TimeScope - Sample Module

Objective

Samples Module

User Interface Specifications:

For the samples tab, the right (content) panel will contain:

1. The user has the option to select any of the following:

   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. dnasample_id (range, ex: 100-210)

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

   3. uuid

4. For dnarun, the filtering controls:

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

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

   3. experiment.name

   4. dataset

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 datasets that will be deleted)

2. PREREQUISITE CHECK:

   1. We only allow dnarun deletion IF the dnaruns are not being used in any dataset
      If there are datasets using those markers:

      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 on dataset A, B, and C. dnarun 2 is being used on dataset D and E. Please delete those datasets first."

         2. Presentation of this message and list of datasets is up to the developer. If it's more performant and user-friendly to have a separate page with a table in it (in case the list is big) then do it that way.

   2. We only allow dnasample deletion IF 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 dnaruns is up to the developer. If it's more performant and user-friendly to have a separate page with a table in it (in case the list is big) then do it that way.

   3. We only allow germplasm deletion IF the germplasms are not associated with any dnarsamples.
      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 dnasamples is up to the developer. If it's more performant and user-friendly to have a separate page with a table in it (in case the list is big) then do it that way.

3. If the user clicks yes, the system then will delete the entities.

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

User interaction and design

Open Questions

Out of Scope