🗃Update database source data to OpenPedCan-analysis v10 release

[logstar]

Description

Updated database building procedure to use OpenPedCan-analysis v10 release data.

Notes for reviewers:

(EDIT 10/12/2021 YZ)

• This PR will be merged around 1pm 10/13, with or without any approval, to test new v10 database in QA environment. FNL team will also need to review and test QA and PRD hosts for MVP1 (most viable product 1) demo on 11/09.
• This PR could not be prepared earlier, because it needs OpenPedCan-analysis v10 release to be merged into dev branch, which was committed around 7pm today, 10/11.
• A review can be added after this PR is merged.
• In the review, please only add comments or suggestions that are directly related code correctness or documentation readability.
• If there is any issue that may directly impact API HTTP connection or result correctness, please report here as soon as possible even without any full review or comprehensive issue analysis.

Related issues:

• 46

• 41

Type of change

• [x] Data model changes. HTTP API is not changed.

Incremented version number to v0.3.2-beta.

Changed

• Changed OpenPedCan-api database source data from OpenPedCan-analysis v9 release to v10 release.
• Updated OpenPedCan-analysis submodule to dev branch v10 release commit.
• Changed db/build_db.sh OPEN_PED_CAN_ANALYSIS_COMMIT from OpenPedCan-analysis dev branch v9 release commit to v10 release commit.
• Renamed OpenPedCan-api database "RMTL" column to "PMTL".
• Changed OpenPedCan-api database "cohort" column "all_cohorts" values to "All Cohorts".
• Renamed OpenPedCan-api database dump file from "postgres_db_open_ped_can_db_schema_bulk_expression.sql.gz" to "open_ped_can_db_postgres_pg_dump.sql.gz".
• Changed /tpm/gene-disease-gtex boxplot title from "Primary tumor and GTEx tissue bulk gene expression" to "Pediatric tumor and GTEx normal adult tissue gene expression".
• Changed /tpm/gene-all-cancer boxplot title from "Primary tumor tissue bulk gene expression" to "Pediatric tumor gene expression".

Added

• Add API_HOST=prd option in tests/curl_test_endpoints.sh to test production API site URL https://openpedcan-api.d3b.io.

How Has This Been Tested?

• [x] Integration test

**Terminal returns for testing local host. Click to expand.**

DEV/QA/PRD RDS databases have not been updated, so only local host can be tested. ```text $ git st On branch logstar/v10-db Your branch is up to date with 'origin/logstar/v10-db'. nothing to commit, working tree clean $ rm tests/http_response_output_files/png/*.png tests/http_response_output_files/json/*.json tests/results/*.tsv $ ./tests/curl_test_endpoints.sh GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000213420&efoId=EFO_0000621 http_code: 200 content_type: application/json time_total: 0.263160 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=EFO_0000621&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.467710 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=EFO_0000621&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.466627 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000213420&efoId=Orphanet_178 http_code: 200 content_type: application/json time_total: 0.269386 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=Orphanet_178&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.317606 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=Orphanet_178&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.511981 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000213420&efoId=MONDO_0016718 http_code: 200 content_type: application/json time_total: 0.259091 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=MONDO_0016718&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.515116 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=MONDO_0016718&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.412261 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000213420&efoId=MONDO_0016680 http_code: 200 content_type: application/json time_total: 0.253453 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=MONDO_0016680&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.419325 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=MONDO_0016680&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.414541 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000213420&efoId=MONDO_0016685 http_code: 200 content_type: application/json time_total: 0.249399 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=MONDO_0016685&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.446541 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000213420&efoId=MONDO_0016685&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.444031 seconds GET http://localhost:8082/tpm/gene-all-cancer/json?ensemblId=ENSG00000213420 http_code: 200 content_type: application/json time_total: 0.222259 seconds GET http://localhost:8082/tpm/gene-all-cancer/plot?ensemblId=ENSG00000213420&yAxisScale=linear http_code: 200 content_type: image/png time_total: 0.994871 seconds GET http://localhost:8082/tpm/gene-all-cancer/plot?ensemblId=ENSG00000213420&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 0.992707 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=EFO_0000621 http_code: 200 content_type: application/json time_total: 0.256225 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=EFO_0000621&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.454627 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=EFO_0000621&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.434664 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=Orphanet_178 http_code: 200 content_type: application/json time_total: 0.263787 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=Orphanet_178&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.470330 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=Orphanet_178&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.470691 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=MONDO_0016718 http_code: 200 content_type: application/json time_total: 0.263121 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=MONDO_0016718&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.473184 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=MONDO_0016718&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.511599 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=MONDO_0016680 http_code: 200 content_type: application/json time_total: 0.251935 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=MONDO_0016680&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.424025 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=MONDO_0016680&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.388942 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=MONDO_0016685 http_code: 200 content_type: application/json time_total: 0.255570 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=MONDO_0016685&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.424910 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000157764&efoId=MONDO_0016685&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.422042 seconds GET http://localhost:8082/tpm/gene-all-cancer/json?ensemblId=ENSG00000157764 http_code: 200 content_type: application/json time_total: 0.223154 seconds GET http://localhost:8082/tpm/gene-all-cancer/plot?ensemblId=ENSG00000157764&yAxisScale=linear http_code: 200 content_type: image/png time_total: 0.989755 seconds GET http://localhost:8082/tpm/gene-all-cancer/plot?ensemblId=ENSG00000157764&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 0.990318 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=EFO_0000621 http_code: 200 content_type: application/json time_total: 0.370653 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=EFO_0000621&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.582368 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=EFO_0000621&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.620442 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=Orphanet_178 http_code: 200 content_type: application/json time_total: 0.376627 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=Orphanet_178&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.432839 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=Orphanet_178&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.458113 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=MONDO_0016718 http_code: 200 content_type: application/json time_total: 0.373949 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=MONDO_0016718&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.439384 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=MONDO_0016718&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.680467 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=MONDO_0016680 http_code: 200 content_type: application/json time_total: 0.366490 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=MONDO_0016680&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.542326 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=MONDO_0016680&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.566345 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=MONDO_0016685 http_code: 200 content_type: application/json time_total: 0.367836 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=MONDO_0016685&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.565089 seconds GET http://localhost:8082/tpm/gene-disease-gtex/plot?ensemblId=ENSG00000273032&efoId=MONDO_0016685&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.593598 seconds GET http://localhost:8082/tpm/gene-all-cancer/json?ensemblId=ENSG00000273032 http_code: 200 content_type: application/json time_total: 0.335203 seconds GET http://localhost:8082/tpm/gene-all-cancer/plot?ensemblId=ENSG00000273032&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.115503 seconds GET http://localhost:8082/tpm/gene-all-cancer/plot?ensemblId=ENSG00000273032&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.205419 seconds $ git st On branch logstar/v10-db Your branch is up to date with 'origin/logstar/v10-db'. nothing to commit, working tree clean ```

For more details about local testing environment, options, and resources, see https://github.com/PediatricOpenTargets/OpenPedCan-api/blob/eb5641f5920c6bfed8943989e4d1b991d21b47aa/README.md.

Checklist

• [x] My code follows the style guidelines of this project
• [x] I have performed a self-review of my own code
• [x] I have commented my code, particularly in hard-to-understand areas
• [x] I have made corresponding changes to the documentation
• [x] My changes generate no new warnings
• [x] I have added tests that prove my fix is effective or that my feature works
• [NA] New and existing unit tests pass locally with my changes
• [NA] Any dependent changes have been merged and published in downstream modules
• [x] I have checked my code and corrected any misspellings
• [ ] I have emojis in my PR and commits 😉

cc @taylordm @chinwallaa @blackdenc

[logstar]

@chris-s-friedman and @afarrel - The 10/14 deadline is postponed this morning. This PR will be merged tomorrow, 10/13, around 1pm with or without any approval, to test new v10 database in QA environment.

cc @chinwallaa @taylordm @blackdenc

[kelseykeith]

Code and Results Review

Everything continues to look good as I move through the TPM boxplot PRs!

• Code is pulling from the correct version of the data (v10).
• Plots have the updated titles and use "All Cohorts" where applicable.
• Results from the API call match data in OpenPedCan-analysis tables.
• Changes to the database function correctly as far as I can tell and names were updated where appropriate.