Job request: 20302
- Organisation:
- The UK Renal Registry
- Workspace:
- renal-short-data-report
- ID:
- plbeglrafglmuxaf
This page shows the technical details of what happened when authorised researcher Louis Fisher requested one or more actions to be run against real patient data in the project, within a secure environment.
By cross-referencing the indicated Requested Actions with the
Pipeline section below, you can infer what
security level
various outputs were written to. Outputs marked as
highly_sensitive
can never be viewed directly by a researcher; they can only
request that code runs against them. Outputs marked as
moderately_sensitive
can be viewed by an approved researcher by logging into a highly
secure environment. Only outputs marked as
moderately_sensitive
can be requested for release to the public, via a controlled
output review service.
Jobs
-
- Job identifier:
-
6rveb2fzshrzghrc
Pipeline
Show project.yaml
version: "3.0"
expectations:
population_size: 1000
actions:
generate_study_population_calculators:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_calculators
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input_calculators.csv.gz
calculate_calculators:
run: python:latest python analysis/scripts/calculate_calculators.py
needs: [generate_study_population_calculators]
outputs:
highly_sensitive:
counts: output/input_calculators_calculated.csv.gz
crcl_gault:
run: python:latest python analysis/scripts/crcl_gault.py
needs: [calculate_calculators]
outputs:
moderately_sensitive:
plots: output/dist*.png
venn: output/venn*.png
counts: output/creatinine_vs_crlc.json
generate_study_population:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range "2019-01-01 to 2023-07-01 by month"
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input*.csv.gz
generate_study_population_ukrr_ethnicity:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ukrr_ethnicity
--output-dir=output
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input_ukrr_ethnicity.csv.gz
join_cohorts:
run: >
cohort-joiner:v0.0.46
--lhs output/input_20*.csv.gz
--rhs output/input_ukrr_ethnicity.csv.gz
--output-dir output/joined
needs: [generate_study_population, generate_study_population_ukrr_ethnicity]
outputs:
highly_sensitive:
cohort: output/joined/input_20*.csv.gz
generate_table_1:
run: python:latest python analysis/scripts/table_1.py --study_def_paths="output/joined/input_*.csv.gz" --demographics="age_band,sex,region,imd,ethnicity"
needs: [join_cohorts]
outputs:
moderately_sensitive:
tables: output/table_1*.csv
get_counts:
run: python:latest python analysis/scripts/combine_operators.py
needs: [join_cohorts]
outputs:
moderately_sensitive:
counts: output/*_count.csv
operator_counts: output/*_count_*.csv
generate_top_5_tables:
run: python:latest python analysis/scripts/top_codes.py
needs: [get_counts]
outputs:
moderately_sensitive:
counts: output/top_5_code_table_*.csv
generate_measures:
run: cohortextractor:latest generate_measures
--study-definition study_definition
--output-dir=output/joined
needs: [join_cohorts]
outputs:
moderately_sensitive:
measure_csv: output/joined/measure_*_rate.csv
plot_ckd:
run: python:latest python analysis/scripts/plot_ckd_over_time.py
needs: [generate_measures]
outputs:
moderately_sensitive:
plots: output/figures/plot_incident_ckd.jpeg
generate_plots:
run: python:latest python analysis/scripts/plot_measures.py
needs: [generate_measures, join_cohorts]
outputs:
moderately_sensitive:
counts: output/figures/plot_*.jpeg
csv: output/figures/plot_*.csv
generate_plots_numeric_values:
run: python:latest python analysis/scripts/plot_numeric_values.py
needs: [join_cohorts]
outputs:
moderately_sensitive:
figures: output/*dis*.jpeg
generate_upset_plots:
run: python:latest python analysis/scripts/ckd_discrepancies.py
needs: [join_cohorts]
outputs:
moderately_sensitive:
figures: output/ckd_staging_*.png
tables: output/ckd_staging_*.csv
time: output/time_diff_ckd.jpeg
dialysis: output/ckd_rrt_upset.csv
dialysis45: output/biochem_4_5_not_coded.csv
generate_study_population_ukrr_jul_22:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ukrr
--index-date-range "2022-07-01"
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/ukrr/input_ukrr_2022-07-01.csv.gz
generate_study_population_ukrr:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ukrr
--index-date-range "2020-01-01"
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/ukrr/input_ukrr*.csv.gz
generate_study_population_ukrr_1:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ukrr_short
--index-date-range "2021-01-01"
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/ukrr/input_ukr*.csv.gz
generate_study_population_ukrr_2:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ukrr_short
--index-date-range "2022-01-01"
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/ukrr/input_uk*.csv.gz
generate_study_population_paeds:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_paeds
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input_paeds.csv.gz
generate_study_population_check_SC:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_check_SC
--output-format csv.gz
--with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input_check_SC.csv.gz
# generate_notebook:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/report.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [generate_plots, get_counts]
# outputs:
# moderately_sensitive:
# notebook: output/report.html
# generate_ukrr_checks:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-checks.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population, generate_study_population_ukrr_ethnicity]
# outputs:
# moderately_sensitive:
# report: output/notebooks/ukrr-checks.html
#generate_ukrr_report:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-report.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [join_acr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/ukrr-report.html
# generate_ukrr_discrepancies:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-discrepancies.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [join_acr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/ukrr-discrepancies.html
ukrr_vs_prim_care_ckd:
run: python:latest python analysis/scripts/ukrr_prim_care_crossover_ckd.py
needs: [join_cohorts]
outputs:
moderately_sensitive:
upset: output/*.png
upset_csv: output/ukrr*overlap_stage.csv
# generate_kidney_week:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/kidney_week.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [join_acr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/kidney_week.html
# generate_ukrr_tables_figures:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-tables-figures.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/ukrr-tables-figures.html
generate_ukrr_tables_figures_1:
run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-tables-figures-2021.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
needs: [generate_study_population_ukrr_1]
outputs:
moderately_sensitive:
report: output/notebooks/ukrr-tables-figures-2021.html
generate_ukrr_tables_figures_2:
run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-tables-figures-2022.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
needs: [generate_study_population_ukrr_2]
outputs:
moderately_sensitive:
report: output/notebooks/ukrr-tables-figures-2022.html
generate_false_positives_ckd:
run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/false-positives-ckd.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
needs: [generate_study_population_ukrr]
outputs:
moderately_sensitive:
report: output/notebooks/false-positives-ckd.html
generate_agreement_by_eGFR:
run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/agreement-by-eGFR.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
needs: [generate_study_population_ukrr]
outputs:
moderately_sensitive:
report: output/notebooks/agreement-by-eGFR.html
# generate_pc_sc_codes1a:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes1a.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes1a.html
# generate_pc_sc_codes1b:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes1b.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes1b.html
# generate_pc_sc_codes2:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes2.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes2.html
# generate_pc_sc_codes3:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes3.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes3.html
# generate_pc_sc_codes4a:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes4a.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes4a.html
# generate_pc_sc_codes4b:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes4b.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes4b.html
# generate_pc_sc_codes4c:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes4c.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes4c.html
# generate_pc_sc_codes5a:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes5a.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes5a.html
# generate_pc_sc_codes5b:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes5b.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/pc-sc-codes5b.html
# generate_ukrr_tables_figures_paeds:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-tables-figures-paeds.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_paeds]
# outputs:
# moderately_sensitive:
# report: output/notebooks/ukrr-tables-figures-paeds.html
# generate_check_SC:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/check-SC.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_check_SC, generate_study_population_ukrr_ethnicity]
# outputs:
# moderately_sensitive:
# report: output/notebooks/check-SC.html
# generate_modality_difference_table:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/modality-difference-table.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/modality-difference-table.html
# generate_incident_analysis:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/incident-analysis.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/incident-analysis.html
# generate_study_population_flowchart:
# run: cohortextractor:latest generate_cohort
# --study-definition study_definition_flowchart
# --output-format csv.gz
# outputs:
# highly_sensitive:
# cohort: output/input_flowchart.csv.gz
# generate_median_age:
# run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/median_age.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
# needs: [generate_study_population_ukrr]
# outputs:
# moderately_sensitive:
# report: output/notebooks/median_age.html
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:07:11
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- renal-short-data-report
- Requested by
- Louis Fisher
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- d50c49a
- Requested actions
-
-
ukrr_vs_prim_care_ckd
-