scout-browser 4.83__py3-none-any.whl → 4.84__py3-none-any.whl

scout/server/extensions/loqus_extension.py

@@ -3,11 +3,15 @@
 * Requires loqusdb version 2.5 or greater.
 * If multiple instances are configured, version will be default's.
 """
+
 import json
 import logging
 import subprocess
 import traceback
 from subprocess import CalledProcessError
+from typing import Dict, Optional
+
+from flask import flash
 
 from scout.exceptions.config import ConfigError
 from scout.utils.scout_requests import get_request_json as api_get
@@ -180,16 +184,9 @@ class LoqusDB:
         }
         return loqus_query
 
-    def get_variant(self, variant_info, loqusdb_id="default"):
-        """Return information for a variant (SNV or SV) from loqusdb
-
-        Args:
-            variant_info(dict)
-            loqusdb_id(string)
+    def get_variant(self, variant_info: dict, loqusdb_id: str = "default") -> Optional[Dict]:
+        """Return information for a variant (SNV or SV) from loqusdb"""
 
-        Returns:
-            loqus_variant(dict)
-        """
         loqus_instance = self.loqusdb_settings.get(loqusdb_id)
         if loqus_instance is None:
             LOG.error(f"Could not find a Loqus instance with id:{loqusdb_id}")
@@ -202,7 +199,7 @@ class LoqusDB:
         return self.get_api_loqus_variant(loqus_instance.get(API_URL), variant_info)
 
     @staticmethod
-    def get_api_loqus_variant(api_url, variant_info):
+    def get_api_loqus_variant(api_url, variant_info) -> dict:
         """get variant data using a Loqus instance available via REST API
 
         SNV/INDELS can be queried in loqus by defining a simple id. For SVs we need to call them
@@ -230,10 +227,15 @@ class LoqusDB:
             search_url = f"{search_url}/?chrom={chrom}&end_chrom={end_chrom}&pos={pos}&end={end}&sv_type={sv_type}"
 
         search_resp = api_get(search_url)
-        if search_resp.get("status_code") != 200:
-            LOG.info(search_resp.get("detail"))
-            return {}
-        return search_resp.get("content")
+
+        if search_resp.get("status_code") == 200:
+            return search_resp.get("content")
+        if search_resp.get("message"):  # An error occurred during the request
+            flash(
+                f"Connection to Loqusdb instance returned error: '{search_resp['message']}'",
+                "warning",
+            )
+        return {}
 
     def get_exec_loqus_variant(self, loqus_instance, variant_info):
         """Get variant data using a local executable instance of Loqus

scout/server/extensions/matchmaker_extension.py

@@ -1,6 +1,7 @@
 """Code for MatchMaker Exchange integration
    Tested with PatientMatcher: https://github.com/Clinical-Genomics/patientMatcher
 """
+
 import datetime
 import json
 import logging

scout/server/extensions/mongo_extension.py

@@ -1,4 +1,5 @@
 """Code for flask mongodb extension in scout"""
+
 import os
 
 from scout.adapter.client import get_connection

scout/server/extensions/rerunner_extension.py

@@ -1,4 +1,5 @@
 """Code for Rerunner integration."""
+
 import logging
 
 LOG = logging.getLogger(__name__)

scout/server/links.py

@@ -159,7 +159,7 @@ def genemania(hgnc_symbol):
 
 
 def genenames(hgnc_id):
-    link = "https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=HGNC:{}"
+    link = "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:{}"
     if not hgnc_id:
         return None
     return link.format(hgnc_id)
@@ -679,9 +679,9 @@ def snp_links(variant_obj):
         if "rs" in snp:
             snp_links[snp] = f"https://www.ncbi.nlm.nih.gov/snp/{snp}"  # dbSNP
         elif snp.isnumeric():
-            snp_links[
-                snp
-            ] = f"https://www.ncbi.nlm.nih.gov/clinvar/variation/{snp}"  # ClinVar variation
+            snp_links[snp] = (
+                f"https://www.ncbi.nlm.nih.gov/clinvar/variation/{snp}"  # ClinVar variation
+            )
 
     return snp_links
 

scout/server/static/bs_styles.css

@@ -333,7 +333,7 @@ body {
 
 /* Closed submenu icon */
 #sidebar-container .list-group .list-group-item[aria-expanded="false"] .submenu-icon::after {
-  content: " \f0d7";
+  content: " \f0da";
   font-family: "Font Awesome 5 Free", ui-monospace;
   font-weight: 900;
   display: inline;
@@ -342,7 +342,7 @@ body {
 }
 /* Opened submenu icon */
 #sidebar-container .list-group .list-group-item[aria-expanded="true"] .submenu-icon::after {
-  content: " \f0da";
+  content: " \f0d7";
   font-family: "Font Awesome 5 Free", ui-monospace;
   font-weight: 900;
   display: inline;
@@ -353,15 +353,15 @@ body {
 
 /* Closed submenu icon - general case */
 .text-body[aria-expanded="false"] .collapse-icon::after {
-  content: " \f0d7";
+  content: " \f0da";
   font-family: "Font Awesome 5 Free", ui-monospace;
   font-weight: 900;
   display: inline;
   text-align: left;
 }
-/* Opened submenu icon - general case */
+/* Open submenu icon - general case */
 .text-body[aria-expanded="true"] .collapse-icon::after {
-  content: " \f0da";
+  content: " \f0d7";
   font-family: "Font Awesome 5 Free", ui-monospace;
   font-weight: 900;
   display: inline;

scout/utils/ensembl_rest_clients.py

@@ -1,4 +1,5 @@
 """Code for talking to ensembl rest API"""
+
 import logging
 from urllib.parse import urlencode
 

scout/utils/scout_requests.py

@@ -1,4 +1,5 @@
 """Code for performing requests"""
+
 import logging
 import urllib.request
 import zlib

scout/utils/sort.py

@@ -0,0 +1,21 @@
+from scout.constants import FILE_TYPE_MAP
+
+
+def get_load_priority(category: str = None, variant_type: str = None, file_type: str = None) -> int:
+    """
+    Returns most urgent, highest load priority (numerically the lowest prio number) for the given variables
+    from a FILE_TYPE_MAP dict of dicts. Helper useful in a sort function.
+    """
+    ordered_file_type_map = sorted(FILE_TYPE_MAP.items(), key=lambda ftm: ftm[1]["load_priority"])
+
+    for ftm in ordered_file_type_map:
+        if file_type and file_type != ftm[0]:
+            continue
+
+        if category and category != ftm[1]["category"]:
+            continue
+
+        if variant_type and variant_type != ftm[1]["variant_type"]:
+            continue
+
+        return ftm[1]["load_priority"]

{scout_browser-4.83.dist-info → scout_browser-4.84.dist-info}/METADATA

@@ -1,12 +1,10 @@
 Metadata-Version: 2.1
 Name: scout-browser
-Version: 4.83
+Version: 4.84
 Summary: Clinical DNA variant visualizer and browser.
 Home-page: https://github.com/Clinical-Genomics/scout
 Author: Måns Magnusson
 Author-email: mans.magnusson@scilifelab.se
-License: UNKNOWN
-Platform: UNKNOWN
 Classifier: Environment :: Web Environment
 Classifier: Intended Audience :: Developers
 Classifier: License :: OSI Approved :: BSD License
@@ -16,6 +14,7 @@ Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Programming Language :: Python :: 3.6
 Description-Content-Type: text/markdown
+License-File: LICENSE
 Requires-Dist: werkzeug <3
 Requires-Dist: Flask >=2.0
 Requires-Dist: Flask-Bootstrap
@@ -338,5 +337,3 @@ be found in [CONTRIBUTING](CONTRIBUTING.md).
 [black-url]: https://github.com/psf/black
 [woke-image]: https://github.com/Clinical-Genomics/scout/actions/workflows/woke.yml/badge.svg
 [woke-url]: https://github.com/Clinical-Genomics/scout/actions/workflows/woke.yml
-
-

{scout_browser-4.83.dist-info → scout_browser-4.84.dist-info}/RECORD

@@ -1,11 +1,11 @@
 scout/__init__.py,sha256=Z4liXvmEcLkC67ElsWvYHfemPKdWgWI5O6MB6XlDM8M,232
-scout/__version__.py,sha256=Kv_DfPRkoZkG-PQ48-r24xj_8hLgmLZ8dm27gihcjb4,21
+scout/__version__.py,sha256=tF83DHOdm3YmXrOU1LzFYhwaXBo2y3-VFlwB8yTrpXw,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
 scout/adapter/mongo/acmg.py,sha256=v2Zuw-6APVmcnBnNXa18WJEu2vj5GUhZNiKMkruJsBI,4170
 scout/adapter/mongo/base.py,sha256=6sN_KofLZS47CpxAnA0x2zhhc0k09riiKOAgaAaDzSI,4206
-scout/adapter/mongo/case.py,sha256=guQ_Jd8gLDl4w7cA3dtAI7RL_F-v2nzwNohF6g-M5qo,59063
+scout/adapter/mongo/case.py,sha256=wXYmyv32gvnCGHgqys3ZGG3gAUyf_buC8LfSzDt4TFo,59238
 scout/adapter/mongo/case_events.py,sha256=slHR4XJF9vRuEbuInJKMMAImLF8m7tHWVfGP42fbXr0,26859
 scout/adapter/mongo/case_group.py,sha256=tG8DuO0rNYepV4k0yCGPqssODErc0HMsAypg3mfhcV0,1575
 scout/adapter/mongo/clinvar.py,sha256=tczC39O3DFDkYgjt2RDgkkG-x1Mvx_99Hw7dAbIQ5gk,19838
@@ -25,9 +25,9 @@ scout/adapter/mongo/query.py,sha256=Mpl8wxfmxFbue5Mixq1jCQcImCPg9D5nf6jCli2WDTM,
 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
-scout/adapter/mongo/variant.py,sha256=wsEwmgD6MjThBqfN4LvdET2bVesF0SQ7ENNP4AfOFEo,34191
+scout/adapter/mongo/variant.py,sha256=SAwYcDY4rL0KaoaV8ZdjyPoz0G_EbC_sRnqA2U53iJU,34623
 scout/adapter/mongo/variant_events.py,sha256=LjUtxJLo3wGBjMI55wPs7sNPeDLq9POw6fgz0dzeuFM,31842
-scout/adapter/mongo/variant_loader.py,sha256=FkW5POGpgRoSfH129VpHxQqII_2OKG4ZChlc45fBcpw,28300
+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=rSsY1ePm8Esn_heE5bU6z2LkKmPhJNiwnB1IeYzKwnU,11057
@@ -40,7 +40,7 @@ scout/build/panel.py,sha256=IrTPFPgqXnbE92vvHpa8NqnTRO7GqWcpPBCtMcdzV84,5348
 scout/build/user.py,sha256=Df_k2H4CxR80yqmgVvl3u3YC9ikr33BLH5fGkxZ3Mlw,942
 scout/build/genes/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
 scout/build/genes/exon.py,sha256=a0oyW69x0tTImu4rxce5pU3Cb_GLSIdbexU0ex_OH7Q,2256
-scout/build/genes/hgnc_gene.py,sha256=hBADu4r0eugglsN4KvaPlVFTmuF7UrQnKomBfjQDvHo,4672
+scout/build/genes/hgnc_gene.py,sha256=3ckEc4jpwcN_bYeAbv_wJrjzWMthm0HJR1dSzAraM_A,678
 scout/build/genes/transcript.py,sha256=qXdS7bU1d-ikgN8UOSyW7u34y-qpgcpVuCccP2tKR80,2416
 scout/build/variant/__init__.py,sha256=Y70EK_8TS69seYSyIvL1Mek1FMo3XPeXcOnYVIOWggA,173
 scout/build/variant/clnsig.py,sha256=uAfrf4RSUGliIp13fW9XqJshodNWxjuAwUbBbNHgmCc,719
@@ -60,16 +60,16 @@ scout/commands/delete/__init__.py,sha256=6Z97FsWMqyKqF64Anl1zwljVNTfjJUCI7yylxIE
 scout/commands/delete/delete_command.py,sha256=X3sH0pP51n1Gmv3e7EbgXggFp_yG4ZtziSNsIpcNu78,12584
 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=nJNrYUUv0rZC8P8vqK84wBKsjths75ThK94tRem9UWY,2111
-scout/commands/download/everything.py,sha256=QDLTsokn0wYmJnB2RtDIQONpkBxUOHB3HbIbGpeC92w,1425
-scout/commands/download/exac.py,sha256=1PQyAdJZyemzfXY6lCVy2SdtPRiDowpogjiGVQ3PALY,1051
-scout/commands/download/hgnc.py,sha256=x5EHcAOqwi2m3nLtZJttBTwU6UfY0FmYS_rNrAt2ME4,889
-scout/commands/download/hpo.py,sha256=7DmoA95VkTIVR6wwqjONXKJvW84HJ36qgixt3bgDcDY,2671
-scout/commands/download/omim.py,sha256=o9qQsprkWo71oOsAOWuz5Itji3YY9Z1I1PJhdj5NMiQ,1415
+scout/commands/download/ensembl.py,sha256=CsTMjYihBtXyfofNIQ2riL9UBzydDbqoNZ7jJVQ15ak,2112
+scout/commands/download/everything.py,sha256=KJ0xKeIx7Rtxv38XRE2RVYBTqec9UXh6LKrozj_6Mwo,1426
+scout/commands/download/exac.py,sha256=Hy-RKnjlPRvvMgkExpyrxdjFXW_kPUvS012SyqYp41E,1052
+scout/commands/download/hgnc.py,sha256=Htp0uOhHDAqSrfIG7xRg2WE8ZKO00chOwW1xqv-OzC8,890
+scout/commands/download/hpo.py,sha256=dIJJKEQqs4bGW3ndSySDgNCzCIrlKh54WY2PgzbfmkI,2672
+scout/commands/download/omim.py,sha256=YxunHYrkDYIo6v-TPxbx7gVMSMX4KB8O6jjbyo9j-Bk,1416
 scout/commands/download/orpha.py,sha256=44WjKauphCcWdVSPop0ohTEKh9BF3M1VFrloratmrl0,1232
 scout/commands/export/__init__.py,sha256=fkolSlzQbEEaMAbC1Nk9-nf1XwPsVaCeobE8kqMrncM,35
 scout/commands/export/case.py,sha256=zY5AYIcqa6l5PhntoaTONmHKiqGRDO_kUd_U4rchBbs,2446
-scout/commands/export/database.py,sha256=IoWE3NYLvZZ54iQDUI1jpOPo_9xVvGb66xgAIywCuE0,2848
+scout/commands/export/database.py,sha256=iQ61Is8jbYj2GpgpSS-7xUDce9JQBliHWgdOLHE4ZWY,2849
 scout/commands/export/exon.py,sha256=-uYsrEjV-q5kVHrFTOq1p7bQ8kdWV1qKonW87NuDbj0,1502
 scout/commands/export/export_command.py,sha256=4jwM1EfCccXlchOyj7VMlgr3DdaY68nZCnTcYVFnrHk,1001
 scout/commands/export/export_handler.py,sha256=8JzNqdMKKiv5k2GVAAO7oI6IVQtsWT0OLh5shO_P4vs,306
@@ -86,9 +86,9 @@ scout/commands/load/case.py,sha256=BD-qoDp5GjVBfTgUM8MihCoNWVgOysOviHO6kqkfcWY,4
 scout/commands/load/cytoband.py,sha256=mPIL7RrcENUtY8oXpKp_Ej69jdvk6M5ax3KlWEvXWeA,935
 scout/commands/load/exons.py,sha256=isxBFR0is5TFvv4j0PHB4KqmHFJHQ0TLQBudrjKmuUI,1887
 scout/commands/load/institute.py,sha256=EYbDeWmpeRl0_jBnsckAp6qua5VyZKpczoHfADfYIDQ,1060
-scout/commands/load/panel.py,sha256=L_APQj0ddQJewC2fUjhn4pQcsCUZ5F2bZOzuSbd7hTQ,2893
+scout/commands/load/panel.py,sha256=dgrOh4T3qghXzpeXu6EKMfR2WOD_RXUfk536HArT06c,2894
 scout/commands/load/region.py,sha256=psICLlMf5WBdSCgXsJZUsM8fICsTJB3Q6U6dB5S6w_8,869
-scout/commands/load/report.py,sha256=yqLJEShX8uKo0pxLTsTyqe-tiysn3tqmlI1wPXKZArw,3563
+scout/commands/load/report.py,sha256=DrnyOJcLbOUUJHzI3jwlj955zYohvjuTeeoeUS_ZU8Q,3564
 scout/commands/load/research.py,sha256=6GBKJY3POQyGxfPwcfj06tcCX48CBTZqq8MSdjevBjM,4426
 scout/commands/load/user.py,sha256=eDHt_byU3DVhI9D-3GwEW_VpQbIF6bPEORAieCTcdUc,1412
 scout/commands/load/variants.py,sha256=Sd9B8R1-04qH83gvXLe5jKXFGoRr9z8u1jAMwwnIg-Q,6442
@@ -103,9 +103,9 @@ scout/commands/update/genes.py,sha256=ngzdPodG9qosQYOMKE9x-rMjniZU3T1d5vmuMrduKJ
 scout/commands/update/hpo.py,sha256=eyCuUlUwPmyP0oLh1olXhdqInlUXDdLe8ylgTlHWi-g,1339
 scout/commands/update/individual.py,sha256=lwVQcKCZj5VxUSO8CcBUsvVRl3ZHgJVe4AE9pcJS7ys,4007
 scout/commands/update/institute.py,sha256=ms8mmTGfCXqxeh_vSB1cdNDGrdHoSSgh9ryhB5GrJQc,1727
-scout/commands/update/omim.py,sha256=ttPivJhFtruG4jXNd6q82Wtf7ajjGsXUC8NkmdZ7q9I,2308
+scout/commands/update/omim.py,sha256=s39qterBGhtBfW7Uc-IJabni93PIhT8shqVbkmQBb9k,2309
 scout/commands/update/panel.py,sha256=990shZ15k5pwHUkd767o8oQ5iqVIpgRA7N_9yv1_eqc,2912
-scout/commands/update/panelapp.py,sha256=GtIWaa7euq0cjeARU1DDFRoL9ZrcHhgHwhaI_w0T0yM,1280
+scout/commands/update/panelapp.py,sha256=T0BPkhxXAd7UPQoKSiJlZgasFsSUO6scCip5o4SStfo,1281
 scout/commands/update/phenotype_groups.py,sha256=Ll0COlEckn1Z7VAJbFbG2EZ5FKFVEcff0sWiUsx-D-g,1980
 scout/commands/update/user.py,sha256=s5s7nh9UABBO9P6L11_j5tsi4iPxzieHw40yDhc4PWM,2497
 scout/commands/view/__init__.py,sha256=ZtRW7UBNf1rPnlCslBVcmjafOPg9WTPpn4xxlAA0wMo,23
@@ -129,7 +129,7 @@ scout/constants/case_tags.py,sha256=Pr9Go_I8udRnrdcRcZdu4swS0Jpdwf8hUdDVGR6d9yY,
 scout/constants/clinvar.py,sha256=TzbnbUsSBML3k1SBVIL3kQh5Hwjq5kqKhtQOOEkfHwU,5586
 scout/constants/clnsig.py,sha256=2u_avIzWO_IPJGcTOoSB7_xqgu5JBl_zZZfT8UVpY90,1359
 scout/constants/disease_parsing.py,sha256=m10iPVzdTsdx7v9ZWvdLjlBrQKR_uyMeJwPbokO9SHY,688
-scout/constants/file_types.py,sha256=kJbG1zyHb8zS0KMRbbU7XVigQLEZNzUmCLFHmI4Zk_k,1298
+scout/constants/file_types.py,sha256=e_wlISYjSde2pJLByUoCCNZpN5gQBXdM1uN6FR077_4,2261
 scout/constants/filters.py,sha256=8nRRb7_17G4P8zMgJ7qrK4NAAuGbPLl-pU5GPP3L4eE,889
 scout/constants/gene_tags.py,sha256=tdzDh6ukJRtHiC8X5YkldijZCS0KrEeXj95sLNlqxuc,3852
 scout/constants/igv_tracks.py,sha256=3-3VzFpCTfuhbEBAitbpY2lQRYXYf-poya3DXs0g9yE,4500
@@ -354,17 +354,17 @@ scout/exceptions/database.py,sha256=P_8HYHFfKT0wK7aH0wFIr3bA5bSjOj956UZKLNJjIpU,
 scout/exceptions/pedigree.py,sha256=bubDeoyOnsYB8-NqAaJhIkDHxJRBAzV7tdJK3xPiwsY,41
 scout/exceptions/vcf.py,sha256=nmHAXuRWL7l5gmGo2uwhPFlGPDnt_MoW0Kvc0KiiHzU,36
 scout/export/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-scout/export/exon.py,sha256=GOjOMPPJNcLruwQyiEq5YH7fHiV2PS9RlCW5iZVaebM,3710
+scout/export/exon.py,sha256=QpFvlKRQsWpQ2inKHAz_bk8ZjmoTFoc1_H_hUhWL8ZQ,3711
 scout/export/gene.py,sha256=6DTJuZUwbsBe3oyKhfov7ZmqM8DbShl5f1IAeZN736k,263
 scout/export/panel.py,sha256=sLSOiePx7QguJUXddsNNgobR-90JI1HFxMV0raZlNzo,5244
 scout/export/transcript.py,sha256=wprCSxGDo2fittTd3IkIqUPnhFj4h4oSNFuyCO9Uyis,400
 scout/export/variant.py,sha256=sxe3-tnVs9cVRtK6I01oo9-hM0DBw0w1bGgvvv2FWUs,7358
 scout/load/__init__.py,sha256=d9cGZ9jMOfnmd9wkyspRFE2m5nxJt8MnpN-8PDlu-7M,212
-scout/load/all.py,sha256=BvamX_hFNb-rM6gc3APAFWvWDGni2CBhJ_ti0HkNRlI,3548
+scout/load/all.py,sha256=F_eb7lWM3wYASEL06qDeNczQTM3QR9Zz76nLgchaN5I,3699
 scout/load/cytoband.py,sha256=vPU8oQm31WMcnaG9QG2le9pe_8g70O1S0q1Ljj3Ce84,1356
 scout/load/disease.py,sha256=eZ-RDTtfO6-YCk0tCHuhCWxw1FSCwHNZEemWXCC4P_w,2747
 scout/load/exon.py,sha256=ONaWJ9EfbhGV8KGXxwlq_jYCoU-JkBpv4r9zDaCjtls,2070
-scout/load/hgnc_gene.py,sha256=rn2vHuECg_LWRzTE9IE1szp6U9HzxX2P0C89kRNNJ5U,3439
+scout/load/hgnc_gene.py,sha256=9bfelQgx71FTeZpn1-5_-Gww_JqFtz8pqMZN6rSXQys,3444
 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
@@ -379,12 +379,12 @@ scout/models/acmg_evaluation.py,sha256=Rn8GvbcUjMS1ZjDaPxuxn2cwWuESxeHOadZn4SREy
 scout/models/clinvar.py,sha256=fTmQYV3yRxQn1JBOwKnovYmkl19H14HKRE2zY9JA93U,3102
 scout/models/disease_term.py,sha256=KFrIkoyImhVDf4YAMYyluQZvDE9GNEa533M_4IMeIlQ,803
 scout/models/event.py,sha256=2v9K7hbSa6bgadolGnGL7OymSibNGRyTZXlnL_SrFTM,1863
-scout/models/hgnc_map.py,sha256=fZ1QE2-FxXZ9LB4yQeH4XLjL_ZMdwZzjlt05Lwaw1TM,4441
+scout/models/hgnc_map.py,sha256=U2v7ie4BxQUVMXvyQoiAcXitNSrEAm_3F7DUkn10ivw,3975
 scout/models/institute.py,sha256=jADVsDmPl2q6GfzoHkfAyyXa3J4E6ghrJl5m1DI6FiI,1854
 scout/models/managed_variant.py,sha256=H6ak7su6n2fRB5o21JdAUNkxsNBeeQjRIgmUAqLB--w,2526
 scout/models/panel.py,sha256=d5IhLcWqB9XiXCKZNzjaxz9f_bogqQ71wbVhAEqmujk,786
 scout/models/phenomodel.py,sha256=UitSXqy41X4R7K6MT6EeLqZsKNKRhlEfnvXa-Brt2NA,1298
-scout/models/phenotype_term.py,sha256=U07Pg5PCsOAu-g_HXbyifVy3sK1QyzDYqH3D4qfbo7Y,925
+scout/models/phenotype_term.py,sha256=jY7dbfPzgE14M1gWqifm5YKkwMlrtfFa_WBHMT1_ogs,927
 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
@@ -405,7 +405,7 @@ scout/parse/hpo_terms.py,sha256=ZJCKFD0rV3jiCuoI8Gm1WNTiaOSRRoKOhZ1bYnqwY6I,5732
 scout/parse/matchmaker.py,sha256=5e9NCFQ2rKXNCJTW-ThXoEylEPl3H41cCfQzPATQ2QM,9524
 scout/parse/mitodel.py,sha256=3uvEXI9v9wIw97NUL7gqLLxHay0mpQpDgKaIxUbIyrE,803
 scout/parse/omim.py,sha256=oFnf1CpEqX2imBvOla1A-3qM6vXpY4B_lc4cgiTSFXc,12464
-scout/parse/orpha.py,sha256=fD-d1W6Y_yUwrpsAxsIFHoUcOUafovItjev4CKw52p0,4391
+scout/parse/orpha.py,sha256=5u9xqGpAn8vgoJ0uVqbYiqQBiNfBwXOiTzX16kAnmFU,4392
 scout/parse/panel.py,sha256=4HYjokWh2sF-effLQxPf4ZzRHsf9grqF1Z9f-HAaRmk,13153
 scout/parse/peddy.py,sha256=uM49GaZMtr8waCsZDvCHDS5JDQ43JUlhdWh9C7f7ZvU,5418
 scout/parse/smn.py,sha256=iOK1N8iYm9dFigsKtWq0Y0ZCa1CH29s9zeR_tH0bPuc,1153
@@ -413,7 +413,7 @@ scout/parse/variant/__init__.py,sha256=5yqCQlAYMqosRabdipFUXqopSMBN4X6jwpNiKiYKl
 scout/parse/variant/callers.py,sha256=o3Dccf_f_TrKHEYAbMMHMpLYUdIjQQHPA8PMuN2KdYM,2248
 scout/parse/variant/clnsig.py,sha256=7egXPwXzaIMTj7dnKnsaHpgZa-STSoBqB1ZlpOS4RYA,4606
 scout/parse/variant/compound.py,sha256=zeRHBwobusCW-ylgurHrnPsc-edeJHeXj6xjXkrbFt8,1493
-scout/parse/variant/conservation.py,sha256=nNG0o7i1AkxZ9lZPodC292CEQ-JAyYEB-qoBr2PoOwk,2948
+scout/parse/variant/conservation.py,sha256=8eHXy57g6ng0eMo38LsIcQ8w_H5mpBSfiMuaXF7aBi4,2949
 scout/parse/variant/coordinates.py,sha256=CU-EyD8NVgTbyIdmYDO3k-zVaMN1EDONjorDwyUSnXU,4742
 scout/parse/variant/deleteriousness.py,sha256=zeFzx218GL-5pKniyci7MVHj3a1cep4nmvoSg7u0ogA,541
 scout/parse/variant/frequency.py,sha256=dKWvuXtG5Ow3QyDMBYdDBgJQGhqZmQWlcEG0YosA87M,7624
@@ -433,7 +433,7 @@ scout/server/__init__.py,sha256=iwhKnzeBJLKxpRVjvzwiRE63_zNpIBfaKLITauVph-0,24
 scout/server/app.py,sha256=H-0MXcqyP897No1bRzETR1m9vUq7Up1jDsVRwdTG9qU,10394
 scout/server/auto.py,sha256=8B6GwfOaUChkTLuLgYQDFMWlxGuHkEegF1argH2G2Ik,401
 scout/server/config.py,sha256=5dIxQ2Fowh5HUpRRmDTAnbAfzAbXrUdmKKzJ2JrccTw,5598
-scout/server/links.py,sha256=TVAyn4_vvKpiZjIEIMdbNZReNrCRgOfvV8ZHCqlgWy0,26996
+scout/server/links.py,sha256=ih5hFdxe_sYHGXY1AtB-_LVf4HHnFirs37Z_eXL5SQM,26998
 scout/server/utils.py,sha256=t9wRs2L2NojrlFeYHtxpIiebU5RljqRCjV7-sut0cT4,12505
 scout/server/blueprints/__init__.py,sha256=iwhKnzeBJLKxpRVjvzwiRE63_zNpIBfaKLITauVph-0,24
 scout/server/blueprints/alignviewers/__init__.py,sha256=XMVed2ekVUAvroqENDHSr2pwM8otqau8ZA-rbH1T2U8,59
@@ -452,7 +452,7 @@ scout/server/blueprints/cases/static/case_images.js,sha256=pb_gG7DNQc-1lADqSII8Y
 scout/server/blueprints/cases/static/case_styles.css,sha256=2Pgc8pFf9DR5HM1sTdAjaRWhjL-bK5bsQnLpH54HZak,541
 scout/server/blueprints/cases/static/edit_pedigree.js,sha256=ntC5fie7SsOYJau8qkke1UHxjiYWY_gBzWcIkGpdJUA,2978
 scout/server/blueprints/cases/static/madeline.js,sha256=KHxKMBVlYVJODNu5QkY9hhsGkDJNoaCoCZZ0DRu0YN0,1175
-scout/server/blueprints/cases/templates/cases/case.html,sha256=d_H1xh_3J4UlgritLCd41T9tpA32bBSfdRVtNlE6PkU,36552
+scout/server/blueprints/cases/templates/cases/case.html,sha256=ZwB24L9D4YjPRPaI4McQQ2VBx5dQvAFPN_LhFXvhp5w,36561
 scout/server/blueprints/cases/templates/cases/case_bionano.html,sha256=PLoRv7hDJcHwxhi-0hC9fQSZc7V_aUYHBhhQqcn_2G8,5946
 scout/server/blueprints/cases/templates/cases/case_report.html,sha256=1tosH5xEl6CCZ1P6qlR5OKvWbAC5z3ewKL_JGdgPMBM,63635
 scout/server/blueprints/cases/templates/cases/case_sma.html,sha256=SAcElb4kH05mkPdEdaEbed-vbgQQGfxioCoNZsHljDc,4962
@@ -531,7 +531,7 @@ scout/server/blueprints/managed_variants/views.py,sha256=wHOClPy2ZCIQvandia90kG6
 scout/server/blueprints/managed_variants/templates/managed_variants/managed_variants.html,sha256=gE1eP1E1A20z7UUuf36onLU75537rrNlR-P9pbwwtnI,17295
 scout/server/blueprints/panels/__init__.py,sha256=usxBF0O7zNX1d9jt-8DRoFZwcfHHS96Gv87LDr1AgG4,53
 scout/server/blueprints/panels/controllers.py,sha256=jpWSxSdu_U6mxBjxQlnIEBNv0nsJ0aHUecWA3gFhcJw,12898
-scout/server/blueprints/panels/forms.py,sha256=rkuYgrbGYZ2luVgnZyclX92ijVjvQU7S6RGSUi0YFEA,695
+scout/server/blueprints/panels/forms.py,sha256=DYlhYpnpv7ehf9JlY3HRFwy-TZ5QDHB0RIRaNTAW1jQ,696
 scout/server/blueprints/panels/views.py,sha256=mJ9WlkmK-ZIysYrMAEDkQ5Y35b76LsrYE9sdP_BvN2Y,15746
 scout/server/blueprints/panels/templates/panels/gene-edit.html,sha256=ZuXxdvjioxHlC0mz54t4q2KBFvP2qXb5VpNIcMVayVM,3649
 scout/server/blueprints/panels/templates/panels/panel.html,sha256=TxFAMRWQfveftJ4wxXJ_swxzq3GeIzwWegnoICQvJTk,15468
@@ -586,7 +586,7 @@ scout/server/blueprints/public/static/ideograms/chromosome-X.png,sha256=Dj7npcW_
 scout/server/blueprints/public/static/ideograms/chromosome-Y.png,sha256=KlOsBLZYFVHRvXvTioT-XE57zSWoYeIwIEXo_rzLBR0,1524
 scout/server/blueprints/public/templates/public/index.html,sha256=kl_-1s4HXRGw_PWacRFHG3cHALBBMN54GJVBnAAZ7LE,3626
 scout/server/blueprints/variant/__init__.py,sha256=SlD8-Aoj9Jq9aVTJjtFfsu-0sUVfkzpiEXcH8z9q6dI,54
-scout/server/blueprints/variant/controllers.py,sha256=xf-UEkSiQrZLPKmwLjruBlI7X2SZ01WmQHrorLoFmPY,25524
+scout/server/blueprints/variant/controllers.py,sha256=2XEBrvq4kXNA2Mj1G6GMfWHphEfgafDewoqFW32Q0PQ,25160
 scout/server/blueprints/variant/utils.py,sha256=3Tj2N6VCPMBcIk6gjDw8l6j2VYfoGugEW09hgxoFNY4,24042
 scout/server/blueprints/variant/verification_controllers.py,sha256=eKzP222e7xuFOaQaI9MLOrD9RWtI8uGB1cJYbcXLzF0,10972
 scout/server/blueprints/variant/views.py,sha256=oM5zA90_DL8eS-gSa1eDRar47xjwzJw2VFx9XCB9hdQ,14711
@@ -604,7 +604,7 @@ scout/server/blueprints/variant/templates/variant/utils.html,sha256=EPwtCxHKhtMD
 scout/server/blueprints/variant/templates/variant/variant.html,sha256=bgO3kb4u45IrgCPUJrHT4paNDOQzcKx5dw0ZYbBmCsc,18914
 scout/server/blueprints/variant/templates/variant/variant_details.html,sha256=J-pF8LRXFnCxIbNfL7klTLj172rlpWF8PznO4ie9Igc,19921
 scout/server/blueprints/variants/__init__.py,sha256=W1KCz9kEbVlNO0o3NvLitYLQoP_3JSJ5KSjhpcjlUBQ,55
-scout/server/blueprints/variants/controllers.py,sha256=FbDMCbaqyCVjogBk5cxrdCPafqulDL-_GjHqmS13B6g,73075
+scout/server/blueprints/variants/controllers.py,sha256=Yoa1tcSGU55AWZSS-7Xizl7HHXLKYzhRu-dqA5J1sAw,72654
 scout/server/blueprints/variants/forms.py,sha256=5BRl2mhiqjuOhsjWXDJjfX95im-NIMxKS-oSbeHiYuM,8944
 scout/server/blueprints/variants/utils.py,sha256=ifFBoyigx0A5KPE4iz9NSpyuUeF1bElrb4ohQLD2GlU,919
 scout/server/blueprints/variants/views.py,sha256=E514mSGAQwV7wGnz8WFsT65uqfztlWcgGFCt4z_lEVU,28137
@@ -621,17 +621,17 @@ scout/server/blueprints/variants/templates/variants/utils.html,sha256=2WriO5n0IG
 scout/server/blueprints/variants/templates/variants/variants.html,sha256=nfSZXVGmsjjUuRC-54G9UsNBMhlNjnvBafN34uL73tY,9333
 scout/server/extensions/__init__.py,sha256=tBhPKg0qc0HuZckWgj3UGexhmA7KQ-hlC50DqWx4UT4,1220
 scout/server/extensions/beacon_extension.py,sha256=YDXQQl5kFcsA4OFHDMVurIKLw_3Gl6yWfcy3lYHl9RE,9904
-scout/server/extensions/bionano_extension.py,sha256=XoKnAmNauatyJWUr63_gPlWyX1JGZfEXV6ge_bZ7VTk,7128
-scout/server/extensions/chanjo_extension.py,sha256=HhkbczCkWv8ATO_zuEPfC_tobjbOSmQHKVB16gXSM98,2258
+scout/server/extensions/bionano_extension.py,sha256=0rWPLMSCRP8uK4_yozo6HTPR6V-oITF492vrGA3wSj0,7129
+scout/server/extensions/chanjo_extension.py,sha256=MEV8l-83yujOw6JK_qc3VILND3S60zZrK-CCrLYRQUQ,2281
 scout/server/extensions/clinvar_extension.py,sha256=e6rrpOnUs-rn3gGfiOQT4UlBRRXRLgot51G3WB44wrU,3746
-scout/server/extensions/gens_extension.py,sha256=zqfzI7vOvPqNIkIl-uULJp-bS634p-4C6T7JsMI3tQw,1002
-scout/server/extensions/ldap_extension.py,sha256=zJLWLfumJoU8w19767g014H2eqv5VJrn-VWPEVeWCj4,2706
-scout/server/extensions/loqus_extension.py,sha256=EqRUfI8QV8OIeAEFGEvVkF4N6XTqPw8N8yXRfiSh5x0,12452
-scout/server/extensions/matchmaker_extension.py,sha256=t5J0R-EIYxCiygcNrhJb1MAdV2xsigmHlQwvw3Pm2DQ,5035
-scout/server/extensions/mongo_extension.py,sha256=Rku2L8bUm3NR5xzqx8Seinsv83eB9oFAWo151UutcTo,1028
+scout/server/extensions/gens_extension.py,sha256=KOF-pP4DiRVQkygthAq6XCHnZwAGHo1kjIxmvW7ItYI,1003
+scout/server/extensions/ldap_extension.py,sha256=nVgJ6YhSyvpg8J4bSYzJwoEvKhP0faWazt3Xk0ixE2U,2746
+scout/server/extensions/loqus_extension.py,sha256=uiqUXQ7Q7DCj6C20TKgL8yLu9DXov95vrJfhq0tvbTM,12602
+scout/server/extensions/matchmaker_extension.py,sha256=m-ecpdaVL8AlRbv2WZ2sGkvNNL0ujuxA3X-xunYBLdA,5036
+scout/server/extensions/mongo_extension.py,sha256=bKB0K5ibp-BWynOTgzBJd5qIYO0S9zRtEyDUw7EoxSQ,1029
 scout/server/extensions/phenopacket_extension.py,sha256=kcEUIOSfkQAlAmUm07hQS1BeUjeN4lBc-InvaNtbFxo,7295
-scout/server/extensions/rerunner_extension.py,sha256=5DkygqZ7o1vt9ZytPdhhGqPavysOXtzAugtYN783qso,1103
-scout/server/static/bs_styles.css,sha256=UU7l0MrdA2BoAEgKvPvEGUzBX0l2nEDzGbiMHGkvpXY,6423
+scout/server/extensions/rerunner_extension.py,sha256=SEwQi5BZR5X70BoD0U7TfyGgGv2WbJbas0v1efuv_r8,1104
+scout/server/static/bs_styles.css,sha256=Y7aq8Es3NHj1OaLPX0eiY5485C8gENptpuYmf7W3o1w,6421
 scout/server/static/custom_images.js,sha256=IUVSlt6GJCXmE1RuSizSMOE89OcFAJnq-ZzA5f2o84s,753
 scout/server/static/favicon.ico,sha256=8aC2QonalUW-D62draMeiII4sZYQSp9BLGQnj-wRlt0,1469
 scout/server/static/humans.txt,sha256=UdqAR07_5LAWWfgH2Ty4RR8BhoHS1WXpx9euKtXqqhs,259
@@ -652,17 +652,18 @@ scout/utils/coordinates.py,sha256=n8WUFn9zohXfjxgFGryyg6mzdl0zBG8uVCdyjhizSpM,60
 scout/utils/date.py,sha256=PT5iNB02rJF4aya8Kd8d6JWagyyhO59GBu2T6EQ6pT0,1333
 scout/utils/dict_utils.py,sha256=nstAbMYQD2KNglY69FD0qSfxYM26eM4QDpp_AqHNQ1U,251
 scout/utils/ensembl_biomart_clients.py,sha256=szth3hpjYYan49URkOxPMp361LgOlv_hr5dsqxJjZDA,1569
-scout/utils/ensembl_rest_clients.py,sha256=MTfMTrBelJodp4M42eOGgWaoU3XlvfoH0Kvam2dcKIM,3038
+scout/utils/ensembl_rest_clients.py,sha256=of6CXQHBnwH4ji5URAZcEqVTebxduLs13lBWv2QTIM4,3039
 scout/utils/gene.py,sha256=uzIGrPBfOkhRGGR9iTSYa00w6PWijjpzSAWRo54wixM,1430
 scout/utils/handle.py,sha256=tLjinHNLADa3IJSxMp_HJe9cbiMlPTsfky4hujplPqU,327
 scout/utils/hgvs.py,sha256=P5i3fIK8WZZlUnjZ8XpMDUG5KDXRCDSOs55DfK5acsc,898
 scout/utils/link.py,sha256=RuCUwnOtGDf9ACaC64_1FqWyWDaBv7dqNEGjmCq59kk,9001
 scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
-scout/utils/scout_requests.py,sha256=owL_XvsrQJG4e0EUuUiY6y_hqKKep2Qljg1nMukzp8Y,12855
+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-4.83.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
-scout_browser-4.83.dist-info/METADATA,sha256=NBrhFdyvFGWQuvC__yBWPsECY6HhzNhVUYdMK1aUsjg,14278
-scout_browser-4.83.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-scout_browser-4.83.dist-info/entry_points.txt,sha256=E6vGg1OwvvKYIsXdHxmlIj7RmcTF0K77Q_PU8laImGg,46
-scout_browser-4.83.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
-scout_browser-4.83.dist-info/RECORD,,
+scout_browser-4.84.dist-info/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
+scout_browser-4.84.dist-info/METADATA,sha256=4IpwKNOjBxH-Kyj_hLJL1mSHA8ZcmKZjERVJ0uIkLG0,14263
+scout_browser-4.84.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+scout_browser-4.84.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
+scout_browser-4.84.dist-info/top_level.txt,sha256=qM75h71bztMaLYsxn1up4c_n2rjc_ZnyaW6Q0K5uOXc,6
+scout_browser-4.84.dist-info/RECORD,,

{scout_browser-4.83.dist-info → scout_browser-4.84.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: bdist_wheel (0.43.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{scout_browser-4.83.dist-info → scout_browser-4.84.dist-info}/entry_points.txt

@@ -1,3 +1,2 @@
 [console_scripts]
 scout = scout.commands:cli
-