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Job request: 23578

Organisation:
Bennett Institute
Workspace:
prophy_effects_sotro_molnup
ID:
6mwiy75w7h22kmc7
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Qing Wen 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:
    prep_descrip_r
    Status:
    Status: Succeeded
    Job identifier:
    hl3epzyxocfgudig

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
      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: 00:01:11

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

Job request

Status
Succeeded
Backend
TPP
Workspace
prophy_effects_sotro_molnup
Requested by
Qing Wen
Branch
main
Force run dependencies
No
Git commit hash
920b974
Requested actions
  • prep_descrip_r

Code comparison

Compare the code used in this job request