Added the function to retrieve the data as #11 from Include FHIR

include_notebooks/include_helper.py

@@ -0,0 +1,27 @@
+import requests
+import pandas as pd
+
+def query_fhir_include(include_cookie, query_statement="https://include-api-fhir-service.includedcc.org/DocumentReference?_tag=HTP&category=RNA-Seq&type=Gene-Expression,Gene-Expression-Quantifications&location:missing=false"):
+
+
+    req = requests.get(query_statement, cookies = {"AWSELBAuthSessionCookie-0" : include_cookie})
+    req_j = req.json()
+    FHIR_SERVER_ROOT =  "https://" + query_statement.split("//")[1].split('/')[0]
+    data = []
+    for entry in req_j['entry']:
+        item = {}
+        item["document_reference_attachement_uri"] = entry['resource']['content'][0]['attachment']['url']
+        item['drs_uri'] = entry['resource']['content'][0]['attachment']['url']
+        item['document_reference_reference'] = entry['fullUrl']
+        item['file_path'] = ""
+        item['specimen_bodySite'] = ""
+        item['condition_code'] =  entry["resource"]['meta']['tag'][0]['code']
+        item['filename'] = entry['resource']['content'][0]['attachment']['title']
+        item['research_study_reference'] = entry["resource"]['meta']['tag'][0]['code']
+        item['patience_reference'] = FHIR_SERVER_ROOT + "/" + entry["resource"]['subject']['reference']
+        item['specimen_reference'] = FHIR_SERVER_ROOT + "/" + entry["resource"]['context']['related'][0]['reference']
+        data.append(item)
+    df = pd.DataFrame(data)
+    df.set_index("document_reference_attachement_uri", inplace=True)
+    return df
+