WIP: Diabetic retinopathy

keep_diabetes_no_dr.json

@@ -0,0 +1,54 @@
+{
+  "name": "keep_diabetes_no_dr",
+  "remarks": [
+    "A blank module"
+  ],
+  "states": {
+    "Initial": {
+      "type": "Initial",
+      "conditional_transition": [
+        {
+          "transition": "Keep",
+          "condition": {
+            "condition_type": "And",
+            "conditions": [
+              {
+                "condition_type": "Active Condition",
+                "codes": [
+                  {
+                    "system": "SNOMED-CT",
+                    "code": 44054006,
+                    "display": "Diabetes mellitus type 2 (disorder)"
+                  }
+                ]
+              },
+              {
+                "condition_type": "Not",
+                "condition": {
+                  "condition_type": "Active Condition",
+                  "codes": [
+                    {
+                      "system": "SNOMED-CT",
+                      "code": "1551000119108",
+                      "display": "Nonproliferative diabetic retinopathy due to type 2 diabetes mellitus (disorder)"
+                    }
+                  ]
+                }
+              }
+            ]
+          }
+        },
+        {
+          "transition": "Terminal"
+        }
+      ]
+    },
+    "Terminal": {
+      "type": "Terminal"
+    },
+    "Keep": {
+      "type": "Terminal"
+    }
+  },
+  "gmf_version": 2
+}

keep_npdr.json

@@ -0,0 +1,36 @@
+{
+  "name": "Generated Keep Module",
+  "states": {
+    "Initial": {
+      "type": "Initial",
+      "name": "Initial",
+      "conditional_transition": [
+        {
+          "transition": "Keep",
+          "condition": {
+            "condition_type": "Active Condition",
+            "codes": [
+              {
+                "system": "SNOMED-CT",
+                "code": "1551000119108",
+                "display": "Nonproliferative diabetic retinopathy due to type 2 diabetes mellitus (disorder)"
+              }
+            ]
+          }
+        },
+        {
+          "transition": "Terminal"
+        }
+      ]
+    },
+    "Terminal": {
+      "type": "Terminal",
+      "name": "Terminal"
+    },
+    "Keep": {
+      "type": "Terminal",
+      "name": "Keep"
+    }
+  },
+  "gmf_version": 2
+}

keep_npdr_no_pdr.json

@@ -0,0 +1,54 @@
+{
+  "name": "keep_npdr_no_pdr",
+  "remarks": [
+    "A blank module"
+  ],
+  "states": {
+    "Initial": {
+      "type": "Initial",
+      "conditional_transition": [
+        {
+          "transition": "Keep",
+          "condition": {
+            "condition_type": "And",
+            "conditions": [
+              {
+                "condition_type": "Active Condition",
+                "codes": [
+                  {
+                    "system": "SNOMED-CT",
+                    "code": "1551000119108",
+                    "display": "Nonproliferative diabetic retinopathy due to type 2 diabetes mellitus (disorder)"
+                  }
+                ]
+              },
+              {
+                "condition_type": "Not",
+                "condition": {
+                  "condition_type": "Active Condition",
+                  "codes": [
+                    {
+                      "system": "SNOMED-CT",
+                      "code": "1501000119109",
+                      "display": "Proliferative diabetic retinopathy due to type II diabetes mellitus (disorder)"
+                    }
+                  ]
+                }
+              }
+            ]
+          }
+        },
+        {
+          "transition": "Terminal"
+        }
+      ]
+    },
+    "Terminal": {
+      "type": "Terminal"
+    },
+    "Keep": {
+      "type": "Terminal"
+    }
+  },
+  "gmf_version": 2
+}

keep_pdr.json

@@ -0,0 +1,36 @@
+{
+  "name": "Generated Keep Module",
+  "states": {
+    "Initial": {
+      "type": "Initial",
+      "name": "Initial",
+      "conditional_transition": [
+        {
+          "transition": "Keep",
+          "condition": {
+            "condition_type": "Active Condition",
+            "codes": [
+              {
+                "system": "SNOMED-CT",
+                "code": "1501000119109",
+                "display": "Proliferative diabetic retinopathy due to type II diabetes mellitus (disorder)"
+              }
+            ]
+          }
+        },
+        {
+          "transition": "Terminal"
+        }
+      ]
+    },
+    "Terminal": {
+      "type": "Terminal",
+      "name": "Terminal"
+    },
+    "Keep": {
+      "type": "Terminal",
+      "name": "Keep"
+    }
+  },
+  "gmf_version": 2
+}

src/main/java/org/mitre/synthea/export/ClinicalNoteExporter.java

@@ -130,6 +130,11 @@ public static String export(Person person, Encounter encounter) {
     person.attributes.put("ehr_medications", encounter.medications);
     person.attributes.put("ehr_careplans", encounter.careplans);
     person.attributes.put("ehr_imaging_studies", encounter.imagingStudies);
+    if (encounter.note == null) {
+      person.attributes.remove("ehr_note");
+    } else {
+      person.attributes.put("ehr_note", encounter.note);
+    }
     person.attributes.put("time", encounter.start);
     if (person.attributes.containsKey(LifecycleModule.QUIT_SMOKING_AGE)) {
       person.attributes.put("quit_smoking_age",

src/main/java/org/mitre/synthea/export/flexporter/Actions.java

@@ -649,13 +649,9 @@ private static void dateFilter(Bundle bundle, String minDateStr, String maxDateS
    * Cascade (current), Delete reference field but leave object, Do nothing
    *
    * @param bundle FHIR Bundle to filter
-   * @param list List of resource types to delete, other types not listed will be kept
+   * @param list List of resource types or FHIRPath to delete, other types not listed will be kept
    */
   public static void deleteResources(Bundle bundle, List<String> list) {
-    // TODO: make this FHIRPath instead of just straight resource types
-
-    Set<String> resourceTypesToDelete = new HashSet<>(list);
-
     Set<String> deletedResourceIDs = new HashSet<>();
 
     Iterator<BundleEntryComponent> itr = bundle.getEntry().iterator();
@@ -665,9 +661,12 @@ public static void deleteResources(Bundle bundle, List<String> list) {
 
       Resource resource = entry.getResource();
       String resourceType = resource.getResourceType().toString();
-      if (resourceTypesToDelete.contains(resourceType)) {
-        deletedResourceIDs.add(resource.getId());
-        itr.remove();
+      for (String applicability : list) {
+        if (applicability.equals(resourceType) || FhirPathUtils.appliesToResource(resource, applicability)) {
+          deletedResourceIDs.add(resource.getId());
+          itr.remove();
+          break;
+        }
       }
     }
 

src/main/java/org/mitre/synthea/world/concepts/HealthRecord.java

@@ -167,6 +167,7 @@ public class Entry implements Serializable {
     public String type;
     public List<Code> codes;
     private BigDecimal cost;
+    public String note;
 
     /**
      * Constructor for Entry.