Fix InatObs#sequences bugs

- Stops this method from zapping `inat_obs_fields` - Refines condition for text :datatype sequences Text must start with 10 ACGT bases
MushroomObserver · Aug 5, 2024 · 4e8049c · 4e8049c
1 parent 9c850c9
commit 4e8049c
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Showing 2 changed files with 31 additions and 33 deletions.
diff --git a/app/classes/inat_obs.rb b/app/classes/inat_obs.rb
@@ -222,9 +222,7 @@ def lng
   end
 
   def sequences
-    obs_sequence_fields =
-      inat_obs_fields.keep_if { |f| sequence_field?(f) }
-
+    obs_sequence_fields = inat_obs_fields.select { |f| sequence_field?(f) }
     obs_sequence_fields.each_with_object([]) do |field, ary|
       # TODO: 2024-06-19 jdc. Need more investigation/test to handle
       # field[:value] blank or not a (pure) lists of bases
@@ -297,7 +295,7 @@ def description
 
   def sequence_field?(field)
     field[:datatype] == "dna" ||
-      field[:name] =~ /DNA/
+      field[:name] =~ /DNA/ && field[:value] =~ /^[ACTG]{,10}/
   end
 
   def fungi?

diff --git a/app/controllers/observations/inat_imports_controller.rb b/app/controllers/observations/inat_imports_controller.rb
@@ -343,35 +343,6 @@ def adjust_consensus_name_naming
       end
     end
 
-    def add_inat_summmary_data(inat_obs)
-      params = {
-        target: @observation,
-        summary: "#{:inat_data_comment.t} #{@observation.created_at}",
-        comment: comment(inat_obs),
-        user: inat_manager
-      }
-
-      Comment.create(params)
-    end
-
-    def comment(inat_obs)
-      <<~COMMENT.gsub(/^\s+/, "")
-        #{:USER.t}: #{inat_obs.inat_user_login}
-        #{:OBSERVED.t}: #{inat_obs.when}\n
-        #{:LAT_LON.t}: #{lat_lon_accuracy(inat_obs)}\n
-        #{:PLACE.t}: #{inat_obs.inat_place_guess}\n
-        #{:ID.t}: #{inat_obs.inat_taxon_name}\n
-        #{:DQA.t}: #{inat_obs.dqa}\n
-        #{:ANNOTATIONS.t}: #{:UNDER_DEVELOPMENT.t}\n
-        #{:PROJECTS.t}: #{inat_obs.inat_project_names}\n
-        #{:SEQUENCES.t}: #{:UNDER_DEVELOPMENT.t}\n
-        #{:OBSERVATION_FIELDS.t}: \n\
-
-        #{obs_fields(inat_obs.inat_obs_fields)}\n
-        #{:TAGS.t}: #{inat_obs.inat_tags.join(" ")}\n
-      COMMENT
-    end
-
     def lat_lon_accuracy(inat_obs)
       "#{inat_obs.inat_location} " \
       "+/-#{inat_obs.inat_public_positional_accuracy} m"
@@ -402,5 +373,34 @@ def obs_fields(fields)
         "&nbsp;&nbsp;#{field[:name]}: #{field[:value]}"
       end.join("\n")
     end
+
+    def add_inat_summmary_data(inat_obs)
+      params = {
+        target: @observation,
+        summary: "#{:inat_data_comment.t} #{@observation.created_at}",
+        comment: comment(inat_obs),
+        user: inat_manager
+      }
+
+      Comment.create(params)
+    end
+
+    def comment(inat_obs)
+      <<~COMMENT.gsub(/^\s+/, "")
+        #{:USER.t}: #{inat_obs.inat_user_login}
+        #{:OBSERVED.t}: #{inat_obs.when}\n
+        #{:LAT_LON.t}: #{lat_lon_accuracy(inat_obs)}\n
+        #{:PLACE.t}: #{inat_obs.inat_place_guess}\n
+        #{:ID.t}: #{inat_obs.inat_taxon_name}\n
+        #{:DQA.t}: #{inat_obs.dqa}\n
+        #{:ANNOTATIONS.t}: #{:UNDER_DEVELOPMENT.t}\n
+        #{:PROJECTS.t}: #{inat_obs.inat_project_names}\n
+        #{:SEQUENCES.t}: #{:UNDER_DEVELOPMENT.t}\n
+        #{:OBSERVATION_FIELDS.t}: \n\
+
+        #{obs_fields(inat_obs.inat_obs_fields)}\n
+        #{:TAGS.t}: #{inat_obs.inat_tags.join(" ")}\n
+      COMMENT
+    end
   end
 end