fix(ontology): add default values for missing comments (DEV-337) (#141)

* fix property comments

* fix default comment for resources

* rename user variable to user_mail

* make return type of getAllGroups optional

* refactor project

* change return type

* refactor ontology creation

* add try except clauses to list creation

* replace typing types with built-in types

* delete knora library readme

* use indent of 4 instead of 3 when dumping json

* improve code after review

Author: irinaschubert

knora/README.md

@@ -163,7 +163,7 @@ def program(user_args: list[str]) -> None:
                 create_ontology(input_file=args.datamodelfile,
                                 lists_file=args.listfile,
                                 server=args.server,
-                                user=args.user,
+                                user_mail=args.user,
                                 password=args.password,
                                 verbose=args.verbose,
                                 dump=args.dump if args.dump else False)

knora/dsp_tools.py

@@ -1,4 +1,4 @@
-from typing import Dict, Optional, Any
+from typing import Optional, Any
 
 from pystrict import strict
 
@@ -28,7 +28,7 @@ def value(self) -> str:
     def permissions(self) -> Optional[Permissions]:
         return self._permissions
 
-    def toJsonLdObj(self, action: Actions) -> Dict[str, Any]:
+    def toJsonLdObj(self, action: Actions) -> dict[str, Any]:
         tmp = {}
         if action == Actions.Create:
             tmp["knora-api:fileValueHasFilename"] = self._value

knora/dsplib/models/bitstream.py

@@ -1,5 +1,5 @@
 import json
-from typing import Dict, Optional, Union
+from typing import Optional, Union
 
 import requests
 from pystrict import strict
@@ -19,11 +19,11 @@ class Connection:
     """
 
     _server: str
-    _prefixes: Union[Dict[str, str], None]
+    _prefixes: Union[dict[str, str], None]
     _token: Union[str, None]
     _log: bool
 
-    def __init__(self, server: str, prefixes: Dict[str, str] = None):
+    def __init__(self, server: str, prefixes: dict[str, str] = None):
         """
         Constructor requiring the server address, the user and password of KNORA
         :param server: Address of the server, e.g https://api.dasch.swiss
@@ -153,12 +153,12 @@ def post(self, path: str, jsondata: Optional[str] = None):
             tmp = path.split('/')
             filename = "POST" + "_".join(tmp) + ".json"
             with open(filename, 'w') as f:
-                json.dump(logobj, f, indent=3)
+                json.dump(logobj, f, indent=4)
         self.on_api_error(req)
         result = req.json()
         return result
 
-    def get(self, path: str, headers: Optional[Dict[str, str]] = None):
+    def get(self, path: str, headers: Optional[dict[str, str]] = None):
         """
         Get data from a server using a HTTP GET request
         :param path: Path of RESTful route

knora/dsplib/models/connection.py

@@ -1,10 +1,12 @@
+from __future__ import annotations
+
 import json
-from typing import List, Optional, Any, Union
+from typing import Optional, Any, Union
 from urllib.parse import quote_plus
 
 from pystrict import strict
 
-from knora.dsplib.models.langstring import LangString, Languages
+from knora.dsplib.models.langstring import LangString
 from .connection import Connection
 from .helpers import Actions, BaseError
 from .model import Model
@@ -211,7 +213,7 @@ def toJsonObj(self, action: Actions):
                 tmp['selfjoin'] = self._selfjoin
         return tmp
 
-    def create(self):
+    def create(self) -> Group:
         jsonobj = self.toJsonObj(Actions.Create)
         jsondata = json.dumps(jsonobj)
         result = self._con.post(Group.ROUTE, jsondata)
@@ -238,14 +240,16 @@ def delete(self):
         return Group.fromJsonObj(self._con, result['group'])
 
     @staticmethod
-    def getAllGroups(con: Connection) -> List['Group']:
-        result = con.get(Group.ROUTE)
-        if 'groups' not in result:
-            raise BaseError("Request got no groups!")
-        return list(map(lambda a: Group.fromJsonObj(con, a), result['groups']))
+    def getAllGroups(con: Connection) -> Optional[list[Group]]:
+        try:
+            result = con.get(Group.ROUTE)
+            return [Group.fromJsonObj(con, group_item) for group_item in result["groups"]]
+        except BaseError:
+            # return None if no groups are found or an error happened
+            return None
 
     @staticmethod
-    def getAllGroupsForProject(con: Connection, proj_shortcode: str) -> List['Group']:
+    def getAllGroupsForProject(con: Connection, proj_shortcode: str) -> list[Group]:
         result = con.get(Group.ROUTE)
         if 'groups' not in result:
             raise BaseError("Request got no groups!")
@@ -265,7 +269,7 @@ def createDefinitionFileObj(self):
         }
         return group
 
-    def print(self):
+    def print(self) -> None:
         print('Group Info:')
         print('  Id:          {}'.format(self._id))
         print('  Name:        {}'.format(self._name))

knora/dsplib/models/group.py

@@ -3,7 +3,7 @@
 from dataclasses import dataclass
 from enum import Enum, unique
 from traceback import format_exc
-from typing import NewType, List, Dict, Optional, Any, Tuple, Union, Pattern
+from typing import NewType, Optional, Any, Tuple, Union, Pattern
 
 from pystrict import strict
 
@@ -23,7 +23,7 @@ class OntoInfo:
     hashtag: bool
 
 
-ContextType = NewType("ContextType", Dict[str, OntoInfo])
+ContextType = NewType("ContextType", dict[str, OntoInfo])
 
 
 def LINE() -> int:
@@ -86,7 +86,7 @@ class Cardinality(Enum):
 @strict
 class ContextIterator:
     _context: 'Context'
-    _prefixes: List[str]
+    _prefixes: list[str]
     _index: int
 
     def __init__(self, context: 'Context'):
@@ -111,10 +111,10 @@ class Context:
     This class holds a JSON-LD context with the ontology IRI's and the associated prefixes
     """
     _context: ContextType
-    _rcontext: Dict[str, str]
+    _rcontext: dict[str, str]
     _exp: Pattern[str]
 
-    common_ontologies  = ContextType({
+    common_ontologies = ContextType({
         "foaf": OntoInfo("http://xmlns.com/foaf/0.1/", False),
         "dc": OntoInfo("http://purl.org/dc/elements/1.1/", False),
         "dcterms": OntoInfo("http://purl.org/dc/terms/", False),
@@ -148,7 +148,7 @@ def __is_iri(self, val: str) -> bool:
         m = self._exp.match(val)
         return m.span()[1] == len(val) if m else False
 
-    def __init__(self, context: Optional[Dict[str, str]] = None):
+    def __init__(self, context: Optional[dict[str, str]] = None):
         """
         THe Constructor of the Context. It takes one optional parameter which as a dict of
         prefix - ontology-iri pairs. If the hashtag "#" is used to append element name, the
@@ -158,17 +158,17 @@ def __init__(self, context: Optional[Dict[str, str]] = None):
         # regexp to test for a complete IRI (including fragment identifier)
         self._exp = re.compile("^(http)s?://([\\w\\.\\-~]+)?(:\\d{,6})?(/[\\w\\-~]+)*(#[\\w\\-~]*)?")
         self._context = ContextType({})
-        
+
         # add ontologies from context, if any
         if context:
             for prefix, onto in context.items():
                 self._context[prefix] = OntoInfo(onto.removesuffix('#'), onto.endswith('#'))
-        
+
         # add standard ontologies (rdf, rdfs, owl, xsl)
         for k, v in self.base_ontologies.items():
             if not self._context.get(k):
                 self._context[k] = v
-        
+
         # add DSP-API internal ontologies (knora-api, salsah-gui)
         for k, v in self.knora_ontologies.items():
             if not self._context.get(k):
@@ -224,7 +224,7 @@ def context(self, value: ContextType) -> None:
             raise BaseError("Error in parameter to context setter")
 
     @property
-    def rcontext(self) -> Dict[str, str]:
+    def rcontext(self) -> dict[str, str]:
         return self._rcontext
 
     def add_context(self, prefix: str, iri: Optional[str] = None) -> None:
@@ -400,15 +400,15 @@ def reduce_iri(self, iristr: str, ontoname: Optional[str] = None) -> str:
         else:
             return iristr
 
-    def toJsonObj(self) -> Dict[str, str]:
+    def toJsonObj(self) -> dict[str, str]:
         """
         Return a python object that can be jsonfied...
         :return: Object to be jsonfied
         """
         return {prefix: oinfo.iri + '#' if oinfo.hashtag else oinfo.iri
                 for prefix, oinfo in self._context.items()}
 
-    def get_externals_used(self) -> Dict[str, str]:
+    def get_externals_used(self) -> dict[str, str]:
         exclude = ["rdf", "rdfs", "owl", "xsd", "knora-api", "salsah-gui"]
         return {prefix: onto.iri for prefix, onto in self._context.items() if prefix not in exclude}
 
@@ -487,7 +487,7 @@ class WithId:
     """
     _tmp: str = None
 
-    def __init__(self, obj: Optional[Dict[str, str]]):
+    def __init__(self, obj: Optional[dict[str, str]]):
         if obj is None:
             return
         self._tmp = obj.get('@id')

knora/dsplib/models/helpers.py

@@ -1,5 +1,5 @@
 from enum import Enum, unique
-from typing import List, Dict, Tuple, Optional, Any, Union
+from typing import Tuple, Optional, Any, Union
 
 from ..models.helpers import BaseError
 
@@ -12,7 +12,7 @@ class Languages(Enum):
     IT = 'it'
 
 
-LangStringParam = Optional[Union[Dict[Union[Languages, str], str], str]]
+LangStringParam = Optional[Union[dict[Union[Languages, str], str], str]]
 
 
 class LangStringIterator:
@@ -53,7 +53,7 @@ class LangString:
     "some:thing": "a string without language specificer"
     ```
     """
-    _langstrs: Dict[Languages, str]
+    _langstrs: dict[Languages, str]
     _simplestring: str
 
     def __init__(self, initvalue: LangStringParam = None):
@@ -204,7 +204,7 @@ def toJsonLdObj(self):
             # return list(map(lambda a: {'@language': a[0].value, '@value': a[1]}, self._langstrs.items()))
 
     @classmethod
-    def fromJsonLdObj(cls, obj: Optional[Union[List[Dict[str, str]], str]]) -> 'LangString':
+    def fromJsonLdObj(cls, obj: Optional[Union[list[dict[str, str]], str]]) -> 'LangString':
         if obj is None:
             return None
         if isinstance(obj, str):
@@ -213,7 +213,7 @@ def fromJsonLdObj(cls, obj: Optional[Union[List[Dict[str, str]], str]]) -> 'Lang
             objs = obj
         else:
             objs = [obj]
-        lstrs: Dict[Languages, str] = {}
+        lstrs: dict[Languages, str] = {}
         for o in objs:
             lang = o.get('@language')
             if lang == 'en':
@@ -239,7 +239,7 @@ def fromJsonObj(cls, obj: Optional[Any]) -> 'LangString':
             objs = obj
         else:
             objs = [obj]
-        lstrs: Dict[Languages, str] = {}
+        lstrs: dict[Languages, str] = {}
         for o in objs:
             lang = o.get('language')
             if lang == 'en':
@@ -268,7 +268,7 @@ def print(self, offset: Optional[int] = None):
     def langstrs(self):
         return self._langstrs
 
-    def createDefinitionFileObj(self) -> Union[str, Dict[str, str]]:
+    def createDefinitionFileObj(self) -> Union[str, dict[str, str]]:
         if self._simplestring:
             return self._simplestring
         langstring = {}

knora/dsplib/models/langstring.py

@@ -38,9 +38,8 @@
 def list_creator(con: Connection,
                  project: Project,
                  parent_node: 'ListNode',
-                 nodes: List[dict]) -> List['ListNode']:
-
-    nodelist: List[ListNode] = []
+                 nodes: list[dict]) -> list['ListNode']:
+    nodelist: list[ListNode] = []
 
     for node in nodes:
         new_node = ListNode(
@@ -96,7 +95,7 @@ class ListNode(Model):
     isRootNode : bool
         Is True if the ListNode is the root node of a list. Cannot be set [read].
 
-    children : List[ListNode]
+    children : list[ListNode]
         Contains a list of child nodes. This attribute is only available for nodes that have been read by the
         method "getAllNodes()" [read].
 
@@ -141,7 +140,7 @@ class ListNode(Model):
     _name: Optional[str]
     _parent: Optional[str]
     _isRootNode: bool
-    _children: Optional[List['ListNode']]
+    _children: Optional[list['ListNode']]
     _rootNodeIri: Optional[str]
 
     def __init__(self,
@@ -153,7 +152,7 @@ def __init__(self,
                  name: Optional[str] = None,
                  parent: Optional[Union['ListNode', str]] = None,
                  isRootNode: bool = False,
-                 children: Optional[List['ListNode']] = None,
+                 children: Optional[list['ListNode']] = None,
                  rootNodeIri: Optional[str] = None):
         """
         This is the constructor for the ListNode object. For
@@ -312,18 +311,18 @@ def isRootNode(self, value: bool) -> None:
         raise BaseError('Property isRootNode cannot be set!')
 
     @property
-    def children(self) -> Optional[List['ListNode']]:
+    def children(self) -> Optional[list['ListNode']]:
         return self._children
 
     @children.setter
-    def children(self, value: List['ListNode']) -> None:
+    def children(self, value: list['ListNode']) -> None:
         self._children = value
 
     @staticmethod
     def __getChildren(con: Connection,
                       parent_iri: str,
                       project_iri: str,
-                      children: List[Any]) -> Optional[List['ListNode']]:
+                      children: list[Any]) -> Optional[list['ListNode']]:
         """
         Internal method! Should not be used directly!
 
@@ -334,7 +333,7 @@ def __getChildren(con: Connection,
         :return: List of ListNode instances
         """
         if children:
-            child_nodes: List[Any] = []
+            child_nodes: list[Any] = []
             for child in children:
 
                 if 'parentNodeIri' not in child:
@@ -530,7 +529,7 @@ def getAllNodes(self) -> 'ListNode':
         return root
 
     @staticmethod
-    def getAllLists(con: Connection, project_iri: Optional[str] = None) -> List['ListNode']:
+    def getAllLists(con: Connection, project_iri: Optional[str] = None) -> list['ListNode']:
         """
         Get all lists. If a project IRI is given, it returns the lists of the specified project
 
@@ -546,7 +545,7 @@ def getAllLists(con: Connection, project_iri: Optional[str] = None) -> List['Lis
             raise BaseError("Request got no lists!")
         return list(map(lambda a: ListNode.fromJsonObj(con, a), result['lists']))
 
-    def _createDefinitionFileObj(self, children: List["ListNode"]):
+    def _createDefinitionFileObj(self, children: list["ListNode"]):
         """
         Create an object that corresponds to the syntax of the input to "create_onto".
         Node: This method must be used only internally (for recursion)!!

knora/dsplib/models/listnode.py

@@ -1,12 +1,10 @@
-from typing import Set
-
 from .connection import Connection
 from .helpers import BaseError
 
 
 class Model:
     _con: Connection
-    _changed: Set[str]
+    _changed: set[str]
 
     def __init__(self, con: Connection):
         if not isinstance(con, Connection):