Job request: 3369
- Organisation:
- Bennett Institute
- Workspace:
- pulse_oximetry_sro
- ID:
- xoatxyw5xsl76isd
This page shows the technical details of what happened when the authorised researcher Colm Andrews 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:
-
xbkhdwwnhlvpfoet
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 10000
actions:
generate_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_cohort --output-format feather
outputs:
highly_sensitive:
cohort: output/input_cohort.feather
count_by_strata:
run: python:latest python analysis/all_time_counts.py
needs: [generate_cohort]
outputs:
moderately_sensitive:
table: output/counts_table_emis.csv
table_historic: output/counts_table_hist_emis.csv
practice_distribution: output/practice_distribution_emis.csv
practice_distribution_historical: output/practice_distribution_historical_emis.csv
per_week: output/code_use_per_week_pulse_oximetry_emis.csv
historic_per_week: output/code_use_per_week_historic_pulse_oximetry_emis.csv
code_table: output/all_pulse_oximetry_codes_emis.csv
historic_code_table: output/all_historic_pulse_oximetry_codes_emis.csv
practice_summ: output/practice_summ_emis.txt
generate_plots:
run: python:latest python analysis/local_graphs.py
needs: [count_by_strata]
outputs:
moderately_sensitive:
plot_per week: output/code_use_per_week_emis.svg
historical_plot_per week: output/historical_code_use_per_week_emis.svg
total_plot_per week: output/total_code_use_per_week_emis.svg
plot_distribution: output/practice_distribution_emis.svg
plot_historical_distribution: output/practice_historical_distribution_emis.svg
plot_total_distribution: output/total_practice_distribution_emis.svg
# hazard_ratio:
# run: r:latest analysis/hr.r
# needs: [generate_cohort]
# outputs:
# moderately_sensitive:
# PHsum: output/Cox_summary.csv
# PHassumpt: output/Cox_assumption.csv
# PHresid: output/deviance_resid.svg
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:02:11
These timestamps are generated and stored using the UTC timezone on the EMIS backend.
Job information
- Status
-
Failed
- Backend
- EMIS
- Workspace
- pulse_oximetry_sro
- Requested by
- Colm Andrews
- Branch
- master
- Force run dependencies
- No
- Git commit hash
- c3660a0
- Requested actions
-
-
count_by_strata
-
Code comparison
Compare the code used in this Job Request