scout-browser 4.88__py3-none-any.whl → 4.89__py3-none-any.whl

scout/__version__.py

@@ -1 +1 @@
-__version__ = "4.88"
+__version__ = "4.89"

scout/adapter/mongo/base.py

@@ -90,7 +90,7 @@ class MongoAdapter(
     def init_app(self, app):
         """Setup via Flask."""
         dbname = app.config["MONGO_DBNAME"]
-        LOG.debug(f"Database name: {dbname}")
+        LOG.info(f"Database name: {dbname}")
         self.setup(app.config["MONGO_DATABASE"])
 
     def setup(self, database):

scout/adapter/mongo/case.py

@@ -4,10 +4,11 @@ import logging
 import operator
 import re
 from copy import deepcopy
-from typing import Any, Dict, List, Optional
+from typing import Any, Dict, List, Optional, Union
 
 import pymongo
 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
@@ -17,6 +18,7 @@ from scout.utils.algorithms import ui_score
 from scout.utils.sort import get_load_priority
 
 LOG = logging.getLogger(__name__)
+EXISTS = "$exists"
 
 
 class CaseHandler(object):
@@ -38,7 +40,7 @@ class CaseHandler(object):
         set_1 = set()
         if len(phenotype_terms) == 0:
             LOG.warning("No phenotype terms provided, please provide ar least one HPO term")
-            return None
+            return []
         # Add all ancestors of all terms
         for term in phenotype_terms:
             hpo_term = self.hpo_term(term)
@@ -73,53 +75,48 @@ class CaseHandler(object):
         self,
         query: Dict[str, Any],
         query_field: str,
-        query_term: str,
+        query_value: str,
         institute_id: str,
     ):
-        """Adds query parameters when search is performed by case or phenotype similarity
-
-        Args:
-            query(dict): cases search query
-            query_field(str) example:"status"
-            query_term(str) example:"active"
-            name_query(dict) args provided by users in cases filter search
-            institute_id(str): institute to search cases for
-        """
+        """Adds query parameters when search is performed by case or phenotype similarity."""
         hpo_terms = []
-        order = None
         CASE_SIMILAR_PROJECTION = {"phenotype_terms": 1}
+
         if query_field == "similar_case":
-            case_obj = self.case(
-                display_name=query_term,
-                institute_id=institute_id,
-                projection=CASE_SIMILAR_PROJECTION,
-            )
+            temp_query_or = {
+                "$or": [
+                    {"display_name": query_value},
+                    {"individuals.display_name": query_value},
+                    {"individuals.subject_id": query_value},
+                    {"_id": query_value},
+                ]
+            }
+            temp_query = {"$and": [{"owner": institute_id}, temp_query_or]}
+            case_obj = self.case_collection.find_one(temp_query, CASE_SIMILAR_PROJECTION)
             if case_obj is None:
                 query["_id"] = {"$in": []}  # No result should be returned by query
                 return
 
             for term in case_obj.get("phenotype_terms", []):
                 hpo_terms.append(term.get("phenotype_id"))
+
             similar_cases = self.cases_by_phenotype(hpo_terms, institute_id, case_obj["_id"])
         else:  # similar HPO terms
-            hpo_terms = list(query_term.replace(" ", "").split(","))
+            hpo_terms = list(query_value.replace(" ", "").split(","))
             similar_cases = self.cases_by_phenotype(hpo_terms, institute_id, None)
 
-        if len(similar_cases) == 0:  # No cases similar to given phenotype
-            query["_id"] = {"$in": []}  # No result should be returned by query
-            return
-
-        similar_case_ids = []
-        order = []
-        for i in similar_cases:
-            similar_case_ids.append(i[0])
-            order.append(i[1])
-        query["_id"] = {"$in": similar_case_ids}
-
-        return order
+        similar_case_ids = [
+            similar_case[0] for similar_case in similar_cases
+        ]  # These are sorted by the most similar to the least
+        self._update_case_id_query(
+            query, similar_case_ids
+        )  # This might mess up the order of the _ids
+        query["_id"]["$in"] = sorted(
+            query["_id"]["$in"], key=lambda idx: similar_case_ids.index(idx)
+        )  # Sort them again by similarity
 
     def _set_genes_of_interest_query(
-        self, query: Dict[str, Any], query_field: str, query_term: str
+        self, query: Dict[str, Any], query_field: str, query_value: str
     ):
         """Adds query parameters when search is aimed at retrieving cases with a certain pinned or causative gene
 
@@ -128,11 +125,11 @@ class CaseHandler(object):
         Args:
             query(dict): cases search query
             query_field(str) "pinned" or "causative"
-            query_term(str) example:"POT1"
+            query_value(str) example:"POT1"
         """
-        hgnc_id = self.hgnc_id(hgnc_symbol=query_term)
+        hgnc_id = self.hgnc_id(hgnc_symbol=query_value)
         if hgnc_id is None:
-            LOG.debug(f"No gene with the HGNC symbol {query_term} found.")
+            LOG.debug(f"No gene with the HGNC symbol {query_value} found.")
             query["_id"] = {"$in": []}  # No result should be returned by query
             return
 
@@ -158,19 +155,21 @@ class CaseHandler(object):
             ]
         )
         case_ids = [case["_id"] for case in cases_with_gene_doc]
-        query["_id"] = {"$in": case_ids}
+        self._update_case_id_query(query, case_ids)
 
-    def _set_case_name_query(self, query: Dict[str, Any], query_term: str):
+    def _set_case_name_query(self, query: Dict[str, Any], query_value: str):
         """Set case query to reg exp search in case and individual display names for parts of the name query."""
 
-        case_name_regex = {"$regex": re.escape(query_term)}
-        query["$or"] = [
+        case_name_regex = {"$regex": re.escape(query_value)}
+        or_options = [
             {"display_name": case_name_regex},
             {"individuals.display_name": case_name_regex},
+            {"individuals.subject_id": case_name_regex},
             {"_id": case_name_regex},
         ]
+        self.update_case_query_or_options(query=query, or_options=or_options)
 
-    def _set_case_phenotype_query(self, query: Dict[str, Any], query_term: str):
+    def _set_case_phenotype_query(self, query: Dict[str, Any], query_value: str):
         """Set case query based on phenotype terms.
 
         The user may have provided multiple query (HPO) terms.
@@ -178,18 +177,12 @@ class CaseHandler(object):
         If the no query term is given (the phenotype query string is empty), instead query for cases
         that lack HPO terms.
         """
-        if query_term != "":
+        if query_value != "":
             query["phenotype_terms.phenotype_id"] = {
-                "$in": list(query_term.replace(" ", "").split(","))
+                "$in": list(query_value.replace(" ", "").split(","))
             }
-            return
 
-        query["$or"] = [
-            {"phenotype_terms": {"$size": 0}},
-            {"phenotype_terms": {"$exists": False}},
-        ]
-
-    def _set_diagnosis_query(self, query: Dict[str, Any], query_term: str):
+    def _set_diagnosis_query(self, query: Dict[str, Any], query_value: str):
         """Set diagnosis query based on query term.
         The user might have provided multiple query terms.
 
@@ -201,92 +194,148 @@ class CaseHandler(object):
 
         The query should be set to check for cases with no HPO terms if the query term is empty.
         """
-        if query_term != "":
-            omim_terms = list(query_term.replace(" ", "").split(","))
-            query["$or"] = [
+        if query_value != "":
+            omim_terms = list(query_value.replace(" ", "").split(","))
+
+            or_options = [
                 {"diagnosis_phenotypes.disease_id": {"$in": omim_terms}},
                 {"diagnosis_phenotypes": {"$in": omim_terms}},
             ]
-            return
 
-        query["$or"] = [
-            {"diagnosis_phenotypes": {"$size": 0}},
-            {"diagnosis_phenotypes": {"$exists": False}},
-        ]
+            self.update_case_query_or_options(query=query, or_options=or_options)
 
-    def _set_synopsis_query(self, query: Dict[str, Any], query_term: str):
-        """Set query to search in the free text synopsis for query_term."""
+    def _set_synopsis_query(self, query: Dict[str, Any], query_value: str):
+        """Set query to search in the free text synopsis for query_value."""
 
-        if query_term != "":
-            query["$text"] = {"$search": re.escape(query_term)}
+        if query_value != "":
+            query["$text"] = {"$search": re.escape(query_value)}
         else:
             query["synopsis"] = ""
 
-    def _populate_name_query(self, query, name_query, owner=None, collaborator=None):
-        """Parses and adds query parameters provided by users in cases search filter.
+    def update_case_query_or_options(self, query: dict, or_options: List[dict]):
+        """Populates the available options in the query $and field"""
+        if not or_options:
+            return
+        query.setdefault("$or", []).extend(or_options)
 
-        Args:
-            query(dict): cases search query
-            name_query(dict): args provided by users in cases filter search
-            owner(dict): an institute id
-            collaborator(dict): an institute id
-        """
-        order = None
-        query_field = name_query.split(":")[0]  # example:status
-        query_term = name_query[name_query.index(":") + 1 :].strip()
+    def populate_case_query(
+        self, query: dict, name_query: Union[str, ImmutableMultiDict], owner=None, collaborator=None
+    ):
+        """Parses and adds query parameters provided by users in cases search filter."""
+
+        def set_case_item_query(query: dict, query_field: str, query_value: str):
+            # Mapping query fields to their corresponding handling functions
+            handlers = {
+                "case": self._set_case_name_query,
+                "exact_pheno": self._set_case_phenotype_query,
+                "exact_dia": self._set_diagnosis_query,
+                "synopsis": self._set_synopsis_query,
+                "panel": set_panel_query,
+                "status": set_status_query,
+                "tags": set_tags_query,
+                "track": set_track_query,
+                "pheno_group": set_pheno_group_query,
+                "cohort": set_cohort_query,
+                "similar_case": set_similar_case_query,
+                "similar_pheno": set_similar_pheno_query,
+                "pinned": set_pinned_gene_query,
+                "causative": set_causative_gene_query,
+                "user": set_user_query,
+            }
 
-        if query_field == "case" and query_term != "":
-            self._set_case_name_query(query, query_term)
+            handler = handlers.get(query_field)
+            if handler:
+                handler(query, query_value)
 
-        if query_field == "exact_pheno":
-            self._set_case_phenotype_query(query, query_term)
+        def set_panel_query(query: dict, query_value: str):
+            """Updates the query with a certain value."""
+            query.update(
+                {"panels": {"$elemMatch": {"panel_name": query_value, "is_default": True}}}
+            )
 
-        if query_field == "exact_dia":
-            self._set_diagnosis_query(query, query_term)
+        def set_status_query(query: dict, query_value: str):
+            """Updates the query with a certain value."""
+            query.update({"status": query_value})
 
-        if query_field == "synopsis":
-            self._set_synopsis_query(query, query_term)
+        def set_tags_query(query: dict, query_value: str):
+            """Updates the query with a certain value."""
+            query.update({"tags": query_value.lower()})
 
-        if query_field == "panel":
-            query["panels"] = {"$elemMatch": {"panel_name": query_term, "is_default": True}}
+        def set_track_query(query: dict, query_value: str):
+            """Updates the query with a certain value."""
+            query.update({"track": query_value})
 
-        if query_field == "status":
-            query["status"] = query_term
+        def set_pheno_group_query(query: dict, query_value: str):
+            """Updates the query with a certain value."""
+            query.update({"phenotype_groups.phenotype_id": query_value})
 
-        if query_field == "tags":
-            query["tags"] = query_term.lower()
+        def set_cohort_query(query: dict, query_value: str):
+            """Updates the query with a certain value."""
+            query.update({"cohorts": query_value})
 
-        if query_field == "track":
-            query["track"] = query_term
+        def set_similar_case_query(query: dict, query_value: str):
+            """Updates the query with a certain value."""
+            self._set_similar_phenotype_query(
+                query, "similar_case", query_value, owner or collaborator
+            )
 
-        if query_field == "pheno_group":
-            if query_term != "":
-                query["phenotype_groups.phenotype_id"] = query_term
-            else:
-                query["$or"] = [
-                    {"phenotype_groups": {"$size": 0}},
-                    {"phenotype_groups": {"$exists": False}},
-                ]
-        if query_field == "cohort":
-            query["cohorts"] = query_term
+        def set_similar_pheno_query(query: dict, query_value: str):
+            """Updates the query with a certain value."""
+            self._set_similar_phenotype_query(
+                query, "similar_pheno", query_value, owner or collaborator
+            )
 
-        if query_term != "" and query_field in ["similar_case", "similar_pheno"]:
-            order = self._set_similar_phenotype_query(
-                query, query_field, query_term, owner or collaborator
+        def set_pinned_gene_query(query: dict, query_value: str):
+            """Updates the query with a certain value."""
+            self._set_genes_of_interest_query(
+                query=query, query_field="pinned", query_value=query_value
             )
 
-        if query_term != "" and query_field in ["pinned", "causative"]:
-            self._set_genes_of_interest_query(query, query_field, query_term)
+        def set_causative_gene_query(query: dict, query_value: str):
+            """Updates the query with a certain value."""
+            self._set_genes_of_interest_query(
+                query=query, query_field="causative", query_value=query_value
+            )
 
-        if query_field == "user":
-            query_terms = query_term.split(" ")
+        def set_user_query(query: dict, query_value: str):
+            # Handling the 'user' field query separately
+            query_terms = query_value.split(" ")
             user_query = {
                 "$and": [{"name": {"$regex": term, "$options": "i"}} for term in query_terms]
             }
             users = self.user_collection.find(user_query)
             query["assignees"] = {"$in": [user["_id"] for user in users]}
 
-        return order
+        if isinstance(name_query, str):
+            # Example: status -> Comes from a GET request from dashboard cases
+            query_field, query_value = name_query.split(":", 1)
+            set_case_item_query(
+                query=query, query_field=query_field.strip(), query_value=query_value.strip()
+            )
+        else:
+            # POST request form from more advanced case search from cases page
+            for query_field in [
+                "case",
+                "exact_pheno",
+                "exact_dia",
+                "synopsis",
+                "panel",
+                "status",
+                "tags",
+                "track",
+                "pheno_group",
+                "cohort",
+                "pinned",
+                "causative",
+                "user",
+                "similar_case",  # In order to be able to sort results by phenotype similarity, keep this at the bottom
+                "similar_pheno",  # In order to be able to sort results by phenotype similarity, keep this at the bottom
+            ]:
+                query_value = name_query.get(query_field)
+                if query_value not in ["", None]:
+                    set_case_item_query(
+                        query=query, query_field=query_field, query_value=query_value.strip()
+                    )
 
     def _update_case_id_query(self, query, id_list):
         """Update a case query ["_id"]["$in"] values using an additional list of case _ids
@@ -300,6 +349,7 @@ class CaseHandler(object):
             query["_id"]["$in"] = list(
                 set(preselected_ids).intersection(set(id_list))
             )  # limit also by case _ids present in id_list
+
         else:  # use id_list for filtering
             query["_id"] = {"$in": id_list}
 
@@ -380,7 +430,6 @@ class CaseHandler(object):
                 query[set_key] = set_value
 
         query = query or {}
-        order = None
         # Prioritize when both owner and collaborator params are present
         if collaborator and owner:
             collaborator = None
@@ -398,14 +447,14 @@ class CaseHandler(object):
             query=query,
             condition=skip_assigned,
             set_key="assignees",
-            set_value={"$exists": False},
+            set_value={EXISTS: False},
         )
 
         _conditional_set_query_value(
             query=query,
             condition=has_causatives,
             set_key="causatives",
-            set_value={"$exists": True, "$ne": []},
+            set_value={EXISTS: True, "$ne": []},
         )
 
         _conditional_set_query_value(
@@ -441,28 +490,28 @@ class CaseHandler(object):
             query=query,
             condition=is_research,
             set_key="is_research",
-            set_value={"$exists": True, "$eq": True},
+            set_value={EXISTS: True, "$eq": True},
         )
 
         _conditional_set_query_value(
             query=query,
             condition=phenotype_terms,
             set_key="phenotype_terms",
-            set_value={"$exists": True, "$ne": []},
+            set_value={EXISTS: True, "$ne": []},
         )
 
         _conditional_set_query_value(
             query=query,
             condition=pinned,
             set_key="suspects",
-            set_value={"$exists": True, "$ne": []},
+            set_value={EXISTS: True, "$ne": []},
         )
 
         _conditional_set_query_value(
             query=query,
             condition=cohort,
             set_key="cohorts",
-            set_value={"$exists": True, "$ne": []},
+            set_value={EXISTS: True, "$ne": []},
         )
 
         _conditional_set_query_value(
@@ -478,7 +527,7 @@ class CaseHandler(object):
 
         if name_query:
             # Case search filter form query
-            order = self._populate_name_query(query, name_query, owner, collaborator)
+            self.populate_case_query(query, name_query, owner, collaborator)
 
         if within_days:
             query["_id"] = {
@@ -507,11 +556,23 @@ class CaseHandler(object):
         if yield_query:
             return query
 
-        if order:
-            return self.case_collection.find(query, projection)
+        if name_query and self.is_pheno_similarity_query(name_query):
+            result_order: list = query["_id"]["$in"]
+            results = self.case_collection.find(query, projection)
+            # Return the result in order of descending phenotype similarity (the same order or the _ids provided in the query)
+            return sorted(list(results), key=lambda res: result_order.index(res["_id"]))
 
         return self.case_collection.find(query, projection).sort("updated_at", -1)
 
+    def is_pheno_similarity_query(self, name_query: Union[str, ImmutableMultiDict]) -> bool:
+        """Return True if the user query contains 'similar_case' or 'similar_pheno' fields."""
+        similar_pheno_keys = ["similar_case", "similar_pheno"]
+
+        if isinstance(name_query, str):
+            return any(key in name_query for key in similar_pheno_keys)
+
+        return any(name_query.get(key) not in [None, ""] for key in similar_pheno_keys)
+
     def rna_cases(self, owner):
         """Retrieve all cases with RNA-seq data for a given institute
 
@@ -521,7 +582,7 @@ class CaseHandler(object):
         Returns:
             list of case _ids
         """
-        EXISTS_NOT_NULL = {"$exists": True, "$nin": [None, ""]}
+        EXISTS_NOT_NULL = {EXISTS: True, "$nin": [None, ""]}
         query = {
             "owner": owner,
             "$or": [
@@ -1001,6 +1062,7 @@ class CaseHandler(object):
             - gene_fusion_report_research: path to the research gene fusions report
             - genome_build: If there is a new genome build
             - has_meivariants: If there are new mei variants
+            - has_outliers: If there are new outlier variants
             - has_strvariants: If there are new strvariants
             - has_svvariants: If there are new svvariants
             - individuals: There could be new individuals
@@ -1008,16 +1070,19 @@ class CaseHandler(object):
             - madeline_info: If there is a new pedigree
             - mme_submission: If case was submitted to MatchMaker Exchange
             - multiqc: If there's an updated multiqc report location
+            - omics_files: If there are updated OMICS files
             - panels: The new gene panels are added
             - pipeline_version: path to the pipeline executable version report file
             - rank_model_version: If there is a new rank model
             - reference_info: path to the pipeline reference version report file
             - rerun_requested: Is set to False since that is probably what happened
             - research_requested: Boolean, if research variants where requested for this case
+            - rna_genome_build: If there is a new RNA genome build ("37" or "38")
             - RNAfusion_inspector: path to the RNA fusion inspector report
             - RNAfusion_inspector_research: path to the research RNA fusion inspector report
             - RNAfusion_report: path to the RNA fusion report
             - RNAfusion_report_research: path to the research RNA fusion report
+            - rna_delivery_report: path to the RNA delivery report
             - smn_tsv: path to static SMN TSV file
             - status: case status
             - sv_rank_model_version: If there is a new sv rank model
@@ -1086,10 +1151,12 @@ class CaseHandler(object):
                 "rerun_requested": case_obj.get("rerun_requested", False),
                 "research_requested": case_obj.get("research_requested", False),
                 "reference_info": case_obj.get("reference_info"),
+                "rna_genome_build": case_obj.get("rna_genome_build"),
                 "RNAfusion_inspector": case_obj.get("RNAfusion_inspector"),
                 "RNAfusion_inspector_research": case_obj.get("RNAfusion_inspector_research"),
                 "RNAfusion_report": case_obj.get("RNAfusion_report"),
                 "RNAfusion_report_research": case_obj.get("RNAfusion_report_research"),
+                "rna_delivery_report": case_obj.get("rna_delivery_report"),
                 "smn_tsv": case_obj.get("smn_tsv"),
                 "status": case_obj.get("status"),
                 "sv_rank_model_version": case_obj.get("sv_rank_model_version"),
@@ -1138,6 +1205,7 @@ class CaseHandler(object):
             "RNAfusion_inspector_research",
             "RNAfusion_report",
             "RNAfusion_report_research",
+            "rna_delivery_report",
             "smn_tsv",
             "sv_rank_model_version",
         ]:

scout/adapter/mongo/omics_variant.py

@@ -9,6 +9,25 @@ LOG = logging.getLogger(__name__)
 
 
 class OmicsVariantHandler:
+
+    def delete_omics_variants_by_category(self, case_id: str, variant_type: str, category: str):
+        """Delete all OMICS variants for a case, given case, variant_type and category."""
+
+        LOG.info(
+            "Deleting old %s %s OMICS variants.",
+            variant_type,
+            category,
+        )
+
+        query = {
+            "case_id": case_id,
+            "variant_type": variant_type,
+            "category": category,
+        }
+        result = self.omics_variant_collection.delete_many(query)
+
+        LOG.info("%s variants deleted", result.deleted_count)
+
     def delete_omics_variants(self, case_id: str, file_type: str):
         """Delete OMICS variants for a case"""
         omics_file_type = OMICS_FILE_TYPE_MAP.get(file_type)

scout/build/case.py

@@ -289,6 +289,7 @@ def build_case(case_data, adapter):
     case_obj["vcf_files"] = case_data.get("vcf_files", {})
     case_obj["omics_files"] = case_data.get("omics_files", {})
     case_obj["delivery_report"] = case_data.get("delivery_report")
+    case_obj["rna_delivery_report"] = case_data.get("rna_delivery_report")
 
     _populate_pipeline_info(case_obj, case_data)