scout-browser 4.98.0__py3-none-any.whl → 4.99.0__py3-none-any.whl

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

@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
 {% from "variants/utils.html" import sv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell %}
-{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell %}
+{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, overlapping_cell, variant_gene_symbols_cell, variant_funct_anno_cell %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - SV variants
@@ -57,18 +57,19 @@ onsubmit="return validateForm()">
         <thead class="table-light thead">
           <tr>
             <th style="width:3%"></th>
-            <th>Rank</th>
-            <th>Score</th>
+            <th title="Rank position">Rank</th>
+            <th title="Rank score">Score</th>
             <th>Callers</th>
             <th>Type</th>
-            <th>Chr</th>
+            <th title="Chromosome">Chr</th>
             <th>Start</th>
             <th>End</th>
             <th>Length</th>
-            <th>Pop Freq</th>
-            <th>Observed</th>
+            <th title="Population Frequency">Pop Freq</th>
+            <th title="Observed database matches">Observed</th>
             <th>Gene(s)</th>
-            <th>Function</th>
+            <th title="Functional annotation">Function</th>
+            <th title="Gene overlapping variants">Overlap</th>
           </tr>
         </thead>
         <tbody>
@@ -121,6 +122,7 @@ onsubmit="return validateForm()">
     <td style="word-wrap:break-word;">
       {{ variant_funct_anno_cell(variant) }}
     </td>
+    <td>{{ overlapping_cell(variant, institute, case) }}</td>
   </tr>
 {% endmacro %}
 

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

@@ -1,5 +1,6 @@
 {% import "bootstrap/wtf.html" as wtf %}
 {% from "utils.html" import comments_table %}
+{% from "cases/utils.html" import pretty_link_variant %}
 {% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, group_assessments_badge, matching_manual_rank, research_assessments_badge %}
 
 {% macro filter_script_main(cytobands) %}
@@ -225,30 +226,25 @@
   </table>
 {% endmacro %}
 
-{% macro svs_table(institute, case, overlapping) %}
+{% macro overlapping_tooltip_table(institute, case, overlapping) %}
   <table class='table table-bordered table-hover table-condensed'>
     <thead>
       <tr>
-        <th>Region</th>
+        <th>Pos</th>
         <th>Type</th>
         <th>Length</th>
         <th>Rank score</th>
       </tr>
     </thead>
     <tbody>
-      {% for sv in overlapping %}
+      {% for variant in overlapping %}
         <tr>
           <td>
-              <a href='{{ url_for("variant.sv_variant",
-                                 institute_id=institute._id,
-                                 case_name=case.display_name,
-                                 variant_id=sv._id) }}'>
-                {{ sv.chromosome }}{{ sv.cytoband_start }}
-              </a>
+            {{ pretty_link_variant(variant, case) }}
           </td>
-          <td class='text-end'>{{ sv.sub_category }}</td>
-          <td class='text-end'>{{ sv.length if sv.length < 100000000000 else "-" }}</td>
-          <td class='text-end'>{{ sv.rank_score }}</td>
+          <td class='text-end'>{{ variant.sub_category }}</td>
+          <td class='text-end'>{{ variant.length if variant.length < 100000000000 else '-' }}</td>
+          <td class='text-end'>{{ variant.rank_score }}</td>
         </tr>
       {% endfor %}
     </tbody>

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

@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
-{% from "variants/utils.html" import compounds_table, svs_table, snv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, mark_heteroplasmic_mt %}
-{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, gene_cell, observed_cell_general  %}
+{% from "variants/utils.html" import snv_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, mark_heteroplasmic_mt %}
+{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, gene_cell, observed_cell_general, overlapping_cell  %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ form.variant_type.data|capitalize }} variants
@@ -59,7 +59,7 @@
               <th style="width:5%" title="Rank score">Score</th>
               <th style="width:4%" title="Chromosome">Chr.</th>
               <th style="width:12%" title="HGNC symbols">Gene</th>
-              <th style="width:6%" title="Pop Freq">Pop Freq</th>
+              <th style="width:6%" title="Population Frequency">Pop Freq</th>
               <th style="width:10%" title="Observed database matches">Observed</th>
               <th style="width:5%" title="CADD score">CADD</th>
               <th style="width:18%" title="Functional annotation">Function</th>
@@ -93,7 +93,7 @@
                   {{ functional_annotation_cell(variant) }}
                 </td>
                 <td>{{ cell_models(variant) }}</td>
-                <td>{{ overlapping_cell(variant) }}</td>
+                <td>{{ overlapping_cell(variant, institute, case) }}</td>
               </tr>
             {% else %}
               <tr>
@@ -159,27 +159,6 @@
   {% endif %}
 {% endmacro %}
 
-{% macro overlapping_cell(variant) %}
-
-  {% if variant.compounds %}
-    {% set ns=namespace(show_compounds=false) %}
-    {% for compound in variant.compounds if not compound.is_dismissed %}
-      {% set ns.show_compounds = true %}
-    {% endfor %}
-    {% if ns.show_compounds %}
-      <a href="#" class="badge bg-primary text-white" data-bs-toggle="popover" data-bs-placement="left"
-        data-bs-html="true" data-bs-trigger="hover click"
-        data-bs-content="{{ compounds_table(institute, case, variant.compounds[:20], is_popover=true) }}">Compounds</a>
-    {% endif %}
-  {% endif %}
-
-  {% if variant.overlapping %}
-  <a href="#" class="badge bg-warning" data-bs-toggle="popover" data-bs-placement="left"
-    data-bs-html="true" data-bs-trigger="hover click"
-    data-bs-content="{{ svs_table(institute, case, variant.overlapping[:20]) }}">Overlapping SVs</a>
-  {% endif %}
-{% endmacro %}
-
 {% block scripts %}
   {{ super() }}
   {{ external_scripts() }}

scout/server/config.py

@@ -38,6 +38,14 @@ ACCREDITATION_BADGE = "swedac-1926-iso17025.png"
 #    discovery_url="https://accounts.google.com/.well-known/openid-configuration",
 # )
 
+# Parameters required for login with Keycloak
+# KEYCLOAK = dict(
+#    client_id="<name_of_client>",
+#    client_secret="secret",
+#    discovery_url="http://localhost:8080/realms/<name_of_realm>/.well-known/openid-configuration",
+#    logout_url="http://localhost:8080/realms/<name_of_realm>/protocol/openid-connect/logout",
+# )
+
 # Chanjo database connection string - used by chanjo report to create coverage reports
 # SQLALCHEMY_DATABASE_URI = "mysql+pymysql://test_user:test_passwordw@127.0.0.1:3306/chanjo"
 

scout/server/utils.py

@@ -244,15 +244,23 @@ def case_has_chanjo2_coverage(case_obj: dict):
 def case_has_alignments(case_obj: dict):
     """Add info on bam/cram files availability to a case dictionary
 
+    This sets the availability of alignments for autosomal chromosomes.
+    If paraphase or de novo assembly alignments, this is also sufficient to set
+    alignment availability.
     Args:
         case_obj(scout.models.Case)
     """
-    case_obj["bam_files"] = False  # Availability of alignments for autosomal chromosomes
+    case_obj["bam_files"] = False
     for ind in case_obj.get("individuals"):
-        bam_path = ind.get("bam_file")
-        if bam_path and os.path.exists(bam_path):
-            case_obj["bam_files"] = True
-            return
+        for alignment_path_key in [
+            "bam_file",
+            "assembly_alignment_path",
+            "paraphase_alignment_path",
+        ]:
+            bam_path = ind.get(alignment_path_key)
+            if bam_path and os.path.exists(bam_path):
+                case_obj["bam_files"] = True
+                return
 
 
 def case_has_mt_alignments(case_obj: dict):
@@ -301,10 +309,19 @@ def case_append_alignments(case_obj: dict):
     """Deconvolute information about files to case_obj.
 
     This function prepares bam/cram files and their indexes for easy access in templates.
+
+    index is set only if it is expected as a separate key on the indiviudal: an
+    attempt at discovery is still made for files with index: None.
     """
     unwrap_settings = [
         {"path": "bam_file", "append_to": "bam_files", "index": "bai_files"},
+        {"path": "assembly_alignment_path", "append_to": "assembly_alignments", "index": None},
         {"path": "mt_bam", "append_to": "mt_bams", "index": "mt_bais"},
+        {
+            "path": "paraphase_alignment_path",
+            "append_to": "paraphase_alignments",
+            "index": None,
+        },
         {"path": "rhocall_bed", "append_to": "rhocall_beds", "index": None},
         {"path": "rhocall_wig", "append_to": "rhocall_wigs", "index": None},
         {"path": "upd_regions_bed", "append_to": "upd_regions_beds", "index": None},

scout/utils/acmg.py

@@ -173,7 +173,7 @@ def get_acmg_criteria(acmg_terms: set) -> tuple:
         finally, check remaining prefixes if no suffix match or stand-alone criteria match
 
     Return a tuple with
-        pvs: This variable indicates if Pathogenicity Very Strong exists
+        pvs_terms: This variable indicates if Pathogenicity Very Strong exists
         ps_terms: Collection of terms with Pathogenicity Strong
         pm_terms: Collection of terms with Pathogenicity moderate
         pp_terms: Collection of terms with Pathogenicity supporting
@@ -182,25 +182,29 @@ def get_acmg_criteria(acmg_terms: set) -> tuple:
         bp_terms: Collection of terms with supporting Benign evidence
     """
 
-    pvs = False
+    pvs_terms = []
     ps_terms = []
     pm_terms = []
     pp_terms = []
 
-    ba = False
+    ba_terms = []
     bs_terms = []
     bp_terms = []
 
     suffix_map = {
+        "_Stand-alone": {"B": ba_terms},
+        "_Very Strong": {"P": pvs_terms},
         "_Strong": {"P": ps_terms, "B": bs_terms},
         "_Moderate": {"P": pm_terms},
         "_Supporting": {"P": pp_terms, "B": bp_terms},
     }
 
     prefix_map = {
+        "PVS": pvs_terms,
         "PS": ps_terms,
         "PM": pm_terms,
         "PP": pp_terms,
+        "BA": ba_terms,
         "BS": bs_terms,
         "BP": bp_terms,
     }
@@ -216,17 +220,12 @@ def get_acmg_criteria(acmg_terms: set) -> tuple:
                     continue
                 break
         else:
-            if term.startswith("PVS"):
-                pvs = True
-            elif term.startswith("BA"):
-                ba = True
-            else:
-                for prefix, term_list in prefix_map.items():
-                    if term.startswith(prefix):
-                        term_list.append(term)
-                        break
+            for prefix, term_list in prefix_map.items():
+                if term.startswith(prefix):
+                    term_list.append(term)
+                    break
 
-    return (pvs, ps_terms, pm_terms, pp_terms, ba, bs_terms, bp_terms)
+    return (pvs_terms, ps_terms, pm_terms, pp_terms, ba_terms, bs_terms, bp_terms)
 
 
 def get_acmg(acmg_terms: set) -> Optional[str]:
@@ -316,19 +315,19 @@ def get_acmg_temperature(acmg_terms: set) -> Optional[dict]:
     if not acmg_terms:
         return {}
 
-    (pvs, ps_terms, pm_terms, pp_terms, ba, bs_terms, bp_terms) = get_acmg_criteria(acmg_terms)
-
-    if ba:
-        points = -8
-    else:
-        points = (
-            8 * pvs
-            + 4 * len(ps_terms)
-            + 2 * len(pm_terms)
-            + len(pp_terms)
-            - 4 * len(bs_terms)
-            - len(bp_terms)
-        )
+    (pvs_terms, ps_terms, pm_terms, pp_terms, ba_terms, bs_terms, bp_terms) = get_acmg_criteria(
+        acmg_terms
+    )
+
+    points = (
+        8 * len(pvs_terms)
+        + 4 * len(ps_terms)
+        + 2 * len(pm_terms)
+        + len(pp_terms)
+        - 8 * len(ba_terms)
+        - 4 * len(bs_terms)
+        - len(bp_terms)
+    )
 
     if points <= -7:
         point_classification = "benign"

scout/utils/ensembl_biomart_clients.py

@@ -4,7 +4,7 @@ from typing import Dict, Iterator
 import requests
 
 LOG = logging.getLogger(__name__)
-SCHUG_BASE = "https://schug-stage.scilifelab.se"
+SCHUG_BASE = "https://schug.scilifelab.se"
 
 BUILDS: Dict[str, str] = {"37": "GRCh37", "38": "GRCh38"}
 

scout/utils/ensembl_rest_clients.py

@@ -1,30 +1,27 @@
 """Code for talking to ensembl rest API"""
 
 import logging
+from typing import Optional
 from urllib.parse import urlencode
 
 import requests
+from flask import flash
 
 LOG = logging.getLogger(__name__)
 
 HEADERS = {"Content-type": "application/json"}
-RESTAPI_37 = "https://grch37.rest.ensembl.org"
-RESTAPI_38 = "https://rest.ensembl.org"
+RESTAPI_URL = "https://rest.ensembl.org"
 
 
 class EnsemblRestApiClient:
     """A class handling requests and responses to and from the Ensembl REST APIs.
-    Endpoints for human build 37: https://grch37.rest.ensembl.org
-    Endpoints for human build 38: http://rest.ensembl.org/
+    Endpoint: http://rest.ensembl.org/
     Documentation: https://github.com/Ensembl/ensembl-rest/wiki
     doi:10.1093/bioinformatics/btu613
     """
 
-    def __init__(self, build="37"):
-        if build == "38":
-            self.server = RESTAPI_38
-        else:
-            self.server = RESTAPI_37
+    def __init__(self):
+        self.server = RESTAPI_URL
 
     def build_url(self, endpoint, params=None):
         """Build an url to query ensembml"""
@@ -34,7 +31,7 @@ class EnsemblRestApiClient:
         return "".join([self.server, endpoint])
 
     @staticmethod
-    def send_request(url):
+    def send_request(url) -> Optional[dict]:
         """Sends the actual request to the server and returns the response
 
         Accepts:
@@ -43,33 +40,29 @@ class EnsemblRestApiClient:
         Returns:
             data(dict): dictionary from json response
         """
-        data = {}
+        error = None
+        data = None
         try:
             response = requests.get(url, headers=HEADERS)
-            if response.status_code == 404:
-                LOG.info("Request failed for url %s\n", url)
-                response.raise_for_status()
-            data = response.json()
-        except requests.exceptions.MissingSchema as err:
-            LOG.info("Request failed for url %s: Error: %s\n", url, err)
-            data = err
-        except requests.exceptions.HTTPError as err:
-            LOG.info("Request failed for url %s: Error: %s\n", url, err)
-            data = err
+            if response.status_code not in [404, 500]:
+
+                data = response.json()
+            else:
+                error = f"Ensembl request failed with code:{response.status_code} for url {url}"
+        except requests.exceptions.MissingSchema:
+            error = f"Ensembl request failed with MissingSchema error for url {url}"
+        except requests.exceptions.HTTPError:
+            error = f"Ensembl request failed with HTTPError error for url {url}"
+
+        if error:
+            flash(error)
         return data
 
-    def liftover(self, build, chrom, start, end=None):
+    def liftover(
+        self, build: str, chrom: str, start: int, end: Optional[int] = None
+    ) -> Optional[dict]:
         """Perform variant liftover using Ensembl REST API
-
-        Args:
-            build(str): genome build: "37" or "38"
-            chrom(str): 1-22,X,Y,MT,M
-            start(int): start coordinate
-            stop(int): stop coordinate or None
-
-        Returns:
-            mappings(list of dict): example:
-                example: https://rest.ensembl.org/map/human/GRCh37/X:1000000..1000100:1/GRCh38?content-type=application/json
+        example: https://rest.ensembl.org/map/human/GRCh37/X:1000000..1000100:1/GRCh38?content-type=application/json
         """
 
         build = "GRCh38" if "38" in str(build) else "GRCh37"

scout/utils/hgvs.py

@@ -6,7 +6,7 @@ LOG = logging.getLogger(__name__)
 VALIDATOR_URL = "https://rest.variantvalidator.org/VariantValidator/variantvalidator/{}/{}/select?content-type=application%2Fjson"
 
 
-def validate_hgvs(build, desc):
+def validate_hgvs(build: str, desc: str) -> bool:
     """Validates a simple hgvs descriptor using the VariantValidator API (https://rest.variantvalidator.org/)
 
     Args:

{scout_browser-4.98.0.dist-info → scout_browser-4.99.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scout-browser
-Version: 4.98.0
+Version: 4.99.0
 Summary: Clinical DNA variant visualizer and browser
 Project-URL: Repository, https://github.com/Clinical-Genomics/scout
 Project-URL: Changelog, https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md
@@ -124,29 +124,25 @@ Instructions on how to run a Scout image connected to your local database or a c
 
 ## Installation
 
-<!-- You can install the latest release of Scout using `pip`:
-
-```bash
-pip install scout-browser
-
-# ... to include optional coverage tools you would use:
-pip install scout-browser[coverage]
-```
-
-If you would like to install Scout for local development: -->
+Here is a quick start. Please see e.g. the [Installation instructions](docs/install.md) for more details.
 
 ```bash
 git clone https://github.com/Clinical-Genomics/scout
 cd scout
-pip install --editable .
 ```
 
-Scout is configured to use `uv` if you like; either run, install, install as a tool or
-```
+Scout is configured to use `uv`; either run, install, or install as a tool.
+
+```bash
 uv sync --frozen
 uv run scout
 ```
 
+You can also install using pip:
+
+```
+pip install --editable .
+```
 
 Scout PDF reports are created using [Flask-WeasyPrint](https://pythonhosted.org/Flask-WeasyPrint/). This library requires external dependencies which need be installed separately (namely Cairo and Pango). See platform-specific instructions for Linux, macOS and Windows available on the WeasyPrint installation [pages](https://doc.courtbouillon.org/weasyprint/stable/first_steps.html#installation).