scout-browser 4.89__py3-none-any.whl → 4.89.2__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
scout/__version__.py CHANGED
@@ -1 +1 @@
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- __version__ = "4.89"
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+ __version__ = "4.89.2"
@@ -335,7 +335,7 @@ class GeneHandler(object):
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  Returns:
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  alias_genes(dict): {<hgnc_alias>: {'true': <hgnc_id>, 'ids': {<hgnc_id_1>, <hgnc_id_2>, ...}}}
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  """
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- LOG.debug("Fetching all genes by alias")
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+
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  # Collect one entry for each alias symbol that exists
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  alias_genes = {}
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scout/parse/panel.py CHANGED
@@ -2,7 +2,7 @@
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  import logging
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  from datetime import datetime
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- from typing import Dict, List, Optional
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+ from typing import Dict, Optional
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  from scout.constants import (
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  INCOMPLETE_PENETRANCE_MAP,
@@ -383,7 +383,7 @@ def parse_panel_app_panel(
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  return gene_panel
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- def get_omim_panel_genes(genemap2_lines, mim2gene_lines, alias_genes):
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+ def get_omim_panel_genes(genemap2_lines: list, mim2gene_lines: list, alias_genes: dict):
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  """Return all genes that should be included in the OMIM-AUTO panel
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  Return the hgnc symbols
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@@ -424,6 +424,19 @@ def get_omim_panel_genes(genemap2_lines, mim2gene_lines, alias_genes):
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  break
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  if hgnc_id_info:
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- yield {"hgnc_id": hgnc_id_info["true"], "hgnc_symbol": hgnc_symbol}
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+ if hgnc_id_info["true"]:
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+ hgnc_id = hgnc_id_info["true"]
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+ elif len(hgnc_id_info.get("ids", ())) == 1:
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+ hgnc_id = list(hgnc_id_info["ids"])[0]
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+ LOG.warning(
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+ "Gene symbol %s does not exist: using an apparently unique alias for hgnc_id %s",
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+ hgnc_symbol,
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+ hgnc_id,
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+ )
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+ else:
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+ LOG.warning(
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+ "Gene symbol %s does not exist, and as an alias it is not unique", hgnc_symbol
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+ )
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+ yield {"hgnc_id": hgnc_id, "hgnc_symbol": hgnc_symbol}
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  else:
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  LOG.warning("Gene symbol %s does not exist", hgnc_symbol)
@@ -1099,7 +1099,9 @@
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  <td>
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  <ul>
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  {% for disease_term in gene.disease_terms %}
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- <li class="d-flex align-items-baseline"><span class="badge bg-secondary m-1">{{ disease_term._id}}</span>&nbsp;<span>{{ disease_term.description }}&nbsp;{{ disease_term.inheritance }}</span></li>
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+ <li class="d-flex align-items-baseline"><span class="badge bg-secondary m-1">{{ disease_term._id}}</span>&nbsp;<span>{{ disease_term.description }}&nbsp;{% if disease_term.source != 'ORPHA' and disease_term.inheritance %}
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+ {% for model in disease_term.inheritance %} {{ inheritance_badge(model,inherit_palette) }}{% endfor %}
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+ {% endif %}</span></li>
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  {% endfor %}
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  </ul>
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  </td>
@@ -1140,7 +1142,7 @@
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  {{ variant_phenotypes(variant) }}
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  </div>
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  <div class="card-body">
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- <table id="panel-table" class="table table-sm table-bordered" style="background-color: transparent; margin-left:-.3rem;>
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+ <table id="panel-table" class="table table-sm table-bordered" style="background-color: transparent; margin-left:-.3rem;">
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  <thead>
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  <tr class="table-secondary">
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  <th>Variant type</th>
@@ -1262,7 +1264,7 @@
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  {{ variant.str_inheritance_mode if variant.str_inheritance_mode else "-" }}
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  </td>
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  <td>
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- {% if variant.str_source.display %}
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+ {% if variant.str_source and variant.str_source.display %}
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  <a style="text-decoration:none;" href="{{variant.str_source_link}}" target="_blank" rel="noopener noreferrer">{{ variant.str_source.display }} </a>
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  {% else %}
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  "-"
@@ -6,11 +6,69 @@
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  {% block css %}
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  <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-1BmE4kWBq78iYhFldvKuhfTAU6auU8tT94WrHftjDbrCEXSU1oBoqyl2QvZ6jIW3" crossorigin="anonymous">
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  <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/all.min.css" integrity="sha512-1ycn6IcaQQ40/MKBW2W4Rhis/DbILU74C1vSrLJxCq57o941Ym01SwNsOMqvEBFlcgUa6xLiPY/NS5R+E6ztJQ==" crossorigin="anonymous" referrerpolicy="no-referrer" />
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- <link rel="stylesheet" href="{{ url_for('static', filename='bs_styles.css') }}">
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  <style>
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  tr.light-grey td{
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  background-color: LightGray;
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  }
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+
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+ /* affected, archived and similar accents */
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+ .bg-danger-light {
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+ background-color: var(--bs-info);
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+ }
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+
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+ /* define colors to be used as class items */
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+ .bg-red {
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+ background-color: var(--bs-red);
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+ }
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+
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+ .bg-orange {
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+ background-color: var(--bs-orange);
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+ }
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+
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+ .bg-blue {
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+ background-color: var(--bs-blue);
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+ }
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+
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+ .bg-teal {
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+ background-color: var(--bs-teal);
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+ }
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+
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+ .bg-green {
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+ background-color: var(--bs-green);
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+ }
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+
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+ .bg-gray {
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+ background-color: var(--bs-gray);
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+ }
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+
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+ .bg-pink {
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+ background-color: var(--bs-pink);
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+ }
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+
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+ .bg-purple {
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+ background-color: var(--bs-purple);
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+ }
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+
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+ .bg-cyan {
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+ background-color: var(--bs-cyan);
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+ }
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+
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+ .bg-gray-400 {
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+ background-color: var(--bs-gray-400);
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+ }
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+
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+ .bg-gray-dark {
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+ background-color: var(--bs-gray-dark);
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+ }
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+
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+ .bg-yellow {
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+ background-color: var(--bs-yellow);
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+ }
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+
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+ .bg-light {
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+ background-color: var(--bs-light);
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+ }
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+ /* End of css colors */
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  </style>
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  {% endblock %}
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@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: scout-browser
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- Version: 4.89
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+ Version: 4.89.2
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  Summary: Clinical DNA variant visualizer and browser.
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  Home-page: https://github.com/Clinical-Genomics/scout
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  Author: Måns Magnusson
@@ -1,5 +1,5 @@
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  scout/__init__.py,sha256=Z4liXvmEcLkC67ElsWvYHfemPKdWgWI5O6MB6XlDM8M,232
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- scout/__version__.py,sha256=uHM9R1HpJEivvV6bRxxdV4CnINQ5HpyCHvuWWIFpq9w,21
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+ scout/__version__.py,sha256=T7ThRIRkePjiRTDa6aeTTkyfBdSPI1nLqcsHeWWi8Ig,23
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  scout/adapter/__init__.py,sha256=-iX_hx2NI1EMAqX0pMd5_90Nnd9uvIMxv9EbefYBzsc,86
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  scout/adapter/client.py,sha256=IuajRsEwTG41ZP14X09Q1Cj94zIgmIvUtlXfcAFn0EA,1513
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  scout/adapter/mongo/__init__.py,sha256=NdHYCUXWUAuX5cUS3-6HCws2hW9uoGep8i0SC-oJd3k,31
@@ -13,7 +13,7 @@ scout/adapter/mongo/cytoband.py,sha256=2NoIAoQ7RPqcipiSymD2O9qH8lXscP3T5ejquOrD7
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  scout/adapter/mongo/disease_terms.py,sha256=4qcQRLuP5xn_RkB2RlNtwCrONmDuWwdlngZrj87BUEo,5637
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  scout/adapter/mongo/event.py,sha256=NnURFhS5odOXk7So_gGMHmALPAJM0PWzESI4FC06azE,19842
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  scout/adapter/mongo/filter.py,sha256=vzBJS_6vq2z76SH8PszdRR-MNuZ7_RA4VJvnkNYUs7s,8937
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- scout/adapter/mongo/hgnc.py,sha256=9jbrkaTtlnnuE5gsSM8ylb8Kero4lC2zCWr-90QlyAY,16420
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+ scout/adapter/mongo/hgnc.py,sha256=FUzzj9at62jW-ypII6mWrfeDTdQzW4BWgXg3bWRTqGo,16372
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  scout/adapter/mongo/hpo.py,sha256=ps2Pix3sGeea7DenboZVP5j7Vh9WAgX3-sgpbAj0Eck,6871
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  scout/adapter/mongo/index.py,sha256=TZPVv6xBWsEtZpBUWp5uhjuPjQMfVss4lZZju49g1Lw,3577
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  scout/adapter/mongo/institute.py,sha256=GQmMKb_VzsvWwadp6gXHlSSpcG5ovF1ozdTzvpTFLpA,7025
@@ -410,7 +410,7 @@ scout/parse/matchmaker.py,sha256=5e9NCFQ2rKXNCJTW-ThXoEylEPl3H41cCfQzPATQ2QM,952
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  scout/parse/mitodel.py,sha256=3uvEXI9v9wIw97NUL7gqLLxHay0mpQpDgKaIxUbIyrE,803
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  scout/parse/omim.py,sha256=nrCaFZgjUKZo9Jfku2-jcNjdsIYHsvjdWcydz4nCpZA,12465
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  scout/parse/orpha.py,sha256=5u9xqGpAn8vgoJ0uVqbYiqQBiNfBwXOiTzX16kAnmFU,4392
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- scout/parse/panel.py,sha256=4HYjokWh2sF-effLQxPf4ZzRHsf9grqF1Z9f-HAaRmk,13153
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+ scout/parse/panel.py,sha256=xNIzUhyCOBIWtH2avbVvJgZioanMztImG6dV1wXnyO4,13722
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  scout/parse/peddy.py,sha256=uM49GaZMtr8waCsZDvCHDS5JDQ43JUlhdWh9C7f7ZvU,5418
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  scout/parse/smn.py,sha256=iOK1N8iYm9dFigsKtWq0Y0ZCa1CH29s9zeR_tH0bPuc,1153
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  scout/parse/omics_variant/__init__.py,sha256=vq8Ew4_Xr2vPy_3Fg0eTpPWsQpWnUXYBhjRndBUvtTw,422
@@ -460,7 +460,7 @@ scout/server/blueprints/cases/static/edit_pedigree.js,sha256=ntC5fie7SsOYJau8qkk
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  scout/server/blueprints/cases/static/madeline.js,sha256=KHxKMBVlYVJODNu5QkY9hhsGkDJNoaCoCZZ0DRu0YN0,1175
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  scout/server/blueprints/cases/templates/cases/case.html,sha256=9Fcn-OFA1yIHchD0PjDs7-Y8I7Qqr8o6cavN0eOi5rI,37183
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  scout/server/blueprints/cases/templates/cases/case_bionano.html,sha256=PLoRv7hDJcHwxhi-0hC9fQSZc7V_aUYHBhhQqcn_2G8,5946
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- scout/server/blueprints/cases/templates/cases/case_report.html,sha256=CzOIec3hbCXCwIQpB0L0vGQPtYvQjJbJXcir61jUM2Q,63091
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+ scout/server/blueprints/cases/templates/cases/case_report.html,sha256=y7aSvMGQoM8jOt93sBrXBvTkhtE7hIVU2jaoSA6FpM8,63309
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  scout/server/blueprints/cases/templates/cases/case_sma.html,sha256=5kpvNPhOO15wTP_WjYX22wQ_B5-pw4jIQweNXYLbsAU,6281
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  scout/server/blueprints/cases/templates/cases/case_tabular_view.html,sha256=ko-LDUKmIoTazMZ2nFWvPEZsgObU07RwqIkDYFjokoY,4317
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  scout/server/blueprints/cases/templates/cases/chanjo2_form.html,sha256=5Wmk7DM8LI3MynqzxeTzAr_EoEBwVVo31djcI5ZlTdo,2164
@@ -649,7 +649,7 @@ scout/server/static/humans.txt,sha256=UdqAR07_5LAWWfgH2Ty4RR8BhoHS1WXpx9euKtXqqh
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  scout/server/static/robots.txt,sha256=fFX0beQN4x3mzR3evnZjrOUYOTNkezYAwqMowTUpmxM,106
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  scout/server/templates/bootstrap_global.html,sha256=yPauZKUzPvDCj6LUrKnCtkYgn7fPt07-Letxqd-hLw8,2634
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  scout/server/templates/layout.html,sha256=-uhRxFA89L0gocv8sPLcODUHmWLNuV6xsjB34Zjq-8o,4635
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- scout/server/templates/report_base.html,sha256=uRSpk-KaE7ZCE0UOGftWH0bGDQVUTU1bpcVKnDKitq0,1335
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+ scout/server/templates/report_base.html,sha256=bNYzoJFgtYMnfxQYeguwQK9c15ZASdmXd72DaiCfZto,2281
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  scout/server/templates/utils.html,sha256=Wd-glkGqmfJeusnqi1fIjCBSgUflWh0V3MOAnr5V_MU,13000
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  scout/server/translations/sv/LC_MESSAGES/messages.mo,sha256=eI53pCtlYj1MXduDicMZRxBhgOV_TlmMUpH7IhncgDY,4452
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  scout/server/translations/sv/LC_MESSAGES/messages.po,sha256=Wp7Mx4LoiFNtzsV1tpAoWjMxYnq8SpfpU9a4XWJ7L6g,4531
@@ -672,9 +672,9 @@ scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
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  scout/utils/scout_requests.py,sha256=JjHOJW1XmenG05mNQ33kvOKq_IicveIfQMcPZeRcQdo,12856
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  scout/utils/sort.py,sha256=1AcbeZ6vdt_UXM3BLDBa3aQmN4qxrqtskxwD19oBhvw,756
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  scout/utils/track_resources.py,sha256=eUjSEe-Ff8BIb4BHPC_COkJocQO2PaWueiPz1GAuiwY,2614
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- scout_browser-4.89.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
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- scout_browser-4.89.dist-info/METADATA,sha256=N51ZBLfSeqt_rWMckEQocMR34WNvAEXjE8FFyDq321M,14260
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- scout_browser-4.89.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
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- scout_browser-4.89.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
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- scout_browser-4.89.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
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- scout_browser-4.89.dist-info/RECORD,,
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+ scout_browser-4.89.2.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
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+ scout_browser-4.89.2.dist-info/METADATA,sha256=stc_17UT_s4jOKJezGHaktPrwY-h3IJqt1VnGQfm6uI,14262
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+ scout_browser-4.89.2.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
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+ scout_browser-4.89.2.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
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+ scout_browser-4.89.2.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
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+ scout_browser-4.89.2.dist-info/RECORD,,