📫Add all-cancer and all-GTEx-tissue plot and summary table endpoints

logstar commented 2 years ago

Description

Added all-cancer and all-GTEx-tissue plot and summary table endpoints.

Resolved #44
Resolved #45

Note for reviewers: In the review, please only add comments or suggestions that are directly related code correctness or documentation readability.

Type of change

[x] New feature (non-breaking change which adds functionality)

Changed

Changed the interface of get_gene_tpm_tbl function by adding a required parameter gtex_sample_group.
Changed the interface of add_gene_tpm_box_group function by adding an optional parameter gtex_box_group.
Changed the behavior of get_gene_tpm_boxplot_summary_tbl function by allowing one sample group to have multiple unique GTEx_tissue_subgroups and GTEx_tissue_subgroup_UBERONs.

Added

Added the following all-cancer and all-GTEx-tissue TPM boxplot and summary table endpoints:
- /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.
Added curl tests for the above all-cancer and all-GTEx-tissue TPM boxplot and summary table endpoints, in tests/curl_test_endpoints.sh.

How Has This Been Tested?

[x] Integration test

**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

[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

logstar commented 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

logstar commented 2 years ago

@afarrel Thank you for reviewing. I will merge this pull request shortly.

kelseykeith commented 1 year ago

Code and Results Review

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

Code is pulling from the correct version of the data (v10).
Results from the API call match data in OpenPedCan-analysis tables.
Plots have the correct boxplots for GTEx tissues, either none, collapsed into a single boxplot, or all tissues.
Plots are the correct size for the number of boxplots they contain and have the correct titles.
Tables also have the correct calculations for the correct grouping of GTEx tissues, either none, collapsed into a single boxplot, or all tissues.
Changes to the database function correctly as far as I can tell and names were updated where appropriate.

PediatricOpenTargets / OpenPedCan-api