Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: 8.3.4 Minor Release
-
Labels:None
-
Story Points:0.1
-
Epic Link:
-
Sprint:Sprint 19
Description
It seems there are a few non-functioning scripts that should be removed from the IGB Scripting language, such as the "Select" script.
These non-functioning scripts should be removed from the IGB command language as it may add confusion to users.
Attachments
Issue Links
- relates to
-
IGBF-525 Remove "select" command as it doesn't actually make a selection, may not be useful
-
- Closed
-
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-568 [ 15637 ] |
| Sprint | Sprint 19 [ 24 ] |
| Assignee | Mason Meyer [ mason ] |
| Rank | Ranked higher |
| Fix Version/s | 8.3.3 Minor Release [ 10000 ] |
| Rank | Ranked higher |
| Sprint | Sprint 19 [ 24 ] | Sprint 18 [ 23 ] |
| Rank | Ranked lower |
| Status | Open [ 1 ] | Testing In Progress [ 10003 ] |
After testing I can confirm that all of the scripts listed on this page (https://wiki.transvar.org/display/igbman/IGB+Script+List) are working except for:
1) select
2) selectfeature
3) the loadmode command parameters "REGION_IN_VIEW" and "CHROMOSOME" (the command works as expected with the other parameters)
Reassigning to David for fixes.
| Assignee | Mason Meyer [ mason ] | David Norris [ dcnorris ] |
| Status | Testing In Progress [ 10003 ] | Open [ 1 ] |
| Rank | Ranked higher |
| Sprint | Sprint 18 [ 23 ] |
| Sprint | Sprint 19 [ 24 ] |
| Rank | Ranked higher |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Story Points | 0.1 |
| Summary | Remove non-functioning scripts from the IGB Scripting Language | Updated Documentation on how to use commands which were misclassified as non-functioning in testing review |
| Assignee | David Norris [ dcnorris ] | Mason Meyer [ mason ] |
| Summary | Updated Documentation on how to use commands which were misclassified as non-functioning in testing review | Fix select and selectfeature commands, and update loadmode documentation to reflect actual options available |
loadmode only accepts the following options
1. no_load
2. region_in_view / visible (they are synonyms in the scripting engine)
3. genome
region_in_view/visible doesn't really load the region in view, but results in the load mode of "Manual". This is actually not a bug, but a case of very poor naming by the original developers.
There is not chromosome load mode, it was removed a few years ago.
select and selectfeature work as expected on the development branch, but required a fix related to case sensitivity to work as expected.
e.g. to test go to the latest Arabidopsis Genome Version and run the following script
select AT1G36940.1
note the selection occurs and the viewer is "jump zoomed" to the position.
Now, load another script with this command instead.
selectfeature AT1G36940.1
The main viewer is not jump zoomed, but is now centered on this selection. To confirm this, simply operate the zoom slider and zoom into a level where you can see the selection of the gene model.
| Status | In Progress [ 3 ] | Needs Testing [ 10002 ] |
| Rank | Ranked higher |
| Rank | Ranked lower |
| Assignee | Mason Meyer [ mason ] | David Norris [ dcnorris ] |
| Status | Needs Testing [ 10002 ] | Open [ 1 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Rank | Ranked lower |
merged fix to master branch for minor release 8.3.4
| Status | In Progress [ 3 ] | Needs Testing [ 10002 ] |
My testing verified that these commands are functioning and we updated the document based on the functioning.
Since the story is resolved, I'll close it.
| Resolution | Done [ 10000 ] | |
| Status | Needs Testing [ 10002 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 15876 ] | Fall 2019 Workflow Update [ 19461 ] |
| Workflow | Fall 2019 Workflow Update [ 19461 ] | Revised Fall 2019 Workflow Update [ 21578 ] |
Add specifics to the description on what should be removed.