Job request: 19149
- Organisation:
- Bennett Institute
- Workspace:
- pax-usernonuser
- ID:
- 73gwt4on3dqino35
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:
-
czn4ucvmsxht2ey5
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
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
describe_trt_preds_all_ci:
run: r:latest analysis/descriptives/describe_trt_preds.R all_ci
needs: [data_process]
outputs:
highly_sensitive:
data1: output/descriptives/psModel_all_ci.rds
moderately_sensitive:
png1: output/descriptives/psOverlap_untrimmed_all_ci.png
png2: output/descriptives/psOverlap_trimmed_all_ci.png
png3: output/descriptives/psCoefs_all_ci.png
csv1: output/descriptives/trimming_descriptives_all_ci.csv
describe_trt_preds_excl_drugs_dnu:
run: r:latest analysis/descriptives/describe_trt_preds.R ci_drugs_dnu
needs: [data_process]
outputs:
highly_sensitive:
data1: output/descriptives/psModel_excl_drugs_dnu.rds
moderately_sensitive:
png1: output/descriptives/psOverlap_untrimmed_excl_drugs_dnu.png
png2: output/descriptives/psOverlap_trimmed_excl_drugs_dnu.png
png3: output/descriptives/psCoefs_excl_drugs_dnu.png
csv1: output/descriptives/trimming_descriptives_excl_drugs_dnu.csv
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
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
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:03:38
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
- 22baad8
- Requested actions
-
-
create_flowchart
-
Code comparison
Compare the code used in this Job Request