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Posted to commits@airavata.apache.org by ma...@apache.org on 2018/01/18 19:22:23 UTC
[airavata] branch develop updated (0d77ff5 -> 0f25c2f)
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a change to branch develop
in repository https://gitbox.apache.org/repos/asf/airavata.git.
from 0d77ff5 AIRAVATA-2645 Generate Python thrift stubs
add c43640f Adding Searching SRA gateway
add 87d323c Log error when failing to execute groovy template
add d70f9af Updating email addresses in gfac-config.yaml
add 274da25 Merge remote-tracking branch 'origin/master'
add 807e1e7 Adding Searching SRA gateway record to the file
add acf3a49 Added the public key generated by the gateway to the data store
add 1d69f66 Added google analytics traching ID for USD gateway
add 625732d Added google analytics tracking ID for testdrive gateway
add e9d64b8 Added google analytics tracking ID for dREG sequencing gateway
add a73ba7b changing dev email address to devjobs
add 15cc7fe added SSC gateway URL
add 1044189 added SSC gateway details
add bcdd119 Merge branch 'AIRAVATA-2571-email-verified'
add 44dd8f1 added Rodeo VM details
add bd4c6d8 airavata PGA gateway installation parameters updated
add 5aec2a8 added google analytics ID
add 80da347 added google analytics ID
add 08f09bc added google analytics ID for SIU gateway
add 5a33b09 added google analytics ID for SimVascular gateway
add ac7330b added google analytics ID for SimCCS gateway
add e101d43 added google analytics ID for IU Cyber gateway
new f13c17f Fixing AIRAVATA-2621
new 0237909 Fixing AIRAVATA-2624 Sampede2 cluster SSH connectivity issue
new 53888e1 Validating port value before overriding
new 0f25c2f Merge branch 'AIRAVATA-2621-bugfix' into develop
The 4 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:
.../group_vars/pga/vars.yml | 39 ++++++++++-----------
.../scigap/{dreg-production => SGCI-SSC}/hosts | 4 +--
.../scigap/dreg-production/group_vars/pga/vars.yml | 1 +
.../scigap/production/pga_config/csbglsu/vars.yml | 1 +
.../production/pga_config/iugateway/vars.yml | 1 +
.../production/pga_config/iugeosurvey/vars.yml | 1 +
.../scigap/production/pga_config/scigap/vars.yml | 1 +
.../{NCSAIndustry => searchingSRA}/vars.yml | 28 +++++++--------
.../production/pga_config/searchingSRA/vault.yml | 18 ++++++++++
.../production/pga_config/simvascular/vars.yml | 1 +
.../production/pga_config/southdakota/vars.yml | 1 +
.../pga_config/southernillinois/vars.yml | 1 +
.../production/pga_config/testdrive/vars.yml | 1 +
dev-tools/ansible/pga-scigap-prod.yml | 1 +
.../roles/gfac/templates/gfac-config.yaml.j2 | 7 +++-
.../org/apache/airavata/gfac/core/GFacUtils.java | 2 +-
.../airavata/gfac/core/context/ProcessContext.java | 40 +++++++++++++++++++++-
.../org/apache/airavata/gfac/impl/Factory.java | 17 ++++-----
.../apache/airavata/gfac/impl/GFacEngineImpl.java | 2 +-
19 files changed, 118 insertions(+), 49 deletions(-)
copy dev-tools/ansible/inventories/scigap/{PICKSC-Production => SGCI-SSC}/group_vars/pga/vars.yml (56%)
copy dev-tools/ansible/inventories/scigap/{dreg-production => SGCI-SSC}/hosts (82%)
copy dev-tools/ansible/inventories/scigap/production/pga_config/{NCSAIndustry => searchingSRA}/vars.yml (65%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/searchingSRA/vault.yml
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[airavata] 01/04: Fixing AIRAVATA-2621
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch develop
in repository https://gitbox.apache.org/repos/asf/airavata.git
commit f13c17fe41bfdd1a4c8e35a88ab16f534190b523
Author: dimuthu.upeksha2@gmail.com <Di...@1234>
AuthorDate: Wed Jan 17 11:30:10 2018 -0500
Fixing AIRAVATA-2621
---
.../airavata/gfac/core/context/ProcessContext.java | 33 +++++++++++++++++++++-
.../apache/airavata/gfac/impl/GFacEngineImpl.java | 2 +-
2 files changed, 33 insertions(+), 2 deletions(-)
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/ProcessContext.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/ProcessContext.java
index 6ca29e3..3f45ff4 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/ProcessContext.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/ProcessContext.java
@@ -43,6 +43,7 @@ import org.apache.airavata.model.status.ProcessState;
import org.apache.airavata.model.status.ProcessStatus;
import org.apache.airavata.model.task.TaskModel;
import org.apache.airavata.registry.cpi.AppCatalog;
+import org.apache.airavata.registry.cpi.AppCatalogException;
import org.apache.airavata.registry.cpi.ExperimentCatalog;
import org.apache.curator.framework.CuratorFramework;
import org.slf4j.Logger;
@@ -620,7 +621,37 @@ public class ProcessContext {
}
}
- public ServerInfo getComputeResourceServerInfo(){
+ public ServerInfo getComputeResourceServerInfo() throws GFacException {
+
+ if (this.jobSubmissionProtocol == JobSubmissionProtocol.SSH) {
+ Optional<JobSubmissionInterface> firstJobSubmissionIface = getComputeResourceDescription()
+ .getJobSubmissionInterfaces().stream()
+ .filter(iface -> iface.getJobSubmissionProtocol() == JobSubmissionProtocol.SSH)
+ .findFirst();
+
+ if (firstJobSubmissionIface.isPresent()) {
+
+ try {
+ SSHJobSubmission sshJobSubmission = appCatalog.getComputeResource()
+ .getSSHJobSubmission(firstJobSubmissionIface.get().getJobSubmissionInterfaceId());
+
+ String alternateHostName = sshJobSubmission.getAlternativeSSHHostName();
+ String hostName = !(alternateHostName == null || alternateHostName.length() == 0) ? alternateHostName :
+ getComputeResourceDescription().getHostName();
+
+ return new ServerInfo(
+ getComputeResourceLoginUserName(),
+ hostName,
+ getComputeResourceCredentialToken(),
+ sshJobSubmission.getSshPort());
+
+ } catch (AppCatalogException e) {
+ throw new GFacException("Failed to fetch ssh job submission for interface " +
+ firstJobSubmissionIface.get().getJobSubmissionInterfaceId(), e);
+ }
+ }
+ }
+
return new ServerInfo(getComputeResourceLoginUserName(),
getComputeResourceDescription().getHostName(),
getComputeResourceCredentialToken());
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/GFacEngineImpl.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/GFacEngineImpl.java
index ac3e755..e81f164 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/GFacEngineImpl.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/GFacEngineImpl.java
@@ -848,7 +848,7 @@ public class GFacEngineImpl implements GFacEngine {
}
private TaskContext getDataStagingTaskContext(ProcessContext processContext, OutputDataObjectType processOutput)
- throws TException, TaskException {
+ throws TException, TaskException, GFacException {
TaskContext taskCtx = new TaskContext();
taskCtx.setParentProcessContext(processContext);
// create new task model for this task
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[airavata] 04/04: Merge branch 'AIRAVATA-2621-bugfix' into develop
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch develop
in repository https://gitbox.apache.org/repos/asf/airavata.git
commit 0f25c2f1dcb3f58a31cfad631d19bfbef714a349
Merge: 0d77ff5 53888e1
Author: Marcus Christie <ma...@iu.edu>
AuthorDate: Thu Jan 18 14:21:54 2018 -0500
Merge branch 'AIRAVATA-2621-bugfix' into develop
Fixes AIRAVATA-2621 and AIRAVATA-2624
.../csbglsu => SGCI-SSC/group_vars/pga}/vars.yml | 51 +++++++++++++---------
.../ansible/inventories/scigap/SGCI-SSC/hosts | 21 +++++++++
.../scigap/dreg-production/group_vars/pga/vars.yml | 1 +
.../scigap/production/pga_config/csbglsu/vars.yml | 1 +
.../production/pga_config/iugateway/vars.yml | 1 +
.../production/pga_config/iugeosurvey/vars.yml | 1 +
.../scigap/production/pga_config/scigap/vars.yml | 1 +
.../pga_config/{csbglsu => searchingSRA}/vars.yml | 26 ++++++-----
.../production/pga_config/searchingSRA/vault.yml | 18 ++++++++
.../production/pga_config/simvascular/vars.yml | 1 +
.../production/pga_config/southdakota/vars.yml | 1 +
.../pga_config/southernillinois/vars.yml | 1 +
.../production/pga_config/testdrive/vars.yml | 1 +
dev-tools/ansible/pga-scigap-prod.yml | 1 +
.../roles/gfac/templates/gfac-config.yaml.j2 | 7 ++-
.../org/apache/airavata/gfac/core/GFacUtils.java | 2 +-
.../airavata/gfac/core/context/ProcessContext.java | 40 ++++++++++++++++-
.../org/apache/airavata/gfac/impl/Factory.java | 17 ++++----
.../apache/airavata/gfac/impl/GFacEngineImpl.java | 2 +-
19 files changed, 151 insertions(+), 43 deletions(-)
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[airavata] 03/04: Validating port value before overriding
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch develop
in repository https://gitbox.apache.org/repos/asf/airavata.git
commit 53888e12f9177d99b17194581f04b3f691305cc8
Author: dimuthu.upeksha2@gmail.com <Di...@1234>
AuthorDate: Wed Jan 17 15:34:29 2018 -0500
Validating port value before overriding
---
.../airavata/gfac/core/context/ProcessContext.java | 17 ++++++++++++-----
1 file changed, 12 insertions(+), 5 deletions(-)
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/ProcessContext.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/ProcessContext.java
index 3f45ff4..2dad12b 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/ProcessContext.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/ProcessContext.java
@@ -639,11 +639,18 @@ public class ProcessContext {
String hostName = !(alternateHostName == null || alternateHostName.length() == 0) ? alternateHostName :
getComputeResourceDescription().getHostName();
- return new ServerInfo(
- getComputeResourceLoginUserName(),
- hostName,
- getComputeResourceCredentialToken(),
- sshJobSubmission.getSshPort());
+ if (sshJobSubmission.getSshPort() > 0) {
+ return new ServerInfo(
+ getComputeResourceLoginUserName(),
+ hostName,
+ getComputeResourceCredentialToken(),
+ sshJobSubmission.getSshPort());
+ } else {
+ return new ServerInfo(
+ getComputeResourceLoginUserName(),
+ hostName,
+ getComputeResourceCredentialToken());
+ }
} catch (AppCatalogException e) {
throw new GFacException("Failed to fetch ssh job submission for interface " +
--
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[airavata] 02/04: Fixing AIRAVATA-2624 Sampede2 cluster SSH
connectivity issue
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch develop
in repository https://gitbox.apache.org/repos/asf/airavata.git
commit 02379098159a81612ed8cf4f73a5cef1e3eae9f9
Author: dimuthu.upeksha2@gmail.com <Di...@1234>
AuthorDate: Wed Jan 17 14:29:51 2018 -0500
Fixing AIRAVATA-2624 Sampede2 cluster SSH connectivity issue
---
.../java/org/apache/airavata/gfac/impl/Factory.java | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/Factory.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/Factory.java
index 37848e7..5ef22e1 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/Factory.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/Factory.java
@@ -22,12 +22,7 @@ package org.apache.airavata.gfac.impl;
import com.google.common.cache.Cache;
import com.google.common.cache.CacheBuilder;
import com.google.common.cache.RemovalListener;
-import com.jcraft.jsch.Channel;
-import com.jcraft.jsch.ChannelExec;
-import com.jcraft.jsch.JSch;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.Session;
-import com.jcraft.jsch.UserInfo;
+import com.jcraft.jsch.*;
import org.apache.airavata.common.exception.AiravataException;
import org.apache.airavata.common.exception.ApplicationSettingsException;
import org.apache.airavata.common.utils.ServerSettings;
@@ -596,7 +591,7 @@ public abstract class Factory {
return new ArchiveTask();
}
- private static class DefaultUserInfo implements UserInfo {
+ private static class DefaultUserInfo implements UserInfo, UIKeyboardInteractive {
private String userName;
private String password;
@@ -637,5 +632,11 @@ public abstract class Factory {
public void showMessage(String s) {
}
- }
+
+ @Override
+ public String[] promptKeyboardInteractive(String destination, String name, String instruction,
+ String[] prompt, boolean[] echo) {
+ return new String[0];
+ }
+ }
}
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