scout-browser 4.92__py3-none-any.whl → 4.93.1__py3-none-any.whl

scout/__version__.py

@@ -1 +1 @@
-__version__ = "4.92"
+__version__ = "4.93.1"

scout/adapter/mongo/base.py

@@ -34,6 +34,7 @@ from flask import current_app
 from .acmg import ACMGHandler
 from .case import CaseHandler
 from .case_group import CaseGroupHandler
+from .ccv import CCVHandler
 from .clinvar import ClinVarHandler
 from .cytoband import CytobandHandler
 from .disease_terms import DiagnosisHandler
@@ -61,6 +62,7 @@ class MongoAdapter(
     ACMGHandler,
     CaseGroupHandler,
     CaseHandler,
+    CCVHandler,
     ClinVarHandler,
     CytobandHandler,
     DiagnosisHandler,
@@ -97,6 +99,7 @@ class MongoAdapter(
         """Setup connection to database."""
         self.db = database
         self.acmg_collection = database.acmg
+        self.ccv_collection = database.ccv
         self.case_collection = database.case
         self.case_group_collection = database.case_group
         self.clinvar_collection = database.clinvar

scout/adapter/mongo/case.py

@@ -11,7 +11,7 @@ from bson import ObjectId
 from werkzeug.datastructures import ImmutableMultiDict
 
 from scout.build.case import build_case
-from scout.constants import ACMG_MAP, FILE_TYPE_MAP, ID_PROJECTION, OMICS_FILE_TYPE_MAP
+from scout.constants import ACMG_MAP, CCV_MAP, FILE_TYPE_MAP, ID_PROJECTION, OMICS_FILE_TYPE_MAP
 from scout.exceptions import ConfigError, IntegrityError
 from scout.parse.variant.ids import parse_document_id
 from scout.utils.algorithms import ui_score
@@ -1272,6 +1272,16 @@ class CaseHandler(object):
                 {"$set": {"case_id": family_id, "variant_specific": new_specific_id}},
             )
 
+        # update ClinGen-CGC-VIGG classification
+        for ccv_obj in self.ccv_collection.find({"case_id": case_obj["_id"]}):
+            LOG.info("update ClinGen-CGC-VIGG classification: %s", ccv_obj["classification"])
+            ccv_variant = self.variant(ccv_obj["variant_specific"])
+            new_specific_id = get_variantid(ccv_variant, family_id)
+            self.ccv_collection.find_one_and_update(
+                {"_id": ccv_obj["_id"]},
+                {"$set": {"case_id": family_id, "variant_specific": new_specific_id}},
+            )
+
         # update events
         institute_obj = self.institute(case_obj["owner"])
         for event_obj in self.events(institute_obj, case=case_obj):
@@ -1344,6 +1354,7 @@ class CaseHandler(object):
                 'mosaic_tags' : [list of variant ids],
                 'cancer_tier': [list of variant ids],
                 'acmg_classification': [list of variant ids]
+                'ccv_classification': [list of variant ids]
                 'is_commented': [list of variant ids]
         """
         updated_variants = {
@@ -1352,6 +1363,7 @@ class CaseHandler(object):
             "mosaic_tags": [],
             "cancer_tier": [],
             "acmg_classification": [],
+            "ccv_classification": [],
             "is_commented": [],
         }
 
@@ -1394,8 +1406,10 @@ class CaseHandler(object):
                 verb = action
                 if action == "acmg_classification":
                     verb = "acmg"
-                elif action == "is_commented":
+                if action == "is_commented":
                     verb = "comment"
+                if action == "ccv_classification":
+                    verb = "ccv"
 
                 old_event = self.event_collection.find_one(
                     {
@@ -1444,6 +1458,17 @@ class CaseHandler(object):
                         acmg_str=str_classif,
                     )
 
+                if action == "ccv_classification":
+                    str_classif = CCV_MAP.get(old_var.get("ccv_classification"))
+                    updated_variant = self.update_ccv(
+                        institute_obj=institute_obj,
+                        case_obj=case_obj,
+                        user_obj=user_obj,
+                        link=link,
+                        variant_obj=new_var,
+                        ccv_str=str_classif,
+                    )
+
                 if action in update_action_map.keys():
                     updated_variant = update_action_map[action](
                         institute_obj,

scout/adapter/mongo/ccv.py

@@ -0,0 +1,131 @@
+# -*- coding: utf-8 -*-
+import logging
+
+import pymongo
+from bson import ObjectId
+
+from scout.build.ccv import build_ccv_evaluation
+from scout.utils.ccv import get_ccv
+
+log = logging.getLogger(__name__)
+
+
+class CCVHandler(object):
+    def submit_ccv_evaluation(
+        self,
+        variant_obj,
+        user_obj,
+        institute_obj,
+        case_obj,
+        link,
+        criteria=None,
+        classification=None,
+    ):
+        """Submit an evaluation to the database
+
+        Get all the relevant information, build an evaluation_obj
+
+        Args:
+            variant_obj(dict)
+            user_obj(dict)
+            institute_obj(dict)
+            case_obj(dict)
+            link(str): variant url
+            criteria(list(dict)):
+                                            [
+                                        {
+                                        'term': str,
+                                        'comment': str,
+                                        'modifier': str,
+                                        'links': list(str)
+                                        },
+                                        .
+                                        .
+                                    ]
+            classification(int)
+        """
+        criteria = criteria or []
+
+        variant_specific = variant_obj["_id"]
+        variant_id = variant_obj["variant_id"]
+        user_id = user_obj["_id"]
+        user_name = user_obj.get("name", user_obj["_id"])
+        institute_id = institute_obj["_id"]
+        case_id = case_obj["_id"]
+
+        evaluation_terms = []
+        for evaluation_info in criteria:
+            term = evaluation_info["term"]
+            if evaluation_info.get("modifier"):
+                term += "_" + evaluation_info.get("modifier")
+            evaluation_terms.append(term)
+
+        if classification is None:
+            classification = get_ccv(evaluation_terms)
+
+        if classification:
+            evaluation_obj = build_ccv_evaluation(
+                variant_specific=variant_specific,
+                variant_id=variant_id,
+                user_id=user_id,
+                user_name=user_name,
+                institute_id=institute_id,
+                case_id=case_id,
+                ccv_classification=classification,
+                ccv_criteria=criteria,
+            )
+
+            self._load_ccv_evaluation(evaluation_obj)
+
+        # Update the ccv classification for the variant:
+        self.update_ccv(institute_obj, case_obj, user_obj, link, variant_obj, classification)
+        return classification
+
+    def _load_ccv_evaluation(self, evaluation_obj):
+        """Load a evaluation object into the database"""
+        res = self.ccv_collection.insert_one(evaluation_obj)
+        return res
+
+    def delete_ccv_evaluation(self, evaluation_obj):
+        """Delete an evaluation from the database
+
+        Args:
+            evaluation_obj(dict)
+
+        """
+        self.ccv_collection.delete_one({"_id": evaluation_obj["_id"]})
+
+    def get_ccv_evaluation(self, evaluation_id):
+        """Get a single evaluation from the database
+
+        Args:
+            evaluation_id(str)
+
+        """
+        return self.ccv_collection.find_one({"_id": ObjectId(evaluation_id)})
+
+    def get_ccv_evaluations(self, variant_obj):
+        """Return all evaluations for a certain variant.
+
+        Args:
+            variant_obj (dict): variant dict from the database
+
+        Returns:
+            pymongo.cursor: database cursor
+        """
+        query = dict(variant_id=variant_obj["variant_id"])
+        res = self.ccv_collection.find(query).sort([("created_at", pymongo.DESCENDING)])
+        return res
+
+    def get_ccv_evaluations_case_specific(self, document_id):
+        """Return all evaluations for a certain variant, in a certain case as determined by document id.
+
+        Args:
+            document_id: variant document id from the db; an md5 hash including the case id.
+
+        Returns:
+            res: pymongo.cursor
+        """
+        query = dict(variant_specific=document_id)
+        res = self.ccv_collection.find(query).sort([("created_at", pymongo.DESCENDING)])
+        return res

scout/adapter/mongo/variant.py

@@ -721,7 +721,7 @@ class VariantHandler(VariantLoader):
     def evaluated_variant_ids_from_events(self, case_id, institute_id):
         """Returns variant ids for variants that have been evaluated
            Return all variants, snvs/indels and svs from case case_id
-            which have an event entry for 'acmg_classification', 'manual_rank', 'dismiss_variant',
+            which have an event entry for 'acmg_classification', 'ccv_classification', 'manual_rank', 'dismiss_variant',
             'cancer_tier', 'mosaic_tags'.
         Args:
             case_id(str)
@@ -732,6 +732,7 @@ class VariantHandler(VariantLoader):
 
         evaluation_verbs = [
             "acmg",
+            "ccv",
             "manual_rank",
             "cancer_tier",
             "dismiss_variant",
@@ -758,7 +759,7 @@ class VariantHandler(VariantLoader):
         """Returns variants that have been evaluated
 
         Return all variants, snvs/indels and svs from case case_id and institute_id
-        which have a entry for 'acmg_classification', 'manual_rank', 'dismiss_variant',
+        which have a entry for 'acmg_classification', 'ccv_classification', 'manual_rank', 'dismiss_variant',
         'cancer_tier' or if they are commented.
 
         Return only if the variants still exist and still have the assessment.
@@ -778,11 +779,11 @@ class VariantHandler(VariantLoader):
         query = {
             "$and": [
                 {"variant_id": {"$in": variant_ids}},
-                {"institute": institute_id},
                 {"case_id": case_id},
                 {
                     "$or": [
                         {"acmg_classification": {"$exists": True}},
+                        {"ccv_classification": {"$exists": True}},
                         {"manual_rank": {"$exists": True}},
                         {"cancer_tier": {"$exists": True}},
                         {"dismiss_variant": {"$exists": True}},

scout/adapter/mongo/variant_events.py

@@ -4,7 +4,7 @@ from typing import Dict, List
 
 import pymongo
 
-from scout.constants import CANCER_TIER_OPTIONS, MANUAL_RANK_OPTIONS, REV_ACMG_MAP
+from scout.constants import CANCER_TIER_OPTIONS, MANUAL_RANK_OPTIONS, REV_ACMG_MAP, REV_CCV_MAP
 
 SANGER_OPTIONS = ["True positive", "False positive", "Not validated"]
 
@@ -931,3 +931,47 @@ class VariantEventHandler(object):
 
         LOG.debug("Variant updated")
         return updated_variant
+
+    def update_ccv(self, institute_obj, case_obj, user_obj, link, variant_obj, ccv_str):
+        """Create an event for updating the ClinGen-CGC-VIGG classification of a variant.
+
+        Arguments:
+            institute_obj (dict): A Institute object
+            case_obj (dict): Case object
+            user_obj (dict): A User object
+            link (str): The url to be used in the event
+            variant_obj (dict): A variant object
+            ccv_str (str): The new ClinGen-CGC-VIGG classification string
+
+        Returns:
+            updated_variant
+        """
+        self.create_event(
+            institute=institute_obj,
+            case=case_obj,
+            user=user_obj,
+            link=link,
+            category="variant",
+            verb="ccv",
+            variant=variant_obj,
+            subject=variant_obj["display_name"],
+        )
+        LOG.info(
+            "Setting ClinGen-CGC-VIGG to {} for: {}".format(ccv_str, variant_obj["display_name"])
+        )
+
+        if ccv_str is None:
+            updated_variant = self.variant_collection.find_one_and_update(
+                {"_id": variant_obj["_id"]},
+                {"$unset": {"ccv_classification": 1}},
+                return_document=pymongo.ReturnDocument.AFTER,
+            )
+        else:
+            updated_variant = self.variant_collection.find_one_and_update(
+                {"_id": variant_obj["_id"]},
+                {"$set": {"ccv_classification": REV_CCV_MAP[ccv_str]}},
+                return_document=pymongo.ReturnDocument.AFTER,
+            )
+
+        LOG.debug("Variant updated")
+        return updated_variant

scout/build/ccv.py

@@ -0,0 +1,59 @@
+import logging
+import datetime
+
+LOG = logging.getLogger(__name__)
+
+
+def build_ccv_evaluation(
+    variant_specific,
+    variant_id,
+    user_id,
+    user_name,
+    institute_id,
+    case_id,
+    ccv_classification,
+    ccv_criteria,
+):
+    """Build a ClinGen-CGC-VIGG evaluation object ready to be inserted to database
+
+    Args:
+        variant_specific(str): md5 string for the specific variant
+        variant_id(str): md5 string for the common variant
+        user_id(str)
+        user_name(str)
+        institute_id(str)
+        case_id(str)
+        ccv_classification(str): The ClinGen-CGC-VIGG classification
+        ccv_criteria(list(dict)): A list of dictionaries with ClinGen-CGC-VIGG criteria
+
+    Returns:
+        evaluation_obj(dict): Correctly formatted evaluation object
+
+    """
+    LOG.info(
+        "Creating ClinGen-CGC-VIGG classification: %s for variant %s",
+        ccv_classification,
+        variant_id,
+    )
+    ccv_criteria = ccv_criteria or []
+    evaluation_obj = dict(
+        variant_specific=variant_specific,
+        variant_id=variant_id,
+        institute_id=institute_id,
+        case_id=case_id,
+        ccv_classification=ccv_classification,
+        user_id=user_id,
+        user_name=user_name,
+        created_at=datetime.datetime.now(),
+    )
+    criteria_objs = []
+    for info in ccv_criteria:
+        criteria_obj = {}
+        for criterion_key in ["term", "comment", "links", "modifier"]:
+            if criterion_key in info:
+                criteria_obj[criterion_key] = info[criterion_key]
+        criteria_objs.append(criteria_obj)
+
+    evaluation_obj["ccv_criteria"] = criteria_objs
+
+    return evaluation_obj

scout/commands/serve.py

@@ -22,7 +22,8 @@ def serve(host, port, debug, livereload, test):
     """Start the web server."""
 
     # Verify the database connectivity before launching the app
-    mongo_client = current_app.config.get("MONGO_DATABASE")._Database__client
+    mongo_client = current_app.config.get("MONGO_DATABASE").client
+
     try:
         mongo_client.server_info()
         if test:

scout/constants/__init__.py

@@ -23,6 +23,7 @@ from .case_tags import (
     VERBS_ICONS_MAP,
     VERBS_MAP,
 )
+from .ccv import CCV_COMPLETE_MAP, CCV_CRITERIA, CCV_MAP, CCV_OPTIONS, REV_CCV_MAP
 from .clinvar import (
     AFFECTED_STATUS,
     ALLELE_OF_ORIGIN,
@@ -126,6 +127,7 @@ COLLECTIONS = [
     "disease_term",
     "variant",
     "acmg",
+    "ccv",
 ]
 
 BUILDS = ["37", "38", "GRCh38"]

scout/constants/case_tags.py

@@ -43,6 +43,7 @@ CASE_REPORT_VARIANT_TYPES = {
     "partial_causatives_detailed": "partial_causatives",
     "suspects_detailed": "suspects",
     "classified_detailed": "acmg_classification",
+    "ccv_classified_detailed": "ccv_classification",
     "tagged_detailed": "manual_rank",
     "tier_detailed": "cancer_tier",
     "dismissed_detailed": "dismiss_variant",
@@ -105,6 +106,7 @@ CASE_TAGS = {
 
 VERBS_MAP = {
     "acmg": "updated ACMG classification for",
+    "ccv": "updated ClinGen-CGC-VIGG classification for",
     "add_case": "added case",
     "add_cohort": "updated cohort for",
     "add_phenotype": "added HPO term for",

scout/constants/ccv.py

@@ -0,0 +1,244 @@
+# -*- coding: utf-8 -*-
+from collections import OrderedDict
+
+# from worst to most certain benign
+CCV_MAP = OrderedDict(
+    [
+        (4, "oncogenic"),
+        (3, "likely_oncogenic"),
+        (0, "uncertain_significance"),
+        (2, "likely_benign"),
+        (1, "benign"),
+    ]
+)
+# <a href="https://cancerhotspots.org" target="_blank">cancerhotspots.org</a>
+REV_CCV_MAP = OrderedDict([(value, key) for key, value in CCV_MAP.items()])
+
+CCV_OPTIONS = [
+    {"code": "oncogenic", "short": "O", "label": "Oncogenic", "color": "danger"},
+    {
+        "code": "likely_oncogenic",
+        "short": "LO",
+        "label": "Likely Oncogenic",
+        "color": "warning",
+    },
+    {
+        "code": "uncertain_significance",
+        "short": "VUS",
+        "label": "Uncertain Significance",
+        "color": "primary",
+    },
+    {"code": "likely_benign", "short": "LB", "label": "Likely Benign", "color": "info"},
+    {"code": "benign", "short": "B", "label": "Benign", "color": "success"},
+]
+
+CCV_COMPLETE_MAP = OrderedDict([(option["code"], option) for option in CCV_OPTIONS])
+
+CCV_CRITERIA = OrderedDict()
+
+CCV_CRITERIA["oncogenicity"] = OrderedDict(
+    [
+        (
+            "Very Strong",
+            OrderedDict(
+                [
+                    (
+                        "OVS1",
+                        {
+                            "short": "Null variant in tumor supressor",
+                            "description": "Null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single-exon or multiexon deletion) in a bona fide tumor suppressor gene.",
+                            "documentation": 'Strength can be modified based on <a href="https://pubmed.ncbi.nlm.nih.gov/30192042/" target="blank">ClinGen’s recommendations for PVS1</a>',
+                        },
+                    )
+                ]
+            ),
+        ),
+        (
+            "Strong",
+            OrderedDict(
+                [
+                    (
+                        "OS1",
+                        {
+                            "short": "Same aa change as known oncogenic variant",
+                            "description": "Same amino acid change as a previously established oncogenic variant (using this standard) regardless of nucleotide change.",
+                        },
+                    ),
+                    (
+                        "OS2",
+                        {
+                            "short": "Well-established functional studies",
+                            "description": "Well-established in vitro or in vivo functional studies, supportive of an oncogenic effect of the variant.",
+                        },
+                    ),
+                    (
+                        "OS3",
+                        {
+                            "short": "Cancer hotspot: high frequency",
+                            "description": "Located in one of the hotspots in cancerhotspots.org with at least 50 samples with a somatic variant at the same amino acid position, and the same amino acid change count in cancerhotspots.org in at least 10 samples.",
+                        },
+                    ),
+                ]
+            ),
+        ),
+        (
+            "Moderate",
+            OrderedDict(
+                [
+                    (
+                        "OM1",
+                        {
+                            "short": "Functional domain",
+                            "description": "Located in a critical and well-established part of a functional domain (eg, active site of an enzyme).",
+                        },
+                    ),
+                    (
+                        "OM2",
+                        {
+                            "short": "Protein length change",
+                            "description": "Protein length changes as a result of in-frame deletions/insertions in a known oncogene or tumor suppressor gene or stop-loss variants in a known tumor suppressor gene.",
+                        },
+                    ),
+                    (
+                        "OM3",
+                        {
+                            "short": "Cancer hotspot: moderate frequency",
+                            "description": "Located in one of the hotspots in cancerhotspots.org with <50 samples with a somatic variant at the same amino acid position, and the same amino acid change count in cancerhotspots.org is at least 10.",
+                        },
+                    ),
+                    (
+                        "OM4",
+                        {
+                            "short": "Missense variant at aa with other oncogenic missense variant",
+                            "description": "Missense variant at an amino acid residue where a different missense variant determined to be oncogenic (using this standard) has been documented. Amino acid difference from reference amino acid should be greater or at least approximately the same as for missense change determined to be oncogenic.",
+                        },
+                    ),
+                ]
+            ),
+        ),
+        (
+            "Supporting",
+            OrderedDict(
+                [
+                    (
+                        "OP1",
+                        {
+                            "short": "Computatinal evidence",
+                            "description": "All used lines of computational evidence support an oncogenic effect of a variant (conservation/evolutionary, splicing effect, etc.).",
+                        },
+                    ),
+                    (
+                        "OP2",
+                        {
+                            "short": "Gene in a malignancy with a single genetic etiology",
+                            "description": "Somatic variant in a gene in a malignancy with a single genetic etiology. Example: retinoblastoma is caused by bi-allelic RB1 inactivation.",
+                        },
+                    ),
+                    (
+                        "OP3",
+                        {
+                            "short": "Cancer hotspots: low frequency",
+                            "description": "Located in one of the hotspots in cancerhotspots.org and the particular amino acid change count in cancerhotspots.org is below 10",
+                        },
+                    ),
+                    (
+                        "OP4",
+                        {
+                            "short": "Absent in population databases",
+                            "description": "Absent from controls (or at an extremely low frequency) in gnomAD.",
+                        },
+                    ),
+                ]
+            ),
+        ),
+    ]
+)
+
+CCV_CRITERIA["benign impact"] = OrderedDict(
+    [
+        (
+            "Very Strong",
+            OrderedDict(
+                [
+                    (
+                        "SBVS1",
+                        {
+                            "short": "MAF is >0.05",
+                            "description": "Minor allele frequency is >5%% in gnomAD in any 5 general continental populations: African, East Asian, European (non-Finnish), Latino, and South Asian.",
+                        },
+                    )
+                ]
+            ),
+        ),
+        (
+            "Strong",
+            OrderedDict(
+                [
+                    (
+                        "SBS1",
+                        {
+                            "short": "MAF is >0.01",
+                            "description": "Minor allele frequency is >1%% in gnomAD in any 5 general continental populations: African, East Asian, European (non-Finnish), Latino, and South Asian.	",
+                        },
+                    ),
+                    (
+                        "SBS2",
+                        {
+                            "short": "Well-established functional studies",
+                            "description": "Well-established in vitro or in vivo functional studies show no oncogenic effects.",
+                        },
+                    ),
+                ]
+            ),
+        ),
+        (
+            "Supporting",
+            OrderedDict(
+                [
+                    (
+                        "SBP1",
+                        {
+                            "short": "Computational evidence",
+                            "description": "All used lines of computational evidence suggest no effect of a variant (conservation/evolutionary, splicing effect, etc.).",
+                        },
+                    ),
+                    (
+                        "SBP2",
+                        {
+                            "short": "Silent mutation (no predicted impact on splicing)",
+                            "description": "A synonymous (silent) variant for which splicing prediction algorithms predict no effect on the splice consensus sequence nor the creation of a new splice site and the nucleotide is not highly conserved.",
+                        },
+                    ),
+                ]
+            ),
+        ),
+    ]
+)
+
+CCV_POTENTIAL_CONFLICTS = [
+    (
+        "OS2",
+        "OS1",
+        "If OS1 is applicable, OS2 can be used only if functional studies are based on the particular nucleotide change of the variant.",
+    ),
+    (
+        "OS3",
+        "OS1",
+        "OS3 cannot be used if OS1 is applicable, unless it is possible to observe hotspots on the basis of the particular nucleotide change.",
+    ),
+    (
+        "OM1",
+        "OVS1",
+        "OM1 cannot be used if OVS1 is applicable.",
+    ),
+    (
+        "OM3",
+        "OM1",
+        "OM3 cannot be used if OM1 is applicable.",
+    ),
+    (
+        "OM3",
+        "OM4",
+        "OM3 cannot be used if OM4 is applicable.",
+    ),
+]

scout/demo/643594.config.yaml

@@ -113,8 +113,8 @@ custom_images:
         path: scout/demo/images/custom_images/640x480_one.png
       - title: A jpg image
         description: A very good description
-        width: 500
-        path: scout/demo/images/custom_images/640x480_two.jpg
+        width: 1300
+        path: scout/demo/images/custom_images/1300x1000.jpg
     section_two:
       - title: An SVG image
         description: Another very good description