scout-browser 4.86__tar.gz → 4.87__tar.gz

{scout-browser-4.86 → scout-browser-4.87}/CHANGELOG.md

@@ -4,6 +4,22 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+## [4.87]
+### Added
+- Option to configure RNA build on case load (default '38')
+### Changed
+- Tooltip on RNA alignments now shows RNA genome build version
+- Updated igv.js to v3.0.4
+### Fixed
+- Style of "SNVs" and "SVs" buttons on WTS Outliers page
+- Chromosome alias files for igv.js
+- Genes track displayed also when RNA alignments are present without splice junctions track on igv browser
+- Genes track displayed again when splice junction tracks are present
+
+## [4.86.1]
+### Fixed
+- Loading and updating PanelApp panels, including PanelApp green
+
 ## [4.86]
 ### Added
 - Display samples' name (tooltip) and affected status directly on caseS page

{scout-browser-4.86/scout_browser.egg-info → scout-browser-4.87}/PKG-INFO

@@ -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-4.87/scout/__version__.py

@@ -0,0 +1 @@
+__version__ = "4.87"

{scout-browser-4.86 → scout-browser-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-browser-4.86 → scout-browser-4.87}/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-browser-4.86 → scout-browser-4.87}/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-browser-4.86 → scout-browser-4.87}/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-browser-4.86 → scout-browser-4.87}/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-browser-4.86 → scout-browser-4.87}/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-browser-4.86 → scout-browser-4.87}/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-browser-4.86 → scout-browser-4.87}/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-browser-4.86 → scout-browser-4.87}/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-browser-4.87/scout/server/blueprints/alignviewers/templates/alignviewers/utils.html

@@ -0,0 +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@3.0.4/dist/igv.min.js" integrity="sha512-iczcEXdlX8PdVb/x5TKY6PntdhIbzWaPicz3ZIeZ41EM2MfFboJKXinNzfcVL+SgEv2dOxezH7GAY5V+rQ9jMQ==" crossorigin="anonymous"></script>
+{% endmacro %}

{scout-browser-4.86 → scout-browser-4.87}/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-browser-4.86 → scout-browser-4.87}/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-browser-4.86 → scout-browser-4.87}/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-browser-4.86 → scout-browser-4.87}/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-browser-4.86 → scout-browser-4.87}/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-browser-4.86 → scout-browser-4.87}/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 → scout-browser-4.87/scout_browser.egg-info}/PKG-INFO

@@ -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 → scout-browser-4.87}/tests/parse/test_parse_case.py

@@ -462,7 +462,7 @@ def test_load_case_int_genome_build(scout_config, key):
         assert parse_case_config(scout_config)
 
 
-@pytest.mark.parametrize("key", ["genome_build", "human_genome_build"])
+@pytest.mark.parametrize("key", ["genome_build", "human_genome_build", "rna_human_genome_build"])
 def test_load_case_str_genome_build(scout_config, key):
     """Test loading a case with a genome build as string: '37' or '38´."""
 

scout-browser-4.86/scout/__version__.py

@@ -1 +0,0 @@
-__version__ = "4.86"

scout-browser-4.86/scout/server/blueprints/alignviewers/templates/alignviewers/utils.html

@@ -1,5 +0,0 @@
-{% 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>
-{% endmacro %}