Job request: 11484
- Organisation:
- University of Manchester
- Workspace:
- broad-spectrum-its
- ID:
- q5v62rqcszdoiobu
This page shows the technical details of what happened when the authorised researcher Billy Zhong 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:
-
6xryioli75m4y7br
-
- Job identifier:
-
cqjxoi7corlblrek
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 30000
actions:
generate_study_population_patient_characteristics_2019:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_patient_characteristics_2019
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_patient_characteristics_2019.csv.gz
generate_study_population_patient_characteristics_2020:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_patient_characteristics_2020
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_patient_characteristics_2020.csv.gz
generate_study_population_patient_characteristics_2021:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_patient_characteristics_2021
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_patient_characteristics_2021.csv.gz
table_1:
run: r:latest analysis/table_1.R
needs: [generate_study_population_patient_characteristics_2019]
outputs:
moderately_sensitive:
table1: output/table1_2019_overallcount.csv
table2: output/table1_2019.csv
table_1_2020:
run: r:latest analysis/table_1_2020.R
needs: [generate_study_population_patient_characteristics_2020]
outputs:
moderately_sensitive:
table1: output/table1_2020_overallcount.csv
table2: output/table1_2020.csv
table_1_2021:
run: r:latest analysis/table_1_2021.R
needs: [generate_study_population_patient_characteristics_2021]
outputs:
moderately_sensitive:
table1: output/table1_2021_overallcount.csv
table2: output/table1_2021.csv
generate_study_population:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition
--index-date-range "2019-01-01 to 2021-12-31 by month"
--skip-existing
--output-dir=output/measures
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv.gz
generate_measures:
run: cohortextractor:latest generate_measures
--study-definition study_definition
--skip-existing
--output-dir=output/measures
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_*.csv
figure_1A:
run: r:latest analysis/figure_1A.R
needs: [generate_measures]
outputs:
moderately_sensitive:
plot1: output/figure_1A.jpeg
### generate study cohort with the date of each prescriptions
generate_study_population_ab_type_2019:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_ab_type_2019
--index-date-range "2019-01-01 to 2019-12-31"
--skip-existing
--output-dir=output/measures
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_ab_type_2019_*.csv.gz
generate_study_population_ab_type_2020:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_ab_type_2020
--index-date-range "2020-01-01 to 2020-12-31"
--skip-existing
--output-dir=output/measures
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_ab_type_2020_*.csv.gz
generate_study_population_ab_type_2021:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_ab_type_2021
--index-date-range "2021-01-01 to 2021-12-31"
--skip-existing
--output-dir=output/measures
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_ab_type_2021_*.csv.gz
conversion_abtype_2019:
run: r:latest analysis/conversion_abtype_2019.R
needs: [generate_study_population_ab_type_2019]
outputs:
highly_sensitive:
rds1: output/measures/abtype_2019.rds
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:49:09
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- broad-spectrum-its
- Requested by
- Billy Zhong
- Branch
- broad_ITS
- Force run dependencies
- No
- Git commit hash
- 2753fe0
- Requested actions
-
-
figure_1A
-
conversion_abtype_2019
-
Code comparison
Compare the code used in this Job Request