[bot] Fast-forward for 25.7.19

.gitignore

@@ -33,6 +33,8 @@ snprc_ehr/.editorconfig
 snprc_ehr/resources/referenceStudy/LoadTaqmanData
 snprc_ehr/resources/referenceStudy/datasetImport/LoadTaqmanData
 snprc_scheduler/.gradle
+snprc_scheduler/resources/views/gen
+snprc_scheduler/resources/web/gen
 snprc_ehr/resources/credits
 */resources/credits/dependencies.txt
 */resources/credits/jars.txt

snprc_ehr/resources/etls/SndPackagesAndSuperPkgs.xml

@@ -33,11 +33,6 @@
             <description>Copy to Staging table</description>
             <source schemaName="snprcSrc" queryName="v_sndGetAllSuperPkgs" />
             <destination schemaName="snprc_ehr" queryName="SndSuperPackageStaging" bulkLoad="true" targetOption="merge">
-                <alternateKeys>
-                    <column name="TopLevelPkgId"/>
-                    <column name = "SuperPkgId"/>
-                    <column name="ObjectId"/>
-                </alternateKeys>
                 <columnTransforms>
                     <column source="createdBy" target="createdBy" transformClass="org.labkey.snprc_ehr.columnTransforms.UserTransform"/>
                     <column source="modifiedBy" target="modifiedBy" transformClass="org.labkey.snprc_ehr.columnTransforms.UserTransform"/>

snprc_ehr/resources/queries/snprc_ehr/HL7BiochemistryPivot.query.xml

@@ -2,7 +2,14 @@
     <metadata>
         <tables xmlns="http://labkey.org/data/xml">
             <table tableName="HL7BiochemistryPivot" tableDbType="NOT_IN_DB">
+                <javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
                 <tableTitle>Biochemistry Results Pivot</tableTitle>
+                <columns>
+                    <column columnName="Key">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
+                 </columns>
             </table>
         </tables>
     </metadata>

snprc_ehr/resources/queries/snprc_ehr/HL7BiochemistryPivot.sql

@@ -1,6 +1,7 @@
 SELECT
     obr.ANIMAL_ID as id,
     obr.OBSERVATION_DATE_TM as date,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
     obr.MESSAGE_ID,
     COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
     obr.PROCEDURE_ID,
@@ -20,6 +21,6 @@ GROUP BY obr.ANIMAL_ID, obr.OBSERVATION_DATE_TM, obr.MESSAGE_ID, COALESCE (lp.Se
 
     IN
     (
-    select DISTINCT TestName as TEST_NAME from snprc_ehr.labwork_panels t
+    select DISTINCT ltrim(Rtrim(TestName)) as TEST_NAME from snprc_ehr.labwork_panels t
     where t.includeInPanel = true AND t.ServiceId.Dataset='Biochemistry'
     )

snprc_ehr/resources/queries/snprc_ehr/HL7BiochemistryPivot/RoutineChemistry.qview.xml

@@ -0,0 +1,43 @@
+<!-- $S is the escape code for / -->
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+    <columns>
+        <column name="Id"/>
+        <column name="Date"/>
+        <column name="CREATININE::RESULT"/>
+        <column name="CREATININE::ABNORMAL_FLAGS"/>
+        <column name="GLUCOSE::RESULT"/>
+        <column name="GLUCOSE::ABNORMAL_FLAGS"/>
+        <column name="BUN$SCREAT RATIO::RESULT"/>
+        <column name="BUN$SCREAT RATIO::ABNORMAL_FLAGS"/>
+        <column name="TOTAL PROTEIN::RESULT"/>
+        <column name="TOTAL PROTEIN::ABNORMAL_FLAGS"/>
+        <column name="ALBUMIN::RESULT"/>
+        <column name="ALBUMIN::ABNORMAL_FLAGS"/>
+        <column name="GLOBULIN (CALC)::RESULT"/>
+        <column name="GLOBULIN (CALC)::ABNORMAL_FLAGS"/>
+        <column name="A$SG RATIO (CALC)::RESULT"/>
+        <column name="A$SG RATIO (CALC)::ABNORMAL_FLAGS"/>
+        <column name="ALT $S SGPT::RESULT"/>
+        <column name="ALT $S SGPT::ABNORMAL_FLAGS"/>
+        <column name="AST $S SGOT::RESULT"/>
+        <column name="AST $S SGOT::ABNORMAL_FLAGS"/>
+        <column name="ALK PHOSPHATASE::RESULT"/>
+        <column name="ALK PHOSPHATASE::ABNORMAL_FLAGS"/>
+        <column name="SODIUM::RESULT"/>
+        <column name="SODIUM::ABNORMAL_FLAGS"/>
+        <column name="POTASSIUM::RESULT"/>
+        <column name="POTASSIUM::ABNORMAL_FLAGS"/>
+        <column name="CHLORIDE::RESULT"/>
+        <column name="CHLORIDE::ABNORMAL_FLAGS"/>
+        <column name="CARBON DIOXIDE::RESULT"/>
+        <column name="CARBON DIOXIDE::ABNORMAL_FLAGS"/>
+        <column name="ANION GAP (CALC)::RESULT"/>
+        <column name="ANION GAP (CALC)::ABNORMAL_FLAGS"/>
+        <column name="COMMENT"/>
+    </columns>
+    <sorts>
+        <sort column="Id"/>
+        <sort column="Date" descending="true"/>
+    </sorts>
+</customView>
+

snprc_ehr/resources/queries/snprc_ehr/HL7CulturePivot.query.xml

@@ -2,7 +2,14 @@
     <metadata>
         <tables xmlns="http://labkey.org/data/xml">
             <table tableName="HL7CulturePivot" tableDbType="NOT_IN_DB">
+                <javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
                 <tableTitle>Culture and Sensitivity Results Pivot</tableTitle>
+                <columns>
+                    <column columnName="Key">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
+                </columns>
             </table>
         </tables>
     </metadata>

snprc_ehr/resources/queries/snprc_ehr/HL7CulturePivot.sql

@@ -1,6 +1,7 @@
 SELECT
     obr.ANIMAL_ID as id,
     obr.OBSERVATION_DATE_TM as date,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
     obr.MESSAGE_ID,
     COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
     obr.PROCEDURE_ID,

snprc_ehr/resources/queries/snprc_ehr/HL7HematologyPivot.query.xml

@@ -2,7 +2,14 @@
     <metadata>
         <tables xmlns="http://labkey.org/data/xml">
             <table tableName="HL7HematologyPivot" tableDbType="NOT_IN_DB">
+                <javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
                 <tableTitle>Hematology Pivot</tableTitle>
+                <columns>
+                    <column columnName="Key">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
+                </columns>
             </table>
         </tables>
     </metadata>

snprc_ehr/resources/queries/snprc_ehr/HL7HematologyPivot.sql

@@ -1,6 +1,7 @@
 SELECT
     obr.ANIMAL_ID as id,
     obr.OBSERVATION_DATE_TM as date,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
     obr.MESSAGE_ID,
     COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
     obr.PROCEDURE_ID,

snprc_ehr/resources/queries/snprc_ehr/HL7HistologyPivot.query.xml

@@ -2,7 +2,14 @@
     <metadata>
         <tables xmlns="http://labkey.org/data/xml">
             <table tableName="HL7HistologyPivot" tableDbType="NOT_IN_DB">
+                <javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
                 <tableTitle>Histology Pivot</tableTitle>
+                <columns>
+                    <column columnName="Key">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
+                </columns>
             </table>
         </tables>
     </metadata>

snprc_ehr/resources/queries/snprc_ehr/HL7HistologyPivot.sql

@@ -1,5 +1,6 @@
 SELECT obr.ANIMAL_ID as id,
        obr.OBSERVATION_DATE_TM as date,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
     obr.MESSAGE_ID,
     COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
     obr.PROCEDURE_ID,

snprc_ehr/resources/queries/snprc_ehr/HL7MiscPivot.query.xml

@@ -2,7 +2,14 @@
     <metadata>
         <tables xmlns="http://labkey.org/data/xml">
             <table tableName="HL7MiscPivot" tableDbType="NOT_IN_DB">
+                <javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
                 <tableTitle>Misc Tests Pivot</tableTitle>
+                <columns>
+                    <column columnName="Key">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
+                </columns>
             </table>
         </tables>
     </metadata>

snprc_ehr/resources/queries/snprc_ehr/HL7MiscPivot.sql

@@ -1,5 +1,6 @@
 SELECT obr.ANIMAL_ID as id,
        obr.OBSERVATION_DATE_TM as date,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
     obr.MESSAGE_ID,
     COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
     obr.PROCEDURE_ID,

snprc_ehr/resources/queries/snprc_ehr/HL7ParasitologyPivot.query.xml

@@ -2,7 +2,14 @@
     <metadata>
         <tables xmlns="http://labkey.org/data/xml">
             <table tableName="HL7ParasitologyPivot" tableDbType="NOT_IN_DB">
+                <javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
                 <tableTitle>Parasitology Pivot</tableTitle>
+                <columns>
+                    <column columnName="Key">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
+                </columns>
             </table>
         </tables>
     </metadata>

snprc_ehr/resources/queries/snprc_ehr/HL7ParasitologyPivot.sql

@@ -1,5 +1,6 @@
 SELECT obr.ANIMAL_ID as id,
        obr.OBSERVATION_DATE_TM as date,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
     obr.MESSAGE_ID,
     COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
     obr.PROCEDURE_ID,

snprc_ehr/resources/queries/snprc_ehr/HL7SurveillancePivot.query.xml

@@ -2,11 +2,16 @@
     <metadata>
         <tables xmlns="http://labkey.org/data/xml">
             <table tableName="HL7SurveillancePivot" tableDbType="NOT_IN_DB">
+                <javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
                 <tableTitle>Surveillance Pivot</tableTitle>
                 <columns>
                     <column columnName="PROCEDURE_NAME">
                         <isHidden>true</isHidden>
                     </column>
+                    <column columnName="Key">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
                 </columns>
             </table>
         </tables>

snprc_ehr/resources/queries/snprc_ehr/HL7SurveillancePivot.sql

@@ -1,14 +1,15 @@
-select Id,
-    date,
-    PROCEDURE_NAME,
-    PROCEDURE_ID,
-    COMMENT,
-    TestName,
-    MAX(ABNORMAL_FLAGS) as ABNORMAL_FLAGS,
-    COALESCE(MAX(RESULT), GROUP_CONCAT(QUALITATIVE_RESULT)) as RESULT
-from snprc_ehr.HL7SurveillancePivotInner
+select spi.Id,
+    spi.date,
+    spi.Id || '-' || CAST(spi.date AS VARCHAR) as key,
+    spi.PROCEDURE_NAME,
+    spi.PROCEDURE_ID,
+    spi.COMMENT,
+    spi.TestName,
+    MAX(spi.ABNORMAL_FLAGS) as ABNORMAL_FLAGS,
+    COALESCE(MAX(spi.RESULT), GROUP_CONCAT(spi.QUALITATIVE_RESULT)) as RESULT
+from snprc_ehr.HL7SurveillancePivotInner as spi
 
-GROUP BY id, date, PROCEDURE_NAME,  PROCEDURE_NAME, PROCEDURE_ID, COMMENT, TestName
+GROUP BY spi.id, spi.date, spi.PROCEDURE_NAME,  spi.PROCEDURE_NAME, spi.PROCEDURE_ID, spi.COMMENT, spi.TestName
     PIVOT RESULT, ABNORMAL_FLAGS BY TestName
 
     IN

snprc_ehr/resources/queries/snprc_ehr/HL7UnknownPivot.query.xml

@@ -2,7 +2,14 @@
     <metadata>
         <tables xmlns="http://labkey.org/data/xml">
             <table tableName="HL7UnknownPivot" tableDbType="NOT_IN_DB">
+                <javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
                 <tableTitle>Unknown Panel Category Pivot</tableTitle>
+                <columns>
+                    <column columnName="Key">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
+                </columns>
             </table>
         </tables>
     </metadata>

snprc_ehr/resources/queries/snprc_ehr/HL7UnknownPivot.sql

@@ -1,6 +1,7 @@
 SELECT
     obr.ANIMAL_ID as id,
     obr.OBSERVATION_DATE_TM as date,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
     obr.MESSAGE_ID,
     COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
     obr.PROCEDURE_ID,

snprc_ehr/resources/queries/snprc_ehr/HL7Urinalysis.query.xml

@@ -2,7 +2,14 @@
     <metadata>
         <tables xmlns="http://labkey.org/data/xml">
             <table tableName="HL7UrinalysisPivot" tableDbType="NOT_IN_DB">
+                <javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
                 <tableTitle>Urinalysis Pivot</tableTitle>
+                <columns>
+                    <column columnName="Key">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
+                </columns>
             </table>
         </tables>
     </metadata>

snprc_ehr/resources/queries/snprc_ehr/HL7UrinalysisPivot.sql

@@ -1,6 +1,7 @@
 SELECT
     obr.ANIMAL_ID as id,
     obr.OBSERVATION_DATE_TM as date,
+    obr.ANIMAL_ID || '-' || CAST(obr.OBSERVATION_DATE_TM AS VARCHAR) as key,
     obr.MESSAGE_ID,
     COALESCE (lp.ServiceId.ServiceName, obr.PROCEDURE_NAME) as PROCEDURE_NAME,
     obr.PROCEDURE_ID,

snprc_ehr/resources/queries/snprc_ehr/MhcDataPivot.sql

@@ -1,25 +1,26 @@
 SELECT
     b.Id,
+    b.modified,
     b.Haplotype,
     b.Ocid,
     b.DataFileSource,
-    b.modified,
     group_concat(b.MhcValue) as MhcValue
 
+
 FROM (
          SELECT
              b.Id,
              b.Haplotype,
              b.Ocid,
              b.MhcValue,
              b.DataFileSource,
-             b.Modified
+             cast(b.modified as varchar) as modified
          FROM snprc_ehr.MhcData as b
-         ) as b
+     ) as b
 
 GROUP BY b.id, b.ocid, b.DataFileSource, b.haplotype, b.modified
 
-PIVOT MhcValue BY Haplotype IN
-(select distinct Haplotype from snprc_ehr.MhcData order by Haplotype
-
-)
+    PIVOT MhcValue BY Haplotype IN
+(
+    select distinct Haplotype from snprc_ehr.MhcData order by Haplotype
+)

snprc_ehr/resources/queries/study/BrowseDataSets.sql

@@ -68,3 +68,5 @@ UNION
 select 'ehr' as schema, 'Colony Management' as CategoryId,'Kinship' as Label, 'kinship' as Name,  true as ShowByDefault, true as isAnimal
 UNION
 select 'ehr' as schema, 'Colony Management' as CategoryId,'Project' as Label, 'project' as Name,  true as ShowByDefault, false as isAnimal
+UNION
+select 'study' as schema, 'Colony Management' as CategoryId,'Offspring' as Label, 'demographicsOffspring' as Name,  true as ShowByDefault, true as isAnimal

snprc_ehr/resources/queries/study/demographicsEarliestHousing.sql

@@ -0,0 +1,17 @@
+/*
+ * Copyright (c) 2017-2018 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+SELECT
+    d.Id AS Id,
+    h.date as FirstHousingDate,
+    h.room as FirstHousingRoom,
+    h.room.area.description as FirstHousingRoomDescription
+FROM study.demographics d
+
+
+--date of first housing
+LEFT JOIN study.housing as h on h.id = d.id and h.qcstate.publicdata = true
+    and h.date = (select min(c1.date) from study.housing as c1
+                   where h.id = c1.id)

snprc_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml

@@ -394,6 +394,11 @@
                 <datatype>varchar</datatype>
             </column>
         </columns>
+        <indices>
+            <index type="unique">
+                <column>caseid</column>
+            </index>
+        </indices>
         <tableTitle>Cases</tableTitle>
     </table>
     <table tableName="matings" tableDbType="TABLE">
@@ -1498,6 +1503,7 @@
                 <datatype>varchar</datatype>
                 <nullable>false</nullable>
                 <columnTitle>Species code (3 char)</columnTitle>
+                <scale>10</scale>
             </column>
             <column columnName="project">
                 <datatype>integer</datatype>