Merge pull request #160 from vemonet/better-import-keys

Improve dependencies versioning

.pre-commit-config.yaml

@@ -16,33 +16,33 @@ repos:
         name: 🪚 Fix end of files
     -   id: trailing-whitespace
         name: ✂️  Trim trailing whitespaces
--   repo: https://github.com/asottile/pyupgrade
-    rev: v2.37.3
-    hooks:
-    -   id: pyupgrade
-        name: ⏫ Running pyupgrade
-        args:
-        - --py3-plus
-        - --keep-runtime-typing
--   repo: https://github.com/myint/autoflake
-    rev: v1.5.3
-    hooks:
-    -   id: autoflake
-        name: ❄️  Running autoflake
-        args:
-        - --recursive
-        - --in-place
-        - --remove-all-unused-imports
-        - --remove-unused-variables
-        - --expand-star-imports
-        - --exclude
-        - __init__.py
-        - --remove-duplicate-keys
--   repo: https://github.com/pycqa/isort
-    rev: 5.10.1
-    hooks:
-    -   id: isort
-        name: 🔄 Formatting imports with isort (python)
+# -   repo: https://github.com/asottile/pyupgrade
+#     rev: v2.37.3
+#     hooks:
+#     -   id: pyupgrade
+#         name: ⏫ Running pyupgrade
+#         args:
+#         - --py3-plus
+#         - --keep-runtime-typing
+# -   repo: https://github.com/myint/autoflake
+#     rev: v1.5.3
+#     hooks:
+#     -   id: autoflake
+#         name: ❄️  Running autoflake
+#         args:
+#         - --recursive
+#         - --in-place
+#         - --remove-all-unused-imports
+#         - --remove-unused-variables
+#         - --expand-star-imports
+#         - --exclude
+#         - __init__.py
+#         - --remove-duplicate-keys
+# -   repo: https://github.com/pycqa/isort
+#     rev: 5.10.1
+#     hooks:
+#     -   id: isort
+#         name: 🔄 Formatting imports with isort (python)
 ci:
     autofix_commit_msg: 🎨 [pre-commit.ci] Auto format from pre-commit.com hooks
     autoupdate_commit_msg: ⬆ [pre-commit.ci] pre-commit autoupdate

docs/getting-started/test-server.md

@@ -1,14 +1,14 @@
 # The nanopub test server
 Throughout this documentation we make use of the
-[nanopub test server](http://test-server.nanopubs.lod.labs.vu.nl/)
+[nanopub test server](https://np.test.knowledgepixels.com/)
 by setting `use_test_server=True` when instantiating `NanopubConf` or `NanopubClient`:
 ```python
 from nanopub import NanopubClient, NanopubConf
 
 client = NanopubClient(use_test_server=True)
 np_conf = NanopubConf(use_test_server=True)
 ```
-This will search and fetch from, and publish to the [nanopub test server](http://test-server.nanopubs.lod.labs.vu.nl/).
+This will search and fetch from, and publish to the [nanopub test server](https://np.test.knowledgepixels.com/).
 
 When learning about nanopub using the testserver is a good idea, because:
 * You are free to experiment with publishing without polluting the production server.
@@ -25,6 +25,6 @@ A manual workaround is:
 1. Open [http://purl.org/np/RA71u9tYPd7ZQifE_6hXjqVim6pkweuvjoi-8ehvLvzg8](http://purl.org/np/RA71u9tYPd7ZQifE_6hXjqVim6pkweuvjoi-8ehvLvzg8)
  in your browser
 2. Notice that the URL changed to [http://server.nanopubs.lod.labs.vu.nl/RA71u9tYPd7ZQifE_6hXjqVim6pkweuvjoi-8ehvLvzg8](http://server.nanopubs.lod.labs.vu.nl/RA71u9tYPd7ZQifE_6hXjqVim6pkweuvjoi-8ehvLvzg8).
-3. Replace 'server' with 'test-server': [http://test-server.nanopubs.lod.labs.vu.nl/RA71u9tYPd7ZQifE_6hXjqVim6pkweuvjoi-8ehvLvzg8](http://test-server.nanopubs.lod.labs.vu.nl/RA71u9tYPd7ZQifE_6hXjqVim6pkweuvjoi-8ehvLvzg8).
+3. Replace 'server' with 'test-server': [https://np.test.knowledgepixels.com/RA71u9tYPd7ZQifE_6hXjqVim6pkweuvjoi-8ehvLvzg8](https://np.test.knowledgepixels.com/RA71u9tYPd7ZQifE_6hXjqVim6pkweuvjoi-8ehvLvzg8).
 
 > **NB**: `NanopubClient.fetch()` does this for you if `use_test_server=True`.

mkdocs.yml

@@ -53,13 +53,13 @@ theme:
       scheme: default
       primary: light blue
       toggle:
-        icon: material/toggle-switch-off-outline
+        icon: material/weather-night
         name: Switch to dark mode
     - media: "(prefers-color-scheme: dark)"
       scheme: slate
       primary: light blue
       toggle:
-        icon: material/toggle-switch
+        icon: material/weather-sunny
         name: Switch to light mode
   features:
     - content.code.annotate
@@ -86,10 +86,12 @@ plugins:
     default_handler: python
     handlers:
       python:
-        rendering:
+        options:
           show_source: true
-    watch:
-      - nanopub
+
+watch:
+  - nanopub
+  - docs
 
 
 # Styled blocks: https://squidfunk.github.io/mkdocs-material/reference/admonitions/#supported-types

nanopub/__main__.py

@@ -47,7 +47,8 @@ def profile():
         p = load_profile()
         print(f' 👤 User profile in \033[1m{DEFAULT_PROFILE_PATH}\033[0m')
         print(str(p))
-    except ProfileError:
+    except ProfileError as e:
+        print(e)
         print(f" ⚠️  No profile could be loaded from {DEFAULT_PROFILE_PATH}")
         print(" ℹ️  Use \033[1mnp setup\033[0m to setup your nanopub profile locally with the interactive CLI")
 
@@ -163,21 +164,23 @@ def setup(
         prompt = ('📬️ Would you like to publish your profile to the nanopub servers? '
                   'This links your ORCID iD to your RSA key, thereby making all your '
                   'publications linkable to you')
-        publish_resp = typer.prompt(prompt, type=Path, default="")
+        publish_resp = typer.prompt(prompt, type=str, default="")
         if publish_resp and publish_resp.lower().startswith("y"):
             publish = True
         else:
             publish = False
 
     if not keypair and not newkeys:
         prompt = '🔓️ Provide the path to your public RSA key: ' \
-                 f'Leave empty for using the one in {USER_CONFIG_DIR}'
-        public_key = typer.prompt(prompt, type=Path, default="")
+            'Leave empty for using the one in: '
+        public_key = typer.prompt(prompt, type=Path,
+                                  default=DEFAULT_PUBLIC_KEY_PATH)
         if not public_key:
             keypair = None
         else:
             prompt = '🔑 Provide the path to your private RSA key: '
-            private_key = typer.prompt(prompt, type=Path)
+            private_key = typer.prompt(prompt, type=Path,
+                                       default=DEFAULT_PRIVATE_KEY_PATH)
             keypair = public_key, private_key
 
     if not keypair:
@@ -194,8 +197,10 @@ def setup(
         public_key_path, private_key = keypair
 
         # Copy the keypair to the default location
-        shutil.copy(public_key_path, USER_CONFIG_DIR / PUBLIC_KEY_FILE)
-        shutil.copy(private_key, USER_CONFIG_DIR / PRIVATE_KEY_FILE)
+        if not os.path.exists(DEFAULT_PUBLIC_KEY_PATH):
+            shutil.copy(public_key_path, USER_CONFIG_DIR / PUBLIC_KEY_FILE)
+        if not os.path.exists(DEFAULT_PRIVATE_KEY_PATH):
+            shutil.copy(private_key, USER_CONFIG_DIR / PRIVATE_KEY_FILE)
 
         print(f'🚚 Your RSA keys have been copied to {USER_CONFIG_DIR}')
 

nanopub/_version.py

@@ -1 +1 @@
-__version__ = "2.0.0"
+__version__ = "2.0.1"

nanopub/client.py

@@ -1,4 +1,5 @@
-"""This module includes a client for the nanopub server.
+"""
+This module includes a client for the nanopub server.
 """
 
 import random
@@ -64,10 +65,10 @@ def find_nanopubs_with_text(
                 retracted. Default is True, returning only publications that are not retracted.
 
         Yields:
-            dicts depicting matching nanopublications.
-            Each dict holds: 'np': the nanopublication uri,
-            'date': date of creation of the nanopublication,
-            'description': A description of the nanopublication (if found in RDF).
+            results (dict): dicts depicting matching nanopublications.
+                Each dict holds: 'np': the nanopublication uri,
+                'date': date of creation of the nanopublication,
+                'description': A description of the nanopublication (if found in RDF).
 
         """
         if len(text) == 0:
@@ -103,10 +104,10 @@ def find_nanopubs_with_pattern(
                 retracted. Default is True, returning only publications that are not retracted.
 
         Yields:
-            dicts depicting matching nanopublications.
-            Each dict holds: 'np': the nanopublication uri,
-            'date': date of creation of the nanopublication,
-            'description': A description of the nanopublication (if found in RDF).
+            results (dict): dicts depicting matching nanopublications.
+                Each dict holds: 'np': the nanopublication uri,
+                'date': date of creation of the nanopublication,
+                'description': A description of the nanopublication (if found in RDF).
 
         """
         params = {}
@@ -145,10 +146,10 @@ def find_things(
                 retracted. Default is True, returning only publications that are not retracted.
 
         Yields:
-            dicts depicting matching nanopublications.
-            Each dict holds: 'np': the nanopublication uri,
-            'date': date of creation of the nanopublication,
-            'description': A description of the nanopublication (if found in RDF).
+            results (dict): dicts depicting matching nanopublications.
+                Each dict holds: 'np': the nanopublication uri,
+                'date': date of creation of the nanopublication,
+                'description': A description of the nanopublication (if found in RDF).
 
         """
         if searchterm == "":

nanopub/definitions.py

@@ -8,7 +8,7 @@
 USER_CONFIG_DIR = Path.home() / ".nanopub"
 DEFAULT_PROFILE_PATH = USER_CONFIG_DIR / "profile.yml"
 
-NANOPUB_TEST_SERVER = 'http://test-server.nanopubs.lod.labs.vu.nl/'
+NANOPUB_TEST_SERVER = 'https://np.test.knowledgepixels.com/'
 # List of servers: https://monitor.petapico.org/.csv
 NANOPUB_SERVER_LIST = [
     'https://np.petapico.org/',
@@ -31,6 +31,7 @@
 MAX_NP_PER_INDEX = 1100
 MAX_TRIPLES_PER_NANOPUB = 1200
 
+RSA_KEY_SIZE = 2048
 
 NANOPUB_GRLC_URLS = [
     "http://grlc.nanopubs.lod.labs.vu.nl/api/local/local/",
@@ -42,4 +43,4 @@
     # "https://grlc.nanopubs.knows.idlab.ugent.be/api/local/local/",
     # "http://grlc.np.scify.org/api/local/local/",
 ]
-NANOPUB_TEST_GRLC_URL = "http://test-grlc.nanopubs.lod.labs.vu.nl/api/local/local/"
+NANOPUB_TEST_GRLC_URL = "https://grlc.test.nps.knowledgepixels.com/api/local/local/"

nanopub/nanopub.py

@@ -92,6 +92,7 @@ def __init__(
         self._assertion += assertion
         self._provenance += provenance
         self._pubinfo += pubinfo
+        self._bnode_count = 0
 
         # Concatenate prefixes declarations from all provided graphs in the main graph
         for user_rdf in [assertion, provenance, pubinfo]:
@@ -157,7 +158,7 @@ def _preformat_graph(self, g: ConjunctiveGraph) -> ConjunctiveGraph:
         g.bind("orcid", ORCID)
         g.bind("ntemplate", NTEMPLATE)
         g.bind("foaf", FOAF)
-        # g = self._replace_blank_nodes(g)
+        g = self._replace_blank_nodes(g)
         return g
 
 
@@ -184,7 +185,8 @@ def sign(self) -> None:
             raise MalformedNanopubError(f"The nanopub have already been signed: {self.source_uri}")
 
         if self.is_valid:
-            signed_g = add_signature(self.rdf, self._conf.profile, self._metadata.namespace, URIRef(str(self._pubinfo.identifier)))
+            self._replace_blank_nodes(self._rdf)
+            signed_g = add_signature(self.rdf, self._conf.profile, self._metadata.namespace, self._pubinfo)
             self.update_from_signed(signed_g)
             log.info(f"Signed {self.source_uri}")
         else:
@@ -221,7 +223,6 @@ def update(self, publish=True) -> None:
             None,
         ))
         self._metadata = extract_np_metadata(self._rdf)
-        print(self._metadata)
         if publish:
             self.publish()
         else:
@@ -362,6 +363,8 @@ def profile(self, value):
     def namespace(self):
         return self._metadata.namespace
 
+
+
     @property
     def introduces_concept(self):
         concepts_introduced = list()
@@ -554,28 +557,44 @@ def _validate_nanopub_arguments(
                     "introduces_concept argument"
                 )
 
-    # TODO: we might to use it to convert blank nodes directly as URI here
-    # instead of doing it through the get_trustyuri() function
-    # def _replace_blank_nodes(self, rdf: ConjunctiveGraph) -> ConjunctiveGraph:
-    #     """Replace blank nodes.
-    #       Replace any blank nodes in the supplied RDF with a corresponding uri in the
-    #     dummy_namespace.'Blank nodes' here refers specifically to rdflib.term.BNode objects. When
-    #     publishing, the dummy_namespace is replaced with the URI of the actual nanopublication.
-    #       For example, if the nanopub's URI is www.purl.org/ABC123 then the blank node will be
-    #     replaced with a concrete URIRef of the form www.purl.org/ABC123#blanknodename where
-    #     'blanknodename' is the name of the rdflib.term.BNode object.
-    #       This is to solve the problem that a user may wish to use the nanopublication to introduce
-    #     a new concept. This new concept needs its own URI (it cannot simply be given the
-    #     nanopublication's URI), but it should still lie within the space of the nanopub.
-    #     Furthermore, the URI the nanopub is published to is not known ahead of time.
-    #     """
-    #     for s, p, o in rdf:
-    #         if isinstance(s, BNode):
-    #             rdf.remove((s, p, o))
-    #             s = self._metadata.namespace[f"_{str(s)}"]
-    #             rdf.add((s, p, o))
-    #         if isinstance(o, BNode):
-    #             rdf.remove((s, p, o))
-    #             o = self._metadata.namespace[f"_{str(o)}"]
-    #             rdf.add((s, p, o))
-    #     return rdf
+
+    def _replace_blank_nodes(self, g: ConjunctiveGraph) -> ConjunctiveGraph:
+        """Replace blank nodes.
+          Replace any blank nodes in the supplied RDF with a corresponding uri in the
+        dummy_namespace.'Blank nodes' here refers specifically to rdflib.term.BNode objects. When
+        publishing, the dummy_namespace is replaced with the URI of the actual nanopublication.
+          For example, if the nanopub's URI is www.purl.org/ABC123 then the blank node will be
+        replaced with a concrete URIRef of the form www.purl.org/ABC123#blanknodename where
+        'blanknodename' is the name of the rdflib.term.BNode object.
+          This is to solve the problem that a user may wish to use the nanopublication to introduce
+        a new concept. This new concept needs its own URI (it cannot simply be given the
+        nanopublication's URI), but it should still lie within the space of the nanopub.
+        Furthermore, the URI the nanopub is published to is not known ahead of time.
+        """
+        bnode_map: dict = {}
+        for s, p, o, c in g.quads():
+            if isinstance(s, BNode):
+                g.remove((s, p, o, c))
+                if str(s) not in bnode_map:
+                    if re.match(r'^[Na-zA-Z0-9]{33}$', str(s)):
+                        # Unnamed BNode looks like N2c21867a547345d9b8a203a7c1cd7e0c
+                        self._bnode_count += 1
+                        bnode_map[str(s)] = self._bnode_count
+                    else:
+                        bnode_map[str(s)] = str(s)
+                s = self._metadata.namespace[f"_{bnode_map[str(s)]}"]
+                g.add((s, p, o, c))
+
+            if isinstance(o, BNode):
+                g.remove((s, p, o, c))
+                if str(o) not in bnode_map:
+                    # if str(o).startswith("N") and len(str(o)) == 33:
+                    if re.match(r'^[Na-zA-Z0-9]{33}$', str(s)):
+                        self._bnode_count += 1
+                        bnode_map[str(o)] = self._bnode_count
+                    else:
+                        bnode_map[str(o)] = str(o)
+                o = self._metadata.namespace[f"_{bnode_map[str(o)]}"]
+
+                g.add((s, p, o, c))
+        return g