Revision history for Perl distribution Convert-Pheno
0.28 2025-04-18T00:00:00Z (Manuel Rueda <mrueda@cpan.org>)
- 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 <fuzzy> 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 <mrueda@cpan.org>)
- DockerHub images now support Linux amd64 and arm64 (M-based Macs)
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