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Job request: 23588

Organisation:
Bennett Institute
Workspace:
prophy_effects_sotro_molnup
ID:
qd6dtuefdrbkgvmy

This page shows the technical details of what happened when authorised researcher Qing Wen 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
version: '3.0'

expectations:
  population_size: 5000

actions:

  gen_dataset_table:
    run: ehrql:v1 generate-dataset analysis/dataset_definition.py --output output/data/dataset_table.csv.gz
    outputs:
      highly_sensitive:
        cohort: output/data/dataset_table.csv.gz

  prep_descrip_r:
    run: r:latest analysis/data_prep_descrip.r
    needs: [gen_dataset_table]
    outputs:
      moderately_sensitive:
        table1: output/tables/table1_sum_num.csv
        table1a: output/tables/table1_sum_rd_m10.csv
        table2: output/tables/table1_sum_num_added.csv
        table2a: output/tables/table1_sum_rd_m10_added.csv
        table3: output/tables/table2_high_risk_extend_rd_m10.csv
        table3a: output/tables/table1_redacted_under8.csv
      highly_sensitive:
        data1: output/data/data4analyses.csv
        data2: output/data/high_risk_cohort.csv
        data3: output/data/high_risk_ever_cohort.csv
        data4: output/data/high_risk_cohort_inc60ddeath.csv

  prep_base_comp_r:
    run: r:latest analysis/prep_base_comp.r
    needs: [prep_descrip_r]
    outputs:
      moderately_sensitive:
        table15: output/tables/sum_continu_vars_output.csv
        table16: output/tables/ttest_output.csv
        table17: output/tables/chisq_output.csv
        table18: output/tables/ranksum_output.csv 
        plot: output/graps/norm_plot_*.png 
      highly_sensitive:
        data15: output/data/high_risk_basecomp_data.csv

  prep_model_surv_r:
    run: r:latest analysis/prep_model_surv.r
    needs: [prep_descrip_r]
    outputs: 
      moderately_sensitive:
        table3: output/tables/table_cox_model_surv0_regn_6m.csv
        table4: output/tables/table_cox_model_surv0_stp_6m.csv
        table3a: output/tables/table_cox_model_surv0_regn_rd2.csv
        table4a: output/tables/table_cox_model_surv0_stp_rd2.csv
      highly_sensitive:
        data5: output/data/high_risk_surv_data.csv

  model_surv_asum_r:
    run: r:latest analysis/model_surv_asum.r  #model_surv_asum.r
    needs: [prep_descrip_r]
    outputs: 
      moderately_sensitive:
        plot: output/graps/plot_*.png 
      highly_sensitive:
        data5: output/data/high_risk_surv_data_plot.csv

  prep_model_1surv_r:
    run: r:latest analysis/prep_model_1surv.r
    needs: [prep_descrip_r]
    outputs:
      moderately_sensitive:
        table5: output/tables/table_cox_model_surv1_regn_12m.csv
        table6: output/tables/table_cox_model_surv1_stp_12m.csv
      highly_sensitive:
        data6: output/data/high_risk_surv_data1.csv

  prep_model_2surv_r:
    run: r:latest analysis/prep_model_2surv.r
    needs: [prep_descrip_r]
    outputs:
      moderately_sensitive:
        table7: output/tables/table_cox_model_surv2_regn_24m.csv
        table8: output/tables/table_cox_model_surv2_stp_24m.csv
      highly_sensitive:
        data7: output/data/high_risk_surv_data2.csv

  prep_descrip_agegp_r:
    run: r:latest analysis/data_prep_descrip_1agegp.r
    needs: [prep_descrip_r]
    outputs:
      highly_sensitive:
        data8: output/data/high_risk_vars_age_rc.csv
      moderately_sensitive:
        table01: output/tables/high_risk_vars_age_rc_table.csv

  ext_cox_surv_r:
    run: r:latest analysis/ext_cox_surv.r
    needs: [prep_descrip_r]
    outputs:
      moderately_sensitive:
        table9: output/tables/table_ext_cox_surv0_regn_6m.csv
        table10: output/tables/table_ext_cox_surv0_stp_6m.csv
      highly_sensitive:
        data8: output/data/ext_high_risk_surv_data.csv

  ext_cox_1surv_r:
    run: r:latest analysis/ext_cox_1surv.r
    needs: [prep_descrip_r]
    outputs:
      moderately_sensitive:
        table11: output/tables/table_ext_cox_surv1_regn_12m.csv
        table12: output/tables/table_ext_cox_surv1_stp_12m.csv
      highly_sensitive:
        data9: output/data/ext_high_risk_surv1_data.csv

  ext_cox_2surv_r:
    run: r:latest analysis/ext_cox_2surv.r
    needs: [prep_descrip_r]
    outputs:
      moderately_sensitive:
        table13: output/tables/table_ext_cox_surv2_regn_24m.csv
        table14: output/tables/table_ext_cox_surv2_stp_24m.csv
      highly_sensitive:
        data10: output/data/ext_high_risk_surv2_data.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:12

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

Job information

Status
Failed
Backend
TPP
Requested by
Qing Wen
Branch
main
Force run dependencies
No
Git commit hash
7737e71
Requested actions
  • prep_base_comp_r

Code comparison

Compare the code used in this Job Request