Job request: 15420
- Organisation:
- Bennett Institute
- Workspace:
- ethnicity-short-data-report-notebook
- ID:
- r2imavmwchzoapvx
This page shows the technical details of what happened when the authorised researcher Colm Andrews 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
-
- Job identifier:
-
ickshbv6lruhn6js
Pipeline
Show project.yaml
### CTV3, PRIMIS, SNOMED analysis
version: '3.0'
expectations:
population_size: 1000
actions:
split_codelist:
run: r:latest analysis/00_trim_snomed_codelist.r
outputs:
highly_sensitive:
data: codelists/ethnicity_*.csv
generate_study_population_5:
run: cohortextractor:latest generate_cohort --study-definition study_definition_5 --output-file output/extract_5/input_5.feather --output-format feather
needs: [split_codelist]
outputs:
highly_sensitive:
cohort: output/extract_5/input_5.feather
generate_dataset_report_5:
run: >
dataset-report:v0.0.9
--input-files output/extract_5/input_5.feather
--output-dir output/extract_5
needs: [generate_study_population_5]
outputs:
moderately_sensitive:
dataset_report: output/extract_5/input_5.html
generate_study_population_16:
run: cohortextractor:latest generate_cohort --study-definition study_definition_16 --output-file output/extract_16/input_16.feather --output-format feather
needs: [split_codelist]
outputs:
highly_sensitive:
cohort: output/extract_16/input_16.feather
generate_dataset_report_16:
run: >
dataset-report:v0.0.9
--input-files output/extract_16/input_16.feather
--output-dir output/extract_16
needs: [generate_study_population_16]
outputs:
moderately_sensitive:
dataset_report: output/extract_16/input_16.html
generate_study_population_time:
run: cohortextractor:latest generate_cohort --study-definition study_definition_time --output-file output/extract_time/input_time.feather --output-format feather
needs: [split_codelist]
outputs:
highly_sensitive:
cohort: output/extract_time/input_time.feather
generate_dataset_report_time:
run: >
dataset-report:v0.0.9
--input-files output/extract_time/input_time.feather
--output-dir output/extract_time
needs: [generate_study_population_time]
outputs:
moderately_sensitive:
dataset_report: output/extract_time/input_time.html
execute_simple_validation_analyses:
run: python:latest python analysis/simple_validation_script.py
needs: [generate_study_population_5]
outputs:
moderately_sensitive:
tables: output/simplified_output/5_group/tables/*.csv
execute_simple_validation_analyses_16:
run: python:latest python analysis/simple_validation_script_16.py
needs: [generate_study_population_16]
outputs:
moderately_sensitive:
tables: output/simplified_output/16_group/tables/simpl*.csv
combine_ons:
run: r:latest analysis/combine_ons.R
needs: [generate_study_population_16]
outputs:
moderately_sensitive:
data: output/ons/ethnic_group*.csv
data2: output/ons/ethnic_group_NA*.csv
data3: output/ons/data_check*.csv
ons_plot:
run: r:latest analysis/ons_plots.R
needs: [combine_ons]
outputs:
moderately_sensitive:
plot_na: output/ons/na_removed/ethnicity_*.png
######## SUS
execute_simple_validation_analyses_sus:
run: python:latest python analysis/sus/simple_validation_script_sus.py
needs: [generate_study_population_5]
outputs:
moderately_sensitive:
tables: output/sus/simplified_output/5_group/tables/*.csv
# figures: output/sus/simplified_output/5_group/figures/*.png
execute_simple_validation_analyses_16_sus:
run: python:latest python analysis/sus/simple_validation_script_16_sus.py
needs: [generate_study_population_16]
outputs:
moderately_sensitive:
tables: output/sus/simplified_output/16_group/tables/simpl*.csv
# combine_ons:
# run: r:latest analysis/combine_ons.R
# needs: [generate_study_population]
# outputs:
# moderately_sensitive:
# data: output/ons/ethnic_group*.csv
# data2: output/ons/ethnic_group_NA*.csv
# data3: output/ons/data_check*.csv
# ons_plot:
# run: r:latest analysis/ons_plots.R
# needs: [combine_ons]
# outputs:
# moderately_sensitive:
# plot_na: output/ons/na_removed/ethnicity_*.png
# iqr:
# run: r:latest analysis/iqr.R
# needs: [generate_study_population]
# outputs:
# moderately_sensitive:
# full: output/simplified_output/5_group/tables/range_fullset.csv
# registered: output/simplified_output/5_group/tables/range_registered.csv
# figures: output/simplified_output/5_group/figures/density*.svg
# ## Only to be run locally
# generate_report:
# run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/draft_report_ethnicity.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [execute_simple_validation_analyses,execute_simple_validation_analyses_16]
# outputs:
# moderately_sensitive:
# notebook: output/draft_report_ethnicity.html
# local_simple_run:
# run: python:latest python analysis/local_simple_run_sot.py
# outputs:
# moderately_sensitive:
# tables: output/released/*.csv
################## over time
time_tables:
run: r:latest analysis/time/times.R
needs: [generate_study_population_time]
outputs:
moderately_sensitive:
data: output/time/*.csv
plots: output/time/*.png
##### draft report
generate_draft_report:
run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/draft_report_ethnicity.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [execute_simple_validation_analyses,execute_simple_validation_analyses_16]
outputs:
moderately_sensitive:
notebook: output/draft_report_ethnicity.html
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:00:29
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- ethnicity-short-data-report-notebook
- Requested by
- Colm Andrews
- Branch
- notebook
- Force run dependencies
- No
- Git commit hash
- ea3c8cc
- Requested actions
-
-
generate_draft_report
-
Code comparison
Compare the code used in this Job Request