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Posted to commits@airavata.apache.org by di...@apache.org on 2018/12/30 03:03:32 UTC
[airavata] branch staging updated (0bf8495 -> f0e1eb4)
This is an automated email from the ASF dual-hosted git repository.
dimuthuupe pushed a change to branch staging
in repository https://gitbox.apache.org/repos/asf/airavata.git.
from 0bf8495 Grant access to localhost separately
add 358a3f8 Adding demo gateway1 for ACS workshop
add fb59d8d Adding demo gateways for ACS workshop
add e9dd9a4 Change Git URL to dREG's repo
add afe33c8 Merge remote-tracking branch 'origin/master'
add b0987c5 Merge remote-tracking branch 'origin/AIRAVATA-2500'
add 9d83c91 Travis: clone full repo for git-describe to work
add 7d4c711 IU Cybergateway: disable password login, IU CAS only
add d365755 IU Cybergateway: automatically assign gateway-user role
add f2b5d2b Added the new google analytics ID
add d900060 Use pga_default_http_port (defaults to 80) in http vhost conf
add c516b73 Added the new google analytics ID for CSBG LSU
add ea1691f Adding analytics var to Simvascular pga_config template
add db71389 Adding supermic email for monitoring
add 957dc95 Fixing output files not staging issues when wildcards are specified
add 0ff8b18 Merge pull request #190 from DImuthuUpe/AIRAVATA-2467
add 3cdb2e3 Removing dev.ultrascan from production deployment
add c303184 Merge remote-tracking branch 'origin/master'
add 3df3bc5 Changed USD Login page wordings on login buttons and headings. Request from gateway PI.
add ed59794 Changed USD Login page wordings on login buttons and headings. Request from gateway PI.
add f2fd1c2 Adding Next Gen Thermodynamics gateway directories
add d15cad4 NextGen Thermodynamics gateway: SSL/CILogon config
add 173b9d6 Changed the CILogon name for next gen TDB
add 1d5b3f2 Changed the CILogon into GSU Login in the Login page CILogon button on request by the gateway PI
add 3f84204 Changed the CILogon name and logo in CILogon button
add c8573c1 Changed the new URL of Searching SRA gateway and added certificates
add f79c7f7 Added vhost server alias for searching SRA
add baf6974 Adding missing emails to gfac config
add a6e5782 Logging improvements
add af87650 Adding max-wall-time-limit into simvascular pga config
add 3dd7c72 Changed the max walltie for SimVascular gateway to 300
add 49f6f1a Bumping prefetch.count to 400
add a0fc98b pga role gains vhost_server_redirect variable, used for CSBGLSU gateway
add e8530a1 Reorganizing DB migration scripts in prep for 0.17 release
add 0f9a519 Fixed the table column constraint
add 61dc421 Merge pull request #199 from rkunalan/fixes
add edba8d3 Added Suranga's email for gateway user account creation notifications
add 433210b Added Rob's gmail to get new user notifications
add 359434f Added new theme to CSBG LSU gateway
add 2dbbfd5 Added new gateway folder: InterACTWEL
add 35e1c12 Switched dreg notification email to sgrc-iu-group@iu.edu from SGG old mail
add cbf0827 Added bigdawg email for monitoring of SIU gateway
add c40d8f1 Added InterACTWEL Jetstream cluster email
add a79b484 Add isUserEnabled to IamAdminServices
add 32a58cf Thrift stub generation for isUserEnabled
add eb07965 Merge branch 'is-user-enabled'
add 3764bba Adding the new R systems gateway
add 05cdb25 Updated storage SSH token
add ea75438 Added Kevin's email to get new user notification
add 0244288 Added Ryan's email
add d679f53 AIRAVATA-2382 Moving max upload filesize to vhost config
add a3520c9 AIRAVATA-2382 Adding comments
add 90dfbb6 AIRAVATA-2382 Increase max file upload size for Simvascular
add 9dd562d Update testdrive to using Let's Encrypt cert
add 7055d80 Adding new rutgers gateway
add d730bbb Adding the SSH key for storage resource
add 20753c8 Added both r-hpc and rutgersgemr gateways to the list
add 22d1db2 Added SSL certificate to GemR gateway
add 0cd309b updated simccs ssl certificates
add f5a051d Adding the new gateway ampgateway
add ad4221d Adding redirect for simccs.org
add 71dffab Bumping up max wall time to 600 min for Simvascular
add 7d57a5e Upgrade Ansible to at least 2.3.1.0 due to sec vulnerability
add 1cced3b Added Carbonate monitoring email
add ac2b8e1 adding R systesm and gw77 email to config
add ffd2b6c Adding new gateway epw gateway
add 18d0e4e IU LDAP ssh account: add user to cybergateway group
add f0565c1 Added API method: isSSHSetupCompleteForUserComputeResourcePreference
add d799876 Regenerate thrift stubs
add 6fad6ca Merge branch 'iu-ldap-cybergateway-group'
add ad3f5eb Merge remote-tracking branch 'origin/master'
add 30bcd6c Adding new gateway epw gateway
add 7f62cd5 adding the credential store token for gateway storage server
add 50fc486 Added CILogon for AMP gateway
add 8bfc54f Added SEAGrid Elastic cluster email for monitoring
add 91b44b1 Added letsencrypt certificate to seagrid gateway
add 1665986 Adding Hubzero gateway to ansible
add 873bd55 Adding storage resource SSH key and SSL certificates
add 85e37cc Added CILogon for HubZero gateway
add a30ec33 Added missing gateways to the list and commented out oiitandy
add 44c3b62 Added nexttdb-production gateway to host in Jetstream cluster
add f22e9c6 Adding SSL for next tdb gateway in jetstream
add 186e764 Adding new Saver-X gateway
add a27eec4 Fixed a typo in gateway domain
add 8a0861e Adde SSL certificates to the saver-x gateway
add 3e8a666 Added gateway storage resource to saver-x gateway
add 07f21f4 Added CILogon to SAVER-X gateway
add caf34aa Added Hubzero and saverx gateways to pga-scigap-prod.yml list
add e1ccbf8 Initial data flow to handle string output type
add 367a68a Validating output file size before reading to avoid OOM issues
add 04d4640 Checking whether argument contains inside each line of output file
add 9c4f74e Merge branch 'master' of https://github.com/apache/airavata into AIRAVATA-2625-FIX
add 21c3a59 Getting file size and validating before downloading
add 356049e Merge branch 'master' into AIRAVATA-2625-FIX
add aeb78ac Changing the string output type file destination to search query field
add fa161fd Fixing typo
add 2d84196 Merge pull request #184 from DImuthuUpe/AIRAVATA-2625-FIX
add 76e2eba Catching all exceptions in PBS parser
add 11929a9 Adding new gateway tenant and gateway for DDStudio
add d18ae10 Updated DDStudio gateway properties
add 161b21f Added SSH key
add 6b779a9 Adding CILogon to DDStudio
add 8b9a7ff Added google analytics to NextTDB gateway
add b173880 Added google analytics to SimCCS
add 241e5a3 Increasing max upload size for SEAGrid
new 89ae6ee Merge branch 'master' into staging
new f0e1eb4 Merge branch 'staging' of https://github.com/apache/airavata into staging
The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
Summary of changes:
.../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 +
.../hosts | 2 +-
.../pga_config/{Kentucky => ampgateway}/vars.yml | 22 +-
.../production/pga_config/ampgateway/vault.yml | 18 +
.../scigap/production/pga_config/csbglsu/vars.yml | 17 +-
.../pga_config/{NCSAIndustry => ddstudio}/vars.yml | 25 +-
.../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/{Kentucky => hubzero}/vars.yml | 24 +-
.../scigap/production/pga_config/hubzero/vault.yml | 18 +
.../pga_config/{Kentucky => interactwel}/vars.yml | 28 +-
.../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/{Kentucky => nexttdb}/vars.yml | 21 +-
.../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/{Kentucky => rutgersgemr}/vars.yml | 26 +-
.../production/pga_config/rutgersgemr/vault.yml | 18 +
.../pga_config/{Kentucky => saverx}/vars.yml | 24 +-
.../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 +
.../roles/pga/templates/pga-ssl-vhost.conf.j2 | 11 +
.../ansible/roles/pga/templates/pga-vhost.conf.j2 | 9 +-
.../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 +
93 files changed, 54021 insertions(+), 40692 deletions(-)
create mode 100644 airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/Model/AppCatalog/AccountProvisioning/Types.php
copy dev-tools/ansible/inventories/scigap/{dreg-production => nexttdb-production}/group_vars/pga/vars.yml (62%)
create mode 100644 dev-tools/ansible/inventories/scigap/nexttdb-production/group_vars/pga/vault.yml
copy dev-tools/ansible/inventories/scigap/{PICKSC-Production => nexttdb-production}/hosts (89%)
copy dev-tools/ansible/inventories/scigap/production/pga_config/{Kentucky => ampgateway}/vars.yml (70%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/ampgateway/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{NCSAIndustry => ddstudio}/vars.yml (71%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/ddstudio/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{searchingSRA => demo1}/vars.yml (79%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/demo1/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{searchingSRA => demo10}/vars.yml (79%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/demo10/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{searchingSRA => demo2}/vars.yml (79%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/demo2/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{searchingSRA => demo3}/vars.yml (79%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/demo3/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{searchingSRA => demo4}/vars.yml (79%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/demo4/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{searchingSRA => demo5}/vars.yml (79%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/demo5/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{searchingSRA => demo6}/vars.yml (79%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/demo6/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{searchingSRA => demo7}/vars.yml (79%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/demo7/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{searchingSRA => demo8}/vars.yml (79%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/demo8/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{searchingSRA => demo9}/vars.yml (79%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/demo9/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{searchingSRA => epwgateway}/vars.yml (66%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/epwgateway/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{Kentucky => hubzero}/vars.yml (68%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/hubzero/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{Kentucky => interactwel}/vars.yml (64%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/interactwel/vault.yml
delete mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/newUltrascan/vars.yml
delete mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/newUltrascan/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{Kentucky => nexttdb}/vars.yml (69%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/nexttdb/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{csbglsu => r-hpc}/vars.yml (66%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/r-hpc/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{Kentucky => rutgersgemr}/vars.yml (66%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/rutgersgemr/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{Kentucky => saverx}/vars.yml (66%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/saverx/vault.yml
rename modules/registry/release-migration-scripts/{0.17-0.18 => 0.16-0.17}/DeltaScripts/sharingCatalog_schema_delta.sql (54%)
rename modules/registry/release-migration-scripts/{0.17-0.18 => 0.16-0.17}/keycloak-migration-replica-catalog/replicaCatalog_lowercase_user_data_dir_example.sql (100%)
rename modules/registry/release-migration-scripts/{0.17-0.18 => 0.16-0.17}/keycloak-migration/credentialStore_keycloak_migration.sql (100%)
rename modules/registry/release-migration-scripts/{0.17-0.18 => 0.16-0.17}/keycloak-migration/expCatalog_keycloak_migration.sql (100%)
rename modules/registry/release-migration-scripts/{0.17-0.18 => 0.16-0.17}/keycloak-migration/profileService_keycloak_migration.sql (100%)
rename modules/registry/release-migration-scripts/{0.17-0.18 => 0.16-0.17}/keycloak-migration/sharingCatalog_keycloak_migration.sql (100%)
delete mode 100644 modules/registry/release-migration-scripts/0.17-0.18/DeltaScripts/appCatalog_schema_delta.sql
delete mode 100644 modules/registry/release-migration-scripts/0.17-0.18/migration-notes.md
delete mode 100644 modules/registry/release-migration-scripts/0.18-0.19/DeltaScripts/appCatalog_schema_delta.sql
[airavata] 01/02: Merge branch 'master' into staging
Posted by di...@apache.org.
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 <di...@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;
+ }
+
+}
[airavata] 02/02: Merge branch 'staging' of
https://github.com/apache/airavata into staging
Posted by di...@apache.org.
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 f0e1eb4a66f724fb13ca26ff52030280fe56b448
Merge: 89ae6ee 0bf8495
Author: Dimuthu Wannipurage <di...@gmail.com>
AuthorDate: Sat Dec 29 22:02:07 2018 -0500
Merge branch 'staging' of https://github.com/apache/airavata into staging
dev-tools/ansible/roles/database/tasks/main.yml | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)