scout-browser 4.91.2__tar.gz → 4.92__tar.gz

{scout-browser-4.91.2 → scout-browser-4.92}/CHANGELOG.md

@@ -4,6 +4,15 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
 
+## [4.92]
+### Added
+- PanelApp link on gene page and on gene panels description
+### Changed
+- Add more filters to the delete variants command (institute ID and text file with list of case IDs)
+- Use the `clinicalgenomics/python3.11-venv:1.0` image everywhere in the Dockerfiles
+### Fixed
+- list/List typing issue on PanelApp extension module
+
 ## [4.91.2]
 ### Fixed
 - Stranger TRGT parsing of `.` in `FORMAT.MC`

{scout-browser-4.91.2/scout_browser.egg-info → scout-browser-4.92}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.91.2
+Version: 4.92
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

scout-browser-4.92/scout/__version__.py

@@ -0,0 +1 @@
+__version__ = "4.92"

{scout-browser-4.91.2 → scout-browser-4.92}/scout/adapter/mongo/query.py

@@ -1,7 +1,7 @@
 import logging
 import re
 from datetime import datetime, timedelta
-from typing import Optional, Union
+from typing import List, Optional, Union
 
 from scout.constants import (
     CLINSIG_MAP,
@@ -19,23 +19,19 @@ LOG = logging.getLogger(__name__)
 
 class QueryHandler(object):
     def build_case_query(
-        self, case_id=None, status=None, older_than=None, analysis_type=[]
+        self,
+        case_ids: Optional[List[str]],
+        institute_id: Optional[List[str]],
+        status: Optional[List[str]],
+        older_than: Optional[int],
+        analysis_type: Optional[List[str]],
     ) -> dict:
-        """Build case query based on case id, status and analysis date
-
-        Args:
-            case_id(str): id of a case
-            status(list): one or more case status
-            older_than(int): to select cases older than a number of months
-            case_ids(list): a list of case _ids
-            analysis_type(list): a list of type of analysis ["wgs", "wes", "panel"]
-
-        Returns:
-            case_query(dict): query dictionary
-        """
+        """Build case query based on case id, status and analysis date."""
         case_query = {}
-        if case_id:
-            case_query["_id"] = case_id
+        if case_ids:
+            case_query["_id"] = {"$in": case_ids}
+        if institute_id:
+            case_query["owner"] = institute_id
         if analysis_type:
             case_query["individuals.analysis_type"] = {"$in": analysis_type}
         if older_than:
@@ -43,6 +39,7 @@ class QueryHandler(object):
             case_query["analysis_date"] = {"$lt": older_than_date}
         if status:
             case_query["status"] = {"$in": list(status)}
+
         return case_query
 
     def delete_variants_query(

{scout-browser-4.91.2 → scout-browser-4.92}/scout/commands/delete/delete_command.py

@@ -29,7 +29,14 @@ VARIANT_CATEGORIES = ["mei", "snv", "sv", "cancer", "cancer_sv", "str"]
 
 @click.command("variants", short_help="Delete variants for one or more cases")
 @click.option("-u", "--user", help="User running this command (email)", required=True)
-@click.option("-c", "--case-id", help="Case id")
+@click.option("-c", "--case-id", help="Case id", multiple=True)
+@click.option(
+    "-f",
+    "--case-file",
+    help="Path to file containing list of case IDs",
+    type=click.Path(exists=True),
+)
+@click.option("-i", "--institute", help="Restrict to cases with specified institute ID")
 @click.option(
     "--status",
     type=click.Choice(CASE_STATUSES),
@@ -42,7 +49,6 @@ VARIANT_CATEGORIES = ["mei", "snv", "sv", "cancer", "cancer_sv", "str"]
     "--analysis-type",
     type=click.Choice(["wgs", "wes", "panel"]),
     multiple=True,
-    default=["wgs"],
     help="Type of analysis",
 )
 @click.option("--rank-threshold", type=click.INT, default=5, help="With rank threshold lower than")
@@ -62,7 +68,9 @@ VARIANT_CATEGORIES = ["mei", "snv", "sv", "cancer", "cancer_sv", "str"]
 @with_appcontext
 def variants(
     user: str,
-    case_id: str,
+    case_id: list,
+    case_file: str,
+    institute: str,
     status: list,
     older_than: int,
     analysis_type: list,
@@ -73,6 +81,12 @@ def variants(
 ) -> None:
     """Delete variants for one or more cases"""
 
+    if case_file and case_id:
+        click.echo(
+            "You should specify either case ID (multiple times if needed) or the path to a text file containing a list of case IDs (one per line)."
+        )
+        return
+
     user_obj = store.user(user)
     if user_obj is None:
         click.echo(f"Could not find a user with email '{user}' in database")
@@ -86,7 +100,16 @@ def variants(
     else:
         click.confirm("Variants are going to be deleted from database. Continue?", abort=True)
 
-    case_query = store.build_case_query(case_id, status, older_than, analysis_type)
+    if case_file:
+        case_id = [line.strip() for line in open(case_file).readlines() if line.strip()]
+
+    case_query = store.build_case_query(
+        case_ids=case_id,
+        institute_id=institute,
+        status=status,
+        older_than=older_than,
+        analysis_type=analysis_type,
+    )
     # Estimate the average size of a variant document in database
     avg_var_size = store.collection_stats("variant").get("avgObjSize", 0)  # in bytes
 

{scout-browser-4.91.2 → scout-browser-4.92}/scout/parse/panelapp.py

@@ -1,12 +1,13 @@
 """Code to parse panel information"""
 
 import logging
-from typing import Dict, List, Optional
+from typing import Dict, Optional
 
 from scout.constants import INCOMPLETE_PENETRANCE_MAP, MODELS_MAP, PANELAPP_CONFIDENCE_EXCLUDE
 from scout.utils.date import get_date
 
 LOG = logging.getLogger(__name__)
+PANELAPP_PANELS_URL = "https://panelapp.genomicsengland.co.uk/panels/"
 
 
 def parse_panel_app_gene(
@@ -90,6 +91,7 @@ def parse_panelapp_panel(
     gene_panel["display_name"] = " - ".join([panel_info["name"], f"[{confidence.upper()}]"])
     gene_panel["institute"] = institute
     gene_panel["panel_type"] = ("clinical",)
+    gene_panel["description"] = f"{PANELAPP_PANELS_URL}{panel_id}"
 
     LOG.info("Parsing panel %s", gene_panel["display_name"])
 

{scout-browser-4.91.2 → scout-browser-4.92}/scout/server/blueprints/genes/templates/genes/gene.html

@@ -84,6 +84,12 @@
                       <a target="_blank" href={{ record.entrez_link }} referrerpolicy="no-referrer" rel="noopener" target="_blank"> {{ entrez_id }}</a>
                     </span>
                   </li>
+                  <li class="list-group-item">
+                    PanelApp
+                    <span class="float-end">
+                      <a target="_blank" href={{ record.panelapp_link }} referrerpolicy="no-referrer" rel="noopener" target="_blank"> {{ symbol }} </a>
+                    </span>
+                  </li>
                   {% if pli_score %}
                   <li class="list-group-item">
                     pLi Score (<a href={{ record.gnomad_link }} referrerpolicy="no-referrer" rel="noopener" target="_blank">GnomAD</a>)

{scout-browser-4.91.2 → scout-browser-4.92}/scout/server/extensions/panelapp_extension.py

@@ -1,5 +1,5 @@
 import logging
-from typing import Optional
+from typing import List, Optional
 
 import requests
 
@@ -41,7 +41,7 @@ class PanelAppClient:
             for type in panel.get("types", []):
                 self.panel_types.add(type["slug"])
 
-    def get_panel_ids(self, signed_off: bool) -> list[int]:
+    def get_panel_ids(self, signed_off: bool) -> List[int]:
         """Returns a list of panel ids contained in a json document with gene panels data."""
 
         def get_ids(json_panels):

{scout-browser-4.91.2 → scout-browser-4.92/scout_browser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.91.2
+Version: 4.92
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson

scout-browser-4.91.2/scout/__version__.py

@@ -1 +0,0 @@
-__version__ = "4.91.2"