got uspdc displaying
Will King
3 years ago
parent
3e65b9fbdd
commit
dd90715400
@ -1,47 +0,0 @@
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import functools
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from flask import (Blueprint, flash, g, redirect, render_template, request, session, url_for)
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from datetime import datetime
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from FormulariesMatching.db_interface import (
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get_db,
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get_connection_details,
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get_trial_summary,
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)
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#setup blueprint
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bp = Blueprint("formularies validation", __name__, url_prefix='/link/formularies')
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@bp.route("/", methods=['GET'])
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def get_remaining():
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#get db connection
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#db_conn = get_db()
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#get required data
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connection_valid = get_connection_details()
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#return html
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return connection_valid
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@bp.route("/<nct_id>", methods=['GET',"POST"])
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def match_trial_to_formulary_groups(nct_id):
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#get db connection
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db_conn = get_db()
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if request.method == "GET":
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pass
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#get list of potential matches for each of the formularies
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#get trial summary
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summary = get_trial_summary(db_conn,nct_id)
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#render template
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return summary
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elif request.method == "POST":
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pass
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#build array of data to insert
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else:
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pass
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@ -0,0 +1,70 @@
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import functools
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from flask import (Blueprint, flash, g, redirect, render_template, request, session, url_for)
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from datetime import datetime
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from FormulariesMatching.db_interface import (
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get_db,
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get_connection_details,
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get_trial_summary,
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)
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import FormulariesMatching.uspdc_db as uspdc
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import FormulariesMatching.uspmmg_db as uspmmg
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import FormulariesMatching.vaform_db as vaform
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FORMULARIES = {
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"USP DC":uspdc,
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# "USP MMG":uspmmg,
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# "VA Formulary":vaform,
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}
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#setup blueprint
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bp = Blueprint("formularies", __name__, url_prefix='/link/formularies')
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@bp.route("/", methods=['GET'])
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def get_remaining_trials():
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#get db connection
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#db_conn = get_db()
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#get required data
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connection_valid = get_connection_details()
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#return html
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return connection_valid
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@bp.route("/<nct_id>", methods=['GET',"POST"])
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def match_trial_to_formulary_groups(nct_id):
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#get db connection
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db_conn = get_db()
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if request.method == "GET":
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#get list of potential matches for each of the formularies
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potential_matches = {}
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class_lists = {}
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for formulary in FORMULARIES:
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potential_matches[formulary] = FORMULARIES[formulary].get_groups_per_nctid(db_conn,nct_id)
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class_lists[formulary] = FORMULARIES[formulary].get_all_formulary_groups(db_conn)
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#get trial summary
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summary = get_trial_summary(db_conn,nct_id)
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#render template
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# return [potential_matches,class_lists,summary]
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return render_template('trial_formularies.html',
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nct_id=nct_id,
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potential_matches=potential_matches,
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class_lists=class_lists,
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summary=summary,
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)
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elif request.method == "POST":
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pass
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#build array of data to insert
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else:
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raise Exception("HTTP method <{}> not implemented".format(request.method))
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@ -0,0 +1,5 @@
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.table {
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width: 100%;
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border-collapse: collapse;
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border: 1px solid;
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}
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Binary file not shown.
@ -0,0 +1,76 @@
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{% extends 'base.html' %}
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{% block header %}
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<h1>
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{% block title %}
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Match Trial {{nct_id}} to Formularies
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{% endblock %}
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</h1>
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{% endblock %}
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{% block content %}
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Based on the drugs associated with a trial,
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the following are the formulary group suggestions.
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<form>
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{% for formulary in potential_matches %}
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<div class=formulary_matches>
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<h2>
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{{ formulary }}
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</h2>
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<p>
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{% for formulary in potential_matches %}
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<table>
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<tr>
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<th>Category</th>
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<th>Class</th>
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<th>Select</th>
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</tr>
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{% for row in potential_matches[formulary] %}
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<tr>
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<td> {{ row[1] }} </td>
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<td> {{ row[2] }} </td>
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<td> <input
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type="checkbox"
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id="{{ formulary,row }}"
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name={{ formulary,row }}
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value="selected">
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</td>
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<!-- add checkbox here -->
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</tr>
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{% endfor %}
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</table>
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</p>
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<p>
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If you've determined it belongs to another class
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<select name="{{ formulary }}-select_box" id="{{ formularay }}-select_box">
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<option disabled selected value> -- select an option -- </option>
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<option value="difficult">
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Difficult to choose
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</option>
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{% for option in class_lists[formulary] %}
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<option value={{ (option[0],option[1]) }}>
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Category:{{ option[0] }} Class:{{ option[1] }}
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<!-- FIX this is really hard to read -->
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<!-- FIX try to add opgroups? -->
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</option>
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{% endfor %}
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</select>
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{% endfor %}
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{% endfor %}
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</p>
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<p>
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<input type="submit" value="Submit">
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</p>
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</form>
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{% endblock %}
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@ -0,0 +1,47 @@
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import psycopg as psyco
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from datetime import datetime
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from flask import current_app, g
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def get_all_formulary_groups(db_conn):
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'''
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Get the list of active formulary groups
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TODO: IMplement for the given formulary
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'''
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sql = '''\
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select distinct "USP Category", "USP Class"
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from "Formularies".usp_dc ud
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order by "USP Category", "USP Class"
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;
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'''
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#query
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with db_conn.cursor() as curse:
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curse.execute(sql)
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return curse.fetchall()
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def get_groups_per_nctid(db_conn, nct_id):
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'''
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Get the list of formulary groups associated with
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the drugs found in a trial identified by NCTID
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'''
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pass
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sql = '''\
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select * from "Formularies".trial_to_uspdc_category_class ttucc
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where nct_id = %(nctid)s
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;
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'''
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#query
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with db_conn.cursor() as curse:
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curse.execute(sql, {"nctid":nct_id})
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return curse.fetchall()
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def store_trial_to_formulary_group_matches():
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pass
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@ -0,0 +1,35 @@
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import psycopg as psyco
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from datetime import datetime
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from flask import current_app, g
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def get_all_formulary_groups(db_conn):
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'''
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Get the list of active formulary groups
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TODO: IMplement for the given formulary
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'''
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sql = '''\
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select distinct "USP Category", "USP Class"
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from "Formularies".usp_dc ud
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order by "USP Category", "USP Class"
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;
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'''
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#query
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with db_conn.cursor() as curse:
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curse.execute(sql)
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return curse.fetchall()
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def get_formulary_groups_per_NCTID(db_conn, nct_id):
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'''
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Get the list of formulary groups associated with
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the drugs found in a trial identified by NCTID
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'''
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pass
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def store_trial_to_formulary_group_matches():
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pass
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@ -0,0 +1,35 @@
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import psycopg as psyco
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from datetime import datetime
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from flask import current_app, g
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def get_all_formulary_groups(db_conn):
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'''
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Get the list of active formulary groups
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TODO: IMplement for the given formulary
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'''
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sql = '''\
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select distinct "USP Category", "USP Class"
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from "Formularies".usp_dc ud
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order by "USP Category", "USP Class"
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;
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'''
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#query
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with db_conn.cursor() as curse:
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curse.execute(sql)
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return curse.fetchall()
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def get_formulary_groups_per_NCTID(db_conn, nct_id):
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'''
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Get the list of formulary groups associated with
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the drugs found in a trial identified by NCTID
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'''
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pass
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def store_trial_to_formulary_group_matches():
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pass
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