nr23730/cbioportal-frontend

React Frontend of cBioPortal :tada:

cbioportal-frontend's Issues

No EvidenceLevelExtension gets shown as "null"

If there is no extension to the evidence level it get's displayed as "null"

@nr23730 should we just change this line to factor that in or is there an underlying issue (e.g. in fhirspark)? I was wondering because it is the string "null".

cbioportal-frontend/src/pages/patientView/therapyRecommendation/MtbTherapyRecommendationTable.tsx

Line 371 in 758bd2e

{therapyRecommendation.evidenceLevelExtension || ''}

It is not clear which clinical data in the form to add therapy recommendations belongs to which sample or patient

If multiple samples of a patient have the same data item, the user cannot differentiate which sample (or if it is patient-level) the item belongs to.

Modals lag and don't open on first click

Steps to reproduce: Open Patient, click on tab MTB, click on Add MTB, click on Add or Add from OncoKB

Modal only opens after click on other tab or field.

Delete therapy recommendation and MTB

fhirspark otherwise wouldn't know with resources to keep / delete.

Related to: nr23730/fhirspark#32

MTB tab calendar feature not working for browser Safari

The browser Safari does not support the current implementation of the calendar feature of MTB entries in the MTB tab.

'More info on cancerdrugs' link in OncoKB card is broken

The current link format leads to a 404 page for every drug.

Refreshing our tabs leads to error message

Steps to reproduce: Open Patient, click on tab MTB, Follow-Up or ClinicalTrialsGov and refresh.

This is probably due to the React router that doesn't know our tabs. We might need to add them there.

mtbStatus

mtbStatus has inconsistencies right now:

When initially created: DRAFT, COMPLETED, ARCHIVED

When changed: Draft, Completed, Archived

Expected from JSON: DRAFT, COMPLETED, ARCHIVED

dbSNP and other default displayed columns not working

In the "official" version this is working but not in our fork.
Probably we need to wait until all the data is loaded properly.

Display who created a therapy recommendation.

We should display the creators of therapy recommendations. As entries are freely editable we should also show users who edited therapy recommendations.
One option would be a mouse-over info icon in the 'Edit' column.

disable inputs on completed mtb

Check permission for MTB tab testing version in prod

The workaround for testing the MTB tab got in the prod version.
We should resolve the underlying issue anyhow that testing is currently not possible for frontend installations.

cbioportal-frontend/src/pages/patientView/therapyRecommendation/MtbTable.tsx

Lines 643 to 644 in 2ba0a02

	this.setState({ loggedIn: true });
	this.setState({ permission: true });

Additional attributes in genetic alterations

• entrezGeneId / clinvar
• hugoSymbol
• alteration / aminoAcidChange
• chromosome
• start
• end
• ref
• alt
• alleleFreqency
• functional-annotation
• dna-chg
• dbSNP id
• read depth
• GnomAD
• cosmic

Editing moves therapy recommendation down

Editing a therapy recommendation moves it down, instead of keeping it's position in the list.

Include fontawesome 4.7.0

Behind a restrictive proxy the Icon may disappear as they are loaded from a CDN. We should ship them with the frontend.

Example:

Presentation of MTB info is ambigous

• Delete button of MTB looks the same as delete button of therapy recommendations
• Date and state field don't have a label

Deal with product alternatives and product combinations

Related to: nr23730/fhirspark#25 and nr23730/fhirspark#26

Disable editing of MTBs only when they are fetched in state 'final'

Currently editing of MTBs is disabled as soon as the state final is selected from the dropdown. Editing should only be disabled for already saved MTBs in state final.
If the state final is selected in the current session the user should still be able to switch the state, other fields should be disabled as before.

Saved MTB sessions don't update on tab switch

Unlike single therapy recommendations, the mtb sessions do not update after saving them and then switching tabs. A page reload is necessary.

Steps to reproduce this error:

• Create new mtb session
• Click 'Save data'
• Switch to different tab in patient view and back to 'MTB' tab

Question: Relation between drug and comments

How much do the comments of a therapy recommendation belong to the selected drug(s)?

--> Could make sense to set drug as a required field.

Typing in field clinical data in therapy recommendation form throws error

To reproduce start typing in the clinical data form field.

OncoKB add all entries in MTB tab doesn't add entries

The feature to add all therapy recommendations from OncoKB doesn't work for our sample patient Testpatient.
Error: Uncaught TypeError: Cannot read property 'chr' of undefined
This probably originates from a particular OncoKB entry as it works for other samples.

Set order/priority for therapy recommendation