Job request: 2539
- Organisation:
- Workspace:
- antipsychotics-prescribing-during-covid-19-master
- ID:
- ztny47wfiyku5i5a
This page shows the technical details of what happened when the authorised researcher Millie Green 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
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- Job identifier:
-
djvb2i26mb53oeen
-
- Job identifier:
-
5vmshm37hb7mudt3
-
- Job identifier:
-
icjxoj37hu4g7o4v
-
- Job identifier:
-
c3ut4wmyj7uwdh5g
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- Job identifier:
-
yogerwr4elzqiugo
Pipeline
Show project.yaml
######################################
# This script defines the project pipeline - it specifys the execution orders for all the code in this
# repo using a series of actions.
######################################
version: '3.0'
expectations:
population_size: 100000
actions:
# Extract data ----
## Cohort data
extract_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output/data --output-format=feather
outputs:
highly_sensitive:
cohort: output/data/input_*.feather
## Ethnicity
extract_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output/data --output-format=feather
outputs:
highly_sensitive:
cohort: output/data/input_ethnicity.feather
# ## Patient to practice lookup
# patient_practice_lookup:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output/data --output-format=feather
# outputs:
# highly_sensitive:
# cohort: output/data/input_practice_count.feather
# Data processing ----
# ## Patient counts
# get_patient_count:
# run: python:latest python analysis/get_patient_counts.py --output-dir=output/data
# needs: [extract_data]
# outputs:
# moderately_sensitive:
# text: output/data/patient_count.json
# ## Practice count
# get_practice_count:
# run: python:latest python analysis/get_practice_count.py --output-dir=output/data
# needs: [patient_practice_lookup]
# outputs:
# moderately_sensitive:
# text: output/data/practice_count.json
## Add ethnicity
join_ethnicity:
run: python:latest python analysis/join_ethnicity.py
needs: [extract_data, extract_ethnicity]
outputs:
highly_sensitive:
cohort: output/data/input*.feather
## Process data
data_process:
run: r:latest analysis/process_data.R
needs: [extract_ethnicity, join_ethnicity]
outputs:
moderately_sensitive:
data: output/data/data_*.rds
tables: output/data/custom_measures_*.csv
# ## Generate measures
# generate_measures:
# run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/data
# needs: [join_ethnicity]
# outputs:
# moderately_sensitive:
# measure_csv: output/data/measure_*.csv
# ### Generate measures, by group
# generate_measures_demographics:
# run: python:latest python analysis/calculate_measures.py
# needs: [join_ethnicity]
# outputs:
# moderately_sensitive:
# measure: output/combined_measure_*.csv
#
# ### Generate measures, by group and demographic
# generate_measures_demographics:
# run: python:latest python analysis/calculate_measures.py
# needs: [join_ethnicity]
# outputs:
# moderately_sensitive:
# measure: output/combined_measure_*.csv
# Results ----
## Figures
summary_figures:
run: r:latest analysis/summary_plots.R
needs: [data_process]
outputs:
moderately_sensitive:
plots: output/figures/plot_*.svg
summary_figures_redacted:
run: r:latest analysis/summary_plots_redacted.R
needs: [data_process]
outputs:
moderately_sensitive:
plots: output/figures/plot*.svg
## Table 1
table_1:
run: r:latest analysis/table_1.R
needs: [join_ethnicity]
outputs:
moderately_sensitive:
plots: output/tables/table1.html
# ## Whole population notebook
# generate_notebook:
# run: jupyter:latest jupyter nbconvert /workspace/notebooks/antipsychotic_measures.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [generate_measures, get_practice_count, get_patient_count]
# outputs:
# moderately_sensitive:
# notebook: output/antipsychotic_measures.html
Timeline
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Created:
-
Started:
-
Finished:
-
Runtime: 20:33:24
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Requested by
- Millie Green
- Branch
- master
- Force run dependencies
- No
- Git commit hash
- df5b0d9
- Requested actions
-
-
extract_data
-
extract_ethnicity
-
join_ethnicity
-
data_process
-
summary_figures
-
Code comparison
Compare the code used in this Job Request