Closed logstar closed 2 years ago
@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
Everything continues to look good as I move through the TPM boxplot PRs!
Description
Updated database building procedure to use OpenPedCan-analysis v10 release data.
Notes for reviewers:
(EDIT 10/12/2021 YZ)
dev
branch, which was committed around 7pm today, 10/11.Related issues:
46
41
Type of change
Incremented version number to v0.3.2-beta.
Changed
OpenPedCan-analysis
submodule todev
branch v10 release commit.db/build_db.sh
OPEN_PED_CAN_ANALYSIS_COMMIT
fromOpenPedCan-analysis
dev
branch v9 release commit to v10 release commit./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"./tpm/gene-all-cancer
boxplot title from "Primary tumor tissue bulk gene expression" to "Pediatric tumor gene expression".Added
API_HOST=prd
option intests/curl_test_endpoints.sh
to test production API site URL https://openpedcan-api.d3b.io.How Has This Been Tested?
**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
cc @taylordm @chinwallaa @blackdenc