From 95762ae6692f6b9d672d15b4fff960ec8e5b14ed Mon Sep 17 00:00:00 2001 From: Daniel Sotirhos Date: Tue, 25 Feb 2025 21:14:37 -0800 Subject: [PATCH] Regenerate canned PFB entities & schema with test_terra_pfb_manifest() --- .../data/manifest/terra/pfb_entities.json | 68 +++++++++++-------- .../data/manifest/terra/pfb_schema.json | 33 ++++++--- 2 files changed, 64 insertions(+), 37 deletions(-) diff --git a/test/service/data/manifest/terra/pfb_entities.json b/test/service/data/manifest/terra/pfb_entities.json index c17ddc5103..aac9b47420 100644 --- a/test/service/data/manifest/terra/pfb_entities.json +++ b/test/service/data/manifest/terra/pfb_entities.json @@ -296,7 +296,7 @@ "b5894cf5-ecdc-4ea6-a0b9-5335ab678c7a" ], "has_input_biomaterial": [ - null + null ], "organ": [ "brain" @@ -305,10 +305,10 @@ "temporal lobe" ], "preservation_method": [ - null + null ], "storage_method": [ - null + null ] }, "relations": [] @@ -330,10 +330,10 @@ "specimens" ], "model_organ": [ - null + null ], "model_organ_part": [ - null + null ], "organ": [ "brain" @@ -380,7 +380,7 @@ "b5894cf5-ecdc-4ea6-a0b9-5335ab678c7a" ], "has_input_biomaterial": [ - null + null ], "organ": [ "brain" @@ -389,7 +389,7 @@ "temporal lobe" ], "preservation_method": [ - null + null ], "storage_method": [ null @@ -416,8 +416,8 @@ "selected_cell_type": [ null ], - "total_estimated_cells_redundant": 0, - "total_estimated_cells": null + "total_estimated_cells": null, + "total_estimated_cells_redundant": 0 }, "relations": [] }, @@ -501,6 +501,9 @@ "project" ], "accessions": [], + "bionetwork_name": [ + "Immune" + ], "contact_names": [ null ], @@ -515,6 +518,9 @@ "institutions": [ "Fake Institution" ], + "is_tissue_atlas_project": [ + false + ], "laboratory": [ null ], @@ -531,16 +537,14 @@ null ], "publications": [], - "is_tissue_atlas_project": [false], - "bionetwork_name": ["Immune"], + "supplementary_links": [ + null + ], "tissue_atlas": [ { "atlas": "Blood", "version": "v1.0" } - ], - "supplementary_links": [ - null ] }, "relations": [] @@ -754,8 +758,8 @@ "selected_cell_type": [ null ], - "total_estimated_cells_redundant": 0, - "total_estimated_cells": 1 + "total_estimated_cells": 1, + "total_estimated_cells_redundant": 0 }, "relations": [] }, @@ -847,6 +851,9 @@ "project" ], "accessions": [], + "bionetwork_name": [ + null + ], "contact_names": [ null ], @@ -862,6 +869,9 @@ "Farmers Trucks", "University" ], + "is_tissue_atlas_project": [ + false + ], "laboratory": [ "John Dear" ], @@ -878,12 +888,10 @@ "Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns." ], "publications": [], - "is_tissue_atlas_project": [false], - "bionetwork_name": [null], - "tissue_atlas": [], "supplementary_links": [ "https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-81547/Results" - ] + ], + "tissue_atlas": [] }, "relations": [] }, @@ -3157,8 +3165,8 @@ "selected_cell_type": [ "peripheral blood mononuclear cell" ], - "total_estimated_cells_redundant": 0, - "total_estimated_cells": 20000 + "total_estimated_cells": 20000, + "total_estimated_cells_redundant": 0 }, "relations": [] }, @@ -3181,8 +3189,8 @@ "selected_cell_type": [ "peripheral blood mononuclear cell" ], - "total_estimated_cells_redundant": 0, - "total_estimated_cells": 20000 + "total_estimated_cells": 20000, + "total_estimated_cells_redundant": 0 }, "relations": [] }, @@ -3284,6 +3292,9 @@ "namespace": "dbgap" } ], + "bionetwork_name": [ + null + ], "contact_names": [ null ], @@ -3298,6 +3309,9 @@ "institutions": [ "Newcastle University" ], + "is_tissue_atlas_project": [ + false + ], "laboratory": [ null ], @@ -3314,12 +3328,10 @@ "The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres" ], "publications": [], - "is_tissue_atlas_project": [false], - "bionetwork_name": [null], - "tissue_atlas": [], "supplementary_links": [ null - ] + ], + "tissue_atlas": [] }, "relations": [] }, diff --git a/test/service/data/manifest/terra/pfb_schema.json b/test/service/data/manifest/terra/pfb_schema.json index 513481e72a..26e2b6852d 100644 --- a/test/service/data/manifest/terra/pfb_schema.json +++ b/test/service/data/manifest/terra/pfb_schema.json @@ -1934,7 +1934,10 @@ "name": "is_tissue_atlas_project", "namespace": "projects", "type": { - "items": ["null", "boolean"], + "items": [ + "null", + "boolean" + ], "type": "array" } }, @@ -1946,17 +1949,23 @@ "fields": [ { "name": "atlas", - "namespace": "projects.tissue_atlas", - "type": ["null", "string"] + "namespace": "projects.tissue_atlas", + "type": [ + "null", + "string" + ] }, { "name": "version", "namespace": "projects.tissue_atlas", - "type": ["null", "string"] + "type": [ + "null", + "string" + ] } ], - "name": "projects.tissue_atlas", - "type": "record" + "name": "projects.tissue_atlas", + "type": "record" }, "type": "array" } @@ -1965,7 +1974,10 @@ "name": "bionetwork_name", "namespace": "projects", "type": { - "items": ["null", "string"], + "items": [ + "null", + "string" + ], "type": "array" } }, @@ -1981,7 +1993,10 @@ "name": "data_use_restriction", "namespace": "projects", "type": { - "items": ["null", "string"], + "items": [ + "null", + "string" + ], "type": "array" } } @@ -2098,4 +2113,4 @@ ], "name": "Entity", "type": "record" -} +} \ No newline at end of file