Updated URLs to 4.4.0

HumanCellAtlas · Dec 8, 2017 · 9a1b5db · 9a1b5db
1 parent 8a0eac8
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Showing 26 changed files with 184 additions and 184 deletions.
diff --git a/json_schema/analysis.json b/json_schema/analysis.json
@@ -76,7 +76,7 @@
         "inputs": {
             "items": {
                 "type": {
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/analysis.json#/definitions/parameter"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/analysis.json#/definitions/parameter"
                 }
             }, 
             "type": "array", 
@@ -89,7 +89,7 @@
         "tasks": {
             "items": {
                 "type": {
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/analysis.json#/definitions/task"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/analysis.json#/definitions/task"
                 }
             }, 
             "type": "array", 
@@ -113,15 +113,15 @@
         "outputs": {
             "items": {
                 "type": {
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/analysis.json#/definitions/file"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/analysis.json#/definitions/file"
                 }
             }, 
             "type": "array", 
             "description": "Output generated by the pipeline run."
         }, 
-        "name": {
-            "type": "string", 
-            "description": "A short, descriptive name for the analysis that need not be unique."
+        "analysis_id": {
+            "type": "number", 
+            "description": "A unique ID for this analysis."
         }, 
         "computational_method": {
             "type": "uri", 
@@ -133,7 +133,7 @@
         }, 
         "core": {
             "description": "Type and schema for this object.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/core.json"
         }, 
         "analysis_run_type": {
             "enum": [
@@ -147,9 +147,9 @@
             "type": "string", 
             "description": "The version of the metadata schemas used for the json files."
         }, 
-        "analysis_id": {
-            "type": "number", 
-            "description": "A unique ID for this analysis."
+        "name": {
+            "type": "string", 
+            "description": "A short, descriptive name for the analysis that need not be unique."
         }
     }
 }
diff --git a/json_schema/assay.json b/json_schema/assay.json
@@ -12,27 +12,27 @@
     "properties": {
         "core": {
             "description": "Type and schema for this object.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/core.json"
         }, 
         "name": {
             "type": "string", 
             "description": "A short, descriptive name for the assay that need not be unique."
         }, 
         "seq": {
             "description": "Information about how a cDNA sample was sequenced.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/seq.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/seq.json"
         }, 
         "rna": {
             "description": "Information about how RNA was converted to cDNA.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/rna.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/rna.json"
         }, 
         "single_cell": {
             "description": "Information on single-cell aspects of an assay.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/single_cell.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/single_cell.json"
         }, 
         "imaging": {
             "description": "Information on image based RNA quantification assays", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/imaging.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/imaging.json"
         }, 
         "assay_id": {
             "type": "string", 

diff --git a/json_schema/assay_bundle.json b/json_schema/assay_bundle.json
@@ -3,37 +3,37 @@
         "assay_ingest": {
             "required": [
                 "hca_ingest", 
-                "content",
+                "content", 
                 "core"
             ], 
             "type": "object", 
             "properties": {
                 "content": {
                     "type": "object", 
                     "description": "Assay content", 
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/assay.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/assay.json"
                 }, 
                 "derivation_protocols": {
                     "items": {
                         "description": "An array of protocols used in derivation of this sample.", 
-                        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/protocol.json"
+                        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/protocol.json"
                     }, 
                     "type": "array"
                 }, 
                 "hca_ingest": {
                     "type": "object", 
                     "description": "core fields added by HCA ingest service", 
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ingest.json"
-                },
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/ingest.json"
+                }, 
                 "core": {
-                    "description": "Type and schema for this object.",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/core.json"
+                    "description": "Type and schema for this object.", 
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/core.json"
                 }
             }
         }
     }, 
     "$schema": "http://json-schema.org/draft-04/schema#", 
-    "type": "object",
+    "type": "object", 
     "description": "A schema for an assay bundle", 
-    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/assay_bundle.json#/definitions/assay_ingest"
+    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/assay_bundle.json#/definitions/assay_ingest"
 }
diff --git a/json_schema/barcode.json b/json_schema/barcode.json
@@ -19,20 +19,20 @@
             ], 
             "description": "The read that the barcode is found in. Should be one of Read 1, Read 2, i7 Index, or i5 Index."
         }, 
-        "size": {
+        "offset": {
             "minimum": 0, 
             "type": "integer", 
-            "description": "Size of barcode in nucleotides.", 
+            "description": "Offset in read of barcode. 0 for beginning of read.", 
             "maximum": 50
         }, 
         "white_list_file": {
             "type": "string", 
             "description": "Name of file containing legitimate barcode sequences. Unused for randomly generated barcodes."
         }, 
-        "offset": {
+        "size": {
             "minimum": 0, 
             "type": "integer", 
-            "description": "Offset in read of barcode. 0 for beginning of read.", 
+            "description": "Size of barcode in nucleotides.", 
             "maximum": 50
         }
     }

diff --git a/json_schema/cell_suspension.json b/json_schema/cell_suspension.json
@@ -1,14 +1,14 @@
 {
     "$schema": "http://json-schema.org/draft-04/schema#", 
-    "title": "cell_suspension", 
+    "description": "Information about the cell suspension derived from the collected or cultured specimen", 
     "properties": {
         "well": {
             "description": "Information about wells in a plate or chip used for single-cell isolation.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/well.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/well.json"
         }, 
         "target_cell_type": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology_json/cell_type_ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/ontology_json/cell_type_ontology.json"
             }, 
             "type": "array", 
             "description": "Cell types present in the suspension."
@@ -21,11 +21,11 @@
         }, 
         "enrichment": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/enrichment.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/enrichment.json"
             }, 
             "type": "array", 
             "description": "How sample was enriched for specific cell type(s)."
         }
     }, 
-    "description": "Information about the cell suspension derived from the collected or cultured specimen"
+    "title": "cell_suspension"
 }
diff --git a/json_schema/contact.json b/json_schema/contact.json
@@ -93,9 +93,10 @@
             ], 
             "description": "Name of country where contact works. Please spell out (except for USA or UK)."
         }, 
-        "institution": {
+        "email": {
+            "pattern": "^.*@.*..*$", 
             "type": "string", 
-            "description": "Name of primary institute where contact works."
+            "description": "An email address for the contact."
         }, 
         "phone": {
             "type": "string", 
@@ -109,10 +110,9 @@
             "type": "string", 
             "description": "Name of lab (often the PI name) within institute where contact works."
         }, 
-        "email": {
-            "pattern": "^.*@.*..*$", 
+        "institution": {
             "type": "string", 
-            "description": "An email address for the contact."
+            "description": "Name of primary institute where contact works."
         }
     }
 }
diff --git a/json_schema/core.json b/json_schema/core.json
@@ -12,9 +12,9 @@
                 "protocol", 
                 "sample", 
                 "file", 
-                "analysis",
-                "assay_bundle",
-                "sample_bundle",
+                "analysis", 
+                "assay_bundle", 
+                "sample_bundle", 
                 "project_bundle"
             ], 
             "description": "The name of the core metadata entity type."

diff --git a/json_schema/death.json b/json_schema/death.json
@@ -11,7 +11,7 @@
     "properties": {
         "cause_of_death": {
             "description": "Cause of death from death report for human donor, from research lab for mouse.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/ontology.json"
         }, 
         "hardy_scale": {
             "minimum": 0, 

diff --git a/json_schema/donor.json b/json_schema/donor.json
@@ -22,7 +22,7 @@
         }, 
         "death": {
             "description": "Information about conditions of death (or info that donor was living at time of collection).", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/death.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/death.json"
         }, 
         "genotype": {
             "type": "string", 
@@ -33,12 +33,11 @@
             "type": "string", 
             "description": "Weight of donor, in kilograms. Can be a range separated by a hyphen."
         }, 
-        "strain": {
-            "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology.json"
-            }, 
-            "type": "array", 
-            "description": "The name of the mouse inbred strain. e.g. C57BL/6."
+        "body_mass_index": {
+            "minimum": 5, 
+            "type": "number", 
+            "description": "The body mass index of the donor.", 
+            "maximum": 100
         }, 
         "alcohol_history": {
             "type": "string", 
@@ -60,7 +59,7 @@
         }, 
         "disease": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology_json/disease_ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/ontology_json/disease_ontology.json"
             }, 
             "type": "array", 
             "description": "Short description of disease status of individual."
@@ -83,15 +82,16 @@
             "type": "string", 
             "description": "Height of donor, in meters. Can be a range separated by a hyphen."
         }, 
-        "body_mass_index": {
-            "minimum": 5, 
-            "type": "number", 
-            "description": "The body mass index of the donor.", 
-            "maximum": 100
+        "strain": {
+            "items": {
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/ontology.json"
+            }, 
+            "type": "array", 
+            "description": "The name of the mouse inbred strain. e.g. C57BL/6."
         }, 
         "ancestry": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/ontology.json"
             }, 
             "type": "array", 
             "description": "An array of ontology terms from EMBL-EBI's Ancestry Ontology describing ancestral groups, uncategorised ancestral groups, and population isolates."
@@ -111,14 +111,14 @@
         }, 
         "medication": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/ontology.json"
             }, 
             "type": "array", 
             "description": "List of medications the donor was currently taking at time of sample donation."
         }, 
         "development_stage": {
             "description": "More detailed (especially for embryos) version of life_stage. e.g. \"E9\" or \"P17\" for mouse.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/ontology.json"
         }
     }
 }
diff --git a/json_schema/enrichment.json b/json_schema/enrichment.json
@@ -8,26 +8,26 @@
     "$schema": "http://json-schema.org/draft-04/schema#", 
     "type": "object", 
     "properties": {
-        "type": {
-            "enum": [
-                "FACS", 
-                "MACS", 
-                "Ficoll gradient"
-            ], 
-            "description": "The method by which enrichment was achieved. e.g. MACS, FACS, Ficoli gradient"
-        }, 
-        "size_min": {
+        "size_max": {
             "minimum": 0.01, 
             "type": "number", 
-            "description": "Minimum size passing selection, in microns.", 
+            "description": "Maximum size passing selection, in microns.", 
             "maximum": 10000
         }, 
-        "size_max": {
+        "size_min": {
             "minimum": 0.01, 
             "type": "number", 
-            "description": "Maximum size passing selection, in microns.", 
+            "description": "Minimum size passing selection, in microns.", 
             "maximum": 10000
         }, 
+        "type": {
+            "enum": [
+                "FACS", 
+                "MACS", 
+                "Ficoll gradient"
+            ], 
+            "description": "The method by which enrichment was achieved. e.g. MACS, FACS, Ficoli gradient"
+        }, 
         "markers": {
             "type": "string", 
             "description": "Space-delimited list of markers (with +/-) used for enrichment. e.g. CD4+ CD8-"

diff --git a/json_schema/file.json b/json_schema/file.json
@@ -10,7 +10,12 @@
     "properties": {
         "core": {
             "description": "Type and schema for this object.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/core.json"
+        }, 
+        "filename": {
+            "pattern": "^.*.fastq$|^.*.fastq.gz$|^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$", 
+            "type": "string", 
+            "description": "A filename for a data file. Must have a valid extension."
         }, 
         "file_format": {
             "enum": [
@@ -21,11 +26,6 @@
                 "png"
             ], 
             "description": "The format that the data file is in. Must be one of: fastq, fastq.gz, tiff, jpg, png."
-        }, 
-        "filename": {
-            "pattern": "^.*.fastq$|^.*.fastq.gz$|^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$", 
-            "type": "string", 
-            "description": "A filename for a data file. Must have a valid extension."
         }
     }
 }