Merge WNPRC's wnprc21.3-SNAPSHOT to LabKey's release21.3-SNAPSHOT

.gitignore

@@ -23,8 +23,6 @@ docker/nginx/key.pem
 
 .storybook-out/
 
-docker/ehrcron/scripts/pg_backup/lkbackup.ini
-
 # generated artifacts from @labkey/build
 */resources/web/*/gen/
 */resources/views/gen/

DBUtils/resources/credits/jars.txt

@@ -1,5 +1,5 @@
 {table}
-Filename|Component|Version|Source|License|LabKey Dev|Purpose
+Filename|Component|Version|Source|License|Dev|Purpose
 jooq-3.8.4.jar|jOOQ|3.8.4|{link:From GitHub|https://github.com/jOOQ/jOOQ}|{link:Apache Software License 2.0|http://www.apache.org/licenses/LICENSE-2.0}|jrichardson|Database-mapping for Java
 jaxb-api-2.3.0.jar|jaxb|2.3.0|Oracle|{link:CDDL 1.1|https://oss.oracle.com/licenses/CDDL+GPL-1.1}{link:GPL2w/ CPE|https://oss.oracle.com/licenses/CDDL+GPL-1.1}|klum|Parsing XML
 {table}

DeviceProxy/resources/credits/jars.txt

@@ -1,5 +1,5 @@
 {table}
-Filename|Component|Version|Source|License|LabKey Dev|Purpose
+Filename|Component|Version|Source|License|Dev|Purpose
 jooq-3.8.4.jar|jOOQ|3.8.4|{link:From GitHub|https://github.com/jOOQ/jOOQ}|{link:Apache Software License 2.0|http://www.apache.org/licenses/LICENSE-2.0}|jrichardson|Database-mapping for Java
 jaxb-api-2.3.0.jar|Java Architecture for XML Binding (JAXB)|2.3.0|Oracle|{link:CDDL|https://oss.oracle.com/licenses/CDDL}|klum|Parsing XML
 {table}

GoogleDrive/resources/credits/jars.txt

@@ -1,5 +1,5 @@
 {table}
-Filename|Component|Version|Source|License|LabKey Dev|Purpose
-google-api-client-1.22.0.jar|Google APIs Client Library for Java|1.22.0|{link:From GitHub|https://github.com/google/google-api-java-client}|{link:Apache Software License 2.0|http://www.apache.org/licenses/LICENSE-2.0}|jrichardson|Used to connect to Google Drive
+Filename|Component|Version|Source|License|WNPRC Dev|Purpose
+google-api-client-1.23.0.jar|Google APIs Client Library for Java|1.23.0|{link:From GitHub|https://github.com/google/google-api-java-client}|{link:Apache Software License 2.0|http://www.apache.org/licenses/LICENSE-2.0}|jrichardson|Used to connect to Google Drive
 google-api-services-drive-v3-rev85-1.23.0.jar|Google Drive API Client Library for Java|v3 rev85 1.23.0|{link:From Google|https://developers.google.com/api-client-library/java/apis/drive/v3}|{link:Apache Software License 2.0|http://www.apache.org/licenses/LICENSE-2.0}|jrichardson|Used to connect to Google Drive
 {table}

WNPRC_Compliance/module.properties

@@ -4,6 +4,6 @@ License: Apache 2.0
 LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
 ModuleClass: org.labkey.wnprc_compliance.WNPRC_ComplianceModule
 Name: WNPRC_Compliance
-SchemaVersion: 20.000
+SchemaVersion: 21.001
 SupportedDatabases: pgsql
 ManageVersion: false

WNPRC_Compliance/resources/credits/jars.txt

@@ -1,5 +1,5 @@
 {table}
-Filename|Component|Version|Source|License|LabKey Dev|Purpose
+Filename|Component|Version|Source|License|WNPRC Dev|Purpose
 jooq-3.8.4.jar|jOOQ|3.8.4|{link:From GitHub|https://github.com/jOOQ/jOOQ}|{link:Apache Software License 2.0|http://www.apache.org/licenses/LICENSE-2.0}|jrichardson|Database-mapping for Java
 pdfbox-2.0.11.jar|Apache PDFBox|2.0.11|{link:From Apache|http://svn.apache.org/repos/asf/pdfbox/trunk/}|{link:Apache Software License 2.0|http://www.apache.org/licenses/LICENSE-2.0}|jrichardson|Generates and manipulates PDFs
 {table}

WNPRC_Compliance/resources/schemas/dbscripts/postgresql/wnprc_compliance-21.000-21.001.sql

@@ -0,0 +1,5 @@
+ALTER TABLE wnprc_compliance.measles_clearances ADD COLUMN IF NOT EXISTS required BOOLEAN DEFAULT true;
+
+ALTER TABLE wnprc_compliance.persons ADD COLUMN IF NOT EXISTS hold BOOLEAN DEFAULT false;
+--update measles_required from wnprc_compliance.measles_clearances using labkey javascript API
+ALTER TABLE wnprc_compliance.persons ADD COLUMN IF NOT EXISTS measles_required BOOLEAN DEFAULT false;

WNPRC_Compliance/resources/schemas/wnprc_compliance.xml

@@ -106,6 +106,8 @@
       <column columnName="modified"/>
       <column columnName="archived_for_access_purposes"/>
       <column columnName="date_of_birth"/>
+      <column columnName="hold"/>
+      <column columnName="measles_required"/>
     </columns>
   </table>
   <table tableName="measles_clearances" tableDbType="TABLE">

WNPRC_Compliance/src/org/labkey/wnprc_compliance/view/unidentifiedCards.jsp

@@ -217,7 +217,7 @@
         WebUtils.VM.submitMarkExempt = function() {
             $exemptDialog.modal('hide');
             var cardData = ko.mapping.toJS(WebUtils.VM.form);
-            WebUtils.API.postJSON("<%=q(urlFor(MarkCardExemptAPI.class))%>", {
+            WebUtils.API.postJSON(<%=q(urlFor(MarkCardExemptAPI.class))%>, {
                         cardId: cardData.selectedCard[0],
                         reason: cardData.notes
             }).then(function(d) {
@@ -236,7 +236,7 @@
 
             //TODO validate here...
             //TODO not sure how this $parent selectedPerson really works here?
-            WebUtils.API.postJSON("<%=q(urlFor(WNPRC_ComplianceController.LinkCardAPI.class))%>", {
+            WebUtils.API.postJSON(<%=q(urlFor(WNPRC_ComplianceController.LinkCardAPI.class))%>, {
                 cardId: cardData.selectedCard[0],
                 personId: personData.selectedPerson
             }).then(function(d) {
@@ -285,7 +285,7 @@
                     } else {
                         // knockout wasn't playing nice here, using jQuery to force button to disabled
                         $(document).on('click', '#radio-person', function () {
-                            $('#link-card-button').removeProp('disabled');
+                            $('#link-card-button').prop('disabled', false);
                         });
                     }
                     WebUtils.VM.listPersons.userMatches((PERSONS in results) ? results[PERSONS] : []);

WNPRC_EHR/resources/credits/jars.txt

@@ -1,6 +1,14 @@
 {table}
-Filename|Component|Version|Source|License|LabKey Dev|Purpose
+Filename|Component|Version|Source|License|WNPRC Dev|Purpose
 joda-time-2.8.1.jar|Joda-Time|2.8.1|{link:From GitHub|https://github.com/JodaOrg/joda-time}|{link:Apache Software License 2.0|http://www.apache.org/licenses/LICENSE-2.0}|jrichardson|Tools for dealing with dates/times in Java
-jsoup-1.10.3.jar|jsoup: Java HTML Parser|1.10.3|{link:From GitHub|https://github.com/jhy/jsoup}|{link:MIT License|https://opensource.org/licenses/MIT}|jricharson|Tools for parsing and manipulating HTML and CSS using the DOM
+jsoup-1.13.1.jar|jsoup: Java HTML Parser|1.10.3|{link:From GitHub|https://github.com/jhy/jsoup}|{link:MIT License|https://opensource.org/licenses/MIT}|jricharson|Tools for parsing and manipulating HTML and CSS using the DOM
 reflections-0.9.10.jar|Reflections|0.9.10|{link:From GitHub|https://github.com/ronmamo/reflections}|{link:WTFPL|http://www.wtfpl.net/about/}|cstevens|Runtime analysis of Java classes and packages
-{table}
+google-api-client-1.23.0.jar|Google API Client for Java|1.30.5|{link:GitHub|https://github.com/googleapis/google-api-java-client}|{link:Apache License 2.0|https://github.com/googleapis/google-api-java-client/blob/master/LICENSE}|ggottfredsen|Library to interact with Google APIs
+google-api-services-calendar-v3-rev255-1.23.0.jar|Google Calendar API Client Library for Java|v3-rev20210708-1.32.1|{link:GitHub|https://github.com/googleapis/google-api-java-client-services/tree/master/clients/google-api-services-calendar/v3}|{link:Apache License 2.0|http://www.apache.org/licenses/LICENSE-2.0}|ggottfredsen|Library for interacting with Google Calendars in Java
+google-http-client-gson-1.23.0.jar|Google HTTP Client Library for Java|1.39.2-sp.1|{link:GitHub|https://github.com/googleapis/google-http-java-client/tree/master/google-http-client-gson}|{link:Apache License 2.0|https://github.com/googleapis/google-http-java-client/blob/master/LICENSE}|ggottfredsen|A flexible, efficient, and powerful Java library for accessing any resource on the web via HTTP
+google-auth-library-oauth2-http-0.19.0.jar|Google Auth Library|1.0.0|{link:GitHub|https://github.com/googleapis/google-auth-library-java/tree/master/oauth2_http}|{link:BSD 3-Clause "New" or "Revised" License|https://github.com/googleapis/google-auth-library-java/blob/master/LICENSE}|ggottfredsen|Contains a wide variety of credentials as well as utility methods to create them and to get Application Default Credentials
+commons-text-1.9.jar|Apache Commons Text|1.9|{link:GitHub|https://github.com/apache/commons-text}|{link:Apache License 2.0|https://github.com/apache/commons-text/blob/master/LICENSE.txt}|ggottfredsen|A library focused on algorithms working on strings
+msal4j-1.11.0.jar|Microsoft Authentication Library (MSAL) for Java|1.11.0|{link:GitHub|https://github.com/AzureAD/microsoft-authentication-library-for-java}|{link:MIT License|https://github.com/AzureAD/microsoft-authentication-library-for-java/blob/dev/LICENSE}|ggottfredsen|Allows to sign in users or apps with Microsoft identities (Azure AD, Microsoft accounts and Azure AD B2C accounts) and obtain tokens to call Microsoft APIs such as Microsoft Graph
+microsoft-graph-2.10.0.jar|Microsoft Graph Java SDK|2.10.0|{link:GitHub|https://github.com/microsoftgraph/msgraph-sdk-java}|{link:MIT License|https://github.com/microsoftgraph/msgraph-sdk-java/blob/dev/LICENSE}|ggottfredsen|Allows for interacting with Microsoft Graph (Calendars/User Accounts/Email/etc.)
+slf4j-nop-1.8.0-beta4.jar|Simple Logging Facade for Java|1.8.0-beta4|{link:GitHub|https://github.com/qos-ch/slf4j/tree/master/slf4j-nop}|{link:MIT License|https://github.com/qos-ch/slf4j/blob/master/LICENSE.txt}|ggottfredsen|Abstraction for various logging frameworks allowing for plugging in a desired framework at deployment time
+{table}

WNPRC_EHR/resources/queries/study/Biopsy/.qview.xml

@@ -6,6 +6,7 @@
        <column name="remark" />
        <column name="type" />
        <column name="nhpbmd" />
+       <column name="billingComplete"/>
        <column name="grossdescription" />
        <column name="performedby" />
        <column name="veterinarian" />

WNPRC_EHR/resources/queries/study/Demographics.query.xml

@@ -81,6 +81,12 @@
                         <!--</fk>-->
                         <url>/ehr/participantView.view?participantId=${dam}</url>
                     </column>
+                    <column columnName="dam_old">
+                        <isHidden>true</isHidden>
+                    </column>
+                    <column columnName="sire_old">
+                        <isHidden>true</isHidden>
+                    </column>
                     <column columnName="sire">
                         <columnTitle>Sire</columnTitle>
                         <!--<fk>-->
@@ -92,6 +98,9 @@
                     </column>
                     <column columnName="origin/source">
                     </column>
+                    <column columnName="origin_old">
+                        <isHidden>true</isHidden>
+                    </column>
                     <column columnName="birth">
                         <formatString>yyyy-MM-dd</formatString>
                         <!--<shownInInsertView>false</shownInInsertView>-->
@@ -102,6 +111,9 @@
                             query.Id~eq=${Id}
                         </url>
                     </column>
+                    <column columnName="birth_old">
+                        <isHidden>true</isHidden>
+                    </column>
                     <column columnName="death">
                         <formatString>yyyy-MM-dd</formatString>
                         <!--<shownInInsertView>false</shownInInsertView>-->
@@ -214,6 +226,9 @@
                     </column>
                     <column columnName="geographic_origin">
                     </column>
+                    <column columnName="geographic_origin_old">
+                        <isHidden>true</isHidden>
+                    </column>
                     <!--<column columnName="behavior">
                         <isHidden>true</isHidden>
                         <shownInInsertView>false</shownInInsertView>

WNPRC_EHR/resources/queries/study/Pedigree.sql

@@ -42,7 +42,8 @@ END
 AS status,
 d.calculated_status as status_code,
 'Demographics' as source,
-d.species as Species
+d.species as Species,
+d.created AS date
 
 --d.qcstate
 
@@ -79,7 +80,8 @@ CAST(p.departdate AS SQL_VARCHAR) as status_code,
 --'Rhesus' as Species
 --null as qcstate
 
-p.species AS species
+p.species AS species,
+COALESCE(p.created,p.modified) AS date
 
 FROM ehr.supplemental_pedigree p
 LEFT JOIN study.demographics d ON (d.id=p.id)

WNPRC_EHR/resources/queries/study/R24DemographicsSrc.sql

@@ -41,7 +41,11 @@ SELECT
   d.dam,
   d.sire,
   d.modified as modified,
-  curdate() as date
+  curdate() as date,
+  CASE d.participantid.activeAssignments.projects
+    WHEN '20210102' THEN true
+    ELSE false
+  END AS U24_Animals
 FROM study.demographics d
 
 LEFT OUTER JOIN study.demographics as ih on d.id = ih.id and ih.origin.code in

WNPRC_EHR/resources/queries/study/WaterOrders.query.xml

@@ -0,0 +1,64 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="waterOrders" tableDbType="TABLE" useColumnOrder="true">
+                <tableUrl />
+                <insertUrl />
+                <importUrl />
+                <updateUrl />
+                <deleteUrl />
+                <columns>
+                    <column columnName="Id">
+
+                    </column>
+                    <column columnName="date">
+                        <columnTitle>Start Date</columnTitle>
+                        <formatString>yyyy-MM-dd hh:mm</formatString>
+                    </column>
+                    <column columnName="enddate">
+                        <columnTitle>End Date</columnTitle>
+                        <formatString>yyyy-MM-dd</formatString>
+                    </column>
+                    <column columnName="volume">
+                        <columnTitle>Water Volume (mL)</columnTitle>
+                    </column>
+                    <column columnName="frequency">
+                        <columnTitle>Frequency</columnTitle>
+                        <fk>
+                            <fkDbSchema>wnprc</fkDbSchema>
+                            <fkTable>husbandry_frequency</fkTable>
+                            <fkColumnName>rowid</fkColumnName>
+                            <fkDisplayColumnName>Meaning</fkDisplayColumnName>
+                        </fk>
+                    </column>
+                    <column columnName="assignedTo">
+                        <columnTitle>Assigned To</columnTitle>
+                        <fk>
+                            <fkDbSchema>ehr_lookups</fkDbSchema>
+                            <fkTable>husbandry_assigned</fkTable>
+                            <fkColumnName>value</fkColumnName>
+                        </fk>
+                    </column>
+                    <column columnName="waterSource">
+                        <columnTitle>Water Source</columnTitle>
+                        <fk>
+                            <fkDbSchema>ehr_lookups</fkDbSchema>
+                            <fkTable>water_source</fkTable>
+                            <fkColumnName>value</fkColumnName>
+                            <fkDisplayColumnName>title</fkDisplayColumnName>
+                        </fk>
+                    </column>
+                    <column columnName="provideFruit">
+                        <columnTitle>Provide Fruit</columnTitle>
+                        <fk>
+                            <fkDbSchema>ehr_lookups</fkDbSchema>
+                            <fkTable>husbandry_fruit</fkTable>
+                            <fkColumnName>value</fkColumnName>
+                        </fk>
+                    </column>
+
+            </columns>
+        </table>
+    </tables>
+</metadata>
+        </query>

WNPRC_EHR/resources/queries/study/WaterOrders/.qview.xml

@@ -0,0 +1,20 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+   <columns>
+       <column name="Id" />
+       <column name="date" />
+       <column name="endDate" />
+       <column name="volume" />
+       <column name="frequency" />
+       <column name="waterSource"/>
+       <column name="assignedTo"/>
+       <column name="provideFruit"/>
+       <column name="qcstate" />
+       <column name="taskid" />
+   </columns>
+   <sorts>
+       <sort column="date" descending="true"/>
+   </sorts>
+  <!--<filters>-->
+      <!--<filter column="qcstate/publicdata" operator="eq" value="true"/>-->
+  <!--</filters>-->
+</customView>

WNPRC_EHR/resources/queries/study/WaterOrders/activeWaterOrders.qview.xml

@@ -0,0 +1,20 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+    <columns>
+        <column name="Id" />
+        <column name="date" />
+        <column name="endDate" />
+        <column name="volume" />
+        <column name="frequency" />
+        <column name="waterSource"/>
+        <column name="assignedTo"/>
+        <column name="provideFruit"/>
+        <column name="qcstate" />
+        <column name="taskid" />
+    </columns>
+    <sorts>
+        <sort column="date" descending="true"/>
+    </sorts>
+    <filters>
+        <filter column="enddatecoalescedfuture" operator="dategte" value="+0d"/>
+    </filters>
+</customView>

WNPRC_EHR/resources/queries/study/WaterRecentWeight.sql

@@ -0,0 +1,27 @@
+SELECT
+voGi.id,
+CAST (voGi.date AS DATE) AS Date,
+voGi.volume,
+voGi.RecentWeight,
+voGi.InnerWeight,
+voGi.objectid
+--voGi.DayDiff
+
+FROM (
+
+SELECT
+    wa.id AS id,
+    wa.date AS date,
+    wa.volume,
+    (SELECT we.weight
+        FROM study.weight we
+        --INNER JOIN study.weight wein
+        --ON we.id = wein.id
+        WHERE we.id = wa.id AND we.date = (SELECT MAX(wen.date) from study.weight wen WHERE wen.id=wa.id AND timestampdiff('SQL_TSI_DAY',wa.date,wen.date)<=0))AS InnerWeight,
+    (SELECT MAX(wen.date)  from study.weight wen WHERE wen.id=wa.id AND timestampdiff('SQL_TSI_DAY',wa.date,wen.date)<=0) AS RecentWeight,
+    wa.objectid
+    --timestampdiff('SQL_TSI_DAY',wa.date ,wa.RecentWeight) AS DayDiff
+
+    FROM study.waterGiven wa
+) voGi
+--GROUP BY voGi.id, voGi.date,voGi.RecentWeight,voGi.InnerWeight

WNPRC_EHR/resources/queries/study/WaterScheduleWithWeight.sql

@@ -0,0 +1,41 @@
+SELECT
+    lsid AS lsid,
+    objectid AS objectIdCoalesced,
+    taskid AS taskid,
+    project AS projectCoalesced,
+    animalId AS animalId,
+    room || '-' || cage  AS location,
+    date AS date,
+    dateOrdered AS dateOrdered,
+    startDateCoalesced AS startDateCoalesced,
+    volume AS volume,
+    provideFruit AS provideFruit,
+    provideFruitTitle AS provideFruitTitle,
+    dataSource AS dataSource,
+    assignedTo AS assignedToCoalesced,
+    assignedToTitle AS assignedToTitleCoalesced,
+    frequency AS frequencyCoalesced,
+    frequencyMeaning AS frequencyMeaningCoalesced,
+    timeofday AS timeofday,
+    displaytimeofday AS displaytimeofday,
+    qcstate AS qcstate,
+
+    --(SELECT max(wg.qcstate) as label FROM study.waterGiven wg WHERE WCO.objectid = wg.treatmentid AND WCO.dateOrdered = wg.dateordered ) AS waterStatus,
+   -- (SELECT timestampdiff(SQL_TSI_HOUR,WCO.date,wg.dateordered ) as diff FROM study.waterGiven wg WHERE WCO.objectid = wg.treatmentid  ) AS difference,
+
+    (SELECT wg.weight AS weightAtDate
+        FROM study.weight wg
+        WHERE wg.id = WCO.animalId AND CAST(substring(CAST(wg.date AS VARCHAR) , 1, 10) AS DATE) <= WCO.date
+        ORDER BY wg.date DESC
+        LIMIT 1
+    ) AS weightAtDate,
+
+    (SELECT wg.date AS weightDate
+        FROM study.weight wg
+        WHERE wg.id = WCO.animalId AND CAST(substring(CAST(wg.date AS VARCHAR) , 1, 10) AS DATE) <= WCO.date
+        ORDER BY wg.date DESC
+        LIMIT 1
+    ) AS weightDate
+
+FROM study.waterScheduleCoalesced WCO
+--WHERE WCO.dateRangeStartDate >= curdate()

WNPRC_EHR/resources/queries/study/biopsy.query.xml

@@ -15,6 +15,9 @@
                   <column columnName="nhpbmd">
                       <columnTitle>NHPBMD</columnTitle>
                   </column>
+                  <column columnName="billingComplete">
+                      <columnTitle>Billing Complete</columnTitle>
+                  </column>
                   <column columnName="remark">
                       <columnTitle>Final Summary Comments</columnTitle>
                   </column>