import { IServerConfig } from './IAppConfig'; export const ServerConfigDefaults: Partial = { app_version: '1.0', api_cache_limit: 450, dat_method: 'none', disabled_tabs: '', genomenexus_url: 'https://v1.genomenexus.org', genomenexus_url_grch38: 'https://grch38.genomenexus.org', genomenexus_website_url: 'https://www.genomenexus.org', genomenexus_isoform_override_source: 'mskcc', g2s_url: 'https://g2s.genomenexus.org', mycancergenome_show: false, digital_slide_archive_iframe_url: 'https://cancer.digitalslidearchive.org/', digital_slide_archive_meta_url: 'https://api.digitalslidearchive.org/api/v1/tcga/image?caseName=', mdacc_heatmap_patient_url: 'https://bioinformatics.mdanderson.org/participant2maps?participant=', mdacc_heatmap_study_meta_url: 'https://bioinformatics.mdanderson.org/study2url?studyid=', mdacc_heatmap_study_url: 'https:// bioinformatics.mdanderson.org/TCGA/NGCHMPortal/?', show_mdacc_heatmap: false, mygene_info_url: 'https://mygene.info/v3/gene/<%= entrezGeneId %>?fields=uniprot', oncoprint_custom_driver_annotation_binary_menu_label: 'Custom driver annotation', oncoprint_custom_driver_annotation_tiers_menu_label: 'Custom driver tiers', oncoprint_custom_driver_annotation_binary_default: true, oncoprint_custom_driver_annotation_tiers_default: true, oncoprint_oncokb_default: true, oncoprint_hotspots_default: true, oncoprint_hide_vus_default: false, oncokb_public_api_url: 'oncokb.org/api/v1', oncokb_merge_icons_by_default: true, pubmed_url: 'https://www.ncbi.nlm.nih.gov/pubmed/<%=pmid%>', show_hotspot: true, show_oncokb: true, show_civic: false, show_pathway_mapper: true, show_mutation_mapper_tool_grch38: true, show_transcript_dropdown: false, show_signal: true, show_ndex: true, survival_show_p_q_values_in_survival_type_table: true, survival_min_group_threshold: 3, skin_description: 'The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets', show_genomenexus: true, // TODO should support more sources such as clinvar,gnomad,sift show_genomenexus_annotation_sources: 'mutation_assessor', survival_initial_x_axis_limit: 0, skin_authorization_message: 'Access to this portal is only available to authorized users.', skin_documentation_about: 'About-Us.md', skin_documentation_software: 'Software-Acknowledgments.md', skin_documentation_baseurl: 'https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/', skin_documentation_markdown: true, skin_email_contact: 'cbioportal at googlegroups dot com', skin_documentation_faq: 'user-guide/faq.md', skin_footer_show_dev: false, skin_login_saml_registration_html: 'Sign in with MSK', skin_documentation_news: 'https://docs.cbioportal.org/news/', skin_documentation_oql: 'user-guide/oql.md', skin_query_max_tree_depth: '3', skin_right_nav_show_data_sets: true, skin_right_nav_show_examples: true, skin_right_nav_show_testimonials: true, skin_right_nav_show_whats_new: true, skin_right_nav_show_twitter: false, skin_citation_rule_text: 'Please cite: Cerami et al., 2012 & Gao et al., 2013', skin_show_about_tab: true, skin_show_data_tab: true, skin_show_faqs_tab: true, skin_show_news_tab: true, skin_show_r_matlab_tab: true, skin_show_tools_tab: true, skin_show_web_api_tab: true, skin_show_tweet_button: false, skin_show_tissue_image_tab: true, quick_search_enabled: false, default_cross_cancer_study_list: 'laml_tcga_pan_can_atlas_2018,acc_tcga_pan_can_atlas_2018,blca_tcga_pan_can_atlas_2018,' + 'lgg_tcga_pan_can_atlas_2018,brca_tcga_pan_can_atlas_2018,cesc_tcga_pan_can_atlas_2018,chol_tcga_pan_can_atlas_2018,' + 'coadread_tcga_pan_can_atlas_2018,dlbc_tcga_pan_can_atlas_2018,esca_tcga_pan_can_atlas_2018,gbm_tcga_pan_can_atlas_2018,' + 'hnsc_tcga_pan_can_atlas_2018,kich_tcga_pan_can_atlas_2018,kirc_tcga_pan_can_atlas_2018,kirp_tcga_pan_can_atlas_2018,' + 'lihc_tcga_pan_can_atlas_2018,luad_tcga_pan_can_atlas_2018,lusc_tcga_pan_can_atlas_2018,meso_tcga_pan_can_atlas_2018,' + 'ov_tcga_pan_can_atlas_2018,paad_tcga_pan_can_atlas_2018,pcpg_tcga_pan_can_atlas_2018,prad_tcga_pan_can_atlas_2018,' + 'sarc_tcga_pan_can_atlas_2018,skcm_tcga_pan_can_atlas_2018,stad_tcga_pan_can_atlas_2018,' + 'tgct_tcga_pan_can_atlas_2018,thym_tcga_pan_can_atlas_2018,thca_tcga_pan_can_atlas_2018,ucs_tcga_pan_can_atlas_2018,' + 'ucec_tcga_pan_can_atlas_2018,uvm_tcga_pan_can_atlas_2018', default_cross_cancer_study_list_name: 'TCGA PanCancer Atlas studies', skin_title: 'cBioPortal for Cancer Genomics', skin_data_sets_header: `The portal currently contains data from the following cancer genomics studies. The table below lists the number of available samples per data type and tumor.`, skin_example_study_queries: `tcga pancancer atlas\n tcga legacy\n tcga -legacy -pancancer\n tcga or icgc\n msk-impact\n -\"cell line\"\n breast\n esophageal OR stomach\n prostate msk\n serous`, skin_login_contact_html: `If you think you have received this message in error, please contact us at cbioportal-access@cbio.mskcc.org`, skin_patientview_filter_genes_profiled_all_samples: false, enable_darwin: false, session_url_length_threshold: '1500', study_view: { tableAttrs: ['CANCER_TYPE', 'CANCER_TYPE_DETAILED'], priority: { CANCER_TYPE: 3000, CANCER_TYPE_DETAILED: 2000, // TODO should have a more generic way to define survival plots priority GENOMIC_PROFILES_SAMPLE_COUNT: 1000, OS_SURVIVAL: 400, DFS_SURVIVAL: 300, DSS_SURVIVAL: 250, PFS_SURVIVAL: 250, MUTATION_COUNT_CNA_FRACTION: 200, MUTATED_GENES_TABLE: 90, STRUCTURAL_VARIANT_GENES_TABLE: 85, CNA_GENES_TABLE: 80, PATIENT_TREATMENTS_TABLE: 75, PATIENT_TREATMENT_GROUPS_TABLE: 75, PATIENT_TREATMENT_TARGET_TABLE: 75, SAMPLE_TREATMENTS_TABLE: 75, SAMPLE_TREATMENT_GROUPS_TABLE: 75, SAMPLE_TREATMENT_TARGET_TABLE: 75, CANCER_STUDIES: 70, SEQUENCED: 60, HAS_CNA_DATA: 50, SAMPLE_COUNT: 40, MUTATION_COUNT: 30, FRACTION_GENOME_ALTERED: 20, GENDER: 9, SEX: 9, AGE: 9, RACE: 8, ETHNICITY: 8, SAMPLE_TYPE: 8, HISTOLOGY: 8, TUMOR_TYPE: 8, SUBTYPE: 8, TUMOR_SITE: 8, }, }, uniprot_id_url: 'https://rest.uniprot.org/uniprotkb/search?query=accession:<%= swissProtAccession %>&format=tsv&fields=id', ensembl_transcript_url: 'http://grch37.ensembl.org/homo_sapiens/Transcript/Summary?t=<%= transcriptId %>', ensembl_transcript_grch38_url: 'http://ensembl.org/homo_sapiens/Transcript/Summary?t=<%= transcriptId %>', query_product_limit: 1000000, clinical_attribute_product_limit: 6500000, skin_show_gsva: false, skin_geneset_hierarchy_default_gsva_score: 0.5, skin_geneset_hierarchy_default_p_value: 0.05, generic_assay_display_text: 'TREATMENT_RESPONSE:Treatment Response,MUTATIONAL_SIGNATURE:Mutational Signature,ARMLEVEL_CNA:Arm-level CNA', saml_logout_local: false, enable_request_body_gzip_compression: false, enable_treatment_groups: false, referenceGenomeVersion: 'hg19', skin_home_page_show_unauthorized_studies: false, skin_home_page_unauthorized_studies_global_message: 'The study is unauthorized. You need to request access.', comparison_categorical_na_values: 'NA', skin_hide_download_controls: false, oncoprint_clinical_tracks_config_json: '', skin_patient_view_mutation_table_columns_show_on_init: '', skin_results_view_mutation_table_columns_show_on_init: '', }; export default ServerConfigDefaults;