open-pathology/generate_yaml.py at main · opensafely/open-pathology · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
"""
Description:
- This script generates the YAML file for the project.

Usage:
- python generate_yaml.py

Output:
- project.yaml
"""

from analysis.config import codelists


# --- YAML HEADER ---

yaml_header = """
version: '4.0'

actions:
"""

# --- YAML MEASURES BODY ----


# Template for measures generation
yaml_template = """
  generate_measures_{test}_tests:
    run: >
      ehrql:v1 generate-measures
        analysis/measure_definition.py
        --output output/{test}_tests/measures.arrow
        --
        --test {test}
    outputs:
      highly_sensitive:
        measures: output/{test}_tests/measures.arrow
  generate_measures_{test}_tests_light:
    run: >
      ehrql:v1 generate-measures
        analysis/measure_definition.py
        --output output/{test}_tests/measures_light.arrow
        --
        --test {test}
        --light
    outputs:
      highly_sensitive:
        measures: output/{test}_tests/measures_light.arrow
  generate_processed_data_{test}_tests:
    run: >
      python:latest
        analysis/write_processed_csv_files.py
        --output-dir output/{test}_tests
        --test {test}
    needs:
      [generate_measures_{test}_tests]
    outputs:
      moderately_sensitive:
        monthly_tables: output/{test}_tests/*deciles_table_counts_per_month*.csv
        monthly_counts: output/{test}_tests/*practice_counts_per_month*.csv
        code_table: output/{test}_tests/top_5_code_table.csv
        event_counts_table: output/{test}_tests/event_counts.csv
  generate_processed_data_{test}_tests_light:
    run: >
      python:latest
        analysis/write_processed_csv_files.py
        --output-dir output/{test}_tests
        --test {test}
        --light
    needs:
      [generate_measures_{test}_tests_light]
    outputs:
      moderately_sensitive:
        monthly_tables: output/{test}_tests/*deciles_table_counts_per_month*_light.csv
        monthly_counts: output/{test}_tests/*practice_counts_per_month*_light.csv
        code_table: output/{test}_tests/top_5_code_table_light.csv
        event_counts_table: output/{test}_tests/event_counts_light.csv
  generate_dataset_test_{test}:
    run: >
        ehrql:v1 generate-dataset
        analysis/dataset_definition.py
        --test-data-file analysis/test_dataset.py
        --output output/tests/{test}_dataset.csv
        --
        --test {test}
    outputs:
      highly_sensitive:
        population: output/tests/{test}_dataset.csv
"""

yaml_body = ""
needs = {}

tests = codelists
del tests["diab_res"]
del tests["alt_numeric"]

for test in tests.keys():
    yaml_body += yaml_template.format(test=test)

yaml_plots = """
  generate_plots:
    run: >
      r:latest
        analysis/plots.r
    outputs:
      moderately_sensitive:
        plots: output*.png
"""

yaml = yaml_header + yaml_body + yaml_plots
with open("project.yaml", "w") as file:
    file.write(yaml)