Release Date - 29 Oct 2018 

GDM Loader download - Rel15_LoaderUI

Deployment Notes: Version 1.5

New Features

TimeScope – Phase 1(Dataset Deletion)

• Compatible with IE and Chrome
• Deployed separately from GDM
• TimeScope will allow system administrators and anyone with admin access to the system to be able to browse and permanently delete bad data. The deletable data will be limited to datasets for the first release of this tool. The ability to delete samples, markers, and dnaruns will come in future releases
• This tool is a GOBii add-on and can be linked to any GDM database instance. It does not have any dependency to our existing UIs, ETL tools, or even the web-services.
• Timescope v1 covers the user module, which is authentication and authorization, and the dataset module.
  • User Module: Authentication:
    • Timescope can connect to any crop database on any given server.
    • To log in, enter the
      • Database Host
      • Databas Port
      • Database Name
      • TimeScope Username, and
      • TimeScope Password
      • <Login>
  • The Landing Page contains a disclaimer of potential damages that can be caused by using TimeScope. It is highly recommended to back up data before proceeding, as actions performed in this tool are not reversible.
  • After a successful logon, you are presented with two tabs, Users and Datasets
• User Module Authorization:
  • Session management has been fully implemented.
  • Session time-out duration is customizable
  • There are 3 types of users:
    • Superadmin - this will be assigned to SysAds. In addition to Timescope database deletion features, this allows them to add, edit, delete any user in the system.
    • Admin - this will be assigned to curators or any user who understands the schema. This grants them the ability to delete GDM data permanently.
    • User – this is a read-only role, ie. The ability to only browse data and not delete anything.
    • Dataset Module:
      • The dataset tab allows superadmins and admins to delete any dataset resulting from the filters.
      • As a SuperAdmin or Admin, you can delete datasets one at a time, a few at a time, or all the datasets resulting from a filter.
      • Filtering Options:
        • by dataset ID, by either entering a single dataet ID or a range of IDs
        • by entering dataset names - either one name or multiple names separated by line
        • by creation date, either by a single date or by a date range
        • by dataet type
        • Prncipal Investigator
• you can delete dataset either by selecting individually or by selecting all.  you can also deselect all
• you can sort by any one of the columns in the table. i.e.....
• to delete datasets, once you've filtered down to the dataets you want ot delete, select one, or more , or all.
• <Delete Selected>
  • you will receive a pop-up asking if you are sure you want to delte the following datasets, which will be listed - you have a choice of saying yes or no
  • if you select 'yes', you are warned again that your action is not reversible, do you want to continue - you have a choice to say 'yes' or cancel
  • you will receive a pop-up informing you that you have successfully deleted datasets with a count of how many datasets were delted as well ascounts for how many markers and DNAruns were updated

Extraction Criteria summary and display:

• A summary file is created in the digest folder containing the extraction criteria used to process the job
• The summary file lists out the dnasamples and/or markers and specifies the name of the file containing the list of dnasamples and/or markers
• The summary file should contain all other information present in the extraction Criteria in tabular format
• The email sent to the users should contain the Extraction Criteria
• All information in the Extraction Criteria should be present in the email with the exception of the list of dnasamples and/or markers, but should point to location containing the file(s)
• If list of dnasample and/or markers is provided, email should simply indicate there was a list of dnasamples and/or markers and not actually list them.

Bug Fixes

• GSD-474 Incorrect repeated data when exporting by sample to FJ from a large dataset
  • Fixes an issue with one of the loaded data orientations when a dataset containing more than 10,000 markers was loaded, which resulted in marker data duplication when output in the flapjack format. Existing data sets are not automatically fixed, and will continue to be incorrect until fixed manually.
• GSD-466 LoaderUI: w/o selecting a PI, A user cannot successfully update a Project
  • In the Project, Experiment, and Dataset forms, Selecting an entity from the left-hand list and updating it, will now push through successfully even without first selecting an entity in the top left dropdown box.
• GSD-463 LoaderUI: Multiplying Analyses for Datasets
  • In the database, the datasets are now being associated once to each selected analysis. There will be no future duplicated analysis IDs in the list of associated analyses for each dataset.
• GSD-462 LoaderUI: Incomplete 2ltr nucleotide support, we need to allow single allele insertions and deletions
  • Validation will now allow two letter nucleotide sources to declare only one allele as an insertion or deletion.
• GSD-456 LoaderUI: Incomplete IUPAC support - 'D' IUPAC code
  • Corrects incorrect interpretation of valid 'D, B, H, and V' IUPAC codes.
• GSD-439 LoaderUI: When using a Template, several datasets (under different Exp/platforms) loaded via Dataset Wizard, using one file to load the markers, samples, and matrix, does not associate the dataset(s) to the correct platform
  • When loading the same allele matrix file to multiple datasets associated with experiments for different platforms, the allele data are now associated with the correct marker/platform combination.
• GSD-429 Free-text entry into GDI marker props table did not work
  • Adding free text in the "Property' tables in all the Wizards is no longer allowed.
• GSD-415 Large chunks of missing data and errors in much of the data when exporting by sample to FJ from a large dataset
  • Fixes an issue with one of the loaded data orientations when a dataset containing more than 10,000 markers was loaded, which resulted in large swathes of null data when output in the flapjack format. Existing data sets are not automatically fixed, and will continue to be incorrect until fixed manually.
• GSD-409 LoaderUI: can move to Next page w/o mapping DS Marker (marker_name)
  • When using the Dataset Wizard, A warning message now appears when a user tries to go to the next step without mapping values for DS Marker Information and the DNArun/DS_DNArun Information tables.
• GSD-391 If VCF alt field is '.' Strange error occurs.
  • VCF files with no ALT field specified (missing data specified with the '.' symbol) no longer suffer a Transformer error.
• GSD-63 long error message if select csv file format but have browsed to txt file
  • When the selected file format (in the dropdown box of allowed formats) and the file type of the file selected by the user do not match, an error message saying "No file with the selected format exists" appears.