Merge branch 'master' into master

Author: sanuann

reproschema/jsonldutils.py

@@ -8,6 +8,9 @@
 def load_file(path_or_url, started=False, http_kwargs={}):
     try:
         data = jsonld.expand(path_or_url)
+        if len(data) == 1:
+            if "@id" not in data[0]:
+                data[0]["@id"] = path_or_url
     except jsonld.JsonLdError as e:
         if 'only "http" and "https"' in str(e):
             lgr.debug("Reloading with local server")
@@ -18,7 +21,9 @@ def load_file(path_or_url, started=False, http_kwargs={}):
                 if "port" not in http_kwargs:
                     raise KeyError("port key missing in http_kwargs")
                 port = http_kwargs["port"]
-            base_url = f"http://localhost:{port}/{root}/"
+            base_url = f"http://localhost:{port}/"
+            if root:
+                base_url += f"{root}/"
             with open(path_or_url) as json_file:
                 data = json.load(json_file)
             try:
@@ -28,6 +33,9 @@ def load_file(path_or_url, started=False, http_kwargs={}):
             finally:
                 if not started:
                     stop_server(stop)
+            if len(data) == 1:
+                if "@id" not in data[0]:
+                    data[0]["@id"] = base_url + os.path.basename(path_or_url)
         else:
             raise
     return data
@@ -99,5 +107,10 @@ def to_newformat(path, format):
     import rdflib as rl
 
     g = rl.Graph()
+    g.bind("rs", "http://schema.repronim.org/")
+    g.bind("sdo", "http://schema.org/")
+    g.bind("nidm", "http://purl.org/nidash/nidm#")
+    g.bind("skos", "http://www.w3.org/2004/02/skos/core#")
+    g.bind("prov", "http://www.w3.org/ns/prov#")
     g.parse(data=nt, format="nt")
     return g.serialize(format=format).decode()

reproschema/tests/contexts/base

@@ -12,6 +12,7 @@
         "prov": "http://www.w3.org/ns/prov#",
         "pav": "http://purl.org/pav/",
         "nidm": "http://purl.org/nidash/nidm#",
+        "uuid": "http://uuid.repronim.org/",
         "reproschema": "http://schema.repronim.org/"
     }
 }

reproschema/tests/data/activities/activity1.jsonld

@@ -12,11 +12,17 @@
         "es": "Durante las últimas 2 semanas, ¿con qué frecuencia le han molestado los siguintes problemas?"
     },
     "messages": [
-		{
-			"message": "Test message: Triggered when item1 value is greater than 1",
-			"jsExpression": "item1 > 1"
-		}
-	],
+      {
+        "message": "Test message: Triggered when item1 value is greater than 1",
+        "jsExpression": "item1 > 1"
+      }
+    ],
+    "compute": [
+        {
+            "variableName": "activity1_total_score",
+            "jsExpression": "item1 + item2"
+        }
+    ],
     "ui": {
         "addProperties": [
             {   "isAbout": "items/item1.jsonld",

reproschema/tests/data/activities/items/item1.jsonld

@@ -48,6 +48,13 @@
             "value": 3
         }
         ]
-    }
+    },
+    "additionalNotesObj": [
+        {
+            "source": "redcap",
+            "column": "notes",
+            "value": "some extra note"
+        }
+    ]
 
 }

reproschema/tests/data/protocols/protocol1_embed.jsonld

@@ -1,5 +1,5 @@
 {
-	"@context": "../../contexts/generic",
+    "@context": "../../contexts/generic",
 	"@type": "reproschema:Protocol",
 	"@id": "protocol1.jsonld",
 	"prefLabel": {

reproschema/tests/data/responses/response1.jsonld

@@ -0,0 +1,11 @@
+{
+    "@context": "../../contexts/generic",
+    "@type": "reproschema:Response",
+    "@id": "uuid:fc963765-1f1b-4ad9-bc4b-0d21b9de5acb",
+    "wasAttributedTo": {
+		"@id": "uuid:2b0aab3d-495f-4eee-98a5-4284b3268a56",
+		"subject_id": "6aabb03d-9e5f-ae5e-c4a5-21b9b326868a"
+    },
+    "isAbout": "../activities/items/item1.jsonld",
+    "value": 1
+}

reproschema/tests/data/responses/responseActivity1.jsonld

@@ -0,0 +1,19 @@
+{
+    "@context": "../../contexts/generic",
+    "@type": "reproschema:ResponseActivity",
+    "@id": "uuid:96496a96-50d6-4b87-a65e-468420e7c80d",
+    "used": [
+        "../activities/items/item1.jsonld",
+        "../activities/activity1.jsonld",
+        "../protocols/protocol1.jsonld"
+    ],
+    "inLanguage": "en",
+    "startedAtTime": "2020-07-23T22:15:37.675Z",
+    "endedAtTime": "2020-07-23T22:15:50.293Z",
+	"wasAssociatedWith": {
+		"version": "0.0.1",
+		"url": "https://schema.repronim.org/ui/#/",
+		"@id": "https://github.com/ReproNim/reproschema-ui"
+	},
+    "prov:generated": "uuid:85d18360-1787-4d3d-b72e-b543ca9b4b1a"
+}

reproschema/tests/test_validate.py

@@ -15,5 +15,5 @@ def test_type_error():
 
 
 def test_url():
-    url = "https://raw.githubusercontent.com/ReproNim/reproschema-py/master/reproschema/tests/data/activities/activity1.jsonld"
+    url = "https://raw.githubusercontent.com/ReproNim/reproschema/1.0.0-rc1/examples/activities/activity1.jsonld"
     assert validate(os.path.abspath("reproschema-shacl.ttl"), url)