scout-browser 4.86__py3-none-any.whl → 4.87__py3-none-any.whl

scout/__version__.py

@@ -1 +1 @@
-__version__ = "4.86"
+__version__ = "4.87"

scout/adapter/mongo/hgnc.py

@@ -7,6 +7,7 @@ from pymongo.errors import BulkWriteError, DuplicateKeyError
 from scout.exceptions import IntegrityError
 
 LOG = logging.getLogger(__name__)
+QUERY_FIELD_EXISTS = {"$exists": True, "$ne": None}
 
 
 class GeneHandler(object):
@@ -364,9 +365,13 @@ class GeneHandler(object):
         Returns:
             mapping(dict): {"ENSG00000121410": 5, ...}
         """
-        pipeline = [{"$group": {"_id": {"ensembl_id": "$ensembl_id", "hgnc_id": "$hgnc_id"}}}]
-        result = self.hgnc_collection.aggregate(pipeline)
-        mapping = {res["_id"]["ensembl_id"]: res["_id"]["hgnc_id"] for res in result}
+        query = {
+            "ensembl_id": QUERY_FIELD_EXISTS,
+            "hgnc_id": QUERY_FIELD_EXISTS,
+        }
+        project = {"ensembl_id": 1, "hgnc_id": 1}
+        result = self.hgnc_collection.find(query, project)
+        mapping = {res["ensembl_id"]: res["hgnc_id"] for res in result}
         return mapping
 
     def hgnc_symbol_ensembl_id_mapping(self) -> Dict[str, str]:
@@ -375,18 +380,13 @@ class GeneHandler(object):
         Returns:
            mapping(dict): {"A1BG": "ENSG00000121410".}
         """
-        pipeline = [
-            {
-                "$group": {
-                    "_id": {
-                        "hgnc_symbol": "$hgnc_symbol",
-                        "ensembl_id": "$ensembl_id",
-                    }
-                }
-            }
-        ]
-        result = self.hgnc_collection.aggregate(pipeline)
-        mapping = {res["_id"]["hgnc_symbol"]: res["_id"]["ensembl_id"] for res in result}
+        query = {
+            "ensembl_id": QUERY_FIELD_EXISTS,
+            "hgnc_symbol": QUERY_FIELD_EXISTS,
+        }
+        project = {"ensembl_id": 1, "hgnc_symbol": 1}
+        result = self.hgnc_collection.find(query, project)
+        mapping = {res["hgnc_symbol"]: res["ensembl_id"] for res in result}
         return mapping
 
     def ensembl_genes(self, build=None, add_transcripts=False, id_transcripts=False):

scout/build/case.py

@@ -211,6 +211,8 @@ def build_case(case_data, adapter):
 
     case_obj["genome_build"] = genome_build
 
+    case_obj["rna_genome_build"] = case_data.get("rna_genome_build", "38")
+
     if case_data.get("rank_model_version"):
         case_obj["rank_model_version"] = str(case_data["rank_model_version"])
 

scout/constants/igv_tracks.py

@@ -4,8 +4,11 @@ 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://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/cytoBand.txt"
+HG19ALIAS_URL = "https://s3.amazonaws.com/igv.org.genomes/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://s3.amazonaws.com/igv.org.genomes/hg38/hg38_alias.tab"
 HG38CYTOBAND_URL = (
     "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt"
 )
@@ -33,6 +36,7 @@ HUMAN_REFERENCE_37 = {
     "fastaURL": HG19REF_URL,
     "indexURL": HG19REF_INDEX_URL,
     "cytobandURL": HG19CYTOBAND_URL,
+    "aliasURL": HG19ALIAS_URL,
 }
 
 # Human genome reference genome build 38. Always displayed
@@ -41,6 +45,7 @@ HUMAN_REFERENCE_38 = {
     "fastaURL": HG38REF_URL,
     "indexURL": HG38REF_INDEX_URL,
     "cytobandURL": HG38CYTOBAND_URL,
+    "aliasURL": HG38ALIAS_URL,
 }
 
 # igv.js track settings common for all users and all cases. Selectable by users

scout/demo/643594.config.yaml

@@ -151,3 +151,4 @@ sv_rank_model_version: '1.5'
 rank_score_threshold: -100
 analysis_date: 2016-10-12 14:00:46
 human_genome_build: '37'
+rna_human_genome_build: '38'

scout/load/panel.py

@@ -117,27 +117,33 @@ def _panelapp_panel_ids() -> List[str]:
     return [panel_info["Panel_Id"] for panel_info in json_lines.get("result", [])]
 
 
-def _parse_panelapp_panel(adapter, panel_id, institute, confidence):
+def _parse_panelapp_panel(
+    panel_id: str,
+    institute: str,
+    confidence: str,
+    ensembl_id_to_hgnc_id_map: Dict[str, int],
+    hgnc_symbol_to_ensembl_id_map: Dict[str, str],
+):
     """fetch and parse lines from a PanelApp panel, given its ID
 
     Args:
         adapter(scout.adapter.MongoAdapter)
         panel_id(str): The panel app panel id
         confidence(str enum green|amber|red): traffic light-style PanelApp level of confidence
+        ensembl_to_hgnc_map: dict[str, int]
+        hgnc_to_ensembl_map: [int, str]
+
 
     Returns:
         parsed_panel(dict). Example:
             {'version': 3.3, 'date': datetime.datetime(2023, 1, 31, 16, 43, 37, 521719), 'display_name': 'Diabetes - neonatal onset - [GREEN]', 'institute': 'cust000', 'panel_type': 'clinical', 'genes': [list of genes], 'panel_id': '55a9041e22c1fc6711b0c6c0'}
 
     """
-    ensembl_gene_hgnc_id_map: Dict[str, int] = adapter.ensembl_to_hgnc_id_mapping()
-    hgnc_symbol_ensembl_gene_map: Dict[str, str] = adapter.hgnc_symbol_ensembl_id_mapping()
-
     json_lines = fetch_resource(PANELAPP_BASE_URL.format("get_panel") + panel_id, json=True)
     parsed_panel = parse_panel_app_panel(
         panel_info=json_lines["result"],
-        ensembl_gene_hgnc_id_map=ensembl_gene_hgnc_id_map,
-        hgnc_symbol_ensembl_gene_map=hgnc_symbol_ensembl_gene_map,
+        ensembl_gene_hgnc_id_map=ensembl_id_to_hgnc_id_map,
+        hgnc_symbol_ensembl_gene_map=hgnc_symbol_to_ensembl_id_map,
         institute=institute,
         confidence=confidence,
     )
@@ -166,8 +172,17 @@ def load_panelapp_panel(adapter, panel_id=None, institute="cust000", confidence=
         LOG.info("Fetching all panel app panels")
         panel_ids: List[str] = _panelapp_panel_ids()
 
+    ensembl_id_to_hgnc_id_map: Dict[str, int] = adapter.ensembl_to_hgnc_id_mapping()
+    hgnc_symbol_to_ensembl_id_map: Dict[int, str] = adapter.hgnc_symbol_ensembl_id_mapping()
+
     for _ in panel_ids:
-        parsed_panel = _parse_panelapp_panel(adapter, _, institute, confidence)
+        parsed_panel = _parse_panelapp_panel(
+            panel_id=_,
+            institute=institute,
+            confidence=confidence,
+            ensembl_id_to_hgnc_id_map=ensembl_id_to_hgnc_id_map,
+            hgnc_symbol_to_ensembl_id_map=hgnc_symbol_to_ensembl_id_map,
+        )
 
         if len(parsed_panel["genes"]) == 0:
             LOG.warning("Panel %s is missing genes. Skipping.", parsed_panel["display_name"])
@@ -201,9 +216,19 @@ def load_panelapp_green_panel(adapter, institute, force):
     }
     genes = set()  # avoid duplicate genes from different panels
     # Loop over all PanelApp panels
+
+    ensembl_id_to_hgnc_id_map: Dict[str, int] = adapter.ensembl_to_hgnc_id_mapping()
+    hgnc_symbol_to_ensembl_id_map: Dict[int, str] = adapter.hgnc_symbol_ensembl_id_mapping()
+
     for _ in panel_ids:
         # And collect their green genes
-        parsed_panel = _parse_panelapp_panel(adapter, _, institute, "green")
+        parsed_panel = _parse_panelapp_panel(
+            panel_id=_,
+            institute=institute,
+            confidence="green",
+            ensembl_id_to_hgnc_id_map=ensembl_id_to_hgnc_id_map,
+            hgnc_symbol_to_ensembl_id_map=hgnc_symbol_to_ensembl_id_map,
+        )
         genes.update({(gene["hgnc_id"], gene["hgnc_symbol"]) for gene in parsed_panel.get("genes")})
 
     green_panel["genes"] = [{"hgnc_id": tup[0], "hgnc_symbol": tup[1]} for tup in genes]

scout/models/case/case_loading_models.py

@@ -409,6 +409,7 @@ class CaseLoader(BaseModel):
     gene_fusion_report_research: Optional[str] = None
     gene_panels: Optional[List[str]] = []
     genome_build: str
+    rna_genome_build: Optional[str] = "38"
     individuals: Union[List[SampleLoader]] = Field([], alias="samples")
     lims_id: Optional[str] = None
     madeline_info: Optional[str] = Field(None, alias="madeline")
@@ -499,15 +500,17 @@ class CaseLoader(BaseModel):
     @model_validator(mode="before")
     @classmethod
     def format_build(cls, values) -> "CaseLoader":
-        """Format the genome build collected from genome_build or human_genome_build keys, so it will be saved as either '37' or '38'."""
-        str_build = str(values.get("genome_build") or values.get("human_genome_build", ""))
-        if "37" in str_build:
-            str_build = "37"
-        elif "38" in str_build:
-            str_build = "38"
-        if str_build not in GENOME_BUILDS:
-            raise ValueError("Genome build must be either '37' or '38'.")
-        values["genome_build"] = str_build
+        """Format the RNA genome build collected from RNA_human_genome_build key."""
+        rna_str_build = str(values.get("rna_human_genome_build", "38"))
+        values["rna_genome_build"] = _get_str_build(rna_str_build)
+        return values
+
+    @model_validator(mode="before")
+    @classmethod
+    def format_rna_build(cls, values) -> "CaseLoader":
+        """Format the genome build collected from genome_build or human_genome_build keys."""
+        dna_str_build = str(values.get("genome_build") or values.get("human_genome_build", ""))
+        values["genome_build"] = _get_str_build(dna_str_build)
         return values
 
     @field_validator("individuals", mode="after")
@@ -567,3 +570,14 @@ class CaseLoader(BaseModel):
                 raise ValueError("Case owner is missing.")
             values["collaborators"] = [values["owner"]]
         return values
+
+
+def _get_str_build(str_build):
+    """Get genome build, as either '37' or '38'."""
+    if "37" in str_build:
+        str_build = "37"
+    elif "38" in str_build:
+        str_build = "38"
+    if str_build not in GENOME_BUILDS:
+        raise ValueError("Genome build must be either '37' or '38'.")
+    return str_build

scout/server/blueprints/alignviewers/controllers.py

@@ -131,7 +131,6 @@ def make_sashimi_tracks(
     Returns:
         display_obj(dict): A display object containing case name, list of genes, locus and tracks
     """
-    build = "38"  # This feature is only available for RNA tracks in build 38
 
     locus = "All"
     variant_obj = None
@@ -141,6 +140,10 @@ def make_sashimi_tracks(
     if omics_variant_id:
         variant_obj = store.omics_variant(variant_id=omics_variant_id)
 
+    build = "38"
+    if "37" in str(case_obj.get("rna_genome_build", "38")):
+        build = "37"
+
     if variant_obj:
         locus = make_locus_from_variant(variant_obj, case_obj, build)
 
@@ -151,19 +154,7 @@ def make_sashimi_tracks(
     # Populate tracks for each individual with splice junction track data
     for ind in case_obj.get("individuals", []):
         if all([ind.get("splice_junctions_bed"), ind.get("rna_coverage_bigwig")]):
-            coverage_wig = ind["rna_coverage_bigwig"]
-            splicej_bed = ind["splice_junctions_bed"]
-            splicej_bed_index = (
-                f"{splicej_bed}.tbi" if os.path.isfile(f"{splicej_bed}.tbi") else None
-            )
-            if splicej_bed_index is None:
-                flash(f"Missing bed file index for individual {ind['display_name']}")
-            track = {
-                "name": ind["display_name"],
-                "coverage_wig": coverage_wig,
-                "splicej_bed": splicej_bed,
-                "splicej_bed_index": splicej_bed_index,
-            }
+            track = make_merged_splice_track(ind)
             display_obj["tracks"].append(track)
         if ind.get("rna_alignment_path"):
             rna_aln = ind["rna_alignment_path"]
@@ -180,6 +171,30 @@ def make_sashimi_tracks(
     return display_obj
 
 
+def make_merged_splice_track(ind: dict) -> dict:
+    """
+    Retrieve individual splice track component and store in a dict for use when generating an IGV.js config.
+
+    Args:
+        ind: dict individual (sample)
+
+    Returns:
+        track: dict with merged track data for igv configuration
+    """
+    coverage_wig = ind["rna_coverage_bigwig"]
+    splicej_bed = ind["splice_junctions_bed"]
+    splicej_bed_index = f"{splicej_bed}.tbi" if os.path.isfile(f"{splicej_bed}.tbi") else None
+    if splicej_bed_index is None:
+        flash(f"Missing bed file index for individual {ind['display_name']}")
+    track = {
+        "name": ind["display_name"],
+        "coverage_wig": coverage_wig,
+        "splicej_bed": splicej_bed,
+        "splicej_bed_index": splicej_bed_index,
+    }
+    return track
+
+
 def make_locus_from_variant(variant_obj: Dict, case_obj: Dict, build: str) -> str:
     """Given a variant obj, construct a locus string across any gene touched for IGV to display.
 

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

@@ -46,10 +46,11 @@
                 // Example of fully specifying a reference GRCh38. Scout is supporting only this for now
                 reference:
                     {
-                        id: "hg38",
+                        id: "{{ reference_track.id }}",
                         fastaURL: "{{ reference_track.fastaURL }}",
                         indexURL: "{{ reference_track.indexURL }}",
-                        cytobandURL: "{{ reference_track.cytobandURL }}"
+                        cytobandURL: "{{ reference_track.cytobandURL }}",
+                        aliasURL: "{{ reference_track.aliasURL }}"
                     },
                 locus: '{{ locus }}',
                 tracks:
@@ -93,8 +94,9 @@
                                     height: 500,
                                   },
                                 ]
-                              }, // end of sashimi track with data
-                              {% if custom_tracks|selectattr("name","equalto", "Genes")|list|length > 0 %}
+                              },
+                            {% endif %}
+                            {% if custom_tracks|selectattr("name","equalto", "Genes")|list|length > 0 %}
                                 { // genes track
                                   name: geneTrack.name,
                                   type: geneTrack.type,
@@ -109,9 +111,8 @@
                                   order: {{counter.loop}},
                                   infoURL: "https://www.ncbi.nlm.nih.gov/gene/?term=$$"
                                 }, // end of genes track
-                              {% endif %}
-                            {% endif %}
-                        {% endfor %}
+                             {% endif %}
+                       {% endfor %}
                     ] // end of tracks
             };
         var igvDiv = document.getElementById("igvDiv");

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

@@ -46,7 +46,8 @@
                         id: "{{ reference_track.id }}",
                         fastaURL: "{{ reference_track.fastaURL }}",
                         indexURL: "{{ reference_track.indexURL }}",
-                        cytobandURL: "{{ reference_track.cytobandURL }}"
+                        cytobandURL: "{{ reference_track.cytobandURL }}",
+                        aliasURL: "{{ reference_track.aliasURL }}"
                     },
                     locus: "{{locus}}",
                     tracks: [

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@3.0.1/dist/igv.min.js"></script>
+  <script src="https://cdn.jsdelivr.net/npm/igv@3.0.4/dist/igv.min.js" integrity="sha512-iczcEXdlX8PdVb/x5TKY6PntdhIbzWaPicz3ZIeZ41EM2MfFboJKXinNzfcVL+SgEv2dOxezH7GAY5V+rQ9jMQ==" crossorigin="anonymous"></script>
 {% endmacro %}

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

@@ -201,7 +201,7 @@
 {% if has_rna_tracks %}
   <div href="#" class="bg-dark list-group-item d-inline-block text-white">
     <form action="{{url_for('alignviewers.sashimi_igv', institute_id=case['owner'], case_name=case['display_name']) }}" target="_blank" rel="noopener">
-      <button role="submit" data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh38" class="btn btn-xs form-control btn-secondary">R<span class="menu-collapsed">NA splicing</span></button>
+      <button role="submit" data-bs-toggle="tooltip" data-bs-placement="top" title="Available in build GRCh{{ case.rna_genome_build or '38' }}" class="btn btn-xs form-control btn-secondary">R<span class="menu-collapsed">NA splicing</span></button>
     </form>
   </div>
 {% endif %}

scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html

@@ -70,27 +70,29 @@
           {% for variant in variants %}
             <tr>
               <td class="text-end">
-                <div class="d-flex flex-row justify-content-between align-items-baseline">
+                <div class="d-flex flex-row justify-content-between">
                 {% if variant.genes %}
                   {{ gene_cell(variant) }}
                 {% else %}
                   {{ variant.gene_name_orig }}
                 {% endif %}
-                {% if case.vcf_files.vcf_snv %}
-                  <form action="{{url_for('variants.variants', institute_id=institute._id, case_name=case.display_name) }}">
-                  <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="{% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %}"></input>
-                  <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
-                  <button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="SNV and INDEL variants view filtered for the gene(s) {% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %} ">SNVs</button>
-                </form>
-                {% endif %}
-                {% if case.vcf_files.vcf_sv %}
-                  <form action="{{url_for('variants.sv_variants', institute_id=institute._id, case_name=case.display_name) }}">
-                  <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="{% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %}"></input>
-                  <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
-                  <button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="SV variants view filtered for the gene(s) {% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %} ">SVs</button>
-                </form>
-                {% endif %}
-                </div>
+                  <div class="d-flex justify-content-center">
+                  {% if case.vcf_files.vcf_snv %}
+                    <form action="{{url_for('variants.variants', institute_id=institute._id, case_name=case.display_name) }}">
+                    <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="{% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %}"></input>
+                    <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
+                    <span><button type="submit" class="btn btn-secondary btn-sm" style="float: right;" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="SNV and INDEL variants view filtered for the gene(s) {% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %} ">SNVs</button></span>
+                    </form>
+                  {% endif %}
+                  {% if case.vcf_files.vcf_sv %}
+                    <form action="{{url_for('variants.sv_variants', institute_id=institute._id, case_name=case.display_name) }}">
+                    <input type="hidden" id="hgnc_symbols" name="hgnc_symbols" value="{% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %}"></input>
+                    <input type="hidden" id="gene_panels" name="gene_panels" value="['']"></input>
+                    <button type="submit" class="btn btn-secondary btn-sm" target="_blank" rel="noopener" data-bs-toggle="tooltip" title="SV variants view filtered for the gene(s) {% for gene in variant.genes %}{{gene.hgnc_symbol}}{{ ", " if not loop.last else "" }}{% endfor %} ">SVs</button></span>
+                  </form>
+                  {% endif %}
+                    </div>
+                 </div>
               </td>
               <td>{{ variant.sub_category }}</td>
               <td class="text-end"> {%  if variant.sub_category == "splicing" %}
@@ -111,7 +113,7 @@
               <td class="text-end">{{ variant.chromosome }}</td>
                 <td class="text-end"><span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span>-<span style="white-space: nowrap;">{{ variant.end|human_longint|safe }}</span>
                 {% if case.has_rna_tracks %}
-                  {{ splice_junctions_button(institute._id, case.display_name, None, variant.omics_variant_id) }}
+                  {{ splice_junctions_button(institute._id, case, None, variant.omics_variant_id) }}
                 {% endif %}
               </tr>
             {% else %}

scout/server/blueprints/variant/templates/variant/buttons.html

@@ -33,13 +33,13 @@
 </div>
 {% endmacro %}
 
-{% macro splice_junctions_button(institute_id, case_name, variant_id, omics_variant_id) %}
+{% macro splice_junctions_button(institute_id, case, variant_id, omics_variant_id) %}
   {% if omics_variant_id %}
-    <a class="btn btn-sm btn-secondary text-white" href="{{url_for('alignviewers.sashimi_igv', institute_id=institute_id, case_name=case_name, omics_variant_id=omics_variant_id)}}" target="_blank"
-    data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh38">RNA splicing</a>
+    <a class="btn btn-sm btn-secondary text-white" href="{{url_for('alignviewers.sashimi_igv', institute_id=institute_id, case_name=case.display_name, omics_variant_id=omics_variant_id)}}" target="_blank"
+    data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh{{ case.rna_genome_build or '38' }}">RNA splicing</a>
   {% else %}
-    <a class="btn btn-sm btn-secondary text-white" href="{{url_for('alignviewers.sashimi_igv', institute_id=institute_id, case_name=case_name, variant_id=variant_id)}}" target="_blank"
-    data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh38">RNA splicing</a>
+    <a class="btn btn-sm btn-secondary text-white" href="{{url_for('alignviewers.sashimi_igv', institute_id=institute_id, case_name=case.display_name, variant_id=variant_id)}}" target="_blank"
+    data-bs-toggle="tooltip" data-bs-placement="top" title="Only available in build GRCh{{ case.rna_genome_build or '38' }}">RNA splicing</a>
   {%  endif  %}
 {% endmacro %}
 

scout/server/blueprints/variant/templates/variant/components.html

@@ -80,7 +80,7 @@
           {% endif %}
           {% if has_rna_tracks %}
             <div class="ms-1">
-              {{ splice_junctions_button(institute._id, case.display_name, variant._id) }}
+              {{ splice_junctions_button(institute._id, case, variant._id) }}
             </div>
           {% endif %}
           {% if variant.alamut_link %}

scout/server/blueprints/variant/templates/variant/sv-variant.html

@@ -274,7 +274,7 @@
         {% endif %}
         {% if rna_tracks %}
           <li class="list-group-item">
-            {{ splice_junctions_button(institute._id, case.display_name, variant._id) }}
+            {{ splice_junctions_button(institute._id, case, variant._id) }}
           </li>
         {% endif %}
       </ul>

scout/server/blueprints/variants/templates/variants/components.html

@@ -143,7 +143,7 @@
 {% endmacro %}
 
 {% macro gene_cell(variant) %}
-  <div class="align-items-center">
+  <div class="d-flex align-items-center">
     {% if variant.category == "cancer" or variant.category == "sv_cancer" %}
       <a data-bs-toggle="tooltip" data-bs-html="true" title="
         <div>

{scout_browser-4.86.dist-info → scout_browser-4.87.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.86
+Version: 4.87
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

{scout_browser-4.86.dist-info → scout_browser-4.87.dist-info}/RECORD

@@ -1,5 +1,5 @@
 scout/__init__.py,sha256=Z4liXvmEcLkC67ElsWvYHfemPKdWgWI5O6MB6XlDM8M,232
-scout/__version__.py,sha256=zYKQx08a1gvbjSpG6DiyHGDUoAWcbw-0P5ZAvghe_Lg,21
+scout/__version__.py,sha256=NDUHhszlscYscmJ7Y40a33-uFqtOH-9gQ_ON88XEv74,21
 scout/adapter/__init__.py,sha256=-iX_hx2NI1EMAqX0pMd5_90Nnd9uvIMxv9EbefYBzsc,86
 scout/adapter/client.py,sha256=IuajRsEwTG41ZP14X09Q1Cj94zIgmIvUtlXfcAFn0EA,1513
 scout/adapter/mongo/__init__.py,sha256=NdHYCUXWUAuX5cUS3-6HCws2hW9uoGep8i0SC-oJd3k,31
@@ -13,7 +13,7 @@ scout/adapter/mongo/cytoband.py,sha256=2NoIAoQ7RPqcipiSymD2O9qH8lXscP3T5ejquOrD7
 scout/adapter/mongo/disease_terms.py,sha256=4qcQRLuP5xn_RkB2RlNtwCrONmDuWwdlngZrj87BUEo,5637
 scout/adapter/mongo/event.py,sha256=NnURFhS5odOXk7So_gGMHmALPAJM0PWzESI4FC06azE,19842
 scout/adapter/mongo/filter.py,sha256=vzBJS_6vq2z76SH8PszdRR-MNuZ7_RA4VJvnkNYUs7s,8937
-scout/adapter/mongo/hgnc.py,sha256=Zcnf_kKJqrJAf62tUFODhL8OQUb695XnL_rzk4D9nes,16411
+scout/adapter/mongo/hgnc.py,sha256=9jbrkaTtlnnuE5gsSM8ylb8Kero4lC2zCWr-90QlyAY,16420
 scout/adapter/mongo/hpo.py,sha256=ps2Pix3sGeea7DenboZVP5j7Vh9WAgX3-sgpbAj0Eck,6871
 scout/adapter/mongo/index.py,sha256=TZPVv6xBWsEtZpBUWp5uhjuPjQMfVss4lZZju49g1Lw,3577
 scout/adapter/mongo/institute.py,sha256=GQmMKb_VzsvWwadp6gXHlSSpcG5ovF1ozdTzvpTFLpA,7025
@@ -31,7 +31,7 @@ scout/adapter/mongo/variant_events.py,sha256=LjUtxJLo3wGBjMI55wPs7sNPeDLq9POw6fg
 scout/adapter/mongo/variant_loader.py,sha256=C05StRMFVChopcolPYXFIbh_S-FhYHu4NvBCpiBLOeE,28327
 scout/build/__init__.py,sha256=GUWEaXTpwsJil_KtrXBQJpZIwCQFSgo8NlK49R9IkA8,521
 scout/build/acmg.py,sha256=M21MrrP_dtEyOuu6t-jBDdaqYcHPMLcwJlt9fHG2ycE,1523
-scout/build/case.py,sha256=RK-FR7Vt1-350xF4UOfAVCdJi74SaMBMV4BmjdtJ2WU,11253
+scout/build/case.py,sha256=wJR3d1n3GMhfQudhSRJM0tust84MuOpOvRcGfx7H6sI,11329
 scout/build/disease.py,sha256=Zew9AF_z1NbbKcO3uJZ2wgni501SkfnYRgnaCZ4m8FY,2020
 scout/build/hpo.py,sha256=LJBCTq-x09D0CSKcUHB8a6ynuUrVh_7Ia0ooA1BxMys,1207
 scout/build/individual.py,sha256=tWK8iKVujuCoZz-rhBVj-RCnlkU19vCSyJtXhlENwS4,5117
@@ -133,7 +133,7 @@ scout/constants/disease_parsing.py,sha256=m10iPVzdTsdx7v9ZWvdLjlBrQKR_uyMeJwPbok
 scout/constants/file_types.py,sha256=3BU2cw40cHMT5IzEGEF_SsIhgYUbnIlUCRmwmB01fzI,3046
 scout/constants/filters.py,sha256=1bcj-z7__yv5eQpjB60wqSHZ3U5U0CVyNbcYT-Wn-vc,957
 scout/constants/gene_tags.py,sha256=tdzDh6ukJRtHiC8X5YkldijZCS0KrEeXj95sLNlqxuc,3852
-scout/constants/igv_tracks.py,sha256=3-3VzFpCTfuhbEBAitbpY2lQRYXYf-poya3DXs0g9yE,4500
+scout/constants/igv_tracks.py,sha256=lrDPCkCjDrTDu80A8wuPjGm6zT_FBrDWv-g9nN_HCsI,4721
 scout/constants/indexes.py,sha256=954b9H72rKI8qSSQbeQDjSl9gYBFGFq0Jd1mTH3Lkmk,5351
 scout/constants/phenotype.py,sha256=MrbXirisR_7GPnxV3NOj3-BoM9CvtGgFZj7PfJu85RM,2331
 scout/constants/query_terms.py,sha256=RrHSBde-UNfdD2D5r1ViHcLfDD-q_sEkLZsPKOE91x4,1556
@@ -154,7 +154,7 @@ scout/demo/643594.clinical.str.vcf.gz,sha256=ElvicUseKkN-DiZOQrFXstxy2jo9lhVMn58
 scout/demo/643594.clinical.str.vcf.gz.tbi,sha256=pyWRI8-DlfGw08S66nYqLOthbaRaNMpAhUACm48iM5A,1695
 scout/demo/643594.clinical.vcf.gz,sha256=ukJjOeF1VuIej02garL_U6aq4Ef8WuO6qOknzK46HPg,408818
 scout/demo/643594.clinical.vcf.gz.tbi,sha256=G4RJMk1GYIDS1IVfXPVkGFtmPN_m0jwwqltdWWuk1A8,7721
-scout/demo/643594.config.yaml,sha256=wHeyFLGiGBViu0RQeELt4IDValaXpqUVfVRSSa1rhEk,5344
+scout/demo/643594.config.yaml,sha256=mxuX82stt0EyTITI18earZyVagdgEP3OHjqd-o-1r9Q,5373
 scout/demo/643594.ped,sha256=P-k5eZY78ZRtajMDQ_rr7Xv5oFhBO-vDc7whg36Jnw4,154
 scout/demo/643594.ped_check.csv,sha256=36HoP13haqQerTEHuJF4R2r6Vh2AQilS1NTr7X6aoZs,444
 scout/demo/643594.peddy.ped,sha256=msfhM3u_5hK_zjHhMas5Ns_KREllRyHN3kdTIVl5J-c,421
@@ -370,7 +370,7 @@ scout/load/exon.py,sha256=ONaWJ9EfbhGV8KGXxwlq_jYCoU-JkBpv4r9zDaCjtls,2070
 scout/load/hgnc_gene.py,sha256=GcSQ01CioYIshAzXAv4msIGDPjTjGBBPBnLX2GvaZJ4,4507
 scout/load/hpo.py,sha256=ZWYjV9j6OfpI-ZZuhTQVEs_xgLa7ST2KuvYLW6ku0PY,2474
 scout/load/institute.py,sha256=etmZ0CZRHOVi3f9R-wn5BK1pZPhtZwq2QYbh2RXXxDc,625
-scout/load/panel.py,sha256=JQqkyUdpvhFnW81n8Sq-iPahDcm1hGBzLfrwUcVqt4k,9446
+scout/load/panel.py,sha256=Zxv-ZlRyk7ZWKy1p0Cod-ATh7TzKqeMbiLu5I6-VEzs,10246
 scout/load/report.py,sha256=TJvblks6Dp5-UDflWRTa8b3fe-A4bT4QnWT2yZLhfLA,820
 scout/load/setup.py,sha256=0qQgfCr53oHL626hG5y0o5vwRnJ4X0IMaTFvMBMRNQE,8183
 scout/load/transcript.py,sha256=mk0Da7GWwqLVRp2xRD9mlzqaomH9R-TL2aKCJx4fEA8,4632
@@ -392,7 +392,7 @@ scout/models/phenotype_term.py,sha256=jY7dbfPzgE14M1gWqifm5YKkwMlrtfFa_WBHMT1_og
 scout/models/user.py,sha256=oercrjpf9fLomqAcN0Fv1BL_XPjOrS_vchURo0RP7es,1134
 scout/models/case/__init__.py,sha256=Sqczn7Wm9KYZtPGAHCvwX_6j9vlaK-0myJtSDlS-448,121
 scout/models/case/case.py,sha256=7r-lR5jr3hNyM0jo-KxQDY7CLjtgtzu26PHOalx1s68,5213
-scout/models/case/case_loading_models.py,sha256=RHUZa71PkWUMu1tLm7cw2JhxQ8jnW1D-_4oF2WMAAmg,20939
+scout/models/case/case_loading_models.py,sha256=mIJ8saxKuskNoXhwlVdlHu90p4CPBvRWtk-l6iK3YLk,21399
 scout/models/variant/__init__.py,sha256=H-IZ2hSTSVS28S8FZzA8j2Cyu1PHQFXyMWJFtCucPAk,40
 scout/models/variant/gene.py,sha256=98CG_JcAklGGFIrUulf1_olQalV65kXQO-gOf7VQZ0A,1095
 scout/models/variant/transcript.py,sha256=rfflEbTs7Bn4HDENqrxtGopQ_0HKnrVLLyBcrj4NpwM,1720
@@ -443,12 +443,12 @@ scout/server/links.py,sha256=WWHQ7CcJxemwR7Cm0n7CvZOfV0dG-_xEAfVff_m_x6U,27013
 scout/server/utils.py,sha256=lhFJI6UkNDD1OPnC53SYG2vjfMNmjp4BBf1tcO8R-ZM,12634
 scout/server/blueprints/__init__.py,sha256=iwhKnzeBJLKxpRVjvzwiRE63_zNpIBfaKLITauVph-0,24
 scout/server/blueprints/alignviewers/__init__.py,sha256=XMVed2ekVUAvroqENDHSr2pwM8otqau8ZA-rbH1T2U8,59
-scout/server/blueprints/alignviewers/controllers.py,sha256=SDTmb4TreWWa1E1SLnQNOfyb-5dcdibpr_t2V9v82rY,12603
+scout/server/blueprints/alignviewers/controllers.py,sha256=Em4YNyQ-MoPFtP2H36KnGFEaNXcRZdUW60iRoqlRluY,12875
 scout/server/blueprints/alignviewers/partial.py,sha256=9hpI00yhvZZCcPVUHlVDp488r1j7vYU5YDXYA6OkWQM,2005
 scout/server/blueprints/alignviewers/views.py,sha256=yQmWqzjdYmqs4e2nzDPLNjgpsNzKhBv1LJGaJi8bnyc,4963
-scout/server/blueprints/alignviewers/templates/alignviewers/igv_sashimi_viewer.html,sha256=ZIbW6e-K2jKWK5WAGK9NkxVywruxm7kxIKRI1w5PaWg,5495
-scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html,sha256=uTJkmnoWfrhZQVRq8fDd4eGBxfrlU7GswvEHCrX-NMk,8496
-scout/server/blueprints/alignviewers/templates/alignviewers/utils.html,sha256=ZGVv4-mCn63QxJ0YfWx_RjgXJaAWfBjM-90i4IinXUY,204
+scout/server/blueprints/alignviewers/templates/alignviewers/igv_sashimi_viewer.html,sha256=37ArJCraTajqWlCvyQYVfSvWCg94pRDIMvf2Y7Oe_j4,5545
+scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html,sha256=u7_OUfcGt-S6BFhwleE4mNprshO870CnzhgLpe4tocg,8564
+scout/server/blueprints/alignviewers/templates/alignviewers/utils.html,sha256=1AhvT-D-dpGvI5MAK6UvK7tkSRi0ybb4mTKD1sTKKQU,336
 scout/server/blueprints/api/__init__.py,sha256=HR6HjS7ot1K_8Lt5eQdNT154z_FCdHGSigy8r2LpNCI,26
 scout/server/blueprints/api/views.py,sha256=pbl78wfhrm1T8JmiJDYF3BbTbfFrlF-hQRbuv2GWI0s,3729
 scout/server/blueprints/cases/__init__.py,sha256=_c17kPFITFYcIVphF4V9bf0PZBer8bU3rtVWQnljKDU,52
@@ -464,7 +464,7 @@ scout/server/blueprints/cases/templates/cases/case_report.html,sha256=5vGSFpFdZN
 scout/server/blueprints/cases/templates/cases/case_sma.html,sha256=SAcElb4kH05mkPdEdaEbed-vbgQQGfxioCoNZsHljDc,4962
 scout/server/blueprints/cases/templates/cases/case_tabular_view.html,sha256=ko-LDUKmIoTazMZ2nFWvPEZsgObU07RwqIkDYFjokoY,4317
 scout/server/blueprints/cases/templates/cases/chanjo2_form.html,sha256=5Wmk7DM8LI3MynqzxeTzAr_EoEBwVVo31djcI5ZlTdo,2164
-scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html,sha256=Az8Oq9ldGtT9snzeDxt1xC68Yp7fp4qZ1eDN7Gr9Wf4,29246
+scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html,sha256=6xWkg0sc1BLQJZXiK-gohVQhUrdwITQ0yWsF61b29qc,29274
 scout/server/blueprints/cases/templates/cases/diseases.html,sha256=ETTQI0Nrl_v86NoX9mFZcvWD-qM1IJoqPmHPWn__Grw,1677
 scout/server/blueprints/cases/templates/cases/gene_panel.html,sha256=lkC_Piqaq-paYr4GUCwQaR8EgGOUXDMoW5sPLDW7yzg,11628
 scout/server/blueprints/cases/templates/cases/index.html,sha256=oUmjFyUvwP4yo21CxcWy-6eepMFI65hpznMEpSEqKfM,1207
@@ -538,7 +538,7 @@ scout/server/blueprints/managed_variants/templates/managed_variants/managed_vari
 scout/server/blueprints/omics_variants/__init__.py,sha256=8UVXrChArhIvMxtgUcG-udvmlTn56q41iy-naOZw5us,37
 scout/server/blueprints/omics_variants/controllers.py,sha256=AnM70stvLniJIU3pFUX-InNjuT-7K0RpuAEYa7vM-jw,3912
 scout/server/blueprints/omics_variants/views.py,sha256=4_wOqAhu_Zl6heqm7ilE8y8xOfy3PU532rkp_H0KZFg,3724
-scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html,sha256=R76aX5qDsSrrUOvfIaGswc7NRwojwFeyK5zcpNXmD6M,12960
+scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html,sha256=lVDXMcY-ukF6GYtJrHvXtw9rISNhkUfrX4nfgPyU_dw,13088
 scout/server/blueprints/panels/__init__.py,sha256=usxBF0O7zNX1d9jt-8DRoFZwcfHHS96Gv87LDr1AgG4,53
 scout/server/blueprints/panels/controllers.py,sha256=apNwdE8gphRTViChoL_yfBJP-H1BfpyAyrIJMv88d9c,12659
 scout/server/blueprints/panels/forms.py,sha256=DYlhYpnpv7ehf9JlY3HRFwy-TZ5QDHB0RIRaNTAW1jQ,696
@@ -601,14 +601,14 @@ scout/server/blueprints/variant/utils.py,sha256=PpIWFiMgtEUIS8A8wD9-5yf_SB42tb1U
 scout/server/blueprints/variant/verification_controllers.py,sha256=eKzP222e7xuFOaQaI9MLOrD9RWtI8uGB1cJYbcXLzF0,10972
 scout/server/blueprints/variant/views.py,sha256=jz5kFRCLhEVRQKFJtKmG0Nq4TX6ofEeyA9zPHE7b1FQ,14768
 scout/server/blueprints/variant/templates/variant/acmg.html,sha256=ubitRnQoADLLOptwMgsPLb1AXhwZgV1YlN504VaC2lY,7754
-scout/server/blueprints/variant/templates/variant/buttons.html,sha256=lQ4inmrlpkb_SHm0KGM8kf7GCUH7TrtyI-yY78THsmE,7180
+scout/server/blueprints/variant/templates/variant/buttons.html,sha256=SnSQhCYiW3lYuZrT22J27OtDaxiVCfWpueOr4jQBOg0,7257
 scout/server/blueprints/variant/templates/variant/cancer-variant.html,sha256=1D9uLIgb06qfhcbl0wB5mRrgARVgfCJfRZhf4wEA2tc,13971
-scout/server/blueprints/variant/templates/variant/components.html,sha256=8sL51D-XR_XRrknZLfZLM4KWz9pHj1CpYsyR9EaAlw4,20863
+scout/server/blueprints/variant/templates/variant/components.html,sha256=hDxXLJkHDTwHApugNcvZkorUR0x10xnFMl256p2DCKA,20850
 scout/server/blueprints/variant/templates/variant/gene_disease_relations.html,sha256=mvw7773Gww3AAOtASL61W5e5cYTc4uB8gJ2zr19NIXw,7283
 scout/server/blueprints/variant/templates/variant/rank_score_results.html,sha256=32RfBrpZ_J-1WYE01Bdd5IC9i1MAzXT7GF27OlElk94,2040
 scout/server/blueprints/variant/templates/variant/sanger.html,sha256=0kVnscTw3KUwjR4QOEuNJMOK9eADGEn9qGNtGx2ST7Y,4507
 scout/server/blueprints/variant/templates/variant/str-variant-reviewer.html,sha256=QETzTkzXhFBd7-20OrLMCd1QSgzOxeE7Lv_Iged5BB0,2220
-scout/server/blueprints/variant/templates/variant/sv-variant.html,sha256=Rn6lAteE2SR8omRRXWVrajcppghoF-tSR23mY4_6Sto,17184
+scout/server/blueprints/variant/templates/variant/sv-variant.html,sha256=Ss1MaXyJngWNry9-eb3EwbUzzsC0RBv0EVvOoS77d1M,17171
 scout/server/blueprints/variant/templates/variant/tx_overview.html,sha256=turyCoOCCd_N80FakxXfIl7q_WViysz1fwx3j312_Lg,6737
 scout/server/blueprints/variant/templates/variant/utils.html,sha256=wstxdK36MtW81MqsQtxbDQFDR7gmPba-kqVNFTVYfpo,21588
 scout/server/blueprints/variant/templates/variant/variant.html,sha256=bgO3kb4u45IrgCPUJrHT4paNDOQzcKx5dw0ZYbBmCsc,18914
@@ -621,7 +621,7 @@ scout/server/blueprints/variants/views.py,sha256=r2T3eLAG_qrZ2vl3Ar2k6K1KRB7J6z5
 scout/server/blueprints/variants/static/form_scripts.js,sha256=o3GCboaesA9Sm1HgejS_yQwt0I-NTkvcl56jiBdLqZs,8319
 scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html,sha256=Y7XQZjjrU_cJGU8EEGEF3QzTVvDfEVudFdygYExVxwI,7429
 scout/server/blueprints/variants/templates/variants/cancer-variants.html,sha256=bX9FLoufo72PBDoWp95DVLltxUrbLeuFmZQObP1oAlw,10132
-scout/server/blueprints/variants/templates/variants/components.html,sha256=oNeLagTLdOy1SRoDCY2tc7mCK26SD9BlLO8vbSpNEvY,16690
+scout/server/blueprints/variants/templates/variants/components.html,sha256=pTHbNKM87AUOzjXn8zbjtweiYzow3Jsbqt9XHJ7GkAk,16697
 scout/server/blueprints/variants/templates/variants/fusion-variants.html,sha256=XGaLgWobzeFHwyQLXr_Yq9THssf8tGU91VbFKdGOFBg,4801
 scout/server/blueprints/variants/templates/variants/indicators.html,sha256=BX6Wg8OpsALCGGozR1eXT57D0Ixrf-OFXVg6G20Wjr0,4400
 scout/server/blueprints/variants/templates/variants/mei-variants.html,sha256=0-wYjaiUByDduWMgmRS4AMg3IppPNtjZL1vvAdFuIPI,5994
@@ -671,9 +671,9 @@ scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
 scout/utils/scout_requests.py,sha256=JjHOJW1XmenG05mNQ33kvOKq_IicveIfQMcPZeRcQdo,12856
 scout/utils/sort.py,sha256=1AcbeZ6vdt_UXM3BLDBa3aQmN4qxrqtskxwD19oBhvw,756
 scout/utils/track_resources.py,sha256=eUjSEe-Ff8BIb4BHPC_COkJocQO2PaWueiPz1GAuiwY,2614
-scout_browser-4.86.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
-scout_browser-4.86.dist-info/METADATA,sha256=LIrl5lLOrztC7-iyc2X-AAASuh6TvvWjA8Tvq09N4xg,14260
-scout_browser-4.86.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
-scout_browser-4.86.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
-scout_browser-4.86.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
-scout_browser-4.86.dist-info/RECORD,,
+scout_browser-4.87.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
+scout_browser-4.87.dist-info/METADATA,sha256=F_tqlSzv0yKyowhxiHzjxDlBNMPncXYZ7z_AxQgqPLk,14260
+scout_browser-4.87.dist-info/WHEEL,sha256=eOLhNAGa2EW3wWl_TU484h7q1UNgy0JXjjoqKoxAAQc,92
+scout_browser-4.87.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
+scout_browser-4.87.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
+scout_browser-4.87.dist-info/RECORD,,