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Posted to commits@airavata.apache.org by ma...@apache.org on 2018/06/15 14:37:10 UTC
[airavata] branch group-based-auth updated (1c5e648 -> 4f334fa)
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a change to branch group-based-auth
in repository https://gitbox.apache.org/repos/asf/airavata.git.
from 1c5e648 AIRAVATA-2827 Upgrade OpenJPA to 2.4.3
new 5b2aa80 AIRAVATA-2827 OpenJPA 2.4.3 upgrade: convert BIT to TINYINT(1)
new 46de1e4 Updating devjobs monitoring email password
new 4f334fa AIRAVATA-2827 Populate JobStatusPK from Job's PK
The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
Summary of changes:
.../scigap/develop/group_vars/all/vault.yml | 66 +++++++++++-----------
.../group-based-auth/group_vars/all/vault.yml | 66 +++++++++++-----------
.../repositories/expcatalog/JobRepository.java | 13 +++--
.../repositories/expcatalog/TaskRepository.java | 7 ++-
.../src/main/resources/appcatalog-mysql.sql | 3 +-
.../src/main/resources/expcatalog-mysql.sql | 4 +-
.../expcatalog/ProcessRepositoryTest.java | 20 +++++--
.../next/DeltaScripts/appCatalog_schema_delta.sql | 11 +++-
.../experimentCatalog_schema_delta.sql | 7 ++-
9 files changed, 117 insertions(+), 80 deletions(-)
--
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[airavata] 03/03: AIRAVATA-2827 Populate JobStatusPK from Job's PK
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch group-based-auth
in repository https://gitbox.apache.org/repos/asf/airavata.git
commit 4f334fa864bab290f21938df5b36d413ed06eed6
Author: Marcus Christie <ma...@apache.org>
AuthorDate: Fri Jun 15 10:35:23 2018 -0400
AIRAVATA-2827 Populate JobStatusPK from Job's PK
---
.../core/repositories/expcatalog/JobRepository.java | 13 +++++++++----
.../core/repositories/expcatalog/TaskRepository.java | 7 ++++++-
.../expcatalog/ProcessRepositoryTest.java | 20 ++++++++++++++++----
3 files changed, 31 insertions(+), 9 deletions(-)
diff --git a/modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/JobRepository.java b/modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/JobRepository.java
index 25af655..3744913 100644
--- a/modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/JobRepository.java
+++ b/modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/JobRepository.java
@@ -69,11 +69,18 @@ public class JobRepository extends ExpCatAbstractRepository<JobModel, JobEntity,
}
- String jobId = jobPK.getJobId();
- String taskId = jobPK.getTaskId();
Mapper mapper = ObjectMapperSingleton.getInstance();
JobEntity jobEntity = mapper.map(jobModel, JobEntity.class);
+ populateParentIds(jobEntity);
+
+ return execute(entityManager -> entityManager.merge(jobEntity));
+ }
+
+ protected void populateParentIds(JobEntity jobEntity) {
+
+ String jobId = jobEntity.getJobId();
+ String taskId = jobEntity.getTaskId();
if (jobEntity.getJobStatuses() != null) {
logger.debug("Populating the Primary Key of JobStatus objects for the Job");
jobEntity.getJobStatuses().forEach(jobStatusEntity -> {
@@ -81,8 +88,6 @@ public class JobRepository extends ExpCatAbstractRepository<JobModel, JobEntity,
jobStatusEntity.setTaskId(taskId);
});
}
-
- return execute(entityManager -> entityManager.merge(jobEntity));
}
public String addJob(JobModel job, String processId) throws RegistryException {
diff --git a/modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/TaskRepository.java b/modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/TaskRepository.java
index 7c2404d..268e7c8 100644
--- a/modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/TaskRepository.java
+++ b/modules/registry-refactoring/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/TaskRepository.java
@@ -40,6 +40,8 @@ import java.util.Map;
public class TaskRepository extends ExpCatAbstractRepository<TaskModel, TaskEntity, String> {
private final static Logger logger = LoggerFactory.getLogger(TaskRepository.class);
+ private final JobRepository jobRepository = new JobRepository();
+
public TaskRepository() { super(TaskModel.class, TaskEntity.class); }
protected String saveTaskModelData(TaskModel taskModel) throws RegistryException {
@@ -95,7 +97,10 @@ public class TaskRepository extends ExpCatAbstractRepository<TaskModel, TaskEnti
if (taskEntity.getJobs() != null) {
logger.debug("Populating the Job objects' Task ID for the Task");
- taskEntity.getJobs().forEach(jobEntity -> jobEntity.setTaskId(taskId));
+ taskEntity.getJobs().forEach(jobEntity -> {
+ jobEntity.setTaskId(taskId);
+ jobRepository.populateParentIds(jobEntity);
+ });
}
}
diff --git a/modules/registry-refactoring/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessRepositoryTest.java b/modules/registry-refactoring/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessRepositoryTest.java
index b454738..dada4d0 100644
--- a/modules/registry-refactoring/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessRepositoryTest.java
+++ b/modules/registry-refactoring/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessRepositoryTest.java
@@ -22,12 +22,10 @@ package org.apache.airavata.registry.core.repositories.expcatalog;
import org.apache.airavata.model.experiment.ExperimentModel;
import org.apache.airavata.model.experiment.ExperimentType;
+import org.apache.airavata.model.job.JobModel;
import org.apache.airavata.model.process.ProcessModel;
import org.apache.airavata.model.scheduling.ComputationalResourceSchedulingModel;
-import org.apache.airavata.model.status.ProcessState;
-import org.apache.airavata.model.status.ProcessStatus;
-import org.apache.airavata.model.status.TaskState;
-import org.apache.airavata.model.status.TaskStatus;
+import org.apache.airavata.model.status.*;
import org.apache.airavata.model.task.TaskModel;
import org.apache.airavata.model.task.TaskTypes;
import org.apache.airavata.model.workspace.Gateway;
@@ -118,6 +116,19 @@ public class ProcessRepositoryTest {
processModel.setProcessDetail("detail");
processModel.setUseUserCRPref(true);
+
+ TaskModel jobSubmissionTask = new TaskModel();
+ jobSubmissionTask.setTaskType(TaskTypes.JOB_SUBMISSION);
+ jobSubmissionTask.setTaskId("job-task-id");
+ JobModel job = new JobModel();
+ job.setProcessId(processId);
+ job.setJobId("job-id");
+ job.setJobDescription("job-description");
+ JobStatus jobStatus = new JobStatus(JobState.SUBMITTED);
+ jobStatus.setStatusId("submitted-job-status-id");
+ job.addToJobStatuses(jobStatus);
+ jobSubmissionTask.addToJobs(job);
+ processModel.addToTasks(jobSubmissionTask);
processRepository.updateProcess(processModel, processId);
ProcessModel retrievedProcess = processRepository.getProcess(processId);
@@ -126,6 +137,7 @@ public class ProcessRepositoryTest {
assertTrue(retrievedProcess.isUseUserCRPref());
assertEquals(1, retrievedProcess.getProcessStatusesSize());
assertEquals(ProcessState.CREATED, retrievedProcess.getProcessStatuses().get(0).getState());
+ assertEquals(2, retrievedProcess.getTasksSize());
ComputationalResourceSchedulingModel computationalResourceSchedulingModel = new ComputationalResourceSchedulingModel();
assertEquals(processId, processRepository.addProcessResourceSchedule(computationalResourceSchedulingModel, processId));
--
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[airavata] 02/03: Updating devjobs monitoring email password
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch group-based-auth
in repository https://gitbox.apache.org/repos/asf/airavata.git
commit 46de1e4096d0fd8cb8ae58e608c65a595b4386d3
Author: Marcus Christie <ma...@apache.org>
AuthorDate: Fri Jun 15 10:04:34 2018 -0400
Updating devjobs monitoring email password
---
.../scigap/develop/group_vars/all/vault.yml | 66 +++++++++++-----------
.../group-based-auth/group_vars/all/vault.yml | 66 +++++++++++-----------
2 files changed, 66 insertions(+), 66 deletions(-)
diff --git a/dev-tools/ansible/inventories/scigap/develop/group_vars/all/vault.yml b/dev-tools/ansible/inventories/scigap/develop/group_vars/all/vault.yml
index b07d280..11b3eff 100644
--- a/dev-tools/ansible/inventories/scigap/develop/group_vars/all/vault.yml
+++ b/dev-tools/ansible/inventories/scigap/develop/group_vars/all/vault.yml
@@ -1,34 +1,34 @@
$ANSIBLE_VAULT;1.1;AES256
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diff --git a/dev-tools/ansible/inventories/scigap/group-based-auth/group_vars/all/vault.yml b/dev-tools/ansible/inventories/scigap/group-based-auth/group_vars/all/vault.yml
index b07d280..aedcb63 100644
--- a/dev-tools/ansible/inventories/scigap/group-based-auth/group_vars/all/vault.yml
+++ b/dev-tools/ansible/inventories/scigap/group-based-auth/group_vars/all/vault.yml
@@ -1,34 +1,34 @@
$ANSIBLE_VAULT;1.1;AES256
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--
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[airavata] 01/03: AIRAVATA-2827 OpenJPA 2.4.3 upgrade: convert BIT
to TINYINT(1)
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch group-based-auth
in repository https://gitbox.apache.org/repos/asf/airavata.git
commit 5b2aa800a1e9e47a713dc07e89eff7130291a118
Author: Marcus Christie <ma...@apache.org>
AuthorDate: Fri Jun 15 09:31:48 2018 -0400
AIRAVATA-2827 OpenJPA 2.4.3 upgrade: convert BIT to TINYINT(1)
---
.../src/main/resources/appcatalog-mysql.sql | 3 ++-
.../src/main/resources/expcatalog-mysql.sql | 4 ++--
.../next/DeltaScripts/appCatalog_schema_delta.sql | 11 ++++++++++-
.../next/DeltaScripts/experimentCatalog_schema_delta.sql | 7 ++++++-
4 files changed, 20 insertions(+), 5 deletions(-)
diff --git a/modules/registry-refactoring/src/main/resources/appcatalog-mysql.sql b/modules/registry-refactoring/src/main/resources/appcatalog-mysql.sql
index 9663dee..39a0069 100644
--- a/modules/registry-refactoring/src/main/resources/appcatalog-mysql.sql
+++ b/modules/registry-refactoring/src/main/resources/appcatalog-mysql.sql
@@ -31,7 +31,7 @@ CREATE TABLE COMPUTE_RESOURCE
DEFAULT_CPU_COUNT INTEGER,
DEFAULT_WALLTIME INTEGER,
ENABLED SMALLINT,
- GATEWAY_USAGE_REPORTING SMALLINT,
+ GATEWAY_USAGE_REPORTING TINYINT(1),
GATEWAY_USAGE_MODULE_LOAD_CMD VARCHAR(500),
GATEWAY_USAGE_EXECUTABLE VARCHAR(255),
PRIMARY KEY (RESOURCE_ID)
@@ -277,6 +277,7 @@ CREATE TABLE APPLICATION_INTERFACE
APPLICATION_DESCRIPTION VARCHAR(500),
GATEWAY_ID VARCHAR(255),
ARCHIVE_WORKING_DIRECTORY SMALLINT,
+ HAS_OPTIONAL_FILE_INPUTS TINYINT(1),
CREATION_TIME TIMESTAMP DEFAULT NOW(),
UPDATE_TIME TIMESTAMP DEFAULT '0000-00-00 00:00:00',
PRIMARY KEY(INTERFACE_ID)
diff --git a/modules/registry-refactoring/src/main/resources/expcatalog-mysql.sql b/modules/registry-refactoring/src/main/resources/expcatalog-mysql.sql
index 29952e5..1dbfe33 100644
--- a/modules/registry-refactoring/src/main/resources/expcatalog-mysql.sql
+++ b/modules/registry-refactoring/src/main/resources/expcatalog-mysql.sql
@@ -237,7 +237,7 @@ CREATE TABLE PROCESS (
EXPERIMENT_DATA_DIR VARCHAR (512),
USERNAME VARCHAR (255),
GROUP_RESOURCE_PROFILE_ID VARCHAR (255) DEFAULT NULL,
- USE_USER_CR_PREF BIT(1),
+ USE_USER_CR_PREF TINYINT(1),
PRIMARY KEY (PROCESS_ID),
FOREIGN KEY (EXPERIMENT_ID) REFERENCES EXPERIMENT(EXPERIMENT_ID) ON DELETE CASCADE
);
@@ -383,7 +383,7 @@ CREATE TABLE QUEUE_STATUS(
HOST_NAME VARCHAR(255),
QUEUE_NAME VARCHAR(255),
CREATED_TIME BIGINT(20),
- QUEUE_UP BIT(1),
+ QUEUE_UP TINYINT(1),
RUNNING_JOBS INT(11),
QUEUED_JOBS INT(11),
PRIMARY KEY (HOST_NAME, QUEUE_NAME, CREATED_TIME)
diff --git a/modules/registry/release-migration-scripts/next/DeltaScripts/appCatalog_schema_delta.sql b/modules/registry/release-migration-scripts/next/DeltaScripts/appCatalog_schema_delta.sql
index def5dcf..272ed9b 100644
--- a/modules/registry/release-migration-scripts/next/DeltaScripts/appCatalog_schema_delta.sql
+++ b/modules/registry/release-migration-scripts/next/DeltaScripts/appCatalog_schema_delta.sql
@@ -28,4 +28,13 @@ alter table COMPUTE_RESOURCE modify column CPUS_PER_NODE int default 0 null;
alter table COMPUTE_RESOURCE modify column DEFAULT_NODE_COUNT int default 0 null;
alter table COMPUTE_RESOURCE modify column DEFAULT_CPU_COUNT int default 0 null;
alter table COMPUTE_RESOURCE modify column DEFAULT_WALLTIME int default 0 null;
-alter table COMPUTE_RESOURCE modify column UPDATE_TIME timestamp default '0000-00-00 00:00:00' null;
\ No newline at end of file
+alter table COMPUTE_RESOURCE modify column UPDATE_TIME timestamp default '0000-00-00 00:00:00' null;
+
+-- AIRAVATA-2827: OpenJPA 2.4.3 upgrade, convert BIT -> TINYINT(1)
+alter table APPLICATION_OUTPUT modify column OUTPUT_STREAMING tinyint(1);
+alter table APPLICATION_INTERFACE modify column ARCHIVE_WORKING_DIRECTORY tinyint(1);
+alter table APPLICATION_INTERFACE modify column HAS_OPTIONAL_FILE_INPUTS tinyint(1);
+alter table APPLICATION_DEPLOYMENT modify column EDITABLE_BY_USER tinyint(1);
+alter table BATCH_QUEUE modify column IS_DEFAULT_QUEUE tinyint(1);
+alter table COMPUTE_RESOURCE modify column GATEWAY_USAGE_REPORTING tinyint(1);
+alter table USER_COMPUTE_RESOURCE_PREFERENCE modify column VALIDATED tinyint(1) default 0;
\ No newline at end of file
diff --git a/modules/registry/release-migration-scripts/next/DeltaScripts/experimentCatalog_schema_delta.sql b/modules/registry/release-migration-scripts/next/DeltaScripts/experimentCatalog_schema_delta.sql
index f70fdd2..9b19987 100644
--- a/modules/registry/release-migration-scripts/next/DeltaScripts/experimentCatalog_schema_delta.sql
+++ b/modules/registry/release-migration-scripts/next/DeltaScripts/experimentCatalog_schema_delta.sql
@@ -22,4 +22,9 @@
alter table EXPERIMENT_INPUT modify METADATA VARCHAR(4096);
-- AIRAVATA-2820
-alter table TASK drop column TASK_INTERNAL_STORE;
\ No newline at end of file
+alter table TASK drop column TASK_INTERNAL_STORE;
+
+-- AIRAVATA-2827: OpenJPA 2.4.3 upgrade, convert BIT -> TINYINT(1)
+alter table PROCESS modify column USE_USER_CR_PREF tinyint(1);
+alter table QUEUE_STATUS modify column QUEUE_UP tinyint(1);
+alter table USER_CONFIGURATION_DATA modify column IS_USE_USER_CR_PREF tinyint(1);
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