Merge pull request #186 from antolinos/issue_185

Issue 185

README.md

@@ -1,7 +1,13 @@
 # ISPyB Project [![Build Status](https://travis-ci.org/antolinos/ispyb.png)](https://travis-ci.org/antolinos/ispyb)
 
 
-## Installing
+1. [Installing](#installing)
+2. [Versioning](#versioning)
+3. [Database creation and update](#database-creation-and-update)
+4. [Database schema](#database-schema)
+5. [Graylog on Widlfly 8.2](#graylog)
+
+# Installing
 
 1. Clone or fork the ISPyB repository and then clone it by typing:
 ```
@@ -147,3 +153,41 @@ Please do not forget to update the database schema :
  https://github.com/ispyb/ISPyB/blob/master/documentation/database/ISPyB_DataModel_5.mwb 
 
 This schema can be updated using MySQLWorkbench (free tool from MySQL).
+
+
+### Graylog
+
+Download [biz.paluch.logging](http://logging.paluch.biz) that provides logging to logstash using the Graylog Extended Logging Format (GELF) 1.0 and 1.1. 
+
+Then create a custom handler on standalone.xml
+```
+  <profile>
+        <subsystem xmlns="urn:jboss:domain:logging:2.0">
+	...
+	<custom-handler name="GelfLogger" class="biz.paluch.logging.gelf.wildfly.WildFlyGelfLogHandler" module="biz.paluch.logging">
+		<level name="INFO"/>
+		<properties>
+		    <property name="host" value="udp:graylog-dau.esrf.fr"/>
+		    <property name="port" value="12201"/>
+		    <property name="version" value="1.0"/>
+		    <property name="facility" value="ispyb-test"/>
+		    <property name="timestampPattern" value="yyyy-MM-dd"/>
+		</properties>
+	</custom-handler>
+	...
+	<logger category="ispyb">
+		<level name="INFO"/>
+		<handlers>
+		    <handler name="ISPYB"/>
+		    <handler name="GelfLogger"/>
+		</handlers>
+	</logger>
+```
+
+I had some problems with the unvalid messages because of timestapPatter. It was fixed by using:
+```
+<property name="timestampPattern" value="yyyy-MM-dd"/>
+```
+
+
+

ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3Service.java

@@ -175,6 +175,8 @@ public List<Session3VO> findByStartDateAndBeamLineNameAndNbShifts(final Integer
 	 */
 	public Session3VO findByAutoProcScalingId(final Integer autoProcScalingId) throws Exception;
 
+	public Session3VO findByAutoProcProgramAttachmentId(final Integer autoProcProgramAttachmentId) throws Exception;
+
 	public void protectSession(Integer sessionId) throws Exception;
 
 	/**
@@ -195,6 +197,8 @@ public List<Session3VO> findByStartDateAndBeamLineNameAndNbShifts(final Integer
 	 */
 	public Integer getNbOfTests(final Integer sesId) throws Exception;
 
+	public Session3VO findByAutoProcProgramId(int autoProcProgramId);
+
 
 
 }

ispyb-ejb/src/main/java/ispyb/server/common/services/sessions/Session3ServiceBean.java

@@ -111,6 +111,19 @@ private static final String FIND_ALL(boolean fetchDataCollectionGroup, boolean f
 			+ " where s.sessionId = g.sessionId and  " + " g.dataCollectionGroupId = c.dataCollectionGroupId and "
 			+ " c.dataCollectionId = api.dataCollectionId and " + " api.autoProcIntegrationId = apshi.autoProcIntegrationId and "
 			+ " apshi.autoProcScalingId = aps.autoProcScalingId and " + " aps.autoProcScalingId = :autoProcScalingId ";
+
+	private static final String FIND_BY_AUTOPROCPROGRAMATTACHMENT_ID = "select s.* from BLSession s, "
+			+ " DataCollectionGroup g, DataCollection c, AutoProcIntegration api, AutoProcProgram autoprocProgram, AutoProcProgramAttachment autoProcProgramAttachment"
+			+ " where s.sessionId = g.sessionId and  g.dataCollectionGroupId = c.dataCollectionGroupId and autoprocProgram.autoProcProgramId = api.autoProcProgramId"
+			+ " and c.dataCollectionId = api.dataCollectionId and autoprocProgram.autoProcProgramId = autoProcProgramAttachment.autoProcProgramId "
+			+ " and autoProcProgramAttachment.autoProcProgramAttachmentId = :autoProcProgramAttachmentId ";
+
+
+	private static final String FIND_BY_AUTOPROCPROGRAM_ID = "select s.* from BLSession s, "
+			+ " DataCollectionGroup g, DataCollection c, AutoProcIntegration api, AutoProcProgram autoprocProgram "
+			+ " where s.sessionId = g.sessionId and  g.dataCollectionGroupId = c.dataCollectionGroupId and autoprocProgram.autoProcProgramId = api.autoProcProgramId"
+			+ " and c.dataCollectionId = api.dataCollectionId and autoprocProgram.autoProcProgramId = :autoProcProgramId ";
+
 
 	private static String getProposalCodeNumberQuery() {
 		String query = "select * " + " FROM BLSession ses, Proposal pro "
@@ -525,6 +538,32 @@ public Session3VO findByAutoProcScalingId(final Integer autoProcScalingId) throw
 		}
 		return null;
 	}
+
+
+	@SuppressWarnings("unchecked")
+	public Session3VO findByAutoProcProgramAttachmentId(final Integer autoProcProgramAttachmentId) throws Exception {
+		String query = FIND_BY_AUTOPROCPROGRAMATTACHMENT_ID;
+		List<Session3VO> col = this.entityManager.createNativeQuery(query, "sessionNativeQuery")
+					.setParameter("autoProcProgramAttachmentId", autoProcProgramAttachmentId).getResultList();
+		if (col != null && col.size() > 0) {
+				return col.get(0);
+		}
+		return null;
+	}
+
+
+	@Override
+	public Session3VO findByAutoProcProgramId(int autoProcProgramId) {
+		String query = FIND_BY_AUTOPROCPROGRAM_ID;
+		@SuppressWarnings("unchecked")
+		List<Session3VO> col = this.entityManager.createNativeQuery(query, "sessionNativeQuery")
+					.setParameter("autoProcProgramId", autoProcProgramId).getResultList();
+		if (col != null && col.size() > 0) {
+				return col.get(0);
+		}
+		return null;
+	}
+
 
 
 	/**
@@ -818,4 +857,6 @@ private void checkChangeRemoveAccess(Session3VO vo) throws AccessDeniedException
 
 
 
+
+
 }