[jira] [Commented] (AIRAVATA-2476) Replace Approved gateways tab with CREATED gateways lsit
[
https://issues.apache.org/jira/browse/AIRAVATA-2476?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16078664#comment-16078664
]
Marcus Christie commented on AIRAVATA-2476:
---
I've updated this in production scigap database:
{code:sql}
begin;
update GATEWAY set GATEWAY_APPROVAL_STATUS = 'DEPLOYED' where
GATEWAY_APPROVAL_STATUS = 'APPROVED';
commit;
{code}
> Replace Approved gateways tab with CREATED gateways lsit
>
>
> Key: AIRAVATA-2476
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2476
> Project: Airavata
> Issue Type: Bug
> Components: PGA PHP Web Gateway
>Affects Versions: 0.17
> Environment: https://dev.scigap.org
>Reporter: Eroma
>Assignee: Sneha Tilak
> Fix For: 0.18
>
>
> Currently the approved list is displayed, but since that is not the state of
> functioning gateway, please change the tab name to CREATED gateways and
> replace the list also with gateways in created state.
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[jira] [Comment Edited] (AIRAVATA-2476) Replace Approved gateways tab with CREATED gateways lsit
[
https://issues.apache.org/jira/browse/AIRAVATA-2476?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16078664#comment-16078664
]
Marcus Christie edited comment on AIRAVATA-2476 at 7/7/17 8:47 PM:
---
I've updated this in production scigap profile_service database:
{code:sql}
begin;
update GATEWAY set GATEWAY_APPROVAL_STATUS = 'DEPLOYED' where
GATEWAY_APPROVAL_STATUS = 'APPROVED';
commit;
{code}
was (Author: marcuschristie):
I've updated this in production scigap database:
{code:sql}
begin;
update GATEWAY set GATEWAY_APPROVAL_STATUS = 'DEPLOYED' where
GATEWAY_APPROVAL_STATUS = 'APPROVED';
commit;
{code}
> Replace Approved gateways tab with CREATED gateways lsit
>
>
> Key: AIRAVATA-2476
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2476
> Project: Airavata
> Issue Type: Bug
> Components: PGA PHP Web Gateway
>Affects Versions: 0.17
> Environment: https://dev.scigap.org
>Reporter: Eroma
>Assignee: Sneha Tilak
> Fix For: 0.18
>
>
> Currently the approved list is displayed, but since that is not the state of
> functioning gateway, please change the tab name to CREATED gateways and
> replace the list also with gateways in created state.
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[jira] [Commented] (AIRAVATA-2369) Gateway provider (who requests for a gateway) clicks User settings in SciGaP portal cannot navigate back to gateway requesting UI
[ https://issues.apache.org/jira/browse/AIRAVATA-2369?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16078045#comment-16078045 ] Marcus Christie commented on AIRAVATA-2369: --- I made that change in AIRAVATA-2235 but I think it was an oversight to not include gateway-provider as well. It's a small fix, I'll commit it. > Gateway provider (who requests for a gateway) clicks User settings in SciGaP > portal cannot navigate back to gateway requesting UI > - > > Key: AIRAVATA-2369 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2369 > Project: Airavata > Issue Type: New Feature > Components: Airavata System, PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://beta.scigap.org/ >Reporter: Eroma >Assignee: Sneha Tilak > Fix For: 0.18 > > > When logged in the button to request for a new gateway is displayed and the > URL is https://beta.scigap.org/admin/dashboard > But if the user clicks on usr Settings link below the username on top > righthand corner there is no way to go back to the dashboard, no dashboard > button or link in the menu bar. user has to log out and login or remember the > URL to type in -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Reopened] (AIRAVATA-2405) Keycloak: search for users with a given role
[ https://issues.apache.org/jira/browse/AIRAVATA-2405?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie reopened AIRAVATA-2405: --- The approach I came up with doesn't work well for a gateway like seagrid.org which has a lot of users. > Keycloak: search for users with a given role > > > Key: AIRAVATA-2405 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2405 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Reporter: Marcus Christie >Assignee: Marcus Christie > Fix For: 0.18 > > > In PGA, admins can search for users that have a selected role. > It would be good to implement this in IamAdminServices in the backend and > then call that from PGA. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2405) Keycloak: search for users with a given role
[ https://issues.apache.org/jira/browse/AIRAVATA-2405?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16079476#comment-16079476 ] Marcus Christie commented on AIRAVATA-2405: --- I've tried a different approach. It's expensive to fetch all of the users and it's expensive to then check the roles of each of those users. So as a compromise I have the code fetch all of the users, then order the user by created date, then take just the most recent 100 and check their roles. This covers the use case where an admin wants to see a list of recent user-pending users. This still isn't a great approach. It suffers from the problem that with a large enough count of users it will take too long to load them all. It's hard to come up with a good solution here without a feature in Keycloak to search for users by role. > Keycloak: search for users with a given role > > > Key: AIRAVATA-2405 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2405 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Reporter: Marcus Christie >Assignee: Marcus Christie > Fix For: 0.18 > > > In PGA, admins can search for users that have a selected role. > It would be good to implement this in IamAdminServices in the backend and > then call that from PGA. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2483) Tried to view an old experiment and throws an exception.
[
https://issues.apache.org/jira/browse/AIRAVATA-2483?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16078234#comment-16078234
]
Marcus Christie commented on AIRAVATA-2483:
---
I ran
{code:sql}
update USER_GROUP set GROUP_ID = lower(GROUP_ID);
{code}
on scigap01 database. However that didn't fix the initial error, still getting
{noformat}
exp ID: CloneofCloneofEcho_L1_136d101d-b6ca-4453-b224-1316b92ed476
exception: Undefined index: scnakandala
{noformat}
The issue is that user scnakandala is the owner of the project that has the
experiment CloneofCloneofEcho_L1_136d101d-b6ca-4453-b224-1316b92ed476. But the
sharing APIs don't return scnakandala as one of the users that can access the
experiment.
> Tried to view an old experiment and throws an exception.
>
>
> Key: AIRAVATA-2483
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2483
> Project: Airavata
> Issue Type: Bug
> Components: PGA PHP Web Gateway
>Affects Versions: 0.17
> Environment: https://testdrive.airavata.org
>Reporter: Eroma
>Assignee: Marcus Christie
> Fix For: 0.18
>
>
> This experiment was an old one. It was listed in Experiment browse and tried
> to view the summary. When clicked on the experiment throws the exception.
> Observation this experiment is from 2016 but all the projects of the user is
> from 2017.
> exp ID: CloneofCloneofEcho_L1_136d101d-b6ca-4453-b224-1316b92ed476
> exception: Undefined index: scnakandala
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[jira] [Commented] (AIRAVATA-2483) Tried to view an old experiment and throws an exception.
[ https://issues.apache.org/jira/browse/AIRAVATA-2483?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16078240#comment-16078240 ] Marcus Christie commented on AIRAVATA-2483: --- Next error is that Clone_of_SLM1-Gamess-Gordon_d9b2ca37-fd2c-48bb-b62e-5f47939c1ec5 doesn't have any record in the SHARING table so it has no owner. > Tried to view an old experiment and throws an exception. > > > Key: AIRAVATA-2483 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2483 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://testdrive.airavata.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > > This experiment was an old one. It was listed in Experiment browse and tried > to view the summary. When clicked on the experiment throws the exception. > Observation this experiment is from 2016 but all the projects of the user is > from 2017. > exp ID: CloneofCloneofEcho_L1_136d101d-b6ca-4453-b224-1316b92ed476 > exception: Undefined index: scnakandala -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2369) Gateway provider (who requests for a gateway) clicks User settings in SciGaP portal cannot navigate back to gateway requesting UI
[ https://issues.apache.org/jira/browse/AIRAVATA-2369?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2369. --- Resolution: Fixed [~eroma_a], This looks fixed to me. If you still are seeing an issue can you describe exactly what issue you are seeing? > Gateway provider (who requests for a gateway) clicks User settings in SciGaP > portal cannot navigate back to gateway requesting UI > - > > Key: AIRAVATA-2369 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2369 > Project: Airavata > Issue Type: New Feature > Components: Airavata System, PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://beta.scigap.org/ >Reporter: Eroma >Assignee: Sneha Tilak > Fix For: 0.18 > > > When logged in the button to request for a new gateway is displayed and the > URL is https://beta.scigap.org/admin/dashboard > But if the user clicks on usr Settings link below the username on top > righthand corner there is no way to go back to the dashboard, no dashboard > button or link in the menu bar. user has to log out and login or remember the > URL to type in -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2489) When special characters are used in experiment name, the experiment browse is empty!
[ https://issues.apache.org/jira/browse/AIRAVATA-2489?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16099084#comment-16099084 ] Marcus Christie commented on AIRAVATA-2489: --- [~eroma_a], Do you get this in dev.seagrid.org as well? I have a fix for this, I hope, that is in dev but I haven't pushed into production yet. > When special characters are used in experiment name, the experiment browse is > empty! > > > Key: AIRAVATA-2489 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2489 > Project: Airavata > Issue Type: Bug > Components: Airavata System, PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: reported by https://sciencegateway.usd.edu/ >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Comment Edited] (AIRAVATA-2492) File transfer slow from alamo.uthscsa.edu to uslims3.uthscsa.edu
[
https://issues.apache.org/jira/browse/AIRAVATA-2492?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16101759#comment-16101759
]
Marcus Christie edited comment on AIRAVATA-2492 at 7/26/17 2:54 PM:
Example of a fast file transfer in seagrid: 6BG archive.tar file transferred
in about 7 minutes.
Experiment ID:
Clone_of_polya_15_nt_unprot_am_prod_02_f762fa5f-b039-4352-812b-11cde23a7732
gfac logs on scigap03:
{noformat}
2017-07-26 09:13:29,653 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Channel creation test succeeded, key
:ccguser_stamp
ede.tacc.xsede.org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:29,653 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Reuse SSH session for
:ccguser_stampede.tacc.xsede.
org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:29,656 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - SSH Session validation succeeded, key
:pga_gf4.ucs.
indiana.edu_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:29,676 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Channel creation test succeeded, key
:pga_gf4.ucs.i
ndiana.edu_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:29,676 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Reuse SSH session for
:pga_gf4.ucs.indiana.edu_22_3
d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:29,676 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - SSH Session validation succeeded, key
:ccguser_stam
pede.tacc.xsede.org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:30,086 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Channel creation test succeeded, key
:ccguser_stamp
ede.tacc.xsede.org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:30,086 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Reuse SSH session for
:ccguser_stampede.tacc.xsede.
org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:30,122 [pool-11-thread-145] INFO
o.a.a.g.impl.HPCRemoteCluster - Executing command cd
/scratch/00421/ccguser/seagrid-
workdirs/PROCESS_ba393353-611c-45fb-a27f-0e8c00c8535e && tar -cvf
/scratch/00421/ccguser/seagrid-workdirs/PROCESS_ba393353-611c-45fb-a27
f-0e8c00c8535e/archive.tar ./*
2017-07-26 09:13:30,680 [Thread-5] INFO o.a.a.g.m.e.EmailBasedMonitor -
[EJM]: 161 new email/s received
2017-07-26 09:14:06,669 [pool-11-thread-145] INFO
o.a.a.g.impl.HPCRemoteCluster - Transferring
from:/scratch/00421/ccguser/seagrid-wor
kdirs/PROCESS_ba393353-611c-45fb-a27f-0e8c00c8535e/archive.tar To:
/var/www/portals/gateway-user-data/seagrid/nastia/polya_15_nt_ful_AMB
ER/Clone_of_polya_15_nt_unprot_am_prod_021500987115/archive.tar
2017-07-26 09:14:06,741 [pool-11-thread-145] INFO o.a.a.gfac.impl.SSHUtils -
Initiating transfer from:/scratch/00421/ccguser/seagrid-w
orkdirs/PROCESS_ba393353-611c-45fb-a27f-0e8c00c8535e/archive.tar To:
/var/www/portals/gateway-user-data/seagrid/nastia/polya_15_nt_ful_A
MBER/Clone_of_polya_15_nt_unprot_am_prod_021500987115/archive.tar, Ignore Empty
file : true
2017-07-26 09:14:07,064 [pool-11-thread-145] INFO o.a.a.gfac.impl.SSHUtils -
Transferring
from:/scratch/00421/ccguser/seagrid-workdirs/PROCESS_ba393353-611c-45fb-a27f-0e8c00c8535e/archive.tar
To:
/var/www/portals/gateway-user-data/seagrid/nastia/polya_15_nt_ful_AMBER/Clone_of_polya_15_nt_unprot_am_prod_021500987115/archive.tar,
File Size : 6057000960, Ignore Empty file : true
...
2017-07-26 09:21:05,861 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - SSH Session validation succeeded, key
:ccguser_stampede.tacc.xsede.org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:21:06,843 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Channel creation test succeeded, key
:ccguser_stampede.tacc.xsede.org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:21:06,843 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Reuse SSH session for
:ccguser_stampede.tacc.xsede.org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:21:06,879 [pool-11-thread-145] INFO
o.a.a.g.impl.HPCRemoteCluster - Executing command rm
/scratch/00421/ccguser/seagrid-workdirs/PROCESS_ba393353-611c-45fb-a27f-0e8c00c8535e/archive.tar
2017-07-26 09:21:07,818 [pool-11-thread-145] INFO
o.a.a.g.impl.task.ArchiveTask - Executing command cd
/var/www/portals/gateway-user-data/seagrid/nastia/polya_15_nt_ful_AMBER/Clone_of_polya_15_nt_unprot_am_prod_021500987115
&& mkdir ARCHIVE && tar -xvf archive.tar -C ARCHIVE && rm archive.tar && chmod
755 -R ARCHIVE/*
2017-07-26 09:23:33,645 [pool-11-thread-145] INFO
o.a.a.g.c.context.TaskContext - expId:
Clone_of_polya_15_nt_unprot_am_prod_02_f762fa5f-b039-4352-812b-11cde23a7732,
processId: PROCESS_ba393353-611c-45fb-a27f-0e8c00c8535e, taskId:
TASK_ca02a6a5-4460-4bc4-ba73-4ba1be7e, type: DATA_STAGING : Task status
changed EXECUTING
[jira] [Commented] (AIRAVATA-2492) File transfer slow from alamo.uthscsa.edu to uslims3.uthscsa.edu
[
https://issues.apache.org/jira/browse/AIRAVATA-2492?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16101768#comment-16101768
]
Marcus Christie commented on AIRAVATA-2492:
---
{quote}
[10:50 AM] Gary Gorbet: No. I can't. This is a test version of something called
"multi-speed, global-fit"; something I only built on Alamo and could not be
built on another cluster without de-stabilizing that cluster for general users.
[10:51 AM] Gary Gorbet: @eroma What is it that you want to test? The general
mechanism of job completion for gw153?
[10:55 AM] Eroma Abeysinghe: @gary as @marcus mentioned we have transferred
much larger files in stampede under 10 minutes. I just wanted to isolate the
issue to connection between alamo and gfac. let me try running one from this
end by cloning one of these delayed ones from PGA and test.
[10:56 AM] Marlon Pierce: @Eroma we may have recent historical data for
transfer speeds from smaller jobs
[10:57 AM] Marlon Pierce: So we could calculate network speeds for those and
see if we are getting really big delays for larger jobs
[11:00 AM] Marcus Christie: @marlon @eroma I looked at one of Eroma's test runs
from 7/7: Ultrascan-alamo_742d2858-edd7-4410-911a-6f4b00df5e69
[11:01 AM] Marcus Christie: It's a really small file though, 10240 bytes and
took 2 seconds judging from gfac logs
{quote}
> File transfer slow from alamo.uthscsa.edu to uslims3.uthscsa.edu
>
>
> Key: AIRAVATA-2492
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2492
> Project: Airavata
> Issue Type: Bug
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>
> Experiment ids in ultrascan.scigap.org:
> US3-AIRA_f200b78e-5d86-499c-b2e6-c3b6fbb3bfa3
> US3-AIRA_b69482ba-b34f-4809-9274-bcda71b8dccc
> Hipchat discussion:
> {quote}
> [11:27 PM] Gary Gorbet: On Alamo, 20 minutes are more elapse from end of job
> until Airavata reports a job status of COMPLETE. Can't *something* be done to
> speed that up!
> Wednesday July 26, 2017
> [9:31 AM] Eroma Abeysinghe: @gary sorry for this. Currently all experiments
> are completed, and two running in alamo. but we found two which took rather
> unusually long time to transfers the files. we are investigating. will keep
> you posted.
> [9:51 AM] Marcus Christie: @gary here's what we've been able to confirm: gfac
> is getting the completed email from the scheduler and processing it
> immediately. Airavata doesn't mark an experiment as being completed until the
> output data staging completes. The output data staging for the jobs you gave
> us to look at took a long time to complete.
> [9:52 AM] Marlon Pierce: You can test network speed in various ways (like
> https://askubuntu.com/questions/7976/how-do-you-test-the-network-speed-betwen-two-boxes,
> which I googled).
> [9:53 AM] Marlon Pierce: It won't fix the problem, but it may help network
> admins diagnose the problem
> [9:53 AM] Marlon Pierce: I'm assuming (maybe incorrectly) that this is an
> issue between Alamo and our servers
> [9:54 AM] Marcus Christie: This is partly because transfer times from alamo
> to lims are happening very slowly, by my rough calculations at about 200kb/s.
> But also the analysis-results.tar file is much larger in these experiments.
> One example we looked at it was about 200 MB and another was about 1.13 GB.
> Looking through the logs back to April this is historically very large for an
> analysis-results.tar file.
> [9:54 AM] Marlon Pierce: But we can confirm this by looking at other servers
> [9:54 AM] Marcus Christie: @marlon this is between alamo and lims. Do we have
> a login on lims?
> [9:56 AM] Marlon Pierce: Oh...where is the LIMS server? At UTHSCSA?
> [9:57 AM] Marlon Pierce: I think it is.
> [9:58 AM] Marcus Christie: @marlon uslims3.uthscsa.edu
> [9:59 AM] Gary Gorbet: That other job completed. But now there is new,
> critical, job that FINISHED 40 minutes ago. Airavata job status is EXECUTING.
> [9:59 AM] Marcus Christie: It would be nice if we could run a command line
> scp transfer test from alamo to uslims3 just to see if it is fundamentally
> limited or this is a slowness in GFac.
> [10:00 AM] Gary Gorbet: That is easy to do. Will do a test and report.
> [10:00 AM] Marcus Christie: Thanks @gary
> [10:01 AM] Gary Gorbet: Transferred a 1.6M file from uslims3 to alamo in
> under a second.
> [10:02 AM] Marcus Christie: Actually I realized that GFac will do the
> transfer from alamo to uslims3 via GFac. It's not a true third party transfer
> but rather the data is streamed through the GFac server. So @marlon was
> right we need to test between alamo -> Gfac and GFac -> uslims3.
> [10:03 AM] Gary Gorbet: This would be alamo/uslims3 to gw153; right?
> [10:03 AM] Marcus Christie: Thanks @gary. So that's our theoretical upper
>
[jira] [Commented] (AIRAVATA-2492) File transfer slow from alamo.uthscsa.edu to uslims3.uthscsa.edu
[
https://issues.apache.org/jira/browse/AIRAVATA-2492?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16101759#comment-16101759
]
Marcus Christie commented on AIRAVATA-2492:
---
Example of a fast file transfer in seagrid: 6BG archive.tar file transferred
in about 7 minutes.
Experiment ID:
Clone_of_polya_15_nt_unprot_am_prod_02_f762fa5f-b039-4352-812b-11cde23a7732
gfac logs on scigap03:
{noformat}
2017-07-26 09:13:29,653 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Channel creation test succeeded, key
:ccguser_stamp
ede.tacc.xsede.org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:29,653 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Reuse SSH session for
:ccguser_stampede.tacc.xsede.
org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:29,656 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - SSH Session validation succeeded, key
:pga_gf4.ucs.
indiana.edu_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:29,676 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Channel creation test succeeded, key
:pga_gf4.ucs.i
ndiana.edu_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:29,676 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Reuse SSH session for
:pga_gf4.ucs.indiana.edu_22_3
d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:29,676 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - SSH Session validation succeeded, key
:ccguser_stam
pede.tacc.xsede.org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:30,086 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Channel creation test succeeded, key
:ccguser_stamp
ede.tacc.xsede.org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:30,086 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Reuse SSH session for
:ccguser_stampede.tacc.xsede.
org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:13:30,122 [pool-11-thread-145] INFO
o.a.a.g.impl.HPCRemoteCluster - Executing command cd
/scratch/00421/ccguser/seagrid-
workdirs/PROCESS_ba393353-611c-45fb-a27f-0e8c00c8535e && tar -cvf
/scratch/00421/ccguser/seagrid-workdirs/PROCESS_ba393353-611c-45fb-a27
f-0e8c00c8535e/archive.tar ./*
2017-07-26 09:13:30,680 [Thread-5] INFO o.a.a.g.m.e.EmailBasedMonitor -
[EJM]: 161 new email/s received
2017-07-26 09:14:06,669 [pool-11-thread-145] INFO
o.a.a.g.impl.HPCRemoteCluster - Transferring
from:/scratch/00421/ccguser/seagrid-wor
kdirs/PROCESS_ba393353-611c-45fb-a27f-0e8c00c8535e/archive.tar To:
/var/www/portals/gateway-user-data/seagrid/nastia/polya_15_nt_ful_AMB
ER/Clone_of_polya_15_nt_unprot_am_prod_021500987115/archive.tar
2017-07-26 09:14:06,741 [pool-11-thread-145] INFO o.a.a.gfac.impl.SSHUtils -
Initiating transfer from:/scratch/00421/ccguser/seagrid-w
orkdirs/PROCESS_ba393353-611c-45fb-a27f-0e8c00c8535e/archive.tar To:
/var/www/portals/gateway-user-data/seagrid/nastia/polya_15_nt_ful_A
MBER/Clone_of_polya_15_nt_unprot_am_prod_021500987115/archive.tar, Ignore Empty
file : true
2017-07-26 09:14:07,064 [pool-11-thread-145] INFO o.a.a.gfac.impl.SSHUtils -
Transferring
from:/scratch/00421/ccguser/seagrid-workdirs/PROCESS_ba393353-611c-45fb-a27f-0e8c00c8535e/archive.tar
To:
/var/www/portals/gateway-user-data/seagrid/nastia/polya_15_nt_ful_AMBER/Clone_of_polya_15_nt_unprot_am_prod_021500987115/archive.tar,
File Size : 6057000960, Ignore Empty file : true
...
2017-07-26 09:21:05,861 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - SSH Session validation succeeded, key
:ccguser_stampede.tacc.xsede.org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:21:06,843 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Channel creation test succeeded, key
:ccguser_stampede.tacc.xsede.org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:21:06,843 [pool-11-thread-145] INFO
o.a.airavata.gfac.impl.Factory - Reuse SSH session for
:ccguser_stampede.tacc.xsede.org_22_3d65bf6d-2c9f-4166-a51b-e76e0022bd3b
2017-07-26 09:21:06,879 [pool-11-thread-145] INFO
o.a.a.g.impl.HPCRemoteCluster - Executing command rm
/scratch/00421/ccguser/seagrid-workdirs/PROCESS_ba393353-611c-45fb-a27f-0e8c00c8535e/archive.tar
2017-07-26 09:21:07,818 [pool-11-thread-145] INFO
o.a.a.g.impl.task.ArchiveTask - Executing command cd
/var/www/portals/gateway-user-data/seagrid/nastia/polya_15_nt_ful_AMBER/Clone_of_polya_15_nt_unprot_am_prod_021500987115
&& mkdir ARCHIVE && tar -xvf archive.tar -C ARCHIVE && rm archive.tar && chmod
755 -R ARCHIVE/*
2017-07-26 09:23:33,645 [pool-11-thread-145] INFO
o.a.a.g.c.context.TaskContext - expId:
Clone_of_polya_15_nt_unprot_am_prod_02_f762fa5f-b039-4352-812b-11cde23a7732,
processId: PROCESS_ba393353-611c-45fb-a27f-0e8c00c8535e, taskId:
TASK_ca02a6a5-4460-4bc4-ba73-4ba1be7e, type: DATA_STAGING : Task status
changed EXECUTING -> COMPLETED
2017-07-26 09:23:33,656
[jira] [Created] (AIRAVATA-2492) File transfer slow from alamo.uthscsa.edu to uslims3.uthscsa.edu
Marcus Christie created AIRAVATA-2492:
-
Summary: File transfer slow from alamo.uthscsa.edu to
uslims3.uthscsa.edu
Key: AIRAVATA-2492
URL: https://issues.apache.org/jira/browse/AIRAVATA-2492
Project: Airavata
Issue Type: Bug
Reporter: Marcus Christie
Assignee: Marcus Christie
Experiment ids in ultrascan.scigap.org:
US3-AIRA_f200b78e-5d86-499c-b2e6-c3b6fbb3bfa3
US3-AIRA_b69482ba-b34f-4809-9274-bcda71b8dccc
Hipchat discussion:
{quote}
[11:27 PM] Gary Gorbet: On Alamo, 20 minutes are more elapse from end of job
until Airavata reports a job status of COMPLETE. Can't *something* be done to
speed that up!
Wednesday July 26, 2017
[9:31 AM] Eroma Abeysinghe: @gary sorry for this. Currently all experiments are
completed, and two running in alamo. but we found two which took rather
unusually long time to transfers the files. we are investigating. will keep you
posted.
[9:51 AM] Marcus Christie: @gary here's what we've been able to confirm: gfac
is getting the completed email from the scheduler and processing it
immediately. Airavata doesn't mark an experiment as being completed until the
output data staging completes. The output data staging for the jobs you gave us
to look at took a long time to complete.
[9:52 AM] Marlon Pierce: You can test network speed in various ways (like
https://askubuntu.com/questions/7976/how-do-you-test-the-network-speed-betwen-two-boxes,
which I googled).
[9:53 AM] Marlon Pierce: It won't fix the problem, but it may help network
admins diagnose the problem
[9:53 AM] Marlon Pierce: I'm assuming (maybe incorrectly) that this is an issue
between Alamo and our servers
[9:54 AM] Marcus Christie: This is partly because transfer times from alamo to
lims are happening very slowly, by my rough calculations at about 200kb/s. But
also the analysis-results.tar file is much larger in these experiments. One
example we looked at it was about 200 MB and another was about 1.13 GB.
Looking through the logs back to April this is historically very large for an
analysis-results.tar file.
[9:54 AM] Marlon Pierce: But we can confirm this by looking at other servers
[9:54 AM] Marcus Christie: @marlon this is between alamo and lims. Do we have a
login on lims?
[9:56 AM] Marlon Pierce: Oh...where is the LIMS server? At UTHSCSA?
[9:57 AM] Marlon Pierce: I think it is.
[9:58 AM] Marcus Christie: @marlon uslims3.uthscsa.edu
[9:59 AM] Gary Gorbet: That other job completed. But now there is new,
critical, job that FINISHED 40 minutes ago. Airavata job status is EXECUTING.
[9:59 AM] Marcus Christie: It would be nice if we could run a command line scp
transfer test from alamo to uslims3 just to see if it is fundamentally limited
or this is a slowness in GFac.
[10:00 AM] Gary Gorbet: That is easy to do. Will do a test and report.
[10:00 AM] Marcus Christie: Thanks @gary
[10:01 AM] Gary Gorbet: Transferred a 1.6M file from uslims3 to alamo in under
a second.
[10:02 AM] Marcus Christie: Actually I realized that GFac will do the transfer
from alamo to uslims3 via GFac. It's not a true third party transfer but rather
the data is streamed through the GFac server. So @marlon was right we need to
test between alamo -> Gfac and GFac -> uslims3.
[10:03 AM] Gary Gorbet: This would be alamo/uslims3 to gw153; right?
[10:03 AM] Marcus Christie: Thanks @gary. So that's our theoretical upper bound.
[10:04 AM] Marcus Christie: @gary that's right
[10:08 AM] Sudhakar Pamidighantam: I think If it is reasonably secure GFac
should do a true third party transfer to avoid this delay.
[10:08 AM] Gary Gorbet: The LIMS work directory for the job has all the output
files. So, it seems to me that gw153 to uslims3 transfers completed. So, why
the EXECUTING gfac status?
{quote}
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[jira] [Commented] (AIRAVATA-2492) File transfer slow from alamo.uthscsa.edu to uslims3.uthscsa.edu
[
https://issues.apache.org/jira/browse/AIRAVATA-2492?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16101724#comment-16101724
]
Marcus Christie commented on AIRAVATA-2492:
---
Some things to check:
* what is the network connection speed between gw153 and alamo and between
gw153 and uslims3?
**
https://askubuntu.com/questions/7976/how-do-you-test-the-network-speed-betwen-two-boxes
* how fast is an scp from alamo->gw153 and from gw153->uslims3? This is
because gfac does a "fake" third party transfer where the data streams through
gfac. This should give us a theoretical upper bound on transfer speed.
* historically how fast are transfer speeds for gfac? Is there a way to query
for them?
* From [~marpierc]: look into tweaking the buffer size in gfac for the transfer
> File transfer slow from alamo.uthscsa.edu to uslims3.uthscsa.edu
>
>
> Key: AIRAVATA-2492
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2492
> Project: Airavata
> Issue Type: Bug
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>
> Experiment ids in ultrascan.scigap.org:
> US3-AIRA_f200b78e-5d86-499c-b2e6-c3b6fbb3bfa3
> US3-AIRA_b69482ba-b34f-4809-9274-bcda71b8dccc
> Hipchat discussion:
> {quote}
> [11:27 PM] Gary Gorbet: On Alamo, 20 minutes are more elapse from end of job
> until Airavata reports a job status of COMPLETE. Can't *something* be done to
> speed that up!
> Wednesday July 26, 2017
> [9:31 AM] Eroma Abeysinghe: @gary sorry for this. Currently all experiments
> are completed, and two running in alamo. but we found two which took rather
> unusually long time to transfers the files. we are investigating. will keep
> you posted.
> [9:51 AM] Marcus Christie: @gary here's what we've been able to confirm: gfac
> is getting the completed email from the scheduler and processing it
> immediately. Airavata doesn't mark an experiment as being completed until the
> output data staging completes. The output data staging for the jobs you gave
> us to look at took a long time to complete.
> [9:52 AM] Marlon Pierce: You can test network speed in various ways (like
> https://askubuntu.com/questions/7976/how-do-you-test-the-network-speed-betwen-two-boxes,
> which I googled).
> [9:53 AM] Marlon Pierce: It won't fix the problem, but it may help network
> admins diagnose the problem
> [9:53 AM] Marlon Pierce: I'm assuming (maybe incorrectly) that this is an
> issue between Alamo and our servers
> [9:54 AM] Marcus Christie: This is partly because transfer times from alamo
> to lims are happening very slowly, by my rough calculations at about 200kb/s.
> But also the analysis-results.tar file is much larger in these experiments.
> One example we looked at it was about 200 MB and another was about 1.13 GB.
> Looking through the logs back to April this is historically very large for an
> analysis-results.tar file.
> [9:54 AM] Marlon Pierce: But we can confirm this by looking at other servers
> [9:54 AM] Marcus Christie: @marlon this is between alamo and lims. Do we have
> a login on lims?
> [9:56 AM] Marlon Pierce: Oh...where is the LIMS server? At UTHSCSA?
> [9:57 AM] Marlon Pierce: I think it is.
> [9:58 AM] Marcus Christie: @marlon uslims3.uthscsa.edu
> [9:59 AM] Gary Gorbet: That other job completed. But now there is new,
> critical, job that FINISHED 40 minutes ago. Airavata job status is EXECUTING.
> [9:59 AM] Marcus Christie: It would be nice if we could run a command line
> scp transfer test from alamo to uslims3 just to see if it is fundamentally
> limited or this is a slowness in GFac.
> [10:00 AM] Gary Gorbet: That is easy to do. Will do a test and report.
> [10:00 AM] Marcus Christie: Thanks @gary
> [10:01 AM] Gary Gorbet: Transferred a 1.6M file from uslims3 to alamo in
> under a second.
> [10:02 AM] Marcus Christie: Actually I realized that GFac will do the
> transfer from alamo to uslims3 via GFac. It's not a true third party transfer
> but rather the data is streamed through the GFac server. So @marlon was
> right we need to test between alamo -> Gfac and GFac -> uslims3.
> [10:03 AM] Gary Gorbet: This would be alamo/uslims3 to gw153; right?
> [10:03 AM] Marcus Christie: Thanks @gary. So that's our theoretical upper
> bound.
> [10:04 AM] Marcus Christie: @gary that's right
> [10:08 AM] Sudhakar Pamidighantam: I think If it is reasonably secure GFac
> should do a true third party transfer to avoid this delay.
> [10:08 AM] Gary Gorbet: The LIMS work directory for the job has all the
> output files. So, it seems to me that gw153 to uslims3 transfers completed.
> So, why the EXECUTING gfac status?
> {quote}
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[jira] [Commented] (AIRAVATA-2458) SiGaP new account verification failed with an exception
[ https://issues.apache.org/jira/browse/AIRAVATA-2458?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16068717#comment-16068717 ] Marcus Christie commented on AIRAVATA-2458: --- Tested account verification and it is working. I think the problem was when I enabled API security but the Keycloak credentials weren't saved in GATEWAY_PROFILE. That is fixed now so account verification is working. I have a code fix for the issue with assigning roles. > SiGaP new account verification failed with an exception > --- > > Key: AIRAVATA-2458 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2458 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.scigap.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > Attachments: Screen Shot 2017-06-29 at 10.15.57 AM.png, Screen Shot > 2017-06-29 at 10.46.06 AM.png > > > 1. Create a new SciGaP account. > 2. Click the account confirmation link in the email > 3. Enter username and password and submit > 4. Exception: Error in authenticating or authorizing user > 5. But it appears the account was confirmed, because the scigap admin > received account creation notification. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2458) SiGaP new account verification failed with an exception
[ https://issues.apache.org/jira/browse/AIRAVATA-2458?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2458. --- Resolution: Fixed > SiGaP new account verification failed with an exception > --- > > Key: AIRAVATA-2458 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2458 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.scigap.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > Attachments: Screen Shot 2017-06-29 at 10.15.57 AM.png, Screen Shot > 2017-06-29 at 10.46.06 AM.png > > > 1. Create a new SciGaP account. > 2. Click the account confirmation link in the email > 3. Enter username and password and submit > 4. Exception: Error in authenticating or authorizing user > 5. But it appears the account was confirmed, because the scigap admin > received account creation notification. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2452) It took 70+ seconds to get the user list to share a project. This is too long
[ https://issues.apache.org/jira/browse/AIRAVATA-2452?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16067245#comment-16067245 ] Marcus Christie commented on AIRAVATA-2452: --- The problem is that the code is fetching user profiles from Keycloak one at a time. I think we can switch it to pull from the Profile Service instead and get them all at once. > It took 70+ seconds to get the user list to share a project. This is too long > - > > Key: AIRAVATA-2452 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2452 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.seagrid.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > > Gave project name to create a new project and clicked 'Share with other Users' > It took 70+ seconds to get the user list. > Is there any way we could reduce this time? Or let users search first and > filter the names as per the search? -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2457) In SciGaP portal notices are not visible to gateway providers.
[ https://issues.apache.org/jira/browse/AIRAVATA-2457?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2457. --- Resolution: Fixed > In SciGaP portal notices are not visible to gateway providers. > -- > > Key: AIRAVATA-2457 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2457 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.scigap.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2456) Last modified date time set in 1970, Hence the immediate experiments are not in Experiment browse.
[ https://issues.apache.org/jira/browse/AIRAVATA-2456?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2456. --- > Last modified date time set in 1970, Hence the immediate experiments are not > in Experiment browse. > -- > > Key: AIRAVATA-2456 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2456 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.seagrid.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > Attachments: Screen Shot 2017-06-28 at 1.48.38 PM.png, Screen Shot > 2017-06-28 at 1.52.30 PM.png > > > Experiment launched have a last updated date time as 01/18/1970, 3:17 AM - > GMT-0400 (EDT) > They appear in project browse and experiment statistics but not in Experiment > browse. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Updated] (AIRAVATA-2304) In Application deployment create page provide the host list which gateway has preferences. Currently the complete list is given in SciGaP
[ https://issues.apache.org/jira/browse/AIRAVATA-2304?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie updated AIRAVATA-2304: -- Priority: Critical (was: Major) > In Application deployment create page provide the host list which gateway has > preferences. Currently the complete list is given in SciGaP > - > > Key: AIRAVATA-2304 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2304 > Project: Airavata > Issue Type: Improvement > Components: PGA PHP Web Gateway >Reporter: Eroma >Assignee: Marcus Christie >Priority: Critical > Fix For: 0.18 > > > In Create Deployment page in 'Application Compute Host' all the resources > available in SciGaP is listed. Even the once the gateway has no > access/allocation. List only the resources gateway has allocations with. > Also the list need to be sorted in alphabetical order. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Updated] (AIRAVATA-2280) When assigning a credential store token to resources, show the description in drop down
[ https://issues.apache.org/jira/browse/AIRAVATA-2280?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie updated AIRAVATA-2280: -- Priority: Critical (was: Major) > When assigning a credential store token to resources, show the description in > drop down > --- > > Key: AIRAVATA-2280 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2280 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Reporter: Eroma >Assignee: Marcus Christie >Priority: Critical > Fix For: 0.18 > > > Currently in Gateway management, we display the token when it comes to > assigning the public keys. Instead show the description so it is more > identifiable and meaningful. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Updated] (AIRAVATA-2420) In testdrive gateway portal, users has no proper navigation to home page once logged in
[ https://issues.apache.org/jira/browse/AIRAVATA-2420?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie updated AIRAVATA-2420: -- Priority: Critical (was: Minor) > In testdrive gateway portal, users has no proper navigation to home page once > logged in > --- > > Key: AIRAVATA-2420 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2420 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway > Environment: https://testdrive.airavata.org >Reporter: Eroma >Assignee: Marcus Christie >Priority: Critical > Fix For: 0.18 > > > Prior to login in on Home page Contact Us exists. > But once logged in user has to click the empty space next to Project in the > top menu bar to get to home page, is kind of hidden -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Updated] (AIRAVATA-2372) When the Gateway base credential store token is not set it appears as it is
[ https://issues.apache.org/jira/browse/AIRAVATA-2372?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie updated AIRAVATA-2372: -- Priority: Critical (was: Minor) > When the Gateway base credential store token is not set it appears as it is > --- > > Key: AIRAVATA-2372 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2372 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://beta.scigap.org >Reporter: Eroma >Assignee: Marcus Christie >Priority: Critical > Fix For: 0.18 > > > In a gateway when the base credential store token is not set it displays a > token in the PGA but actually it is just display and it is not set in the > gateway. > Guessing the values in the dropdown is listed in the alphabetical order but > this kind of confuses the user. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2372) When the Gateway base credential store token is not set it appears as it is
[ https://issues.apache.org/jira/browse/AIRAVATA-2372?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16070327#comment-16070327 ] Marcus Christie commented on AIRAVATA-2372: --- Setting the base credential store token for a gateway works as intended. However I did find a bug. In the list of gateways under *Approved Gateways* tab in scigap, the displayed base credential store token is not correct. The problem is that the list of tokens available in the template are only scigap's SSH tokens. The tokens are fetched for each gateway. Eroma said since scigap admins can't change the base credential store token for other gateways that this is lower priority and only scigap admins will see this so also low priority. > When the Gateway base credential store token is not set it appears as it is > --- > > Key: AIRAVATA-2372 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2372 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://beta.scigap.org >Reporter: Eroma >Assignee: Marcus Christie >Priority: Critical > Fix For: 0.18 > > > In a gateway when the base credential store token is not set it displays a > token in the PGA but actually it is just display and it is not set in the > gateway. > Guessing the values in the dropdown is listed in the alphabetical order but > this kind of confuses the user. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2372) When the Gateway base credential store token is not set it appears as it is
[ https://issues.apache.org/jira/browse/AIRAVATA-2372?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2372. --- Resolution: Won't Fix > When the Gateway base credential store token is not set it appears as it is > --- > > Key: AIRAVATA-2372 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2372 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://beta.scigap.org >Reporter: Eroma >Assignee: Marcus Christie >Priority: Critical > Fix For: 0.18 > > > In a gateway when the base credential store token is not set it displays a > token in the PGA but actually it is just display and it is not set in the > gateway. > Guessing the values in the dropdown is listed in the alphabetical order but > this kind of confuses the user. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2420) In testdrive gateway portal, users has no proper navigation to home page once logged in
[ https://issues.apache.org/jira/browse/AIRAVATA-2420?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2420. --- Resolution: Fixed [~eroma_a] I think this is no longer an issue with the new base theme. If you look at dev.testdrive.airavata.org you can click on the *PHP Gateway* in the upper left to get back to the home page, and that seems very reasonable and expected behavior. And we should be moving the new code into production here within the next week. > In testdrive gateway portal, users has no proper navigation to home page once > logged in > --- > > Key: AIRAVATA-2420 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2420 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway > Environment: https://testdrive.airavata.org >Reporter: Eroma >Assignee: Marcus Christie >Priority: Critical > Fix For: 0.18 > > > Prior to login in on Home page Contact Us exists. > But once logged in user has to click the empty space next to Project in the > top menu bar to get to home page, is kind of hidden -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2457) In SciGaP portal notices are not visible to gateway providers.
[ https://issues.apache.org/jira/browse/AIRAVATA-2457?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2457. --- Resolution: Fixed > In SciGaP portal notices are not visible to gateway providers. > -- > > Key: AIRAVATA-2457 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2457 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.scigap.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2449) When experiments are searched in Experiment Statistics, and tried to view the summary, throws an exception
[ https://issues.apache.org/jira/browse/AIRAVATA-2449?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2449. --- Resolution: Fixed > When experiments are searched in Experiment Statistics, and tried to view the > summary, throws an exception > -- > > Key: AIRAVATA-2449 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2449 > Project: Airavata > Issue Type: Bug >Affects Versions: 0.17 > Environment: https://dev.seagrid.org >Reporter: Eroma >Assignee: Marcus Christie >Priority: Blocker > Fix For: 0.18 > > > 1. Search for Gaussian experiments of last 6 months for a specific user. > 2. Lists all the experiments. > 3. Some of them don't have the application, its empty in Experiment summary > 4. When clicked on one of them gets: Class 'WSIS' not found > 5. Exception is thrown when tried to view the summary, when clicked stats > nothing is displayed no exception thrown > 6. Seems like the exception is not because the interface ID is no longer, its > because as the gateway admin i am trying to view someone else's experiment > summary. > 7. investigation: The empty application exists for application interface ID > which no longer exists in the app_catalog -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2449) When experiments are searched in Experiment Statistics, and tried to view the summary, throws an exception
[ https://issues.apache.org/jira/browse/AIRAVATA-2449?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16070240#comment-16070240 ] Marcus Christie commented on AIRAVATA-2449: --- I think this one was fixed by changes in AIRAVATA-2452. [~eroma_a] can you please test again? > When experiments are searched in Experiment Statistics, and tried to view the > summary, throws an exception > -- > > Key: AIRAVATA-2449 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2449 > Project: Airavata > Issue Type: Bug >Affects Versions: 0.17 > Environment: https://dev.seagrid.org >Reporter: Eroma >Assignee: Marcus Christie >Priority: Blocker > Fix For: 0.18 > > > 1. Search for Gaussian experiments of last 6 months for a specific user. > 2. Lists all the experiments. > 3. Some of them don't have the application, its empty in Experiment summary > 4. When clicked on one of them gets: Class 'WSIS' not found > 5. Exception is thrown when tried to view the summary, when clicked stats > nothing is displayed no exception thrown > 6. Seems like the exception is not because the interface ID is no longer, its > because as the gateway admin i am trying to view someone else's experiment > summary. > 7. investigation: The empty application exists for application interface ID > which no longer exists in the app_catalog -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Updated] (AIRAVATA-2449) When experiments are searched in Experiment Statistics, and tried to view the summary, throws an exception
[ https://issues.apache.org/jira/browse/AIRAVATA-2449?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie updated AIRAVATA-2449: -- Priority: Blocker (was: Major) > When experiments are searched in Experiment Statistics, and tried to view the > summary, throws an exception > -- > > Key: AIRAVATA-2449 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2449 > Project: Airavata > Issue Type: Bug >Affects Versions: 0.17 > Environment: https://dev.seagrid.org >Reporter: Eroma >Assignee: Marcus Christie >Priority: Blocker > Fix For: 0.18 > > > 1. Search for Gaussian experiments of last 6 months for a specific user. > 2. Lists all the experiments. > 3. Some of them don't have the application, its empty in Experiment summary > 4. When clicked on one of them gets: Class 'WSIS' not found > 5. Exception is thrown when tried to view the summary, when clicked stats > nothing is displayed no exception thrown > 6. Seems like the exception is not because the interface ID is no longer, its > because as the gateway admin i am trying to view someone else's experiment > summary. > 7. investigation: The empty application exists for application interface ID > which no longer exists in the app_catalog -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2419) Keycloak: enable and test Keycloak based authorization
[ https://issues.apache.org/jira/browse/AIRAVATA-2419?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16068417#comment-16068417 ] Marcus Christie commented on AIRAVATA-2419: --- Enabled now in dev SciGaP environment. > Keycloak: enable and test Keycloak based authorization > -- > > Key: AIRAVATA-2419 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2419 > Project: Airavata > Issue Type: Bug > Components: Security >Reporter: Marcus Christie >Assignee: Marcus Christie > Fix For: 0.18 > > -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2304) In Application deployment create page provide the host list which gateway has preferences. Currently the complete list is given in SciGaP
[
https://issues.apache.org/jira/browse/AIRAVATA-2304?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16070697#comment-16070697
]
Marcus Christie commented on AIRAVATA-2304:
---
I also disabled the *Create a new Application Deployment* button when there are
no compute resource preferences and display a message to the user:
{quote}
You cannot create any application deployments until you create at least one
compute resource preference.
{quote}
And there is a link to the gateway management page where user can create
compute resource preference.
> In Application deployment create page provide the host list which gateway has
> preferences. Currently the complete list is given in SciGaP
> -
>
> Key: AIRAVATA-2304
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2304
> Project: Airavata
> Issue Type: Improvement
> Components: PGA PHP Web Gateway
>Reporter: Eroma
>Assignee: Marcus Christie
>Priority: Critical
> Fix For: 0.18
>
>
> In Create Deployment page in 'Application Compute Host' all the resources
> available in SciGaP is listed. Even the once the gateway has no
> access/allocation. List only the resources gateway has allocations with.
> Also the list need to be sorted in alphabetical order.
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[jira] [Assigned] (AIRAVATA-2420) In testdrive gateway portal, users has no proper navigation to home page once logged in
[ https://issues.apache.org/jira/browse/AIRAVATA-2420?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie reassigned AIRAVATA-2420: - Assignee: Marcus Christie > In testdrive gateway portal, users has no proper navigation to home page once > logged in > --- > > Key: AIRAVATA-2420 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2420 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway > Environment: https://testdrive.airavata.org >Reporter: Eroma >Assignee: Marcus Christie >Priority: Minor > Fix For: 0.18 > > > Prior to login in on Home page Contact Us exists. > But once logged in user has to click the empty space next to Project in the > top menu bar to get to home page, is kind of hidden -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Created] (AIRAVATA-2477) For gateway request, store admin password in credential store
Marcus Christie created AIRAVATA-2477: - Summary: For gateway request, store admin password in credential store Key: AIRAVATA-2477 URL: https://issues.apache.org/jira/browse/AIRAVATA-2477 Project: Airavata Issue Type: Bug Components: PGA PHP Web Gateway Reporter: Marcus Christie Assignee: Sneha Tilak Looks like currently the code is storing the admin password provided by a gateway requester in the identityServerPasswordToken field of the Gateway object. Instead the code should store the username and password in the credential store, get back a credential store token, and save this token in the identityServerPasswordToken field of the Gateway object. See AdminUtilities::create_pwd_token for how to generate a password token. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2478) Email link for email change confirmation throws an exception
[ https://issues.apache.org/jira/browse/AIRAVATA-2478?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2478. --- Resolution: Fixed Note: this happens whenever the email change confirmation link is clicked and the user isn't still logged in (or the link opens in a different browser from the one the user requested the email address change in). Should be fixed now. > Email link for email change confirmation throws an exception > > > Key: AIRAVATA-2478 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2478 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.seagrid.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > Attachments: Screen Shot 2017-07-04 at 12.49.25 PM.png > > > Clicked the link on email sent to confirm email address change. exception > thrown: Cannot access protected property Exception::$message -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2468) When requesting for a gateway validate the email address format.
[ https://issues.apache.org/jira/browse/AIRAVATA-2468?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16071828#comment-16071828 ] Marcus Christie commented on AIRAVATA-2468: --- Looks like email validation is working. When I give 'test' as an email I get the error 'The email must be a valid email address.' One issue though is that the previously supplied values are missing in the form. > When requesting for a gateway validate the email address format. > > > Key: AIRAVATA-2468 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2468 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.scigap.org >Reporter: Eroma >Assignee: Sneha Tilak > Fix For: 0.18 > > > When requesting for a gateway, gave 'test' as the email and when saved. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2463) Throws system exception when tried to submit gateway request with already existing gateway name
[ https://issues.apache.org/jira/browse/AIRAVATA-2463?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16071829#comment-16071829 ] Marcus Christie commented on AIRAVATA-2463: --- A meaningful error message is now displayed thanks to Sneha's changes. However, there is still the issue that the form values aren't redisplayed so the user can correct and resubmit. > Throws system exception when tried to submit gateway request with already > existing gateway name > --- > > Key: AIRAVATA-2463 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2463 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.scigap.org >Reporter: Eroma >Assignee: Sneha Tilak > Fix For: 0.18 > > > Instead of a system exception user should be provided with meaningful error > message, and given the opportunity to fix and resubmit the request. When > checking for duplicates, should not restrict if the existing gateway name is > from a CANCELLED or DENIED request. Only should restrict gateway requests in > other states. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2469) New gateway providers cannot create a gateway request.
[ https://issues.apache.org/jira/browse/AIRAVATA-2469?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16071826#comment-16071826 ] Marcus Christie commented on AIRAVATA-2469: --- [~tilaks26], that is right. I think adding gateway-provider to the verifyadmin filter will fix this issue. > New gateway providers cannot create a gateway request. > -- > > Key: AIRAVATA-2469 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2469 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.scigap.org >Reporter: Eroma >Assignee: Sneha Tilak > Fix For: 0.18 > > > For newly created users, cannot create a new gateway request. When the > request is submitted getting error, "You need to be an admin to use this > service." > No record is created because gateway request has no record of this gateway > request. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2469) New gateway providers cannot create a gateway request.
[ https://issues.apache.org/jira/browse/AIRAVATA-2469?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16072668#comment-16072668 ] Marcus Christie commented on AIRAVATA-2469: --- I'm fixing this as part of another issue. > New gateway providers cannot create a gateway request. > -- > > Key: AIRAVATA-2469 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2469 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.scigap.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > > For newly created users, cannot create a new gateway request. When the > request is submitted getting error, "You need to be an admin to use this > service." > No record is created because gateway request has no record of this gateway > request. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2470) When existing gateway provider tries to update the second part of the gateway reqest
[ https://issues.apache.org/jira/browse/AIRAVATA-2470?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2470. --- Resolution: Fixed > When existing gateway provider tries to update the second part of the gateway > reqest > > > Key: AIRAVATA-2470 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2470 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.scigap.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > Attachments: Screen Shot 2017-07-02 at 10.40.54 AM.png > > > 1. Existing gateway provider creates a gateway request > 2. SciGaP admin gets notification > 3. SciGaP admin approves the request > 4. Gateway provider gets notified about the gateway request update > 5. Logs in to portal, and clicks Update request > 6. Exception thrown - Error getting gateway-profile, reason: Could not find > Gateway with ID: f37a6727-bb6d-4e69-a213-0f55386ec90b -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2470) When existing gateway provider tries to update the second part of the gateway reqest
[ https://issues.apache.org/jira/browse/AIRAVATA-2470?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16072673#comment-16072673 ] Marcus Christie commented on AIRAVATA-2470: --- [~eroma_a], this should be fixed now. Can you try again? > When existing gateway provider tries to update the second part of the gateway > reqest > > > Key: AIRAVATA-2470 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2470 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.scigap.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > Attachments: Screen Shot 2017-07-02 at 10.40.54 AM.png > > > 1. Existing gateway provider creates a gateway request > 2. SciGaP admin gets notification > 3. SciGaP admin approves the request > 4. Gateway provider gets notified about the gateway request update > 5. Logs in to portal, and clicks Update request > 6. Exception thrown - Error getting gateway-profile, reason: Could not find > Gateway with ID: f37a6727-bb6d-4e69-a213-0f55386ec90b -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2448) user with uppercase letters in username cannot reset password with keycloak migration
[ https://issues.apache.org/jira/browse/AIRAVATA-2448?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2448. --- Resolution: Fixed Should be fixed now. > user with uppercase letters in username cannot reset password with keycloak > migration > - > > Key: AIRAVATA-2448 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2448 > Project: Airavata > Issue Type: Bug > Components: Airavata System, PGA PHP Web Gateway, Security >Affects Versions: 0.17 > Environment: https://dev.seagrid.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > > 1. Existing user with upper case username tries to login > 2. Login fails, no message is displayed saying reset password. Message > displayed: "Invalid username or password. Please try again." > 3. User tries forgot password link and that also failed. > 4. Password reset of username with upper case letters should be handled. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2376) Duplicating experiment records in Experiment statistics and Experiment browse
[
https://issues.apache.org/jira/browse/AIRAVATA-2376?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16068337#comment-16068337
]
Marcus Christie commented on AIRAVATA-2376:
---
I found an example of an experiment with two statuses in the same second but
only one status in LATEST_EXPERIMENT_STATUS:
In EXPERIMENT_STATUS table:
| CREATED |
LT_Cu2Se_HangChi_order_13_8A_grad_3_restart_f231677b-141c-4eb1-a477-dbc75ca7a42b
|
2017-06-28 18:56:50.938000 |
| LAUNCHED |
LT_Cu2Se_HangChi_order_13_8A_grad_3_restart_f231677b-141c-4eb1-a477-dbc75ca7a42b
|
2017-06-28 18:56:52.167000 |
| EXECUTING |
LT_Cu2Se_HangChi_order_13_8A_grad_3_restart_f231677b-141c-4eb1-a477-dbc75ca7a42b
|
2017-06-28 18:56:52.485000 |
In LATEST_EXPERIMENT_STATUS:
{code:sql}
select * from LATEST_EXPERIMENT_STATUS where EXPERIMENT_ID =
'LT_Cu2Se_HangChi_order_13_8A_grad_3_restart_f231677b-141c-4eb1-a477-dbc75ca7a42b';
{code}
|
LT_Cu2Se_HangChi_order_13_8A_grad_3_restart_f231677b-141c-4eb1-a477-dbc75ca7a42b
| EXECUTING | 2017-06-28 18:56:52.485000 |
> Duplicating experiment records in Experiment statistics and Experiment browse
> -
>
> Key: AIRAVATA-2376
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2376
> Project: Airavata
> Issue Type: Bug
> Components: PGA PHP Web Gateway, Registry API
>Affects Versions: 0.17
> Environment: https://seagrid.org and all other gateways as well
>Reporter: Eroma
>Assignee: Marcus Christie
>Priority: Critical
> Fix For: 0.17
>
>
> When experiments are launched there are two records in EXPERIMENT SUMMARY
> table for LAUNCHED and EXECUTING state which has the exact same state change
> time. In PGA however two records show up for the same experiment and with
> same status. e.g.: two exact records for a single experiment. This only
> appears until the experiment is FAILED or COMPLETED. But both users and
> gateway admins notices this and this needs fixing.
> h3. Resources
> * MySQL JDBC driver configuration:
> **
> https://dev.mysql.com/doc/connector-j/5.1/en/connector-j-reference-configuration-properties.html
> ** uses sendFractionalSeconds
> ** added in [MySQL Connector/J
> 5.1.37|https://docs.oracle.com/cd/E17952_01/connector-j-relnotes-en/news-5-1-37.html]
> * https://issues.apache.org/jira/browse/OPENJPA-2159
> * MariaDB JDBC driver configuration:
> ** https://mariadb.com/kb/en/mariadb/about-mariadb-connector-j/
> ** uses useFractionalSeconds
> * MariaDB JDBC driver defaults to useFractionalSeconds as true since 1.1.8
> ** https://mariadb.com/kb/en/mariadb/mariadb-java-client-118-changelog/
> * [MariaDB TIMESTAMP|https://mariadb.com/kb/en/mariadb/timestamp/]
> * [Microseconds in
> MariaDB|https://mariadb.com/kb/en/mariadb/microseconds-in-mariadb/]
> * How to specify TIMESTAMP precision in JPA annotations?
> ** [Confused why they seem to use scale instead of precision in
> OpenJPA|https://issues.apache.org/jira/browse/OPENJPA-2555]
> * [Supporting evidence that we need to use MariaDB driver when using MariaDB
> server|https://issues.alfresco.com/jira/browse/MNT-17613]
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[jira] [Resolved] (AIRAVATA-2376) Duplicating experiment records in Experiment statistics and Experiment browse
[ https://issues.apache.org/jira/browse/AIRAVATA-2376?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2376. --- Resolution: Fixed > Duplicating experiment records in Experiment statistics and Experiment browse > - > > Key: AIRAVATA-2376 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2376 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway, Registry API >Affects Versions: 0.17 > Environment: https://seagrid.org and all other gateways as well >Reporter: Eroma >Assignee: Marcus Christie >Priority: Critical > Fix For: 0.17 > > > When experiments are launched there are two records in EXPERIMENT SUMMARY > table for LAUNCHED and EXECUTING state which has the exact same state change > time. In PGA however two records show up for the same experiment and with > same status. e.g.: two exact records for a single experiment. This only > appears until the experiment is FAILED or COMPLETED. But both users and > gateway admins notices this and this needs fixing. > h3. Resources > * MySQL JDBC driver configuration: > ** > https://dev.mysql.com/doc/connector-j/5.1/en/connector-j-reference-configuration-properties.html > ** uses sendFractionalSeconds > ** added in [MySQL Connector/J > 5.1.37|https://docs.oracle.com/cd/E17952_01/connector-j-relnotes-en/news-5-1-37.html] > * https://issues.apache.org/jira/browse/OPENJPA-2159 > * MariaDB JDBC driver configuration: > ** https://mariadb.com/kb/en/mariadb/about-mariadb-connector-j/ > ** uses useFractionalSeconds > * MariaDB JDBC driver defaults to useFractionalSeconds as true since 1.1.8 > ** https://mariadb.com/kb/en/mariadb/mariadb-java-client-118-changelog/ > * [MariaDB TIMESTAMP|https://mariadb.com/kb/en/mariadb/timestamp/] > * [Microseconds in > MariaDB|https://mariadb.com/kb/en/mariadb/microseconds-in-mariadb/] > * How to specify TIMESTAMP precision in JPA annotations? > ** [Confused why they seem to use scale instead of precision in > OpenJPA|https://issues.apache.org/jira/browse/OPENJPA-2555] > * [Supporting evidence that we need to use MariaDB driver when using MariaDB > server|https://issues.alfresco.com/jira/browse/MNT-17613] -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2452) It took 70+ seconds to get the user list to share a project. This is too long
[ https://issues.apache.org/jira/browse/AIRAVATA-2452?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16068297#comment-16068297 ] Marcus Christie commented on AIRAVATA-2452: --- I fixed this by loading all user profiles from the UserProfileService. The problem with this approach is that it won't scale as a gateway gets more and more users. We need to move toward having the user search first for users and then fetching user profiles matching that search. That's a bigger change, but I think we can tackle that when we do the Django implementation of PGA. > It took 70+ seconds to get the user list to share a project. This is too long > - > > Key: AIRAVATA-2452 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2452 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.seagrid.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > > Gave project name to create a new project and clicked 'Share with other Users' > It took 70+ seconds to get the user list. > Is there any way we could reduce this time? Or let users search first and > filter the names as per the search? -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2452) It took 70+ seconds to get the user list to share a project. This is too long
[ https://issues.apache.org/jira/browse/AIRAVATA-2452?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2452. --- Resolution: Fixed > It took 70+ seconds to get the user list to share a project. This is too long > - > > Key: AIRAVATA-2452 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2452 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.seagrid.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > > Gave project name to create a new project and clicked 'Share with other Users' > It took 70+ seconds to get the user list. > Is there any way we could reduce this time? Or let users search first and > filter the names as per the search? -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Comment Edited] (AIRAVATA-2454) Error exception 'Class 'WSIS' not found' when tried to view a shared project sumamry
[ https://issues.apache.org/jira/browse/AIRAVATA-2454?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16068306#comment-16068306 ] Marcus Christie edited comment on AIRAVATA-2454 at 6/29/17 1:10 PM: I think this one is fixed by changes in AIRAVATA-2452. Can you test again Eroma? was (Author: marcuschristie): I think this one is fixed. Can you test again Eroma? > Error exception 'Class 'WSIS' not found' when tried to view a shared project > sumamry > > > Key: AIRAVATA-2454 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2454 > Project: Airavata > Issue Type: Bug > Components: Airavata System, PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.seagrid.org/ >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > > 1. User A logged in through CILogon using campus login (IU) > 2. Created a project and shared with a user B who has gmail account as the > gateway username. User B logged in through CILogon using gmail. > 3. User B logs in and tries to view the project summary of the shared project > 4. User B was given write permission > 5. When clicked view project summary exception thrown -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2454) Error exception 'Class 'WSIS' not found' when tried to view a shared project sumamry
[ https://issues.apache.org/jira/browse/AIRAVATA-2454?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2454. --- Resolution: Fixed I think this one is fixed. Can you test again Eroma? > Error exception 'Class 'WSIS' not found' when tried to view a shared project > sumamry > > > Key: AIRAVATA-2454 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2454 > Project: Airavata > Issue Type: Bug > Components: Airavata System, PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.seagrid.org/ >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > > 1. User A logged in through CILogon using campus login (IU) > 2. Created a project and shared with a user B who has gmail account as the > gateway username. User B logged in through CILogon using gmail. > 3. User B logs in and tries to view the project summary of the shared project > 4. User B was given write permission > 5. When clicked view project summary exception thrown -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2453) Database migration scripts for 0.18
[ https://issues.apache.org/jira/browse/AIRAVATA-2453?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2453. --- Resolution: Fixed > Database migration scripts for 0.18 > --- > > Key: AIRAVATA-2453 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2453 > Project: Airavata > Issue Type: Bug >Reporter: Marcus Christie >Assignee: Marcus Christie > -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2482) Gateway admin-read-only cannot view Gateway management interface. Exception thorwn
[
https://issues.apache.org/jira/browse/AIRAVATA-2482?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16075228#comment-16075228
]
Marcus Christie commented on AIRAVATA-2482:
---
This was a role permission issue. I added access to {{getGateway}} for
admin-read-only role.
See
https://github.com/apache/airavata/commit/160f70e585098a079c2e6b8168a86ec01cc8ecea
> Gateway admin-read-only cannot view Gateway management interface. Exception
> thorwn
> --
>
> Key: AIRAVATA-2482
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2482
> Project: Airavata
> Issue Type: Bug
> Components: Airavata System, PGA PHP Web Gateway
>Affects Versions: 0.17
> Environment: https://dev.seagrid.org and
> https://dev.testdrive.airavata.org
>Reporter: Eroma
>Assignee: Marcus Christie
> Fix For: 0.18
>
>
> In both gateways admin-read-only role users cannot view the gateway
> management page. Getting exception:
> Airavata \ API \ Error \ AuthorizationException
> User is not authenticated or authorized.
> seagrid gateway user is a created account with keycloak and testdrive user
> account is through CILogon
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[jira] [Resolved] (AIRAVATA-2246) Python 3 compatibility in Python thrift stubs
[ https://issues.apache.org/jira/browse/AIRAVATA-2246?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2246. --- Resolution: Fixed > Python 3 compatibility in Python thrift stubs > - > > Key: AIRAVATA-2246 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2246 > Project: Airavata > Issue Type: Bug > Components: Airavata Client >Reporter: Marcus Christie >Assignee: Marcus Christie > > The current Python thrift stubs depend on Python 2. Would be great moving > forward to have a Python 3 compatible version. > Looks like the latest unreleased version of Thrift supports generating Python > 3 compatible stubs. -- This message was sent by Atlassian JIRA (v6.3.15#6346)
[jira] [Commented] (AIRAVATA-2371) Deploy Keycloak integration testing environment on Jetstream
[
https://issues.apache.org/jira/browse/AIRAVATA-2371?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15983560#comment-15983560
]
Marcus Christie commented on AIRAVATA-2371:
---
For the accord integration we just used the Keycloak master admin username and
password to administrative purposes. I think we should use a separate
privileged user account created in that realm, like what we did for the WSO2IS
integration.
So how to do that? We need to create a user in the realm and then give that
user the {{realm-admin}} role of the {{realm-management}} client. Here's what
it says in the manual:
{quote}
The account that logs in needs to have proper permissions in order to be able
to invoke Admin REST API operations. Specifically - realm-admin role of
realm-management client is required for user to administer the realm within
which the user is defined.
{quote}
http://www.keycloak.org/docs/3.0/server_admin/topics/admin-cli.html
> Deploy Keycloak integration testing environment on Jetstream
>
>
> Key: AIRAVATA-2371
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2371
> Project: Airavata
> Issue Type: Bug
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>
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[jira] [Resolved] (AIRAVATA-2367) When users logs in to the gateway using CILogon the email notification is not sent to gateway admins
[ https://issues.apache.org/jira/browse/AIRAVATA-2367?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2367. --- Resolution: Fixed This needs to be tested but should be fixed. > When users logs in to the gateway using CILogon the email notification is not > sent to gateway admins > > > Key: AIRAVATA-2367 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2367 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway > Environment: http://accord.scigap.org/ >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > > When a user uses CILogon and logs in to the gateway for the first time does > not trigger the notification email for th gateway admin to provide gateway > access. > First login to the gateway through CILogon should be treated as the > confirmation and gateway admin need to be notified. -- This message was sent by Atlassian JIRA (v6.3.15#6346)
[jira] [Commented] (AIRAVATA-2342) Integrate Keycloak with PGA
[ https://issues.apache.org/jira/browse/AIRAVATA-2342?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15989392#comment-15989392 ] Marcus Christie commented on AIRAVATA-2342: --- When testing on Jetstream I ran into a problem where PHP curl wasn't able to verify the iam.scigap.org SSL certificate. I'm not sure why since it worked fine on my laptop. Ultimately what I did is I got the CA certificate from http://certmgr.techservices.illinois.edu/intermediate1.txt and configured it as the cafile-path in pga_config.php. > Integrate Keycloak with PGA > --- > > Key: AIRAVATA-2342 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2342 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway, Security >Reporter: Marcus Christie >Assignee: Marcus Christie > Fix For: 0.18 > > > Integrate Keycloak with PGA. Essentially, replace WSO2 IS with Keycloak. > The initial motivating use case is integration of Keycloak with CILogon. -- This message was sent by Atlassian JIRA (v6.3.15#6346)
[jira] [Created] (AIRAVATA-2373) Increase open file descriptor limits for RabbitMQ server
Marcus Christie created AIRAVATA-2373:
-
Summary: Increase open file descriptor limits for RabbitMQ server
Key: AIRAVATA-2373
URL: https://issues.apache.org/jira/browse/AIRAVATA-2373
Project: Airavata
Issue Type: Bug
Components: GFac
Reporter: Marcus Christie
Assignee: Marcus Christie
Ran into a problem on gw56 where GFac wasn't able to make a connection to
RabbitMQ because RabbitMQ hit the open file descriptor limit of 1024.
Using
http://clouddoc.stratus.com/1.5.1.0/en-us/Content/Help/P03_Support/C02_InstallGuide/C05_OpenStackInstall/T_RabbitMQLimits.htm
as a guide I created a file called /etc/default/rabbitmq-server on gw56 with
the following contents:
{noformat}
ulimit -n 65536
{noformat}
Then I restarted RabbitMQ. I verified the new limit:
{noformat}
[root@gw56 ~]# grep -e Limit -e files /proc/$(cat /var/run/rabbitmq/pid)/limits
Limit Soft Limit Hard Limit Units
Max open files6553665536files
{noformat}
Then I restarted GFac and it was able to connect to the process_launch queue
again.
It would be good to research if this is the best way to increase open file
limits and then get it into the Ansible scripts.
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[jira] [Created] (AIRAVATA-2374) Create init scripts for airavata servers
Marcus Christie created AIRAVATA-2374: - Summary: Create init scripts for airavata servers Key: AIRAVATA-2374 URL: https://issues.apache.org/jira/browse/AIRAVATA-2374 Project: Airavata Issue Type: Bug Reporter: Marcus Christie Assignee: Marcus Christie Fix For: 0.18 -- This message was sent by Atlassian JIRA (v6.3.15#6346)
[jira] [Created] (AIRAVATA-2375) PGA: when sharing disabled, all users' projects are displayed in browse projects
Marcus Christie created AIRAVATA-2375: - Summary: PGA: when sharing disabled, all users' projects are displayed in browse projects Key: AIRAVATA-2375 URL: https://issues.apache.org/jira/browse/AIRAVATA-2375 Project: Airavata Issue Type: Bug Reporter: Marcus Christie Fix For: 0.18 -- This message was sent by Atlassian JIRA (v6.3.15#6346)
[jira] [Commented] (AIRAVATA-2373) Increase open file descriptor limits for RabbitMQ server
[
https://issues.apache.org/jira/browse/AIRAVATA-2373?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15982834#comment-15982834
]
Marcus Christie commented on AIRAVATA-2373:
---
Also, can we add a Zabbix alert for this? And can we add it as part of the
Ansible scripts?
> Increase open file descriptor limits for RabbitMQ server
>
>
> Key: AIRAVATA-2373
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2373
> Project: Airavata
> Issue Type: Bug
> Components: GFac
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>
> Ran into a problem on gw56 where GFac wasn't able to make a connection to
> RabbitMQ because RabbitMQ hit the open file descriptor limit of 1024.
> Using
> http://clouddoc.stratus.com/1.5.1.0/en-us/Content/Help/P03_Support/C02_InstallGuide/C05_OpenStackInstall/T_RabbitMQLimits.htm
> as a guide I created a file called /etc/default/rabbitmq-server on gw56 with
> the following contents:
> {noformat}
> ulimit -n 65536
> {noformat}
> Then I restarted RabbitMQ. I verified the new limit:
> {noformat}
> [root@gw56 ~]# grep -e Limit -e files /proc/$(cat
> /var/run/rabbitmq/pid)/limits
> Limit Soft Limit Hard Limit Units
> Max open files6553665536files
> {noformat}
> Then I restarted GFac and it was able to connect to the process_launch queue
> again.
> It would be good to research if this is the best way to increase open file
> limits and then get it into the Ansible scripts.
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[jira] [Created] (AIRAVATA-2506) Sharing Registry: Error updating user when changed
Marcus Christie created AIRAVATA-2506:
-
Summary: Sharing Registry: Error updating user when changed
Key: AIRAVATA-2506
URL: https://issues.apache.org/jira/browse/AIRAVATA-2506
Project: Airavata
Issue Type: Improvement
Components: Airavata System
Reporter: Marcus Christie
Fix For: 0.19
Exception:
{noformat}
2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
o.a.a.s.r.m.SharingServiceDBEventHandler - New DB Event message to sharing
service.
2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
o.a.a.s.r.m.SharingServiceDBEventHandler - DB Event message to sharing service
from user.profile
2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
o.a.a.s.r.m.SharingServiceDBEventHandler - User profile specific DB Event
communicated by user.profile
2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
o.a.a.s.r.m.SharingServiceDBEventHandler - Updating user. User Id :
eabey...@iu.edu
2017-08-04 20:35:41,874 [pool-15-thread-1] ERROR
o.a.a.s.r.s.SharingRegistryServerHandler - null
java.lang.NullPointerException: null
at
org.apache.airavata.sharing.registry.server.SharingRegistryServerHandler.updatedUser(SharingRegistryServerHandler.java:180)
at
org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3992)
at
org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3976)
at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
at
org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
2017-08-04 20:35:41,874 [pool-18-thread-3] ERROR
o.a.a.s.r.m.SharingServiceDBEventHandler - Error processing message.
org.apache.airavata.sharing.registry.models.SharingRegistryException: null
Stack trace:java.lang.NullPointerException
at
org.apache.airavata.sharing.registry.server.SharingRegistryServerHandler.updatedUser(SharingRegistryServerHandler.java:180)
at
org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3992)
at
org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3976)
at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
at
org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
at
org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result$updatedUser_resultStandardScheme.read(SharingRegistryService.java:15260)
at
org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result$updatedUser_resultStandardScheme.read(SharingRegistryService.java:15238)
at
org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result.read(SharingRegistryService.java:15182)
at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:89)
at
org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Client.recv_updatedUser(SharingRegistryService.java:757)
at
org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Client.updatedUser(SharingRegistryService.java:744)
at
org.apache.airavata.sharing.registry.messaging.SharingServiceDBEventHandler.onMessage(SharingServiceDBEventHandler.java:104)
at
org.apache.airavata.messaging.core.impl.MessageConsumer.handleDelivery(MessageConsumer.java:70)
at
com.rabbitmq.client.impl.ConsumerDispatcher$5.run(ConsumerDispatcher.java:144)
at
com.rabbitmq.client.impl.ConsumerWorkService$WorkPoolRunnable.run(ConsumerWorkService.java:99)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
{noformat}
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[jira] [Commented] (AIRAVATA-2501) In application deployment, default node count and CPU count are mandatory
[ https://issues.apache.org/jira/browse/AIRAVATA-2501?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16114719#comment-16114719 ] Marcus Christie commented on AIRAVATA-2501: --- [~eroma_a], Just want to clarify. The desired behavior is that you want to be able to leave the default values in the deployment blank so that queue or gateway level defaults will take effect instead? Is the issue that now if you supply a 0 for a default value that that 0 will then be displayed to the user for the application? > In application deployment, default node count and CPU count are mandatory > - > > Key: AIRAVATA-2501 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2501 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: all dev and production gateways >Reporter: Eroma >Assignee: Marcus Christie >Priority: Minor > Fix For: 0.19 > > > When creating an application deployment currently the default values for node > and CPU are mandatory. If the user doesn't want to give a default value has > to give 0. > When given 0 in deployment the default values are not set to 0 at experiment > creation. Default values set at queue level or gateway level will be > displayed to the user, not the 0 put in deployment. > Minor issue, its just that user has to give 0 to bypass. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2502) In gateways CILogon is enabled, it to be the main login mechanism
[ https://issues.apache.org/jira/browse/AIRAVATA-2502?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16114725#comment-16114725 ] Marcus Christie commented on AIRAVATA-2502: --- [~eroma_a], I think we can make the order of options configurable. It might take a while before I get to the code changes to change the order of options. In the meantime, for USD we could go ahead and create a Login with USD credentials button fairly quickly (would need to register with CILogon and do some Keycloak configuration, but should take too long). Do you think it is worth it? So they would have these options: * username/password * Login with USD Credentials * Login with CILogon > In gateways CILogon is enabled, it to be the main login mechanism > - > > Key: AIRAVATA-2502 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2502 > Project: Airavata > Issue Type: Improvement > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://sciencegateway.usd.edu >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > > 1. CILogon to be the more focused login to use > 2. First option: Users to have clear indication ‘Login with USD credentials” > and directly take them to USD without needing to select the institute. > 3. Second option: “Login with other institute credentials” This for other > users login to gateway. Here there should be list of institutes to select and > login. > 4. Third option: Create or log in with a local gateway account. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Created] (AIRAVATA-2505) Update Airavata to Thrift 0.10.0
Marcus Christie created AIRAVATA-2505: - Summary: Update Airavata to Thrift 0.10.0 Key: AIRAVATA-2505 URL: https://issues.apache.org/jira/browse/AIRAVATA-2505 Project: Airavata Issue Type: Improvement Reporter: Marcus Christie Assignee: Marcus Christie We need Thrift 0.10.0 to generate Python 3 compatible stubs. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Assigned] (AIRAVATA-2506) Sharing Registry: Error updating user when changed
[
https://issues.apache.org/jira/browse/AIRAVATA-2506?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Marcus Christie reassigned AIRAVATA-2506:
-
Assignee: Marcus Christie
> Sharing Registry: Error updating user when changed
> --
>
> Key: AIRAVATA-2506
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2506
> Project: Airavata
> Issue Type: Improvement
> Components: Airavata System
>Reporter: Marcus Christie
>Assignee: Marcus Christie
> Fix For: 0.19
>
>
> Exception:
> {noformat}
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - New DB Event message to sharing
> service.
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - DB Event message to sharing
> service from user.profile
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - User profile specific DB Event
> communicated by user.profile
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - Updating user. User Id :
> eabey...@iu.edu
> 2017-08-04 20:35:41,874 [pool-15-thread-1] ERROR
> o.a.a.s.r.s.SharingRegistryServerHandler - null
> java.lang.NullPointerException: null
> at
> org.apache.airavata.sharing.registry.server.SharingRegistryServerHandler.updatedUser(SharingRegistryServerHandler.java:180)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3992)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3976)
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
> at
> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> 2017-08-04 20:35:41,874 [pool-18-thread-3] ERROR
> o.a.a.s.r.m.SharingServiceDBEventHandler - Error processing message.
> org.apache.airavata.sharing.registry.models.SharingRegistryException: null
> Stack trace:java.lang.NullPointerException
> at
> org.apache.airavata.sharing.registry.server.SharingRegistryServerHandler.updatedUser(SharingRegistryServerHandler.java:180)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3992)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3976)
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
> at
> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result$updatedUser_resultStandardScheme.read(SharingRegistryService.java:15260)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result$updatedUser_resultStandardScheme.read(SharingRegistryService.java:15238)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result.read(SharingRegistryService.java:15182)
> at
> org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:89)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Client.recv_updatedUser(SharingRegistryService.java:757)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Client.updatedUser(SharingRegistryService.java:744)
> at
> org.apache.airavata.sharing.registry.messaging.SharingServiceDBEventHandler.onMessage(SharingServiceDBEventHandler.java:104)
> at
> org.apache.airavata.messaging.core.impl.MessageConsumer.handleDelivery(MessageConsumer.java:70)
> at
> com.rabbitmq.client.impl.ConsumerDispatcher$5.run(ConsumerDispatcher.java:144)
> at
> com.rabbitmq.client.impl.ConsumerWorkService$WorkPoolRunnable.run(ConsumerWorkService.java:99)
> at
>
[jira] [Resolved] (AIRAVATA-2461) In SciGaP portal users should not have compute resource, storage resource and crendetial store configuration enabled
[ https://issues.apache.org/jira/browse/AIRAVATA-2461?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2461. --- Resolution: Fixed > In SciGaP portal users should not have compute resource, storage resource and > crendetial store configuration enabled > - > > Key: AIRAVATA-2461 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2461 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.scigap.org/ >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.19 > > > For general public SciGaP portal is to request gateways. These UIs are not > meaningful and they could confuse users. User profile can exist. > Its ok to leave those options for SciGaP admins, But they will not be used or > tested in release 0.18 -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2489) When special characters are used in experiment name, the experiment browse is empty!
[ https://issues.apache.org/jira/browse/AIRAVATA-2489?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2489. --- Resolution: Fixed > When special characters are used in experiment name, the experiment browse is > empty! > > > Key: AIRAVATA-2489 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2489 > Project: Airavata > Issue Type: Bug > Components: Airavata System, PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: reported by https://sciencegateway.usd.edu/ >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2460) Hide Identity server configuration in gateway management
[ https://issues.apache.org/jira/browse/AIRAVATA-2460?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2460. --- Resolution: Fixed > Hide Identity server configuration in gateway management > - > > Key: AIRAVATA-2460 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2460 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.seagrid.org/ >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.19 > > > This UI is not used at gateway level. Currently we add this for each gateway > using SciGaP portal, but it involves manual intervention at database level. > The current function need to be extended to make all automatic using SciGaP > portal. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2443) In a gateway should not have gateway-provider role or non active roles
[ https://issues.apache.org/jira/browse/AIRAVATA-2443?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2443. --- Resolution: Fixed > In a gateway should not have gateway-provider role or non active roles > -- > > Key: AIRAVATA-2443 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2443 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: http://149.165.156.11/ >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > > In Admin Dashboard --> Users > 1. Users can be assigned gateway provider role. This role is specifically for > SciGaP portal, not for generic gateways. > 2. When gateway provider role is given, user is presented with gateway > request UI when logged in > 3. Currently in the gateway there are roles that are not meaningful to > gateway admins such as, ofline_access and uma_authorization. > 4. These need to be blocked in the gateway UI -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-1902) PGA Project should have restrictions when naming. Project name is used to create the directories in storage.
[
https://issues.apache.org/jira/browse/AIRAVATA-1902?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16109095#comment-16109095
]
Marcus Christie commented on AIRAVATA-1902:
---
I'm deploying a fix to dev scigap environment now.
I tested with the following as a project id/name/description to test escaping
HTML and handling single and double quotes:
{noformat}
!@#$%^&*()"'_+=-0987654321test
{noformat}
> PGA Project should have restrictions when naming. Project name is used to
> create the directories in storage.
>
>
> Key: AIRAVATA-1902
> URL: https://issues.apache.org/jira/browse/AIRAVATA-1902
> Project: Airavata
> Issue Type: Bug
> Components: PGA PHP Web Gateway
>Affects Versions: 0.16
> Environment: dev.seagrid.org
>Reporter: Eroma
>Assignee: Marcus Christie
> Fix For: 0.18
>
> Attachments: Screen Shot 2016-10-24 at 10.35.44 AM.png, Screen Shot
> 2.png
>
>
> Currently can provide any character when creating the project in PGA. With
> storage, a directory is creating under each gateway users name using the
> project name and all experiments under the specific project will be grouped
> in to the project directory in storage.
> Since name can't contain special characters when creating the directory in
> server; project names are automatically altered
> E.g.: Project name in PGA: 03/14/2016 is converted to 03_14_2016 in storage.
> This way users will not be able to search for their projects in storage.
--
This message was sent by Atlassian JIRA
(v6.4.14#64029)
[jira] [Created] (AIRAVATA-2507) Increase Keycloak access token lifetime from default of 5 minutes
Marcus Christie created AIRAVATA-2507: - Summary: Increase Keycloak access token lifetime from default of 5 minutes Key: AIRAVATA-2507 URL: https://issues.apache.org/jira/browse/AIRAVATA-2507 Project: Airavata Issue Type: Bug Components: PGA PHP Web Gateway Affects Versions: 0.18 Reporter: Marcus Christie Assignee: Marcus Christie Default Keycloak Access token lifetime is 5 minutes. This means if the user is idle in the PGA for 5 minutes or more then they get logged out and can't successful submit their work. In some cases this means the user loses work. Here is [documentation on various timeouts in Keycloak|http://www.keycloak.org/docs/2.5/server_admin/topics/sessions/timeouts.html]. I think two are relevant here: * Access Token Lifespan - this is the main one that affects access token lifetime. I think we should make this 30 minutes (at least). * SSO Session Idle - this timeout also affects access token lifetime. It defaults to 30 minutes. It resets whenever there is an authentication or the use of a refresh token. Thus, Keycloak recommends that the Access Token Lifespan be less than the SSO Session Idle. I think we should make SSO Session Idle to 1 hour. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2507) Increase Keycloak access token lifetime from default of 5 minutes
[ https://issues.apache.org/jira/browse/AIRAVATA-2507?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16118812#comment-16118812 ] Marcus Christie commented on AIRAVATA-2507: --- Created branch AIRAVATA\-2507 off of master, and I've merged it into develop for testing. Still needs testing. I think I'll test this one once I fix setting the admin password when creating the Keycloak tenant. > Increase Keycloak access token lifetime from default of 5 minutes > - > > Key: AIRAVATA-2507 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2507 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.18 >Reporter: Marcus Christie >Assignee: Marcus Christie > > Default Keycloak Access token lifetime is 5 minutes. This means if the user > is idle in the PGA for 5 minutes or more then they get logged out and can't > successful submit their work. In some cases this means the user loses work. > Here is [documentation on various timeouts in > Keycloak|http://www.keycloak.org/docs/2.5/server_admin/topics/sessions/timeouts.html]. > I think two are relevant here: > * Access Token Lifespan - this is the main one that affects access token > lifetime. I think we should make this 30 minutes (at least). > * SSO Session Idle - this timeout also affects access token lifetime. It > defaults to 30 minutes. It resets whenever there is an authentication or the > use of a refresh token. Thus, Keycloak recommends that the Access Token > Lifespan be less than the SSO Session Idle. I think we should make SSO > Session Idle to 1 hour. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2506) Sharing Registry: Error updating user when changed
[
https://issues.apache.org/jira/browse/AIRAVATA-2506?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16118855#comment-16118855
]
Marcus Christie commented on AIRAVATA-2506:
---
I tested this but it didn't work. I think it is because these two lines should
be reversed:
{code}
83 //AIRAVATA-2506: Sharing Service treats
airavataInternalUserId as the userId. AiravataAPIServerHandler
84 //also treats airavataInternalUserId as the userId
when creating entities, entityTypes using the sharing
85 //service.
86
userProfile.setUserId(userProfile.getAiravataInternalUserId());
87
ThriftUtils.createThriftFromBytes(dBEventMessageContext.getPublisher().getPublisherContext().getEntityDataModel(),
userProfile);
{code}
I'll make the change and test.
> Sharing Registry: Error updating user when changed
> --
>
> Key: AIRAVATA-2506
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2506
> Project: Airavata
> Issue Type: Improvement
> Components: Airavata System
>Reporter: Marcus Christie
>Assignee: Supun Chathuranga Nakandala
> Fix For: 0.19
>
>
> Exception:
> {noformat}
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - New DB Event message to sharing
> service.
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - DB Event message to sharing
> service from user.profile
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - User profile specific DB Event
> communicated by user.profile
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - Updating user. User Id :
> eabey...@iu.edu
> 2017-08-04 20:35:41,874 [pool-15-thread-1] ERROR
> o.a.a.s.r.s.SharingRegistryServerHandler - null
> java.lang.NullPointerException: null
> at
> org.apache.airavata.sharing.registry.server.SharingRegistryServerHandler.updatedUser(SharingRegistryServerHandler.java:180)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3992)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3976)
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
> at
> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> 2017-08-04 20:35:41,874 [pool-18-thread-3] ERROR
> o.a.a.s.r.m.SharingServiceDBEventHandler - Error processing message.
> org.apache.airavata.sharing.registry.models.SharingRegistryException: null
> Stack trace:java.lang.NullPointerException
> at
> org.apache.airavata.sharing.registry.server.SharingRegistryServerHandler.updatedUser(SharingRegistryServerHandler.java:180)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3992)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3976)
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
> at
> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result$updatedUser_resultStandardScheme.read(SharingRegistryService.java:15260)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result$updatedUser_resultStandardScheme.read(SharingRegistryService.java:15238)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result.read(SharingRegistryService.java:15182)
> at
> org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:89)
> at
>
[jira] [Assigned] (AIRAVATA-2506) Sharing Registry: Error updating user when changed
[
https://issues.apache.org/jira/browse/AIRAVATA-2506?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Marcus Christie reassigned AIRAVATA-2506:
-
Assignee: Marcus Christie (was: Supun Chathuranga Nakandala)
> Sharing Registry: Error updating user when changed
> --
>
> Key: AIRAVATA-2506
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2506
> Project: Airavata
> Issue Type: Improvement
> Components: Airavata System
>Reporter: Marcus Christie
>Assignee: Marcus Christie
> Fix For: 0.19
>
>
> Exception:
> {noformat}
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - New DB Event message to sharing
> service.
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - DB Event message to sharing
> service from user.profile
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - User profile specific DB Event
> communicated by user.profile
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - Updating user. User Id :
> eabey...@iu.edu
> 2017-08-04 20:35:41,874 [pool-15-thread-1] ERROR
> o.a.a.s.r.s.SharingRegistryServerHandler - null
> java.lang.NullPointerException: null
> at
> org.apache.airavata.sharing.registry.server.SharingRegistryServerHandler.updatedUser(SharingRegistryServerHandler.java:180)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3992)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3976)
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
> at
> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> 2017-08-04 20:35:41,874 [pool-18-thread-3] ERROR
> o.a.a.s.r.m.SharingServiceDBEventHandler - Error processing message.
> org.apache.airavata.sharing.registry.models.SharingRegistryException: null
> Stack trace:java.lang.NullPointerException
> at
> org.apache.airavata.sharing.registry.server.SharingRegistryServerHandler.updatedUser(SharingRegistryServerHandler.java:180)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3992)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3976)
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
> at
> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result$updatedUser_resultStandardScheme.read(SharingRegistryService.java:15260)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result$updatedUser_resultStandardScheme.read(SharingRegistryService.java:15238)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result.read(SharingRegistryService.java:15182)
> at
> org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:89)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Client.recv_updatedUser(SharingRegistryService.java:757)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Client.updatedUser(SharingRegistryService.java:744)
> at
> org.apache.airavata.sharing.registry.messaging.SharingServiceDBEventHandler.onMessage(SharingServiceDBEventHandler.java:104)
> at
> org.apache.airavata.messaging.core.impl.MessageConsumer.handleDelivery(MessageConsumer.java:70)
> at
> com.rabbitmq.client.impl.ConsumerDispatcher$5.run(ConsumerDispatcher.java:144)
> at
> com.rabbitmq.client.impl.ConsumerWorkService$WorkPoolRunnable.run(ConsumerWorkService.java:99)
> at
>
[jira] [Created] (AIRAVATA-2508) Set admin password when creating Keycloak tenant
Marcus Christie created AIRAVATA-2508: - Summary: Set admin password when creating Keycloak tenant Key: AIRAVATA-2508 URL: https://issues.apache.org/jira/browse/AIRAVATA-2508 Project: Airavata Issue Type: Bug Affects Versions: 0.18 Reporter: Marcus Christie Assignee: Marcus Christie Relates to AIRAVATA-2491. Also should test AIRAVATA-2507 when testing this one. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Assigned] (AIRAVATA-2506) Sharing Registry: Error updating user when changed
[
https://issues.apache.org/jira/browse/AIRAVATA-2506?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Marcus Christie reassigned AIRAVATA-2506:
-
Assignee: Supun Chathuranga Nakandala (was: Marcus Christie)
> Sharing Registry: Error updating user when changed
> --
>
> Key: AIRAVATA-2506
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2506
> Project: Airavata
> Issue Type: Improvement
> Components: Airavata System
>Reporter: Marcus Christie
>Assignee: Supun Chathuranga Nakandala
> Fix For: 0.19
>
>
> Exception:
> {noformat}
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - New DB Event message to sharing
> service.
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - DB Event message to sharing
> service from user.profile
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - User profile specific DB Event
> communicated by user.profile
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - Updating user. User Id :
> eabey...@iu.edu
> 2017-08-04 20:35:41,874 [pool-15-thread-1] ERROR
> o.a.a.s.r.s.SharingRegistryServerHandler - null
> java.lang.NullPointerException: null
> at
> org.apache.airavata.sharing.registry.server.SharingRegistryServerHandler.updatedUser(SharingRegistryServerHandler.java:180)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3992)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3976)
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
> at
> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> 2017-08-04 20:35:41,874 [pool-18-thread-3] ERROR
> o.a.a.s.r.m.SharingServiceDBEventHandler - Error processing message.
> org.apache.airavata.sharing.registry.models.SharingRegistryException: null
> Stack trace:java.lang.NullPointerException
> at
> org.apache.airavata.sharing.registry.server.SharingRegistryServerHandler.updatedUser(SharingRegistryServerHandler.java:180)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3992)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3976)
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
> at
> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result$updatedUser_resultStandardScheme.read(SharingRegistryService.java:15260)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result$updatedUser_resultStandardScheme.read(SharingRegistryService.java:15238)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result.read(SharingRegistryService.java:15182)
> at
> org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:89)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Client.recv_updatedUser(SharingRegistryService.java:757)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Client.updatedUser(SharingRegistryService.java:744)
> at
> org.apache.airavata.sharing.registry.messaging.SharingServiceDBEventHandler.onMessage(SharingServiceDBEventHandler.java:104)
> at
> org.apache.airavata.messaging.core.impl.MessageConsumer.handleDelivery(MessageConsumer.java:70)
> at
> com.rabbitmq.client.impl.ConsumerDispatcher$5.run(ConsumerDispatcher.java:144)
> at
> com.rabbitmq.client.impl.ConsumerWorkService$WorkPoolRunnable.run(ConsumerWorkService.java:99)
>
[jira] [Resolved] (AIRAVATA-2504) When tried to logout from email verification getting an error
[
https://issues.apache.org/jira/browse/AIRAVATA-2504?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Marcus Christie resolved AIRAVATA-2504.
---
Resolution: Fixed
[~eroma_a],
The problem was that the Keycloak 'pga' client for realm 'new-mexico-state'
wasn't configured with the correct redirect URIs.
It was configured with these redirect URIs:
* https://cia.nmsu.edu
* https://cia.nmsu.edu/callback-url
I added the following, correct redirect URIs:
* https://sciencegateway.nmsu.edu
* https://sciencegateway.nmsu.edu/callback-url
What happened is {{https://cia.nmsu.edu}} was probably entered into the gateway
request. The Keycloak realm creation code will automatically populate the
redirect URIs from this value. However, when it was actually deployed it had a
different domain {{https://sciencegateway.nmsu.edu}}.
*Whenever the domain of a gateway is different from what was provided in the
gateway request at tenant creation time, we'll have to go into Keycloak and fix
the redirect URIs.*
> When tried to logout from email verification getting an error
> -
>
> Key: AIRAVATA-2504
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2504
> Project: Airavata
> Issue Type: Bug
> Components: Keycloak Authentication, PGA PHP Web Gateway
>Affects Versions: 0.18
> Environment: sciencegateway.nmsu.edu
>Reporter: Eroma
>Assignee: Marcus Christie
> Fix For: 0.18
>
>
> 1. Created a new account in sciencegateway.nmsu.edu gateway
> 2. When the email verification email was received clicked the link and logged
> in to the gateway verify
> 3. Got the message that says "Your New Mexico State Science Gateway account
> is pending approval. You will be notified via email upo"
> 4. Clicked logout and getting error screen with message
> WE'RE SORRY ...
> Invalid redirect uri
> 5. URL of the error screen:
> https://iam.scigap.org/auth/realms/new-mexico-state/protocol/openid-connect/logout?redirect_uri=https%3A%2F%2Fsciencegateway.nmsu.edu
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[jira] [Commented] (AIRAVATA-2506) Sharing Registry: Error updating user when changed
[
https://issues.apache.org/jira/browse/AIRAVATA-2506?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16116934#comment-16116934
]
Marcus Christie commented on AIRAVATA-2506:
---
I've took a look at the code. Looks like it is trying to look up an existing
SHARING_USER record. The primary key would be a composite key of
(user_id=eabey...@iu.edu, domain_id=...) (I'm not sure what gateway this is
for. However, on dbdev.scigap.org all of the USER_IDs in SHARING_USER have the
form {{username@domain}}, which could explain why the existing record can't be
found.
I'm not sure why USER_ID would be in the form of {{username@domain}} since the
primary key of SHARING_USER is (user_id, domain_id).
I'll ask [~scnakandala] if he has any insight.
> Sharing Registry: Error updating user when changed
> --
>
> Key: AIRAVATA-2506
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2506
> Project: Airavata
> Issue Type: Improvement
> Components: Airavata System
>Reporter: Marcus Christie
>Assignee: Marcus Christie
> Fix For: 0.19
>
>
> Exception:
> {noformat}
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - New DB Event message to sharing
> service.
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - DB Event message to sharing
> service from user.profile
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - User profile specific DB Event
> communicated by user.profile
> 2017-08-04 20:35:41,869 [pool-18-thread-3] INFO
> o.a.a.s.r.m.SharingServiceDBEventHandler - Updating user. User Id :
> eabey...@iu.edu
> 2017-08-04 20:35:41,874 [pool-15-thread-1] ERROR
> o.a.a.s.r.s.SharingRegistryServerHandler - null
> java.lang.NullPointerException: null
> at
> org.apache.airavata.sharing.registry.server.SharingRegistryServerHandler.updatedUser(SharingRegistryServerHandler.java:180)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3992)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3976)
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
> at
> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> 2017-08-04 20:35:41,874 [pool-18-thread-3] ERROR
> o.a.a.s.r.m.SharingServiceDBEventHandler - Error processing message.
> org.apache.airavata.sharing.registry.models.SharingRegistryException: null
> Stack trace:java.lang.NullPointerException
> at
> org.apache.airavata.sharing.registry.server.SharingRegistryServerHandler.updatedUser(SharingRegistryServerHandler.java:180)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3992)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Processor$updatedUser.getResult(SharingRegistryService.java:3976)
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
> at
> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result$updatedUser_resultStandardScheme.read(SharingRegistryService.java:15260)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result$updatedUser_resultStandardScheme.read(SharingRegistryService.java:15238)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$updatedUser_result.read(SharingRegistryService.java:15182)
> at
> org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:89)
> at
> org.apache.airavata.sharing.registry.service.cpi.SharingRegistryService$Client.recv_updatedUser(SharingRegistryService.java:757)
> at
>
[jira] [Commented] (AIRAVATA-2382) Ansible: parameterize max upload size in .htaccess in PGA role
[ https://issues.apache.org/jira/browse/AIRAVATA-2382?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16116942#comment-16116942 ] Marcus Christie commented on AIRAVATA-2382: --- This is also needed by SIU. > Ansible: parameterize max upload size in .htaccess in PGA role > -- > > Key: AIRAVATA-2382 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2382 > Project: Airavata > Issue Type: Bug >Reporter: Marcus Christie >Assignee: Marcus Christie > Fix For: 0.18 > > -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2441) Can we structure PGA theme to have a separate landing page and light branding in the app?
[ https://issues.apache.org/jira/browse/AIRAVATA-2441?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16129413#comment-16129413 ] Marcus Christie commented on AIRAVATA-2441: --- I've done this now for https://sciencegateway.siu.edu/ > Can we structure PGA theme to have a separate landing page and light branding > in the app? > - > > Key: AIRAVATA-2441 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2441 > Project: Airavata > Issue Type: Improvement >Reporter: Marcus Christie >Assignee: Marcus Christie > > This is an idea offered by Levi McGranahan. The problem is that currently the > PGA theme affects every page of the PGA and sometimes the CSS that one wants > to include in the PGA theme collides with the CSS used in the PGA itself. > Levi suggested having a separate "landing page" (the home page) that could be > defined by the theme and would use the theme's CSS and but then once you log > into PGA there is only PGA CSS so no collision. Once logged into the PGA we > could display a brand image of a certain size in the header, and maybe other > light branding elements but PGA would have control of the layout. > The thinking is that this aligns much better with how organizations are > already ready to brand web applications. They already have templates for > landing pages with their own CSS. So making a landing page should be easy > (this is true of the IU Cybergateway). What is much harder is getting an > organization's branding CSS to work well with PGA's CSS. > The scope of this issue is to first evaluate whether this is possible and how > much effort will be involved. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2441) Can we structure PGA theme to have a separate landing page and light branding in the app?
[ https://issues.apache.org/jira/browse/AIRAVATA-2441?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2441. --- Resolution: Fixed > Can we structure PGA theme to have a separate landing page and light branding > in the app? > - > > Key: AIRAVATA-2441 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2441 > Project: Airavata > Issue Type: Improvement >Reporter: Marcus Christie >Assignee: Marcus Christie > > This is an idea offered by Levi McGranahan. The problem is that currently the > PGA theme affects every page of the PGA and sometimes the CSS that one wants > to include in the PGA theme collides with the CSS used in the PGA itself. > Levi suggested having a separate "landing page" (the home page) that could be > defined by the theme and would use the theme's CSS and but then once you log > into PGA there is only PGA CSS so no collision. Once logged into the PGA we > could display a brand image of a certain size in the header, and maybe other > light branding elements but PGA would have control of the layout. > The thinking is that this aligns much better with how organizations are > already ready to brand web applications. They already have templates for > landing pages with their own CSS. So making a landing page should be easy > (this is true of the IU Cybergateway). What is much harder is getting an > organization's branding CSS to work well with PGA's CSS. > The scope of this issue is to first evaluate whether this is possible and how > much effort will be involved. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2505) Update Airavata to Thrift 0.10.0
[ https://issues.apache.org/jira/browse/AIRAVATA-2505?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16129417#comment-16129417 ] Marcus Christie commented on AIRAVATA-2505: --- So far we haven't encountered any problems in the dev environment. I think I'll merge this to the develop branch on Monday. (I would merge it today but I'm out of the office the next two days and don't want to be away in case the Thrift upgrade breaks something). > Update Airavata to Thrift 0.10.0 > > > Key: AIRAVATA-2505 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2505 > Project: Airavata > Issue Type: Improvement >Reporter: Marcus Christie >Assignee: Marcus Christie > > We need Thrift 0.10.0 to generate Python 3 compatible stubs. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2441) Can we structure PGA theme to have a separate landing page and light branding in the app?
[ https://issues.apache.org/jira/browse/AIRAVATA-2441?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16129405#comment-16129405 ] Marcus Christie commented on AIRAVATA-2441: --- Updated notes on the base-pga-theme: https://github.com/SciGaP/base-pga-theme/commit/f22819bdbdf804a0ee58c38ff18b871caa69282e > Can we structure PGA theme to have a separate landing page and light branding > in the app? > - > > Key: AIRAVATA-2441 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2441 > Project: Airavata > Issue Type: Improvement >Reporter: Marcus Christie >Assignee: Marcus Christie > > This is an idea offered by Levi McGranahan. The problem is that currently the > PGA theme affects every page of the PGA and sometimes the CSS that one wants > to include in the PGA theme collides with the CSS used in the PGA itself. > Levi suggested having a separate "landing page" (the home page) that could be > defined by the theme and would use the theme's CSS and but then once you log > into PGA there is only PGA CSS so no collision. Once logged into the PGA we > could display a brand image of a certain size in the header, and maybe other > light branding elements but PGA would have control of the layout. > The thinking is that this aligns much better with how organizations are > already ready to brand web applications. They already have templates for > landing pages with their own CSS. So making a landing page should be easy > (this is true of the IU Cybergateway). What is much harder is getting an > organization's branding CSS to work well with PGA's CSS. > The scope of this issue is to first evaluate whether this is possible and how > much effort will be involved. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Created] (AIRAVATA-2381) Ansible: parameterize setting debug flag in PGA role
Marcus Christie created AIRAVATA-2381: - Summary: Ansible: parameterize setting debug flag in PGA role Key: AIRAVATA-2381 URL: https://issues.apache.org/jira/browse/AIRAVATA-2381 Project: Airavata Issue Type: Bug Components: PGA PHP Web Gateway Reporter: Marcus Christie Assignee: Marcus Christie -- This message was sent by Atlassian JIRA (v6.3.15#6346)
[jira] [Created] (AIRAVATA-2382) Ansible: parameterize max upload size in .htaccess in PGA role
Marcus Christie created AIRAVATA-2382: - Summary: Ansible: parameterize max upload size in .htaccess in PGA role Key: AIRAVATA-2382 URL: https://issues.apache.org/jira/browse/AIRAVATA-2382 Project: Airavata Issue Type: Bug Reporter: Marcus Christie Assignee: Marcus Christie -- This message was sent by Atlassian JIRA (v6.3.15#6346)
[jira] [Assigned] (AIRAVATA-2324) Increase the length of gateway acronym in SciGaP gateway request
[ https://issues.apache.org/jira/browse/AIRAVATA-2324?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie reassigned AIRAVATA-2324: - Assignee: Marcus Christie (was: Anuj Bhandar) > Increase the length of gateway acronym in SciGaP gateway request > > > Key: AIRAVATA-2324 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2324 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.scigap.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > -- This message was sent by Atlassian JIRA (v6.3.15#6346)
[jira] [Resolved] (AIRAVATA-2324) Increase the length of gateway acronym in SciGaP gateway request
[ https://issues.apache.org/jira/browse/AIRAVATA-2324?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2324. --- Resolution: Fixed > Increase the length of gateway acronym in SciGaP gateway request > > > Key: AIRAVATA-2324 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2324 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://dev.scigap.org >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.18 > > -- This message was sent by Atlassian JIRA (v6.3.15#6346)
[jira] [Resolved] (AIRAVATA-2383) LSF walltime calculation
[
https://issues.apache.org/jira/browse/AIRAVATA-2383?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Marcus Christie resolved AIRAVATA-2383.
---
Resolution: Fixed
> LSF walltime calculation
>
>
> Key: AIRAVATA-2383
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2383
> Project: Airavata
> Issue Type: Bug
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>
> LSF script walltime format is wrong. Here's an example script created:
> {noformat}
> #!/bin/bash
> # LSF batch job submission script generated by Apache Airavata
> #BSUB -L /bin/bash
> #BSUB -q short
> #BSUB -n 1
> #BSUB -J A1460597667
> #BSUB -u gw56j...@scigap.org
> #BSUB -W 00:30:00
> #BSUB -o
> /scratch/scigap0/PROCESS_01a85937-e308-498e-b14a-e0529135f046/Quantum_Espresso.stdout
> #BSUB -e
> /scratch/scigap0/PROCESS_01a85937-e308-498e-b14a-e0529135f046/Quantum_Espresso.stderr
> module load icc/13.0.1 openmpi/1.6.5 espresso/5.3.0
> cd /scratch/scigap0/PROCESS_01a85937-e308-498e-b14a-e0529135f046
> mpirun -np /opt/apps/icc-13.0.1/openmpi-1.6.5/espresso/5.3.0/bin/pw.x <
> Al.sample.in > Al.sample.out
> {noformat}
> Walltime is the {{#BSUB -W 00:30:00}} parameter. It should be {{#BSUB -W
> 00:30}} because walltime in LSF is HH:MM.
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[jira] [Created] (AIRAVATA-2383) LSF walltime calculation
Marcus Christie created AIRAVATA-2383:
-
Summary: LSF walltime calculation
Key: AIRAVATA-2383
URL: https://issues.apache.org/jira/browse/AIRAVATA-2383
Project: Airavata
Issue Type: Bug
Reporter: Marcus Christie
Assignee: Marcus Christie
LSF script walltime format is wrong. Here's an example script created:
{noformat}
#!/bin/bash
# LSF batch job submission script generated by Apache Airavata
#BSUB -L /bin/bash
#BSUB -q short
#BSUB -n 1
#BSUB -J A1460597667
#BSUB -u gw56j...@scigap.org
#BSUB -W 00:30:00
#BSUB -o
/scratch/scigap0/PROCESS_01a85937-e308-498e-b14a-e0529135f046/Quantum_Espresso.stdout
#BSUB -e
/scratch/scigap0/PROCESS_01a85937-e308-498e-b14a-e0529135f046/Quantum_Espresso.stderr
module load icc/13.0.1 openmpi/1.6.5 espresso/5.3.0
cd /scratch/scigap0/PROCESS_01a85937-e308-498e-b14a-e0529135f046
mpirun -np /opt/apps/icc-13.0.1/openmpi-1.6.5/espresso/5.3.0/bin/pw.x <
Al.sample.in > Al.sample.out
{noformat}
Walltime is the {{#BSUB -W 00:30:00}} parameter. It should be {{#BSUB -W
00:30}} because walltime in LSF is HH:MM.
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[jira] [Commented] (AIRAVATA-2383) LSF walltime calculation
[
https://issues.apache.org/jira/browse/AIRAVATA-2383?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16008679#comment-16008679
]
Marcus Christie commented on AIRAVATA-2383:
---
Commits for this issue:
*
https://github.com/apache/airavata/commit/31a67053d4f83fc9ff10e3d64c12f6da63ffd1aa
*
https://github.com/apache/airavata/commit/9ef08205c1f030b9252177c2076b310a16f1764c
* https://github.com/apache/airavata/commit/7b48f1514
> LSF walltime calculation
>
>
> Key: AIRAVATA-2383
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2383
> Project: Airavata
> Issue Type: Bug
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>
> LSF script walltime format is wrong. Here's an example script created:
> {noformat}
> #!/bin/bash
> # LSF batch job submission script generated by Apache Airavata
> #BSUB -L /bin/bash
> #BSUB -q short
> #BSUB -n 1
> #BSUB -J A1460597667
> #BSUB -u gw56j...@scigap.org
> #BSUB -W 00:30:00
> #BSUB -o
> /scratch/scigap0/PROCESS_01a85937-e308-498e-b14a-e0529135f046/Quantum_Espresso.stdout
> #BSUB -e
> /scratch/scigap0/PROCESS_01a85937-e308-498e-b14a-e0529135f046/Quantum_Espresso.stderr
> module load icc/13.0.1 openmpi/1.6.5 espresso/5.3.0
> cd /scratch/scigap0/PROCESS_01a85937-e308-498e-b14a-e0529135f046
> mpirun -np /opt/apps/icc-13.0.1/openmpi-1.6.5/espresso/5.3.0/bin/pw.x <
> Al.sample.in > Al.sample.out
> {noformat}
> Walltime is the {{#BSUB -W 00:30:00}} parameter. It should be {{#BSUB -W
> 00:30}} because walltime in LSF is HH:MM.
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[jira] [Resolved] (AIRAVATA-2371) Deploy Keycloak integration testing environment on Jetstream
[ https://issues.apache.org/jira/browse/AIRAVATA-2371?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2371. --- Resolution: Fixed > Deploy Keycloak integration testing environment on Jetstream > > > Key: AIRAVATA-2371 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2371 > Project: Airavata > Issue Type: Bug >Reporter: Marcus Christie >Assignee: Marcus Christie > Fix For: 0.18 > > -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2432) Use Docker image for running Thrift to generate stub files
[ https://issues.apache.org/jira/browse/AIRAVATA-2432?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2432. --- Resolution: Fixed > Use Docker image for running Thrift to generate stub files > -- > > Key: AIRAVATA-2432 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2432 > Project: Airavata > Issue Type: Bug >Reporter: Marcus Christie >Assignee: Marcus Christie > > Integrate Docker images into running Thrift for stub generation. The purpose > of this is to make it easier for developers to use Thrift without needing to > install Thrift, which can be fairly tricky. > I've tested this locally using the Dockerfile that comes with Apache Thrift's > 0.10.0 release. However, it might be better to use the official Thrift Docker > images instead: https://hub.docker.com/_/thrift/. That way one doesn't have > to build the images and can just download them from Docker Hub. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Updated] (AIRAVATA-2434) Keycloak: what happens if you log in through CILogon but then update your email address?
[ https://issues.apache.org/jira/browse/AIRAVATA-2434?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie updated AIRAVATA-2434: -- Fix Version/s: 0.18 > Keycloak: what happens if you log in through CILogon but then update your > email address? > > > Key: AIRAVATA-2434 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2434 > Project: Airavata > Issue Type: Task >Reporter: Marcus Christie >Assignee: Marcus Christie > Fix For: 0.18 > > > Once the CILogon integration is available for testing I want to test this > scenario > * log in through CILogon > * On the user profile editor edit the user email (this will update the email > in Keycloak as well) > * log out and try to log back in > My main question is: is Keycloak able to log the same user back in even > though that user changed their email address? Or does an additional Keycloak > account get created? > If Keycloak gets confused when the email address changes in Keycloak we may > need some way to prevent editing the email address for users that > authenticate through Keycloak. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Created] (AIRAVATA-2434) Keycloak: what happens if you log in through CILogon but then update your email address?
Marcus Christie created AIRAVATA-2434: - Summary: Keycloak: what happens if you log in through CILogon but then update your email address? Key: AIRAVATA-2434 URL: https://issues.apache.org/jira/browse/AIRAVATA-2434 Project: Airavata Issue Type: Task Reporter: Marcus Christie Assignee: Marcus Christie Once the CILogon integration is available for testing I want to test this scenario * log in through CILogon * On the user profile editor edit the user email (this will update the email in Keycloak as well) * log out and try to log back in My main question is: is Keycloak able to log the same user back in even though that user changed their email address? Or does an additional Keycloak account get created? If Keycloak gets confused when the email address changes in Keycloak we may need some way to prevent editing the email address for users that authenticate through Keycloak. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Created] (AIRAVATA-2450) Keycloak: restrictions on what is allowed for realm ids?
Marcus Christie created AIRAVATA-2450: - Summary: Keycloak: restrictions on what is allowed for realm ids? Key: AIRAVATA-2450 URL: https://issues.apache.org/jira/browse/AIRAVATA-2450 Project: Airavata Issue Type: Bug Reporter: Marcus Christie Assignee: Marcus Christie -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2450) Keycloak: restrictions on what is allowed for realm ids?
[ https://issues.apache.org/jira/browse/AIRAVATA-2450?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2450. --- Resolution: Fixed > Keycloak: restrictions on what is allowed for realm ids? > > > Key: AIRAVATA-2450 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2450 > Project: Airavata > Issue Type: Bug >Reporter: Marcus Christie >Assignee: Marcus Christie > -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2450) Keycloak: restrictions on what is allowed for realm ids?
[
https://issues.apache.org/jira/browse/AIRAVATA-2450?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16061423#comment-16061423
]
Marcus Christie commented on AIRAVATA-2450:
---
Code I used to test:
{code}
FileInputStream fis = null;
KeyStore ks = null;
try {
fis = new
java.io.FileInputStream("/Users/machrist/Airavata/airavata/modules/configuration/server/src/main/resources/client_truststore.jks");
ks = KeyStore.getInstance(KeyStore.getDefaultType());
ks.load(fis, "airavata".toCharArray());
} catch (Exception e) {
throw new RuntimeException("Failed to load trust store KeyStore
instance", e);
} finally {
if (fis != null) {
try {
fis.close();
} catch (IOException e) {
logger.error("Failed to close trust store FileInputStream",
e);
}
}
}
String adminUrl = "https://iamdev.scigap.org/auth;;
String realm = "master";
String username = "";
String password = "";
ResteasyClient resteasyClient = new ResteasyClientBuilder()
.connectionPoolSize(10)
.trustStore(ks)
.build();
Keycloak client = KeycloakBuilder.builder()
.serverUrl(adminUrl)
.realm(realm)
.username(username)
.password(password)
.clientId("admin-cli")
.resteasyClient(resteasyClient)
.build();
// create realm
RealmRepresentation newRealmDetails = new RealmRepresentation();
newRealmDetails.setEnabled(true);
newRealmDetails.setId("abc-123");
newRealmDetails.setDisplayName("ABC 123");
newRealmDetails.setRealm("abc-123");
// Following two settings allow duplicate email addresses
newRealmDetails.setLoginWithEmailAllowed(false);
newRealmDetails.setDuplicateEmailsAllowed(true);
client.realms().create(newRealmDetails);
List realms = client.realms().findAll();
for (RealmRepresentation realmRepresentation : realms) {
System.out.println("Realm: " + realmRepresentation.getId() + ",
name=" + realmRepresentation.getRealm() + ", description=" +
realmRepresentation.getDisplayName());
}
{code}
> Keycloak: restrictions on what is allowed for realm ids?
>
>
> Key: AIRAVATA-2450
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2450
> Project: Airavata
> Issue Type: Bug
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>
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[jira] [Commented] (AIRAVATA-2450) Keycloak: restrictions on what is allowed for realm ids?
[
https://issues.apache.org/jira/browse/AIRAVATA-2450?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16061422#comment-16061422
]
Marcus Christie commented on AIRAVATA-2450:
---
Looks like Keycloak doesn't allow creating two realm ids that differ only by
case. I tried creating one through the API with id "abc-123" and "ABC-123". I
couldn't create the second one and got a {{HTTP 409 Conflict}} error.
I think we should just lowercase whatever we use for realm ids, and change any
spaces or special characters to hyphens, just to keep it simple.
> Keycloak: restrictions on what is allowed for realm ids?
>
>
> Key: AIRAVATA-2450
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2450
> Project: Airavata
> Issue Type: Bug
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>
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[jira] [Resolved] (AIRAVATA-2415) Keycloak: allow gateway admin account to log into portal
[ https://issues.apache.org/jira/browse/AIRAVATA-2415?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2415. --- Resolution: Fixed > Keycloak: allow gateway admin account to log into portal > > > Key: AIRAVATA-2415 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2415 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway, Security >Reporter: Marcus Christie >Assignee: Marcus Christie > Fix For: 0.18 > > > The Keycloak username and password given at gateway request creation cannot > be used to login to the Gateway by the admin. This is only for PGA and > Keycloak communication. Need to implement using this account for gateway > login as well. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2406) Review user migration
[ https://issues.apache.org/jira/browse/AIRAVATA-2406?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2406. --- Resolution: Fixed > Review user migration > - > > Key: AIRAVATA-2406 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2406 > Project: Airavata > Issue Type: Bug > Components: Security >Reporter: Marcus Christie >Assignee: Marcus Christie > Fix For: 0.18 > > > With Anuj's help we were able to migrate production seagrid from IS to 1) > Keycloak and 2) user profile service. This task is to review the migrated > data and document what work is still needed. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Resolved] (AIRAVATA-2440) With keycloak, my username is changed, results a new data directory creation
[ https://issues.apache.org/jira/browse/AIRAVATA-2440?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2440. --- Resolution: Fixed > With keycloak, my username is changed, results a new data directory creation > > > Key: AIRAVATA-2440 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2440 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: http://149.165.156.11/ >Reporter: Eroma >Assignee: Marcus Christie > Fix For: 0.17 > > > When login to PGA i gave ProdEroma2017 as the username. But once i am logged > in to the gateway, my username is displayed as proderoma2017. > In storage, now i have tow directories, ProdEroma2017 and proderoma2017. > When i clicked, 'Storage' from the main gateway menu, its empty. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (AIRAVATA-2405) Keycloak: search for users with a given role
[ https://issues.apache.org/jira/browse/AIRAVATA-2405?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16063185#comment-16063185 ] Marcus Christie commented on AIRAVATA-2405: --- Looks like there is an open issue to search for users with a particular role: https://issues.jboss.org/browse/KEYCLOAK-1902 I think the only way to implement this now is to get all of the users and iterate over them and filter them in code. > Keycloak: search for users with a given role > > > Key: AIRAVATA-2405 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2405 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Reporter: Marcus Christie >Assignee: Marcus Christie > Fix For: 0.18 > > > In PGA, admins can search for users that have a selected role. > It would be good to implement this in IamAdminServices in the backend and > then call that from PGA. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
