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fix: order link-outs alphabetically
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@holtgrewe
holtgrewe committed Aug 1, 2023
1 parent b12c3ac commit 389a3f1
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141 changes: 74 additions & 67 deletions variants/vueapp/src/components/VariantDetailsGene.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -196,77 +196,80 @@ const props = withDefaults(defineProps<Props>(), {
</div>
<div class="card-body pb-2 pt-2">
<div>
<strong> HGNC: </strong>
<strong> ENSEMBL: </strong>
<a
:href="`https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/${gene?.hgnc?.hgnc_id}`"
:href="`https://www.ensembl.org/Homo_sapiens/Gene/Summary?g=${gene?.hgnc?.ensembl_gene_id}`"
target="_blank"
>
<i-mdi-launch />
{{ gene?.hgnc?.hgnc_id }}
{{ gene?.hgnc?.ensembl_gene_id }}
</a>
</div>
<div>
<strong> ENSEMBL: </strong>
<strong> HGNC: </strong>
<a
:href="`https://www.ensembl.org/Homo_sapiens/Gene/Summary?g=${gene?.hgnc?.ensembl_gene_id}`"
:href="`https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/${gene?.hgnc?.hgnc_id}`"
target="_blank"
>
<i-mdi-launch />
{{ gene?.hgnc?.ensembl_gene_id }}
{{ gene?.hgnc?.hgnc_id }}
</a>
</div>
<div v-if="gene?.hgnc?.refseq_accession?.length">
<strong> RefSeq: </strong>
<template v-for="(accession, index) in gene.hgnc.refseq_accession">
<div v-if="gene?.hgnc?.mgd_id?.length">
<strong>MGI: </strong>
<template v-for="(mgd_id, index) in gene.hgnc.mgd_id">
<template v-if="index > 0">, </template>
<a
:href="`https://www.ncbi.nlm.nih.gov/nuccore/?term=${accession}+AND+srcdb_refseq[PROP]`"
:href="`https://www.informatics.jax.org/marker/${mgd_id}`"
target="_blank"
>
<i-mdi-launch />
{{ accession }}
{{ mgd_id }}
</a>
</template>
</div>
<div v-if="gene?.hgnc?.uniprot_ids?.length">
<strong> UniProt: </strong>
<template v-for="(uniprotid, index) in gene.hgnc.uniprot_ids">
<span class="text-muted" v-else> No MGI </span>
<div v-if="gene?.hgnc?.pubmed_id?.length">
<strong>Primary PMID: </strong>
<template v-for="(pmid, index) in gene.hgnc.pubmed_id">
<template v-if="index > 0">, </template>
<a
:href="`https://www.uniprot.org/uniprotkb/${uniprotid}/entry`"
:href="`https://pubmed.ncbi.nlm.nih.gov/${pmid}/`"
target="_blank"
>
{{ uniprotid }}
<i-mdi-launch />
{{ pmid }}
</a>
</template>
</div>
<div v-if="gene?.hgnc?.pubmed_id?.length">
<strong>Primary PMID: </strong>
<template v-for="(pmid, index) in gene.hgnc.pubmed_id">
<div v-else class="text-muted">No primary PMID</div>
<div v-if="gene?.hgnc?.refseq_accession?.length">
<strong> RefSeq: </strong>
<template v-for="(accession, index) in gene.hgnc.refseq_accession">
<template v-if="index > 0">, </template>
<a
:href="`https://pubmed.ncbi.nlm.nih.gov/${pmid}/`"
:href="`https://www.ncbi.nlm.nih.gov/nuccore/?term=${accession}+AND+srcdb_refseq[PROP]`"
target="_blank"
>
<i-mdi-launch />
{{ pmid }}
{{ accession }}
</a>
</template>
</div>
<div v-if="gene?.hgnc?.mgd_id?.length">
<strong>MGI: </strong>
<template v-for="(mgd_id, index) in gene.hgnc.mgd_id">
<div v-else class="text-muted">No RefSeq</div>
<div v-if="gene?.hgnc?.uniprot_ids?.length">
<strong> UniProt: </strong>
<template v-for="(uniprotid, index) in gene.hgnc.uniprot_ids">
<template v-if="index > 0">, </template>
<a
:href="`https://www.informatics.jax.org/marker/${mgd_id}`"
:href="`https://www.uniprot.org/uniprotkb/${uniprotid}/entry`"
target="_blank"
>
<i-mdi-launch />
{{ mgd_id }}
{{ uniprotid }}
</a>
</template>
</div>
<span class="text-muted" v-else> No MGI </span>
<div class="text-muted" v-else>No UniProt</div>
</div>
</div>
</div>
Expand All @@ -283,104 +286,117 @@ const props = withDefaults(defineProps<Props>(), {
<div class="col-6 p-0">
<div>
<a
:href="`https://www.deciphergenomics.org/gene/${gene?.hgnc?.symbol}`"
:href="`https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=${gene?.hgnc?.cosmic}`"
target="_blank"
v-if="gene?.hgnc?.cosmic"
>
<i-mdi-launch />
DECIPHER
COSMIC
</a>
<span v-else>COSMIC</span>
</div>

<div>
<a
:href="`https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=${gene?.hgnc?.cosmic}`"
:href="`https://www.deciphergenomics.org/gene/${gene?.hgnc?.symbol}`"
target="_blank"
v-if="gene?.hgnc?.cosmic"
>
<i-mdi-launch />
COSMIC
DECIPHER
</a>
<span v-else>COSMIC</span>
</div>
<div>
<a
:href="`https://medlineplus.gov/genetics/gene/${gene?.hgnc?.symbol}/`"
:href="`https://search.thegencc.org/genes/${gene?.hgnc?.hgnc_id}`"
target="_blank"
>
<i-mdi-launch />
MedLinePlus
GenCC
</a>
</div>
<div>
<a
:href="`https://www.omim.org/entry/${gene?.hgnc?.omim_id[0]}`"
:href="`${props.hgmdProPrefix}/gene.php?gene=${gene?.hgnc?.symbol}`"
target="_blank"
v-if="gene?.hgnc?.omim_id.length"
v-if="props.hgmdProEnabled"
>
<i-mdi-launch />
OMIM
HGMD Pro
</a>
<span v-else>OMIM</span>
<span class="text-muted" v-else>
<i-mdi-launch />
HGMD Pro
</span>
</div>
<div>
<a
:href="`https://www.malacards.org/search/results?query=+[GE]+${gene?.hgnc?.symbol}`"
:href="`https://www.kegg.jp/kegg-bin/search_pathway_text?map=map&keyword=${gene?.hgnc?.symbol}&mode=1&viewImage=true`"
target="_blank"
>
<i-mdi-launch />
MalaCards
KEGG
</a>
</div>
<div>
<a
:href="`https://mastermind.genomenon.com/detail?gene=${gene?.hgnc?.symbol}&disease=all%20diseases`"
:href="`https://medlineplus.gov/genetics/gene/${gene?.hgnc?.symbol}/`"
target="_blank"
>
<i-mdi-launch />
MASTERMIND
MedLinePlus
</a>
</div>
<div>
<a
:href="`https://www.kegg.jp/kegg-bin/search_pathway_text?map=map&keyword=${gene?.hgnc?.symbol}&mode=1&viewImage=true`"
:href="`https://www.omim.org/entry/${gene?.hgnc?.omim_id[0]}`"
target="_blank"
v-if="gene?.hgnc?.omim_id.length"
>
<i-mdi-launch />
KEGG
OMIM
</a>
<span v-else>OMIM</span>
</div>
</div>
<div class="col-6 p-0">
<div>
<a
:href="`${props.hgmdProPrefix}/gene.php?gene=${gene?.hgnc?.symbol}`"
:href="`https://pubmed.ncbi.nlm.nih.gov/?term=${gene?.hgnc?.hgnc_id}`"
target="_blank"
v-if="props.hgmdProEnabled"
>
<i-mdi-launch />
HGMD Pro
PubMed
</a>
<span class="text-muted" v-else>
<i-mdi-launch />
HGMD Pro
</span>
</div>
<div v-if="props.smallVar">

<div>
<a
:href="`https://stuart.radboudumc.nl/metadome/dashboard/transcript/${smallVar.ensembl_transcript_id}`"
:href="`https://www.malacards.org/search/results?query=+[GE]+${gene?.hgnc?.symbol}`"
target="_blank"
>
<i-mdi-launch />
MetaDome
MalaCards
</a>
</div>
<div>
<a
:href="`https://search.thegencc.org/genes/${gene?.hgnc?.hgnc_id}`"
:href="`https://mastermind.genomenon.com/detail?gene=${gene?.hgnc?.symbol}&disease=all%20diseases`"
target="_blank"
>
<i-mdi-launch />
GenCC
MASTERMIND
</a>
</div>

<div v-if="props.smallVar">
<a
:href="`https://stuart.radboudumc.nl/metadome/dashboard/transcript/${smallVar.ensembl_transcript_id}`"
>
<i-mdi-launch />
MetaDome
</a>
</div>

<div>
<template v-if="gene?.hgnc?.uniprot_ids?.length">
<template v-for="(uniprotid, index) in gene.hgnc.uniprot_ids">
Expand All @@ -406,15 +422,6 @@ const props = withDefaults(defineProps<Props>(), {
VarSome
</a>
</div>
<div>
<a
:href="`https://pubmed.ncbi.nlm.nih.gov/?term=${gene?.hgnc?.hgnc_id}`"
target="_blank"
>
<i-mdi-launch />
PubMed
</a>
</div>
</div>
</div>
</div>
Expand Down
44 changes: 22 additions & 22 deletions variants/vueapp/src/components/VariantDetailsVariantTools.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -230,9 +230,9 @@ const umdpredictorLinkout = computed((): str => {
</div>
<div class="card-body p-2">
<div>
<a :href="ucscLinkout" target="_blank">
<a :href="dgvLinkout" target="_blank">
<i-mdi-launch />
UCSC Genome Browser
DGV
</a>
</div>
<div>
Expand All @@ -241,12 +241,6 @@ const umdpredictorLinkout = computed((): str => {
ENSEBML
</a>
</div>
<div>
<a :href="dgvLinkout" target="_blank">
<i-mdi-launch />
DGV
</a>
</div>
<div>
<a :href="gnomadLinkout" target="_blank">
<i-mdi-launch />
Expand Down Expand Up @@ -275,36 +269,42 @@ const umdpredictorLinkout = computed((): str => {
</div>
<div>
<a
:href="`https://varseak.bio/ssp.php?gene={{ smallVar.symbol }}&hgvs={{ smallVar.hgvs_c }}`"
v-if="props.umdPredictorApiToken"
:href="umdpredictorLinkout"
target="_blank"
>
<i-mdi-launch />
VarSeak Splice Site Predictor
UMD Predictor
</a>
<span v-else-if="smallVar?.release !== 'GRCh37'" class="text-muted">
<i-mdi-launch />
UMD Predictor (not available for GRCh38)
</span>
<span v-else class="text-muted">
<i-mdi-launch />
UMD Predictor (API token not configured)
</span>
</div>
<div>
<a :href="varsomeLinkout" target="_blank">
<a :href="ucscLinkout" target="_blank">
<i-mdi-launch />
varsome
UCSC Genome Browser
</a>
</div>
<div>
<a
v-if="props.umdPredictorApiToken"
:href="umdpredictorLinkout"
:href="`https://varseak.bio/ssp.php?gene={{ smallVar.symbol }}&hgvs={{ smallVar.hgvs_c }}`"
target="_blank"
>
<i-mdi-launch />
UMD Predictor
VarSeak Splice Site Predictor
</a>
<span v-else-if="smallVar?.release !== 'GRCh37'" class="text-muted">
<i-mdi-launch />
UMD Predictor (not available for GRCh38)
</span>
<span v-else class="text-muted">
</div>
<div>
<a :href="varsomeLinkout" target="_blank">
<i-mdi-launch />
UMD Predictor (API token not configured)
</span>
varsome
</a>
</div>
</div>
</div>
Expand Down

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