├── .gitattributes ├── .github └── workflows │ └── build.yml ├── .gitignore ├── .idea ├── .name ├── codeStyles │ └── codeStyleConfig.xml ├── compiler.xml ├── cpic-data.iml ├── data_source_mapping.xml ├── encodings.xml ├── gradle.xml ├── jarRepositories.xml ├── jsLibraryMappings.xml ├── libraries-with-intellij-classes.xml ├── markdown-exported-files.xml ├── misc.xml ├── sqlDataSources.xml ├── sqldialects.xml └── vcs.xml ├── .yarn ├── plugins │ └── @yarnpkg │ │ └── plugin-interactive-tools.cjs └── releases │ └── yarn-3.5.0.cjs ├── .yarnrc.yml ├── CHANGELOG.md ├── LICENSE.md ├── Makefile ├── README.md ├── data.tsv ├── gradle └── wrapper │ ├── gradle-wrapper.jar │ └── gradle-wrapper.properties ├── gradlew ├── gradlew.bat ├── package.json ├── settings.gradle ├── src ├── main │ ├── design │ │ ├── diagram │ │ │ ├── api-layers │ │ │ │ └── CPIC API diagram.sketch │ │ │ ├── api │ │ │ │ └── CPIC_API_diagram.graphml │ │ │ ├── prioritization │ │ │ │ └── Gene-Drug Pair Prioritization.pxm │ │ │ │ │ ├── .blank │ │ │ │ │ ├── QuickLook │ │ │ │ │ ├── Preview.tiff │ │ │ │ │ └── Thumbnail.tiff │ │ │ │ │ ├── document │ │ │ │ │ ├── info │ │ │ │ │ └── meta │ │ │ │ │ └── layers │ │ │ │ │ └── Layer-4F812445-C2CD-4010-A8AB-7916A57CA431-20151124-141760.data │ │ │ ├── relationships │ │ │ │ ├── Dockerfile │ │ │ │ ├── README.md │ │ │ │ ├── Service Ecosystem Diagram.Rmd │ │ │ │ └── diagram.dot │ │ │ ├── warfarin │ │ │ │ ├── README.md │ │ │ │ ├── warfarin_pediatric_recommendation_diagram.graphml │ │ │ │ ├── warfarin_recommendation_diagram.graphml │ │ │ │ └── warfarin_recommendation_diagram.txt │ │ │ └── workflow-uml │ │ │ │ ├── atazanavir_cds.puml │ │ │ │ ├── gene_workflow.puml │ │ │ │ └── generate.sh │ │ └── logo │ │ │ ├── CPIC Compact Logo.sketch │ │ │ ├── CPIC Full Logo.sketch │ │ │ ├── CPIC Square Logo.sketch │ │ │ └── CPIC.ai │ ├── java │ │ └── org │ │ │ └── cpicpgx │ │ │ ├── DataArtifactArchive.java │ │ │ ├── DataImport.java │ │ │ ├── FrequencyGenerator.java │ │ │ ├── ProgressReport.java │ │ │ ├── db │ │ │ ├── ConnectionFactory.java │ │ │ ├── DbLookup.java │ │ │ ├── FileHistoryWriter.java │ │ │ ├── FlywayClean.java │ │ │ ├── FlywayMigrate.java │ │ │ └── LookupMethod.java │ │ │ ├── exception │ │ │ └── NotFoundException.java │ │ │ ├── exporter │ │ │ ├── AlleleDefinitionExporter.java │ │ │ ├── AlleleFunctionalityReferenceExporter.java │ │ │ ├── AlleleSummaryExporter.java │ │ │ ├── BaseExporter.java │ │ │ ├── ChangelogExporter.java │ │ │ ├── ClinVarSubmission.java │ │ │ ├── ClinVarWorkbook.java │ │ │ ├── DiplotypePhenotypeExporter.java │ │ │ ├── DrugResourceCreator.java │ │ │ ├── DrugResourceExporter.java │ │ │ ├── DrugReviewExporter.java │ │ │ ├── FrequencyCreator.java │ │ │ ├── FrequencyExporter.java │ │ │ ├── GeneCdsExporter.java │ │ │ ├── GeneResourceCreator.java │ │ │ ├── GeneResourceExporter.java │ │ │ ├── GuidelineExporter.java │ │ │ ├── GuidelineStarterPack.java │ │ │ ├── PairsExporter.java │ │ │ ├── PhenotypesExporter.java │ │ │ ├── RecommendationCreator.java │ │ │ ├── RecommendationExporter.java │ │ │ ├── TermsExporter.java │ │ │ └── TestAlertExporter.java │ │ │ ├── importer │ │ │ ├── AlleleDefinitionImporter.java │ │ │ ├── AlleleFrequencyImporter.java │ │ │ ├── BaseDirectoryImporter.java │ │ │ ├── DiplotypePhenotypeImporter.java │ │ │ ├── DrugImporter.java │ │ │ ├── FrequencyProcessor.java │ │ │ ├── FunctionReferenceImporter.java │ │ │ ├── GeneCdsImporter.java │ │ │ ├── GenePhenotypeImporter.java │ │ │ ├── GeneReferenceImporter.java │ │ │ ├── GuidelineImporter.java │ │ │ ├── PairDiffImporter.java │ │ │ ├── PairImporter.java │ │ │ ├── PharmVarApiImporter.java │ │ │ ├── PublicationCatalog.java │ │ │ ├── RecommendationImporter.java │ │ │ └── TestAlertImporter.java │ │ │ ├── model │ │ │ ├── AlleleDistribution.java │ │ │ ├── DrugGenePair.java │ │ │ ├── EntityType.java │ │ │ ├── FileType.java │ │ │ └── GnomadPopulation.java │ │ │ ├── stats │ │ │ ├── AbstractStatistics.java │ │ │ ├── DatabaseStatistics.java │ │ │ ├── GitHubStatistics.java │ │ │ ├── StatisticsCollector.java │ │ │ ├── StatisticsReport.java │ │ │ ├── StatsWriter.java │ │ │ └── model │ │ │ │ ├── GitHubAsset.java │ │ │ │ ├── GitHubRelease.java │ │ │ │ └── StatisticType.java │ │ │ ├── util │ │ │ ├── ActivityScoreComparator.java │ │ │ ├── CompareWorkbooks.java │ │ │ ├── Constants.java │ │ │ ├── DbHarness.java │ │ │ ├── FileStoreClient.java │ │ │ ├── HttpUtils.java │ │ │ ├── RowWrapper.java │ │ │ ├── TextUtils.java │ │ │ └── WorkbookWrapper.java │ │ │ └── workbook │ │ │ ├── AbstractWorkbook.java │ │ │ ├── AlleleDefinitionWorkbook.java │ │ │ ├── AlleleFunctionalityReferenceWorkbook.java │ │ │ ├── AlleleSummaryWorkbook.java │ │ │ ├── DiplotypeWorkbook.java │ │ │ ├── DrugResourceWorkbook.java │ │ │ ├── DrugReviewWorkbook.java │ │ │ ├── FrequencyWorkbook.java │ │ │ ├── GeneCdsWorkbook.java │ │ │ ├── GeneResourceWorkbook.java │ │ │ ├── GuidelineWorkbook.java │ │ │ ├── PairWorkbook.java │ │ │ ├── PhenotypesWorkbook.java │ │ │ ├── RecommendationWorkbook.java │ │ │ ├── SheetWrapper.java │ │ │ ├── TermsWorkbook.java │ │ │ └── TestAlertWorkbook.java │ ├── node │ │ ├── checkenv.js │ │ ├── cpicapi.js │ │ ├── db │ │ │ ├── bootstrap.mjs │ │ │ ├── bootstrap_api.mjs │ │ │ ├── dump.mjs │ │ │ ├── index.js │ │ │ └── pg.js │ │ ├── log │ │ │ └── index.js │ │ ├── lookupPublication.js │ │ ├── makePairUpdates.js │ │ ├── updateGenes.js │ │ └── updatePublications.js │ └── resources │ │ ├── db │ │ ├── clinvar │ │ │ ├── README.md │ │ │ ├── clinvar_dataload.sql │ │ │ ├── clinvar_download.sh │ │ │ └── clinvar_schema.sql │ │ ├── migration │ │ │ ├── V10__pair_data_update.sql │ │ │ ├── V11__guideline_in_drug_model.sql │ │ │ ├── V12__pair_data_update.sql │ │ │ ├── V13__add_publications.sql │ │ │ ├── V14__add_highlighted_publications.sql │ │ │ ├── V15__pair_data_update.sql │ │ │ ├── V16__update_ibuprofen_ATC.sql │ │ │ ├── V18__allele_status_lookup.sql │ │ │ ├── V19__new_publication.sql │ │ │ ├── V1__Initial_bootstrap.sql │ │ │ ├── V20__update_sequence_IDs.sql │ │ │ ├── V21__recommendation_lookup_fn.sql │ │ │ ├── V22__ppi_release.sql │ │ │ ├── V23__helpful_views.sql │ │ │ ├── V24__new_drug_flowcharts.sql │ │ │ ├── V25__phenytoin_guideline_update.sql │ │ │ ├── V26__validate_pair_pmids.sql │ │ │ ├── V27__reference_allele.sql │ │ │ ├── V28__more_allele_frequency.sql │ │ │ ├── V29__gene_notes_on_diplotype.sql │ │ │ ├── V2__initial_data.sql │ │ │ ├── V30__fix_diplotype_note_column_name.sql │ │ │ ├── V31__structural_variant_alleles.sql │ │ │ ├── V32__more_notes.sql │ │ │ ├── V33__remove_allele_frequency.sql │ │ │ ├── V34__add_constraints_to_publication.sql │ │ │ ├── V35__opioid_release.sql │ │ │ ├── V36__update_allele_view.sql │ │ │ ├── V37__remove_unused column.sql │ │ │ ├── V38__gene_urls.sql │ │ │ ├── V39__guideline_summary_view.sql │ │ │ ├── V3__views.sql │ │ │ ├── V40__fix_flowchart_urls.sql │ │ │ ├── V41__publication_files.sql │ │ │ ├── V42__aminoglycosides_guideline.sql │ │ │ ├── V43__seq_loc_unique_key.sql │ │ │ ├── V44__functionmethods.sql │ │ │ ├── V45__sequence_location_position.sql │ │ │ ├── V46__fix_dbsnpid_column.sql │ │ │ ├── V47__guideline_fns.sql │ │ │ ├── V48__update_guideline_allele_fn.sql │ │ │ ├── V49__fix_allele_findings.sql │ │ │ ├── V4__flow_charts.sql │ │ │ ├── V50__fix_IFNL3_lookup.sql │ │ │ ├── V51__fix_guideline_allele_fn.sql │ │ │ ├── V52__recommendation_alleles_view.sql │ │ │ ├── V53__statins_guideline.sql │ │ │ ├── V54__publication_index.sql │ │ │ ├── V55__allele_frequency_cache.sql │ │ │ ├── V56__gene_legacy_names.sql │ │ │ ├── V57__pgkb_recs_fn_update.sql │ │ │ ├── V58__stats_table.sql │ │ │ ├── V59__remove_allele_guideline.sql │ │ │ ├── V60__reference_allele.sql │ │ │ ├── V61__G6PD_guideline_prep.sql │ │ │ ├── V62__G6PD_flow_charts.sql │ │ │ ├── V63__fosphenytoin_flow_chart.sql │ │ │ ├── V64__recommendation_flags.sql │ │ │ ├── V65__frequency_flags.sql │ │ │ ├── V66__ssri_snri_guideline.sql │ │ │ ├── V67__frequency_view_fix.sql │ │ │ ├── V68__fix_function_definitions.sql │ │ │ ├── V69__change_log_releases.sql │ │ │ ├── V6__nsaid_release.sql │ │ │ ├── V70__fix_allele_freq_view.sql │ │ │ ├── V71__fix_guideline_summary_view.sql │ │ │ ├── V72__gene_cds_changelog.sql │ │ │ ├── V73__clinpgx_guideline_update.sql │ │ │ ├── V74__supplemental_file_cleanup.sql │ │ │ ├── V75__hydrazaline_guideline.sql │ │ │ ├── V7__nsaid_pair_data.sql │ │ │ ├── V8__data_progress_view.sql │ │ │ └── V9__file_view.sql │ │ └── stats.sql │ │ ├── logback.xml │ │ └── org │ │ └── cpicpgx │ │ └── exporter │ │ ├── FunctionColumnDefinitions.tsv │ │ └── SubmissionTemplate.xlsx └── test │ ├── java │ └── org │ │ └── cpicpgx │ │ ├── db │ │ └── ConnectionFactoryTest.java │ │ ├── importer │ │ ├── AlleleDefinitionImporterTest.java │ │ ├── BaseDirectoryImporterTest.java │ │ ├── DiplotypePhenotypeImporterTest.java │ │ └── FunctionReferenceImporterTest.java │ │ └── util │ │ ├── ActivityScoreComparatorTest.java │ │ ├── FileStoreClientTest.java │ │ ├── RowWrapperTest.java │ │ └── TextUtilsTest.java │ └── 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