fixing 500 error caused when it is an insertion but we don't know the…

… inserted sequence
WormBase · Jun 13, 2019 · 736e1da · 736e1da
1 parent 64426dd
commit 736e1da
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Showing 2 changed files with 25 additions and 19 deletions.
diff --git a/src/rest_api/classes/pcr_oligo/widgets/sequence.clj b/src/rest_api/classes/pcr_oligo/widgets/sequence.clj
@@ -4,17 +4,19 @@
    [rest-api.classes.generic-fields :as generic]
    [rest-api.formatters.object :as obj :refer [pack-obj]]))
 
-; tested with WBPaper00006202_Y41D4B_1.1
 (defn segment [p]
-  {:data (when-let [refseqobj (sequence-fns/genomic-obj p)]
-	   (let [s (sequence-fns/get-sequence refseqobj)]
-	     {:dna s
-              :length (count s)
-              :start (:start refseqobj)
-              :stop (:stop refseqobj)
-              :end (:stop refseqobj)
-              :ref (:seqname refseqobj)
-              :refseq (:seqname refseqobj)}))
+  {:data (if (contains? p :oligo/id);e.g. OK2488_external_b
+           {:dna (:oligo/sequence p)
+            :length (:oligo/length p)}
+           (when-let [refseqobj (sequence-fns/genomic-obj p)] ;e.g. cenix:10-b12
+             (let [s (sequence-fns/get-sequence refseqobj)]
+               {:dna s
+                :length (count s)
+                :start (:start refseqobj)
+                :stop (:stop refseqobj)
+                :end (:stop refseqobj)
+                :ref (:seqname refseqobj)
+                :refseq (:seqname refseqobj)})))
    :description "Sequence/segment data about this PCR product"})
 
 (defn oligos [p]

diff --git a/src/rest_api/classes/variation/widgets/molecular_details.clj b/src/rest_api/classes/variation/widgets/molecular_details.clj
@@ -290,9 +290,11 @@
 
                  length-change (if-let [insertion (:variation/insertion variation)]
                                  (or (if-let [insertion-str (let [insertion (or (:variation.insertion/text insertion)
-                                                                                (:transposon-family/id
-                                                                                  (first
-                                                                                    (:variation/transposon-insertion variation))))]
+                                                                                (or
+                                                                                  (:transposon-family/id
+                                                                                    (first
+                                                                                      (:variation/transposon-insertion variation)))
+                                                                                  "-"))]
                                                               (if (= insertion "Mos") "<Mos>" insertion))]
                                        (if (contains? variation :variation/deletion)
                                          (- (count insertion-str)
@@ -415,12 +417,14 @@
                                       (contains? variation :variation/insertion)
                                       (let [insertion (:variation/insertion variation)
                                             insert-str (or (if-let [insert-value (:variation.insertion/text insertion)]
-                                                              (if (= strand "+")
-                                                                insert-value
-                                                                (generic-functions/dna-reverse-complement insert-value)))
-                                                           (:transposon-family/id
-                                                             (first
-                                                               (:variation/transposon-insertion variation))))]
+                                                             (if (= strand "+")
+                                                               insert-value
+                                                               (generic-functions/dna-reverse-complement insert-value)))
+                                                           (or
+                                                             (:transposon-family/id
+                                                               (first
+                                                                 (:variation/transposon-insertion variation)))
+                                                             "-"))]
                                         (str/replace
                                           (:sequence wildtype-positive)
                                           #"\-+"