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Job request: 3769

Organisation:
Workspace:
antipsychotics-prescribing-during-covid-19-master
ID:
it7r4vdiespcr3uy
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 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:
    extract_data
    Status:
    Status: Succeeded
    Job identifier:
    wmyipftkn4gczbgz
  • Action:
    extract_ethnicity
    Status:
    Status: Failed
    Job identifier:
    h4xitlirgdx4ckio
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    data_process
    Status:
    Status: Failed
    Job identifier:
    5mu3azvdkqh7xpu7
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    table_2
    Status:
    Status: Failed
    Job identifier:
    2gdrrp4yhfqwp2uu
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    summary_figures
    Status:
    Status: Failed
    Job identifier:
    oh3gxrxk3f53vjn5
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    table_1
    Status:
    Status: Failed
    Job identifier:
    p4qqarv7x5rr2ctj
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    join_ethnicity
    Status:
    Status: Failed
    Job identifier:
    3lawe6b3kuozdyku
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
######################################

# This script defines the project pipeline - it specifys the execution orders for all the code in this
# repo using a series of actions.

######################################

version: '3.0'

expectations:
  population_size: 100000

actions:

  # Extract data ----
  
  ## Cohort data
  extract_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-03-01 to 2021-04-01 by month" --output-dir=output/data --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_*.feather
  
  ## Ethnicity      
  extract_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output/data --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_ethnicity.feather
  
  # Data processing ----
  
  ## Add ethnicity
  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs: [extract_data, extract_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/data/input*.feather
  
  ## Process data
  data_process:
    run: r:latest analysis/process/process_data.R
    needs: [extract_ethnicity, join_ethnicity]
    outputs:
      moderately_sensitive:
        data: output/data/data_*.rds
 
  # Results ----
  
  ## Figures
  summary_figures:
    run: r:latest analysis/descriptive/summary_plots.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        plot1: output/figures/total_*.png
        plot2: output/figures/new_*.png
        
  ## Table 1
  table_1:
    run: r:latest analysis/descriptive/table_1.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        plots: output/tables/table1.csv
  
  ## Table 2
  table_2:
    run: r:latest analysis/descriptive/table_2.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        plots: output/tables/table2*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 33:07:23

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

Job request

Status
Failed
Backend
EMIS
Workspace
antipsychotics-prescribing-during-covid-19-master
Requested by
Millie Green
Branch
master
Force run dependencies
No
Git commit hash
03458de
Requested actions
  • extract_data
  • extract_ethnicity
  • join_ethnicity
  • data_process
  • summary_figures
  • table_1
  • table_2

Code comparison

Compare the code used in this job request