From fc6a6d424df71f2fe7af2e5b66c08f0fae3acaaf Mon Sep 17 00:00:00 2001
From: Manuel Luypaert <manuel.luypaert@wormbase.org>
Date: Thu, 9 Jul 2020 18:24:29 +0100
Subject: [PATCH] Added gene/{id}/update-other-names PUT and DELETE REST API
 endpoints to add/delete a set of other-names from a gene its other-names #304

---
 src/wormbase/names/entity.clj | 21 +++++++++++++++++++++
 src/wormbase/names/gene.clj   | 26 ++++++++++++++++++++++++++
 src/wormbase/specs/gene.clj   |  4 +++-
 3 files changed, 50 insertions(+), 1 deletion(-)

diff --git a/src/wormbase/names/entity.clj b/src/wormbase/names/entity.clj
index aa230afb..fa4f4e8a 100644
--- a/src/wormbase/names/entity.clj
+++ b/src/wormbase/names/entity.clj
@@ -195,6 +195,27 @@
                 (not-found
                  (format "%s '%s' does not exist" ent-ns (last lur)))))))))))
 
+(defn update-multi-card
+  [identify-fn uiident dt-transact-fn attr]
+  (fn handle-multi-card [request identifier]
+    (let [{conn :conn payload :body-params} request
+          ent-ns (namespace uiident)
+          data (some-> payload :data)
+          [lur entity] (identify-fn request identifier)]
+      (when (and entity data)
+        (let [build-tx (fn [id attr ^String val] (vec [dt-transact-fn id attr val]))
+              ;;retriev db-id to add values to
+              db-id (:db/id entity)
+              ;;build transaction statements to make
+              txes (map #(build-tx db-id attr %) data)
+              ;;transact data to datomic
+              tx-result @(d/transact-async conn txes)]
+          (when-let [db-after (:db-after tx-result)]
+            (if-let [updated (wdb/pull db-after [attr uiident] lur)]
+              (ok (or (attr updated) []))
+              (not-found
+               (format "%s '%s' does not exist" ent-ns (last lur))))))))))
+
 (defn status-changer
   "Return a handler to change the status of an entity to `to-status`.
 
diff --git a/src/wormbase/names/gene.clj b/src/wormbase/names/gene.clj
index 50640841..c116fb07 100644
--- a/src/wormbase/names/gene.clj
+++ b/src/wormbase/names/gene.clj
@@ -443,6 +443,32 @@
                            (nil? (:cgc-name data)))
                       (bad-request! {:message "CGC name cannot be removed from an uncloned gene."}))
                     (update-gene request identifier)))}})
+    (sweet/context "/update-other-names" []
+      (sweet/resource
+       {:put
+        {:summary "Add a set of other-names to a gene."
+         :x-name ::add-other-names-gene
+         :parameters {:body-params {:data ::wsg/update-other-names
+                                    :prov ::wsp/provenance}}
+         :responses (-> wnu/default-responses
+                        (dissoc conflict)
+                        (assoc bad-request {:schema ::wsv/error-response})
+                        (wnu/response-map))
+         :handler (fn [request]
+                    (let [add-other-names (wne/update-multi-card identify :gene/id :db/add ':gene/other-names)]
+                      (add-other-names request identifier)))}
+        :delete
+        {:summary "Delete a set of other-names from a gene."
+         :x-name ::delete-other-names-gene
+         :parameters {:body-params {:data ::wsg/update-other-names
+                                    :prov ::wsp/provenance}}
+         :responses (-> wnu/default-responses
+                        (dissoc conflict)
+                        (assoc bad-request {:schema ::wsv/error-response})
+                        (wnu/response-map))
+         :handler (fn [request]
+                    (let [delete-other-names (wne/update-multi-card identify :gene/id :db/retract ':gene/other-names)]
+                      (delete-other-names request identifier)))}}))
     (sweet/context "/merge/:from-identifier" [from-identifier]
       (sweet/resource
        {:post
diff --git a/src/wormbase/specs/gene.clj b/src/wormbase/specs/gene.clj
index 00f82553..7776a834 100644
--- a/src/wormbase/specs/gene.clj
+++ b/src/wormbase/specs/gene.clj
@@ -85,7 +85,6 @@
 
 (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)
@@ -94,6 +93,9 @@
 (s/def ::updated (stc/spec {:spec (s/keys :req-un [:gene/id])
                             :description "The response data from updating a Gene."}))
 
+(s/def ::update-other-names (stc/spec {:spec :gene/other-names
+                                        :description "A collection of other names."}))
+
 (s/def ::merge (stc/spec {:spec (s/keys :req-un [:gene/biotype])
                           :description "The data requried to update a Gene."}))