Job request: 9052
- Organisation:
- King's College London
- Workspace:
- early-inflammatory-arthritis
- ID:
- vbij446lnfm37mn6
This page shows the technical details of what happened when the authorised researcher Mark Russell requested one or more actions to be run against real patient data within a secure environment.
By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.
The output security levels are:
-
highly_sensitive
- Researchers can never directly view these outputs
- Researchers can only request code is run against them
-
moderately_sensitive
- Can be viewed by an approved researcher by logging into a highly secure environment
- These are the only outputs that can be requested for public release via a controlled output review service.
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 400000
actions:
generate_study_population_allpts:
run: cohortextractor:latest generate_cohort --study-definition study_definition_allpts
outputs:
highly_sensitive:
cohort: output/input_allpts.csv
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
create_cohorts_allpts:
run: stata-mp:latest analysis/001_define_covariates_allpts.do
needs: [generate_study_population_allpts]
outputs:
highly_sensitive:
log1: logs/cleaning_dataset_allpts.log
data1: output/data/file_eia_allpts.dta
create_cohorts:
run: stata-mp:latest analysis/000_define_covariates.do
needs: [generate_study_population]
outputs:
highly_sensitive:
log1: logs/cleaning_dataset.log
data1: output/data/file_eia_all.dta
run_baseline_tables_allpts:
run: stata-mp:latest analysis/101_baseline_characteristics_allpts.do
needs: [create_cohorts_allpts]
outputs:
moderately_sensitive:
log1: logs/descriptive_tables_allpts.log
doc1: output/tables/baseline_allpts.csv
run_baseline_tables:
run: stata-mp:latest analysis/100_baseline_characteristics.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/descriptive_tables.log
doc1: output/tables/baseline_bydiagnosis.csv
doc2: output/tables/baseline_byyear.csv
doc3: output/tables/referral_bydiag_nomiss.csv
doc4: output/tables/referral_byyear_nomiss.csv
doc5: output/tables/referral_byregion_nomiss.csv
doc6: output/tables/drug_bydiag_miss.csv
doc7: output/tables/drug_byyear_miss.csv
doc8: output/tables/drug_byyear_ra_miss.csv
doc9: output/tables/drug_byyear_psa_miss.csv
doc10: output/tables/drug_byyear_undiff_miss.csv
doc11: output/tables/drug_byyearanddisease.csv
doc12: output/tables/drug_byyearandregion.csv
doc13: output/tables/diag_count_bymonth.csv
doc14: output/tables/appt_count_bymonth.csv
figure1: output/figures/incidence_twoway_rounded.svg
figure2: output/figures/incidence_twoway_appt.svg
run_itsa_models:
run: stata-mp:latest analysis/200_itsa_models.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/itsa_models.log
figure1: output/figures/ITSA_diagnostic_delay_newey.svg
figure2: output/figures/ITSA_diagnostic_delay_prais.svg
figure3: output/figures/ITSA_diagnostic_delay_GP_newey.svg
figure4: output/figures/ITSA_diagnostic_delay_GP_prais.svg
doc1: output/tables/gp_to_appt_ITSA_table.csv
run_itsa_models_drugs:
run: stata-mp:latest analysis/201_itsa_models_drugs.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/itsa_models_drugs.log
figure1: output/figures/ITSA_csDMARD_delay_newey.svg
figure2: output/figures/ITSA_csDMARD_delay_prais.svg
figure3: output/figures/ITSA_csDMARD_delay_newey_sensitivity.svg
figure4: output/figures/ITSA_csDMARD_delay_prais_sensitivity.svg
doc1: output/tables/appt_to_csdmard_ITSA_table.csv
run_box_plots:
run: stata-mp:latest analysis/300_box_plots.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/box_plots.log
figure 1: output/figures/regional_qs1_bar_overall.svg
figure 2: output/figures/regional_qs1_bar_2019.svg
figure 3: output/figures/regional_qs1_bar_2020.svg
figure 4: output/figures/regional_qs2_bar_overall.svg
figure 5: output/figures/regional_qs2_bar_2019.svg
figure 6: output/figures/regional_qs2_bar_2020.svg
figure 7: output/figures/regional_qs2_bar_GP_overall.svg
figure 8: output/figures/regional_qs2_bar_GP_2019.svg
figure 9: output/figures/regional_qs2_bar_GP_2020.svg
figure 10: output/figures/regional_csdmard_bar_overall.svg
figure 11: output/figures/regional_csdmard_bar_2019.svg
figure 12: output/figures/regional_csdmard_bar_2020.svg
run_redacted_tables:
run: stata-mp:latest analysis/400_redacted_tables.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/redacted_tables.log
doc1: output/tables/table_1_rounded_bydiag.csv
doc2: output/tables/table_mean_bydiag_rounded.csv
doc3: output/tables/table_median_bydiag_rounded.csv
doc4: output/tables/table_median_bydiag_rounded_to21.csv
doc5: output/tables/ITSA_tables_appt_delay_rounded.csv
doc6: output/tables/ITSA_tables_csdmard_delay_rounded.csv
doc7: output/tables/drug_byyearanddisease_rounded.csv
doc8: output/tables/first_csdmard_rounded.csv
doc9: output/tables/drug_byyearandregion_rounded.csv
doc10: output/tables/referral_byregion_rounded.csv
run_redacted_tables_allpts:
run: stata-mp:latest analysis/401_redacted_tables_allpts.do
needs: [create_cohorts_allpts]
outputs:
moderately_sensitive:
log1: logs/redacted_tables_allpts.log
doc1: output/tables/table_1_rounded_allpts.csv
Timeline
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Created:
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Started:
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Finished:
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Runtime:
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job request
- Status
-
Failed
JobRequestError: Internal error
- Backend
- TPP
- Workspace
- early-inflammatory-arthritis
- Requested by
- Mark Russell
- Branch
- main
- Force run dependencies
- Yes
- Git commit hash
- 8c72f5a
- Requested actions
-
-
generate_study_population -
create_cohorts -
run_baseline_tables -
run_itsa_models -
run_itsa_models_drugs -
run_box_plots -
run_redacted_tables
-
Code comparison
Compare the code used in this job request