Extractor: Extract Metadata only

Objective

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 

   2. User must select at least one item from the filter section and/or enter a list or file in the Included Samples section 

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

         1. Principal Investigator 

         2. Project 

         3. Platforms 

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

      3. Upon selection of one or more items in 'Filters',  

         1. User can select any of the following 

            1. Germplasm Name 

            2. External Code 

            3. DNA Sample 

         2. User can provide  

            1. no list nor file of samples 

            2. a list of samples entered into the text box 

            3. a file with a list of samples 

         3.  <Submit> 

      4. When use selects zero items in the Filter section 

         1. User can select any of the following 

            1. Germplasm Name 

            2. External Code 

            3. DNA Sample 

         2. User must provide a list or a file of samples 

         3.  <Submit> 

   3. There should be no marker.file in gobii_bundle/crops/<crop>/extractor/output/<netID>/meta_data/by_sample 

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 Platforms from the filter section and/or enter a list, a file, or a Marker Group in the Included Markers section 

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

      2. Upon selection of one or more Platforms in 'Filters',  

         1. User can provide  

            1. no list nor file of markers 

            2. a list of markers 

            3. a file with a list of markers 

            4. one or more Marker Groups selected 

         2.  <Submit> 

      3. When user selects zero items in the Filter section 

         1. User must provide one of the following 

            1. a list of markers 

            2. a file with a list of markers, 

            3. one or more Marker Groups selected 

         2.  <Submit> 

   3. There should be no sample.file in gobii_bundle/crops/<crop>/extractor/output/<netID>/meta_data/by_marker 

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. 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