From 000192831760a91669090c2ce606d6b8b0c43103 Mon Sep 17 00:00:00 2001 From: bkmartinjr Date: Thu, 21 Jan 2021 15:01:10 -0800 Subject: [PATCH] wire e2e gene set loading prototype --- client/src/actions/index.js | 11 + client/src/reducers/genesets.js | 3292 +------------------ server/app/app.py | 14 + server/cli/launch.py | 23 +- server/common/annotations/annotations.py | 12 +- server/common/annotations/local_file_csv.py | 97 +- server/common/config/client_config.py | 1 + server/common/config/dataset_config.py | 46 +- server/common/rest.py | 43 +- server/data_common/data_adaptor.py | 15 +- server/default_config.py | 5 +- 11 files changed, 279 insertions(+), 3280 deletions(-) diff --git a/client/src/actions/index.js b/client/src/actions/index.js index 5de720b0..fd8749a3 100644 --- a/client/src/actions/index.js +++ b/client/src/actions/index.js @@ -52,6 +52,16 @@ async function userInfoFetch(dispatch) { }); } +async function genesetsFetch(dispatch) { + return fetchJson("genesets").then((response) => { + const genesets = response?.genesets ?? {}; + dispatch({ + type: "geneset: initial load", + init: genesets, + }); + }) +} + function prefetchEmbeddings(annoMatrix) { /* prefetch requests for all embeddings @@ -74,6 +84,7 @@ const doInitialDataLoad = () => schemaFetch(dispatch), userColorsFetchAndLoad(dispatch), userInfoFetch(dispatch), + genesetsFetch(dispatch), ]); const baseDataUrl = `${globals.API.prefix}${globals.API.version}`; diff --git a/client/src/reducers/genesets.js b/client/src/reducers/genesets.js index caa4beea..b714b1b4 100644 --- a/client/src/reducers/genesets.js +++ b/client/src/reducers/genesets.js @@ -1,3239 +1,41 @@ -/* -Reducers for geneset data. UI state is controlled from a separate reducer. -*/ - -/** - * This is sample / mock data which will be removed once we connect to the backend. - */ -const testGeneSets = new Map(); - -const _testGeneSets = [ - { - "BLADDER.EPITHELIAL_UROTHELIAL.UMBRELLA_CELL": "Epcam", - "BLADDER.EPITHELIAL_UROTHELIAL.BASAL_CELL": "Epcam", - "BLADDER.MESENCHYMAL.NA": "Dcn", - "FAT.NA.MESENCHYMAL_PROGENITORS": "Pdgfra", - "FAT.IMMUNE_CELLS.B_CELLS": "Cd19", - "FAT.IMMUNE_CELLS.T_CELLS": "Cd3g", - "FAT.IMMUNE_CELLS.NK_CELLS": "Irf8", - "FAT.IMMUNE_CELLS.MYELOID": "Itgam", - "FAT.NA.ENDOTHELIAL_CELLS": "Pecam1", - "HEART_AND_AORTA.VASCULAR_ENDOTHELIAL.NA": "Fabp4", - "HEART_AND_AORTA.FIBROBLASTS.NA": "Ddr2", - "HEART_AND_AORTA.ATRIAL_CARDIOMYOCYTES.NA": "Nppa", - "HEART_AND_AORTA.ENDOCARDIAL.NA": "NPR3", - "HEART_AND_AORTA.IMMUNE.NA": "C1qa", - "HEART_AND_AORTA.MYOFIBROBLASTS.NA": "Tcf21", - "HEART_AND_AORTA.SMOOTH_MUSCLE.NA": "Myh11", - "HEART_AND_AORTA.CARDIOMYOCYTES.NA": "TNNI3", - "HEART_AND_AORTA.AORTIC_ENDOTHELIAL.NA": "Ehd3", - "HEART_AND_AORTA.ENDOTHELIAL.NA": "Cdh5", - "HEART_AND_AORTA.ANTIGEN_PRESENTING.NA": "Ptprc", - "HEART_AND_AORTA.MACROPHAGES.NA": "Selplg", - "KIDNEY.FENESTRATED_ENDOTHELIAL_CELLS.NA": "Plvap", - "KIDNEY.MESANGIAL_CELLS.NA": "Des", - "KIDNEY.PODOCYTES.NA": "Podxl", - "KIDNEY.TUBULE.PROXIMAL_BRUSH_BORDER_CELLS": "WIL1", - "KIDNEY.TUBULE.DISTAL_COLLECTING_DUCT_PRINCIPAL_CELLS": "KCNE1", - "PANCREAS.EXOCRINE.ACINAR_CELLS": "AMY2B", - "PANCREAS.EXOCRINE.DUCTAL_CELLS": "Krt19", - "PANCREAS.ENDOCRINE.BETA": "Ins1", - "PANCREAS.ENDOCRINE.ALPHA": "Gcg", - "PANCREAS.ENDOCRINE.DELTA": "SST", - "PANCREAS.ENDOCRINE.PP": "Ppy", - "PANCREAS.NA.ENDOTHELIAL": "Kdr", - "PANCREAS.NA.IMMUNE": "Ptprc", - "PANCREAS.NA.STELLATE_CELLS": "Pdgfra", - "SPLEEN.IMMUNE.B_CELLS": "Cd79a", - "SPLEEN.IMMUNE.T_CELLS": "Cd4", - "TRACHEA.EPITHELIUM.CILIATED": "Epcam", - "TRACHEA.EPITHELIUM.SECRETORY": "Epcam", - "TRACHEA.EPITHELIUM.NEUROENDOCRINE": "Epcam", - "TRACHEA.EPITHELIUM.BASAL": "Epcam", - "TRACHEA.NA.MESENCHYMAL": "Pdgfrb", - "TRACHEA.NA.IMMUNE": "Ptprc", - "TRACHEA.NA.ENDOTHELIAL": "Pecam1", - "TONGUE.EPITHELIUM.PROLIFERATIVE_BASAL": "Top2a", - "TONGUE.EPITHELIUM.BASAL_KERATINOCYTES": "Krt10", - "TONGUE.EPITHELIUM.SUPRABASAL_BASAL_KERATINOCYTES": "Krt14", - "TONGUE.EPITHELIUM.FILIFORM_ASSOCIATED_KERATINOCYTES": "KRT84", - "TONGUE.EPITHELIUM.TASTE_RECEPTOR_CELLS": "Krt8", - "MARROW.WHOLE_MARROW.T_CELLS": "AHNAK", - "MARROW.WHOLE_MARROW.NK_CELLS": "KLRB1A", - "MARROW.WHOLE_MARROW.NKT_CELLS": "AHNAK", - "MARROW.WHOLE_MARROW.IMMATURE_T_CELLS": "Cd3e", - "MARROW.WHOLE_MARROW.IMMATURE_NK": "KLRB1A", - "MARROW.WHOLE_MARROW.IMMATURE_NKT": "Cd3e", - "MARROW.WHOLE_MARROW.PRE_NK": "Mki67", - "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.PRO_B": "Dntt", - "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.LATE_PRO_B": "PAX5", - "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.IMMATURE_B": "Chchd10", - "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.MATURE_NAIVE_B": "Cd79a", - "MARROW.TER119_B220_FACTION.LATE_PRO_B": "VPREB1", - "MARROW.TER119_B220_FACTION.INTERMEDIATE_PRE_B": "PAX5", - "MARROW.TER119_B220_FACTION.IMMATURE_B": "PAX5", - "MARROW.TER119_B220_FACTION.MATURE_NAIVE_B": "PAX5", - "MARROW.UNFRACTIONED_MARROW.HEMATOPOIETIC_PRECURSOR_CELLS": "Kit", - "MARROW.UNFRACTIONED_MARROW.PROERYTHOBLASTS": "TFRC", - "MARROW.UNFRACTIONED_MARROW.ERYTHOBLASTS": "BPGM", - "MARROW.UNFRACTIONED_MARROW.PROLIFERATING_GRANULOPOIETIC_CELLS": "Ltf", - "MARROW.UNFRACTIONED_MARROW.GRANULOCYTES": "Ltf", - "MARROW.UNFRACTIONED_MARROW.BASOPHILS": "Ccl3", - "MARROW.UNFRACTIONED_MARROW.PROLIFERATING_PROMONOCYTE": "AHNAK", - "MARROW.UNFRACTIONED_MARROW.MATURE_MONOCYTES": "AHNAK", - "MARROW.UNFRACTIONED_MARROW.BM_MACROPHAGES": "AHNAK", - "MARROW.SUBFRACTIONATION.HPC_CLUSTERS": "Kit", - "MARROW.SUBFRACTIONATION.QUIESCENT_HSC_ENRICHED_FRACTION": "Cd48", - "MARROW.SUBFRACTIONATION.MPPS": "Stmn1", - "MARROW.SUBFRACTIONATION.MEGAKARYOCYTE_ERYTHROCYTE_PROGENITOR": "Tgm2", - "MARROW.SUBFRACTIONATION.COMMON_LYMPHOCYTE_PROGENITOR_LINEAGE": "Dntt", - "MARROW.MYELOID_CELLS.GRANULOCYTE_MONOCYTE_PROGENITORS": "Flt3", - "MARROW.MYELOID_CELLS.MATURE_MONOCYTES": "Cd68", - "MARROW.MYELOID_CELLS.MACROPHAGES": "Cd68", - "MARROW.MYELOID_CELLS.GRANULOCYTE_1": "Ltf", - "MARROW.MYELOID_CELLS.GRANULOCYTE_2_BASOPHILS": "Ccl3", - "LUNG.EPITHELIAL.MULTICILIATED": "FOXJ1", - "LUNG.EPITHELIAL.ALVEOLAR_TYPE_2": "SFTPA1", - "LUNG.ENDOTHELIAL.NA": "Pecam1", - "LUNG.STROMAL.NA": "Col1a1", - "LUNG.IMMUNE.ALVEOLAR_MACROPHAGES": "MARCO", - "LUNG.IMMUNE.INTERSTITIAL_MACROPHAGES": "Csf1r", - "LUNG.IMMUNE.DENDRITIC_CELLS": "ITGAX", - "LUNG.IMMUNE.INVADING_MONOCYTES": "Itgam", - "LUNG.IMMUNE.NON_CANONICAL_1": "Itgam", - "LUNG.IMMUNE.NON_CANONICAL_2": "Itgam", - "LUNG.STROMA.ADVENTITIAL_FIBROBLAST": "Serpinf1", - "LUNG.STROMA.SCA1_ADVENTITIAL_FIBROBLAST": "Scara5", - "LUNG.STROMA.ALVEOLAR_FIBROBLAST": "SLC7A10", - "LUNG.STROMA.MESOTHELIAL_CELL": "MSLN", - "LUNG.STROMA.MYOFIBROBLAST": "Hhip", - "LUNG.STROMA.PERICYTE": "TRPC6", - "LUNG.STROMA.SMOOTH_MUSCLE_CELL": "Acta2", - "LUNG.STROMA.CHONDROCYTE": "Sox9", - "LUNG.EPITHELIUM.ALVEOLAR_EPITHELIAL_TYPE_1_CELL": "Clic5", - "LUNG.EPITHELIUM.ALVEOLAR_EPITHELIAL_TYPE_2_CELL": "SFTPA1", - "LUNG.EPITHELIUM.CILIATED_CELL": "FOXJ1", - "LUNG.EPITHELIUM.NEUROENDOCRINE_CELL": "CALCA", - "LUNG.EPITHELIUM.BASAL_CELL": "Krt5", - "LUNG.EPITHELIUM.CLUB_CELL": "SCGB1A1", - "LUNG.EPITHELIUM.GOBLET_CELL": "MUC5B", - "LUNG.IMMUNE.ALVEOLAR_MACROPHAGE": "MARCO", - "LUNG.IMMUNE.B_CELL": "Cd79a", - "LUNG.IMMUNE.BASOPHIL": "FCER1A", - "LUNG.IMMUNE.CLASSICAL_MONOCYTE": "Cd14", - "LUNG.IMMUNE.DENDRITIC_CELL": "Flt3", - "LUNG.IMMUNE.INTERSTITIAL_MACROPHAGE": "C1qa", - "LUNG.IMMUNE.NATURAL_KILLER_CELL": "Nkg7", - "LUNG.IMMUNE.NEUTROPHIL": "Retnlg", - "LUNG.IMMUNE.NONCLASSICAL_MONOCYTE": "EMR4", - "LUNG.IMMUNE.CD4_T_CELL": "Cd4", - "LUNG.IMMUNE.CD8_T_CELL": "Cd8b1", - "LUNG.IMMUNE.INTERMEDIATE_MONOCYTE": "Plac8", - "LUNG.IMMUNE.NATURAL_KILLER_T_CELL": "CXCR6", - "LUNG.IMMUNE.PLASMACYTOID_DENDRITIC_CELL": "Siglech", - "LUNG.IMMUNE.PROLIFERATING_ALVEOLAR_MACROPHAGE": "Mki67", - "LUNG.IMMUNE.PROLIFERATING_NK_T_CELL": "CXCR6", - "LUNG.ENDOTHELIUM.ARTERY_CELL": "DKK2", - "LUNG.ENDOTHELIUM.CAPILLARY_TYPE_1_CELL": "Plvap", - "LUNG.ENDOTHELIUM.CAPILLARY_TYPE_2_CELL": "Ednrb", - "LUNG.ENDOTHELIUM.LYMPHATIC_CELL": "PROX1", - "LUNG.ENDOTHELIUM.VEIN_CELL": "SLC6A2", - "LUNG.NEURONAL_GLIA.GLIAL_CELL": "Arhgap42", - "LIVER.NA.ENDOTHELIUM": "Pecam1", - "LIVER.NA.STELLATE_CELLS": "Dcn", - "LIVER.HEPATOCYTES.PERICENTRAL_PERIPORTAL_MIDLOBULAR": "Alb", - "LIVER.IMMUNE.KUPFFER_MACROPHAGE": "Emr1", - "LIVER.IMMUNE.NK_NKT_CELLS": "Zap70", - "LIVER.IMMUNE.CIRCULATING_B_CELLS": "Cd79a", - "LIVER.IMMUNE.MACROPHAGES_MONOCYTES": "Mrc1", - "LIVER.IMMUNE.T_CELLS": "Cd3e", - "LIVER.CHOLANGIOCYTES_BILE_DUCT_EPITHELIAL_CELLS.NA": "Epcam", - "LIVER.IMMUNE.NEUTROPHILS": "Csf3r", - "LIVER.IMMUNE.PLASMACYTOID_DENDRITIC": "Siglech", - "LIVER.ERYTHROCYTES.NA": "BPGM", - "LARGE_INTESTINES.PROXIMAL_COLON.ENTEROCYTES": "HOXB6", - "LARGE_INTESTINES.PROXIMAL_COLON.GOBLET_CELLS": "HOXB6", - "LARGE_INTESTINES.PROXIMAL_COLON.CHROMAFFIN_CELLS_ENTERENDOCRINE": "HOXB6", - "LARGE_INTESTINES.PROXIMAL_COLON.TUFT_CELLS": "HOXB6", - "LARGE_INTESTINES.PROXIMAL_COLON.PROLIFERATING_STEM": "Lgr5", - "LARGE_INTESTINES.DISTAL_COLON.ENTEROCYTES": "Hoxb13", - "LARGE_INTESTINES.DISTAL_COLON.GOBLET_CELLS": "Hoxb13", - "LARGE_INTESTINES.DISTAL_COLON.CHROMAFFIN_CELLS_ENTERENDOCRINE": "Hoxb13", - "LARGE_INTESTINES.DISTAL_COLON.TUFT_CELLS": "Hoxb13", - "LARGE_INTESTINES.DISTAL_COLON.PROLIFERATING_STEM": "Lgr5", - "LIMB_MUSCLE.SATELLITE_CELLS_1.NA": "Vcam1", - "LIMB_MUSCLE.SATELLITE_CELLS_2.NA": "Vcam1", - "LIMB_MUSCLE.IMMUNE.MACROPHAGE": "Ptprc", - "LIMB_MUSCLE.IMMUNE.T_CELL": "Ptprc", - "LIMB_MUSCLE.IMMUNE.B_CELL": "Ptprc", - "LIMB_MUSCLE.NA.MESENCYHMAL_STEM_CELLS_MSC": "Atn1", - "LIMB_MUSCLE.NA.ENOTHELIAL": "Pecam1", - "LIMB_MUSCLE.NA.CHONDROCYTES_OR_MSC_PROGENITORS": "Chodl", - "DIAPHRAM.SATELLITE_CELLS.NA": "PAX7", - "DIAPHRAM.FIBRO_ADIOPEGNIC_PROGENITORS_MSC.NA": "Pdgfra", - "DIAPHRAM.ENDOTHELIAL_CELLS.NA": "Pecam1", - "DIAPHRAM.IMMUNE.B_CELLS": "Cd19", - "DIAPHRAM.IMMUNE.T_CELLS": "Cd19", - "DIAPHRAM.IMMUNE.MACROPHAGE": "Itgam", - "SKIN.INTERFOLLICULAR_EPIDERMIS.STEM_CELL": "Krt14", - "SKIN.INTERFOLLICULAR_EPIDERMIS.ACTIVELY_DIVIDNG_STEM_CELLS": "Top2a", - "SKIN.INTERFOLLICULAR_EPIDERMIS.DIFFERENTIATED_PROGENY": "Krt10", - "SKIN.BULGE_CELLS.OUTER_BULGE": "Dkk3", - "SKIN.BULGE_CELLS.INNER_BULGE": "Fgf18", - "MAMMARY_GLAND.EPITHELIAL_CELLS.T_CELLS": "Cd3e", - "MAMMARY_GLAND.EPITHELIAL_CELLS.B_CELLS": "Cd74", - "MAMMARY_GLAND.EPITHELIAL_CELLS.MACROPHAGES": "Cd74", - "MAMMARY_GLAND.EPITHELIAL_CELLS.BASAL": "Krt14", - "MAMMARY_GLAND.EPITHELIAL_CELLS.LUMINAL": "Krt8", - "MAMMARY_GLAND.EPITHELIAL_CELLS.LUMINAL_PROGENITORS": "Krt8", - "MAMMARY_GLAND.EPITHELIAL_CELLS.HORMONE_RESPONSIVE_LUMINAL": "Krt8", - "MAMMARY_GLAND.ENDOTHELIAL_CELLS.NA": "Esam", - "MAMMARY_GLAND.STROMAL_CELLS.NA": "VIM", - "THYMUS.IMMUNE.DN1_THYMOCYTES": "Cd44", - "THYMUS.IMMUNE.DP_CELLS": "Dntt", - "THYMUS.IMMUNE.IMMUNE": "Cd8b1", - "THYMUS.IMMUNE.PROLIFERATING_THYMOCYTES": "Top2a", - "THYMUS.STROMAL_CELLS.LYMPHOCYTE": "Zbtb7b", - "THYMUS.STROMAL_CELLS.STROMAL_CELLS": "Cd3e", - "THYMUS.STROMAL_CELLS.DENDRITIC_CELLS": "Ptprc", - "THYMUS.STROMAL_CELLS.MESENCHYMAL_CELLS": "IGFBP7", - "THYMUS.STROMAL_CELLS.THYMIC_EPITHELIAL_CELLS": "Krt5", - "BRAIN.MICROGLIA.NA": "Cx3cr1", - "BRAIN.NON_PARENCHYMAL_MACROPHAGES.NA": "Cx3cr1", - "BRAIN.OLIGODENDROCYTE_PROGENITOR_CELLS.NA": "Pdgfra", - "BRAIN.MATURE_MYELINATING_OLIGODENDROCYTES.NA": "Mog", - "BRAIN.BRAIN_ENDOTHELIAL_CELLS.NA": "Pecam1", - "BRAIN.ASTROCYTE.NA": "Aldh1l1", - "BRAIN.BERGMAN_GLIA.NA": "Gdf10", - "BRAIN.EXCITATORY_NEURONS.NA": "SLC17A7", - "BRAIN.INHIBITORY_NEURON.NA": "GAD1", - }, - { - "BLADDER.EPITHELIAL_UROTHELIAL.UMBRELLA_CELL": "Upk3a", - "BLADDER.EPITHELIAL_UROTHELIAL.BASAL_CELL": "Krt5", - "BLADDER.MESENCHYMAL.NA": "Car3", - "FAT.NA.MESENCHYMAL_PROGENITORS": "Cd34", - "FAT.IMMUNE_CELLS.B_CELLS": "Ptprc", - "FAT.IMMUNE_CELLS.T_CELLS": "Cd8a", - "FAT.IMMUNE_CELLS.NK_CELLS": "GZMA", - "FAT.IMMUNE_CELLS.MYELOID": "Cd68", - "FAT.NA.ENDOTHELIAL_CELLS": "Cdh5", - "HEART_AND_AORTA.VASCULAR_ENDOTHELIAL.NA": "Cdh5", - "HEART_AND_AORTA.FIBROBLASTS.NA": "Col3a1", - "HEART_AND_AORTA.ATRIAL_CARDIOMYOCYTES.NA": "MYL7", - "HEART_AND_AORTA.ENDOCARDIAL.NA": "Pecam1", - "HEART_AND_AORTA.IMMUNE.NA": "H2-Eb1", - "HEART_AND_AORTA.MYOFIBROBLASTS.NA": "", - "HEART_AND_AORTA.SMOOTH_MUSCLE.NA": "Acta2", - "HEART_AND_AORTA.CARDIOMYOCYTES.NA": "", - "HEART_AND_AORTA.AORTIC_ENDOTHELIAL.NA": "", - "HEART_AND_AORTA.ENDOTHELIAL.NA": "Pecam1", - "HEART_AND_AORTA.ANTIGEN_PRESENTING.NA": "H2-Eb1", - "HEART_AND_AORTA.MACROPHAGES.NA": "Cd14", - "KIDNEY.FENESTRATED_ENDOTHELIAL_CELLS.NA": "", - "KIDNEY.MESANGIAL_CELLS.NA": "VIM", - "KIDNEY.PODOCYTES.NA": "WT1", - "KIDNEY.TUBULE.PROXIMAL_BRUSH_BORDER_CELLS": "", - "KIDNEY.TUBULE.DISTAL_COLLECTING_DUCT_PRINCIPAL_CELLS": "SCNN1A", - "PANCREAS.EXOCRINE.ACINAR_CELLS": "CPA1", - "PANCREAS.EXOCRINE.DUCTAL_CELLS": "HNF1B", - "PANCREAS.ENDOCRINE.BETA": "Ins2", - "PANCREAS.ENDOCRINE.ALPHA": "Mafb", - "PANCREAS.ENDOCRINE.DELTA": "Hhex", - "PANCREAS.ENDOCRINE.PP": "HNF1B", - "PANCREAS.NA.ENDOTHELIAL": "Pecam1", - "PANCREAS.NA.IMMUNE": "", - "PANCREAS.NA.STELLATE_CELLS": "Pdgfrb", - "SPLEEN.IMMUNE.B_CELLS": "Ccr2", - "SPLEEN.IMMUNE.T_CELLS": "Cd8b1", - "TRACHEA.EPITHELIUM.CILIATED": "Cdh1", - "TRACHEA.EPITHELIUM.SECRETORY": "Cdh1", - "TRACHEA.EPITHELIUM.NEUROENDOCRINE": "Cdh1", - "TRACHEA.EPITHELIUM.BASAL": "Cdh1", - "TRACHEA.NA.MESENCHYMAL": "Col1a1", - "TRACHEA.NA.IMMUNE": "", - "TRACHEA.NA.ENDOTHELIAL": "", - "TONGUE.EPITHELIUM.PROLIFERATIVE_BASAL": "Cdc20", - "TONGUE.EPITHELIUM.BASAL_KERATINOCYTES": "Sbsn", - "TONGUE.EPITHELIUM.SUPRABASAL_BASAL_KERATINOCYTES": "Krt10", - "TONGUE.EPITHELIUM.FILIFORM_ASSOCIATED_KERATINOCYTES": "KRT36", - "TONGUE.EPITHELIUM.TASTE_RECEPTOR_CELLS": "Krt19", - "MARROW.WHOLE_MARROW.T_CELLS": "Thy1", - "MARROW.WHOLE_MARROW.NK_CELLS": "KLRB1C", - "MARROW.WHOLE_MARROW.NKT_CELLS": "Thy1", - "MARROW.WHOLE_MARROW.IMMATURE_T_CELLS": "Cd4", - "MARROW.WHOLE_MARROW.IMMATURE_NK": "KLRB1C", - "MARROW.WHOLE_MARROW.IMMATURE_NKT": "Cd4", - "MARROW.WHOLE_MARROW.PRE_NK": "Stmn1", - "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.PRO_B": "Rag1", - "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.LATE_PRO_B": "Rag1", - "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.IMMATURE_B": "Cd79a", - "MARROW.UNFRACTIONED_FRACTIONATED_MARROW.MATURE_NAIVE_B": "Cd79b", - "MARROW.TER119_B220_FACTION.LATE_PRO_B": "PAX5", - "MARROW.TER119_B220_FACTION.INTERMEDIATE_PRE_B": "Rag1", - "MARROW.TER119_B220_FACTION.IMMATURE_B": "Cd19", - "MARROW.TER119_B220_FACTION.MATURE_NAIVE_B": "Cd19", - "MARROW.UNFRACTIONED_MARROW.HEMATOPOIETIC_PRECURSOR_CELLS": "Stmn1", - "MARROW.UNFRACTIONED_MARROW.PROERYTHOBLASTS": "Mki67", - "MARROW.UNFRACTIONED_MARROW.ERYTHOBLASTS": "", - "MARROW.UNFRACTIONED_MARROW.PROLIFERATING_GRANULOPOIETIC_CELLS": "Pglyrp1", - "MARROW.UNFRACTIONED_MARROW.GRANULOCYTES": "Pglyrp1", - "MARROW.UNFRACTIONED_MARROW.BASOPHILS": "FCER1A", - "MARROW.UNFRACTIONED_MARROW.PROLIFERATING_PROMONOCYTE": "Mpeg1", - "MARROW.UNFRACTIONED_MARROW.MATURE_MONOCYTES": "Mpeg1", - "MARROW.UNFRACTIONED_MARROW.BM_MACROPHAGES": "Mpeg1", - 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"LIMB_MUSCLE.NA.ENOTHELIAL": "", - "LIMB_MUSCLE.NA.CHONDROCYTES_OR_MSC_PROGENITORS": "", - "DIAPHRAM.SATELLITE_CELLS.NA": "PAX3", - "DIAPHRAM.FIBRO_ADIOPEGNIC_PROGENITORS_MSC.NA": "", - "DIAPHRAM.ENDOTHELIAL_CELLS.NA": "", - "DIAPHRAM.IMMUNE.B_CELLS": "Cd3d", - "DIAPHRAM.IMMUNE.T_CELLS": "Cd3d", - "DIAPHRAM.IMMUNE.MACROPHAGE": "Fcer1g", - "SKIN.INTERFOLLICULAR_EPIDERMIS.STEM_CELL": "Krt10", - "SKIN.INTERFOLLICULAR_EPIDERMIS.ACTIVELY_DIVIDNG_STEM_CELLS": "", - "SKIN.INTERFOLLICULAR_EPIDERMIS.DIFFERENTIATED_PROGENY": "", - "SKIN.BULGE_CELLS.OUTER_BULGE": "Cd34", - "SKIN.BULGE_CELLS.INNER_BULGE": "", - "MAMMARY_GLAND.EPITHELIAL_CELLS.T_CELLS": "Cd3d", - "MAMMARY_GLAND.EPITHELIAL_CELLS.B_CELLS": "", - "MAMMARY_GLAND.EPITHELIAL_CELLS.MACROPHAGES": "Cd14", - "MAMMARY_GLAND.EPITHELIAL_CELLS.BASAL": "Krt5", - "MAMMARY_GLAND.EPITHELIAL_CELLS.LUMINAL": "Krt18", - "MAMMARY_GLAND.EPITHELIAL_CELLS.LUMINAL_PROGENITORS": "Cd14", - "MAMMARY_GLAND.EPITHELIAL_CELLS.HORMONE_RESPONSIVE_LUMINAL": "ESR1", - 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"BLADDER.MESENCHYMAL.NA": "Scara5", - "FAT.NA.MESENCHYMAL_PROGENITORS": "", - "FAT.IMMUNE_CELLS.B_CELLS": "", - "FAT.IMMUNE_CELLS.T_CELLS": "Cd4", - "FAT.IMMUNE_CELLS.NK_CELLS": "Nkg7", - "FAT.IMMUNE_CELLS.MYELOID": "C1qa", - "FAT.NA.ENDOTHELIAL_CELLS": "Ptprc", - "HEART_AND_AORTA.VASCULAR_ENDOTHELIAL.NA": "Cav1", - "HEART_AND_AORTA.FIBROBLASTS.NA": "Col1a1", - "HEART_AND_AORTA.ATRIAL_CARDIOMYOCYTES.NA": "SLN", - "HEART_AND_AORTA.ENDOCARDIAL.NA": "", - "HEART_AND_AORTA.IMMUNE.NA": "", - "HEART_AND_AORTA.MYOFIBROBLASTS.NA": "", - "HEART_AND_AORTA.SMOOTH_MUSCLE.NA": "Tagln", - "HEART_AND_AORTA.CARDIOMYOCYTES.NA": "", - "HEART_AND_AORTA.AORTIC_ENDOTHELIAL.NA": "", - "HEART_AND_AORTA.ENDOTHELIAL.NA": "Tek", - "HEART_AND_AORTA.ANTIGEN_PRESENTING.NA": "Cd86", - "HEART_AND_AORTA.MACROPHAGES.NA": "Cd3e", - "KIDNEY.FENESTRATED_ENDOTHELIAL_CELLS.NA": "", - "KIDNEY.MESANGIAL_CELLS.NA": "Acta2", - "KIDNEY.PODOCYTES.NA": "Mme", - "KIDNEY.TUBULE.PROXIMAL_BRUSH_BORDER_CELLS": "", - "KIDNEY.TUBULE.DISTAL_COLLECTING_DUCT_PRINCIPAL_CELLS": "AQP2", - 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"BRAIN.MICROGLIA.NA": "", - "BRAIN.NON_PARENCHYMAL_MACROPHAGES.NA": "", - "BRAIN.OLIGODENDROCYTE_PROGENITOR_CELLS.NA": "", - "BRAIN.MATURE_MYELINATING_OLIGODENDROCYTES.NA": "", - "BRAIN.BRAIN_ENDOTHELIAL_CELLS.NA": "", - "BRAIN.ASTROCYTE.NA": "", - "BRAIN.BERGMAN_GLIA.NA": "", - "BRAIN.EXCITATORY_NEURONS.NA": "", - "BRAIN.INHIBITORY_NEURON.NA": "", - }, -]; - -for (const grp of _testGeneSets) { - for (const gsName of Object.getOwnPropertyNames(grp)) { - let gs = testGeneSets.get(gsName); - if (gs === undefined) { - gs = new Set(); - testGeneSets.set(gsName, gs); - } - const gene = grp[gsName]; - if (gene !== "") gs.add(gene); - } -} - /** + * Gene set state. Geneset UI state is in a different reducer. + * * geneset reducer state is a Map object, where: * key: the gene set name, a string. * val: the genes in the gene set, which is a Set of string + * + * Ie, Map> */ const GeneSets = ( state = { - genesets: new Map(testGeneSets), + genesets: new Map(), }, action ) => { switch (action.type) { + /** + * Initial, load-time bootstrap. + * { + * type: "geneset: initial load" + * init: Array>> + * } + */ + case "geneset: initial load": { + const { init } = action; + const genesets = new Map(state.genesets); + for (const gs of init) { + const genes = new Set(); + for (const gene of gs[1]) { + genes.add(gene); + } + genesets.set(gs[0], genes); + } + return { + genesets, + }; + } + /** * { * type: "geneset: create", @@ -3243,14 +45,13 @@ const GeneSets = ( */ case "geneset: create": { const { name, genes } = action; - const { genesets } = state; - if (genesets.has(name) !== undefined) + if (state.genesets.has(name) !== undefined) throw new Error("geneset: create -- name already defined."); - const newGenesets = new Map(genesets); // clone - newGenesets.set(name, new Set(genes || [])); + const genesets = new Map(state.genesets); // clone + genesets.set(name, new Set(genes || [])); return { - genesets: newGenesets, + genesets, }; } @@ -3262,14 +63,13 @@ const GeneSets = ( */ case "geneset: delete": { const { name } = action; - const { genesets } = state; - if (!genesets.has(name)) + if (!state.genesets.has(name)) throw new Error("geneset: delete -- name does not exist."); - const newGenesets = new Map(genesets); // clone - newGenesets.delete(name); + const genesets = new Map(state.genesets); // clone + genesets.delete(name); return { - genesets: newGenesets, + genesets, }; } @@ -3282,18 +82,17 @@ const GeneSets = ( */ case "geneset: add genes": { const { name, genes } = action; - const { genesets } = state; - if (!genesets.has(name)) + if (!state.genesets.has(name)) throw new Error("geneset: add genes -- name does not exist."); - const newGenesets = new Map(genesets); // clone - const newGenes = new Set(genesets.get(name)); // clone + const genesets = new Map(state.genesets); // clone + const newGenes = new Set(state.genesets.get(name)); // clone for (const gene of genes) { newGenes.add(gene); } - newGenesets.set(name, newGenes); + genesets.set(name, newGenes); return { - genesets: newGenesets, + genesets, }; } @@ -3306,18 +105,17 @@ const GeneSets = ( */ case "geneset: del genes": { const { name, genes } = action; - const { genesets } = state; - if (!genesets.has(name)) + if (!state.genesets.has(name)) throw new Error("geneset: add genes -- name does not exist."); - const newGenesets = new Map(genesets); // clone - const newGenes = new Set(genesets.get(name)); // clone + const genesets = new Map(state.genesets); // clone + const newGenes = new Set(state.genesets.get(name)); // clone for (const gene of genes) { newGenes.delete(gene); } - newGenesets.set(name, newGenes); + genesets.set(name, newGenes); return { - genesets: newGenesets, + genesets, }; } diff --git a/server/app/app.py b/server/app/app.py index 5f924703..a2fe26b7 100644 --- a/server/app/app.py +++ b/server/app/app.py @@ -318,6 +318,19 @@ class LayoutObsAPI(DatasetResource): return common_rest.layout_obs_put(request, data_adaptor) +class GenesetsAPI(DatasetResource): + @cache_control(public=True, no_store=True) + @rest_get_data_adaptor + def get(self, data_adaptor): + return common_rest.genesets_get(request, data_adaptor) + + @requires_authentication + @cache_control(no_store=True) + @rest_get_data_adaptor + def put(self, data_adaptor): + return common_rest.genesets_put(request, data_adaptor) + + def get_api_base_resources(bp_base): """Add resources that are accessed from the api_base_url""" api = Api(bp_base) @@ -343,6 +356,7 @@ def get_api_dataroot_resources(bp_dataroot, url_dataroot=None): add_resource(AnnotationsObsAPI, "/annotations/obs") add_resource(AnnotationsVarAPI, "/annotations/var") add_resource(DataVarAPI, "/data/var") + add_resource(GenesetsAPI, "/genesets") # Display routes add_resource(ColorsAPI, "/colors") # Computation routes diff --git a/server/cli/launch.py b/server/cli/launch.py index a05fd6a1..b0e24bc3 100644 --- a/server/cli/launch.py +++ b/server/cli/launch.py @@ -36,12 +36,12 @@ def annotation_args(func): ) @click.option( "--annotations-dir", + "--data-dir", default=DEFAULT_CONFIG.default_dataset_config.user_annotations__local_file_csv__directory, show_default=False, multiple=False, metavar="", - help="Directory of where to save output annotations; filename will be specified in the application. " - "Incompatible with --annotations-file.", + help="Directory of where to save annotations and gene sets; filename will be specified in the application. Incompatible with --annotations-file and --genesets-file.", ) @click.option( "--experimental-annotations-ontology", @@ -57,6 +57,21 @@ def annotation_args(func): metavar="", help="Location of OBO file defining cell annotation autosuggest terms.", ) + @click.option( + "--disable-genesets-save", + is_flag=True, + default=not DEFAULT_CONFIG.default_dataset_config.user_annotations__genesets__readonly, + show_default=False, + help="Disable saving gene sets. If disabled, users will be able to make changes to gene sets but all changes will be lost on browser refresh.", + ) + @click.option( + "--genesets-file", + default=DEFAULT_CONFIG.default_dataset_config.user_annotations__local_file_csv__genesets_file, + show_default=True, + multiple=False, + metavar="", + help="CSV file to initialize editing of gene sets; will be altered in-place. Incompatible with --data-dir.", + ) @functools.wraps(func) def wrapper(*args, **kwargs): return func(*args, **kwargs) @@ -325,6 +340,8 @@ def launch( disable_annotations, annotations_file, annotations_dir, + genesets_file, + disable_genesets_save, backed, disable_diffexp, experimental_annotations_ontology, @@ -389,6 +406,8 @@ def launch( user_annotations__enable=not disable_annotations, user_annotations__local_file_csv__file=annotations_file, user_annotations__local_file_csv__directory=annotations_dir, + user_annotations__local_file_csv__genesets_file=genesets_file, + user_annotations__genesets__readonly=disable_genesets_save, user_annotations__ontology__enable=experimental_annotations_ontology, user_annotations__ontology__obo_location=experimental_annotations_ontology_obo, presentation__max_categories=max_category_items, diff --git a/server/common/annotations/annotations.py b/server/common/annotations/annotations.py index a8443075..d57cb270 100644 --- a/server/common/annotations/annotations.py +++ b/server/common/annotations/annotations.py @@ -8,7 +8,7 @@ from server.common.utils.type_conversion_utils import get_schema_type_hint_of_ar class Annotations(metaclass=ABCMeta): - """ baseclass for annotations, including ontologies""" + """ baseclass for annotations, including ontologies and gene sets""" """ our default ontology is the PURL for the Cell Ontology. See http://www.obofoundry.org/ontology/cl.html """ @@ -64,6 +64,16 @@ class Annotations(metaclass=ABCMeta): """Write the labels (df) to a persistent storage such that it can later be read""" pass + @abstractmethod + def read_genesets(self, data_adaptor): + """Return the genesets as a list of list, ie, [['gsname', ['gene1', 'gene2']], ...] """ + pass + + @abstractmethod + def write_genesets(self, gs, data_adaptor): + """Write the genesets (gs) to a persistent storage such that it can later be read""" + pass + @abstractmethod def update_parameters(self, parameters, data_adaptor): """Update configuration parameters that describe information about the annotations feature""" diff --git a/server/common/annotations/local_file_csv.py b/server/common/annotations/local_file_csv.py index 545b8a6e..4604f4cd 100644 --- a/server/common/annotations/local_file_csv.py +++ b/server/common/annotations/local_file_csv.py @@ -4,6 +4,7 @@ import re import threading from datetime import datetime from hashlib import blake2b +import csv import pandas as pd from flask import session, has_request_context, current_app @@ -16,14 +17,16 @@ from server.common.errors import AnnotationsError class AnnotationsLocalFile(Annotations): CXG_ANNO_COLLECTION = "cxg_anno_collection" - def __init__(self, output_dir, output_file): + def __init__(self, output_dir, label_output_file, genesets_output_file): super().__init__() self.output_dir = output_dir - self.output_file = output_file - # lock used to protect label file write ops + self.label_output_file = label_output_file + self.genesets_output_file = genesets_output_file + # lock used to protect label and geneset file write ops self.label_lock = threading.RLock() + self.genesets_lock = threading.RLock() - # cache the most recent annotations + # cache the most recent annotations. We don't cache genesets as they are small self.last_fname = None self.last_labels = None @@ -51,7 +54,7 @@ class AnnotationsLocalFile(Annotations): if not current_app.auth.is_user_authenticated(): return pd.DataFrame() - fname = self._get_filename(data_adaptor) + fname = self._get_celllabels_filename(data_adaptor) with self.label_lock: if fname is not None and os.path.exists(fname) and os.path.getsize(fname) > 0: # returned the cached labels if possible, otherwise read them from the file @@ -81,7 +84,7 @@ class AnnotationsLocalFile(Annotations): f"which was last modified on {lastmodstr}\n" ) - fname = self._get_filename(data_adaptor) + fname = self._get_celllabels_filename(data_adaptor) self._backup(fname) if not df.empty: with open(fname, "w", newline="") as f: @@ -95,6 +98,62 @@ class AnnotationsLocalFile(Annotations): self.last_fname = fname self.last_labels = df + def read_genesets(self, data_adaptor): + if has_request_context(): + if not current_app.auth.is_user_authenticated(): + return {} + + fname = self._get_genesets_filename(data_adaptor) + gs = [] + with self.genesets_lock: + if fname is not None and os.path.exists(fname) and os.path.getsize(fname) > 0: + with open(fname, newline="") as f: + sample = f.read(1024) + f.seek(0) + sniffer = csv.Sniffer() + dialect = sniffer.sniff(sample) + dialect.skipinitialspace = True + reader = csv.reader(f, dialect) + haveReadHeader = False + + for row in reader: + if len(row) == 0: + continue + # if row starts with '#' it is a comment + if row[0].startswith("#"): + continue + # if this is the first non-comment row, assume it is a header + if not haveReadHeader: + haveReadHeader = True + continue + gs.append([row[0], row[1:]]) + + return gs + + def write_genesets(self, genesets, data_adaptor): + with self.genesets_lock: + lastmod = data_adaptor.get_last_mod_time() + lastmodstr = "'unknown'" if lastmod is None else lastmod.isoformat(timespec="seconds") + header = ( + f"# Geneset generated on {datetime.now().isoformat(timespec='seconds')} " + f"using cellxgene version {cellxgene_version}\n" + f"# Input data file was {data_adaptor.get_location()}, " + f"which was last modified on {lastmodstr}\n" + ) + + fname = self._get_genesets_filename(data_adaptor) + self._backup(fname) + if len(genesets) > 0: + gsRows = [[gs[0]] + gs[1] for gs in genesets] + with open(fname, "w", newline="") as f: + if header is not None: + f.write(header) + writer = csv.writer(f) + writer.writerow(["name", "genes..."]) # CSV column header row + writer.writerows(gsRows) + else: + open(fname, "w").close() + def _get_userdata_idhash(self, data_adaptor): """ Return a short hash that weakly identifies the user and dataset. @@ -109,16 +168,26 @@ class AnnotationsLocalFile(Annotations): if self.output_dir: return self.output_dir - if self.output_file: + if self.label_output_file: return os.path.dirname(self.path.abspath(self.output_dir)) return os.getcwd() - def _get_filename(self, data_adaptor): + def _get_celllabels_filename(self, data_adaptor): """ return the current annotation file name """ - if self.output_file: - return self.output_file + if self.label_output_file: + return self.label_output_file + return self._get_filename(data_adaptor, "celllabels") + + def _get_genesets_filename(self, data_adaptor): + """ return the current annotation file name """ + if self.genesets_output_file: + return self.genesets_output_file + + return self._get_filename(data_adaptor, "genesets") + + def _get_filename(self, data_adaptor, anno_name): # we need to generate a file name, which we can only do if we have a UID and collection name if session is None: raise AnnotationsError("unable to determine file name for annotations") @@ -131,7 +200,7 @@ class AnnotationsLocalFile(Annotations): raise AnnotationsError("unable to determine file name for annotations") idhash = self._get_userdata_idhash(data_adaptor) - return os.path.join(self._get_output_dir(), f"{collection}-{idhash}.csv") + return os.path.join(self._get_output_dir(), f"{collection}-{anno_name}-{idhash}.csv") def _backup(self, fname, max_backups=9): """ @@ -179,9 +248,9 @@ class AnnotationsLocalFile(Annotations): else: params["annotations_cell_ontology_enabled"] = False - if self.output_file is not None: - # user has hard-wired the name of the annotation data collection - fname = os.path.basename(self.output_file) + if self.label_output_file is not None: + # user has hard-wired the name of the annotation cell label data collection + fname = os.path.basename(self.label_output_file) collection_fname = os.path.splitext(fname)[0] params["annotations-data-collection-is-read-only"] = True params["annotations-data-collection-name"] = collection_fname diff --git a/server/common/config/client_config.py b/server/common/config/client_config.py index 8a70c0b6..c7578d7a 100644 --- a/server/common/config/client_config.py +++ b/server/common/config/client_config.py @@ -44,6 +44,7 @@ def get_client_config(app_config, data_adaptor): "annotations": False, "annotations_file": None, "annotations_dir": None, + "annotations_genesets_readonly": dataset_config.user_annotations__genesets__readonly, "annotations_cell_ontology_enabled": False, "annotations_cell_ontology_obopath": None, "annotations_cell_ontology_terms": None, diff --git a/server/common/config/dataset_config.py b/server/common/config/dataset_config.py index 7586ec2f..7565df41 100644 --- a/server/common/config/dataset_config.py +++ b/server/common/config/dataset_config.py @@ -42,6 +42,10 @@ class DatasetConfig(BaseConfig): self.user_annotations__hosted_tiledb_array__hosted_file_directory = default_config["user_annotations"][ "hosted_tiledb_array" ]["hosted_file_directory"] + self.user_annotations__genesets__readonly = default_config["user_annotations"]["genesets"]["readonly"] + self.user_annotations__local_file_csv__genesets_file = default_config["user_annotations"]["local_file_csv"][ + "genesets_file" + ] self.embeddings__names = default_config["embeddings"]["names"] self.embeddings__enable_reembedding = default_config["embeddings"]["enable_reembedding"] @@ -98,6 +102,9 @@ class DatasetConfig(BaseConfig): self.validate_correct_type_of_configuration_attribute( "user_annotations__local_file_csv__file", (type(None), str) ) + self.validate_correct_type_of_configuration_attribute( + "user_annotations__local_file_csv__genesets_file", (type(None), str) + ) self.validate_correct_type_of_configuration_attribute("user_annotations__ontology__enable", bool) self.validate_correct_type_of_configuration_attribute( "user_annotations__ontology__obo_location", (type(None), str) @@ -108,6 +115,8 @@ class DatasetConfig(BaseConfig): self.validate_correct_type_of_configuration_attribute( "user_annotations__hosted_tiledb_array__hosted_file_directory", (type(None), str) ) + self.validate_correct_type_of_configuration_attribute("user_annotations__genesets__readonly", bool) + if self.user_annotations__enable: server_config = self.app_config.server_config if not self.app__authentication_enable: @@ -132,14 +141,22 @@ class DatasetConfig(BaseConfig): def handle_local_file_csv_annotations(self): dirname = self.user_annotations__local_file_csv__directory - filename = self.user_annotations__local_file_csv__file - if filename is not None and dirname is not None: + annotation_filename = self.user_annotations__local_file_csv__file + if annotation_filename is not None and dirname is not None: raise ConfigurationError("'annotations-file' and 'annotations-dir' may not be used together.") + genesets_filename = self.user_annotations__local_file_csv__genesets_file + if genesets_filename is not None and dirname is not None: + raise ConfigurationError("'genesets-file' and 'annotations-dir' may not be used together.") - if filename is not None: - lf_name, lf_ext = splitext(filename) + if annotation_filename is not None: + lf_name, lf_ext = splitext(annotation_filename) if lf_ext and lf_ext != ".csv": - raise ConfigurationError(f"annotation file type must be .csv: {filename}") + raise ConfigurationError(f"annotation file type must be .csv: {annotation_filename}") + + if genesets_filename is not None: + lf_name, lf_ext = splitext(genesets_filename) + if lf_ext and lf_ext != ".csv": + raise ConfigurationError(f"genesets file type must be .csv: {genesets_filename}") if dirname is not None and not isdir(dirname): try: @@ -147,16 +164,23 @@ class DatasetConfig(BaseConfig): except OSError: raise ConfigurationError("Unable to create directory specified by --annotations-dir") - self.user_annotations = AnnotationsLocalFile(dirname, filename) + self.user_annotations = AnnotationsLocalFile(dirname, annotation_filename, genesets_filename) # if the user has specified a fixed label file, go ahead and validate it # so that we can remove errors early in the process. server_config = self.app_config.server_config - if server_config.single_dataset__datapath and self.user_annotations__local_file_csv__file: - with server_config.matrix_data_cache_manager.data_adaptor( - self.tag, server_config.single_dataset__datapath, self.app_config - ) as data_adaptor: - data_adaptor.check_new_labels(self.user_annotations.read_labels(data_adaptor)) + if server_config.single_dataset__datapath: + if self.user_annotations__local_file_csv__file: + with server_config.matrix_data_cache_manager.data_adaptor( + self.tag, server_config.single_dataset__datapath, self.app_config + ) as data_adaptor: + data_adaptor.check_new_labels(self.user_annotations.read_labels(data_adaptor)) + + if self.user_annotations__local_file_csv__genesets_file: + with server_config.matrix_data_cache_manager.data_adaptor( + self.tag, server_config.single_dataset__datapath, self.app_config + ) as data_adaptor: + data_adaptor.check_new_genesets(self.user_annotations.read_genesets(data_adaptor)) def handle_hosted_tiledb_annotations(self): self.validate_correct_type_of_configuration_attribute("user_annotations__hosted_tiledb_array__db_uri", str) diff --git a/server/common/rest.py b/server/common/rest.py index ca140709..dc7b800a 100644 --- a/server/common/rest.py +++ b/server/common/rest.py @@ -196,9 +196,6 @@ def annotations_var_get(request, data_adaptor): try: labels = None - annotations = data_adaptor.dataset_config.user_annotations - if annotations is not None: - labels = annotations.read_labels(data_adaptor) return make_response( data_adaptor.annotation_to_fbs_matrix(Axis.VAR, fields, labels), HTTPStatus.OK, @@ -328,3 +325,43 @@ def layout_obs_put(request, data_adaptor): return abort_and_log(HTTPStatus.NOT_IMPLEMENTED, str(e)) except (ValueError, DisabledFeatureError, FilterError) as e: return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True) + + +def genesets_get(request, data_adaptor): + preferred_mimetype = request.accept_mimetypes.best_match(["application/json"]) + if preferred_mimetype != "application/json": + return abort(HTTPStatus.NOT_ACCEPTABLE) + + annotations = data_adaptor.dataset_config.user_annotations + genesets = annotations.read_genesets(data_adaptor) + return make_response(jsonify({"genesets": genesets}), HTTPStatus.OK) + + +def genesets_put(request, data_adaptor): + annotations = data_adaptor.dataset_config.user_annotations + if annotations is None: + return abort(HTTPStatus.NOT_IMPLEMENTED) + + if data_adaptor.dataset_config.user_annotations__genesets__readonly: + return abort(HTTPStatus.NOT_IMPLEMENTED) + + anno_collection = request.args.get("annotation-collection-name", default=None) + + if anno_collection is not None: + if not annotations.is_safe_collection_name(anno_collection): + return abort(HTTPStatus.BAD_REQUEST, "Bad annotation collection name") + annotations.set_collection(anno_collection) + + args = request.get_json() + try: + genesets = args["genesets"] + if type(genesets) is list: + gs = data_adaptor.check_new_genesets(genesets) + annotations.write_genesets(gs, data_adaptor) + else: + pass + annotations.write_genesets([], data_adaptor) + res = json.dumps({"status": "OK"}) + return make_response(res, HTTPStatus.OK, {"Content-Type": "application/json"}) + except (ValueError, DisabledFeatureError, KeyError) as e: + return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True) diff --git a/server/data_common/data_adaptor.py b/server/data_common/data_adaptor.py index cb1e3c57..4faa55bc 100644 --- a/server/data_common/data_adaptor.py +++ b/server/data_common/data_adaptor.py @@ -266,6 +266,19 @@ class DataAdaptor(metaclass=ABCMeta): return labels_df + def check_new_genesets(self, genesets): + """Check gene sets, return if correct, else raise error""" + + # server_config.single_dataset__var_names + + print("<<<<<<<<>>>>>>>>>>> NEED TO IMPLEMENT check_new_genesets") + # XXX TODO - + # 1. check that all gs names are legal & non-duplicative. + # 2. check that all genes exist in var.index or var-index + # 3. de-dup genes + + return genesets + def data_frame_to_fbs_matrix(self, filter, axis): """ Retrieves data 'X' and returns in a flatbuffer Matrix. @@ -338,7 +351,7 @@ class DataAdaptor(metaclass=ABCMeta): @staticmethod def normalize_embedding(embedding): """Normalize embedding layout to meet client assumptions. - Embedding is an ndarray, shape (n_obs, n)., where n is normally 2 + Embedding is an ndarray, shape (n_obs, n)., where n is normally 2 """ # scale isotropically diff --git a/server/default_config.py b/server/default_config.py index 20922ef9..d000141f 100644 --- a/server/default_config.py +++ b/server/default_config.py @@ -191,10 +191,13 @@ dataset: hosted_file_directory: null local_file_csv: directory: null - file: null + file: null # annotations file name + genesets_file: null # gene sets file name ontology: enable: false obo_location: null + genesets: + readonly: true embeddings: names : []