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From dimuthu...@apache.org
Subject [airavata] 01/02: Merge branch 'master' into staging
Date Sun, 30 Dec 2018 03:03:33 GMT
This is an automated email from the ASF dual-hosted git repository.

dimuthuupe pushed a commit to branch staging
in repository https://gitbox.apache.org/repos/asf/airavata.git

commit 89ae6eef1fcb927534aab61016b4e87e1df22a48
Merge: a6ef239 241e5a3
Author: Dimuthu Wannipurage <dimuthu.upeksha2@gmail.com>
AuthorDate: Fri Dec 28 15:00:17 2018 -0500

    Merge branch 'master' into staging
    
    # Conflicts:
    #	airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java
    #	airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/API/Airavata.php
    #	airavata-services/profile-service/profile-service-stubs/src/main/java/org/apache/airavata/service/profile/iam/admin/services/cpi/IamAdminServices.java
    #	modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
    #	modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cluster/RemoteCluster.java
    #	modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/BESRemoteCluster.java
    #	modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/HPCRemoteCluster.java
    #	modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/LocalRemoteCluster.java
    #	modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java
    #	modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/SCPDataStageTask.java
    #	modules/gfac/gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java
    #	modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/cpi/impl/SimpleOrchestratorImpl.java

 .../api/server/handler/AiravataServerHandler.java  |    30 +
 .../java/org/apache/airavata/api/Airavata.java     | 77016 +++++++++++--------
 .../main/resources/lib/Airavata/API/Airavata.php   | 10997 +--
 .../Model/AppCatalog/AccountProvisioning/Types.php |   345 +
 .../Iam/Admin/Services/CPI/IamAdminServices.php    |   294 +
 .../core/impl/TenantManagementKeycloakImpl.java    |    19 +
 .../core/interfaces/TenantManagementInterface.java |    10 +
 .../profile/handlers/IamAdminServicesHandler.java  |    14 +
 .../iam/admin/services/cpi/IamAdminServices.java   |  4589 +-
 .../scigap/dreg-production/group_vars/pga/vars.yml |     4 +-
 .../group_vars/pga/vars.yml                        |    37 +-
 .../nexttdb-production/group_vars/pga/vault.yml    |    18 +
 .../inventories/scigap/nexttdb-production/hosts    |    21 +
 .../pga_config/{csbglsu => ampgateway}/vars.yml    |    23 +-
 .../production/pga_config/ampgateway/vault.yml     |    18 +
 .../scigap/production/pga_config/csbglsu/vars.yml  |    17 +-
 .../pga_config/{csbglsu => ddstudio}/vars.yml      |    30 +-
 .../production/pga_config/ddstudio/vault.yml       |    17 +
 .../pga_config/{searchingSRA => demo1}/vars.yml    |    14 +-
 .../scigap/production/pga_config/demo1/vault.yml   |    17 +
 .../pga_config/{searchingSRA => demo10}/vars.yml   |    14 +-
 .../scigap/production/pga_config/demo10/vault.yml  |    17 +
 .../pga_config/{searchingSRA => demo2}/vars.yml    |    14 +-
 .../scigap/production/pga_config/demo2/vault.yml   |    17 +
 .../pga_config/{searchingSRA => demo3}/vars.yml    |    14 +-
 .../scigap/production/pga_config/demo3/vault.yml   |    17 +
 .../pga_config/{searchingSRA => demo4}/vars.yml    |    14 +-
 .../scigap/production/pga_config/demo4/vault.yml   |    17 +
 .../pga_config/{searchingSRA => demo5}/vars.yml    |    14 +-
 .../scigap/production/pga_config/demo5/vault.yml   |    17 +
 .../pga_config/{searchingSRA => demo6}/vars.yml    |    14 +-
 .../scigap/production/pga_config/demo6/vault.yml   |    17 +
 .../pga_config/{searchingSRA => demo7}/vars.yml    |    14 +-
 .../scigap/production/pga_config/demo7/vault.yml   |    17 +
 .../pga_config/{searchingSRA => demo8}/vars.yml    |    14 +-
 .../scigap/production/pga_config/demo8/vault.yml   |    17 +
 .../pga_config/{searchingSRA => demo9}/vars.yml    |    14 +-
 .../scigap/production/pga_config/demo9/vault.yml   |    17 +
 .../{searchingSRA => epwgateway}/vars.yml          |    23 +-
 .../production/pga_config/epwgateway/vault.yml     |    18 +
 .../production/pga_config/georgiastate/vars.yml    |     6 +-
 .../pga_config/{iugateway => hubzero}/vars.yml     |    31 +-
 .../scigap/production/pga_config/hubzero/vault.yml |    18 +
 .../pga_config/{csbglsu => interactwel}/vars.yml   |    25 +-
 .../production/pga_config/interactwel/vault.yml    |    18 +
 .../production/pga_config/iugateway/vars.yml       |     4 +-
 .../production/pga_config/iugeosurvey/vars.yml     |    17 +-
 .../production/pga_config/newUltrascan/vars.yml    |    73 -
 .../production/pga_config/newUltrascan/vault.yml   |    18 -
 .../pga_config/{csbglsu => nexttdb}/vars.yml       |    26 +-
 .../scigap/production/pga_config/nexttdb/vault.yml |    18 +
 .../pga_config/{csbglsu => r-hpc}/vars.yml         |    25 +-
 .../scigap/production/pga_config/r-hpc/vault.yml   |    18 +
 .../pga_config/{csbglsu => rutgersgemr}/vars.yml   |    25 +-
 .../production/pga_config/rutgersgemr/vault.yml    |    18 +
 .../pga_config/{iugateway => saverx}/vars.yml      |    31 +-
 .../scigap/production/pga_config/saverx/vault.yml  |    18 +
 .../scigap/production/pga_config/seagrid/vars.yml  |    11 +-
 .../production/pga_config/searchingSRA/vars.yml    |    15 +-
 .../pga_config/simvascular/files/pga_config.php.j2 |     7 +-
 .../production/pga_config/simvascular/vars.yml     |     3 +
 .../production/pga_config/southdakota/vars.yml     |     8 +-
 .../production/pga_config/testdrive/vars.yml       |    10 +-
 dev-tools/ansible/pga-scigap-prod.yml              |    14 +-
 dev-tools/ansible/requirements.txt                 |     2 +-
 .../gfac/templates/airavata-server.properties.j2   |     2 +-
 .../roles/gfac/templates/gfac-config.yaml.j2       |    11 +
 dev-tools/ansible/roles/pga/defaults/main.yml      |     7 +
 .../roles/pga/templates/pga-ssl-vhost.conf.j2      |    13 +
 .../ansible/roles/pga/templates/pga-vhost.conf.j2  |    11 +-
 .../accountprovisioning/SSHAccountManager.java     |    25 +-
 .../accountprovisioning/SSHAccountProvisioner.java |     9 +
 .../provisioner/IULdapSSHAccountProvisioner.java   |   165 +-
 .../IULdapSSHAccountProvisionerProvider.java       |     6 +-
 .../provisioner/TestSSHAccountProvisioner.java     |     5 +
 .../monitor/email/parser/PBSEmailParser.java       |     2 +-
 .../src/main/resources/appcatalog-mysql.sql        |     2 +-
 .../DeltaScripts/appCatalog_schema_delta.sql       |    38 +-
 .../DeltaScripts/credentialStore_schema_delta.sql  |     8 -
 .../DeltaScripts/expCatalog_schema_delta.sql       |     8 -
 .../DeltaScripts/replicaCatalog_schema_delta.sql   |     8 -
 .../DeltaScripts/sharingCatalog_schema_delta.sql   |    21 +
 .../DeltaScripts/workFlow_schema_delta.sql         |     8 -
 ...licaCatalog_lowercase_user_data_dir_example.sql |     0
 .../credentialStore_keycloak_migration.sql         |     0
 .../expCatalog_keycloak_migration.sql              |     0
 .../profileService_keycloak_migration.sql          |     0
 .../sharingCatalog_keycloak_migration.sql          |     0
 .../0.16-0.17/migration-notes.md                   |     9 +-
 .../DeltaScripts/appCatalog_schema_delta.sql       |    30 -
 .../0.17-0.18/migration-notes.md                   |    17 -
 .../DeltaScripts/appCatalog_schema_delta.sql       |    36 -
 .../airavata-apis/airavata_api.thrift              |     9 +
 .../iam-admin-services-cpi.thrift                  |     5 +
 94 files changed, 54069 insertions(+), 40695 deletions(-)

diff --cc modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/PBSEmailParser.java
index 45dce11,0000000..14a4497
mode 100644,000000..100644
--- a/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/PBSEmailParser.java
+++ b/modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/PBSEmailParser.java
@@@ -1,106 -1,0 +1,106 @@@
 +/**
 + *
 + * 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.monitor.email.parser;
 +
 +import org.apache.airavata.common.exception.AiravataException;
 +import org.apache.airavata.model.status.JobState;
 +import org.apache.airavata.monitor.JobStatusResult;
 +import org.slf4j.Logger;
 +import org.slf4j.LoggerFactory;
 +
 +import javax.mail.Message;
 +import javax.mail.MessagingException;
 +import java.io.IOException;
 +import java.util.regex.Matcher;
 +import java.util.regex.Pattern;
 +
 +public class PBSEmailParser implements EmailParser {
 +    private static final Logger log = LoggerFactory.getLogger(PBSEmailParser.class);
 +    public static final String BEGUN_EXECUTION = "Begun execution";
 +    public static final String EXECUTION_TERMINATED = "Execution terminated";
 +    public static final String ABORTED_BY_PBS_SERVER = "Aborted by PBS Server";
 +
 +    static final String REGEX = "[a-zA-Z ]*:[ ]*(?<" + JOBID + ">[a-zA-Z0-9-_\\.]*)\\s+[a-zA-Z
]*:[ ]*(?<" +
 +            JOBNAME + ">[a-zA-Z0-9-\\.]*)\\s[\\S|\\s]*(?<" + STATUS + ">" + BEGUN_EXECUTION
+ "|" +
 +            EXECUTION_TERMINATED + "|" + ABORTED_BY_PBS_SERVER + ")";
 +
 +    private static final String REGEX_EXIT_STATUS = "Exit_status=(?<" + EXIT_STATUS +
">[\\d]+)";
 +
 +    @Override
 +    public JobStatusResult parseEmail(Message message) throws MessagingException, AiravataException
{
 +        JobStatusResult jobStatusResult = new JobStatusResult();
 +//        log.info("Parsing -> " + message.getSubject());
 +        try {
 +            String content = ((String) message.getContent());
 +            parseContent(content, jobStatusResult);
-         } catch (IOException e) {
++        } catch (Exception e) {
 +            throw new AiravataException("[EJM]: Error while reading content of the email
message");
 +        }
 +        return jobStatusResult;
 +    }
 +
 +    void parseContent(String content, JobStatusResult jobStatusResult) throws MessagingException,
AiravataException {
 +        content = content.replaceAll("[^\\x00-\\x7F]", "");
 +        Pattern pattern = Pattern.compile(REGEX);
 +        Matcher matcher = pattern.matcher(content);
 +        if (matcher.find()) {
 +            jobStatusResult.setJobId(matcher.group(JOBID));
 +            jobStatusResult.setJobName(matcher.group(JOBNAME));
 +            String statusLine = matcher.group(STATUS);
 +            jobStatusResult.setState(getJobState(statusLine, content));
 +        } else {
 +            log.error("[EJM]: No matched found for content => \n" + content);
 +        }
 +    }
 +
 +    private JobState getJobState(String statusLine, String content) {
 +        switch (statusLine) {
 +            case BEGUN_EXECUTION:
 +                return JobState.ACTIVE;
 +            case EXECUTION_TERMINATED:
 +                int exitStatus = getExitStatus(content);
 +                if (exitStatus == 0) {
 +                    // TODO - Remove rabbitmq client script line from the script.
 +                    return JobState.COMPLETE;
 +                } else if (exitStatus == 271) {
 +                    return JobState.CANCELED;
 +                } else {
 +                    return JobState.FAILED;
 +                }
 +            case ABORTED_BY_PBS_SERVER:
 +                return JobState.FAILED;
 +            default:
 +                return JobState.UNKNOWN;
 +        }
 +    }
 +
 +    private int getExitStatus(String content) {
 +        Pattern pattern = Pattern.compile(REGEX_EXIT_STATUS);
 +        Matcher matcher = pattern.matcher(content);
 +        if (matcher.find()) {
 +            String group = matcher.group(EXIT_STATUS);
 +            if (group != null && !group.trim().isEmpty()) {
 +                return Integer.valueOf(group.trim());
 +            }
 +        }
 +        return -1;
 +    }
 +
 +}


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