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Job request: 13733

Organisation:
University of Bristol
Workspace:
post-covid-gastrointestinal
ID:
qybnvinaafelzs7o
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Marwa Al Arab 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:
    vax_eligibility_inputs
    Status:
    Status: Succeeded
    Job identifier:
    ntg44srksxchh5gl
  • Action:
    generate_study_population_prelim
    Status:
    Status: Failed
    Job identifier:
    7ykapaddhkyp3svt
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_study_population_prevax
    Status:
    Status: Failed
    Job identifier:
    5o3s3e2leu5h6zwq
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_study_population_vax
    Status:
    Status: Failed
    Job identifier:
    kxkcj35lpfrio74g
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    preprocess_data_prevax
    Status:
    Status: Failed
    Job identifier:
    oed5u37dgv5mtplk
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    preprocess_data_vax
    Status:
    Status: Failed
    Job identifier:
    oykvt7oplydx734j
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    preprocess_data_unvax
    Status:
    Status: Failed
    Job identifier:
    sqx6sfk6rt35ie3o
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_index_dates
    Status:
    Status: Failed
    Job identifier:
    xxjx5a4gtblt4bue
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_study_population_unvax
    Status:
    Status: Failed
    Job identifier:
    ntqmiuqr64hozled
    Error:
    cancelled_by_user: Cancelled by user

Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create_project_actions.R 
  ## Edit and run create_project_actions.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  vax_eligibility_inputs:
    run: r:latest analysis/metadates.R
    outputs:
      highly_sensitive:
        study_dates_json: output/study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

  generate_study_population_prelim:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prelim
      --output-format feather
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_prelim.feather

  generate_index_dates:
    run: r:latest analysis/prelim.R
    needs:
    - vax_eligibility_inputs
    - generate_study_population_prelim
    outputs:
      highly_sensitive:
        index_dates: output/index_dates.csv

  generate_study_population_prevax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax
      --output-format feather
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_prevax.feather

  generate_study_population_vax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
      --output-format feather
    needs:
    - generate_index_dates
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_vax.feather

  generate_study_population_unvax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax
      --output-format feather
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_unvax.feather

  preprocess_data_prevax:
    run: r:latest analysis/preprocess/preprocess_data.R prevax
    needs:
    - generate_index_dates
    - generate_study_population_prevax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_prevax_stage0.txt
        describe_venn: output/not-for-review/describe_venn_prevax.txt
      highly_sensitive:
        cohort: output/input_prevax.rds
        venn: output/venn_prevax.rds

  preprocess_data_vax:
    run: r:latest analysis/preprocess/preprocess_data.R vax
    needs:
    - generate_index_dates
    - generate_study_population_vax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_vax_stage0.txt
        descrive_venn: output/not-for-review/describe_venn_vax.txt
      highly_sensitive:
        cohort: output/input_vax.rds
        venn: output/venn_vax.rds

  preprocess_data_unvax:
    run: r:latest analysis/preprocess/preprocess_data.R unvax
    needs:
    - generate_index_dates
    - generate_study_population_unvax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_unvax_stage0.txt
        describe_venn: output/not-for-review/describe_venn_unvax.txt
      highly_sensitive:
        cohort: output/input_unvax.rds
        venn: output/venn_unvax.rds

  stage1_data_cleaning_all:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R all
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_*.csv
        QA_rules: output/review/descriptives/QA_summary_*.csv
        IE_criteria: output/review/descriptives/Cohort_flow_*.csv
        histograms: output/not-for-review/numeric_histograms_*.svg
      highly_sensitive:
        cohort: output/input_*.rds

  # stage1_end_date_table_prevax:
  #   run: r:latest analysis/preprocess/create_follow_up_end_date.R prevax
  #   needs:
  #   - preprocess_data_prevax
  #   - preprocess_data_vax
  #   - preprocess_data_unvax
  #   #- stage1_data_cleaning_all
  #   - vax_eligibility_inputs
  #   outputs:
  #     highly_sensitive:
  #       end_date_table: output/follow_up_end_dates_prevax_*.rds

  # stage1_end_date_table_vax:
  #   run: r:latest analysis/preprocess/create_follow_up_end_date.R vax
  #   needs:
  #   - preprocess_data_prevax
  #   - preprocess_data_vax
  #   - preprocess_data_unvax
  #   #- stage1_data_cleaning_all
  #   - vax_eligibility_inputs
  #   outputs:
  #     highly_sensitive:
  #       end_date_table: output/follow_up_end_dates_vax_*.rds

  # stage1_end_date_table_unvax:
  #   run: r:latest analysis/preprocess/create_follow_up_end_date.R unvax
  #   needs:
  #   - preprocess_data_prevax
  #   - preprocess_data_vax
  #   - preprocess_data_unvax
  #   #- stage1_data_cleaning_all
  #   - vax_eligibility_inputs
  #   outputs:
  #     highly_sensitive:
  #       end_date_table: output/follow_up_end_dates_unvax_*.rds

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:12

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

Job request

Status
Failed
Backend
TPP
Workspace
post-covid-gastrointestinal
Requested by
Marwa Al Arab
Branch
main
Force run dependencies
Yes
Git commit hash
e422428
Requested actions
  • vax_eligibility_inputs
  • generate_study_population_prelim
  • generate_index_dates
  • generate_study_population_prevax
  • generate_study_population_vax
  • generate_study_population_unvax
  • preprocess_data_prevax
  • preprocess_data_vax
  • preprocess_data_unvax

Code comparison

Compare the code used in this job request