README.md aktualisiert

README.md

@@ -98,7 +98,7 @@ The MeDaX pipeline consists of the following components:
 
 ## ✍️ Citation
 
-If you use the MeDaX pipeline in your research, please cite: 10.5281/zenodo.15229077 and Mazein, I and Gebhardt, T et al. [MeDaX, a knowledge graph on FHIR.](https://doi.org/10.3233/shti240423)
+If you use the MeDaX pipeline in your research, please cite the software [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15229076.svg)](https://doi.org/10.5281/zenodo.15229076) and out latest paper: Mazein, I and Gebhardt, T et al. [MeDaX, a knowledge graph on FHIR.](https://doi.org/10.3233/shti240423)
 
 ## 🙏 Acknowledgements
 

fhirImport.py

@@ -32,7 +32,10 @@ def getBundle(url: str, search: str):
 
     
     if url is not None:
-        link = url + '?_format=json'
+        if '?' in url:
+            link = url + '&_format=json'
+        else:
+            link = url + '?_format=json'
     else:
         link = fhir_server + search + '&_format=json'
 

import_fhir_to_nx_diGraph.py

@@ -24,18 +24,21 @@ from fhirImport import getPatientEverything, getBundle
 def load_multiple_fhir_patients(n):
     #graph = nx.DiGraph()
     init = True
+    initLoad = True
     ids = []
     #get n ids
     nextIds = True
     while len(ids) < n and nextIds:
-        if init:
+        if initLoad:
             complex = os.getenv('COMPLEX_PATIENTS')
             if complex and complex.upper() != 'TRUE':
                 bundle = getBundle(None, '/Patient?_count=' + str(n))
             else:
                 bundle = getBundle(None, '/Patient?_has:Observation:subject:status=final&_count=' + str(n))
+            initLoad = False
         else:
-            bundle = getBundle(None, nextLink)
+            print("NEXT LINK: ", nextLink, flush=True)
+            bundle = getBundle(nextLink, None)
 
         if not 'entry' in bundle.json():
             print("ERROR -- No data found in the fhir bundle. Check the request and if the server is up and responding")