Job request: 13557
- Organisation:
- ONS
- Workspace:
- covid_mental_health
- ID:
- 6ozy4cpnnfnghca2
This page shows the technical details of what happened when the authorised researcher Klaudia Rzepnicka requested one or more actions to be run against real patient data in the project, within a secure environment.
By cross-referencing the list of jobs with the
pipeline section below, you can infer what
security level
various outputs were written to. Researchers can never directly
view outputs marked as
highly_sensitive
;
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:
-
qnedrohiknuxxvo2
Pipeline
Show project.yaml
# describes how each step in your analysis should be run
version: '3.0'
expectations:
population_size: 1000
actions:
# combine_codelists:
# run: r:latest analysis/combine_codelists.R
# outputs:
# highly_sensitive:
# cmd: 'codelists/ons-cmd-codes.csv'
#smi: 'codelists/ons-smi-codes.csv'
#self_harm : 'codelists/ons-self-harm-codes.csv'
generate_wide_non_health:
run: cohortextractor:latest generate_cohort --study-definition study_definition_non_health --with-end-date-fix
#needs: [combine_codelists]
outputs:
highly_sensitive:
cohort: output/input_non_health.csv
generate_wide_health_mh:
run: cohortextractor:latest generate_cohort --study-definition study_definition_health_mh --with-end-date-fix
#needs: [combine_codelists]
outputs:
highly_sensitive:
cohort: output/input_health_mh.csv
generate_wide_health_non_mh:
run: cohortextractor:latest generate_cohort --study-definition study_definition_health_non_mh --with-end-date-fix
#needs: [combine_codelists]
outputs:
highly_sensitive:
cohort: output/input_health_non_mh.csv
combine_wide_data:
run: r:latest analysis/combine_wide_data.R
needs: [generate_wide_non_health, generate_wide_health_mh, generate_wide_health_non_mh]
outputs:
highly_sensitive:
cohort: output/input_cis_wide.csv
transform_cis_wide_to_long:
run: r:latest analysis/cis_wide_to_long.R
needs: [combine_wide_data]
outputs:
highly_sensitive:
cohort: output/input_cis_long.csv
reconcile_snomed_ctv3:
run: r:latest analysis/reconcile_snomed_ctv3.R
needs: [transform_cis_wide_to_long]
outputs:
highly_sensitive:
cohort: output/input_reconciled.csv
bmi: output/bmi_summary_table_info_before_cap.csv
derive_exposed:
run: r:latest analysis/exposed_population.R
needs: [reconcile_snomed_ctv3]
outputs:
highly_sensitive:
cohort: output/cis_exposed.csv
derive_controls:
run: r:latest analysis/control_population.R
needs: [reconcile_snomed_ctv3]
outputs:
highly_sensitive:
cohort: output/cis_control.csv
perform_matching:
run: r:latest analysis/create_controls.R
needs: [derive_exposed, derive_controls]
outputs:
highly_sensitive:
incidence: output/incidence_group.csv
prevalence: output/prevalence_group.csv
exacerbated: output/exacerbated_group.csv
adjust_matched_groups:
run: r:latest analysis/adjust_groups.R
needs: [perform_matching]
outputs:
highly_sensitive:
incidence: output/adjusted_incidence_group.csv
prevalence: output/adjusted_prevalence_group.csv
descriptive_stats:
run: r:latest analysis/descriptive_statistics.R
needs: [adjust_matched_groups]
outputs:
moderately_sensitive:
incidence_cat_stats: output/incidence_cat_stats.csv
incidence_con_stats: output/incidence_con_stats.csv
prevalence_cat_stats: output/prevalence_cat_stats.csv
prevalence_con_stats: output/prevalence_con_stats.csv
incidence_bmi: output/incidence_cont_bmi_stats.csv
prevalence_bmi: output/prevalence_cont_bmi_stats.csv
cumulative_incidence:
run: r:latest analysis/cumulative_incidence_curves.R
needs: [adjust_matched_groups]
outputs:
highly_sensitive:
inc_t: output/incidence_t.csv
prev_t: output/prevalence_t.csv
moderately_sensitive:
inc_surv: output/incidence_surv.jpg
prev_surv: output/prevalence_surv.jpg
hazard_ratios:
run: r:latest analysis/hazard_ratios.R
needs: [cumulative_incidence]
outputs:
moderately_sensitive:
temp: output/inc_hr_placeholder.csv
temp2: output/prev_hr_placeholder.csv
cox_inc1: output/cox_graph_inc_no_adj.jpg
cox_inc2: output/cox_graph_inc_min_adj.jpg
cox_inc3: output/cox_graph_inc_full_adj.jpg
cox_prev1: output/cox_graph_prev_no_adj.jpg
cox_prev2: output/cox_graph_prev_min_adj.jpg
cox_prev3: output/cox_graph_prev_full_adj.jpg
res_inc1: output/res_no_inc.jpg
res_inc2: output/res_min_inc.jpg
res_inc3: output/res_full_inc.jpg
res_prev1: output/res_no_prev.jpg
res_prev2: output/res_min_prev.jpg
res_prev3: output/res_full_prev.jpg
sch_res1: output/schoenfled_inc_no.csv
sch_res2: output/schoenfled_inc_min.csv
sch_res3: output/schoenfled_inc_full.csv
sch_res4: output/schoenfled_prev_no.csv
sch_res5: output/schoenfled_prev_min.csv
sch_res6: output/schoenfled_prev_full.csv
event_rates_incidence:
run: r:latest analysis/event_rates_incidence.R
needs: [cumulative_incidence]
outputs:
moderately_sensitive:
incidence_event_rates: output/event_counts_and_rates_incidence.csv
event_rates_prevalence:
run: r:latest analysis/event_rates_prevalence.R
needs: [cumulative_incidence]
outputs:
moderately_sensitive:
incidence_event_rates: output/event_counts_and_rates_prevalence.csv
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime:
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- covid_mental_health
- Requested by
- Klaudia Rzepnicka
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 0e0b08a
- Requested actions
-
-
run_all
-
Code comparison
Compare the code used in this Job Request