csrlite 0.2.0__py3-none-any.whl → 0.2.1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (21) hide show
  1. csrlite/__init__.py +71 -58
  2. csrlite/ae/__init__.py +1 -1
  3. csrlite/ae/ae_listing.py +494 -494
  4. csrlite/ae/ae_specific.py +483 -483
  5. csrlite/ae/ae_summary.py +401 -401
  6. csrlite/ae/ae_utils.py +62 -62
  7. csrlite/common/config.py +34 -34
  8. csrlite/common/count.py +293 -293
  9. csrlite/common/parse.py +308 -308
  10. csrlite/common/plan.py +365 -365
  11. csrlite/common/rtf.py +137 -85
  12. csrlite/common/utils.py +33 -33
  13. csrlite/common/yaml_loader.py +71 -71
  14. csrlite/disposition/__init__.py +2 -2
  15. csrlite/disposition/disposition.py +332 -332
  16. csrlite/ie/ie.py +405 -0
  17. {csrlite-0.2.0.dist-info → csrlite-0.2.1.dist-info}/METADATA +68 -68
  18. csrlite-0.2.1.dist-info/RECORD +20 -0
  19. csrlite-0.2.0.dist-info/RECORD +0 -19
  20. {csrlite-0.2.0.dist-info → csrlite-0.2.1.dist-info}/WHEEL +0 -0
  21. {csrlite-0.2.0.dist-info → csrlite-0.2.1.dist-info}/top_level.txt +0 -0
csrlite/__init__.py CHANGED
@@ -1,58 +1,71 @@
1
- import logging
2
- import sys
3
-
4
- from .ae.ae_listing import ( # AE listing functions
5
- ae_listing,
6
- study_plan_to_ae_listing,
7
- )
8
- from .ae.ae_specific import ( # AE specific functions
9
- ae_specific,
10
- study_plan_to_ae_specific,
11
- )
12
- from .ae.ae_summary import ( # AE summary functions
13
- ae_summary,
14
- study_plan_to_ae_summary,
15
- )
16
- from .common.config import config
17
- from .common.count import (
18
- count_subject,
19
- count_subject_with_observation,
20
- )
21
- from .common.parse import (
22
- StudyPlanParser,
23
- parse_filter_to_sql,
24
- )
25
- from .common.plan import ( # Core classes
26
- load_plan,
27
- )
28
- from .disposition.disposition import study_plan_to_disposition_summary
29
-
30
- # Configure logging
31
- logging.basicConfig(
32
- level=config.logging_level,
33
- format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
34
- stream=sys.stdout,
35
- )
36
- logger = logging.getLogger("csrlite")
37
-
38
- # Main exports for common usage
39
- __all__ = [
40
- # Primary user interface
41
- "load_plan",
42
- # AE analysis (direct pipeline wrappers)
43
- "ae_summary",
44
- "ae_specific",
45
- "ae_listing",
46
- # AE analysis (StudyPlan integration)
47
- "study_plan_to_ae_summary",
48
- "study_plan_to_ae_specific",
49
- "study_plan_to_ae_listing",
50
- # Disposition analysis
51
- "study_plan_to_disposition_summary",
52
- # Count functions
53
- "count_subject",
54
- "count_subject_with_observation",
55
- # Parse utilities
56
- "StudyPlanParser",
57
- "parse_filter_to_sql",
58
- ]
1
+ import logging
2
+ import sys
3
+
4
+ from .ae.ae_listing import ( # AE listing functions
5
+ ae_listing,
6
+ study_plan_to_ae_listing,
7
+ )
8
+ from .ae.ae_specific import ( # AE specific functions
9
+ ae_specific,
10
+ study_plan_to_ae_specific,
11
+ )
12
+ from .ae.ae_summary import ( # AE summary functions
13
+ ae_summary,
14
+ study_plan_to_ae_summary,
15
+ )
16
+ from .common.config import config
17
+ from .common.count import (
18
+ count_subject,
19
+ count_subject_with_observation,
20
+ )
21
+ from .common.parse import (
22
+ StudyPlanParser,
23
+ parse_filter_to_sql,
24
+ )
25
+ from .common.plan import ( # Core classes
26
+ load_plan,
27
+ )
28
+ from .disposition.disposition import study_plan_to_disposition_summary
29
+ from .ie.ie import (
30
+ ie_ard,
31
+ ie_df,
32
+ ie_rtf,
33
+ study_plan_to_ie_listing,
34
+ study_plan_to_ie_summary,
35
+ )
36
+
37
+ # Configure logging
38
+ logging.basicConfig(
39
+ level=config.logging_level,
40
+ format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
41
+ stream=sys.stdout,
42
+ )
43
+ logger = logging.getLogger("csrlite")
44
+
45
+ # Main exports for common usage
46
+ __all__ = [
47
+ # Primary user interface
48
+ "load_plan",
49
+ # AE analysis (direct pipeline wrappers)
50
+ "ae_summary",
51
+ "ae_specific",
52
+ "ae_listing",
53
+ # AE analysis (StudyPlan integration)
54
+ "study_plan_to_ae_summary",
55
+ "study_plan_to_ae_specific",
56
+ "study_plan_to_ae_listing",
57
+ # Disposition analysis
58
+ "study_plan_to_disposition_summary",
59
+ # Count functions
60
+ "count_subject",
61
+ "count_subject_with_observation",
62
+ # Parse utilities
63
+ "StudyPlanParser",
64
+ "parse_filter_to_sql",
65
+ # IE analysis
66
+ "ie_ard",
67
+ "ie_df",
68
+ "ie_rtf",
69
+ "study_plan_to_ie_summary",
70
+ "study_plan_to_ie_listing",
71
+ ]
csrlite/ae/__init__.py CHANGED
@@ -1 +1 @@
1
- # pyre-strict
1
+ # pyre-strict