Merge remote-tracking branch 'origin/develop' into fb_long_is_the_new_int

Author: labkey-matthewb

EHR_App/test/src/org/labkey/test/tests/EHR_AppTest.java

@@ -12,6 +12,8 @@
 import org.labkey.test.util.PostgresOnlyTest;
 
 import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
 
 @Category({EHR.class})
 public class EHR_AppTest extends AbstractGenericEHRTest implements PostgresOnlyTest
@@ -120,6 +122,17 @@ public void preTest()
         goToEHRFolder();
     }
 
+    @Override
+    protected List<String> skipLinksForValidation()
+    {
+        List<String> links = new ArrayList<>(super.skipLinksForValidation());
+        links.add("Issue_Tracker");
+        links.add("ehr-colonyOverview.view");
+        links.add("ehr-updateTable.view");
+        links.add("ehr-populateLookupData.view");
+        return links;
+    }
+
     @Test
     public void testSteps()
     {

Viral_Load_Assay/resources/schemas/dbscripts/postgresql/Viral_Load_Assay-0.00-11.10.sql

@@ -34,10 +34,12 @@ CREATE TABLE Viral_Load_Assay.assays
 -- ----------------------------
 -- Records of assays
 -- ----------------------------
+-- @SkipOnEmptySchemasBegin
 INSERT INTO Viral_Load_Assay.assays
 (assayName, virus)
 VALUES
 ('SIVmac239-Gag', 'SIVmac239');
+-- @SkipOnEmptySchemasEnd
 
 -- ----------------------------
 -- Table structure for vl_category
@@ -71,8 +73,10 @@ WITH (OIDS=FALSE);
 -- ----------------------------
 -- Records of vl_instrument
 -- ----------------------------
+-- @SkipOnEmptySchemasBegin
 INSERT INTO Viral_Load_Assay.vl_instrument VALUES ('LC480');
 INSERT INTO Viral_Load_Assay.vl_instrument VALUES ('Light Cycler');
+-- @SkipOnEmptySchemasEnd
 
 -- ----------------------------
 -- Table structure for vl_sampletype
@@ -105,7 +109,9 @@ WITH (OIDS=FALSE);
 -- ----------------------------
 -- Records of vl_technique
 -- ----------------------------
+-- @SkipOnEmptySchemasBegin
 INSERT INTO Viral_Load_Assay.vl_technique VALUES ('Lifson 1-Step VL');
+-- @SkipOnEmptySchemasEnd
 
 -- ----------------------------
 -- Table structure for vl_virus
@@ -122,5 +128,3 @@ WITH (OIDS=FALSE);
 -- Records of vl_virus
 -- ----------------------------
 INSERT INTO Viral_Load_Assay.vl_virus VALUES ('SIVmac239');
-
-

Viral_Load_Assay/resources/schemas/dbscripts/postgresql/Viral_Load_Assay-12.20-12.21.sql

@@ -13,6 +13,9 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+
+-- @SkipOnEmptySchemasBegin
 INSERT INTO viral_load_assay.vl_instrument VALUES ('ABI 7500');
+-- @SkipOnEmptySchemasEnd
 
 DROP TABLE viral_load_assay.vl_category;

Viral_Load_Assay/resources/schemas/dbscripts/postgresql/Viral_Load_Assay-12.22-12.23.sql

@@ -13,4 +13,6 @@ CREATE TABLE viral_load_assay.fluors (
   constraint PK_fluors PRIMARY KEY (name)
 );
 
-INSERT INTO viral_load_assay.fluors (name) VALUES ('FAM');
+-- @SkipOnEmptySchemasBegin
+INSERT INTO viral_load_assay.fluors (name) VALUES ('FAM');
+-- @SkipOnEmptySchemasEnd

Viral_Load_Assay/resources/schemas/dbscripts/postgresql/Viral_Load_Assay-12.26-12.27.sql

@@ -1,6 +1,8 @@
+-- @SkipOnEmptySchemasBegin
 INSERT INTO viral_load_assay.vl_instrument (instrument)
   SELECT 'LC96'
   WHERE
     NOT EXISTS (
         SELECT instrument FROM viral_load_assay.vl_instrument WHERE instrument = 'LC96'
-    );
+    );
+-- @SkipOnEmptySchemasEnd

Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/ViralLoadAssayDataProvider.java

@@ -34,12 +34,6 @@
 import java.util.List;
 import java.util.Set;
 
-/**
- * Created with IntelliJ IDEA.
- * User: bimber
- * Date: 9/28/12
- * Time: 4:17 PM
- */
 public class ViralLoadAssayDataProvider extends AbstractAssayDataProvider
 {
     public ViralLoadAssayDataProvider(Module m)

…ditLog/audit/EHR Client Errors.qview.xml … API Actions/EHR Client Errors.qview.xmlehr/resources/queries/auditLog/audit/EHR Client Errors.qview.xml renamed to ehr/resources/queries/auditLog/Client API Actions/EHR Client Errors.qview.xml ehr/resources/queries/auditLog/audit/EHR Client Errors.qview.xml renamed to ehr/resources/queries/auditLog/Client API Actions/EHR Client Errors.qview.xml

@@ -3,15 +3,12 @@
         <column name="CreatedBy"/>
         <column name="Date"/>
         <column name="EventType"/>
-        <column name="Key1"/>
-        <column name="Key2"/>
-        <!--<column name="Key3"/>-->
-
+        <column name="SubType"/>
+        <column name="String1"/>
         <column name="Comment" />
     </columns>
     <filters>
-        <filter column="EventType" operator="eq" value="Client API Actions"/>
-        <filter column="Key1" operator="neqornull" value="LabKey Server Backup" />
+        <filter column="SubType" operator="neqornull" value="LabKey Server Backup" />
     </filters>
    <sorts>
        <sort column="Date" descending="true"/>

ehr/resources/schemas/dbscripts/postgresql/ehr-0.000-24.000.sql

@@ -276,6 +276,7 @@ CREATE TABLE ehr.notificationTypes
     CONSTRAINT PK_notificationTypes PRIMARY KEY (NotificationType)
 );
 
+-- @SkipOnEmptySchemasBegin
 INSERT into ehr.notificationTypes
 (NotificationType, description)
 VALUES
@@ -285,6 +286,7 @@ VALUES
 ('Animal Care Service Request', ''),
 ('Colony Validation - General', 'Subscribing to this notification will result in emails for general colony records issues like records needing attention, animals missing from the demographics table, etc.')
 ;
+-- @SkipOnEmptySchemasEnd
 
 CREATE TABLE ehr.notificationRecipients
 (
@@ -407,6 +409,7 @@ CREATE TABLE ehr.qcStateMetadata
     CONSTRAINT PK_qcStateMetadata PRIMARY KEY (QCStateLabel)
 );
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO ehr.qcStateMetadata
 (QCStateLabel,draftData,isDeleted,isRequest)
 VALUES
@@ -421,6 +424,7 @@ VALUES
 ('Request: Approved', TRUE, FALSE, TRUE),
 ('Request: Complete', FALSE, FALSE, TRUE)
 ;
+-- @SkipOnEmptySchemasEnd
 
 DROP TABLE IF EXISTS ehr.module_properties;
 
@@ -507,12 +511,14 @@ ALTER TABLE ehr.reports
   add column description varchar(4000)
 ;
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO ehr.qcStateMetadata
 (QCStateLabel,draftData,isDeleted,isRequest)
 VALUES
 ('Completed', FALSE, FALSE, FALSE),
 ('Scheduled', TRUE, FALSE, FALSE)
 ;
+-- @SkipOnEmptySchemasEnd
 
 ALTER TABLE ehr.formTypes ADD COLUMN configJson text;
 
@@ -601,6 +607,7 @@ ALTER table ehr.qcStateMetadata
 
 DELETE from ehr.qcStateMetadata;
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO ehr.qcStateMetadata
 (QCStateLabel,DraftData,isDeleted,isRequest,allowFutureDates)
 VALUES
@@ -616,6 +623,7 @@ VALUES
 ('Request: Complete', FALSE, FALSE, TRUE, TRUE),
 ('Scheduled', TRUE, FALSE, FALSE, TRUE)
 ;
+-- @SkipOnEmptySchemasEnd
 
 UPDATE ehr.qcStateMetadata
 SET DraftData = FALSE
@@ -625,10 +633,12 @@ ALTER table ehr.reports
   add column sort_order integer
   ;
 
+-- @SkipOnEmptySchemasBegin
 insert into ehr.notificationtypes
 (notificationtype,description) VALUES
 ('Incompleted Treatments', 'An email will be sent each day at 8:30, 15:30 and 20:30 notifying of any incompleted treatments')
 ;
+-- @SkipOnEmptySchemasEnd
 
 CREATE TABLE ehr.automatic_alerts (
     rowid serial not null,
@@ -685,13 +695,15 @@ UPDATE ehr.qcStateMetadata
 SET DraftData = TRUE
 WHERE QCStateLabel = 'Review Requested';
 
+-- @SkipOnEmptySchemasBegin
 insert into ehr.notificationtypes
 (notificationtype,description) VALUES
 ('Blood Draw Request Completed', 'An email will be sent each time a blood draw request is completed'),
 ('Blood Draw Request Denied', 'An email will be sent each time a blood draw request is denied'),
 ('Clinpath Request Completed', 'An email will be sent each time a clinpath request is completed'),
 ('Clinpath Request Denied', 'An email will be sent each time a clinpath request is denied')
 ;
+-- @SkipOnEmptySchemasEnd
 
 alter TABLE ehr.notificationRecipients
   add column Recipient2 integer
@@ -779,10 +791,12 @@ alter TABLE ehr.protocol
   add column maxAnimals integer
 ;
 
+-- @SkipOnEmptySchemasBegin
 insert into ehr.notificationtypes
 (notificationtype,description) VALUES
 ('Prenatal Death', 'An email will be sent each time a prenatal death is reported')
 ;
+-- @SkipOnEmptySchemasEnd
 
 delete from ehr.notificationtypes where notificationtype in (
 'Clinpath Abnormal Results',
@@ -803,6 +817,7 @@ delete from ehr.notificationtypes where notificationtype in (
 
 delete from ehr.notificationtypes where notificationtype = 'Colony Validation - General';
 
+-- @SkipOnEmptySchemasBegin
 insert into ehr.notificationtypes
 (notificationtype,description) VALUES
 ('Clinpath Abnormal Results', 'An email will be sent periodically to summarize abnormal clinpath results'),
@@ -819,6 +834,7 @@ insert into ehr.notificationtypes
 ('Overdue Weight Alerts', 'An email will be sent daily to summarize animals overdue for weights.'),
 ('Site Error Alerts', 'An hourly email will be sent if a new site error is reported.')
 ;
+-- @SkipOnEmptySchemasEnd
 
 drop TABLE ehr.client_errors;
 
@@ -1263,8 +1279,10 @@ ALTER TABLE ehr.reports ADD subjectIdFieldName varchar(200);
 
 ALTER TABLE ehr.project ADD alwaysavailable bool;
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO ehr.qcstateMetadata (QCStateLabel,draftData,isDeleted,isRequest)
 VALUES ('Request: Sample Delivered', TRUE, FALSE, TRUE);
+-- @SkipOnEmptySchemasEnd
 
 CREATE TABLE ehr.protocolexemptions (
   rowid SERIAL,
@@ -1337,7 +1355,9 @@ CREATE INDEX snomed_tags_taskid ON ehr.snomed_tags (taskid);
 
 CREATE INDEX treatment_times_container_treatmentid ON ehr.treatment_times (container, treatmentid);
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO ehr.qcStateMetadata (QCStateLabel,DraftData,isDeleted,isRequest,allowFutureDates) VALUES ('Request: Cancelled', false, false, true, true);
+-- @SkipOnEmptySchemasEnd
 
 ALTER TABLE ehr.project ADD projecttype varchar(100);
 
@@ -1634,6 +1654,7 @@ DROP FUNCTION ehr.handleAddContactToProtocol();
 DELETE FROM ehr.qcStateMetadata WHERE QCStateLabel = 'Started';
 DELETE FROM ehr.status WHERE Label = 'Started';
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO ehr.qcStateMetadata
     (QCStateLabel,draftData,isDeleted,isRequest)
 VALUES
@@ -1642,7 +1663,7 @@ INSERT INTO ehr.status
     (label,Description,PublicData,DraftData,isDeleted,isRequest,allowFutureDates)
 VALUES
        ('Started', 'Record has started, but not completed',TRUE,FALSE,FALSE,FALSE,FALSE);
-
+-- @SkipOnEmptySchemasEnd
 
 -- ehr-17.21-17.22.sql
 -- contents of ehr-17.21-17.22.sql script are not in rolled up ehr-0.00-18.10.sql, since they got added and merged after the rollup.
@@ -1781,6 +1802,7 @@ DROP FUNCTION ehr.addConstraintToFormFrameworkTypes();
 DELETE FROM ehr.qcStateMetadata WHERE QCStateLabel = 'Request: On Hold';
 DELETE FROM ehr.status WHERE Label = 'Request: On Hold';
 
+-- @SkipOnEmptySchemasBegin
 INSERT INTO ehr.qcStateMetadata
 (QCStateLabel, draftData, isDeleted, isRequest, allowFutureDates)
 VALUES
@@ -1790,6 +1812,7 @@ INSERT INTO ehr.status
 (label, description, publicData, draftData, isDeleted, isRequest, allowFutureDates)
 VALUES
 ('Request: On Hold', 'Request has been put on hold', FALSE, FALSE, FALSE, TRUE, TRUE);
+-- @SkipOnEmptySchemasEnd
 
 CREATE INDEX snomed_tags_recordid ON ehr.snomed_tags (recordid);