Merge branch 'master' of https://github.com/wormbase/wormbase_rest

WormBase · May 9, 2019 · 06e3593 · 06e3593
2 parents 21dd5ca + 59cc313
commit 06e3593
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Showing 11 changed files with 242 additions and 170 deletions.
diff --git a/src/rest_api/classes/cds.clj b/src/rest_api/classes/cds.clj
@@ -16,7 +16,7 @@
    {:overview overview/widget
     :location location/widget
     :feature feature/widget
-    ;:sequences sequences/widget
+    :sequences sequences/widget
     :reagents reagents/widget
     :external_links external-links/widget
     :references references/widget}

diff --git a/src/rest_api/classes/cds/widgets/overview.clj b/src/rest_api/classes/cds/widgets/overview.clj
@@ -7,7 +7,6 @@
 
 (defn description [cds]
   {:data (:cds.detailed-description/text (first (:cds/detailed-description cds)))
-   :d (:db/id cds)
    :description (str "description of the CDS " (:cds/id cds))})
 
 (defn partial-field [cds]

diff --git a/src/rest_api/classes/cds/widgets/sequences.clj b/src/rest_api/classes/cds/widgets/sequences.clj
@@ -7,21 +7,15 @@
     [rest-api.classes.generic-functions :as generic-functions]
     [rest-api.formatters.object :as obj :refer [pack-obj]]))
 
-(defn unspliced-sequence-context [c]
-  {:data (when-let [transcript  (-> c
+(defn cds-sequence [c]
+  {:data (when-let [transcript  (or
+                                 (-> c
                                     :transcript.corresponding-cds/_cds
                                     first
-                                    :transcript/_corresponding-cds)]
-          (sequence-fns/transcript-sequence-features transcript 0 "unspliced"))
-   :description "the unpliced sequence of the sequence"})
-
-(defn spliced-sequence-context [c]
-  {:data (when-let [transcript  (-> c
-                                    :transcript.corresponding-cds/_cds
-                                    first
-                                    :transcript/_corresponding-cds)]
-          (sequence-fns/transcript-sequence-features transcript 0 "spliced"))
-   :description "the unpliced sequence of the sequence"})
+                                    :transcript/_corresponding-cds)
+                                 c)]
+          (sequence-fns/transcript-sequence-features transcript 0 :cds))
+   :description "the spliced sequence of the transcripts without UTR"})
 
 (defn protein-sequence [c]
   {:data (when-let [peptide (some->> (:cds/corresponding-protein c)
@@ -46,9 +40,6 @@
 
 (def widget
   {:name generic/name-field
-   :predicted_exon_structure generic/predicted-exon-structure
    :print_blast print-blast
    :protein_sequence protein-sequence
-   :predicted_unit generic/predicted-units
-   :unspliced_sequence_context unspliced-sequence-context
-   :spliced_sequence_context spliced-sequence-context})
+   :cds_sequence cds-sequence})
diff --git a/src/rest_api/classes/generic_fields.clj b/src/rest_api/classes/generic_fields.clj
@@ -89,9 +89,7 @@
                                  [(some->> (:cds.corresponding-protein/_protein object)
                                            (map :cds/_corresponding-protein)
                                            (filter #(not= "history" (:method/id (:locatable/method %))))
-                                           (map :gene.corresponding-cds/_cds)
-                                           first
-                                           (map :gene/_corresponding-cds))
+                                           first)
                                   "gene"]
 
                                  :else
@@ -535,19 +533,33 @@
                                  (corresponding-all-gene gene object role nil))))
 
                  "cds"
-                 (when-let [ths (:transcript.corresponding-cds/_cds object)]
-                   (let [genes
-                         (distinct
-                           (flatten
-                             (for [th ths
-                                   :let [ghs (:gene.corresponding-transcript/_transcript
-                                               (:transcript/_corresponding-cds th))]]
-                               (for [gh ghs
-                                     :let [gene (:gene/_corresponding-transcript gh)]]
-                                 gene))))]
-                     (flatten
-                       (for [gene genes]
-                         (corresponding-all-gene gene object role nil)))))
+                 (or
+                   (when-let [ths (:transcript.corresponding-cds/_cds object)]
+                     (let [genes
+                           (distinct
+                             (flatten
+                               (for [th ths
+                                     :let [ghs (:gene.corresponding-transcript/_transcript
+                                                 (:transcript/_corresponding-cds th))]]
+                                 (for [gh ghs
+                                       :let [gene (:gene/_corresponding-transcript gh)]]
+                                   gene))))]
+                       (flatten
+                         (for [gene genes]
+                           (corresponding-all-gene gene object role nil)))))
+                   (when-let [ths (:transposon.corresponding-cds/_cds object)]
+                     (let [genes
+                           (distinct
+                             (flatten
+                               (for [th ths
+                                     :let [ghs (:gene.corresponding-transposon/_transposon
+                                                 (:transposon/_corresponding-cds th))]]
+                                 (for [gh ghs
+                                       :let [gene (:gene/_corresponding-transposon gh)]]
+                                   gene))))]
+                       (flatten
+                         (for [gene genes]
+                           (corresponding-all-gene gene object role nil))))))
 
                  "protein" ;; need to make it filter for only the row with the protein
                  (when-let [cdshs (:cds.corresponding-protein/_protein object)]

diff --git a/src/rest_api/classes/pseudogene.clj b/src/rest_api/classes/pseudogene.clj
@@ -17,7 +17,7 @@
     :feature feature/widget
     :genetics genetics/widget
     :reagents reagents/widget
-    ;:sequences sequences/widget
+    :sequences sequences/widget
     :expression expression/widget
     :location location/widget
     }

diff --git a/src/rest_api/classes/pseudogene/widgets/sequences.clj b/src/rest_api/classes/pseudogene/widgets/sequences.clj
@@ -12,7 +12,7 @@
            (name strand-kw))
    :description "strand orientation of the sequence"})
 
-(defn print-sequence [p]
+(defn sequence-context [p]
   {:data (when-let [refseqobj (sequence-fns/genomic-obj p)]
            (when-let [dna-sequence (sequence-fns/get-sequence refseqobj)]
              (let [strand (if-let [strand-kw (:locatable/strand p)]
@@ -36,4 +36,4 @@
   {:name generic/name-field
    :predicted_exon_structure generic/predicted-exon-structure
    :strand strand
-   :print_sequence print-sequence})
+   :sequence_context sequence-context})