Deleting Markers
Definitions
- The Markers tab is used to delete markers from GDM. It has a more extensive search filter compared to the Datasets tab.
Markers can only be deleted IF the they are not being used in any dataset AND any marker_groups.
- Only users with "Superadmin" and "Admin" roles can perform a delete action.
- Users with "User" role can only view dataset information using this feature, and cannot delete any information.
- All delete actions are permanent and will impact GDM immediately.
- It is highly recommended to back up data in GDM before proceeding, as actions performed in this tool are not reversible.
Filtering
Filters are used to reduce the records displayed in the table, and users can use this feature to only show records of interest. Use two or more filters to get an intersection list of markers that meet all filtering criteria.
There are two parts to the filtering. The left-hand side has a similar functionality to the filters found in the Dataset tab. At the bottom of it, a summary of the right-hand side selections will be specified under the "Current Filters" field.
The right-hand side filters give the option to select multiple items per category. Each election will affect the items that will be shown in the succeeding category (this will be further explained in the table below).
A small notch/arrow that sits below the Submit Query button can collapse the filters to give more space to the results table. The double arrowhead on the top-right side of the filter panel can also collapse/expand it.
| Filter | Defintion | Influence on other filters |
|---|---|---|
| Marker ID | Used to get marker records with specific database IDs. The first field is used to get all IDs greater than or equal to the specified ID, and the second is used to get IDs smaller than or equal to the specified ID. Use the two fields together to get IDs within a range. | None |
| Marker Names | Use this filter to get marker(s) with specific names. Specify list of names with one name per line. Delimiters such as commas, colons and tabs are not allowed. | None |
| Platforms | Use this filter to search for markers belonging to specific Platforms. This list always shows all the platforms in the database. | Will affect the list of Vendor-Protocols, Projects, Experiments and Datasets |
| Vendor-Protocols | Use this filter to search for markers belonging to specific Vendor-Protocols. If Platforms are selected, the list will only show Vendor-Protocols under the selected Platforms. | Will affect the list of Projects, Experiments and Datasets |
| Projects | Use this filter to search for markers belonging to specific Projects. If Platforms or Vendor-Protocols are selected, the list will only show Projects under the selected Platforms and/or Vendor-Protocols. | Will affect the list of Experiments and Datasets |
| Experiments | Use this filter to search for markers belonging to specific Experiments. If Platforms, Vendor-Protocols, or Projects are selected, the list will only show Experiments under the selected Platforms, Vendor-Protocols and/or Projects. | Will affect the list of Datasets |
| Analyses | Use this filter to search for markers related to specific Analyses. This list always shows all the analyses in the database. | Will affect the list of Datasets |
| Datasets | Use this filter to search for markers belonging to specific Datasets. If Platforms, Vendor-Protocols, Projects or Experiments are selected, the list will only show Datasets under the selected Platforms, Vendor-Protocols, Projects and/or Experiments. | None |
| Mapsets | Use this filter to search for markers related to specific Mapsets. This list always shows all the mapsets in the database. | Will affect the list of Linkage Groups |
| Linkage Groups | Use this filter to search for markers belonging to specific Linkage Groups. If Mapsets are selected, the list will only show Linkage Groups under the selected Mapsets. | None |
In the right-side filter, there are number indicators beside each category that gets updated with each change of selection, indicating how many items are in that list.
Each list has a search bar that reduces the number of items as you type.
There's also an information button beside the search bars that will indicate if a certain list is being filtered or not.
Viewing Additional Marker Details
Clicking on a row in the results table will show additional marker detail if the marker is associated to a Dataset, a Linkage Group or a Marker Group.
This is useful when checking if a marker is related to a dataset or a marker group. Again, markers are only allowed to be deleted IF the they are not being used in any dataset AND any marker_groups.
Deleting Markers
STEP 1 : FILTER
- Use filters to search for the markers to be deleted.
- Select marker(s) by clicking on the checkbox next to it
STEP 2: SELECT MARKERS TO DELETE
- Click on red "Delete Selected" button above the table.
- A confirmation box will pop-up with the list of files you have selected for deletion.
- Click "Yes" to proceed, and "No" to abort.
STEP 3: PREREQUISITE CHECK
If "Yes" is selected, each of the markers will be checked whether or not it is associated with a marker group or a dataset. A warning will pop-up with a list of markers that cannot be deleted and the datasets or marker groups with which they are associated. This list can also be exported to a file and be used as a reference.
- In the warning dialog, the dataset ID will be enclosed in a parenthesis beside the dataset name.
- A marker can be associated with multiple datasets. In which case, all the datasets need to be deleted first before that marker can be deleted.
A marker cannot be deleted if it is associated with a dataset or a marker group.
STEP 4: CONFIRM FINAL WARNING
If there are selected markers that are not associated with a dataset or marker group, there will be a final warning to confirm permanent deletion.
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.
Deletion Summary
Upon completion of deletion, a summary page of what was deleted will be displayed and will contain:
Total number of rows deleted
Filtering criteria (This field will be empty if there was no search query performed prior to deleting the markers)
Deletion duration
A summary of the most recent filters used before the delete was submitted, will be included in the confirmation dialog when markers are deleted.