Provisional Classification Summary - Case Level Evidence

[jimmyzhen]

Create a table view for all Case Level evidence (Individual evidence primarily since other types of evidence can't be scored) associated with the provisional classification.

Table header title "Genetic Evidence: Case Level (variants, segregation)

Table columns include:

1. Variant type
2. Variant
3. Reference
4. Sex
5. Age
6. Ethnicity
7. Phenotypes
8. Associations
9. Segregations (sub-column - Number of affected, Number of unaffected, LOD score)
10. Previous testing
11. Methods of detection
12. Score (sub-column - Proband (default), Seg)

Sortable columns include:

1. Variant type
2. Variant
3. Reference

Could they also include:

4. Sex
5. Age
6. Ethnicity
7. Methods of detection
8. Score (depending on east of implementation)

[selinad]

@jimmyzhen a bug 🐛 (dang): When "No Modification" become new value as the new Calculated Classification = last saved and I save without modifying, it saves as "No Modification" 🙀

Great catch! 🎣

[selinad]

Change this blue text (in above screenshot) slightly: "Heads up! The Last Saved Classification below is based on the matrix above. You can edit this Classification based on the same Matrix, view the Evidence Summary page for it, or return to the Record Curation page." to "Heads up! The Last Saved Classification (below) is based on the above Classification Matrix. You may edit it by selecting "Edit Classification," click "Evidence Summary" to view all evidence associated with it, or return to the record by clicking "Record Curation page."

[selinad]

@jimmyzhen @wrightmw do you think the red note should be here when you edit a classification (above one) and the setting is No Modification?

[selinad]

@jimmyzhen notice above that when I went to edit the one that incorrectly saved as "No Modification," it shows last saved as "Moderate" (see above comment screenshot)

[selinad]

@jimmyzhen @wrightmw: should we add a note by the Print PDF button on Evidence Summary?

e.g. For best printing, choose "Landscape" for layout, 50% for Scale, "Minimum" for Margins, and select "Background graphics"

[jimmyzhen]

@selinad I am fine with adding such note.

[selinad]

@wrightmw @jimmyzhen I pounded some more -- looks great. Scored some of @wrightmw's data too, which I'd forgotten to do previously and everything behaves. A future request could be to enter curator associated with evidence (let's see if that will be something that is desired after they use it a bit). 👍 great job!

[wrightmw]

Me too @selinad wrt to the note about best printing option,

[jimmyzhen]

@selinad @wrightmw I have updated the same instance with the latest requested changes. Please give it another round of testing. Thanks!

[selinad]

Hi @jimmyzhen

Thanks for the updated instance!

[removed as I was confused]

[selinad]

[removed as I was confused]

@jimmyzhen I apologize, but I think the note I put in red was confusing:

"If you would like to 1) save the new "Calculated Classification" highlighted in blue or 2) change your Last Saved Classification value based on this new "Calculated Classification" value, make sure to edit the highlighted fields and click Save. You may also choose to mark your Classification as Provisional."

Can you please change to:
"Click Save to save the Calculated Classification (highlighted in blue) without modification, or modify the Classification value in the pull-down and hit Save. You may also choose to mark your Classification as Provisional."

[selinad]

@jimmyzhen -- I believe we can shorten the yellow message from:

"The Total Points shown above is based on the the set of saved evidence and accompanying scores that existed when the "View Classification Matrix" button was clicked. To save a Classification for this Gene Disease Record based on this evidence, please see the section below. Otherwise, click "Cancel" to return to your previous page."

to

"The Total Points shown above are based on the the set of saved evidence and accompanying scores existing when the "View Classification Matrix" button was clicked. To save a Classification for this Gene Disease Record based on this evidence, please see the section below."

[wrightmw]

@selinad I just took a screenshot of that! But happy for text to change ;-)

[selinad]

@wrightmw -- screenshot of what? :)

[wrightmw]

@selinad The Classification Matrix tables...but I'm obviously fine with text changes.

[selinad]

@jimmyzhen so sorry -- text change to blue one as well:

"The Last Saved Classification (above) is based on the above Classification Matrix. You may edit it by selecting "Edit Classification," click "Evidence Summary" to view all evidence associated with it, or return to the record by clicking "Record Curation page."

to

"Select "Edit Classification" to edit the Last Saved Classification or click "Evidence Summary" to view all evidence associated with the saved Classification. If you don't wish to save, click "Record Curation page" to add more evidence."

@wrightmw sorry --I think you are working on the help doc. Could you put a placeholder in those spots? thx.

[selinad]

@jimmyzhen I like the new red text here. Any chance it could span more width? (e.g. start closer to the left). If not, no worries!

[selinad]

@wrightmw do you think this message needs to be in red? I feel like it should be in blue...

[selinad]

@jimmyzhen all is working great! Apologies for my original confusion, which my own text caused. The bug 🐛 is gone. If you are able to make the text changes, that would be great. The only other thing I might do is change the red text (above) to blue -- it is not so much a warning as instructions, although happy for @wrightmw to weigh in.

Thank you! Really. Great. Job.

[snehitp]

Go to bed, guys.

[jimmyzhen]

@selinad @wrightmw I've addressed the latest round of changes and updated the same instance. Please feel free to review it again.

Meanwhile, I will start the process of bringing up a release candidate.

[wrightmw]

@jimmyzhen Thanks so much for this work. Above and beyond! @selinad No worries, re. keep changing all the texts... we can always update any changed figures later. As for the blue vs red text debate, it should be blue because it's instructional rather than a warning ... but I don't think this should delay a release candidate.

[selinad]

Hi @jimmyzhen -- thank you! All the text changes look great. I appreciate the changes -- they are so much clearer for the user.

Also, thx @wrightmw -- @jimmyzhen has made it blue in his updates. Looks great!

@jimmyzhen I think it's good to go!

[jimmyzhen]

Included in R13 release.