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🔥 HAPI FHIR - Java API for HL7 FHIR Clients and Servers
http://hapifhir.io
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hapi fhir post replace backslashn with space #1218

Open utkinnina opened 5 years ago

utkinnina commented 5 years ago

Hi, can't find any documentation, limitations or restrictions , so opening a bug.

Describe the bug when using hapi fhir post transaction bundle and string filed contains the backslash n('\n') , backslash n replaced with space

To Reproduce

  1. create bundle with 2 resources: patient and clinical impression
  2. fill clinical impression resource with summary that include "\n" (backslash n) f.e. "summary":"Chief Complaint:\nAbdominal pain for last 4 days. Described as sudden onset, like 'someone punching me in the stomach'. \nPain began after returning from a golf outing where patient consumed roast beef and pizza." },
  3. post the same bundle programmatically using IGeneric client instance execute = (Bundle)igenericclientinstance.transaction().withBundle(bundle).execute();
  4. result -> backslash n replaces with space
  5. post the bundle manually using web wizard (web-> server home/action -> transaction)
  6. result -> backskash n remained

Expected behavior IGeneric client should not format data inside.

Environment (please complete the following information):

thanks in advance, Nina

jamesagnew commented 5 years ago

Hi @utkinnina, thanks for the bug report! Would you be able to provide a complete code snippet that demonstrates this issue?

utkinnina commented 5 years ago

Hi @jamesagnew , thank you for quick response.

  1. here is the bundle I post:

{
"type":"transaction", "resourceType":"Bundle", "entry":[
{
"fullUrl":"urn:uuid:47709cc7-b3ec-4abc-9d26-3df3d3d57907", "resource":{
"resourceType":"Patient", "identifier":[
{
"system":"http://www.imi-mimic.de/patients", "value":"6547582" } ], "active":true, "name":[
{
"use":"official", "family":"Smith", "given":[
"jJn" ] } ], "gender":"male", "birthDate":"1936-07-15", "deceasedBoolean":false, "communication":[
{
"language":{
"coding":[
{
"system":"urn:ietf:bcp:47", "code":"en", "display":"English" } ], "text":"English" }, "preferred":true } ], "maritalStatus":{
"coding":[
{
"system":"http://hl7.org/fhir/v3/MaritalStatus", "code":"M", "display":"Married" } ], "text":"A current marriage contract is active" }, "contact":[
{
"relationship":[
{
"coding":[
{
"system":"http://hl7.org/fhir/v2/0131", "code":"N" } ] }, {
"coding":[
{
"system":"http://hl7.org/fhir/v3/RoleCode", "code":"WIFE" } ] } ], "name":{
"use":"usual", "family":"McGregor", "given":[
"Dolores" ] }, "telecom":[
{
"system":"phone", "value":"069-555-0383", "use":"mobile" } ] } ] }, "request":{
"method":"POST", "url":"Patient" } }, {
"resource":{
"resourceType":"ClinicalImpression", "id":" admitting note", "status":"completed", "subject":{
"reference":"urn:uuid:47709cc7-b3ec-4abc-9d26-3df3d3d57907" }, "code":{
"coding":[
{
"system":"UMLS", "code":"C1317082", "display":"Admission history and physical note" } ] }, "effectivePeriod":{
"start":"2018-09-16T08:00:00+01:00", "end":"2018-09-16T08:30:00+01:00" }, "date":"2018-09-16", "summary":"Chief Complaint:\n Abdominal pain for last 4 days. Described as sudden onset, like 'someone punching me in the stomach'. The pain has been unrelenting and worsening over time.\n\nHistory of present illness: \nPain began after returning from a golf outing where patient consumed roast beef and pizza. Reports episode of nausea and one episode of emesis; denies blood. Appetite remains poor. No bowel movement and no rectal bleeding. Denies fever, chills or sweats. Has been taking ibuprofen and acetaminophen without relief. Denies similar pain before. \n\nRisk factors:\nDiabetes Type 2, Chronic Obstructive Pulmonary Disease, Chronic Renal Insufficiency, Abdominal Aortic Aneurysm (5.8 cm, endovascular repair 2014), Hypertension, Hyperlipidemia, Benign Prostate Hyperplasia, Diverticulosis\n\nSocial history: \n82-year-old active male. Reports occasional alcohol 2-3 drinks per week. 1ppd smoker x 50 years; quit 5 years ago. Denies recreational drugs. Married x 52 years; wife Delores McGregor: (715) 555-1212. Three grown children, alive and well. DPOA on file: Full resuscitative efforts, however patient does not wish for sustained or prolonged measures if no reasonable hope for recovery.\n\nFamily history: Non-contributory\n\nInitial Exam:\n A&O x3, in visible distress. Cardiac: NSR, no ectopy, +1 murmur, Lung Sounds clear throughout, Abdomen distended but no peritoneal sighs. Patient reports pain with palpation. BS faint x 4 quads. RUQ Abdominal Ultrasound: Common Bile Duct dilation 7-9mm. Abdominal CT: Inflammatory stranding around the pancreas. \n\nConsults: GI and Surgical \n\nRecommend: ERCP, Admit to Step Down Unit" }, "request":{
"method":"POST", "url":"ClinicalImpression" } } ] }

  1. if i go to hapi fhir server https://fhirtest.uhn.ca/transaction and post it i received the response { "resourceType": "Bundle", "id": "4241842e-665d-4782-9748-116819526485", "type": "transaction-response", "link": [ { "relation": "self", "url": "http://hapi.fhir.org/baseDstu3" } ], "entry": [ { "response": { "status": "201 Created", "location": "Patient/1452146/_history/1", "etag": "1", "lastModified": "2019-02-25T10:16:57.607+00:00" } }, { "response": { "status": "201 Created", "location": "ClinicalImpression/1452147/_history/1", "etag": "1", "lastModified": "2019-02-25T10:16:57.607+00:00" } } ] }

where http://hapi.fhir.org/baseDstu3/ClinicalImpression/1452147 contains summary with backslashn

  1. if i use hapi fhir api with the following code where bundle is the same json parsed to Bundle object and fhirServer is the base url: FhirContext CTX = FhirContext.forDstu3(); IGenericClient serverClient = CTX.newRestfulGenericClient(fhirServer); CTX.setPerformanceOptions(new PerformanceOptionsEnum[]{PerformanceOptionsEnum.DEFERRED_MODEL_SCANNING}); CTX.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER); serverClient.transaction().withBundle(bundle).execute();

and than i check the db i see that the backslashn was replaced with space

p.s. i am using jsonParser = CTX.newJsonParser(); for create Bundle from json input and i already checked that the json parser does not replace the backslashn

jamesagnew commented 5 years ago

I used the following code snippet:

    FhirContext ctx = FhirContext.forDstu3();
    IGenericClient client = ctx.newRestfulGenericClient("http://hapi.fhir.org/baseDstu3");

    ClinicalImpression impression = new ClinicalImpression();
    impression.setDescription("line1\nline2");
    client.create().resource(impression).execute();

And it successfully and correctly created the following resource: http://hapi.fhir.org/baseDstu3/ClinicalImpression/1455375

Can you please provide a complete runnable code snippet like this one that shows your issue?

jamesagnew commented 5 years ago

(Note, please reduce the code snippet to the bare minimum required in order to demonstrate the issue)

utkinnina commented 5 years ago

@jamesagnew please see my previous comment, line System.out.println(((ClinicalImpression)inputBundleEntry.get(1).getResource()).getSummary()); there I print to the console the summary from clinical impression object after the parsing, but from the input

than i post the whole bundle to the db , and query the clinical impression object that was created String resourseFullUrl = baseServerUrl + "/" + outputBundleEntry.get(1).getResponse().getLocation(); and than i print the summary System.out.println(execute1.getSummary()); where i print the summary from the object that is already created in the db and i query it by location

the prints are different, because in the created object the backslashn are missing

jamesagnew commented 5 years ago

I just ran this code snippet and the ClinicalImpresion it stored in the server looks correct to me.

http://hapi.fhir.org/baseDstu3/ClinicalImpression/1478163

  "summary": "Chief Complaint:\nAbdominal pain for last 4 days. Described as sudden onset, like 'someone punching me in the stomach'. The pain has been unrelenting and worsening over time.\n\nHistory of present illness: \nPain began after returning from a golf outing where patient consumed roast beef and pizza. Reports episode of nausea and one episode of emesis; denies blood.  Appetite remains poor. No bowel movement and no rectal bleeding. Denies fever, chills or sweats. Has been taking ibuprofen and acetaminophen without relief. Denies similar pain before. \n\nRisk factors:\nDiabetes Type 2, Chronic Obstructive Pulmonary Disease, Chronic Renal Insufficiency, Abdominal Aortic Aneurysm (5.8 cm, endovascular repair 2014), Hypertension, Hyperlipidemia, Benign Prostate Hyperplasia, Diverticulosis\n\nSocial history: \n82-year-old active male. Reports occasional alcohol 2-3 drinks per week. 1ppd smoker x 50 years; quit 5 years ago. Denies recreational drugs. Married x 52 years; wife Delores McGregor: (715) 555-1212. Three grown children, alive and well. DPOA on file: Full resuscitative efforts, however patient does not wish for sustained or prolonged measures if no reasonable hope for recovery.\n\nFamily history: Non-contributory\n\nInitial Exam:\n A&O x3, in visible distress. Cardiac: NSR, no ectopy, +1 murmur, Lung Sounds clear throughout, Abdomen distended but no peritoneal sighs. Patient reports pain with palpation. BS faint x 4 quads. RUQ Abdominal Ultrasound: Common Bile Duct dilation 7-9mm. Abdominal CT: Inflammatory stranding around the pancreas. \n\nConsults:  GI and Surgical \n\nRecommend: ERCP, Admit to Step Down Unit"
}
utkinnina commented 5 years ago

WOW @jamesagnew
here is mine http://hapi.fhir.org/baseDstu3/ClinicalImpression/1478166/

jamesagnew commented 5 years ago

Please try to reduce the code snippet down to the absolute bare minimum required to demonstrate the issue. Remove every single line that is not necessary in order to demonstrate the issue. I'm looking for a code snippet like the one I posted above.

utkinnina commented 5 years ago

package com.ge.acutecare.awslambda.hospital.gateway.handlers;

import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.model.base.resource.BaseOperationOutcome; import ca.uhn.fhir.model.primitive.IdDt; import ca.uhn.fhir.parser.IParser; import ca.uhn.fhir.rest.client.api.IGenericClient; import org.hl7.fhir.dstu3.model.Bundle; import org.hl7.fhir.dstu3.model.ClinicalImpression; import org.hl7.fhir.dstu3.model.OperationOutcome; import org.hl7.fhir.dstu3.model.Patient; import org.junit.Test;

import java.util.Iterator; import java.util.List;

public class HapiFhirbackslashNTest { FhirContext CTX = FhirContext.forDstu3(); IParser jsonParser = CTX.newJsonParser(); String baseServerUrl = "http://hapi.fhir.org/baseDstu3";

@Test
public void testParseWinBackslashNShortVersion() {
    IGenericClient serverClient = CTX.newRestfulGenericClient(baseServerUrl);

    String strP1 = "{  \n" +
            "   \"type\":\"transaction\",\n" +
            "   \"resourceType\":\"Bundle\",\n" +
            "   \"entry\":[  \n" +
            "      {  \n" +
            "         \"fullUrl\":\"urn:uuid:47709cc7-b3ec-4abc-9d26-3df3d3d57907\",\n" +
            "         \"resource\":{  \n" +
            "            \"resourceType\":\"Patient\",\n" +
            "            \"identifier\":[  \n" +
            "               {  \n" +
            "                  \"system\":\"http://www.imi-mimic.de/patients\",\n" +
            "                  \"value\":\"test123\"\n" +
            "               }\n" +
            "            ],\n" +
            "            \"active\":true,\n" +
            "            \"name\":[  \n" +
            "               {  \n" +
            "                  \"use\":\"official\",\n" +
            "                  \"family\":\"Smith\",\n" +
            "                  \"given\":[  \n" +
            "                     \"jon\"\n" +
            "                  ]\n" +
            "               }\n" +
            "            ],\n" +
            "            \"gender\":\"male\",\n" +
            "            \"birthDate\":\"1936-07-15\",\n" +
            "            \"deceasedBoolean\":false,\n" +
            "            \"communication\":[  \n" +
            "               {  \n" +
            "                  \"language\":{  \n" +
            "                     \"coding\":[  \n" +
            "                        {  \n" +
            "                           \"system\":\"urn:ietf:bcp:47\",\n" +
            "                           \"code\":\"en\",\n" +
            "                           \"display\":\"English\"\n" +
            "                        }\n" +
            "                     ],\n" +
            "                     \"text\":\"English\"\n" +
            "                  },\n" +
            "                  \"preferred\":true\n" +
            "               }\n" +
            "            ],\n" +
            "            \"maritalStatus\":{  \n" +
            "               \"coding\":[  \n" +
            "                  {  \n" +
            "                     \"system\":\"http://hl7.org/fhir/v3/MaritalStatus\",\n" +
            "                     \"code\":\"M\",\n" +
            "                     \"display\":\"Married\"\n" +
            "                  }\n" +
            "               ],\n" +
            "               \"text\":\"A current marriage contract is active\"\n" +
            "            },\n" +
            "            \"contact\":[  \n" +
            "               {  \n" +
            "                  \"relationship\":[  \n" +
            "                     {  \n" +
            "                        \"coding\":[  \n" +
            "                           {  \n" +
            "                              \"system\":\"http://hl7.org/fhir/v2/0131\",\n" +
            "                              \"code\":\"N\"\n" +
            "                           }\n" +
            "                        ]\n" +
            "                     },\n" +
            "                     {  \n" +
            "                        \"coding\":[  \n" +
            "                           {  \n" +
            "                              \"system\":\"http://hl7.org/fhir/v3/RoleCode\",\n" +
            "                              \"code\":\"WIFE\"\n" +
            "                           }\n" +
            "                        ]\n" +
            "                     }\n" +
            "                  ],\n" +
            "                  \"name\":{  \n" +
            "                     \"use\":\"usual\",\n" +
            "                     \"family\":\"McGregor\",\n" +
            "                     \"given\":[  \n" +
            "                        \"Dolores\"\n" +
            "                     ]\n" +
            "                  },\n" +
            "                  \"telecom\":[  \n" +
            "                     {  \n" +
            "                        \"system\":\"phone\",\n" +
            "                        \"value\":\"069-555-0383\",\n" +
            "                        \"use\":\"mobile\"\n" +
            "                     }\n" +
            "                  ]\n" +
            "               }\n" +
            "            ]\n" +
            "         },\n" +
            "         \"request\":{  \n" +
            "            \"method\":\"POST\",\n" +
            "            \"url\":\"Patient\"\n" +
            "         }\n" +
            "      },\n" +
            "      {  \n" +
            "         \"resource\":{  \n" +
            "            \"resourceType\":\"ClinicalImpression\",\n" +
            "            \"id\":\" admitting note\",\n" +
            "            \"status\":\"completed\",\n" +
            "            \"subject\":{  \n" +
            "               \"reference\":\"urn:uuid:47709cc7-b3ec-4abc-9d26-3df3d3d57907\"\n" +
            "            },\n" +
            "            \"code\":{  \n" +
            "               \"coding\":[  \n" +
            "                  {  \n" +
            "                     \"system\":\"UMLS\",\n" +
            "                     \"code\":\"C1317082\",\n" +
            "                     \"display\":\"Admission history and physical note\"\n" +
            "                  }\n" +
            "               ]\n" +
            "            },\n" +
            "            \"effectivePeriod\":{  \n" +
            "               \"start\":\"2018-09-16T08:00:00+01:00\",\n" +
            "               \"end\":\"2018-09-16T08:30:00+01:00\"\n" +
            "            },\n" +
            "            \"date\":\"2018-09-16\",\n" +
            "            \"summary\":\"Chief Complaint:\\nAbdominal pain for last 4 days. Described as sudden onset, like 'someone punching me in the stomach'. The pain has been unrelenting and worsening over time.\\n\\nHistory of present illness: \\nPain began after returning from a golf outing where patient consumed roast beef and pizza. Reports episode of nausea and one episode of emesis; denies blood.  Appetite remains poor. No bowel movement and no rectal bleeding. Denies fever, chills or sweats. Has been taking ibuprofen and acetaminophen without relief. Denies similar pain before. \\n\\nRisk factors:\\nDiabetes Type 2, Chronic Obstructive Pulmonary Disease, Chronic Renal Insufficiency, Abdominal Aortic Aneurysm (5.8 cm, endovascular repair 2014), Hypertension, Hyperlipidemia, Benign Prostate Hyperplasia, Diverticulosis\\n\\nSocial history: \\n82-year-old active male. Reports occasional alcohol 2-3 drinks per week. 1ppd smoker x 50 years; quit 5 years ago. Denies recreational drugs. Married x 52 years; wife Delores McGregor: (715) 555-1212. Three grown children, alive and well. DPOA on file: Full resuscitative efforts, however patient does not wish for sustained or prolonged measures if no reasonable hope for recovery.\\n\\nFamily history: Non-contributory\\n\\nInitial Exam:\\n A&O x3, in visible distress. Cardiac: NSR, no ectopy, +1 murmur, Lung Sounds clear throughout, Abdomen distended but no peritoneal sighs. Patient reports pain with palpation. BS faint x 4 quads. RUQ Abdominal Ultrasound: Common Bile Duct dilation 7-9mm. Abdominal CT: Inflammatory stranding around the pancreas. \\n\\nConsults:  GI and Surgical \\n\\nRecommend: ERCP, Admit to Step Down Unit\"\n" +
            "         },\n" +
            "         \"request\":{  \n" +
            "            \"method\":\"POST\",\n" +
            "            \"url\":\"ClinicalImpression\"\n" +
            "         }\n" +
            "      }\n" +
            "   ]\n" +
            "}";

    Bundle inputBundle = jsonParser.parseResource(Bundle.class, strP1);
    String originalSummary = ((ClinicalImpression) inputBundle.getEntry().get(1).getResource()).getSummary();
    Bundle execute = serverClient.transaction().withBundle(inputBundle).execute();

    ClinicalImpression queryClinicalImpressionResult = (ClinicalImpression)serverClient.search()
        .byUrl(baseServerUrl + "/" + execute.getEntry().get(1).getResponse().getLocation())
        .execute();

    if (queryClinicalImpressionResult.getSummary().equals(originalSummary)) {

        System.out.println("\033[1;31m" + "same summary" + "\033[0m");
    }else {
        System.out.println("\033[1;31m" + "not same summary" + "\033[0m");
        System.out.println("\033[0;31m" + "original: " + "\033[0m");
        System.out.println(originalSummary);
        System.out.println("\033[0;31m" + "stored in db: " + "\033[0m");
        System.out.println(queryClinicalImpressionResult.getSummary());
    }
}

}

utkinnina commented 5 years ago

@jamesagnew done, please try again

jamesagnew commented 5 years ago

So this requires a patient to be submitted along with the impression, and for it to be in a transaction?

sent from my phone.

On Tue, Feb 26, 2019, 01:52 utkinnina notifications@github.com wrote:

@jamesagnew https://github.com/jamesagnew done, please try again

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/jamesagnew/hapi-fhir/issues/1218#issuecomment-467318207, or mute the thread https://github.com/notifications/unsubscribe-auth/ADTfnc2x0hvL9sDagAQRcEcWqSNTrVCBks5vRNmQgaJpZM4bOhgk .

utkinnina commented 5 years ago

@jamesagnew , i am not sure i understand you. my use case is to post bundles of patient data to db that we implement with hapi fhir. transaction? - yes, it should be atomic in my use case

jamesagnew commented 5 years ago

I'm asking you to trim out anything that isn't neccessary in order to demonstrate your issue. There is a higher likelihood that we will have time to investigate this if we don't need to be the ones to figure out whether the fact that you are including a transaction with two resources is relevant to this issue.

Please see this link if this isn't clear: https://github.com/jamesagnew/hapi-fhir/wiki/Getting-Help

utkinnina commented 5 years ago

@jamesagnew , understand, thanks! so my answer is - the bug reproducing requires a ClinicalImpression to be submitted along with the patient, and for it to be in a transaction

jamesagnew commented 5 years ago

So if you remove the patient from the bundle it stops happening?

jamesagnew commented 5 years ago

That is bizarre.

utkinnina commented 5 years ago

aaa, just a moment! i did not try without a patient

utkinnina commented 5 years ago

hi @jamesagnew , sorry for delay. below the shortest code to demonstrate it. i guess the bug happen because the is resource inside the bundle. not relate to the patient. i removed the patient, and put clinical impression only inside the bundle and the backslash n was replaced alsoe

utkinnina commented 5 years ago

import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.parser.IParser; import ca.uhn.fhir.rest.client.api.IGenericClient; import org.hl7.fhir.dstu3.model.Bundle; import org.hl7.fhir.dstu3.model.ClinicalImpression; import org.junit.Test;

public class HapiFhirbackslashNTest {

FhirContext CTX = FhirContext.forDstu3();
IParser jsonParser = CTX.newJsonParser();
String baseServerUrl = "http://hapi.fhir.org/baseDstu3";

@Test
public void testParseWinBackslashNShortVersion() {
    IGenericClient serverClient = CTX.newRestfulGenericClient(baseServerUrl);

    String strP1 = "{  \n" +
            "   \"type\":\"transaction\",\n" +
            "   \"resourceType\":\"Bundle\",\n" +
            "   \"entry\":[  \n" +
            "      {  \n" +
            "         \"resource\":{  \n" +
            "            \"resourceType\":\"ClinicalImpression\",\n" +
            "            \"id\":\"Pena admitting note\",\n" +
            "            \"status\":\"completed\",\n" +
            "            \"subject\":{  \n" +
            "               \"reference\":\"Patient/423119\"\n" +
            "            },\n" +
            "            \"code\":{  \n" +
            "               \"coding\":[  \n" +
            "                  {  \n" +
            "                     \"system\":\"UMLS\",\n" +
            "                     \"code\":\"C1317082\",\n" +
            "                     \"display\":\"Admission history and physical note\"\n" +
            "                  }\n" +
            "               ]\n" +
            "            },\n" +
            "            \"effectivePeriod\":{  \n" +
            "               \"start\":\"2018-09-15T15:00:00\",\n" +
            "               \"end\":\"2018-09-15T15:30:00\"\n" +
            "            },\n" +
            "            \"date\":\"2018-09-15\",\n" +
            "            \"summary\": \"Chief Complaint: \\nAbdominal pain for last 4 days. Described as sudden onset, like 'someone punching me in the stomach'. The pain has been unrelenting and worsening over time.\\n\\nHistory of present illness: \\nPain began after returning from a golf outing where patient consumed roast beef and pizza. Reports episode of nausea and one episode of emesis; denies blood.  Appetite remains poor. No bowel movement and no rectal bleeding. Denies fever, chills or sweats. Has been taking ibuprofen and acetaminophen without relief. Denies similar pain before.\\n\\n\"\n" +
            "         },\n" +
            "         \"request\":{  \n" +
            "            \"method\":\"POST\",\n" +
            "            \"url\":\"ClinicalImpression\"\n" +
            "         }\n" +
            "      }\n" +
            "   ]\n" +
            "}";
    Bundle inputBundle = jsonParser.parseResource(Bundle.class, strP1);
    String originalSummary = ((ClinicalImpression) inputBundle.getEntry().get(0).getResource()).getSummary();
    Bundle execute = serverClient.transaction().withBundle(inputBundle).execute();

    ClinicalImpression queryClinicalImpressionResult = (ClinicalImpression)serverClient.search()
        .byUrl(baseServerUrl + "/" + execute.getEntry().get(0).getResponse().getLocation())
        .execute();

    if (queryClinicalImpressionResult.getSummary().equals(originalSummary)) {

        System.out.println("\033[1;31m" + "same summary" + "\033[0m");
    }else {
        System.out.println("\033[1;31m" + "not same summary" + "\033[0m");
        System.out.println("\033[0;31m" + "original: " + "\033[0m");
        System.out.println(originalSummary);
        System.out.println("\033[0;31m" + "stored in db: " + "\033[0m");
        System.out.println(queryClinicalImpressionResult.getSummary());
    }
}

}

jamesagnew commented 5 years ago

Running this test gives me the following:

/usr/lib/jvm/java-11-openjdk-amd64/bin/java -ea -Didea.test.cyclic.buffer.size=1048576 -javaagent:/snap/intellij-idea-ultimate/114/lib/idea_rt.jar=37835:/snap/intellij-idea-ultimate/114/bin -Dfile.encoding=UTF-8 -classpath /snap/intellij-idea-ultimate/114/lib/idea_rt.jar:/snap/intellij-idea-ultimate/114/plugins/junit/lib/junit-rt.jar:/snap/intellij-idea-ultimate/114/plugins/junit/lib/junit5-rt.jar:/home/james/git/hapi-fhir/hapi-fhir-jpaserver-base/target/test-classes:/home/james/git/hapi-fhir/hapi-fhir-jpaserver-base/target/classes:/home/james/.m2/repository/org/codehaus/woodstox/woodstox-core-asl/4.4.1/woodstox-core-asl-4.4.1.jar:/home/james/.m2/repository/javax/xml/stream/stax-api/1.0-2/stax-api-1.0-2.jar:/home/james/.m2/repository/org/codehaus/woodstox/stax2-api/3.1.4/stax2-api-3.1.4.jar:/home/james/.m2/repository/net/sf/saxon/Saxon-HE/9.5.1-5/Saxon-HE-9.5.1-5.jar:/home/james/.m2/repository/org/apache/commons/commons-csv/1.3/commons-csv-1.3.jar:/home/james/git/hapi-fhir/hapi-fhir-base/target/classes:/home/james/.m2/repository/com/google/code/gson/gson/2.8.5/gson-2.8.5.jar:/home/james/.m2/repository/org/apache/commons/commons-lang3/3.8.1/commons-lang3-3.8.1.jar:/home/james/.m2/repository/org/apache/commons/commons-text/1.6/commons-text-1.6.jar:/home/james/.m2/repository/commons-codec/commons-codec/1.11/commons-codec-1.11.jar:/home/james/.m2/repository/commons-io/commons-io/2.6/commons-io-2.6.jar:/home/james/.m2/repository/org/slf4j/slf4j-api/1.7.25/slf4j-api-1.7.25.jar:/home/james/.m2/repository/org/slf4j/jcl-over-slf4j/1.7.25/jcl-over-slf4j-1.7.25.jar:/home/james/git/hapi-fhir/hapi-fhir-client/target/classes:/home/james/.m2/repository/org/apache/httpcomponents/httpclient/4.5.3/httpclient-4.5.3.jar:/home/james/.m2/repository/org/apache/httpcomponents/httpcore/4.4.6/httpcore-4.4.6.jar:/home/james/git/hapi-fhir/hapi-fhir-server/target/classes:/home/james/git/hapi-fhir/hapi-fhir-jpaserver-subscription/target/classes:/home/james/git/hapi-fhir/hapi-fhir-jpaserver-searchparam/target/classes:/home/james/.m2/repository/org/springframework/retry/spring-retry/1.2.2.RELEASE/spring-retry-1.2.2.RELEASE.jar:/home/james/git/hapi-fhir/hapi-fhir-jpaserver-model/target/classes:/home/james/git/hapi-fhir/hapi-fhir-validation/target/classes:/home/james/.m2/repository/ca/uhn/hapi/fhir/hapi-fhir-utilities/3.8.0-SNAPSHOT/hapi-fhir-utilities-3.8.0-SNAPSHOT.jar:/home/james/git/hapi-fhir/hapi-fhir-converter/target/classes:/home/james/.m2/repository/org/glassfish/jaxb/jaxb-runtime/2.3.1/jaxb-runtime-2.3.1.jar:/home/james/.m2/repository/org/glassfish/jaxb/txw2/2.3.1/txw2-2.3.1.jar:/home/james/.m2/repository/com/sun/istack/istack-commons-runtime/3.0.7/istack-commons-runtime-3.0.7.jar:/home/james/.m2/repository/org/jvnet/staxex/stax-ex/1.8/stax-ex-1.8.jar:/home/james/.m2/repository/com/sun/xml/fastinfoset/FastInfoset/1.2.15/FastInfoset-1.2.15.jar:/home/james/git/hapi-fhir/hapi-fhir-structures-dstu2/target/classes:/home/james/git/hapi-fhir/hapi-fhir-structures-dstu3/target/classes:/home/james/git/hapi-fhir/hapi-fhir-structures-r4/target/classes:/home/james/git/hapi-fhir/hapi-fhir-structures-hl7org-dstu2/target/classes:/home/james/.m2/repository/xpp3/xpp3_min/1.1.4c/xpp3_min-1.1.4c.jar:/home/james/git/hapi-fhir/hapi-fhir-validation-resources-dstu2/target/classes:/home/james/git/hapi-fhir/hapi-fhir-validation-resources-dstu3/target/classes:/home/james/git/hapi-fhir/hapi-fhir-validation-resources-r4/target/classes:/home/james/.m2/repository/ch/qos/logback/logback-classic/1.2.3/logback-classic-1.2.3.jar:/home/james/.m2/repository/ch/qos/logback/logback-core/1.2.3/logback-core-1.2.3.jar:/home/james/.m2/repository/net/ttddyy/datasource-proxy/1.4.9/datasource-proxy-1.4.9.jar:/home/james/.m2/repository/org/javassist/javassist/3.22.0-GA/javassist-3.22.0-GA.jar:/home/james/.m2/repository/com/fasterxml/jackson/core/jackson-annotations/2.9.7/jackson-annotations-2.9.7.jar:/home/james/.m2/repository/com/helger/ph-schematron/5.0.4/ph-schematron-5.0.4.jar:/home/james/.m2/repository/com/helger/ph-xml/9.1.1/ph-xml-9.1.1.jar:/home/james/.m2/repository/com/helger/ph-collection/9.1.1/ph-collection-9.1.1.jar:/home/james/.m2/repository/com/helger/ph-jaxb/9.1.1/ph-jaxb-9.1.1.jar:/home/james/.m2/repository/org/glassfish/jaxb/jaxb-core/2.2.11/jaxb-core-2.2.11.jar:/home/james/.m2/repository/com/helger/ph-commons/9.1.1/ph-commons-9.1.1.jar:/home/james/.m2/repository/com/google/code/findbugs/jsr305/3.0.2/jsr305-3.0.2.jar:/home/james/.m2/repository/org/thymeleaf/thymeleaf/3.0.11.RELEASE/thymeleaf-3.0.11.RELEASE.jar:/home/james/.m2/repository/ognl/ognl/3.1.12/ognl-3.1.12.jar:/home/james/.m2/repository/org/attoparser/attoparser/2.0.5.RELEASE/attoparser-2.0.5.RELEASE.jar:/home/james/.m2/repository/org/unbescape/unbescape/1.1.6.RELEASE/unbescape-1.1.6.RELEASE.jar:/home/james/.m2/repository/org/thymeleaf/thymeleaf-spring5/3.0.11.RELEASE/thymeleaf-spring5-3.0.11.RELEASE.jar:/home/james/.m2/repository/org/jscience/jscience/4.3.1/jscience-4.3.1.jar:/home/james/.m2/repository/org/javolution/javolution/5.2.3/javolution-5.2.3.jar:/home/james/.m2/repository/net/riotopsys/json_patch/0.0.0/json_patch-0.0.0.jar:/home/james/.m2/repository/com/github/dnault/xml-patch/0.3.0/xml-patch-0.3.0.jar:/home/james/.m2/repository/org/jdom/jdom2/2.0.6/jdom2-2.0.6.jar:/home/james/.m2/repository/jaxen/jaxen/1.1.6/jaxen-1.1.6.jar:/home/james/.m2/repository/net/sf/jopt-simple/jopt-simple/4.9/jopt-simple-4.9.jar:/home/james/.m2/repository/javax/interceptor/javax.interceptor-api/1.2/javax.interceptor-api-1.2.jar:/home/james/.m2/repository/javax/annotation/javax.annotation-api/1.3.2/javax.annotation-api-1.3.2.jar:/home/james/.m2/repository/javax/xml/bind/jaxb-api/2.3.1/jaxb-api-2.3.1.jar:/home/james/.m2/repository/javax/activation/javax.activation-api/1.2.0/javax.activation-api-1.2.0.jar:/home/james/.m2/repository/org/apache/derby/derby/10.14.2.0/derby-10.14.2.0.jar:/home/james/.m2/repository/org/apache/commons/commons-dbcp2/2.5.0/commons-dbcp2-2.5.0.jar:/home/james/.m2/repository/org/apache/commons/commons-pool2/2.6.0/commons-pool2-2.6.0.jar:/home/james/.m2/repository/commons-logging/commons-logging/1.2/commons-logging-1.2.jar:/home/james/.m2/repository/junit/junit/4.12/junit-4.12.jar:/home/james/.m2/repository/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar:/home/james/.m2/repository/org/springframework/spring-core/5.1.3.RELEASE/spring-core-5.1.3.RELEASE.jar:/home/james/.m2/repository/org/springframework/spring-jcl/5.1.3.RELEASE/spring-jcl-5.1.3.RELEASE.jar:/home/james/.m2/repository/org/springframework/spring-orm/5.1.3.RELEASE/spring-orm-5.1.3.RELEASE.jar:/home/james/.m2/repository/org/springframework/spring-jdbc/5.1.3.RELEASE/spring-jdbc-5.1.3.RELEASE.jar:/home/james/.m2/repository/org/springframework/spring-context/5.1.3.RELEASE/spring-context-5.1.3.RELEASE.jar:/home/james/.m2/repository/org/springframework/spring-aop/5.1.3.RELEASE/spring-aop-5.1.3.RELEASE.jar:/home/james/.m2/repository/org/springframework/spring-expression/5.1.3.RELEASE/spring-expression-5.1.3.RELEASE.jar:/home/james/.m2/repository/org/springframework/spring-beans/5.1.3.RELEASE/spring-beans-5.1.3.RELEASE.jar:/home/james/.m2/repository/org/springframework/data/spring-data-jpa/2.1.3.RELEASE/spring-data-jpa-2.1.3.RELEASE.jar:/home/james/.m2/repository/org/springframework/data/spring-data-commons/2.1.3.RELEASE/spring-data-commons-2.1.3.RELEASE.jar:/home/james/.m2/repository/org/aspectj/aspectjrt/1.9.1/aspectjrt-1.9.1.jar:/home/james/.m2/repository/org/springframework/spring-messaging/5.1.3.RELEASE/spring-messaging-5.1.3.RELEASE.jar:/home/james/.m2/repository/org/springframework/spring-tx/5.1.3.RELEASE/spring-tx-5.1.3.RELEASE.jar:/home/james/.m2/repository/org/springframework/spring-context-support/5.1.3.RELEASE/spring-context-support-5.1.3.RELEASE.jar:/home/james/.m2/repository/org/springframework/spring-webmvc/5.1.3.RELEASE/spring-webmvc-5.1.3.RELEASE.jar:/home/james/.m2/repository/org/springframework/spring-web/5.1.3.RELEASE/spring-web-5.1.3.RELEASE.jar:/home/james/.m2/repository/org/springframework/spring-websocket/5.1.3.RELEASE/spring-websocket-5.1.3.RELEASE.jar:/home/james/.m2/repository/org/hibernate/hibernate-core/5.4.1.Final/hibernate-core-5.4.1.Final.jar:/home/james/.m2/repository/org/jboss/logging/jboss-logging/3.3.2.Final/jboss-logging-3.3.2.Final.jar:/home/james/.m2/repository/javax/persistence/javax.persistence-api/2.2/javax.persistence-api-2.2.jar:/home/james/.m2/repository/net/bytebuddy/byte-buddy/1.9.5/byte-buddy-1.9.5.jar:/home/james/.m2/repository/antlr/antlr/2.7.7/antlr-2.7.7.jar:/home/james/.m2/repository/org/jboss/spec/javax/transaction/jboss-transaction-api_1.2_spec/1.1.1.Final/jboss-transaction-api_1.2_spec-1.1.1.Final.jar:/home/james/.m2/repository/org/jboss/jandex/2.0.5.Final/jandex-2.0.5.Final.jar:/home/james/.m2/repository/com/fasterxml/classmate/1.3.4/classmate-1.3.4.jar:/home/james/.m2/repository/org/dom4j/dom4j/2.1.1/dom4j-2.1.1.jar:/home/james/.m2/repository/org/hibernate/common/hibernate-commons-annotations/5.1.0.Final/hibernate-commons-annotations-5.1.0.Final.jar:/home/james/.m2/repository/org/hibernate/hibernate-entitymanager/5.4.1.Final/hibernate-entitymanager-5.4.1.Final.jar:/home/james/.m2/repository/org/hibernate/hibernate-ehcache/5.4.1.Final/hibernate-ehcache-5.4.1.Final.jar:/home/james/.m2/repository/net/sf/ehcache/ehcache/2.10.6/ehcache-2.10.6.jar:/home/james/.m2/repository/org/hibernate/hibernate-validator/5.4.1.Final/hibernate-validator-5.4.1.Final.jar:/home/james/.m2/repository/javax/validation/validation-api/2.0.1.Final/validation-api-2.0.1.Final.jar:/home/james/.m2/repository/com/sun/activation/javax.activation/1.2.0/javax.activation-1.2.0.jar:/home/james/.m2/repository/javax/mail/javax.mail-api/1.6.0/javax.mail-api-1.6.0.jar:/home/james/.m2/repository/com/sun/mail/javax.mail/1.6.1/javax.mail-1.6.1.jar:/home/james/.m2/repository/javax/el/javax.el-api/3.0.0/javax.el-api-3.0.0.jar:/home/james/.m2/repository/org/glassfish/javax.el/3.0.0/javax.el-3.0.0.jar:/home/james/.m2/repository/org/hibernate/hibernate-search-orm/5.11.1.Final/hibernate-search-orm-5.11.1.Final.jar:/home/james/.m2/repository/org/hibernate/hibernate-search-engine/5.11.1.Final/hibernate-search-engine-5.11.1.Final.jar:/home/james/.m2/repository/org/apache/lucene/lucene-misc/5.5.5/lucene-misc-5.5.5.jar:/home/james/.m2/repository/org/apache/lucene/lucene-facet/5.5.5/lucene-facet-5.5.5.jar:/home/james/.m2/repository/org/apache/lucene/lucene-queryparser/5.5.5/lucene-queryparser-5.5.5.jar:/home/james/.m2/repository/org/jboss/logging/jboss-logging-processor/2.1.0.Final/jboss-logging-processor-2.1.0.Final.jar:/home/james/.m2/repository/org/jboss/logging/jboss-logging-annotations/2.1.0.Final/jboss-logging-annotations-2.1.0.Final.jar:/home/james/.m2/repository/org/jboss/jdeparser/jdeparser/2.0.2.Final/jdeparser-2.0.2.Final.jar:/home/james/.m2/repository/org/apache/lucene/lucene-highlighter/5.5.5/lucene-highlighter-5.5.5.jar:/home/james/.m2/repository/org/apache/lucene/lucene-analyzers-common/5.5.5/lucene-analyzers-common-5.5.5.jar:/home/james/.m2/repository/org/apache/lucene/lucene-core/5.5.5/lucene-core-5.5.5.jar:/home/james/.m2/repository/org/apache/lucene/lucene-join/5.5.5/lucene-join-5.5.5.jar:/home/james/.m2/repository/org/apache/lucene/lucene-memory/5.5.5/lucene-memory-5.5.5.jar:/home/james/.m2/repository/org/apache/lucene/lucene-queries/5.5.5/lucene-queries-5.5.5.jar:/home/james/.m2/repository/org/apache/lucene/lucene-analyzers-phonetic/5.5.5/lucene-analyzers-phonetic-5.5.5.jar:/home/james/.m2/repository/com/google/guava/guava/25.0-jre/guava-25.0-jre.jar:/home/james/.m2/repository/org/checkerframework/checker-compat-qual/2.0.0/checker-compat-qual-2.0.0.jar:/home/james/.m2/repository/com/google/errorprone/error_prone_annotations/2.1.3/error_prone_annotations-2.1.3.jar:/home/james/.m2/repository/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar:/home/james/.m2/repository/org/codehaus/mojo/animal-sniffer-annotations/1.14/animal-sniffer-annotations-1.14.jar:/home/james/.m2/repository/org/eclipse/jetty/jetty-servlets/9.4.14.v20181114/jetty-servlets-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/jetty-continuation/9.4.14.v20181114/jetty-continuation-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/jetty-http/9.4.14.v20181114/jetty-http-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/jetty-io/9.4.14.v20181114/jetty-io-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/jetty-servlet/9.4.14.v20181114/jetty-servlet-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/jetty-security/9.4.14.v20181114/jetty-security-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/jetty-server/9.4.14.v20181114/jetty-server-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/jetty-util/9.4.14.v20181114/jetty-util-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/jetty-webapp/9.4.14.v20181114/jetty-webapp-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/jetty-xml/9.4.14.v20181114/jetty-xml-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/websocket/websocket-api/9.4.14.v20181114/websocket-api-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/websocket/websocket-client/9.4.14.v20181114/websocket-client-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/jetty-client/9.4.14.v20181114/jetty-client-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/websocket/websocket-common/9.4.14.v20181114/websocket-common-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/websocket/websocket-server/9.4.14.v20181114/websocket-server-9.4.14.v20181114.jar:/home/james/.m2/repository/org/eclipse/jetty/websocket/websocket-servlet/9.4.14.v20181114/websocket-servlet-9.4.14.v20181114.jar:/home/james/.m2/repository/org/springframework/spring-test/5.1.3.RELEASE/spring-test-5.1.3.RELEASE.jar:/home/james/.m2/repository/com/icegreen/greenmail/1.5.6/greenmail-1.5.6.jar:/home/james/.m2/repository/com/icegreen/greenmail-spring/1.5.6/greenmail-spring-1.5.6.jar:/home/james/.m2/repository/org/apache/commons/commons-collections4/4.1/commons-collections4-4.1.jar:/home/james/.m2/repository/com/github/ben-manes/caffeine/caffeine/2.6.2/caffeine-2.6.2.jar:/home/james/.m2/repository/com/google/guava/guava-testlib/23.0/guava-testlib-23.0.jar:/home/james/.m2/repository/org/hamcrest/java-hamcrest/2.0.0.0/java-hamcrest-2.0.0.0.jar:/home/james/.m2/repository/org/mockito/mockito-core/2.23.4/mockito-core-2.23.4.jar:/home/james/.m2/repository/net/bytebuddy/byte-buddy-agent/1.9.3/byte-buddy-agent-1.9.3.jar:/home/james/.m2/repository/org/objenesis/objenesis/2.6/objenesis-2.6.jar com.intellij.rt.execution.junit.JUnitStarter -ideVersion5 -junit4 ca.uhn.fhir.jpa.provider.dstu3.HapiFhirbackslashNTest,testParseWinBackslashNShortVersion
2019-03-04 05:47:55.634 [main] INFO  ca.uhn.fhir.util.VersionUtil [VersionUtil.java:72] HAPI FHIR version 3.8.0-SNAPSHOT - Rev 25907eeb50
2019-03-04 05:47:55.641 [main] INFO  ca.uhn.fhir.context.FhirContext [FhirContext.java:171] Creating new FHIR context for FHIR version [DSTU3]
2019-03-04 05:47:56.077 [main] INFO  ca.uhn.fhir.util.XmlUtil [DependencyLogImpl.java:75] FHIR XML procesing will use StAX implementation 'Woodstox XML-processor' version '4.4.1'
same summary

Process finished with exit code 0

What is the output you see?

utkinnina commented 5 years ago

/usr/lib/jvm/java-8-openjdk-amd64/bin/java -ea -Didea.test.cyclic.buffer.size=1048576 -javaagent:/opt/idea-IC-181.5281.24/lib/idea_rt.jar=42684:/opt/idea-IC-181.5281.24/bin -Dfile.encoding=UTF-8 -classpath 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com.intellij.rt.execution.junit.JUnitStarter -ideVersion5 -junit4 com.ge.acutecare.awslambda.hospital.gateway.handlers.HapiFhirbackslashNTest,testParseWinBackslashNShortVersion SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. not same summary original: Chief Complaint: Abdominal pain for last 4 days. Described as sudden onset, like 'someone punching me in the stomach'. The pain has been unrelenting and worsening over time.

History of present illness: Pain began after returning from a golf outing where patient consumed roast beef and pizza. Reports episode of nausea and one episode of emesis; denies blood. Appetite remains poor. No bowel movement and no rectal bleeding. Denies fever, chills or sweats. Has been taking ibuprofen and acetaminophen without relief. Denies similar pain before.

stored in db: Chief Complaint: Abdominal pain for last 4 days. Described as sudden onset, like 'someone punching me in the stomach'. The pain has been unrelenting and worsening over time. History of present illness: Pain began after returning from a golf outing where patient consumed roast beef and pizza. Reports episode of nausea and one episode of emesis; denies blood. Appetite remains poor. No bowel movement and no rectal bleeding. Denies fever, chills or sweats. Has been taking ibuprofen and acetaminophen without relief. Denies similar pain before.

Process finished with exit code 0

utkinnina commented 5 years ago

THAT is bizarre :) but my HAPI FHIR Version HAPI FHIR Server - 3.5.0

jamesagnew commented 5 years ago

No kidding!

Well, I don't think we've addressed any bugs related to this in the last 2 releases, but it would be worth trying to upgrade to the latest version (3.7.0) just to see.

Failing that, can you try to replicate this issue within this project: https://github.com/FirelyTeam/fhirstarters/tree/master/java/hapi-fhirstarters-client-skeleton

That project has a bare-minimum set of dependencies. If it works there we know this is a conflict with something your project is depending on and it's just a matter or figuring out what.

utkinnina commented 5 years ago

ok @jamesagnew , thank you very much for helping me! I am working in a big project and unfortunately it is not my decision about upgrade. I would highly recommend to my team to perform it any way.

jamesagnew commented 5 years ago

Well- you don't necessarily need to upgrade. Even just trying a one-time deploy using the latest version of HAPI FHIR would be enough to confirm or rule out that this is a version thing.

I'm more curious about other dependencies in your project- there is probably some sort of conflict or bad interaction somewhere. I'm guessing you'll probably need to gradually introduce dependencies from your "real" project into the test one until it breaks to figure out what's going on.

utkinnina commented 5 years ago

I'll try to reproduce it in "clear" project, without any other dependencies, I don't mind to deploy the server using latest hapi fhir, but I guess the bug is not depend on server deployment as I can reproduce it connecting to "http://hapi.fhir.org/baseDstu3" so I really don't need to deploy the server, but I do want to reproduce it with latest hapi fhir client., that's why i need "clear" project