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Job request: 21050

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
openprompt-cohort-profile
ID:
ha53ball55ogmjgc
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alasdair Henderson requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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: 1000

actions:

  create_dummy_data: 
    run: >
      ehrql:v0
        create-dummy-tables 
        analysis/dataset_definition.py output/dummydata 
        -- 
        --day=0
    outputs: 
      highly_sensitive:
        openprompt_dummy: output/dummydata/open_prompt.csv

  edit_dummy_data:
    run: > 
      r:latest
        analysis/00_dummy_data_editing/edit_automatic_dummy_data.R
    needs: [create_dummy_data]
    outputs: 
      highly_sensitive: 
        openprompt_dummy_edited: output/dummydata/dummy_edited/open_prompt.csv

  scrape_all_data: 
    run: >
      ehrql:v0
        generate-dataset
        analysis/scrape_data_response_dates.py
        --output output/openprompt_all.csv
        --dummy-tables output/dummydata/dummy_edited
    needs: [edit_dummy_data]
    outputs:
      highly_sensitive: 
        openprompt_all: output/openprompt_all.csv

  generate_openprompt_survey1: 
    run: >
      ehrql:v0
        generate-dataset 
        analysis/dataset_definition.py 
        --output output/openprompt_survey1.csv
        --dummy-tables output/dummydata/dummy_edited
        --
        --day=0
        --window=5
    needs: [edit_dummy_data]
    outputs:
      highly_sensitive:
        openprompt_survey1: output/openprompt_survey1.csv

  generate_openprompt_survey2: 
    run: >
      ehrql:v0
        generate-dataset 
        analysis/dataset_definition.py 
        --output output/openprompt_survey2.csv
        --dummy-tables output/dummydata/dummy_edited
        --
        --day=30
        --window=5
    needs: [edit_dummy_data]
    outputs:
      highly_sensitive:
        openprompt_survey2: output/openprompt_survey2.csv

  generate_openprompt_survey3: 
    run: >
      ehrql:v0
        generate-dataset 
        analysis/dataset_definition.py 
        --output output/openprompt_survey3.csv
        --dummy-tables output/dummydata/dummy_edited
        --
        --day=60
        --window=5
    needs: [edit_dummy_data]
    outputs:
      highly_sensitive:
        openprompt_survey3: output/openprompt_survey3.csv

  generate_openprompt_survey4: 
    run: >
      ehrql:v0
        generate-dataset 
        analysis/dataset_definition.py 
        --output output/openprompt_survey4.csv
        --dummy-tables output/dummydata/dummy_edited
        --
        --day=90
        --window=5
    needs: [edit_dummy_data]
    outputs:
      highly_sensitive:
        openprompt_survey4: output/openprompt_survey4.csv

  extract_linked_tpp_info: 
    run: >
      ehrql:v0
        generate-dataset 
        analysis/add_tpp_data.py 
        --output output/openprompt_linked_tpp.csv.gz
    outputs:
      highly_sensitive:
        linked_tpp_data: output/openprompt_linked_tpp.csv.gz
  
  extract_tpp_demographics: 
    run: >
      ehrql:v0
        generate-dataset 
        analysis/extract_tpp_demographics.py 
        --output output/opensafely_tpp_demographics.csv.gz
    outputs:
      highly_sensitive:
        tpp_demog_data: output/opensafely_tpp_demographics.csv.gz
  
  datacombine_and_figure1:
      run: >
        r:latest analysis/01_data_import/101_data_combine.R
      needs: [scrape_all_data, generate_openprompt_survey1, generate_openprompt_survey2, generate_openprompt_survey3, generate_openprompt_survey4]
      outputs: 
        highly_sensitive: 
          openprompt_combined: output/openprompt_raw.gz.parquet
        moderately_sensitive:
          openprompt_raw_skim: output/data_properties/op_raw_skim.txt
          openprompt_raw_tab: output/data_properties/op_raw_tabulate.txt
          openprompt_mapped_skim: output/data_properties/op_mapped_skim.txt
          openprompt_mapped_tab: output/data_properties/op_mapped_tabulate.txt
          raw_summ_base_s: output/data_properties/op_baseline_skim.txt
          raw_summ_base_t: output/data_properties/op_baseline_tabulate.txt
          raw_summ_survey1_s: output/data_properties/op_survey1_skim.txt
          raw_summ_survey1_t: output/data_properties/op_survey1_tabulate.txt
          raw_summ_survey2_s: output/data_properties/op_survey2_skim.txt
          raw_summ_survey2_t: output/data_properties/op_survey2_tabulate.txt
          raw_summ_survey3_s: output/data_properties/op_survey3_skim.txt
          raw_summ_survey3_t: output/data_properties/op_survey3_tabulate.txt
          raw_summ_survey4_s: output/data_properties/op_survey4_skim.txt
          raw_summ_survey4_t: output/data_properties/op_survey4_tabulate.txt
          check_days_after_baseline: output/data_properties/sample_day_lags.pdf
          p1a_jpeg: output/plots/p1a_index_dates.jpeg
          p1b_jpeg: output/plots/p1b_recorded_question_responses.jpeg
          p1c_jpeg: output/plots/p1c_anyresponse_hist.jpeg
          p1d_jpeg: output/plots/p1d_ltfu.jpeg
          p1_jpeg: output/plots/p1_fup.jpeg
  
  import_linked_tpp: 
    run: >
      r:latest analysis/01_data_import/102_import_linked_tpp.R
    needs: [extract_linked_tpp_info]
    outputs: 
      highly_sensitive: 
        linked_tpp_data_edited: output/openprompt_linked_tpp_edited.gz.parquet
      moderately_sensitive:
        openprompt_tpp_skim: output/data_properties/op_tpp_skim.txt
        openprompt_tpp_tab: output/data_properties/op_tpp_tabulate.txt

  export_table1_stats: 
    run: >
      r:latest analysis/02_baseline_descriptive/201_table1stats.R
    needs: [datacombine_and_figure1, import_linked_tpp]
    outputs: 
      moderately_sensitive: 
        table1: output/tables/table1.html
        table1_stats: output/tables/table1_stats.csv

# Then need to run analysis/02_baseline_descriptive/002-map-making.R to produce the Figure 2 for the paper

  export_table2_fup_stats: 
    run: >
      r:latest analysis/03_followup_responses/301_followup_table.R
    needs: [datacombine_and_figure1]
    outputs:
      moderately_sensitive: 
        table2: output/tables/table2_followup.html
        table2_stats: output/tables/table2_fup_stats.csv

# Then need to run analysis/03_followup_responses/302_followup_plots.R

  export_data_agreement: 
    run: > 
      r:latest analysis/04_data_agreement/401_data_agreement.R
    needs: [datacombine_and_figure1, import_linked_tpp]
    outputs: 
      moderately_sensitive: 
        venndiagram_jpeg: output/plots/venn.jpeg
        venndiagram_pdf: output/plots/venn.pdf
        agreementdata: output/tables/table3_agreement.csv
        
  export_data_representativeness: 
    run: > 
      r:latest analysis/05_representativeness/501_demographic_representativeness.R
    needs: [datacombine_and_figure1, extract_tpp_demographics]
    outputs: 
      moderately_sensitive: 
        table3_stats: output/tables/table3_rep_stats.csv
        table3: output/tables/table3_represetativeness.html
  
# Then need to run analysis/05_representativeness/502_representativeness_plot.R to produce the Figure 4 for the paper

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:16:23

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

Job information

Status
Succeeded
Backend
TPP
Workspace
openprompt-cohort-profile
Requested by
Alasdair Henderson
Branch
main
Force run dependencies
Yes
Git commit hash
6fd40bd
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request