Support alternate validator / newer validation result property names and do additional aggregations

home/fhirvalidation.py

@@ -29,7 +29,8 @@ class Validator():
     def fhir_operation_validate(self, resource_type, resource, send_pretty=False):
 
         headers = {'User-Agent': 'Bulk FHIR validator',
-                   'Content-Type': 'application/fhir+json'}
+                   'Content-Type': 'application/fhir+json',
+                   'Accept': 'application/fhir+json'}
 
         if send_pretty:
             data = json.dumps(resource, indent=4)
@@ -55,14 +56,21 @@ class Validator():
         df = pd.DataFrame()
 
         for issue in outcome.get('issue'):
-            diagnostics = issue.get('diagnostics')
+            diagnostics = issue.get('details').get('text')
+            if not diagnostics:
+                # fallback to (old?) HAPI validator properties
+                diagnostics = issue.get('diagnostics')
 
             diagnostics_aggregated = remove_value_code(diagnostics)
             diagnostics_aggregated = remove_array_index(diagnostics_aggregated)
 
             severity = issue.get('severity')
 
-            location = issue.get('location')
+            location = issue.get('expression')
+            if not location:
+                # fallback to (old?) HAPI validator properties
+                location = issue.get('location')
+
             location = location[0]
             location_aggregated = remove_array_index(location)
 
@@ -188,18 +196,45 @@ def get_next_page_url(bundle_dict):
 
 
 def remove_value_code(diagnostics):
-    find_value_code = re.search(r"Coding provided \(.+?\#(.+?)\) is not in the value set", diagnostics)
 
-    if not find_value_code:
-        find_value_code = re.search(r"Unknown code in fragment CodeSystem \'.+?\#(.+?)\'", diagnostics)
 
+    find_value_code = re.search(r"Coding provided \(.+?\#(.+?)\)", diagnostics)
     if find_value_code:
         value_code = find_value_code.groups()[0]
-        diagnostics_removed_valuecode = diagnostics.replace(value_code, "REMOVEDCODE")
+        diagnostics = diagnostics.replace(value_code, "REMOVEDCODE")
-    else:
-        diagnostics_removed_valuecode = diagnostics
 
-    return diagnostics_removed_valuecode
+    find_value_code = re.search(r"code provided \(.+?\#(.+?)\) was not found", diagnostics)
+    if find_value_code:
+        value_code = find_value_code.groups()[0]
+        diagnostics = diagnostics.replace(value_code, "REMOVEDCODE")
+
+    find_value_code = re.search(r"Unknown code in fragment CodeSystem \'.+?\#(.+?)\'", diagnostics)
+    if find_value_code:
+        value_code = find_value_code.groups()[0]
+        diagnostics = diagnostics.replace(value_code, "REMOVEDCODE")
+
+    find_value_code = re.search(r"code \`(.+?)\` was not found in the code system", diagnostics)
+    if find_value_code:
+        value_code = find_value_code.groups()[0]
+        diagnostics = diagnostics.replace(value_code, "REMOVEDCODE")
+
+    find_value_code = re.search(r"Invalid display \`(.+?)\` for code \`.+?\#(.+?)\`. A valid display is \`(.+?)\`", diagnostics)
+    if find_value_code:
+        value_display = find_value_code.groups()[0]
+        value_code = find_value_code.groups()[1]
+        valid_display = find_value_code.groups()[2]
+        diagnostics = diagnostics.replace(value_code, "REMOVEDCODE")
+        diagnostics = diagnostics.replace(value_display, "REMOVEDDISPLAY")
+        diagnostics = diagnostics.replace(valid_display, "REMOVEDVALIDDISPLAY")
+
+    find_value_code = re.search(r"Invalid display \`(.+?)\` for code \`.+?\#(.+?)\`", diagnostics)
+    if find_value_code:
+        value_display = find_value_code.groups()[0]
+        value_code = find_value_code.groups()[1]
+        diagnostics = diagnostics.replace(value_code, "REMOVEDCODE")
+        diagnostics = diagnostics.replace(value_display, "REMOVEDDISPLAY")
+
+    return diagnostics
 
 
 def remove_array_index(diagnostics):
@@ -256,7 +291,13 @@ def render_validation_outcome(resource, outcome, resource_url=None, do_print_lin
     summary_html = ''
 
     for issue in issues_sorted:
-        location_element = issue['location'][0]
+
+        location_element = issue.get('expression')
+
+        if not location_element:
+            # Fallback to old(?) HAPI validator properties
+            location_element = issue['location'][0]
+
         location_line = select_location_line(issue)
 
         match issue['severity']:
@@ -285,8 +326,14 @@ def render_validation_outcome(resource, outcome, resource_url=None, do_print_lin
 
         issue_html += '</small><br>'
 
+
+        diagnostics = issue.get('details').get('text')
+        if not diagnostics:
+            # fallback to (old?) HAPI validator properties
+            diagnostics = issue.get('diagnostics')
+
         issue_html += f'{issue["severity"]} for element <i><b>{location_element}</b></i> (beginning at line ' + str(
-            location_line) + f'):<br><b>{issue["diagnostics"]}</b>'
+            location_line) + f'):<br><b>{diagnostics}</b>'
 
         issue_html += '</li></span>'