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Posted to commits@airavata.apache.org by ma...@apache.org on 2020/04/23 00:39:01 UTC
[airavata] branch master updated (6e51d46 -> 56b3f0a)
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a change to branch master
in repository https://gitbox.apache.org/repos/asf/airavata.git.
from 6e51d46 Merge remote-tracking branch 'origin/airavata-3281'
add b07d1d0 AIRAVATA-3268 Add overrideFilename to app input model
add cf0bb4b AIRAVATA-3268 migrate input_values to override_filename
add 3cb9347 Attaching overrideFileName to destination
add 5209ef3 AIRAVATA-3268 Use overrideFilename on command line
new e78ff86 Merge branch 'airavata-3268'
add af5cc07 AIRAVATA-3126 Add ComputeResourceReservation data model and entity
add d698f9b AIRAVATA-3126 Update logic to get active reservation
add 3fb981b AIRAVATA-3126 Prevent MariaDB ON UPDATE CURRENT_TIMESTAMP
add 6f35091 WIP
new 56b3f0a Merge branch 'AIRAVATA-3126--Implement-compute-resource-reservation-addition'
The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
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Summary of changes:
.../appcatalog/groupresourceprofile/ttypes.py | 217 +++++-
.../lib/airavata/model/application/io/ttypes.py | 16 +-
.../resources/lib/airavata/model/group/ttypes.py | 3 +
.../resources/lib/airavata/model/sharing/ttypes.py | 15 +-
.../ComputeResourcePolicy.java | 32 +-
.../ComputeResourceReservation.java | 820 +++++++++++++++++++++
.../GroupComputeResourcePreference.java | 189 ++++-
.../groupresourceprofile/GroupResourceProfile.java | 108 +--
.../model/application/io/InputDataObjectType.java | 115 ++-
airavata-api/airavata-model-utils/pom.xml | 6 +
.../util/GroupComputeResourcePreferenceUtil.java | 30 +-
.../GroupComputeResourcePreferenceUtilTest.java | 116 +++
.../airavata/helix/impl/task/TaskContext.java | 9 +
.../task/submission/config/GroovyMapBuilder.java | 12 +-
.../org/apache/airavata/common/utils/JPAUtils.java | 146 +++-
.../src/main/resources/META-INF/persistence.xml | 1 +
.../init/03-appcatalog-migrations.sql | 11 +
.../init/04-expcatalog-migrations.sql | 4 +
.../cpi/impl/SimpleOrchestratorImpl.java | 5 +-
modules/registry/registry-core/README.md | 13 +
.../appcatalog/ApplicationInputEntity.java | 11 +
....java => ComputeResourceReservationEntity.java} | 93 ++-
.../appcatalog/GroupComputeResourcePrefEntity.java | 15 +-
.../GroupSSHAccountProvisionerConfig.java | 2 +-
.../entities/expcatalog/ExperimentInputEntity.java | 13 +-
.../entities/expcatalog/ProcessInputEntity.java | 13 +-
.../core/repositories/AbstractRepository.java | 10 +-
.../appcatalog/GroupResourceProfileRepository.java | 29 +-
.../core/utils/JPAUtil/AppCatalogJPAUtils.java | 11 +-
.../src/main/resources/META-INF/persistence.xml | 1 +
.../src/main/resources/appcatalog-derby.sql | 7 +
.../src/main/resources/appcatalog-mysql.sql | 9 +
.../src/main/resources/expcatalog-derby.sql | 2 +
.../src/main/resources/expcatalog-mysql.sql | 2 +
.../GroupResourceProfileRepositoryTest.java | 257 ++++++-
.../expcatalog/ExperimentRepositoryTest.java | 4 +
.../DeltaScripts/appCatalog_schema_delta.sql | 4 +
.../experimentCatalog_schema_delta.sql | 4 +
.../next/DeltaScripts/appCatalog_schema_delta.sql | 8 +
.../application_io_models.thrift | 5 +-
.../group_resource_profile_model.thrift | 13 +-
41 files changed, 2176 insertions(+), 205 deletions(-)
create mode 100644 airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/groupresourceprofile/ComputeResourceReservation.java
copy modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/GrpComputePrefRepository.java => airavata-api/airavata-model-utils/src/main/java/org/apache/airavata/model/util/GroupComputeResourcePreferenceUtil.java (51%)
create mode 100644 airavata-api/airavata-model-utils/src/test/java/org/apache/airavata/model/util/GroupComputeResourcePreferenceUtilTest.java
create mode 100644 modules/ide-integration/src/main/resources/database_scripts/init/03-appcatalog-migrations.sql
create mode 100644 modules/ide-integration/src/main/resources/database_scripts/init/04-expcatalog-migrations.sql
create mode 100644 modules/registry/registry-core/README.md
copy modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/{GroupSSHAccountProvisionerConfig.java => ComputeResourceReservationEntity.java} (52%)
[airavata] 01/02: Merge branch 'airavata-3268'
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/airavata.git
commit e78ff86e7ff3a180ba9edf725352b013d24f77e3
Merge: 6e51d46 5209ef3
Author: Marcus Christie <ma...@iu.edu>
AuthorDate: Wed Apr 22 20:27:17 2020 -0400
Merge branch 'airavata-3268'
.../lib/airavata/model/application/io/ttypes.py | 16 ++-
.../resources/lib/airavata/model/group/ttypes.py | 3 +
.../resources/lib/airavata/model/sharing/ttypes.py | 15 ++-
.../model/application/io/InputDataObjectType.java | 115 ++++++++++++++++++++-
.../task/submission/config/GroovyMapBuilder.java | 12 ++-
.../init/03-appcatalog-migrations.sql | 3 +
.../init/04-expcatalog-migrations.sql | 4 +
.../cpi/impl/SimpleOrchestratorImpl.java | 5 +-
.../appcatalog/ApplicationInputEntity.java | 11 ++
.../entities/expcatalog/ExperimentInputEntity.java | 13 ++-
.../entities/expcatalog/ProcessInputEntity.java | 13 ++-
.../src/main/resources/appcatalog-derby.sql | 1 +
.../src/main/resources/appcatalog-mysql.sql | 1 +
.../src/main/resources/expcatalog-derby.sql | 2 +
.../src/main/resources/expcatalog-mysql.sql | 2 +
.../expcatalog/ExperimentRepositoryTest.java | 4 +
.../DeltaScripts/appCatalog_schema_delta.sql | 4 +
.../experimentCatalog_schema_delta.sql | 4 +
.../application_io_models.thrift | 5 +-
19 files changed, 219 insertions(+), 14 deletions(-)
diff --cc modules/registry/release-migration-scripts/0.18-0.19/DeltaScripts/experimentCatalog_schema_delta.sql
index 7f1c2c8,7a97d50..487a324
--- a/modules/registry/release-migration-scripts/0.18-0.19/DeltaScripts/experimentCatalog_schema_delta.sql
+++ b/modules/registry/release-migration-scripts/0.18-0.19/DeltaScripts/experimentCatalog_schema_delta.sql
@@@ -115,15 -115,6 +115,19 @@@ wher
g.OAUTH_CLIENT_ID is null
or g.OAUTH_CLIENT_SECRET is null;
+-- AIRAVATA-3303 Slashes in experiment id
+set FOREIGN_KEY_CHECKS=0;
+
+update EXPERIMENT set EXPERIMENT_ID = REPLACE(EXPERIMENT_ID, "/", "_") where EXPERIMENT_ID like '%/%';
+update EXPERIMENT_INPUT set EXPERIMENT_ID = REPLACE(EXPERIMENT_ID, "/", "_") where EXPERIMENT_ID like '%/%';
+update EXPERIMENT_OUTPUT set EXPERIMENT_ID = REPLACE(EXPERIMENT_ID, "/", "_") where EXPERIMENT_ID like '%/%';
+update EXPERIMENT_STATUS set EXPERIMENT_ID = REPLACE(EXPERIMENT_ID, "/", "_") where EXPERIMENT_ID like '%/%';
+update EXPERIMENT_ERROR set EXPERIMENT_ID = REPLACE(EXPERIMENT_ID, "/", "_") where EXPERIMENT_ID like '%/%';
+update USER_CONFIGURATION_DATA set EXPERIMENT_ID = REPLACE(EXPERIMENT_ID, "/", "_") where EXPERIMENT_ID like '%/%';
+update PROCESS set EXPERIMENT_ID = REPLACE(EXPERIMENT_ID, "/", "_") where EXPERIMENT_ID like '%/%';
+
+set FOREIGN_KEY_CHECKS=1;
++
+ -- AIRAVATA-3268: add overrideFilename to EXPERIMENT_INPUT, PROCESS_INPUT
+ ALTER TABLE EXPERIMENT_INPUT ADD COLUMN IF NOT EXISTS OVERRIDE_FILENAME VARCHAR(255);
+ ALTER TABLE PROCESS_INPUT ADD COLUMN IF NOT EXISTS OVERRIDE_FILENAME VARCHAR(255);
[airavata] 02/02: Merge branch
'AIRAVATA-3126--Implement-compute-resource-reservation-addition'
Posted by ma...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/airavata.git
commit 56b3f0ab77b7b68e3ebb4179a66eb4189b8d66fb
Merge: e78ff86 6f35091
Author: Marcus Christie <ma...@iu.edu>
AuthorDate: Wed Apr 22 20:30:52 2020 -0400
Merge branch 'AIRAVATA-3126--Implement-compute-resource-reservation-addition'
.../appcatalog/groupresourceprofile/ttypes.py | 217 +++++-
.../ComputeResourcePolicy.java | 32 +-
.../ComputeResourceReservation.java | 820 +++++++++++++++++++++
.../GroupComputeResourcePreference.java | 189 ++++-
.../groupresourceprofile/GroupResourceProfile.java | 108 +--
airavata-api/airavata-model-utils/pom.xml | 6 +
.../util/GroupComputeResourcePreferenceUtil.java | 44 ++
.../GroupComputeResourcePreferenceUtilTest.java | 116 +++
.../airavata/helix/impl/task/TaskContext.java | 9 +
.../org/apache/airavata/common/utils/JPAUtils.java | 146 +++-
.../src/main/resources/META-INF/persistence.xml | 1 +
.../init/03-appcatalog-migrations.sql | 8 +
modules/registry/registry-core/README.md | 13 +
....java => ComputeResourceReservationEntity.java} | 93 ++-
.../appcatalog/GroupComputeResourcePrefEntity.java | 15 +-
.../GroupSSHAccountProvisionerConfig.java | 2 +-
.../core/repositories/AbstractRepository.java | 10 +-
.../appcatalog/GroupResourceProfileRepository.java | 29 +-
.../core/utils/JPAUtil/AppCatalogJPAUtils.java | 11 +-
.../src/main/resources/META-INF/persistence.xml | 1 +
.../src/main/resources/appcatalog-derby.sql | 6 +
.../src/main/resources/appcatalog-mysql.sql | 8 +
.../GroupResourceProfileRepositoryTest.java | 257 ++++++-
.../next/DeltaScripts/appCatalog_schema_delta.sql | 8 +
.../group_resource_profile_model.thrift | 13 +-
25 files changed, 1981 insertions(+), 181 deletions(-)
diff --cc modules/ide-integration/src/main/resources/database_scripts/init/03-appcatalog-migrations.sql
index 4022bf3,a07c0f0..cf6f9c7
--- a/modules/ide-integration/src/main/resources/database_scripts/init/03-appcatalog-migrations.sql
+++ b/modules/ide-integration/src/main/resources/database_scripts/init/03-appcatalog-migrations.sql
@@@ -1,3 -1,10 +1,11 @@@
use app_catalog;
+ALTER TABLE APPLICATION_INPUT ADD COLUMN OVERRIDE_FILENAME VARCHAR(255);
+ -- AIRAVATA-3126
+ CREATE TABLE IF NOT EXISTS COMPUTE_RESOURCE_RESERVATION -- ComputeResourceReservationEntity
+ (RESERVATION_ID VARCHAR(255) NOT NULL, END_TIME TIMESTAMP NOT NULL, RESERVATION_NAME VARCHAR(255) NOT NULL, START_TIME TIMESTAMP NOT NULL, RESOURCE_ID VARCHAR(255) NOT NULL, GROUP_RESOURCE_PROFILE_ID VARCHAR(255) NOT NULL, PRIMARY KEY (RESERVATION_ID)
+ )ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ CREATE TABLE IF NOT EXISTS COMPUTE_RESOURCE_RESERVATION_QUEUE (RESERVATION_ID VARCHAR(255), QUEUE_NAME VARCHAR(255) NOT NULL
+ )ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ CREATE INDEX I_CMPTN_Q_RESERVATION_ID ON COMPUTE_RESOURCE_RESERVATION_QUEUE (RESERVATION_ID);
+ ALTER TABLE COMPUTE_RESOURCE_RESERVATION ADD CONSTRAINT FK_COMPUTE_RESOURCE_RESERVATION FOREIGN KEY (RESOURCE_ID, GROUP_RESOURCE_PROFILE_ID) REFERENCES GROUP_COMPUTE_RESOURCE_PREFERENCE (RESOURCE_ID, GROUP_RESOURCE_PROFILE_ID) ON DELETE CASCADE;
diff --cc modules/registry/release-migration-scripts/next/DeltaScripts/appCatalog_schema_delta.sql
index b9f4385,c25b3b1..6dacaa4
--- a/modules/registry/release-migration-scripts/next/DeltaScripts/appCatalog_schema_delta.sql
+++ b/modules/registry/release-migration-scripts/next/DeltaScripts/appCatalog_schema_delta.sql
@@@ -20,21 -20,11 +20,29 @@@
use app_catalog;
+-- AIRAVATA-3276 Replace JSON configuration: "toggle": ["isRequired"] ->
+-- "isRequired": true. Toggling requiredToAddedToCommandLine no longer needed.
+
+-- replace toggle with is isRequired
+update APPLICATION_INPUT
+set METADATA = REGEXP_REPLACE(METADATA, '"toggle": \\[[^}]+\\]', CONCAT('"isRequired": ', IF(IS_REQUIRED=1, 'true', 'false')))
+-- showOptions has "toggle" but not "isRequired"
+where METADATA rlike '"showOptions": {"toggle": \\[[^}]+\\]'
+ and NOT METADATA rlike '"showOptions": {.*"isRequired": (true|false)'
+;
+
+-- remove toggle since isRequired is already there
+update APPLICATION_INPUT
+set METADATA = REGEXP_REPLACE(METADATA, '(, )?"toggle": \\[[^}]+\\](, )?', '')
+-- showOptions has BOTH "toggle" and "isRequired"
+where METADATA rlike '"showOptions": {"toggle": \\[[^}]+\\]'
+ and METADATA rlike '"showOptions": {.*"isRequired": (true|false)'
+;
+ -- AIRAVATA-3126
+ CREATE TABLE IF NOT EXISTS COMPUTE_RESOURCE_RESERVATION -- ComputeResourceReservationEntity
+ (RESERVATION_ID VARCHAR(255) NOT NULL, END_TIME TIMESTAMP NOT NULL DEFAULT 0, RESERVATION_NAME VARCHAR(255) NOT NULL, START_TIME TIMESTAMP NOT NULL DEFAULT 0, RESOURCE_ID VARCHAR(255) NOT NULL, GROUP_RESOURCE_PROFILE_ID VARCHAR(255) NOT NULL, PRIMARY KEY (RESERVATION_ID)
+ )ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ CREATE TABLE IF NOT EXISTS COMPUTE_RESOURCE_RESERVATION_QUEUE (RESERVATION_ID VARCHAR(255), QUEUE_NAME VARCHAR(255) NOT NULL
+ )ENGINE=InnoDB DEFAULT CHARSET=latin1;
+ CREATE INDEX IF NOT EXISTS I_CMPTN_Q_RESERVATION_ID ON COMPUTE_RESOURCE_RESERVATION_QUEUE (RESERVATION_ID);
+ ALTER TABLE COMPUTE_RESOURCE_RESERVATION ADD CONSTRAINT FK_COMPUTE_RESOURCE_RESERVATION FOREIGN KEY IF NOT EXISTS (RESOURCE_ID, GROUP_RESOURCE_PROFILE_ID) REFERENCES GROUP_COMPUTE_RESOURCE_PREFERENCE (RESOURCE_ID, GROUP_RESOURCE_PROFILE_ID) ON DELETE CASCADE;