From d528c03e26222f48a0e943608925825547044ca1 Mon Sep 17 00:00:00 2001
From: Paul Bugni <pbugni@u.washington.edu>
Date: Wed, 23 Jun 2021 10:21:04 -0700
Subject: [PATCH] Early work on CSV file upload API.  Not functional - checking
 in to capture WIP.

---
 script_facade/api/fhir.py   | 37 +++++++++++++++++++++++++++++++++++++
 tests/test_api.py           | 10 ++++++++++
 tests/test_api/patients.csv |  2 ++
 3 files changed, 49 insertions(+)
 create mode 100644 tests/test_api/patients.csv

diff --git a/script_facade/api/fhir.py b/script_facade/api/fhir.py
index 85a38ef..3f059a8 100644
--- a/script_facade/api/fhir.py
+++ b/script_facade/api/fhir.py
@@ -1,4 +1,6 @@
+import csv
 from flask import Blueprint, request, current_app
+import io
 import timeit
 
 from script_facade.client.client_106 import rx_history_query, patient_lookup_query
@@ -57,3 +59,38 @@ def patient_search(fhir_version):
 
     patient_bundle = patient_lookup_query(patient_fname, patient_lname, patient_dob)
     return patient_bundle
+
+
+@blueprint.route('/upload/patient/csv', methods=['POST'])
+def upload_patient_csv():
+    """Given a CSV file (via request.files) upload contents"""
+
+    def decode_file(binary_data):
+        """Convert binary file data to file like string buffer
+
+        Flask reads in multipart files as binary, which the csv lib can't
+        handle.
+
+        :returns: StringIO buffer of utf-8 decoded strings for file like use
+        """
+        buffer = io.StringIO()
+        last_pos = binary_data.tell()
+        while True:
+            line = binary_data.readline()
+            pos = binary_data.tell()
+            if pos == last_pos:
+                # Position stops progressing at EOF
+                break
+            last_pos = pos
+            buffer.write(line.decode('utf-8'))
+
+        buffer.seek(0)
+        return buffer
+
+    contents = request.files['file']
+    csv.register_dialect('generic', skipinitialspace=True)
+    reader = csv.DictReader(decode_file(contents), dialect='generic')
+    for row in reader:
+        if 'provider_last_name' in row:
+            # Upsert provider
+            pass
diff --git a/tests/test_api.py b/tests/test_api.py
index 8c0c3be..c343365 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -1,3 +1,4 @@
+import os
 import pytest
 from conftest import load_json
 
@@ -20,3 +21,12 @@ def test_medication_order(client, mocker, med_order_bundle):
         }
       )
     assert response.status_code == 200
+
+
+def test_upload_patient(client, datadir):
+    file = open(os.path.join(datadir, 'patients.csv'), 'rb')
+    data = {'filename': 'patients.csv', 'file': file}
+    client.post(
+        '/upload/patient/csv',
+        content_type='multipart/form-data',
+        data=data)
diff --git a/tests/test_api/patients.csv b/tests/test_api/patients.csv
new file mode 100644
index 0000000..9e664d5
--- /dev/null
+++ b/tests/test_api/patients.csv
@@ -0,0 +1,2 @@
+first_name, last_name, birthdate
+John, Hancock, 1737-01-23