Closed logstar closed 1 year ago
Updates/progress on this issue:
OpenPedCan-analysis
submodule to v11 release.OpenPedCan-api
, with help from @blackdenc . The swap space prevents docker container from being terminated when exceeding RAM limit.db/build_tools/tpm_data_lists.R
to be compatible with v11 release. Checked whether v11 data are compatible with db/build_tools/tpm_data_lists.R
assertions/assumptions related to cohort
, experimental_strategy
, Kids_First_Biospecimen_ID
, cancer_group
, EFO
, MONDO
, etc.I will continue working on this issue in the next week, with the following action items:
db/build_tools/build_db.R
assertions/assumptions.OpenPedCan-api
and database instances.src/get_gene_tpm_tbl.R
assertions/assumptions.Let me know if you have questions or suggestions.
Updates/progress on this issue:
db/build_tools/build_db.R
. Added comments to improve readability.src/get_gene_tpm_tbl.R
and src/get_gene_tpm_boxplot_tbl.R
.I will continue working on this issue in the next week, with the following action items:
src/get_gene_tpm_boxplot_summary_tbl.R
and src/get_gene_tpm_boxplot.R
.dev
AWS RDS server.Let me know if you have questions or suggestions.
I will continue working on the following action items next week:
README.md
to clarify that differential gene expression (DGE) database table uses v10 data, whereas TPM database table uses v11 data. As DGE endpoints have not been integrated to MTP, this will not cause inconsistent data versions on MTP.
After OpenPedCan-analysis v11 data release, update API database using v11 data with the following steps:
./db/build_db.sh
.tests/r_test_scripts/test_endpoint_http.R
to use the updated EFO IDs.DB_LOCATION=local docker-compose up
.tests/run_tests.sh
locally.Two branches in this repository are currently deployed remotely.
de-heatmap
branch is deployed on remote DEV API and database server for reviewing https://github.com/PediatricOpenTargets/OpenPedCan-api/pull/60.main
branch, i.e., releasev0.4.0-beta
, is deployed on remote QA and PRD API and database servers for integration with MTP.v10-dge
branch contains the latest version of locally developed API and database server, which is under review at https://github.com/PediatricOpenTargets/OpenPedCan-api/pull/65, butv10-dge
branch is not deployed remotely.Therefore, the branch for v11 data release should be developed based on
v10-dge
. After the v11 update PR is created, previous PRs can be reviewed, to separate all v11 update PR changes into multiple PRs, which could facilitate the reviewing process.After v11 update PR is approved and merged, the changes will be deployed to QA API HTTP server, and QA API database needs to be updated with v11 database. Then, the updated QA API site needs to be evaluated by FNL team for integration with MTP.
cc @jharenza @chinwallaa @taylordm @afarrel @ewafula @kelseykeith