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

GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.10-17.11.sql

@@ -0,0 +1,45 @@
+/*
+ * Copyright (c) 2011 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (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.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+CREATE TABLE geneticscore.taqman_probes (
+  rowid serial,
+  probe varchar(100),
+  target varchar(1000),
+
+  container ENTITYID,
+  created TIMESTAMP,
+  createdby USERID,
+  modified TIMESTAMP,
+  modifiedby USERID,
+
+  CONSTRAINT PK_taqman_probes PRIMARY KEY (rowid)
+);
+
+CREATE TABLE geneticscore.test_significance (
+  rowid serial,
+  probe varchar(100),
+  genotype varchar(100),
+  label varchar(1000),
+  comment varchar(4000),
+
+  container ENTITYID,
+  created TIMESTAMP,
+  createdby USERID,
+  modified TIMESTAMP,
+  modifiedby USERID,
+
+  CONSTRAINT PK_test_significance PRIMARY KEY (rowid)
+);

GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.10-17.11.sql

@@ -0,0 +1,45 @@
+/*
+ * Copyright (c) 2011 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (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.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+CREATE TABLE geneticscore.taqman_probes (
+  rowid int identity(1,1),
+  probe varchar(100),
+  target varchar(1000),
+
+  container ENTITYID,
+  created DATETIME,
+  createdby USERID,
+  modified DATETIME,
+  modifiedby USERID,
+
+  CONSTRAINT PK_taqman_probes PRIMARY KEY (rowid)
+);
+
+CREATE TABLE geneticscore.test_significance (
+  rowid int identity(1,1),
+  probe varchar(100),
+  genotype varchar(100),
+  label varchar(1000),
+  comment varchar(4000),
+
+  container ENTITYID,
+  created DATETIME,
+  createdby USERID,
+  modified DATETIME,
+  modifiedby USERID,
+
+  CONSTRAINT PK_test_significance PRIMARY KEY (rowid)
+);

GeneticsCore/resources/schemas/geneticscore.xml

@@ -58,6 +58,74 @@
             </ns:column>
             <ns:column columnName="modifiedby">
 
+            </ns:column>
+        </ns:columns>
+    </ns:table>
+    <ns:table tableName="taqman_probes" tableDbType="TABLE">
+        <ns:javaCustomizer>org.labkey.ldk.query.DefaultTableCustomizer</ns:javaCustomizer>
+        <ns:tableTitle>Taqman Probes</ns:tableTitle>
+        <ns:pkColumnName>rowId</ns:pkColumnName>
+        <ns:columns>
+            <ns:column columnName="rowid">
+                <ns:columnTitle>Row Id</ns:columnTitle>
+            </ns:column>
+            <ns:column columnName="probe">
+
+            </ns:column>
+            <ns:column columnName="target">
+
+            </ns:column>
+            <ns:column columnName="container">
+                <ns:columnTitle>Folder</ns:columnTitle>
+            </ns:column>
+            <ns:column columnName="created">
+
+            </ns:column>
+            <ns:column columnName="createdby">
+
+            </ns:column>
+            <ns:column columnName="modified">
+
+            </ns:column>
+            <ns:column columnName="modifiedby">
+
+            </ns:column>
+        </ns:columns>
+    </ns:table>
+    <ns:table tableName="test_significance" tableDbType="TABLE">
+        <ns:javaCustomizer>org.labkey.ldk.query.DefaultTableCustomizer</ns:javaCustomizer>
+        <ns:tableTitle>Genetic Test Significance</ns:tableTitle>
+        <ns:pkColumnName>rowId</ns:pkColumnName>
+        <ns:columns>
+            <ns:column columnName="rowid">
+                <ns:columnTitle>Row Id</ns:columnTitle>
+            </ns:column>
+            <ns:column columnName="probe">
+
+            </ns:column>
+            <ns:column columnName="genotype">
+
+            </ns:column>
+            <ns:column columnName="label">
+
+            </ns:column>
+            <ns:column columnName="comment">
+
+            </ns:column>
+            <ns:column columnName="container">
+                <ns:columnTitle>Folder</ns:columnTitle>
+            </ns:column>
+            <ns:column columnName="created">
+
+            </ns:column>
+            <ns:column columnName="createdby">
+
+            </ns:column>
+            <ns:column columnName="modified">
+
+            </ns:column>
+            <ns:column columnName="modifiedby">
+
             </ns:column>
         </ns:columns>
     </ns:table>

GeneticsCore/src/org/labkey/GeneticsCore/GeneticsCoreModule.java

@@ -39,7 +39,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 17.10;
+        return 17.11;
     }
 
     @Override

GeneticsCore/src/org/labkey/GeneticsCore/notification/GeneticsCoreNotification.java

@@ -106,6 +106,7 @@ public String getMessageBodyHTML(Container c, User u)
         getParentageFreezerSamplesNotFlagged(c, u, msg);
 
         getParentageConflicts(c, u, msg);
+        getAncestryConflicts(c, u, msg);
 
         return msg.toString();
     }
@@ -157,6 +158,18 @@ public void getParentageConflicts(Container c, User u, StringBuilder msg)
         }
     }
 
+    public void getAncestryConflicts(Container c, User u, StringBuilder msg)
+    {
+        TableInfo ti = QueryService.get().getUserSchema(u, c, "study").getTable("geneticAncestryConflicts");
+        TableSelector ts = new TableSelector(ti, PageFlowUtil.set("Id"));
+        long count = ts.getRowCount();
+        if (count > 0)
+        {
+            ActionURL url = QueryService.get().urlFor(u, c, QueryAction.executeQuery, "study", "geneticAncestryConflicts");
+            msg.append("<b>WARNING: There are " + count + " animals with duplicate or conflicting genetic ancestry calls.</b><p>  <a href='" + AppProps.getInstance().getBaseServerUrl() + url.toString() + "'>Click here to view these animals</a><hr>");
+        }
+    }
+
     public void getActiveExclusions(Container c, User u, StringBuilder msg, String flag, int interval)
     {
         SimpleFilter filter = new SimpleFilter();

ONPRC_EHR_ComplianceDB/module.properties

@@ -0,0 +1,3 @@
+Name: ONPRC_EHR_ComplianceDB
+ModuleClass: org.labkey.api.module.SimpleModule
+ModuleDependencies: EHR_ComplianceDB

ONPRC_EHR_ComplianceDB/resources/queries/EHR_ComplianceDB/Measles45DayAlert.query.xml

@@ -0,0 +1,49 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="Measles45DayAlert" tableDbType="NOT_IN_DB">
+                <tableTitle>Measles 45 Day Overdue Report</tableTitle>
+                <columns>
+                    <column columnName="employeeId">
+                        <isKeyField>true</isKeyField>
+                        <fk>
+                            <fkDbSchema>ehr_compliancedb</fkDbSchema>
+                            <fkTable>employees</fkTable>
+                            <fkColumnName>employeeId</fkColumnName>
+                        </fk>
+                    </column>
+                    <column columnName="requirementName">
+                        <columnTitle>Requirement Name</columnTitle>
+                        <fk>
+                            <fkDbSchema>ehr_compliancedb</fkDbSchema>
+                            <fkTable>requirements</fkTable>
+                            <fkColumnName>requirementName</fkColumnName>
+                        </fk>
+                        <facetingBehavior>ALWAYS_OFF</facetingBehavior>
+                    </column>
+                    <column columnName="DaysOverDue">
+                        <conditionalFormats>
+                            <conditionalFormat>
+                                <filters>
+                                    <filter operator="gte" value="0"/>
+                                    <filter operator="lte" value="14"/>
+                                </filters>
+                                <backgroundColor>E3170D</backgroundColor>
+                            </conditionalFormat>
+                            <conditionalFormat>
+                                <filters>
+                                    <filter operator="gte" value="15"/>
+                                </filters>
+                                <backgroundColor>FBEC5D</backgroundColor>
+                            </conditionalFormat>
+                        </conditionalFormats>
+                    </column>
+                    <column columnName="isRequired">
+                        <columnTitle>Is Required?</columnTitle>
+                        <facetingBehavior>ALWAYS_OFF</facetingBehavior>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

ONPRC_EHR_ComplianceDB/resources/queries/EHR_ComplianceDB/Measles45DayAlert.sql

@@ -0,0 +1,47 @@
+SELECT
+	emp.employeeid,
+	emp.Name,
+	emp.email,
+	emp.unit,
+	emp.category,
+	emp.location,
+	emp.majorudds,
+	emp.notes,
+	emp.requirementname,
+	--c.date,
+	Case
+       When (c.requirementname is null) Then emp.date
+       When (c.requirementname is not null) Then c.date
+       ELSE ''
+	End AS DateCompleted,
+	emp.comment,
+	emp.trainer,
+	Case
+       When (c.requirementname is null) Then TIMESTAMPDIFF('SQL_TSI_DAY', emp.date, now())
+       When (c.requirementname is not null) Then '-1'
+       ELSE ''
+	End as DaysOverDue
+	FROM ehr_compliancedb.completiondates c
+	RIGHT JOIN (
+       SELECT
+       c1.employeeid,
+       emp.email,
+       emp.Firstname + ' ' + emp.Lastname as Name,
+       emp.unit,
+       emp.category,
+       emp.location,
+       emp.majorudds,
+       emp.notes,
+       emp.isActive,
+       c1.requirementname,
+       c1.date,
+       c1.result,
+       c1.comment,
+       c1.trainer
+       FROM ehr_compliancedb.completiondates c1, ehr_compliancedb.employees emp
+       Where c1.employeeid = emp.employeeid
+       And c1.requirementname like 'Occupational Health - Measles Compliant - Initial'
+       And emp.endDate is null
+       ) emp
+	ON c.employeeid = emp.employeeid
+	And c.requirementname like 'Occupational Health - Measles Compliant'

ONPRC_EHR_ComplianceDB/resources/queries/EHR_ComplianceDB/employees.query.xml

@@ -0,0 +1,30 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="employees" tableDbType="NOT_IN_DB">
+                <tableTitle>Employees</tableTitle>
+                <columns>
+                    <column columnName="majorudds">
+                        <columnTitle>Host</columnTitle>
+                    </column>
+                    <!--<column columnName="barrier">-->
+                    <!--<columnTitle>West Campus Level 1</columnTitle>-->
+                    <!--</column>-->
+                    <!--<column columnName="animals">-->
+                    <!--<columnTitle>West Campus Level 2</columnTitle>-->
+                    <!--</column>-->
+                    <!--<column columnName="contactsSla">-->
+                    <!--<columnTitle>West Campus Level 3</columnTitle>-->
+                    <!--</column>-->
+                    <!--<column columnName="tissue">-->
+                    <!--<columnTitle>West Campus Level 4</columnTitle>-->
+                    <!--</column>-->
+                    <!--<column columnName="isemployee">-->
+                    <!--<isHidden>true</isHidden>-->
+                    <!--</column>-->
+
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

ONPRC_EHR_ComplianceDB/resources/queries/EHR_ComplianceDB/employees/.qview.xml

@@ -0,0 +1,27 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView">
+    <columns>
+        <column name="employeeid"/>
+        <column name="lastName"/>
+        <column name="firstName"/>
+        <column name="middleName"/>
+        <column name="email"/>
+        <column name="personid"/>
+        <column name="type"/>
+        <column name="majorudds"/>
+        <column name="title"/>
+        <column name="unit"/>
+        <column name="supervisor"/>
+        <column name="emergencycontact" />
+        <column name="emergencycontactdaytimephone" />
+        <column name="emergencycontactnighttimephone" />
+        <column name="category"/>
+        <column name="location"/>
+        <column name="startdate"/>
+        <column name="enddate"/>
+        <column name="notes"/>
+    </columns>
+    <sorts>
+        <sort column="lastName" descending="false"/>
+        <sort column="firstName" descending="false"/>
+    </sorts>
+</customView>

ONPRC_EHR_ComplianceDB/resources/queries/EHR_ComplianceDB/requirements.query.xml

@@ -0,0 +1,23 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="Requirements" tableDbType="NOT_IN_DB">
+                <tableTitle>Requirements</tableTitle>
+                <columns>
+                    <!--<column columnName="access">-->
+                    <!--<columnTitle>West Campus Level 1</columnTitle>-->
+                    <!--</column>-->
+                    <!--<column columnName="animals">-->
+                    <!--<columnTitle>West Campus Level 2</columnTitle>-->
+                    <!--</column>-->
+                    <!--<column columnName="contactsSla">-->
+                    <!--<columnTitle>West Campus Level 3</columnTitle>-->
+                    <!--</column>-->
+                    <!--<column columnName="tissues">-->
+                    <!--<columnTitle>West Campus Level 4</columnTitle>-->
+                    <!--</column>-->
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>