Job request: 4234
- Organisation:
- The London School of Hygiene & Tropical Medicine
- Workspace:
- covid-vaccine-neuro-research
- ID:
- zcbijnzymesrcyjx
This page shows the technical details of what happened when the authorised researcher John Tazare 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
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lepyjijm3c74hdx3
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tnvah35fwibyozyz
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aimowrrhzk77a3mr
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oots2daidn6yicgl
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o7sepshz6zcw22nv
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zjzljmlcalf5wudz
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exmnlawenf3kazbc
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i3hwidsuass2yj2s
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j4huibnyijgali6i
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y6gystyntpnpdj7s
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c7pc6azq47gqgzgp
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mavjgilus2luwsjp
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hsqipqh6juhdto27
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lsymyvvvodbr4n2q
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- Job identifier:
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ct5gdymikddez2hm
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- Job identifier:
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y5qwbv6ekk3aocxb
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 5000
actions:
# extract relevant cohorts
generate_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sccs_and_historical_cohort
outputs:
highly_sensitive:
cohort: output/input_sccs_and_historical_cohort.csv
apply_exclusion_criteria:
run: stata-mp:latest analysis/apply_exclusion_criteria.do
needs: [generate_cohort]
outputs:
moderately_sensitive:
log: output/logs/apply_exclusion_criteria.log
highly_sensitive:
cohort_controls: output/input_historical_controls.csv
cohort_az_cases: output/input_AZ_cases.csv
cohort_pfizer_cases: output/input_PF_cases.csv
cohort_moderna_cases: output/input_MOD_cases.csv
denominators: output/tables/denominators*
# main analyses
SCCS_first_dose_only_primary_AZ:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do AZ
needs: [apply_exclusion_criteria]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_AZ.log
results: output/tables/results_summary_primary_AZ*
highly_sensitive:
sccs_pop_BP: output/temp_data/sccs_popn_BP_AZ*
sccs_pop_TM: output/temp_data/sccs_popn_TM_AZ*
sccs_pop_GBS: output/temp_data/sccs_popn_GBS_AZ*
sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_AZ*
sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_AZ*
sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_AZ*
SCCS_first_dose_only_primary_PF:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do PF
needs: [apply_exclusion_criteria]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_PF.log
results: output/tables/results_summary_primary_PF*
highly_sensitive:
sccs_pop_BP: output/temp_data/sccs_popn_BP_PF*
sccs_pop_TM: output/temp_data/sccs_popn_TM_PF*
sccs_pop_GBS: output/temp_data/sccs_popn_GBS_PF*
sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_PF*
sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_PF*
sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_PF*
SCCS_first_dose_only_primary_MOD:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_primary.do MOD
needs: [apply_exclusion_criteria]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_neuro_primary_MOD.log
results: output/tables/results_summary_primary_MOD*
highly_sensitive:
sccs_pop_BP: output/temp_data/sccs_popn_BP_MOD*
sccs_pop_TM: output/temp_data/sccs_popn_TM_MOD*
sccs_pop_GBS: output/temp_data/sccs_popn_GBS_MOD*
sccs_cutp_BP: output/temp_data/sccs_cutp_data_BP_MOD*
sccs_cutp_TM: output/temp_data/sccs_cutp_data_TM_MOD*
sccs_cutp_GBS: output/temp_data/sccs_cutp_data_GBS_MOD*
# baseline tables (AZ and PF only due to small MOD numbers)
SCCS_baseline_tables_AZ:
run: stata-mp:latest analysis/SCCS_baseline_tables.do AZ
needs: [SCCS_first_dose_only_primary_AZ]
outputs:
moderately_sensitive:
log: output/logs/SCCS_baseline_tables_AZ.log
tables: output/tables/baseline_AZ/*
SCCS_baseline_tables_PF:
run: stata-mp:latest analysis/SCCS_baseline_tables.do PF
needs: [SCCS_first_dose_only_primary_PF]
outputs:
moderately_sensitive:
log: output/logs/SCCS_baseline_tables_PF.log
tables: output/tables/baseline_PF/*
# check assumptions
SCCS_assumption_checking_AZ:
run: stata-mp:latest analysis/SCCS_assumption_checking.do AZ
needs: [SCCS_first_dose_only_primary_AZ]
outputs:
moderately_sensitive:
log: output/logs/SCCS_assumption_checking_AZ.log
plots_S1: output/plots/S1_exposure_centered_interval_AZ*
plots_S2: output/plots/S2_censored_futime_AZ*
SCCS_assumption_checking_PF:
run: stata-mp:latest analysis/SCCS_assumption_checking.do PF
needs: [SCCS_first_dose_only_primary_PF]
outputs:
moderately_sensitive:
log: output/logs/SCCS_assumption_checking_PF.log
plots_S1: output/plots/S1_exposure_centered_interval_PF*
plots_S2: output/plots/S2_censored_futime_PF*
# sensitivity analyses
## stratified analyses
SCCS_stratified_analyses_AZ:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_stratified.do AZ
needs: [SCCS_first_dose_only_primary_AZ]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_stratified_AZ.log
results: output/tables/results_summary_stratified_AZ.csv
SCCS_stratified_analyses_PF:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_stratified.do PF
needs: [SCCS_first_dose_only_primary_PF]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_stratified_PF.log
results: output/tables/results_summary_stratified_PF.csv
## changing risk windows
SCCS_vary_risk_windows_AZ:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_risk.do AZ
needs: [SCCS_first_dose_only_primary_AZ]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_risk_AZ.log
results: output/tables/results_summary_sens_risk_AZ.csv
SCCS_vary_risk_windows_PF:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro_sens_risk.do PF
needs: [SCCS_first_dose_only_primary_PF]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_neuro_sens_risk_PF.log
results: output/tables/results_summary_sens_risk_PF.csv
## second doses
SCCS_second_dose_AZ:
run: stata-mp:latest analysis/SCCS_first_second_dose_analyses_neuro.do AZ
needs: [SCCS_first_dose_only_primary_AZ, apply_exclusion_criteria]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_second_dose_analyses_neuro_AZ.log
results: output/tables/results_summary_second_doses_AZ.csv
SCCS_second_dose_PF:
run: stata-mp:latest analysis/SCCS_first_second_dose_analyses_neuro.do PF
needs: [SCCS_first_dose_only_primary_PF, apply_exclusion_criteria]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_second_dose_analyses_neuro_PF.log
results: output/tables/results_summary_second_doses_PF*
## AZ vs Pfizer
SCCS_comparative_AZ_Pfizer:
run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_sens_AZ_vs_PF.do
needs: [SCCS_first_dose_only_primary_AZ, SCCS_first_dose_only_primary_PF]
outputs:
moderately_sensitive:
log: output/logs/SCCS_first_dose_only_analyses_sens_AZ_vs_PF.log
results: output/tables/results_summary_sens_AZ_vs_PF.csv
Timeline
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Created:
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Finished:
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Runtime:
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- covid-vaccine-neuro-research
- Requested by
- John Tazare
- Branch
- main
- Force run dependencies
- Yes
- Git commit hash
- 3aaefeb
- Requested actions
-
-
run_all
-
Code comparison
Compare the code used in this Job Request