Perf/optimize research export

Build.sbt

@@ -28,7 +28,8 @@ val appDependencies = Seq(
   "com.h2database" % "h2" % "1.4.193",
   "com.jcraft" % "jsch" % "0.1.54",
   "ca.uhn.hapi.fhir" % "hapi-fhir-base" % "5.7.0",
-  "ca.uhn.hapi.fhir" % "hapi-fhir-structures-r5" % "5.7.0"
+  "ca.uhn.hapi.fhir" % "hapi-fhir-structures-r5" % "5.7.0",
+  "org.apache.commons" % "commons-csv" % "1.10.0"
 )
 
 

Dockerfile

@@ -64,11 +64,12 @@ RUN --mount=type=cache,target=/root/.ivy2 \
 WORKDIR $PROJECT_HOME/app/target/universal
 RUN unzip femr-*.zip && rm femr-*.zip
 
-FROM openjdk:8-jre-alpine
+FROM eclipse-temurin:8-jre-alpine-3.23
 
 RUN apk update
-RUN apk add --no-cache bash python3 py3-pip gcc python3-dev musl-dev linux-headers mariadb-client mariadb-connector-c mariadb-connector-c-dev
-RUN pip3 install psutil
+#RUN apk add --no-cache bash python3 py3-pip gcc python3-dev musl       -dev linux-headers mariadb-client mariadb-connector-c mariadb-connector-c-dev
+#RUN pip3 install psutil
+RUN apk add --no-cache bash python3 py3-pip py3-psutil gcc python3-dev musl-dev linux-headers mariadb-client mariadb-connector-c mariadb-connector-c-dev
 
 #database variables
 ARG APP_VERSION
@@ -86,4 +87,4 @@ EXPOSE 9000
 
 # run fEMR using env variables
 #ENTRYPOINT url=$DB_URL usr=$DB_USER pass=$DB_PASS sbt ~run
-ENTRYPOINT ["/bin/bash", "-c", "/opt/bin/femr/bin/femr"]
+ENTRYPOINT ["/bin/bash", "-c", "rm -f /opt/bin/femr/RUNNING_PID; exec /opt/bin/femr/bin/femr -Dpidfile.path=/dev/null"]

app/femr/business/helpers/LogicDoer.java

@@ -93,9 +93,9 @@ public static String getCsvFilePath() {
                 path += File.separator;
             return path;
         } catch (Exception ex) {
-            //If config doesn't exist, default to "photos"
-            path = "../Upload/Csv";
-            return path;
+            //If config doesn't exist, default to "../Upload/CSV"
+            return ".." + File.separator + "Upload" + File.separator + "CSV" + File.separator;
+
         }
 
     }

app/femr/common/models/ResearchExportItem.java

@@ -32,122 +32,110 @@ public class ResearchExportItem {
     private Integer weeksPregnant;
     private String dayOfVisit;
     private Integer tripId;
+
     private List<String> chiefComplaints;
     private List<String> prescribedMedications;
     private List<String> dispensedMedications;
     private Map<String, Float> vitalMap;
     private Map<String, String> tabFieldMap;
+
     private String trip_team;
     private String trip_country;
 
     public UUID getPatientId() {
         return patientId;
     }
-
     public void setPatientId(UUID patientId) {
         this.patientId = patientId;
     }
 
     public String getGender() {
         return gender;
     }
-
     public void setGender(String gender) {
         this.gender = gender;
     }
 
     public Integer getAge() {
         return age;
     }
-
     public void setAge(Integer age) {
         this.age = age;
     }
 
     public Boolean getIsPregnant() {
         return isPregnant;
     }
-
     public void setIsPregnant(Boolean isPregnant) {
         this.isPregnant = isPregnant;
     }
 
     public Integer getWeeksPregnant() {
         return weeksPregnant;
     }
-
     public void setWeeksPregnant(Integer weeksPregnant) {
         this.weeksPregnant = weeksPregnant;
     }
 
     public List<String> getChiefComplaints() {
         return chiefComplaints;
     }
-
     public void setChiefComplaints(List<String> chiefComplaints) {
         this.chiefComplaints = chiefComplaints;
     }
 
     public List<String> getPrescribedMedications() {
         return prescribedMedications;
     }
-
     public void setPrescribedMedications(List<String> prescribedMedications) {
         this.prescribedMedications = prescribedMedications;
     }
 
     public List<String> getDispensedMedications() {
         return dispensedMedications;
     }
-
     public void setDispensedMedications(List<String> dispensedMedications) {
         this.dispensedMedications = dispensedMedications;
     }
 
     public Map<String, Float> getVitalMap() {
         return vitalMap;
     }
-
     public void setVitalMap(Map<String, Float> vitalMap) {
         this.vitalMap = vitalMap;
     }
 
     public Map<String, String> getTabFieldMap() {
         return tabFieldMap;
     }
-
     public void setTabFieldMap(Map<String, String> tabFieldMap) {
         this.tabFieldMap = tabFieldMap;
     }
 
     public String getDayOfVisit() {
         return dayOfVisit;
     }
-
     public void setDayOfVisit(String day) {
         this.dayOfVisit = day;
     }
 
     public Integer getTripId() {
         return tripId;
     }
-
     public void setTripId(Integer tripId) {
         this.tripId = tripId;
     }
 
     public String getTrip_team() {
         return trip_team;
     }
-
     public void setTrip_team(String trip_team) {
         this.trip_team = trip_team;
     }
 
     public String getTrip_country() {
         return trip_country;
     }
-
     public void setTrip_country(String trip_country) {
         this.trip_country = trip_country;
     }

app/femr/ui/controllers/ResearchController.java

@@ -83,10 +83,11 @@ public Result indexGet() {
         filterViewModel.setMissionTrips(missionItemServiceResponse.getResponseObject());
 
         // Set Default Start (30 Days Ago) and End Date (Today)
+        // temporarily "-365 * 10" modified for development to default to last ten years
         Calendar today = Calendar.getInstance();
         SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd");
         filterViewModel.setEndDate(dateFormat.format(today.getTime()));
-        today.add(Calendar.DAY_OF_MONTH, -120);
+        today.add(Calendar.DAY_OF_MONTH, -365 * 10);
         filterViewModel.setStartDate(dateFormat.format(today.getTime()));
 
 
@@ -130,6 +131,9 @@ public Result exportPost() {
         // This does weird stuff and isn't reliable.
         //ServiceResponse<File> exportServiceResponse = researchService.retrieveCsvExportFile(filterItem);
         ServiceResponse<File> exportServiceResponse = researchService.exportPatientsByTrip(filterItem.getMissionTripId());
+        if (exportServiceResponse == null) {
+            return internalServerError("Export Failed");
+        }
 
         File csvFile = exportServiceResponse.getResponseObject();
 

app/femr/util/stringhelpers/StringUtils.java

@@ -23,6 +23,8 @@
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
 import java.util.Date;
+import java.util.List;
+import java.util.Map;
 
 /**
  * This class contains utilities for manipulating strings. If you add something here, please clearly document the
@@ -240,14 +242,67 @@ public static String outputBloodPressureOrNA(String systolic, String diastolic)
      * @return The user friendly trip title or null if parameters were null
      */
     public static String generateMissionTripTitle(String teamName, String country, Date startDate, Date endDate){
-
         if (StringUtils.isNullOrWhiteSpace(teamName) || StringUtils.isNullOrWhiteSpace(country) || startDate == null || endDate == null){
-
             return null;
         }
-
         String tripTitle = teamName + "-" + country + "-(" + dateUtils.getFriendlyInternationalDate(startDate) + "-" + dateUtils.getFriendlyInternationalDate(endDate) + ")";
         return tripTitle;
     }
 
+    /**
+     * Converts a list of strings into a single semicolon-separated value.
+     * Example:
+     * ["headache", "nausea"] → "headache; nausea"
+     * @param list the list of strings to join; may be null or empty
+     * @return a semicolon-separated string, or an empty string if the list is null or empty
+     */
+    public static String joinList(List<String> list) {
+        if (list == null || list.isEmpty()) return "";
+        return String.join("; ", list);
+    }
+
+    /**
+     * Converts a map of string keys to float values into a flattened
+     * semicolon-separated representation suitable for a single CSV column.
+     * Format:
+     * { "bp": 120.0, "hr": 80.0 }
+     * → "bp=120.0; hr=80.0"
+     * @param map the map of string keys to float values; may be null or empty
+     * @return a semicolon-delimited {@code key=value} string, or empty string for null/empty input
+     */
+    public static String joinFloatMap(Map<String, Float> map) {
+        if (map == null || map.isEmpty()) return "";
+        StringBuilder sb = new StringBuilder();
+        boolean first = true;
+        for (Map.Entry<String, Float> e : map.entrySet()) {
+            if (!first) sb.append("; ");
+            sb.append(e.getKey()).append("=").append(e.getValue());
+            first = false;
+        }
+        return sb.toString();
+    }
+
+    /**
+     * Converts a map of string keys to string values into a flattened
+     * semicolon-separated representation for a single CSV cell.
+     * Format:
+     * { "field1": "value1", "field2": "value2" }
+     * → "field1=value1; field2=value2"
+     * @param map the map of string keys to string values; may be null or empty
+     * @return a semicolon-delimited {@code key=value} string, or empty string for null/empty input
+     */
+    public static String joinStringMap(Map<String, String> map) {
+        if (map == null || map.isEmpty()) return "";
+        StringBuilder sb = new StringBuilder();
+        boolean first = true;
+        for (Map.Entry<String, String> e : map.entrySet()) {
+            if (!first) sb.append("; ");
+            sb.append(e.getKey()).append("=").append(e.getValue());
+            first = false;
+        }
+        return sb.toString();
+    }
+
 }
+
+

public/js/research/filter-menu.js

@@ -157,10 +157,60 @@ var filterMenuModule = (function () {
         return false;
     };
 
-    var exportData = function () {
+    var exportData = async function (e) {
+      if (e) {
+        e.preventDefault();
+        e.stopPropagation();
+      }
+
+      const btn = document.getElementById("export-button");
+      btn.disabled = true;
+      btn.value = "Exporting…";
+
+      // form is often a jQuery object in this codebase
+      var formEl = form && form.jquery ? form[0] : form;
+      if (!formEl) {
+        alert("Export failed (form not found).");
+        btn.disabled = false;
+        btn.value = "Export Data";
+        return false;
+      }
+
+      try {
+        const resp = await fetch(formEl.action, {
+          method: "POST",
+          body: new FormData(formEl),
+          credentials: "same-origin"
+        });
+
+        if (!resp.ok) {
+          alert("Export failed (" + resp.status + ")");
+          btn.disabled = false;
+          btn.value = "Export Data";
+          return false;
+        }
+
+        const blob = await resp.blob();
+        const url = window.URL.createObjectURL(blob);
+        const a = document.createElement("a");
+        a.href = url;
+
+        const cd = resp.headers.get("content-disposition") || "";
+        const match = cd.match(/filename="?([^"]+)"?/i);
+        a.download = match ? match[1] : "research_export.csv";
+
+        document.body.appendChild(a);
+        a.click();
+        a.remove();
+        window.URL.revokeObjectURL(url);
 
-        $(form).submit();
+        alert("Research export completed!");
+      } catch (err) {
+        alert("Export failed.");
+      }
 
+        btn.disabled = false;
+        btn.value = "Export Data";
         return false;
     };