cdiscbuilder 1.2.1__tar.gz → 1.2.2__tar.gz

{cdiscbuilder-1.2.1 → cdiscbuilder-1.2.2}/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2026 Ming-Chun Chen
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2026 Ming-Chun Chen
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{cdiscbuilder-1.2.1 → cdiscbuilder-1.2.2}/MANIFEST.in

@@ -1,3 +1,3 @@
-include src/cdiscbuilder/adam/schema.yaml
-recursive-include src/cdiscbuilder/adam/adam_spec/tests/data *.yaml
-include src/cdiscbuilder/metadata/*.yaml
+include src/cdiscbuilder/adam/schema.yaml
+recursive-include src/cdiscbuilder/adam/adam_spec/tests/data *.yaml
+include src/cdiscbuilder/metadata/*.yaml

{cdiscbuilder-1.2.1/src/cdiscbuilder.egg-info → cdiscbuilder-1.2.2}/PKG-INFO

@@ -1,195 +1,196 @@
-Metadata-Version: 2.4
-Name: cdiscbuilder
-Version: 1.2.1
-Summary: A package to convert ODM XML to SDTM/ADaM Datasets
-Author-email: Ming-Chun Chen <hellomingchun@gmail.com>
-Requires-Python: >=3.9
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: pandas
-Requires-Dist: pyyaml
-Requires-Dist: polars>=0.20.0
-Requires-Dist: reactable>=0.1.6
-Dynamic: license-file
-
-# CDISC Builder
-
-**`cdiscbuilder`** is a Python package designed to simplify the transformation of clinical trial data from **ODM (Operational Data Model)** XML format into **CDISC SDTM (Study Data Tabulation Model)** and **ADaM (Analysis Data Model)** datasets.
-
-It provides a flexible, configuration-driven approach to data mapping, allowing users to define rules using simple YAML files or Python dictionaries without harcoding complex logic.
-
-## Key Features
-
--   **ODM XML Parsing**: Efficiently parses CDISC ODM strings and files into workable dataframes.
--   **Configurable Mappings**: Define your mapping rules (source columns, hardcoded values, custom logic) in YAML.
--   **Schema Validation**: Ensures your configuration files adhere to strict standards before processing.
--   **Metadata-Driven Findings**: Powerful processor for Findings domains (VS, LB, FA, etc.) using granular metadata.
--   **Excel/Parquet Output**: Generates regulatory-compliant datasets in modern formats.
-
-## Installation
-
-```bash
-pip install cdiscbuilder
-```
-
-## Quick Start
-
-### 1. Command Line Interface
-
-You can generate datasets directly from your terminal:
-
-```bash
-# Generate SDTM datasets from an ODM XML file
-cdisc-sdtm --xml study_data.xml --output ./sdtm_data
-```
-
-### 2. Python API
-
-```python
-from cdiscbuilder.sdtm import create_sdtm_datasets
-
-# Define paths
-xml_file = "study_data.xml"
-config_dir = "path/to/my/specs" 
-output_dir = "./sdtm_outputs"
-
-# Generate Datasets
-create_sdtm_datasets(config_dir, xml_file, output_dir)
-```
-
-## Configuration
-
-For detailed and complete references on how to structure mapping specifications, see:
-* **[SDTM Mapping Specification](file:///c:/Users/mingc/Documents/projects/cdiscbuilder/cdisc_builder/docs/SDTM_MAPPING_SPECIFICATION.md)**: Details on the intermediate `odm_long.csv` schema, wide vs. findings domains, regex extraction, and validation rules.
-* **[ADaM Mapping Specification](file:///c:/Users/mingc/Documents/projects/cdiscbuilder/cdisc_builder/docs/ADAM_MAPPING_SPECIFICATION.md)**: Details on ADaM yaml configuration schema, inheritance, SQL-like derivations, conditions, and aggregations.
-
-The package comes with standard configurations for common domains (`DM`, `AE`, `VS`, etc.) in `src/cdisc_builder/specs`. You can override these or add new ones by creating your own configuration directory.
-
-### Example YAML (`DM.yaml`)
-
-```yaml
-DM:
-    - formoid: "FORM.DEMOG"
-      keys: ["StudyOID", "StudySubjectID"]
-      columns:
-          STUDYID:
-              source: StudyOID
-              type: str
-          USUBJID:
-              source: StudySubjectID
-              prefix: "PPT-"
-              type: str
-          AGE:
-              source: IT.AGE
-              type: int
-              type: str
-          SEX:
-              source: I_DEMOG_SEX
-              type: str
-              value_mapping:
-                  "M": "Male"
-                  "F": "Female"
-
-```
-### Finding Domains (Dynamic Mapping)
-
-For domains like `IE`, `LB`, `FA` where many input items map to a single `Test Code` / `Test Name` pair, use `type: finding`.
-
-```yaml
-IE:
-  - type: finding
-    formoid: "F_ELIGIBILITY"
-    # Filter rows using Regex
-    item_group_regex: "IG_ELIGI_.*"
-    item_oid_regex: "I_ELIGI_.*"
-    
-    columns:
-      # Extract part of the OID for the Short Code
-      IETESTCD:
-        source: ItemOID
-        regex_extract: "I_ELIGI_(.*)"
-      
-      # Use Metadata from parsed XML for the Description
-      IETEST:
-        source: Metadata.Question
-      
-      IEORRES:
-        source: Value
-```
-
-### Advanced Mapping Features
-
-**Prefixing**:
-```yaml
-USUBJID:
-  source: StudySubjectID
-  prefix: "PPT-"
-```
-
-**Substring Extraction** (extracts chars 3-5 before mapping):
-```yaml
-SITEID:
-  source: FULL_ID
-  substring_start: 3
-  substring_length: 3
-
-**Fallback** (use secondary source if primary is missing):
-```yaml
-SUBJID:
-  source: RFSTDTC
-  fallback: USUBJID
-```
-```
-
-**Default Values**:
-```yaml
-CUSTOM_COL:
-  source: ORG_COL
-  value_mapping:
-    "A": "Alpha"
-  mapping_default: "Other" # used if not A
-  # mapping_default_source: "AnotherCol" # Fallback to column value
-```
-
-**Case Sensitive Mapping**:
-By default, mapping is case-sensitive. You can disable this to map values regardless of case (e.g. "Yes", "yes", "YES" -> "Y"). Unmapped values preserve their original casing.
-```yaml
-RESP:
-  source: INPUT_VAL
-  value_mapping:
-    "Yes": "Y"
-    "No": "N"
-  case_sensitive: false
-```
-
-## Development
-
-This project uses modern tools for testing and maintaining code quality:
-
-### 1. Running Tests
-Run the automated test suite using `pytest`:
-```bash
-# Using standard pip/virtual environment
-pytest
-
-# Using uv
-uv run pytest
-```
-
-### 2. Code Quality
-We use `black` for code formatting, `ruff` for linting, and `mypy` for type checking:
-
-```bash
-# Code Formatting (in-place rewrite)
-uv run --with black black src/
-
-# Linting and style checks
-uv run --with ruff ruff check src/
-
-# Type Checking
-uv run --with mypy mypy src/
-```
-
-## License
-
-[MIT License](LICENSE)
+Metadata-Version: 2.4
+Name: cdiscbuilder
+Version: 1.2.2
+Summary: A package to convert ODM XML to SDTM/ADaM Datasets
+Author-email: Ming-Chun Chen <hellomingchun@gmail.com>
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas
+Requires-Dist: pyyaml
+Requires-Dist: polars>=0.20.0
+Requires-Dist: reactable>=0.1.6
+Requires-Dist: pyarrow
+Dynamic: license-file
+
+# CDISC Builder
+
+**`cdiscbuilder`** is a Python package designed to simplify the transformation of clinical trial data from **ODM (Operational Data Model)** XML format into **CDISC SDTM (Study Data Tabulation Model)** and **ADaM (Analysis Data Model)** datasets.
+
+It provides a flexible, configuration-driven approach to data mapping, allowing users to define rules using simple YAML files or Python dictionaries without harcoding complex logic.
+
+## Key Features
+
+-   **ODM XML Parsing**: Efficiently parses CDISC ODM strings and files into workable dataframes.
+-   **Configurable Mappings**: Define your mapping rules (source columns, hardcoded values, custom logic) in YAML.
+-   **Schema Validation**: Ensures your configuration files adhere to strict standards before processing.
+-   **Metadata-Driven Findings**: Powerful processor for Findings domains (VS, LB, FA, etc.) using granular metadata.
+-   **Excel/Parquet Output**: Generates regulatory-compliant datasets in modern formats.
+
+## Installation
+
+```bash
+pip install cdiscbuilder
+```
+
+## Quick Start
+
+### 1. Command Line Interface
+
+You can generate datasets directly from your terminal:
+
+```bash
+# Generate SDTM datasets from an ODM XML file
+cdisc-sdtm --xml study_data.xml --output ./sdtm_data
+```
+
+### 2. Python API
+
+```python
+from cdiscbuilder.sdtm import create_sdtm_datasets
+
+# Define paths
+xml_file = "study_data.xml"
+config_dir = "path/to/my/specs" 
+output_dir = "./sdtm_outputs"
+
+# Generate Datasets
+create_sdtm_datasets(config_dir, xml_file, output_dir)
+```
+
+## Configuration
+
+For detailed and complete references on how to structure mapping specifications, see:
+* **[SDTM Mapping Specification](file:///c:/Users/mingc/Documents/projects/cdiscbuilder/cdisc_builder/docs/SDTM_MAPPING_SPECIFICATION.md)**: Details on the intermediate `odm_long.csv` schema, wide vs. findings domains, regex extraction, and validation rules.
+* **[ADaM Mapping Specification](file:///c:/Users/mingc/Documents/projects/cdiscbuilder/cdisc_builder/docs/ADAM_MAPPING_SPECIFICATION.md)**: Details on ADaM yaml configuration schema, inheritance, SQL-like derivations, conditions, and aggregations.
+
+The package comes with standard configurations for common domains (`DM`, `AE`, `VS`, etc.) in `src/cdisc_builder/specs`. You can override these or add new ones by creating your own configuration directory.
+
+### Example YAML (`DM.yaml`)
+
+```yaml
+DM:
+    - formoid: "FORM.DEMOG"
+      keys: ["StudyOID", "StudySubjectID"]
+      columns:
+          STUDYID:
+              source: StudyOID
+              type: str
+          USUBJID:
+              source: StudySubjectID
+              prefix: "PPT-"
+              type: str
+          AGE:
+              source: IT.AGE
+              type: int
+              type: str
+          SEX:
+              source: I_DEMOG_SEX
+              type: str
+              value_mapping:
+                  "M": "Male"
+                  "F": "Female"
+
+```
+### Finding Domains (Dynamic Mapping)
+
+For domains like `IE`, `LB`, `FA` where many input items map to a single `Test Code` / `Test Name` pair, use `type: finding`.
+
+```yaml
+IE:
+  - type: finding
+    formoid: "F_ELIGIBILITY"
+    # Filter rows using Regex
+    item_group_regex: "IG_ELIGI_.*"
+    item_oid_regex: "I_ELIGI_.*"
+    
+    columns:
+      # Extract part of the OID for the Short Code
+      IETESTCD:
+        source: ItemOID
+        regex_extract: "I_ELIGI_(.*)"
+      
+      # Use Metadata from parsed XML for the Description
+      IETEST:
+        source: Metadata.Question
+      
+      IEORRES:
+        source: Value
+```
+
+### Advanced Mapping Features
+
+**Prefixing**:
+```yaml
+USUBJID:
+  source: StudySubjectID
+  prefix: "PPT-"
+```
+
+**Substring Extraction** (extracts chars 3-5 before mapping):
+```yaml
+SITEID:
+  source: FULL_ID
+  substring_start: 3
+  substring_length: 3
+
+**Fallback** (use secondary source if primary is missing):
+```yaml
+SUBJID:
+  source: RFSTDTC
+  fallback: USUBJID
+```
+```
+
+**Default Values**:
+```yaml
+CUSTOM_COL:
+  source: ORG_COL
+  value_mapping:
+    "A": "Alpha"
+  mapping_default: "Other" # used if not A
+  # mapping_default_source: "AnotherCol" # Fallback to column value
+```
+
+**Case Sensitive Mapping**:
+By default, mapping is case-sensitive. You can disable this to map values regardless of case (e.g. "Yes", "yes", "YES" -> "Y"). Unmapped values preserve their original casing.
+```yaml
+RESP:
+  source: INPUT_VAL
+  value_mapping:
+    "Yes": "Y"
+    "No": "N"
+  case_sensitive: false
+```
+
+## Development
+
+This project uses modern tools for testing and maintaining code quality:
+
+### 1. Running Tests
+Run the automated test suite using `pytest`:
+```bash
+# Using standard pip/virtual environment
+pytest
+
+# Using uv
+uv run pytest
+```
+
+### 2. Code Quality
+We use `black` for code formatting, `ruff` for linting, and `mypy` for type checking:
+
+```bash
+# Code Formatting (in-place rewrite)
+uv run --with black black src/
+
+# Linting and style checks
+uv run --with ruff ruff check src/
+
+# Type Checking
+uv run --with mypy mypy src/
+```
+
+## License
+
+[MIT License](LICENSE)