Job request: 21050

Organisation:: The London School of Hygiene & Tropical Medicine
Workspace:: openprompt-cohort-profile
ID:: ha53ball55ogmjgc

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

Action:

extract_linked_tpp_info

Status:

Status: Succeeded

Job identifier:

sjn4pu2b62lmtfwi
Action:

extract_tpp_demographics

Status:

Status: Succeeded

Job identifier:

i3e7xy4wri3px4u2
Action:

create_dummy_data

Status:

Status: Succeeded

Job identifier:

wtzt4376febak4iy
Action:

edit_dummy_data

Status:

Status: Succeeded

Job identifier:

fectboxpdpa7zj2g
Action:

generate_openprompt_survey1

Status:

Status: Succeeded

Job identifier:

xllal7zkzht35q6j
Action:

generate_openprompt_survey2

Status:

Status: Succeeded

Job identifier:

uwhnmuvfly34r4zp
Action:

generate_openprompt_survey3

Status:

Status: Succeeded

Job identifier:

pygjvknrbl4puhlv
Action:

generate_openprompt_survey4

Status:

Status: Succeeded

Job identifier:

e5qvvgex4eem6fti
Action:

scrape_all_data

Status:

Status: Succeeded

Job identifier:

xcjat64nnjr3etva
Action:

datacombine_and_figure1

Status:

Status: Succeeded

Job identifier:

zwhvbvebq7zrmnx5
Action:

export_data_representativeness

Status:

Status: Succeeded

Job identifier:

nrgwk26ojg6p5lbn
Action:

export_table2_fup_stats

Status:

Status: Succeeded

Job identifier:

ivoqykra24kkhtfh
Action:

import_linked_tpp

Status:

Status: Succeeded

Job identifier:

nphhc4vx4isn2qef
Action:

export_data_agreement

Status:

Status: Succeeded

Job identifier:

4oz52rhfm4ypsltk
Action:

export_table1_stats

Status:

Status: Succeeded

Job identifier:

smqeehshonn37fwm

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: 1 year, 1 month ago 09 Nov 2023 16:45:06 UTC
Started: 1 year, 1 month ago 09 Nov 2023 16:45:09 UTC
Finished: 1 year, 1 month ago 09 Nov 2023 18:12:52 UTC
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