From 52ad091c057f0f4e77ae2ac317d7fae4557d4e51 Mon Sep 17 00:00:00 2001
From: CalebSLane <c.steelelane@gmail.com>
Date: Tue, 30 Jul 2024 13:39:33 -0700
Subject: [PATCH 1/6] add back fixes that don't interfere else where for menu
 not behaving correctly

---
 frontend/src/components/Style.css        |  11 ++-
 frontend/src/components/layout/Header.js | 112 +++++++++++------------
 2 files changed, 64 insertions(+), 59 deletions(-)

diff --git a/frontend/src/components/Style.css b/frontend/src/components/Style.css
index 21b271161..d1f629f5b 100644
--- a/frontend/src/components/Style.css
+++ b/frontend/src/components/Style.css
@@ -498,13 +498,18 @@ button {
   padding-left: 1rem !important;
 }
 
-.cds--side-nav__link:hover {
+.top-level-menu-item > a {
+  pointer-events: auto !important;
+  text-decoration: none !important;
+}
+
+.top-level-menu-item > a:hover {
   background-color: var(--cds-background-hover, #072655);
 }
 
-/* .cds--side-nav__link {
+#mainHeader .cds--side-nav__link {
   pointer-events: none
-} */
+}
 
 @media screen and (max-width: 792px) {
   .banner h5 {
diff --git a/frontend/src/components/layout/Header.js b/frontend/src/components/layout/Header.js
index aa41f26d5..28a0e619c 100644
--- a/frontend/src/components/layout/Header.js
+++ b/frontend/src/components/layout/Header.js
@@ -192,6 +192,7 @@ function OEHeader(props) {
               }}
             >
               <SideNavMenu
+                className="top-level-menu-item"
                 aria-label={intl.formatMessage({
                   id: menuItem.menu.displayKey,
                 })}
@@ -200,18 +201,25 @@ function OEHeader(props) {
                 })}
                 key={"menu_" + index + "_" + level}
                 defaultExpanded={menuItem.expanded}
-                onClick={(e) => {
-                  setMenuItemExpanded(e, menuItem, path);
-                }}
+                // onClick={(e) => { // not supported yet, but if it becomes so we can simplify the functionality here by having this here and not have a span around it
+                //   setMenuItemExpanded(e, menuItem, path);
+                // }}
               >
-                {menuItem.childMenus.map((childMenuItem, index) => {
-                  return generateMenuItems(
-                    childMenuItem,
-                    index,
-                    level + 1,
-                    path + ".childMenus[" + index + "]",
-                  );
-                })}
+                <span
+                  onClick={(e) => {
+                    e.preventDefault();
+                    e.stopPropagation();
+                  }}
+                >
+                  {menuItem.childMenus.map((childMenuItem, index) => {
+                    return generateMenuItems(
+                      childMenuItem,
+                      index,
+                      level + 1,
+                      path + ".childMenus[" + index + "]",
+                    );
+                  })}
+                </span>
               </SideNavMenu>
             </span>
           </React.Fragment>
@@ -223,6 +231,7 @@ function OEHeader(props) {
               id={menuItem.menu.elementId}
               href={menuItem.menu.actionURL}
               target={menuItem.menu.openInNewWindow ? "_blank" : ""}
+              className="top-level-menu-item"
             >
               {renderSideNavMenuItemLabel(menuItem, level)}
             </SideNavMenuItem>
@@ -231,7 +240,14 @@ function OEHeader(props) {
       } else {
         return (
           <React.Fragment key={path}>
-            <SideNavMenuItem className="reduced-padding-nav-menu-item">
+            <SideNavMenuItem
+              className="reduced-padding-nav-menu-item"
+              id={menuItem.menu.elementId}
+              href={menuItem.menu.actionURL}
+              target={menuItem.menu.openInNewWindow ? "_blank" : ""}
+              style={{ width: "100%" }}
+              rel="noreferrer"
+            >
               <span style={{ display: "flex", width: "100%" }}>
                 {!menuItem.menu.actionURL &&
                   !hasActiveChildMenu(menuItem) &&
@@ -284,27 +300,19 @@ function OEHeader(props) {
   const renderSingleNavButton = (menuItem, index, level, path) => {
     const marginValue = (level - 1) * 0.5 + "rem";
     return (
-      <a
-        id={menuItem.menu.elementId}
-        href={menuItem.menu.actionURL}
-        target={menuItem.menu.openInNewWindow ? "_blank" : ""}
-        style={{ width: "100%" }}
-        rel="noreferrer"
+      <button
+        className={"custom-sidenav-button"}
+        style={{ width: "100%", marginLeft: marginValue }}
+        onClick={() => {
+          if (menuItem.menu.openInNewWindow) {
+            window.open(menuItem.menu.actionURL);
+          } else {
+            window.location.href = menuItem.menu.actionURL;
+          }
+        }}
       >
-        <button
-          className={"custom-sidenav-button"}
-          style={{ marginLeft: marginValue }}
-          onClick={() => {
-            if (menuItem.menu.openInNewWindow) {
-              window.open(menuItem.menu.actionURL);
-            } else {
-              window.location.href = menuItem.menu.actionURL;
-            }
-          }}
-        >
-          {renderSideNavMenuItemLabel(menuItem, level)}
-        </button>
-      </a>
+        {renderSideNavMenuItemLabel(menuItem, level)}
+      </button>
     );
   };
 
@@ -329,31 +337,23 @@ function OEHeader(props) {
     const marginValue = (level - 1) * 0.5 + "rem";
     return (
       <>
-        <a
-          id={menuItem.menu.elementId}
-          href={menuItem.menu.actionURL}
-          target={menuItem.menu.openInNewWindow ? "_blank" : ""}
-          style={{ width: "100%" }}
-          rel="noreferrer"
-        >
-          <button
-            className={
-              menuItem.menu.actionURL
-                ? "custom-sidenav-button"
-                : "custom-sidenav-button-unclickable"
+        <button
+          className={
+            menuItem.menu.actionURL
+              ? "custom-sidenav-button"
+              : "custom-sidenav-button-unclickable"
+          }
+          style={{ marginLeft: marginValue }}
+          onClick={() => {
+            if (menuItem.menu.openInNewWindow) {
+              window.open(menuItem.menu.actionURL);
+            } else {
+              window.location.href = menuItem.menu.actionURL;
             }
-            style={{ marginLeft: marginValue }}
-            onClick={() => {
-              if (menuItem.menu.openInNewWindow) {
-                window.open(menuItem.menu.actionURL);
-              } else {
-                window.location.href = menuItem.menu.actionURL;
-              }
-            }}
-          >
-            {renderSideNavMenuItemLabel(menuItem, level)}
-          </button>
-        </a>
+          }}
+        >
+          {renderSideNavMenuItemLabel(menuItem, level)}
+        </button>
         {menuItem.childMenus.length > 0 && (
           <button
             id={menuItem.menu.displayKey + "_dropdown"}

From 6f08e1f400003cd2f459b0af9c4a95daecb3daf0 Mon Sep 17 00:00:00 2001
From: CalebSLane <c.steelelane@gmail.com>
Date: Mon, 12 Aug 2024 11:06:21 -0700
Subject: [PATCH 2/6] WHONet report work

---
 .../analysis/daoimpl/AnalysisDAOImpl.java     |   1 -
 .../WHONETCSVRoutineSampleExportReport.java   |   1 -
 .../WHONETCIRoutineColumnBuilder.java         | 198 ++----
 .../WHONETCSVRoutineColumnBuilder.java        | 621 ++----------------
 .../WHONETRoutineColumnBuilder.java           |  45 +-
 .../reportBeans/WHONETTBColumnBuilder.java    | 148 -----
 .../reports/service/WHONetReportService.java  |  14 +
 .../service/WHONetReportServiceImpl.java      | 175 +++++
 .../test/service/TestService.java             |   2 +
 .../test/service/TestServiceImpl.java         |   8 +
 .../action/util/TestReflexUtil.java           | 134 +++-
 11 files changed, 412 insertions(+), 935 deletions(-)
 delete mode 100644 src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETTBColumnBuilder.java
 create mode 100644 src/main/java/org/openelisglobal/reports/service/WHONetReportService.java
 create mode 100644 src/main/java/org/openelisglobal/reports/service/WHONetReportServiceImpl.java

diff --git a/src/main/java/org/openelisglobal/analysis/daoimpl/AnalysisDAOImpl.java b/src/main/java/org/openelisglobal/analysis/daoimpl/AnalysisDAOImpl.java
index bb3ce2df3..c01526540 100644
--- a/src/main/java/org/openelisglobal/analysis/daoimpl/AnalysisDAOImpl.java
+++ b/src/main/java/org/openelisglobal/analysis/daoimpl/AnalysisDAOImpl.java
@@ -1220,7 +1220,6 @@ public List<Analysis> getAllAnalysisByTestsAndStatusAndCompletedDateRange(List<I
             String sql = "from Analysis a where a.test.id IN (:testList) and a.statusId IN (:analysisStatusList)"
                     + " and a.sampleItem.sample.statusId IN (:sampleStatusList) and a.completedDate"
                     + " BETWEEN :lowDate AND :highDate order by a.sampleItem.sample.accessionNumber";
-
             for (Integer testId : testIdList) {
                 testList.add(testId);
             }
diff --git a/src/main/java/org/openelisglobal/reports/action/implementation/WHONETCSVRoutineSampleExportReport.java b/src/main/java/org/openelisglobal/reports/action/implementation/WHONETCSVRoutineSampleExportReport.java
index a85eb38d3..f880768ea 100644
--- a/src/main/java/org/openelisglobal/reports/action/implementation/WHONETCSVRoutineSampleExportReport.java
+++ b/src/main/java/org/openelisglobal/reports/action/implementation/WHONETCSVRoutineSampleExportReport.java
@@ -67,7 +67,6 @@ public byte[] runReport() throws UnsupportedEncodingException, IOException, Ille
         buffer.write(WHONETcsvRoutineColumnBuilder.getColumnNamesLine().getBytes("windows-1252"));
 
         writeResultsToBuffer(buffer);
-        WHONETcsvRoutineColumnBuilder.closeResultSet();
 
         return buffer.toByteArray();
     }
diff --git a/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETCIRoutineColumnBuilder.java b/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETCIRoutineColumnBuilder.java
index adc6c7627..bb6238b3a 100644
--- a/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETCIRoutineColumnBuilder.java
+++ b/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETCIRoutineColumnBuilder.java
@@ -1,9 +1,5 @@
 package org.openelisglobal.reports.action.implementation.reportBeans;
 
-import static org.openelisglobal.reports.action.implementation.reportBeans.WHONETCSVRoutineColumnBuilder.Strategy.NONE;
-
-import java.sql.Date;
-import org.openelisglobal.common.services.StatusService;
 import org.openelisglobal.reports.action.implementation.Report.DateRange;
 
 /**
@@ -19,157 +15,75 @@
  */
 public abstract class WHONETCIRoutineColumnBuilder extends WHONETCSVRoutineColumnBuilder {
 
-    protected static final String WHONET_SELECT =
-            // "SELECT
-            // t.id,t.method_id,t.uom_id,t.description,t.loinc,t.reporting_description,"
-            // + "t.sticker_req_flag , t.is_active , t.active_begin , t.active_end ,
-            // t.is_reportable,"
-            // +
-            // "t.time_holding,t.time_wait,t.time_ta_average,t.time_ta_warning,t.time_ta_max,"
-            // + "label_qty,t.lastupdated,t.label_id,t.test_trailer_id,"
-            // +
-            // "t.test_section_id,t.scriptlet_id,t.test_format_id,t.local_code,t.sort_order,"
-            // + "t.name,t.orderable,t.guid,t.name_localization_id,"
-            // +
-            // "t.reporting_name_localization_id,t.default_test_result_id,t.notify_results,"
-            // + "t.in_lab_only,t.antimicrobial_resistance "
-            // + "FROM test t WHERE t.antimicrobial_resistance = true"
-            // + "\n ";
-
-            "select s.accession_number,pe.last_name, pe.first_name,t.id,t.description,t.loinc,t.guid"
-                    + " from analysis a" + " join sample_item si on a.sampitem_id = si.id"
-                    + " join sample s on si.samp_id = s.id" + " join sample_human sh on sh.samp_id = s.id"
-                    + " join patient pa on pa.id = sh.patient_id" + " join person pe on pe.id = pa.person_id"
-                    + " join test t on t.id = a.test_id" + " left join result r on r.analysis_id = a.id"
-                    + " where t.antimicrobial_resistance = true" + "\n ";
-
-    /**
-     * The basic SQL SELECT to get start on finding a sample, sample_item, patient
-     * and organization
-     */
-    protected static final String SELECT_SAMPLE_PATIENT_ORGANIZATION = "SELECT DISTINCT s.id as sample_id, s.accession_number, s.entered_date, s.received_date,"
-            + " s.collection_date, s.status_id \n"
-            + ", pat.national_id, pat.external_id, pat.birth_date, per.first_name, per.last_name," + " pat.gender \n"
-            + ", o.short_name as organization_code, o.name AS organization_name \n" + " ";
-    /**
-     * The column select which puts all demographic and result columns in the result
-     * set.
-     */
-    protected static final String SELECT_ALL_DEMOGRAPHIC_AND_RESULTS = "\n, demo.*, result.*" + "\n ";
-    /**
-     * the basic SQL FROM clause for the selection from basic lab tables for sample,
-     * sample_item, patient & organization
-     */
-    protected static final String FROM_SAMPLE_PATIENT_ORGANIZATION = " FROM sample as s, patient as pat, person as per, sample_human as sh, requester_type AS rq,"
-            + " sample_requester AS sq, organization AS o \n" + " ";
+    protected static final String WHONET_SELECT = "select r.value as result_value," //
+            + " s.accession_number as lab_no, s.collection_date, s.entered_date," //
+            + " pe.last_name, pe.first_name," //
+            + " pa.national_id, pa.gender, pa.birth_date,"
+            + " t.id as test_id, t.name as test_name, t.description as test_description, t.loinc, t.guid," //
+            + " tos.description as sample_type" //
+            + " from sample_item si" + " join analysis a on a.sampitem_id = si.id" //
+            + " join sample s on si.samp_id = s.id" //
+            + " join sample_human sh on sh.samp_id = s.id" + " join sample_requester sr1 on sr1.sample_id = s.id"
+            + " join type_of_sample tos on si.typeosamp_id = tos.id" //
+            + " join patient pa on pa.id = sh.patient_id" //
+            + " join person pe on pe.id = pa.person_id" + " join test t on t.id = a.test_id" //
+            + " left join result r on r.analysis_id = a.id" //
+            + " where t.antimicrobial_resistance = true"
+            + " and sr1.requester_type_id = (SELECT id from requester_type rt where rt.requester_type = 'organization')";
 
     protected DateRange dateRange;
     // protected String projectStr;
 
     /** */
     public WHONETCIRoutineColumnBuilder(DateRange dateRange) {
-        super(StatusService.AnalysisStatus.Finalized);
+        super();
         this.dateRange = dateRange;
-        // this.projectStr = projectStr;
-        defineAllObservationHistoryTypes();
-        defineAllTestsAndResults();
-        // defineAllProjectTags();
-        defineAllReportColumns();
     }
 
-    protected abstract void defineAllReportColumns();
-
     @Override
-    public abstract void makeSQL();
-
-    /**
-     * Useful when building the SQL String
-     *
-     * @param lowDate
-     * @param highDate
-     * @return String starting "WHERE ..." joining patient, sample, organization
+    public abstract void searchForWHONetResults();
+
+    // protected void defineBasicColumns() {
+    // // // patient fields
+    // // add("national_id", "IDENTIFIER", NONE);
+    // // add("first_name", "FIRST NAME", NONE);
+    // // add("last_name", "LAST NAME", NONE);
+    // // add("gender", "SEX", NONE);
+    // // add("birth_date", "BIRTHDATE", DATE);
+    // // add("entered_date", "DATE ENTERED", DATE_TIME); // interview date
+
+    // // // add("organization_code", "CODEREFERER", NONE);
+    // // // add("organization_name", "REFERER", NONE);
+
+    // // // specimen fields
+    // // add("lab_no", "LABNO", NONE);
+    // // add("collection_date", "DATE COLLECTED", DATE_TIME); // collection date
+    // // add("sample_type", "SPECIMEN TYPE", NONE);
+
+    // // add("test_name", "ANTIBIOTIC", NONE);
+    // // add("organism", "ORGANISM", NONE);
+    // // add("loinc", "LOINC", NONE);
+    // // add("guid", "GUID", NONE);
+
+    // }
+    /*
+     * add("accession_number", "LABNO", NONE); add("national_id", "IDENTIFIER",
+     * NONE); add("entered_date", "AGEYEARS", AGE_YEARS); add("entered_date",
+     * "AGEMONTHS", AGE_MONTHS); add("entered_date", "AGEWEEKS", AGE_WEEKS);//
+     * reception date add("entered_date", "DATEENTERED", DATE_TIME); // interview
+     * date add("collection_date", "DATECOLLECT", DATE_TIME); // collection date
      */
-    protected String buildWhereSamplePatienOrgSQL(Date lowDate, Date highDate) {
-        String WHERE_SAMPLE_PATIENT_ORG = " WHERE " + "\n pat.id = sh.patient_id " + "\n AND sh.samp_id = s.id "
-                + "\n AND s.entered_date >= '" + formatDateForDatabaseSql(lowDate) + "'" + "\n AND s.entered_date <= '"
-                + formatDateForDatabaseSql(highDate) + "'" + "\n " + "\n AND sq.requester_type_id = rq.id "
-                + "\n AND sq.sample_id= s.id " + "\n AND pat.person_id = per.id " + "\n AND o.id = sq.requester_id   "
-        // + ((GenericValidator.isBlankOrNull(projectStr))?"": " AND sp.proj_id = " +
-        // projectStr)
-        ;
-        return WHERE_SAMPLE_PATIENT_ORG;
-    }
 
-    protected void appendRepeatingObservation(SQLConstant aOhTypeName, int maxCols, Date lowDate, Date highDate) {
-        appendCrosstabPreamble(aOhTypeName);
-
-        query.append(" crosstab( ' SELECT s.id as s_id, type, value FROM Sample AS s  LEFT JOIN ( SELECT"
-                + " DISTINCT s.id as s_id , oh.observation_history_type_id AS type, oh.value AS value,"
-                + " oh.id  FROM Sample as s, Observation_History AS oh WHERE oh.sample_id = s.id AND"
-                + " s.entered_date >= date(''" + formatDateForDatabaseSql(lowDate) + "'') "
-                + " AND s.entered_date <= date(''" + formatDateForDatabaseSql(highDate)
-                + "'') AND oh.observation_history_type_id = (select id FROM observation_history_type"
-                + " WHERE type_name = ''" + aOhTypeName + "'')  ORDER by 1,2, oh.id desc ) AS repeatCols"
-                + " ON s.id = repeatCols.s_id" + " WHERE s.entered_date >= date(''" + formatDateForDatabaseSql(lowDate)
-                + "'') " + " AND s.entered_date <= date(''" + formatDateForDatabaseSql(highDate) + "'')" + "' )"
-                + " AS " + aOhTypeName + " ( s_id NUMERIC(10) ");
-        for (int col = 1; col <= maxCols; col++) {
-            query.append(", \"").append(aOhTypeName).append(col).append("\" VARCHAR(100)");
-        }
-        query.append(" )\n ");
-        appendCrosstabPostfix(lowDate, highDate, aOhTypeName);
-    }
+    // add("released_date", "DATEVALIDATION", DATE_TIME ); // validation date
 
-    protected void appendOtherDiseaseCrosstab(Date lowDate, Date highDate, SQLConstant diseaseListName,
-            SQLConstant otherColumnName) {
-        appendCrosstabPreamble(otherColumnName);
-        query.append(" crosstab( "
-                + " 'SELECT DISTINCT s.id, oh.observation_history_type_id AS ohType, oh.value AS value "
-                + " FROM  Sample as s, Observation_History AS oh, Observation_history_type as oht "
-                + " WHERE s.entered_date >= ''" + formatDateForDatabaseSql(lowDate) + "''"
-                + "   AND s.entered_date <= ''" + formatDateForDatabaseSql(highDate)
-                + "''   AND s.id = oh.sample_id    AND oh.observation_history_type_id = oht.id    AND"
-                + " oh.observation_history_type_id = (select id FROM observation_history_type WHERE" + " type_name = ''"
-                + diseaseListName + "'') " + "   AND oh.value !~ ''^[0-9]+$'' " + " ORDER by 1,2,3' ) AS "
-                + otherColumnName + " ( s_id NUMERIC(10), " + otherColumnName + " varChar(100) ) " + "\n");
-        appendCrosstabPostfix(lowDate, highDate, otherColumnName);
-    }
-
-    protected void defineBasicColumns() {
-        add("accession_number", "LABNO", NONE);
-        add("last_name", "Last Name", NONE);
-        add("first_name", "First Name", NONE);
-        add("id", "ID", NONE);
-        add("description", "Description", NONE);
-        add("loinc", "LOINC", NONE);
-        add("guid", "GUID", NONE);
-
-        /*
-         * add("accession_number", "LABNO", NONE); add("national_id", "IDENTIFIER",
-         * NONE); add("gender", "SEX", NONE); add("birth_date", "BIRTHDATE", DATE);
-         * add("entered_date", "AGEYEARS", AGE_YEARS); add("entered_date", "AGEMONTHS",
-         * AGE_MONTHS); add("entered_date", "AGEWEEKS", AGE_WEEKS); add("received_date",
-         * "DATERECPT", DATE_TIME); // reception date add("entered_date", "DATEENTERED",
-         * DATE_TIME); // interview date add("collection_date", "DATECOLLECT",
-         * DATE_TIME); // collection date
-         */
-
-        // add("released_date", "DATEVALIDATION", DATE_TIME ); // validation date
-
-        /*
-         * add("organization_code", "CODEREFERER", NONE); add("organization_name",
-         * "REFERER", NONE); add("program", "PROGRAM", PROGRAM); add("status_id",
-         * "STATUS", SAMPLE_STATUS);
-         */
-
-        // add("external_id", "SUJETSIT", NONE);
-        // add("last_name", "NOM", NONE);
-        // add("first_name", "PRENOM", NONE);
+    /*
+     * add("organization_code", "CODEREFERER", NONE); add("organization_name",
+     * "REFERER", NONE); add("program", "PROGRAM", PROGRAM); add("status_id",
+     * "STATUS", SAMPLE_STATUS);
+     */
 
-    }
+    // add("external_id", "SUJETSIT", NONE);
+    // add("last_name", "NOM", NONE);
+    // add("first_name", "PRENOM", NONE);
 
-    @Override
-    protected void addAllResultsColumns() {
-        super.addAllResultsColumns();
-    }
 }
diff --git a/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETCSVRoutineColumnBuilder.java b/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETCSVRoutineColumnBuilder.java
index 9a2ad27bc..c3e2b24fe 100644
--- a/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETCSVRoutineColumnBuilder.java
+++ b/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETCSVRoutineColumnBuilder.java
@@ -17,42 +17,19 @@
  */
 package org.openelisglobal.reports.action.implementation.reportBeans;
 
-import static org.apache.commons.validator.GenericValidator.isBlankOrNull;
-import static org.openelisglobal.reports.action.implementation.reportBeans.WHONETCSVRoutineColumnBuilder.Strategy.DICT;
-import static org.openelisglobal.reports.action.implementation.reportBeans.WHONETCSVRoutineColumnBuilder.Strategy.TEST_RESULT;
-
-import java.sql.Connection;
-import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
-import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Date;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
-import org.hibernate.Session;
-import org.hibernate.SessionFactory;
-import org.hibernate.jdbc.ReturningWork;
 import org.openelisglobal.analyte.service.AnalyteService;
-import org.openelisglobal.analyte.valueholder.Analyte;
-import org.openelisglobal.common.log.LogEvent;
-import org.openelisglobal.common.services.IStatusService;
-import org.openelisglobal.common.services.StatusService;
-import org.openelisglobal.common.services.StatusService.OrderStatus;
 import org.openelisglobal.common.util.DateUtil;
-import org.openelisglobal.common.util.StringUtil;
 import org.openelisglobal.observationhistorytype.service.ObservationHistoryTypeService;
-import org.openelisglobal.observationhistorytype.valueholder.ObservationHistoryType;
 import org.openelisglobal.result.service.ResultService;
-import org.openelisglobal.result.valueholder.Result;
 import org.openelisglobal.spring.util.SpringContext;
 import org.openelisglobal.test.service.TestService;
-import org.openelisglobal.test.service.TestServiceImpl;
-import org.openelisglobal.test.valueholder.Test;
 import org.openelisglobal.testresult.service.TestResultService;
-import org.openelisglobal.testresult.valueholder.TestResult;
-import org.openelisglobal.typeoftestresult.service.TypeOfTestResultServiceImpl;
 
 /**
  * @author pahill (pahill@uw.edu)
@@ -60,6 +37,46 @@
  */
 public abstract class WHONETCSVRoutineColumnBuilder {
 
+    public static class WHONetRow {
+        private String nationalId;
+        private String firstName;
+        private String lastName;
+        private String sex;
+        private String birthdate;
+        private String enteredDate;
+        private String labNo;
+        private String collectionDate;
+        private String sampleType;
+        private String antibiotic;
+        private String organism;
+        private String result;
+
+        private String delimeter = "\t";
+
+        public WHONetRow(String nationalId, String firstName, String lastName, String sex, String birthdate,
+                String enteredDate, String labNo, String collectionDate, String sampleType, String antibiotic,
+                String organism, String result) {
+            this.nationalId = nationalId;
+            this.firstName = firstName;
+            this.lastName = lastName;
+            this.sex = sex;
+            this.birthdate = birthdate;
+            this.enteredDate = enteredDate;
+            this.labNo = labNo;
+            this.collectionDate = collectionDate;
+            this.sampleType = sampleType;
+            this.antibiotic = antibiotic;
+            this.organism = organism;
+            this.result = result;
+        }
+
+        public String getRow() {
+            List<String> rowValues = Arrays.asList(nationalId, firstName, lastName, sex, birthdate, enteredDate, labNo,
+                    collectionDate, sampleType, antibiotic, organism, result);
+            return String.join(delimeter, rowValues);
+        }
+    }
+
     // these are used so we are not passing around strings in the methods that are
     // appended to sql
     // this is to cover any potential sql injection that could be introduced by a
@@ -79,50 +96,11 @@ public String toString() {
         }
     }
 
-    /** */
-    public WHONETCSVRoutineColumnBuilder(StatusService.AnalysisStatus validStatusFilter) {
-        // we'll round up everything via hibernate first.
-        ResourceTranslator.GenderTranslator.getInstance();
-
-        if (validStatusFilter != null) {
-            validStatusId = SpringContext.getBean(IStatusService.class).getStatusID(validStatusFilter);
-        }
-    }
-
-    /**
-     * The list of all columns that can be exported for lookup when report is
-     * generated
-     */
-    private final Map<String, CSVRoutineColumn> columnsByDbName = new HashMap<>();
-
-    /**
-     * The list of columns in order of definition, so that we can generate
-     * JasperReports XML in order for display
-     */
-    private final List<CSVRoutineColumn> columnsInOrder = new ArrayList<>();
-
-    /**
-     * In order as postgres would order varchar columns (alphabetical ignoring
-     * case?).
-     */
-    protected List<ObservationHistoryType> allObHistoryTypes;
-
-    /** All possible tests, so we can have 1 result per test. */
-    protected List<Test> allTests;
-
-    /**
-     * This table provide a mapping from test name (CSV column heading also) to the
-     * TestResult record so we can look at the result type (Dictionary vs. constant
-     * etc.)
-     */
-    protected Map<String, TestResult> testResultsByTestName;
-
-    protected String validStatusId;
-
     protected static final SimpleDateFormat postgresDateFormat = new SimpleDateFormat("yyyy-MM-dd");
     private static final SimpleDateFormat postgresDateTime = new SimpleDateFormat("yyyy-MM-dd hh:mm:ss");
 
-    protected ResultSet resultSet;
+    protected List<WHONetRow> rows;
+    protected int index = -1;
 
     protected String eol = System.getProperty("line.separator");
 
@@ -132,54 +110,6 @@ public WHONETCSVRoutineColumnBuilder(StatusService.AnalysisStatus validStatusFil
     protected TestService testService = SpringContext.getBean(TestService.class);
     protected TestResultService testResultService = SpringContext.getBean(TestResultService.class);
 
-    // This is the largest value possible for a postgres column name. The code will
-    // convert the
-    // test description to a column name so we need to truncate
-    // It's actually 63 but UTF_8 makes 55 safer.
-    private static final int MAX_POSTGRES_COL_NAME = 55;
-
-    /**
-     * the test have to be sorted by the name, because they have to match the pivot
-     * table order in the results
-     */
-    @SuppressWarnings("unchecked")
-    protected void defineAllTestsAndResults() {
-        if (allTests == null) {
-            allTests = testService.getAllOrderBy("description");
-        }
-        if (testResultsByTestName == null) {
-            testResultsByTestName = new HashMap<>();
-            List<TestResult> allTestResults = testResultService.getAllTestResults();
-            for (TestResult testResult : allTestResults) {
-                String key = TestServiceImpl.getLocalizedTestNameWithType(testResult.getTest());
-                testResultsByTestName.put(key, testResult);
-            }
-        }
-    }
-
-    /** map to provide appropriate tag to identify the project. */
-
-    // static Map<String /* project Id */, String /* project tag */> projectTagById
-    // = new HashMap<String, String>();
-    /*
-     * static { defineAllProjectTags(); }
-     *
-     * public static void defineAllProjectTags() { ProjectService projectService =
-     * new ProjectServiceImpl(); List<Project> allProjects =
-     * projectService.getAllProjects(); for (Project project : allProjects) { String
-     * projectTag; // Watch the order on these 1st 2! if
-     * (project.getNameKey().contains("ARVF")) { projectTag = "ARVS"; } else if
-     * (project.getNameKey().contains("ARV")) { projectTag = "ARVB"; } else if
-     * (project.getNameKey().contains("VLS")) { projectTag = "VLS"; } else { //
-     * otherwise we use the letters from the Sample ID prefix, which // at some
-     * locations for some projects is undefined. String code =
-     * project.getProgramCode(); projectTag = (code == null)?"":code.substring(1);
-     * // drop the L } projectTagById.put(project.getId(), projectTag); } }
-     */
-    protected StringBuilder query;
-
-    private String gendCD4CountAnalyteId;
-
     /**
      * The various ways that columns are converted for CSV export
      *
@@ -205,33 +135,7 @@ public void buildDataSource() throws SQLException {
     }
 
     protected void buildResultSet() throws SQLException {
-        // MAKE SURE ALL GENERATED QUERIES STAY SQL INJECTION SAFE
-        makeSQL();
-        String sql = query.toString();
-        // LogEvent.logWarn(this.getClass().getSimpleName(), "buildResultSet", sql);
-        // LogEvent.logInfo(this.getClass().getName(), "method unkown", "===1===\n" +
-        // sql.substring(0, 7000)); // the SQL is
-        // chunked out only because Eclipse thinks printing really big strings to the
-        // console must be wrong, so it truncates them
-        // LogEvent.logInfo(this.getClass().getSimpleName(), "method unkown",
-        // "===2===\n" +
-        // sql.substring(7000));
-        // Session session =
-        // HibernateUtil.getSession().getSessionFactory().openSession();
-        // PreparedStatement stmt = session.connection().prepareStatement(sql,
-        // ResultSet.TYPE_SCROLL_SENSITIVE,
-        // ResultSet.CONCUR_READ_ONLY);
-        // resultSet = stmt.executeQuery();
-        Session session = SpringContext.getBean(SessionFactory.class).openSession();
-        resultSet = session.doReturningWork(new ReturningWork<ResultSet>() {
-
-            @Override
-            public ResultSet execute(Connection connection) throws SQLException {
-
-                return connection.prepareStatement(sql, ResultSet.TYPE_SCROLL_SENSITIVE, ResultSet.CONCUR_READ_ONLY)
-                        .executeQuery();
-            }
-        });
+        searchForWHONetResults();
     }
 
     protected synchronized String formatDateForDatabaseSql(Date date) {
@@ -239,11 +143,6 @@ protected synchronized String formatDateForDatabaseSql(Date date) {
         return postgresDateFormat.format(date);
     }
 
-    private synchronized String formatDateTimeForDatabaseSql(Date date) {
-        // SimpleDateFormat is not thread safe
-        return postgresDateTime.format(date);
-    }
-
     protected synchronized Date parseDateForDatabaseSql(String date) throws ParseException {
         // SimpleDateFormat is not thread safe
         return postgresDateFormat.parse(date);
@@ -277,387 +176,7 @@ protected String datetimeToLocalDateTime(String value) {
         }
     }
 
-    public String getValue(CSVRoutineColumn column, String accessionNumber) throws SQLException, ParseException {
-        String value;
-        // look in the data source for a value
-        try {
-            value = resultSet.getString(trimToPostgresMaxColumnName(column.dbName));
-        } catch (RuntimeException e) {
-            // if you end up where it is because the result set doesn't return a
-            // column of the right name
-            // Check MAX_POSTGRES_COL_NAME if this fails on a long name
-            LogEvent.logInfo(this.getClass().getSimpleName(), "getValue",
-                    "Internal Error: Unable to find db column \"" + column.dbName + "\" in data.");
-            return "?" + column.csvName + "?";
-        }
-
-        String result = column.translate(value, accessionNumber);
-        // translate should never return null, "" is better while it is doing
-        // translation.
-        if (result == null) {
-            LogEvent.logInfo(this.getClass().getSimpleName(), "getValue", "A null found " + column.dbName);
-        }
-        return result;
-    }
-
-    protected String prepareColumnName(String columnName) {
-        // trim and escape the column name so it is more safe from sql injection
-        if (!columnName.matches("(?i)[a-zàâçéèêëîïôûùüÿñæœ0-9_ ()%/\\[\\]+\\-]+")) {
-            LogEvent.logWarn(this.getClass().getSimpleName(), "prepareColumnName",
-                    "potentially dangerous character detected in '" + columnName + "'");
-        }
-        return "\"" + trimToPostgresMaxColumnName(columnName = columnName.replace("\"", "\\\"")) + "\"";
-    }
-
-    private String trimToPostgresMaxColumnName(String name) {
-        if (name.length() <= MAX_POSTGRES_COL_NAME) {
-            return name;
-        } else {
-            return name.substring(0, MAX_POSTGRES_COL_NAME);
-        }
-    }
-
-    public void add(String dbName, String csvTitle) {
-        add(dbName, csvTitle, DICT);
-    }
-
-    public void add(String dbName, String csvTitle, Strategy strat) {
-        CSVRoutineColumn col = new CSVRoutineColumn(dbName, csvTitle, strat);
-        columnsByDbName.put(dbName, col);
-        columnsInOrder.add(col);
-    }
-
-    public void add(String dbName, String csvTitle, ICSVRoutineColumnCustomStrategy customStrategy) {
-        CSVRoutineColumn col = new CSVRoutineColumn(dbName, csvTitle, Strategy.CUSTOM, customStrategy);
-        columnsByDbName.put(dbName, col);
-        columnsInOrder.add(col);
-    }
-
-    /**
-     * A utility routine for finding the project short tag (used in exporting etc.)
-     * from a projectId.
-     */
-    /*
-     * public static String translateProjectId(String projectId) { return (projectId
-     * == null) ? null : projectTagById.get(projectId); }
-     */
-    public class CSVRoutineColumn {
-        public String csvName;
-        public String dbName;
-        public Strategy strategy;
-        public ICSVRoutineColumnCustomStrategy customStrategy;
-
-        public CSVRoutineColumn(String dbName, String csvName, Strategy strategy) {
-            this.csvName = csvName;
-            this.dbName = dbName;
-            this.strategy = strategy;
-        }
-
-        public CSVRoutineColumn(String dbName, String csvName, Strategy strategy,
-                ICSVRoutineColumnCustomStrategy customStrategy) {
-            this.csvName = csvName;
-            this.dbName = dbName;
-            this.strategy = strategy;
-            this.customStrategy = customStrategy;
-        }
-
-        public String translate(String value, String accessionNumber) throws SQLException, ParseException {
-            switch (strategy) {
-            case CUSTOM:
-                return customStrategy.translate(value, accessionNumber, csvName, dbName);
-            case DICT_RAW:
-                return isBlankOrNull(value) ? ""
-                        : ResourceTranslator.DictionaryTranslator.getInstance().translateRaw(value);
-            case DICT_PLUS:
-                return isBlankOrNull(value) ? ""
-                        : ResourceTranslator.DictionaryTranslator.getInstance().translateOrNot(value);
-            case DICT:
-                return isBlankOrNull(value) ? ""
-                        : ResourceTranslator.DictionaryTranslator.getInstance().translate(value);
-            case PROGRAM:
-                return isBlankOrNull(value) ? ""
-                        : ResourceTranslator.DictionaryTranslator.getInstance().translate(value);
-            case DATE:
-                return isBlankOrNull(value) ? "" : datetimeToLocalDate(value);
-            case DATE_TIME:
-                return isBlankOrNull(value) ? "" : datetimeToLocalDateTime(value);
-            case AGE_YEARS:
-            case AGE_MONTHS:
-            case AGE_WEEKS:
-                return isBlankOrNull(value) ? "" : translateAge(strategy, value);
-            case GENDER:
-                return isBlankOrNull(value) ? "" : ResourceTranslator.GenderTranslator.getInstance().translate(value);
-            case DROP_ZERO:
-                return ("0".equals(value) || value == null) ? "" : value;
-            case TEST_RESULT:
-                return isBlankOrNull(value) ? "" : translateTestResult(csvName, value);
-            case GEND_CD4:
-                return isBlankOrNull(value) ? "" : translateGendResult(getGendCD4CountAnalyteId(), value);
-            case LOG:
-                return isBlankOrNull(value) ? "" : translateLog(value);
-            case SAMPLE_STATUS:
-                OrderStatus orderStatus = SpringContext.getBean(IStatusService.class).getOrderStatusForID(value);
-                if (orderStatus == null) {
-                    return "?";
-                }
-                switch (orderStatus) {
-                case Entered:
-                    return "Entered"; // entered,
-                case Started:
-                    return "Started"; // commenced,
-                case Finished:
-                    return "Finished"; // Finished,
-                case NonConforming_depricated:
-                    return "Non-conforming"; // Non-conforming, Non-conformes
-                }
-
-            case DEBUG:
-                LogEvent.logInfo(this.getClass().getSimpleName(), "translate",
-                        "Processing Column Value: " + csvName + " \"" + value + "\"");
-            case BLANK:
-                return "";
-            default:
-                return isBlankOrNull(value) ? "" : value;
-            }
-        }
-
-        private String translateGendResult(String gendResultAnalyteId, String sampleItemId) {
-            // 'generated CD4 Count'
-            Result gendCD4Result = resultService.getResultForAnalyteAndSampleItem(gendResultAnalyteId, sampleItemId);
-            if (gendCD4Result == null) {
-                return "";
-            }
-            String value = gendCD4Result.getValue(true);
-            return (value == null) ? "" : value;
-        }
-
-        /**
-         * The log value of the given value as a floating-point value.
-         *
-         * @param value
-         * @return The log value
-         */
-        private String translateLog(String value) {
-            try {
-                double d = Double.parseDouble(value);
-                return String.valueOf(Math.log10(d));
-            } catch (NumberFormatException e) {
-                return "";
-            }
-        }
-
-        public String translateAge(Strategy strategy, String end) throws SQLException, ParseException {
-            Date birthday = resultSet.getDate("birth_date");
-            Date endDate = parseDateTimeForDatabaseSql(end);
-            if ((birthday != null) && (endDate != null)) {
-                switch (strategy) {
-                case AGE_YEARS:
-                    return String.valueOf(DateUtil.getAgeInYears(birthday, endDate));
-                case AGE_MONTHS:
-                    return String.valueOf(DateUtil.getAgeInMonths(birthday, endDate));
-                case AGE_WEEKS:
-                    return String.valueOf(DateUtil.getAgeInWeeks(birthday, endDate));
-                }
-                return "";
-            }
-            return "";
-        }
-
-        /**
-         * @param value
-         * @return @
-         * @throws SQLException
-         */
-        public String translateTestResult(String testName, String value) throws SQLException {
-            TestResult testResult = testResultsByTestName.get(testName);
-            // if it is not in the table then its just a value in the result
-            // that was NOT selected from a list, thus no translation
-            if (testResult == null) {
-                return value;
-            }
-            String type = testResult.getTestResultType();
-            // if it is in the table D have to be translated through the
-            // dictionary, otherwise don't
-            if (TypeOfTestResultServiceImpl.ResultType.DICTIONARY.getCharacterValue().equals(type)) {
-                return ResourceTranslator.DictionaryTranslator.getInstance().translateRaw(value);
-            } else if (TypeOfTestResultServiceImpl.ResultType.MULTISELECT.getCharacterValue().equals(type)) {
-                return findMultiSelectItemsForTest(testResult.getTest().getId());
-            }
-            return value;
-        }
-
-        /**
-         * @param testId
-         * @return
-         * @throws SQLException
-         */
-        private String findMultiSelectItemsForTest(String testId) throws SQLException {
-            String sampleId = resultSet.getString("sample_id");
-            List<Result> results = resultService.getResultsForTestAndSample(sampleId, testId);
-            StringBuilder multi = new StringBuilder();
-            for (Result result : results) {
-                multi.append(ResourceTranslator.DictionaryTranslator.getInstance()
-                        .translateRaw(result.getValue().replace(",", ".")));
-                multi.append(",");
-            }
-
-            if (multi.length() > 0) {
-                multi.setLength(multi.length() - 1);
-            }
-
-            return multi.toString();
-        }
-    }
-
-    public abstract void makeSQL();
-
-    protected void defineAllObservationHistoryTypes() {
-        allObHistoryTypes = ohtService.getAllOrdered("typeName", false);
-    }
-
-    /**
-     * For every sample, one row per sample item, one column per test result for
-     * that sample item.
-     *
-     * @param lowDate
-     * @param highDate
-     */
-    protected void appendResultCrosstab(java.sql.Date lowDate, java.sql.Date highDate) {
-        // A list of analytes which should not show up in the regular results,
-        // because they are not the primary results, but, for example, is a
-        // conclusion.
-        // String excludeAnalytes = getExcludedAnalytesSet();
-        SQLConstant listName = SQLConstant.RESULT;
-        query.append(", \n\n ( SELECT si.samp_id, si.id AS sampleItem_id, si.sort_order AS sampleItemNo, " + listName
-                + ".* " + " FROM sample_item AS si JOIN \n ");
-
-        // Begin cross tab / pivot table
-        query.append(" crosstab( \n" + " 'SELECT si.id, t.description, replace(replace(replace(replace(r.value ,E''\\n"
-                + "'', '' ''), E''\\t'', '' ''), E''\\r" + "'', '' ''),'','',''.'') \n"
-                + " FROM clinlims.result AS r join clinlims.analysis AS a on a.id = r.analysis_id \n"
-                + "  join clinlims.sample_item AS si on si.id = a.sampitem_id \n"
-                + "  join clinlims.sample AS s on s.id = si.samp_id \n"
-                + " join clinlims.test_result AS tr on r.test_result_id = tr.id \n"
-                + " join clinlims.test AS t on tr.test_id = t.id \n"
-                + " left join sample_projects sp on si.samp_id = sp.samp_id \n" + "\n"
-                + " WHERE sp.id IS NULL AND s.entered_date >= date(''" + formatDateForDatabaseSql(lowDate)
-                + "'')  AND s.entered_date <= date(''" + formatDateForDatabaseSql(highDate) + " '') " + "\n "
-                // sql injection safe as user cannot overwrite validStatusId in database
-                + ((validStatusId == null) ? "" : " AND a.status_id = " + validStatusId)
-                // + (( excludeAnalytes == null)?"":
-                // " AND r.analyte_id NOT IN ( " + excludeAnalytes) + ")"
-                // + " AND a.test_id = t.id "
-                + "\n ORDER BY 1, 2 "
-                + "\n ', 'SELECT t.description FROM test t where t.is_active = ''Y'' ORDER BY 1' ) ");
-        // end of cross tab
-
-        // Name the test pivot table columns . We'll name them all after the
-        // resource name, because some tests have fancy characters in them and
-        // somewhere
-        // between iReport, Java and postgres a complex name (e.g. one including
-        // a beta, " HCG Quant") get messed up and isn't found.
-        query.append("\n as " + listName + " ( " // inner use of the list name
-                + "\"si_id\" numeric(10) ");
-        for (Test col : allTests) {
-            String testName = TestServiceImpl.getLocalizedTestNameWithType(col);
-            query.append("\n, " + prepareColumnName(testName) + " varchar(200) ");
-        }
-        query.append(" ) \n");
-        // left join all sample Items from the right sample range to the results table.
-        query.append("\n ON si.id = " + listName + ".si_id " // the inner use a few lines above
-                + "\n ORDER BY si.samp_id, si.id " + "\n) AS " + listName + "\n "); // outer re-use the list name to
-        // name this sparse matrix of
-        // results.
-    }
-
-    /**
-     * @return
-     */
-    private String getExcludedAnalytesSet() {
-        String[] excludedAnalytes = new String[] { getGendCD4CountAnalyteId() };
-        StringBuilder sb = new StringBuilder();
-        for (String a : excludedAnalytes) {
-            sb.append(a).append(",");
-        }
-        sb.setLength(sb.length() - 1);
-        return sb.toString();
-    }
-
-    protected void appendObservationHistoryCrosstab(java.sql.Date lowDate, java.sql.Date highDate) {
-        appendCrosstabPreamble(SQLConstant.DEMO);
-        query.append( // any Observation History items
-                "\n crosstab( " + "\n 'SELECT DISTINCT oh.sample_id as samp_id, oht.type_name, value "
-                        + "\n FROM observation_history AS oh, sample AS s, observation_history_type AS oht "
-                        + "\n WHERE s.entered_date >= date(''" + formatDateForDatabaseSql(lowDate) + "'') "
-                        + "\n AND s.entered_date <= date(''" + formatDateForDatabaseSql(highDate) + "'')"
-                        + "\n AND s.id = oh.sample_id AND oh.observation_history_type_id = oht.id order by 1;' "
-                        + "\n , "
-                        + "\n 'SELECT DISTINCT oht.type_name FROM observation_history_type AS oht ORDER BY 1;' " + // must
-                                                                                                                   // be
-                                                                                                                   // the
-                                                                                                                   // same
-                                                                                                                   // list
-                                                                                                                   // as
-                                                                                                                   // the
-                                                                                                                   // column
-                                                                                                                   // definition
-                                                                                                                   // for
-                                                                                                                   // the
-                                                                                                                   // demo
-                                                                                                                   // table
-                                                                                                                   // below.
-                        "\n ) \n ");
-
-        // in the following list of observation history items, all valid values
-        // are listed in alphabetical order (since that is how crosstab lists
-        // them), so that that the queries constructed don't have to filter the
-        // exceptional ones.
-        // It is the column name list defined in the constructor of this class
-        // which picks the right column to display (and in what order). That
-        // list is also used to generated the JasperReport XML
-        // That list skips the OH types which actually repeat (priorDiseases,
-        // priorARVTreatmentINNs) which are returned as as crosstab set of
-        // columns either specially named columns (disease acronyms for each
-        // diseases) or with with n after their name (priorARVTreatmentINNs1, 2,
-        // ... )
-        query.append(" as demo ( " + " \"s_id\"                           numeric(10) ");
-        for (ObservationHistoryType oht : allObHistoryTypes) {
-            // this is sql injection safe as users currently have no way of modifying fields
-            // in ObservationHistoryTypes
-            query.append("\n," + oht.getTypeName() + " varchar(100) ");
-        }
-        query.append(" ) \n");
-        appendCrosstabPostfix(lowDate, highDate, SQLConstant.DEMO);
-    }
-
-    protected void appendCrosstabPreamble(SQLConstant listName) {
-        query.append(", \n\n ( SELECT s.id AS samp_id, " + listName + ".* " + " FROM sample AS s LEFT JOIN \n ");
-    }
-
-    protected void appendCrosstabPostfix(java.sql.Date lowDate, java.sql.Date highDate, SQLConstant listName) {
-        query.append("\n ON s.id = " + listName + ".s_id " + " AND s.entered_date >= '"
-                + formatDateForDatabaseSql(lowDate) + "'" + " AND s.entered_date <= '"
-                + formatDateForDatabaseSql(highDate) + "'" + " ORDER BY 1 " + "\n) AS " + listName + "\n ");
-    }
-
-    protected Object pad20(Object translate) {
-        // uncomment the following lines to help make everything line up when
-        // debugging output.
-        // String strIn = (String)translate;
-        // int len = strIn.length();
-        // len = ( len > 30 )? 30: len;
-        // translate = translate + " ".substring(len);
-        return translate;
-    }
-
-    /** Generate a column to the list of all columns. One for each possible test. */
-    protected void addAllResultsColumns() {
-        /*
-         * for (Test test : allTests) { String testTag =
-         * TestServiceImpl.getLocalizedTestNameWithType(test); add(testTag,
-         * TestServiceImpl.getLocalizedTestNameWithType(test), TEST_RESULT); }
-         */
-    }
+    public abstract void searchForWHONetResults();
 
     /**
      * Useful for the 1st line of a CSV files. This produces a completely escaped
@@ -666,14 +185,11 @@ protected void addAllResultsColumns() {
      * @return one string with all names.
      */
     public String getColumnNamesLine() {
-        StringBuilder line = new StringBuilder();
-        for (CSVRoutineColumn column : columnsInOrder) {
-            line.append(StringUtil.escapeCSVValue(column.csvName));
-            line.append(",");
-        }
-        line.setLength(line.length() - 1);
-        line.append(eol);
-        return line.toString();
+
+        return new StringBuilder()
+                .append(new WHONetRow("NATIONAL ID", "FIRST NAME", "LAST NAME", "SEX", "BIRTHDATE", "DATE ENTERED",
+                        "LABNO", "DATE COLLECTED", "SPECIMEN TYPE", "ANTIBIOTIC", "ORGANISM", "RESULT").getRow())
+                .append(eol).toString();
     }
 
     /**
@@ -682,43 +198,10 @@ public String getColumnNamesLine() {
      * @throws SQLException
      */
     public String nextLine() throws SQLException, ParseException {
-        StringBuilder line = new StringBuilder();
-        String accessionNumber = null;
-        for (CSVRoutineColumn column : columnsInOrder) {
-            // OK this is a little hocky. Some of the custom translation strategies need the
-            // accession number and MOST of the time
-            // they are called after the accession number column. Not sure what to do if
-            // they are ever called before.
-            String translatedValue = StringUtil.escapeCSVValue(getValue(column, accessionNumber));
-            if (accessionNumber == null && "accession_number".equals(column.dbName)) {
-                accessionNumber = translatedValue;
-            }
-            line.append(translatedValue);
-            line.append(",");
-        }
-        line.setLength(line.length() - 1);
-        line.append(eol);
-        return line.toString();
+        return new StringBuilder().append(rows.get(index).getRow()).append(eol).toString();
     }
 
     public boolean next() throws SQLException {
-        return resultSet.next();
-    }
-
-    /**
-     * @throws SQLException
-     */
-    public void closeResultSet() throws SQLException {
-        resultSet.close();
-        resultSet = null;
-    }
-
-    protected String getGendCD4CountAnalyteId() {
-        if (gendCD4CountAnalyteId == null) {
-            Analyte a = new Analyte();
-            a.setAnalyteName("generated CD4 Count");
-            gendCD4CountAnalyteId = analyteService.getAnalyteByName(a, false).getId();
-        }
-        return gendCD4CountAnalyteId;
+        return ++index < rows.size();
     }
 }
diff --git a/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETRoutineColumnBuilder.java b/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETRoutineColumnBuilder.java
index ad416830b..027bed202 100644
--- a/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETRoutineColumnBuilder.java
+++ b/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETRoutineColumnBuilder.java
@@ -18,8 +18,9 @@
 package org.openelisglobal.reports.action.implementation.reportBeans;
 
 import java.sql.Date;
-import org.openelisglobal.common.log.LogEvent;
 import org.openelisglobal.reports.action.implementation.Report.DateRange;
+import org.openelisglobal.reports.service.WHONetReportService;
+import org.openelisglobal.spring.util.SpringContext;
 
 /**
  * @author pahill (pahill@uw.edu)
@@ -35,47 +36,13 @@ public WHONETRoutineColumnBuilder(DateRange dateRange) {
         super(dateRange);
     }
 
-    /**
-     * @see org.openelisglobal.reports.action.implementation.reportBeans.CIRoutineColumnBuilder#defineAllReportColumns()
-     */
-    @Override
-    protected void defineAllReportColumns() {
-        defineBasicColumns();
-        addAllResultsColumns();
-    }
-
-    /**
-     * @see org.openelisglobal.reports.action.implementation.reportBeans.CIRoutineColumnBuilder#makeSQL()
-     */
     @Override
-    public void makeSQL() {
-        query = new StringBuilder();
+    public void searchForWHONetResults() {
+        WHONetReportService reportService = SpringContext.getBean(WHONetReportService.class);
         Date lowDate = dateRange.getLowDate();
         Date highDate = dateRange.getHighDate();
-
-        query.append(WHONET_SELECT);
-        /*
-         * query.append(SELECT_SAMPLE_PATIENT_ORGANIZATION); // more cross tabulation of
-         * other columns goes where query.append(SELECT_ALL_DEMOGRAPHIC_AND_RESULTS);
-         *
-         * // FROM clause for ordinary lab (sample and patient) tables
-         * query.append(FROM_SAMPLE_PATIENT_ORGANIZATION);
-         *
-         * // all observation history from expressions
-         * appendObservationHistoryCrosstab(lowDate, highDate);
-         *
-         * appendResultCrosstab(lowDate, highDate);
-         *
-         * // and finally the join that puts these all together. Each cross table should
-         * be // listed here otherwise it's not in the result and you'll get a full join
-         * query.append(buildWhereSamplePatienOrgSQL(lowDate, highDate) // insert
-         * joining of any other crosstab here. + "\n AND s.id = demo.samp_id " +
-         * "\n AND s.id = result.samp_id " + "\n ORDER BY s.accession_number"); // no
-         * don't insert another crosstab or table here, go up before the main WHERE //
-         * clause
-         */
-        LogEvent.logTrace("WHONETRoutineColumnBuilder:", "Log SQL", query.toString());
-
+        rows = reportService.getWHONetRows(lowDate, highDate);
         return;
     }
+
 }
diff --git a/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETTBColumnBuilder.java b/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETTBColumnBuilder.java
deleted file mode 100644
index fa72cfd33..000000000
--- a/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETTBColumnBuilder.java
+++ /dev/null
@@ -1,148 +0,0 @@
-/*
- * The contents of this file are subject to the Mozilla Public License
- * Version 1.1 (the "License"); you may not use this file except in
- * compliance with the License. You may obtain a copy of the License at
- * http://www.mozilla.org/MPL/
- *
- * Software distributed under the License is distributed on an "AS IS"
- * basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the
- * License for the specific language governing rights and limitations under
- * the License.
- *
- * The Original Code is OpenELIS code.
- *
- * Copyright (C) The Minnesota Department of Health.  All Rights Reserved.
- *
- * Contributor(s): CIRG, University of Washington, Seattle WA.
- */
-package org.openelisglobal.reports.action.implementation.reportBeans;
-
-import java.sql.Date;
-import java.util.HashMap;
-import java.util.List;
-import org.openelisglobal.reports.action.implementation.Report.DateRange;
-import org.openelisglobal.reports.action.implementation.reportBeans.WHONETCSVRoutineColumnBuilder.SQLConstant;
-import org.openelisglobal.test.service.TestServiceImpl;
-import org.openelisglobal.test.valueholder.Test;
-import org.openelisglobal.testresult.valueholder.TestResult;
-
-/**
- * @author pahill (pahill@uw.edu)
- * @since May 18, 2011
- */
-public class WHONETTBColumnBuilder extends WHONETRoutineColumnBuilder {
-
-    /**
-     * @param dateRange
-     * @param projectStr
-     */
-    public WHONETTBColumnBuilder(DateRange dateRange) {
-        super(dateRange);
-    }
-
-    /**
-     * @see org.openelisglobal.reports.action.implementation.reportBeans.CIRoutineColumnBuilder#defineAllReportColumns()
-     */
-    @Override
-    protected void defineAllReportColumns() {
-        defineBasicColumns();
-        addAllResultsColumns();
-    }
-
-    @Override
-    @SuppressWarnings("unchecked")
-    protected void defineAllTestsAndResults() {
-        if (allTests == null) {
-            allTests = testService.getTbTest();
-        }
-        if (testResultsByTestName == null) {
-            testResultsByTestName = new HashMap<>();
-            List<TestResult> allTestResults = testResultService.getAllTestResults();
-            for (TestResult testResult : allTestResults) {
-                String key = TestServiceImpl.getLocalizedTestNameWithType(testResult.getTest());
-                testResultsByTestName.put(key, testResult);
-            }
-        }
-    }
-
-    @Override
-    protected void appendResultCrosstab(java.sql.Date lowDate, java.sql.Date highDate) {
-        // A list of analytes which should not show up in the regular results,
-        // String excludeAnalytes = getExcludedAnalytesSet();
-        SQLConstant listName = SQLConstant.RESULT;
-        query.append(", \n\n ( SELECT si.samp_id, si.id AS sampleItem_id, si.sort_order AS sampleItemNo, " + listName
-                + ".* " + " FROM sample_item AS si JOIN \n ");
-
-        // Begin cross tab / pivot table
-        query.append(" crosstab( \n" + " 'SELECT si.id, t.description, replace(replace(replace(replace(r.value ,E''\\n"
-                + "'', '' ''), E''\\t'', '' ''), E''\\r" + "'', '' ''),'','',''.'') \n"
-                + " FROM clinlims.result AS r join clinlims.analysis AS a on a.id = r.analysis_id \n"
-                + "  join clinlims.sample_item AS si on si.id = a.sampitem_id \n"
-                + "  join clinlims.sample AS s on s.id = si.samp_id \n"
-                + " join clinlims.test_result AS tr on r.test_result_id = tr.id \n"
-                + " join clinlims.test AS t on tr.test_id = t.id \n"
-                + " JOIN test_section ts ON t.test_section_id = ts.id \n"
-                + " left join sample_projects sp on si.samp_id = sp.samp_id \n" + "\n"
-                + " WHERE sp.id IS NULL AND ts.name = ''TB'' AND s.entered_date >= date(''"
-                + formatDateForDatabaseSql(lowDate) + "'')  AND s.entered_date <= date(''"
-                + formatDateForDatabaseSql(highDate) + " '') " + "\n "
-                // sql injection safe as user cannot overwrite validStatusId in database
-                + ((validStatusId == null) ? "" : " AND a.status_id = " + validStatusId)
-                // + (( excludeAnalytes == null)?"":
-                // " AND r.analyte_id NOT IN ( " + excludeAnalytes) + ")"
-                // + " AND a.test_id = t.id "
-                + "\n" + " ORDER BY 1, 2 \n"
-                + " ', 'SELECT t.description FROM test t JOIN test_section ts ON t.test_section_id ="
-                + " ts.id where t.is_active = ''Y'' AND ts.name = ''TB'' ORDER BY 1' ) ");
-        // end of cross tab
-
-        // Name the test pivot table columns . We'll name them all after the
-        // resource name, because some tests have fancy characters in them and
-        // somewhere
-        // between iReport, Java and postgres a complex name (e.g. one including
-        // a beta, " HCG Quant") get messed up and isn't found.
-        query.append("\n as " + listName + " ( " // inner use of the list name
-                + "\"si_id\" numeric(10) ");
-        for (Test col : allTests) {
-            String testName = TestServiceImpl.getLocalizedTestNameWithType(col);
-            query.append("\n, " + prepareColumnName(testName) + " varchar(200) ");
-        }
-        query.append(" ) \n");
-        // left join all sample Items from the right sample range to the results table.
-        query.append("\n ON si.id = " + listName + ".si_id " // the inner use a few lines above
-                + "\n ORDER BY si.samp_id, si.id " + "\n) AS " + listName + "\n "); // outer re-use the list name to
-        // name this sparse matrix of
-        // results.
-    }
-
-    /**
-     * @see org.openelisglobal.reports.action.implementation.reportBeans.CIRoutineColumnBuilder#makeSQL()
-     */
-    @Override
-    public void makeSQL() {
-        query = new StringBuilder();
-        Date lowDate = dateRange.getLowDate();
-        Date highDate = dateRange.getHighDate();
-        query.append(SELECT_SAMPLE_PATIENT_ORGANIZATION);
-        // more cross tabulation of other columns goes where
-        query.append(SELECT_ALL_DEMOGRAPHIC_AND_RESULTS);
-
-        // FROM clause for ordinary lab (sample and patient) tables
-        query.append(FROM_SAMPLE_PATIENT_ORGANIZATION);
-
-        // all observation history from expressions
-        appendObservationHistoryCrosstab(lowDate, highDate);
-
-        appendResultCrosstab(lowDate, highDate);
-
-        // and finally the join that puts these all together. Each cross table should be
-        // listed here otherwise it's not in the result and you'll get a full join
-        query.append(buildWhereSamplePatienOrgSQL(lowDate, highDate)
-                // insert joining of any other crosstab here.
-                + "\n AND s.id = demo.samp_id " + "\n AND s.id = result.samp_id " + "\n ORDER BY s.accession_number ");
-        // no don't insert another crosstab or table here, go up before the main WHERE
-        // clause
-        System.out.println("query.toString(): " + query.toString());
-        return;
-    }
-}
diff --git a/src/main/java/org/openelisglobal/reports/service/WHONetReportService.java b/src/main/java/org/openelisglobal/reports/service/WHONetReportService.java
new file mode 100644
index 000000000..f0063be92
--- /dev/null
+++ b/src/main/java/org/openelisglobal/reports/service/WHONetReportService.java
@@ -0,0 +1,14 @@
+package org.openelisglobal.reports.service;
+
+import java.sql.Date;
+import java.util.List;
+import org.openelisglobal.reports.action.implementation.reportBeans.WHONETCSVRoutineColumnBuilder.WHONetRow;
+import org.openelisglobal.sampleitem.valueholder.SampleItem;
+
+public interface WHONetReportService {
+
+    List<SampleItem> getAntimicrobialEntries(Date lowDate, Date highDate);
+
+    List<WHONetRow> getWHONetRows(Date lowDate, Date highDate);
+
+}
diff --git a/src/main/java/org/openelisglobal/reports/service/WHONetReportServiceImpl.java b/src/main/java/org/openelisglobal/reports/service/WHONetReportServiceImpl.java
new file mode 100644
index 000000000..6aad45db0
--- /dev/null
+++ b/src/main/java/org/openelisglobal/reports/service/WHONetReportServiceImpl.java
@@ -0,0 +1,175 @@
+package org.openelisglobal.reports.service;
+
+import java.sql.Date;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+import javax.annotation.PostConstruct;
+import org.openelisglobal.analysis.service.AnalysisService;
+import org.openelisglobal.analysis.valueholder.Analysis;
+import org.openelisglobal.common.log.LogEvent;
+import org.openelisglobal.common.services.IStatusService;
+import org.openelisglobal.common.services.StatusService.AnalysisStatus;
+import org.openelisglobal.common.services.StatusService.OrderStatus;
+import org.openelisglobal.common.util.DateUtil;
+import org.openelisglobal.patient.valueholder.Patient;
+import org.openelisglobal.reports.action.implementation.reportBeans.WHONETCSVRoutineColumnBuilder.WHONetRow;
+import org.openelisglobal.result.service.ResultService;
+import org.openelisglobal.result.valueholder.Result;
+import org.openelisglobal.sample.service.SampleService;
+import org.openelisglobal.sample.valueholder.Sample;
+import org.openelisglobal.samplehuman.service.SampleHumanService;
+import org.openelisglobal.sampleitem.service.SampleItemService;
+import org.openelisglobal.sampleitem.valueholder.SampleItem;
+import org.openelisglobal.test.service.TestService;
+import org.openelisglobal.test.valueholder.Test;
+import org.openelisglobal.testreflex.action.util.TestReflexUtil;
+import org.openelisglobal.testreflex.service.TestReflexService;
+import org.openelisglobal.typeofsample.service.TypeOfSampleService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+@Service
+public class WHONetReportServiceImpl implements WHONetReportService {
+
+    @Autowired
+    private SampleService sampleService;
+    @Autowired
+    private AnalysisService analysisService;
+    @Autowired
+    private ResultService resultService;
+    @Autowired
+    private SampleHumanService sampleHumanService;
+    @Autowired
+    private TestService testService;
+    @Autowired
+    private TypeOfSampleService sampleTypeService;
+    @Autowired
+    private SampleItemService sampleItemService;
+    @Autowired
+    private IStatusService statusService;
+    @Autowired
+    private TestReflexService testReflexService;
+
+    private List<Integer> ANALYSIS_STATUS_IDS;
+    private List<Integer> SAMPLE_STATUS_IDS;
+
+    @PostConstruct
+    private void initialize() {
+        ANALYSIS_STATUS_IDS = Arrays
+                .asList(statusService.getStatusID(AnalysisStatus.SampleRejected),
+                        statusService.getStatusID(AnalysisStatus.NotStarted),
+                        statusService.getStatusID(AnalysisStatus.Canceled),
+                        statusService.getStatusID(AnalysisStatus.TechnicalAcceptance),
+                        statusService.getStatusID(AnalysisStatus.TechnicalRejected),
+                        statusService.getStatusID(AnalysisStatus.BiologistRejected),
+                        statusService.getStatusID(AnalysisStatus.NonConforming_depricated),
+                        statusService.getStatusID(AnalysisStatus.Finalized))
+                .stream().map(val -> Integer.parseInt(val)).collect(Collectors.toList());
+        SAMPLE_STATUS_IDS = Arrays
+                .asList(statusService.getStatusID(OrderStatus.Entered), statusService.getStatusID(OrderStatus.Started),
+                        statusService.getStatusID(OrderStatus.Finished),
+                        statusService.getStatusID(OrderStatus.NonConforming_depricated))
+                .stream().map(val -> Integer.parseInt(val)).collect(Collectors.toList());
+    }
+
+    @Override
+    public List<SampleItem> getAntimicrobialEntries(Date lowDate, Date highDate) {
+        List<Test> tests = testService.getAllMatching("antimicrobialResistance", Boolean.TRUE);
+        List<Integer> testIds = tests.stream().map(e -> Integer.parseInt(e.getId())).collect(Collectors.toList());
+
+        Map<String, SampleItem> sampleItems = new HashMap<>();
+        List<Analysis> analysises = analysisService.getAllAnalysisByTestsAndStatusAndCompletedDateRange(testIds,
+                ANALYSIS_STATUS_IDS, SAMPLE_STATUS_IDS, lowDate, highDate);
+
+        System.out.println(
+                "analysises" + String.join(", ", analysises.stream().map(e -> e.getId()).collect(Collectors.toList())));
+        analysises.stream().forEach(e -> sampleItems.putIfAbsent(e.getSampleItem().getId(), e.getSampleItem()));
+        System.out.println("sampleItems"
+                + String.join(", ", analysises.stream().map(e -> e.getId()).collect(Collectors.toList())));
+
+        return new ArrayList<SampleItem>(sampleItems.values());
+    }
+
+    @Override
+    public List<WHONetRow> getWHONetRows(Date lowDate, Date highDate) {
+        List<SampleItem> sampleItems = getAntimicrobialEntries(lowDate, highDate);
+        return createRowsFromSampleItems(sampleItems);
+    }
+
+    private List<WHONetRow> createRowsFromSampleItems(List<SampleItem> sampleItems) {
+        List<WHONetRow> rows = new ArrayList<>();
+
+        List<String> triggerTestIds = testService.getTriggeringAntimicrobialResistanceTests().stream()
+                .map(e -> e.getId()).collect(Collectors.toList());
+
+        for (SampleItem sampleItem : sampleItems) {
+            Sample sample = sampleItem.getSample();
+            Patient patient = sampleHumanService.getPatientForSample(sample);
+            List<Analysis> analysises = analysisService.getAnalysesBySampleItem(sampleItem);
+
+            // for every analysis in the sampleItem, find any that are a triggering
+            // antimicrobial resistance analysis
+            System.out.println("analysises"
+                    + String.join(", ", analysises.stream().map(e -> e.getId()).collect(Collectors.toList())));
+
+            for (Analysis potentialTriggerAnalysis : analysises) {
+                if (triggerTestIds.contains(potentialTriggerAnalysis.getTest().getId())) {
+                    Analysis triggerAnalysis = potentialTriggerAnalysis;
+                    // find the exact result that triggers further analysis
+                    List<Result> results = resultService.getResultsByAnalysis(triggerAnalysis);
+                    System.out.println("results"
+                            + String.join(", ", results.stream().map(e -> e.getId()).collect(Collectors.toList())));
+                    for (Result triggerResult : results) {
+                        System.out.println("triggerResult" + triggerResult.getId());
+                        System.out.println("testResult" + triggerResult.getTestResult().getId());
+
+                        TestReflexUtil testReflexUtil = new TestReflexUtil();
+
+                        // find the analysis that was triggered by the trigger test
+                        for (Analysis potentialReflexAnalysis : analysises) {
+                            if (testReflexUtil.isTestTriggeredByResult(potentialReflexAnalysis.getTest(), triggerResult)) {
+                                Analysis reflexAnalysis =  potentialReflexAnalysis;
+                                // get the results from the the reflex test
+                                List<Result> reflexResults = resultService.getResultsByAnalysis(reflexAnalysis);
+                                if (reflexResults.size() == 0) {
+                                    // if there's no results for the second test, we still need the info of the
+                                    // trigger test and reflex test name
+                                    rows.add(new WHONetRow(patient.getNationalId(), patient.getPerson().getFirstName(),
+                                            patient.getPerson().getLastName(), patient.getGender(),
+                                            patient.getBirthDateForDisplay(), sample.getEnteredDateForDisplay(),
+                                            sample.getAccessionNumber(),
+                                            DateUtil.convertTimestampToStringDate(sampleItem.getCollectionDate()),
+                                            sampleItem.getTypeOfSample().getDescription(),
+                                            reflexAnalysis.getTest().getName(),
+                                            resultService.getSimpleResultValue(triggerResult), ""));
+                                } else {
+                                    // else add the info of both tests/results
+                                    for (Result reflexResult : reflexResults) {
+                                        rows.add(new WHONetRow(patient.getNationalId(), patient.getPerson().getFirstName(),
+                                                patient.getPerson().getLastName(), patient.getGender(),
+                                                patient.getBirthDateForDisplay(), sample.getEnteredDateForDisplay(),
+                                                sample.getAccessionNumber(),
+                                                DateUtil.convertTimestampToStringDate(sampleItem.getCollectionDate()),
+                                                sampleItem.getTypeOfSample().getDescription(),
+                                                reflexAnalysis.getTest().getName(),
+                                                resultService.getSimpleResultValue(triggerResult),
+                                                resultService.getSimpleResultValue(reflexResult)));
+                                    }
+                                }
+                            }
+
+                        }
+                    }
+                }
+            }
+
+        }
+
+        return rows;
+    }
+
+}
diff --git a/src/main/java/org/openelisglobal/test/service/TestService.java b/src/main/java/org/openelisglobal/test/service/TestService.java
index 95949b1bf..b12a4b787 100644
--- a/src/main/java/org/openelisglobal/test/service/TestService.java
+++ b/src/main/java/org/openelisglobal/test/service/TestService.java
@@ -132,4 +132,6 @@ public interface TestService extends BaseObjectService<Test, String> {
     void activateTests(List<String> testNames);
 
     void activateTestsAndDeactivateOthers(List<String> asList);
+
+    List<Test> getTriggeringAntimicrobialResistanceTests();
 }
diff --git a/src/main/java/org/openelisglobal/test/service/TestServiceImpl.java b/src/main/java/org/openelisglobal/test/service/TestServiceImpl.java
index f5f12fb5b..bf25f3b34 100644
--- a/src/main/java/org/openelisglobal/test/service/TestServiceImpl.java
+++ b/src/main/java/org/openelisglobal/test/service/TestServiceImpl.java
@@ -8,6 +8,7 @@
 import java.util.Map;
 import java.util.Optional;
 import java.util.Vector;
+import java.util.stream.Collectors;
 import javax.annotation.PostConstruct;
 import javax.servlet.http.HttpServletRequest;
 import org.openelisglobal.common.action.IActionConstants;
@@ -33,6 +34,7 @@
 import org.openelisglobal.test.valueholder.TestSection;
 import org.openelisglobal.testanalyte.service.TestAnalyteService;
 import org.openelisglobal.testanalyte.valueholder.TestAnalyte;
+import org.openelisglobal.testreflex.action.util.TestReflexUtil;
 import org.openelisglobal.testresult.service.TestResultService;
 import org.openelisglobal.testresult.valueholder.TestResult;
 import org.openelisglobal.typeofsample.service.TypeOfSampleService;
@@ -742,4 +744,10 @@ public List<Test> getTbTest() {
     public List<Panel> getTbPanelsByMethod(String method) {
         return getBaseObjectDAO().getTbPanelsByMethod(method);
     }
+
+    @Override
+    public List<Test> getTriggeringAntimicrobialResistanceTests() {
+        return getAllMatching("antimicrobialResistance", Boolean.TRUE).stream()
+                .filter(e -> TestReflexUtil.isTriggeringReflexTestId(e.getId())).collect(Collectors.toList());
+    }
 }
diff --git a/src/main/java/org/openelisglobal/testreflex/action/util/TestReflexUtil.java b/src/main/java/org/openelisglobal/testreflex/action/util/TestReflexUtil.java
index b6a218130..b8a5215c7 100644
--- a/src/main/java/org/openelisglobal/testreflex/action/util/TestReflexUtil.java
+++ b/src/main/java/org/openelisglobal/testreflex/action/util/TestReflexUtil.java
@@ -44,6 +44,7 @@
 import org.openelisglobal.spring.util.SpringContext;
 import org.openelisglobal.test.service.TestService;
 import org.openelisglobal.test.service.TestServiceImpl;
+import org.openelisglobal.test.valueholder.Test;
 import org.openelisglobal.testanalyte.valueholder.TestAnalyte;
 import org.openelisglobal.testreflex.action.bean.ReflexRule;
 import org.openelisglobal.testreflex.action.bean.ReflexRuleOptions;
@@ -142,6 +143,15 @@ public static boolean testIsTriggeringReflexWithSibs(String testId) {
         return false;
     }
 
+    public static List<TestReflex> getReflexTests(String testId) {
+        if (isTriggeringReflexTestId(testId)) {
+            return TEST_TO_REFLEX_MAP.get(testId);
+        } else {
+            return new ArrayList<>();
+        }
+
+    }
+
     public static String makeReflexTestName(TestReflex testReflex) {
         return TestServiceImpl.getUserLocalizedTestName(testReflex.getAddedTest());
     }
@@ -320,20 +330,10 @@ private List<TestReflex> getReflexTests(TestReflexBean reflexBean) {
         if (reflexBean.getResult().getTestResult() == null) {
             return new ArrayList<>();
         }
-        String resultType = testService.getResultType(reflexBean.getResult().getTestResult().getTest());
         List<TestReflex> reflexesForResult = reflexResolver.getTestReflexesForResult(reflexBean.getResult());
-        if (resultType.equals("D")) {
-            reflexesForResult = applyDictionaryRelationRulesForReflex(reflexBean.getResult());
-        } else if (!resultType.equals("D")) {
-            if (resultType.equals("N")) {
-                reflexesForResult = reflexesForResult.stream()
-                        .filter(test -> applyNumericRelationRulesForReflex(test, reflexBean))
-                        .collect(Collectors.toList());
-            } else {
-                reflexesForResult = reflexesForResult.stream()
-                        .filter(test -> applyTextRelationRulesForReflex(test, reflexBean)).collect(Collectors.toList());
-            }
-        }
+        reflexesForResult = reflexesForResult.stream()
+                .filter(e -> isTestTriggeredByResult(e.getAddedTest(), reflexBean.getResult()))
+                .collect(Collectors.toList());
         return reflexesForResult;
     }
 
@@ -483,54 +483,48 @@ private List<TestReflex> applyDictionaryRelationRulesForReflex(Result result) {
         return reflexTests;
     }
 
-    private Boolean applyNumericRelationRulesForReflex(TestReflex reflexTest, TestReflexBean reflexBean) {
+    private Boolean applyNumericRelationRulesForReflex(TestReflex reflexTest, Result result) {
         if (reflexTest.getRelation() == null) {
             return false;
         }
         switch (reflexTest.getRelation()) {
         case EQUALS:
-            return Double.valueOf(reflexTest.getNonDictionaryValue())
-                    .equals(Double.valueOf(reflexBean.getResult().getValue()));
+            return Double.valueOf(reflexTest.getNonDictionaryValue()).equals(Double.valueOf(result.getValue()));
         case NOT_EQUALS:
-            return !(Double.valueOf(reflexTest.getNonDictionaryValue())
-                    .equals(Double.valueOf(reflexBean.getResult().getValue())));
+            return !(Double.valueOf(reflexTest.getNonDictionaryValue()).equals(Double.valueOf(result.getValue())));
         case GREATER_THAN:
-            return Double.valueOf(reflexTest.getNonDictionaryValue()) < Double
-                    .valueOf(reflexBean.getResult().getValue());
+            return Double.valueOf(reflexTest.getNonDictionaryValue()) < Double.valueOf(result.getValue());
         case LESS_THAN:
-            return Double.valueOf(reflexTest.getNonDictionaryValue()) > Double
-                    .valueOf(reflexBean.getResult().getValue());
+            return Double.valueOf(reflexTest.getNonDictionaryValue()) > Double.valueOf(result.getValue());
         case GREATER_THAN_OR_EQUAL:
-            return Double.valueOf(reflexTest.getNonDictionaryValue()) <= Double
-                    .valueOf(reflexBean.getResult().getValue());
+            return Double.valueOf(reflexTest.getNonDictionaryValue()) <= Double.valueOf(result.getValue());
         case LESS_THAN_OR_EQUAL:
-            return Double.valueOf(reflexTest.getNonDictionaryValue()) >= Double
-                    .valueOf(reflexBean.getResult().getValue());
+            return Double.valueOf(reflexTest.getNonDictionaryValue()) >= Double.valueOf(result.getValue());
         case INSIDE_NORMAL_RANGE:
-            return Double.valueOf(reflexBean.getResult().getValue()) >= reflexBean.getResult().getMinNormal()
-                    && Double.valueOf(reflexBean.getResult().getValue()) <= reflexBean.getResult().getMaxNormal();
+            return Double.valueOf(result.getValue()) >= result.getMinNormal()
+                    && Double.valueOf(result.getValue()) <= result.getMaxNormal();
         case OUTSIDE_NORMAL_RANGE:
-            return !(Double.valueOf(reflexBean.getResult().getValue()) >= reflexBean.getResult().getMinNormal()
-                    && Double.valueOf(reflexBean.getResult().getValue()) <= reflexBean.getResult().getMaxNormal());
+            return !(Double.valueOf(result.getValue()) >= result.getMinNormal()
+                    && Double.valueOf(result.getValue()) <= result.getMaxNormal());
         case BETWEEN:
             String value1 = reflexTest.getNonDictionaryValue().split("-")[0];
             String value2 = reflexTest.getNonDictionaryValue().split("-")[1];
-            return Double.valueOf(reflexBean.getResult().getValue()) >= Double.valueOf(value1)
-                    && Double.valueOf(reflexBean.getResult().getValue()) <= Double.valueOf(value2);
+            return Double.valueOf(result.getValue()) >= Double.valueOf(value1)
+                    && Double.valueOf(result.getValue()) <= Double.valueOf(value2);
         default:
             return false;
         }
     }
 
-    private Boolean applyTextRelationRulesForReflex(TestReflex reflexTest, TestReflexBean reflexBean) {
+    private Boolean applyTextRelationRulesForReflex(TestReflex reflexTest, Result result) {
         if (reflexTest.getRelation() == null) {
             return false;
         }
         switch (reflexTest.getRelation()) {
         case EQUALS:
-            return reflexTest.getNonDictionaryValue().equals(reflexBean.getResult().getValue());
+            return reflexTest.getNonDictionaryValue().equals(result.getValue());
         case NOT_EQUALS:
-            return !(reflexTest.getNonDictionaryValue().equals(reflexBean.getResult().getValue()));
+            return !(reflexTest.getNonDictionaryValue().equals(result.getValue()));
         default:
             return false;
         }
@@ -828,4 +822,74 @@ private boolean isConclusion(Result result) {
         return analyte != null
                 && (CONCLUSION_ANAYLETE_ID.equals(analyte.getId()) || CD4_ANAYLETE.getId().equals(analyte.getId()));
     }
+
+    public boolean isTestTriggeredByResult(Test potentialReflexTest, Result potentialTriggerResult) {
+        String resultType = testService.getResultType(potentialTriggerResult.getTestResult().getTest());
+        if (resultType.equals("D")) {
+            return doesDictionaryRelationRulesForReflexApply(potentialReflexTest, potentialTriggerResult);
+        } else if (!resultType.equals("D")) {
+            if (resultType.equals("N")) {
+                return doesNumericRulesForReflexApply(potentialReflexTest, potentialTriggerResult);
+            } else {
+                return doesGenericRulesForReflexApply(potentialReflexTest, potentialTriggerResult);
+            }
+        }
+        return false;
+    }
+
+    public boolean doesDictionaryRelationRulesForReflexApply(Test potentialReflexTest, Result potentialTriggerResult) {
+        return reflexResolver.getTestReflexsByAnalyteAndTest(potentialTriggerResult).stream().anyMatch(reflexTest -> {
+            if (reflexTest.getAddedTest().getId().equals(potentialReflexTest.getId())) {
+                if (reflexTest.getRelation() != null) {
+                    switch (reflexTest.getRelation()) {
+                    case EQUALS:
+                        if (reflexTest.getTestResult().getValue().equals(potentialTriggerResult.getValue())) {
+                            return true;
+                        }
+                        break;
+                    case NOT_EQUALS:
+                        if (!(reflexTest.getTestResult().getValue().equals(potentialTriggerResult.getValue()))) {
+                            return true;
+                        }
+                        break;
+                    case INSIDE_NORMAL_RANGE:
+                        List<ResultLimit> resultLimits = SpringContext.getBean(ResultLimitService.class)
+                                .getResultLimits(potentialTriggerResult.getTestResult().getTest());
+                        if (!resultLimits.isEmpty()
+                                && StringUtils.isNotBlank(resultLimits.get(0).getDictionaryNormalId())) {
+                            if (potentialTriggerResult.getValue().equals(resultLimits.get(0).getDictionaryNormalId())) {
+                                return true;
+                            }
+                        }
+                        break;
+                    case OUTSIDE_NORMAL_RANGE:
+                        List<ResultLimit> limits = SpringContext.getBean(ResultLimitService.class)
+                                .getResultLimits(potentialTriggerResult.getTestResult().getTest());
+                        if (!limits.isEmpty() && StringUtils.isNotBlank(limits.get(0).getDictionaryNormalId())) {
+                            if (!(potentialTriggerResult.getValue().equals(limits.get(0).getDictionaryNormalId()))) {
+                                return true;
+                            }
+                        }
+                        break;
+                    default:
+                        break;
+                    }
+                }
+            }
+            return false;
+
+        });
+    }
+
+    private boolean doesNumericRulesForReflexApply(Test potentialReflexTest, Result potentialTriggerResult) {
+        List<TestReflex> reflexesForResult = reflexResolver.getTestReflexesForResult(potentialTriggerResult);
+        return reflexesForResult.stream().anyMatch(test -> test.getAddedTest().equals(potentialReflexTest)
+                && applyNumericRelationRulesForReflex(test, potentialTriggerResult));
+    }
+
+    private boolean doesGenericRulesForReflexApply(Test potentialReflexTest, Result potentialTriggerResult) {
+        List<TestReflex> reflexesForResult = reflexResolver.getTestReflexesForResult(potentialTriggerResult);
+        return reflexesForResult.stream().anyMatch(test -> test.getAddedTest().equals(potentialReflexTest)
+                && applyTextRelationRulesForReflex(test, potentialTriggerResult));
+    }
 }

From 729c728906dbb2f4e3404fd0db003a9d9af1969a Mon Sep 17 00:00:00 2001
From: CalebSLane <c.steelelane@gmail.com>
Date: Mon, 12 Aug 2024 11:06:52 -0700
Subject: [PATCH 3/6] 2.8.1.39

---
 pom.xml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/pom.xml b/pom.xml
index 577de72a5..ddfc69452 100644
--- a/pom.xml
+++ b/pom.xml
@@ -16,7 +16,7 @@
     <minor.version>8</minor.version>
     <state.version>1</state.version>
     <!-- 0 = alpha, 1 = beta, 2 = rc, 3 = deployable -->
-    <fix.version>38</fix.version>
+    <fix.version>39</fix.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <liquibase.propertyFile>${project.basedir}/liquibase/liquibase.properties</liquibase.propertyFile>
     <castor.version>1.4.1</castor.version>
@@ -84,10 +84,10 @@
       <version>2.12.0</version>
     </dependency>
     <dependency>
-            <groupId>com.fasterxml.jackson.datatype</groupId>
-            <artifactId>jackson-datatype-jsr310</artifactId>
-            <version>2.12.3</version>
-        </dependency>
+      <groupId>com.fasterxml.jackson.datatype</groupId>
+      <artifactId>jackson-datatype-jsr310</artifactId>
+      <version>2.12.3</version>
+    </dependency>
     <!-- APACHE ASSORTED DEPENDENCIES -->
     <dependency>
       <groupId>org.apache.httpcomponents</groupId>
@@ -681,4 +681,4 @@
       </plugin>
     </plugins>
   </build>
-</project>
+</project>
\ No newline at end of file

From 2cce8807f0f08ebde7d27e08e1141124431d8fb7 Mon Sep 17 00:00:00 2001
From: CalebSLane <c.steelelane@gmail.com>
Date: Mon, 12 Aug 2024 11:55:17 -0700
Subject: [PATCH 4/6] format

---
 pom.xml                                            |  2 +-
 .../reportBeans/WHONETCSVRoutineColumnBuilder.java |  1 -
 .../reports/service/WHONetReportServiceImpl.java   | 14 +++++++-------
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/pom.xml b/pom.xml
index ddfc69452..de3118b7c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -681,4 +681,4 @@
       </plugin>
     </plugins>
   </build>
-</project>
\ No newline at end of file
+</project>
diff --git a/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETCSVRoutineColumnBuilder.java b/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETCSVRoutineColumnBuilder.java
index c3e2b24fe..703774749 100644
--- a/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETCSVRoutineColumnBuilder.java
+++ b/src/main/java/org/openelisglobal/reports/action/implementation/reportBeans/WHONETCSVRoutineColumnBuilder.java
@@ -185,7 +185,6 @@ protected String datetimeToLocalDateTime(String value) {
      * @return one string with all names.
      */
     public String getColumnNamesLine() {
-
         return new StringBuilder()
                 .append(new WHONetRow("NATIONAL ID", "FIRST NAME", "LAST NAME", "SEX", "BIRTHDATE", "DATE ENTERED",
                         "LABNO", "DATE COLLECTED", "SPECIMEN TYPE", "ANTIBIOTIC", "ORGANISM", "RESULT").getRow())
diff --git a/src/main/java/org/openelisglobal/reports/service/WHONetReportServiceImpl.java b/src/main/java/org/openelisglobal/reports/service/WHONetReportServiceImpl.java
index 6aad45db0..bcf31d3b8 100644
--- a/src/main/java/org/openelisglobal/reports/service/WHONetReportServiceImpl.java
+++ b/src/main/java/org/openelisglobal/reports/service/WHONetReportServiceImpl.java
@@ -10,7 +10,6 @@
 import javax.annotation.PostConstruct;
 import org.openelisglobal.analysis.service.AnalysisService;
 import org.openelisglobal.analysis.valueholder.Analysis;
-import org.openelisglobal.common.log.LogEvent;
 import org.openelisglobal.common.services.IStatusService;
 import org.openelisglobal.common.services.StatusService.AnalysisStatus;
 import org.openelisglobal.common.services.StatusService.OrderStatus;
@@ -131,8 +130,9 @@ private List<WHONetRow> createRowsFromSampleItems(List<SampleItem> sampleItems)
 
                         // find the analysis that was triggered by the trigger test
                         for (Analysis potentialReflexAnalysis : analysises) {
-                            if (testReflexUtil.isTestTriggeredByResult(potentialReflexAnalysis.getTest(), triggerResult)) {
-                                Analysis reflexAnalysis =  potentialReflexAnalysis;
+                            if (testReflexUtil.isTestTriggeredByResult(potentialReflexAnalysis.getTest(),
+                                    triggerResult)) {
+                                Analysis reflexAnalysis = potentialReflexAnalysis;
                                 // get the results from the the reflex test
                                 List<Result> reflexResults = resultService.getResultsByAnalysis(reflexAnalysis);
                                 if (reflexResults.size() == 0) {
@@ -149,10 +149,10 @@ private List<WHONetRow> createRowsFromSampleItems(List<SampleItem> sampleItems)
                                 } else {
                                     // else add the info of both tests/results
                                     for (Result reflexResult : reflexResults) {
-                                        rows.add(new WHONetRow(patient.getNationalId(), patient.getPerson().getFirstName(),
-                                                patient.getPerson().getLastName(), patient.getGender(),
-                                                patient.getBirthDateForDisplay(), sample.getEnteredDateForDisplay(),
-                                                sample.getAccessionNumber(),
+                                        rows.add(new WHONetRow(patient.getNationalId(),
+                                                patient.getPerson().getFirstName(), patient.getPerson().getLastName(),
+                                                patient.getGender(), patient.getBirthDateForDisplay(),
+                                                sample.getEnteredDateForDisplay(), sample.getAccessionNumber(),
                                                 DateUtil.convertTimestampToStringDate(sampleItem.getCollectionDate()),
                                                 sampleItem.getTypeOfSample().getDescription(),
                                                 reflexAnalysis.getTest().getName(),

From 61e5b8a10a58da93a7c44f9284956986c2391d3e Mon Sep 17 00:00:00 2001
From: CalebSLane <c.steelelane@gmail.com>
Date: Mon, 12 Aug 2024 12:50:12 -0700
Subject: [PATCH 5/6] change ids of navs to communicate functionality

---
 frontend/cypress/pages/HomePage.js       | 44 ++++++++++++------------
 frontend/src/components/layout/Header.js | 19 +++++-----
 2 files changed, 32 insertions(+), 31 deletions(-)

diff --git a/frontend/cypress/pages/HomePage.js b/frontend/cypress/pages/HomePage.js
index 4175ff469..c22181af3 100755
--- a/frontend/cypress/pages/HomePage.js
+++ b/frontend/cypress/pages/HomePage.js
@@ -19,8 +19,8 @@ class HomePage {
 
   goToOrderPage() {
     this.openNavigationMenu();
-    cy.get("#menu_sample").click();
-    cy.get("#menu_sample_add").click();
+    cy.get("#menu_sample_dropdown").click();
+    cy.get("#menu_sample_add_nav").click();
     return new OrderEntityPage();
   }
 
@@ -32,69 +32,69 @@ class HomePage {
 
   goToBatchOrderEntry() {
     this.openNavigationMenu();
-    cy.get("#menu_sample").click();
-    cy.get("#menu_sample_batch_entry").click();
+    cy.get("#menu_sample_dropdown").click();
+    cy.get("#menu_sample_batch_entry_nav").click();
     return new BatchOrderEntry();
   }
 
   goToPatientEntry() {
     this.openNavigationMenu();
-    cy.get("#menu_patient").click();
-    cy.get("#menu_patient_add_or_edit").click();
+    cy.get("#menu_patient_dropdown").click();
+    cy.get("#menu_patient_add_or_edit_nav").click();
     return new PatientEntryPage();
   }
 
   goToModifyOrderPage() {
     this.openNavigationMenu();
-    cy.get("#menu_sample").click();
-    cy.get("#menu_sample_edit").click();
+    cy.get("#menu_sample_dropdown").click();
+    cy.get("#menu_sample_edit_nav").click();
     return new ModifyOrderPage();
   }
   goToWorkPlanPlanByTest() {
     this.openNavigationMenu();
-    cy.get("#menu_workplan").click();
-    cy.get("#menu_workplan_test").click();
+    cy.get("#menu_workplan_dropdown").click();
+    cy.get("#menu_workplan_test_nav").click();
     return new WorkPlan();
   }
 
   goToWorkPlanPlanByPanel() {
     this.openNavigationMenu();
-    cy.get("#menu_workplan").click();
-    cy.get("#menu_workplan_panel").click();
+    cy.get("#menu_workplan_dropdown").click();
+    cy.get("#menu_workplan_panel_nav").click();
     return new WorkPlan();
   }
 
   goToWorkPlanPlanByUnit() {
     this.openNavigationMenu();
-    cy.get("#menu_workplan").click();
-    cy.get("#menu_workplan_bench").click();
+    cy.get("#menu_workplan_dropdown").click();
+    cy.get("#menu_workplan_bench_nav").click();
     return new WorkPlan();
   }
 
   goToWorkPlanPlanByPriority() {
     this.openNavigationMenu();
-    cy.get("#menu_workplan").click();
-    cy.get("#menu_workplan_priority").click();
+    cy.get("#menu_workplan_dropdown").click();
+    cy.get("#menu_workplan_priority_nav").click();
     return new WorkPlan();
   }
 
   goToReportNCE() {
     this.openNavigationMenu();
-    cy.get("#menu_nonconformity").click();
-    cy.get("#menu_non_conforming_report").click();
+    cy.get("#menu_nonconformity_dropdown").click();
+    cy.get("#menu_non_conforming_report_nav").click();
     return new NonConform();
   }
 
   goToViewNCE() {
     this.openNavigationMenu();
-    cy.get("#menu_nonconformity").click();
-    cy.get("#menu_non_conforming_view").click();
+    cy.get("#menu_nonconformity_dropdown").click();
+    cy.get("#menu_non_conforming_view_nav").click();
     return new NonConform();
   }
   goToCorrectiveActions() {
     this.openNavigationMenu();
-    cy.get("#menu_nonconformity").click();
-    cy.get("#menu_non_conforming_corrective_actions").click();
+    cy.get("#menu_nonconformity_dropdown").click();
+    cy.get("#menu_non_conforming_corrective_actions_nav").click();
     return new NonConform();
   }
 }
diff --git a/frontend/src/components/layout/Header.js b/frontend/src/components/layout/Header.js
index 28a0e619c..f4e080bb1 100644
--- a/frontend/src/components/layout/Header.js
+++ b/frontend/src/components/layout/Header.js
@@ -184,9 +184,9 @@ function OEHeader(props) {
     if (menuItem.menu.isActive) {
       if (level === 0 && menuItem.childMenus.length > 0) {
         return (
-          <React.Fragment key={path}>
+          <span id={menuItem.menu.elementId} key={path}>
             <span
-              id={menuItem.menu.elementId}
+              id={menuItem.menu.elementId + "_dropdown"}
               onClick={(e) => {
                 setMenuItemExpanded(e, menuItem, path);
               }}
@@ -222,27 +222,26 @@ function OEHeader(props) {
                 </span>
               </SideNavMenu>
             </span>
-          </React.Fragment>
+          </span>
         );
       } else if (level === 0) {
         return (
-          <React.Fragment key={path}>
+          <span key={path} id={menuItem.menu.elementId}>
             <SideNavMenuItem
-              id={menuItem.menu.elementId}
+              id={menuItem.menu.elementId + "_nav"}
               href={menuItem.menu.actionURL}
               target={menuItem.menu.openInNewWindow ? "_blank" : ""}
               className="top-level-menu-item"
             >
               {renderSideNavMenuItemLabel(menuItem, level)}
             </SideNavMenuItem>
-          </React.Fragment>
+          </span>
         );
       } else {
         return (
-          <React.Fragment key={path}>
+          <span id={menuItem.menu.elementId} key={path}>
             <SideNavMenuItem
               className="reduced-padding-nav-menu-item"
-              id={menuItem.menu.elementId}
               href={menuItem.menu.actionURL}
               target={menuItem.menu.openInNewWindow ? "_blank" : ""}
               style={{ width: "100%" }}
@@ -277,7 +276,7 @@ function OEHeader(props) {
                 </span>
               );
             })}
-          </React.Fragment>
+          </span>
         );
       }
     } else {
@@ -303,6 +302,7 @@ function OEHeader(props) {
       <button
         className={"custom-sidenav-button"}
         style={{ width: "100%", marginLeft: marginValue }}
+        id={menuItem.menu.elementId + "_nav"}
         onClick={() => {
           if (menuItem.menu.openInNewWindow) {
             window.open(menuItem.menu.actionURL);
@@ -338,6 +338,7 @@ function OEHeader(props) {
     return (
       <>
         <button
+          id={menuItem.menu.elementId + "_nav"}
           className={
             menuItem.menu.actionURL
               ? "custom-sidenav-button"

From 2cbd5850c06face70ce2acfb08406aa73cd6c604 Mon Sep 17 00:00:00 2001
From: CalebSLane <c.steelelane@gmail.com>
Date: Mon, 12 Aug 2024 19:43:18 -0700
Subject: [PATCH 6/6] fix broken reflexes for dictionary

---
 .../testreflex/action/util/TestReflexUtil.java           | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/openelisglobal/testreflex/action/util/TestReflexUtil.java b/src/main/java/org/openelisglobal/testreflex/action/util/TestReflexUtil.java
index b8a5215c7..6b2440240 100644
--- a/src/main/java/org/openelisglobal/testreflex/action/util/TestReflexUtil.java
+++ b/src/main/java/org/openelisglobal/testreflex/action/util/TestReflexUtil.java
@@ -330,7 +330,13 @@ private List<TestReflex> getReflexTests(TestReflexBean reflexBean) {
         if (reflexBean.getResult().getTestResult() == null) {
             return new ArrayList<>();
         }
-        List<TestReflex> reflexesForResult = reflexResolver.getTestReflexesForResult(reflexBean.getResult());
+        String resultType = testService.getResultType(reflexBean.getResult().getTestResult().getTest());
+        List<TestReflex> reflexesForResult;
+        if (resultType.equals("D")) {
+            reflexesForResult = reflexResolver.getTestReflexsByAnalyteAndTest(reflexBean.getResult());
+        } else {
+            reflexesForResult = reflexResolver.getTestReflexesForResult(reflexBean.getResult());
+        }
         reflexesForResult = reflexesForResult.stream()
                 .filter(e -> isTestTriggeredByResult(e.getAddedTest(), reflexBean.getResult()))
                 .collect(Collectors.toList());
@@ -876,6 +882,7 @@ public boolean doesDictionaryRelationRulesForReflexApply(Test potentialReflexTes
                     }
                 }
             }
+
             return false;
 
         });