Changed tag from 4.0 to 4.0.0

HumanCellAtlas · Nov 21, 2017 · 5eeab02 · 5eeab02
1 parent fc98079
commit 5eeab02
Show file tree

Hide file tree

Showing 19 changed files with 63 additions and 63 deletions.
diff --git a/json_schema/analysis.json b/json_schema/analysis.json
@@ -7,7 +7,7 @@
             "type": "array",
             "items": {
                 "type": {
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/analysis.json#/definitions/task"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/analysis.json#/definitions/task"
                 }
             }
         },
@@ -30,7 +30,7 @@
         "outputs": {
             "items": {
                 "type": {
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/analysis.json#/definitions/file"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/analysis.json#/definitions/file"
                 }
             },
             "description": "Output generated by the pipeline run.",
@@ -58,7 +58,7 @@
         "inputs": {
             "items": {
                 "type": {
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/analysis.json#/definitions/parameter"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/analysis.json#/definitions/parameter"
                 }
             },
             "type": "array",
@@ -78,7 +78,7 @@
         },
         "core": {
             "description": "Type and schema for this object.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/core.json"
         }
     },
     "type": "object",

diff --git a/json_schema/assay.json b/json_schema/assay.json
@@ -6,7 +6,7 @@
     "properties": {
         "core": {
             "description": "Type and schema for this object.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/core.json"
         },
         "assay_id": {
             "description": "A unique ID for this assay.",
@@ -22,19 +22,19 @@
         },
         "imaging": {
             "description": "Information on image based RNA quantification assays",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/imaging.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/imaging.json"
         },
         "rna": {
             "description": "Information about how RNA was converted to cDNA.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/rna.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/rna.json"
         },
         "seq": {
             "description": "Information about how a cDNA sample was sequenced.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/seq.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/seq.json"
         },
         "single_cell": {
             "description": "Information on single-cell aspects of an assay.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/single_cell.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/single_cell.json"
         }
     },
     "required": [

diff --git a/json_schema/assay_bundle.json b/json_schema/assay_bundle.json
@@ -11,18 +11,18 @@
             ],
             "properties": {
                 "hca_ingest": {
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ingest.json",
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ingest.json",
                     "description": "core fields added by HCA ingest service",
                     "type": "object"
                 },
                 "content": {
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/assay.json",
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/assay.json",
                     "description": "Assay content",
                     "type": "object"
                 },
                 "derivation_protocols": {
                     "items": {
-                        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/protocol.json",
+                        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/protocol.json",
                         "description": "An array of protocols used in derivation of this sample."
                     },
                     "type": "array"
@@ -31,6 +31,6 @@
         }
     },
     "items": {
-        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/assay_bundle.json#/definitions/assay_ingest"
+        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/assay_bundle.json#/definitions/assay_ingest"
     }
 }
diff --git a/json_schema/cell_suspension.json b/json_schema/cell_suspension.json
@@ -6,14 +6,14 @@
             "description": "Cell types present in the suspension.",
             "type": "array",
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology_json/cell_type_ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology_json/cell_type_ontology.json"
             }
         },
         "enrichment": {
             "description": "How sample was enriched for specific cell type(s).",
             "type": "array",
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/enrichment.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/enrichment.json"
             }
         },
         "total_estimated_cells": {
@@ -23,7 +23,7 @@
             "type": "number"
         },
         "well": {
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/well.json",
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/well.json",
             "description": "Information about wells in a plate or chip used for single-cell isolation."
         }
     },

diff --git a/json_schema/death.json b/json_schema/death.json
@@ -6,7 +6,7 @@
     "properties": {
         "cause_of_death": {
             "description": "Cause of death from death report for human donor, from research lab for mouse.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json"
         },
         "cold_perfused": {
             "description": "Yes if perfused with cold fluid to help preserve tissues before heart stopped. No otherwise.",

diff --git a/json_schema/donor.json b/json_schema/donor.json
@@ -26,7 +26,7 @@
             "description": "An array of ontology terms from EMBL-EBI's Ancestry Ontology describing ancestral groups, uncategorised ancestral groups, and population isolates.",
             "type": "array",
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json"
             }
         },
         "body_mass_index": {
@@ -37,17 +37,17 @@
         },
         "death": {
             "description": "Information about conditions of death (or info that donor was living at time of collection).",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/death.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/death.json"
         },
         "development_stage": {
             "description": "More detailed (especially for embryos) version of life_stage. e.g. \"E9\" or \"P17\" for mouse.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json"
         },
         "disease": {
             "description": "Short description of disease status of individual.",
             "type": "array",
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology_json/disease_ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology_json/disease_ontology.json"
             }
         },
         "genotype": {
@@ -77,7 +77,7 @@
             "description": "List of medications the donor was currently taking at time of sample donation.",
             "type": "array",
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json"
             }
         },
         "nutritional_state": {
@@ -105,7 +105,7 @@
             "description": "The name of th mouse inbred strain. e.g. C57BL/6.",
             "type": "array",
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json"
             }
         },
         "weight": {

diff --git a/json_schema/file.json b/json_schema/file.json
@@ -22,7 +22,7 @@
         },
         "core": {
             "description": "Type and schema for this object.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/core.json"
         }
     },
     "required": [

diff --git a/json_schema/immortalized_cell_line.json b/json_schema/immortalized_cell_line.json
@@ -13,7 +13,7 @@
         },
         "cell_type": {
             "description": "What cell type the line was derived from. CLO ontology.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology_json/cell_type_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology_json/cell_type_ontology.json"
         },
         "date_established": {
             "description": "When the cell line was established.",
@@ -22,7 +22,7 @@
         },
         "disease": {
             "description": "A disease associated with the cell line. EFO ontology.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology_json/disease_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology_json/disease_ontology.json"
         },
         "karyotype": {
             "description": "The karyotype of the cell line.",
@@ -36,10 +36,10 @@
         },
         "publication": {
             "description": "The publication in which the cell line creation was cited.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/publication.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/publication.json"
         },
         "cell_cycle": {
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json",
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json",
             "description": "The cell cycle phase, if known."
         }
     },

diff --git a/json_schema/organoid.json b/json_schema/organoid.json
@@ -4,7 +4,7 @@
     "properties": {
         "model_for_organ": {
             "description": "Organ that this organoid is a model system for.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json"
         }
     },
     "title": "organoid",

diff --git a/json_schema/primary_cell_line.json b/json_schema/primary_cell_line.json
@@ -5,7 +5,7 @@
     "properties": {
         "cell_type": {
             "description": "The cell type that the cell line was derived from. Should be a CLO ontology.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology_json/cell_type_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology_json/cell_type_ontology.json"
         },
         "date_established": {
             "description": "When the cell line was established, in date-time format.",
@@ -14,7 +14,7 @@
         },
         "disease": {
             "description": "Free text describing any disease association to the cell type. Should be found in EFO ontology.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology_json/disease_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology_json/disease_ontology.json"
         },
         "passage_number": {
             "description": "The number of passages the cell line has been through.",
@@ -23,7 +23,7 @@
             "type": "integer"
         },
         "cell_cycle": {
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json",
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json",
             "description": "The cell cycle phase if the cell line is synchronized growing cells or the phase is known."
         }
     },

diff --git a/json_schema/project.json b/json_schema/project.json
@@ -30,17 +30,17 @@
         "contributors": {
             "description": "List of people contributing to the project.",
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/contact.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/contact.json"
             },
             "type": "array"
         },
         "core": {
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/core.json",
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/core.json",
             "description": "type and schema for this object"
         },
         "experimental_design": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json",
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/ontology.json",
                 "description": "A short description of overall experiment type. e.g. \"single cell RNA sequencing.\""
             },
             "type": "array"
@@ -69,7 +69,7 @@
         },
         "publications": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/publication.json",
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/publication.json",
                 "description": "An array of publication modules."
             },
             "type": "array"
@@ -84,7 +84,7 @@
         "submitters": {
             "description": "List of people submitting data to the project.",
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/contact.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0.0/json_schema/https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.0/json_schema/contact.json"
             },
             "type": "array"
         },