Added gene other-names support to DB scheme and /gene REST API patter…

…n search #304

resources/schema/definitions.edn

@@ -23,6 +23,9 @@
        :valueType :db.type/string
        :cardinality :db.cardinality/one
        :unique :db.unique/value}
+  #:db{:ident :gene/other-names
+       :valueType :db.type/string
+       :cardinality :db.cardinality/many}
   #:db{:ident :gene/status
        :valueType :db.type/ref
        :cardinality :db.cardinality/one}

src/wormbase/names/entity.clj

@@ -305,26 +305,16 @@
                  (count numbers))})))
 
 (defn build-find-query
-  [find-attrs unqualified-attrs rule-head]
+  [rule-head]
   ;; generated symbols are used to bind result variables in the datalog query.
   ;; this is done to avoid confusion with variable names used to bind
   ;; predicates.
-  (let [query-vars (repeatedly (count unqualified-attrs)
-                               (partial gensym "?"))
-        rule-clause (cons (symbol rule-head) '(?pattern ?name ?eid))
-        var->ident (zipmap query-vars find-attrs)
-        q-spec {:in '[$ % ?pattern]
-                :where
-                [rule-clause
-                 '[?eid ?id-ident ?id]]}
-        get-else-clauses (->> query-vars
-                              (map (fn [sym]
-                                     [(list 'get-else '$ '?eid (sym var->ident) "") sym]))
-                              (vec))]
-    (-> q-spec
-        (update :where (fn [clause]
-                         (concat clause get-else-clauses)))
-        (assoc :find query-vars :keys find-attrs))))
+  (let [rule-clause (cons (symbol rule-head) '(?pattern ?name ?eid))
+        q-spec {:find '[[?eid ...]]
+                :in '[$ % ?pattern]
+                :where [rule-clause
+                       '[?eid ?id-ident ?id]]}]
+    q-spec))
 
 (defn finder
   [entity-type unqualified-attrs]
@@ -336,9 +326,11 @@
               find-attrs (map (partial keyword entity-type) unqualified-attrs)
               rule-head (str entity-type "-name")
               matching-rules (wnm/make-rules rule-head find-attrs)
-              query (build-find-query find-attrs unqualified-attrs rule-head)
-              regexp-pattern (re-pattern (str "^" s-pattern))
-              q-result (d/q query db matching-rules regexp-pattern)
+              query (build-find-query rule-head)
+              matching-pattern (re-pattern (str "^" s-pattern))
+              pull-pattern (vec find-attrs)
+              q-ids (d/q query db matching-rules matching-pattern)
+              q-result (d/pull-many db pull-pattern q-ids)
               res {:matches (if (seq q-result)
                               (vec (map #(wnu/unqualify-keys % entity-type) q-result))
                               [])}]

src/wormbase/names/gene.clj

@@ -341,7 +341,7 @@
        :responses (wnu/http-responses-for-read {:schema ::wsg/find-result})
        :parameters {:query-params ::wsc/find-request}
        :x-name ::find-gene
-       :handler (wne/finder "gene" ["cgc-name" "sequence-name" "id"])}
+       :handler (wne/finder "gene" ["cgc-name" "sequence-name" "id" "other-names"])}
       :post
       {:summary "Create new names for a gene (cloned or un-cloned)"
        :x-name ::new-gene

src/wormbase/specs/gene.clj

@@ -12,6 +12,8 @@
 
 (s/def ::name (s/and string?))
 
+(s/def ::names-coll (s/coll-of ::name))
+
 (s/def :gene/id (stc/spec {:spec ::name
                            :swagger/example "WBGene00000421"
                            :description "The primary identifier of a Gene."}))
@@ -20,6 +22,10 @@
                                  :swagger/example "unc-22"
                                  :description "The CGC name."}))
 
+(s/def :gene/other-names (stc/spec {:spec (s/nilable ::names-coll)
+                                 :swagger/example "[\"UNCoordinated-22\", \"Other-name\"]"
+                                 :description "Alternative gene name(s)."}))
+
 (s/def :gene/sequence-name (stc/spec {:spec (s/nilable ::name)
                                       :swagger/example "AAH1.1"
                                       :description "The sequence name of the Gene."}))
@@ -77,6 +83,7 @@
 
 (s/def ::update (stc/spec {:spec (s/and (s/keys :opt-un [:gene/cgc-name
                                                          :gene/sequence-name
+                                                         :gene/other-names
                                                          :gene/biotype
                                                          :gene/species])
                                         seq)
@@ -166,7 +173,8 @@
 
 (s/def ::find-match (stc/spec {:spec (s/keys :req-un [:gene/id]
                                              :opt-un [:gene/cgc-name
-                                                      :gene/sequence-name])
+                                                      :gene/sequence-name
+                                                      :gene/other-names])
                                :description "A mappings describing a search result match."}))
 (s/def ::matches (stc/spec {:spec (s/coll-of ::find-match :kind vector?)
                             :description "A collection of search result matches."}))