├── .circleci └── config.yml ├── .codecov.yml ├── .gitignore ├── CONTRIBUTORS.md ├── Events.md ├── Extractors.md ├── LICENSE.txt ├── README.md ├── Transformer.md ├── project ├── build.properties ├── plugins.sbt └── project │ └── assembly.sbt └── src ├── main ├── resources │ ├── cnam │ │ ├── dcir.conf │ │ └── mco.conf │ ├── config │ │ ├── bulk │ │ │ ├── default.conf │ │ │ └── paths │ │ │ │ └── cmap.conf │ │ ├── fall │ │ │ ├── default.conf │ │ │ ├── paths │ │ │ │ ├── cmap.conf │ │ │ │ ├── cnam.conf │ │ │ │ ├── save.conf │ │ │ │ └── test.conf │ │ │ └── template.conf │ │ ├── pioglitazone │ │ │ ├── default.conf │ │ │ ├── paths │ │ │ │ ├── cmap.conf │ │ │ │ ├── cnam.conf │ │ │ │ └── test.conf │ │ │ └── template.conf │ │ ├── rosiglitazone │ │ │ ├── default.conf │ │ │ ├── paths │ │ │ │ ├── cmap.conf │ │ │ │ ├── cnam.conf │ │ │ │ └── test.conf │ │ │ └── template.conf │ │ └── test │ │ │ └── default.conf │ ├── polytechnique │ │ ├── dcir.conf │ │ ├── had.conf │ │ ├── mco.conf │ │ └── ssr.conf │ ├── test.conf │ └── test │ │ ├── dcir.conf │ │ └── mco.conf └── scala │ └── fr │ └── polytechnique │ └── cmap │ └── cnam │ ├── Main.scala │ ├── etl │ ├── config │ │ ├── BaseConfig.scala │ │ ├── CaseClassConfig.scala │ │ ├── Config.scala │ │ ├── ConfigLoader.scala │ │ └── study │ │ │ └── StudyConfig.scala │ ├── datatypes │ │ ├── Addable.scala │ │ ├── Period.scala │ │ ├── RemainingPeriod.scala │ │ └── Subtractable.scala │ ├── events │ │ ├── AnyEvent.scala │ │ ├── Classification.scala │ │ ├── Diagnosis.scala │ │ ├── Dispensation.scala │ │ ├── Drug.scala │ │ ├── DrugPrescription.scala │ │ ├── Event.scala │ │ ├── EventBuilder.scala │ │ ├── Exposure.scala │ │ ├── FollowUp.scala │ │ ├── HospitalStay.scala │ │ ├── Interaction.scala │ │ ├── MedicalAct.scala │ │ ├── MedicalTakeOverReason.scala │ │ ├── Molecule.scala │ │ ├── NgapAct.scala │ │ ├── ObservationPeriod.scala │ │ ├── Outcome.scala │ │ ├── PractionnerClaimSpeciality.scala │ │ ├── Trackloss.scala │ │ └── package.scala │ ├── extractors │ │ ├── ColumnNames.scala │ │ ├── EventRowExtractor.scala │ │ ├── Extractor.scala │ │ ├── ExtractorConfig.scala │ │ ├── SimpleExtractor.scala │ │ ├── codes │ │ │ ├── ExtractorCodes.scala │ │ │ └── SimpleExtractorCodes.scala │ │ ├── events │ │ │ ├── acts │ │ │ │ ├── DcirMedicalActExtractor.scala │ │ │ │ ├── HadCcamActExtractor.scala │ │ │ │ ├── McoCcamActExtractor.scala │ │ │ │ ├── McoCeCcamActExtractor.scala │ │ │ │ ├── MedicalActsConfig.scala │ │ │ │ ├── SsrActExtractor.scala │ │ │ │ └── SsrCeActExtractor.scala │ │ │ ├── classifications │ │ │ │ └── GhmExtractor.scala │ │ │ ├── diagnoses │ │ │ │ ├── DiagnosesConfig.scala │ │ │ │ ├── HadDiagnosisExtractor.scala │ │ │ │ ├── ImbCimDiagnosisExtractor.scala │ │ │ │ ├── McoDiagnosisExtractor.scala │ │ │ │ └── SsrDiagnosisExtractor.scala │ │ │ ├── drugs │ │ │ │ ├── DrugConfig.scala │ │ │ │ ├── DrugExtractor.scala │ │ │ │ ├── classification │ │ │ │ │ ├── DrugClassConfig.scala │ │ │ │ │ ├── PharmacologicalClassConfig.scala │ │ │ │ │ └── families │ │ │ │ │ │ ├── Antidepresseurs.scala │ │ │ │ │ │ ├── Antiepileptics.scala │ │ │ │ │ │ ├── Antihypertenseurs.scala │ │ │ │ │ │ ├── Cardiac.scala │ │ │ │ │ │ ├── Hypnotiques.scala │ │ │ │ │ │ ├── Neuroleptiques.scala │ │ │ │ │ │ ├── Opioids.scala │ │ │ │ │ │ └── ProtonPumpInhibitors.scala │ │ │ │ └── level │ │ │ │ │ ├── Cip13Level.scala │ │ │ │ │ ├── DrugClassificationLevel.scala │ │ │ │ │ ├── MoleculeCombinationLevel.scala │ │ │ │ │ ├── PharmacologicalLevel.scala │ │ │ │ │ └── TherapeuticLevel.scala │ │ │ ├── hospitalstays │ │ │ │ ├── HadHospitalStaysExtractor.scala │ │ │ │ ├── McoHospitalStaysExtractor.scala │ │ │ │ ├── McoceEmergenciesExtractor.scala │ │ │ │ └── SsrHospitalStaysExtractor.scala │ │ │ ├── molecules │ │ │ │ ├── DcirMoleculePurchases.scala │ │ │ │ ├── MoleculePurchases.scala │ │ │ │ └── MoleculePurchasesConfig.scala │ │ │ ├── ngapacts │ │ │ │ ├── DcirNgapActExtractor.scala │ │ │ │ ├── McoCeNgapActExtractor.scala │ │ │ │ ├── NgapActClassConfig.scala │ │ │ │ └── NgapActConfig.scala │ │ │ ├── prestations │ │ │ │ ├── McoCeSpecialtyExtractor.scala │ │ │ │ ├── PractitionerClaimSpecialityConfig.scala │ │ │ │ └── PractitionerClaimSpecialityExtractor.scala │ │ │ └── takeoverreasons │ │ │ │ └── HadTakeOverReasonExtractor.scala │ │ ├── patients │ │ │ ├── AllPatientExtractor.scala │ │ │ ├── DcirPatients.scala │ │ │ ├── HadPatients.scala │ │ │ ├── IrBenPatients.scala │ │ │ ├── McoPatients.scala │ │ │ ├── McocePatients.scala │ │ │ ├── PatientExtractor.scala │ │ │ ├── PatientUtils.scala │ │ │ └── PatientsConfig.scala │ │ └── sources │ │ │ ├── dcir │ │ │ ├── DcirRowExtractor.scala │ │ │ ├── DcirSimpleExtractor.scala │ │ │ └── DcirSource.scala │ │ │ ├── had │ │ │ ├── HadRowExtractor.scala │ │ │ ├── HadSimpleExtractor.scala │ │ │ └── HadSource.scala │ │ │ ├── imb │ │ │ ├── ImbRowExtractor.scala │ │ │ ├── ImbSimpleExtractor.scala │ │ │ └── ImbSource.scala │ │ │ ├── mco │ │ │ ├── McoRowExtractor.scala │ │ │ ├── McoSimpleExtractor.scala │ │ │ └── McoSource.scala │ │ │ ├── mcoce │ │ │ ├── McoCeRowExtractor.scala │ │ │ ├── McoCeSimpleExtractor.scala │ │ │ └── McoCeSource.scala │ │ │ ├── ssr │ │ │ ├── SsrRowExtractor.scala │ │ │ ├── SsrSimpleExtractor.scala │ │ │ └── SsrSource.scala │ │ │ └── ssrce │ │ │ ├── SsrCeRowExtractor.scala │ │ │ ├── SsrCeSimpleExtractor.scala │ │ │ └── SsrCeSource.scala │ ├── filters │ │ ├── EventFilters.scala │ │ ├── EventFiltersImplicits.scala │ │ ├── PatientFilters.scala │ │ └── PatientFiltersImplicits.scala │ ├── implicits │ │ └── package.scala │ ├── patients │ │ └── Patient.scala │ ├── sources │ │ ├── SourceManager.scala │ │ ├── SourceReader.scala │ │ ├── SourceSanitizer.scala │ │ ├── Sources.scala │ │ ├── data │ │ │ ├── DataSourceManager.scala │ │ │ ├── DcirFilters.scala │ │ │ ├── DcirSource.scala │ │ │ ├── DcirSourceSanitizer.scala │ │ │ ├── DoublonFinessPmsi.scala │ │ │ ├── HadFilters.scala │ │ │ ├── HadSource.scala │ │ │ ├── HadSourceSanitizer.scala │ │ │ ├── McoCeSource.scala │ │ │ ├── McoFilters.scala │ │ │ ├── McoSource.scala │ │ │ ├── McoSourceSanitizer.scala │ │ │ ├── SsrCeSource.scala │ │ │ ├── SsrFilters.scala │ │ │ ├── SsrSource.scala │ │ │ └── SsrSourceSanitizer.scala │ │ ├── general │ │ │ └── GeneralSource.scala │ │ └── value │ │ │ ├── DosagesSource.scala │ │ │ ├── IrBenSource.scala │ │ │ ├── IrImbSource.scala │ │ │ ├── IrNatSource.scala │ │ │ └── IrPhaSource.scala │ └── transformers │ │ ├── TransformerConfig.scala │ │ ├── drugprescription │ │ └── DrugPrescriptionTransformer.scala │ │ ├── exposures │ │ ├── ExposureDuration.scala │ │ ├── ExposurePeriodAdder.scala │ │ ├── ExposureTransformer.scala │ │ └── ExposuresTransformerConfig.scala │ │ ├── follow_up │ │ ├── Columns.scala │ │ ├── FollowUpTransformer.scala │ │ ├── FollowUpTransformerConfig.scala │ │ └── FollowUpTransformerUtilities.scala │ │ ├── interaction │ │ ├── ExposureN.scala │ │ ├── InteractionTransformer.scala │ │ ├── InteractionTransformerConfig.scala │ │ └── NLevelInteractionTransformer.scala │ │ ├── observation │ │ ├── Columns.scala │ │ ├── ObservationPeriodTransformer.scala │ │ └── ObservationPeriodTransformerConfig.scala │ │ ├── outcomes │ │ ├── OutcomesTransformer.scala │ │ └── OutcomesTransformerConfig.scala │ │ ├── patients │ │ └── PatientFilters.scala │ │ └── tracklosses │ │ ├── TracklossTransformer.scala │ │ └── TracklossesConfig.scala │ ├── exceptions │ └── package.scala │ ├── study │ ├── bulk │ │ ├── BulkConfig.scala │ │ ├── BulkConfigLoader.scala │ │ ├── BulkMain.scala │ │ └── extractors │ │ │ ├── DcirSourceExtractor.scala │ │ │ ├── HadSourceExtractor.scala │ │ │ ├── ImbSourceExtractor.scala │ │ │ ├── McoCeSourceExtractor.scala │ │ │ ├── McoSourceExtractor.scala │ │ │ ├── PatientExtractor.scala │ │ │ ├── SourceExtractor.scala │ │ │ ├── SsrCeSourceExtractor.scala │ │ │ └── SsrSourceExtractor.scala │ ├── fall │ │ ├── FallMain.scala │ │ ├── FallMainExtract.scala │ │ ├── FallMainTransform.scala │ │ ├── codes │ │ │ └── FractureCodes.scala │ │ ├── config │ │ │ ├── FallConfig.scala │ │ │ ├── FallConfigLoader.scala │ │ │ ├── FallDrugClassConfig.scala │ │ │ └── FracturesTransformerConfig.scala │ │ ├── extractors │ │ │ ├── ActsExtractor.scala │ │ │ ├── CardiacExtractor.scala │ │ │ ├── ControlDrugs.scala │ │ │ ├── DiagnosisExtractor.scala │ │ │ ├── DrugsExtractor.scala │ │ │ ├── EpilepticsExtractor.scala │ │ │ ├── FallHospitalStayExtractor.scala │ │ │ ├── HTAExtractor.scala │ │ │ ├── IPPExtractor.scala │ │ │ └── OpioidsExtractor.scala │ │ ├── follow_up │ │ │ └── FallStudyFollowUps.scala │ │ ├── fractures │ │ │ ├── BodySite.scala │ │ │ ├── FracturesTransformer.scala │ │ │ ├── FracturesTransformerImplicits.scala │ │ │ ├── HospitalizedFractures.scala │ │ │ ├── LiberalFractures.scala │ │ │ ├── PrivateAmbulatoryFractures.scala │ │ │ ├── PublicAmbulatoryFractures.scala │ │ │ └── Surgery.scala │ │ ├── liberalActs │ │ │ └── LiberalActsTransformer.scala │ │ ├── readme.md │ │ └── statistics │ │ │ ├── DiagnosisCounter.scala │ │ │ └── EventStatistics.scala │ ├── pioglitazone │ │ ├── PioglitazoneConfig.scala │ │ ├── PioglitazoneMain.scala │ │ ├── PioglitazoneStudyCodes.scala │ │ ├── extractors │ │ │ ├── Diagnoses.scala │ │ │ └── MedicalActs.scala │ │ └── outcomes │ │ │ ├── BroadBladderCancer.scala │ │ │ ├── CancerDefinition.scala │ │ │ ├── NaiveBladderCancer.scala │ │ │ ├── NarrowBladderCancer.scala │ │ │ └── PioglitazoneOutcomeTransformer.scala │ └── rosiglitazone │ │ ├── RosiglitazoneConfig.scala │ │ ├── RosiglitazoneMain.scala │ │ ├── RosiglitazoneStudyCodes.scala │ │ ├── extractors │ │ └── Diagnoses.scala │ │ └── outcomes │ │ ├── HeartFailure.scala │ │ ├── Infarctus.scala │ │ ├── OutcomeDefinition.scala │ │ └── RosiglitazoneOutcomeTransformer.scala │ └── util │ ├── ColumnUtilities.scala │ ├── DrugEventsTransformerHelper.scala │ ├── Locales.scala │ ├── LoggerLevels.scala │ ├── Path.scala │ ├── RichDataFrame.scala │ ├── collections │ ├── RichSeq.scala │ └── implicits │ │ └── package.scala │ ├── datetime │ ├── Period.scala │ ├── RichDate.scala │ ├── RichInt.scala │ ├── RichLong.scala │ └── implicits │ │ └── package.scala │ ├── functions │ └── package.scala │ ├── package.scala │ └── reporting │ ├── JsonSerializable.scala │ ├── MainMetadata.scala │ ├── OperationMetadata.scala │ ├── OperationReporter.scala │ ├── OperationTypes.scala │ └── package.scala └── test ├── resources ├── DCIR │ ├── ER_BIO_F.csv │ ├── ER_CAM_F.csv │ ├── ER_ETE_F.csv │ ├── ER_PHA_F.csv │ ├── ER_PRS_F.csv │ └── ER_UCD_F.csv ├── IR_BEN_R.csv ├── IR_IMB_R.csv ├── PMSI │ ├── T_HAD19A.csv │ ├── T_HAD19B.csv │ ├── T_HAD19C.csv │ ├── T_HAD19D.csv │ ├── T_MCO06A.csv │ ├── T_MCO06B.csv │ ├── T_MCO06C.csv │ ├── T_MCO06D.csv │ ├── T_MCO07A.csv │ ├── T_MCO07B.csv │ ├── T_MCO07C.csv │ ├── T_MCO07D.csv │ ├── T_MCO08A.csv │ ├── T_MCO08B.csv │ ├── T_MCO08C.csv │ ├── T_MCO08D.csv │ ├── T_MCO08MED.csv │ ├── T_MCO08UM.csv │ ├── T_MCOaa_nnFBSTC.csv │ ├── T_MCOaa_nnFCSTC.csv │ ├── T_SSR19B.csv │ ├── T_SSR19C.csv │ ├── T_SSR19CCAM.csv │ ├── T_SSR19CSARR.csv │ └── T_SSR19D.csv ├── SAS │ └── dataereanof.sas7bdat ├── config │ ├── cox-cumulative-purchase.conf │ ├── cox-cumulative-time.conf │ ├── filtering-broad.conf │ ├── filtering-narrow.conf │ ├── filtering-reuse-events.conf │ ├── filtering-reuse-flat-events.conf │ ├── mlpp-default.conf │ ├── mlpp-new-exposure.conf │ └── sas-default.conf ├── expected │ ├── DCIR.parquet │ ├── ER_CAM_F.parquet │ ├── ER_PHA_F.parquet │ ├── ER_PRS_F.parquet │ ├── ER_UCD_F.parquet │ ├── IR_BEN_R.parquet │ ├── IR_IMB_R.parquet │ ├── IR_PHA_R.parquet │ └── MCO.parquet ├── extractors │ ├── Imb.gz.parquet │ └── dummy.parquet ├── fake.conf ├── statistics │ └── IR_BEN_R.csv ├── test-input │ ├── DCIR.parquet │ ├── DCIR_w_BIO.parquet │ ├── DOSE_PER_MOLECULE.CSV │ ├── HAD.parquet │ ├── IR_BEN_R.parquet │ ├── IR_IMB_R.parquet │ ├── IR_IMB_R_null.parquet │ │ ├── ._SUCCESS.crc │ │ ├── .part-00000-95ff3836-ebd0-4f6c-88a9-55c81f9b4302-c000.snappy.parquet.crc │ │ ├── .part-00001-95ff3836-ebd0-4f6c-88a9-55c81f9b4302-c000.snappy.parquet.crc │ │ ├── _SUCCESS │ │ ├── part-00000-95ff3836-ebd0-4f6c-88a9-55c81f9b4302-c000.snappy.parquet │ │ └── part-00001-95ff3836-ebd0-4f6c-88a9-55c81f9b4302-c000.snappy.parquet │ ├── IR_PHA_R.parquet │ ├── IR_PHA_R_With_molecules.parquet │ ├── MCO.parquet │ ├── MCO_CE.parquet │ ├── SSR.parquet │ ├── SSR_C.parquet │ ├── SSR_SEJ.parquet │ ├── events.parquet │ ├── flat-events.parquet │ └── old_events.parquet ├── test-joined │ └── SSR.parquet │ │ ├── ._SUCCESS.crc │ │ ├── .part-00000-4659fc3c-6a63-4ab1-bcfe-620d052a165a-c000.snappy.parquet.crc │ │ ├── _SUCCESS │ │ └── part-00000-4659fc3c-6a63-4ab1-bcfe-620d052a165a-c000.snappy.parquet └── value_tables │ ├── DOSE_PER_MOLECULE.CSV │ ├── IR_NAT_V.csv │ ├── IR_NAT_V.parquet │ ├── IR_PHA_R_124.29.csv │ ├── IR_PHA_R_With_Molecules_Combination.csv │ └── IR_PHA_R_With_molecules.parquet └── scala └── fr └── polytechnique └── cmap └── cnam ├── Discipline.scala ├── SharedContext.scala ├── etl ├── config │ ├── CaseClassConfigSuite.scala │ └── ConfigLoaderSuite.scala ├── datatypes │ ├── PeriodSuite.scala │ └── RemainingPeriodSuite.scala ├── events │ ├── ClassificationSuite.scala │ ├── DiagnosisSuite.scala │ ├── DrugSuite.scala │ ├── EventSuite.scala │ ├── ExposureSuite.scala │ ├── FollowUpSuite.scala │ ├── HospitalStaySuite.scala │ ├── MedicalActSuite.scala │ ├── MedicalTakeOverReasonSuite.scala │ ├── MoleculeSuite.scala │ ├── NgapActSuite.scala │ └── PractionnerClaimSpecialitySuite.scala ├── extractors │ ├── EventRowExtractorSuite.scala │ ├── events │ │ ├── acts │ │ │ ├── DcirBiologyActsSuite.scala │ │ │ ├── DcirMedicalActsSuite.scala │ │ │ ├── HadMedicalActsSuite.scala │ │ │ ├── McoCEMedicalActsSuite.scala │ │ │ ├── McoMedicalActsSuite.scala │ │ │ ├── MedicalActsConfigSuite.scala │ │ │ ├── SsrCEMedicalActsSuite.scala │ │ │ └── SsrMedicalActsSuite.scala │ │ ├── classifications │ │ │ └── GHMClassificationsSuite.scala │ │ ├── diagnoses │ │ │ ├── HadDiagnosesSuite.scala │ │ │ ├── ImbDiagnosesSuite.scala │ │ │ ├── McoDiagnosesSuite.scala │ │ │ └── SsrDiagnosesSuite.scala │ │ ├── drugs │ │ │ ├── DrugsExtractorSuite.scala │ │ │ ├── PharmacologicalClassConfigSuite.scala │ │ │ └── level │ │ │ │ ├── Cip13LevelSuite.scala │ │ │ │ ├── DrugClassficationLevelSuite.scala │ │ │ │ ├── MoleculeCombinationSuite.scala │ │ │ │ ├── PharmacologicalSuite.scala │ │ │ │ └── TherapeuticSuite.scala │ │ ├── hospitalstays │ │ │ ├── HadHospitalStayExtractorSuite.scala │ │ │ ├── McoHospitalStayExtractorSuite.scala │ │ │ ├── McoceEmergenciesExtractorSuite.scala │ │ │ └── SSrHospitalStayExtractorSuite.scala │ │ ├── molecules │ │ │ ├── DcirMoleculePurchasesSuite.scala │ │ │ └── MoleculePurchasesSuite.scala │ │ ├── ngapacts │ │ │ ├── DcirNgapActsExtractorSuite.scala │ │ │ └── McoNgapActsExtractorSuite.scala │ │ ├── prestations │ │ │ └── PractitionerClaimSpecialityExtractorSuite.scala │ │ └── takeoverreasons │ │ │ └── HadTakeOveReasonSuite.scala │ ├── patients │ │ ├── AllPatientExtractorSuite.scala │ │ ├── DcirPatientsSuite.scala │ │ ├── HadPatientsSuite.scala │ │ ├── IrBenPatientsSuite.scala │ │ ├── McoPatientsSuite.scala │ │ └── McocePatientsSuite.scala │ └── sources │ │ ├── dcir │ │ └── DcirRowExtractorSuite.scala │ │ ├── had │ │ ├── HadRowExtractorSuite.scala │ │ └── HadSourceSuite.scala │ │ ├── mco │ │ ├── McoRowExtractorSuite.scala │ │ └── McoSourceSuite.scala │ │ ├── mcoce │ │ └── McoCeRowExtractorSuite.scala │ │ ├── ssr │ │ ├── SsrRowExtractorSuite.scala │ │ └── SsrSourceSuite.scala │ │ └── ssrce │ │ └── SsrCeRowExtractorSuite.scala ├── filters │ ├── PatientFiltersImplicitsSuite.scala │ └── PatientFiltersSuite.scala ├── sources │ ├── SourceReaderSuite.scala │ ├── data │ │ ├── DataSourceManagerSuite.scala │ │ ├── DcirFiltersSuite.scala │ │ ├── DcirSourceSuite.scala │ │ ├── HadFiltersSuite.scala │ │ ├── HadSourceSuite.scala │ │ ├── McoCeSourceSuite.scala │ │ ├── McoFiltersSuite.scala │ │ ├── McoSourceSuite.scala │ │ └── SsrFiltersSuite.scala │ ├── general │ │ └── GeneralSourceSuite.scala │ └── value │ │ ├── DosagesSourceSuite.scala │ │ └── IrImbSourceSuite.scala └── transformers │ ├── drugprescription │ └── DrugPrescriptionTransformerSuite.scala │ ├── exposures │ ├── ExposureDurationSuite.scala │ ├── ExposurePeriodAdderSuite.scala │ └── ExposureTransformerSuite.scala │ ├── follow_up │ ├── FollowUpSuite.scala │ └── FollowUpTransformerSuite.scala │ ├── interaction │ ├── ExposureNSuite.scala │ └── NLevelInteractionTransformerSuite.scala │ ├── observation │ └── ObservationPeriodTransformerSuite.scala │ ├── outcomes │ └── OutcomeSuite.scala │ ├── patients │ └── PatientFiltersSuite.scala │ └── tracklosses │ └── TracklossTransformerSuite.scala ├── study ├── bulk │ └── extractors │ │ ├── DcirSourceExtractorSuite.scala │ │ ├── HadSourceExtractorSuite.scala │ │ ├── ImbSourceExtractorSuite.scala │ │ ├── McoCeSourceExtractorSuite.scala │ │ ├── McoSourceExtractorSuite.scala │ │ ├── SourceExtractorSuite.scala │ │ ├── SsrCeSourceExtractorSuite.scala │ │ └── SsrSourceExtractorSuite.scala ├── fall │ ├── FallMainExtractorTransformSuite.scala │ ├── FallMainSuite.scala │ ├── config │ │ └── FallConfigSuite.scala │ ├── extractors │ │ └── FallHospitalStayExtractorSuite.scala │ ├── fractures │ │ ├── BodySiteSuite.scala │ │ ├── FracturesImplicitsSuite.scala │ │ ├── FracturesTransformerSuite.scala │ │ ├── HospitalizedFracturesSuite.scala │ │ ├── LiberalFracturesSuite.scala │ │ ├── PrivateAmbulatoryFracturesSuite.scala │ │ └── PublicAmbulatoryFracturesSuite.scala │ └── statistics │ │ └── DiagnosisCounterSuite.scala ├── pioglitazone │ ├── PioglitazoneConfigSuite.scala │ ├── PioglitazoneMainSuite.scala │ └── outcomes │ │ ├── BroadBladderCancerSuite.scala │ │ ├── NaiveBladderCancerSuite.scala │ │ └── NarrowBladderCancerSuite.scala └── rosiglitazone │ ├── RosiglitazoneConfigSuite.scala │ └── outcomes │ ├── HeartFailureSuite.scala │ ├── InfarctusSuite.scala │ ├── OutcomeDefinitionSuite.scala │ └── RosiglitazoneOutcomeTransformerSuite.scala └── util ├── ColumnUtilitiesSuite.scala ├── FunctionsSuite.scala ├── PathSuite.scala ├── RichDataFrameSuite.scala ├── collections ├── RichSeqSuite.scala └── implicits │ └── CollectionsImplicitsSuite.scala ├── datetime ├── PeriodSuite.scala ├── RichDateSuite.scala ├── RichIntSuite.scala ├── RichLongSuite.scala └── implicits │ └── DatetimeImplicitsSuite.scala └── reporting ├── JsonSerializableSuite.scala └── OperationReporterSuite.scala /.circleci/config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/X-DataInitiative/SCALPEL-Extraction/HEAD/.circleci/config.yml -------------------------------------------------------------------------------- /.codecov.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/X-DataInitiative/SCALPEL-Extraction/HEAD/.codecov.yml -------------------------------------------------------------------------------- /.gitignore: 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