Use new signature (#74)

Author: labkey-adam

OpenLdapSync/module.properties

@@ -3,5 +3,4 @@ Label: Open LDAP Sync
 Description: This module can be used to sync LabKey users with an LDAP server
 License: Apache 2.0
 LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
-ConsolidateScripts: false
 ManageVersion: false

OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSyncRunner.java

@@ -62,7 +62,6 @@
 import static org.labkey.openldapsync.ldap.LdapSettings.FIRSTNAME_FIELD_PROP;
 
 /**
- * Created with IntelliJ IDEA.
  * User: bimber
  * Date: 1/21/13
  * Time: 5:18 PM
@@ -568,14 +567,14 @@ private void initPreviouslySyncedRecords()
         SimpleFilter filter = new SimpleFilter(FieldKey.fromString("provider"), _wrapper.getProviderName(), CompareType.EQUAL);
         TableSelector ts = new TableSelector(ti, filter, null);
 
-        ts.forEach(new Selector.ForEachBlock<LdapSyncModel>()
+        ts.forEach(LdapSyncModel.class, new Selector.ForEachBlock<LdapSyncModel>()
         {
             @Override
             public void exec(LdapSyncModel model)
             {
                 _syncedRecordMap.put(model.getSourceId(), model);
             }
-        }, LdapSyncModel.class);
+        });
     }
 
     private User createUser(LdapEntry ldapEntry) throws LdapException

SequenceAnalysis/module.properties

@@ -1,3 +1,2 @@
 ModuleClass: org.labkey.sequenceanalysis.SequenceAnalysisModule
-ConsolidateScripts: false
 ManageVersion: false

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java

@@ -2,7 +2,6 @@
 
 import org.apache.commons.io.FileUtils;
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
@@ -220,7 +219,7 @@ private void processContainer(Container c, Logger log) throws IOException
             TableInfo tableRefNtSequences = SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_REF_NT_SEQUENCES);
             TableSelector ntTs = new TableSelector(tableRefNtSequences, new SimpleFilter(FieldKey.fromString("container"), c.getId()), null);
             final Set<String> expectedSequences = new HashSet<>(10000, 1000);
-            ntTs.forEach(m -> {
+            ntTs.forEach(RefNtSequenceModel.class, m -> {
                 if (m.getSequenceFile() == null || m.getSequenceFile() == 0)
                 {
                     log.error("sequence record lacks a sequence file Id: " + m.getRowid());
@@ -244,7 +243,7 @@ private void processContainer(Container c, Logger log) throws IOException
                 {
                     expectedSequences.add(d.getFile().getName());
                 }
-            }, RefNtSequenceModel.class);
+            });
 
             if (sequenceDir.exists())
             {

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java

@@ -839,10 +839,10 @@ public void apppendSequenceLength(User u, Logger log)
         TableSelector ts = new TableSelector(ti, PageFlowUtil.set("rowid", "sequenceFile"), new SimpleFilter(FieldKey.fromString("seqLength"), null, CompareType.ISBLANK), null);
 
         log.info(ts.getRowCount() + " total sequences to migrate");
-        ts.forEach(new Selector.ForEachBlock<RefNtSequenceModel>()
+        ts.forEach(RefNtSequenceModel.class, new Selector.ForEachBlock<>()
         {
             @Override
-            public void exec(RefNtSequenceModel nt) throws SQLException, StopIteratingException
+            public void exec(RefNtSequenceModel nt) throws StopIteratingException
             {
                 try (InputStream is = nt.getSequenceInputStream())
                 {
@@ -864,7 +864,7 @@ public void exec(RefNtSequenceModel nt) throws SQLException, StopIteratingExcept
                     stopIterating();
                 }
             }
-        }, RefNtSequenceModel.class);
+        });
     }
 
     public static class TestCase extends Assert

blast/module.properties

@@ -1,3 +1,2 @@
 ModuleClass: org.labkey.blast.BLASTModule
-ConsolidateScripts: false
 ManageVersion: false

cluster/module.properties

@@ -3,5 +3,4 @@ Label: Cluster
 Description: This module enables integration between the LabKey pipeline and clusters, including HTCondor and Slurm clusters
 License: Apache 2.0
 LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
-ConsolidateScripts: false
 ManageVersion: false

jbrowse/module.properties

@@ -1,3 +1,2 @@
 ModuleClass: org.labkey.jbrowse.JBrowseModule
-ConsolidateScripts: false
 ManageVersion: false

omerointegration/module.properties

@@ -1,5 +1,4 @@
 ModuleClass: org.labkey.omerointegration.OmeroIntegrationModule
 License: Apache 2.0
 LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
-ConsolidateScripts: false
 ManageVersion: false