Fixing example sbgrid

biocaddie · Sep 5, 2016 · abc307f · abc307f
1 parent 30afc02
commit abc307f
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Showing 4 changed files with 136 additions and 78 deletions.
diff --git a/code/validate_instances.py b/code/validate_instances.py
@@ -5,9 +5,8 @@
 from os.path import join
 
 
-def validate_instance(filename, error_printing):
+def validate_instance(path, filename, error_printing):
     schemasPath = os.path.abspath("../json-schemas")
-    path = "../examples"
     datasetSchema = json.load(open(join(schemasPath,"dataset_schema.json")))
     instrumentSchema = json.load(open(join(schemasPath,"instrument_schema.json")))
     resolver = RefResolver('file://'+schemasPath+'/'+"dataset_schema.json", datasetSchema) #, base_uri=schemasPath)
@@ -30,9 +29,10 @@ def validate_instance(filename, error_printing):
     print("...done")
 
 
-validate_instance("179.json", 2)
-#validate_instance("ClinicalTrials.gov-NCT00001372.json", 2)
-#validate_instance("PDB-5AEM.json", 2)
-#validate_instance("Uniprot-P77967.json", 2)
-#validate_instance("DBgap-phs000979.v1.p1.json", 2)
+path = "../examples"
+validate_instance(path, "SBGrid-179.json", 2)
+#validate_instance(path, "ClinicalTrials.gov-NCT00001372.json", 2)
+#validate_instance(path, "PDB-5AEM.json", 2)
+#validate_instance(path, "Uniprot-P77967.json", 2)
+#validate_instance(path, "DBgap-phs000979.v1.p1.json", 2)
 
diff --git a/examples/179.json b/examples/179.json
diff --git a/examples/SBGrid-179.json b/examples/SBGrid-179.json
@@ -0,0 +1,128 @@
+{
+	"identifiers":
+	[
+		{"identifier" : "10.15785/SBGRID/179","identifierSource" : "DOI"}
+	],
+	"title":"X-Ray Diffraction data from Nup37-Nup120 full-length complex from Schizosaccharomyces pombe, source of 4FHN structure",
+	"types":
+	[
+		{"information": {"value":"X-Ray Diffraction"} }
+	],
+	"isAbout": [ {"name": "Nup37-Nup120 full-length complex from Schizosaccharomyces pombe"} ],
+	"creators":
+	[
+		{"firstName":"Silvija", "lastName":"Bilokapic" },
+		{"firstName":"Thomas", "lastName":"Schwartz" }
+
+	],
+	"distributions":
+	[
+		{
+			"dates": [
+				{
+					"date": "2010-02-19",
+					"type": {
+						"value": "creation"
+					}
+				},
+				{
+					"date": "2015-10-06",
+					"type": {
+						"value": "publication date"
+					}
+				}
+			],
+			"access": {
+				"landingPage": "https://data.sbgrid.org/dataset/179",
+				"accessURL": "rsync://data.sbgrid.org/10.15785/SBGRID/179"
+			},
+			"storedIn":
+			{
+				"name": "Structural Biology Data Grid",
+				"identifiers": [
+					{
+						"identifier": "https://data.sbgrid.org",
+						"identifierSource": "HTTP"
+					},
+					{
+						"identifier": "https://www.biosharing.org/biodbcore-000683",
+						"identifierSource": "BioSharing"
+					}
+				]
+			}
+		},
+		{
+			"access": {
+				"landingPage": "https://data.sbgrid.org/dataset/179",
+				"accessURL": "rsync://sbgrid.icm.uu.se/10.15785/SBGRID/179"
+			},
+			"storedIn":
+			{
+				"name": "Structural Biology Data Grid",
+				"identifiers": [
+					{
+						"identifier": "https://data.sbgrid.org",
+						"identifierSource": "HTTP"
+					},
+					{
+						"identifier": "https://www.biosharing.org/biodbcore-000683",
+						"identifierSource": "BioSharing"
+					}
+				]
+			}
+		},
+		{
+			"access": {
+				"landingPage": "https://data.sbgrid.org/dataset/179",
+				"accessURL": "rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/179"
+			},
+			"storedIn":
+			{
+				"name": "Structural Biology Data Grid",
+				"identifiers": [
+					{
+						"identifier": "https://data.sbgrid.org",
+						"identifierSource": "HTTP"
+					},
+					{
+						"identifier": "https://www.biosharing.org/biodbcore-000683",
+						"identifierSource": "BioSharing"
+					}
+				]
+			}
+		},
+		{
+			"access": {
+				"landingPage": "https://data.sbgrid.org/dataset/179",
+				"accessURL": "rsync://sbgrid.ncpss.org/10.15785/SBGRID/179"
+			},
+			"storedIn":
+			{
+				"name": "Structural Biology Data Grid",
+				"identifiers": [
+					{
+						"identifier": "https://data.sbgrid.org",
+						"identifierSource": "HTTP"
+					},
+					{
+						"identifier": "https://www.biosharing.org/biodbcore-000683",
+						"identifierSource": "BioSharing"
+					}
+				]
+			}
+		}
+	],
+	"relatedIdentifiers":
+	[
+		{"identifier":"10.15785/SBGRID/180","identifierSource":"DOI","relationType":"relatedTo"},
+		{"identifier":"10.1073/pnas.1205151109", "identifierSource":"DOI", "relationType":"isCitedBy"},
+		{"identifier":"4FHN", "identifierSource":"PDB", "relationType":"relatedTo"}
+	],
+	"extraProperties":
+	[
+		{
+			"category":"data_class",
+			"values": [ { "value": "experimental dataset" } ]
+		}
+	]
+}
diff --git a/json-schemas/dataset_distribution_schema.json b/json-schemas/dataset_distribution_schema.json
@@ -55,7 +55,7 @@
         "$ref": "license_schema.json#"
       }
     },
-    "accessInformation" : {
+    "access" : {
       "description": "The information about access modality for the dataset distribution.",
       "$ref" : "access_schema.json#"
     },