Closed logstar closed 2 years ago
Hi @logstar , I reviewed your code, tables, and plots. It looks good but before I approve I want to review the title names: eg Pediatric primary and relapsed tumor and GTEx normal adult tissue gene expression. While this is fine, would a more succinct title be Pediatric Tumors and GTEx normal adult tissue gene expression (since you have the primary tumors, relapsed tumors, and normal tissue in the legend right below which can serve two purposes, legend and subtitle.)
What are your thoughts. I'm ready to approve pending this design decision. If the larger group wants the longer descriptive title that's fine.
Hi @logstar , I reviewed your code, tables, and plots. It looks good but before I approve I want to review the title names: eg Pediatric primary and relapsed tumor and GTEx normal adult tissue gene expression. While this is fine, would a more succinct title be Pediatric Tumors and GTEx normal adult tissue gene expression (since you have the primary tumors, relapsed tumors, and normal tissue in the legend right below which can serve two purposes, legend and subtitle.)
What are your thoughts. I'm ready to approve pending this design decision. If the larger group wants the longer descriptive title that's fine.
@afarrel Thank you for reviewing. I think we could keep the longer title, to distinguish primary-and-relapse from primary-only and relapse-only. The title originally uses only "pediatric tumor", but changed to more descriptive ones, which was described in https://github.com/PediatricOpenTargets/OpenPedCan-api/issues/56#issue-1056141024.
Hi @logstar , I reviewed your code, tables, and plots. It looks good. Thanks for your hard work on this.
Hi @afarrel . Thank you for reviewing. I will merge this PR after coordinating with @blackdenc . This PR requires a new database instance to be used for QA site, which needs to be configured by @blackdenc .
Everything continues to look good!
broad_tumor_descriptor
) appropriately.
Description
Added relapse tumors samples to
/tpm/*
endpoint results and plots.Notes for reviewers:
Type of change
Changed
includeTumorDesc
to determine how independent primary and relapse tumor samples should be handled./tpm/gene-disease-gtex/json
/tpm/gene-disease-gtex/plot
/tpm/gene-all-cancer/json
/tpm/gene-all-cancer/plot
/tpm/gene-all-cancer-collapsed-gtex/json
/tpm/gene-all-cancer-collapsed-gtex/plot
/tpm/gene-all-cancer-gtex/json
/tpm/gene-all-cancer-gtex/plot
tests/curl_test_endpoints.sh
.get_gene_tpm_tbl
function:gtex_sample_group
parameter value choices to"require"
and"exclude"
.relapse_sample_group
.min_n_per_sample_group
parameter.specimen_descriptor
to returned table.src/add_gene_tpm_box_group.R
. The procedure inadd_gene_tpm_box_group
function is integrated intoget_gene_tpm_boxplot_tbl
function.get_gene_tpm_boxplot_tbl
function:gtex_histology_group
.spec_desc_group
.min_n_per_box
.x_labels
column tox_label
.box_group
column.histology_group
column.specimen_descriptor
column.specimen_descriptor_fill
column.specimen_descriptor_x_label
column.box_sample_count
column.x_label_sample_count
column.tpm_boxplot_summary_tbl
function:specimen_descriptor_fill
column.box_sample_count
column.src/ggplot2_publication_theme.R
tosrc/ggplot2_boxplot_theme.R
.results/test-*.tsv
toresults/tsv/test-*.tsv
.Added
bulk_expression
schema andbulk_expression_tpm_histology
table.specimen_descriptor
column to OpenPedCan-api databasebulk_expression
schema andbulk_expression_tpm_histology
table. Thespecimen_descriptor
column describes whether a specimen is obtained from primary tumor, or relapse tumor, or normal tissue.tests/run_tests.sh
to test API.tests/r_test_scripts/test_endpoint_http.R
to test API HTTP server, which outputstests/results/endpoint_response_times.tsv
andtests/plots/endpoint_response_time_boxplot.png
to summarize HTTP response times.src/get_tpm_endpoint_tbl.R
to callget_gene_tpm_tbl
andget_gene_tpm_boxplot_tbl
with proper parameters according to HTTP request query parameters.How Has This Been Tested?
Task link/Screenshot/Terminal returns:
For more details about local testing environment, options, and resources, see
README.md
of this PR branch.Checklist
cc @taylordm @chinwallaa