Merge pull request #98 from HumanCellAtlas/analysis_updates

Analysis updates
HumanCellAtlas · Dec 14, 2017 · f2343c5 · f2343c5
2 parents f73bcd5 + 32001ec
commit f2343c5
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Showing 23 changed files with 88 additions and 86 deletions.
diff --git a/json_schema/analysis.json b/json_schema/analysis.json
@@ -22,7 +22,6 @@
                 "name",
                 "start_time",
                 "stop_time",
-                "log",
                 "disk_size",
                 "docker_image",
                 "cpus",
@@ -87,7 +86,7 @@
         "file": {
             "additionalProperties": false,
             "required": [
-                "checksum",
+                "name",
                 "file_path",
                 "format"
             ],
@@ -101,6 +100,9 @@
                 },
                 "format": {
                     "type": "string"
+                },
+                "name": {
+                    "type": "string"
                 }
             }
         }
@@ -110,7 +112,7 @@
     "properties": {
         "inputs": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis.json#/definitions/parameter"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis.json#/definitions/parameter"
             },
             "type": "array",
             "description": "Input parameters used in the pipeline run, these can be files or string values (settings)."
@@ -121,7 +123,7 @@
         },
         "tasks": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis.json#/definitions/task"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis.json#/definitions/task"
             },
             "type": "array",
             "description": "Descriptions of tasks in the workflow."
@@ -144,7 +146,7 @@
         },
         "outputs": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis.json#/definitions/file"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis.json#/definitions/file"
             },
             "type": "array",
             "description": "Output generated by the pipeline run."
@@ -164,7 +166,7 @@
         },
         "core": {
             "description": "Type and schema for this object.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
         },
         "analysis_run_type": {
             "enum": [

diff --git a/json_schema/analysis_bundle.json b/json_schema/analysis_bundle.json
@@ -11,22 +11,22 @@
                 "content": {
                     "type": "object",
                     "description": "Analysis content",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis.json"
                 },
                 "core": {
                     "description": "Type and schema for this object.",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
                 },
                 "hca_ingest": {
                     "type": "object",
                     "description": "core fields added by HCA ingest service",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ingest.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ingest.json"
                 }
             }
         }
     },
     "$schema": "http://json-schema.org/draft-04/schema#",
     "type": "object",
     "description": "A schema for a analysis bundle",
-    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis_bundle.json#/definitions/analysis_ingest"
+    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis_bundle.json#/definitions/analysis_ingest"
 }
diff --git a/json_schema/assay.json b/json_schema/assay.json
@@ -12,27 +12,27 @@
     "properties": {
         "core": {
             "description": "Type and schema for this object.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
         },
         "name": {
             "type": "string",
             "description": "A short, descriptive name for the assay that need not be unique."
         },
         "seq": {
             "description": "Information about how a cDNA sample was sequenced.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/seq.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/seq.json"
         },
         "rna": {
             "description": "Information about how RNA was converted to cDNA.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/rna.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/rna.json"
         },
         "single_cell": {
             "description": "Information on single-cell aspects of an assay.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/single_cell.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/single_cell.json"
         },
         "imaging": {
             "description": "Information on image based RNA quantification assays",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/imaging.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/imaging.json"
         },
         "assay_id": {
             "type": "string",

diff --git a/json_schema/assay_bundle.json b/json_schema/assay_bundle.json
@@ -11,19 +11,19 @@
                 "content": {
                     "type": "object",
                     "description": "Assay content",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/assay.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/assay.json"
                 },
                 "derivation_protocols": {
                     "items": {
                         "description": "An array of protocols used in derivation of this sample.",
-                        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/protocol.json"
+                        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/protocol.json"
                     },
                     "type": "array"
                 },
                 "hca_ingest": {
                     "type": "object",
                     "description": "core fields added by HCA ingest service",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ingest.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ingest.json"
                 },
                 "has_input": {
                     "type": "string",
@@ -38,13 +38,13 @@
                 },
                 "core": {
                     "description": "Type and schema for this object.",
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
                 }
             }
         }
     },
     "$schema": "http://json-schema.org/draft-04/schema#",
     "type": "object",
     "description": "A schema for an assay bundle",
-    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/assay_bundle.json#/definitions/assay_ingest"
+    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/assay_bundle.json#/definitions/assay_ingest"
 }
diff --git a/json_schema/cell_suspension.json b/json_schema/cell_suspension.json
@@ -4,11 +4,11 @@
     "properties": {
         "well": {
             "description": "Information about wells in a plate or chip used for single-cell isolation.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/well.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/well.json"
         },
         "target_cell_type": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology_json/cell_type_ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/cell_type_ontology.json"
             },
             "type": "array",
             "description": "Cell types present in the suspension."
@@ -21,7 +21,7 @@
         },
         "enrichment": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/enrichment.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/enrichment.json"
             },
             "type": "array",
             "description": "How sample was enriched for specific cell type(s)."

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.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/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).",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/death.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/death.json"
         },
         "genotype": {
             "type": "string",
@@ -59,7 +59,7 @@
         },
         "disease": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology_json/disease_ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/disease_ontology.json"
             },
             "type": "array",
             "description": "Short description of disease status of individual."
@@ -84,14 +84,14 @@
         },
         "strain": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
             },
             "type": "array",
             "description": "The name of the mouse inbred strain. e.g. C57BL/6."
         },
         "ancestry": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/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": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/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.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
         }
     }
 }
diff --git a/json_schema/file.json b/json_schema/file.json
@@ -10,7 +10,7 @@
     "properties": {
         "core": {
             "description": "Type and schema for this object.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
         },
         "filename": {
             "pattern": "^.*.fastq$|^.*.fastq.gz$|^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$",

diff --git a/json_schema/immortalized_cell_line.json b/json_schema/immortalized_cell_line.json
@@ -11,7 +11,7 @@
         },
         "cell_type": {
             "description": "What cell type the line was derived from. CLO ontology.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology_json/cell_type_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/cell_type_ontology.json"
         },
         "date_established": {
             "type": "string",
@@ -24,7 +24,7 @@
         },
         "disease": {
             "description": "A disease associated with the cell line. EFO ontology.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology_json/disease_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/disease_ontology.json"
         },
         "passage_number": {
             "minimum": 0,
@@ -34,15 +34,15 @@
         },
         "publication": {
             "description": "The publication in which the cell line creation was cited.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/publication.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/publication.json"
         },
         "karyotype": {
             "type": "string",
             "description": "The karyotype of the cell line."
         },
         "cell_cycle": {
             "description": "The cell cycle phase, if known.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
         }
     }
 }
diff --git a/json_schema/organoid.json b/json_schema/organoid.json
@@ -7,7 +7,7 @@
     "properties": {
         "model_for_organ": {
             "description": "Organ that this organoid is a model system for.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
         }
     },
     "title": "organoid"

diff --git a/json_schema/primary_cell_line.json b/json_schema/primary_cell_line.json
@@ -7,7 +7,7 @@
     "properties": {
         "cell_type": {
             "description": "The cell type that the cell line was derived from. Should be a CLO ontology.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology_json/cell_type_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/cell_type_ontology.json"
         },
         "date_established": {
             "type": "string",
@@ -16,7 +16,7 @@
         },
         "disease": {
             "description": "Free text describing any disease association to the cell type. Should be found in EFO ontology.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology_json/disease_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/disease_ontology.json"
         },
         "passage_number": {
             "minimum": 0,
@@ -26,7 +26,7 @@
         },
         "cell_cycle": {
             "description": "The cell cycle phase if the cell line is synchronized growing cells or the phase is known.",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
         }
     }
 }
diff --git a/json_schema/project.json b/json_schema/project.json
@@ -19,7 +19,7 @@
     "properties": {
         "core": {
             "description": "type and schema for this object",
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json"
         },
         "related_projects": {
             "items": {
@@ -34,14 +34,14 @@
         },
         "contributors": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/contact.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/contact.json"
             },
             "type": "array",
             "description": "List of people contributing to the project."
         },
         "submitters": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/contact.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/contact.json"
             },
             "type": "array",
             "description": "List of people submitting data to the project."
@@ -66,14 +66,14 @@
         "experimental_design": {
             "items": {
                 "description": "A short description of overall experiment type. e.g. \"single cell RNA sequencing.\"",
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json"
             },
             "type": "array"
         },
         "publications": {
             "items": {
                 "description": "An array of publication modules.",
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/publication.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/publication.json"
             },
             "type": "array"
         },