scout-browser 4.96.0__py3-none-any.whl → 4.98.0__py3-none-any.whl

scout/server/blueprints/variants/views.py

@@ -67,8 +67,7 @@ def variants(institute_id, case_name):
 
     variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False)
 
-    if request.form.get("hpo_clinical_filter"):
-        case_obj["hpo_clinical_filter"] = True
+    controllers.set_hpo_clinical_filter(case_obj, request.form)
 
     user_obj = store.user(current_user.email)
     if request.method == "POST":
@@ -97,14 +96,12 @@ def variants(institute_id, case_name):
 
     controllers.populate_force_show_unaffected_vars(institute_obj, form)
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_id, category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
+    # Populate custom soft filters
+    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
+
     # populate available panel choices
     form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj)
 
@@ -161,7 +158,9 @@ def variants(institute_id, case_name):
         cytobands=cytobands,
         dismiss_variant_options=DISMISS_VARIANT_OPTIONS,
         expand_search=controllers.get_expand_search(request.form),
-        filters=available_filters,
+        filters=controllers.populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         form=form,
         genetic_models_palette=GENETIC_MODELS_PALETTE,
         inherit_palette=INHERITANCE_PALETTE,
@@ -210,15 +209,12 @@ def str_variants(institute_id, case_name):
     controllers.populate_force_show_unaffected_vars(institute_obj, form)
     controllers.update_form_hgnc_symbols(store, case_obj, form)
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_id, category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
-
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
+    # Populate custom soft filters
+    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
+
     # populate available panel choices
     form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj)
 
@@ -254,7 +250,9 @@ def str_variants(institute_id, case_name):
         cytobands=cytobands,
         dismiss_variant_options=DISMISS_VARIANT_OPTIONS,
         expand_search=controllers.get_expand_search(request.form),
-        filters=available_filters,
+        filters=controllers.populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         form=form,
         inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
@@ -282,8 +280,7 @@ def sv_variants(institute_id, case_name):
         variant_type = "clinical"
     variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False)
 
-    if request.form.get("hpo_clinical_filter"):
-        case_obj["hpo_clinical_filter"] = True
+    controllers.set_hpo_clinical_filter(case_obj, request.form)
 
     if "dismiss_submit" in request.form:  # dismiss a list of variants
         controllers.dismiss_variant_list(
@@ -299,15 +296,12 @@ def sv_variants(institute_id, case_name):
     controllers.activate_case(store, institute_obj, case_obj, current_user)
     form = controllers.populate_sv_filters_form(store, institute_obj, case_obj, category, request)
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_obj["_id"], category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
-
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
+    # Populate custom soft filters
+    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
+
     genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
     cytobands = store.cytoband_by_chrom(genome_build)
 
@@ -334,7 +328,9 @@ def sv_variants(institute_id, case_name):
         cytobands=cytobands,
         dismiss_variant_options=DISMISS_VARIANT_OPTIONS,
         expand_search=controllers.get_expand_search(request.form),
-        filters=available_filters,
+        filters=controllers.populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         form=form,
         inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
@@ -361,8 +357,7 @@ def mei_variants(institute_id, case_name):
     )
     variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False)
 
-    if request.form.get("hpo_clinical_filter"):
-        case_obj["hpo_clinical_filter"] = True
+    controllers.set_hpo_clinical_filter(case_obj, request.form)
 
     if "dismiss_submit" in request.form:  # dismiss a list of variants
         controllers.dismiss_variant_list(
@@ -393,15 +388,12 @@ def mei_variants(institute_id, case_name):
         # set chromosome to all chromosomes
         form.chrom.data = request.args.get("chrom", "")
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_obj["_id"], category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
-
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
+    # Populate custom soft filters
+    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
+
     # populate available panel choices
     form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj)
 
@@ -431,7 +423,9 @@ def mei_variants(institute_id, case_name):
         cytobands=cytobands,
         dismiss_variant_options=DISMISS_VARIANT_OPTIONS,
         expand_search=controllers.get_expand_search(request.form),
-        filters=available_filters,
+        filters=controllers.populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         form=form,
         inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
@@ -507,15 +501,12 @@ def cancer_variants(institute_id, case_name):
     # update status of case if visited for the first time
     controllers.activate_case(store, institute_obj, case_obj, current_user)
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_id, category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
-
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
+    # Populate custom soft filters
+    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
+
     form.gene_panels.choices = controllers.gene_panel_choices(store, institute_obj, case_obj)
 
     genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
@@ -550,7 +541,9 @@ def cancer_variants(institute_id, case_name):
             **CANCER_SPECIFIC_VARIANT_DISMISS_OPTIONS,
         },
         expand_search=controllers.get_expand_search(request.form),
-        filters=available_filters,
+        filters=controllers.populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         result_size=result_size,
         show_dismiss_block=controllers.get_show_dismiss_block(),
         total_variants=variants_stats.get(variant_type, {}).get(category, "NA"),
@@ -574,9 +567,6 @@ def cancer_sv_variants(institute_id, case_name):
         variant_type = "clinical"
     variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False)
 
-    if request.form.get("hpo_clinical_filter"):
-        case_obj["hpo_clinical_filter"] = True
-
     if "dismiss_submit" in request.form:  # dismiss a list of variants
         controllers.dismiss_variant_list(
             store,
@@ -591,15 +581,12 @@ def cancer_sv_variants(institute_id, case_name):
     controllers.activate_case(store, institute_obj, case_obj, current_user)
     form = controllers.populate_sv_filters_form(store, institute_obj, case_obj, category, request)
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_obj["_id"], category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
-
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
+    # Populate custom soft filters
+    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
+
     genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
     cytobands = store.cytoband_by_chrom(genome_build)
 
@@ -630,7 +617,9 @@ def cancer_sv_variants(institute_id, case_name):
             **CANCER_SPECIFIC_VARIANT_DISMISS_OPTIONS,
         },
         expand_search=controllers.get_expand_search(request.form),
-        filters=available_filters,
+        filters=controllers.populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         form=form,
         inherit_palette=INHERITANCE_PALETTE,
         institute=institute_obj,
@@ -660,9 +649,6 @@ def fusion_variants(institute_id, case_name):
         variant_type = "clinical"
     variants_stats = store.case_variants_count(case_obj["_id"], institute_id, variant_type, False)
 
-    if request.form.get("hpo_clinical_filter"):
-        case_obj["hpo_clinical_filter"] = True
-
     if "dismiss_submit" in request.form:  # dismiss a list of variants
         controllers.dismiss_variant_list(
             store,
@@ -679,15 +665,12 @@ def fusion_variants(institute_id, case_name):
         store, institute_obj, case_obj, category, request
     )
 
-    # populate filters dropdown
-    available_filters = list(store.filters(institute_obj["_id"], category))
-    form.filters.choices = [
-        (filter.get("_id"), filter.get("display_name")) for filter in available_filters
-    ]
-
     # Populate chromosome select choices
     controllers.populate_chrom_choices(form, case_obj)
 
+    # Populate custom soft filters
+    controllers.populate_institute_soft_filters(form=form, institute_obj=institute_obj)
+
     genome_build = "38" if "38" in str(case_obj.get("genome_build", "37")) else "37"
     cytobands = store.cytoband_by_chrom(genome_build)
 
@@ -717,7 +700,9 @@ def fusion_variants(institute_id, case_name):
             **DISMISS_VARIANT_OPTIONS,
         },
         expand_search=controllers.get_expand_search(request.form),
-        filters=available_filters,
+        filters=controllers.populate_persistent_filters_choices(
+            institute_id=institute_id, category=category, form=form
+        ),
         form=form,
         institute=institute_obj,
         manual_rank_options=MANUAL_RANK_OPTIONS,

scout/server/extensions/beacon_extension.py

@@ -1,5 +1,5 @@
 """Scout supports integration with the Clinical Genomics SciLifeLab Beacon
-   cgbeacon2: https://github.com/Clinical-Genomics/cgbeacon2
+cgbeacon2: https://github.com/Clinical-Genomics/cgbeacon2
 """
 
 import datetime

scout/server/extensions/bionano_extension.py

@@ -1,10 +1,10 @@
 """
-    Connect to BioNano Access server via its API.
+Connect to BioNano Access server via its API.
 
-    The server API we connect to is described in the following document:
-    https://bionano.com/wp-content/uploads/2023/01/30462-Bionano-Access-API-Guide-1.pdf
-    For further development, the server has a Swagger-like demo interface at https://bionano-access.scilifelab.se/Bnx/
-    which is useful for details, and for sniffing actual message content structure, required cookie variable names etc.
+The server API we connect to is described in the following document:
+https://bionano.com/wp-content/uploads/2023/01/30462-Bionano-Access-API-Guide-1.pdf
+For further development, the server has a Swagger-like demo interface at https://bionano-access.scilifelab.se/Bnx/
+which is useful for details, and for sniffing actual message content structure, required cookie variable names etc.
 """
 
 import json

scout/server/extensions/chanjo2_extension.py

@@ -1,5 +1,5 @@
 import logging
-from typing import Dict
+from typing import Dict, List
 
 import requests
 from flask import current_app
@@ -8,6 +8,9 @@ REF_CHROM = "14"
 MT_CHROM = "MT"
 LOG = logging.getLogger(__name__)
 
+CHANJO_BUILD_37 = "GRCh37"
+CHANJO_BUILD_38 = "GRCh38"
+
 
 class Chanjo2Client:
     """Runs requests to chanjo2 and returns results in the expected format."""
@@ -44,3 +47,39 @@ class Chanjo2Client:
             coverage_stats[ind["individual_id"]] = coverage_info
 
         return coverage_stats
+
+    def get_gene_complete_coverage(
+        self, hgnc_id: int, threshold: int = 15, individuals: dict = {}, build: str = "38"
+    ) -> bool:
+        """
+        Return complete coverage for hgnc_id at a coverage threshold.
+        """
+        chanjo_build = CHANJO_BUILD_37 if "37" in build else CHANJO_BUILD_38
+        chanjo2_gene_cov_url: str = "/".join(
+            [current_app.config.get("CHANJO2_URL"), "coverage/d4/genes/summary"]
+        )
+
+        gene_cov_query = {
+            "build": chanjo_build,
+            "coverage_threshold": threshold,
+            "hgnc_gene_ids": [hgnc_id],
+            "interval_type": "genes",
+            "samples": [],
+        }
+        for ind in individuals:
+            if not ind.get("d4_file"):
+                continue
+
+            gene_cov_query["samples"].append(
+                {"coverage_file_path": ind["d4_file"], "name": ind["individual_id"]}
+            )
+
+        resp = requests.post(chanjo2_gene_cov_url, json=gene_cov_query)
+        gene_cov = resp.json()
+
+        full_coverage = bool(gene_cov)
+        for sample in gene_cov.keys():
+            if gene_cov[sample]["coverage_completeness_percent"] < 100:
+                full_coverage = False
+
+        return full_coverage

scout/server/extensions/chanjo_extension.py

@@ -1,5 +1,5 @@
 """
-    Generate coverage reports using chanjo and chanjo-report. Documentation under -> `docs/admin-guide/chanjo_coverage_integration.md`
+Generate coverage reports using chanjo and chanjo-report. Documentation under -> `docs/admin-guide/chanjo_coverage_integration.md`
 """
 
 import json

scout/server/extensions/matchmaker_extension.py

@@ -1,5 +1,5 @@
 """Code for MatchMaker Exchange integration
-   Tested with PatientMatcher: https://github.com/Clinical-Genomics/patientMatcher
+Tested with PatientMatcher: https://github.com/Clinical-Genomics/patientMatcher
 """
 
 import datetime

scout/server/static/bs_styles.css

@@ -269,6 +269,8 @@ li.nav-item {
 
 /* Introduce small space in between list elements */
 body {
+	min-width: 1000px;
+ 	overflow-x: scroll;
 	background-color: var(--bg-color);
 	font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";
 }

scout/server/templates/layout.html

@@ -43,6 +43,7 @@
                 <div class="dropdown-divider" ></div>
                 <a class="dropdown-item" href="https://clinical-genomics.github.io/scout" referrerpolicy="no-referrer" rel="noopener" target='_blank'>User guide</a>
                 <a class="dropdown-item" href="https://github.com/Clinical-Genomics/scout/issues" referrerpolicy="no-referrer" rel="noopener" target='_blank'>Open issues</a>
+                <a class="dropdown-item mb-1" href="https://github.com/Clinical-Genomics/scout/releases/tag/v{{ SCOUT_VERSION[:-2] if SCOUT_VERSION.endswith('.0') and SCOUT_VERSION.count('.') > 1 else SCOUT_VERSION }}" referrerpolicy="no-referrer" rel="noopener" target='_blank'>Release notes v{{SCOUT_VERSION}}</a>
               </div>
             </li>
             {% block top_nav %}{% endblock %}

scout/server/utils.py

@@ -330,6 +330,11 @@ def case_append_alignments(case_obj: dict):
         # Add sample name
         sample_name = f"{case_obj.get('display_name', '')} - {individual.get('display_name', '')}"
         append_safe(case_obj, "sample_names", sample_name)
+        append_safe(
+            case_obj,
+            "track_items_soft_clips_settings",
+            individual.get("analysis_type", "") not in ["wes", "panel"],
+        )
 
         # Process all file settings
         for setting in unwrap_settings:

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.scilifelab.se"
+SCHUG_BASE = "https://schug-stage.scilifelab.se"
 
 BUILDS: Dict[str, str] = {"37": "GRCh37", "38": "GRCh38"}
 
@@ -29,15 +29,6 @@ class EnsemblBiomartHandler:
     def stream_resource(self, interval_type: str) -> Iterator[str]:
         """Use schug web to fetch genes, transcripts or exons from a remote Ensembl biomart in the right genome build and save them to file."""
 
-        def yield_resource_lines(iterable) -> str:
-            """Removes the last element from an iterator."""
-            it = iter(iterable)
-            current = next(it)
-            for i in it:
-                yield current
-                current = i
-
         shug_url: str = f"{SCHUG_BASE}{SCHUG_RESOURCE_URL[interval_type]}{self.build}"
 
-        # return all lines except the last, which contains the "[success]" string
-        return yield_resource_lines(self.stream_get(shug_url))
+        return self.stream_get(shug_url)

scout/utils/scout_requests.py

@@ -324,7 +324,7 @@ def fetch_constraint():
     Returns:
         exac_lines(iterable(str))
     """
-    path = "/release/v4.0/constraint/gnomad.v4.0.constraint_metrics.tsv"
+    path = "/release/4.1/constraint/gnomad.v4.1.constraint_metrics.tsv"
     mirror_urls = [
         f"https://storage.googleapis.com/gcp-public-data--gnomad{path}",
         f"https://gnomad-public-us-east-1.s3.amazonaws.com{path}",

{scout_browser-4.96.0.dist-info → scout_browser-4.98.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scout-browser
-Version: 4.96.0
+Version: 4.98.0
 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