Feature/areg 126

applications/portal/backend/api/mappers/antibody_mapper.py

@@ -22,10 +22,11 @@
 def extract_base_url(url):
     return urlsplit(url).hostname
 
-@cache
+
 def get_vendor_domains(vendor_id):
-    return [vd.base_url for vd in VendorDomain.objects.filter(
-                        vendor_id=vendor_id)]
+    return [vd.base_url for vd in VendorDomain.objects.filter(vendor_id=vendor_id, status=STATUS.CURATED)]
+
+
 class AntibodyMapper(IDAOMapper):
 
     def from_dto(self, dto: AntibodyDTO) -> Antibody:
@@ -128,8 +129,7 @@ def to_dto(self, dao: Antibody) -> AntibodyDTO:
             ab.sourceOrganism = dao.source_organism.name
         if dao.species and not ab.targetSpecies:
             ab.targetSpecies = [s.name for s in dao.species.all()]
-
-
+
         ab.url = get_url_if_permitted(dao)
 
         ab.showLink = dao.show_link if dao.show_link is not None else (dao.vendor and dao.vendor.show_link)

applications/portal/backend/api/models.py

@@ -277,7 +277,7 @@ def import_save(self):
         if first_save:
             super().save()
             self._handle_duplicates()
-        
+
         if self.catalog_num:
             self.catalog_num_search = catalog_number_chunked(self.catalog_num, self.cat_alt)
 
@@ -312,13 +312,11 @@ def save(self, *args, update_search=True, **kwargs):
         if update_search and self.status == STATUS.CURATED:
             refresh_search_view()
 
-
     def _has_target_species_raw_changed(self, old_instance):
         if old_instance:
             return self.target_species_raw != old_instance.target_species_raw
         return self.target_species_raw is not None
 
-
     def delete(self, *args, **kwargs):
         super(Antibody, self).delete(*args, **kwargs)
         if self.status == STATUS.CURATED:
@@ -400,10 +398,6 @@ def _synchronize_target_species(self, old_species):
 
         self._fill_target_species_raw_from_species()
 
-
-
-
-
     def _target_species_from_raw(self):
         species = []
         if self.target_species_raw:
@@ -439,70 +433,68 @@ def get_duplicate(self) -> Optional['Antibody']:
             return duplicate_antibodies[0]
         return None
 
-    def set_vendor_from_name_url(self, url, name=None):
-        """
-        Sets vendor from name and url.
-
-        if the name exists:
-            if the url exists:
-                return existing vendor
-            else:
-                create new vendor domain and associate to existing vendor
+    @staticmethod
+    def get_alt_url_with_and_without_www(url):
+        if "www." in url:
+            alt_url = url.replace("www.", "")
         else:
-            if the url exists:
-                try to guess a vendor just by the url and add a vendor synonym
-            else if the url doesn't exist:
-                create a new vendor with the name from url
-            else:
-                do nothing
-        """
+            alt_url = "www." + url
+        return alt_url
 
-        base_url = url and extract_base_url(url)
+    def check_vendor_name_or_create(self, name, base_url):
         try:
-            # First, try to match by exact name
             vendor = Vendor.objects.get(name__iexact=name or base_url)
-            self.vendor = vendor
-            if base_url:
-                self.add_vendor_domain(base_url, vendor)
         except Vendor.MultipleObjectsReturned:
             log.exception("Multiple vendors with name %s", name)
-            vendor = self.vendor = Vendor.objects.filter(name__iexact=name or base_url)[0]
-            if base_url:
-                self.add_vendor_domain(base_url, vendor)
+            vendor = Vendor.objects.filter(name__iexact=name)[0]
         except Vendor.DoesNotExist:
-            # Then, try to match by domain
-
-            vds = VendorDomain.objects.filter(base_url__iexact=base_url, status=STATUS.CURATED)
-            if len(vds) == 0:
-                # If the domain is not matched, try to match by domain with and without www
-
-                if "www." in base_url:
-                    alt_base_url = base_url.replace("www.", "")
-                else:
-                    alt_base_url = "www." + base_url
-                vds = VendorDomain.objects.filter(base_url__iexact=alt_base_url, status=STATUS.CURATED)
-
-                if len(vds) == 0:
-                    # As it doesn't match, create a new vendor
-                    vendor_name = name or base_url
-                    log.info("Creating new Vendor `%s` on domain  to `%s`",
-                             vendor_name, base_url)
-                    vendor = Vendor(name=vendor_name,
-                                    commercial_type=self.commercial_type)
-                    vendor.save()
-                    self.vendor = vendor
-                    if base_url:
-                        self.add_vendor_domain(base_url, vendor)
-                    return
-
-
-            # Vendor domain matched one way or the other, so associate to existing vendor
-            if len(vds) > 1:
-                log.error("Unexpectedly found multiple vendor domains for %s", base_url)
-
-            self.vendor = vds[0].vendor
-            if name:
-                VendorSynonym.objects.create(vendor=self.vendor, name=name)
+            if not self.vendor:  ## if vendor is not set by vendor domain
+                vendor_name = name or base_url
+                log.info(
+                    "Creating new Vendor `%s` on domain  to `%s`", vendor_name, base_url
+                )
+                vendor = Vendor(name=vendor_name, commercial_type=self.commercial_type)
+                vendor.save()
+                self.vendor = vendor
+                self.add_vendor_domain(base_url, vendor)
+            return
+
+        if not self.vendor:
+            self.vendor = vendor
+            self.add_vendor_domain(base_url, vendor)
+
+    def set_vendor_from_name_url(self, url, name=None):
+        """
+        If a new antibody is submitted with some vendor name and URL
+        should be treated with following rules:
+        - If both domain and vendor name are not recognized,
+            a new vendor is created and the new domain is attached to the vendor.
+        - If both domain and vendor name are recognized,
+            the domain is prioritized. And vendor name is added as a synonym.
+        - If the domain is not recognized but vendor name is recognized,
+            the new domain is attached to the vendor recognized.
+        - If domain is recognized and vendor name is not recognized,
+            we add a vendor synonym
+        """
+
+        base_url = url and extract_base_url(url)
+        vds = VendorDomain.objects.filter(
+            base_url__iexact=base_url, status=STATUS.CURATED
+        )
+        alt_url = self.get_alt_url_with_and_without_www(url=base_url)
+        vds_alt = VendorDomain.objects.filter(
+            base_url__iexact=alt_url, status=STATUS.CURATED
+        )
+        vds_total = vds.union(vds_alt)
+
+        self.vendor = vds_total[0].vendor if len(vds_total) > 0 else None
+
+        self.check_vendor_name_or_create(name, base_url)
+        if len(vds_total) > 1:
+            log.error("Unexpectedly found multiple vendor domains for %s", base_url)
+
+        if len(vds_total) >= 1 and name:
+            VendorSynonym.objects.create(vendor=self.vendor, name=name)
 
     def add_vendor_domain(self, base_url, vendor):
         try:

applications/portal/backend/api/services/antibody_service.py

@@ -46,6 +46,9 @@ def create_antibody(body: AddAntibodyDTO, userid: str) -> AntibodyDTO:
     antibody.uid = userid
     antibody.save()
 
+    if antibody.get_duplicate():
+        raise DuplicatedAntibody(antibody_mapper.to_dto(antibody))
+
     return antibody_mapper.to_dto(antibody)
 
 
@@ -61,7 +64,12 @@ def get_antibody(antibody_id: int, status=STATUS.CURATED, filters=None) -> List[
 
 def get_antibody_by_accession(accession: int) -> List[AntibodyDTO]:
     try:
-        return antibody_mapper.to_dto(Antibody.objects.get(accession=accession).select_related("vendor", "source_organism").prefetch_related("species").prefetch_related("applications"))
+        return antibody_mapper.to_dto(
+            Antibody.objects.select_related("vendor", "source_organism")
+            .prefetch_related("species")
+            .prefetch_related("applications")
+            .get(accession=accession)
+        )
     except Antibody.DoesNotExist:
         raise
     except Antibody.MultipleObjectsReturned: