MRUEDA / Convert-Pheno-0.26 / Changes 
Revision history for Perl distribution Convert-Pheno

0.26 2024-12-18T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Fixed issue with excluded/negated boolean values in <pxf2bff>

0.25 2024-11-09T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - 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 <mrueda@cpan.org>)

 - 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 <mrueda@cpan.org>)

 - Reduced RAM usage in -iomop -stream when loading mandatory tables from PostgreSQL dump

0.22 2024-07-13T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - 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 <mrueda@cpan.org>)

 - 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 <mrueda@cpan.org>)

 - Encapsulated default values in Default.pm
 - Refactored REDCap.pm code to be used with CSV.pm
 - Implemented basic <csv2bff> and <csv2pxf> 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 <mrueda@cpan.org>)

 - 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 <mrueda@cpan.org>)

 - 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 <mrueda@cpan.org>)

 - Fixed typo in _info.VISIT_OCCURENCE -> _info.VISIT_OCCURRENCE

0.16 2023-12-26T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Implemented restriction on I/O format duplication (ibff->obff)

0.15 2023-11-30T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - 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 <mrueda@cpan.org>)

 - 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 <mrueda@cpan.org>)

 - Pushing new version after passing all tests

0.12_3 2023-09-12T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - 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 <mrueda@cpan.org>)

 - Added Data::Leaf::Walker to cpanfile/Makefile.PL

0.12_1 2023-09-06T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - 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 <mrueda@cpan.org>)

 - Pushing new version after passing all tests

0.11_4 2023-07-17T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Modified t/args.t to make it 'MSWin32' and 'cygwin' compatible

0.11_3 2023-07-17T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - Changed getpwuid to $ENV{'USERNAME'} to make 'MSWin32' compatible

0.11_2 2023-07-10T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)

 - 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 <mrueda@cpan.org>)

 - 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 <mrueda@cpan.org>)
 - 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 <mrueda@cpan.org>)
 - 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