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Objective
Currently extract metadata outputs dnaruns and markers that are only associated with a dataset. The objective for this requirement is to redo this functionality to allow users to extract meta information regardless of their association with a dataset.
Requirements:
As a GDM user I want to extract sample metadata without samples being associated with a dataset
Extract Sample Metadata
User logs into Extractor and selects By Samples tab
User selects Format: Sample Metadata
user cannot select Mapset - this combo box should be greyed out when metadata is selected
any selected Mapset under Extraction Criteria should be removed.
User must select at least one item from either ( b.i ) or ( b.ii ) below:
User can select zero, one, or more of the following items in 'Filters'
Principal Investigator
Project
Platforms
User cannot select a Dataset Type – this combo box will be greyed out when Metadata is selected and any dataset type previously selected should be removed from the combo box and from the Extraction Criteria.
User cannot select a Platform – this list box will be greyed out when Metadata is selected
In “Included Samples” frame:
User can select any of the following
Germplasm Name
External Code
DNA Sample
User must provide one of the following
a list of samples entered into the text box
a file with a list of samples
<Submit>
The output folder should not contain
dataset file
marker.file
As a GDM user I want to extract marker metadata without markers being associated with a dataset
Extract Marker Metadata
User logs into Extractor and selects By Markers tab
User selects Format: Marker Metadata
User must select at least one item from either ( b.i ) or ( b.ii ) below:
User can select:
Platform - one or more
User cannot select a Dataset Type – this combo box will be greyed out when Metadata is selected
In “Included Markers” frame:
User can select any of the following
a list of markers
a file with a list of markers
one or more Marker Groups
<Submit>
The output folder should not contain
dataset file
sample.file
Extract By Samples and Extract By Markers tabs, Filter of Dataset Type, and Select Format radio buttons
By default, Dataset Types is a selectable combo box
By default, radio button for Hapmap format is selected
If User selects a Dataset type in the combo box
and User then selects Sample/Marker Metadata as the format
a System Message popup tells the user “you cannot select dataset type for extract metadata only”
user must close the popup (select x in the upper right corner) before able to continue (same as how the popup works when submitting a job)
Data types combo box shows ‘Select a Dataset Type’ greyed out and unselectable (no longer displaying the dataset type previously selected)
Requirement | User Story | Importance | Jira Issue | Notes | |||||||
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Discussion Tue Nov 26
Discussion included:
Need a req to remove the requirement to select dataset type?
Grey out platforms from Filters – don't need for extract metadata?
Do we want new tabs for both extract Sample Metadata and Extract Marker Metadata?
More discussion needs to be had as to the best/easiest approach
User interaction and design
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Question | Answer | Date Answered |
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Sample: Should we be able to extract germplasm or external_code w/o selecting any filter at all? they can both be loaded to the germplasm table with no association to any other entititySample: Project is the minimum required in order to load samples to the dnasample table. Is that all we want to require for metadata extract? | you will need to either select one thing from the filter section.and/or enter a list or file in the selection section | |