Job request: 8501
- Organisation:
- ISARIC
- Workspace:
- hdruk-os-covid-paeds
- ID:
- xezzt54btr4emwhb
This page shows the technical details of what happened when the authorised researcher James Farrell 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:
-
coijrsbfenh25m5b
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- Job identifier:
-
ciolizs7bibxzmjw
-
- Job identifier:
-
bwiqv2komsntuj7y
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- Job identifier:
-
a7ruvsn5nlir6vyl - Error:
- cancelled_by_user: Cancelled by user
-
- Job identifier:
-
2istmcwj5ulm3ni3 - Error:
- cancelled_by_user: Cancelled by user
-
- Job identifier:
-
2y54m6nqwoq47wer - Error:
- cancelled_by_user: Cancelled by user
-
- Job identifier:
-
jqnwbomxbz4klvxt - Error:
- cancelled_by_user: Cancelled by user
-
- Job identifier:
-
mvewkyzji3ywzrie - Error:
- cancelled_by_user: Cancelled by user
-
- Job identifier:
-
zgvzycsqdlm5e3ut - Error:
- Internal error: this usually means a platform issue rather than a problem for users to fix. The tech team are automatically notified of these errors and will be investigating.
-
- Job identifier:
-
54owggq2drbg7ipl - Error:
- dependency_failed: Not starting as dependency failed
-
- Job identifier:
-
s67q6kfbr3b5oxzk - Error:
- dependency_failed: Not starting as dependency failed
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- Job identifier:
-
jlpvfs7ytnovcfqj - Error:
- dependency_failed: Not starting as dependency failed
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format csv.gz
outputs:
highly_sensitive:
cohort: output/input.csv.gz
generate_dummy_data:
run: r:latest analysis/generate_dummy_data.R
needs: [generate_study_population]
outputs:
highly_sensitive:
dummy_data_admissions: output/dummy_data/dummy_data_admissions.csv.gz
dummy_data_outpatient: output/dummy_data/dummy_data_outpatient.csv.gz
dummy_data_gp: output/dummy_data/dummy_data_gp.csv.gz
dummy_data_testing_negative: output/dummy_data/dummy_data_testing_negative.csv.gz
dummy_data_testing_positive: output/dummy_data/dummy_data_testing_positive.csv.gz
generate_admissions:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_admissions
--index-date-range "2018-10-01 to 2022-01-31 by week"
--output-format csv.gz
--skip-existing
--output-dir=output/data_weekly
dummy_data_file: output/dummy_data/dummy_data_admissions.csv.gz
needs: [generate_dummy_data]
outputs:
highly_sensitive:
data_admissions: output/data_weekly/input_admissions_20*.csv.gz
generate_outpatient:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_outpatient
--index-date-range "2019-03-11 to 2022-01-31 by week"
--output-format csv.gz
--skip-existing
--output-dir=output/data_weekly
dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
needs: [generate_dummy_data]
outputs:
highly_sensitive:
data_outpatient: output/data_weekly/input_outpatient_20*.csv.gz
generate_gp:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_gp
--index-date-range "2018-12-31 to 2022-01-31 by week"
--output-format csv.gz
--skip-existing
--output-dir=output/data_weekly
dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
needs: [generate_dummy_data]
outputs:
highly_sensitive:
data_gp_contacts: output/data_weekly/input_gp_20*.csv.gz
generate_covid_tests_negative:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_covid_tests_negative
--index-date-range "2019-12-30 to 2022-01-31 by week"
--output-format csv.gz
--skip-existing
--output-dir=output/data_weekly
dummy_data_file: output/dummy_data/dummy_data_testing_negative.csv.gz
needs: [generate_dummy_data]
outputs:
highly_sensitive:
data_negative_tests: output/data_weekly/input_covid_tests_negative_20*.csv.gz
generate_covid_tests_positive:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_covid_tests_positive
--index-date-range "2019-12-30 to 2022-01-31 by week"
--output-format csv.gz
--skip-existing
--output-dir=output/data_weekly
dummy_data_file: output/dummy_data/dummy_data_testing_positive.csv.gz
needs: [generate_dummy_data]
outputs:
highly_sensitive:
data_positive_tests: output/data_weekly/input_covid_tests_positive_20*.csv.gz
process_patient_data:
run: r:latest analysis/01_process_patient_data.R
needs: [generate_study_population]
outputs:
highly_sensitive:
data_patient: output/data/data_patient.rds
data_id: output/data/data_id.rds
process_admissions_data:
run: r:latest analysis/01_process_admissions_data.R
needs: [generate_admissions, process_patient_data]
outputs:
highly_sensitive:
data_admissions: output/data/data_admissions.rds
moderately_sensitive:
diagnostics_admissions: output/diagnostics/diagnostics_admissions.csv
plots_admissions: output/descriptives/data_admissions/*.jpeg
process_outpatient_data:
run: r:latest analysis/01_process_outpatient_data.R
needs: [generate_outpatient, process_patient_data]
outputs:
highly_sensitive:
data_outpatient: output/data/data_outpatient.rds
moderately_sensitive:
diagnostics_outpatient: output/diagnostics/diagnostics_outpatient.csv
plots_outpatient: output/descriptives/data_outpatient/*.jpeg
process_gp_data:
run: r:latest analysis/01_process_gp_data.R
needs: [generate_gp, process_patient_data]
outputs:
highly_sensitive:
data_gp: output/data/data_gp.rds
moderately_sensitive:
diagnostics_gp: output/diagnostics/diagnostics_gp.csv
plots_gp: output/descriptives/data_gp/*.jpeg
process_testing_data:
run: r:latest analysis/01_process_testing_data.R
needs: [generate_covid_tests_negative, generate_covid_tests_positive, process_patient_data]
outputs:
highly_sensitive:
data_testing: output/data/data_testing.rds
moderately_sensitive:
diagnostics_testing: output/diagnostics/diagnostics_testing.csv
plots_testing: output/descriptives/data_testing/*.jpeg
Timeline
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Created:
-
Started:
-
Finished:
-
Runtime: 138:55:03
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- hdruk-os-covid-paeds
- Requested by
- James Farrell
- Branch
- main
- Force run dependencies
- Yes
- Git commit hash
- 5b7616e
- Requested actions
-
-
run_all
-
Code comparison
Compare the code used in this Job Request