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Job request: 9895

Workspace:
mabs-sgtf
ID:
5m7zuqfkri5y62up

This page shows the technical details of what happened when 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 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

  • Action:
    sgtf_report
    Status:
    Status: Succeeded
    Job identifier:
    qb2xnfwx4akjw4yz

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
        
  extract_sgtf_weekly_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sgtf_weekly --index-date-range "2020-03-01 to 2022-05-30 by week" --output-dir=output/data --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/data/input_sgtf_weekly_*.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_process_sgtf:
    run: r:latest analysis/process/process_data_sgtf.R
    needs: [extract_sgtf_weekly_data]
    outputs:
      highly_sensitive:
        data: output/data/weekly_sgtf_counts*.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, data_process_sgtf]
    outputs:
      moderately_sensitive:
        html: output/coverage/sgtf_report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Succeeded
Backend
TPP
Workspace
mabs-sgtf
Requested by
Millie Green
Branch
sgtf
Force run dependencies
No
Git commit hash
98733a4
Requested actions
  • sgtf_report