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Job request: 834

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
hh-classification-research
ID:
ihs3zl7ij2nxvcd2
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Kevin Wing 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:
    generate_cohort
    Status:
    Status: Succeeded
    Job identifier:
    e5nw4lzpclborgtw
  • Action:
    prepare_data
    Status:
    Status: Succeeded
    Job identifier:
    heoqzficpsxrmgcn
  • Action:
    output_table1
    Status:
    Status: Failed
    Job identifier:
    bo23c65se5tadcco
    Error:
    nonzero_exit: Job exited with an error code

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 100000

actions:
  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  prepare_data:
    run: stata-mp:latest analysis/01_hhClassif_cr_analysis_dataset.do
    needs: [generate_cohort]
    outputs:
      highly_sensitive:
        allvars: output/hhClassif_analysis_dataset.dta
      moderately_sensitive:
        log1: released_outputs/01_hhClassif_cr_analysis_dataset.log

  data_checks:
    run: stata-mp:latest analysis/02_hhClassif_an_data_checks.do
    needs: [prepare_data]
    outputs:
      moderately_sensitive:
        log: released_outputs/02_hhClassif_an_data_checks.log

  output_table1:
    run: stata-mp:latest analysis/03b_hhClassif_an_descriptive_table_1.do
    needs: [prepare_data]
    outputs:
      moderately_sensitive:
        log: released_outputs/03b_hhClassif_an_descriptive_table_1.log

  output_descriptive:
    run: stata-mp:latest analysis/02_hh_an_caseFreq_descriptive_plots.do
    needs: [prepare_data]
    outputs:
      moderately_sensitive:
        graph1: released_outputs/an_caseFreq_descr_overall_HH_Histogram.svg
        graph2: released_outputs/an_caseFreq_descr_overall_HH_HistogramOverlay.svg
        log1: released_outputs/02_hh_an_caseFreq_descriptive_plots.log
        log2: released_outputs/an_caseDescrTable.txt

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:07:13

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

Job request

Status
Failed
Backend
TPP
Workspace
hh-classification-research
Requested by
Kevin Wing
Branch
master
Force run dependencies
Yes
Git commit hash
a9040df
Requested actions
  • output_table1

Code comparison

Compare the code used in this job request