fix(create-ontology): within an ontology, references to the ontology itself are not possible (DEV-135)

.github/workflows/ckeck-pr-title.yml

@@ -12,9 +12,9 @@ jobs:
       # check PR title
       - uses: deepakputhraya/action-pr-title@master
         with:
-          regex: '([a-z])+(\(([a-z\-_ ])+\))?!?: [a-z]([a-zA-Z-\.\d \(\)\[\]#_])+$' # Regex the title should match.
-          allowed_prefixes: 'fix,refactor,feat,docs,chore,style,test' # title should start with the given prefix
-          disallowed_prefixes: 'feature,hotfix' # title should not start with the given prefix
+          regex: '([a-z])+(\(([a-z\-_ ])+\))?!?: [a-z]([a-zA-Z-\.\d \(\)\[\]#_,])+$' # Regex the title should match.
+          allowed_prefixes: "fix,refactor,feat,docs,chore,style,test" # title should start with the given prefix
+          disallowed_prefixes: "feature,hotfix" # title should not start with the given prefix
           prefix_case_sensitive: true # title prefix are case insensitive
           min_length: 7 # Min length of the title
           max_length: 120 # Max length of the title

.gitignore

@@ -68,3 +68,6 @@ out.json
 # bazel
 /bazel-*
 /.ijwb/
+
+# for testing in development
+tmp/

Makefile

@@ -54,7 +54,7 @@ install-requirements: ## install requirements
 .PHONY: install
 install: ## install from source (runs setup.py)
 	python3 -m pip install --upgrade pip
-	pip3 install .
+	pip3 install -e .
 
 .PHONY: test
 test: clean local-tmp clone-dsp-repo dsp-stack ## run all tests

docs/dsp-tools-create.md

@@ -48,6 +48,8 @@ A complete data model definition for DSP looks like this:
 
 ### "prefixes" object
 
+(optional)
+
 `"prefixes": { "prefix": "<iri>", ...}`
 
 The `prefixes` object contains the prefixes of external ontologies that are used in the current project. All prefixes
@@ -64,14 +66,21 @@ full qualified IRI each time it is used. So, instead of writing a property calle
 }
 ```
 
+Note that prefixes can be defined for the ontologies defined in this file, but this is only necessary if the ontology
+needs to be referred to explicitly by another ontology within the same file.
+
 ### "$schema" object
 
+(required)
+
 The `$schema` object refers to the JSON schema for DSP data model definitions and is mandatory.
 
 `"$schema": "https://raw.githubusercontent.com/dasch-swiss/dsp-tools/main/knora/dsplib/schemas/ontology.json"`
 
 ### "project" object
 
+(required)
+
 `"project": {"key": "<value>", ...}`
 
 The `project` object contains all resources and properties of the ontology as well as some information about the
@@ -128,38 +137,50 @@ In the following section all fields of the `project` object are explained in det
 
 ### Shortcode
 
+(required)
+
 `"shortcode": "<4-hex-characters>"`
 
 The shortcode has to be unique and is represented by a 4 digit hexadecimal string. The shortcode has to be provided by the DaSCH.
 
 ### Shortname
 
+(required)
+
 `"shortname": "<string>"`
 
 The shortname has to be unique. It should be in the form of a [xsd:NCNAME](https://www.w3.org/TR/xmlschema11-2/#NCName). This means a
 string without blanks or special characters but `-` and `_` are allowed (although not as first character).
 
 ### Longname
 
+(required)
+
 `"longname": "<string>"`
 
 The longname is a string that provides the full name of the project.
 
 ### Descriptions
 
+(required)
+
 `"descriptions": {"<lang>": "<string>", ...}`
 
 The description is represented as a collection of strings with language tags (currently "en", "de", "fr" and "it" are
 supported). It is the description of the project.
 
 ### Keywords
 
+(required)
+
 `"keywords": ["<string>", "<string>", ...]`
 
 Keywords are represented as an array of strings and are used to describe and/or tag the project.
 
 ### Lists
 
+(optional)
+
 `"lists": [<list-definition>,<list-definition>,...]`
 
 Lists can be used to provide controlled vocabularies and can be "flat" or "hierarchical". One advantage of the use of
@@ -331,6 +352,8 @@ The `lists` element is optional. If not used, it should be omitted.
 
 ### Groups
 
+(optional)
+
 `"groups": [<group-definition>, <group-definition>,...]`
 
 The `groups` object contains groups definitions. This is used to specify the permissions a user gets. A project may
@@ -364,6 +387,8 @@ The `groups` element is optional. If not used, it should be omitted. It is curre
 
 ### Users
 
+(optional)
+
 `"users": [<user-definition>, <user-definition>,...]`
 
 This object contains user definitions. A user has the following elements:
@@ -410,6 +435,8 @@ The `users` element is optional. If not used, it should be omitted.
 
 ### Ontologies
 
+(required)
+
 An ontology is a formal representation of a set of terminologies which finally represent real world objects.
 Dependencies, attributes and relations of and between the individual components of the set are recorded in a logical,
 formal language. In contrast to a taxonomy, which defines a mere hierarchical structure within a range of terms, an
@@ -467,19 +494,25 @@ Example of an `ontologies` object:
 
 #### Name
 
+(required)
+
 `"name": "<string>"`
 
 The ontology's (short) name should be in the form of a [xsd:NCNAME](https://www.w3.org/TR/xmlschema11-2/#NCName). This
 means a string without blanks or special characters but `-` and `_` are allowed (although not as first character).
 
 #### Label
 
+(required)
+
 `"label": "<string>"`
 
 A string that provides the full name of the ontology.
 
 #### Properties
 
+(required)
+
 `"properties": [<property-definition>, <property-definition>, ...]`
 
 A `properties` array contains all properties used to describe resources in the ontology. A property has to be of a
@@ -896,11 +929,11 @@ Represents a node of a (possibly hierarchical) list
 
 - `Radio`: A GUI element for _ListValue_. A set of radio buttons. This works only with flat lists.
     - _gui_attributes_:
-        - `hlist=<list-name>` (mandatory): The reference of a [list](#lists) root node
+        - `hlist=<list-name>` (required): The reference of a [list](#lists) root node
 - `List`: A GUI element for _ListValue_. A list of values to select one from. This GUI element should be chosen for
   hierarchical lists or flat lists that could be expanded to hierarchical lists in the future.
     - _gui_attributes_:
-        - `hlist=<list-name>` (mandatory): The reference of a [list](#lists) root node
+        - `hlist=<list-name>` (required): The reference of a [list](#lists) root node
 
 *Example:*
 
@@ -1029,6 +1062,8 @@ Example of a `properties` object:
 
 #### Resources
 
+(required)
+
 The resource classes are the primary entities of the data model. They are the actual objects inside a terminology space.
 A resource class can be seen as a template for the representation of a real object that is represented in the DSP. A
 resource class defines properties (_data fields_). For each of these properties a data type as well as the cardinality

knora/dsplib/models/connection.py

@@ -69,7 +69,7 @@ def get_token(self) -> str:
     def token(self) -> str:
         return self._token
 
-    def start_logging(self):
+    def start_logging(self) -> None:
         self._log = True
 
     def stop_logging(self):

knora/dsplib/models/helpers.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, Union, Pattern
+from typing import NewType, List, Dict, Optional, Any, Tuple, Union, Pattern
 
 from pystrict import strict
 
@@ -26,7 +26,7 @@ class OntoInfo:
 ContextType = NewType("ContextType", Dict[str, OntoInfo])
 
 
-def LINE():
+def LINE() -> int:
     return sys._getframe(1).f_lineno
 
 
@@ -94,7 +94,7 @@ def __init__(self, context: 'Context'):
         self._prefixes = [x for x in self._context.context]
         self._index = 0
 
-    def __next__(self):
+    def __next__(self) -> Tuple[Optional[str], Optional[OntoInfo]]:
         if len(self._context.context) == 0 and self._index == 0:
             return None, None
         elif self._index < len(self._context.context):
@@ -112,9 +112,9 @@ class Context:
     """
     _context: ContextType
     _rcontext: Dict[str, str]
-    _exp: Pattern
+    _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),
@@ -123,19 +123,19 @@ class Context:
         "bibtex": OntoInfo("http://purl.org/net/nknouf/ns/bibtex", True),
         "bibo": OntoInfo("http://purl.org/ontology/bibo/", False),
         "cidoc": OntoInfo("http://purl.org/NET/cidoc-crm/core", True)
-    }
+    })
 
-    knora_ontologies: ContextType = {
+    knora_ontologies = ContextType({
         "knora-api": OntoInfo("http://api.knora.org/ontology/knora-api/v2", True),
         "salsah-gui": OntoInfo("http://api.knora.org/ontology/salsah-gui/v2", True)
-    }
+    })
 
-    base_ontologies: ContextType = {
+    base_ontologies = ContextType({
         "rdf": OntoInfo("http://www.w3.org/1999/02/22-rdf-syntax-ns", True),
         "rdfs": OntoInfo("http://www.w3.org/2000/01/rdf-schema", True),
         "owl": OntoInfo("http://www.w3.org/2002/07/owl", True),
         "xsd": OntoInfo("http://www.w3.org/2001/XMLSchema", True)
-    }
+    })
 
     def __is_iri(self, val: str) -> bool:
         """
@@ -164,7 +164,7 @@ def __init__(self, context: Optional[Dict[str, str]] = None):
             cleaned_input: Dict[str, str] = {prefix: onto for (prefix, onto) in context.items()
                                              if self.base_ontologies.get(prefix) is None and self.knora_ontologies.get(
                     prefix) is None}
-            self._context = {}
+            self._context = ContextType({})
             for prefix, onto in cleaned_input.items():
                 self._context[prefix] = OntoInfo(onto[:-1], True) if onto.endswith('#') else OntoInfo(onto, False)
             #
@@ -180,14 +180,14 @@ def __init__(self, context: Optional[Dict[str, str]] = None):
                 if self._context.get(cc[0]) is None:
                     self._context[cc[0]] = cc[1]
         else:
-            self._context = {
+            self._context = ContextType({
                 "rdf": OntoInfo("http://www.w3.org/1999/02/22-rdf-syntax-ns", True),
                 "rdfs": OntoInfo("http://www.w3.org/2000/01/rdf-schema", True),
                 "owl": OntoInfo("http://www.w3.org/2002/07/owl", True),
                 "xsd": OntoInfo("http://www.w3.org/2001/XMLSchema", True),
                 "knora-api": OntoInfo("http://api.knora.org/ontology/knora-api/v2", True),
                 "salsah-gui": OntoInfo("http://api.knora.org/ontology/salsah-gui/v2", True)
-            }
+            })
         self._rcontext = dict(map(lambda x: (x[1].iri, x[0]), self._context.items()))
 
     def __len__(self) -> int:
@@ -196,7 +196,7 @@ def __len__(self) -> int:
     def __getitem__(self, key: str) -> OntoInfo:
         return self._context[key]
 
-    def __setitem__(self, key: str, value: OntoInfo):
+    def __setitem__(self, key: str, value: OntoInfo) -> None:
         self._context[key] = value
         self._rcontext[value.iri] = key
 
@@ -283,7 +283,7 @@ def iri_from_prefix(self, prefix: str) -> Optional[str]:
 
     def prefix_from_iri(self, iri: str) -> Optional[str]:
         """
-        Get the IRI from a full context that has or has not a a trailing "#". It first searches in the normal list
+        Get the IRI from a full context that has or has not a trailing "#". It first searches in the normal list
         of contexted. If the iri is not found there, it looks in the list common (external) ontologies. If the
         ontology is found there, this ontology is added to the list of known ontology and it's prefix is returned.
         If nothing is found, None is returns

knora/dsplib/models/project.py

@@ -515,7 +515,7 @@ def getAllProjects(con: Connection) -> List['Project']:
             raise BaseError("Request got no projects!")
         return list(map(lambda a: Project.fromJsonObj(con, a), result['projects']))
 
-    def print(self):
+    def print(self) -> None:
         """
         print info to stdout
 

knora/dsplib/models/resourceclass.py

@@ -669,12 +669,11 @@ def toJsonObj(self, lastModificationDate: LastModificationDate, action: Actions,
         def resolve_resref(resref: str):
             tmp = resref.split(':')
             if len(tmp) > 1:
-                if tmp[0]:
+                if tmp[0] and self._context.iri_from_prefix(tmp[0]) != self._ontology_id:
                     self._context.add_context(tmp[0])
                     return {"@id": resref}  # fully qualified name in the form "prefix:name"
                 else:
-                    return {"@id": self._context.prefix_from_iri(self._ontology_id) + ':' + tmp[
-                        1]}  # ":name" in current ontology
+                    return {"@id": self._context.prefix_from_iri(self._ontology_id) + ':' + tmp[1]}  # ":name" in current ontology
             else:
                 return {"@id": "knora-api:" + resref}  # no ":", must be from knora-api!
 

knora/dsplib/schemas/ontology.json

@@ -221,12 +221,14 @@
                 },
                 "properties": {
                     "type": "array",
+                    "minItems": 1,
                     "items": {
                         "$ref": "#/definitions/property"
                     }
                 },
                 "resources": {
                     "type": "array",
+                    "minItems": 1,
                     "items": {
                         "$ref": "#/definitions/resource"
                     }
@@ -482,6 +484,7 @@
                 },
                 "keywords": {
                     "type": "array",
+                    "minItems": 1,
                     "items": {
                         "type": "string"
                     }
@@ -512,6 +515,7 @@
                 },
                 "ontologies": {
                     "type": "array",
+                    "minItems": 1,
                     "items": {
                         "$ref": "#/definitions/ontology"
                     }
@@ -521,6 +525,7 @@
                 "shortcode",
                 "shortname",
                 "longname",
+                "descriptions",
                 "ontologies",
                 "keywords"
             ],

knora/dsplib/utils/onto_create_lists.py

@@ -1,5 +1,5 @@
 import json
-from typing import List
+from typing import Any, Dict, List
 
 from .expand_all_lists import expand_lists_from_excel
 from .onto_validate import validate_ontology
@@ -8,7 +8,7 @@
 from ..models.project import Project
 
 
-def list_creator(con: Connection, project: Project, parent_node: ListNode, nodes: List[dict]):
+def list_creator(con: Connection, project: Project, parent_node: ListNode, nodes: List[Dict[Any, Any]]) -> List[Dict[Any, Any]]:
     """
     Creates the list on the DSP server
 
@@ -35,7 +35,7 @@ def list_creator(con: Connection, project: Project, parent_node: ListNode, nodes
 
 
 def create_lists(input_file: str, lists_file: str, server: str, user: str, password: str, verbose: bool,
-                 dump: bool = False):
+                 dump: bool = False) -> Dict[str, Any]:
     """
     Creates the lists on the DSP server