Merge oncokb-curation feature branch into master

[calvinlu3]

No description provided.

[calvinlu3]

Issue list:

• We need to pass in Pageable to getAllGenes endpoint, but oncokb-core does not have spring-data dependency

• Solution 1: Add spring-boot-starter-data-jpa dependency to the core. A drawback of this approach is that our spring version is very old, so we need to use an older version of spring-data that is compatible. In older version of spring-data, the method Pageable.unpaged() is not available, so we need to use new PageRequest(0, Integer.MAX_VALUE) to get all genes.

• Solution 2 ✔️ : Use the org.oncokb.oncokb_curation.client.Pageable in the java client and manually set the Page fields.

org.oncokb.oncokb_curation.client.Pageable pageable = new org.oncokb.oncokb_curation.client.Pageable();
pageable.setPage(0);
pageable.setSize(Integer.MAX_VALUE);

---

• In Gene model, we are applying @JsonIgnore annotation to the ensemblGenes field. As a result, this field is not included in our java client generated model.

Usages:

1. In oncokb-core, we are using this field in genomicLocationShouldBeAnnotated(...) method to determine if a GL/HGVSg should be annoated by GenomeNexus.
2. We are also using this field in PrivateUtilsApi.utilsEnsemblGenesGet(...) to get ensemble genes from entrez gene id. This is used in the AnnotationPage in oncokb-public.

• Solution 1: Remove @JsonIgnore, so that ensemblGenes can be pulled from the Gene entity.
• Solution 2 ✔️: Keep annotation, but provide and endpoint in EnsembleGeneResource to fetch ensembl genes by gene id. With this approach, we also need to cache all ensemblGenes in oncokb-core and create a mapping with allTranscriptGenes to quickly fetch the ensembl gene.

---

• Missing properties in Gene schema produced by SpringDoc.

• Adding @JsonIgnoreProperties in EnsemblGene causes the Gene schema to not include "geneAliases", "ensemblGenes", "alterations"

@ManyToOne
@JsonIgnoreProperties(value = { "geneAliases", "ensemblGenes", "alterations" }, allowSetters = true)
private Gene gene;

Related issue from springdoc and it seems like a bug.

1. Increasing the springdoc version to 1.7.0 did not make a difference
2. Created a new JHipster project with the same JDL models.

• Interesting thing is that this new project does not have the same problem. The properties ignored in EnsemblGene does not affect the Gene schema.
• Replacing all the java models in oncokb-curation with the newly generated models from this test application did not resolve the issue either.