demo-rfc80-poc branch has some issues with legacy functionality

[alisman]

I found this because a fair number of e2e tests are failing

https://app.circleci.com/pipelines/github/cBioPortal/cbioportal-frontend/14029/workflows/956c88e1-d402-4277-8db2-8b9ee60619d7/jobs/166171/tests

One example is failure of this endpoint. Need to figure out what we might have changed in rfc80 backend that would cause this. Hunch is that it has to do with configuration.

https://genie-public-beta.cbioportal.org/results/coexpression?cancer_study_list=prad_tcga_pan_can_atlas_2018&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Cgistic&case_set_id=prad_tcga_pan_can_atlas_2018_cnaseq&gene_list=CDKN2A%2520MDM2%2520MDM4%2520TP53&geneset_list=%20&tab_index=tab_visualize&Action=Submit

[alisman]

The following produces error

java.lang.IllegalStateException: A Cursor is already closed.

curl 'http://localhost:8082/api/molecular-profiles/co-expressions/fetch?molecularProfileIdA=coadread_tcga_pub_rna_seq_mrna&molecularProfileIdB=coadread_tcga_pub_rna_seq_mrna&threshold=0' \
  -H 'Accept: application/json' \
  -H 'Accept-Language: en-US,en;q=0.9' \
  -H 'Cache-Control: no-cache' \
  -H 'Connection: keep-alive' \
  -H 'Content-Type: application/json' \
  -H 'Cookie: _ga=GA1.1.1887007066.1710956751; _ga_5260NDGD6Z=GS1.1.1721930557.11.1.1721930574.0.0.0' \
  -H 'Origin: http://localhost:8082' \
  -H 'Pragma: no-cache' \
  -H 'Referer: http://localhost:8082/results/coexpression?cancer_study_list=coadread_tcga_pub&cancer_study_id=coadread_tcga_pub&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=coadread_tcga_pub_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=coadread_tcga_pub_gistic&Z_SCORE_THRESHOLD=2.0&case_set_id=coadread_tcga_pub_nonhypermut&gene_list=KRAS%20NRAS%20BRAF&gene_set_choice=user-defined-list' \
  -H 'Sec-Fetch-Dest: empty' \
  -H 'Sec-Fetch-Mode: cors' \
  -H 'Sec-Fetch-Site: same-origin' \
  -H 'User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/131.0.0.0 Safari/537.36' \
  -H 'sec-ch-ua: "Google Chrome";v="131", "Chromium";v="131", "Not_A Brand";v="24"' \
  -H 'sec-ch-ua-mobile: ?0' \
  -H 'sec-ch-ua-platform: "macOS"' \
  --data-raw '{"sampleListId":"coadread_tcga_pub_nonhypermut","entrezGeneId":3845}'

[alisman]

@haynescd best we can tell, this has to do with interaction between @transactional(readOnly=true) decorator and the new CustomDataSourceConfiguration. Various articles suggest that data source configuration needs to be set up to support transactions.

As the comments in our code suggest, there is some legit reason for using transactions for readonly operation. 🤷