v0.6.1-beta

Changelog for this release version

v0.6.1-beta

Changed

• Updated database using OpenPedCan-analysis v12 final release data.
• Changed db/build_db.sh to download OpenPedCan-analysis api-data using db/build_tools/download_api_data.sh.
• Changed db/build_tools/build_db_docker_cmd.sh to compress intermediate CSV files.

Added

• Added db/build_tools/download_api_data.sh to download OpenPedCan-analysis api-data.

v0.6.0-beta

Changed

• Changed the interface of get_gene_tpm_tbl function:
  • Added a required parameter tcga_sample_group.
• Changed the interface of get_tpm_endpoint_tbl function:
  • Added a required parameter tcga_sample_group.
• Updated db/db.Dockerfile PostgreSQL docker image to version 12.13.

Added

• Added OpenPedCan-analysis TCGA TPM data to the database.
• Added the following TCGA expanded TPM boxplot and summary table endpoints:
  • /tpm/gene-disease-tcga/plot
  • /tpm/gene-disease-tcga/json
  • /tpm/gene-disease-tcga-gtex/plot
  • /tpm/gene-disease-tcga-gtex/json
  • /tpm/gene-all-cancer-tcga/plot
  • /tpm/gene-all-cancer-tcga/json
  • /tpm/gene-all-cancer-tcga-gtex/plot
  • /tpm/gene-all-cancer-tcga-gtex/json
• Added tests in tests/r_test_scripts/test_endpoint_http.R to test the added TCGA expanded TPM boxplot and summary table endpoints.

v0.5.3-beta

Changed

• Updated database using OpenPedCan-analysis v11 TPM data and independent sample lists.
• Updated tests/r_test_scripts/test_endpoint_http.R according to OpenPedCan-analysis v11 TPM data.

v0.5.2-beta

Changed

• Updated database using v10 differential gene expression (DGE) data.
• Installed libxml2 in Dockerfile.
• Updated tests for DGE heatmap endpoints, according to v10 DGE data.

v0.5.1-beta

Changed

• Changed the interfaces of the following endpoints by adding two required parameters, includeBoxplot and boxplotYAxisScale, to determine whether to add boxplots with certain Y-axis scales on the sides of the differential gene expression (DGE) heatmaps or not.
  • /dge/top-gene-disease-gtex-diff-exp/plot
  • /dge/gene-all-cancer-gtex-diff-exp/plot

v0.5.0-beta

Added

• Added the following differential gene expression (DGE) endpoints to transfer DGE heatmap PNG plots and JSON tables via HTTP GET method.
  • /dge/top-gene-disease-gtex-diff-exp/json: Transfer a JSON table of one disease and top differentially expressed genes.
  • /dge/top-gene-disease-gtex-diff-exp/plot: Transfer a PNG heatmap of one disease and top differentially expressed genes.
  • /dge/gene-all-cancer-gtex-diff-exp/json: Transfer a DGE JSON table of one gene and all diseases.
  • /dge/gene-all-cancer-gtex-diff-exp/plot: Transfer a DGE PNG heatmap of one gene and all diseases.
• Added DGE database table BULK_EXP_SCHEMA.BULK_EXP_DIFF_EXP_TBL, which is declared in ../OpenPedCan-api-secrets/common_db.env and db/r_interfaces/db_env_vars.R and constructed in db/build_tools/build_db.R and db/build_tools/build_db_docker_cmd.sh.
• Added the following R scripts to implement the added DGE endpoints.
  • src/get_one_efo_top_ensg_diff_exp_heatmap.R
  • src/get_one_efo_top_ensg_diff_exp_heatmap_tbl.R
  • src/get_one_efo_top_ensg_diff_exp_tbl.R
  • src/get_one_ensg_all_efo_diff_exp_heatmap.R
  • src/get_one_ensg_all_efo_diff_exp_heatmap_tbl.R
  • src/get_one_ensg_all_efo_diff_exp_tbl.R
• Added tests in tests/r_test_scripts/test_endpoint_http.R to test the added DGE endpoints.