scout-browser 4.91.2__py3-none-any.whl → 4.92__py3-none-any.whl

scout/__version__.py

@@ -1 +1 @@
-__version__ = "4.91.2"
+__version__ = "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/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/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/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/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.dist-info → scout_browser-4.92.dist-info}/METADATA

@@ -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.dist-info → scout_browser-4.92.dist-info}/RECORD

@@ -1,5 +1,5 @@
 scout/__init__.py,sha256=Z4liXvmEcLkC67ElsWvYHfemPKdWgWI5O6MB6XlDM8M,232
-scout/__version__.py,sha256=c-e8ef0PPzsi3EtzC80FCudBi3MZOAKf5jphOkGjfF8,23
+scout/__version__.py,sha256=ANcNj-w6TB4wETdZ9CZJYc1ZGU2Q1cA11Hzzi92m9BE,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
@@ -22,7 +22,7 @@ scout/adapter/mongo/matchmaker.py,sha256=amTvFOlUbrt1RmecY_8hPY6bO3j79lc2UbmzlCQ
 scout/adapter/mongo/omics_variant.py,sha256=VdkNG_l6vcr3UF25EixEfvIdMGkSGeNaMjLRhQHS_lc,7521
 scout/adapter/mongo/panel.py,sha256=d1oMEYAiDGybLmlbbf3-fQdCdU0-T7x2XdIUwZGthYk,20031
 scout/adapter/mongo/phenomodel.py,sha256=cypSS8YRzu98Bf1kC0orfrLNn_ZQSYCK8e4mNR5PaPY,2572
-scout/adapter/mongo/query.py,sha256=MzeMUND_BPHgJLGDEbOVgwf4ic8M9ZXFcyroQd0LMJQ,33314
+scout/adapter/mongo/query.py,sha256=Zk5BV9GZYVlGoSRRjP88TpvB4teVpvHgHnSDV0W-kS0,33157
 scout/adapter/mongo/rank_model.py,sha256=wvDNI4OLf-f7ZYZ_Q_6qi0myxOJCNNJR_-2-_0u2K2M,5712
 scout/adapter/mongo/transcript.py,sha256=3U1qtyxZ1DnrzdBJm_emJXISMYFKJuX_zAKynUt8NMY,7417
 scout/adapter/mongo/user.py,sha256=QoQnRWqi_dV3ZwGzBonEU6Ap9TgMDf2x_C5UIqG0pa0,2569
@@ -58,7 +58,7 @@ scout/commands/serve.py,sha256=fImJrgMBYQTD18xODjGqN6NgXjTe8seI_awd9vF04rU,1564
 scout/commands/utils.py,sha256=T29f-1wTq3uoxqtv6QOqBdMBl7tLeEn8DYXnnv3gowI,306
 scout/commands/wipe_database.py,sha256=TvCoXZCT-mvTqsZaFstV5u5FM8KAQstB3JxyGHYMLtg,1005
 scout/commands/delete/__init__.py,sha256=6Z97FsWMqyKqF64Anl1zwljVNTfjJUCI7yylxIEnsUY,35
-scout/commands/delete/delete_command.py,sha256=X3sH0pP51n1Gmv3e7EbgXggFp_yG4ZtziSNsIpcNu78,12584
+scout/commands/delete/delete_command.py,sha256=_x897Du0nTsYmSG_5LAIm6Z9sjKcaCrtAR7cwuNwl4I,13285
 scout/commands/download/__init__.py,sha256=mfDzxqKzJ0LgfPBN_fehkdX5BPy1FJ3rauA3ORLIjCM,39
 scout/commands/download/download_command.py,sha256=m5CKefst3qhs4urfNu1A2TERisUb_5WPn-wn9bGCDr0,736
 scout/commands/download/ensembl.py,sha256=CsTMjYihBtXyfofNIQ2riL9UBzydDbqoNZ7jJVQ15ak,2112
@@ -414,7 +414,7 @@ scout/parse/mitodel.py,sha256=3uvEXI9v9wIw97NUL7gqLLxHay0mpQpDgKaIxUbIyrE,803
 scout/parse/omim.py,sha256=nrCaFZgjUKZo9Jfku2-jcNjdsIYHsvjdWcydz4nCpZA,12465
 scout/parse/orpha.py,sha256=5u9xqGpAn8vgoJ0uVqbYiqQBiNfBwXOiTzX16kAnmFU,4392
 scout/parse/panel.py,sha256=J28e_MkKeB5r4hOutb3qimxUT7G5yg8x1Ca4bAs0I_c,9577
-scout/parse/panelapp.py,sha256=1UAKBm48tKlfDpNb_VH_kfqO8tgduXRSIQnWa61Fzrc,3944
+scout/parse/panelapp.py,sha256=Idz6cGvQnyI-nn6yCTc6EGSRp1gX-CXN6Y4ayAee-_A,4076
 scout/parse/peddy.py,sha256=uM49GaZMtr8waCsZDvCHDS5JDQ43JUlhdWh9C7f7ZvU,5418
 scout/parse/smn.py,sha256=iOK1N8iYm9dFigsKtWq0Y0ZCa1CH29s9zeR_tH0bPuc,1153
 scout/parse/omics_variant/__init__.py,sha256=vq8Ew4_Xr2vPy_3Fg0eTpPWsQpWnUXYBhjRndBUvtTw,422
@@ -500,7 +500,7 @@ scout/server/blueprints/diagnoses/templates/diagnoses/disease_term.html,sha256=8
 scout/server/blueprints/genes/__init__.py,sha256=LPHrbmfVhZpLGGdExFbJp_Du1NKCsVOO_eaevpsNLC8,52
 scout/server/blueprints/genes/controllers.py,sha256=LCuGPQymKxA7sES49z_j2_B3prKmNY-ME0VK892VoPs,3629
 scout/server/blueprints/genes/views.py,sha256=lFJ7izYu0CbUJo3j5TesrUhIwreZUYw9_dDqd6iG8m4,1512
-scout/server/blueprints/genes/templates/genes/gene.html,sha256=X1WR-sHYGnWyhQfgN77TqC3_yoweaqu7MjwUvAO9UBo,10872
+scout/server/blueprints/genes/templates/genes/gene.html,sha256=a--c-IjzNKN_JW7z9jbNCnk3bLD_oVeFvf5x8IAmynA,11197
 scout/server/blueprints/genes/templates/genes/genes.html,sha256=x6jXKijvuEX9GvIedHW4O_BerYXiWEmAdYT0HTiGnhI,1130
 scout/server/blueprints/genes/templates/genes/layout.html,sha256=cZMLe2cInq24z0sZpPxDm_kEiAe5VQbOR-8XWn6wlvI,1601
 scout/server/blueprints/institutes/__init__.py,sha256=kGSyYrBC1QaEQBDdoMkMLfaowV7roaV5DowICi_0RSQ,65
@@ -644,7 +644,7 @@ scout/server/extensions/ldap_extension.py,sha256=nVgJ6YhSyvpg8J4bSYzJwoEvKhP0faW
 scout/server/extensions/loqus_extension.py,sha256=uiqUXQ7Q7DCj6C20TKgL8yLu9DXov95vrJfhq0tvbTM,12602
 scout/server/extensions/matchmaker_extension.py,sha256=mNytCYnZX1hgdq1otkvnyOkh4dj9SVgQthJAfKb8TMI,5024
 scout/server/extensions/mongo_extension.py,sha256=bKB0K5ibp-BWynOTgzBJd5qIYO0S9zRtEyDUw7EoxSQ,1029
-scout/server/extensions/panelapp_extension.py,sha256=UoPFGKqXJtAfbw3WRTxvHZweNI4jVgYgrhWkgVJouRo,2732
+scout/server/extensions/panelapp_extension.py,sha256=UnHhyG7iSMy3ERQg5Sl3DOkmKjsLPgAEfPkzlfn2BrY,2738
 scout/server/extensions/phenopacket_extension.py,sha256=kcEUIOSfkQAlAmUm07hQS1BeUjeN4lBc-InvaNtbFxo,7295
 scout/server/extensions/rerunner_extension.py,sha256=SEwQi5BZR5X70BoD0U7TfyGgGv2WbJbas0v1efuv_r8,1104
 scout/server/static/bs_styles.css,sha256=Y7aq8Es3NHj1OaLPX0eiY5485C8gENptpuYmf7W3o1w,6421
@@ -677,9 +677,9 @@ scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
 scout/utils/scout_requests.py,sha256=lgPumNI_EikBZR1m9ztZI_mZAfV29y1KGoiBv9kejzQ,12797
 scout/utils/sort.py,sha256=1AcbeZ6vdt_UXM3BLDBa3aQmN4qxrqtskxwD19oBhvw,756
 scout/utils/track_resources.py,sha256=eUjSEe-Ff8BIb4BHPC_COkJocQO2PaWueiPz1GAuiwY,2614
-scout_browser-4.91.2.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
-scout_browser-4.91.2.dist-info/METADATA,sha256=i0cvLLKs7eoxwwbjjU2KDltcnzEuNtgCDumaZZKLUCs,14262
-scout_browser-4.91.2.dist-info/WHEEL,sha256=tZoeGjtWxWRfdplE7E3d45VPlLNQnvbKiYnx7gwAy8A,92
-scout_browser-4.91.2.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
-scout_browser-4.91.2.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
-scout_browser-4.91.2.dist-info/RECORD,,
+scout_browser-4.92.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
+scout_browser-4.92.dist-info/METADATA,sha256=Z78U2w0_9MMsAmsc1pLdjEAkA2k2J06aUwZ2R6VIbJM,14260
+scout_browser-4.92.dist-info/WHEEL,sha256=tZoeGjtWxWRfdplE7E3d45VPlLNQnvbKiYnx7gwAy8A,92
+scout_browser-4.92.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
+scout_browser-4.92.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
+scout_browser-4.92.dist-info/RECORD,,