Job request: 24241
- Organisation:
- University of Bristol
- Workspace:
- metformin-covid-main
- ID:
- iyhydtn7moiozneb
This page shows the technical details of what happened when the authorised researcher Alain Amstutz 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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4ump5gu2hxqgcvsu
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5b6xhuj75aczt2rj
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ziyj6cdetnlkna4t
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tri5dqlic3ljgljh
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doaskwusdhbnrnox - Error:
- nonzero_exit: Job exited with an error
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cpthkyo3nc7wu2dg - Error:
- dependency_failed: Not starting as dependency failed
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jgodosmvtohaa6fm - Error:
- dependency_failed: Not starting as dependency failed
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kzge7qy44izjhy4w - Error:
- dependency_failed: Not starting as dependency failed
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6d63warciskpetww - Error:
- dependency_failed: Not starting as dependency failed
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dssnu52baf6twit5 - Error:
- dependency_failed: Not starting as dependency failed
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gft6btoltipwishy - Error:
- dependency_failed: Not starting as dependency failed
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b3ddmurbarlqsxn4 - Error:
- dependency_failed: Not starting as dependency failed
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u3ucyr5cwo3lbkfl - Error:
- dependency_failed: Not starting as dependency failed
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2xjkxlbdtjmdiqt4 - Error:
- dependency_failed: Not starting as dependency failed
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ffabgageavk3njou - Error:
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hfc3nc532dquxupn - Error:
- dependency_failed: Not starting as dependency failed
Pipeline
Show project.yaml
version: '3.0'
# Ignore this`expectation` block. It is required but not used, and will be removed in future versions.
expectations:
population_size: 1000
actions:
study_dates:
run: r:latest analysis/metadates.R
outputs:
highly_sensitive:
study_dates_json: output/study_dates.json
generate_dataset_dm_algo:
run: ehrql:v1 generate-dataset analysis/dataset_definition_dm_algo.py --output output/dataset_dm_algo.arrow
needs:
- study_dates
outputs:
highly_sensitive:
dataset: output/dataset_dm_algo.arrow
data_process_dm_algo:
run: r:latest analysis/data_process_dm_algo.R
needs:
- generate_dataset_dm_algo
outputs:
highly_sensitive:
dataset: output/data/data_processed_dm_algo.csv.gz
#generate_dataset:
# run: ehrql:v1 generate-dataset analysis/dataset_definition_landmark.py --output output/dataset.arrow
# needs:
# - study_dates
# outputs:
# highly_sensitive:
# dataset: output/dataset.arrow
generate_dataset:
run: ehrql:v1 generate-dataset analysis/dataset_definition_t2dm.py --output output/dataset.arrow
needs:
- study_dates
- generate_dataset_dm_algo
- data_process_dm_algo
outputs:
highly_sensitive:
dataset: output/dataset.arrow
#data_process:
# run: r:latest analysis/data_process.R
# needs:
# - generate_dataset
# - data_process_dm_algo
# outputs:
# highly_sensitive:
# rds: output/data/data_processed.rds
# feather: output/data/data_plots.feather
# moderately_sensitive:
# csv: output/data_properties/*.csv
data_process:
run: r:latest analysis/data_process.R
needs:
- generate_dataset
outputs:
highly_sensitive:
rds: output/data/data_processed.rds
feather: output/data/data_plots.feather
moderately_sensitive:
csv: output/data_properties/*.csv
km_estimates_metfin:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/metfin
--exposure=exp_bin_metfin_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_metfin_anytime
--censor_date=out_date_severecovid
--max_fup=730
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/metfin/*.csv
km_estimates_metfin_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/metfin_mono
--exposure=exp_bin_metfin_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_metfin_mono_anytime
--censor_date=out_date_severecovid
--max_fup=730
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/metfin_mono/*.csv
km_estimates_dpp4_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/dpp4_mono
--exposure=exp_bin_dpp4_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_dpp4_mono_anytime
--censor_date=out_date_severecovid
--max_fup=730
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/dpp4_mono/*.csv
km_estimates_tzd_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/tzd_mono
--exposure=exp_bin_tzd_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_tzd_mono_anytime
--censor_date=out_date_severecovid
--max_fup=730
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/tzd_mono/*.csv
km_estimates_sglt2_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/sglt2_mono
--exposure=exp_bin_sglt2_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_sglt2_mono_anytime
--censor_date=out_date_severecovid
--max_fup=730
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/sglt2_mono/*.csv
km_estimates_sulfo_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/sulfo_mono
--exposure=exp_bin_sulfo_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_sulfo_mono_anytime
--censor_date=out_date_severecovid
--max_fup=730
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/sulfo_mono/*.csv
km_estimates_glp1_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/glp1_mono
--exposure=exp_bin_glp1_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_glp1_mono_anytime
--censor_date=out_date_severecovid
--max_fup=730
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/glp1_mono/*.csv
km_estimates_megli_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/megli_mono
--exposure=exp_bin_megli_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_megli_mono_anytime
--censor_date=out_date_severecovid
--max_fup=730
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/megli_mono/*.csv
km_estimates_agi_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/agi_mono
--exposure=exp_bin_agi_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_agi_mono_anytime
--censor_date=out_date_severecovid
--max_fup=730
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/agi_mono/*.csv
km_estimates_insulin_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/insulin_mono
--exposure=exp_bin_insulin_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_insulin_mono_anytime
--censor_date=out_date_severecovid
--max_fup=730
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/insulin_mono/*.csv
plot_km_estimates:
run: r:latest analysis/km_plot.R
needs:
- km_estimates_metfin
- km_estimates_metfin_mono
- km_estimates_dpp4_mono
- km_estimates_tzd_mono
- km_estimates_sglt2_mono
- km_estimates_sulfo_mono
- km_estimates_glp1_mono
- km_estimates_megli_mono
- km_estimates_agi_mono
- km_estimates_insulin_mono
outputs:
moderately_sensitive:
plot: output/data_properties/*.png
# km_estimates_metfin:
# run: kaplan-meier-function:v0.0.2
# --df_input=output/data/data_plots.feather
# --dir_output=output/km_estimates_metfin.feather ### double-check!!!
# --exposure=exp_bin_metfin_anytime
# --origin_date=elig_date_t2dm
# --event_date=exp_date_metfin_anytime
# --censor_date=out_date_severecovid
# --plot=TRUE
# needs:
# - data_process
# outputs:
# highly_sensitive:
# output: output/km_estimates_metfin.feather
Timeline
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Created:
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Started:
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Finished:
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Runtime: 25:17:00
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- metformin-covid-main
- Requested by
- Alain Amstutz
- Branch
- main
- Force run dependencies
- Yes
- Git commit hash
- d5e1268
- Requested actions
-
-
study_dates -
generate_dataset_dm_algo -
data_process_dm_algo -
generate_dataset -
data_process -
km_estimates_metfin -
km_estimates_metfin_mono -
km_estimates_dpp4_mono -
km_estimates_tzd_mono -
km_estimates_sglt2_mono -
km_estimates_sulfo_mono -
km_estimates_glp1_mono -
km_estimates_megli_mono -
km_estimates_agi_mono -
km_estimates_insulin_mono -
plot_km_estimates
-
Code comparison
Compare the code used in this Job Request