Merge pull request #72 from mcode/dev

Dev
mcode · Apr 8, 2024 · 72560f9 · 72560f9
2 parents 0d2b0a0 + 4f92fd9
commit 72560f9
Show file tree

Hide file tree

Showing 19 changed files with 227 additions and 128 deletions.
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # EHR FHIR Server
 
-This subproject hosts a HAPI FHIR server that is based on the now-deprecated [hapi-fhir-jpaserver-example](https://github.com/jamesagnew/hapi-fhir/tree/master/hapi-fhir-jpaserver-example). The new repo is found [here](https://github.com/hapifhir/hapi-fhir-jpaserver-starter).
+This sub-project hosts a HAPI FHIR server that is based on the now-deprecated [hapi-fhir-jpaserver-example](https://github.com/jamesagnew/hapi-fhir/tree/master/hapi-fhir-jpaserver-example). The new repo is found [here](https://github.com/hapifhir/hapi-fhir-jpaserver-starter).
 
 ## Running the server
 

diff --git a/bundlefile/HypoxemiaPatientBundle.json b/bundlefile/HypoxemiaPatientBundle.json
@@ -203,7 +203,7 @@
 				],
 				"address": {
 					"line": [
-						"773  Wiseman Street"
+						"773 Wiseman Street"
 					],
 					"city": "Knoxville",
 					"state": "Tennessee",

diff --git a/dockerRunnerDev.sh b/dockerRunnerDev.sh
@@ -21,18 +21,18 @@ echo "loading data into test-ehr..."
 gradle loadData
 
 # Continuous Load Data command whenever fhirResourcesToLoad directory changes
-reources_modify_time=$(stat -c %Y fhirResourcesToLoad)
+resources_modify_time=$(stat -c %Y fhirResourcesToLoad)
 while sleep 1
 do
-    new_reources_modify_time=$(stat -c %Y fhirResourcesToLoad)
+    new_resources_modify_time=$(stat -c %Y fhirResourcesToLoad)
 
-    if [[ "$reources_modify_time" != "$new_reources_modify_time" ]] 
+    if [[ "$resources_modify_time" != "$new_resources_modify_time" ]] 
     then
         echo "loading data into test-ehr..."
         gradle loadData
     fi
 
-    reources_modify_time=$new_reources_modify_time
+    resources_modify_time=$new_resources_modify_time
 
 done ) & LOAD_DATA_PID=$!
 

diff --git a/fhirResourcesToLoad/medication_turalio.json b/fhirResourcesToLoad/medication_turalio.json
@@ -31,7 +31,7 @@
             {
               "system": "http://snomed.info/sct",
               "code": "2183126",
-              "display": "Product containing only turaliio"
+              "display": "Product containing only turalio"
             }
           ]
         },

diff --git a/fhirResourcesToLoad/rems_smith_medicationstatement_turalio.json b/fhirResourcesToLoad/rems_smith_medicationstatement_turalio.json
@@ -30,7 +30,7 @@
                     {
                       "system": "http://snomed.info/sct",
                       "code": "2183126",
-                      "display": "Product containing only turaliio"
+                      "display": "Product containing only turalio"
                     }
                   ]
                 },

diff --git a/fhirResourcesToLoad/rems_snow_medicationrequest_acetaminophen.json b/fhirResourcesToLoad/rems_snow_medicationrequest_acetaminophen.json
@@ -0,0 +1,78 @@
+{
+  "resourceType": "MedicationRequest",
+  "id": "pat017-mr-acetaminophen",
+  "meta": {
+    "versionId": "1",
+    "lastUpdated": "2023-12-18T21:12:33.000+00:00",
+    "source": "#aquj6ECLPVYNYbuX",
+    "profile": [
+      "http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest"
+    ]
+  },
+  "identifier": [
+    {
+      "type": {
+        "coding": [
+          {
+            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+            "code": "PLAC",
+            "display": "Placer Identifier"
+          }
+        ]
+      },
+      "system": "http://myprescribingsystem.com/ordernumber",
+      "value": "605153"
+    }
+  ],
+  "status": "draft",
+  "intent": "order",
+  "medicationCodeableConcept": {
+    "coding": [
+      {
+        "system": "http://www.nlm.nih.gov/research/umls/rxnorm",
+        "code": "993781",
+        "display": "Acetaminophen 300 MG / Codeine Phosphate 30 MG Oral Tablet"
+      },
+      {
+        "system": "http://hl7.org/fhir/sid/ndc",
+        "code": "00093015001"
+      }
+    ],
+    "text": "Acetaminophen 300 mg / Codeine 30 mg oral tablet"
+  },
+  "subject": {
+    "reference": "Patient/pat017",
+    "display": "Jon Snow"
+  },
+  "authoredOn": "2023-06-05",
+  "requester": {
+    "reference": "Practitioner/pra1234",
+    "display": "Jane Doe"
+  },
+  "reasonCode": [
+    {
+      "text": "Post dental surgery"
+    }
+  ],
+  "dosageInstruction": [
+    {
+      "text": "1 tab tid prn pain"
+    }
+  ],
+  "dispenseRequest": {
+    "numberOfRepeatsAllowed": 1,
+    "quantity": {
+      "value": 10,
+      "unit": "each",
+      "system": "http://unitsofmeasure.org",
+      "code": "{each}"
+    },
+    "performer": {
+      "identifier": {
+        "system": "http://terminology.hl7.org/CodeSystem/NCPDPProviderIdentificationNumber",
+        "value": "0999017"
+      },
+      "display": "Our Pharmacy"
+    }
+  }
+}
diff --git a/fhirResourcesToLoad/rems_snow_medicationrequest_addyi.json b/fhirResourcesToLoad/rems_snow_medicationrequest_addyi.json
@@ -0,0 +1,93 @@
+{
+  "resourceType": "MedicationRequest",
+  "id": "pat017-mr-addyi",
+  "medicationCodeableConcept": {
+    "coding": [
+      {
+        "system": "http://www.nlm.nih.gov/research/umls/rxnorm",
+        "code": "1666386",
+        "display": "Addyi 100 MG Oral Tablet"
+      },
+      {
+          "system": "http://hl7.org/fhir/sid/ndc",
+          "code": "58604-214-03"
+      }
+    ]
+  },
+  "status": "active",
+  "intent": "order",
+  "subject": {
+    "reference": "Patient/pat017",
+    "display": "Jon Snow"
+  },
+  "authoredOn": "2024-02-29",
+  "requester": {
+    "reference": "Practitioner/pra1234",
+    "display": "Jane Doe"
+  },
+  "reasonCode": [
+    {
+      "coding": [
+        {
+          "system": "http://snomed.info/sct",
+          "code": "270903007",
+          "display": "Hypoactive sexual desire disorder (HSDD)"
+        }
+      ]
+    }
+  ],
+  "insurance": [
+    {
+      "reference": "Coverage/cov017"
+    }
+  ],
+  "dosageInstruction": [
+    {
+      "sequence": 1,
+      "text": "100mg before bed",
+      "timing": {
+        "repeat": {
+          "frequency": 1,
+          "period": 1,
+          "periodUnit": "d"
+        }
+      },
+      "route": {
+        "coding": [
+          {
+            "system": "http://snomed.info/sct",
+            "code": "26643006",
+            "display": "Oral route (qualifier value)"
+          }
+        ]
+      },
+      "doseAndRate": [
+        {
+          "type": {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/dose-rate-type",
+                "code": "ordered",
+                "display": "Ordered"
+              }
+            ]
+          },
+          "doseQuantity": {
+            "value": 100,
+            "unit": "mg",
+            "system": "http://unitsofmeasure.org",
+            "code": "mg"
+          }
+        }
+      ]
+    }
+  ],
+  "dispenseRequest": {
+    "quantity": {
+      "value": 28,
+      "system": "http://terminology.hl7.org/CodeSystem/v3-orderableDrugForm",
+      "code": "TAB"
+    },
+    "numberOfRepeatsAllowed": 2
+  }
+}
diff --git a/fhirResourcesToLoad/rems_snow_medicationstatement_turalio.json b/fhirResourcesToLoad/rems_snow_medicationstatement_turalio.json
@@ -30,7 +30,7 @@
                     {
                       "system": "http://snomed.info/sct",
                       "code": "2183126",
-                      "display": "Product containing only turaliio"
+                      "display": "Product containing only turalio"
                     }
                   ]
                 },

diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java b/src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java
@@ -224,7 +224,7 @@ protected void initialize() throws ServletException {
     setPagingProvider(databaseBackedPagingProvider);
 
     /*
-     * This interceptor formats the output using nice colourful
+     * This interceptor formats the output using nice colorful
      * HTML output when the request is detected to come from a
      * browser.
      */
@@ -419,7 +419,7 @@ protected void initialize() throws ServletException {
   private ServerConformanceR4 createConformance(RestfulServer theRestfulServer, IFhirSystemDao<Bundle, Meta> theSystemDao, DaoConfig theDaoConfig, ISearchParamRegistry theSearchParamRegistry, IValidationSupport theValidationSupport){
      ServerConformanceR4 con = new ServerConformanceR4(theRestfulServer, theSystemDao,
             theDaoConfig, theSearchParamRegistry, theValidationSupport);
-    // this isnt autowiring so force it.
+    // this isn't autowiring so force it.
     myApplicationContext.getAutowireCapableBeanFactory().autowireBean(con);
     return con;
   }

diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/JettyConfiguration.java b/src/main/java/ca/uhn/fhir/jpa/starter/JettyConfiguration.java
@@ -14,7 +14,6 @@
 import org.eclipse.jetty.io.ByteBufferOutputStream;
 import org.eclipse.jetty.server.Dispatcher;
 import org.eclipse.jetty.server.Request;
-import org.eclipse.jetty.server.handler.AbstractHandler;
 import org.eclipse.jetty.server.handler.ErrorHandler;
 import org.eclipse.jetty.util.StringUtil;
 

diff --git a/src/main/java/org/hl7/codex/rems/script/Message.java b/src/main/java/org/hl7/codex/rems/script/Message.java
@@ -1,14 +1,11 @@
 package org.hl7.codex.rems.script;
 
-//import java.io.Serializable;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlElement;
 
 @XmlRootElement(name="Message")
-//public class Message implements Serializable {
 public class Message {
     protected Header header; 
-    //protected Body body;
 
     @XmlElement(name="Header")
         public Header getHeader() {
@@ -17,14 +14,4 @@ public Header getHeader() {
     public void setHeader(Header header) {
         this.header = header;
     }
-
-    /*
-    @XmlElement(name="Body")
-    public Body getBody() {
-        return body;
-    }
-    public void setBody(Body body) {
-        this.body = body;
-    }
-    */
 }
diff --git a/src/main/java/org/hl7/codex/rems/script/NcpdpScriptController.java b/src/main/java/org/hl7/codex/rems/script/NcpdpScriptController.java
@@ -26,9 +26,6 @@ public class NcpdpScriptController {
 
     private static final String APPLICATION_XML = "application/xml";
 
-    @Autowired
-    private org.springframework.core.env.Environment environment;
-
     @Autowired
     private JpaRestfulServer jpaRestfulServer;
 
@@ -59,7 +56,7 @@ public RxFillStatusMessage getScriptResponse(@RequestBody RxFillMessage payload)
         RequestDetails requestDetails = new SystemRequestDetails();
         requestDetails.setRequestId(header.getPrescriberOrderNumber());
 
-        // retrieve the MedicationRequeest
+        // retrieve the MedicationRequest
         MedicationRequest medicationRequest = null;
         try {
             medicationRequest = medicationRequestDao.read(id, requestDetails);

diff --git a/src/main/java/org/hl7/davinci/ehrserver/authproxy/AuthProxy.java b/src/main/java/org/hl7/davinci/ehrserver/authproxy/AuthProxy.java
@@ -62,7 +62,7 @@ public void getAuth(@RequestParam Map<String, String> reqParamValue, HttpServlet
    * passed in by the request to associate the request with a launch id, and uses that launch id
    * to append extra parameters to the token response.
    * @param body - Custom object to serialize the incoming request body
-   * @return - returns the custom built reponse
+   * @return - returns the custom built response
    */
   @PostMapping(value = "/token",  consumes = MediaType.APPLICATION_FORM_URLENCODED_VALUE)
   public ResponseEntity<TokenResponse> getToken(TokenRequest body) {

diff --git a/src/main/java/org/hl7/davinci/ehrserver/authproxy/PayloadDAO.java b/src/main/java/org/hl7/davinci/ehrserver/authproxy/PayloadDAO.java
@@ -1,19 +1,12 @@
 package org.hl7.davinci.ehrserver.authproxy;
 
-import org.hl7.davinci.ehrserver.requestgenerator.database.Key;
-
 public interface PayloadDAO {
 
   public void createPayload(Payload payload);
 
-
-  // create a new user record in the users table
-//  public void create(String launchId, String launchUrl, String patientId, String template, String request);
-
   // get a user with the passed id
   public Payload getPayload(String id);
 
-
   // update launch id to be a code
   public void updateCode(String launchId, String code);
 

diff --git a/src/main/java/org/hl7/davinci/ehrserver/authproxy/PayloadMapper.java b/src/main/java/org/hl7/davinci/ehrserver/authproxy/PayloadMapper.java
@@ -1,6 +1,5 @@
 package org.hl7.davinci.ehrserver.authproxy;
 
-import org.hl7.davinci.ehrserver.requestgenerator.database.Key;
 import org.springframework.jdbc.core.RowMapper;
 
 import java.sql.ResultSet;

diff --git a/...rg/hl7/davinci/ehrserver/interceptor/QuestionnaireResponseSearchParameterInterceptor.java b/...rg/hl7/davinci/ehrserver/interceptor/QuestionnaireResponseSearchParameterInterceptor.java
@@ -3,10 +3,6 @@
 import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
 import org.hl7.fhir.r4.model.Enumerations.SearchParamType;
 
-import java.util.ArrayList;
-import java.util.List;
-
-import org.hl7.fhir.r4.model.Enumeration;
 import org.hl7.fhir.r4.model.SearchParameter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

diff --git a/src/main/java/org/hl7/davinci/ehrserver/requestgenerator/database/KeyDAO.java b/src/main/java/org/hl7/davinci/ehrserver/requestgenerator/database/KeyDAO.java
@@ -1,13 +1,11 @@
 package org.hl7.davinci.ehrserver.requestgenerator.database;
 
-import javax.sql.DataSource;
 import java.util.List;
 
 public interface KeyDAO {
 
   public void createKey(Key key);
 
-
   // create a new user record in the users table
   public void create(String id, String e, String n, String kty);