handle deprecations

src/vfbquery/term_info_queries.py

@@ -87,6 +87,11 @@ def get_types_str(self, show_types: bool) -> str:
     def return_type(self, type_list: List[str]) -> str:
         return " ".join([typ.replace("_", " ") for typ in type_list])
 
+    def is_deprecated(self) -> bool:
+        """True if this entity carries the 'Deprecated' tag (mirrors the
+        Neo4j :Deprecated label) in its types or unique_facets."""
+        return "Deprecated" in (self.types or []) or "Deprecated" in (self.unique_facets or [])
+
 
 @dataclass_json
 @dataclass
@@ -290,6 +295,11 @@ def link(self):
             return self.homepage
         return self.site.iri
 
+    def site_deprecated(self) -> bool:
+        """True if the cross-referenced site is deprecated; such xrefs must not
+        be turned into external links."""
+        return bool(self.site) and self.site.is_deprecated()
+
 
 @dataclass_json
 @dataclass
@@ -621,6 +631,9 @@ def get_xref_list(self):
         results = list()
         if self.xrefs:
             for xref in self.xrefs:
+                # never build a link to a deprecated site
+                if xref.site_deprecated():
+                    continue
                 results.append(xref.get_ext_link())
             # sort xrefs alphabetically (by site)
             results = sorted(results, key=lambda d: d['label'])
@@ -694,6 +707,9 @@ def get_thumbnail(self):
     def get_cluster_image(self):
         image_array = list()
         try:
+            # don't build an image URL from a deprecated site
+            if self.xrefs[0].site_deprecated():
+                return None
             image_array.append(self.get_image(self.xrefs[0].link_base + self.xrefs[0].accession + "/snapshot.png",
                                               self.term.core.label, self.term.core.short_form))
         except Exception as e:

src/vfbquery/vfb_connectivity.py

@@ -242,6 +242,8 @@ def _build_connectivity_cypher(upstream_id, downstream_id, weight,
         "-[r:synapsed_to]->"
         "(n2:Individual:Neuron:has_neuron_connectivity)-[:INSTANCEOF]->(c2)"
         f"\nWHERE r.weight[0] >= {weight}"
+        # deprecated neurons are obsolete and must not appear in connectivity
+        "\nAND NOT n1:Deprecated AND NOT n2:Deprecated"
     )
 
     # Database filtering
@@ -256,6 +258,10 @@ def _build_connectivity_cypher(upstream_id, downstream_id, weight,
 
     if not group_by_class:
         # Per-neuron results
+        # Show the source site + accession as plain text even when the site is
+        # deprecated (these columns are passed through to the results table and
+        # are not rendered as links downstream); deprecated *neurons* are still
+        # excluded above.
         clauses.append(
             "OPTIONAL MATCH (n1)-[r1:database_cross_reference]->"
             "(s1:Individual:Site {is_data_source:[True]})"
@@ -291,6 +297,8 @@ def _build_connectivity_cypher(upstream_id, downstream_id, weight,
         # Count total upstream neurons (with optional db filtering)
         total_match = (
             "MATCH (c1)<-[:INSTANCEOF]-(all_n1:Individual:has_neuron_connectivity)"
+            # keep the percent_connected denominator consistent: exclude deprecated neurons
+            "\nWHERE NOT all_n1:Deprecated"
         )
         if exclude_dbs:
             db_list = str(exclude_dbs)

src/vfbquery/vfb_queries.py

@@ -1345,6 +1345,9 @@ def term_info_parse_object(results, short_form):
             xrefs_out = []
             for x in vfbTerm.xrefs:
                 site = getattr(x, 'site', None)
+                # never build a link to a deprecated site
+                if site is not None and getattr(site, 'is_deprecated', None) and site.is_deprecated():
+                    continue
                 label = getattr(site, 'label', '') if site else ''
                 acc = x.accession if getattr(x, 'accession', None) and x.accession != "None" else ''
                 if acc:
@@ -2268,8 +2271,9 @@ def get_instances(short_form: str, return_dataframe=True, limit: int = -1):
                apoc.text.format("[%s](%s)",[i.label,i.short_form]) AS label,
                apoc.text.join(i.uniqueFacets, '|') AS tags,
                apoc.text.format("[%s](%s)",[p.label,p.short_form]) AS parent,
-               REPLACE(apoc.text.format("[%s](%s)",[site.label,site.short_form]), '[null](null)', '') AS source,
-               REPLACE(apoc.text.format("[%s](%s)",[rx.accession[0],site.link_base[0] + rx.accession[0]]), '[null](null)', '') AS source_id,
+               // Deprecated sites: show the source/accession text but no link.
+               CASE WHEN site:Deprecated THEN COALESCE(site.label,'') ELSE REPLACE(apoc.text.format("[%s](%s)",[site.label,site.short_form]), '[null](null)', '') END AS source,
+               CASE WHEN site:Deprecated THEN COALESCE(rx.accession[0],'') ELSE REPLACE(apoc.text.format("[%s](%s)",[rx.accession[0],site.link_base[0] + rx.accession[0]]), '[null](null)', '') END AS source_id,
                apoc.text.format("[%s](%s)",[CASE WHEN templ.symbol[0] <> '' THEN templ.symbol[0] ELSE templ.label END,templ.short_form]) AS template,
                apoc.text.format("[%s](%s)",[ds.label,ds.short_form]) AS dataset,
                REPLACE(apoc.text.format("[%s](%s)",[lic.label,lic.short_form]), '[null](null)', '') AS license,
@@ -2727,8 +2731,8 @@ def get_similar_neurons(neuron, similarity_score='NBLAST_score', return_datafram
             r.{similarity_score}[0] AS score,
             apoc.text.join(coalesce(n2.uniqueFacets, []), '|') AS tags,
             type,
-            REPLACE(apoc.text.format("[%s](%s)",[site.label,site.short_form]), '[null](null)', '') AS source,
-            REPLACE(apoc.text.format("[%s](%s)",[rx.accession[0], (site.link_base[0] + rx.accession[0])]), '[null](null)', '') AS source_id,
+            CASE WHEN site:Deprecated THEN COALESCE(site.label,'') ELSE REPLACE(apoc.text.format("[%s](%s)",[site.label,site.short_form]), '[null](null)', '') END AS source,
+            CASE WHEN site:Deprecated THEN COALESCE(rx.accession[0],'') ELSE REPLACE(apoc.text.format("[%s](%s)",[rx.accession[0], (site.link_base[0] + rx.accession[0])]), '[null](null)', '') END AS source_id,
             REPLACE(apoc.text.format("[%s](%s)",[CASE WHEN templ.symbol[0] <> '' THEN templ.symbol[0] ELSE templ.label END,templ.short_form]), '[null](null)', '') AS template,
             coalesce(technique.label, '') AS technique,
             REPLACE(apoc.text.format("[![%s](%s '%s')](%s)",[n2.label + " aligned to " + CASE WHEN templ.symbol[0] <> '' THEN templ.symbol[0] ELSE templ.label END, REPLACE(COALESCE(ri.thumbnail[0],""),"thumbnailT.png","thumbnail.png"), n2.label + " aligned to " + CASE WHEN templ.symbol[0] <> '' THEN templ.symbol[0] ELSE templ.label END, templ.short_form + "," + n2.short_form]), "[![null]( 'null')](null)", "") as thumbnail
@@ -4560,15 +4564,19 @@ def _owlery_query_to_results(owl_query_string: str, short_form: str, return_data
                         for xref in xrefs:
                             if xref.get('is_data_source', False):
                                 site_info = xref.get('site', {})
+                                # Deprecated sites: show the source/accession
+                                # text but never build a link to them.
+                                site_tags = (site_info.get('types') or []) + (site_info.get('unique_facets') or [])
+                                is_deprecated = 'Deprecated' in site_tags
                                 site_label = site_info.get('symbol') or site_info.get('label', '')
                                 site_short_form = site_info.get('short_form', '')
-                                if site_label and site_short_form:
-                                    source = f"[{site_label}]({site_short_form})"
-                                
+                                if site_label:
+                                    source = site_label if (is_deprecated or not site_short_form) else f"[{site_label}]({site_short_form})"
+
                                 accession = xref.get('accession', '')
                                 link_base = xref.get('link_base', '')
-                                if accession and link_base:
-                                    source_id = f"[{accession}]({link_base}{accession})"
+                                if accession:
+                                    source_id = accession if (is_deprecated or not link_base) else f"[{accession}]({link_base}{accession})"
                                 break
                     row['source'] = source
                     row['source_id'] = source_id