better search for deleted terms

server/xpub-model/entities/manuscript/data-access.js

@@ -522,7 +522,7 @@ class Manuscript extends EpmcBaseModel {
     return manuscripts
   }
 
-  static async searchArticleIds(id, user, trx) {
+  static async searchArticleIds(id, user, excludeDeleted = true, trx) {
     const { isAdmin, manuscriptIds } = await Manuscript.isAdmin(user)
 
     const manuscripts = await Manuscript.query(trx)
@@ -535,6 +535,9 @@ class Manuscript extends EpmcBaseModel {
         if (!isAdmin) {
           q.whereIn('id', manuscriptIds)
         }
+        if (excludeDeleted) {
+          q.whereNull('deleted')
+        }
       })
       .eager('[journal, notes, organization]')
       .modifyEager('notes', builder => {

server/xpub-model/entities/manuscript/index.js

@@ -415,7 +415,7 @@ const Manuscript = {
     }
   },
 
-  findByArticleId: async (id, userId, ftp, trx) => {
+  findByArticleId: async (id, userId, ftp = false, trx) => {
     let manuscript = null
     if (id.toUpperCase().startsWith('EMS')) {
       manuscript = await ManuscriptAccess.selectById(id.toUpperCase(), trx)
@@ -425,6 +425,7 @@ const Manuscript = {
       const manuscripts = await ManuscriptAccess.searchArticleIds(
         searchId,
         userId,
+        ftp,
         trx,
       )
       manuscript = manuscripts.pop()