Merge pull request #1399 from synthetichealth/module_cleanup

Module cleanup

src/main/resources/modules/appendicitis.json

@@ -309,8 +309,7 @@
         "Avg operative time is ~55 minutes",
         "https://www.ncbi.nlm.nih.gov/pubmed/17658102"
       ],
-      "direct_transition": "Appendicitis_Symptom1_Ends",
-      "name": "Appendectomy"
+      "direct_transition": "End_Appendicitis"
     },
     "Appendicitis_Symptom1_Ends": {
       "type": "Symptom",
@@ -407,8 +406,28 @@
     },
     "Transfer_To_Inpatient": {
       "type": "EncounterEnd",
-      "direct_transition": "Appendectomy_Encounter",
-      "name": "Transfer_To_Inpatient"
+      "direct_transition": "Appendectomy_Encounter"
+    },
+    "End_Appendicitis": {
+      "type": "ConditionEnd",
+      "condition_onset": "Appendicitis",
+      "conditional_transition": [
+        {
+          "transition": "End_Rupture",
+          "condition": {
+            "condition_type": "PriorState",
+            "name": "Rupture"
+          }
+        },
+        {
+          "transition": "Appendicitis_Symptom1_Ends"
+        }
+      ]
+    },
+    "End_Rupture": {
+      "type": "ConditionEnd",
+      "direct_transition": "Appendicitis_Symptom1_Ends",
+      "condition_onset": "Rupture"
     }
   },
   "gmf_version": 1

src/main/resources/modules/covid19/end_outcomes.json

@@ -20,7 +20,7 @@
           "display": "Pneumonia (disorder)"
         }
       ],
-      "direct_transition": "End Mild Respiratory Distress"
+      "direct_transition": "End Hypoxemia"
     },
     "End ARDS": {
       "type": "ConditionEnd",
@@ -150,6 +150,17 @@
         }
       ],
       "direct_transition": "End Heart Failure"
+    },
+    "End Hypoxemia": {
+      "type": "ConditionEnd",
+      "direct_transition": "End Mild Respiratory Distress",
+      "codes": [
+        {
+          "system": "SNOMED-CT",
+          "code": 389087006,
+          "display": "Hypoxemia (disorder)"
+        }
+      ]
     }
   },
   "gmf_version": 1

src/main/resources/modules/home_health_treatment.json

@@ -19,7 +19,7 @@
       ],
       "direct_transition": "Referral_Home_Health_Care",
       "encounter_class": "urgentcare",
-      "reason": "Transition_To_Home"
+      "reason": "home_health_reason"
     },
     "Referral_Home_Health_Care": {
       "type": "Procedure",
@@ -65,7 +65,7 @@
       ],
       "direct_transition": "Initial_Patient_Assessment",
       "encounter_class": "home",
-      "reason": "Transition_To_Home"
+      "reason": "home_health_reason"
     },
     "Initial_Patient_Assessment": {
       "type": "Procedure",
@@ -126,7 +126,7 @@
       ],
       "direct_transition": "Begin_Visit",
       "encounter_class": "home",
-      "reason": "Transition_To_Home"
+      "reason": "home_health_reason"
     },
     "Begin_Visit": {
       "type": "Counter",
@@ -225,7 +225,7 @@
           "display": "Patient discharge (procedure)"
         }
       ],
-      "direct_transition": "End_Transition_To_Home"
+      "direct_transition": "Last Visit"
     },
     "Nursing_Care": {
       "type": "Procedure",
@@ -352,30 +352,40 @@
           }
         ]
       },
-      "direct_transition": "Transition_To_Home"
+      "conditional_transition": [
+        {
+          "transition": "Default_Home_Health_Reason",
+          "condition": {
+            "condition_type": "Attribute",
+            "attribute": "home_health_reason",
+            "operator": "is nil"
+          }
+        },
+        {
+          "transition": "Face_to_Face_Encounter"
+        }
+      ]
     },
     "Reset Home Health": {
       "type": "SetAttribute",
       "attribute": "home_health",
-      "direct_transition": "Wait Until Home Health",
+      "direct_transition": "Reset Home Health Reason",
       "value": false
     },
-    "Transition_To_Home": {
-      "type": "ConditionOnset",
-      "target_encounter": "Face_to_Face_Encounter",
-      "codes": [
-        {
-          "system": "SNOMED-CT",
-          "code": 1871000124103,
-          "display": "Transition from acute care to home-health care (finding)"
-        }
-      ],
-      "direct_transition": "Face_to_Face_Encounter"
+    "Default_Home_Health_Reason": {
+      "type": "SetAttribute",
+      "attribute": "home_health_reason",
+      "direct_transition": "Face_to_Face_Encounter",
+      "value_code": {
+        "system": "SNOMED-CT",
+        "code": "1871000124103",
+        "display": "Transition from acute care to home-health care (finding)"
+      }
     },
-    "End_Transition_To_Home": {
-      "type": "ConditionEnd",
-      "direct_transition": "Last Visit",
-      "condition_onset": "Transition_To_Home"
+    "Reset Home Health Reason": {
+      "type": "SetAttribute",
+      "attribute": "home_health_reason",
+      "direct_transition": "Wait Until Home Health"
     }
   },
   "gmf_version": 1

src/main/resources/modules/metabolic_syndrome_care.json

@@ -288,7 +288,18 @@
       "remarks": [
         "setting prediabetes as severity 0 makes some things easier"
       ],
-      "direct_transition": "Diagnose_Prediabetes"
+      "conditional_transition": [
+        {
+          "transition": "Check_CarePlan",
+          "condition": {
+            "condition_type": "PriorState",
+            "name": "Diagnose_Diabetes"
+          }
+        },
+        {
+          "transition": "Diagnose_Prediabetes"
+        }
+      ]
     },
     "Diagnose_Prediabetes": {
       "type": "ConditionOnset",

src/main/resources/modules/opioid_addiction.json

@@ -645,7 +645,7 @@
       "distributed_transition": [
         {
           "distribution": 0.98747,
-          "transition": "End_Directed_Use_Overdose_Encounter"
+          "transition": "End_Directed_Use_Overdose"
         },
         {
           "distribution": 0.01253,
@@ -683,7 +683,7 @@
       "distributed_transition": [
         {
           "distribution": 0.98747,
-          "transition": "End_Misuse_Overdose_Encounter"
+          "transition": "End_Misuse_Overdose"
         },
         {
           "distribution": 0.01253,
@@ -738,19 +738,7 @@
         }
       },
       "unit": "hours",
-      "conditional_transition": [
-        {
-          "condition": {
-            "condition_type": "Attribute",
-            "attribute": "opioid_addiction_careplan",
-            "operator": "is nil"
-          },
-          "transition": "Opioid_Addiction_CarePlan"
-        },
-        {
-          "transition": "End_Addiction_Overdose_Encounter"
-        }
-      ]
+      "direct_transition": "End_Addiction_Overdose"
     },
     "Opioid_Addiction_CarePlan": {
       "type": "CarePlanStart",
@@ -928,6 +916,33 @@
       ],
       "direct_transition": "Recovery_Management",
       "assign_to_attribute": "opioid_drug_addiction"
+    },
+    "End_Addiction_Overdose": {
+      "type": "ConditionEnd",
+      "conditional_transition": [
+        {
+          "condition": {
+            "condition_type": "Attribute",
+            "attribute": "opioid_addiction_careplan",
+            "operator": "is nil"
+          },
+          "transition": "Opioid_Addiction_CarePlan"
+        },
+        {
+          "transition": "End_Addiction_Overdose_Encounter"
+        }
+      ],
+      "condition_onset": "Addiction_Overdose"
+    },
+    "End_Misuse_Overdose": {
+      "type": "ConditionEnd",
+      "direct_transition": "End_Misuse_Overdose_Encounter",
+      "condition_onset": "Misuse_Overdose"
+    },
+    "End_Directed_Use_Overdose": {
+      "type": "ConditionEnd",
+      "direct_transition": "End_Directed_Use_Overdose_Encounter",
+      "condition_onset": "Directed_Use_Overdose"
     }
   },
   "gmf_version": 1

src/main/resources/modules/pregnancy.json

@@ -1919,11 +1919,11 @@
     "Miscarriage_Fatal_Pregnancy_Complication_Ends": {
       "type": "ConditionEnd",
       "referenced_by_attribute": "fatal_pregnancy_complication",
-      "direct_transition": "End_Miscarriage_Followup_Encounter"
+      "direct_transition": "History_of_Miscarriage"
     },
     "End_Miscarriage_Followup_Encounter": {
       "type": "EncounterEnd",
-      "direct_transition": "Miscarriage_Ends"
+      "direct_transition": "End_Miscarriage_Condition"
     },
     "Wait_For_Induced_Abortion": {
       "type": "Delay",
@@ -2129,24 +2129,6 @@
         }
       ]
     },
-    "Miscarriage_Ends": {
-      "type": "ConditionEnd",
-      "condition_onset": "Become_Pregnant",
-      "conditional_transition": [
-        {
-          "transition": "Anemia_End_2",
-          "condition": {
-            "condition_type": "Attribute",
-            "attribute": "anemia_pregnancy",
-            "operator": "==",
-            "value": 1
-          }
-        },
-        {
-          "transition": "Unset_Pregnant_Attribute"
-        }
-      ]
-    },
     "Abortion_Ends": {
       "type": "ConditionEnd",
       "condition_onset": "Become_Pregnant",
@@ -2326,6 +2308,40 @@
       ],
       "assign_to_attribute": "fatal_pregnancy_complication",
       "direct_transition": "End_Initial_Visit_Towards_Ectopic_Pregnancy"
+    },
+    "Miscarriage_Ends_Pregnancy": {
+      "type": "ConditionEnd",
+      "condition_onset": "Become_Pregnant",
+      "conditional_transition": [
+        {
+          "transition": "Anemia_End_2",
+          "condition": {
+            "condition_type": "Attribute",
+            "attribute": "anemia_pregnancy",
+            "operator": "==",
+            "value": 1
+          }
+        },
+        {
+          "transition": "Unset_Pregnant_Attribute"
+        }
+      ]
+    },
+    "End_Miscarriage_Condition": {
+      "type": "ConditionEnd",
+      "direct_transition": "Miscarriage_Ends_Pregnancy",
+      "referenced_by_attribute": "miscarriage"
+    },
+    "History_of_Miscarriage": {
+      "type": "ConditionOnset",
+      "codes": [
+        {
+          "system": "SNOMED-CT",
+          "code": 161744009,
+          "display": "Past pregnancy history of miscarriage (situation)"
+        }
+      ],
+      "direct_transition": "End_Miscarriage_Followup_Encounter"
     }
   },
   "gmf_version": 1