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Job request: 9813

Organisation:
Bennett Institute
Workspace:
mabs-report
ID:
k2zoldpk7f2p45tv
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:
    extract_data
    Status:
    Status: Failed
    Job identifier:
    dd6nv5u5c6v76szq
  • Action:
    report_data
    Status:
    Status: Failed
    Job identifier:
    jzs53k3b4mklkhui
  • Action:
    stp_report
    Status:
    Status: Failed
    Job identifier:
    3jcokbkksfyz44hl
  • Action:
    data_process
    Status:
    Status: Failed
    Job identifier:
    fwq52ycjxzv2rwcm
  • Action:
    data_properties
    Status:
    Status: Failed
    Job identifier:
    ajodnnazfdz6qpvb
  • Action:
    sa_symptomatic_test
    Status:
    Status: Failed
    Job identifier:
    obadjgy3skuutph6

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: 500000

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
    
  extract_sgtf_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sgtf --output-dir=output/data --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/data/input_sgtf.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-avs-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-avs-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
        
  # SGTF ----
  sgtf_mabs_report:
    run: r:latest -e 'rmarkdown::render("analysis/descriptive/sgtf.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/coverage")'
    needs: [data_process]
    outputs:
      moderately_sensitive:
        html: output/coverage/sgtf.html
  
  sgtf_report:
    run: r:latest -e 'rmarkdown::render("analysis/descriptive/sgtf_report.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/coverage")'
    needs: [extract_sgtf_data]
    outputs:
      moderately_sensitive:
        html: output/coverage/sgtf_report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:19

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

Job information

Status
Failed
Backend
TPP
Workspace
mabs-report
Requested by
Millie Green
Branch
report
Force run dependencies
No
Git commit hash
11b1cb7
Requested actions
  • extract_data
  • data_process
  • data_properties
  • sa_symptomatic_test
  • report_data
  • stp_report

Code comparison

Compare the code used in this Job Request