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Posted to commits@airavata.apache.org by sc...@apache.org on 2015/09/05 09:06:01 UTC
[13/16] airavata git commit: check unclosed entity managers
check unclosed entity managers
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/4e57f5b9
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/4e57f5b9
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/4e57f5b9
Branch: refs/heads/master
Commit: 4e57f5b9e0304aa5c4091380999e2ea2c5837f44
Parents: 840ae1a
Author: Chathuri Wimalasena <ch...@apache.org>
Authored: Fri Sep 4 15:54:00 2015 -0400
Committer: Supun Nakandala <sc...@apache.org>
Committed: Sat Sep 5 12:24:24 2015 +0530
----------------------------------------------------------------------
.../catalog/resources/ExperimentResource.java | 2 -
.../catalog/resources/GatewayResource.java | 2 -
.../catalog/resources/JobResource.java | 2 -
.../catalog/resources/JobStatusResource.java | 6 +--
.../catalog/resources/ProcessErrorResource.java | 6 +--
.../catalog/resources/ProcessInputResource.java | 4 +-
.../resources/ProcessOutputResource.java | 4 +-
.../catalog/resources/ProcessResource.java | 2 -
.../ProcessResourceScheduleResource.java | 6 +--
.../resources/ProcessStatusResource.java | 6 +--
.../catalog/resources/ProjectResource.java | 2 +
.../catalog/resources/TaskResource.java | 2 -
.../src/main/resources/expcatalog-derby.sql | 2 +-
.../src/main/resources/expcatalog-mysql.sql | 2 +-
.../src/test/resources/expcatalog-derby.sql | 40 +++++++++++++++-----
15 files changed, 51 insertions(+), 37 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentResource.java
index ab1def4..f60ff0a 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentResource.java
@@ -413,8 +413,6 @@ public class ExperimentResource extends AbstractExpCatResource {
}
break;
default:
- em.getTransaction().commit();
- em.close();
logger.error("Unsupported resource type for experiment resource.", new UnsupportedOperationException());
throw new UnsupportedOperationException();
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/GatewayResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/GatewayResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/GatewayResource.java
index 3c1c93e..15ead2d 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/GatewayResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/GatewayResource.java
@@ -296,8 +296,6 @@ public class GatewayResource extends AbstractExpCatResource {
}
break;
default:
- em.getTransaction().commit();
- em.close();
logger.error("Unsupported resource type for gateway resource.", new IllegalArgumentException());
throw new IllegalArgumentException("Unsupported resource type for gateway resource.");
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobResource.java
index a8e6d11..d4c1a99 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobResource.java
@@ -250,8 +250,6 @@ public class JobResource extends AbstractExpCatResource {
}
break;
default:
- em.getTransaction().commit();
- em.close();
logger.error("Unsupported resource type for job resource.", new UnsupportedOperationException());
throw new UnsupportedOperationException();
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobStatusResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobStatusResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobStatusResource.java
index b41a071..ded56b4 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobStatusResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobStatusResource.java
@@ -118,12 +118,12 @@ public class JobStatusResource extends AbstractExpCatResource {
public void save() throws RegistryException{
EntityManager em = null;
try {
- em = ExpCatResourceUtils.getEntityManager();
- em.getTransaction().begin();
- JobStatus jobStatus;
if(jobId == null || statusId == null || processId == null){
throw new RegistryException("Does not have the job id or status id or task id");
}
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
+ JobStatus jobStatus;
JobStatusPK jobStatusPK = new JobStatusPK();
jobStatusPK.setJobId(jobId);
jobStatusPK.setStatusId(statusId);
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessErrorResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessErrorResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessErrorResource.java
index 7f84a74..05915b4 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessErrorResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessErrorResource.java
@@ -127,12 +127,12 @@ public class ProcessErrorResource extends AbstractExpCatResource {
public void save() throws RegistryException{
EntityManager em = null;
try {
- em = ExpCatResourceUtils.getEntityManager();
- em.getTransaction().begin();
- ProcessError processError;
if(processId == null || errorId == null){
throw new RegistryException("Does not have the process id or error id");
}
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
+ ProcessError processError;
ProcessErrorPK processErrorPK = new ProcessErrorPK();
processErrorPK.setProcessId(processId);
processErrorPK.setErrorId(errorId);
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessInputResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessInputResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessInputResource.java
index d2437a0..823ec2b 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessInputResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessInputResource.java
@@ -171,11 +171,11 @@ public class ProcessInputResource extends AbstractExpCatResource {
public void save() throws RegistryException{
EntityManager em = null;
try {
- em = ExpCatResourceUtils.getEntityManager();
- em.getTransaction().begin();
if(processId == null){
throw new RegistryException("Does not have the process id");
}
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
ProcessInput processInput;
ProcessInputPK processInputPk = new ProcessInputPK();
processInputPk.setProcessId(processId);
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessOutputResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessOutputResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessOutputResource.java
index bee0ef7..8e930ac 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessOutputResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessOutputResource.java
@@ -153,11 +153,11 @@ public class ProcessOutputResource extends AbstractExpCatResource {
public void save() throws RegistryException{
EntityManager em = null;
try {
- em = ExpCatResourceUtils.getEntityManager();
- em.getTransaction().begin();
if(processId == null){
throw new RegistryException("Does not have the process id");
}
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
ProcessOutput processOutput;
ProcessOutputPK processOutputPK = new ProcessOutputPK();
processOutputPK.setProcessId(processId);
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResource.java
index 51a91ce..9adb7dc 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResource.java
@@ -447,8 +447,6 @@ public class ProcessResource extends AbstractExpCatResource {
}
break;
default:
- em.getTransaction().commit();
- em.close();
logger.error("Unsupported resource type for task resource.", new UnsupportedOperationException());
throw new UnsupportedOperationException();
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResourceScheduleResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResourceScheduleResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResourceScheduleResource.java
index 4975ae9..c510305 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResourceScheduleResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResourceScheduleResource.java
@@ -134,12 +134,12 @@ public class ProcessResourceScheduleResource extends AbstractExpCatResource {
public void save() throws RegistryException{
EntityManager em = null;
try {
- em = ExpCatResourceUtils.getEntityManager();
- em.getTransaction().begin();
- ProcessResourceSchedule processResourceSchedule;
if(processId == null){
throw new RegistryException("Does not have the process id");
}
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
+ ProcessResourceSchedule processResourceSchedule;
processResourceSchedule = em.find(ProcessResourceSchedule.class, processId);
if(processResourceSchedule == null){
processResourceSchedule = new ProcessResourceSchedule();
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessStatusResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessStatusResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessStatusResource.java
index de8c81b..53eba4f 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessStatusResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessStatusResource.java
@@ -109,12 +109,12 @@ public class ProcessStatusResource extends AbstractExpCatResource {
public void save() throws RegistryException{
EntityManager em = null;
try {
- em = ExpCatResourceUtils.getEntityManager();
- em.getTransaction().begin();
- ProcessStatus processStatus;
if(processId == null || statusId == null){
throw new RegistryException("Does not have the process id or status id");
}
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
+ ProcessStatus processStatus;
ProcessStatusPK processStatusPK = new ProcessStatusPK();
processStatusPK.setStatusId(statusId);
processStatusPK.setProcessId(processId);
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProjectResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProjectResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProjectResource.java
index f77c2b9..eabd8b0 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProjectResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProjectResource.java
@@ -101,6 +101,8 @@ public class ProjectResource extends AbstractExpCatResource {
Query q = generator.deleteQuery(em);
q.executeUpdate();
} else {
+ em.getTransaction().commit();
+ em.close();
logger.error("Unsupported resource type for project resource.", new IllegalArgumentException());
throw new IllegalArgumentException("Unsupported resource type for project resource.");
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskResource.java
index 962f0d0..ad3de43 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskResource.java
@@ -250,8 +250,6 @@ public class TaskResource extends AbstractExpCatResource {
}
break;
default:
- em.getTransaction().commit();
- em.close();
logger.error("Unsupported resource type for task resource.", new UnsupportedOperationException());
throw new UnsupportedOperationException();
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/main/resources/expcatalog-derby.sql
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/resources/expcatalog-derby.sql b/modules/registry/registry-core/src/main/resources/expcatalog-derby.sql
index c395099..5dd1777 100644
--- a/modules/registry/registry-core/src/main/resources/expcatalog-derby.sql
+++ b/modules/registry/registry-core/src/main/resources/expcatalog-derby.sql
@@ -308,7 +308,7 @@ CREATE TABLE JOB (
WORKING_DIR varchar(255),
STDOUT CLOB,
STDERR CLOB,
- EXIT_CODE INTEGER(11),
+ EXIT_CODE INT,
PRIMARY KEY (JOB_ID, PROCESS_ID),
FOREIGN KEY (PROCESS_ID) REFERENCES PROCESS(PROCESS_ID) ON DELETE CASCADE
);
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/main/resources/expcatalog-mysql.sql
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/resources/expcatalog-mysql.sql b/modules/registry/registry-core/src/main/resources/expcatalog-mysql.sql
index 12b61ec..b3d05b7 100644
--- a/modules/registry/registry-core/src/main/resources/expcatalog-mysql.sql
+++ b/modules/registry/registry-core/src/main/resources/expcatalog-mysql.sql
@@ -310,7 +310,7 @@ CREATE TABLE JOB (
WORKING_DIR varchar(255),
STDOUT LONGTEXT,
STDERR LONGTEXT,
- EXIT_CODE INTEGER(11),
+ EXIT_CODE INT(11),
PRIMARY KEY (JOB_ID, PROCESS_ID),
FOREIGN KEY (PROCESS_ID) REFERENCES PROCESS(PROCESS_ID) ON DELETE CASCADE
);
http://git-wip-us.apache.org/repos/asf/airavata/blob/4e57f5b9/modules/registry/registry-core/src/test/resources/expcatalog-derby.sql
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/test/resources/expcatalog-derby.sql b/modules/registry/registry-core/src/test/resources/expcatalog-derby.sql
index ac8c913..31aa701 100644
--- a/modules/registry/registry-core/src/test/resources/expcatalog-derby.sql
+++ b/modules/registry/registry-core/src/test/resources/expcatalog-derby.sql
@@ -294,30 +294,33 @@ CREATE TABLE TASK_ERROR (
TRANSIENT_OR_PERSISTENT SMALLINT,
ROOT_CAUSE_ERROR_ID_LIST CLOB,
PRIMARY KEY (ERROR_ID, TASK_ID),
- FOREIGN KEY (TASK_ID) REFERENCES TASK(TASK_ID) ON DELETE CASCADE
-);
+ FOREIGN KEY (TASK_ID) REFERENCES TASK(TASK_ID) ON DELETE CASCADE);
CREATE TABLE JOB (
JOB_ID varchar(255),
TASK_ID varchar(255),
- JOB_DESCRIPTION varchar(255),
+ PROCESS_ID varchar(255),
+ JOB_DESCRIPTION CLOB,
CREATION_TIME timestamp DEFAULT '0000-00-00 00:00:00',
COMPUTE_RESOURCE_CONSUMED varchar(255),
JOB_NAME varchar(255),
WORKING_DIR varchar(255),
- PRIMARY KEY (JOB_ID, TASK_ID),
- FOREIGN KEY (TASK_ID) REFERENCES TASK(TASK_ID) ON DELETE CASCADE
+ STDOUT CLOB,
+ STDERR CLOB,
+ EXIT_CODE INT,
+ PRIMARY KEY (JOB_ID, PROCESS_ID),
+ FOREIGN KEY (PROCESS_ID) REFERENCES PROCESS(PROCESS_ID) ON DELETE CASCADE
);
CREATE TABLE JOB_STATUS (
STATUS_ID varchar(255),
JOB_ID varchar(255),
- TASK_ID varchar(255),
+ PROCESS_ID varchar(255),
STATE varchar(255),
TIME_OF_STATE_CHANGE timestamp DEFAULT '0000-00-00 00:00:00',
REASON CLOB,
- PRIMARY KEY (STATUS_ID, JOB_ID, TASK_ID),
- FOREIGN KEY (JOB_ID, TASK_ID) REFERENCES JOB(JOB_ID, TASK_ID) ON DELETE CASCADE
+ PRIMARY KEY (STATUS_ID, JOB_ID, PROCESS_ID),
+ FOREIGN KEY (JOB_ID, PROCESS_ID) REFERENCES JOB(JOB_ID, PROCESS_ID) ON DELETE CASCADE
);
CREATE TABLE CONFIGURATION
@@ -329,4 +332,23 @@ CREATE TABLE CONFIGURATION
PRIMARY KEY(CONFIG_KEY, CONFIG_VAL, CATEGORY_ID)
);
-INSERT INTO CONFIGURATION (CONFIG_KEY, CONFIG_VAL, EXPIRE_DATE, CATEGORY_ID) VALUES('registry.version', '0.15', CURRENT_TIMESTAMP ,'SYSTEM');
\ No newline at end of file
+INSERT INTO CONFIGURATION (CONFIG_KEY, CONFIG_VAL, EXPIRE_DATE, CATEGORY_ID) VALUES('registry.version', '0.16', CURRENT_TIMESTAMP ,'SYSTEM');
+
+CREATE TABLE COMMUNITY_USER
+(
+ GATEWAY_ID VARCHAR(256) NOT NULL,
+ COMMUNITY_USER_NAME VARCHAR(256) NOT NULL,
+ TOKEN_ID VARCHAR(256) NOT NULL,
+ COMMUNITY_USER_EMAIL VARCHAR(256) NOT NULL,
+ PRIMARY KEY (GATEWAY_ID, COMMUNITY_USER_NAME, TOKEN_ID)
+);
+
+CREATE TABLE CREDENTIALS
+(
+ GATEWAY_ID VARCHAR(256) NOT NULL,
+ TOKEN_ID VARCHAR(256) NOT NULL,
+ CREDENTIAL BLOB NOT NULL,
+ PORTAL_USER_ID VARCHAR(256) NOT NULL,
+ TIME_PERSISTED TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+ PRIMARY KEY (GATEWAY_ID, TOKEN_ID)
+);
\ No newline at end of file