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Job request: 12428

Organisation:
Bennett Institute
Workspace:
mabs-report
ID:
7snfe3opfp3mt5po

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

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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

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

  # Data processing ----
  data_process:
    run: r:latest analysis/process/process_data.R
    needs: [extract_data]
    outputs:
      highly_sensitive:
        data: output/data/data_processed*.rds
      moderately_sensitive:
        csv: output/coverage/n_excl_more_trtmnts_implausible_trtmnt_date.csv
  
  # 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
  
  hosp_after_pos_test:
    run: r:latest analysis/descriptive/discharge_adm_after_pos_test.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        redacted_table: output/coverage/table_admitted_after_pos_test.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

  stp_decile_values_report:
    run: r:latest -e 'rmarkdown::render("analysis/descriptive/stp-decile-values.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/variation")'
    needs: [data_process, extract_stp_data]
    outputs:
      moderately_sensitive:
        html: output/variation/stp-decile-values.html
        csv1: output/variation/table_stp_coverage.csv  
        csv2: output/variation/stp_decile_values.csv
        csv3: output/variation/stp_decile_values_weekly.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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:14:06

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

Job information

Status
Succeeded
Backend
TPP
Workspace
mabs-report
Requested by
Linda Nab
Branch
report
Force run dependencies
No
Git commit hash
cfce452
Requested actions
  • extract_data
  • extract_stp_data
  • data_process
  • data_properties
  • sa_symptomatic_test
  • report_data
  • stp_decile_values_report

Code comparison

Compare the code used in this Job Request