ZFIN-9258 synchronize abbrev and name for transcripts (ZFIN#1121)

* ZFIN-9258 synchronize abbrev and name for transcripts * fix accessor for HTPDataset change * Update db.changelog.master.xml --------- Co-authored-by: Ryan Taylor <[email protected]>
rtaylorzfin · Aug 16, 2024 · 2560c08 · 2560c08
1 parent 4bd56bc
commit 2560c08
Show file tree

Hide file tree

Showing 6 changed files with 143 additions and 16 deletions.
diff --git a/source/org/zfin/db/postGmakePostloaddb/1160/ZFIN-9258.sql b/source/org/zfin/db/postGmakePostloaddb/1160/ZFIN-9258.sql
@@ -0,0 +1,90 @@
+--liquibase formatted sql
+--changeset cmpich:ZFIN-9258.sql
+
+insert into marker_history_reason
+VALUES ('Renamed to conform with Ensembl transcript nomenclature');
+insert into marker_history_reason
+VALUES ('Same transcript');
+
+
+select count(*)
+from marker
+where exists(select * from transcript where mrkr_zdb_id = tscript_mrkr_zdb_id and mrkr_abbrev != mrkr_name);
+
+CREATE TEMP TABLE marker_name_temp as
+select mrkr_zdb_id, mrkr_name, mrkr_abbrev
+from marker
+where exists(select * from transcript where mrkr_zdb_id = tscript_mrkr_zdb_id and mrkr_abbrev != mrkr_name);
+
+-- still problem transcript as they have a conflict when setting abbrev = name
+select *
+from marker as m
+where exists(
+        select * from marker_name_temp as mnt where mnt.mrkr_zdb_id = m.mrkr_zdb_id
+    )
+  and exists(select * from marker as m2 where m2.mrkr_abbrev = m.mrkr_name);
+
+-- remove conflicting records
+delete from marker_name_temp where
+        mrkr_zdb_id in ('ZDB-TSCRIPT-090929-18263', 'ZDB-TSCRIPT-090929-18262', 'ZDB-TSCRIPT-090929-3084', 'ZDB-TSCRIPT-090929-5042',
+                              'ZDB-TSCRIPT-090929-14197', 'ZDB-TSCRIPT-110325-1463');
+
+update marker as m
+set mrkr_abbrev = lower(mrkr_name),
+    mrkr_name   = lower(mrkr_name)
+where exists(
+        select * from marker_name_temp as mnt where mnt.mrkr_zdb_id = m.mrkr_zdb_id
+    );
+
+create temp table data_alias_temp as
+select * from data_alias where exists (
+                                       select * from marker_name_temp where mrkr_zdb_id = dalias_data_zdb_id and dalias_alias = mrkr_abbrev
+                                   );
+
+
+create temp table marker_alias_temp as
+select get_id('DALIAS') as id, mrkr_abbrev, mrkr_zdb_id
+from marker_name_temp;
+
+delete from marker_alias_temp as mat where
+    exists (
+            select * from data_alias where exists (
+                                                   select * from marker_name_temp as mn where mn.mrkr_zdb_id = dalias_data_zdb_id and dalias_alias = mrkr_abbrev
+                                                                                          and mat.mrkr_zdb_id = mn.mrkr_zdb_id
+                                               )
+        );
+
+insert into zdb_active_data
+select id from marker_alias_temp;
+
+insert into data_alias (dalias_zdb_id, dalias_data_zdb_id, dalias_alias, dalias_alias_lower, dalias_group_id)
+select id, mrkr_zdb_id, mrkr_abbrev, lower(mrkr_abbrev), 1
+from marker_alias_temp;
+
+insert into marker_alias_temp
+    select dalias_zdb_id, dalias_alias, dalias_data_zdb_id from data_alias_temp;
+
+create temp table id_temp as
+    select get_id('NOMEN') as id,
+           mrkr_zdb_id
+    from marker_name_temp;
+
+insert into zdb_active_data
+select id from id_temp;
+
+
+insert into marker_history (mhist_zdb_id, mhist_mrkr_zdb_id, mhist_event, mhist_reason, mhist_date,
+                            mhist_mrkr_prev_name, mhist_mrkr_abbrev_on_mhist_date, mhist_mrkr_name_on_mhist_date, mhist_dalias_zdb_id)
+select it.id,
+       mn.mrkr_zdb_id,
+       'reassigned',
+       'Renamed to conform with Ensembl transcript nomenclature',
+       now(),
+       mn.mrkr_abbrev,
+       mn.mrkr_name,
+       mn.mrkr_name,
+       mat.id
+from marker_name_temp as mn, id_temp as it, marker_alias_temp as mat
+where mn.mrkr_zdb_id = it.mrkr_zdb_id
+and mn.mrkr_zdb_id = mat.mrkr_zdb_id;
+
diff --git a/source/org/zfin/db/postGmakePostloaddb/1160/db.changelog.master.xml b/source/org/zfin/db/postGmakePostloaddb/1160/db.changelog.master.xml
@@ -5,6 +5,11 @@
         xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog
                       http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.1.xsd">
 
+
     <include file="source/org/zfin/db/postGmakePostloaddb/1160/ZFIN-9318.sql" />
 
+    <include file="source/org/zfin/db/postGmakePostloaddb/1160/ZFIN-9244.sql" />
+    <include file="source/org/zfin/db/postGmakePostloaddb/1160/ZFIN-9258.sql" />
+
+
 </databaseChangeLog>
diff --git a/source/org/zfin/marker/MarkerHistory.java b/source/org/zfin/marker/MarkerHistory.java
@@ -5,7 +5,9 @@
 import org.zfin.infrastructure.PublicationAttribution;
 
 import javax.persistence.*;
+import java.util.ArrayList;
 import java.util.Date;
+import java.util.List;
 import java.util.Set;
 
 @Entity
@@ -88,7 +90,10 @@ public enum Reason {
         RENAMED_TO_CONFORM_WITH_HUMAN_NOMENCLATURE("renamed to conform with human nomenclature"),
         RENAMED_TO_CONFORM_WITH_MOUSE_NOMENCLATURE("renamed to conform with mouse nomenclature"),
         RENAMED_TO_CONFORM_WITH_ZEBRAFISH_GUIDELINES("renamed to conform with zebrafish guidelines"),
-        SAME_MARKER("same marker");
+        SAME_MARKER("same marker"),
+        RENAMED_TO_CONFORM_WITH_ENSEMBL_TRANSCRIPT_NOMENCLATURE("Renamed to conform with Ensembl transcript nomenclature"),
+        SAME_TRANSCRIPT("same transcript");
+
 //        RENAMED_THROUGH_THE_NOMENCLATURE_PIPELINE("renamed through the nomenclature pipeline");
 
         private String value;
@@ -105,6 +110,33 @@ public static Reason getReason(String reasonValue) {
             return null;
         }
 
+        static List<Reason> transcriptReasons = new ArrayList<>();
+        static {
+            transcriptReasons.add(NOT_SPECIFIED);
+            transcriptReasons.add(PER_GENE_FAMILY_REVISION);
+            transcriptReasons.add(RENAMED_TO_CONFORM_WITH_ZEBRAFISH_GUIDELINES);
+            transcriptReasons.add(PER_PERSONAL_COMMUNICATION_WITH_AUTHORS);
+            transcriptReasons.add(RENAMED_TO_CONFORM_WITH_HUMAN_NOMENCLATURE);
+            transcriptReasons.add(RENAMED_TO_CONFORM_WITH_MOUSE_NOMENCLATURE);
+            transcriptReasons.add(SAME_MARKER);
+        }
+
+        static List<Reason> markerReasons = new ArrayList<>();
+        static {
+            markerReasons.add(NOT_SPECIFIED);
+            markerReasons.add(RENAMED_TO_CONFORM_WITH_ENSEMBL_TRANSCRIPT_NOMENCLATURE);
+            markerReasons.add(RENAMED_TO_CONFORM_WITH_ZEBRAFISH_GUIDELINES);
+            markerReasons.add(SAME_TRANSCRIPT);
+        }
+
+        public static List<Reason> getTranscriptReasons() {
+            return transcriptReasons;
+        }
+
+        public static List<Reason> getMarkerReasons() {
+            return markerReasons;
+        }
+
         public String toString() {
             return value;
         }
@@ -273,15 +305,12 @@ public void setOldMarkerName(String oldMarkerName) {
     }
 
     public String getOldSymbol() {
-        switch (event) {
-            case REASSIGNED:
-                return (markerAlias == null ? "" : markerAlias.getAlias());
-            case MERGED:
-                return (markerAlias == null ? "" : markerAlias.getAlias());
-            case RENAMED:
-                return oldMarkerName;
-        }
-        return "";
+        return switch (event) {
+            case REASSIGNED -> (markerAlias == null ? "" : markerAlias.getAlias());
+            case MERGED -> (markerAlias == null ? "" : markerAlias.getAlias());
+            case RENAMED -> oldMarkerName;
+            default -> "";
+        };
     }
 
     public String getNewValue() {

diff --git a/source/org/zfin/marker/agr/BasicRNASeqMetaDatasetInfo.java b/source/org/zfin/marker/agr/BasicRNASeqMetaDatasetInfo.java
@@ -81,7 +81,7 @@ public AllRNASeqMetaDatasetDTO getAllDatasetInfo() {
                                     datasetId.setPreferredCrossReference(preferredCrossReference);
 
                                 }
-                                datasetId.setSecondaryId(htpSecondaryIds);
+                                datasetId.setAlternateIds(htpSecondaryIds);
                             }
                             dto.setDatasetId(datasetId);
 

diff --git a/source/org/zfin/marker/agr/HtpIDDTO.java b/source/org/zfin/marker/agr/HtpIDDTO.java
@@ -15,7 +15,7 @@
 public class HtpIDDTO {
 
     private String primaryId;
-    private List<String> secondaryId;
+    private List<String> alternateIds;
     private List<CrossReferenceDTO> crossReferences;
     private CrossReferenceDTO preferredCrossReference;
 

diff --git a/source/org/zfin/marker/presentation/MarkerEditController.java b/source/org/zfin/marker/presentation/MarkerEditController.java
@@ -23,7 +23,10 @@
 import org.zfin.nomenclature.presentation.Nomenclature;
 import org.zfin.publication.Publication;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Locale;
+import java.util.Objects;
 
 import static org.zfin.repository.RepositoryFactory.getInfrastructureRepository;
 import static org.zfin.repository.RepositoryFactory.getPublicationRepository;
@@ -60,11 +63,11 @@ private Nomenclature getNomenclatureForMarker(Marker marker) {
         nomenclature.setReason("");
         nomenclature.setComments("");
         if (marker.getMarkerType().getType().equals(Marker.Type.TSCRIPT)) {
-            nomenclature.putMeta("reasons", Arrays.stream(MarkerHistory.TranscriptReason.values())
-                .map(MarkerHistory.TranscriptReason::toString)
+            nomenclature.putMeta("reasons", MarkerHistory.Reason.getTranscriptReasons().stream()
+                .map(MarkerHistory.Reason::toString)
                 .toArray());
         } else {
-            nomenclature.putMeta("reasons", Arrays.stream(MarkerHistory.Reason.values())
+            nomenclature.putMeta("reasons", MarkerHistory.Reason.getMarkerReasons().stream()
                 .map(MarkerHistory.Reason::toString)
                 .toArray());
         }