Revision history for Perl distribution Convert-Pheno 0.29 2025-12-23XXT00:00:00Z (Manuel Rueda ) - Updated icd10.db SQLite database - Fixed typo in t/redcap2bff/in/redcap_mapping.yaml 0.28 2025-04-18T00:00:00Z (Manuel Rueda ) - Internal parameter 'ncpuhost' renamed to 'threadshost' - BFF.pm renamed to Bff2Pxf.pm - Organized some modules into DB and Utils - <--slq2csv> CSVs now mantain the order of header fields from <.sql> (i.e., easier csv import) - OMOP information moved from OMOP.pm to OMOP::Definitions.pm - String similarity functions moved to Similarity.pm - Added --search mode (default: 0.9 token-based + 0.1 Levenshtein distance) - Added --levenshtein-weight parameter - In 'omop2bff' conversion: - Added property "_visit" to 'interventionsOrProcedures' term - Added 'P' string to age (to conform with ISO8601) generated via condition_start_date + birth_datetime - Added DateTime::Format::ISO8601 module to simplify ome time-related calculations - Added "basic" 'bff2omop' conversion. To be further tested and improved in next releases - Added 'visitId' property to 'mapping.json' schema that lands in "_visit.id" on array-based terms 0.27 2025-01-16T00:00:00Z (Manuel Rueda ) - DockerHub images now support Linux amd64 and arm64 (M-based Macs) 0.26 2024-12-18T00:00:00Z (Manuel Rueda ) - Fixed issue with excluded/negated boolean values in 0.25 2024-11-09T00:00:00Z (Manuel Rueda ) - Changed the default 'ontology_term' from {id => 'NCIT:NA0000', label => 'NA'} to {id => 'NCIT:C126101', label => 'Not Available'} - Expanded coverage for 'procedure' term in omop2bff*/bff2pxf - omop2bff now accepts measurements with empty values '\\N' and assigns defaults when needed 0.24 2024-07-18T00:00:00Z (Manuel Rueda ) - Switched read_csv from Text::CSV_XS functional interface to incremental reading to reduce RAM usage 0.23 2024-07-17T00:00:00Z (Manuel Rueda ) - Reduced RAM usage in -iomop -stream when loading mandatory tables from PostgreSQL dump 0.22 2024-07-13T00:00:00Z (Manuel Rueda ) - Reduced memory usage in -iomop -stream by emptying CONCEPT, PERSON and VISIT_OCCURRENCE during AoH -> HoH step - Reduced memory usage in -iomop -no-stream by avoiding data duplication during transposition - Added Devel::Size to production for use with -verbose (+ added to cpanfile/Makefile.PL) - Implemented --max-lines-sql option to --stream mode 0.21 2024-06-01T00:00:00Z (Manuel Rueda ) - Updated the default value for the 'treatment.interval' object - Fixed a warning that occurred in exact searches when the string contained leading numbers - Modified database search behavior to exclude numbers from the search - Fixed an OMOP --stream mode error where processing a single table with undefined values incorrectly flagged entries as duplicates, yielding only one individual 0.20 2024-05-23T00:00:00Z (Manuel Rueda ) - Encapsulated default values in Default.pm - Refactored REDCap.pm code to be used with CSV.pm - Implemented basic and conversions (experimental) - Mapping file changes: o Required properties in mappind file now only are 'project','id' and 'sex' o Added project.baselineFieldsToPropagate o Added new properties along with their schemas, This is the current list: * age,ageOfOnset,assignTermIdFromHeader,bodySite,dateOfProcedure,dictionary,drugDose,drugUnit,duration,durationUnit,familyHistory,fields,mapping,procedureCodeLabel,selector,terminology,unit - Fixed issue with hpo.db that had leading and trailing white spaces in columns 0.19 2024-04-24T00:00:00Z (Manuel Rueda ) - Updated how to obtain nproc for FreeBSD - Moved t/{ohdsi,protobuff}.t to xt/ - Added experimental -ojsond (JSON-LD) (to be used with -i{bff|pxf} - Extended Unicode support - Separated Windows builds into a distinct workflow due to JSONLD dependency issues - Dynamically load JSONLD module with require (if installed) 0.18 2024-02-29T00:00:00Z (Manuel Rueda ) - Updated resources in PXF.pm - Added info.REDCap_columns to REDCap.pm - Renamed keys in REDCap mapping (schema|src|files): o radio -> selector o dict -> dictionary o map -> mapping - Added info.convertPheno to individuals.json - Added project.version to mapping (schema|src|files) - Refactored CSV.pm and IO.pm to IO::CSVHandler and IO::FileIO - Implemented -o{csv,jsonf} (to be used with -i{bff|pxf} 0.17 2024-02-03T00:00:00Z (Manuel Rueda ) - Fixed typo in _info.VISIT_OCCURENCE -> _info.VISIT_OCCURRENCE 0.16 2023-12-26T00:00:00Z (Manuel Rueda ) - Implemented restriction on I/O format duplication (ibff->obff) 0.15 2023-11-30T00:00:00Z (Manuel Rueda ) - Changed 'windows-latest' to 'windows-2019' in GHA build-and-test.yml - Refactored .pm to improve readibility and maintanability 0.14 2023-11-21T00:00:00Z (Manuel Rueda ) - Fixed error on pxf.{json,yaml} @pxf-tools-cli examples (v1.0.0-RC3) o label": "Vitamin E" -> label": "atorvastatin" 0.13 2023-09-12T00:00:00Z (Manuel Rueda ) - Pushing new version after passing all tests 0.12_3 2023-09-12T00:00:00Z (Manuel Rueda ) - Added support for Windows Server OS - Added changes to pass windows-latest tests in GitHub o Replaced PerlIO::gzip by core IO::Uncompress::G[un]zip o Adapted t/{args,cli.t} 0.12_2 2023-09-07T00:00:00Z (Manuel Rueda ) - Added Data::Leaf::Walker to cpanfile/Makefile.PL 0.12_1 2023-09-06T00:00:00Z (Manuel Rueda ) - Extended the documentation (e.g., docs/tbl/*md) - Excluded unnecessary files in CPAN via MANIFEST.SKIP - Changed Google Drive location of ohdsi.db - Increased coverage of PXF<-->BFF term mapping - Added READMEs to t/*/in/ - Updated t/pxf2bff/in/pxf.json and added YAML version 0.12 2023-07-19T00:00:00Z (Manuel Rueda ) - Pushing new version after passing all tests 0.11_4 2023-07-17T00:00:00Z (Manuel Rueda ) - Modified t/args.t to make it 'MSWin32' and 'cygwin' compatible 0.11_3 2023-07-17T00:00:00Z (Manuel Rueda ) - Changed getpwuid to $ENV{'USERNAME'} to make 'MSWin32' compatible 0.11_2 2023-07-10T00:00:00Z (Manuel Rueda ) - Modified Python binding to work in Conda env - Increased Perl version from 5.16 to 5.26 0.11_1 2023-07-09T00:00:00Z (Manuel Rueda ) - Reverted change in Makefile.PL for 'IO::Socket::SSL' - IO::Socker::SSL only is used if installed 0.11 2023-07-09T00:00:00Z (Manuel Rueda ) - Uncommented 'IO::Socket::SSL' in Makefile.PL to pass self-validation of mapping schema in t/ - Changed cnag.crg.eu to cnag.eu 0.10 2023-07-03T00:00:00Z (Manuel Rueda ) - Added share/db/{omim,hpo}.db SQLite databases - Modified source to accomodate such dbs Note: Versions < 0.10 were primarily for testing deployment on CPAN