EVA-3475 - Release count endpoints v2 #177

tcezard · 2024-03-14T10:45:27Z

No description provided.

apriltuesday

I guess there's some updates to be made to support the lists of taxonomies/assemblies, but here are my comments on the rest (mostly naming things)

eva-release/src/main/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsv2Controller.java

eva-release/src/main/java/uk/ac/ebi/eva/release/dto/ReleaseStatsPerSpeciesV2Dto.java

eva-release/src/main/java/uk/ac/ebi/eva/release/models/ReleaseStatsView.java

apriltuesday · 2024-03-18T15:00:13Z

eva-release/src/main/java/uk/ac/ebi/eva/release/models/ReleaseStatsPerAssemblyView.java

+
+import org.hibernate.annotations.Type;
+
+import javax.persistence.*;


Should avoid wildcard imports

In case IntelliJ puts a wildcard when you format using the shortcut, you can change the default value in
File -> Settings -> Editor -> Code -Style -> Java -> Imports tab

Class count to use import with '*': Set this value to something like 50 (default is 5)

eva-release/src/main/java/uk/ac/ebi/eva/release/services/ReleaseStatsServicev2.java

eva-release/src/main/java/uk/ac/ebi/eva/release/dto/ReleaseStatsPerV2Dto.java

eva-release/src/main/java/uk/ac/ebi/eva/release/dto/ReleaseStatsPerAssemblyV2Dto.java

eva-release/src/main/java/uk/ac/ebi/eva/release/dto/ReleaseStatsPerV2Dto.java

nitin-ebi · 2024-03-20T14:53:22Z

eva-release/src/main/java/uk/ac/ebi/eva/release/dto/ReleaseStatsPerSpeciesV2Dto.java

+
+public class ReleaseStatsPerSpeciesV2Dto extends ReleaseStatsPerV2Dto {
+
+    @Id


Suggested change

@Id

nitin-ebi · 2024-03-20T14:54:12Z

eva-release/src/main/java/uk/ac/ebi/eva/release/dto/ReleaseStatsPerAssemblyV2Dto.java

+
+public class ReleaseStatsPerAssemblyV2Dto extends ReleaseStatsPerV2Dto {
+
+    @Id


Suggested change

@Id

nitin-ebi · 2024-03-20T14:54:26Z

eva-release/src/main/java/uk/ac/ebi/eva/release/dto/ReleaseStatsPerAssemblyV2Dto.java

+    @Id
+    private String assemblyAccession;
+
+    @Id


Suggested change

@Id

nitin-ebi · 2024-03-20T15:08:21Z

eva-release/src/main/java/uk/ac/ebi/eva/release/dto/ReleaseStatsPerV2Dto.java

+package uk.ac.ebi.eva.release.dto;
+
+import javax.persistence.Id;
+import java.util.Objects;


unused imports

nitin-ebi · 2024-03-20T15:45:39Z

eva-release/src/main/java/uk/ac/ebi/eva/release/models/ReleaseStatsPerAssemblyView.java

+    @Id
+    private String assemblyAccession;
+
+    private String rsType;


Suggested change

private String rsType;

@Id

private String rsType;

If you don't intend this to be part of ID, you should probably remove it from ReleaseStatsPerAssemblyViewPK as well

nitin-ebi · 2024-03-20T15:52:14Z

eva-release/src/main/java/uk/ac/ebi/eva/release/models/ReleaseStatsPerAssemblyView.java

+    private Long count;
+
+    @Column(name="new")
+    protected Long newAddition;


Suggested change

protected Long newAddition;

private Long newAddition;

nitin-ebi · 2024-03-20T16:02:49Z

eva-release/src/main/java/uk/ac/ebi/eva/release/models/ReleaseStatsPerTaxonomyView.java

+    private int taxonomyId;
+    @Id
+    private int releaseVersion;
+    private String rsType;


Suggested change

private String rsType;

@Id

private String rsType;

If you don't intend this to be part of ID, you should probably remove it from ReleaseStatsPerAssemblyView as well

nitin-ebi · 2024-03-20T16:03:59Z

eva-release/src/main/java/uk/ac/ebi/eva/release/models/ReleaseStatsPerTaxonomyView.java

+    private Long count;
+
+    @Column(name="new")
+    protected Long newAddition;


Suggested change

protected Long newAddition;

private Long newAddition;

nitin-ebi · 2024-03-21T06:49:45Z

eva-release/src/main/java/uk/ac/ebi/eva/release/services/ReleaseStatsServicev2.java

+            if (!keyToDto.containsKey(key)) {
+                keyToDto.put(key, new ReleaseStatsPerSpeciesV2Dto());
+            }
+            ReleaseStatsPerSpeciesV2Dto dto = keyToDto.get(key);


Suggested change

if (!keyToDto.containsKey(key)) {

keyToDto.put(key, new ReleaseStatsPerSpeciesV2Dto());

}

ReleaseStatsPerSpeciesV2Dto dto = keyToDto.get(key);

ReleaseStatsPerSpeciesV2Dto dto = keyToDto.computeIfAbsent(key, k -> new ReleaseStatsPerSpeciesV2Dto());

Optional

Change PK to be embeded to enable join with taxonomy Join with evapro.taxonomy to get scientific name and common name

Co-authored-by: April Shen <[email protected]>

tcezard · 2024-03-25T13:55:25Z

Please take a new look now that we're using the wide version of the aggregate table

apriltuesday · 2024-03-26T11:27:33Z

eva-release/src/main/java/uk/ac/ebi/eva/release/models/ReleaseStatsPerAssemblyV2.java

+import java.util.Objects;
+
+@Entity
+@IdClass(ReleaseStatsPerAssemblyV2PK.class)


Should this be an @EmbeddedId as in the taxonomy model? (I'm not sure I understand the reason to use one form vs. another, just wondering if they should be the same.)

I mostly copied the old data model way but it was incompatible with joining with Taxonomy which is why I switch it to using @EmbeddedId.
You're right though that we should keep them consistent so I updated this class to use @EmbeddedId as well.

eva-release/src/main/java/uk/ac/ebi/eva/release/mappers/ReleaseStatsPerAssemblyMapper.java

eva-release/src/main/java/uk/ac/ebi/eva/release/dto/ReleaseStatsV2Dto.java

nitin-ebi · 2024-03-26T09:30:23Z

eva-release/src/main/java/uk/ac/ebi/eva/release/mappers/ReleaseStatsMapperUtils.java

+        this.releaseInfoRepository = releaseInfoRepository;
+    }
+
+    public Map<Integer, String> getReleasesFtp() {


Since this is a util class, It will be better to have this as a method with a parameter (can also be static)

I think I was trying to find a way to provide the FTP as a singleton so that we're not making the same query to the database too many time.
There might be a better way of doing that.

eva-release/pom.xml

Co-authored-by: nitin-ebi <[email protected]> Co-authored-by: April Shen <[email protected]>

…dified

initial version of the v2 endpoints

b942d60

tcezard marked this pull request as draft March 14, 2024 10:45

tcezard marked this pull request as ready for review March 17, 2024 22:52

tcezard requested review from nitin-ebi and apriltuesday March 17, 2024 22:52

v2 endpoints for both Assembly and taxonomy

4f01662

tcezard force-pushed the EVA3475_release_count_v2 branch from 75ee6fa to 4f01662 Compare March 17, 2024 22:56

apriltuesday reviewed Mar 19, 2024

View reviewed changes

nitin-ebi approved these changes Mar 21, 2024

View reviewed changes

tcezard and others added 5 commits March 24, 2024 11:04

Support postgesql arrays

005f9c1

Change PK to be embeded to enable join with taxonomy Join with evapro.taxonomy to get scientific name and common name

Apply suggestions from code review

6e3325e

Co-authored-by: April Shen <[email protected]>

Address review comments

fe73193

Add release folder

3fdf00d

Switch to using the Wide version of the aggregate count table

21ab750

tcezard requested review from apriltuesday and nitin-ebi March 25, 2024 13:55

Fix endpoint with new RS

3c24d26

apriltuesday approved these changes Mar 26, 2024

View reviewed changes

nitin-ebi approved these changes Mar 26, 2024

View reviewed changes

tcezard and others added 4 commits March 27, 2024 10:47

Apply suggestions from code review

a2da081

Co-authored-by: nitin-ebi <[email protected]> Co-authored-by: April Shen <[email protected]>

Update the application.properties to ensure the Table will not get mo…

59f9dc0

…dified

Use EmbeddedId in ReleaseStatsPerAssemblyV2

cadf7d9

Provide releaseLink via join on the database

15c60e2

tcezard merged commit f384731 into EBIvariation:master Apr 9, 2024
1 check passed

tcezard self-assigned this Jun 28, 2024

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

EVA-3475 - Release count endpoints v2 #177

EVA-3475 - Release count endpoints v2 #177

tcezard commented Mar 14, 2024

apriltuesday left a comment

apriltuesday Mar 18, 2024

nitin-ebi Mar 20, 2024

nitin-ebi Mar 20, 2024

nitin-ebi Mar 20, 2024

nitin-ebi Mar 20, 2024

nitin-ebi Mar 20, 2024

nitin-ebi Mar 20, 2024

nitin-ebi Mar 20, 2024

nitin-ebi Mar 20, 2024

nitin-ebi Mar 20, 2024

nitin-ebi Mar 21, 2024

tcezard commented Mar 25, 2024

apriltuesday Mar 26, 2024

tcezard Mar 27, 2024

nitin-ebi Mar 26, 2024

tcezard Mar 27, 2024


		import org.hibernate.annotations.Type;

		import javax.persistence.*;


		public class ReleaseStatsPerSpeciesV2Dto extends ReleaseStatsPerV2Dto {

		@Id


		public class ReleaseStatsPerAssemblyV2Dto extends ReleaseStatsPerV2Dto {

		@Id

EVA-3475 - Release count endpoints v2 #177

EVA-3475 - Release count endpoints v2 #177

Conversation

tcezard commented Mar 14, 2024

apriltuesday left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

tcezard commented Mar 25, 2024

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment