Files

• .dockerignore
• .gitattributes
• .gitignore
• CITATION.cff
• Changes
• LICENSE
• MANIFEST
• META.json
• META.yml
• Makefile.PL
• README.md
• VERSION
• api/perl/README.md
• api/perl/json_bridge.pl
• api/perl/main.pl
• api/perl/openapi.json
• api/perl/t/main.t
• api/perl/t/simplest.t
• api/perl/worker.pl
• api/python/README.md
• api/python/main.py
• api/python/test_api.py
• api/python/test_binding.py
• bin/convert-pheno
• cpanfile
• lib/Convert/Pheno.pm
• lib/Convert/Pheno/Audit/Terminology.pm
• lib/Convert/Pheno/BFF/Biosample.pm
• lib/Convert/Pheno/BFF/DerivedEntities.pm
• lib/Convert/Pheno/BFF/ToOMOP.pm
• lib/Convert/Pheno/BFF/ToPXF.pm
• lib/Convert/Pheno/CBioPortal/ToBFF.pm
• lib/Convert/Pheno/CDISC/DefineXML.pm
• lib/Convert/Pheno/CDISC/ODM/Detector.pm
• lib/Convert/Pheno/CDISC/ODM/Metadata.pm
• lib/Convert/Pheno/CDISC/ODM/Parser.pm
• lib/Convert/Pheno/CDISC/ODM/Record.pm
• lib/Convert/Pheno/CDISC/ODM/Util.pm
• lib/Convert/Pheno/CDISC/ODM/V1.pm
• lib/Convert/Pheno/CDISC/ODM/V2.pm
• lib/Convert/Pheno/CDISC/SDTM/Normalizer.pm
• lib/Convert/Pheno/CDISC/SDTM/Terminology.pm
• lib/Convert/Pheno/CDISC/SDTM/ToBFF.pm
• lib/Convert/Pheno/CLI/Args.pm
• lib/Convert/Pheno/CSV.pm
• lib/Convert/Pheno/ClinicalCDM/Claims.pm
• lib/Convert/Pheno/ClinicalCDM/I2B2.pm
• lib/Convert/Pheno/ClinicalCDM/ToBFF.pm
• lib/Convert/Pheno/ClinicalCDM/Util.pm
• lib/Convert/Pheno/Context.pm
• lib/Convert/Pheno/ConversionRequest.pm
• lib/Convert/Pheno/DB/Bundle.pm
• lib/Convert/Pheno/DB/SQLite.pm
• lib/Convert/Pheno/DB/Similarity.pm
• lib/Convert/Pheno/Emit/OMOP.pm
• lib/Convert/Pheno/Execution/Files.pm
• lib/Convert/Pheno/ExecutionContext.pm
• lib/Convert/Pheno/FHIR/Profile/MCode.pm
• lib/Convert/Pheno/FHIR/ToBFF.pm
• lib/Convert/Pheno/FHIR/Util.pm
• lib/Convert/Pheno/HTTP/Jobs.pm
• lib/Convert/Pheno/HTTP/Projects.pm
• lib/Convert/Pheno/HTTP/Service.pm
• lib/Convert/Pheno/IO/Atomic.pm
• lib/Convert/Pheno/IO/CSVHandler.pm
• lib/Convert/Pheno/IO/FileIO.pm
• lib/Convert/Pheno/JSONLD.pm
• lib/Convert/Pheno/Mapping/Compiler.pm
• lib/Convert/Pheno/Mapping/Metadata.pm
• lib/Convert/Pheno/Mapping/Shared.pm
• lib/Convert/Pheno/Model/Bundle.pm
• lib/Convert/Pheno/OMOP/Definitions.pm
• lib/Convert/Pheno/OMOP/ParticipantStream.pm
• lib/Convert/Pheno/OMOP/ToBFF.pm
• lib/Convert/Pheno/OMOP/ToBFF/Biosamples.pm
• lib/Convert/Pheno/OMOP/ToBFF/Individuals.pm
• lib/Convert/Pheno/OMOP/Vocabulary.pm
• lib/Convert/Pheno/OpenEHR/ToBFF.pm
• lib/Convert/Pheno/Operations.pm
• lib/Convert/Pheno/PXF/ToBFF.pm
• lib/Convert/Pheno/PXF/ToBFF/Biosamples.pm
• lib/Convert/Pheno/PXF/ToBFF/Individuals.pm
• lib/Convert/Pheno/Pipeline.pm
• lib/Convert/Pheno/Runner.pm
• lib/Convert/Pheno/Sink/FileSet.pm
• lib/Convert/Pheno/Source.pm
• lib/Convert/Pheno/Source/CBioPortal.pm
• lib/Convert/Pheno/Source/CDISC/DatasetJSON.pm
• lib/Convert/Pheno/Source/CDISC/DatasetXML.pm
• lib/Convert/Pheno/Source/CDISC/ODM.pm
• lib/Convert/Pheno/Source/ClinicalCDM.pm
• lib/Convert/Pheno/Source/FHIR.pm
• lib/Convert/Pheno/Source/OMOP.pm
• lib/Convert/Pheno/Source/OpenEHR.pm
• lib/Convert/Pheno/Source/Result.pm
• lib/Convert/Pheno/Source/Structured.pm
• lib/Convert/Pheno/Source/TablePackage.pm
• lib/Convert/Pheno/Source/Tabular.pm
• lib/Convert/Pheno/Tabular/REDCap/Dictionary.pm
• lib/Convert/Pheno/Tabular/Record.pm
• lib/Convert/Pheno/Tabular/ToBFF.pm
• lib/Convert/Pheno/Utils/Default.pm
• lib/Convert/Pheno/Utils/Schema.pm
• lib/convertpheno.py
• share/db/README
• share/db/concepts_candidates_2_exposure.csv
• share/db/manifest.json
• share/db/v0/cdisc.db
• share/db/v0/hpo.db
• share/db/v0/icd10.db
• share/db/v0/ncit.db
• share/db/v0/omim.db
• share/ex/perl.pl
• share/ex/python.py
• share/schema/dataset-json-1.1.json
• share/schema/mapping-v2.json
• share/schema/public-conversions.json
• t/00-load.t
• t/01-api-bff-pxf.t
• t/02-api-tabular.t
• t/03-api-omop.t
• t/04-api-stream-omop.t
• t/05-errors.t
• t/06-mapping-errors.t
• t/07-api-bff-omop.t
• t/08-jsonld.t
• t/09-pxf-behavior.t
• t/10-bff2omop-behavior.t
• t/11-mapping-utils.t
• t/12-db-similarity.t
• t/13-db-sqlite.t
• t/14-csvhandler-utils.t
• t/15-convertpheno-orchestration.t
• t/16-omop-behavior.t
• t/17-context-bundle.t
• t/18-cli-entities.t
• t/19-cli-regression.t
• t/20-cli-stream-omop.t
• t/21-openehr-behavior.t
• t/21-term-audit.t
• t/22-fileio-gzip.t
• t/23-cli-help.t
• t/24-tabular-raw-values.t
• t/25-json-bridge.t
• t/26-omop-biosamples.t
• t/27-operation-registry.t
• t/28-ontology-cache.t
• t/29-atomic-output.t
• t/30-source-sink-boundaries.t
• t/31-mapping-v2.t
• t/32-datasetjson.t
• t/33-datasetjson-omop.t
• t/34-fhir.t
• t/35-fhir-omop.t
• t/36-cdisc-odm.t
• t/37-cbioportal.t
• t/38-datasetxml.t
• t/39-ohdsi-vocabulary.t
• t/40-db-bundle.t
• t/41-http-artifact-service.t
• t/42-clinical-cdm.t
• t/43-service-jobs.t
• t/44-job-controls.t
• t/45-ontology-inspection.t
• t/46-job-recovery.t
• t/47-job-deletion.t
• t/48-job-publication.t
• t/49-job-mapping-audit.t
• t/50-resource-directory.t
• t/51-omop-job-output.t
• t/52-projects.t
• t/53-desktop-examples.t
• t/54-bff-omop-mapping.t
• t/55-dataset-id.t
• t/58-concurrent-jobs.t
• t/59-job-metadata-lock.t
• t/README.md
• t/bff2csv/out/individuals.csv
• t/bff2jsonf/out/individuals.fold.json
• t/bff2omop/in/README.md
• t/bff2omop/in/individuals.json
• t/bff2omop/in/local-terms.json
• t/bff2omop/in/terminology.yaml
• t/bff2omop/out/eunomia_CONDITION_OCCURRENCE.csv
• t/bff2omop/out/eunomia_OBSERVATION.csv
• t/bff2omop/out/eunomia_PERSON.csv
• t/bff2omop/out/eunomia_PROCEDURE_OCCURRENCE.csv
• t/bff2pxf/in/README
• t/bff2pxf/in/individuals.json
• t/bff2pxf/out/pxf.json
• t/cbioportal2bff/in/acyc_mgh_2016/LICENSE
• t/cbioportal2bff/in/acyc_mgh_2016/README.md
• t/cbioportal2bff/in/acyc_mgh_2016/case_lists/cases_all.txt
• t/cbioportal2bff/in/acyc_mgh_2016/data_clinical_patient.txt
• t/cbioportal2bff/in/acyc_mgh_2016/data_clinical_sample.txt
• t/cbioportal2bff/in/acyc_mgh_2016/meta_clinical_patient.txt
• t/cbioportal2bff/in/acyc_mgh_2016/meta_clinical_sample.txt
• t/cbioportal2bff/in/acyc_mgh_2016/meta_study.txt
• t/cbioportal2bff/in/cbioportal_mapping.yaml
• t/cdiscodm2bff/in/README
• t/cdiscodm2bff/in/cdisc_odm_data.xml
• t/cdiscodm2bff/in/cdisc_odm_dictionary.csv
• t/cdiscodm2bff/in/generic_mapping.yaml
• t/cdiscodm2bff/in/generic_odm_v1.xml
• t/cdiscodm2bff/in/generic_odm_v2.xml
• t/cdiscodm2bff/out/individuals.json
• t/cdiscodm2pxf/out/pxf.json
• t/csv2bff/in/csv_data.csv
• t/csv2bff/in/csv_mapping.yaml
• t/csv2bff/out/individuals.json
• t/csv2omop/out/csv_CONDITION_OCCURRENCE.csv
• t/csv2omop/out/csv_DRUG_EXPOSURE.csv
• t/csv2omop/out/csv_MEASUREMENT.csv
• t/csv2omop/out/csv_OBSERVATION.csv
• t/csv2omop/out/csv_PERSON.csv
• t/csv2pxf/out/pxf.json
• t/datasetjson2bff/in/README.md
• t/datasetjson2bff/in/ae.json
• t/datasetjson2bff/in/cm.json
• t/datasetjson2bff/in/dm.json
• t/datasetjson2bff/in/ex.json
• t/datasetjson2bff/in/lb.json
• t/datasetjson2bff/in/mh.json
• t/datasetjson2bff/in/pr.json
• t/datasetjson2bff/in/qs.json
• t/datasetjson2bff/in/sdtm_terminology.yaml
• t/datasetjson2bff/in/ts.json
• t/datasetjson2bff/in/vs.json
• t/datasetjson2bff/out/README.md
• t/datasetjson2bff/out/individuals.json
• t/datasetjson2bff/out/terminology/individuals.json
• t/datasetjson2omop/out/CONDITION_OCCURRENCE.csv
• t/datasetjson2omop/out/DRUG_EXPOSURE.csv
• t/datasetjson2omop/out/MEASUREMENT.csv
• t/datasetjson2omop/out/OBSERVATION.csv
• t/datasetjson2omop/out/PERSON.csv
• t/datasetjson2omop/out/PROCEDURE_OCCURRENCE.csv
• t/datasetjson2pxf/out/pxf.json
• t/datasetxml2bff/in/README.md
• t/datasetxml2bff/in/define.xml
• t/datasetxml2bff/in/dm.xml
• t/datasetxml2bff/in/lb.xml
• t/datasetxml2bff/in/mh.xml
• t/datasetxml2bff/in/terminology/define.xml
• t/datasetxml2bff/in/terminology/dm.xml
• t/datasetxml2bff/in/ts.xml
• t/datasetxml2bff/out/README.md
• t/datasetxml2bff/out/individuals.json
• t/datasetxml2bff/out/terminology/individuals.json
• t/fhir2bff/in/README.md
• t/fhir2bff/in/mcode-patient-bundle-jenny-m.json
• t/fhir2bff/in/patient-bundle.json
• t/fhir2bff/out/biosamples.json
• t/fhir2bff/out/cohorts.json
• t/fhir2bff/out/datasets.json
• t/fhir2bff/out/individuals.json
• t/fhir2omop/out/CONDITION_OCCURRENCE.csv
• t/fhir2omop/out/DRUG_EXPOSURE.csv
• t/fhir2omop/out/MEASUREMENT.csv
• t/fhir2omop/out/OBSERVATION.csv
• t/fhir2omop/out/PERSON.csv
• t/fhir2omop/out/PROCEDURE_OCCURRENCE.csv
• t/fhir2pxf/out/pxf.json
• t/fixtures/README.md
• t/fixtures/http-omop-request.json
• t/fixtures/ohdsi-concepts.tsv
• t/fixtures/ohdsi-maps-to.tsv
• t/i2b22bff/in/CONCEPT_DIMENSION.csv
• t/i2b22bff/in/OBSERVATION_FACT.csv
• t/i2b22bff/in/PATIENT_DIMENSION.csv
• t/i2b22bff/in/README.md
• t/i2b22bff/in/VISIT_DIMENSION.csv
• t/i2b22bff/out/individuals.json
• t/lib/Test/ConvertPheno.pm
• t/lib/concurrent-conversion-worker.pl
• t/lib/metadata-lock-probe.pl
• t/lib/queue-blocking-worker.pl
• t/omop2bff/in/CONCEPT.csv
• t/omop2bff/in/DRUG_EXPOSURE.csv
• t/omop2bff/in/PERSON.csv
• t/omop2bff/in/README.md
• t/omop2bff/in/gz/CONCEPT.csv.gz
• t/omop2bff/in/gz/DRUG_EXPOSURE.csv.gz
• t/omop2bff/in/gz/PERSON.csv.gz
• t/omop2bff/in/gz/omop_cdm_eunomia.sql.gz
• t/omop2bff/in/mimic_specimen/CONCEPT.csv
• t/omop2bff/in/mimic_specimen/PERSON.csv
• t/omop2bff/in/mimic_specimen/SPECIMEN.csv
• t/omop2bff/in/omop_cdm_eunomia.sql
• t/omop2bff/in/specimen_quantity/CONCEPT.csv
• t/omop2bff/in/specimen_quantity/PERSON.csv
• t/omop2bff/in/specimen_quantity/SPECIMEN.csv
• t/omop2bff/out/biosamples.json
• t/omop2bff/out/individuals.json
• t/omop2bff/out/individuals_csv.json
• t/omop2bff/out/individuals_csv.json.gz
• t/omop2bff/out/individuals_drug_exposure.json.gz
• t/omop2bff/out/ohdsi.json
• t/omop2pxf/out/pxf.json
• t/openehr2bff/in/README.md
• t/openehr2bff/in/compo_corona.json
• t/openehr2bff/in/gecco_personendaten.json
• t/openehr2bff/in/gecco_personendaten_patient.json
• t/openehr2bff/in/ips_canonical.json
• t/openehr2bff/in/laboratory_report.json
• t/openehr2bff/out/individuals.json
• t/openehr2pxf/out/pxf.json
• t/pcornet2bff/in/DEATH.csv
• t/pcornet2bff/in/DEMOGRAPHIC.csv
• t/pcornet2bff/in/DIAGNOSIS.csv
• t/pcornet2bff/in/ENCOUNTER.csv
• t/pcornet2bff/in/LAB_RESULT_CM.csv
• t/pcornet2bff/in/PRESCRIBING.csv
• t/pcornet2bff/in/PROCEDURES.csv
• t/pcornet2bff/in/README.md
• t/pcornet2bff/in/VITAL.csv
• t/pcornet2bff/out/individuals.json
• t/pxf2bff/in/README
• t/pxf2bff/in/pxf.json
• t/pxf2bff/in/pxf.yaml
• t/pxf2bff/in/pxf_biosamples.json
• t/pxf2bff/out/biosamples.json
• t/pxf2bff/out/individuals.json
• t/pxf2bff/out/individuals.yaml
• t/pxf2csv/out/pxf.csv
• t/pxf2jsonf/out/pxf.fold.json
• t/redcap2bff/in/redcap_data.csv
• t/redcap2bff/in/redcap_dictionary.csv
• t/redcap2bff/in/redcap_mapping.yaml
• t/redcap2bff/out/individuals.json
• t/redcap2pxf/out/pxf.json
• t/schema/malformed.json
• t/sentinel2bff/in/DEATH.csv
• t/sentinel2bff/in/DEMOGRAPHIC.csv
• t/sentinel2bff/in/DIAGNOSIS.csv
• t/sentinel2bff/in/ENCOUNTER.csv
• t/sentinel2bff/in/LAB_RESULT.csv
• t/sentinel2bff/in/PRESCRIBING.csv
• t/sentinel2bff/in/PROCEDURE.csv
• t/sentinel2bff/in/README.md
• t/sentinel2bff/in/VITAL_SIGNS.csv
• t/sentinel2bff/out/individuals.json
• xt/bff2omop.t
• xt/csv2omop.t
• xt/desktop-large-file.t
• xt/minion-evaluation.t
• xt/ohdsi.t
• xt/protobuff.t
• xt/self-validate-schema.t