Extractor: Extract Metadata only

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 

1. User logs into Extractor and selects By Samples tab 

   1. User selects Format: Sample Metadata 

      1. user cannot select Mapset - this combo box should be greyed out when metadata is selected

      2. any selected Mapset under Extraction Criteria should be removed.

   2. User must select at least one item from either ( b.i ) or ( b.ii ) below:

      1. User can select zero, one, or more of the following items in 'Filters'  

         1. Principal Investigator 

         2. Project 

         3. Platforms 

         4. 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.

         5. User cannot select a Platform – this list box will be greyed out when Metadata is selected 

      2. In “Included Samples” frame:  

         1. User can select any of the following 

            1. Germplasm Name 

            2. External Code 

            3. DNA Sample 

         2. User must provide one of the following

            1. a list of samples entered into the text box 

            2. a file with a list of samples 

      3.  <Submit> 

2. The output folder should not contain

   1. dataset file

   2. marker.file 

As a GDM user I want to extract marker metadata without markers being associated with a dataset 

 Extract Marker Metadata 

1. User logs into Extractor and selects By Markers tab 

   1. User selects Format: Marker Metadata 

   2. User must select at least one item from either ( b.i ) or ( b.ii ) below: 

      1. User can select:

         1. Platform - one or more

         2. User cannot select a Dataset Type – this combo box will be greyed out when Metadata is selected

      2. In “Included Markers” frame:   

         1. User can select any of the following

            1. a list of markers 

            2. a file with a list of markers 

            3. one or more Marker Groups

      3.  <Submit> 

   3. The output folder should not contain

      1. dataset file

      2.  sample.file 

Extract By Samples and Extract By Markers tabs, Filter of Dataset Type, and Select Format radio buttons

1. By default, Dataset Types is a selectable combo box

2. By default, radio button for Hapmap format is selected

3. If User selects a Dataset type in the combo box

   1. and User then selects Sample/Marker Metadata as the format

      1. a System Message popup tells the user “you cannot select dataset type for extract metadata only”

         1. 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)

      2. Data types combo box shows ‘Select a Dataset Type’ greyed out and unselectable (no longer displaying the dataset type previously selected)

    

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

Open Questions

Out of Scope