Merge pull request #104 from apdavison/rename-scope

Rename "scope" to "release_status"

Author: apdavison

README.md

@@ -80,28 +80,28 @@ Using these classes, it is possible to list all metadata matching a particular c
 ```
 
 ```
->>> datasets = DatasetVersion.list(client, techniques=whole_cell_patch, scope="in progress")
+>>> datasets = DatasetVersion.list(client, techniques=whole_cell_patch, release_status="in progress")
 ```
 
 For research products that are versioned, such as datasets, models, and software, certain attributes may be inherited from the parent (e.g. a DatasetVersion generally inherits its name from a Dataset). In this case, we have a convenience method to retrieve the parent's name:
 
 ```
->>> print(datasets[0].get_name(client, scope="in progress"))
+>>> print(datasets[0].get_name(client, release_status="in progress"))
 'Cholinergic interneurons in the striatum - Single cell patch clamp recordings'
 ```
 
 If you know the unique identifier of an object, you can retrieve it directly:
 
 ```
->>> dataset = DatasetVersion.from_id("17196b79-04db-4ea4-bb69-d20aab6f1d62", client, scope="in progress")
+>>> dataset = DatasetVersion.from_id("17196b79-04db-4ea4-bb69-d20aab6f1d62", client, release_status="in progress")
 ```
 
 Links between metadata in the Knowledge Graph are not followed automatically,
 to avoid unnecessary network traffic, but can be followed with the `resolve()` method:
 
 ```
->>> license = dataset.license.resolve(client, scope="in progress")
->>> authors = [author.resolve(client, scope="in progress") for author in dataset.authors]
+>>> license = dataset.license.resolve(client, release_status="in progress")
+>>> authors = [author.resolve(client, release_status="in progress") for author in dataset.authors]
 ```
 
 The associated metadata is accessible as attributes of the Python objects, e.g.:

builder/additional_methods/DatasetVersion.py.txt

@@ -1,6 +1,6 @@
     def download(self, local_path, client, accept_terms_of_use=False):
         if accepted_terms_of_use(client, accept_terms_of_use=accept_terms_of_use):
-            repo = self.repository.resolve(client, scope=self.scope or None)
+            repo = self.repository.resolve(client, release_status=self.release_status or None)
             if (repo.iri.value.startswith("https://object.cscs.ch/v1/AUTH")
                 or repo.iri.value.startswith("https://data-proxy.ebrains.eu/api/v1/public")
             ):

builder/additional_methods/Person.py.txt

@@ -6,7 +6,7 @@
     def me(cls, client, allow_multiple=False, follow_links=None):
         user_info = client.user_info()
         possible_matches = cls.list(
-            client, scope="in progress", space="common",
+            client, release_status="in progress", space="common",
             follow_links=follow_links,
             family_name=user_info.family_name,
             given_name=user_info.given_name

builder/additional_methods/ScholarlyArticle.py.txt

@@ -1,7 +1,7 @@
     def get_journal(self, client, with_volume=False, with_issue=False):
         journal = volume = issue = None
         if self.is_part_of:
-            issue_or_volume = self.is_part_of.resolve(client, scope=self.scope, follow_links={"is_part_of": {}})
+            issue_or_volume = self.is_part_of.resolve(client, release_status=self.release_status, follow_links={"is_part_of": {}})
             if isinstance(issue_or_volume, PublicationIssue):
                 volume = issue_or_volume.is_part_of
                 issue = issue_or_volume

builder/fairgraph_module_template.py.txt

@@ -46,6 +46,6 @@ class {{ class_name }}({{base_class}}, OM{{ class_name }}):
     existence_query_properties = {{ existence_query_properties }}
     {%- endif %}
 
-    def __init__(self {%- for arg in constructor_arguments -%}, {{arg}}=None{%- endfor -%}, id=None, data=None, space=None, scope=None):
+    def __init__(self {%- for arg in constructor_arguments -%}, {{arg}}=None{%- endfor -%}, id=None, data=None, space=None, release_status=None):
         return {{ base_class }}.__init__(self, {{ standard_init_properties }}data=data {%- for arg in constructor_arguments -%}, {{arg}}={{arg}}{%- endfor -%})
 {{ additional_methods }}

builder/update_openminds.py

@@ -13,20 +13,14 @@
 
 OPENMINDS_VERSION = "latest"
 
-name_map = {
-    "scope": "model_scope",  # this is because 'scope' is already a keyword
-                             # we could rename the 'scope' keyword to 'stage'
-                             # but we would have the same problem, as there is
-                             # a property named 'stage'
-                             # Suggested resolution: rename the property "scope" in openMINDS to "hasScope"
-}
 
 global_aliases = {
     "short_name": "alias",
     "full_name": "name",
     "has_versions": "versions",
     "has_entity": "entities",
-    "hashes": "hash"
+    "hashes": "hash",
+    "scope": "model_scope"
 }
 
 
@@ -235,20 +229,17 @@
 }
 
 def generate_python_name(json_name):
-    if json_name in name_map:
-        python_name = name_map[json_name]
-    else:
-        python_name = re.sub("(.)([A-Z][a-z]+)", r"\1_\2", json_name.strip())
-        python_name = re.sub("([a-z0-9])([A-Z])", r"\1_\2", python_name).lower()
-        replacements = [
-            ("-", "_"), (".", "_"), ("+", "plus"), ("#", "sharp"), (",", "comma"), ("(", ""), (")", "")
-        ]
-        for before, after in replacements:
-            python_name = python_name.replace(before, after)
-        if python_name[0] in number_names:  # Python variables can't start with a number
-            python_name = number_names[python_name[0]] + python_name[1:]
-        if not python_name.isidentifier():
-            raise NameError(f"Cannot generate a valid Python name from '{json_name}'")
+    python_name = re.sub("(.)([A-Z][a-z]+)", r"\1_\2", json_name.strip())
+    python_name = re.sub("([a-z0-9])([A-Z])", r"\1_\2", python_name).lower()
+    replacements = [
+        ("-", "_"), (".", "_"), ("+", "plus"), ("#", "sharp"), (",", "comma"), ("(", ""), (")", "")
+    ]
+    for before, after in replacements:
+        python_name = python_name.replace(before, after)
+    if python_name[0] in number_names:  # Python variables can't start with a number
+        python_name = number_names[python_name[0]] + python_name[1:]
+    if not python_name.isidentifier():
+        raise NameError(f"Cannot generate a valid Python name from '{json_name}'")
     return python_name
 
 
@@ -665,7 +656,7 @@ def get_type(prop):
         else:
             base_class = "KGObject"
             default_space = get_default_space(module_name, class_name)
-            standard_init_properties = "id=id, space=space, scope=scope, "
+            standard_init_properties = "id=id, space=space, release_status=release_status, "
         properties = []
         plurals_special_cases = {
             # because this is a single item (PropertyValueList), but that item contains a list

fairgraph/base.py

@@ -56,7 +56,7 @@ class Resolvable:  # all
     def resolve(
         self,
         client: KGClient,
-        scope: Optional[str] = None,
+        release_status: Optional[str] = None,
         use_cache: bool = True,
         follow_links: Optional[Dict[str, Any]] = None,
     ):