Repository: airavata Updated Branches: refs/heads/master 60e657d45 -> 39a0365d8
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/39a0365d Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/39a0365d Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/39a0365d Branch: refs/heads/master Commit: 39a0365d84ca3c50a1712acea66f9b5bf27b5409 Parents: 60e657d Author: Chathuri Wimalasena <[email protected]> Authored: Fri Sep 4 15:54:00 2015 -0400 Committer: Chathuri Wimalasena <[email protected]> Committed: Fri Sep 4 15:54:00 2015 -0400 ---------------------------------------------------------------------- .../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/39a0365d/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/39a0365d/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/39a0365d/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/39a0365d/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/39a0365d/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/39a0365d/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/39a0365d/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/39a0365d/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/39a0365d/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/39a0365d/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/39a0365d/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/39a0365d/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/39a0365d/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/39a0365d/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/39a0365d/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
