Added test to validate BDbag-AGR-example.json and fixed the file

biocaddie · Mar 22, 2018 · 805562c · 805562c
1 parent ebbd22a
commit 805562c
Show file tree

Hide file tree

Showing 2 changed files with 49 additions and 22 deletions.
diff --git a/json-instances/BDbag-AGR-example.json b/json-instances/BDbag-AGR-example.json
@@ -1,8 +1,8 @@
 {
-    "identifiers": [{
+    "identifier": {
         "identifier": "http://identifiers.org/minid:b9j69h",
         "identifierSource": "minid"
-    }],
+    },
     "title": "AGR Data set with identifier-based references to data in cloud storage",
     "description": "AGR Data set with identifier-based references to data in cloud storage",
     "dates": [{
@@ -13,10 +13,10 @@
         }
     }],
     "creators": [{
-        "identifiers": [{
+        "identifier": {
             "identifier": "http://orcid.org/0000-0003-2280-917X",
             "identifierSource": "orcid"
-        }],
+        },
         "affiliations": [{"name": "University of Southern California / Information Science"}],
         "firstName": "Michel",
         "fullName": "Mike d'Arcy",
@@ -25,18 +25,22 @@
     "types": [{"information": {"value": "model organism data"}}],
     "hasPart": [
         {
-            "identifiers": [{
+            "identifier": {
                 "identifier": "minid:b9n39d",
                 "identifierSource": "minid"
-            }],
+            },
             "title": "A list of disease ontology terms obtained from the Disease Ontology website.",
             "types": [{"information": {"value": "ontology terms"}}],
+            "creators": [ {} ],
             "distributions": [{
                 "identifier": {
                     "identifier": "minid:b9n39d",
                     "identifierSource": ""
                 },
-                "access": {"accessURL": "/data/DO/do_1.0.obo"},
+                "access": {
+                    "accessURL": "/data/DO/do_1.0.obo",
+                    "landingPage": ""
+                },
                 "conformsTo": [{
                     "name": "obo format",
                     "type": {
@@ -53,18 +57,22 @@
             }]
         },
         {
-            "identifiers": [{
+            "identifier": {
                 "identifier": "minid:b9hd64",
                 "identifierSource": "minid"
-            }],
+            },
             "title": "A list of gene ontology terms obtained from the Gene Ontology Consortium.",
             "types": [{"information": {"value": "ontology terms"}}],
+            "creators": [ {} ],
             "distributions": [{
                 "identifier": {
                     "identifier": "minid:b9hd64",
                     "identifierSource": ""
                 },
-                "access": {"accessURL": "data/GO/go_1.0.obo"},
+                "access": {
+                    "accessURL": "data/GO/go_1.0.obo",
+                    "landingPage": ""
+                },
                 "conformsTo": [{
                     "name": "obo format",
                     "type": {
@@ -81,12 +89,13 @@
             }]
         },
         {
-            "identifiers": [{
+            "identifier": {
                 "identifier": "minid:b9px1z",
                 "identifierSource": "minid"
-            }],
+            },
             "title": "A list of sequence ontology terms obtained from the Sequence Ontology website.",
             "types": [{"information": {"value": "ontology terms"}}],
+            "creators": [ {} ],
             "dates": [{
                 "date": "2.6.2018",
                 "type": {
@@ -99,7 +108,10 @@
                     "identifier": "minid:b9px1z",
                     "identifierSource": ""
                 },
-                "access": {"accessURL": "data/SO/so_1.0.obo"},
+                "access": {
+                    "accessURL": "data/SO/so_1.0.obo",
+                    "landingPage": ""
+                },
                 "conformsTo": [{
                     "name": "obo format",
                     "type": {
@@ -116,18 +128,22 @@
             }]
         },
         {
-            "identifiers": [{
+            "identifier": {
                 "identifier": "minid:b9dm68",
                 "identifierSource": "minid"
-            }],
+            },
             "title": "Flybase MOD data",
             "types": [{"information": {"value": "MOD data"}}],
+            "creators": [ {} ],
             "distributions": [{
                 "identifier": {
                     "identifier": "minid:b9dm68",
                     "identifierSource": ""
                 },
-                "access": {"accessURL": "data/FB_1.0.4_4.tar.gz"},
+                "access": {
+                    "accessURL": "data/FB_1.0.4_4.tar.gz",
+                    "landingPage": ""
+                },
                 "conformsTo": [{
                     "name": "tar.gz",
                     "type": {
@@ -144,18 +160,22 @@
             }]
         },
         {
-            "identifiers": [{
+            "identifier": {
                 "identifier": "minid:b9cm3t",
                 "identifierSource": "minid"
-            }],
+            },
             "title": "A list of gene ontology associations for Drosophila obtained from the Gene Ontology Consortium.",
             "types": [{"information": {"value": "gene association data"}}],
+            "creators": [ {} ],
             "distributions": [{
                 "identifier": {
                     "identifier": "minid:b9cm3t",
                     "identifierSource": ""
                 },
-                "access": {"accessURL": "data/GO/ANNOT/gene_association.fb.gz"},
+                "access": {
+                    "accessURL": "data/GO/ANNOT/gene_association.fb.gz",
+                    "landingPage": ""
+                },
                 "conformsTo": [{
                     "name": "tar.gz",
                     "type": {
@@ -172,18 +192,22 @@
             }]
         },
         {
-            "identifiers": [{
+            "identifier": {
                 "identifier": "http://identifiers.org/minid:b9m393",
                 "identifierSource": "minid"
-            }],
+            },
             "title": "JSON files containing orthology derived from DIOPT v6.2 http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl",
             "types": [{"information": {"value": "orthology data"}}],
+            "creators": [ {} ],
             "distributions": [{
                 "identifier": {
                     "identifier": "http://identifiers.org/minid:b9m393",
                     "identifierSource": "minid"
                 },
-                "access": {"accessURL": "data/ORTHO/orthology_FlyBase_1.0.0_2.json.tar.gz"},
+                "access": {
+                    "accessURL": "data/ORTHO/orthology_FlyBase_1.0.0_2.json.tar.gz",
+                    "landingPage": ""
+                },
                 "conformsTo": [
                     {
                         "name": "tar.gz",

diff --git a/tests/test_dats_model.py b/tests/test_dats_model.py
@@ -55,6 +55,9 @@ def test_validate_instance(self):
         folder_path = os.path.join(self.path, "datamed")
         self.assertTrue(dats_model.validate_dataset(folder_path, "E-GEOD-70652-dats.json", 1))
 
+    def test_validate_dataset_10(self):
+        self.assertTrue(dats_model.validate_dataset(self.path, "BDbag-AGR-example.json", 1))
+