close_db)
+
+
+
+
+def select_remaing_trials_to_analyze(db_conn):
+    '''
+    This will get the set of trials that need to be analyzed.
+    '''
+    sql = '''
+    select distinct nct_id 
+    from "DiseaseBurden".trial_to_icd10 tti 
+    where tti.approved is null
+    order by nct_id
+    ;
+    '''
+    with db_conn.cursor() as cursor:
+        cursor.execute(sql)
+        return cursor.fetchall()
+
+
+def select_analyzed_trials(db_conn):
+    '''
+    This will get the set of trials that have been analyzed.
+    '''
+    sql = '''
+    select distinct nct_id, max(approval_timestamp)
+    from "DiseaseBurden".trial_to_icd10 tti 
+    where tti.approved in ('accepted','rejected')
+    group by nct_id
+    order by max(approval_timestamp) desc
+    ;
+    '''
+    with db_conn.cursor() as cursor:
+        cursor.execute(sql)
+        return cursor.fetchall()
+
+def select_unmatched_trials(db_conn):
+    '''
+    This will get the set of trials that have been analyzed.
+    '''
+    sql = '''
+    select distinct nct_id
+    from "DiseaseBurden".trial_to_icd10 tti 
+    where tti.approved = 'unmatched'
+    order by nct_id
+    ;
+    '''
+    with db_conn.cursor() as cursor:
+        cursor.execute(sql)
+        return cursor.fetchall()
+
+
+def get_trial_conditions_and_proposed_matches(db_conn, nct_id):
+    sql = '''
+        select *
+        from "DiseaseBurden".trial_to_icd10 tti 
+        where nct_id = %s
+        '''
+    with db_conn.cursor() as cursor:
+        cursor.execute(sql,[nct_id])
+        return cursor.fetchall()
+
+
+def store_validation(db_conn, list_of_insert_data):
+    sql = """
+    update "DiseaseBurden".trial_to_icd10
+    set approved=%s, approval_timestamp=%s
+    where id=%s
+    ; 
+    """
+    with db_conn.cursor() as cursor:
+        for l in list_of_insert_data:
+            cursor.execute(sql, l)
+    db_conn.commit()
+
+def get_trial_summary(db_conn,nct_id):
+    sql_summary ="""
+select 
+    s.nct_id,
+    brief_title ,
+    official_title ,
+    bs.description as brief_description,
+    dd.description as detailed_description
+from ctgov.studies s 
+    left join ctgov.brief_summaries bs
+        on bs.nct_id = s.nct_id 
+    left join ctgov.detailed_descriptions dd 
+        on dd.nct_id = s.nct_id 
+where s.nct_id = %s
+;
+"""
+    sql_conditions="""
+--conditions mentioned
+select * from ctgov.conditions c 
+where c.nct_id = %s
+;
+"""
+    sql_keywords="""
+select nct_id ,downcase_name 
+from ctgov.keywords k 
+where k.nct_id = %s
+;
+"""
+    with db_conn.cursor() as curse:
+        curse.execute(sql_summary,[nct_id])
+        summary = curse.fetchall()
+
+        curse.execute(sql_keywords,[nct_id])
+        keywords = curse.fetchall()
+
+        curse.execute(sql_conditions,[nct_id])
+        conditions = curse.fetchall()
+
+    return {"summary":summary, "keywords":keywords, "conditions":conditions}
+
+def get_list_icd10_codes(db_conn):
+    sql = """
+    select distinct code 
+    from "DiseaseBurden".icd10_to_cause itc 
+    order by code;
+    """
+    with db_conn.cursor() as curse:
+        curse.execute(sql)
+        codes = curse.fetchall()
+    
+    return [ x[0] for x in codes ]
+
+def record_suggested_matches(db_conn, nct_id,condition,icd10_code):
+    sql1 = """
+    INSERT INTO "DiseaseBurden".trial_to_icd10 
+    (nct_id,"condition",ui,"source",approved,approval_timestamp)
+    VALUES (%s,%s,%s,'hand matched','accepted',%s)
+    ;
+    """
+
+
+    with db_conn.cursor() as curse:
+        curse.execute(sql1,[nct_id,condition,icd10_code,datetime.now()])
+    db_conn.commit()

FormulariesMatching/FormulariesMatching/templates/base.html

@@ -0,0 +1,22 @@
+<!doctype html>
+<title>{% block title %}{% endblock %} - ClinicalTrialsProject</title>
+<!--<link rel="stylesheet" href="{{ url_for('static', filename='style.css') }}">-->
+
+<nav>
+  <h1>Nav</h1>
+  <ul>
+    <li>
+      <a href="{{ url_for('hello') }}">Linking Home</a>
+    </li>
+    <li>
+      <a href="{{ url_for('formularies validation.get_remaining') }}">Linking Formularies</a>
+    </li>
+  </ul>
+</nav>
+
+<section class="content">
+  <header>
+    {% block header %}{% endblock %}
+  </header>
+  {% block content %}{% endblock %}
+</section>

FormulariesMatching/FormulariesMatching/templates/formulary_index.html

@@ -0,0 +1,49 @@
+{% extends 'base.html' %}
+
+{% block header %}
+  <h1>{% block title %} ICD-10 to Trial Conditions Validation {% endblock %}</h1>
+{% endblock %}
+
+{% block content %}
+
+<h2>Trials to Validate</h2>
+
+<table>
+<th>Trials</th>
+{% for trial in list_to_validate %}
+<tr><td>
+    <a href="{{ url_for('.validate_trial', nct_id=trial[0] ) }}">
+        {{ trial [0] }}
+    </a>
+</td></tr> 
+{% endfor %}
+</table>
+
+<h2>Trials that have been Validated</h2>
+
+<table>
+<th>Trials Links</th>
+{% for trial in validated_list %}
+<tr><td>
+    <a href="{{ url_for('.validate_trial', nct_id=trial[0] ) }}">
+        {{ trial [0] }}
+    </a> 
+    (Most recently updated {{trial[1]}})
+</td></tr> 
+{% endfor %}
+</table>
+
+<h2>Trials that don't have a good match</h2>
+
+<table>
+<th>Trial Links</th>
+{% for trial in unmatched_list %}
+<tr><td>
+    <a href="{{ url_for('.validate_trial', nct_id=trial[0] ) }}">
+        {{ trial [0] }}
+    </a>
+</td></tr> 
+{% endfor %}
+</table>
+
+{% endblock %}

FormulariesMatching/FormulariesMatching/templates/icd10_index.html

@@ -0,0 +1,49 @@
+{% extends 'base.html' %}
+
+{% block header %}
+  <h1>{% block title %} ICD-10 to Trial Conditions Validation {% endblock %}</h1>
+{% endblock %}
+
+{% block content %}
+
+<h2>Trials to Validate</h2>
+
+<table>
+<th>Trials</th>
+{% for trial in list_to_validate %}
+<tr><td>
+    <a href="{{ url_for('.validate_trial', nct_id=trial[0] ) }}">
+        {{ trial [0] }}
+    </a>
+</td></tr> 
+{% endfor %}
+</table>
+
+<h2>Trials that have been Validated</h2>
+
+<table>
+<th>Trials Links</th>
+{% for trial in validated_list %}
+<tr><td>
+    <a href="{{ url_for('.validate_trial', nct_id=trial[0] ) }}">
+        {{ trial [0] }}
+    </a> 
+    (Most recently updated {{trial[1]}})
+</td></tr> 
+{% endfor %}
+</table>
+
+<h2>Trials that don't have a good match</h2>
+
+<table>
+<th>Trial Links</th>
+{% for trial in unmatched_list %}
+<tr><td>
+    <a href="{{ url_for('.validate_trial', nct_id=trial[0] ) }}">
+        {{ trial [0] }}
+    </a>
+</td></tr> 
+{% endfor %}
+</table>
+
+{% endblock %}

FormulariesMatching/FormulariesMatching/templates/index.html

@@ -0,0 +1,24 @@
+{% extends 'base.html' %}
+
+{% block header %}
+<h1>
+{% block title %}
+Formulary Matching
+{% endblock %}
+</h1>
+{% endblock %}
+
+
+
+
+{% block content %}
+
+This is the home page for matching things to clinical trials
+
+There are a few major efforts related to matching.
+
+The first is to match trials to IDC10 codes
+
+The second is to link trials to formulary groups.
+
+{% endblock %}

FormulariesMatching/requirements.txt

@@ -0,0 +1,6 @@
+flask
+psycopg[binary]
+datetime
+watchdog
+waitress
+python-dotenv

FormulariesMatching/setup.py

@@ -0,0 +1,12 @@
+from setuptools import setup
+
+setup(
+    name='FormulariesMatching',
+    packages=['FormulariesMatching'],
+    include_package_data=True,
+    install_requires=[
+        'flask',
+        'psycopg[binary]',
+        'datetime',
+    ],
+)

FormulariesMatching/start.sh

@@ -0,0 +1 @@
+waitress-serve --port=5000 --call 'Icd10ConditionsMatching:create_app'

sample.env

@@ -1,6 +1,6 @@
 
 #Postgres Info
-POSTGRES_HOST=
+POSTGRES_HOST=will-office
 POSTGRES_DB=aact_db
 POSTGRES_PORT=5432
 POSTGRES_USER=root