diff --git a/auto_gen_concept_templates b/auto_gen_concept_templates/README.md similarity index 100% rename from auto_gen_concept_templates rename to auto_gen_concept_templates/README.md diff --git a/auto_gen_concept_templates/autogen.py b/auto_gen_concept_templates/autogen.py new file mode 100644 index 0000000..d1b7753 --- /dev/null +++ b/auto_gen_concept_templates/autogen.py @@ -0,0 +1,106 @@ +import gspread +from gspread_dataframe import set_with_dataframe, get_as_dataframe +import pandas as pd + +mapping_sources = [ + { + 'spreadsheet_name': 'AIREADI MOCA Data Dictionary and Mappings v0.3', + 'worksheet_name': 'MOCA Data Dictionary with Extensions', + 'process': True, + 'tag': 'MOCA', + }, + { + 'spreadsheet_name': 'REDCap Data Dictionary and OMOP Mappings', + 'worksheet_name': '_master REDCap Data Dictionary with Extensions', + 'process': False, + 'tag': 'RedCap', + }, +] +outputs = [ + { + 'name': 'concept_manual.csv', + 'columns': { + 'concept_name': {'MOCA': 'TARGET_CONCEPT_NAME'}, + 'SRC_CODE': {'default': ''}, + 'concept_id': {'MOCA': 'TARGET_CONCEPT_ID'}, + 'vocabulary_id': {'MOCA': 'TARGET_VOCABULARY_ID'}, + 'domain_id': {'MOCA': 'TARGET_DOMAIN_ID'}, + 'v6_domain_id': {'default': 'survey_conduct'}, + 'concept_class_id': {'MOCA': 'TARGET_CONCEPT_CLASS_ID'}, + 'standard_concept': {'MOCA': 'TARGET_STANDARD_CONCEPT'}, + 'valid_start_date': {'default': '1/1/1970'}, + 'valid_end_date': {'default': ''}, + 'invalid_reason': {'default': ''}, + } + }, + { + 'name': 'concept_relationship_manual.csv', + 'columns': { + 'concept_name': {'MOCA': 'TARGET_CONCEPT_NAME'}, + 'concept_id_1': {'MOCA': 'TARGET_CONCEPT_ID'}, + 'SRC_CODE': {'default': ''}, + 'vocabulary_id_1': {'MOCA': 'TARGET_VOCABULARY_ID'}, + 'relationship_id': {'default': ''}, + 'concept_id_2': {'default': '606671'}, + 'temp name': {'default': 'Montreal Cognitive Assessment version 8.1'}, + 'temp domain': {'default': 'Measurement'}, + 'vocabulary_id_2': {'default': 'SNOMED'}, + 'temp class': {'default': 'Staging / Scales'}, + 'concept_code_2': {'default': '1148423001'}, + 'temp standard': {'default': 'S'}, + 'relationship_valid_start_date': {'default': ''}, + 'relationship_valid_end_date': {'default': ''}, + 'invalid_reason': {'default': ''}, + 'confidence': {'default': '1'}, + 'predicate_id': {'default': 'skos:broadMatch'}, + 'mapping_source': {'default': 'ManualMapping'}, + 'mapping_justification': {'default': 'ManualMappingCuration'}, + 'mapping_tool': {'default': ''}, + 'Notes': {'default': ''}, + } + }, +] + + +def main(): + gc = gspread.service_account() + + for source in mapping_sources: + if not source['process']: + continue + + spreadsheet = gc.open(source['spreadsheet_name']) + mapping = spreadsheet.worksheet(source['worksheet_name']) + df_all = get_as_dataframe(mapping) + df = df_all.copy()[df_all['TARGET_CONCEPT_ID'] > 2000000000] + tag = source['tag'] + + for ofile in outputs: + columns = ofile['columns'] + result_data = {} + + # Process each column in the output specification + for col_name, source_def in columns.items(): + if tag in source_def: + # Use the source column from the dataframe + source_col = source_def[tag] + if source_col in df.columns: + result_data[col_name] = df[source_col].values + else: + print(f"Warning: Column '{source_col}' not found in source data") + result_data[col_name] = [source_def.get('default', '')] * len(df) + else: + # Use default value for all rows + default_value = source_def.get('default', '') + result_data[col_name] = [default_value] * len(df) + + # Create DataFrame from the result data + result_df = pd.DataFrame(result_data) + + # Save to CSV + filename = 'output/' + ofile['name'] + result_df.to_csv(filename, index=False) + print(f"Saved {filename} with {len(result_df)} rows") + +if __name__ == "__main__": + main() diff --git a/auto_gen_concept_templates/output/concept_manual.csv b/auto_gen_concept_templates/output/concept_manual.csv new file mode 100644 index 0000000..5e4e903 --- /dev/null +++ b/auto_gen_concept_templates/output/concept_manual.csv @@ -0,0 +1,31 @@ +concept_name,SRC_CODE,concept_id,vocabulary_id,domain_id,v6_domain_id,concept_class_id,standard_concept,valid_start_date,valid_end_date,invalid_reason +Trail drawings score,,2005200344.0,SNOMED,Measurement,survey_conduct,Staging / Scales,S,1/1/1970,, +Time taken to do trails in seconds,,2005200345.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Cube drawings score,,2005200346.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Time taken to do cube in seconds,,2005200347.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Clock drawings score,,2005200348.0,LOINC,Observation,survey_conduct,Survey,S,1/1/1970,, +Time taken to do clock in seconds,,2005200349.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Animal name recall task score,,2005200350.0,AIREADI-MOCA,Measurement,survey_conduct,Observable Entity,S,1/1/1970,, +Time in seconds to perform the animal name recall task,,2005200351.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Words correctly repeated (1st trial) score,,2005200352.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Time in seconds to perform the words correctly repeated (1st trial),,2005200353.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Words correctly repeated (2nd trial) score,,2005200354.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Time in seconds to perform the words correctly repeated (2nd trial),,2005200355.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Repeating digits score,,2005200356.0,SNOMED,Observation,survey_conduct,Observable Entity,S,1/1/1970,, +Time in seconds to perform the repeating digits task,,2005200357.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Letter tapping score,,2005200358.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Time in seconds to perform the letter tapping task,,2005200359.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Serial 7 subtraction score,,2005200360.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Time in seconds to perform the serial 7 subtraction task,,2005200361.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Repeats sentences II score,,2005200362.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Time in seconds to perform repeats sentences II task,,2005200363.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Maximal one-minute recall of words beginning with 'F' score,,2005200364.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Time in seconds to perform the words beginning with 'F' recall task,,2005200365.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +MOCA abstraction score,,2005200366.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Time in seconds to perform MOCA abstraction task,,2005200367.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +MOCA delayed recall with no cue score,,2005200368.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Time in seconds to perform the MOCA delayed recall with no cue task,,2005200369.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +"MOCA orientation date, month, year, day, place, city score",,2005200370.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +"Time in seconds to perform the MOCA orientation date, month, year, day, place, city task",,2005200371.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, +Age in years (3-4 year span),,2005200372.0,AIREADI-MOCA,Observation,survey_conduct,Observable Entity,S,1/1/1970,, +"MOCA delayed recall with no cue, cue, and multiple choice cue (Combined score)",,2005200373.0,AIREADI-MOCA,Measurement,survey_conduct,Assessment Item ,S,1/1/1970,, diff --git a/auto_gen_concept_templates/output/concept_relationship_manual.csv b/auto_gen_concept_templates/output/concept_relationship_manual.csv new file mode 100644 index 0000000..882984e --- /dev/null +++ b/auto_gen_concept_templates/output/concept_relationship_manual.csv @@ -0,0 +1,31 @@ +concept_name,concept_id_1,SRC_CODE,vocabulary_id_1,relationship_id,concept_id_2,temp name,temp domain,vocabulary_id_2,temp class,concept_code_2,temp standard,relationship_valid_start_date,relationship_valid_end_date,invalid_reason,confidence,predicate_id,mapping_source,mapping_justification,mapping_tool,Notes +Trail drawings score,2005200344.0,,SNOMED,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Time taken to do trails in seconds,2005200345.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Cube drawings score,2005200346.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Time taken to do cube in seconds,2005200347.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Clock drawings score,2005200348.0,,LOINC,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Time taken to do clock in seconds,2005200349.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Animal name recall task score,2005200350.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Time in seconds to perform the animal name recall task,2005200351.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Words correctly repeated (1st trial) score,2005200352.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Time in seconds to perform the words correctly repeated (1st trial),2005200353.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Words correctly repeated (2nd trial) score,2005200354.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Time in seconds to perform the words correctly repeated (2nd trial),2005200355.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Repeating digits score,2005200356.0,,SNOMED,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Time in seconds to perform the repeating digits task,2005200357.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Letter tapping score,2005200358.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Time in seconds to perform the letter tapping task,2005200359.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Serial 7 subtraction score,2005200360.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Time in seconds to perform the serial 7 subtraction task,2005200361.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Repeats sentences II score,2005200362.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Time in seconds to perform repeats sentences II task,2005200363.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Maximal one-minute recall of words beginning with 'F' score,2005200364.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Time in seconds to perform the words beginning with 'F' recall task,2005200365.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +MOCA abstraction score,2005200366.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Time in seconds to perform MOCA abstraction task,2005200367.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +MOCA delayed recall with no cue score,2005200368.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +Time in seconds to perform the MOCA delayed recall with no cue task,2005200369.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scales,1148423001,S,,,,1,skos:broadMatch,ManualMapping,ManualMappingCuration,, +"MOCA orientation date, month, year, day, place, city score",2005200370.0,,AIREADI-MOCA,,606671,Montreal Cognitive Assessment version 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