This page shows the technical details of what happened when authorised researcher Venexia Walker requested one or more actions to be run against real patient data in the post-covid-vaccinated 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
| ID | Status | Action |
|---|---|---|
| bknhtzxe6i67lry3 | succeeded | stage4_table2_both |
Pipeline
Show Hide project.yaml
version: '3.0'
expectations:
population_size: 500000
actions:
active_analyses:
run: r:latest analysis/active_analyses.R
outputs:
highly_sensitive:
active_analyses: output/active_analyses.rds
vax_eligibility_inputs:
run: r:latest analysis/vax_eligibility_inputs.R
outputs:
highly_sensitive:
vax_study_dates_json: output/vax_study_dates.json
vax_jcvi_groups: output/vax_jcvi_groups.csv
vax_eligible_dates: output/vax_eligible_dates.csv
generate_study_population_electively_unvaccinated:
run: cohortextractor:latest generate_cohort --study-definition study_definition_electively_unvaccinated --output-format feather
needs: [vax_eligibility_inputs]
outputs:
highly_sensitive:
cohort: output/input_electively_unvaccinated.feather
generate_study_population_vaccinated:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated --output-format feather
outputs:
highly_sensitive:
cohort: output/input_vaccinated.feather
generate_study_population_index:
run: cohortextractor:latest generate_cohort --study-definition study_definition_index --output-format feather
outputs:
highly_sensitive:
cohort: output/input_index.feather
preprocess_data:
run: r:latest analysis/preprocess_data.R
needs: [generate_study_population_index, generate_study_population_vaccinated, generate_study_population_electively_unvaccinated]
outputs:
moderately_sensitive:
describe: output/describe_*.txt
highly_sensitive:
cohort: output/input_*.rds
venn: output/venn_*.rds
stage1_data_cleaning_both:
run: r:latest analysis/Stage1_data_cleaning.R both
needs: [preprocess_data]
outputs:
moderately_sensitive:
refactoring: output/meta_data_factors_*.csv
QA_rules: output/QA_summary_*.csv
IE_criteria: output/Cohort_flow_*.csv
highly_sensitive:
cohort: output/input_*_stage1.rds
stage2_missing_table1_both:
run: r:latest analysis/Stage2_missing_table1.R both
needs: [stage1_data_cleaning_both]
outputs:
moderately_sensitive:
Missing_RangeChecks: output/Check_missing_range_*.csv
DateChecks: output/Check_dates_range_*.csv
Descriptive_Table: output/Table1_*.csv
stage4_table2_both:
run: r:latest analysis/table_2.R both
needs: [active_analyses, stage1_data_cleaning_both]
outputs:
moderately_sensitive:
table2: output/table2_*.csv
venn_both:
run: r:latest analysis/venn_diagram.R both
needs: [active_analyses, preprocess_data, stage1_data_cleaning_both]
outputs:
moderately_sensitive:
venn_digram: output/venn_diagram_*.svg
venn_diagram_number_check: output/venn_diagram_number_check_*.csv
State
State is inferred from the related Jobs.
Status: Succeeded
Timings
Timings set to UTC timezone.
- Created:
- Started:
- Finished:
- Runtime: 12:08:32
Config
-
- Backend:
-
TPP
-
- Workspace:
- post-covid-vaccinated
-
- Branch:
main
-
- Creator:
- venexia
-
- Force run dependencies:
- False
-
- Git Commit Hash:
- 9a9278e
-
Requested actions:
stage4_table2_both