Closed logstar closed 2 years ago
@chris-s-friedman @afarrel - Would you be able to review this PR before this Thursday? I will open a new PR probably on this Thursday to address #51 , so the DEV site will be updated to the new PR.
cc @chinwallaa @taylordm
@afarrel Thank you for reviewing. I will merge this pull request shortly.
Everything continues to look good as I move through the TPM PRs.
Description
Added all-cancer and all-GTEx-tissue plot and summary table endpoints.
Note for reviewers: In the review, please only add comments or suggestions that are directly related code correctness or documentation readability.
Type of change
Changed
get_gene_tpm_tbl
function by adding a required parametergtex_sample_group
.add_gene_tpm_box_group
function by adding an optional parametergtex_box_group
.get_gene_tpm_boxplot_summary_tbl
function by allowing one sample group to have multiple uniqueGTEx_tissue_subgroup
s andGTEx_tissue_subgroup_UBERON
s.Added
/tpm/gene-all-cancer-collapsed-gtex/plot
transfers boxplot with all GTEx tissues collapsed into one box./tpm/gene-all-cancer-collapsed-gtex/json
transfers summary table with all GTEx tissues collapsed into one sample group./tpm/gene-all-cancer-gtex/plot
transfers boxplot with each GTEx tissue subgroup as one box./tpm/gene-all-cancer-gtex/json
transfers summary table with each GTEx tissue subgroup as one sample group.curl
tests for the above all-cancer and all-GTEx-tissue TPM boxplot and summary table endpoints, intests/curl_test_endpoints.sh
.How Has This Been Tested?
**Terminal returns for testing DEV host. Click to expand.**
```text $ git st On branch acg Your branch is up to date with 'origin/acg'. 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: 0.258172 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: 1.436654 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: 1.420492 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000213420&efoId=Orphanet_178 http_code: 200 content_type: application/json time_total: 0.263910 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: 1.310420 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: 1.457913 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000213420&efoId=MONDO_0016718 http_code: 200 content_type: application/json time_total: 0.267860 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: 1.454943 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: 1.447156 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000213420&efoId=MONDO_0016680 http_code: 200 content_type: application/json time_total: 0.263423 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: 1.541460 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: 1.426151 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000213420&efoId=MONDO_0016685 http_code: 200 content_type: application/json time_total: 0.255761 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: 1.429106 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: 1.455311 seconds GET http://localhost:8082/tpm/gene-all-cancer/json?ensemblId=ENSG00000213420 http_code: 200 content_type: application/json time_total: 0.225743 seconds GET http://localhost:8082/tpm/gene-all-cancer/plot?ensemblId=ENSG00000213420&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.007589 seconds GET http://localhost:8082/tpm/gene-all-cancer/plot?ensemblId=ENSG00000213420&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 0.994899 seconds GET http://localhost:8082/tpm/gene-all-cancer-collapsed-gtex/json?ensemblId=ENSG00000213420 http_code: 200 content_type: application/json time_total: 0.257944 seconds GET http://localhost:8082/tpm/gene-all-cancer-collapsed-gtex/plot?ensemblId=ENSG00000213420&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.302714 seconds GET http://localhost:8082/tpm/gene-all-cancer-collapsed-gtex/plot?ensemblId=ENSG00000213420&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.277916 seconds GET http://localhost:8082/tpm/gene-all-cancer-gtex/json?ensemblId=ENSG00000213420 http_code: 200 content_type: application/json time_total: 0.287717 seconds GET http://localhost:8082/tpm/gene-all-cancer-gtex/plot?ensemblId=ENSG00000213420&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.287103 seconds GET http://localhost:8082/tpm/gene-all-cancer-gtex/plot?ensemblId=ENSG00000213420&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.256290 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=EFO_0000621 http_code: 200 content_type: application/json time_total: 0.267169 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: 1.519475 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: 1.398836 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=Orphanet_178 http_code: 200 content_type: application/json time_total: 0.261575 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: 1.453257 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: 1.409980 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=MONDO_0016718 http_code: 200 content_type: application/json time_total: 0.260170 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: 1.456813 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: 1.441518 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=MONDO_0016680 http_code: 200 content_type: application/json time_total: 0.262513 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: 1.472196 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: 1.441619 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000157764&efoId=MONDO_0016685 http_code: 200 content_type: application/json time_total: 0.263992 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: 1.567861 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: 1.387683 seconds GET http://localhost:8082/tpm/gene-all-cancer/json?ensemblId=ENSG00000157764 http_code: 200 content_type: application/json time_total: 0.235271 seconds GET http://localhost:8082/tpm/gene-all-cancer/plot?ensemblId=ENSG00000157764&yAxisScale=linear http_code: 200 content_type: image/png time_total: 0.991376 seconds GET http://localhost:8082/tpm/gene-all-cancer/plot?ensemblId=ENSG00000157764&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 0.981801 seconds GET http://localhost:8082/tpm/gene-all-cancer-collapsed-gtex/json?ensemblId=ENSG00000157764 http_code: 200 content_type: application/json time_total: 0.251346 seconds GET http://localhost:8082/tpm/gene-all-cancer-collapsed-gtex/plot?ensemblId=ENSG00000157764&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.246673 seconds GET http://localhost:8082/tpm/gene-all-cancer-collapsed-gtex/plot?ensemblId=ENSG00000157764&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.264880 seconds GET http://localhost:8082/tpm/gene-all-cancer-gtex/json?ensemblId=ENSG00000157764 http_code: 200 content_type: application/json time_total: 0.276227 seconds GET http://localhost:8082/tpm/gene-all-cancer-gtex/plot?ensemblId=ENSG00000157764&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.257954 seconds GET http://localhost:8082/tpm/gene-all-cancer-gtex/plot?ensemblId=ENSG00000157764&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.225313 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=EFO_0000621 http_code: 200 content_type: application/json time_total: 0.376670 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: 1.609124 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: 1.594647 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=Orphanet_178 http_code: 200 content_type: application/json time_total: 0.400856 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: 1.493592 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: 1.376393 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=MONDO_0016718 http_code: 200 content_type: application/json time_total: 0.367889 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: 1.374106 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: 1.568900 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=MONDO_0016680 http_code: 200 content_type: application/json time_total: 0.373818 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: 1.567342 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: 1.568448 seconds GET http://localhost:8082/tpm/gene-disease-gtex/json?ensemblId=ENSG00000273032&efoId=MONDO_0016685 http_code: 200 content_type: application/json time_total: 0.375137 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: 1.589693 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: 1.668127 seconds GET http://localhost:8082/tpm/gene-all-cancer/json?ensemblId=ENSG00000273032 http_code: 200 content_type: application/json time_total: 0.337727 seconds GET http://localhost:8082/tpm/gene-all-cancer/plot?ensemblId=ENSG00000273032&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.097545 seconds GET http://localhost:8082/tpm/gene-all-cancer/plot?ensemblId=ENSG00000273032&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.096425 seconds GET http://localhost:8082/tpm/gene-all-cancer-collapsed-gtex/json?ensemblId=ENSG00000273032 http_code: 200 content_type: application/json time_total: 0.366653 seconds GET http://localhost:8082/tpm/gene-all-cancer-collapsed-gtex/plot?ensemblId=ENSG00000273032&yAxisScale=linear http_code: 200 content_type: image/png time_total: 1.460458 seconds GET http://localhost:8082/tpm/gene-all-cancer-collapsed-gtex/plot?ensemblId=ENSG00000273032&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 1.422966 seconds GET http://localhost:8082/tpm/gene-all-cancer-gtex/json?ensemblId=ENSG00000273032 http_code: 200 content_type: application/json time_total: 0.416603 seconds GET http://localhost:8082/tpm/gene-all-cancer-gtex/plot?ensemblId=ENSG00000273032&yAxisScale=linear http_code: 200 content_type: image/png time_total: 2.418889 seconds GET http://localhost:8082/tpm/gene-all-cancer-gtex/plot?ensemblId=ENSG00000273032&yAxisScale=log10 http_code: 200 content_type: image/png time_total: 2.402400 seconds $ git st On branch acg Your branch is up to date with 'origin/acg'. nothing to commit, working tree clean ```For more details about local testing environment, options, and resources, see https://github.com/PediatricOpenTargets/OpenPedCan-api/blob/55afd9c5162e8c8304cecc351feb02be7170e379/README.md.
Checklist
cc @taylordm @chinwallaa