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Fixing IGV and MT dropdown menu bug. #517

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merged 1 commit into from May 25, 2022
Merged

Fixing IGV and MT dropdown menu bug. #517

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351 changes: 178 additions & 173 deletions variants/templates/variants/filter_result/row.html
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Expand Up @@ -448,205 +448,210 @@
{% endif %}
<td>
<div class="btn-group sodar-list-btn-group pr-2">
<button
class="btn btn-primary sodar-list-btn"
type="button"
data-toggle="modal"
data-target="#variantcarriermodal-{{ entry.release }}-{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}"
onclick="showVariantCarrierModal(this, '{{ entry.release }}', '{{ entry.chromosome }}', '{{ entry.start }}', '{{ entry.reference }}', '{{ entry.alternative }}');"
>
<span class="iconify" data-icon="mdi:binoculars"></span>
</button>
{% if entry.release == "GRCh37" %}
<a class="btn btn-primary dropdown-toggle sodar-list-dropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
MT
</a>
<div class="dropdown-menu dropdown-menu-right">
<a
href="https://www.genecascade.org/MTc2021/ChrPos102.cgi?chromosome={{ entry.chromosome }}&position={{ entry.start }}&ref={{ entry.reference }}&alt={{ entry.alternative }}"
data-toggle="tooltip"
target="_blank"
title="Open variant in MutationTaster 2021"
class="btn btn-primary dropdown-item">
MT 2021
</a>
<a
href="https://www.genecascade.org/MT85/ChrPos85.cgi?chromosome={{ entry.chromosome }}&position={{ entry.start }}&ref={{ entry.reference }}&alt={{ entry.alternative }}"
data-toggle="tooltip"
target="_blank"
title="Open variant in MutationTaster 85"
class="btn btn-primary dropdown-item">
MT 85
</a>
</div>
{% else %}
<span
class="btn btn-disabled sodar-list-btn btn-outline-secondary"
data-toggle="tooltip"
title="MutationTaster not available for genome {{ entry.release }}"
<div class="btn-group sodar-list-btn-group">
<button
class="btn btn-primary sodar-list-btn"
type="button"
data-toggle="modal"
data-target="#variantcarriermodal-{{ entry.release }}-{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}"
onclick="showVariantCarrierModal(this, '{{ entry.release }}', '{{ entry.chromosome }}', '{{ entry.start }}', '{{ entry.reference }}', '{{ entry.alternative }}');"
>
MT
</span>
{% endif %}
{% if ga4gh_beacon_network_widget_enabled or kiosk_mode %}
<a
data-toggle="popover"
tabindex="0"
data-trigger="focus"
data-content="<iframe
src='https://beacon-network.org:443/#/widget?rs={{ entry.release }}&chrom={{ entry.chromosome }}&pos={{ entry.start }}&ref={{ entry.reference }}&allele={{ entry.alternative }}'
style='width: 100%; height: 300px; overflow: auto;'
marginwidth='0' marginheight='0' frameborder='0' vspace='0' hspace='0'>
</iframe>"
data-html="true"
data-tooltip="tooltip"
title="Query GA4GH Beacon Network"
class="btn btn-warning sodar-list-btn"
>
<i class="iconify" data-icon="fa-solid:podcast" aria-hidden="true"></i>
</a>
{% endif %}
<button
type="button"
onclick="javascript:$.ajax({url: 'http://127.0.0.1:60151/goto?locus=chr{{ entry.chromosome }}:{{ entry.start }}-{{ entry.end }}'})"
title="Go to locus in IGV"
class="btn btn-secondary sodar-list-btn">
IGV
</button>
<button type="button" class="btn btn-secondary dropdown-toggle dropdown-toggle-split sodar-list-dropdown" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
<span class="sr-only">Toggle Dropdown</span>
</button>
<div class="dropdown-menu dropdown-menu-right" style="z-index: 1030;">
{% linkout_available_for "ucsc" entry.release as ucsc_available %}
{% if ucsc_available %}
<a class="dropdown-item" href="https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg19&position={{ entry.chromosome }}:{{ entry.start }}-{{ entry.end }}" target="_blank">
Locus @UCSC
<span class="iconify" data-icon="mdi:binoculars"></span>
</button>
{% if entry.release == "GRCh37" %}
<a class="btn btn-primary dropdown-toggle sodar-list-dropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
MT
</a>
<div class="dropdown-menu dropdown-menu-right"">
<a
href="https://www.genecascade.org/MTc2021/ChrPos102.cgi?chromosome={{ entry.chromosome }}&position={{ entry.start }}&ref={{ entry.reference }}&alt={{ entry.alternative }}"
data-toggle="tooltip"
target="_blank"
title="Open variant in MutationTaster 2021"
class="btn btn-primary dropdown-item">
MT 2021
</a>
<a
href="https://www.genecascade.org/MT85/ChrPos85.cgi?chromosome={{ entry.chromosome }}&position={{ entry.start }}&ref={{ entry.reference }}&alt={{ entry.alternative }}"
data-toggle="tooltip"
target="_blank"
title="Open variant in MutationTaster 85"
class="btn btn-primary dropdown-item">
MT 85
</a>
</div>
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="UCSC browser not available for reference {{ entry.release }}">
Locus @UCSC
<span
class="btn btn-disabled sodar-list-btn btn-outline-secondary"
data-toggle="tooltip"
title="MutationTaster not available for genome {{ entry.release }}"
>
MT
</span>
{% endif %}

{% linkout_available_for "ensembl" entry.release as ensembl_available %}
{% if ensembl_available %}
<a class="dropdown-item" href="https://{% if entry.release == "GRCh37" %}grch37{% else %}www{% endif %}.ensembl.org/Homo_sapiens/Location/View?r={{ entry.chromosome }}:{{ entry.start }}-{{ entry.end }}" target="_blank">
Locus @EnsEMBL
</div>
<div class="btn-group sodar-list-btn-group">
{% if ga4gh_beacon_network_widget_enabled or kiosk_mode %}
<a
data-toggle="popover"
tabindex="0"
data-trigger="focus"
data-content="<iframe
src='https://beacon-network.org:443/#/widget?rs={{ entry.release }}&chrom={{ entry.chromosome }}&pos={{ entry.start }}&ref={{ entry.reference }}&allele={{ entry.alternative }}'
style='width: 100%; height: 300px; overflow: auto;'
marginwidth='0' marginheight='0' frameborder='0' vspace='0' hspace='0'>
</iframe>"
data-html="true"
data-tooltip="tooltip"
title="Query GA4GH Beacon Network"
class="btn btn-warning sodar-list-btn"
>
<i class="iconify" data-icon="fa-solid:podcast" aria-hidden="true"></i>
</a>
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="ENSEMBL browser not available for reference {{ entry.release }}">
Locus @EnsEMBL
</span>
{% endif %}
<button
type="button"
onclick="javascript:$.ajax({url: 'http://127.0.0.1:60151/goto?locus=chr{{ entry.chromosome }}:{{ entry.start }}-{{ entry.end }}'})"
title="Go to locus in IGV"
class="btn btn-secondary sodar-list-btn"
>
IGV
</button>
<button type="button" class="btn btn-secondary dropdown-toggle dropdown-toggle-split sodar-list-dropdown" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
<span class="sr-only">Toggle Dropdown</span>
</button>
<div class="dropdown-menu dropdown-menu-right" style="z-index: 1030;">
{% linkout_available_for "ucsc" entry.release as ucsc_available %}
{% if ucsc_available %}
<a class="dropdown-item" href="https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg19&position={{ entry.chromosome }}:{{ entry.start }}-{{ entry.end }}" target="_blank">
Locus @UCSC
</a>
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="UCSC browser not available for reference {{ entry.release }}">
Locus @UCSC
</span>
{% endif %}

{% linkout_available_for "dgv" entry.release as dgv_available %}
{% if dgv_available %}
<a class="dropdown-item" href="http://dgv.tcag.ca/gb2/gbrowse/dgv2_hg19/?name={{ entry.chromosome }}:{{ entry.start }}-{{ entry.end }};search=Search" target="_blank">
Locus @DGV
</a>
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="DGV browser not available for reference {{ entry.release }}">
Locus @DGV
</span>
{% endif %}
{% linkout_available_for "ensembl" entry.release as ensembl_available %}
{% if ensembl_available %}
<a class="dropdown-item" href="https://{% if entry.release == "GRCh37" %}grch37{% else %}www{% endif %}.ensembl.org/Homo_sapiens/Location/View?r={{ entry.chromosome }}:{{ entry.start }}-{{ entry.end }}" target="_blank">
Locus @EnsEMBL
</a>
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="ENSEMBL browser not available for reference {{ entry.release }}">
Locus @EnsEMBL
</span>
{% endif %}

{% linkout_available_for "gnomad" entry.release as gnomad_available %}
{% if gnomad_available %}
<a class="dropdown-item" href="http://gnomad.broadinstitute.org/region/{{ entry.chromosome }}-{{ entry.start }}-{{ entry.end }}" target="_blank">
Locus @gnomAD
</a>
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="gnomAD browser not available for reference {{ entry.release }}">
Locus @gnomAD
</span>
{% endif %}
{% linkout_available_for "dgv" entry.release as dgv_available %}
{% if dgv_available %}
<a class="dropdown-item" href="http://dgv.tcag.ca/gb2/gbrowse/dgv2_hg19/?name={{ entry.chromosome }}:{{ entry.start }}-{{ entry.end }};search=Search" target="_blank">
Locus @DGV
</a>
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="DGV browser not available for reference {{ entry.release }}">
Locus @DGV
</span>
{% endif %}

<div class="dropdown-divider"></div>
{% linkout_available_for "gnomad" entry.release as gnomad_available %}
{% if gnomad_available %}
<a class="dropdown-item" href="http://gnomad.broadinstitute.org/region/{{ entry.chromosome }}-{{ entry.start }}-{{ entry.end }}" target="_blank">
Locus @gnomAD
</a>
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="gnomAD browser not available for reference {{ entry.release }}">
Locus @gnomAD
</span>
{% endif %}

<a href="javascript:humanSplicingFinder('{{ symbol }}', '{{ entry.hgvs_c }}');"
data-toggle="tooltip"
title="Query Human Splicing Finder"
class="dropdown-item">
Query Human Splicing Finder
</a>
<div class="dropdown-divider"></div>

<a href="https://varseak.bio/ssp.php?gene={{ symbol|urlencode }}&hgvs={{ entry.hgvs_c|urlencode }}&&transcript={{ entry.refseq_transcript_id }}"
data-toggle="tooltip"
title="Query varSEAK Splice Site Prediction"
target="_blank"
class="dropdown-item">
Query varSEAK Splicing
</a>
<a href="javascript:humanSplicingFinder('{{ symbol }}', '{{ entry.hgvs_c }}');"
data-toggle="tooltip"
title="Query Human Splicing Finder"
class="dropdown-item">
Query Human Splicing Finder
</a>

{% if "missense_variant" in entry.effect %}
<a href="javascript:polyPhen2('{{ symbol }}', '{{ entry.hgvs_p }}');"
<a href="https://varseak.bio/ssp.php?gene={{ symbol|urlencode }}&hgvs={{ entry.hgvs_c|urlencode }}&&transcript={{ entry.refseq_transcript_id }}"
data-toggle="tooltip"
title="Query PolyPhen 2"
title="Query varSEAK Splice Site Prediction"
target="_blank"
class="dropdown-item">
Query PolyPhen 2
Query varSEAK Splicing
</a>
{% else %}
<span class="dropdown-item disabled">
PolyPhen 2: missense only
</span>
{% endif %}

{% linkout_available_for "umd" entry.release as umd_available %}
{% if umd_available %}
{% if entry.reference|length != 1 or entry.alternative|length != 1 %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="UMD Predictor can only predict SNVs">
UMD Predictor: SNV only
{% if "missense_variant" in entry.effect %}
<a href="javascript:polyPhen2('{{ symbol }}', '{{ entry.hgvs_p }}');"
data-toggle="tooltip"
title="Query PolyPhen 2"
class="dropdown-item">
Query PolyPhen 2
</a>
{% else %}
<span class="dropdown-item disabled">
PolyPhen 2: missense only
</span>
{% elif umd_predictor_api_token %}
<a href="{% linkout_base_url "umd" entry.release %}chromosome=chr{{ entry.chromosome }}&c_position={{ entry.start }}&wt_nucleotide={{ entry.reference }}&mutant_nucleotide={{ entry.alternative }}&token={{ umd_predictor_api_token }}"
{% endif %}

{% linkout_available_for "umd" entry.release as umd_available %}
{% if umd_available %}
{% if entry.reference|length != 1 or entry.alternative|length != 1 %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="UMD Predictor can only predict SNVs">
UMD Predictor: SNV only
</span>
{% elif umd_predictor_api_token %}
<a href="{% linkout_base_url "umd" entry.release %}chromosome=chr{{ entry.chromosome }}&c_position={{ entry.start }}&wt_nucleotide={{ entry.reference }}&mutant_nucleotide={{ entry.alternative }}&token={{ umd_predictor_api_token }}"
data-toggle="tooltip"
title="Query UMD Predictor"
target="_blank"
class="dropdown-item">
Query UMD Predictor
</a>
{# #}
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="Configure your UMD Predictor API token in the user settings.">
UMD Predictor: no key
</span>
{% endif %}
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="UMD not available for reference {{ entry.release }}">
UMD Predictor
</span>
{% endif %}

{% linkout_available_for "varsome" entry.release as varsome_available %}
{% if varsome_available %}
<a href="{% linkout_base_url "varsome" entry.release %}{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}"
data-toggle="tooltip"
title="Query UMD Predictor"
title="View variant in varsome"
target="_blank"
class="dropdown-item">
Query UMD Predictor
Query Varsome
</a>
{# #}
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="Configure your UMD Predictor API token in the user settings.">
UMD Predictor: no key
<span class="dropdown-item disabled" data-toggle="tooltip" title="Varsome not available for reference {{ entry.release }}">
Query Varsome
</span>
{% endif %}
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="UMD not available for reference {{ entry.release }}">
UMD Predictor
</span>
{% endif %}

{% linkout_available_for "varsome" entry.release as varsome_available %}
{% if varsome_available %}
<a href="{% linkout_base_url "varsome" entry.release %}{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}"
data-toggle="tooltip"
title="View variant in varsome"
target="_blank"
class="dropdown-item">
Query Varsome
</a>
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="Varsome not available for reference {{ entry.release }}">
Query Varsome
</span>
{% endif %}

{% linkout_available_for "variant_validator" entry.release as vv_available %}
{% if vv_available %}
<a
data-toggle="modal"
data-target="#variantvalidatormodal-{{ entry.release }}-{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}"
title="Submit variant to VariantValidator"
onclick="if ($('#variantvalidatormodal-{{ entry.release }}-{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}').find('.variant-validator-results').children().length == 0){$('#variantvalidatormodalsubmit-{{ entry.release }}-{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}').click();}"
class="dropdown-item">
Query VariantValidator
</a>
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="VariantValidator not available for reference {{ entry.release }}">
Query VariantValidator
</span>
{% endif %}
{% linkout_available_for "variant_validator" entry.release as vv_available %}
{% if vv_available %}
<a
data-toggle="modal"
data-target="#variantvalidatormodal-{{ entry.release }}-{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}"
title="Submit variant to VariantValidator"
onclick="if ($('#variantvalidatormodal-{{ entry.release }}-{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}').find('.variant-validator-results').children().length == 0){$('#variantvalidatormodalsubmit-{{ entry.release }}-{{ entry.chromosome }}-{{ entry.start }}-{{ entry.reference }}-{{ entry.alternative }}').click();}"
class="dropdown-item">
Query VariantValidator
</a>
{% else %}
<span class="dropdown-item disabled" data-toggle="tooltip" title="VariantValidator not available for reference {{ entry.release }}">
Query VariantValidator
</span>
{% endif %}
</div>
</div>
</div>
<!-- Modal -->
Expand Down