User Interface Specifications:

For samples, there will be three additional tabs in the right (content) panel:

1. The additional tabs will be:

   1. Germplasm

   2. Dnasample

   3. Dnarun

2. For germplasm, the filtering controls:

   1. germplasm_id (range, ex: 100-210)

   2. germplasm.name list (text area: line-separated list)

3. For dnasample, the filtering controls:

   1. project.name/project_id

   2. filtering controls from #2 above

   3. dnasample_id (range, ex: 100-210)

   4. dnasample.name list (text area: line-separated list)

   5. uuid

4. For dnarun, the filtering controls:

   1. filtering controls from #3 above, which includes controls from #2

   2. dnarun_id (range, ex: 100-210)

   3. dnarun.name list (text area: line-separated list)

   4. experiment.name/experiment_id

   5. dataset.name/dataset_id

      1. include option ‘none’

5. A submit button to query the database

6. A clear button to clear the current filters and result set

7. A table listing the data resulting from the filters

   • This table will provide pagination for optimal performance

   • This table will provide a capability to select rows individually

   • And a select all button to select all rows

8. A delete button to delete the rows selected

9. For the result table: All the columns wherein an ID is displayed should have a column next to it displaying the names. Columns should be sortable.

Functional Specifications:

Upon selecting a set of markers from the result table and clicking the delete button, the system will:

1. Prompt the user to confirm what will be deleted (basic yes-no prompt window with a list of all the germplasm/dnasamples/dnaruns that will be deleted)

2. PREREQUISITE CHECK:

   1. We only allow dnarun deletion IFF the dnaruns are not associated with any datasets
      If there are dnaruns associated with datasets:

      1. Provide a window/prompt/page that displays the list of dataset references for the dnaruns, and do not allow deletion if there are references. Basically, you have to delete the datasets first.

         1. A message that essentially displays: "dnarun 1 is being used in dataset A, B, and C. dnarun 2 is being used in dataset D and E. Please delete those datasets first."

         2. Presentation of this message and list of datasets should be consistent with that of the Marker Module

   2. We only allow dnasample deletion IFF the dnasamples are not associated with any dnaruns.
      If there are dnaruns associated with those dnasamples:

      1. Provide a window/prompt/page that displays the list of dnarun references for the dnasamples, and do not allow deletion if there are references. Basically, you have to delete the dnaruns first.

         1. A message that essentially displays: "dnasample 1 is associated with dnarun A, B, and C. dnasample 2 is being used on dnarun D and E. Please delete those dnaruns first."

         2. Presentation of this message and list of datasets should be consistent with that of the Marker Module

   3. We only allow germplasm deletion IFF the germplasms are not associated with any dnasamples.
      If there are dnasamples associated with those germplasms:

      1. Provide a window/prompt/page that displays the list of dnasample references for the germplasms, and do not allow deletion if there are references. Basically, you have to delete the dnasamples first.

         1. A message that essentially displays: "germplasm 1 is associated with dnasample A, B, and C. germplasm 2 is being used on dnasample D and E. Please delete those dnasamples first."

         2. Presentation of this message and list of datasets should be consistent with that of the Marker Module

3. If the user clicks yes, the system will delete the entities provided they meet all pre-requisite checks.

4. If the user clicks no, the operation will simply abort.

Everytime a deletion is being made, show:

Prompt Messages:

A warning message box will be shown that clearly indicates that the operation is final and the data will be deleted, providing a quick statistics on how many rows there are (ex. Are you sure you want to delete 102321 markers?). The user is then provided with the ability to cancel or go through with the operation.

Result Report Page:

Upon completion of deletion, a summary page of what was deleted will be displayed. This will contain:

• Total number of rows deleted

• Filtering criteria

• Deletion duration

Add a Footer: This should show one or two sentences that warns the user to do regular backups or at least one backup before using this tool to allow for recoverability in case of user mistakes.

Logging:

Log a detailed list of what gets deleted per operation. The developer has the flexibility to use whatever library (or stay with basic stdout) s/he wants. The only requirement is that the following gets logged:

1. For every deletion, log the actual SQL (or the JOOQ equivalent) that ran.

2. The username of the user who ran the deletion operation

3. Timestamp of deletion

4. Result of deletion

   1. Total number of rows deleted

   2. Filtering criteria

   3. Deletion duration

Requirements:

New features

- Updated 'Genotype Calls' API extract genotypes by search query to include 'Dna sample names', 'Dna sample UUIDs' and 'Germplasm names' and their respective Ids to Genotypes Extract search query.

- Updated 'Genotypes Calls' API to extract by Marker names alone.

- Added 'Get CallSets' for genotypes extract query(Dnarun metadata).

- Added 'Get Variants' for genotypes extract query(Marker metadata).

- Added Search Samples API.

- Added Search CallSets API.

- Added Search Variants API.

- Added sepUnphased and unknownString fields to Calls and fileFormat object.

- Default page size for List Genotypes API has been increased from 1000 to 100000.

- Updated the reference documentation(https://gobiibrapi.docs.apiary.io/).

Bug fixes

- Fixed project id to map to sample group id instead of observation unit id in samples object.

- Temporary file buffers are cleaned automatically.

- Fixed bug in List Genotypes by extract query API when page size is equal to dnarun size or its multiples.