Merge pull request ReproNim#8 from Remi-Gau/remi_schema_creator

Remi schema creator

.github/workflows/pythonpackage.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: [macos-latest, ubuntu-18.04]
-        python-version: [3.7, 3.8]
+        python-version: [3.7, 3.8, 3.9]
 
     steps:
     - uses: actions/checkout@v2

reproschema/cli.py

@@ -57,13 +57,19 @@ def validate(shapefile, path):
     default="n-triples",
     show_default=True,
 )
+@click.option(
+    "--prefixfile", default=None, type=click.Path(exists=True, dir_okay=False)
+)
+@click.option(
+    "--contextfile", default=None, type=click.Path(exists=True, dir_okay=False)
+)
 @click.argument("path", nargs=1, type=str)
-def convert(path, format):
+def convert(path, format, prefixfile, contextfile):
     if not (path.startswith("http") or os.path.exists(path)):
         raise ValueError(f"{path} must be a URL or an existing file or directory")
     from .jsonldutils import to_newformat
 
-    print(to_newformat(path, format))
+    print(to_newformat(path, format, prefixfile, contextfile))
 
 
 @main.command()

reproschema/jsonldutils.py

@@ -75,7 +75,7 @@ def validate_data(data, shape_file_path):
     return conforms, v_text
 
 
-def to_newformat(path, format):
+def to_newformat(path, format, prefixfile=None, contextfile=None):
     """Convert a JSONLD document to n-triples format
 
     Since PyLD requires an http url, a local server is started to serve the
@@ -87,6 +87,11 @@ def to_newformat(path, format):
         A local path or remote url to convert to n-triples
     format: str of enum
         Returned format jsonld, n-triples, turtle
+    prefixfile: str
+        Prefixes to use when converting to turtle (ignored otherwise)
+    contextfile: str
+        Context to use for compaction when returning jsonld. If not provided,
+        a jsonld graph is returned.
 
     Returns
     -------
@@ -99,6 +104,10 @@ def to_newformat(path, format):
         raise ValueError(f"{format} not in {supported_formats}")
     data = load_file(path)
     if format == "jsonld":
+        if contextfile is not None:
+            with open(contextfile) as fp:
+                context = json.load(fp)
+            data = jsonld.compact(data, context)
         return json.dumps(data, indent=2)
     kwargs = {"algorithm": "URDNA2015", "format": "application/n-quads"}
     nt = jsonld.normalize(data, kwargs)
@@ -112,5 +121,10 @@ def to_newformat(path, format):
     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#")
+    if prefixfile is not None:
+        with open(prefixfile) as fp:
+            prefixes = json.load(fp)
+        for key, value in prefixes.items():
+            g.bind(key, value)
     g.parse(data=nt, format="nt")
     return g.serialize(format=format).decode()

reproschema/models/README.md

@@ -0,0 +1,8 @@
+# README
+
+## reproschema file creation
+
+The creation reproschema protocols, activities and items (or Field) are handled
+by 3 python classes with the same names contained in their dedicated modules.
+
+They all inherit from the same base class.

reproschema/models/activity.py

@@ -1,5 +1,7 @@
 from .base import SchemaBase
 
+DEFAULT_LANG = "en"
+
 
 class Activity(SchemaBase):
     """
@@ -8,47 +10,41 @@ class to deal with reproschema activities
 
     schema_type = "reproschema:Activity"
 
+    visible = True
+    required = False
+    skippable = True
+
     def __init__(self, version=None):
         super().__init__(version)
-        self.schema["ui"] = {"shuffle": [], "order": [], "addProperties": []}
-
-    def set_ui_shuffle(self, shuffle=False):
-        self.schema["ui"]["shuffle"] = shuffle
-
-    def set_URI(self, URI):
-        self.URI = URI
-
-    def get_URI(self):
-        return self.URI
-
-    # TODO
-    # preamble
-    # compute
-    # citation
-    # image
 
-    def set_defaults(self, name):
-        self._ReproschemaSchema__set_defaults(name)  # this looks wrong
-        self.set_ui_shuffle(False)
+    def set_defaults(self, name="default"):
+        self._SchemaBase__set_defaults(name)
+        self.set_preamble()
+        self.set_ui_default()
 
-    def update_activity(self, item_info):
-
-        # TODO
-        # - remove the hard coding on visibility and valueRequired
-
-        # update the content of the activity schema with new item
+    def set_compute(self, variable, expression):
+        self.schema["compute"] = [
+            {"variableName": variable, "jsExpression": expression}
+        ]
 
-        item_info["URI"] = "items/" + item_info["name"]
+    def append_item(self, item):
+        # See comment and TODO of the append_activity Protocol class
 
-        append_to_activity = {
-            "variableName": item_info["name"],
-            "isAbout": item_info["URI"],
-            "isVis": item_info["visibility"],
-            "valueRequired": False,
+        property = {
+            "variableName": item.get_basename(),
+            "isAbout": item.get_URI(),
+            "isVis": item.visible,
+            "requiredValue": item.required,
         }
+        if item.skippable:
+            property["allow"] = ["reproschema:Skipped"]
 
-        self.schema["ui"]["order"].append(item_info["URI"])
-        self.schema["ui"]["addProperties"].append(append_to_activity)
+        self.schema["ui"]["order"].append(item.get_URI())
+        self.schema["ui"]["addProperties"].append(property)
+
+    """
+    writing, reading, sorting, unsetting
+    """
 
     def sort(self):
         schema_order = [
@@ -59,9 +55,15 @@ def sort(self):
             "description",
             "schemaVersion",
             "version",
+            "preamble",
+            "citation",
+            "image",
+            "compute",
             "ui",
         ]
         self.sort_schema(schema_order)
+        self.sort_ui()
 
-        ui_order = ["shuffle", "order", "addProperties"]
-        self.sort_ui(ui_order)
+    def write(self, output_dir):
+        self.sort()
+        self._SchemaBase__write(output_dir)