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MNDeployment #3234

CyVerse (iPlant) member node

Added by Dave Vieglais almost 10 years ago. Updated over 3 years ago.

Status:
Testing
Priority:
Normal
Assignee:
Target version:
Start date:
2013-01-30
Due date:
% Done:

50%

Latitude:
32.22
Longitude:
-110.93
MN Description:
CyVerse provides life scientists with powerful computational infrastructure to handle huge datasets and complex analyses, thus enabling data-driven discovery. Our extensible platforms provide data storage, bioinformatics tools, image analyses, cloud services, APIs, and more.
Base URL:
NodeIdentifier:
urn:node:CYVERSE
MN Tier:
Tier 1
Software stack:
iRODS
MN_Date_Online:
Name:
CyVerse
Logo URL:
member-node-info/production/graphics/web/CYVERSE.png
Date Upcoming:
2018-07-05
Date Deprecated:
Information URL:
http://www.cyverse.org/
Version:
Sprint:

Description

The Botanical Information and ecology Network (BIEN) , which is a project of the iPlant Collaborative has been identified as a potential member node. This issue is to track progress on that goal. Note that BIEN is a postgres database, with iRODS used for a different part of the iPlant overall project.

An initial contact is Nirav Merchant, but also Mark Schildhauer who is coordinating BIEN development.

Need to determine the relationship between BIEN and the iRODS data system use at iPlant, and whether they would represent the same MN or two distinct MNs.

OTHER CONTACTS
* Shelley Littin littin@cyverse.org, Coordinator, Marketing & Communications
* Tina Lee tinal.cyverse@gmail.com, User Engagement Officer
* Ramona L. Walls rwalls@cyverse.org, Senior Scientific Analyst

Cyverse_logo.png - pulled from website (8.38 KB) Amy Forrester, 2018-07-02 18:53

cyverse_cmyk.png (72 KB) Amy Forrester, 2018-07-05 13:48

649
654

Subtasks

Task #3534: Contact Schildhauer and Merchant to plan trajectory for iPlant MNClosedMatthew Jones

Story #8564: (CyVerse) Testing & Development NewRob Nahf

Task #8565: Develop or Implement MN SoftwareClosedAmy Forrester

Task #8566: Test RegistrationIn ProgressRob Nahf

Task #8567: Display as UpcomingClosedDave Vieglais

Story #8568: (CyVerse) Move to productionNew

Task #8572: Cyverse - MN CommunicationsClosedAmy Forrester

Task #8643: (Cyverse) Implement in Production EnvironmentNew

Task #8644: (Cyverse) Register in ProductionNew

Task #8645: (Cyverse) Mutual acceptanceNewAmy Forrester

Task #8646: (cyverse) Formal AnnouncementNew


Related issues

Blocked by Infrastructure - Story #4073: iRODS MN Stack development Closed

History

#2 Updated by John Cobb over 9 years ago

  • translation missing: en.field_remaining_hours set to 0.0
  • Due date set to 2013-07-31
  • Target version set to Deploy by end of Y4Q4

#3 Updated by Matthew Jones over 9 years ago

  • Assignee set to Matthew Jones
  • Subject changed from Deploy an iPlant BIEN member node to iPlant BIEN member node

#4 Updated by Matthew Jones over 9 years ago

  • Description updated (diff)

#5 Updated by Matthew Jones over 9 years ago

  • Description updated (diff)

#6 Updated by Matthew Jones over 9 years ago

  • Due date changed from 2013-07-31 to 2014-01-31
  • Target version changed from Deploy by end of Y4Q4 to Deploy by end of Y5Q2

#7 Updated by John Cobb almost 9 years ago

BIEN iPlant software infrastructure is iRODs based. MN deployment needs a iRODS SW deployment as a pre-requisite. Y5Q2 target deployment me need to be revised in light of this requirement and DataONE CCIT work plans.

#8 Updated by Bruce Wilson almost 9 years ago

  • Subject changed from iPlant BIEN member node to iPlant member node

#9 Updated by Bruce Wilson almost 9 years ago

  • Description updated (diff)

#10 Updated by Laura Moyers over 8 years ago

  • Software stack set to iRODS

#11 Updated by Bruce Wilson over 8 years ago

  • Due date deleted (2014-01-31)
  • Target version deleted (Deploy by end of Y5Q2)
  • Start date deleted (2013-01-30)

Pulling out of Y5Q2, as this going depends on the work with iRODS being done by the DFC node (#3532)

#12 Updated by Laura Moyers about 6 years ago

  • Subject changed from iPlant member node to CyVerse (iPlant) member node

iPlant is now known as CyVerse but the website is still http://www.iplantcollaborative.org/

#14 Updated by Laura Moyers over 5 years ago

  • MN Tier set to Tier 1
  • NodeIdentifier set to urn:node:CYVERSE

Meeting 12/16/16: CyVerse wishes to proceed with a MN representing the content in the Data Commons Repository (DCR). This is a (currently) small repository of public content, with identifiers, based in iRODS. The intent is to piggy-back off of Lisa Stillwell's iRODS work toward the DFC MN. CyVerse does have the resources to develop/deploy an iRODS MN. They currently have an internal replication scheme, so initially don't anticipate replicating their content to other MNs.

Follow-up meeting 3rd/4th week of January.

#15 Updated by Laura Moyers over 5 years ago

  • Status changed from New to Planning
  • Target version set to Deploy by end of Y3Q2
  • % Done changed from 0 to 10

See meeting notes from 20 January 2017: https://epad.dataone.org/pad/p/CyVerse_and_DataONE

#16 Updated by Laura Moyers over 5 years ago

  • Target version changed from Deploy by end of Y3Q2 to Deploy by end of Y3Q3

#17 Updated by Laura Moyers about 5 years ago

  • Latitude set to 32.22
  • Longitude set to -110.93
  • Base URL set to http://www.cyverse.org/

#18 Updated by Laura Moyers almost 5 years ago

  • Target version changed from Deploy by end of Y3Q3 to Deploy by end of Y3Q4
  • Assignee changed from Matthew Jones to Mark Servilla

Administrative POCs: Nirav Merchant and Ramona Walls (rwalls@cyverse.org)
Technical POCs: Dennis at CyVerse, Mike Conway (michael_conway@unc.edu) with Lisa Stillwell (lisa@renci.org) as consultant (Lisa developed first iRODS implementation for DFC (the DataNet Federation Consortium)

Meeting notes in epad: https://epad.dataone.org/pad/p/CyVerse_and_DataONE

Last email from Ramona 23 August 2017:

I think might be good if we scheduled another call sometime soon. Dennis has done quite a bit of work on publishing to DataONE, but we have some questions that I think only someone from DataONE can answer, but for which it might be good to have the whole group on the call.

The questions have to do with the unit of publication to DataONE (a single file versus a collection of files), size limits on DataONE objects, requirements on making metadata and data available via API, possible use of Bagit, and probably some other things I am forgetting.

Currently trying to set up a call for Thursday, 31 August.

#19 Updated by Laura Moyers almost 5 years ago

Actual start date of 9/14/16 when serious discussions and plans for development began.

#20 Updated by Laura Moyers almost 5 years ago

  • Target version changed from Deploy by end of Y3Q4 to Deploy by end of Y4Q1

#21 Updated by Mark Servilla almost 5 years ago

Conference call with Ramona, Dennis, Mike, Laura, Mark on 31 August (see epad: https://epad.dataone.org/pad/p/CyVerse_and_DataONE). Provided more technical information for Mike and Dennis to ponder.

#22 Updated by Amy Forrester over 4 years ago

10/18/2017 -email From: Dennis Roberts

Hi Everyone,
I just wanted to provide a brief update. The member node service along with the DataONE event logger has been running in our development environments for about a week.
We’re currently in the process of changing our deployment strategy from Docker Compose to Kubernetes. I haven’t tried to package up the member node service or the event logger for Docker Compose because that would ultimately be wasted effort. The next step in the switch to Kubernetes will be to get our automated QA tests working against Kubernetes. Once that’s done, we’ll be able to deploy the member node service and event logger in our QA environment. We can coordinate testing as soon as we get the member node service deployed.
The last remaining task for the member node service is to create a utility to generate the Object Reuse and Exchange files for our data sets. I don’t believe that this has to be done before we can begin testing the member node service, but it will be necessary before we move it to production.

#23 Updated by Amy Forrester over 4 years ago

2/8/18 {Nirav Merchant}: The work has gone through QA on our side, it is bundled in the bigger Kubernetes upgrade for Discovery Environment (DE) happening end of this month, so I am hoping we will see it in production soon.

Contact is Sarah Roberts(sarahr@cyverse.org)

#25 Updated by Amy Forrester about 4 years ago

  • % Done changed from 10 to 50
  • Status changed from Planning to Testing

#26 Updated by Amy Forrester almost 4 years ago

  • Logo URL set to https://github.com/DataONEorg/member-node-info/blob/master/production/graphics/originals/Cyverse_logo.png
  • File Cyverse_logo.png added
649

#27 Updated by Rob Nahf almost 4 years ago

re: data planning for their Member Node, their initial plan is to expose the curated set of packages that are relatively stable, and have DOIs assigned. They manufacture the Datacite metadata for these packages, and it is a metadata format we support, so testing in STAGE makes sense.

Yet, there is a strong possibility that they will need to support mutable data, so would want to upgrade their API to v2, to leverage the seriesID. Meeting July 5th to help assess the situation.

Testing of their current api will be useful, and will be of great service to them for demonstrations in mid July.

#28 Updated by Amy Forrester almost 4 years ago

  • Logo URL changed from https://github.com/DataONEorg/member-node-info/blob/master/production/graphics/originals/Cyverse_logo.png to https://github.com/DataONEorg/member-node-info/blob/master/production/graphics/originals/cyverse_cmyk.png
  • Name set to CyVerse
  • Information URL set to http://www.cyverse.org/
  • File cyverse_cmyk.png added
  • MN Description set to CyVerse provides life scientists with powerful computational infrastructure to handle huge datasets and complex analyses, thus enabling data-driven discovery. Our extensible platforms provide data storage, bioinformatics tools, image analyses, cloud services, APIs, and more.
  • Base URL deleted (http://www.cyverse.org/)
654

information provided by Shelley Littin littin@cyverse.org

#29 Updated by Amy Forrester almost 4 years ago

  • Date Upcoming set to 2018-07-05

#30 Updated by Amy Forrester almost 4 years ago

  • Description updated (diff)

#31 Updated by Mark Servilla almost 4 years ago

  • Assignee changed from Mark Servilla to Rob Nahf

#32 Updated by Amy Forrester over 3 years ago

  • Logo URL changed from https://github.com/DataONEorg/member-node-info/blob/master/production/graphics/originals/cyverse_cmyk.png to member-node-info/production/graphics/web/CYVERSE.png

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