Closed jimmyzhen closed 6 years ago
@jimmyzhen ClinVar VariationID: 10000 does not load data in this instance. It doesn't load in this test instance but it does work in the normal demo and prod interfaces.
@jimmyzhen ClinVar VariationID: 17000 did work in the test instance when I created it as part of 10001 Affiliation but when I went back in and tried to enter VariationID: 17000 as part of Affiliation 10002 it would no longer load any data. In other words, it seems like this loading issue arises when a curator from an Affiliation tries to enter a ClinVar VariationID that has already been entered by a curator from a different Affiliation.
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oooh -- good catch @wrightmw ! Same in GCI (probably obvious)
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@wrightmw @jimmyzhen I'm thinking we don't need this text any more (on Evaluation Summary)
To clarify -- this was confusing the 2nd time through when I'd already saved as Provisional
@selinad Do you mean get rid or it altogether or just the second time around? I think H & S requested this text.
@jimmyzhen @wrightmw I may be confused -- I thought it was possible to save an interpretation as LP or P, just not as Provisional. I got this trying to save going around the 2nd time after an Approved
@jimmyzhen this note works great the first time around when there has not bee a previously saved Provisional. One change to text if possible:
"The option to save an Interpretation as Provisional will not appear when the saved calculated or modified value is "Likely Pathogenic" or "Pathogenic" and there is no associated disease."
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I thought it was possible to save an Interoperation as LP or P, just not as Provisional. I got this trying to save going around the 2nd time after an Approved
@selinad, in regards to your comments above, you need to provide an explanation to the modified pathogenicity before you can save the interpretation.
@jimmyzhen sorry, I think my point is why is the warning bar there -- I can save it if it's not provisional (after providing a reason)
@jimmyzhen it does not happen if I haven't saved as Provisional before
@jimmyzhen If I get a warning I can't save as Provisional then go back and add a disease and View Summary again, it gives me the Provisional box. The provisional box should only appear after a Save of the Classification
Need a space between sentences in this text:
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@jimmyzhen If I had Modified to LP, then go back around and add more and get Calculated of P, then it still says "LP" for Modification, but if I change to P it makes me give a reason...is the same logic being used in GCI and VCI? thx!
@selinad, I don't know whether they are using the very same logic, although they kinda behave similarly.
@jimmyzhen here's what it does in GCI
@jimmyzhen An empty "Provisional Classification entered by" field in editable box is filled upon saving. Perhaps get rid of this from editable box and only display once saved?
It's looking pretty fantastic so far @jimmyzhen ... you've done an amazing job with this!
@jimmyzhen it happens even when I don't have to add a disease -- in this case, had just made a change to another criteria and saved -- you can see I was presented with Provisional option:
@selinad According to the screen shot(s), there is a disease associated with the interpretation...
@jimmyzhen adding a 2nd Prov and 2nd Approved Interpretation works GREAT!
@selinad, @wrightmw, I can't seem to be able to reproduce the problem anymore.
@selinad I don't think that bug is fixed because I am getting the same issue
Here is the one for Provisional:
Suggested text: "When ready, you may save this Interpretation as Approved. Once you have saved it as Approved, you will not be able to undo it, but you will be able to save a new current Approved Interpretation, archiving the current one and retaining access to its Evaluation Summary."
@selinad re. text above...
Suggested text: "When ready, you may save this Provisional Interpretation as Approved. Once you have saved it as Approved it will become uneditable, but you will be able to save a new current Approved Interpretation, thus archiving this current one and retaining access to its Evaluation Summary."
Looks good @wrightmw -- thank you!
[x] @jimmyzhen for saved Provisional and Approved snapshot boxes, change "Classification" to "interpretation" (VCI Summary page)
[x] @jimmyzhen when Provisional exists and not Approved and someone comes back to Summary, the Evaluation Summary box stays open like it is, but Approval box needs to disappear and button goes on snapshot for most current Saved Provisional (per GCI workflow)
[ ] documents show new Status buttons for header
@jimmyzhen I think the above also occurs if I add a disease back....
p.s. love the "Approve this Saved Provisional" button!!!!
@jimmyzhen Just been looking at your new instance. It looks phenomenal! Love the orange "Approve this Saved Provisional" button!
And I am now able to work on the same variant as part of different Affiliations. Great!
@jimmyzhen @selinad
When you first visit an Interpretation, you get to see "All Existing Interpretations", which is great, but this is not behaving quite right.
Here are the headers for the existing Interpretations I randomly created:
1) An APPROVED "likely pathogenic" interpretation from the Hereditary Cancer WG Affiliation
2) An APPROVED/NEW PROVISIONAL "benign" interpretation by the Rett/Angelman
3) A PROVISIONAL VUS interpretation by the RASopathy EP
4) An IN PROGRESS interpretaion by the KCNQ1 EP.. for this one I have only Saved an Evaluation Summary... nothing else
5) I started an Interpretation as BCM-Education...added evidence ...but I have not saved an Evaluation Summary yet... so no status
Now when I go in as a different Affiliation, this time as "No Affiliation" and I go to the Evidence View for the above 5 examples, here is my header:
[x] Rett/Angelman says "PROVISIONAL" but it is actually "APPROVED/NEW PROVISIONAL"
[ ] For BCM-Education because I have not saved an Evaluation yet, it is not marked as IN PROGRESS in the headers but when I go back to my dashboard (acting as BCM-Education) it says "In progress":
Therefore, we are inconsistently showing the "In Progress" status.
Btw, as you can see I can definitely work on the same variant as different Affiliations. Whatever you did with the elastic search is working! Great!
@jimmyzhen @wrightmw this is what I saw before. I started an Interpretation, saved as BA1 Met -- you can see it responds I saved, but I don't get update button. Also criteria bar does not change... @jimmyzhen let me know if I should make a ticket....I believe a curator was writing in about this and I asked for more info.
Note criteria bar -- also, Summary shows no criteria saved
I then try to do PM2 and have the same problem:
First time in for a new variant and BS1 seems to work (and after this I was able to modify it to PM2 and it saved....almost as if saving as BS1 first works, but saving as BA1 or PM2 first doesn't work. Summary looks as expected)
@jimmyzhen when I clicked on the orange Approved button, it went back to In progress and I was not able to get the chance to Approve:
@jimmyzhen @wrightmw If I go go back to Summary to Approve a saved Provisional that was benign after adding more evidence and it's now pathogenic, I get this, which is very nice.
However, if I click to save it as Approved (orange button), I get this, which seems correct, but we may need to make certain curators aren't thinking they are saving the pathogenic....I'm not sure what to do for this, or whether we should worry right now?
Could we have some "simple feedback" on the save evaluation part saying not yet saved? When they click button, it would say saved?
@jimmyzhen steps for buggy thing
@jimmyzhen thoughts:
we have this text in GCI -- analogous text could be helpful in eliminating confusion in VCI (or maybe it is there and not displaying....sorry):
the white is hard to see in the orange bar...should we make this text black so we can see Provisional vs. Approved?
@selinad,
the white is hard to see in the orange bar...should we make this text black so we can see Provisional vs. Approved?
I made the text bold and it seems to read better now:
we have this text in GCI -- analogous text could be helpful in eliminating confusion in VCI (or maybe it is there and not displaying...
There is currently a similar paragraph of note text in the VCI (see the screen shot above). Although it may not be exactly the same text you see in GCI, it is there when the approval form entry panel shows.
@selinad,
However, if I click to save it as Approved (orange button), I get this, which seems correct, but we may need to make certain curators aren't thinking they are saving the pathogenic....I'm not sure what to do for this, or whether we should worry right now?...Could we have some "simple feedback" on the save evaluation part saying not yet saved? When they click button, it would say saved?
There is also a paragraph of note text in the VCI being shown when the provisional form entry panel is displayed (upon saving the evaluation). You may choose to update it if it suits the needs. For anything more complicated or needing a more well thought-out user experience, I would suggest we look into that in subsequent releases if this is not a showstopper.
Testing steps
add variant 21135
add some evaluations for benign
go to Summary
Save summary. @jimmyzhen this looks great -- were we going to remove "In Progress" though? I thought it disappeared upon first save.
go back and add another evaluation
return to Summary and save a new one -- all looks good
save this as Provisional -- all looks good
return to interpretation and make another evaluation
return to Summary -- all looks good
modify to LP and give reason, save again; expect to see old provisional and ability to approve it, but see this (should still let me Approve original one, right? But, saved behavior good since there is no disease):
go back out and add disease
go back to Summary -- looks good except that still can't approve 1st provisional even though I haven't saved a second Provisional
save a new Provisional --- looks great
save a first approved -- looks great!
went back to delete Disease -- great note on modal
changed to VUS in summary and saved. All looked good
saved Provisional and got correct status!
saved as Approved
All in all looks great!!! Just the one bug when I saved as LP (see above) and there was missing ability to save the existing Prov as Approved....
Dashboard -- was I supposed to see this as Approved? It shows none
here is is when I go into it:
Previous error I reported whereby "Approved/New Provisional" was being incorrectly reported as just "Provisional" in the "All Existing Interpretations" section has now been fixed. Thanks Jimmy! @selinad I have added some Affiliations for you in this new testing instance... you should see them next time you logout and back in again.
@wrightmw @jimmyzhen -- I was not able to see any status in the Dashboard for the VCI, but was able to see the Approved + New Provisional for the GCI (one the Dashboard.
@jimmyzhen sorry -- I see your checkmark and I did a shift refresh and can see buttons on Dashboard! Now works great!!!!
..when I go back to the dashboard it says just "Provisional":
Whereas, as I said earlier... in the "All Existing Interpretations" section this is now reporting correctly. Which is fantastic! Thanks Jimmy!
@jimmyzhen please see comments to your comments :-) @selinad,
Please see my responses to your feedback from your testing last night:
were we going to remove "In Progress" though? I thought it disappeared upon first save.
"In progress" remains until the 1st Provisional is saved.
modify to LP and give reason, save again; expect to see old provisional and ability to approve it, but see this (should still let me Approve original one, right? go back to Summary -- looks good except that still can't approve 1st provisional even though I haven't saved a second Provisional
As the way it is implemented now, I am disabling the ability to approve a saved Provisional as soon as the user saves changes in the Summary. The thinking behind it is that the user should provision the newly saved changes in the Summary again prior to approving it.
Hi @jimmyzhen , @wrightmw discovered a bug when we were demo'ing for the curators. The current approved moves to archived -- it should have a green flag instead of a file box
@wrightmw confirmed this is independent of whether disease added or not
@jimmyzhen feedback from curators: 1) loved the workflow and no confusion around it! 2) adding "current" before green flag and "archived" before file would be good -- if this is not possible, could we make the icons a tad larger -- feedback was the file box looked like a trash can =:-0
@jimmyzhen would it be "quick" to have the gray "View Approved Summary" (or Provisional) have a blue border? NOT NECESSARY at all (they were fine with it being gray) but if quick it may make it more obvious it's clickable.
@jimmyzhen one more bug, which seems to be related to a long variant name -- problems on Dashboard display
@selinad, @wrightmw,
Please use the following instance to review the changes and fixes in regards to your comments and reports above: https://jz-approval-workflow.demo.clinicalgenome.org
Thanks!
@jimmyzhen looks GREAT!!!! I couldn't break it! Nicely done. Only 2 small items:
it doesn't seem like the tiestamp for Saved Summary updates all the time. I saved one at 8:27 and one at 8:29 and it remained at 8:27.
still a wrap problem -- I don't think there is a need to stress about it now, though (24229)
Implement the Provisional Interpretation section, which consists of the following requirements: