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Job request: 8328

Organisation:
Bennett Institute
Workspace:
mabs-main
ID:
ijj4vfv6zyzd3smd
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Millie Green 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

  • Action:
    data_process
    Status:
    Status: Failed
    Job identifier:
    riqidmb5j5nn3vud
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    sa_symptomatic_test
    Status:
    Status: Failed
    Job identifier:
    t5bjwsgs7kf5l34y
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    obs_vs_exp_report
    Status:
    Status: Failed
    Job identifier:
    rt3xgc35avl4cxb4
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    report_data
    Status:
    Status: Failed
    Job identifier:
    5u56oe7hkdb5bil7
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    data_properties
    Status:
    Status: Failed
    Job identifier:
    cu5nrkj3xuywordz
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    outcomes_report
    Status:
    Status: Failed
    Job identifier:
    wi5e7vctuvdt56il
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    stp_report
    Status:
    Status: Failed
    Job identifier:
    krikjlomrrfmfiys
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
################################################################################
#
# Description: This script defines the project pipeline - it specifys the 
#              execution orders for all the code in this repo using a series of 
#              actions.
#
# Author(s): M Green
# Date last updated: 15/02/2022
#
################################################################################

version: '3.0'

expectations:
  population_size: 100000

actions:
  
  # Extract data ----
  extract_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/data/input.csv.gz
  
  extract_stp_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_stp --output-dir=output/data --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/data/input_stp.csv.gz
  
  # Data processing ----
  data_process:
    run: r:latest analysis/process/process_data.R
    needs: [extract_data]
    outputs:
      highly_sensitive:
        data: output/data/data_processed*.rds
  
  # Data summaries ----
  data_properties:
    run: r:latest analysis/descriptive/data_properties.R output/data/data_processed.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        cohort: output/data_properties/data_processed*.txt
        
  # Sensitivity anslysis ----
  sa_symptomatic_test:
    run: r:latest -e 'rmarkdown::render("analysis/descriptive/sa_symptomatic_test.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/coverage")'
    needs: [data_process]
    outputs:
      moderately_sensitive:
        html: output/coverage/sa_symptomatic_test.html
  
  # Report ----
  report_data:
    run: r:latest analysis/descriptive/coverage_report_data.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        redacted_tables: output/coverage/table_*.csv
        unredacted_tables: output/coverage/for-checks/table_*.csv
  
  # Variation by STP ----
  stp_report:
    run: r:latest -e 'rmarkdown::render("analysis/descriptive/mabs-and-abs-by-stp.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/variation")'
    needs: [data_process, extract_stp_data]
    outputs:
      moderately_sensitive:
        html: output/variation/mabs-and-abs-by-stp.html
        figures: output/variation/figure_*.csv
        csvs: output/variation/table_*.csv
        
  # Obs vs exp ----
  obs_vs_exp_report:
    run: r:latest -e 'rmarkdown::render("analysis/descriptive/obs-vs-exp.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/variation")'
    needs: [data_process]
    outputs:
      moderately_sensitive:
        html: output/variation/obs-vs-exp.html

  # Crude count of outcomes ----
  outcomes_report:
    run: r:latest -e 'rmarkdown::render("analysis/descriptive/crude_outcomes.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/effectiveness/counts")'
    needs: [data_process]
    outputs:
      moderately_sensitive:
        html: output/effectiveness/counts/crude_outcomes.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:09:28

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

Job request

Status
Failed
Backend
TPP
Workspace
mabs-main
Requested by
Millie Green
Branch
main
Force run dependencies
No
Git commit hash
0050c24
Requested actions
  • data_process
  • data_properties
  • sa_symptomatic_test
  • report_data
  • stp_report
  • obs_vs_exp_report
  • outcomes_report

Code comparison

Compare the code used in this job request