csrlite 0.3.0__py3-none-any.whl → 0.3.2__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 (27) hide show
  1. csrlite/__init__.py +91 -110
  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/cm/cm_listing.py +497 -497
  8. csrlite/cm/cm_summary.py +327 -327
  9. csrlite/common/config.py +34 -34
  10. csrlite/common/count.py +293 -293
  11. csrlite/common/parse.py +308 -308
  12. csrlite/common/plan.py +365 -365
  13. csrlite/common/rtf.py +166 -137
  14. csrlite/common/utils.py +33 -33
  15. csrlite/common/yaml_loader.py +71 -71
  16. csrlite/disposition/__init__.py +2 -2
  17. csrlite/disposition/disposition.py +332 -332
  18. csrlite/ie/{ie_summary.py → ie.py} +405 -292
  19. csrlite/pd/pd_listing.py +461 -461
  20. {csrlite-0.3.0.dist-info → csrlite-0.3.2.dist-info}/METADATA +68 -68
  21. csrlite-0.3.2.dist-info/RECORD +23 -0
  22. {csrlite-0.3.0.dist-info → csrlite-0.3.2.dist-info}/WHEEL +1 -1
  23. csrlite/ie/ie_listing.py +0 -109
  24. csrlite/mh/mh_listing.py +0 -209
  25. csrlite/mh/mh_summary.py +0 -333
  26. csrlite-0.3.0.dist-info/RECORD +0 -26
  27. {csrlite-0.3.0.dist-info → csrlite-0.3.2.dist-info}/top_level.txt +0 -0
csrlite/__init__.py CHANGED
@@ -1,110 +1,91 @@
1
- import logging
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- import sys
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-
4
- from .ae.ae_listing import ( # AE listing functions
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- ae_listing,
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- study_plan_to_ae_listing,
7
- )
8
- from .ae.ae_specific import ( # AE specific functions
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- ae_specific,
10
- study_plan_to_ae_specific,
11
- )
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- from .ae.ae_summary import ( # AE summary functions
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- ae_summary,
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- study_plan_to_ae_summary,
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- )
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- from .cm.cm_listing import ( # CM listing functions
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- cm_listing,
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- study_plan_to_cm_listing,
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- )
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- from .cm.cm_summary import (
21
- cm_summary,
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- study_plan_to_cm_summary,
23
- )
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- from .common.config import config
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- from .common.count import (
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- count_subject,
27
- count_subject_with_observation,
28
- )
29
- from .common.parse import (
30
- StudyPlanParser,
31
- parse_filter_to_sql,
32
- )
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- from .common.plan import ( # Core classes
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- load_plan,
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- )
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- from .disposition.disposition import study_plan_to_disposition_summary
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- from .ie.ie_listing import (
38
- ie_listing_df,
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- ie_listing_rtf,
40
- study_plan_to_ie_listing,
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- )
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- from .ie.ie_summary import (
43
- ie_ard,
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- ie_df,
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- ie_rtf,
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- study_plan_to_ie_summary,
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- )
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- from .mh.mh_listing import (
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- mh_listing,
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- study_plan_to_mh_listing,
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- )
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- from .mh.mh_summary import (
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- mh_summary,
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- study_plan_to_mh_summary,
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- )
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- from .pd.pd_listing import (
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- pd_listing,
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- study_plan_to_pd_listing,
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- )
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-
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- # Configure logging
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- logging.basicConfig(
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- level=config.logging_level,
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- format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
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- stream=sys.stdout,
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- )
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- logger = logging.getLogger("csrlite")
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-
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- # Main exports for common usage
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- __all__ = [
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- # Primary user interface
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- "load_plan",
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- # AE analysis (direct pipeline wrappers)
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- "ae_summary",
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- "ae_specific",
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- "ae_listing",
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- # AE analysis (StudyPlan integration)
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- "study_plan_to_ae_summary",
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- "study_plan_to_ae_specific",
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- "study_plan_to_ae_listing",
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- # CM analysis
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- "cm_listing",
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- "study_plan_to_cm_listing",
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- "cm_summary",
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- "study_plan_to_cm_summary",
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- # Disposition analysis
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- "study_plan_to_disposition_summary",
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- # Count functions
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- "count_subject",
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- "count_subject_with_observation",
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- # Parse utilities
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- "StudyPlanParser",
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- "parse_filter_to_sql",
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- # IE analysis
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- "ie_ard",
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- "ie_df",
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- "ie_rtf",
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- "study_plan_to_ie_summary",
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- "ie_listing_df",
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- "ie_listing_rtf",
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- "study_plan_to_ie_listing",
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- # PD analysis
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- "pd_listing",
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- "study_plan_to_pd_listing",
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- # MH analysis
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- "mh_listing",
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- "study_plan_to_mh_listing",
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- "mh_summary",
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- "study_plan_to_mh_summary",
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- ]
1
+ import logging
2
+ import sys
3
+
4
+ from .ae.ae_listing import ( # AE listing functions
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+ ae_listing,
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+ study_plan_to_ae_listing,
7
+ )
8
+ from .ae.ae_specific import ( # AE specific functions
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+ ae_specific,
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+ study_plan_to_ae_specific,
11
+ )
12
+ from .ae.ae_summary import ( # AE summary functions
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+ ae_summary,
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+ study_plan_to_ae_summary,
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+ )
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+ from .cm.cm_listing import ( # CM listing functions
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+ cm_listing,
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+ study_plan_to_cm_listing,
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+ )
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+ from .cm.cm_summary import (
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+ cm_summary,
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+ study_plan_to_cm_summary,
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+ )
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+ from .common.config import config
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+ from .common.count import (
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+ count_subject,
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+ count_subject_with_observation,
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+ )
29
+ from .common.parse import (
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+ StudyPlanParser,
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+ parse_filter_to_sql,
32
+ )
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+ from .common.plan import ( # Core classes
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+ load_plan,
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+ )
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+ from .disposition.disposition import study_plan_to_disposition_summary
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+ from .ie.ie import (
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+ ie_ard,
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+ ie_df,
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+ ie_rtf,
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+ study_plan_to_ie_listing,
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+ study_plan_to_ie_summary,
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+ )
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+ from .pd.pd_listing import (
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+ pd_listing,
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+ study_plan_to_pd_listing,
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+ )
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+
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+ # Configure logging
50
+ logging.basicConfig(
51
+ level=config.logging_level,
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+ format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
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+ stream=sys.stdout,
54
+ )
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+ logger = logging.getLogger("csrlite")
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+
57
+ # Main exports for common usage
58
+ __all__ = [
59
+ # Primary user interface
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+ "load_plan",
61
+ # AE analysis (direct pipeline wrappers)
62
+ "ae_summary",
63
+ "ae_specific",
64
+ "ae_listing",
65
+ # AE analysis (StudyPlan integration)
66
+ "study_plan_to_ae_summary",
67
+ "study_plan_to_ae_specific",
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+ "study_plan_to_ae_listing",
69
+ # CM analysis
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+ "cm_listing",
71
+ "study_plan_to_cm_listing",
72
+ "cm_summary",
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+ "study_plan_to_cm_summary",
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+ # Disposition analysis
75
+ "study_plan_to_disposition_summary",
76
+ # Count functions
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+ "count_subject",
78
+ "count_subject_with_observation",
79
+ # Parse utilities
80
+ "StudyPlanParser",
81
+ "parse_filter_to_sql",
82
+ # IE analysis
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+ "ie_ard",
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+ "ie_df",
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+ "ie_rtf",
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+ "study_plan_to_ie_summary",
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+ "study_plan_to_ie_listing",
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+ # PD analysis
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+ "pd_listing",
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+ "study_plan_to_pd_listing",
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+ ]
csrlite/ae/__init__.py CHANGED
@@ -1 +1 @@
1
- # pyre-strict
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+ # pyre-strict