Merge branch 'main' into version_4.60

CHANGELOG.md

@@ -8,6 +8,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
 ### Added
 - Mitochondrial deletion signatures (mitosign) can be uploaded and shown with mtDNA report
 - A `Type of analysis` column on Causatives and Validated variants pages
+- List of "safe" gene panels available for matching causatives and managed variants in institute settings, to avoid secondary findings
 ### Changed
 - Hide removed gene panels by default in panels page
 - Removed option for filtering cancer SVs by Tumor and Normal alt AF

scout/adapter/mongo/institute.py

@@ -43,6 +43,7 @@ def update_institute(
         remove_sanger=None,
         phenotype_groups=None,
         gene_panels=None,
+        gene_panels_matching=None,
         group_abbreviations=None,
         add_groups=None,
         sharing_institutes=None,
@@ -63,6 +64,7 @@ def update_institute(
             remove_sanger(str): Email adress for sanger user to be removed
             phenotype_groups(iterable(str)): New phenotype groups
             gene_panels(dict): a dictionary of panels with key=panel_name and value=display_name
+            gene_panels_matching(dict): panels to limit search of matching variants (managed, causatives) to. Dict with key=panel_name and value=display_name
             group_abbreviations(iterable(str))
             add_groups(bool): If groups should be added. If False replace groups
             sharing_institutes(list(str)): Other institutes to share cases with
@@ -94,9 +96,6 @@ def update_institute(
             )
             updates["$push"] = {"sanger_recipients": sanger_recipient}
 
-        if sanger_recipients is not None:
-            updates["$set"]["sanger_recipients"] = sanger_recipients  # can be empty list
-
         if remove_sanger:
             LOG.info(
                 "Removing sanger recipient {0} from institute: {1}".format(
@@ -105,27 +104,21 @@ def update_institute(
             )
             updates["$pull"] = {"sanger_recipients": remove_sanger}
 
-        if coverage_cutoff:
-            LOG.info(
-                "Updating coverage cutoff for institute: {0} to {1}".format(
-                    internal_id, coverage_cutoff
-                )
-            )
-            updates["$set"]["coverage_cutoff"] = coverage_cutoff
-
-        if frequency_cutoff:
-            LOG.info(
-                "Updating frequency cutoff for institute: {0} to {1}".format(
-                    internal_id, frequency_cutoff
-                )
-            )
-            updates["$set"]["frequency_cutoff"] = frequency_cutoff
-
-        if display_name:
-            LOG.info(
-                "Updating display name for institute: {0} to {1}".format(internal_id, display_name)
-            )
-            updates["$set"]["display_name"] = display_name
+        # Set a number of items
+        GENERAL_SETTINGS = {
+            "cohorts": cohorts,
+            "collaborators": sharing_institutes,
+            "coverage_cutoff": coverage_cutoff,
+            "display_name": display_name,
+            "frequency_cutoff": frequency_cutoff,
+            "gene_panels": gene_panels,
+            "gene_panels_matching": gene_panels_matching,
+            "loqusdb_id": loqusdb_ids,
+            "sanger_recipients": sanger_recipients,
+        }
+        for key, value in GENERAL_SETTINGS.items():
+            if value not in [None, ""]:
+                updates["$set"][key] = value
 
         if phenotype_groups is not None:
             if group_abbreviations:
@@ -145,19 +138,6 @@ def update_institute(
                 existing_groups[hpo_term] = {"name": description, "abbr": abbreviation}
             updates["$set"]["phenotype_groups"] = existing_groups
 
-        if gene_panels is not None:
-            updates["$set"]["gene_panels"] = gene_panels
-
-        if sharing_institutes is not None:
-            updates["$set"]["collaborators"] = sharing_institutes
-
-        if cohorts is not None:
-            updates["$set"]["cohorts"] = cohorts
-
-        if loqusdb_ids:
-            LOG.warning("Updating loqusdb id for institute: %s to %s", internal_id, loqusdb_ids)
-            updates["$set"]["loqusdb_id"] = loqusdb_ids
-
         if alamut_key is not None:
             updates["$set"]["alamut_key"] = (
                 alamut_key if alamut_key != "" else None
@@ -192,6 +172,24 @@ def institute(self, institute_id):
 
         return institute_obj
 
+    def safe_genes_filter(self, institute_id):
+        """Returns a list of "safe" HGNC IDs to filter variants with. These genes are retrieved from the institute.gene_panels_matching
+        Can be used to limit secondary findings when retrieving other causatives or matching managed variants
+
+        Args:
+            institute_id(str): _id of an institute
+
+        Returns:
+            safe_genes(list of HGNC ids)
+        """
+        safe_genes = []
+        institute_obj = self.institute(institute_id)
+        if not institute_obj:
+            return safe_genes  # return an empty list
+        for panel_name in institute_obj.get("gene_panels_matching", {}).keys():
+            safe_genes += self.panel_to_genes(panel_name=panel_name, gene_format="hgnc_id")
+        return safe_genes
+
     def institutes(self, institute_ids=None):
         """Fetch all institutes.
 

scout/server/blueprints/cases/controllers.py

@@ -329,12 +329,19 @@ def case(store, institute_obj, case_obj):
             for img in case_obj["custom_images"][img_section]:
                 img["data"] = b64encode(img["data"]).decode("utf-8")
 
+    # Limit secondary findings according to institute settings
+    limit_genes = store.safe_genes_filter(institute_obj["_id"])
+
     data = {
         "institute": institute_obj,
         "case": case_obj,
         "status_class": STATUS_MAP.get(case_obj["status"]),
-        "other_causatives": [var for var in store.check_causatives(case_obj=case_obj)],
-        "managed_variants": [var for var in store.check_managed(case_obj=case_obj)],
+        "other_causatives": [
+            var for var in store.check_causatives(case_obj=case_obj, limit_genes=limit_genes)
+        ],
+        "managed_variants": [
+            var for var in store.check_managed(case_obj=case_obj, limit_genes=limit_genes)
+        ],
         "comments": store.events(institute_obj, case=case_obj, comments=True),
         "hpo_groups": pheno_groups,
         "case_groups": case_groups,

scout/server/blueprints/cases/templates/cases/case.html

@@ -54,9 +54,17 @@ <h4 class="">
                   <span class="badge bg-sm bg-secondary">Internal ID: {{case._id}}</span>
               </h4>
             </div>
-            <div class="col-sm-8">
+            <div class="col-sm-6">
               {{ variants_buttons() }}
             </div>
+            <div class="col-sm-2">
+              Safe variant matching:
+              {% if institute.gene_panels_matching %}
+                <span class="badge rounded-pill bg-warning text-dark" data-bs-toggle="tooltip" data-bs-placement="left" title="To avoid incidental findings, eventual matching causatives and managed variants displayed on case page are filteres using a list of 'safe' panels. Modify institute settings to edit list of 'safe' panels. Current safe panels: {{ institute.gene_panels_matching.values()|list }}">on</span>
+              {% else %}
+                <span class="badge rounded-pill bg-info" data-bs-toggle="tooltip" data-bs-placement="left" title="Matching causatives and managed variants displayed on case page are NOT filtered by gene panel. Use caution to avoid incidental findings.">off</span>
+              {% endif %}
+            </div>
         </div> <!--end of div class="row" -->
       </div>
 

scout/server/blueprints/institutes/controllers.py

@@ -274,6 +274,7 @@ def populate_institute_form(form, institute_obj):
     for panel in available_panels:
         panel_set.add((panel["panel_name"], panel["display_name"]))
     form.gene_panels.choices = sorted(panel_set, key=lambda tup: tup[1])
+    form.gene_panels_matching.choices = sorted(panel_set, key=lambda tup: tup[1])
 
     return default_phenotypes
 
@@ -294,6 +295,7 @@ def update_institute_settings(store, institute_obj, form):
     sharing_institutes = []
     phenotype_groups = []
     gene_panels = {}
+    gene_panels_matching = {}
     group_abbreviations = []
     cohorts = []
 
@@ -317,6 +319,12 @@ def update_institute_settings(store, institute_obj, form):
             continue
         gene_panels[panel_name] = panel_obj["display_name"]
 
+    for panel_name in form.getlist("gene_panels_matching"):
+        panel_obj = store.gene_panel(panel_name)
+        if panel_obj is None:
+            continue
+        gene_panels_matching[panel_name] = panel_obj["display_name"]
+
     for cohort in form.getlist("cohorts"):
         cohorts.append(cohort.strip())
 
@@ -328,6 +336,7 @@ def update_institute_settings(store, institute_obj, form):
         display_name=form.get("display_name"),
         phenotype_groups=phenotype_groups,
         gene_panels=gene_panels,
+        gene_panels_matching=gene_panels_matching,
         group_abbreviations=group_abbreviations,
         add_groups=False,
         sharing_institutes=sharing_institutes,

scout/server/blueprints/institutes/forms.py

@@ -72,7 +72,12 @@ class InstituteForm(FlaskForm):
     pheno_abbrev = StringField("Abbreviation", validators=[validators.Optional()])
 
     gene_panels = NonValidatingSelectMultipleField(
-        "Gene panels for variants filtering", validators=[validators.Optional()]
+        "Gene panels available for variants filtering", validators=[validators.Optional()]
+    )
+
+    gene_panels_matching = NonValidatingSelectMultipleField(
+        "Gene panels available for other variants matching (managed and causatives variants)",
+        validators=[validators.Optional()],
     )
 
     pheno_groups = NonValidatingSelectMultipleField("Custom phenotype groups", choices=hpo_tuples)

scout/server/blueprints/institutes/templates/overview/utils.html

@@ -85,6 +85,15 @@ <h3 class="header">General Institute Settings</h3>
 
             <div class="row mt-3 d-flex align-items-center">
 
+              <div class="col-4">
+                {{ form.institutes.label(class="control-label",data_bs_toggle="tooltip", data_bs_placement="top", title="Allow case sharing only with preselected institutes.") }}
+                <select multiple="multiple" class="selectpicker" name="institutes" data-style="btn-secondary">
+                {% for choice in form.institutes.choices %}
+                  <option value="{{choice[0]}}" {% if choice[0] in institute.get("collaborators", []) %} selected {% endif %}>{{choice[1]}}</option>
+                {% endfor %}
+                </select>
+              </div>
+
               <div class="col-4">
                 {{ form.gene_panels.label(class="control-label",data_bs_toggle="tooltip", data_bs_placement="top", title="Select gene panels that will be available for variants filtering.") }}
                 <select multiple="multiple" name="gene_panels" class="selectpicker ml-3" data-style="btn-secondary">
@@ -95,6 +104,19 @@ <h3 class="header">General Institute Settings</h3>
               </div>
 
               <div class="col-4">
+                {{ form.gene_panels_matching.label(class="control-label",data_bs_toggle="tooltip", data_bs_placement="top", title="Limit incidental findings by looking for matching managed and causatives variants only in these panels") }}
+                <select multiple="multiple" name="gene_panels_matching" class="selectpicker ml-3" data-style="btn-secondary">
+                  {% for choice in form.gene_panels_matching.choices or [] %}
+                    <option value="{{choice[0]}}" {% if institute.gene_panels_matching and choice[0] in institute.gene_panels_matching.keys() %} selected {% endif %}>{{choice[1]}}</option>
+                  {% endfor %}
+                </select>
+              </div>
+
+            <div>
+
+            <div class="row mt-3 d-flex align-items-center">
+
+              <div class="col-5">
                 {{ form.pheno_groups.label(class="control-label",data_bs_toggle="tooltip", data_bs_placement="top", title="Phenotype groups are used to quickly assign a certain phenotype to a case, on the case page.") }}
                 <select multiple="multiple" name="pheno_groups" class="selectpicker" data-style="btn-secondary">
                   {% for choice in form.pheno_groups.choices or [] %}
@@ -103,7 +125,7 @@ <h3 class="header">General Institute Settings</h3>
                 </select>
               </div>
 
-              <div class="col-4">
+              <div class="col-7">
                 <div class="col-3">
                   {{form.cohorts.label(class="control-label",data_bs_toggle="tooltip", data_bs_placement="top", title="Categories used to subdivide patients")}}
                 </div>
@@ -115,18 +137,9 @@ <h3 class="header">General Institute Settings</h3>
                   </select>
                 </div>
               </div>
-
             </div>
 
             <div class="row mt-3 d-flex align-items-center">
-              <div class="col-4">
-                {{ form.institutes.label(class="control-label",data_bs_toggle="tooltip", data_bs_placement="top", title="Allow case sharing only with preselected institutes.") }}
-                <select multiple="multiple" class="selectpicker" name="institutes" data-style="btn-secondary">
-                {% for choice in form.institutes.choices %}
-                  <option value="{{choice[0]}}" {% if choice[0] in institute.get("collaborators", []) %} selected {% endif %}>{{choice[1]}}</option>
-                {% endfor %}
-                </select>
-              </div>
               {% if "admin" in current_user.roles %}
                 <!-- Admins can modify loqusdb settings -->
                 <div class="col-4">