Job request: 7208

Organisation:: ISARIC
Workspace:: hdruk-os-covid-paeds
ID:: jsgj5drx3qdmw2ch

This page shows the technical details of what happened when the authorised researcher James Farrell requested one or more actions to be run against real patient data within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

highly_sensitive
- Researchers can never directly view these outputs
- Researchers can only request code is run against them
moderately_sensitive
- Can be viewed by an approved researcher by logging into a highly secure environment
- These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

Action:

generate_outpatient_2019_high

Status:

Succeeded

Job identifier:

itnmyoklbxm62ukx
Action:

generate_admissions_2020_high

Status:

Failed

Job identifier:

bormywmx2iucnnpu

Error:

nonzero_exit: Job exited with error code 1
Action:

generate_outpatient_2020_high

Status:

Failed

Job identifier:

qttaoyttpmitv3ao

Error:

nonzero_exit: Job exited with error code 1
Action:

generate_admissions_2022

Status:

Succeeded

Job identifier:

sjae7xfgfjkrenya
Action:

generate_contact_counts

Status:

Succeeded

Job identifier:

23o2txtypd3k472v
Action:

generate_admissions_2021_high

Status:

Failed

Job identifier:

affvziqjnrrpbiuq

Error:

nonzero_exit: Job exited with error code 1
Action:

generate_outpatient_2019

Status:

Succeeded

Job identifier:

jcldzv7wyyd5tkcq
Action:

generate_gp_2020

Status:

Succeeded

Job identifier:

msfrawrcx25ggrdv
Action:

generate_admissions_2018

Status:

Succeeded

Job identifier:

2keatg2f5aoy4y4m
Action:

generate_gp_2019

Status:

Succeeded

Job identifier:

37q5762ccgha2yqp
Action:

generate_outpatient_2021

Status:

Succeeded

Job identifier:

uhrqerqbx2uwjlbo
Action:

generate_admissions_2022_high

Status:

Succeeded

Job identifier:

fzqbqlzmajupnndy
Action:

generate_study_population

Status:

Succeeded

Job identifier:

7xpdjby2wtnhi45s
Action:

generate_gp_2019_high

Status:

Failed

Job identifier:

jhm2tw5ersabubwj

Error:

nonzero_exit: Job exited with error code 1
Action:

generate_gp_2021_high

Status:

Failed

Job identifier:

ijslah5emtxxyb2r

Error:

nonzero_exit: Job exited with error code 1
Action:

generate_gp_2021

Status:

Failed

Job identifier:

rorgkzp6v2taogcv

Error:

nonzero_exit: Job exited with error code 1
Action:

generate_admissions_2019

Status:

Succeeded

Job identifier:

36tyisacvomclagv
Action:

generate_gp_2022

Status:

Succeeded

Job identifier:

6zaom5nzgejdsl6n
Action:

generate_outpatient_2022_high

Status:

Succeeded

Job identifier:

4mljxuij6osrrobv
Action:

generate_gp_2020_high

Status:

Succeeded

Job identifier:

wzwolvzbhthgwqua
Action:

generate_gp_2022_high

Status:

Succeeded

Job identifier:

oed532qgyqyv5rmp
Action:

generate_admissions_2021

Status:

Succeeded

Job identifier:

ovlyxvxsw2f2y2vi
Action:

generate_outpatient_2020

Status:

Succeeded

Job identifier:

3eabql3534io2api
Action:

generate_admissions_2019_high

Status:

Failed

Job identifier:

os6jlflvti4orx3y

Error:

nonzero_exit: Job exited with error code 1
Action:

generate_admissions_2018_high

Status:

Failed

Job identifier:

fx6tmdhqr3wi7gmi

Error:

nonzero_exit: Job exited with error code 1
Action:

generate_outpatient_2021_high

Status:

Failed

Job identifier:

u44l7v3qjgwynqa2

Error:

nonzero_exit: Job exited with error code 1
Action:

generate_admissions_2020

Status:

Failed

Job identifier:

mbqwpg7eocdmeopm

Error:

nonzero_exit: Job exited with error code 1
Action:

generate_outpatient_2022

Status:

Succeeded

Job identifier:

li6lbhhd7sejwxgy
Action:

descriptives_count_data

Status:

Succeeded

Job identifier:

265gmdtqpepnhy6n
Action:

process_data

Status:

Failed

Job identifier:

5z4j2bzrogahs7mf

Error:

dependency_failed: Not starting as dependency failed
Action:

descriptives

Status:

Failed

Job identifier:

s6ych5puvc6sgpun

Error:

dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml

version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_contact_counts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_contact_counts --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_contact_counts.csv.gz

  descriptives_count_data:
    run: r:latest analysis/00_count_data.R
    needs: [generate_contact_counts]
    outputs:
      moderately_sensitive:
        plots: output/descriptive/counts/*.jpeg
        tables: output/descriptive/counts/*.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input.csv.gz

  generate_admissions_2018:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2018 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2018.csv.gz

  generate_admissions_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2019 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2019.csv.gz

  generate_admissions_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2020 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2020.csv.gz

  generate_admissions_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2021 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2021.csv.gz

  generate_admissions_2022:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2022 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2022.csv.gz

  generate_admissions_2018_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2018_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2018_high.csv.gz

  generate_admissions_2019_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2019_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2019_high.csv.gz

  generate_admissions_2020_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2020_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2020_high.csv.gz

  generate_admissions_2021_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2021_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2021_high.csv.gz

  generate_admissions_2022_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2022_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2022_high.csv.gz

  generate_gp_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2019 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2019.csv.gz

  generate_gp_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2020 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2020.csv.gz

  generate_gp_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2021 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2021.csv.gz

  generate_gp_2022:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2022 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2022.csv.gz

  generate_gp_2019_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2019_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2019_high.csv.gz

  generate_gp_2020_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2020_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2020_high.csv.gz

  generate_gp_2021_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2021_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2021_high.csv.gz

  generate_gp_2022_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2022_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2022_high.csv.gz

  generate_outpatient_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2019 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2019.csv.gz

  generate_outpatient_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2020 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2020.csv.gz

  generate_outpatient_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2021 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2021.csv.gz

  generate_outpatient_2022:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2022 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2022.csv.gz

  generate_outpatient_2019_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2019_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2019_high.csv.gz

  generate_outpatient_2020_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2020_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2020_high.csv.gz

  generate_outpatient_2021_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2021_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2021_high.csv.gz

  generate_outpatient_2022_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2022_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2022_high.csv.gz

  process_data:
    run: r:latest analysis/01_process_data.R
    needs: [generate_study_population, 
            generate_admissions_2018, generate_admissions_2019, generate_admissions_2020, generate_admissions_2021, generate_admissions_2022,
            generate_admissions_2018_high, generate_admissions_2019_high, generate_admissions_2020_high, generate_admissions_2021_high, generate_admissions_2022_high,
            generate_gp_2019, generate_gp_2020, generate_gp_2021, generate_gp_2022,
            generate_gp_2019_high, generate_gp_2020_high, generate_gp_2021_high, generate_gp_2022_high,
            generate_outpatient_2019, generate_outpatient_2020, generate_outpatient_2021, generate_outpatient_2022,
            generate_outpatient_2019_high, generate_outpatient_2020_high, generate_outpatient_2021_high, generate_outpatient_2022_high]
    outputs:
      highly_sensitive:
        data1: output/data/*.rds
      moderately_sensitive:
        diagnostics: output/diagnostics/*.csv
    
  descriptives:
    run: r:latest analysis/02_summary.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        plots: output/descriptive/plots/*.jpeg

Timeline

Created: 3 years, 11 months ago 25 Apr 2022 13:32:06 UTC
Started: 3 years, 11 months ago 25 Apr 2022 14:02:54 UTC
Finished: 3 years, 11 months ago 26 Apr 2022 08:15:00 UTC
Runtime: 264:13:36

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job request

Status: Failed
Backend: TPP
Workspace: hdruk-os-covid-paeds
Requested by: James Farrell
Branch: main
Force run dependencies: Yes
Git commit hash: 08c3e11
Requested actions: run_all

Code comparison

Compare the code used in this job request