Release 2.0

Owned by Yaw Nti-Addae
Last updated: Apr 28, 2020 by Deb Weigand

Release Date -  

GDM Loader download - Rel20_LoaderUI

Deployment Notes: Version 2.0


 Software QA Test Case

  File Modified

Microsoft Excel Spreadsheet Rel 2.0 - FlapJack with BrAPI-TestCases.xlsx

Mar 20, 2019 by Deb Weigand

Microsoft Excel Spreadsheet Rel 2.0 - ownCloud-TestCases.xlsx

Mar 20, 2019 by Deb Weigand


New FeaturesDescription
ownCloud

Web-based file browser that allows for easy access to GDM files

 read more...
  • Bundle ownCloud with GDM as a 
    • separate container (preferred)
  • Configure ownCloud to user-authentication - same as used by GDM
  • Configure ownCloud with the following folder structure, for each crop:
    • Crops [/data/gobii_bundle/crops]
      • <cropname>
        • extractor
          • done
          • inprogress
          • instructions
          • output
        • files
        • hdf5
        • loader
          • digest
          • done
          • inprogress
          • instructions
          • qc
      • notices
        • confidentiality.txt
    • logs - should be at same level as crops
  • Configure ownCloud so there is no ability to "File/Folder Delete" 
  • file types we need to be able to view:
    • .txt
    • .genotype
    • .log
    • .file
    • .json
    • digest. files
    • digest.dataset_marker
    • digest.dataset_dnarun
    • digest.dnarun
    • digest.dnasample
    • digest.germplasm
    • digest.marker
    • digest.marker_linkage_group
    • digest.linkage_group
Marker Tools Portal

A portal that will consolidate all GOBii related tools in one view, which also allows users to add/link their own tools to the portal.

To be able to see all web-based tools in one space, as well as desktop tools to download, and web-sites of interest

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  • Tabs: Default Applications to be shipped out with MarkerPortal
    • tab for web based tools
      • GDM - one for each crop
      • KDCompute
      • ownCloud
      • TimeScope
      • EIB Galaxy Demo
    • tab for desktop tools to download
      • GDM Loader
      • Flapjack
      • TASSEL 5
    • tab for web sites of interest
      • GOBii Project
      • EIB Platform
  • Allow sys-admins to register more tools by directly modifying MPortal's configuration file
  • Each application should allow for specification of documentation link
    • GDM -
      • User Manual
      • Technical Documentation
      • APIs
    • TimeScope
    • KDC - Data QC
    • EIB Galaxy Demo
      • EIB Galaxy
      • Galaxy
    • Flapjack
    • TASSEL 5
Import GDM dataset into Flapjack

BrAPI implementation to view GOBII datasets directly in Flapjack, without having to use the GOBii extractor UI.

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  • The user will be able to use the FlapJack *Import Data* tool to specify the url of a GOBII server and do the following: 
    • Select a "Study" (which is the same as a GOBii project); 
    • Select a "Marrix" (a GOBii dataset, concatenated with the experiment name, from within the project); 
    • View the resutlting dataset in FlapJack. 
  • The data should conform to several criteria: 
    • The list of studies (projects) should be filtered to those for which there exist datasets that have been loaded into the system; 
    • The list of matrices (datasets) should also be filtered in this way;
  • The names of the matrices should include the number of alleles in the matrix. This number can be derived, in theory, by multiplying the number of markers by the number samples in the dataset. 
  • Matrices with a large number of alleles will be flagged as a high risk for processing and download delay. It will be up to FlapJack to determine the threshold for this warning.
  • When the extract results in error, the error condition should be reported to the user in a graceful way. An example of this error, as reported by email, is attached.  Ideally, the error reported should be similar to what you get in an email notification.
PortainerA container designed for System Administrators to monitor local and remote container environments.
GDM public documentationUp to date, Public, Downloadable Documentation


Bugs
Issue keySummary
GSD-443Extractor - warning pop-up when pasting more than 200 items in a List cannot be closed
GSD-464Extractor: All Contacts showing up in 'All Principal Investigators' dropdown in the Extractor
GSD-467LoaderUI: w/o selecting a PI, select Add New for Project needs a proper error message
GSD-490TimeScope: Cannot filter by current date
GSD-494LoaderUI: Anyone added as a contact wth any role selected can log into the LoaderUI
GSD-495TimeScope: A SuperAdmin can change username for any/all users
GSD-500TimeScope: req 4.e missed: what should be displayed once connected to a DB
GSD-509LoaderUI: should disallow 2 letter nucleotide 
GSD-469Extractor: Two emails sent after a Failed extraction
GSD-472Extract by marker or sample into hapmap or FJ format incorrectly reports as failed if one of the datasets containing the marker or sample is not available - but the ouput file has errors
GSD-473Small request to please add dataset name in the QC notification message
GSD-475Triple email on extract by market simple request with marker file list.
GSD-486Extractor: GR-127 Req 2.2 missed - list entered in text box should not appear in email
GSD-541Extractor: Unable to successfully extract multiple datasets using the 'By Dataset' tab
GSD-496Incorrect permissions applied to the "notices" folder under gobii-crops
GSD-491Extract By Sample sets Project Id to '0' in Instruction file if a Project name is selected and then user selects 'All Projects', resulting in a failed extract