scout-browser 4.100.2__py3-none-any.whl → 4.102.0__py3-none-any.whl

scout/adapter/mongo/case.py

@@ -6,7 +6,7 @@ import operator
 import re
 from collections import OrderedDict
 from copy import deepcopy
-from typing import Any, Dict, List, Optional
+from typing import Any, Dict, List, Optional, Tuple
 
 import pymongo
 from bson import ObjectId
@@ -928,21 +928,35 @@ class CaseHandler(object):
 
             self.load_omics_variants(case_obj=case_obj, build=build, file_type=omics_file)
 
-    def _load_clinical_variants(self, case_obj: dict, build: str, update: bool = False):
-        """Load variants in the order specified by CLINICAL_ORDERED_FILE_TYPE_MAP."""
+    def get_load_type_categories(self, case_obj: dict) -> List[Tuple[str, str]]:
+        """Return an (ordered) list of tuples pairing variant type and category for loading.
+
+        It is important for predictable variant collisions to retain the order specified in
+        the file type map CLINICAL_ORDERED_FILE_TYPE_MAP. Hence the set operation is made in parallel
+        with the list construction."""
+
         CLINICAL_ORDERED_FILE_TYPE_MAP = OrderedDict(
             (key, value)
             for key, value in ORDERED_FILE_TYPE_MAP.items()
             if value["variant_type"] != "research"
         )
-        load_type_cat = set()
+
+        load_type_cat = []
+        cat_seen = set()
         for file_name, vcf_dict in CLINICAL_ORDERED_FILE_TYPE_MAP.items():
             if not case_obj["vcf_files"].get(file_name):
                 LOG.debug("didn't find {}, skipping".format(file_name))
                 continue
-            load_type_cat.add((vcf_dict["variant_type"], vcf_dict["category"]))
+            pair = (vcf_dict["variant_type"], vcf_dict["category"])
+            if pair not in cat_seen:
+                cat_seen.add(pair)
+                load_type_cat.append(pair)
+        return load_type_cat
+
+    def _load_clinical_variants(self, case_obj: dict, build: str, update: bool = False):
+        """Load variants in the order specified by CLINICAL_ORDERED_FILE_TYPE_MAP."""
 
-        for variant_type, category in load_type_cat:
+        for variant_type, category in self.get_load_type_categories(case_obj):
             if update:
                 self.delete_variants(
                     case_id=case_obj["_id"],

scout/adapter/mongo/clinvar.py

@@ -1,10 +1,10 @@
 # -*- coding: utf-8 -*-
 import logging
+import re
 from datetime import datetime
 from typing import List, Optional
 
 import pymongo
-from bson import ObjectId
 from bson.objectid import ObjectId
 from pymongo import ReturnDocument
 
@@ -393,14 +393,14 @@ class ClinVarHandler(object):
             self.clinvar_collection.delete_one({"_id": object_id})
 
         # in any case remove reference to it in the submission object 'case_data' list field
-        self.clinvar_submission_collection.find_one_and_update(
-            {"_id": ObjectId(submission_id)}, {"$pull": {"case_data": object_id}}
-        )
 
         return self.clinvar_submission_collection.find_one_and_update(
-            {"_id": submission_id},
-            {"$set": {"updated_at": datetime.now()}},
-            return_document=pymongo.ReturnDocument.AFTER,
+            {"_id": ObjectId(submission_id)},
+            {
+                "$set": {"updated_at": datetime.now()},
+                "$pull": {"case_data": {"$regex": f"^{re.escape(object_id)}"}},
+            },
+            return_document=ReturnDocument.AFTER,
         )
 
     def case_to_clinVars(self, case_id):

scout/adapter/mongo/hgnc.py

@@ -1,5 +1,5 @@
 import logging
-from typing import Dict, Set
+from typing import Dict, Optional, Set
 
 import intervaltree
 from pymongo.errors import BulkWriteError, DuplicateKeyError
@@ -44,7 +44,9 @@ class GeneHandler(object):
 
         return result
 
-    def hgnc_gene_caption(self, hgnc_identifier, build=None):
+    def hgnc_gene_caption(
+        self, hgnc_identifier: Optional[int] = None, build: Optional[str] = None
+    ) -> Optional[dict]:
         """Fetch the current hgnc gene symbol and similar caption info for a gene in a lightweight dict
         Avoid populating transcripts, exons etc that would be added on a full gene object. Use hgnc_gene() if
         you need to use those.
@@ -57,6 +59,9 @@ class GeneHandler(object):
             gene_caption(dict): light pymongo document with keys "hgnc_symbol", "description", "chromosome", "start", "end".
         """
 
+        if not hgnc_identifier:
+            return
+
         query = {"hgnc_id": int(hgnc_identifier)}
 
         if build in ["37", "38"]:

scout/adapter/mongo/omics_variant.py

@@ -1,4 +1,5 @@
 import logging
+import os
 from typing import Dict, Iterable, List, Optional
 
 from pymongo import ASCENDING, DESCENDING
@@ -130,6 +131,13 @@ class OmicsVariantHandler:
 
         nr_inserted = 0
 
+        file_path = case_obj["omics_files"].get(file_type) if case_obj.get("omics_files") else None
+        if file_path is None or os.path.exists(file_path) is False:
+            LOG.warning(
+                f"File '{file_path}' not found on disk. Please update case {case_obj['_id']} with a valid file path for {file_type}."
+            )
+            return
+
         file_handle = open(case_obj["omics_files"].get(file_type), "r")
 
         for omics_info in parse_omics_file(file_handle, omics_file_type=omics_file_type):

scout/adapter/mongo/variant_loader.py

@@ -642,7 +642,6 @@ class VariantLoader(object):
         Returns:
             nr_inserted(int)
         """
-
         institute_id = case_obj["owner"]
 
         nr_inserted = 0
@@ -659,9 +658,14 @@ class VariantLoader(object):
                 continue
 
             LOG.info(f"Loading'{vcf_file_key}' variants")
-            variant_file = case_obj["vcf_files"].get(vcf_file_key)
+            variant_file = (
+                case_obj["vcf_files"].get(vcf_file_key) if case_obj.get("vcf_files") else None
+            )
 
             if not variant_file or not self._has_variants_in_file(variant_file):
+                LOG.warning(
+                    f"File '{variant_file}' not found on disk. Please update case {case_obj['_id']} with a valid file path for variant category: '{category}'."
+                )
                 continue
 
             vcf_obj = VCF(variant_file)

scout/constants/__init__.py

@@ -78,6 +78,7 @@ from .indexes import ID_PROJECTION, INDEXES
 from .panels import PANELAPP_CONFIDENCE_EXCLUDE
 from .phenotype import (
     COHORT_TAGS,
+    HPO_LINK_URL,
     HPO_URL,
     HPOTERMS_URL,
     ORPHA_URLS,

scout/constants/file_types.py

@@ -1,6 +1,6 @@
 from collections import OrderedDict
 
-# Variants in Scout will be loadedfor a case  in the same order as these ordered dictionaries
+# Variants in Scout will be loaded for a case in the same order as these ordered dictionaries
 ORDERED_FILE_TYPE_MAP = OrderedDict(
     [
         ("vcf_cancer", {"category": "cancer", "variant_type": "clinical"}),

scout/constants/igv_tracks.py

@@ -4,11 +4,15 @@ HG19REF_URL = (
 )
 HG19REF_INDEX_URL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/1kg_v37/human_g1k_v37_decoy.fasta.fai"
 HG19CYTOBAND_URL = "https://raw.githubusercontent.com/Clinical-Genomics/reference-files/refs/heads/master/rare-disease/region/grch37_cytoband.bed"
-HG19ALIAS_URL = "https://igv.org/genomes/data/hg19/hg19_alias.tab"
+HG19ALIAS_URL = (
+    "https://raw.githubusercontent.com/igvteam/igv-data/refs/heads/main/data/hg19/hg19_alias.tab"
+)
 
 HG38REF_URL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa"
 HG38REF_INDEX_URL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai"
-HG38ALIAS_URL = "https://igv.org/genomes/data/hg38/hg38_alias.tab"
+HG38ALIAS_URL = (
+    "https://raw.githubusercontent.com/igvteam/igv-data/refs/heads/main/data/hg38/hg38_alias.tab"
+)
 HG38CYTOBAND_URL = "https://igv-genepattern-org.s3.amazonaws.com/genomes/hg38/cytoBandIdeo.txt.gz"
 
 HG38GENES_URL = "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz"

scout/constants/phenotype.py

@@ -2,6 +2,7 @@ HPO_URL = "http://purl.obolibrary.org/obo/hp/hpoa/{}"
 HPOTERMS_URL = (
     "https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo"
 )
+HPO_LINK_URL = "https://hpo.jax.org/browse/term/"
 
 ORPHA_URLS = {
     "orpha_to_hpo": "https://www.orphadata.com/data/xml/en_product4.xml",

scout/load/hpo.py

@@ -1,6 +1,6 @@
 import logging
 from datetime import datetime
-from typing import Dict, Iterable, Optional
+from typing import Iterable, Optional
 
 from click import progressbar
 
@@ -45,7 +45,13 @@ def load_hpo_terms(
         if not gene_info:
             continue
 
-        hgnc_id = gene_info["true"]
+        if gene_info["true"] is not None:
+            hgnc_id = gene_info["true"]
+        elif len(gene_info["ids"]) == 1:
+            # unique aliases can be used
+            hgnc_id = list(gene_info["ids"])[0]
+        else:
+            continue
 
         if hpo_id not in hpo_terms:
             continue

scout/server/blueprints/alignviewers/controllers.py

@@ -8,7 +8,11 @@ from flask_login import current_user
 
 from scout.constants import CASE_SPECIFIC_TRACKS, HUMAN_REFERENCE, IGV_TRACKS
 from scout.server.extensions import config_igv_tracks, store
-from scout.server.utils import case_append_alignments, find_index
+from scout.server.utils import (
+    case_append_alignments,
+    find_index,
+    get_case_genome_build,
+)
 from scout.utils.ensembl_rest_clients import EnsemblRestApiClient
 
 LOG = logging.getLogger(__name__)
@@ -88,7 +92,8 @@ def make_igv_tracks(
         display_obj["locus"] = "chr{0}:{1}-{2}".format(chromosome, start, stop)
 
     # Set genome build for displaying alignments:
-    if "38" in str(case_obj.get("genome_build", "37")) or chromosome == "M":
+
+    if get_case_genome_build(case_obj) == "38" or chromosome == "M":
         build = "38"
     else:
         build = "37"
@@ -137,10 +142,7 @@ def make_sashimi_tracks(
     """
 
     locus = "All"
-
-    build = "38"
-    if "37" in str(case_obj.get("rna_genome_build", "38")):
-        build = "37"
+    build = "37" if "37" in str(case_obj.get("rna_genome_build", "38")) else "38"
 
     if variant_id:
         variant_obj = store.variant(document_id=variant_id)

scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html

@@ -35,6 +35,8 @@
   $(document).ready(function () {
       var div = $("#igvDiv")[0],
               options = {
+                    loadDefaultGenomes: false,
+                    genomeList: "https://raw.githubusercontent.com/igvteam/igv-data/main/genomes/web/genomes.json",
                     showNavigation: true,
                     showRuler: true,
                     {% if display_center_guide %}

scout/server/blueprints/alignviewers/templates/alignviewers/utils.html

@@ -1,5 +1,5 @@
 {% macro igv_script() %}
   <link rel="shortcut icon" href="//igv.org/web/img/favicon.ico">
   <!-- IGV JS-->
-  <script src="https://cdn.jsdelivr.net/npm/igv@3.2.0/dist/igv.min.js" integrity="sha512-MHnbGQeONlQXyEs6PgiW2bhwywJW5IwUnRKfQKrPaVSrzopctBTU1VtOiEXMf/ZPBk47eFimlVRxdff+sdsyAg==" crossorigin="anonymous"></script>
+  <script src="https://cdn.jsdelivr.net/npm/igv@3.3.0/dist/igv.min.js" integrity="sha512-U3drIflKJksG0+kiVuqYrQaI9SsloPhKfISeZr8bzVpO/oRFz7hE1vdJirvDyYIfv51CSucKJgcLAdupqitBcQ==" crossorigin="anonymous"></script>
 {% endmacro %}

scout/server/blueprints/cases/controllers.py

@@ -22,6 +22,7 @@ from scout.constants import (
     CUSTOM_CASE_REPORTS,
     DATE_DAY_FORMATTER,
     GENOME_REGION,
+    HPO_LINK_URL,
     INHERITANCE_PALETTE,
     MITODEL_HEADER,
     MT_COV_STATS_HEADER,
@@ -66,6 +67,7 @@ from scout.server.utils import (
     case_has_mt_alignments,
     case_has_mtdna_report,
     case_has_rna_tracks,
+    get_case_genome_build,
     get_case_mito_chromosome,
     institute_and_case,
 )
@@ -157,7 +159,12 @@ def coverage_report_contents(base_url, institute_obj, case_obj):
     return html_body_content
 
 
-def _populate_case_groups(store, case_obj, case_groups, case_group_label):
+def _populate_case_groups(
+    store: MongoAdapter,
+    case_obj: dict,
+    case_groups: Dict[str, List[str]],
+    case_group_label: Dict[str, str],
+):
     """Case groups allow display of information about user linked cases together on one case.
     Notably variantS lists show shared annotations and alignment views show all alignments
     available for the group.
@@ -178,20 +185,21 @@ def _populate_case_groups(store, case_obj, case_groups, case_group_label):
             case_group_label[group] = store.case_group_label(group)
 
 
-def _get_partial_causatives(store: MongoAdapter, case_obj: Dict) -> List[Dict]:
-    """Return any partial causatives a case has, populated as causative objs.
-    Args:
-        store(adapter.MongoAdapter)
-        case_obj(models.Case)
-    Returns:
-        partial(list(dict))
+def _get_partial_causatives(store: MongoAdapter, institute_obj: dict, case_obj: dict) -> List[Dict]:
+    """Check for partial causatives and associated phenotypes.
+    Return any partial causatives a case has, populated as causative objs.
     """
 
     partial_causatives = []
     if case_obj.get("partial_causatives"):
         for var_id, values in case_obj["partial_causatives"].items():
+            variant_obj = store.variant(var_id)
+            if variant_obj:
+                decorated_variant_obj = _get_decorated_var(
+                    store, var_obj=variant_obj, institute_obj=institute_obj, case_obj=case_obj
+                )
             causative_obj = {
-                "variant": store.variant(var_id) or var_id,
+                "variant": decorated_variant_obj or var_id,
                 "disease_terms": values.get("diagnosis_phenotypes"),
                 "hpo_terms": values.get("phenotype_terms"),
             }
@@ -287,7 +295,7 @@ def bionano_case(store, institute_obj, case_obj) -> Dict:
     return data
 
 
-def sma_case(store, institute_obj, case_obj):
+def sma_case(store: MongoAdapter, institute_obj: dict, case_obj: dict) -> dict:
     """Preprocess a case for tabular view, SMA."""
 
     _populate_case_individuals(case_obj)
@@ -299,11 +307,31 @@ def sma_case(store, institute_obj, case_obj):
         "case": case_obj,
         "comments": store.events(institute_obj, case=case_obj, comments=True),
         "events": _get_events(store, institute_obj, case_obj),
-        "region": GENOME_REGION[case_obj.get("genome_build", "38")],
+        "region": GENOME_REGION[get_case_genome_build(case_obj)],
     }
     return data
 
 
+def _get_suspects_or_causatives(
+    store: MongoAdapter, institute_obj: dict, case_obj: dict, kind: str = "suspects"
+) -> list:
+    """Fetch the variant objects for suspects and causatives and decorate them.
+    If no longer available, append variant_id instead."""
+
+    marked_vars = []
+    for variant_id in case_obj.get(kind, []):
+        variant_obj = store.variant(variant_id)
+        if variant_obj:
+            marked_vars.append(
+                _get_decorated_var(
+                    store, var_obj=variant_obj, institute_obj=institute_obj, case_obj=case_obj
+                )
+            )
+        else:
+            marked_vars.append(variant_id)
+    return marked_vars
+
+
 def case(
     store: MongoAdapter, institute_obj: dict, case_obj: dict, hide_matching: bool = True
 ) -> dict:
@@ -331,22 +359,16 @@ def case(
     case_group_label = {}
     _populate_case_groups(store, case_obj, case_groups, case_group_label)
 
-    # Fetch the variant objects for suspects and causatives
-    suspects = [
-        store.variant(variant_id) or variant_id for variant_id in case_obj.get("suspects", [])
-    ]
+    suspects = _get_suspects_or_causatives(store, institute_obj, case_obj, "suspects")
     _populate_assessments(suspects)
-    causatives = [
-        store.variant(variant_id) or variant_id for variant_id in case_obj.get("causatives", [])
-    ]
+
+    causatives = _get_suspects_or_causatives(store, institute_obj, case_obj, "causatives")
     _populate_assessments(causatives)
 
-    # get evaluated variants
     evaluated_variants = store.evaluated_variants(case_obj["_id"], case_obj["owner"])
     _populate_assessments(evaluated_variants)
 
-    # check for partial causatives and associated phenotypes
-    partial_causatives = _get_partial_causatives(store, case_obj)
+    partial_causatives = _get_partial_causatives(store, institute_obj, case_obj)
     _populate_assessments(partial_causatives)
 
     case_obj["clinvar_variants"] = store.case_to_clinVars(case_obj["_id"])
@@ -367,9 +389,7 @@ def case(
     for hpo_term in itertools.chain(
         case_obj.get("phenotype_groups") or [], case_obj.get("phenotype_terms") or []
     ):
-        hpo_term["hpo_link"] = "http://hpo.jax.org/app/browse/term/{}".format(
-            hpo_term["phenotype_id"]
-        )
+        hpo_term["hpo_link"] = f"{HPO_LINK_URL}{hpo_term['phenotype_id']}"
 
     _set_rank_model_links(case_obj)
 
@@ -471,7 +491,7 @@ def case(
         "tissue_types": SAMPLE_SOURCE,
         "report_types": CUSTOM_CASE_REPORTS,
         "mme_nodes": matchmaker.connected_nodes,
-        "gens_info": gens.connection_settings(case_obj.get("genome_build")),
+        "gens_info": gens.connection_settings(get_case_genome_build(case_obj)),
         "display_rerunner": rerunner.connection_settings.get("display", False),
         "hide_matching": hide_matching,
         "audits": store.case_events_by_verb(
@@ -676,7 +696,9 @@ def case_report_variants(store: MongoAdapter, case_obj: dict, institute_obj: dic
             add_bayesian_acmg_classification(var_obj)
             add_bayesian_ccv_classification(var_obj)
             evaluated_variants_by_type[eval_category].append(
-                _get_decorated_var(var_obj=var_obj, institute_obj=institute_obj, case_obj=case_obj)
+                _get_decorated_var(
+                    store, var_obj=var_obj, institute_obj=institute_obj, case_obj=case_obj
+                )
             )
 
     for var_obj in store.evaluated_variants(
@@ -689,7 +711,9 @@ def case_report_variants(store: MongoAdapter, case_obj: dict, institute_obj: dic
     data["variants"] = evaluated_variants_by_type
 
 
-def _get_decorated_var(var_obj: dict, institute_obj: dict, case_obj: dict) -> dict:
+def _get_decorated_var(
+    store: MongoAdapter, var_obj: dict, institute_obj: dict, case_obj: dict
+) -> dict:
     """Decorate a variant object for display using the variant controller"""
     return variant_decorator(
         store=store,
@@ -719,7 +743,9 @@ def _append_evaluated_variant_by_type(
             add_bayesian_ccv_classification(var_obj)
 
             evaluated_variants_by_type[eval_category].append(
-                _get_decorated_var(var_obj=var_obj, institute_obj=institute_obj, case_obj=case_obj)
+                _get_decorated_var(
+                    store, var_obj=var_obj, institute_obj=institute_obj, case_obj=case_obj
+                )
             )
 
 
@@ -765,6 +791,7 @@ def case_report_content(store: MongoAdapter, institute_obj: dict, case_obj: dict
     data["genetic_models"] = dict(GENETIC_MODELS)
     data["report_created_at"] = datetime.datetime.now().strftime("%Y-%m-%d %H:%M")
     data["current_scout_version"] = __version__
+    data["hpo_link_url"] = HPO_LINK_URL
 
     case_report_variants(store, case_obj, institute_obj, data)
 
@@ -1395,6 +1422,7 @@ def matchmaker_matches(request, institute_id, case_name):
             pat_matches = parse_matches(patient_id, server_resp["content"]["matches"])
         matches[patient_id] = pat_matches
 
+    data["hpo_link_url"] = HPO_LINK_URL
     data["matches"] = matches
     return data
 

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

@@ -2,6 +2,8 @@
 {% from "utils.html" import comments_table, variant_related_comments_table %}
 {% from "variant/gene_disease_relations.html" import inheritance_badge %}
 {% from "variants/components.html" import fusion_variants_header, default_fusion_variant_cells %}
+{% from "variant/variant_details.html" import frequencies_table, old_observations_table %}
+{% from "variant/components.html" import clinsig_table %}
 
 {% extends "report_base.html" %}
 
@@ -192,7 +194,7 @@
   	              <ul>
   	                {% for pheno in case.phenotype_terms %}
   	                  <li>
-  	                  {{pheno.feature}} - (<a style="text-decoration:none;" href="https://hpo.jax.org/app/browse/term/{{pheno.phenotype_id}}" target="_blank">{{pheno.phenotype_id}})</a>
+  	                  {{pheno.feature}} - (<a style="text-decoration:none;" href="{{ hpo_link_url }}{{pheno.phenotype_id}}" target="_blank">{{pheno.phenotype_id}})</a>
                       {% for feature_ind in pheno.individuals %} <!-- display eventual individual-level HPO terms -->
                         {% for case_ind in case.individuals %}
                           {% if feature_ind.individual_name == case_ind.display_name %}
@@ -588,78 +590,14 @@
       <table class="table table-sm">
         <tr>
           <td style="width:60%;">
-            {{ genotype_table(variant) }}
+            {{ genotype_table(variant) }}<br>
+            {{ clinsig_table(variant) }}
           </td>
           <td style="width:3%"></td>
           <td>
-            <table id="panel-table" class="table table-sm" style="background-color: transparent">
-              <thead>
-                <tr>
-                  <th>Pop. frequency
-                    {% if variant.frequency == 'common' %}
-                      <span class="badge bg-danger">{{variant.frequency}}</span>
-                    {% elif variant.frequency == 'uncommon' %}
-                      <span class="badge bg-warning text-dark">{{variant.frequency}}</span>
-                    {% else %}
-                      <span class="badge bg-success">{{variant.frequency}}</span>
-                    {% endif %}
-                  </th>
-                  <th>
-                  </th>
-                </tr>
-              </thead>
-              <tbody>
-                <tr>
-                  <td>
-                    {% if variant.dbsnp_id %}
-                      <a style="text-decoration:none;" href="{{ variant.thousandg_link }}" rel="noopener" target="_blank">1000G</a>
-                    {% else %}
-                      1000G
-                    {% endif %}
-                  </td>
-                  <td>
-                    {% if variant.max_thousand_genomes_frequency %}
-                      {{ variant.max_thousand_genomes_frequency|human_decimal }} <small>(max)</small> |
-                    {% endif %}
-                    {{ variant.thousand_genomes_frequency|human_decimal if variant.thousand_genomes_frequency }}
-                    {% if not variant.max_thousand_genomes_frequency and not variant.thousand_genomes_frequency %}
-                      <span class="text-muted">Not annotated</span>
-                    {% endif %}
-                  </td>
-                </tr>
-                <tr>
-                  <td><a style="text-decoration:none;" title="Exome Aggregation Consortium" rel="noopener" target="_blank" href="{{ variant.exac_link }}">ExAC</a></td>
-                  <td>
-                    {% if variant.max_exac_frequency %}
-                      {{ variant.max_exac_frequency|human_decimal }} <small>(max)</small> |
-                    {% endif %}
-                    {{ variant.exac_frequency|human_decimal if variant.exac_frequency }}
-                    {% if not variant.max_exac_frequency and not variant.exac_frequency %}
-                      <span class="text-muted">Not annotated</span>
-                    {% endif %}
-                  </td>
-                </tr>
-                <tr>
-                  <td><a style="text-decoration:none;" title="genome Aggregation Database" rel="noopener" target="_blank" href="{{ variant.gnomad_link }}">gnomAD</a></td>
-                  <td>
-                    {% if 'gnomad_frequency' in variant%}
-                      {% if variant.max_gnomad_frequency %}
-                        {{ variant.max_gnomad_frequency|human_decimal }}
-                        <small>(max)</small> |
-                      {% endif %}
-                      {{ variant.gnomad_frequency|human_decimal if variant.gnomad_frequency }}
-                    {% else %}
-                      <span class="text-muted">Not annotated</span>
-                    {% endif %}
-                  </td>
-                  <td>
-                  </td>
-                </tr>
-              </tbody>
-            </table>
+          {{ frequencies_table(variant) }}
+          {{ old_observations_table(variant) }}
           </td>
-        </tr>
-      </table>
       <table id="panel-table" class="table table-sm" style="background-color: transparent">
         <thead>
           <tr>
@@ -1074,25 +1012,8 @@
         </td>
         <td style="width:3%"></td>
         <td>
-          <table id="panel-table" class="table table-sm" style="background-color: transparent">
-            <thead>
-              <th colspan=2>Pop. frequency</th>
-            </thead>
-            <tbody>
-              {% for freq_name, value, link in variant.frequencies %}
-                <tr>
-                  <td>{{ freq_name }}</td>
-                  <td>
-                    {% if value %}
-                      <span class="badge bg-secondary">{{ value|human_decimal }}</span>
-                    {% else %}
-                      <span class="text-muted">Not annotated</span>
-                    {% endif %}
-                  </td>
-                </tr>
-              {% endfor %}
-            </tbody>
-          </table>
+          {{ frequencies_table(variant) }}
+          {{ old_observations_table(variant) }}
         </td>
       </tr>
     </table>

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

@@ -85,7 +85,7 @@
         <ul class="list-group list-group-flush">
           {% for hpo in case.mme_submission.features %}
             <li class="list-group-item">
-              <a class="text-white" target="_blank" href="http://hpo.jax.org/app/browse/term/{{hpo.id}}">
+              <a class="text-white" target="_blank" href="{{hpo_link_url}}{{hpo.id}}">
               <span class="badge bg-sm bg-info">{{hpo.id}}</span>
               </a>{{hpo.label}}
             </li>

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

@@ -191,7 +191,7 @@
 {% endmacro %}
 
 {% macro hpo_panel(case, institute, config) %}
-  {% set url = 'https://hpo.jax.org/app/' %}
+  {% set url = 'https://hpo.jax.org/' %}
     <div id="phenotypes_panel" class="panel-heading">
       <h6 class="mt-3"><span class="fa fa-stethoscope"></span>&nbsp;Phenotype terms (<a target="_blank" class="" href="{{ url }}" rel="noopener">HPO</a>)</h6>
     </div>