add hgvsg column and link out to genome nexus #2971
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leexgh
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| } | ||
| else { | ||
| return ( | ||
| <a href={`https://www.genomenexus.org/variant/${hgvsgData}`} target="_blank" rel="noopener noreferrer"> |
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lets make a helper in urls.ts to make these links. the host should only be in once place in our code
| <img | ||
| height='16' | ||
| width='16' | ||
| src={require("./GenomeNexusLogo.png")} |
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would be best if we accomplished this with css. so, make a
|
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||
| if (status !== null) { | ||
| // show loading circle | ||
| if (status === TableCellStatus.LOADING) { |
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it's weird that we have a separate case for loading. one would think that would take care of loading state.
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cBioPortal/cbioportal#6988
issue created about the loading state
| @@ -0,0 +1,22 @@ | |||
| .hgvsg-data a, | |||
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lets discuss using SASS for nesting these defs
| @@ -232,7 +232,18 @@ export function extractGenomicLocation(mutation: Mutation) | |||
| // TODO remove when done refactoring mutation mapper | |||
| export function genomicLocationString(genomicLocation: GenomicLocation) | |||
| { | |||
| return `${genomicLocation.chromosome},${genomicLocation.start},${genomicLocation.end},${genomicLocation.referenceAllele},${genomicLocation.variantAllele}`; | |||
| // mapping chromosome X with 23 | |||
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would be good to have a test for this function
src/shared/lib/MutationUtils.ts
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| return `${genomicLocation.chromosome},${genomicLocation.start},${genomicLocation.end},${genomicLocation.referenceAllele},${genomicLocation.variantAllele}`; | ||
| // mapping chromosome X with 23 | ||
| let chromosome = ""; | ||
| if (genomicLocation.chromosome === "X") { |
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you should use a switch statement instead of if/else when testing against a single value (genomicLocation.chromosome). Good to get in habit of using switch in these kinds of situations. You could also use a an enum with a default. If genomicLocation.chromosome exists in enum, you use it's value. If not, you use Enum.default.
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@alisman fixed, thanks |
leexgh
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@tmazor @schultzn could you take a look and give some feedback on the hgvsg column? this column links out to Genome Nexus variant page |
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@leexgh as discussed in person: let's hide the hgvsg column for now (make it optional) and do a new PR that adds a tooltip for the protein change column with a link to Genome Nexus. |
leexgh
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leexgh
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- hgvsg is shown by default - the hgvsg will be shorted with ... if the ref or var is too long
add hgvsg column in mutation table and link out to genome nexus
...and the whole hgvsg will show in tooltip