Page Comparison

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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  

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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 the filter section and/or enter a list or file in the Included Samples section 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 Upon selection of one or more items in 'Filters',

         1. selected and any dataset type previously selected should be removed from the combo box and from the Extraction Criteria.

         2. 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 can provide  

            no list nor file of samples 

            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> 

      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> 

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

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 

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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 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 

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

         1. User can provide  

            no list nor file of markers 

            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 selected 

      3.  <Submit> 

      4. 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 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)

    

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