scout-browser 4.103.2__py3-none-any.whl → 4.103.3__py3-none-any.whl

scout/server/app.py

@@ -311,20 +311,31 @@ def register_filters(app):
 
     @app.template_filter()
     def format_variant_canonical_transcripts(variant: dict) -> List[str]:
-        """Formats canonical transcripts for all genes in a variant."""
-
         lines = set()
         genes = variant.get("genes") or []
 
         for gene in genes:
+            gene_symbol = gene.get("hgnc_symbol", "")
+            hgvs = gene.get("hgvs_identifier")
             transcripts = gene.get("transcripts") or []
+
+            canonical_tx = None
+            primary_tx = None
+            tx_id = None
+
+            protein = None
+
             for tx in transcripts:
+                tx_id = tx.get("transcript_id")
                 if not tx.get("is_canonical"):
+                    if tx.get("is_primary"):
+                        primary_tx = tx_id
                     continue
-                canonical_tx = tx.get("transcript_id")
+                canonical_tx = tx_id
                 protein = tx.get("protein_sequence_name")
-            line_components = [f"{canonical_tx} ({gene.get('hgnc_symbol', '')})"]
-            hgvs = gene.get("hgvs_identifier")
+                break
+
+            line_components = [f"{canonical_tx or primary_tx or tx_id} ({gene_symbol})"]
             if hgvs:
                 line_components.append(hgvs)
             if protein:

scout/server/blueprints/institutes/views.py

@@ -145,7 +145,9 @@ def gene_variants(institute_id):
 
     institute_choices = [
         (inst["_id"], f"{inst['display_name']} ({inst['_id']})")
-        for inst in user_institutes(store, current_user)
+        for inst in sorted(
+            user_institutes(store, current_user), key=lambda i: i["display_name"].lower()
+        )
     ]
     form = GeneVariantFiltersForm()
     form.institute.choices = institute_choices

scout/server/blueprints/variants/controllers.py

@@ -1023,7 +1023,7 @@ def download_str_variants(case_obj, variant_objs):
         variant_line.append(str(variant.get("variant_rank", "")))  # index
         variant_line.append(variant.get("str_repid", variant.get("str_trid", "")))  # Repeat locus
         variant_line.append(
-            variant.get("str_display_ru", variant.get("str_ru", ""))
+            variant.get("str_display_ru", variant.get("str_ru", variant.get("str_motifs", "")))
         )  # Reference repeat unit
         variant_line.append(str(get_str_mc(variant) or "."))  # Estimated size
         variant_line.append(str(variant.get("str_ref", "")))  # Reference size

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

@@ -241,8 +241,12 @@
       {% endfor %}
     {%endif%}
   </div>"
-  title="">{% if variant.str_repid %} {{ variant.str_repid }} {% elif variant.str_trid %} {{ variant.str_trid  }} {% else %}
-  {% for gene in variant.genes %} {{ gene.symbol }} {% endfor %} {% endif %}
+  title="">{% if variant.str_repid %} {{ variant.str_repid }}
+  {% elif variant.genes %}
+    {% for gene in variant.genes %} {{ gene.symbol or gene.hgnc_symbol }} {% endfor %}
+  {% else %}
+    {{ variant.str_trid }}
+  {% endif %}
   </a>
   {% for gene in variant.genes %}
       {% if variant.str_disease %}

scout/server/blueprints/variants/views.py

@@ -230,6 +230,7 @@ def str_variants(institute_id, case_name):
         case_obj["_id"], category=category, query=query, build=genome_build
     ).sort(
         [
+            ("genes.hgnc_symbol", pymongo.ASCENDING),
             ("str_repid", pymongo.ASCENDING),
             ("str_trid", pymongo.ASCENDING),
             ("chromosome", pymongo.ASCENDING),

{scout_browser-4.103.2.dist-info → scout_browser-4.103.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scout-browser
-Version: 4.103.2
+Version: 4.103.3
 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

{scout_browser-4.103.2.dist-info → scout_browser-4.103.3.dist-info}/RECORD

@@ -449,7 +449,7 @@ scout/resources/cytoBand_hg19.txt.gz,sha256=pheUD5b9NlVuvwwnbKwDc2FG80Yg70gvPxVX
 scout/resources/cytoBand_hg38.txt.gz,sha256=sqSVmvPlktQ-0hTiTapJM-5UgyV6xDoYZuTF0kPuETs,6105
 scout/resources/custom_igv_tracks/mane.bb,sha256=flEexDxHmbX7IwwrMM0P5DWOxcSCjmHxGNlyg_WqElQ,3519360
 scout/server/__init__.py,sha256=iwhKnzeBJLKxpRVjvzwiRE63_zNpIBfaKLITauVph-0,24
-scout/server/app.py,sha256=NB3WXI2Xa8Wdfnonkoxb0mWeEV9gYOJhqvYc_h4ajTw,14633
+scout/server/app.py,sha256=7iyp2gFhCRPr1zdRRYD-z3TanSjvbnEkI_YQiTSKxD8,14879
 scout/server/auto.py,sha256=8B6GwfOaUChkTLuLgYQDFMWlxGuHkEegF1argH2G2Ik,401
 scout/server/config.py,sha256=JcT9rUDcAdm9oSk7Wwbu-Aut96-xvBQnMeQTt_-6rXs,6401
 scout/server/links.py,sha256=aFCvrtXrc1gnhNhnifapVdUZOZKEpBD2zSxWXdvQLEk,28154
@@ -519,7 +519,7 @@ scout/server/blueprints/genes/templates/genes/layout.html,sha256=cZMLe2cInq24z0s
 scout/server/blueprints/institutes/__init__.py,sha256=kGSyYrBC1QaEQBDdoMkMLfaowV7roaV5DowICi_0RSQ,65
 scout/server/blueprints/institutes/controllers.py,sha256=nYAkZ2SRBQsXYm-rfMkfyxBTWGSrpsgnvGdZ9Qqsqk0,37115
 scout/server/blueprints/institutes/forms.py,sha256=1xz_p51YIlWv-VhkCD3WS0K1z1S1oPYuWNaUNAQOchk,6858
-scout/server/blueprints/institutes/views.py,sha256=LG-uTAEUxbkHvvk0YDeDak2v366lAhmFjsyGYbZGI48,9354
+scout/server/blueprints/institutes/views.py,sha256=jBDLXw0vdAetaXqgZF3vd0EPCOpO11g0B3MTML7iTco,9425
 scout/server/blueprints/institutes/static/form_scripts.js,sha256=8Sn7omeXeeUbiXJPfT0Qb4CaBJ_KtZZWw7N2he7EDx0,747
 scout/server/blueprints/institutes/static/select2_darktheme.css,sha256=Nq_va597W_e5y-52B4ClwSJzACq0WFbPU8SIp3DtKIo,1818
 scout/server/blueprints/institutes/static/timeline_styles.css,sha256=Vq48ffIidpQmDQhAzfW47O9mGQZEWdlbMtOE8AK-ZEU,2122
@@ -636,10 +636,10 @@ scout/server/blueprints/variant/templates/variant/utils.html,sha256=Chek9j4v8R7s
 scout/server/blueprints/variant/templates/variant/variant.html,sha256=Pn4OSSgXjbsLXUbEKOqKKhyNsny4Ay-hoBFY1xDZ-dw,20741
 scout/server/blueprints/variant/templates/variant/variant_details.html,sha256=Bs59vFzJMav7D65aNLOQZ5985t0ZK49uyE1go_h5MdQ,21960
 scout/server/blueprints/variants/__init__.py,sha256=W1KCz9kEbVlNO0o3NvLitYLQoP_3JSJ5KSjhpcjlUBQ,55
-scout/server/blueprints/variants/controllers.py,sha256=NbRM4tVrWsLLOVH-Jun80K0ZwJ9MObCJtQjnBXE2hjM,74730
+scout/server/blueprints/variants/controllers.py,sha256=82pBTGMuqq1FCII9j0FlAsewQjD3XMZvYZ6IKJgvDd0,74757
 scout/server/blueprints/variants/forms.py,sha256=X4lw2UhSAAkaAMgpBK5yz8B8RvcirjjgjOyctN8g1xw,12599
 scout/server/blueprints/variants/utils.py,sha256=ifFBoyigx0A5KPE4iz9NSpyuUeF1bElrb4ohQLD2GlU,919
-scout/server/blueprints/variants/views.py,sha256=kBzO4uyI4EjaSEt5YKEkOOouwJQqTuRPatdkSFu5jkA,28472
+scout/server/blueprints/variants/views.py,sha256=7dEiz0g_ZhROmIouOaDa2tCUl0S6bAbzED6E9Ady4HA,28526
 scout/server/blueprints/variants/static/form_scripts.js,sha256=o3GCboaesA9Sm1HgejS_yQwt0I-NTkvcl56jiBdLqZs,8319
 scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html,sha256=MbhtOx_szaTH4wPz6SkgA1JWrFri5Vsayty4YXUky4M,7164
 scout/server/blueprints/variants/templates/variants/cancer-variants.html,sha256=Y9UsAUOHn6pIi4p2n57EApJQeaxmbxLdmds5y1ceXyw,9717
@@ -647,7 +647,7 @@ scout/server/blueprints/variants/templates/variants/components.html,sha256=Oa3MU
 scout/server/blueprints/variants/templates/variants/fusion-variants.html,sha256=XGaLgWobzeFHwyQLXr_Yq9THssf8tGU91VbFKdGOFBg,4801
 scout/server/blueprints/variants/templates/variants/indicators.html,sha256=5IPiNgEB_JmYpvD6_Mpx9wd1gmKpsVnTm-HKfuBsKXg,5081
 scout/server/blueprints/variants/templates/variants/mei-variants.html,sha256=Lb_xNjUh15UCM7s3AvRGYpKSvQmJZYZU5qU-zoRs3UU,6008
-scout/server/blueprints/variants/templates/variants/str-variants.html,sha256=qZMQDlHrjmMhVmwc0AmQ5YrL7Q-Q-8kPd4_Ekn8IXPw,11132
+scout/server/blueprints/variants/templates/variants/str-variants.html,sha256=bMDUOB_YyZHjh3Z9LxlhlcTIG436X8rIlG1EgGrosa4,11160
 scout/server/blueprints/variants/templates/variants/sv-variants.html,sha256=jmpofUnCsXXFcvMHniuOMIJN37FV1E7dPY6phLhdDf4,6714
 scout/server/blueprints/variants/templates/variants/utils.html,sha256=VVDCG1oiRM3v0W8Ga03Ym3m1dCYkjgmy1m9PJrGuDQ0,53768
 scout/server/blueprints/variants/templates/variants/variants.html,sha256=Nhgbkf0UCYHFZNE-4ilbp7PbYckXx3irTJZcaFohH5s,8461
@@ -695,8 +695,8 @@ scout/utils/link.py,sha256=HpQvwu0hmuCrs7TcAExLmOzEGr3glWuu8iaW0ao5pEA,9011
 scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
 scout/utils/scout_requests.py,sha256=6R8boknrfwlmrRQ2txD81lfVtqUK_iabywEiVyIiZfQ,12685
 scout/utils/track_resources.py,sha256=eUjSEe-Ff8BIb4BHPC_COkJocQO2PaWueiPz1GAuiwY,2614
-scout_browser-4.103.2.dist-info/METADATA,sha256=oshdlGBA8Vvvoq4aDmTKYG-Kg_uPjB8XnhRxS9EH_7U,15527
-scout_browser-4.103.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-scout_browser-4.103.2.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
-scout_browser-4.103.2.dist-info/licenses/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
-scout_browser-4.103.2.dist-info/RECORD,,
+scout_browser-4.103.3.dist-info/METADATA,sha256=3hBmvP8CtVpqYAwDzR4kK6FU9WoU8u6ft-4ufmm5b5A,15527
+scout_browser-4.103.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+scout_browser-4.103.3.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
+scout_browser-4.103.3.dist-info/licenses/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
+scout_browser-4.103.3.dist-info/RECORD,,