Commit 803de13f authored by hammonds's avatar hammonds
Browse files

Merge branch 'master' into 'master'

Master

See merge request DM/dm!25
parents a86d7052 213215b3
......@@ -106,7 +106,7 @@ This node will be responsible for providing the data storage web service, the po
To install _dm_ compnents for the data-storage node
* cd DM\_INSTALL\_DIR/production
* edit etc/dm.deploy.conf to change DM\_CA\_HOST to data-storage
* ./sbin/install\_dm\_deploy\_data\_storage.sh
* ./sbin/dm\_deploy\_data\_storage.sh
- This deploy process will install components and prompt for user input as necessary. Prompts will ask for a number of system passwords, some existing and some being set by this process, node names for the DS web service node and file locations. These include
- __postgres__ admin account - This will be used to manage the postgres itself. Each developer can set this to a unique value.
- __dm__ db management account - This will be for mananging the 'dm' database in postgres. Each developer can set this to a unique value.
......@@ -121,7 +121,7 @@ This node will provide _daq_, _proc_ and _cat_ web services. These services wil
To install _dm_ components on the exp-station:
* cd DM\_INSTALL\_DIR/production
* Edit the file etc/dm.deploy.conf to ensure that the DM\_CA\_HOST is set to the data-storage node.
* ./sbin/install\_dm\_deploy\_exp\_station.sh
* ./sbin/dm\_deploy\_exp\_station.sh
- This will start the installation process which will prompt for
- DM DS Web Service Host (data-storage in this case
- DM DS Web Servervice Installation directory (where the web service is installed on node data-storage)
......@@ -194,11 +194,11 @@ Each step in a workflow can define inputs and outputs which can then be used in
If needed the test system can be restarted running a couple of startup commands. Change directory the DM install directory and then
* data-storage
* DM\_INSTALL\_DIR/production/etc/init.d/dm-db-services restart
* DM\_INSTALL\_DIR/production/etc/init.d/dm-ds-services restart
* DM\_INSTALL\_DIR/production/etc/init.d/dm-monitor-services restart
* exp-station
* DM\_INSTALL\_DIR/production/etc/init.d/dm-db-services restart
* DM\_INSTALL\_DIR/production/etc/init.d/dm-daq-services restart
* DM\_INSTALL\_DIR/production/etc/init.d/dm-monitor-services restart
This may be necessary if, for instance, the system has been rebooted. These commands restart several services in the install directory. If you have modified something in only one of these services you may be able to restart that service. For instance if only the data storage web service needs to be rebooted then you can run
......
Release 3.3.0 (05/04/2020)
- Change log4j version from 1.2.7 to 2.13.2. Code changes to adapt were
necessary. Changed config file from log4j.properties to log4j2.xml
- change jar file for postgresql from 9.3-1102.jdbc41 to 42.2.8. The underlying
postgresql in support changed from 9.3 to 9.6 a while ago.
Release 3.2.2 (02/24/2020)
=============================
- Added user documentation (Getting Started guide)
......
......@@ -14,7 +14,7 @@ DM_DAQ_WEB_SERVICE_URL=https://DM_HOSTNAME:33336
DM_CAT_WEB_SERVICE_URL=https://DM_HOSTNAME:44436
DM_PROC_WEB_SERVICE_URL=https://DM_HOSTNAME:55536
DM_APS_DB_WEB_SERVICE_URL=https://DM_HOSTNAME:11236
DM_SOFTWARE_VERSION=3.2.2
DM_SOFTWARE_VERSION=3.3.0
LDAP_SERVER_URL='ldaps://dmid-vm.xray.aps.anl.gov:636'
LDAP_DN_FORMAT='uid=%%s,ou=people,o=aps.anl.gov,dc=aps,dc=anl,dc=gov'
LDAP_UTIL_ADMIN_DN='uid=DM_SYSTEM_UNIX_ACCOUNT,ou=People,o=aps.anl.gov,dc=aps,dc=anl,dc=gov'
......
......@@ -14,7 +14,7 @@ DM_DAQ_WEB_SERVICE_URL=https://DM_HOSTNAME:33336
DM_CAT_WEB_SERVICE_URL=https://DM_HOSTNAME:44436
DM_PROC_WEB_SERVICE_URL=https://DM_HOSTNAME:55536
DM_APS_DB_WEB_SERVICE_URL=https://DM_HOSTNAME:11236
DM_SOFTWARE_VERSION=2.2.2
DM_SOFTWARE_VERSION=3.3.0
LDAP_SERVER_URL='ldaps://dmid-vm.xray.aps.anl.gov:636'
LDAP_DN_FORMAT='uid=%%s,ou=people,o=aps.anl.gov,dc=aps,dc=anl,dc=gov'
LDAP_UTIL_ADMIN_DN='uid=DM_SYSTEM_UNIX_ACCOUNT,ou=People,o=aps.anl.gov,dc=aps,dc=anl,dc=gov'
......
......@@ -29,12 +29,14 @@ dist.jar=${dist.dir}/dm-api.jar
dist.javadoc.dir=${dist.dir}/javadoc
endorsed.classpath=
excludes=
file.reference.log4j-1.2.17.jar=../lib/log4j-1.2.17.jar
file.reference.log4j-core-2.13.2.jar=../lib/log4j-core-2.13.2.jar
file.reference.log4j-api-2.13.2.jar=../lib/log4j-api-2.13.2.jar
includes=**
jar.compress=false
javac.classpath=\
${reference.DmBase.jar}:\
${file.reference.log4j-1.2.17.jar}
${file.reference.log4j-core-2.13.2.jar}:\
${file.reference.log4j-api-2.13.2.jar}
# Space-separated list of extra javac options
javac.compilerargs=
javac.deprecation=false
......
......@@ -29,7 +29,8 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.net.ssl.HttpsURLConnection;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
/**
* DM REST Web Service API class.
......@@ -49,7 +50,7 @@ public class DmRestApi {
private static final String DefaultSessionId = "defaultSession";
private static final boolean httpsInitialized = initializeHttpsConnection();
private static final Logger logger = Logger.getLogger(DmRestApi.class.getName());
private static final Logger logger = LogManager.getLogger(DmRestApi.class.getName());
private static boolean initializeHttpsConnection() {
HttpsURLConnection.setDefaultSSLSocketFactory(new NoServerVerificationSSLSocketFactory());
......
......@@ -30,14 +30,16 @@ dist.javadoc.dir=${dist.dir}/javadoc
endorsed.classpath=
excludes=
file.reference.gson-2.3.1.jar=../lib/gson-2.3.1.jar
file.reference.log4j-1.2.17.jar=../lib/log4j-1.2.17.jar
file.reference.log4j-core-2.13.2.jar=../lib/log4j-core-2.13.2.jar
file.reference.log4j-api-2.13.2.jar=../lib/log4j-api-2.13.2.jar
file.reference.primefaces-6.0.jar=../lib/primefaces-6.0.jar
file.reference.jaxb-osgi.jar=/local/DataManagement/support/opt/payara/glassfish/modules/jaxb-osgi.jar
file.reference.jaxb-api-2.3.1.jar=../lib/jaxb-api-2.3.1.jar
includes=**
jar.compress=false
javac.classpath=\
${file.reference.log4j-1.2.17.jar}:\
${file.reference.log4j-core-2.13.2.jar}:\
${file.reference.log4j-api-2.13.2.jar}:\
${file.reference.gson-2.3.1.jar}:\
${file.reference.primefaces-6.0.jar}:\
${file.reference.jaxb-api-2.3.1.jar}:\
......
package gov.anl.aps.dm.common.exceptions;
import gov.anl.aps.dm.common.constants.DmStatus;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
/**
* DM exception factory class.
......@@ -10,7 +11,7 @@ import org.apache.log4j.Logger;
public class DmExceptionFactory {
private static final Logger logger
= Logger.getLogger(DmExceptionFactory.class.getName());
= LogManager.getLogger(DmExceptionFactory.class.getName());
/**
* Generate DM exception.
......
......@@ -7,14 +7,15 @@ import gov.anl.aps.dm.common.exceptions.DmException;
import java.lang.reflect.Type;
import java.util.LinkedList;
import java.util.List;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
/**
* DM object factory class.
*/
public class DmObjectFactory {
private static final Logger logger = Logger.getLogger(DmObjectFactory.class.getName());
private static final Logger logger = LogManager.getLogger(DmObjectFactory.class.getName());
private static final Gson gson = new GsonBuilder().create();
/**
......
......@@ -6,7 +6,8 @@ import java.security.spec.InvalidKeySpecException;
import java.util.Random;
import javax.crypto.SecretKeyFactory;
import javax.crypto.spec.PBEKeySpec;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.primefaces.util.Base64;
/**
......@@ -21,7 +22,7 @@ public class CryptUtility {
private static final char[] SaltCharset = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789".toCharArray();
private static final String SaltDelimiter = "$";
private static final Logger logger = Logger.getLogger(CryptUtility.class.getName());
private static final Logger logger = LogManager.getLogger(CryptUtility.class.getName());
/**
* Generate random string.
......
......@@ -9,7 +9,8 @@ import javax.net.SocketFactory;
import javax.net.ssl.SSLContext;
import javax.net.ssl.SSLSocketFactory;
import javax.net.ssl.TrustManager;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
/**
* SSL socket factory that does not verify server credentials.
......@@ -22,7 +23,7 @@ import org.apache.log4j.Logger;
*/
public class NoServerVerificationSSLSocketFactory extends SSLSocketFactory {
private static final Logger logger = Logger.getLogger(NoServerVerificationSSLSocketFactory.class.getName());
private static final Logger logger = LogManager.getLogger(NoServerVerificationSSLSocketFactory.class.getName());
private SSLSocketFactory factory;
......
......@@ -1040,8 +1040,9 @@ exists or setup the property manually. For example like this:
<copyfiles files="${reference.DmApi.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
<copyfiles files="${file.reference.gson-2.3.1.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
<copyfiles files="${file.reference.itext-2.1.7.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
<copyfiles files="${file.reference.log4j-1.2.17.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
<copyfiles files="${file.reference.postgresql-9.3-1102.jdbc41.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
<copyfiles files="${file.reference.log4j-core-2.13.2.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
<copyfiles files="${file.reference.log4j-api-2.13.2.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
<copyfiles files="${file.reference.postgresql-42.2.8.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
<copyfiles files="${file.reference.org-netbeans-modules-java-j2seproject-copylibstask.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
<copyfiles files="${file.reference.poi-3.10.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
<copyfiles files="${file.reference.primefaces-6.0.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>
......@@ -1053,8 +1054,9 @@ exists or setup the property manually. For example like this:
<copyfiles files="${reference.DmApi.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
<copyfiles files="${file.reference.gson-2.3.1.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
<copyfiles files="${file.reference.itext-2.1.7.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
<copyfiles files="${file.reference.log4j-1.2.17.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
<copyfiles files="${file.reference.postgresql-9.3-1102.jdbc41.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
<copyfiles files="${file.reference.log4j-core-2.13.2.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
<copyfiles files="${file.reference.log4j-api-2.13.2.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
<copyfiles files="${file.reference.postgresql-42.2.8.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
<copyfiles files="${file.reference.org-netbeans-modules-java-j2seproject-copylibstask.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
<copyfiles files="${file.reference.poi-3.10.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
<copyfiles files="${file.reference.primefaces-6.0.jar}" todir="${build.web.dir}/WEB-INF/lib"/>
......
......@@ -33,10 +33,11 @@ endorsed.classpath=\
excludes=
file.reference.gson-2.3.1.jar=../lib/gson-2.3.1.jar
file.reference.itext-2.1.7.jar=lib/itext-2.1.7.jar
file.reference.log4j-1.2.17.jar=../lib/log4j-1.2.17.jar
file.reference.log4j-core-2.13.2.jar=../lib/log4j-core-2.13.2.jar
file.reference.log4j-api-2.13.2.jar=../lib/log4j-api-2.13.2.jar
file.reference.org-netbeans-modules-java-j2seproject-copylibstask.jar=lib/org-netbeans-modules-java-j2seproject-copylibstask.jar
file.reference.poi-3.10.jar=lib/poi-3.10.jar
file.reference.postgresql-9.3-1102.jdbc41.jar=lib/postgresql-9.3-1102.jdbc41.jar
file.reference.postgresql-42.2.8.jar=lib/postgresql-42.2.8.jar
file.reference.primefaces-6.0.jar=../lib/primefaces-6.0.jar
includes=**
j2ee.compile.on.save=true
......@@ -56,8 +57,9 @@ javac.classpath=\
${reference.DmApi.jar}:\
${file.reference.gson-2.3.1.jar}:\
${file.reference.itext-2.1.7.jar}:\
${file.reference.log4j-1.2.17.jar}:\
${file.reference.postgresql-9.3-1102.jdbc41.jar}:\
${file.reference.log4j-core-2.13.2.jar}:\
${file.reference.log4j-api-2.13.2.jar}:\
${file.reference.postgresql-42.2.8.jar}:\
${file.reference.org-netbeans-modules-java-j2seproject-copylibstask.jar}:\
${file.reference.poi-3.10.jar}:\
${file.reference.primefaces-6.0.jar}
......
......@@ -23,11 +23,15 @@
<path-in-war>WEB-INF/lib</path-in-war>
</library>
<library dirs="200">
<file>${file.reference.log4j-1.2.17.jar}</file>
<file>${file.reference.log4j-core-2.13.2.jar}</file>
<path-in-war>WEB-INF/lib</path-in-war>
</library>
<library dirs="200">
<file>${file.reference.postgresql-9.3-1102.jdbc41.jar}</file>
<file>${file.reference.log4j-api-2.13.2.jar}</file>
<path-in-war>WEB-INF/lib</path-in-war>
</library>
<library dirs="200">
<file>${file.reference.postgresql-42.2.8.jar}</file>
<path-in-war>WEB-INF/lib</path-in-war>
</library>
<library dirs="200">
......
......@@ -15,12 +15,13 @@ import javax.annotation.PostConstruct;
import javax.faces.model.DataModel;
import javax.faces.model.ListDataModel;
import javax.faces.model.SelectItem;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.primefaces.event.data.FilterEvent;
public abstract class DmEntityController<EntityType extends DmEntity, FacadeType extends DmEntityDbFacade<EntityType>> implements Serializable {
private static final Logger logger = Logger.getLogger(DmEntityController.class.getName());
private static final Logger logger = LogManager.getLogger(DmEntityController.class.getName());
private static final int NUMBER_OF_ROWS_FOR_DISPLAY_LIST = 25;
private static final int NUMBER_OF_ROWS_FOR_SELECT_LIST = 10;
......
......@@ -24,13 +24,14 @@ import javax.faces.component.UIComponent;
import javax.faces.context.FacesContext;
import javax.faces.convert.Converter;
import javax.faces.convert.FacesConverter;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
@Named("experimentController")
@SessionScoped
public class ExperimentController extends DmEntityController<Experiment, ExperimentDbFacade> {
private static final Logger logger = Logger.getLogger(ExperimentController.class.getName());
private static final Logger logger = LogManager.getLogger(ExperimentController.class.getName());
@EJB
private ExperimentDbFacade experimentDbFacade;
......
......@@ -9,13 +9,14 @@ import javax.faces.component.UIComponent;
import javax.faces.context.FacesContext;
import javax.faces.convert.Converter;
import javax.faces.convert.FacesConverter;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
@Named("experimentRoleTypeController")
@SessionScoped
public class ExperimentRoleTypeController extends DmEntityController<ExperimentRoleType, ExperimentRoleTypeDbFacade> {
private static final Logger logger = Logger.getLogger(ExperimentRoleTypeController.class.getName());
private static final Logger logger = LogManager.getLogger(ExperimentRoleTypeController.class.getName());
@EJB
private ExperimentRoleTypeDbFacade experimentRoleTypeDbFacade;
......
......@@ -23,13 +23,14 @@ import javax.faces.component.UIComponent;
import javax.faces.context.FacesContext;
import javax.faces.convert.Converter;
import javax.faces.convert.FacesConverter;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
@Named("experimentStationController")
@SessionScoped
public class ExperimentStationController extends DmEntityController<ExperimentStation, ExperimentStationDbFacade> {
private static final Logger logger = Logger.getLogger(ExperimentStationController.class.getName());
private static final Logger logger = LogManager.getLogger(ExperimentStationController.class.getName());
@EJB
private ExperimentStationDbFacade experimentStationDbFacade;
......
......@@ -12,13 +12,14 @@ import javax.faces.component.UIComponent;
import javax.faces.context.FacesContext;
import javax.faces.convert.Converter;
import javax.faces.convert.FacesConverter;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
@Named("experimentTypeController")
@SessionScoped
public class ExperimentTypeController extends DmEntityController<ExperimentType, ExperimentTypeDbFacade> {
private static final Logger logger = Logger.getLogger(ExperimentTypeController.class.getName());
private static final Logger logger = LogManager.getLogger(ExperimentTypeController.class.getName());
@EJB
private ExperimentTypeDbFacade experimentTypeDbFacade;
......
......@@ -19,7 +19,8 @@ import javax.enterprise.context.SessionScoped;
import javax.faces.context.ExternalContext;
import javax.faces.context.FacesContext;
import javax.inject.Named;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
/**
* Login controller.
......@@ -37,7 +38,7 @@ public class LoginController implements Serializable {
private UserInfo user = null;
private boolean isAdmin;
private static final Logger logger = Logger.getLogger(LoginController.class.getName());
private static final Logger logger = LogManager.getLogger(LoginController.class.getName());
/**
* Constructor.
......
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