Job request: 6332
- Organisation:
- University of Bristol
- Workspace:
- post-covid-vaccinated
- ID:
- btw2vpm74rm7f7ak
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 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.
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Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 400000
actions:
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml DIRECTLY
## This file is created by create_project_actions.R
## Edit and run create_project_actions.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
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_vaccinated:
run: r:latest analysis/preprocess_data.R vaccinated
needs:
- generate_study_population_index
- generate_study_population_vaccinated
- generate_study_population_electively_unvaccinated
outputs:
moderately_sensitive:
describe: output/describe_input_vaccinated_*.txt
highly_sensitive:
cohort: output/input_vaccinated.rds
venn: output/venn_vaccinated.rds
preprocess_data_electively_unvaccinated:
run: r:latest analysis/preprocess_data.R electively_unvaccinated
needs:
- generate_study_population_index
- generate_study_population_vaccinated
- generate_study_population_electively_unvaccinated
outputs:
moderately_sensitive:
describe: output/describe_input_electively_unvaccinated_*.txt
highly_sensitive:
cohort: output/input_electively_unvaccinated.rds
venn: output/venn_electively_unvaccinated.rds
stage1_data_cleaning_both:
run: r:latest analysis/Stage1_data_cleaning.R both
needs:
- preprocess_data_vaccinated
- preprocess_data_electively_unvaccinated
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:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
table2: output/table2_*.csv
stage4_venn_diagram_both:
run: r:latest analysis/venn_diagram.R both
needs:
- preprocess_data_vaccinated
- preprocess_data_electively_unvaccinated
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
venn_diagram: output/venn_diagram_*.svg
venn_diagram_number_check: output/venn_diagram_number_check_*.csv
## Apply cox model for ami
Analysis_cox_ami:
run: r:latest analysis/01_pipe.R ami
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_ami.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_ami.html
analyses_not_run: output/analyses_not_run_ami.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_ami.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_ami.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_ami.csv
compiled_event_counts: output/compiled_event_counts_ami.csv
## Apply cox model for stroke_isch
Analysis_cox_stroke_isch:
run: r:latest analysis/01_pipe.R stroke_isch
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_stroke_isch.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_stroke_isch.html
analyses_not_run: output/analyses_not_run_stroke_isch.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_stroke_isch.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_stroke_isch.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_stroke_isch.csv
compiled_event_counts: output/compiled_event_counts_stroke_isch.csv
## Apply cox model for dvt
Analysis_cox_dvt:
run: r:latest analysis/01_pipe.R dvt
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_dvt.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_dvt.html
analyses_not_run: output/analyses_not_run_dvt.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_dvt.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_dvt.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_dvt.csv
compiled_event_counts: output/compiled_event_counts_dvt.csv
## Apply cox model for pe
Analysis_cox_pe:
run: r:latest analysis/01_pipe.R pe
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_pe.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_pe.html
analyses_not_run: output/analyses_not_run_pe.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_pe.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_pe.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_pe.csv
compiled_event_counts: output/compiled_event_counts_pe.csv
## Apply cox model for tia
Analysis_cox_tia:
run: r:latest analysis/01_pipe.R tia
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_tia.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_tia.html
analyses_not_run: output/analyses_not_run_tia.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_tia.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_tia.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_tia.csv
compiled_event_counts: output/compiled_event_counts_tia.csv
## Apply cox model for stroke_sah_hs
Analysis_cox_stroke_sah_hs:
run: r:latest analysis/01_pipe.R stroke_sah_hs
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_stroke_sah_hs.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_stroke_sah_hs.html
analyses_not_run: output/analyses_not_run_stroke_sah_hs.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_stroke_sah_hs.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_stroke_sah_hs.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_stroke_sah_hs.csv
compiled_event_counts: output/compiled_event_counts_stroke_sah_hs.csv
## Apply cox model for hf
Analysis_cox_hf:
run: r:latest analysis/01_pipe.R hf
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_hf.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_hf.html
analyses_not_run: output/analyses_not_run_hf.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_hf.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_hf.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_hf.csv
compiled_event_counts: output/compiled_event_counts_hf.csv
## Apply cox model for angina
Analysis_cox_angina:
run: r:latest analysis/01_pipe.R angina
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_angina.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_angina.html
analyses_not_run: output/analyses_not_run_angina.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_angina.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_angina.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_angina.csv
compiled_event_counts: output/compiled_event_counts_angina.csv
## Apply cox model for ate
Analysis_cox_ate:
run: r:latest analysis/01_pipe.R ate
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_ate.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_ate.html
analyses_not_run: output/analyses_not_run_ate.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_ate.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_ate.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_ate.csv
compiled_event_counts: output/compiled_event_counts_ate.csv
## Apply cox model for vte
Analysis_cox_vte:
run: r:latest analysis/01_pipe.R vte
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_vte.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_vte.html
analyses_not_run: output/analyses_not_run_vte.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_vte.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_vte.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_vte.csv
compiled_event_counts: output/compiled_event_counts_vte.csv
## Apply cox model for depression
Analysis_cox_depression:
run: r:latest analysis/01_pipe.R depression
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_depression.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_depression.html
analyses_not_run: output/analyses_not_run_depression.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_depression.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_depression.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_depression.csv
compiled_event_counts: output/compiled_event_counts_depression.csv
## Apply cox model for anxiety_general
Analysis_cox_anxiety_general:
run: r:latest analysis/01_pipe.R anxiety_general
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_anxiety_general.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_anxiety_general.html
analyses_not_run: output/analyses_not_run_anxiety_general.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_anxiety_general.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_anxiety_general.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_anxiety_general.csv
compiled_event_counts: output/compiled_event_counts_anxiety_general.csv
## Apply cox model for anxiety_ocd
Analysis_cox_anxiety_ocd:
run: r:latest analysis/01_pipe.R anxiety_ocd
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_anxiety_ocd.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_anxiety_ocd.html
analyses_not_run: output/analyses_not_run_anxiety_ocd.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_anxiety_ocd.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_anxiety_ocd.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_anxiety_ocd.csv
compiled_event_counts: output/compiled_event_counts_anxiety_ocd.csv
## Apply cox model for anxiety_ptsd
Analysis_cox_anxiety_ptsd:
run: r:latest analysis/01_pipe.R anxiety_ptsd
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_anxiety_ptsd.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_anxiety_ptsd.html
analyses_not_run: output/analyses_not_run_anxiety_ptsd.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_anxiety_ptsd.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_anxiety_ptsd.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_anxiety_ptsd.csv
compiled_event_counts: output/compiled_event_counts_anxiety_ptsd.csv
## Apply cox model for eating_disorders
Analysis_cox_eating_disorders:
run: r:latest analysis/01_pipe.R eating_disorders
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_eating_disorders.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_eating_disorders.html
analyses_not_run: output/analyses_not_run_eating_disorders.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_eating_disorders.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_eating_disorders.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_eating_disorders.csv
compiled_event_counts: output/compiled_event_counts_eating_disorders.csv
## Apply cox model for serious_mental_illness
Analysis_cox_serious_mental_illness:
run: r:latest analysis/01_pipe.R serious_mental_illness
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_serious_mental_illness.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_serious_mental_illness.html
analyses_not_run: output/analyses_not_run_serious_mental_illness.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_serious_mental_illness.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_serious_mental_illness.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_serious_mental_illness.csv
compiled_event_counts: output/compiled_event_counts_serious_mental_illness.csv
## Apply cox model for self_harm_10plus
Analysis_cox_self_harm_10plus:
run: r:latest analysis/01_pipe.R self_harm_10plus
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_self_harm_10plus.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_self_harm_10plus.html
analyses_not_run: output/analyses_not_run_self_harm_10plus.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_self_harm_10plus.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_self_harm_10plus.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_self_harm_10plus.csv
compiled_event_counts: output/compiled_event_counts_self_harm_10plus.csv
## Apply cox model for self_harm_15plus
Analysis_cox_self_harm_15plus:
run: r:latest analysis/01_pipe.R self_harm_15plus
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_self_harm_15plus.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_self_harm_15plus.html
analyses_not_run: output/analyses_not_run_self_harm_15plus.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_self_harm_15plus.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_self_harm_15plus.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_self_harm_15plus.csv
compiled_event_counts: output/compiled_event_counts_self_harm_15plus.csv
## Apply cox model for suicide
Analysis_cox_suicide:
run: r:latest analysis/01_pipe.R suicide
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_suicide.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_suicide.html
analyses_not_run: output/analyses_not_run_suicide.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_suicide.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_suicide.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_suicide.csv
compiled_event_counts: output/compiled_event_counts_suicide.csv
## Apply cox model for addiction
Analysis_cox_addiction:
run: r:latest analysis/01_pipe.R addiction
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
compiled_hrs_html: output/suppressed_compiled_HR_results_addiction.html
compiled_event_counts_html: output/suppressed_compiled_event_counts_addiction.html
analyses_not_run: output/analyses_not_run_addiction.csv
compiled_hrs_csv: output/suppressed_compiled_HR_results_addiction.csv
compiled_event_counts_csv: output/suppressed_compiled_event_counts_addiction.csv
highly_sensitive:
compiled_hrs: output/compiled_HR_results_addiction.csv
compiled_event_counts: output/compiled_event_counts_addiction.csv
Timeline
-
Created:
-
Started:
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Finished:
-
Runtime: 182:52:25
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- post-covid-vaccinated
- Requested by
- Venexia Walker
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 430b38e
- Requested actions
-
-
Analysis_cox_stroke_sah_hs
-
Analysis_cox_hf
-
Analysis_cox_angina
-
Analysis_cox_ate
-
Analysis_cox_vte
-
Analysis_cox_depression
-
Analysis_cox_anxiety_general
-
Analysis_cox_anxiety_ocd
-
Analysis_cox_anxiety_ptsd
-
Analysis_cox_eating_disorders
-
Analysis_cox_serious_mental_illness
-
Analysis_cox_self_harm_10plus
-
Analysis_cox_self_harm_15plus
-
Analysis_cox_suicide
-
Analysis_cox_addiction
-