ghga-transpiler 2.3.2__tar.gz → 2.4.1__tar.gz

{ghga_transpiler-2.3.2/src/ghga_transpiler.egg-info → ghga_transpiler-2.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ghga_transpiler
-Version: 2.3.2
+Version: 2.4.1
 Summary: GHGA-Transpiler - excel to JSON converter
 Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
 License: Apache 2.0

{ghga_transpiler-2.3.2 → ghga_transpiler-2.4.1}/pyproject.toml

@@ -21,7 +21,7 @@ classifiers = [
     "Intended Audience :: Developers",
 ]
 name = "ghga_transpiler"
-version = "2.3.2"
+version = "2.4.1"
 description = "GHGA-Transpiler - excel to JSON converter"
 dependencies = [
     "typer >= 0.12",

{ghga_transpiler-2.3.2 → ghga_transpiler-2.4.1}/src/ghga_transpiler/configs/2.0.yaml

@@ -28,6 +28,9 @@ worksheets:
   - settings:
       end_column: 7
       name: analysis_method_supporting_files
+      transformations:
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
     sheet_name: AnalysisMethodSupportingFile
   - settings:
       end_column: 7
@@ -64,6 +67,9 @@ worksheets:
   - settings:
       end_column: 7
       name: individual_supporting_files
+      transformations:
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
     sheet_name: IndividualSupportingFile
   - settings:
       end_column: 21
@@ -119,10 +125,15 @@ worksheets:
           !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
         attributes:
           !!python/object/apply:ghga_transpiler.transformations.to_attributes []
+        sequencing_read_length:
+          !!python/name:ghga_transpiler.transformations.to_string
     sheet_name: ExperimentMethod
   - settings:
       end_column: 7
       name: experiment_method_supporting_files
+      transformations:
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
     sheet_name: ExperimentMethodSupportingFile
   - settings:
       end_column: 8
@@ -136,10 +147,17 @@ worksheets:
           !!python/object/apply:ghga_transpiler.transformations.to_list []
         format:
           !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        sequencing_lane_id:
+          !!python/name:ghga_transpiler.transformations.to_string
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
     sheet_name: ResearchDataFile
   - settings:
       end_column: 7
       name: process_data_files
+      transformations:
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
     sheet_name: ProcessDataFile
   - settings:
       end_column: 7

{ghga_transpiler-2.3.2 → ghga_transpiler-2.4.1}/src/ghga_transpiler/configs/2.1.yaml

@@ -30,6 +30,9 @@ worksheets:
   - settings:
       end_column: 7
       name: analysis_method_supporting_files
+      transformations:
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
     sheet_name: AnalysisMethodSupportingFile
   - settings:
       end_column: 7
@@ -66,6 +69,9 @@ worksheets:
   - settings:
       end_column: 7
       name: individual_supporting_files
+      transformations:
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
     sheet_name: IndividualSupportingFile
   - settings:
       end_column: 21
@@ -121,10 +127,15 @@ worksheets:
           !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
         attributes:
           !!python/object/apply:ghga_transpiler.transformations.to_attributes []
+        sequencing_read_length:
+          !!python/name:ghga_transpiler.transformations.to_string
     sheet_name: ExperimentMethod
   - settings:
       end_column: 7
       name: experiment_method_supporting_files
+      transformations:
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
     sheet_name: ExperimentMethodSupportingFile
   - settings:
       end_column: 8
@@ -138,10 +149,17 @@ worksheets:
           !!python/object/apply:ghga_transpiler.transformations.to_list []
         format:
           !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        sequencing_lane_id:
+          !!python/name:ghga_transpiler.transformations.to_string
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
     sheet_name: ResearchDataFile
   - settings:
       end_column: 7
       name: process_data_files
+      transformations:
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
     sheet_name: ProcessDataFile
   - settings:
       end_column: 7

ghga_transpiler-2.4.1/src/ghga_transpiler/configs/2.2.yaml

@@ -0,0 +1,192 @@
+ghga_metadata_version: 2.2.0
+default_settings:
+  header_row: 1
+  start_row: 7
+  start_column: 1
+  transformations:
+    attributes:
+      !!python/object/apply:ghga_transpiler.transformations.to_attributes []
+    format:
+      !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+worksheets:
+  - settings:
+      end_column: 7
+      name: analyses
+      transformations:
+        research_data_files:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+    sheet_name: Analysis
+  - settings:
+      end_column: 17
+      name: analysis_methods
+      transformations:
+        reference_type:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        parameters:
+          !!python/object/apply:ghga_transpiler.transformations.to_attributes []
+        software_versions:
+          !!python/object/apply:ghga_transpiler.transformations.to_attributes []
+        attributes:
+          !!python/object/apply:ghga_transpiler.transformations.to_attributes []
+    sheet_name: AnalysisMethod
+  - settings:
+      end_column: 7
+      name: analysis_method_supporting_files
+      transformations:
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
+    sheet_name: AnalysisMethodSupportingFile
+  - settings:
+      end_column: 7
+      name: studies
+      transformations:
+        affiliations:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        attributes:
+          !!python/object/apply:ghga_transpiler.transformations.to_attributes []
+        types:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
+        attributes:
+          !!python/object/apply:ghga_transpiler.transformations.to_attributes []
+    sheet_name: Study
+  - settings:
+      end_column: 10
+      name: individuals
+      transformations:
+        phenotypic_features_terms:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        phenotypic_features_ids:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        diagnosis_ids:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        diagnosis_terms:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        sex:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        ancestry_terms:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        ancestry_ids:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+    sheet_name: Individual
+  - settings:
+      end_column: 7
+      name: individual_supporting_files
+      transformations:
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
+    sheet_name: IndividualSupportingFile
+  - settings:
+      end_column: 21
+      name: samples
+      transformations:
+        type:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        storage:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        disease_or_healthy:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        case_control_status:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
+        biospecimen_age_at_sampling:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        biospecimen_vital_status_at_sampling:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        biospecimen_isolation:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        biospecimen_storage:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        attributes:
+          !!python/object/apply:ghga_transpiler.transformations.to_attributes []
+    sheet_name: Sample
+  - settings:
+      end_column: 23
+      name: experiment_methods
+      transformations:
+        library_type:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        library_selection_methods:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
+        library_preparation_kit_retail_name:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        primer:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        end_bias:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        target_regions:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        rnaseq_strandedness:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        instrument_model:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        sequencing_layout:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        flow_cell_type:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        sample_barcode_read:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        sequencing_layout:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        attributes:
+          !!python/object/apply:ghga_transpiler.transformations.to_attributes []
+        sequencing_read_length:
+          !!python/name:ghga_transpiler.transformations.to_string
+    sheet_name: ExperimentMethod
+  - settings:
+      end_column: 7
+      name: experiment_method_supporting_files
+      transformations:
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
+    sheet_name: ExperimentMethodSupportingFile
+  - settings:
+      end_column: 8
+      name: experiments
+    sheet_name: Experiment
+  - settings:
+      end_column: 9
+      name: research_data_files
+      transformations:
+        experiments:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        format:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        sequencing_lane_id:
+          !!python/name:ghga_transpiler.transformations.to_string
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
+    sheet_name: ResearchDataFile
+  - settings:
+      end_column: 7
+      name: process_data_files
+      transformations:
+        included_in_submission:
+          !!python/name:ghga_transpiler.transformations.to_boolean
+    sheet_name: ProcessDataFile
+  - settings:
+      end_column: 7
+      name: datasets
+      transformations:
+        types: !!python/object/apply:ghga_transpiler.transformations.to_list []
+    sheet_name: Dataset
+  - settings:
+      end_column: 11
+      name: data_access_policies
+      transformations:
+        data_use_modifier_terms:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
+        data_use_permission_term:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        data_use_modifier_ids:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+    sheet_name: DataAccessPolicy
+  - settings:
+      end_column: 4
+      name: data_access_committees
+    sheet_name: DataAccessCommittee
+  - settings:
+      end_column: 9
+      name: publications
+      transformations:
+        xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
+    sheet_name: Publication

{ghga_transpiler-2.3.2 → ghga_transpiler-2.4.1}/src/ghga_transpiler/transformations.py

@@ -20,6 +20,11 @@
 from collections.abc import Callable
 
 
+def to_string(value: int | str) -> str:
+    """Converts a value to string"""
+    return str(value)
+
+
 def split_by_semicolon(value: str) -> list[str]:
     """Splits a string by semicolon"""
     return [elem.strip() for elem in value.split(";")]
@@ -64,3 +69,18 @@ def snake_case_list(value: str) -> list[str]:
 def to_snake_case_list() -> Callable:
     """Returns a function that converts a semicolon separated string into a list of snake-cased strings"""
     return snake_case_list
+
+
+def to_boolean(value: bool | str) -> bool:
+    """Converts common string boolean values to bool.
+
+    Accepts: true/false in any casing (e.g., "true", "False", "TRUE").
+    """
+    if isinstance(value, bool):
+        return value
+    normalized = value.strip().casefold()
+    if normalized == "true":
+        return True
+    if normalized == "false":
+        return False
+    raise ValueError(f"Invalid boolean string: {value!r}")

{ghga_transpiler-2.3.2 → ghga_transpiler-2.4.1/src/ghga_transpiler.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ghga_transpiler
-Version: 2.3.2
+Version: 2.4.1
 Summary: GHGA-Transpiler - excel to JSON converter
 Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
 License: Apache 2.0

{ghga_transpiler-2.3.2 → ghga_transpiler-2.4.1}/src/ghga_transpiler.egg-info/SOURCES.txt

@@ -21,6 +21,7 @@ src/ghga_transpiler/configs/1.0.yaml
 src/ghga_transpiler/configs/1.1.yaml
 src/ghga_transpiler/configs/2.0.yaml
 src/ghga_transpiler/configs/2.1.yaml
+src/ghga_transpiler/configs/2.2.yaml
 src/ghga_transpiler/configs/__init__.py
 tests/test_convert_workbook.py
 tests/test_create_config.py