Closed hitz closed 9 years ago
page to create a new provisional.
page to edit existing provisional data. First, have a view of login user's provisional.
then, click button Calculate Again will get new summary below
HI @kgliu0101 Thanks so much for this!
Here are a few comments:
PAGE TO CREATE A NEW PROVISIONAL
Number of years since first clinical publication Score: 2 Year of First Publication: 1994
Number of clinical publications with clincial evidence Score: 2 Number of Publcations: x
Number of probands associated with a pathogenic variant Score: 2 Individual probands not associated with Family: 1 Individual probands associated with Family: 3
Experimental Data Combined Score: 3.5
[indent these]
Expression (0.5 points each) Score: 1.0 Number of pieces of evidence: 2
Protein Interactions (0.5 points each) Score: 0.5 Number of pieces of evidence: 1
Protein Interactions (0.5 points each) Score: 0.5 Number of pieces of evidence: 1
Model Systems (2 points each) Score: 2 Number of pieces of evidence: 1
[end indent]
Total Score: 9.5
PAGE TO EDIT PROVISIONAL DATA
I think Recalculate (rather than Calculate again) button should be on GDM page - you can't recalculate from the Summary page. The curator could Edit their classification, but that is different from recalculating from the evidence.
@kgliu0101 I'm not sure I understand the red note - it just changes their classification, not any data underneath (also, I don't think @forresttanaka has any red notes - red is reserved for errors).
Add Summary data, link and button in record title panel.
gdm with Summary and Provisional Classification.
gdm with pathogenic data and assessed as Supports, but without Summary.
gdm without assessed pathogenic data.
Display Summary data as one line in record title panel.
Hi @kgliu0101 - looking good - here is my similar version with some changes in wording
matching above?
Thanks @kgliu0101 Looks good!
There is one more thing you could try, if you like, since there is more room than I thought.
You could put the following in a 2nd column:
Total Score: 17 (Definitive) Provisional Classification: Strong [Edit Classification]
That way, you would have 3 columns:
1. Current Summary Generated: 2015....
2. Total Score: 17 (Definitive) Provisional Classification: Strong [Edit Classification]
3. [Button]
This might highlight the scoring part.
3 columns, button moves left little, Summary & Provisional Classification, Edit Classification.
Note for new calculation.
Hi @kgliu0101 - thanks so much - it's coming along!
I like the addition of the note since the header still has the Summary/Classification from before the user hit Generate New Summary.
Slight change to wording - @forresttanaka, do we need a blue box for a note here?: The calculated values below are based on the set of curated evidence saved prior to selecting "Generate New Summary." To save these values as the "Current Summary & Provisional Classification" calculated values and make a new Provisional Classification, click the Save button below.
Could you implement the following text changes?
@selinad Have a look
Great! Thanks, @kgliu0101
2 things (both on me):
Also, are you requiring a reason if they change the Provisional Score, or did we decide we could not implement that?
Thanks!
changed Note and Proband(s)
change "Proband(s) from Families" to "Number of proband ..."
Thanks @kgliu0101 - let's use the 2nd one.
Change the text under Proband Score to be: Number of probands with variants assessed as "supports" pathogenicity
Changed. But it's pretty long and hard to stay as one line
Great! The "16" is still floating inbetwen - can it be on the same line as "Number of probands....supports"?
Thanks! Selina
"16" at top line
Excellent! Thanks for your hard work on this, @kgliu0101
Thanks @kgliu0101 - I can't see it...?
this one
change to Definitive
should be this one
Thank you @kgliu0101 - that looks perfect!
Hi Kang,
I don't have time for thorough testing by any means - @tsneddon can test more thoroughly on Monday. A couple of quick things:
Sorry I can't test any more before I go! Thanks for your hard work putting up the instance on a Friday night.
Yes, there seems to be issues with generating a summary. One I can add is that I can assess on a variant without selecting any of the drop-downs. However, when I make a summary all the scores are zero. I only get the correct score if I select one of the drop-downs from 'Evaluation of Pathogenicity'. If this is required it should be stated in the Edit Variant Information view and a user should not be able to make an assessment without selecting one of the drop-downs or putting some text in the comments box. This is the GDM in progress: https://90-kl-summary-and-provisional-c326264-kangliu.demo.clinicalgenome.org/curation-central/?gdm=3e144866-16d9-11e5-b451-60f81dc5b05a Let me know when this and Selina's issues are fixed and I will review the new instance.
@tsneddon and @selinad, currently, pathogenicity of one variant in a gdm is shared in all curators. And each curator assesses to the variant pathogenicity. That is different to the mechanism that each curator makes his/her own pathogenicity and assesses to it only (can not assess other's). Please let me know which one you prefer and I will edit relevant code.
@kgliu0101 I'm a little confused by your last message. Please clarify what the current situation is and what alternative you are proposing.
Another comment: I added Exp 1 to the following instance and saved as 'Supports': https://90-kl-summary-and-provisional-c326264-kangliu.demo.clinicalgenome.org/curation-central/?gdm=3e144866-16d9-11e5-b451-60f81dc5b05a&pmid=2345676 I also added variationID:177872 but I can NOT save any information including an assessment on this variant.
I also added variationID:177872 but I can NOT save any information including an assessment on this variant.
Traced this to an object not being embedded, so there will have to be a change to __init__.py
. I’ll work on that first thing this morning in a new branch.
I just noticed the 90_kl_summary_and_provisional branch is 82 commits behind dev. I’ve made embedding changes (including for this exact problem) in recent dev merges, so I think we can assume for now that I fixed this problem already.
Thanks @forresttanaka, so I can continue to assess on this instance?: https://90-kl-summary-and-provisional-c326264-kangliu.demo.clinicalgenome.org/
@kgliu0101 Your branch should be updated and a new instance brought up.
@tsneddon I would recommend that you not continue to test on this instance until the the code base behind it (on a new instance) is brought up to date.
@tsneddon I can only address assessing variants, and I worked on that towards the end of last week, probably within the 82-commit window. So how much assessing variants proves on this instance, I’m not clear.
Please move these comments if they should be somewhere else (I've lost track from afar):
Here is the GDM URL for the following: https://90-kl-summary-and-provisional-fa45a47-kangliu.demo.clinicalgenome.org/curation-central/?gdm=34adcf73-a559-41d8-985a-b0eb947fc2a3
Here's what I tried in order, generated summary, and it worked!:
What did not work:
Features:
Experimental Count is showing but not Experimental Score
I can see "Final Experimental Score" 3. If you mean no score for each experimental evidence (Expression, Biochemical Function, Model System), that is what we decided last week. Since Final Experimental Score is range-based but not directly equal to sum of each evidence score, we decided not showing them.
Hmm...I vaguely remember this, but not necessarily for experimental. Fine for beta and we can discuss again.
Let me check Models again - I may have been confused, it may be working ok.
@kgliu0101 I have to stop testing now, but I think the scoring is all working well!!!
@selinad - I think we are OK not including the # of pieces of contradictory evidence for this initial release but it should be a priority for the next 3-week release. I will start testing now...
Initial comments:
...still testing...
@tsneddon Regarding item 3... do you get an error message in the console (command+option+i in Chrome) when you try to set an assessment?
@tsneddon Item 1. I changed tile of field "Shared Phenotype(s) (free text):" to "Phenotype(s) (free text):". Item 2. GDM status is currently set as "Summary/Provisional Classifications" if there is a summary generated, no who did it. Is it necessary to set the status per user?
other items are related to test data in gdm 9ffd7c1e-16d9-11e5-b283-60f81dc5b05a. Some of them may missing required item because of schema change. I suggest starting from a new gdm for testing.
@mrmin123 - no error, just nothing happens when I click on save.
@kgliu0101 - re: #2, I don't see a summary and there is no evidence added so I don't think Selina could have made a summary. Why then is Status: Summary/Provisional Classifications and not Status: In progress?
This is a view of the GDM that calculates the current summary and provisional assertions.
Apparently summaries and assertions are PER curator. Summary is autogenerated.