Job request: 20441
- Organisation:
- Bennett Institute
- Workspace:
- pax-usernonuser
- ID:
- 3gitckftsytgm5du
This page shows the technical details of what happened when the authorised researcher Linda Nab 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:
-
kpra46oh65u7uy5p
-
- Job identifier:
-
ou3ssl4fxvh7cjuk
-
- Job identifier:
-
yuihavyl3nis2tpu
-
- Job identifier:
-
3wogbguduk6pivoa
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 5000
actions:
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Data extraction
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input.csv.gz
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_study_population_pax_trt:
run: cohortextractor:latest generate_cohort --study-definition study_definition_pax_trt --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_pax_trt.csv.gz
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Data cleaning and description
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
data_process:
run: r:latest analysis/data_process.R
needs: [generate_study_population]
outputs:
highly_sensitive:
data1: output/data/data_processed.rds
data2: output/data/data_processed_grace6.rds
data3: output/data/data_processed_grace7.rds
data4: output/data/data_processed_grace8.rds
data1_excl: output/data/data_processed_excl_contraindicated.rds
data2_excl: output/data/data_processed_excl_contraindicated_grace6.rds
data3_excl: output/data/data_processed_excl_contraindicated_grace7.rds
data4_excl: output/data/data_processed_excl_contraindicated_grace8.rds
rds1: output/data_properties/n_excluded.rds
rds2: output/data_properties/n_excluded_contraindicated.rds
data_process_flowchart:
run: r:latest analysis/data_process_flowchart.R
needs: [generate_study_population_flowchart]
outputs:
highly_sensitive:
data: output/data/data_flowchart_processed.rds
data_properties:
run: r:latest analysis/data_properties/data_properties.R output/data/data_processed.rds output/data_properties
needs: [data_process]
outputs:
moderately_sensitive:
txt1: output/data_properties/data_processed_skim.txt
txt2: output/data_properties/data_processed_coltypes.txt
txt3: output/data_properties/data_processed_tabulate.txt
create_flowchart:
run: r:latest analysis/flowchart.R
needs: [data_process_flowchart, data_process]
outputs:
moderately_sensitive:
csv1: output/flowchart/flowchart.csv
csv2: output/flowchart/flowchart_redacted.csv
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Descriptive analyses
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
describe_distr_trt_init:
run: r:latest analysis/descriptives/describe_distr_trt_init.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/descriptives/distr_pax_init.csv
csv2: output/descriptives/distr_pax_init_red.csv
describe_outcomes_in_trt_window:
run: r:latest analysis/descriptives/describe_outcomes_in_trt_window.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/descriptives/outcomes_in_trt_window.csv
csv2: output/descriptives/outcomes_in_trt_window_red.csv
csv3: output/descriptives/outcomes_day0.csv
describe_prop_trt:
run: r:latest analysis/descriptives/describe_prop_trt.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/descriptives/prop_trt.csv
csv2: output/descriptives/prop_trt_red.csv
describe_trt_contra:
run: r:latest analysis/descriptives/describe_trt_contra.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/descriptives/trt_contra.csv
csv2: output/descriptives/trt_contra_red.csv
csvs1: output/descriptives/n_codes_*.csv
describe_trt_preds_all_ci_pax:
run: r:latest analysis/descriptives/describe_trt_preds.R all_ci Paxlovid
needs: [data_process]
outputs:
highly_sensitive:
model1: output/descriptives/psModel_Paxlovid_all_ci.rds
moderately_sensitive:
csv1: output/descriptives/psDens_untrimmed_Paxlovid_all_ci.csv
csv2: output/descriptives/psDens_trimmed_Paxlovid_all_ci.csv
csv3: output/descriptives/psCoefs_Paxlovid_all_ci.csv
csv4: output/descriptives/trimming_descriptives_Paxlovid_all_ci.csv
describe_trt_preds_all_ci_sot:
run: r:latest analysis/descriptives/describe_trt_preds.R all_ci Sotrovimab
needs: [data_process]
outputs:
highly_sensitive:
data1: output/descriptives/psModel_Sotrovimab_all_ci.rds
moderately_sensitive:
csv1: output/descriptives/psDens_untrimmed_Sotrovimab_all_ci.csv
csv2: output/descriptives/psDens_trimmed_Sotrovimab_all_ci.csv
csv3: output/descriptives/psCoefs_Sotrovimab_all_ci.csv
csv4: output/descriptives/trimming_descriptives_Sotrovimab_all_ci.csv
describe_trt_preds_all_ci_mol:
run: r:latest analysis/descriptives/describe_trt_preds.R all_ci Molnupiravir
needs: [data_process]
outputs:
highly_sensitive:
data1: output/descriptives/psModel_Molnupiravir_all_ci.rds
moderately_sensitive:
csv1: output/descriptives/psDens_untrimmed_Molnupiravir_all_ci.csv
csv2: output/descriptives/psDens_trimmed_Molnupiravir_all_ci.csv
csv3: output/descriptives/psCoefs_Molnupiravir_all_ci.csv
csv4: output/descriptives/trimming_descriptives_Molnupiravir_all_ci.csv
visualise_trt_preds_dens:
run: r:latest analysis/descriptives/visualise_trt_preds_dens.R
needs: [describe_trt_preds_all_ci_pax, describe_trt_preds_all_ci_sot, describe_trt_preds_all_ci_mol]
outputs:
moderately_sensitive:
png1: output/descriptives/psOverlap_untrimmed_*_all_ci.png
png2: output/descriptives/psOverlap_trimmed_*_all_ci.png
create_table1:
run: r:latest analysis/descriptives/table1.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/tables/table1.csv
csv2: output/tables/table1_red.csv
csv3: output/tables/table1_red_unf.csv
csv4: output/tables/table1_full.csv
csv5: output/tables/table1_full_red.csv
csv6: output/tables/table1_full_red_unf.csv
csv7: output/tables/table1_trt_untrt.csv
csv8: output/tables/table1_trt_untrt_red.csv
csv9: output/tables/table1_trt_untrt_red_unf.csv
describe_trt_groups:
run: r:latest analysis/descriptives/describe_trt_groups.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/descriptives/trt_groups.csv
csv2: output/descriptives/trt_groups_red.csv
describe_fup_outcomes:
run: r:latest analysis/descriptives/describe_fup_outcomes.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/descriptives/overview_fup_outcomes.csv
csv2: output/descriptives/overview_fup_outcomes_red.csv
describe_postest_pop:
run: r:latest analysis/descriptives/describe_postest_pop.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/descriptives/postest_pop.csv
csv2: output/descriptives/postest_pop_red.csv
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Sequential trials
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
data_prepare_seq_trials:
run: r:latest analysis/seq_trials/prepare_data.R
needs: [data_process]
outputs:
highly_sensitive:
data1: output/data/data_seq_trials_monthly.feather
data2: output/data/data_seq_trials_bimonthly.feather
data3: output/data/data_seq_trials_weekly.feather
describe_size_trials:
run: r:latest analysis/seq_trials/descriptives/describe_size_trials.R
needs: [data_prepare_seq_trials]
outputs:
moderately_sensitive:
csv1: output/seq_trials/descriptives/data_flow_seq_trials_monthly.csv
csv2: output/seq_trials/descriptives/data_flow_seq_trials_bimonthly.csv
csv3: output/seq_trials/descriptives/data_flow_seq_trials_weekly.csv
csv4: output/seq_trials/descriptives/data_flow_seq_trials_monthly_red.csv
csv5: output/seq_trials/descriptives/data_flow_seq_trials_bimonthly_red.csv
csv6: output/seq_trials/descriptives/data_flow_seq_trials_weekly_red.csv
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:53:01
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- pax-usernonuser
- Requested by
- Linda Nab
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 6a35eb5
- Requested actions
-
-
describe_trt_preds_all_ci_pax
-
describe_trt_preds_all_ci_sot
-
describe_trt_preds_all_ci_mol
-
visualise_trt_preds_dens
-
Code comparison
Compare the code used in this Job Request