airavata.git
5 days agoIncreased the size of uploading files for MIGA gateway master
eroma2014 [Thu, 12 May 2022 19:42:39 +0000 (15:42 -0400)] 
Increased the size of uploading files for MIGA gateway

6 days agoAnsible: disabling usd deploy until we get valid certs
Marcus Christie [Wed, 11 May 2022 21:32:50 +0000 (17:32 -0400)] 
Ansible: disabling usd deploy until we get valid certs

3 weeks agoRemoved CIRC email from the notification list.
eroma2014 [Mon, 25 Apr 2022 19:14:11 +0000 (15:14 -0400)] 
Removed CIRC email from the notification list.

4 weeks agoAnsible: trecx app id for prod amos gateway
Marcus Christie [Fri, 15 Apr 2022 17:44:36 +0000 (13:44 -0400)] 
Ansible: trecx app id for prod amos gateway

5 weeks agoAnsible: production branch of lrose-sgci django app
Marcus Christie [Wed, 13 Apr 2022 18:31:51 +0000 (14:31 -0400)] 
Ansible: production branch of lrose-sgci django app

5 weeks agoAnsible: global floods - django app and geo db config
Marcus Christie [Wed, 6 Apr 2022 21:36:07 +0000 (17:36 -0400)] 
Ansible: global floods - django app and geo db config

5 weeks agoAIRAVATA-3411 Ansible: tusd_upload_dir for prod inventory
Marcus Christie [Wed, 6 Apr 2022 21:04:54 +0000 (17:04 -0400)] 
AIRAVATA-3411 Ansible: tusd_upload_dir for prod inventory

6 weeks agoAIRAVATA-3590 remove xmlbeans
PJ Fanning [Tue, 5 Apr 2022 13:43:11 +0000 (15:43 +0200)] 
AIRAVATA-3590 remove xmlbeans

6 weeks agoAIRAVATA-3590 upgrade log4j and commons-io
PJ Fanning [Thu, 17 Mar 2022 12:42:39 +0000 (13:42 +0100)] 
AIRAVATA-3590 upgrade log4j and commons-io

6 weeks agoupdate versions
PJ Fanning [Thu, 17 Mar 2022 13:24:53 +0000 (14:24 +0100)] 
update versions

6 weeks agojackson 2.9.10.8
PJ Fanning [Thu, 17 Mar 2022 13:19:25 +0000 (14:19 +0100)] 
jackson 2.9.10.8

6 weeks agoUpdate email-config.yaml.j2
Eroma Abeysinghe [Mon, 4 Apr 2022 17:23:00 +0000 (13:23 -0400)] 
Update email-config.yaml.j2

Adding HTCONDOR jetstream cluster email for monitoring

6 weeks agoCommenting out htcondor email configs
Dimuthu Wannipurage [Mon, 4 Apr 2022 13:53:45 +0000 (09:53 -0400)] 
Commenting out htcondor email configs

6 weeks agoMerge branch 'htcondor-new'
Dimuthu Wannipurage [Mon, 4 Apr 2022 13:46:19 +0000 (09:46 -0400)] 
Merge branch 'htcondor-new'

# Conflicts:
# modules/orchestrator/orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java

6 weeks agoUpdating Helix version
Dimuthu Wannipurage [Mon, 4 Apr 2022 13:41:20 +0000 (09:41 -0400)] 
Updating Helix version

8 weeks agoAnsible: Updating Helix download URLs
Marcus Christie [Mon, 21 Mar 2022 13:42:26 +0000 (09:42 -0400)] 
Ansible: Updating Helix download URLs

8 weeks agoMerge pull request #276 from apache/AIRAVATA-3549
Marcus Christie [Mon, 21 Mar 2022 13:35:43 +0000 (09:35 -0400)] 
Merge pull request #276 from apache/AIRAVATA-3549

Fetching intermediate outputs for an running experiment

2 months agoAnsible: update/downgrade zabbix agent to 4.0.x
Marcus Christie [Fri, 11 Mar 2022 23:02:51 +0000 (18:02 -0500)] 
Ansible: update/downgrade zabbix agent to 4.0.x

2 months agoUpdate email-config.yaml.j2
Eroma Abeysinghe [Fri, 11 Mar 2022 19:56:07 +0000 (14:56 -0500)] 
Update email-config.yaml.j2

Added Pinnacle UCMerced cluster email for monitoring.

2 months agoAnsible: pubad django app config
Marcus Christie [Mon, 7 Mar 2022 22:38:51 +0000 (17:38 -0500)] 
Ansible: pubad django app config

2 months agoAnsible: disabling global floods app until we get it working
Marcus Christie [Thu, 3 Mar 2022 20:32:17 +0000 (15:32 -0500)] 
Ansible: disabling global floods app until we get it working

2 months agoAIRAVATA-3585 update regex to include React generated files
Marcus Christie [Mon, 28 Feb 2022 22:22:00 +0000 (17:22 -0500)] 
AIRAVATA-3585 update regex to include React generated files

2 months agoUpdate email-config.yaml.j2
Eroma Abeysinghe [Mon, 21 Feb 2022 17:32:25 +0000 (12:32 -0500)] 
Update email-config.yaml.j2

Added Slurm <slurm@br003.ib.bridges2.psc.edu> for email monitoring

2 months agoAIRAVATA-3549 Only allow fetching intermediate outputs when job itself is ACTIVE 276/head
Marcus Christie [Wed, 16 Feb 2022 22:33:15 +0000 (17:33 -0500)] 
AIRAVATA-3549 Only allow fetching intermediate outputs when job itself is ACTIVE

2 months agoAIRAVATA-3549 Allow users with READ access to get intermediate output status
Marcus Christie [Wed, 16 Feb 2022 14:29:32 +0000 (09:29 -0500)] 
AIRAVATA-3549 Allow users with READ access to get intermediate output status

3 months agoAIRAVATA-3549 code simplification, relying on final COMPLETED process status
Marcus Christie [Thu, 10 Feb 2022 18:57:12 +0000 (13:57 -0500)] 
AIRAVATA-3549 code simplification, relying on final COMPLETED process status

3 months agoAIRAVATA-3549 Add CompletingTask to get COMPLETED status on intermediate output fetch...
Marcus Christie [Thu, 10 Feb 2022 16:13:34 +0000 (11:13 -0500)] 
AIRAVATA-3549 Add CompletingTask to get COMPLETED status on intermediate output fetching process

Also updated Orchestrator to not update experiment status when receiving
an intermediate output fetching process status event.

3 months agoAIRAVATA-3549 When fetching intermediate URI_COLLECTION, update process output with...
Marcus Christie [Thu, 10 Feb 2022 15:00:43 +0000 (10:00 -0500)] 
AIRAVATA-3549 When fetching intermediate URI_COLLECTION, update process output with data product URIs

3 months agoMerge branch 'ultrascan-mainteinence'
Dimuthu Wannipurage [Thu, 3 Feb 2022 17:55:28 +0000 (12:55 -0500)] 
Merge branch 'ultrascan-mainteinence'

3 months agoAIRAVATA-3570 Ansible: include web component build dir
Marcus Christie [Wed, 26 Jan 2022 21:29:36 +0000 (16:29 -0500)] 
AIRAVATA-3570 Ansible: include web component build dir

3 months agoAIRAVATA-3549 Add intermediate output methods for all users
Marcus Christie [Wed, 26 Jan 2022 19:48:12 +0000 (14:48 -0500)] 
AIRAVATA-3549 Add intermediate output methods for all users

3 months agoMerge branch 'AIRAVATA-3550'
Marcus Christie [Tue, 18 Jan 2022 14:05:07 +0000 (09:05 -0500)] 
Merge branch 'AIRAVATA-3550'

3 months agoMerge branch 'airavata-3319'
Marcus Christie [Tue, 18 Jan 2022 13:55:21 +0000 (08:55 -0500)] 
Merge branch 'airavata-3319'

4 months agoFixing the issue of standard out and error files are not getting registered
Dimuthu Wannipurage [Fri, 14 Jan 2022 18:53:53 +0000 (13:53 -0500)] 
Fixing the issue of standard out and error files are not getting registered

4 months agoAvoiding premature helix manager closure ultrascan-mainteinence
Dimuthu Wannipurage [Fri, 14 Jan 2022 04:06:29 +0000 (23:06 -0500)] 
Avoiding premature helix manager closure

4 months agoGracefully cleaning up the helix manager to avoid stale zookeeper connections
Dimuthu Wannipurage [Fri, 14 Jan 2022 03:49:04 +0000 (22:49 -0500)] 
Gracefully cleaning up the helix manager to avoid stale zookeeper connections

4 months agoRelevant changes from htcondor branch htcondor-new 278/head
Dimuthu Wannipurage [Fri, 14 Jan 2022 01:45:20 +0000 (20:45 -0500)] 
Relevant changes from htcondor branch

4 months agoAIRAVATA-3549 Add method to check on status of intermediate output fetching
Marcus Christie [Fri, 7 Jan 2022 22:27:51 +0000 (17:27 -0500)] 
AIRAVATA-3549 Add method to check on status of intermediate output fetching

4 months agoAIRAVATA-3549 Orch: update intermediate output fetching process to FAILED if fails...
Marcus Christie [Fri, 7 Jan 2022 17:25:18 +0000 (12:25 -0500)] 
AIRAVATA-3549 Orch: update intermediate output fetching process to FAILED if fails to launch

4 months agoAIRAVATA-3549 API validation that experiment is executing and there aren't already...
Marcus Christie [Fri, 7 Jan 2022 17:24:24 +0000 (12:24 -0500)] 
AIRAVATA-3549 API validation that experiment is executing and there aren't already executing intermediate output tasks

4 months agoUpdated the redirect URI for the geo gateway
eroma2014 [Wed, 5 Jan 2022 20:57:17 +0000 (15:57 -0500)] 
Updated the redirect URI for the geo gateway

4 months agoPrioritizing external parameters when constructing the slurm script
Dimuthu Wannipurage [Thu, 24 Dec 2020 00:24:04 +0000 (19:24 -0500)] 
Prioritizing external parameters when constructing the slurm script

4 months agoUpdating the slurm script to override parmaters with pre job commands
Dimuthu Wannipurage [Wed, 23 Dec 2020 22:36:23 +0000 (17:36 -0500)] 
Updating the slurm script to override parmaters with pre job commands

4 months agoIgnoring sym links empty directories when building the archive
Dimuthu Wannipurage [Wed, 5 Jan 2022 07:16:10 +0000 (02:16 -0500)] 
Ignoring sym links empty directories when building the archive

4 months agoMerge branch 'AIRAVATA-3549' into develop
Dimuthu Wannipurage [Wed, 5 Jan 2022 01:19:44 +0000 (20:19 -0500)] 
Merge branch 'AIRAVATA-3549' into develop

4 months agoOptimizing the un-archiving process by separating out chain comands
Dimuthu Wannipurage [Wed, 5 Jan 2022 00:46:23 +0000 (19:46 -0500)] 
Optimizing the un-archiving process by separating out chain comands

4 months agoMinor logging enhancement
Dimuthu Wannipurage [Tue, 4 Jan 2022 23:49:03 +0000 (18:49 -0500)] 
Minor logging enhancement

4 months agoAIRAVATA-3549 Derive the parent process for intermediate output fetching process
Marcus Christie [Tue, 4 Jan 2022 21:08:15 +0000 (16:08 -0500)] 
AIRAVATA-3549 Derive the parent process for intermediate output fetching process

4 months agoAIRAVATA-3549 Regenerated thrift stubs - removing parentProcessId
Marcus Christie [Tue, 4 Jan 2022 21:03:32 +0000 (16:03 -0500)] 
AIRAVATA-3549 Regenerated thrift stubs - removing parentProcessId

4 months agoMinor enhancement
Dimuthu Wannipurage [Mon, 3 Jan 2022 03:53:12 +0000 (22:53 -0500)] 
Minor enhancement

4 months agoMerge branch 'AIRAVATA-3549' into develop
Dimuthu Wannipurage [Mon, 3 Jan 2022 02:02:47 +0000 (21:02 -0500)] 
Merge branch 'AIRAVATA-3549' into develop

4 months agoFine grained state publish mechanism for helix tasks
Dimuthu Wannipurage [Mon, 3 Jan 2022 02:02:07 +0000 (21:02 -0500)] 
Fine grained state publish mechanism for helix tasks

4 months agoMerge branch 'AIRAVATA-3549' into develop
Dimuthu Wannipurage [Mon, 3 Jan 2022 00:03:20 +0000 (19:03 -0500)] 
Merge branch 'AIRAVATA-3549' into develop

4 months agoAdding a parent process id field to fetch intermediate outputs as they are bound...
Dimuthu Wannipurage [Mon, 3 Jan 2022 00:01:04 +0000 (19:01 -0500)] 
Adding a parent process id field to fetch intermediate outputs as they are bound to parent process data path

4 months agoMerge branch 'AIRAVATA-3549' into develop
Dimuthu Wannipurage [Sat, 1 Jan 2022 23:52:49 +0000 (18:52 -0500)] 
Merge branch 'AIRAVATA-3549' into develop

# Conflicts:
# modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/TaskContext.java

4 months agoMaking task context load on demand
Dimuthu Wannipurage [Sat, 1 Jan 2022 23:49:11 +0000 (18:49 -0500)] 
Making task context load on demand

4 months agoMerge branch 'AIRAVATA-3549' into develop
Dimuthu Wannipurage [Fri, 31 Dec 2021 06:54:58 +0000 (01:54 -0500)] 
Merge branch 'AIRAVATA-3549' into develop

# Conflicts:
# modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/ExperimentConsumer.java

4 months agoFixing the bug in deserializing intermediate output event
Dimuthu Wannipurage [Fri, 31 Dec 2021 06:53:42 +0000 (01:53 -0500)] 
Fixing the bug in deserializing intermediate output event

4 months agoMinor bug fix of missing intermediate output filter in ExperimentConsumer
Dimuthu Wannipurage [Fri, 31 Dec 2021 02:54:59 +0000 (21:54 -0500)] 
Minor bug fix of missing intermediate output filter in ExperimentConsumer

4 months agoMerge branch 'AIRAVATA-3549' into develop
Dimuthu Wannipurage [Thu, 30 Dec 2021 19:35:16 +0000 (14:35 -0500)] 
Merge branch 'AIRAVATA-3549' into develop

4 months agoMerge pull request #275 from apache/log4j-upgrade
Dimuthu Wannipurage [Fri, 17 Dec 2021 20:19:32 +0000 (15:19 -0500)] 
Merge pull request #275 from apache/log4j-upgrade

Upgrading log4j v1 to log4j 2.16.0 to address recent security vulnerabilities

5 months agoMerge branch 'log4j-upgrade' into develop
Dimuthu Wannipurage [Fri, 17 Dec 2021 05:27:43 +0000 (00:27 -0500)] 
Merge branch 'log4j-upgrade' into develop

5 months agoAdding mistakenly deleted api-server start code log4j-upgrade 275/head
Dimuthu Wannipurage [Fri, 17 Dec 2021 05:26:57 +0000 (00:26 -0500)] 
Adding mistakenly deleted api-server start code

5 months agoMerge branch 'log4j-upgrade' into develop
Dimuthu Wannipurage [Fri, 17 Dec 2021 01:57:43 +0000 (20:57 -0500)] 
Merge branch 'log4j-upgrade' into develop

5 months agoUpgrading from log4j -> log4j2 + refactoring
Dimuthu Wannipurage [Fri, 17 Dec 2021 01:56:39 +0000 (20:56 -0500)] 
Upgrading from log4j -> log4j2 + refactoring

5 months agoMerge branch 'AIRAVATA-3550' into develop
Marcus Christie [Wed, 15 Dec 2021 23:04:25 +0000 (18:04 -0500)] 
Merge branch 'AIRAVATA-3550' into develop

5 months agoAIRAVATA-3550 newer version of assembly plugin for faster api server assembly
Marcus Christie [Wed, 15 Dec 2021 23:04:12 +0000 (18:04 -0500)] 
AIRAVATA-3550 newer version of assembly plugin for faster api server assembly

5 months agoAIRAVATA-3549 Initial API/Orch changes for fetching intermediate outputs
Marcus Christie [Wed, 15 Dec 2021 21:54:03 +0000 (16:54 -0500)] 
AIRAVATA-3549 Initial API/Orch changes for fetching intermediate outputs

5 months agoSupporting intermediate transfers at helix level
Dimuthu Wannipurage [Wed, 15 Dec 2021 21:14:22 +0000 (16:14 -0500)] 
Supporting intermediate transfers at helix level

5 months agoAIRAVATA-3549 Thrift stubs generated for fetchExperimentOutputs
Marcus Christie [Wed, 15 Dec 2021 20:37:53 +0000 (15:37 -0500)] 
AIRAVATA-3549 Thrift stubs generated for fetchExperimentOutputs

5 months agoAnsible: removing beta.distantreader.scigap.org
Marcus Christie [Tue, 14 Dec 2021 17:23:25 +0000 (12:23 -0500)] 
Ansible: removing beta.distantreader.scigap.org

5 months agoAIRAVATA-3319 Ansible: add more external IDP userinfo configs
Marcus Christie [Fri, 10 Dec 2021 21:49:06 +0000 (16:49 -0500)] 
AIRAVATA-3319 Ansible: add more external IDP userinfo configs

5 months agoMerge branch 'develop' of github.com:apache/airavata into develop
eroma2014 [Fri, 3 Dec 2021 14:38:52 +0000 (09:38 -0500)] 
Merge branch 'develop' of github.com:apache/airavata into develop

5 months agoAdding Dev RNAMake gateway CILogon
eroma2014 [Fri, 3 Dec 2021 14:38:23 +0000 (09:38 -0500)] 
Adding Dev RNAMake gateway CILogon

5 months agoMerge branch 'master' into develop
Marcus Christie [Thu, 2 Dec 2021 23:44:21 +0000 (18:44 -0500)] 
Merge branch 'master' into develop

5 months agoAdding Dev RNAMake gateway
eroma2014 [Fri, 3 Dec 2021 04:05:52 +0000 (23:05 -0500)] 
Adding Dev RNAMake gateway

5 months agoAdding Dev RNAMake gateway
eroma2014 [Fri, 3 Dec 2021 04:05:04 +0000 (23:05 -0500)] 
Adding Dev RNAMake gateway

5 months agoAIRAVATA-3546 Ansible: update certbot, ca certs
Marcus Christie [Thu, 2 Dec 2021 23:44:01 +0000 (18:44 -0500)] 
AIRAVATA-3546 Ansible: update certbot, ca certs

5 months agoAdding Dev RNAMake gateway
eroma2014 [Thu, 2 Dec 2021 17:56:44 +0000 (12:56 -0500)] 
Adding Dev RNAMake gateway

5 months agoMerge branch 'AIRAVATA-3546' into develop
Marcus Christie [Tue, 30 Nov 2021 22:23:20 +0000 (17:23 -0500)] 
Merge branch 'AIRAVATA-3546' into develop

5 months agoAIRAVATA-3546 Update certbot, ca certs
Marcus Christie [Tue, 30 Nov 2021 22:23:04 +0000 (17:23 -0500)] 
AIRAVATA-3546 Update certbot, ca certs

6 months agoAdding DeepPDB gateway SSH key and cilogon
eroma2014 [Tue, 9 Nov 2021 21:47:54 +0000 (16:47 -0500)] 
Adding DeepPDB gateway SSH key and cilogon

6 months agoAdding DeepPDB gateway
eroma2014 [Tue, 9 Nov 2021 21:11:46 +0000 (16:11 -0500)] 
Adding DeepPDB gateway

6 months agoAdding DeepPDB gateway
eroma2014 [Tue, 9 Nov 2021 20:13:13 +0000 (15:13 -0500)] 
Adding DeepPDB gateway

6 months agoMerge branch 'airavata-3525'
Marcus Christie [Mon, 8 Nov 2021 14:14:45 +0000 (09:14 -0500)] 
Merge branch 'airavata-3525'

6 months agoAnsible: adding global-floods-django-app to deploy
Marcus Christie [Fri, 5 Nov 2021 18:57:25 +0000 (14:57 -0400)] 
Ansible: adding global-floods-django-app to deploy

6 months agoAnsible: changing trecx-django-app git url
Marcus Christie [Fri, 29 Oct 2021 13:58:27 +0000 (09:58 -0400)] 
Ansible: changing trecx-django-app git url

6 months agoRevert "Change in name of AMOS gateway"
Marcus Christie [Thu, 21 Oct 2021 21:31:01 +0000 (17:31 -0400)] 
Revert "Change in name of AMOS gateway"

This reverts commit bd256279db788bd482d4927c9b2a7b9031c1c7c8.

6 months agoAIRAVATA-3533 Support redirecting from old HTTPS domain to new HTTPS domain
Marcus Christie [Thu, 21 Oct 2021 20:27:52 +0000 (16:27 -0400)] 
AIRAVATA-3533 Support redirecting from old HTTPS domain to new HTTPS domain

6 months agoChange in name of AMOS gateway
eroma2014 [Thu, 21 Oct 2021 17:47:11 +0000 (13:47 -0400)] 
Change in name of AMOS gateway

7 months agoAdding new scigateway.ucmerced.edu gateway with cilogon
eroma2014 [Fri, 15 Oct 2021 17:12:25 +0000 (13:12 -0400)] 
Adding new scigateway.ucmerced.edu gateway with cilogon

7 months agoAdding new scigateway.ucmerced.edu gateway with cilogon
eroma2014 [Fri, 15 Oct 2021 15:13:00 +0000 (11:13 -0400)] 
Adding new scigateway.ucmerced.edu gateway with cilogon

7 months agoAdding new scigateway.ucmerced.edu gateway
eroma2014 [Wed, 13 Oct 2021 19:43:00 +0000 (15:43 -0400)] 
Adding new scigateway.ucmerced.edu gateway

7 months agoAdding new scigateway.ucmerced.edu gateway
eroma2014 [Wed, 13 Oct 2021 19:42:23 +0000 (15:42 -0400)] 
Adding new scigateway.ucmerced.edu gateway

7 months agoAdding new scigateway.ucmerced.edu gateway
eroma2014 [Wed, 13 Oct 2021 19:40:45 +0000 (15:40 -0400)] 
Adding new scigateway.ucmerced.edu gateway

7 months agoremoved the alias added for amp gateway
eroma2014 [Fri, 8 Oct 2021 18:03:57 +0000 (14:03 -0400)] 
removed the alias added for amp gateway

7 months agoUpdating the AMP gateway new domain
eroma2014 [Fri, 8 Oct 2021 17:29:19 +0000 (13:29 -0400)] 
Updating the AMP gateway new domain

7 months agoAIRAVATA-3524: workaround for timeout when adding all users to group
Marcus Christie [Thu, 7 Oct 2021 20:49:40 +0000 (16:49 -0400)] 
AIRAVATA-3524: workaround for timeout when adding all users to group

7 months agoMerge branch 'airavata-3525' into develop
Marcus Christie [Wed, 6 Oct 2021 17:39:18 +0000 (13:39 -0400)] 
Merge branch 'airavata-3525' into develop

7 months agoAIRAVATA-3525 Fix the OPTIONS setting for MySQL/MariaDB
Marcus Christie [Wed, 6 Oct 2021 17:37:24 +0000 (13:37 -0400)] 
AIRAVATA-3525 Fix the OPTIONS setting for MySQL/MariaDB