[28/35] airavata git commit: AIRAVATA-2500 Thrift stub code generation

[machristie]

http://git-wip-us.apache.org/repos/asf/airavata/blob/3184c238/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/API/Airavata.php
--
diff --git 
a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/API/Airavata.php
 
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/API/Airavata.php
index 18bfcf5..c8976ba 100644
--- 
a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/API/Airavata.php
+++ 
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/API/Airavata.php
@@ -3428,6 +3428,71 @@ interface AiravataIf {
*/
   public function 
deleteGatewayStoragePreference(\Airavata\Model\Security\AuthzToken $authzToken, 
$gatewayID, $storageId);
   /**
+   * @param \Airavata\Model\Security\AuthzToken $authzToken
+   * @return 
\Airavata\Model\AppCatalog\AccountProvisioning\SSHAccountProvisioner[]
+   * @throws \Airavata\API\Error\InvalidRequestException
+   * @throws \Airavata\API\Error\AiravataClientException
+   * @throws \Airavata\API\Error\AiravataSystemException
+   * @throws \Airavata\API\Error\AuthorizationException
+   */
+  public function 
getSSHAccountProvisioners(\Airavata\Model\Security\AuthzToken $authzToken);
+  /**
+   * Check if user has an SSH account on the given compute resource. This
+   * method will only work if the compute resource has an 
SSHAccountProvisioner configured for it.
+   * 
+   * @param \Airavata\Model\Security\AuthzToken $authzToken
+   * @param string $computeResourceId
+   * @param string $userId
+   * @return bool
+   * @throws \Airavata\API\Error\InvalidRequestException
+   * @throws \Airavata\API\Error\AiravataClientException
+   * @throws \Airavata\API\Error\AiravataSystemException
+   * @throws \Airavata\API\Error\AuthorizationException
+   */
+  public function doesUserHaveSSHAccount(\Airavata\Model\Security\AuthzToken 
$authzToken, $computeResourceId, $userId);
+  /**
+   * Setup and return a UserComputeResourcePreference object for this user to 
SSH into the given compute resource with
+   * the given SSH credential. This method will only work if the compute 
resource has an SSHAccountProvisioner
+   * configured for it. The returned UserComputeResourcePreference object is 
not saved; it is up to the client to
+   * call addUserComputeResourcePreference to persist it.
+   * 
+   * @param \Airavata\Model\Security\AuthzToken $authzToken
+   * @param string $computeResourceId
+   * @param string $userId
+   * @param string $airavataCredStoreToken
+   * @return 
\Airavata\Model\AppCatalog\UserResourceProfile\UserComputeResourcePreference 
User specific preferences for a Computer Resource
+   * 
+   * computeResourceId:
+   *   Corelate the preference to a compute resource.
+   * 
+   * 
+   * loginUserName:
+   *   If turned true, Airavata will override the preferences of better 
alternatives exist.
+   * 
+   * 
+   * preferredBatchQueue:
+   *  Gateways can choose a defualt batch queue based on average job 
dimention, reservations or other metrics.
+   * 
+   * scratchLocation:
+   *  Path to the local scratch space on a HPC cluster. Typically used to 
create working directory for job execution.
+   * 
+   * allocationProjectNumber:
+   *  Typically used on HPC machines to charge computing usage to a account 
number. For instance, on XSEDE once an
+   *allocation is approved, an allocation number is assigned. Before 
passing this number with job submittions, the
+   *account to be used has to be added to the allocation.
+   * 
+   * resourceSpecificCredentialStoreToken:
+   *  Resource specific credential store token. If this token is specified, 
then it is superceeded by the gateway's
+   *   default credential store.
+   * 
+   * 
+   * @throws \Airavata\API\Error\InvalidRequestException
+   * @throws \Airavata\API\Error\AiravataClientException
+   * @throws \Airavata\API\Error\AiravataSystemException
+   * @throws \Airavata\API\Error\AuthorizationException
+   */
+  public function 
setupUserComputeResourcePreferencesForSSH(\Airavata\Model\Security\AuthzToken 
$authzToken, $computeResourceId, $userId, $airavataCredStoreToken);
+  /**
* Register User Resource Profile.
* 
* @param UserResourceProfile
@@ -12720,6 +12785,200 @@ class AiravataClient implements 
\Airavata\API\AiravataIf {
 throw new \Exception("deleteGatewayStoragePreference failed: unknown 
result");
   }
 
+  public function 
getSSHAccountProvisioners(\Airavata\Model\Security\AuthzToken $authzToken)
+  {
+$this->send_getSSHAccountProvisioners($authzToken);
+return $this->recv_getSSHAccountProvisioners();
+  }
+
+  public function 
send_getSSHAccountProvisioners(\Airavata\Model\Security\AuthzToken $authzToken)
+  {
+$args = new \Airavata\API\Airavata_getSSHAccountProvisioners_args();
+$args->authzToken = $authzToken;
+$bin_accel = 

[17/35] airavata git commit: AIRAVATA-2500 Add creation of scratch location

[machristie]

AIRAVATA-2500 Add creation of scratch location


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/8c748c66
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/8c748c66
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/8c748c66

Branch: refs/heads/AIRAVATA-2500
Commit: 8c748c66b5f4c40847432b6abe5b1ca535188be9
Parents: 3d161b8
Author: Marcus Christie 
Authored: Wed Aug 23 17:19:05 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:07:56 2017 -0400

--
 .../accountprovisioning/SSHAccountManager.java  | 11 ++-
 .../airavata/accountprovisioning/SSHUtil.java   | 79 +++-
 2 files changed, 84 insertions(+), 6 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/8c748c66/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
--
diff --git 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
index d565fe9..a56a632 100644
--- 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
+++ 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
@@ -34,6 +34,8 @@ import org.apache.airavata.registry.api.RegistryService;
 import org.apache.airavata.registry.api.client.RegistryServiceClientFactory;
 import org.apache.airavata.registry.api.exception.RegistryServiceException;
 import org.apache.thrift.TException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.util.HashMap;
 import java.util.List;
@@ -43,6 +45,8 @@ import java.util.stream.Collectors;
 
 public class SSHAccountManager {
 
+private final static Logger logger = 
LoggerFactory.getLogger(SSHAccountManager.class);
+
 // TODO: change return type to one that returns some details of the SSH 
account setup, for example the scratch location
 public static void setupSSHAccount(String gatewayId, String 
computeResourceId, String username, SSHCredential sshCredential) {
 
@@ -84,8 +88,9 @@ public class SSHAccountManager {
 // Install SSH key
 sshAccountProvisioner.installSSHKey(username, 
sshCredential.getPublicKey());
 
+// TODO: replace hard coded port 22 with port from SSHJobSubmission 
interface
 // Verify can authenticate to host
-boolean validated = SSHUtil.validate(username, 
computeResourceDescription.getHostName(), 22, sshCredential);
+boolean validated = 
SSHUtil.validate(computeResourceDescription.getHostName(), 22, username, 
sshCredential);
 if (!validated) {
 throw new RuntimeException("Failed to validate installation of key 
for [" + username
 + "] on [" + computeResourceDescription.getHostName() + "] 
using SSH Account Provisioner ["
@@ -93,8 +98,10 @@ public class SSHAccountManager {
 }
 
 // create the scratch location on the host
-// TODO: create the scratch location
 String scratchLocation = 
sshAccountProvisioner.getScratchLocation(username);
+SSHUtil.execute(computeResourceDescription.getHostName(), 22, 
username, sshCredential, "mkdir -p " + scratchLocation);
+
+// TODO: return information about provisioned account
 }
 
 private static Map resolveProvisionerConfig(String 
gatewayId, String provisionerName, Map provisionerConfig) {

http://git-wip-us.apache.org/repos/asf/airavata/blob/8c748c66/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHUtil.java
--
diff --git 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHUtil.java
 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHUtil.java
index 4b5452a..2550270 100644
--- 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHUtil.java
+++ 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHUtil.java
@@ -20,12 +20,14 @@
 
 package org.apache.airavata.accountprovisioning;
 
-import com.jcraft.jsch.JSch;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.Session;
+import com.jcraft.jsch.*;
 import org.apache.airavata.model.credential.store.SSHCredential;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
+import java.io.ByteArrayOutputStream;

[12/35] airavata git commit: AIRAVATA-2500 SSHAccountManager: install SSH key and verify

[machristie]

AIRAVATA-2500 SSHAccountManager: install SSH key and verify


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/3d161b81
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/3d161b81
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/3d161b81

Branch: refs/heads/AIRAVATA-2500
Commit: 3d161b8161975be658259739047e36df3bd6ef38
Parents: 2a90139
Author: Marcus Christie 
Authored: Mon Aug 14 12:38:53 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:07:56 2017 -0400

--
 .../accountprovisioning/SSHAccountManager.java  | 104 ++-
 .../airavata/accountprovisioning/SSHUtil.java   |  83 +++
 2 files changed, 162 insertions(+), 25 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/3d161b81/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
--
diff --git 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
index dcb819b..d565fe9 100644
--- 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
+++ 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
@@ -25,43 +25,48 @@ import org.apache.airavata.common.utils.ServerSettings;
 import 
org.apache.airavata.credential.store.client.CredentialStoreClientFactory;
 import org.apache.airavata.credential.store.cpi.CredentialStoreService;
 import org.apache.airavata.credential.store.exception.CredentialStoreException;
+import 
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisionerConfigParam;
+import 
org.apache.airavata.model.appcatalog.computeresource.ComputeResourceDescription;
+import 
org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference;
 import org.apache.airavata.model.credential.store.PasswordCredential;
+import org.apache.airavata.model.credential.store.SSHCredential;
 import org.apache.airavata.registry.api.RegistryService;
 import org.apache.airavata.registry.api.client.RegistryServiceClientFactory;
 import org.apache.airavata.registry.api.exception.RegistryServiceException;
 import org.apache.thrift.TException;
 
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
+import java.util.function.Function;
+import java.util.stream.Collectors;
 
 public class SSHAccountManager {
 
-// TODO: need private key too to verify
-public static void setupSSHAccount(String gatewayId, String hostname, 
String username, String sshPublicKey) {
-
-// TODO: finish implementing
+// TODO: change return type to one that returns some details of the SSH 
account setup, for example the scratch location
+public static void setupSSHAccount(String gatewayId, String 
computeResourceId, String username, SSHCredential sshCredential) {
 
 // get compute resource preferences for the gateway and hostname
+// TODO: close the registry service client transport when done with it
+RegistryService.Client registryServiceClient = 
getRegistryServiceClient();
+ComputeResourcePreference computeResourcePreference = null;
+ComputeResourceDescription computeResourceDescription = null;
+try {
+computeResourcePreference = 
registryServiceClient.getGatewayComputeResourcePreference(gatewayId, 
computeResourceId);
+computeResourceDescription = 
registryServiceClient.getComputeResource(computeResourceId);
+} catch(TException e) {
+throw new RuntimeException(e);
+}
 
 // get the account provisioner and config values for the preferences
-String provisionerName = null;
-Map provisionerConfig = null;
-
-CredentialStoreService.Client credentialStoreServiceClient = 
getCredentialStoreClient();
-// Resolve any CRED_STORE_PASSWORD_TOKEN config parameters to passwords
-Map resolvedConfig = new HashMap<>();
-for (Map.Entry configEntry : 
provisionerConfig.entrySet() ) {
-if (configEntry.getKey().getType() == 
ConfigParam.ConfigParamType.CRED_STORE_PASSWORD_TOKEN) {
-try {
-PasswordCredential password = 
credentialStoreServiceClient.getPasswordCredential(configEntry.getValue(), 
gatewayId);
-resolvedConfig.put(configEntry.getKey(), 
password.getPassword());
-} catch (TException e) {
-  

[32/35] airavata git commit: AIRAVATA-2500 Thrift stub code generation

[machristie]

AIRAVATA-2500 Thrift stub code generation


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/fab19005
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/fab19005
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/fab19005

Branch: refs/heads/AIRAVATA-2500
Commit: fab19005af44bec99634aa5d9233948803428d16
Parents: 71d33ea
Author: Marcus Christie 
Authored: Thu Sep 7 15:16:43 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:08:05 2017 -0400

--
 .../Model/AppCatalog/GatewayProfile/Types.php   |  23 
 .../ComputeResourcePreference.java  | 114 ++-
 2 files changed, 133 insertions(+), 4 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/fab19005/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/Model/AppCatalog/GatewayProfile/Types.php
--
diff --git 
a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/Model/AppCatalog/GatewayProfile/Types.php
 
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/Model/AppCatalog/GatewayProfile/Types.php
index da3071a..63e39bc 100644
--- 
a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/Model/AppCatalog/GatewayProfile/Types.php
+++ 
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/Model/AppCatalog/GatewayProfile/Types.php
@@ -118,6 +118,10 @@ class ComputeResourcePreference {
* @var array
*/
   public $sshAccountProvisionerConfig = null;
+  /**
+   * @var string
+   */
+  public $sshAccountProvisionerAdditionalInfo = null;
 
   public function __construct($vals=null) {
 if (!isset(self::$_TSPEC)) {
@@ -194,6 +198,10 @@ class ComputeResourcePreference {
 'type' => TType::STRING,
 ),
   ),
+17 => array(
+  'var' => 'sshAccountProvisionerAdditionalInfo',
+  'type' => TType::STRING,
+  ),
 );
 }
 if (is_array($vals)) {
@@ -245,6 +253,9 @@ class ComputeResourcePreference {
   if (isset($vals['sshAccountProvisionerConfig'])) {
 $this->sshAccountProvisionerConfig = 
$vals['sshAccountProvisionerConfig'];
   }
+  if (isset($vals['sshAccountProvisionerAdditionalInfo'])) {
+$this->sshAccountProvisionerAdditionalInfo = 
$vals['sshAccountProvisionerAdditionalInfo'];
+  }
 }
   }
 
@@ -392,6 +403,13 @@ class ComputeResourcePreference {
 $xfer += $input->skip($ftype);
   }
   break;
+case 17:
+  if ($ftype == TType::STRING) {
+$xfer += 
$input->readString($this->sshAccountProvisionerAdditionalInfo);
+  } else {
+$xfer += $input->skip($ftype);
+  }
+  break;
 default:
   $xfer += $input->skip($ftype);
   break;
@@ -498,6 +516,11 @@ class ComputeResourcePreference {
   }
   $xfer += $output->writeFieldEnd();
 }
+if ($this->sshAccountProvisionerAdditionalInfo !== null) {
+  $xfer += $output->writeFieldBegin('sshAccountProvisionerAdditionalInfo', 
TType::STRING, 17);
+  $xfer += 
$output->writeString($this->sshAccountProvisionerAdditionalInfo);
+  $xfer += $output->writeFieldEnd();
+}
 $xfer += $output->writeFieldStop();
 $xfer += $output->writeStructEnd();
 return $xfer;

http://git-wip-us.apache.org/repos/asf/airavata/blob/fab19005/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
--
diff --git 
a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
 
b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
index 3edf60c..d758e9d 100644
--- 
a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
+++ 
b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
@@ -105,6 +105,7 @@ public class ComputeResourcePreference implements 
org.apache.thrift.TBase, SchemeFactory> schemes = 
new HashMap();
   static {
@@ -128,6 +129,7 @@ public class ComputeResourcePreference implements 
org.apache.thrift.TBase sshAccountProvisionerConfig; // optional
+  private String sshAccountProvisionerAdditionalInfo; // optional
 
   /** The set of fields this struct contains, along with convenience 

[23/35] airavata git commit: AIRAVATA-2500 Implement API method to get provisioner metadata

[machristie]

AIRAVATA-2500 Implement API method to get provisioner metadata


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/643d35b3
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/643d35b3
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/643d35b3

Branch: refs/heads/AIRAVATA-2500
Commit: 643d35b3884d1014a47c3a1b50fc6580d0dabeb1
Parents: 469a7e7
Author: Marcus Christie 
Authored: Thu Sep 7 09:41:17 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:07:57 2017 -0400

--
 .../server/handler/AiravataServerHandler.java   | 56 ++--
 .../accountprovisioning/SSHAccountManager.java  |  3 +-
 .../SSHAccountProvisioner.java  | 10 ++--
 .../SSHAccountProvisionerFactory.java   | 14 ++---
 .../SSHAccountProvisionerProvider.java  |  3 +-
 .../IULdapSSHAccountProvisioner.java| 10 
 .../IULdapSSHAccountProvisionerProvider.java| 31 ++-
 .../SSHAccountProvisionerFactoryTest.java   |  4 +-
 .../provisioner/TestSSHAccountProvisioner.java  | 10 
 .../TestSSHAccountProvisionerProvider.java  | 10 
 .../airavata-apis/airavata_api.thrift   | 12 ++---
 .../account_provisioning_model.thrift   | 12 +++--
 12 files changed, 107 insertions(+), 68 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/643d35b3/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
--
diff --git 
a/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
 
b/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
index bb3f2c0..febb703 100644
--- 
a/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
+++ 
b/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
@@ -19,7 +19,10 @@
  */
 package org.apache.airavata.api.server.handler;
 
+import org.apache.airavata.accountprovisioning.ConfigParam;
 import org.apache.airavata.accountprovisioning.SSHAccountManager;
+import org.apache.airavata.accountprovisioning.SSHAccountProvisionerFactory;
+import org.apache.airavata.accountprovisioning.SSHAccountProvisionerProvider;
 import org.apache.airavata.api.Airavata;
 import org.apache.airavata.api.airavata_apiConstants;
 import org.apache.airavata.api.server.util.ThriftClientPool;
@@ -38,6 +41,7 @@ import org.apache.airavata.messaging.core.Type;
 import org.apache.airavata.model.WorkflowModel;
 import 
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisioner;
 import 
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisionerConfigParam;
+import 
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisionerConfigParamType;
 import 
org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
 import org.apache.airavata.model.appcatalog.appdeployment.ApplicationModule;
 import 
org.apache.airavata.model.appcatalog.appinterface.ApplicationInterfaceDescription;
@@ -3969,30 +3973,48 @@ public class AiravataServerHandler implements 
Airavata.Iface {
 
 @Override
 @SecurityCheck
-public List 
getSSHAccountProvisionerNames(AuthzToken authzToken) throws 
InvalidRequestException, AiravataClientException, AiravataSystemException, 
AuthorizationException, TException {
+public List getSSHAccountProvisioners(AuthzToken 
authzToken) throws InvalidRequestException, AiravataClientException, 
AiravataSystemException, AuthorizationException, TException {
 
-// TODO: implement
-return null;
-}
-
-@Override
-@SecurityCheck
-public List 
getSSHAccountProvisionerConfigParams(AuthzToken authzToken, String 
provisionerName) throws InvalidRequestException, AiravataClientException, 
AiravataSystemException, AuthorizationException, TException {
-
-// TODO: implement
-return null;
+List sshAccountProvisioners = new ArrayList<>();
+List sshAccountProvisionerProviders = 
SSHAccountProvisionerFactory.getSSHAccountProvisionerProviders();
+for (SSHAccountProvisionerProvider provider : 
sshAccountProvisionerProviders) {
+// TODO: Move this Thrift conversion to utility class
+SSHAccountProvisioner sshAccountProvisioner = new 
SSHAccountProvisioner();
+
sshAccountProvisioner.setCanCreateAccount(provider.canCreateAccount());
+
sshAccountProvisioner.setCanInstallSSHKey(provider.canInstallSSHKey());
+

[19/35] airavata git commit: AIRAVATA-2500 Persist SSH account provisioner and config

[machristie]

AIRAVATA-2500 Persist SSH account provisioner and config


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/ac2823a6
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/ac2823a6
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/ac2823a6

Branch: refs/heads/AIRAVATA-2500
Commit: ac2823a604abca6e0db6314dd7658c1325bb94c3
Parents: 722aabd
Author: Marcus Christie 
Authored: Fri Sep 1 12:33:40 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:07:56 2017 -0400

--
 .../accountprovisioning/SSHAccountManager.java  |  5 +-
 .../catalog/impl/GwyResourceProfileImpl.java| 10 ++
 .../model/ComputeResourcePreference.java| 31 +--
 .../SSHAccountProvisionerConfiguration.java | 98 
 .../SSHAccountProvisionerConfigurationPK.java   | 57 
 .../ComputeHostPreferenceResource.java  | 50 +++---
 .../app/catalog/util/AppCatalogJPAUtils.java|  8 ++
 .../util/AppCatalogThriftConversion.java|  8 +-
 .../src/main/resources/META-INF/persistence.xml |  1 +
 .../src/main/resources/appcatalog-derby.sql | 11 +++
 .../src/main/resources/appcatalog-mysql.sql | 13 ++-
 .../DeltaScripts/appCatalog_schema_delta.sql| 31 +++
 .../gateway_resource_profile_model.thrift   |  2 +-
 13 files changed, 300 insertions(+), 25 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/ac2823a6/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
--
diff --git 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
index f9ed22a..74c0dd2 100644
--- 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
+++ 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
@@ -25,7 +25,6 @@ import org.apache.airavata.common.utils.ServerSettings;
 import 
org.apache.airavata.credential.store.client.CredentialStoreClientFactory;
 import org.apache.airavata.credential.store.cpi.CredentialStoreService;
 import org.apache.airavata.credential.store.exception.CredentialStoreException;
-import 
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisionerConfigParam;
 import 
org.apache.airavata.model.appcatalog.computeresource.ComputeResourceDescription;
 import 
org.apache.airavata.model.appcatalog.computeresource.JobSubmissionInterface;
 import 
org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol;
@@ -181,11 +180,11 @@ public class SSHAccountManager {
 }
 }
 
-private static Map convertConfigParams(String 
provisionerName, Map 
thriftConfigParams) {
+private static Map convertConfigParams(String 
provisionerName, Map thriftConfigParams) {
 List configParams = 
SSHAccountProvisionerFactory.getSSHAccountProvisionerConfigParams(provisionerName);
 Map configParamMap = 
configParams.stream().collect(Collectors.toMap(ConfigParam::getName, 
Function.identity()));
 
-return 
thriftConfigParams.entrySet().stream().collect(Collectors.toMap(entry -> 
configParamMap.get(entry.getKey().getName()), entry -> entry.getValue()));
+return 
thriftConfigParams.entrySet().stream().collect(Collectors.toMap(entry -> 
configParamMap.get(entry.getKey()), entry -> entry.getValue()));
 }
 
 private static RegistryService.Client getRegistryServiceClient() {

http://git-wip-us.apache.org/repos/asf/airavata/blob/ac2823a6/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/impl/GwyResourceProfileImpl.java
--
diff --git 
a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/impl/GwyResourceProfileImpl.java
 
b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/impl/GwyResourceProfileImpl.java
index ccfb08a..78a6f0f 100644
--- 
a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/impl/GwyResourceProfileImpl.java
+++ 
b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/impl/GwyResourceProfileImpl.java
@@ -89,6 +89,11 @@ public class GwyResourceProfileImpl implements 
GwyResourceProfile {
 if 

[16/35] airavata git commit: AIRAVATA-2500 Finish implementing SSHAccountManager

[machristie]

AIRAVATA-2500 Finish implementing SSHAccountManager


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/0d1e90f6
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/0d1e90f6
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/0d1e90f6

Branch: refs/heads/AIRAVATA-2500
Commit: 0d1e90f612831337588867f2589819eefcadde0a
Parents: 8c748c6
Author: Marcus Christie 
Authored: Thu Aug 24 14:23:10 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:07:56 2017 -0400

--
 .../accountprovisioning/SSHAccountManager.java  | 41 ++--
 1 file changed, 30 insertions(+), 11 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/0d1e90f6/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
--
diff --git 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
index a56a632..ec7cfc1 100644
--- 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
+++ 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
@@ -27,7 +27,11 @@ import 
org.apache.airavata.credential.store.cpi.CredentialStoreService;
 import org.apache.airavata.credential.store.exception.CredentialStoreException;
 import 
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisionerConfigParam;
 import 
org.apache.airavata.model.appcatalog.computeresource.ComputeResourceDescription;
+import 
org.apache.airavata.model.appcatalog.computeresource.JobSubmissionInterface;
+import 
org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol;
+import org.apache.airavata.model.appcatalog.computeresource.SSHJobSubmission;
 import 
org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference;
+import 
org.apache.airavata.model.appcatalog.userresourceprofile.UserComputeResourcePreference;
 import org.apache.airavata.model.credential.store.PasswordCredential;
 import org.apache.airavata.model.credential.store.SSHCredential;
 import org.apache.airavata.registry.api.RegistryService;
@@ -47,24 +51,37 @@ public class SSHAccountManager {
 
 private final static Logger logger = 
LoggerFactory.getLogger(SSHAccountManager.class);
 
-// TODO: change return type to one that returns some details of the SSH 
account setup, for example the scratch location
-public static void setupSSHAccount(String gatewayId, String 
computeResourceId, String username, SSHCredential sshCredential) {
+public static UserComputeResourcePreference setupSSHAccount(String 
gatewayId, String computeResourceId, String username, SSHCredential 
sshCredential) {
 
 // get compute resource preferences for the gateway and hostname
-// TODO: close the registry service client transport when done with it
 RegistryService.Client registryServiceClient = 
getRegistryServiceClient();
 ComputeResourcePreference computeResourcePreference = null;
 ComputeResourceDescription computeResourceDescription = null;
+SSHJobSubmission sshJobSubmission = null;
 try {
 computeResourcePreference = 
registryServiceClient.getGatewayComputeResourcePreference(gatewayId, 
computeResourceId);
 computeResourceDescription = 
registryServiceClient.getComputeResource(computeResourceId);
+// Find the SSHJobSubmission
+for (JobSubmissionInterface jobSubmissionInterface : 
computeResourceDescription.getJobSubmissionInterfaces()) {
+if (jobSubmissionInterface.getJobSubmissionProtocol() == 
JobSubmissionProtocol.SSH) {
+sshJobSubmission = 
registryServiceClient.getSSHJobSubmission(jobSubmissionInterface.getJobSubmissionInterfaceId());
+break;
+}
+}
 } catch(TException e) {
 throw new RuntimeException(e);
+} finally {
+if 
(registryServiceClient.getInputProtocol().getTransport().isOpen()) {
+
registryServiceClient.getInputProtocol().getTransport().close();
+}
+}
+
+if (sshJobSubmission == null) {
+throw new RuntimeException("Compute resource [" + 
computeResourceId + "] does not have an SSH Job Submission interface.");
 }
 
 // get the account provisioner and config values for the preferences
 if (!computeResourcePreference.isSetSshAccountProvisioner()) {
-

[04/35] airavata git commit: Added IU Geology Survey Group gateway directory vara.yml

[machristie]

Added IU Geology Survey Group gateway directory vara.yml


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/862c25be
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/862c25be
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/862c25be

Branch: refs/heads/AIRAVATA-2500
Commit: 862c25be80db341369c40781ea8d3f531eb76bfd
Parents: 2f471d1
Author: Eroma Abeysinghe 
Authored: Mon Aug 14 16:41:52 2017 -0400
Committer: Eroma Abeysinghe 
Committed: Mon Aug 14 16:41:52 2017 -0400

--
 .../production/pga_config/iugeosurvey/vars.yml  | 61 
 1 file changed, 61 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/862c25be/dev-tools/ansible/inventories/scigap/production/pga_config/iugeosurvey/vars.yml
--
diff --git 
a/dev-tools/ansible/inventories/scigap/production/pga_config/iugeosurvey/vars.yml
 
b/dev-tools/ansible/inventories/scigap/production/pga_config/iugeosurvey/vars.yml
new file mode 100644
index 000..bbbaf31
--- /dev/null
+++ 
b/dev-tools/ansible/inventories/scigap/production/pga_config/iugeosurvey/vars.yml
@@ -0,0 +1,61 @@
+#
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
+---
+pga_repo: "https://github.com/apache/airavata-php-gateway.git;
+git_branch: "master"
+user: "pga"
+group: "pga"
+doc_root_dir: "/var/www/portals/{{ gateway_id }}"
+vhost_servername: "geosurveyiu.scigap.org"
+vhost_ssl: true
+# TODO: have Ansible manage these files as well
+ssl_certificate_file: "/etc/letsencrypt/live/geosurveyiu.scigap.org/cert.pem"
+ssl_certificate_chain_file: 
"/etc/letsencrypt/live/geosurveyiu.scigap.org/fullchain.pem"
+ssl_certificate_key_file: 
"/etc/letsencrypt/live/geosurveyiu.scigap.org/privkey.pem"
+
+## Keycloak related variables
+tenant_domain: "{{ gateway_id }}"
+admin_username: "admin"
+admin_password: "{{ vault_admin_password }}"
+oauth_client_key: "{{ vault_oauth_client_key }}"
+oauth_client_secret: "{{ vault_oauth_client_secret }}"
+oidc_discovery_url: "https://iam.scigap.org/auth/realms/{{ tenant_domain 
}}/.well-known/openid-configuration"
+
+auth_options:
+  - name: "IU Geology Survey"
+oauth_grant_type: "password"
+oauth_callback_url: "https://{{ vhost_servername }}/callback-url"
+
+gateway_id: "iu-geology-survey"
+# relative to document root dir
+experiment_data_dir: "{{ user_data_dir }}/{{ gateway_id }}"
+gateway_data_store_resource_id: 
"gf4.ucs.indiana.edu_61552681-96f0-462a-a36c-a62a010bffc6"
+#gateway_data_store_ssh_public_key: "ssh-rsa 
B3NzaC1yc2EDAQABAAABAQDEuA1indjdczBXg2qrmD0bB0QfKq0u2q3o25DegTaty5LoogW+APEvXmwc2g6PzkM75MgfMsTErMQaQ3/PoElADQKg2/NePz05YWobn9zrPZFeRWfOqWMjFDx72cffHKBzgnahFDBlR/YJhf4IZJ+EOA1zMiMF2oZQmEYQtbQFhbKPF+jrScEQeuXVuXWSS2sKNAVKj3pY4kmi9kEOYELee/O6ghBUfrVhB95vDKJPgmQSuo3pgkLRdflTBSAQ54UchwjXi2RA9Xv0RXJF/JyyRGn6bSbRxYhsm5RJeiBVj4ua7p2b36rSYVqtVsTKEonx5kYdKzwyjJXWpjB2KtQp"
+
+## Portal related variables
+super_admin_portal: "false"
+admin_emails: "['sgrc-iu-gr...@iu.edu','wangy...@indiana.edu']"
+portal_email_username: "pga.airav...@gmail.com"
+portal_email_password: "{{ vault_portal_email_password }}"
+#portal_theme: "gsu-gateway-theme"
+#portal_theme_repo: "https://github.com/SciGaP/gsu-gateway-theme;
+portal_title: "IU Geology Survey"
+...

[20/35] airavata git commit: AIRAVATA-2500: generated Thrift stub code

[machristie]

http://git-wip-us.apache.org/repos/asf/airavata/blob/722aabd4/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/accountprovisioning/SSHAccountProvisioner.java
--
diff --git 
a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/accountprovisioning/SSHAccountProvisioner.java
 
b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/accountprovisioning/SSHAccountProvisioner.java
new file mode 100644
index 000..fb0a965
--- /dev/null
+++ 
b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/accountprovisioning/SSHAccountProvisioner.java
@@ -0,0 +1,600 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+/**
+ * Autogenerated by Thrift Compiler (0.9.3)
+ *
+ * DO NOT EDIT UNLESS YOU ARE SURE THAT YOU KNOW WHAT YOU ARE DOING
+ *  @generated
+ */
+package org.apache.airavata.model.appcatalog.accountprovisioning;
+
+import org.apache.thrift.scheme.IScheme;
+import org.apache.thrift.scheme.SchemeFactory;
+import org.apache.thrift.scheme.StandardScheme;
+
+import org.apache.thrift.scheme.TupleScheme;
+import org.apache.thrift.protocol.TTupleProtocol;
+import org.apache.thrift.protocol.TProtocolException;
+import org.apache.thrift.EncodingUtils;
+import org.apache.thrift.TException;
+import org.apache.thrift.async.AsyncMethodCallback;
+import org.apache.thrift.server.AbstractNonblockingServer.*;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.Map;
+import java.util.HashMap;
+import java.util.EnumMap;
+import java.util.Set;
+import java.util.HashSet;
+import java.util.EnumSet;
+import java.util.Collections;
+import java.util.BitSet;
+import java.nio.ByteBuffer;
+import java.util.Arrays;
+import javax.annotation.Generated;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+@SuppressWarnings({"cast", "rawtypes", "serial", "unchecked"})
+@Generated(value = "Autogenerated by Thrift Compiler (0.9.3)")
+public class SSHAccountProvisioner implements 
org.apache.thrift.TBase, 
java.io.Serializable, Cloneable, Comparable {
+  private static final org.apache.thrift.protocol.TStruct STRUCT_DESC = new 
org.apache.thrift.protocol.TStruct("SSHAccountProvisioner");
+
+  private static final org.apache.thrift.protocol.TField NAME_FIELD_DESC = new 
org.apache.thrift.protocol.TField("name", 
org.apache.thrift.protocol.TType.STRING, (short)1);
+  private static final org.apache.thrift.protocol.TField 
CAN_CREATE_ACCOUNT_FIELD_DESC = new 
org.apache.thrift.protocol.TField("canCreateAccount", 
org.apache.thrift.protocol.TType.BOOL, (short)2);
+  private static final org.apache.thrift.protocol.TField 
CAN_INSTALL_SSHKEY_FIELD_DESC = new 
org.apache.thrift.protocol.TField("canInstallSSHKey", 
org.apache.thrift.protocol.TType.BOOL, (short)3);
+
+  private static final Map schemes = 
new HashMap();
+  static {
+schemes.put(StandardScheme.class, new 
SSHAccountProvisionerStandardSchemeFactory());
+schemes.put(TupleScheme.class, new 
SSHAccountProvisionerTupleSchemeFactory());
+  }
+
+  private String name; // required
+  private boolean canCreateAccount; // required
+  private boolean canInstallSSHKey; // required
+
+  /** The set of fields this struct contains, along with convenience methods 
for finding and manipulating them. */
+  public enum _Fields implements org.apache.thrift.TFieldIdEnum {
+NAME((short)1, "name"),
+CAN_CREATE_ACCOUNT((short)2, "canCreateAccount"),
+CAN_INSTALL_SSHKEY((short)3, "canInstallSSHKey");
+
+private static final Map byName = new HashMap();
+
+static {
+  for (_Fields field : EnumSet.allOf(_Fields.class)) {
+byName.put(field.getFieldName(), field);
+  }
+}
+
+/**
+ * Find the _Fields constant that matches fieldId, or null if its not 
found.
+ */
+public static _Fields findByThriftId(int fieldId) {
+  switch(fieldId) {
+case 1: // NAME
+  return NAME;
+case 2: // CAN_CREATE_ACCOUNT
+  return 

[24/35] airavata git commit: AIRAVATA-2500 Thrift stub generation

[machristie]

http://git-wip-us.apache.org/repos/asf/airavata/blob/469a7e79/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
--
diff --git 
a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
 
b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
index 0d52abb..5601424 100644
--- 
a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
+++ 
b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
@@ -23,32 +23,15 @@
  */
 package org.apache.airavata.model.appcatalog.gatewayprofile;
 
+import org.apache.thrift.EncodingUtils;
+import org.apache.thrift.protocol.TTupleProtocol;
 import org.apache.thrift.scheme.IScheme;
 import org.apache.thrift.scheme.SchemeFactory;
 import org.apache.thrift.scheme.StandardScheme;
-
 import org.apache.thrift.scheme.TupleScheme;
-import org.apache.thrift.protocol.TTupleProtocol;
-import org.apache.thrift.protocol.TProtocolException;
-import org.apache.thrift.EncodingUtils;
-import org.apache.thrift.TException;
-import org.apache.thrift.async.AsyncMethodCallback;
-import org.apache.thrift.server.AbstractNonblockingServer.*;
-import java.util.List;
-import java.util.ArrayList;
-import java.util.Map;
-import java.util.HashMap;
-import java.util.EnumMap;
-import java.util.Set;
-import java.util.HashSet;
-import java.util.EnumSet;
-import java.util.Collections;
-import java.util.BitSet;
-import java.nio.ByteBuffer;
-import java.util.Arrays;
+
 import javax.annotation.Generated;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+import java.util.*;
 
 @SuppressWarnings({"cast", "rawtypes", "serial", "unchecked"})
 /**
@@ -127,7 +110,7 @@ public class ComputeResourcePreference implements 
org.apache.thrift.TBase
 sshAccountProvisionerConfig; // optional
+  private Map sshAccountProvisionerConfig; // optional
 
   /** The set of fields this struct contains, along with convenience methods 
for finding and manipulating them. */
   public enum _Fields implements org.apache.thrift.TFieldIdEnum {
@@ -281,7 +264,7 @@ public class ComputeResourcePreference implements 
org.apache.thrift.TBase
 __this__sshAccountProvisionerConfig = new 
HashMap(other.sshAccountProvisionerConfig.size());
-  for 
(Map.Entry other_element : other.sshAccountProvisionerConfig.entrySet()) {
-
-
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisionerConfigParam
 other_element_key = other_element.getKey();
-String other_element_value = other_element.getValue();
-
-
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisionerConfigParam
 __this__sshAccountProvisionerConfig_copy_key = new 
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisionerConfigParam(other_element_key);
-
-String __this__sshAccountProvisionerConfig_copy_value = 
other_element_value;
-
-
__this__sshAccountProvisionerConfig.put(__this__sshAccountProvisionerConfig_copy_key,
 __this__sshAccountProvisionerConfig_copy_value);
-  }
+  Map __this__sshAccountProvisionerConfig = new 
HashMap(other.sshAccountProvisionerConfig);
   this.sshAccountProvisionerConfig = __this__sshAccountProvisionerConfig;
 }
   }
@@ -752,18 +724,18 @@ public class ComputeResourcePreference implements 
org.apache.thrift.TBase();
+  this.sshAccountProvisionerConfig = new HashMap();
 }
 this.sshAccountProvisionerConfig.put(key, val);
   }
 
-  public 
Map
 getSshAccountProvisionerConfig() {
+  public Map getSshAccountProvisionerConfig() {
 return this.sshAccountProvisionerConfig;
   }
 
-  public void 
setSshAccountProvisionerConfig(Map
 sshAccountProvisionerConfig) {
+  public void setSshAccountProvisionerConfig(Map 
sshAccountProvisionerConfig) {
 this.sshAccountProvisionerConfig = sshAccountProvisionerConfig;
   }
 
@@ -908,7 +880,7 @@ public class ComputeResourcePreference implements 
org.apache.thrift.TBase)value);
+setSshAccountProvisionerConfig((Map)value);
   }
   break;
 
@@ -1767,13 +1739,12 @@ public class ComputeResourcePreference implements 

[21/35] airavata git commit: AIRAVATA-2500: generated Thrift stub code

[machristie]

http://git-wip-us.apache.org/repos/asf/airavata/blob/722aabd4/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
--
diff --git 
a/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
 
b/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
index 851f96e..6214caf 100644
--- 
a/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
+++ 
b/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
@@ -2621,11 +2621,34 @@ public class Airavata {
  */
 public boolean 
deleteGatewayStoragePreference(org.apache.airavata.model.security.AuthzToken 
authzToken, String gatewayID, String storageId) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
 
-public List 
getSSHAccountProvisionerNames(org.apache.airavata.model.security.AuthzToken 
authzToken) throws org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
+public 
List
 getSSHAccountProvisionerNames(org.apache.airavata.model.security.AuthzToken 
authzToken) throws org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
 
 public 
List
 
getSSHAccountProvisionerConfigParams(org.apache.airavata.model.security.AuthzToken
 authzToken, String provisionerName) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
 
 /**
+ * Setup and return a UserComputeResourcePreference object for this user 
to SSH into the given compute resource with
+ * the given SSH credential. This method will only work if the compute 
resource has an SSHAccountProvisioner
+ * configured for it. The returned UserComputeResourcePreference object is 
not saved; it is up to the client to
+ * call addUserComputeResourcePreference to persist it.
+ * 
+ * @param authzToken
+ * @param computeResourceId
+ * @param username
+ * @param airavataCredStoreToken
+ */
+public 
org.apache.airavata.model.appcatalog.userresourceprofile.UserComputeResourcePreference
 
setupUserComputeResourcePreferencesForSSH(org.apache.airavata.model.security.AuthzToken
 authzToken, String computeResourceId, String username, String 
airavataCredStoreToken) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
+
+/**
+ * Check if user has an SSH account on the given compute resource. This
+ * method will only work if the compute resource has an 
SSHAccountProvisioner configured for it.
+ * 
+ * @param authzToken
+ * @param computeResourceId
+ * @param username
+ */
+public boolean 
doesUserHaveSSHAccount(org.apache.airavata.model.security.AuthzToken 
authzToken, String computeResourceId, String username) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
+
+/**
  * Register User Resource Profile.
  * 
  * @param UserResourceProfile
@@ -3299,6 +3322,10 @@ public class Airavata {
 
 public void 
getSSHAccountProvisionerConfigParams(org.apache.airavata.model.security.AuthzToken
 authzToken, String provisionerName, 
org.apache.thrift.async.AsyncMethodCallback resultHandler) throws 
org.apache.thrift.TException;
 
+public void 
setupUserComputeResourcePreferencesForSSH(org.apache.airavata.model.security.AuthzToken
 authzToken, String computeResourceId, String username, String 
airavataCredStoreToken, org.apache.thrift.async.AsyncMethodCallback 
resultHandler) throws org.apache.thrift.TException;
+
+public void 
doesUserHaveSSHAccount(org.apache.airavata.model.security.AuthzToken 
authzToken, String computeResourceId, String username, 
org.apache.thrift.async.AsyncMethodCallback resultHandler) throws 
org.apache.thrift.TException;
+
 

[30/35] airavata git commit: AIRAVATA-2500 Thrift stub code generation

[machristie]

AIRAVATA-2500 Thrift stub code generation


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/3184c238
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/3184c238
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/3184c238

Branch: refs/heads/AIRAVATA-2500
Commit: 3184c23874cf15aef991859bbb87b9d1e0892f9d
Parents: 643d35b
Author: Marcus Christie 
Authored: Thu Sep 7 09:42:32 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:08:05 2017 -0400

--
 .../java/org/apache/airavata/api/Airavata.java  | 36866 -
 .../resources/lib/Airavata/API/Airavata.php |  8436 ++--
 .../Model/AppCatalog/GatewayProfile/Types.php   |   120 +-
 .../SSHAccountProvisioner.java  |   159 +-
 .../ComputeResourcePreference.java  |25 +-
 5 files changed, 22774 insertions(+), 22832 deletions(-)
--

[31/35] airavata git commit: Integrate IULdapSSHAccountProvisioner with fixes

[machristie]

Integrate IULdapSSHAccountProvisioner with fixes


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/74371129
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/74371129
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/74371129

Branch: refs/heads/AIRAVATA-2500
Commit: 743711290ee07336005ee7a4d023cdce5325a6f6
Parents: 1c2ab27
Author: Marcus Christie 
Authored: Mon Sep 18 15:12:16 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:08:05 2017 -0400

--
 .../IULdapSSHAccountProvisioner.java| 242 ++-
 .../IULdapSSHAccountProvisionerProvider.java|  47 ++--
 .../SSHAccountProvisionerFactoryTest.java   |   4 -
 .../TestSSHAccountProvisionerProvider.java  |   2 +-
 4 files changed, 153 insertions(+), 142 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/74371129/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/provisioner/IULdapSSHAccountProvisioner.java
--
diff --git 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/provisioner/IULdapSSHAccountProvisioner.java
 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/provisioner/IULdapSSHAccountProvisioner.java
index 331c01c..d0c204f 100644
--- 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/provisioner/IULdapSSHAccountProvisioner.java
+++ 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/provisioner/IULdapSSHAccountProvisioner.java
@@ -21,152 +21,158 @@
 package org.apache.airavata.accountprovisioning.provisioner;
 
 import org.apache.airavata.accountprovisioning.ConfigParam;
+import org.apache.airavata.accountprovisioning.SSHAccountManager;
 import org.apache.airavata.accountprovisioning.SSHAccountProvisioner;
-import org.apache.directory.api.ldap.model.cursor.CursorException;
-import org.apache.directory.ldap.client.api.*;
-import org.apache.directory.api.ldap.model.cursor.EntryCursor;
-import org.apache.directory.api.ldap.model.entry.Attribute;
+import org.apache.directory.api.ldap.model.entry.DefaultAttribute;
 import org.apache.directory.api.ldap.model.entry.Entry;
-import org.apache.directory.api.ldap.model.entry.Modification;
-import org.apache.directory.api.ldap.model.entry.DefaultEntry;
+import org.apache.directory.api.ldap.model.entry.ModificationOperation;
 import org.apache.directory.api.ldap.model.exception.LdapException;
-import org.apache.directory.api.ldap.model.message.SearchScope;
-import org.apache.directory.api.ldap.model.message.DeleteResponse;
+import org.apache.directory.api.ldap.model.message.ModifyRequest;
+import org.apache.directory.api.ldap.model.message.ModifyRequestImpl;
+import org.apache.directory.api.ldap.model.message.ModifyResponse;
 import org.apache.directory.api.ldap.model.message.ResultCodeEnum;
-import org.junit.Assert;
+import org.apache.directory.api.ldap.model.name.Dn;
+import org.apache.directory.ldap.client.api.LdapConnection;
+import org.apache.directory.ldap.client.api.LdapNetworkConnection;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.util.HashMap;
 import java.util.Map;
-import java.util.List;
+import java.util.function.Function;
 
 public class IULdapSSHAccountProvisioner implements SSHAccountProvisioner  {
 
-String ldaphost, adminDN, ldap_username, ldap_password, adminPass, 
ldapBaseDN;
-int ldapport, ldapPortId;
-LdapConnection connection;
+private final static Logger logger = 
LoggerFactory.getLogger(SSHAccountManager.class);
+public static final String LDAP_PUBLIC_KEY_OBJECT_CLASS = "ldapPublicKey";
+public static final String SSH_PUBLIC_KEY_ATTRIBUTE_NAME = "sshPublicKey";
+
+private String ldapHost, ldapUsername, ldapPassword, ldapBaseDN, 
canonicalScratchLocation;
+private int ldapPort;
 @Override
 public void init(Map config) {
 
-// TODO: implement
-ldapServerName =  config.get(new 
ConfigParam("ldaphost"));//"bazooka.hps.iu.edu"
-ldapPortId = config.get(new ConfigParam("ldapport"));//"636"
-ldap_username = config.get(new 
ConfigParam("ldap_username"));//"cn=sgrcusr"
-ldap_password = config.get(new ConfigParam("ldap_password"));//"lore 
footwork engorge"
-ldapBaseDN = config.get(new ConfigParam( "ldapBaseDN" 
));//"dc=rt,dc=iu,dc=edu"
-try {
-connection = new LdapNetworkConnection(ldaphost, ldapport, true);
-
-
-System.out.println( "binding connection:" );
-String 

[09/35] airavata git commit: UAB CILogon config

[machristie]

UAB CILogon config


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/6488090f
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/6488090f
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/6488090f

Branch: refs/heads/AIRAVATA-2500
Commit: 6488090f90eab30e37c4ca39cc0fa24025aeaffb
Parents: d537890
Author: Marcus Christie 
Authored: Wed Aug 16 11:33:36 2017 -0400
Committer: Marcus Christie 
Committed: Wed Aug 16 11:33:36 2017 -0400

--
 .../inventories/scigap/production/pga_config/uab/vars.yml| 4 
 1 file changed, 4 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/6488090f/dev-tools/ansible/inventories/scigap/production/pga_config/uab/vars.yml
--
diff --git 
a/dev-tools/ansible/inventories/scigap/production/pga_config/uab/vars.yml 
b/dev-tools/ansible/inventories/scigap/production/pga_config/uab/vars.yml
index 4355173..ac5dda5 100644
--- a/dev-tools/ansible/inventories/scigap/production/pga_config/uab/vars.yml
+++ b/dev-tools/ansible/inventories/scigap/production/pga_config/uab/vars.yml
@@ -42,6 +42,10 @@ oidc_discovery_url: "https://iam.scigap.org/auth/realms/{{ 
tenant_domain }}/.wel
 auth_options:
   - name: "The University of Alabama at Birmingham Science Gateway"
 oauth_grant_type: "password"
+  - name: "CILogon"
+oauth_grant_type: "authorization_code"
+oauth_authorize_url_extra_params: "kc_idp_hint=cilogon"
+logo: "/assets/cilogon-logo-24x24-b.png"
 oauth_callback_url: "https://{{ vhost_servername }}/callback-url"
 
 gateway_id: "alabama-birmingham"

[26/35] airavata git commit: AIRAVATA-2500 Thrift stub generation

[machristie]

AIRAVATA-2500 Thrift stub generation


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/469a7e79
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/469a7e79
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/469a7e79

Branch: refs/heads/AIRAVATA-2500
Commit: 469a7e791db59ca277685f47a422e8805d3c4042
Parents: ac2823a
Author: Marcus Christie 
Authored: Fri Sep 1 17:12:46 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:07:57 2017 -0400

--
 .../java/org/apache/airavata/api/Airavata.java  | 782 +--
 .../ComputeResourcePreference.java  |  78 +-
 2 files changed, 415 insertions(+), 445 deletions(-)
--

[27/35] airavata git commit: AIRAVATA-2500 Thrift stub code generation

[machristie]

http://git-wip-us.apache.org/repos/asf/airavata/blob/3184c238/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/Model/AppCatalog/GatewayProfile/Types.php
--
diff --git 
a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/Model/AppCatalog/GatewayProfile/Types.php
 
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/Model/AppCatalog/GatewayProfile/Types.php
index f0b329d..da3071a 100644
--- 
a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/Model/AppCatalog/GatewayProfile/Types.php
+++ 
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/Model/AppCatalog/GatewayProfile/Types.php
@@ -110,6 +110,14 @@ class ComputeResourcePreference {
* @var int
*/
   public $reservationEndTime = null;
+  /**
+   * @var string
+   */
+  public $sshAccountProvisioner = null;
+  /**
+   * @var array
+   */
+  public $sshAccountProvisionerConfig = null;
 
   public function __construct($vals=null) {
 if (!isset(self::$_TSPEC)) {
@@ -170,6 +178,22 @@ class ComputeResourcePreference {
   'var' => 'reservationEndTime',
   'type' => TType::I64,
   ),
+15 => array(
+  'var' => 'sshAccountProvisioner',
+  'type' => TType::STRING,
+  ),
+16 => array(
+  'var' => 'sshAccountProvisionerConfig',
+  'type' => TType::MAP,
+  'ktype' => TType::STRING,
+  'vtype' => TType::STRING,
+  'key' => array(
+'type' => TType::STRING,
+  ),
+  'val' => array(
+'type' => TType::STRING,
+),
+  ),
 );
 }
 if (is_array($vals)) {
@@ -215,6 +239,12 @@ class ComputeResourcePreference {
   if (isset($vals['reservationEndTime'])) {
 $this->reservationEndTime = $vals['reservationEndTime'];
   }
+  if (isset($vals['sshAccountProvisioner'])) {
+$this->sshAccountProvisioner = $vals['sshAccountProvisioner'];
+  }
+  if (isset($vals['sshAccountProvisionerConfig'])) {
+$this->sshAccountProvisionerConfig = 
$vals['sshAccountProvisionerConfig'];
+  }
 }
   }
 
@@ -335,6 +365,33 @@ class ComputeResourcePreference {
 $xfer += $input->skip($ftype);
   }
   break;
+case 15:
+  if ($ftype == TType::STRING) {
+$xfer += $input->readString($this->sshAccountProvisioner);
+  } else {
+$xfer += $input->skip($ftype);
+  }
+  break;
+case 16:
+  if ($ftype == TType::MAP) {
+$this->sshAccountProvisionerConfig = array();
+$_size0 = 0;
+$_ktype1 = 0;
+$_vtype2 = 0;
+$xfer += $input->readMapBegin($_ktype1, $_vtype2, $_size0);
+for ($_i4 = 0; $_i4 < $_size0; ++$_i4)
+{
+  $key5 = '';
+  $val6 = '';
+  $xfer += $input->readString($key5);
+  $xfer += $input->readString($val6);
+  $this->sshAccountProvisionerConfig[$key5] = $val6;
+}
+$xfer += $input->readMapEnd();
+  } else {
+$xfer += $input->skip($ftype);
+  }
+  break;
 default:
   $xfer += $input->skip($ftype);
   break;
@@ -418,6 +475,29 @@ class ComputeResourcePreference {
   $xfer += $output->writeI64($this->reservationEndTime);
   $xfer += $output->writeFieldEnd();
 }
+if ($this->sshAccountProvisioner !== null) {
+  $xfer += $output->writeFieldBegin('sshAccountProvisioner', 
TType::STRING, 15);
+  $xfer += $output->writeString($this->sshAccountProvisioner);
+  $xfer += $output->writeFieldEnd();
+}
+if ($this->sshAccountProvisionerConfig !== null) {
+  if (!is_array($this->sshAccountProvisionerConfig)) {
+throw new TProtocolException('Bad type in structure.', 
TProtocolException::INVALID_DATA);
+  }
+  $xfer += $output->writeFieldBegin('sshAccountProvisionerConfig', 
TType::MAP, 16);
+  {
+$output->writeMapBegin(TType::STRING, TType::STRING, 
count($this->sshAccountProvisionerConfig));
+{
+  foreach ($this->sshAccountProvisionerConfig as $kiter7 => $viter8)
+  {
+$xfer += $output->writeString($kiter7);
+$xfer += $output->writeString($viter8);
+  }
+}
+$output->writeMapEnd();
+  }
+  $xfer += $output->writeFieldEnd();
+}
 $xfer += $output->writeFieldStop();
 $xfer += $output->writeStructEnd();
 return $xfer;
@@ -711,15 +791,15 @@ class GatewayResourceProfile {
 case 3:
   if ($ftype == TType::LST) {
 $this->computeResourcePreferences = array();
-$_size0 = 0;
-$_etype3 = 0;
-$xfer += 

[14/35] airavata git commit: AIRAVATA-2500 Update thrift API and regenerated

[machristie]

http://git-wip-us.apache.org/repos/asf/airavata/blob/2a901394/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
--
diff --git 
a/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
 
b/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
index 6ef1610..851f96e 100644
--- 
a/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
+++ 
b/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
@@ -2621,6 +2621,10 @@ public class Airavata {
  */
 public boolean 
deleteGatewayStoragePreference(org.apache.airavata.model.security.AuthzToken 
authzToken, String gatewayID, String storageId) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
 
+public List 
getSSHAccountProvisionerNames(org.apache.airavata.model.security.AuthzToken 
authzToken) throws org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
+
+public 
List
 
getSSHAccountProvisionerConfigParams(org.apache.airavata.model.security.AuthzToken
 authzToken, String provisionerName) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
+
 /**
  * Register User Resource Profile.
  * 
@@ -3291,6 +3295,10 @@ public class Airavata {
 
 public void 
deleteGatewayStoragePreference(org.apache.airavata.model.security.AuthzToken 
authzToken, String gatewayID, String storageId, 
org.apache.thrift.async.AsyncMethodCallback resultHandler) throws 
org.apache.thrift.TException;
 
+public void 
getSSHAccountProvisionerNames(org.apache.airavata.model.security.AuthzToken 
authzToken, org.apache.thrift.async.AsyncMethodCallback resultHandler) throws 
org.apache.thrift.TException;
+
+public void 
getSSHAccountProvisionerConfigParams(org.apache.airavata.model.security.AuthzToken
 authzToken, String provisionerName, 
org.apache.thrift.async.AsyncMethodCallback resultHandler) throws 
org.apache.thrift.TException;
+
 public void 
registerUserResourceProfile(org.apache.airavata.model.security.AuthzToken 
authzToken, 
org.apache.airavata.model.appcatalog.userresourceprofile.UserResourceProfile 
userResourceProfile, org.apache.thrift.async.AsyncMethodCallback resultHandler) 
throws org.apache.thrift.TException;
 
 public void 
getUserResourceProfile(org.apache.airavata.model.security.AuthzToken 
authzToken, String userId, String gatewayID, 
org.apache.thrift.async.AsyncMethodCallback resultHandler) throws 
org.apache.thrift.TException;
@@ -8275,6 +8283,77 @@ public class Airavata {
   throw new 
org.apache.thrift.TApplicationException(org.apache.thrift.TApplicationException.MISSING_RESULT,
 "deleteGatewayStoragePreference failed: unknown result");
 }
 
+public List 
getSSHAccountProvisionerNames(org.apache.airavata.model.security.AuthzToken 
authzToken) throws org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException
+{
+  send_getSSHAccountProvisionerNames(authzToken);
+  return recv_getSSHAccountProvisionerNames();
+}
+
+public void 
send_getSSHAccountProvisionerNames(org.apache.airavata.model.security.AuthzToken
 authzToken) throws org.apache.thrift.TException
+{
+  getSSHAccountProvisionerNames_args args = new 
getSSHAccountProvisionerNames_args();
+  args.setAuthzToken(authzToken);
+  sendBase("getSSHAccountProvisionerNames", args);
+}
+
+public List recv_getSSHAccountProvisionerNames() throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException
+{
+  getSSHAccountProvisionerNames_result result = new 
getSSHAccountProvisionerNames_result();
+  receiveBase(result, "getSSHAccountProvisionerNames");
+  if (result.isSetSuccess()) {
+return result.success;
+  }
+  if (result.ire != null) {
+throw result.ire;
+  }
+  if (result.ace != null) {
+throw result.ace;
+  }
+  if 

[34/35] airavata git commit: AIRAVATA-2500 SSHAccountManager bug fixes

[machristie]

AIRAVATA-2500 SSHAccountManager bug fixes


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/31f3906b
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/31f3906b
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/31f3906b

Branch: refs/heads/AIRAVATA-2500
Commit: 31f3906b6123bb1ce57cd9030f05f15d343cd9f9
Parents: 3184c23
Author: Marcus Christie 
Authored: Thu Sep 7 13:11:03 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:08:05 2017 -0400

--
 .../apache/airavata/accountprovisioning/SSHAccountManager.java | 6 --
 1 file changed, 4 insertions(+), 2 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/31f3906b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
--
diff --git 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
index 8493dc1..70c144c 100644
--- 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
+++ 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
@@ -165,7 +165,7 @@ public class SSHAccountManager {
 PasswordCredential password = 
credentialStoreServiceClient.getPasswordCredential(configEntry.getValue(), 
gatewayId);
 resolvedConfig.put(configEntry.getKey(), 
password.getPassword());
 } catch (TException e) {
-throw new RuntimeException("Failed to get password 
needed to configure " + provisionerName);
+throw new RuntimeException("Failed to get password 
needed to configure " + provisionerName, e);
 }
 } else {
 resolvedConfig.put(configEntry.getKey(), 
configEntry.getValue());
@@ -182,6 +182,8 @@ public class SSHAccountManager {
 }
 
 private static Map convertConfigParams(String 
provisionerName, Map thriftConfigParams) {
+// TODO: also check that all required parameters are present?
+// TODO: also, this doesn't handle optional entries which should be 
skipped if missing from thriftConfigParams
 List configParams = 
SSHAccountProvisionerFactory.getSSHAccountProvisionerConfigParams(provisionerName);
 Map configParamMap = 
configParams.stream().collect(Collectors.toMap(ConfigParam::getName, 
Function.identity()));
 
@@ -204,7 +206,7 @@ public class SSHAccountManager {
 try {
 String credServerHost = 
ServerSettings.getCredentialStoreServerHost();
 int credServerPort = 
Integer.valueOf(ServerSettings.getCredentialStoreServerPort());
-return CredentialStoreClientFactory.createAiravataCSClient(null, 
0);
+return 
CredentialStoreClientFactory.createAiravataCSClient(credServerHost, 
credServerPort);
 } catch (CredentialStoreException | ApplicationSettingsException e) {
 throw new RuntimeException("Failed to create credential store 
service client", e);
 }

[08/35] airavata git commit: Changes to the vars.yml, added the key for data storage access

[machristie]

Changes to the vars.yml, added the key for data storage access


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/d5378905
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/d5378905
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/d5378905

Branch: refs/heads/AIRAVATA-2500
Commit: d53789056fe011f224b154812d20478aa09be3a8
Parents: 4b1c437
Author: Eroma Abeysinghe 
Authored: Tue Aug 15 14:32:24 2017 -0400
Committer: Eroma Abeysinghe 
Committed: Tue Aug 15 14:32:24 2017 -0400

--
 .../production/pga_config/csbglsu/vault.yml   | 18 ++
 1 file changed, 18 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/d5378905/dev-tools/ansible/inventories/scigap/production/pga_config/csbglsu/vault.yml
--
diff --git 
a/dev-tools/ansible/inventories/scigap/production/pga_config/csbglsu/vault.yml 
b/dev-tools/ansible/inventories/scigap/production/pga_config/csbglsu/vault.yml
new file mode 100644
index 000..389345b
--- /dev/null
+++ 
b/dev-tools/ansible/inventories/scigap/production/pga_config/csbglsu/vault.yml
@@ -0,0 +1,18 @@
+$ANSIBLE_VAULT;1.1;AES256
+37373436626563633733323039346662383239383061336466343737393938656462636137346131
+303137343664326361353339643737643739313031310a356263326561396432613635653138
+66306332326430373161353835386561356238616135663933363864663039343131636430316265
+3731613866633663360a383131363564373532303438313837633766656131346132653964333735
+66386332336132313833613335613763633133386430346535383662643730376233643931323038
+35633238623962343165333935323936303366393465623733616431303638313562336236346635
+3535323930336337353738643061626164366430613961633662646266613961656264656431
+33353839353637333266343538653133383232366563363965323662626437396264383734656137
+30356534386264326636313465643534396639323232613637613031613736323433373238336437
+61373732316536363861643131366364653764363964356334366430336130336233383837653131
+623130396433306532393161303961393064366538353530643261316630613836653761
+3739613531313839666162613164626134613935356635323037393063656361303237613437
+64636163373962666562383164653334323335623065373063396564376465633238316332346336
+6635613038313137306563383935663864326234373963383536383864316330383561376430
+3332323237376665313939323831353334363834383832346562666132666265653135633030
+38373634366433623731393561646330383466353062646338373837383336323361623362663264
+3661

[05/35] airavata git commit: Added IU Geology Survey Group gateway directory vault.yml

[machristie]

Added IU Geology Survey Group gateway directory vault.yml


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/5ad47345
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/5ad47345
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/5ad47345

Branch: refs/heads/AIRAVATA-2500
Commit: 5ad4734521c5e6ab8fb5eae8dd4b770bee553dff
Parents: 862c25b
Author: Eroma Abeysinghe 
Authored: Mon Aug 14 16:42:54 2017 -0400
Committer: Eroma Abeysinghe 
Committed: Mon Aug 14 16:42:54 2017 -0400

--
 .../production/pga_config/iugeosurvey/vault.yml   | 18 ++
 1 file changed, 18 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/5ad47345/dev-tools/ansible/inventories/scigap/production/pga_config/iugeosurvey/vault.yml
--
diff --git 
a/dev-tools/ansible/inventories/scigap/production/pga_config/iugeosurvey/vault.yml
 
b/dev-tools/ansible/inventories/scigap/production/pga_config/iugeosurvey/vault.yml
new file mode 100644
index 000..fc2f7c5
--- /dev/null
+++ 
b/dev-tools/ansible/inventories/scigap/production/pga_config/iugeosurvey/vault.yml
@@ -0,0 +1,18 @@
+$ANSIBLE_VAULT;1.1;AES256
+66636531313965303866643038636339303766383030653235633538623237323036336434336435
+633039663263633738353137653639396461656163390a323064393931376165373038323437
+39313937363536663364633562393039643935313838363837376335386261303665
+303134633730370a613937303739323839303633303164373466386239613436643737653266
+3634663032613064666462623161373733363661303269643961336564313036383366356164
+66383439326331316336313437393537626139323066356366383366613437303866323638363831
+39373561653365626664326431363562333037616538303234313762633262663631633832646338
+63316335356161343134663366643037633666366563386339353332346261333230393730316364
+3530346530386536656332386135353138646533643465303266613166616161393038626461
+3861303264333939333162623664383565383935313832383034333632336465363263366639
+63643738316237313134653038363266383161353862363332353262333166623736323734336339
+61333233343230373665346336393530613936636533643732613539333634396566313962386331
+64623062313161633265646535313334643563613365353439313935383239353334623030396230
+3234343163636535346665323064326436313332663732353166383463363130306561353366
+36336432386131383062353065356434653233356361343533393462356361643363396261306431
+36316133353530376435643732653034356362333164373233376530383430303731333737646338
+3930

[22/35] airavata git commit: AIRAVATA-2500: generated Thrift stub code

[machristie]

AIRAVATA-2500: generated Thrift stub code


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/722aabd4
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/722aabd4
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/722aabd4

Branch: refs/heads/AIRAVATA-2500
Commit: 722aabd4c4fcde001ace20416ea16027a1299224
Parents: 8f2f135
Author: Marcus Christie 
Authored: Thu Aug 31 09:17:23 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:07:56 2017 -0400

--
 .../java/org/apache/airavata/api/Airavata.java  | 4698 +++---
 .../SSHAccountProvisioner.java  |  600 +++
 .../SSHAccountProvisionerConfigParam.java   |  733 +++
 .../SSHAccountProvisionerConfigParamType.java   |   62 +
 4 files changed, 5345 insertions(+), 748 deletions(-)
--

[01/35] airavata git commit: Added Diana's email to admin emails [Forced Update!]

[machristie]

Repository: airavata
Updated Branches:
  refs/heads/AIRAVATA-2500 daedef2eb -> 743711290 (forced update)


Added Diana's email to admin emails


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/67f6fad3
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/67f6fad3
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/67f6fad3

Branch: refs/heads/AIRAVATA-2500
Commit: 67f6fad3b77f16b4e3ffbdfa0bc5fd52b32c4452
Parents: 21a7505
Author: Eroma Abeysinghe 
Authored: Mon Aug 7 11:54:26 2017 -0400
Committer: Eroma Abeysinghe 
Committed: Mon Aug 7 11:54:26 2017 -0400

--
 .../inventories/scigap/PICKSC-Production/group_vars/pga/vars.yml   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/67f6fad3/dev-tools/ansible/inventories/scigap/PICKSC-Production/group_vars/pga/vars.yml
--
diff --git 
a/dev-tools/ansible/inventories/scigap/PICKSC-Production/group_vars/pga/vars.yml
 
b/dev-tools/ansible/inventories/scigap/PICKSC-Production/group_vars/pga/vars.yml
index 32e556e..d71f02f 100644
--- 
a/dev-tools/ansible/inventories/scigap/PICKSC-Production/group_vars/pga/vars.yml
+++ 
b/dev-tools/ansible/inventories/scigap/PICKSC-Production/group_vars/pga/vars.yml
@@ -66,7 +66,7 @@ gateway_data_store_ssh_public_key: "ssh-rsa 
B3NzaC1yc2EDAQABAAABAQCZG7vi
 
 ## Portal related variables
 super_admin_portal: "false"
-admin_emails: "['sgrc-iu-gr...@iu.edu']"
+admin_emails: "['sgrc-iu-gr...@iu.edu','dugas...@ad.nmsu.edu']"
 portal_email_username: "pga.airav...@gmail.com"
 portal_email_password: "{{ vault_portal_email_password }}"
 # The portal theme is included in the dreg-gateway branch of 
airavata-php-gateway

[02/35] airavata git commit: Update Ansible deploy for dREG gateway (Keycloak migration)

[machristie]

Update Ansible deploy for dREG gateway (Keycloak migration)


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/ccd25183
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/ccd25183
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/ccd25183

Branch: refs/heads/AIRAVATA-2500
Commit: ccd251830eca38e2d1fba0d0640fca77a6ca3dd0
Parents: 67f6fad
Author: Marcus Christie 
Authored: Tue Aug 8 17:27:44 2017 -0400
Committer: Marcus Christie 
Committed: Wed Aug 9 11:20:25 2017 -0400

--
 .../dreg-production/group_vars/pga/vars.yml | 14 +---
 .../dreg-production/group_vars/pga/vault.yml| 34 ++--
 2 files changed, 27 insertions(+), 21 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/ccd25183/dev-tools/ansible/inventories/scigap/dreg-production/group_vars/pga/vars.yml
--
diff --git 
a/dev-tools/ansible/inventories/scigap/dreg-production/group_vars/pga/vars.yml 
b/dev-tools/ansible/inventories/scigap/dreg-production/group_vars/pga/vars.yml
index 5eed223..a192f6b 100644
--- 
a/dev-tools/ansible/inventories/scigap/dreg-production/group_vars/pga/vars.yml
+++ 
b/dev-tools/ansible/inventories/scigap/dreg-production/group_vars/pga/vars.yml
@@ -25,8 +25,8 @@ real_user_data_dir: "/data/gateway-user-data"
 ## Airavata Client related variables
 airavata_server: "tls://{{ groups['api-orch'][0] }}"
 airavata_port: "9930"
-# FIXME: temporarily turn off SSL verification for WSO2 IS
-auth_verify_peer: "false"
+airavata_profile_service_server: "{{ groups['api-orch'][0] }}"
+oauth_service_url: "https://iam.scigap.org/auth;
 
 pga_repo: "https://github.com/apache/airavata-php-gateway.git;
 git_branch: "dreg-gateway"
@@ -41,15 +41,21 @@ ssl_certificate_chain_file: 
"/etc/letsencrypt/live/dreg.dnasequence.org/fullchai
 ssl_certificate_key_file: 
"/etc/letsencrypt/live/dreg.dnasequence.org/privkey.pem"
 pga_ssl_vhost_template: "{{ inventory_dir }}/files/pga-ssl-vhost.conf.j2"
 
-## WSO2 IS related variables
-tenant_domain: "dreg.cornell"
+## Keycloak related variables
+tenant_domain: "{{ gateway_id }}"
 admin_username: "admin"
 admin_password: "{{ vault_admin_password }}"
 oauth_client_key: "{{ vault_oauth_client_key }}"
 oauth_client_secret: "{{ vault_oauth_client_secret }}"
+oidc_discovery_url: "https://iam.scigap.org/auth/realms/{{ tenant_domain 
}}/.well-known/openid-configuration"
 # dREG gateway automatically gives users the gateway-user role so they don't 
have to wait on admin approval
 initial_role_name: "gateway-user"
 
+auth_options:
+  - name: "dREG"
+oauth_grant_type: "password"
+oauth_callback_url: "https://{{ vhost_servername }}/callback-url"
+
 gateway_id: "cornelldna"
 # relative to document root dir
 experiment_data_dir: "{{ user_data_dir }}/cornell-dnasequence"

http://git-wip-us.apache.org/repos/asf/airavata/blob/ccd25183/dev-tools/ansible/inventories/scigap/dreg-production/group_vars/pga/vault.yml
--
diff --git 
a/dev-tools/ansible/inventories/scigap/dreg-production/group_vars/pga/vault.yml 
b/dev-tools/ansible/inventories/scigap/dreg-production/group_vars/pga/vault.yml
index eaca63b..d10aef2 100644
--- 
a/dev-tools/ansible/inventories/scigap/dreg-production/group_vars/pga/vault.yml
+++ 
b/dev-tools/ansible/inventories/scigap/dreg-production/group_vars/pga/vault.yml
@@ -1,18 +1,18 @@
 $ANSIBLE_VAULT;1.1;AES256
-37653231363231666433316261313238643763633234663866393832386236643436623566303263
-3334323065363831656435383564623034393661323037300a34326331633131366134613661
-39633030386362623966303630653462373762373034323134356539313036376563613335383135
-3962646533323362370a383064616634303730373232353663386165313666303732396635643562
-39313037323264656236323337643862636265626138656435303064353531616264633435643965
-3861613861303933313436643635666337643533343264326637653864356563343532333262
-3532333533643733396437336665373734303230623864303234316235343764376636353236
-323631386334323963306138326562373461613138373539356534313362313766313164
-35386534313033623563613635343163633564613636636236316633623263313437626337663530
-64313166323263353266623135616236653463356439363530373630653232363863303238356265
-65363630393364636238643861386161356635666331336530626533666434373931393237643861
-3338366365343931306439373565306432383665343366636161643938396136383234386232
-33343238636238373936663365316663653532616364636336363936316235353164636365613738
-33346462386230623735376132306663633932363838643935373539316565626435646565393833
-66623065373162623964363665646436356464643366633764323232343736353032616561643637

[29/35] airavata git commit: AIRAVATA-2500 Thrift stub code generation

[machristie]

http://git-wip-us.apache.org/repos/asf/airavata/blob/3184c238/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
--
diff --git 
a/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
 
b/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
index d92d222..48fdbd8 100644
--- 
a/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
+++ 
b/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
@@ -2621,9 +2621,7 @@ public class Airavata {
  */
 public boolean 
deleteGatewayStoragePreference(org.apache.airavata.model.security.AuthzToken 
authzToken, String gatewayID, String storageId) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
 
-public 
List
 getSSHAccountProvisionerNames(org.apache.airavata.model.security.AuthzToken 
authzToken) throws org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
-
-public 
List
 
getSSHAccountProvisionerConfigParams(org.apache.airavata.model.security.AuthzToken
 authzToken, String provisionerName) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
+public 
List
 getSSHAccountProvisioners(org.apache.airavata.model.security.AuthzToken 
authzToken) throws org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
 
 /**
  * Check if user has an SSH account on the given compute resource. This
@@ -2631,9 +2629,9 @@ public class Airavata {
  * 
  * @param authzToken
  * @param computeResourceId
- * @param username
+ * @param userId
  */
-public boolean 
doesUserHaveSSHAccount(org.apache.airavata.model.security.AuthzToken 
authzToken, String computeResourceId, String username) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
+public boolean 
doesUserHaveSSHAccount(org.apache.airavata.model.security.AuthzToken 
authzToken, String computeResourceId, String userId) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
 
 /**
  * Setup and return a UserComputeResourcePreference object for this user 
to SSH into the given compute resource with
@@ -2643,10 +2641,10 @@ public class Airavata {
  * 
  * @param authzToken
  * @param computeResourceId
- * @param username
+ * @param userId
  * @param airavataCredStoreToken
  */
-public 
org.apache.airavata.model.appcatalog.userresourceprofile.UserComputeResourcePreference
 
setupUserComputeResourcePreferencesForSSH(org.apache.airavata.model.security.AuthzToken
 authzToken, String computeResourceId, String username, String 
airavataCredStoreToken) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
+public 
org.apache.airavata.model.appcatalog.userresourceprofile.UserComputeResourcePreference
 
setupUserComputeResourcePreferencesForSSH(org.apache.airavata.model.security.AuthzToken
 authzToken, String computeResourceId, String userId, String 
airavataCredStoreToken) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
 
 /**
  * Register User Resource Profile.
@@ -3318,13 +3316,11 @@ public class Airavata {
 
 public void 
deleteGatewayStoragePreference(org.apache.airavata.model.security.AuthzToken 
authzToken, String gatewayID, 

[06/35] airavata git commit: Changes to the vars.yml, added the key for data storage access

[machristie]

Changes to the vars.yml, added the key for data storage access


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/8f57d7c3
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/8f57d7c3
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/8f57d7c3

Branch: refs/heads/AIRAVATA-2500
Commit: 8f57d7c3fe3584c543fe8a9dbbf3af2a817ee7ee
Parents: 5ad4734
Author: Eroma Abeysinghe 
Authored: Mon Aug 14 16:52:19 2017 -0400
Committer: Eroma Abeysinghe 
Committed: Mon Aug 14 16:52:19 2017 -0400

--
 .../inventories/scigap/production/pga_config/iugeosurvey/vars.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/8f57d7c3/dev-tools/ansible/inventories/scigap/production/pga_config/iugeosurvey/vars.yml
--
diff --git 
a/dev-tools/ansible/inventories/scigap/production/pga_config/iugeosurvey/vars.yml
 
b/dev-tools/ansible/inventories/scigap/production/pga_config/iugeosurvey/vars.yml
index bbbaf31..d9a3588 100644
--- 
a/dev-tools/ansible/inventories/scigap/production/pga_config/iugeosurvey/vars.yml
+++ 
b/dev-tools/ansible/inventories/scigap/production/pga_config/iugeosurvey/vars.yml
@@ -48,7 +48,7 @@ gateway_id: "iu-geology-survey"
 # relative to document root dir
 experiment_data_dir: "{{ user_data_dir }}/{{ gateway_id }}"
 gateway_data_store_resource_id: 
"gf4.ucs.indiana.edu_61552681-96f0-462a-a36c-a62a010bffc6"
-#gateway_data_store_ssh_public_key: "ssh-rsa 
B3NzaC1yc2EDAQABAAABAQDEuA1indjdczBXg2qrmD0bB0QfKq0u2q3o25DegTaty5LoogW+APEvXmwc2g6PzkM75MgfMsTErMQaQ3/PoElADQKg2/NePz05YWobn9zrPZFeRWfOqWMjFDx72cffHKBzgnahFDBlR/YJhf4IZJ+EOA1zMiMF2oZQmEYQtbQFhbKPF+jrScEQeuXVuXWSS2sKNAVKj3pY4kmi9kEOYELee/O6ghBUfrVhB95vDKJPgmQSuo3pgkLRdflTBSAQ54UchwjXi2RA9Xv0RXJF/JyyRGn6bSbRxYhsm5RJeiBVj4ua7p2b36rSYVqtVsTKEonx5kYdKzwyjJXWpjB2KtQp"
+gateway_data_store_ssh_public_key: "ssh-rsa 
B3NzaC1yc2EDAQABAAABAQDEuA1indjdczBXg2qrmD0bB0QfKq0u2q3o25DegTaty5LoogW+APEvXmwc2g6PzkM75MgfMsTErMQaQ3/PoElADQKg2/NePz05YWobn9zrPZFeRWfOqWMjFDx72cffHKBzgnahFDBlR/YJhf4IZJ+EOA1zMiMF2oZQmEYQtbQFhbKPF+jrScEQeuXVuXWSS2sKNAVKj3pY4kmi9kEOYELee/O6ghBUfrVhB95vDKJPgmQSuo3pgkLRdflTBSAQ54UchwjXi2RA9Xv0RXJF/JyyRGn6bSbRxYhsm5RJeiBVj4ua7p2b36rSYVqtVsTKEonx5kYdKzwyjJXWpjB2KtQp"
 
 ## Portal related variables
 super_admin_portal: "false"

[07/35] airavata git commit: Changes to the vars.yml, added the key for data storage access

[machristie]

Changes to the vars.yml, added the key for data storage access


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/4b1c4372
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/4b1c4372
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/4b1c4372

Branch: refs/heads/AIRAVATA-2500
Commit: 4b1c4372eee4dd4877a19d2d144b9e44b8f02133
Parents: 8f57d7c
Author: Eroma Abeysinghe 
Authored: Tue Aug 15 14:32:07 2017 -0400
Committer: Eroma Abeysinghe 
Committed: Tue Aug 15 14:32:07 2017 -0400

--
 .../production/pga_config/csbglsu/vars.yml  | 61 
 dev-tools/ansible/pga-scigap-prod.yml   |  4 +-
 2 files changed, 64 insertions(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/4b1c4372/dev-tools/ansible/inventories/scigap/production/pga_config/csbglsu/vars.yml
--
diff --git 
a/dev-tools/ansible/inventories/scigap/production/pga_config/csbglsu/vars.yml 
b/dev-tools/ansible/inventories/scigap/production/pga_config/csbglsu/vars.yml
new file mode 100644
index 000..b34e099
--- /dev/null
+++ 
b/dev-tools/ansible/inventories/scigap/production/pga_config/csbglsu/vars.yml
@@ -0,0 +1,61 @@
+#
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
+---
+pga_repo: "https://github.com/apache/airavata-php-gateway.git;
+git_branch: "master"
+user: "pga"
+group: "pga"
+doc_root_dir: "/var/www/portals/{{ gateway_id }}"
+vhost_servername: "csbglsu.scigap.org"
+vhost_ssl: false
+# TODO: have Ansible manage these files as well
+#ssl_certificate_file: "/etc/letsencrypt/live/csbglsu.scigap.org/cert.pem"
+#ssl_certificate_chain_file: 
"/etc/letsencrypt/live/csbglsu.scigap.org/fullchain.pem"
+#ssl_certificate_key_file: 
"/etc/letsencrypt/live/csbglsu.scigap.org/privkey.pem"
+
+## Keycloak related variables
+tenant_domain: "{{ gateway_id }}"
+admin_username: "admin"
+admin_password: "{{ vault_admin_password }}"
+oauth_client_key: "{{ vault_oauth_client_key }}"
+oauth_client_secret: "{{ vault_oauth_client_secret }}"
+oidc_discovery_url: "https://iam.scigap.org/auth/realms/{{ tenant_domain 
}}/.well-known/openid-configuration"
+
+auth_options:
+  - name: "LSU Computational Sys Biology"
+oauth_grant_type: "password"
+oauth_callback_url: "https://{{ vhost_servername }}/callback-url"
+
+gateway_id: "lsu-computational-sys-biology"
+# relative to document root dir
+experiment_data_dir: "{{ user_data_dir }}/{{ gateway_id }}"
+gateway_data_store_resource_id: 
"gf4.ucs.indiana.edu_61552681-96f0-462a-a36c-a62a010bffc6"
+gateway_data_store_ssh_public_key: "ssh-rsa 
B3NzaC1yc2EDAQABAAABAQDc/WQnD40zGuO+bIMsWc0ey8oxDzEj/dPFPg8LN7oNn/V7pi74mF2D57wgA8KsxcpsNydcReSXZhx6FynlK6iABDZP5QdREmhm87gkrMQUA/ZI7R2q7ekchbRtCnrGwU/pdHBh4penaiScs08o7OPfqJJp/TfgwH92dA9dThqGf9hD1Y0nmWECfvX56rXAggcgZl+Q6IFD0VFinFMkqZRWFFi4Zm7yiKCNWYXvXlIGjFOlDp0/ONGg5wjpCFivhI934Uk6Y69hSMhnFJc6g1JHD4PLaBILlUjwEikmH6KL3ii6Wt30pou+tIihBDBv0ODR4jDiOeBJGkcisWeh3Uzj"
+
+## Portal related variables
+super_admin_portal: "false"
+admin_emails: "['sgrc-iu-gr...@iu.edu','mbrylin...@lsu.edu']"
+portal_email_username: "pga.airav...@gmail.com"
+portal_email_password: "{{ vault_portal_email_password }}"
+#portal_theme: "gsu-gateway-theme"
+#portal_theme_repo: "https://github.com/SciGaP/gsu-gateway-theme;
+portal_title: "LSU Computational Sys Biology"
+...

http://git-wip-us.apache.org/repos/asf/airavata/blob/4b1c4372/dev-tools/ansible/pga-scigap-prod.yml
--
diff --git a/dev-tools/ansible/pga-scigap-prod.yml 
b/dev-tools/ansible/pga-scigap-prod.yml
index ea2fea1..45b80c3 100644
--- a/dev-tools/ansible/pga-scigap-prod.yml
+++ b/dev-tools/ansible/pga-scigap-prod.yml
@@ -41,5 +41,7 @@
 - include: pga-single-vhost.yml vars_dir="{{ inventory_dir }}/pga_config/uab"
 - include: pga-single-vhost.yml vars_dir="{{ inventory_dir 
}}/pga_config/ultrascan"
 - include: pga-single-vhost.yml vars_dir="{{ 

[15/35] airavata git commit: AIRAVATA-2500 Update thrift API and regenerated

[machristie]

AIRAVATA-2500 Update thrift API and regenerated


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/2a901394
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/2a901394
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/2a901394

Branch: refs/heads/AIRAVATA-2500
Commit: 2a90139402c9c82350138adc4dc3bc59d56cee93
Parents: 77baac4
Author: Marcus Christie 
Authored: Mon Aug 14 12:36:19 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:07:56 2017 -0400

--
 .../java/org/apache/airavata/api/Airavata.java  | 35330 +
 .../ComputeResourcePreference.java  |   285 +-
 .../gatewayprofile/GatewayResourceProfile.java  |72 +-
 .../account_provisioning_model.thrift   | 2 +-
 .../gateway_resource_profile_model.thrift   | 2 +-
 5 files changed, 19411 insertions(+), 16280 deletions(-)
--

[10/35] airavata git commit: AIRAVATA-2500 Implement SSHAccountProvisionerFactory

[machristie]

AIRAVATA-2500 Implement SSHAccountProvisionerFactory


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/77baac43
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/77baac43
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/77baac43

Branch: refs/heads/AIRAVATA-2500
Commit: 77baac438f9a59629a9fc21a904dc7397245a029
Parents: 1c39e2e
Author: Marcus Christie 
Authored: Thu Aug 10 15:24:26 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:07:40 2017 -0400

--
 .../accountprovisioning/ConfigParam.java| 32 +++--
 .../accountprovisioning/SSHAccountManager.java  | 37 +-
 .../SSHAccountProvisioner.java  |  9 ---
 .../SSHAccountProvisionerFactory.java   | 28 +---
 .../SSHAccountProvisionerProvider.java  | 37 ++
 .../IULdapSSHAccountProvisioner.java|  7 --
 .../IULdapSSHAccountProvisionerProvider.java| 44 
 ...ta.accountprovisioning.SSHAccountProvisioner | 22 --
 ...ntprovisioning.SSHAccountProvisionerProvider | 22 ++
 .../SSHAccountProvisionerFactoryTest.java   | 75 
 .../provisioner/TestSSHAccountProvisioner.java  | 71 ++
 .../TestSSHAccountProvisionerProvider.java  | 66 +
 ...ntprovisioning.SSHAccountProvisionerProvider | 21 ++
 .../account_provisioning_model.thrift   |  2 +-
 .../gateway_resource_profile_model.thrift   |  2 +-
 15 files changed, 420 insertions(+), 55 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/77baac43/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/ConfigParam.java
--
diff --git 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/ConfigParam.java
 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/ConfigParam.java
index beb8bbc..cf27b7f 100644
--- 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/ConfigParam.java
+++ 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/ConfigParam.java
@@ -24,7 +24,7 @@ public class ConfigParam {
 
 public enum ConfigParamType {
 STRING,
-CRED_TOKEN,
+CRED_STORE_PASSWORD_TOKEN,
 }
 
 private boolean optional = false;
@@ -32,36 +32,58 @@ public class ConfigParam {
 private String description;
 private ConfigParamType type = ConfigParamType.STRING;
 
+public ConfigParam(String name) {
+this.name = name;
+}
+
 public boolean isOptional() {
 return optional;
 }
 
-public void setOptional(boolean optional) {
+public ConfigParam setOptional(boolean optional) {
 this.optional = optional;
+return this;
 }
 
 public String getName() {
 return name;
 }
 
-public void setName(String name) {
+public ConfigParam setName(String name) {
 this.name = name;
+return this;
 }
 
 public String getDescription() {
 return description;
 }
 
-public void setDescription(String description) {
+public ConfigParam setDescription(String description) {
 this.description = description;
+return this;
 }
 
 public ConfigParamType getType() {
 return type;
 }
 
-public void setType(ConfigParamType type) {
+public ConfigParam setType(ConfigParamType type) {
 this.type = type;
+return this;
+}
+
+@Override
+public boolean equals(Object o) {
+if (this == o) return true;
+if (!(o instanceof ConfigParam)) return false;
+
+ConfigParam that = (ConfigParam) o;
+
+return name.equals(that.name);
 }
 
+@Override
+public int hashCode() {
+return name.hashCode();
+}
 }

http://git-wip-us.apache.org/repos/asf/airavata/blob/77baac43/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
--
diff --git 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
index 4e00e4e..dcb819b 100644
--- 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
+++ 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
@@ -20,12 +20,18 @@
 
 package 

[03/35] airavata git commit: Added WVState University gateway directory

[machristie]

Added WVState University gateway directory


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/2f471d10
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/2f471d10
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/2f471d10

Branch: refs/heads/AIRAVATA-2500
Commit: 2f471d104dcd7a03ee5f46d758e51fee06825077
Parents: ccd2518
Author: Eroma Abeysinghe 
Authored: Mon Aug 14 15:54:52 2017 -0400
Committer: Eroma Abeysinghe 
Committed: Mon Aug 14 15:54:52 2017 -0400

--
 .../scigap/production/pga_config/wvsu/vars.yml  | 71 
 .../scigap/production/pga_config/wvsu/vault.yml | 18 +
 2 files changed, 89 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/2f471d10/dev-tools/ansible/inventories/scigap/production/pga_config/wvsu/vars.yml
--
diff --git 
a/dev-tools/ansible/inventories/scigap/production/pga_config/wvsu/vars.yml 
b/dev-tools/ansible/inventories/scigap/production/pga_config/wvsu/vars.yml
new file mode 100644
index 000..d8d3dda
--- /dev/null
+++ b/dev-tools/ansible/inventories/scigap/production/pga_config/wvsu/vars.yml
@@ -0,0 +1,71 @@
+#
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
+---
+pga_repo: "https://github.com/apache/airavata-php-gateway.git;
+git_branch: "master"
+user: "pga"
+group: "pga"
+doc_root_dir: "/var/www/portals/{{ gateway_id }}"
+vhost_servername: "sciencegateway.wvstateu.edu"
+#vhost_serveralias: "www.seagrid.org"
+#vhost_servername: "beta.seagrid.org"
+vhost_ssl: True
+# TODO: have Ansible manage these files as well
+ssl_certificate_file: 
"/etc/letsencrypt/live/sciencegateway.wvstateu.edu/cert.pem"
+ssl_certificate_chain_file: 
"/etc/letsencrypt/live/sciencegateway.wvstateu.edu/fullchain.pem"
+ssl_certificate_key_file: 
"/etc/letsencrypt/live/sciencegateway.wvstateu.edu/privkey.pem"
+#ssl_certificate_file: "/etc/letsencrypt/live/beta.seagrid.org/cert.pem"
+#ssl_certificate_chain_file: 
"/etc/letsencrypt/live/beta.seagrid.org/fullchain.pem"
+#ssl_certificate_key_file: "/etc/letsencrypt/live/beta.seagrid.org/privkey.pem"
+
+
+## Keycloak related variables
+tenant_domain: "{{ gateway_id }}"
+admin_username: "admin"
+admin_password: "{{ vault_admin_password }}"
+oauth_client_key: "{{ vault_oauth_client_key }}"
+oauth_client_secret: "{{ vault_oauth_client_secret }}"
+oidc_discovery_url: "https://iam.scigap.org/auth/realms/{{ tenant_domain 
}}/.well-known/openid-configuration"
+
+auth_options:
+  - name: "WVirginia State University"
+oauth_grant_type: "password"
+ # - name: "CILogon"
+  #  oauth_grant_type: "authorization_code"
+ #   oauth_authorize_url_extra_params: "kc_idp_hint=cilogon"
+  #  logo: "/assets/cilogon-logo-24x24-b.png"
+oauth_callback_url: "https://{{ vhost_servername }}/callback-url"
+
+gateway_id: "wvirginia-state-university"
+# relative to document root dir
+experiment_data_dir: "{{ user_data_dir }}/wvirginia-state-university"
+gateway_data_store_resource_id: 
"gf4.ucs.indiana.edu_61552681-96f0-462a-a36c-a62a010bffc6"
+gateway_data_store_ssh_public_key: "ssh-rsa 
B3NzaC1yc2EDAQABAAABAQCHm/f06vFCah0lVLnykei1cwkKMGwaCdn//BjZtG/9OnV7fjDzjISBCuz+LEC/FJKv3BaByAQ0Tvq0GxIgBzR31r2Qpp7yKJyl1THpftrshPOD2M1FOJfebc9QAnVKdQQpIGtA5/viOnZfV0nnEXqiKjafsAdwnSP3097XSvD7UvQGwkhmG4oIbs66RTh19gUB3/4QZZBEbUDBaeHrxzwS/NXaQorCfrZt2mJCNeFLdhiqqg2JbT4g4X/Crps6es/o3fN6mRsFnRu9Y5Xhh/FFyT/u8IiW18FzHaH9hfOhyxeKRQCk0nJV+aREcmJ3wIk7VRA/bKGWcVDqZRHRvcPR"
+
+## Portal related variables
+super_admin_portal: "false"
+admin_emails: "['smalka...@wvstateu.edu', 'sgrc-iu-gr...@iu.edu']"
+portal_email_username: "pga.airav...@gmail.com"
+portal_email_password: "{{ vault_portal_email_password }}"
+#portal_theme: "base"
+#portal_theme_repo: "https://github.com/SciGaP/seagrid-website-theme.git;
+portal_title: "WVirginia State University"
+...

[11/35] airavata git commit: AIRAVATA-2500 Initial interfaces, APIs for account provisioning

[machristie]

AIRAVATA-2500 Initial interfaces, APIs for account provisioning


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/1c39e2ea
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/1c39e2ea
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/1c39e2ea

Branch: refs/heads/AIRAVATA-2500
Commit: 1c39e2ea715f736d25d874c36a519ee0ed250162
Parents: 6488090
Author: Marcus Christie 
Authored: Wed Aug 9 15:54:07 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:07:40 2017 -0400

--
 modules/compute-account-provisioning/pom.xml| 67 +
 .../accountprovisioning/ConfigParam.java| 67 +
 .../accountprovisioning/SSHAccountManager.java  | 69 ++
 .../SSHAccountProvisioner.java  | 43 +++
 .../SSHAccountProvisionerFactory.java   | 49 +
 .../IULdapSSHAccountProvisioner.java| 75 
 ...ta.accountprovisioning.SSHAccountProvisioner | 22 ++
 pom.xml |  1 +
 .../airavata-apis/airavata_api.thrift   | 11 +++
 .../account_provisioning_model.thrift   | 40 +++
 .../gateway_resource_profile_model.thrift   |  5 +-
 11 files changed, 448 insertions(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/1c39e2ea/modules/compute-account-provisioning/pom.xml
--
diff --git a/modules/compute-account-provisioning/pom.xml 
b/modules/compute-account-provisioning/pom.xml
new file mode 100644
index 000..ee89d33
--- /dev/null
+++ b/modules/compute-account-provisioning/pom.xml
@@ -0,0 +1,67 @@
+
+
+
+http://maven.apache.org/POM/4.0.0;
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance;
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 
http://maven.apache.org/xsd/maven-4.0.0.xsd;>
+
+airavata
+org.apache.airavata
+0.17-SNAPSHOT
+../../pom.xml
+
+4.0.0
+
+compute-account-provisioning
+
+
+
+airavata-credential-store
+org.apache.airavata
+${project.version}
+
+
+registry-api-stubs
+org.apache.airavata
+${project.version}
+
+
+com.jcraft
+jsch
+0.1.50
+
+
+org.slf4j
+slf4j-api
+
+
+junit
+junit
+test
+
+
+com.google.code.gson
+gson
+2.3.1
+
+
+
+
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata/blob/1c39e2ea/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/ConfigParam.java
--
diff --git 
a/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/ConfigParam.java
 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/ConfigParam.java
new file mode 100644
index 000..beb8bbc
--- /dev/null
+++ 
b/modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/ConfigParam.java
@@ -0,0 +1,67 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+ */
+
+package org.apache.airavata.accountprovisioning;
+
+public class ConfigParam {
+
+public enum ConfigParamType {
+STRING,
+CRED_TOKEN,
+}
+
+private boolean optional = false;
+private String name;
+private String description;
+private ConfigParamType type = ConfigParamType.STRING;
+
+public boolean isOptional() {
+return optional;
+}
+
+public void setOptional(boolean optional) {
+this.optional = optional;
+}
+
+public String getName() {
+return name;
+}
+
+public void setName(String 

[18/35] airavata git commit: AIRAVATA-2500 Implement doesUserHaveSSHAccount and setup SSH account methods in API

[machristie]

AIRAVATA-2500 Implement doesUserHaveSSHAccount and setup SSH account methods in 
API


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/8f2f1353
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/8f2f1353
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/8f2f1353

Branch: refs/heads/AIRAVATA-2500
Commit: 8f2f135374c96f92ffb7eb1775bdfdecb144fb20
Parents: 0d1e90f
Author: Marcus Christie 
Authored: Thu Aug 31 09:16:03 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 15:07:56 2017 -0400

--
 airavata-api/airavata-api-server/pom.xml|  5 ++
 .../server/handler/AiravataServerHandler.java   | 55 
 .../accountprovisioning/SSHAccountManager.java  | 42 ---
 .../SSHAccountProvisionerProvider.java  |  1 +
 .../airavata-apis/airavata_api.thrift   | 24 -
 .../account_provisioning_model.thrift   |  2 +
 6 files changed, 122 insertions(+), 7 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/airavata/blob/8f2f1353/airavata-api/airavata-api-server/pom.xml
--
diff --git a/airavata-api/airavata-api-server/pom.xml 
b/airavata-api/airavata-api-server/pom.xml
index ada0b8f..a4d10af 100644
--- a/airavata-api/airavata-api-server/pom.xml
+++ b/airavata-api/airavata-api-server/pom.xml
@@ -93,6 +93,11 @@
 services-security
 ${project.version}
 
+
+org.apache.airavata
+compute-account-provisioning
+${project.version}
+
 
 
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/8f2f1353/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
--
diff --git 
a/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
 
b/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
index 4ae91ea..bb3f2c0 100644
--- 
a/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
+++ 
b/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
@@ -19,6 +19,7 @@
  */
 package org.apache.airavata.api.server.handler;
 
+import org.apache.airavata.accountprovisioning.SSHAccountManager;
 import org.apache.airavata.api.Airavata;
 import org.apache.airavata.api.airavata_apiConstants;
 import org.apache.airavata.api.server.util.ThriftClientPool;
@@ -35,6 +36,8 @@ import org.apache.airavata.messaging.core.MessagingFactory;
 import org.apache.airavata.messaging.core.Publisher;
 import org.apache.airavata.messaging.core.Type;
 import org.apache.airavata.model.WorkflowModel;
+import 
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisioner;
+import 
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisionerConfigParam;
 import 
org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
 import org.apache.airavata.model.appcatalog.appdeployment.ApplicationModule;
 import 
org.apache.airavata.model.appcatalog.appinterface.ApplicationInterfaceDescription;
@@ -3964,6 +3967,58 @@ public class AiravataServerHandler implements 
Airavata.Iface {
 }
 }
 
+@Override
+@SecurityCheck
+public List 
getSSHAccountProvisionerNames(AuthzToken authzToken) throws 
InvalidRequestException, AiravataClientException, AiravataSystemException, 
AuthorizationException, TException {
+
+// TODO: implement
+return null;
+}
+
+@Override
+@SecurityCheck
+public List 
getSSHAccountProvisionerConfigParams(AuthzToken authzToken, String 
provisionerName) throws InvalidRequestException, AiravataClientException, 
AiravataSystemException, AuthorizationException, TException {
+
+// TODO: implement
+return null;
+}
+
+@Override
+@SecurityCheck
+public boolean doesUserHaveSSHAccount(AuthzToken authzToken, String 
computeResourceId, String username) throws InvalidRequestException, 
AiravataClientException, AiravataSystemException, AuthorizationException, 
TException {
+String gatewayId = authzToken.getClaimsMap().get(Constants.GATEWAY_ID);
+return SSHAccountManager.doesUserHaveSSHAccount(gatewayId, 
computeResourceId, username);
+}
+
+@Override
+@SecurityCheck
+public UserComputeResourcePreference 
setupUserComputeResourcePreferencesForSSH(AuthzToken authzToken, String 
computeResourceId, String username, String airavataCredStoreToken) 

[25/35] airavata git commit: AIRAVATA-2500 Thrift stub generation

[machristie]

http://git-wip-us.apache.org/repos/asf/airavata/blob/469a7e79/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
--
diff --git 
a/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
 
b/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
index 6214caf..d92d222 100644
--- 
a/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
+++ 
b/airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
@@ -2626,27 +2626,27 @@ public class Airavata {
 public 
List
 
getSSHAccountProvisionerConfigParams(org.apache.airavata.model.security.AuthzToken
 authzToken, String provisionerName) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
 
 /**
- * Setup and return a UserComputeResourcePreference object for this user 
to SSH into the given compute resource with
- * the given SSH credential. This method will only work if the compute 
resource has an SSHAccountProvisioner
- * configured for it. The returned UserComputeResourcePreference object is 
not saved; it is up to the client to
- * call addUserComputeResourcePreference to persist it.
+ * Check if user has an SSH account on the given compute resource. This
+ * method will only work if the compute resource has an 
SSHAccountProvisioner configured for it.
  * 
  * @param authzToken
  * @param computeResourceId
  * @param username
- * @param airavataCredStoreToken
  */
-public 
org.apache.airavata.model.appcatalog.userresourceprofile.UserComputeResourcePreference
 
setupUserComputeResourcePreferencesForSSH(org.apache.airavata.model.security.AuthzToken
 authzToken, String computeResourceId, String username, String 
airavataCredStoreToken) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
+public boolean 
doesUserHaveSSHAccount(org.apache.airavata.model.security.AuthzToken 
authzToken, String computeResourceId, String username) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
 
 /**
- * Check if user has an SSH account on the given compute resource. This
- * method will only work if the compute resource has an 
SSHAccountProvisioner configured for it.
+ * Setup and return a UserComputeResourcePreference object for this user 
to SSH into the given compute resource with
+ * the given SSH credential. This method will only work if the compute 
resource has an SSHAccountProvisioner
+ * configured for it. The returned UserComputeResourcePreference object is 
not saved; it is up to the client to
+ * call addUserComputeResourcePreference to persist it.
  * 
  * @param authzToken
  * @param computeResourceId
  * @param username
+ * @param airavataCredStoreToken
  */
-public boolean 
doesUserHaveSSHAccount(org.apache.airavata.model.security.AuthzToken 
authzToken, String computeResourceId, String username) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
+public 
org.apache.airavata.model.appcatalog.userresourceprofile.UserComputeResourcePreference
 
setupUserComputeResourcePreferencesForSSH(org.apache.airavata.model.security.AuthzToken
 authzToken, String computeResourceId, String username, String 
airavataCredStoreToken) throws 
org.apache.airavata.model.error.InvalidRequestException, 
org.apache.airavata.model.error.AiravataClientException, 
org.apache.airavata.model.error.AiravataSystemException, 
org.apache.airavata.model.error.AuthorizationException, 
org.apache.thrift.TException;
 
 /**
  * Register User Resource Profile.
@@ -3322,10 +3322,10 @@ public class Airavata {
 
 public void 
getSSHAccountProvisionerConfigParams(org.apache.airavata.model.security.AuthzToken
 authzToken, String provisionerName, 
org.apache.thrift.async.AsyncMethodCallback resultHandler) throws 
org.apache.thrift.TException;
 
-public void 
setupUserComputeResourcePreferencesForSSH(org.apache.airavata.model.security.AuthzToken
 authzToken, String computeResourceId, String username, String 

[13/35] airavata git commit: AIRAVATA-2500 Update thrift API and regenerated

[machristie]

http://git-wip-us.apache.org/repos/asf/airavata/blob/2a901394/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
--
diff --git 
a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
 
b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
index b1c092b..0d52abb 100644
--- 
a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
+++ 
b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java
@@ -103,6 +103,8 @@ public class ComputeResourcePreference implements 
org.apache.thrift.TBase, SchemeFactory> schemes = 
new HashMap();
   static {
@@ -124,6 +126,8 @@ public class ComputeResourcePreference implements 
org.apache.thrift.TBase
 sshAccountProvisionerConfig; // optional
 
   /** The set of fields this struct contains, along with convenience methods 
for finding and manipulating them. */
   public enum _Fields implements org.apache.thrift.TFieldIdEnum {
@@ -148,7 +152,9 @@ public class ComputeResourcePreference implements 
org.apache.thrift.TBase byName = new HashMap();
 
@@ -191,6 +197,10 @@ public class ComputeResourcePreference implements 
org.apache.thrift.TBase 
metaDataMap;
   static {
 Map<_Fields, org.apache.thrift.meta_data.FieldMetaData> tmpMap = new 
EnumMap<_Fields, org.apache.thrift.meta_data.FieldMetaData>(_Fields.class);
@@ -267,6 +277,12 @@ public class ComputeResourcePreference implements 
org.apache.thrift.TBase
 __this__sshAccountProvisionerConfig = new 
HashMap(other.sshAccountProvisionerConfig.size());
+  for 
(Map.Entry other_element : other.sshAccountProvisionerConfig.entrySet()) {
+
+
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisionerConfigParam
 other_element_key = other_element.getKey();
+String other_element_value = other_element.getValue();
+
+
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisionerConfigParam
 __this__sshAccountProvisionerConfig_copy_key = new 
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisionerConfigParam(other_element_key);
+
+String __this__sshAccountProvisionerConfig_copy_value = 
other_element_value;
+
+
__this__sshAccountProvisionerConfig.put(__this__sshAccountProvisionerConfig_copy_key,
 __this__sshAccountProvisionerConfig_copy_value);
+  }
+  this.sshAccountProvisionerConfig = __this__sshAccountProvisionerConfig;
+}
   }
 
   public ComputeResourcePreference deepCopy() {
@@ -352,6 +386,8 @@ public class ComputeResourcePreference implements 
org.apache.thrift.TBase();
+}
+this.sshAccountProvisionerConfig.put(key, val);
+  }
+
+  public 
Map
 getSshAccountProvisionerConfig() {
+return this.sshAccountProvisionerConfig;
+  }
+
+  public void 
setSshAccountProvisionerConfig(Map
 sshAccountProvisionerConfig) {
+this.sshAccountProvisionerConfig = sshAccountProvisionerConfig;
+  }
+
+  public void unsetSshAccountProvisionerConfig() {
+this.sshAccountProvisionerConfig = null;
+  }
+
+  /** Returns true if field sshAccountProvisionerConfig is set (has been 
assigned a value) and false otherwise */
+  public boolean isSetSshAccountProvisionerConfig() {
+return this.sshAccountProvisionerConfig != null;
+  }
+
+  public void setSshAccountProvisionerConfigIsSet(boolean value) {
+if (!value) {
+  this.sshAccountProvisionerConfig = null;
+}
+  }
+
   public void setFieldValue(_Fields field, Object value) {
 switch (field) {
 case COMPUTE_RESOURCE_ID:
@@ -803,6 +896,22 @@ public class ComputeResourcePreference implements 
org.apache.thrift.TBase)value);
+  }
+  break;
+
 }
   }
 
@@ -850,6 +959,12 @@ public class ComputeResourcePreference implements 
org.apache.thrift.TBase(2*_map0.size);
+
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisionerConfigParam
 _key1;
+String _val2;
+for (int _i3 = 0; _i3 < _map0.size; ++_i3)
+{
+  _key1 = new 
org.apache.airavata.model.appcatalog.accountprovisioning.SSHAccountProvisionerConfigParam();
+  _key1.read(iprot);
+  _val2 = 

[4/4] airavata-django-portal git commit: Requiring Django session for REST API

[machristie]

Requiring Django session for REST API


Project: http://git-wip-us.apache.org/repos/asf/airavata-django-portal/repo
Commit: 
http://git-wip-us.apache.org/repos/asf/airavata-django-portal/commit/4147972a
Tree: 
http://git-wip-us.apache.org/repos/asf/airavata-django-portal/tree/4147972a
Diff: 
http://git-wip-us.apache.org/repos/asf/airavata-django-portal/diff/4147972a

Branch: refs/heads/master
Commit: 4147972a1c157f570abdc5baaa6f243154f4c586
Parents: e8e0fc4
Author: Marcus Christie 
Authored: Tue Sep 19 14:06:34 2017 -0400
Committer: Marcus Christie 
Committed: Tue Sep 19 14:06:34 2017 -0400

--
 django_airavata/settings.py | 10 ++
 1 file changed, 10 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/airavata-django-portal/blob/4147972a/django_airavata/settings.py
--
diff --git a/django_airavata/settings.py b/django_airavata/settings.py
index c0b55d9..c803a33 100644
--- a/django_airavata/settings.py
+++ b/django_airavata/settings.py
@@ -129,6 +129,16 @@ USE_TZ = True
 STATIC_URL = '/static/'
 STATICFILES_DIRS = [os.path.join(BASE_DIR, "django_airavata", "static")]
 
+# Django REST Framework configuration
+REST_FRAMEWORK = {
+'DEFAULT_AUTHENTICATION_CLASSES': (
+'rest_framework.authentication.SessionAuthentication',
+),
+'DEFAULT_PERMISSION_CLASSES': (
+'rest_framework.permissions.IsAuthenticated',
+),
+}
+
 AUTHENTICATION_BACKENDS = [
 'django_airavata.apps.auth.backends.KeycloakBackend'
 ]

[3/4] airavata-django-portal git commit: Namespacing API urls

[machristie]

Namespacing API urls


Project: http://git-wip-us.apache.org/repos/asf/airavata-django-portal/repo
Commit: 
http://git-wip-us.apache.org/repos/asf/airavata-django-portal/commit/e8e0fc44
Tree: 
http://git-wip-us.apache.org/repos/asf/airavata-django-portal/tree/e8e0fc44
Diff: 
http://git-wip-us.apache.org/repos/asf/airavata-django-portal/diff/e8e0fc44

Branch: refs/heads/master
Commit: e8e0fc44f4c7764dfb48d3f9a227a2ad7d5898f2
Parents: c975f46
Author: Marcus Christie 
Authored: Mon Sep 18 10:09:54 2017 -0400
Committer: Marcus Christie 
Committed: Mon Sep 18 10:09:54 2017 -0400

--
 django_airavata/apps/api/serializers.py | 6 +++---
 django_airavata/apps/api/urls.py| 1 +
 django_airavata/apps/api/views.py   | 4 ++--
 3 files changed, 6 insertions(+), 5 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/airavata-django-portal/blob/e8e0fc44/django_airavata/apps/api/serializers.py
--
diff --git a/django_airavata/apps/api/serializers.py 
b/django_airavata/apps/api/serializers.py
index 7f38bf1..12442dd 100644
--- a/django_airavata/apps/api/serializers.py
+++ b/django_airavata/apps/api/serializers.py
@@ -42,13 +42,13 @@ class GatewayIdDefaultField(serializers.CharField):
 self.default = settings.GATEWAY_ID
 
 class ProjectSerializer(serializers.Serializer):
-url = FullyEncodedHyperlinkedIdentityField(view_name='project-detail', 
lookup_field='projectID', lookup_url_kwarg='project_id')
+url = 
FullyEncodedHyperlinkedIdentityField(view_name='django_airavata_api:project-detail',
 lookup_field='projectID', lookup_url_kwarg='project_id')
 projectID = serializers.CharField(read_only=True)
 name = serializers.CharField(required=True)
 description = serializers.CharField(required=False)
 owner = GatewayUsernameDefaultField()
 gatewayId = GatewayIdDefaultField()
-experiments = 
FullyEncodedHyperlinkedIdentityField(view_name='project-experiments', 
lookup_field='projectID', lookup_url_kwarg='project_id')
+experiments = 
FullyEncodedHyperlinkedIdentityField(view_name='django_airavata_api:project-experiments',
 lookup_field='projectID', lookup_url_kwarg='project_id')
 
 def create(self, validated_data):
 return Project(**validated_data)
@@ -65,7 +65,7 @@ class ExperimentSerializer(serializers.Serializer):
 
 experimentId = serializers.CharField(read_only=True)
 projectId = serializers.CharField(required=True)
-project = FullyEncodedHyperlinkedIdentityField(view_name='project-detail', 
lookup_field='projectId', lookup_url_kwarg='project_id')
+project = 
FullyEncodedHyperlinkedIdentityField(view_name='django_airavata_api:project-detail',
 lookup_field='projectId', lookup_url_kwarg='project_id')
 gatewayId = GatewayIdDefaultField()
 experimentType = serializers.CharField(required=True)
 userName = GatewayUsernameDefaultField()

http://git-wip-us.apache.org/repos/asf/airavata-django-portal/blob/e8e0fc44/django_airavata/apps/api/urls.py
--
diff --git a/django_airavata/apps/api/urls.py b/django_airavata/apps/api/urls.py
index 750e677..1c5e19b 100644
--- a/django_airavata/apps/api/urls.py
+++ b/django_airavata/apps/api/urls.py
@@ -12,6 +12,7 @@ logger = logging.getLogger(__name__)
 router = routers.SimpleRouter()
 router.register(r'projects', views.ProjectViewSet, base_name='project')
 
+app_name = 'django_airavata_api'
 urlpatterns = [
 url(r'^$', views.api_root),
 # url(r'^projects/$', views.ProjectList.as_view(), 
name='api_project_list'),

http://git-wip-us.apache.org/repos/asf/airavata-django-portal/blob/e8e0fc44/django_airavata/apps/api/views.py
--
diff --git a/django_airavata/apps/api/views.py 
b/django_airavata/apps/api/views.py
index 1181fa3..416fa5a 100644
--- a/django_airavata/apps/api/views.py
+++ b/django_airavata/apps/api/views.py
@@ -17,8 +17,8 @@ from django.views.decorators.csrf import csrf_exempt
 @api_view(['GET'])
 def api_root(request, format=None):
 return Response({
-'projects': reverse('project-list', request=request, format=format),
-'experiments': reverse('api_experiment_list', request=request, 
format=format)
+'projects': reverse('django_airavata_api:project-list', 
request=request, format=format),
+'experiments': reverse('django_airavata_api:api_experiment_list', 
request=request, format=format)
 })
 
 class GenericAPIBackedViewSet(GenericViewSet):

[1/4] airavata-django-portal git commit: Adding project's experiments to ProjectViewSet

[machristie]

Repository: airavata-django-portal
Updated Branches:
  refs/heads/master 4253233ff -> 4147972a1


Adding project's experiments to ProjectViewSet


Project: http://git-wip-us.apache.org/repos/asf/airavata-django-portal/repo
Commit: 
http://git-wip-us.apache.org/repos/asf/airavata-django-portal/commit/0a2bc1c5
Tree: 
http://git-wip-us.apache.org/repos/asf/airavata-django-portal/tree/0a2bc1c5
Diff: 
http://git-wip-us.apache.org/repos/asf/airavata-django-portal/diff/0a2bc1c5

Branch: refs/heads/master
Commit: 0a2bc1c50cc53dfd030c6bec170f2d380ebf2404
Parents: 4253233
Author: Marcus Christie 
Authored: Mon Sep 18 09:19:59 2017 -0400
Committer: Marcus Christie 
Committed: Mon Sep 18 09:19:59 2017 -0400

--
 django_airavata/apps/api/serializers.py |  4 ++--
 django_airavata/apps/api/urls.py| 10 +-
 django_airavata/apps/api/views.py   | 17 +++--
 3 files changed, 18 insertions(+), 13 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/airavata-django-portal/blob/0a2bc1c5/django_airavata/apps/api/serializers.py
--
diff --git a/django_airavata/apps/api/serializers.py 
b/django_airavata/apps/api/serializers.py
index d13b718..7f38bf1 100644
--- a/django_airavata/apps/api/serializers.py
+++ b/django_airavata/apps/api/serializers.py
@@ -42,13 +42,13 @@ class GatewayIdDefaultField(serializers.CharField):
 self.default = settings.GATEWAY_ID
 
 class ProjectSerializer(serializers.Serializer):
-url = FullyEncodedHyperlinkedIdentityField(view_name='project-detail', 
lookup_field='projectID', lookup_url_kwarg='pk')
+url = FullyEncodedHyperlinkedIdentityField(view_name='project-detail', 
lookup_field='projectID', lookup_url_kwarg='project_id')
 projectID = serializers.CharField(read_only=True)
 name = serializers.CharField(required=True)
 description = serializers.CharField(required=False)
 owner = GatewayUsernameDefaultField()
 gatewayId = GatewayIdDefaultField()
-experiments = 
FullyEncodedHyperlinkedIdentityField(view_name='api_project_experiments_list', 
lookup_field='projectID', lookup_url_kwarg='project_id')
+experiments = 
FullyEncodedHyperlinkedIdentityField(view_name='project-experiments', 
lookup_field='projectID', lookup_url_kwarg='project_id')
 
 def create(self, validated_data):
 return Project(**validated_data)

http://git-wip-us.apache.org/repos/asf/airavata-django-portal/blob/0a2bc1c5/django_airavata/apps/api/urls.py
--
diff --git a/django_airavata/apps/api/urls.py b/django_airavata/apps/api/urls.py
index 544c07b..750e677 100644
--- a/django_airavata/apps/api/urls.py
+++ b/django_airavata/apps/api/urls.py
@@ -5,6 +5,10 @@ from django.conf.urls import include, url
 from rest_framework import routers
 from rest_framework.urlpatterns import format_suffix_patterns
 
+import logging
+
+logger = logging.getLogger(__name__)
+
 router = routers.SimpleRouter()
 router.register(r'projects', views.ProjectViewSet, base_name='project')
 
@@ -13,10 +17,14 @@ urlpatterns = [
 # url(r'^projects/$', views.ProjectList.as_view(), 
name='api_project_list'),
 # More specific, longer URLs should come before less specific, shorter ones
 # since the regular expression for project_id allows any character, even 
'/'
-url(r'^projects/(?P.+)/experiments/$', 
views.ProjectExperimentList.as_view(), name='api_project_experiments_list'),
+# url(r'^projects/(?P.+)/experiments/$', 
views.ProjectExperimentList.as_view(), name='api_project_experiments_list'),
 # url(r'^projects/(?P.+)/$', views.ProjectDetail.as_view(), 
name='api_project_detail'),
 url(r'^experiments/$', views.ExperimentList.as_view(), 
name='api_experiment_list'),
 url(r'^', include(router.urls)),
 ]
 
+if logger.isEnabledFor(logging.DEBUG):
+for url in router.urls:
+logger.debug("router url: {}".format(url))
+
 urlpatterns = format_suffix_patterns(urlpatterns)
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-django-portal/blob/0a2bc1c5/django_airavata/apps/api/views.py
--
diff --git a/django_airavata/apps/api/views.py 
b/django_airavata/apps/api/views.py
index 2de3ba8..1181fa3 100644
--- a/django_airavata/apps/api/views.py
+++ b/django_airavata/apps/api/views.py
@@ -2,7 +2,7 @@
 from . import serializers
 
 from rest_framework import status, mixins
-from rest_framework.decorators import api_view
+from rest_framework.decorators import api_view, detail_route
 from rest_framework.views import APIView
 from rest_framework.viewsets import GenericViewSet
 from rest_framework.response import Response
@@ -81,6 +81,7 @@ class 

[2/4] airavata-django-portal git commit: Fix calling ProjectViewSet directly to get project list

[machristie]

Fix calling ProjectViewSet directly to get project list


Project: http://git-wip-us.apache.org/repos/asf/airavata-django-portal/repo
Commit: 
http://git-wip-us.apache.org/repos/asf/airavata-django-portal/commit/c975f46f
Tree: 
http://git-wip-us.apache.org/repos/asf/airavata-django-portal/tree/c975f46f
Diff: 
http://git-wip-us.apache.org/repos/asf/airavata-django-portal/diff/c975f46f

Branch: refs/heads/master
Commit: c975f46f65eed677d12c16927a5aa25a5832260e
Parents: 0a2bc1c
Author: Marcus Christie 
Authored: Mon Sep 18 09:30:47 2017 -0400
Committer: Marcus Christie 
Committed: Mon Sep 18 09:44:56 2017 -0400

--
 django_airavata/apps/workspace/views.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/airavata-django-portal/blob/c975f46f/django_airavata/apps/workspace/views.py
--
diff --git a/django_airavata/apps/workspace/views.py 
b/django_airavata/apps/workspace/views.py
index 6967f25..b7d8d8f 100644
--- a/django_airavata/apps/workspace/views.py
+++ b/django_airavata/apps/workspace/views.py
@@ -13,7 +13,7 @@ logger = logging.getLogger(__name__)
 @login_required
 def projects_list(request):
 
-response = ProjectList().get(request)
+response = ProjectViewSet.as_view({'get': 'list'})(request)
 projects_json = JSONRenderer().render(response.data)
 
 return render(request, 'django_airavata_workspace/projects_list.html', {