scout-browser 4.83__py3-none-any.whl → 4.84__py3-none-any.whl

scout/models/hgnc_map.py

@@ -2,6 +2,8 @@ from __future__ import unicode_literals
 
 from typing import List, Optional
 
+from pydantic import BaseModel, Field, field_validator, model_validator
+
 
 class Exon(dict):
     """Exon dictionary
@@ -66,90 +68,51 @@ class HgncTranscript(dict):
                 self["mane_plus_clinical"] = mane_plus_clinical
 
 
-class HgncGene(dict):
-    """HgncGene dictionary
-
-    'hgnc_id': int, # This is the hgnc id, required:
-    'hgnc_symbol': str, # The primary symbol, required
-    'ensembl_id': str, # required
-    'build': str, # '37' or '38', defaults to '37', required
-
-    'chromosome': str, # required
-    'start': int, # required
-    'end': int, # required
-
-    'description': str, # Gene description
-    'aliases': list(), # Gene symbol aliases, includes hgnc_symbol, str
-    'entrez_id': int,
-    'omim_id': int,
-    'pli_score': float,
-    'primary_transcripts': list(), # List of refseq transcripts (str)
-    'ucsc_id': str,
-    'uniprot_ids': list(), # List of str
-    'vega_id': str,
-
-    # Inheritance information
-    'inheritance_models': list(), # List of model names
-    'incomplete_penetrance': bool, # Acquired from HPO
-
-    # Phenotype information
-    'phenotypes': list(), # List of dictionaries with phenotype information
-    """
-
-    def __init__(
-        self,
-        hgnc_id,
-        hgnc_symbol,
-        ensembl_id,
-        chrom,
-        start,
-        end,
-        description=None,
-        aliases=None,
-        entrez_id=None,
-        omim_id=None,
-        pli_score=None,
-        primary_transcripts=None,
-        ucsc_id=None,
-        uniprot_ids=None,
-        vega_id=None,
-        inheritance_models=None,
-        incomplete_penetrance=False,
-        phenotypes=None,
-        build="37",
-    ):
-        super(HgncGene, self).__init__()
-        self["hgnc_id"] = int(hgnc_id)
-        self["hgnc_symbol"] = hgnc_symbol
-        self["ensembl_id"] = ensembl_id
-
-        self["chromosome"] = chrom
-        self["start"] = int(start)
-        self["end"] = int(end)
-        self["length"] = self["end"] - self["start"]
-
-        self["description"] = description
-        self["aliases"] = aliases
-        self["primary_transcripts"] = primary_transcripts
-        self["inheritance_models"] = inheritance_models
-        self["phenotypes"] = phenotypes
-
-        self["entrez_id"] = entrez_id
-        if entrez_id:
-            self["entrez_id"] = int(entrez_id)
-
-        self["omim_id"] = omim_id
-        if omim_id:
-            self["omim_id"] = int(omim_id)
-
-        self["ucsc_id"] = ucsc_id
-        self["uniprot_ids"] = uniprot_ids
-        self["vega_id"] = vega_id
-
-        self["pli_score"] = pli_score
-        if pli_score:
-            self["pli_score"] = float(pli_score)
-
-        self["incomplete_penetrance"] = incomplete_penetrance
-
-        self["build"] = build
+class HgncGene(BaseModel):
+    hgnc_id: int
+    hgnc_symbol: str
+    build: str
+    chromosome: str
+    start: int
+    end: int
+    length: int
+    description: Optional[str] = None
+    ensembl_id: Optional[str] = Field(None, alias="ensembl_gene_id")
+    aliases: Optional[List[str]] = Field(None, alias="previous_symbols")
+    entrez_id: Optional[int] = None
+    omim_id: Optional[int] = None
+    primary_transcripts: Optional[List[str]] = Field(None, alias="ref_seq")
+    ucsc_id: Optional[str] = None
+    uniprot_ids: Optional[List[str]] = None
+    vega_id: Optional[str] = None
+    inheritance_models: Optional[List[str]] = None
+    incomplete_penetrance: Optional[bool] = False
+    phenotypes: Optional[List[dict]] = None
+    pli_score: Optional[float] = None
+    constraint_lof_oe: Optional[float] = None
+    constraint_lof_oe_ci_lower: Optional[float] = None
+    constraint_lof_oe_ci_upper: Optional[float] = None
+    constraint_lof_z: Optional[float] = None
+    constraint_mis_oe: Optional[float] = None
+    constraint_mis_oe_ci_lower: Optional[float] = None
+    constraint_mis_oe_ci_upper: Optional[float] = None
+    constraint_mis_z: Optional[float] = None
+
+    @model_validator(mode="before")
+    def set_gene_length(cls, values) -> "HgncGene":
+        """Set gene length."""
+        if None in [values.get("end"), values.get("start")]:
+            values.update({"length": None})
+        else:
+            values.update({"length": values.get("end") - values.get("start")})
+        return values
+
+    @field_validator("phenotypes", mode="before")
+    @classmethod
+    def set_phenotypes_inheritance(cls, phenotypes) -> Optional[List[dict]]:
+        """Convert field 'inheritance' of each phenotype in phenotypes from set to list."""
+        for phenotype in phenotypes:
+            phenotype["inheritance_models"] = list(phenotype.get("inheritance", {}))
+            phenotype.pop("inheritance", None)
+
+        return phenotypes

scout/models/phenotype_term.py

@@ -14,9 +14,9 @@ class HpoTerm(BaseModel):
     """
 
     hpo_id: str  # id field in the hpo.obo file
-    hpo_number: Optional[
-        int
-    ] = None  # id field in the hpo.obo file, stripped of the 'HP:' part and the zeroes
+    hpo_number: Optional[int] = (
+        None  # id field in the hpo.obo file, stripped of the 'HP:' part and the zeroes
+    )
     description: str  # name field in the hpo.obo file
     ancestors: List = []
     all_ancestors: List = []

scout/parse/orpha.py

@@ -1,4 +1,5 @@
 """Code for parsing ORPHA formatted files"""
+
 import logging
 from typing import Any, Dict, List
 from xml.etree.ElementTree import Element

scout/parse/variant/conservation.py

@@ -1,4 +1,5 @@
 """Code for parsing conservation"""
+
 import logging
 import numbers
 

scout/server/blueprints/cases/templates/cases/case.html

@@ -65,7 +65,7 @@
                 <span class="badge rounded-pill bg-info text-body" data-bs-toggle="tooltip" data-bs-placement="left" title="Matching causatives and managed variants displayed on case page are NOT filtered by gene panel. Use caution to avoid incidental findings.">off</span>
               {% endif %}
             </div>
-        </div> <!--end of div class="row" -->
+        </div> <!--end of row -->
         <div class="row">
           <form id="case_status_form" method="POST" action="{{ url_for('cases.status', institute_id=institute._id, case_name=case.display_name) }}">
               <div class="btn-toolbar ms-2" role="toolbar">
@@ -105,7 +105,7 @@
                     {{ 'Inactive' if case.status == 'ignored' else 'Ignored' }}
                   </button>
                 </div>
-                <div class="btn-group ms-2 role="group">
+                <div class="btn-group ms-2" role="group">
                   <select name="tags" id="status_tags_case" multiple class="selectpicker" data-style="btn btn-secondary">
                     {% for tag, data in case_tag_options.items() %}
                       <option {% if 'tags' in case and tag~"" in case.tags %} selected {% endif %} value="{{ tag }}" title="{{ data.label }}">
@@ -119,103 +119,65 @@
         </div>
       </div>
 
+      {{ matching_variants() }}
+
       <div class="card panel-default" >
-        <div class="row mt-0">
-          <div class="col-sm-12 col-md-12 ms-3">
-           <div data-bs-toggle='tooltip' class="panel-heading" title="Check if there are any variants in this case
-              marked as causative in another case for this institute, or are on the managed variants list.">
-             <strong>{% if hide_matching == false %}
-               <a href="{{ url_for('cases.case', institute_id=institute._id, case_name=case.display_name, hide_matching='True') }}" class="text-body"><span class="me-1 fa fa-caret-right"></span>Search for matching causatives and managed variants</a>
-             {% else %}
-               <a href="{{ url_for('cases.case', institute_id=institute._id, case_name=case.display_name, hide_matching='False') }}" class="text-body"><span class="me-1 fa fa-caret-down"></span>Search for matching causatives and managed variants</a>
-             {% endif %}
-             </strong>
-           </div>
-          </div>
+        <div class="row">
+          <div class="col">{{ causatives_list(causatives, partial_causatives, evaluated_variants, institute, case, manual_rank_options, cancer_tier_options) }}</div>
+          <div class="col">{{ suspects_list(suspects, institute, case, manual_rank_options, cancer_tier_options) }}</div>
+          <!-- end of data sharing panels -->
         </div>
-        {% if hide_matching == false %}
-        {% if other_causatives|length > 0 %}
-          <div class="row mt-0 ms-3">
-            <div class="col-xs-12 col-md-12 ms-3">{{ matching_causatives(other_causatives, institute, case) }}</div>
-          </div>
-        {% endif %}
-        {% if default_other_causatives|length > 0%}
-          <div class="row mt-0 ms-3">
-            <div class="col-xs-12 col-md-12 ms-3">{{ matching_causatives(default_other_causatives, institute, case, default=True) }}</div>
-          </div>
-        {% endif %}
-        {% if managed_variants|length > 0%}
-          <div class="row mt-0 ms-3">
-            <div class="col-sm-12 col-md-12 ms-3">{{ matching_managed_variants(managed_variants, institute, case) }}</div>
-          </div>
-        {% endif %}
-        {% if default_managed_variants|length > 0%}
-          <div class="row mt-0 ms-3">
-            <div class="col-sm-12 col-md-12 ms-3">{{ matching_managed_variants(default_managed_variants, institute, case, default=True) }}</div>
-          </div>
-        {% endif %}
-        {% if other_causatives|length == 0 and default_other_causatives|length == 0 and managed_variants|length == 0 and default_managed_variants|length == 0%}
-          <div class="row mt-0 ms-3">
-            <div class="col-sm-12 col-md-12 ms-3">No matching causatives or managed variants found</div>
-          </div>
-        {% endif %}
-      {% endif %}
-      <div class="row">
-        <div class="col">{{ causatives_list(causatives, partial_causatives, evaluated_variants, institute, case, manual_rank_options, cancer_tier_options) }}</div>
-        <div class="col">{{ suspects_list(suspects, institute, case, manual_rank_options, cancer_tier_options) }}</div>
-        <!-- end of data sharing panels -->
-      </div>
 
-      <div class="row">
-        {% if case.track == 'cancer' %}
-          <div class="col-sm-12 col-md-12 mt-3">{{ cancer_individuals_table(case, institute, tissue_types, gens_info) }}</div>
-        {% else %}
-          <div class="mt-3 col-sm-8 col-md-{{"8" if case.madeline_info and case.individuals|length > 1 else "12"}}">{{ individuals_table(case, institute, tissue_types, display_rerunner, gens_info) }}</div>
-          {% if case.madeline_info and case.individuals|length > 1 %}
-            <div class="col-sm-4">
-              {{ pedigree_panel(case) }}
-            </div>
+        <div class="row">
+          {% if case.track == 'cancer' %}
+            <div class="col-sm-12 col-md-12 mt-3">{{ cancer_individuals_table(case, institute, tissue_types, gens_info) }}</div>
+          {% else %}
+            <div class="mt-3 col-sm-8 col-md-{{"8" if case.madeline_info and case.individuals|length > 1 else "12"}}">{{ individuals_table(case, institute, tissue_types, display_rerunner, gens_info) }}</div>
+            {% if case.madeline_info and case.individuals|length > 1 %}
+              <div class="col-sm-4">
+                {{ pedigree_panel(case) }}
+              </div>
+            {% endif %}
           {% endif %}
-        {% endif %}
-      </div>
-
-      <div class="row mt-3">
-        <div class="col-6">{{ synopsis_panel() }}</div>
-        <div class="col-6">{{ comments_panel(institute, case, current_user, comments) }}</div>
-      </div>
+        </div>
 
-      <div class="row">
-        <div class="col-sm-12">
-          {{ insert_multi_image_panel() }}
+        <div class="row mt-3">
+          <div class="col-6">{{ synopsis_panel() }}</div>
+          <div class="col-6">{{ comments_panel(institute, case, current_user, comments) }}</div>
         </div>
-      </div>
 
-      <div class="row">
-        <div class="col-sm-12">
-          {{ custom_image_panels() }}
+        <div class="row">
+          <div class="col-sm-12">
+            {{ insert_multi_image_panel() }}
+          </div>
         </div>
-      </div>
 
-      <!-- CASE DIAGNOSES AND PHENOTYPES -->
-      <div class="panel-default">
-        <div class="panel-heading"><span class="fa fa-user-md"></span>&nbsp;Phenotypes & diagnoses</div>
         <div class="row">
-          <div class="col-sm-6 ">
-            <div class="card h-100">
-              <div class="card-body">
-                {{ hpo_panel(case, institute, config) }}
+          <div class="col-sm-12">
+            {{ custom_image_panels() }}
+          </div>
+        </div>
+
+        <!-- CASE DIAGNOSES AND PHENOTYPES -->
+        <div class="panel-default">
+          <div class="panel-heading"><span class="fa fa-user-md"></span>&nbsp;Phenotypes & diagnoses</div>
+          <div class="row">
+            <div class="col-sm-6 ">
+              <div class="card h-100">
+                <div class="card-body">
+                  {{ hpo_panel(case, institute, config) }}
+                </div>
               </div>
             </div>
-          </div>
-          <div class="col-sm-6">
-            <div class="card h-100">
-              <div class="card-body">
-                {{ hpo_genelist_panel(case, institute, config) }}
+            <div class="col-sm-6">
+              <div class="card h-100">
+                <div class="card-body">
+                  {{ hpo_genelist_panel(case, institute, config) }}
+                </div>
               </div>
             </div>
-          </div>
-        </div> <!--end of <div class="row">-->
-        </div>
+          </div> <!--end of row>-->
+        </div> <!--end of card panel-default  -->
 
           <!-- diagnoses-related code-->
         {% if not case.track == 'cancer' %}
@@ -259,8 +221,8 @@
       {{ reanalysis_modal(institute, case) }}
       {{ beacon_modal(institute, case) }}
       {{ matchmaker_modal(institute, case, suspects, mme_nodes) }}
-  </div><!-- end of <div containter> -->
-</div><!-- end of <div col> -->
+  </div><!-- end of containter -->
+</div><!-- end of col -->
 {% endmacro %}
 
 {% macro variants_buttons() %}
@@ -398,7 +360,7 @@
           </div>
         {% endfor %}
       {% endif %}
-      </div> <!-- end of <div class="list-group" style="max-height:200px; overflow-y: scroll;" -->
+      </div> <!-- end of list-group -->
     </div>
   </div>
 {% endmacro %}
@@ -574,6 +536,51 @@
 </div>
 {% endmacro %}
 
+{% macro matching_variants() %}
+<div class="card mt-3">
+  <div class="row mt-0 ms-3">
+    <div class="col-sm-12 col-md-12">
+      <div data-bs-toggle='tooltip' class="panel-heading" title="Check if there are any variants in this case
+        marked as causative in another case for this institute, or are on the managed variants list.">
+        <strong>
+        {% if hide_matching == false %}
+          <a href="{{ url_for('cases.case', institute_id=institute._id, case_name=case.display_name, hide_matching='True') }}" class="text-body"><span class="me-1 fa fa-caret-down"></span>Search for matching causatives and managed variants</a>
+        {% else %}
+          <a href="{{ url_for('cases.case', institute_id=institute._id, case_name=case.display_name, hide_matching='False') }}" class="text-body"><span class="me-1 fa fa-caret-right"></span>Search for matching causatives and managed variants</a>
+        {% endif %}
+        </strong>
+      </div>
+    </div>
+    {% if hide_matching == false %}
+      {% if other_causatives|length > 0 %}
+        <div class="row mt-0 ms-3">
+          <div class="col-xs-12 col-md-12">{{ matching_causatives(other_causatives, institute, case) }}</div>
+        </div>
+      {% endif %}
+      {% if default_other_causatives|length > 0%}
+        <div class="row mt-0 ms-3">
+          <div class="col-xs-12 col-md-12">{{ matching_causatives(default_other_causatives, institute, case, default=True) }}</div>
+        </div>
+      {% endif %}
+      {% if managed_variants|length > 0%}
+        <div class="row mt-0 ms-3">
+          <div class="col-sm-12 col-md-12">{{ matching_managed_variants(managed_variants, institute, case) }}</div>
+        </div>
+      {% endif %}
+      {% if default_managed_variants|length > 0%}
+        <div class="row mt-0 ms-3">
+          <div class="col-sm-12 col-md-12">{{ matching_managed_variants(default_managed_variants, institute, case, default=True) }}</div>
+        </div>
+      {% endif %}
+      {% if other_causatives|length == 0 and default_other_causatives|length == 0 and managed_variants|length == 0 and default_managed_variants|length == 0%}
+        <div class="row mt-0 ms-3">
+          <div class="col-sm-12 col-md-12">No matching causatives or managed variants found</div>
+        </div>
+      {% endif %}
+    {% endif %}
+  </div>
+</div>
+{% endmacro %}
 
 {% block scripts %}
 {{ super() }}

scout/server/blueprints/panels/forms.py

@@ -1,4 +1,5 @@
 """Code for panel gene form"""
+
 from flask_wtf import FlaskForm
 from wtforms import BooleanField, SelectMultipleField, StringField
 

scout/server/blueprints/variant/controllers.py

@@ -486,26 +486,21 @@ def observations(store: MongoAdapter, loqusdb: LoqusDB, variant_obj: dict) -> Di
     loqus_query = loqusdb.get_loqus_query(variant_obj, category)
 
     for loqus_id in inst_loqus_ids:  # Loop over all loqusdb instances of an institute
-        obs_data[loqus_id] = {}
-        loqus_settings = loqusdb.loqusdb_settings.get(loqus_id)
+        # collect observation on that loqusdb instance
+        obs_data[loqus_id] = loqusdb.get_variant(loqus_query, loqusdb_id=loqus_id)
 
-        if loqus_settings is None:  # An instance might have been renamed or removed
+        if obs_data[loqus_id] is None:
             flash(
-                f"Could not connect to the preselected loqusdb '{loqus_id}' instance",
+                f"Could not find a Loqus instance with id:{loqus_id}",
                 "warning",
             )
-            obs_data[loqus_id]["total"] = "N/A"
+            obs_data[loqus_id]["observations"] = "N/A"
             continue
-        obs_data[loqus_id] = loqusdb.get_variant(
-            loqus_query, loqusdb_id=loqus_id
-        )  # collect observation on that loqus instance
-
-        if not obs_data[loqus_id]:  # data is an empty dictionary
-            # Collect count of variants in variant's case
-            obs_data[loqus_id] = loqusdb.get_variant(loqus_query, loqusdb_id=loqus_id)
-            if obs_data[loqus_id].get("total"):
-                obs_data[loqus_id]["observations"] = 0
+
+        if obs_data[loqus_id] == {}:  # Variant was not found
+            obs_data[loqus_id]["observations"] = 0
             continue
+
         # Check if the current case is represented in the loqusdb instance
         obs_data[loqus_id]["case_match"] = variant_obj["case_id"] in obs_data[loqus_id].get(
             "families", []

scout/server/blueprints/variants/controllers.py

@@ -3,12 +3,10 @@ import logging
 import re
 from typing import Any, Dict, List, Optional
 
-import bson
 from flask import Response, flash, session, url_for
 from flask_login import current_user
 from markupsafe import Markup
 from pymongo.cursor import CursorType
-from pymongo.errors import DocumentTooLarge
 from werkzeug.datastructures import Headers, ImmutableMultiDict, MultiDict
 from wtforms import DecimalField
 
@@ -513,7 +511,7 @@ def update_variant_genes(store, variant_obj, genome_build):
 
     if variant_genes is not None:
         for gene_obj in variant_genes:
-            # If there is no hgnc id there is nothin we can do
+            # If there is no hgnc id there is nothing we can do
             if not gene_obj["hgnc_id"]:
                 continue
             # Else we collect the gene object and check the id
@@ -530,27 +528,6 @@ def update_variant_genes(store, variant_obj, genome_build):
     return has_changed
 
 
-def update_variant_store(store, variant_obj):
-    """
-    Update variants in db store if anything changed.
-    Args:
-        store(scout.adapter.MongoAdapter)
-        variant_obj(scout.models.Variant)
-
-        update(boolean): upsert only if this is set true
-
-        get_compounds(bool): if compounds should be added to added to the returned variant object
-
-    """
-    try:
-        variant_obj = store.update_variant(variant_obj)
-    except DocumentTooLarge:
-        flash(
-            f"An error occurred while updating info for variant: {variant_obj['_id']} (pymongo_errors.DocumentTooLarge: {len(bson.BSON.encode(variant_obj))})",
-            "warning",
-        )
-
-
 def _compound_follow_filter_freq(compound, compound_var_obj, query_form):
     """When compound follow filter is selected, apply relevant settings from the query filter onto dismissing compounds.
 
@@ -895,11 +872,18 @@ def parse_variant(
     compounds_have_changed = False
     if get_compounds:
         compounds_have_changed = update_compounds(store, variant_obj, case_dismissed_vars)
+        if update and compounds_have_changed:
+            store.variant_update_field(
+                variant_id=variant_obj["_id"],
+                field_name="compounds",
+                field_value=variant_obj["compounds"],
+            )
 
     genes_have_changed = update_variant_genes(store, variant_obj, genome_build)
-
-    if update and (compounds_have_changed or genes_have_changed):
-        update_variant_store(store, variant_obj)
+    if update and genes_have_changed:
+        store.variant_update_field(
+            variant_id=variant_obj["_id"], field_name="genes", field_value=variant_obj["genes"]
+        )
 
     variant_obj["comments"] = store.events(
         institute_obj,

scout/server/extensions/bionano_extension.py

@@ -6,6 +6,7 @@
     For further development, the server has a Swagger-like demo interface at https://bionano-access.scilifelab.se/Bnx/
     which is useful for details, and for sniffing actual message content structure, required cookie variable names etc.
 """
+
 import json
 import logging
 from typing import Dict, Iterable, List, Optional, Tuple

scout/server/extensions/chanjo_extension.py

@@ -9,21 +9,22 @@ from flask_babel import Babel
 from markupsafe import Markup
 
 LOG = logging.getLogger(__name__)
-try:
-    from chanjo_report.server.app import configure_template_filters
-    from chanjo_report.server.blueprints import report_bp
-    from chanjo_report.server.extensions import api as chanjo_api
-except ImportError as error:
-    chanjo_api = None
-    report_bp = None
-    configure_template_filters = None
-    LOG.warning("chanjo-report is not properly installed! %s.", error)
 
 
 class ChanjoReport:
     """Interfaces with chanjo-report. Creates the /reports endpoints in scout domain. Use Babel to set report language."""
 
     def init_app(self, app):
+        try:
+            from chanjo_report.server.app import configure_template_filters
+            from chanjo_report.server.blueprints import report_bp
+            from chanjo_report.server.extensions import api as chanjo_api
+        except ImportError as error:
+            chanjo_api = None
+            report_bp = None
+            configure_template_filters = None
+            LOG.error(error)
+
         if not chanjo_api:
             raise ImportError(
                 "An SQL db path was given, but chanjo-report could not be registered."

scout/server/extensions/gens_extension.py

@@ -2,6 +2,7 @@
 
 * Requires gens version 1.1.1 or greater
 """
+
 import logging
 
 LOG = logging.getLogger(__name__)

scout/server/extensions/ldap_extension.py

@@ -43,9 +43,11 @@ class LdapManager(LDAPConn):
         self.tls = Tls(
             local_private_key_file=app.config["LDAP_CLIENT_PRIVATE_KEY"],
             local_certificate_file=app.config["LDAP_CLIENT_CERT"],
-            validate=app.config["LDAP_REQUIRE_CERT"]
-            if app.config.get("LDAP_CLIENT_CERT")
-            else ssl.CERT_NONE,
+            validate=(
+                app.config["LDAP_REQUIRE_CERT"]
+                if app.config.get("LDAP_CLIENT_CERT")
+                else ssl.CERT_NONE
+            ),
             version=app.config["LDAP_TLS_VERSION"],
             ca_certs_file=app.config["LDAP_CA_CERTS_FILE"],
             valid_names=app.config["LDAP_VALID_NAMES"],