Merge from onprc19.1 & onprc19.1Prod r.63271 to 65949

EHR_ComplianceDB/resources/queries/ehr_compliancedb/completionDates/.qview.xml

@@ -22,6 +22,7 @@
         <column name="comment"/>
         <column name="trainer"/>
         <column name="employeeid/enddate"/>
+        <column name="FileName"/>
     </columns>
     <sorts>
         <sort column="employeeid/lastName" descending="false"/>

EHR_ComplianceDB/resources/schemas/dbscripts/postgresql/EHR_ComplianceDB-12.38-12.39.sql

@@ -0,0 +1 @@
+ALTER TABLE ehr_compliancedb.CompletionDates ADD COLUMN FileName varchar(500);

EHR_ComplianceDB/resources/schemas/dbscripts/postgresql/EHR_ComplianceDB-12.39-12.40.sql

@@ -0,0 +1 @@
+ALTER TABLE ehr_compliancedb.Employees ALTER COLUMN Notes TYPE VARCHAR (4000);

EHR_ComplianceDB/resources/schemas/dbscripts/sqlserver/EHR_ComplianceDB-12.38-12.39.sql

@@ -0,0 +1 @@
+ALTER TABLE ehr_compliancedb.CompletionDates ADD FileName nvarchar(500);

EHR_ComplianceDB/resources/schemas/dbscripts/sqlserver/EHR_ComplianceDB-12.39-12.40.sql

@@ -0,0 +1,2 @@
+ALTER TABLE ehr_compliancedb.Employees ALTER COLUMN Notes NVARCHAR (4000);
+

EHR_ComplianceDB/resources/schemas/ehr_compliancedb.xml

@@ -93,18 +93,15 @@
             </column>
             <column columnName="lastName">
                 <columnTitle>Last Name</columnTitle>
-                <displayWidth>100</displayWidth>
                 <facetingBehavior>ALWAYS_OFF</facetingBehavior>
             </column>
             <column columnName="firstName">
                 <nullable>true</nullable>
                 <columnTitle>First Name</columnTitle>
-                <displayWidth>100</displayWidth>
                 <facetingBehavior>ALWAYS_OFF</facetingBehavior>
             </column>
             <column columnName="middleName">
                 <columnTitle>Middle Name</columnTitle>
-                <displayWidth>100</displayWidth>
                 <facetingBehavior>ALWAYS_OFF</facetingBehavior>
             </column>
             <column columnName="email">
@@ -201,10 +198,12 @@
             <column columnName="startdate">
                 <nullable>true</nullable>
                 <columnTitle>Start Date</columnTitle>
+                <formatString>Date</formatString>
             </column>
             <column columnName="enddate">
                 <nullable>true</nullable>
                 <columnTitle>End Date</columnTitle>
+                <formatString>Date</formatString>
             </column>
             <column columnName="notes">
                 <nullable>true</nullable>
@@ -511,6 +510,7 @@
             <column columnName="date">
                 <nullable>false</nullable>
                 <columnTitle>Date Completed</columnTitle>
+                <formatString>Date</formatString>
             </column>
             <column columnName="result">
                 <nullable>true</nullable>
@@ -529,6 +529,10 @@
                 <nullable>true</nullable>
                 <columnTitle>Comment</columnTitle>
             </column>
+            <column columnName="FileName">
+                <columnTitle>FileName</columnTitle>
+                <isHidden>false</isHidden>
+            </column>
             <column columnName="container">
                 <isUserEditable>false</isUserEditable>
                 <isHidden>true</isHidden>
@@ -709,6 +713,7 @@
             <column columnName="date">
                 <nullable>true</nullable>
                 <columnTitle>Date Completed</columnTitle>
+                <formatString>Date</formatString>
             </column>
             <column columnName="container">
                 <isUserEditable>false</isUserEditable>

EHR_ComplianceDB/resources/views/publicPage.html

@@ -19,7 +19,13 @@
                 xtype: 'ldk-linkbutton',
                 text: '<li>View Employee List</li>',
                 href: LABKEY.ActionURL.buildURL('query', 'executeQuery', null, {schemaName: 'EmployeeData', 'query.queryName': 'Employees'})
-            },{
+            },
+//                {
+//                xtype: 'ldk-linkbutton',
+//                text: '<li>View Respirator Protection Quarantine Report</li>',
+//                href: LABKEY.ActionURL.buildURL('query', 'executeQuery', null, {schemaName: 'EmployeeData', 'query.queryName': 'RespiratorProtectionQuarantine'})
+//            },
+                {
                 xtype: 'ldk-linkbutton',
                 text: '<li>View Private Section (authorized users only)</li>',
                 href: LABKEY.ActionURL.buildURL('project', 'start', container),

EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/EHR_ComplianceDBModule.java

@@ -49,7 +49,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 12.38;
+        return 12.40;
     }
 
     @Override

ehr/api-src/org/labkey/api/ehr/EHRService.java

@@ -19,19 +19,21 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.AbstractTableInfo;
 import org.labkey.api.data.Container;
+import org.labkey.api.data.CoreSchema;
+import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.TableCustomizer;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.ehr.dataentry.DataEntryForm;
 import org.labkey.api.ehr.dataentry.DataEntryFormFactory;
 import org.labkey.api.ehr.dataentry.SingleQueryFormProvider;
 import org.labkey.api.ehr.demographics.DemographicsProvider;
 import org.labkey.api.ehr.demographics.ProjectValidator;
-import org.labkey.api.ehr.history.HistoryDataSource;
-import org.labkey.api.ehr.history.LabworkType;
+import org.labkey.api.ehr.history.*;
 import org.labkey.api.ldk.table.ButtonConfigFactory;
 import org.labkey.api.module.Module;
 import org.labkey.api.query.BatchValidationException;
 import org.labkey.api.query.DetailsURL;
+import org.labkey.api.query.ExprColumn;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.resource.Resource;
 import org.labkey.api.security.User;
@@ -126,6 +128,32 @@ static public void setInstance(EHRService instance)
     /** @return the project validator set by the EHR module, note a center specific module may have overridden the default */
     abstract public ProjectValidator getProjectValidator();
 
+    public enum EndingOption
+    {
+        /** end date is not set, or any day in the future */
+        activeAfterMidnightTonight(new SQLFragment(" WHEN (CAST(" + ExprColumn.STR_TABLE_ALIAS + ".enddate AS DATE) > {fn curdate()}) THEN " + CoreSchema.getInstance().getSchema().getSqlDialect().getBooleanTRUE())),
+        /** ends anytime today */
+        endsToday(new SQLFragment("WHEN (" + ExprColumn.STR_TABLE_ALIAS + ".enddate IS NOT NULL AND CAST(" + ExprColumn.STR_TABLE_ALIAS + ".enddate AS DATE) = {fn curdate()}) THEN " + CoreSchema.getInstance().getSchema().getSqlDialect().getBooleanTRUE())),
+        /** consider records that start/stop on today's date to be active */
+        allowSameDay(new SQLFragment(" WHEN (" + ExprColumn.STR_TABLE_ALIAS + ".enddate IS NOT NULL AND CAST(" + ExprColumn.STR_TABLE_ALIAS + ".enddate AS DATE) = {fn curdate()} AND CAST(" + ExprColumn.STR_TABLE_ALIAS + ".date as DATE) = {fn curdate()}) THEN " + CoreSchema.getInstance().getSchema().getSqlDialect().getBooleanTRUE())),
+        /** end time must be before right now */
+        endingBeforeNow(new SQLFragment(" WHEN (" + ExprColumn.STR_TABLE_ALIAS + ".enddate >= {fn now()}) THEN " + CoreSchema.getInstance().getSchema().getSqlDialect().getBooleanTRUE()));
+
+        private final SQLFragment _sql;
+
+        EndingOption(SQLFragment sql)
+        {
+            _sql = sql;
+        }
+
+        public SQLFragment getSql()
+        {
+            return _sql;
+        }
+    }
+
+    public abstract void addIsActiveCol(AbstractTableInfo ti, boolean includeExpired, EndingOption... endOptions);
+
     /** Categories where pre-configured reports can be offered to the user */
     public enum REPORT_LINK_TYPE
     {

ehr/api-src/org/labkey/api/ehr/history/DefaultLabworkType.java

@@ -230,6 +230,10 @@ protected String getLine(Results rs, boolean redacted) throws SQLException
         StringBuilder sb = new StringBuilder();
         String testId = getTestId(rs);
         Double result = _resultField == null ?  null : rs.getDouble(FieldKey.fromString(_resultField));
+        if (rs.wasNull())
+        {
+            result = null;
+        }
         String units = _unitsField == null ?  null : rs.getString(FieldKey.fromString(_unitsField));
         String qualResult = _qualResultField == null ?  null : rs.getString(FieldKey.fromString(_qualResultField));
 

ehr/api-src/org/labkey/api/ehr/history/LabworkType.java

@@ -39,4 +39,9 @@ public interface LabworkType
     Map<String, List<String>> getResults(Container c, User u, List<String> runIds, boolean redacted);
 
     Map<String, List<String>> getResults(Container c, User u, String id, Date minDate, Date maxDate, boolean redacted);
+
+    default boolean showPerformedBy()
+    {
+        return true;
+    }
 }

ehr/api-src/org/labkey/api/ehr/table/DurationColumn.java

@@ -17,6 +17,7 @@
 
 import org.apache.commons.lang3.time.DurationFormatUtils;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.DataColumn;
 import org.labkey.api.data.RenderContext;
@@ -32,9 +33,11 @@
 public class DurationColumn extends DataColumn
 {
 
-    String _startDateColumn;
-    String _endDateColumn;
-    private String _durationFormat;
+    protected final String _startDateColumn;
+    protected final String _endDateColumn;
+    private final String _durationFormat;
+
+    private boolean _dropTime;
 
     public DurationColumn(ColumnInfo col, String startDateColumn, String endDateColumn)
     {
@@ -49,6 +52,12 @@ public DurationColumn(ColumnInfo col, String startDateColumn, String endDateColu
         _durationFormat = durationFormat;
     }
 
+    /** Treat all times as if they were at midnight of the same day */
+    public void setDropTime(boolean dropTime)
+    {
+        _dropTime = dropTime;
+    }
+
     @Override
     public Class getDisplayValueClass()
     {
@@ -60,12 +69,24 @@ public Class getDisplayValueClass()
     @Override
     public Object getDisplayValue(RenderContext ctx)
     {
-        return getFormattedDuration((Date)ctx.get(getMappedFieldKey(_startDateColumn)), (Date)ctx.get(getMappedFieldKey(_endDateColumn)));
+        Date startDate = (Date)ctx.get(getMappedFieldKey(_startDateColumn));
+        Date endDate = (Date)ctx.get(getMappedFieldKey(_endDateColumn));
+
+        return getFormattedDuration(startDate, endDate);
+    }
+
+    private void dropTime(@NotNull Calendar cal)
+    {
+        cal.set(Calendar.HOUR_OF_DAY, 0);
+        cal.set(Calendar.MINUTE, 0);
+        cal.set(Calendar.SECOND, 0);
+        cal.set(Calendar.MILLISECOND, 0);
     }
 
-    protected String getFormattedDuration(Date startDate, Date endDate)
+    /** Convert from dates to calendars, dealing with nulls */
+    public final String getFormattedDuration(@Nullable Date startDate, @Nullable Date endDate)
     {
-        if (startDate == null || _durationFormat == null)
+        if (startDate == null)
             return null;
 
         Calendar startCal = Calendar.getInstance();
@@ -74,6 +95,20 @@ protected String getFormattedDuration(Date startDate, Date endDate)
         Calendar endCal = Calendar.getInstance();
         endCal.setTime(endDate == null ? new Date() : endDate);
 
+        if (_dropTime)
+        {
+            // Snap to midnight so that days work based on calendar day instead of 24-hour periods
+            dropTime(startCal);
+            dropTime(endCal);
+        }
+        return getFormattedDuration(startCal, endCal);
+    }
+
+    protected String getFormattedDuration(@NotNull Calendar startCal, @NotNull Calendar endCal)
+    {
+        if (_durationFormat == null)
+            return null;
+
         String formattedDuration;
         try
         {
@@ -113,24 +148,4 @@ protected FieldKey getMappedFieldKey(String colName)
     {
         return new FieldKey(getBoundColumn().getFieldKey().getParent(), colName);
     }
-
-    public String getStartDateColumn()
-    {
-        return _startDateColumn;
-    }
-
-    public void setStartDateColumn(String startDateColumn)
-    {
-        _startDateColumn = startDateColumn;
-    }
-
-    public String getEndDateColumn()
-    {
-        return _endDateColumn;
-    }
-
-    public void setEndDateColumn(String endDateColumn)
-    {
-        _endDateColumn = endDateColumn;
-    }
 }

ehr/resources/queries/study/treatment_order.query.xml

@@ -62,6 +62,11 @@
                             <fkDbSchema>ehr_lookups</fkDbSchema>
                             <fkTable>treatment_frequency</fkTable>
                             <fkColumnName>rowid</fkColumnName>
+                            <filters>
+                                <filterGroup>
+                                    <filter column="active" operator="eq" value="true"/> <!-- filter applied only during insert and update, will not be used during grid view -->
+                                </filterGroup>
+                            </filters>
                         </fk>
                     </column>
                     <column columnName="route">

ehr/resources/reports/schemas/study/Pedigree/Pedigree.r

@@ -13,10 +13,10 @@ library(Rlabkey)
 #str(labkey.data);
 #warnings();
 
-labkey.acceptSelfSignedCerts();
+labkey.setCurlOptions(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)
 
 
-if ((length(labkey.data$id) == 0) | (is.na(labkey.data$dam) & is.na(labkey.data$sire))){
+if ((length(labkey.data$id) == 0) || all(is.na(labkey.data$dam) & is.na(labkey.data$sire))) {
     png(filename="${imgout:myscatterplot}", width = 650, height = 150);
     plot(0, 0, type='n', xaxt='n', yaxt='n', bty='n', ann=FALSE  )
     title(main = "No pedigree data found for selected animal(s).", sub = NULL, xlab = NULL, ylab = NULL,
@@ -200,17 +200,17 @@ if ((length(labkey.data$id) == 0) | (is.na(labkey.data$dam) & is.na(labkey.data$
         if (length(damIndex) == 0) damIndex <- which(allPed$Id == ped$Dam[i]);
         if (length(sireIndex) == 0) sireIndex <- which(allPed$Id == ped$Sire[i]);
 
-        if((is.na(ped$Sire[i]))& (!is.na(ped$Dam[i]))){
-            xt <- sample (1:30,1)
+        if(is.na(ped$Sire[i])){
+            xt <- sample (1:99,1)
             #typeof(ped$Sire);
             #typeof(xt);
             ped$Sire[i] <- paste('xxs',xt)
             ped$Sire[i] <- paste (ped$Sire[i], "Unknown Sire", sep="\n")
             #print(ped$Dam[i])
             #print(ped$Sire[i])
         }
-        if((is.na(ped$Dam[i]))& (!is.na(ped$Sire[i]))){
-                xt <- sample (1:30,1)
+        if(is.na(ped$Dam[i])){
+                xt <- sample (1:99,1)
                 #typeof(ped$Sire);
                 #typeof(xt);
                 ped$Dam[i] <- paste ('xxd',xt);

ehr/resources/schemas/ehr_lookups.xml

@@ -2637,7 +2637,9 @@
                     <fkColumnName>entityid</fkColumnName>
                 </fk>
             </column>
-            <column columnName="datedisabled" />
+            <column columnName="datedisabled">
+                <columnTitle>Date Disabled</columnTitle>
+            </column>
         </columns>
     </table>
     <table tableName="labwork_services" tableDbType="TABLE" useColumnOrder="true">

ehr/resources/views/groupOverlaps.html

@@ -162,8 +162,11 @@
                 return;
             }
 
+            // By Kollil, 3/22/2018 : In 17.2 the filter is not working. Removed the the line 168 and added the filterArray at line 169.
+            // The Animal group search is working fine now after this change.
             if (groupName)
-                config.removeableFilters = [LABKEY.Filter.create('groupId/name', groupName, LABKEY.Filter.Types.EQUAL)];
+                //config.removeableFilters = [LABKEY.Filter.create('groupId/name', groupName, LABKEY.Filter.Types.EQUAL)];
+                config.filterArray = [LABKEY.Filter.create('groupId/name', groupName, LABKEY.Filter.Types.EQUAL)];
 
             var params = {
                 StartDate: start,
@@ -172,7 +175,8 @@
 
             config.parameters = params;
 
-            LDK.Utils.getReadOnlyQWP(config).render(this.qwpDiv.id);
+            LDK.Utils.getReadOnlyQWP(config);
+
         }
 
     });

ehr/resources/views/housingOverlaps.html

@@ -200,7 +200,7 @@
             if (!LABKEY.Utils.isEmptyObj(params))
                 config.parameters = params;
 
-            LDK.Utils.getReadOnlyQWP(config).render(this.qwpDiv.id);
+            LDK.Utils.getReadOnlyQWP(config);
         }
 
     }).render(webpart.wrapperDivId);