Merge pull request #131 from Capitains/dev

Nemo 2.0.0

.travis.yml

@@ -18,4 +18,4 @@ deploy:
   password: $PYPASS
   on:
     tags: true
-    python: "3.5"
+    python: "3.5"

CHANGES.mD

@@ -1,6 +1,13 @@
 Change logs
 ===
 
+## 2.0.0 - 22/10/2019
+
+By @sonofmun
+
+- Minor changes to make Nemo compatible with MyCapytain 3.0.0
+- This version is no longer compatible with earlier versions of MyCapytain. Please upgrade to MyCapytain 3.0.0.
+
 ## 1.0.4 - 22/10/2019
 
 By @ponteineptique

flask_nemo/__init__.py

@@ -9,7 +9,8 @@
 from urllib.parse import quote
 from operator import itemgetter
 from warnings import warn
-from collections import Callable, OrderedDict
+from collections import OrderedDict
+from collections.abc import Callable
 from copy import deepcopy as copy
 from pkg_resources import resource_filename
 
@@ -498,6 +499,7 @@ def expose_ancestors_or_children(self, member, collection, lang=None):
         x = {
             "id": member.id,
             "label": str(member.get_label(lang)),
+            "is_resource": isinstance(member, ResourceCollection),
             "model": str(member.model),
             "type": str(member.type),
             "size": member.size,

flask_nemo/chunker.py

@@ -14,7 +14,7 @@ def default_chunker(text, getreffs):
     :rtype: [(str, str)]
     """
     level = len(text.citation)
-    return [tuple([reff.split(":")[-1]]*2) for reff in getreffs(level=level)]
+    return [tuple([str(reff)]*2) for reff in getreffs(level=level)]
 
 
 def scheme_chunker(text, getreffs):
@@ -34,7 +34,7 @@ def scheme_chunker(text, getreffs):
         level = 2
     elif types == ["book", "line"]:
         return line_chunker(text, getreffs)
-    return [tuple([reff.split(":")[-1]]*2) for reff in getreffs(level=level)]
+    return [tuple([str(reff)]*2) for reff in getreffs(level=level)]
 
 
 def line_chunker(text, getreffs, lines=30):
@@ -50,7 +50,7 @@ def line_chunker(text, getreffs, lines=30):
     :rtype: [(str, str)]
     """
     level = len(text.citation)
-    source_reffs = [reff.split(":")[-1] for reff in getreffs(level=level)]
+    source_reffs = [str(reff) for reff in getreffs(level=level)]
     reffs = []
     i = 0
     while i + lines - 1 < len(source_reffs):
@@ -72,7 +72,7 @@ def level_chunker(text, getreffs, level=1):
     :rtype: [(str, str)]
     """
     references = getreffs(level=level)
-    return [(ref.split(":")[-1], ref.split(":")[-1]) for ref in references]
+    return [(str(ref), str(ref)) for ref in references]
 
 
 def level_grouper(text, getreffs, level=None, groupby=20):
@@ -87,7 +87,7 @@ def level_grouper(text, getreffs, level=None, groupby=20):
     if level is None or level > len(text.citation):
         level = len(text.citation)
 
-    references = [ref.split(":")[-1] for ref in getreffs(level=level)]
+    references = [str(ref) for ref in getreffs(level=level)]
     _refs = OrderedDict()
 
     for key in references:

flask_nemo/data/templates/collection.html

@@ -14,7 +14,7 @@ <h1>
     <section class="card-columns">
         <ul>
         {% for coll in collections.members %}
-            {% if coll.model == 'http://w3id.org/dts-ontology/resource' %}
+            {% if coll.is_resource %}
             <li class="card">
                 [{{coll.lang}}] {{ coll.label }}<br />
                 <a class="card-link" href="{{url_for('.r_references_semantic', objectId=coll.id, semantic=coll.semantic)}}">Browse</a>

flask_nemo/plugins/annotations_api.py

@@ -34,7 +34,7 @@ class AnnotationsApiPlugin(PluginPrototype):
 
     def __init__(self, queryinterface, *args, **kwargs):
         super(AnnotationsApiPlugin, self).__init__(*args, **kwargs)
-        self.__queryinterface__ = queryinterface
+        self._queryinterface = queryinterface
 
     # TODO we should have a response at the base of annotations/api that returns link types and link relations
     # showing the next level of options 
@@ -63,13 +63,13 @@ def r_annotations(self):
             except ValueError:
                 return "invalid urn", 400
 
-            count, annotations = self.__queryinterface__.getAnnotations(urn, wildcard=wildcard, include=include,
-                                                                        exclude=exclude, limit=limit, start=start,
-                                                                        expand=expand)
+            count, annotations = self._queryinterface.getAnnotations(urn, wildcard=wildcard, include=include,
+                                                                     exclude=exclude, limit=limit, start=start,
+                                                                     expand=expand)
         else:
             #  Note that this implementation is not done for too much annotations
             #  because we do not implement pagination here
-            count, annotations = self.__queryinterface__.getAnnotations(None, limit=limit, start=start, expand=expand)
+            count, annotations = self._queryinterface.getAnnotations(None, limit=limit, start=start, expand=expand)
         mapped = []
         response = {
             "@context": type(self).JSONLD_CONTEXT,
@@ -102,7 +102,7 @@ def r_annotation(self, sha):
         :return: annotation contents
         :rtype: {str: Any}
         """
-        annotation = self.__queryinterface__.getResource(sha)
+        annotation = self._queryinterface.getResource(sha)
         if not annotation:
             return "invalid resource uri", 404
         response = {
@@ -125,7 +125,7 @@ def r_annotation_body(self, sha):
         :return: annotation contents
         :rtype: {str: Any}
         """
-        annotation = self.__queryinterface__.getResource(sha)
+        annotation = self._queryinterface.getResource(sha)
         if not annotation:
             return "invalid resource uri", 404
         # TODO this should inspect the annotation content

flask_nemo/query/annotation.py

@@ -25,16 +25,16 @@ def __init__(self, objectId, subreference=None, **kwargs):
                 subreference = None
         elif isinstance(objectId, tuple):
             objectId, subreference = objectId
-        self.__objectId__ = objectId
-        self.__subreference__ = subreference
+        self._objectId = objectId
+        self._subreference = subreference
 
     @property
     def objectId(self):
-        return self.__objectId__
+        return self._objectId
 
     @property
     def subreference(self):
-        return self.__subreference__
+        return self._subreference
 
     def to_json(self):
         """ Method to call to get a serializable object for json.dump or jsonify based on the target
@@ -84,45 +84,45 @@ class AnnotationResource(object):
     SLUG = "annotation"
 
     def __init__(self, uri, target, type_uri, resolver, target_class=Target, mimetype=None, slug=None, **kwargs):
-        self.__uri__ = uri
+        self._uri = uri
         if not isinstance(target, Target):
-            self.__target__ = target_class(target)
+            self._target = target_class(target)
         else:
-            self.__target__ = target
-        self.__type_uri__ = type_uri
-        self.__slug__ = slug or deepcopy(type(self).SLUG)
-        self.__sha__ = hashlib.sha256(
+            self._target = target
+        self._type_uri = type_uri
+        self._slug = slug or deepcopy(type(self).SLUG)
+        self._sha = hashlib.sha256(
             "{uri}::{type_uri}".format(uri=uri, type_uri=type_uri).encode('utf-8')
         ).hexdigest()
 
-        self.__content__ = None
-        self.__resolver__ = resolver
-        self.__retriever__ = None
-        self.__mimetype__ = mimetype
+        self._content = None
+        self._resolver = resolver
+        self._retriever = None
+        self._mimetype = mimetype
 
     @property
     def mimetype(self):
-        return self.__mimetype__
+        return self._mimetype
 
     @property
     def sha(self):
-        return self.__sha__
+        return self._sha
 
     @property
     def uri(self):
-        return self.__uri__
+        return self._uri
 
     @property
     def type_uri(self):
-        return self.__type_uri__
+        return self._type_uri
 
     @property
     def slug(self):
-        return self.__slug__
+        return self._slug
 
     @property
     def target(self):
-        return self.__target__
+        return self._target
 
     @property
     def expandable(self):
@@ -135,10 +135,10 @@ def read(self):
         :return: the contents of the resource
         :rtype: str or bytes or flask.response
         """
-        if not self.__content__:
-            self.__retriever__ = self.__resolver__.resolve(self.uri)
-            self.__content__, self.__mimetype__ = self.__retriever__.read(self.uri)
-        return self.__content__
+        if not self._content:
+            self._retriever = self._resolver.resolve(self.uri)
+            self._content, self._mimetype = self._retriever.read(self.uri)
+        return self._content
 
     def expand(self): 
         """ Expand the contents of the Annotation if it is expandable  (i.e. if it references  multiple resources)

flask_nemo/query/interface.py

@@ -1,4 +1,5 @@
-from MyCapytain.common.reference import URN
+from MyCapytain.common.reference import URN, BaseReferenceSet, BaseReference
+from MyCapytain.errors import CitationDepthError
 from flask_nemo.query.proto import QueryPrototype
 from flask_nemo.query.annotation import AnnotationResource
 from werkzeug.exceptions import NotFound
@@ -20,24 +21,28 @@ class SimpleQuery(QueryPrototype):
 
     """
 
+    # ToDo: We should probably make a real use (and not just test fixes)
+    #       of BaseReferenceSet and BaseReference here. This seems silly
+    #       that we are restringing stuff here.
+
     def __init__(self, annotations, resolver=None):
         super(SimpleQuery, self).__init__(None)
-        self.__annotations__ = []
-        self.__nemo__ = None
-        self.__resolver__ = resolver
+        self._annotations = []
+        self._nemo = None
+        self._resolver = resolver
 
         for resource in annotations:
             if isinstance(resource, tuple):
                 target, body, type_uri = resource
-                self.__annotations__.append(AnnotationResource(
-                    body, target, type_uri, self.__resolver__
+                self._annotations.append(AnnotationResource(
+                    body, target, type_uri, self._resolver
                 ))
             else:
-                self.__annotations__.append(resource)
+                self._annotations.append(resource)
 
     @property
     def textResolver(self):
-        return self.__nemo__.resolver
+        return self._nemo.resolver
 
     def process(self, nemo):
         """ Register nemo and parses annotations
@@ -46,16 +51,16 @@ def process(self, nemo):
 
         :param nemo: Nemo
         """
-        self.__nemo__ = nemo
-        for annotation in self.__annotations__:
+        self._nemo = nemo
+        for annotation in self._annotations:
             annotation.target.expanded = frozenset(
-                self.__getinnerreffs__(
+                self._getinnerreffs(
                     objectId=annotation.target.objectId,
                     subreference=annotation.target.subreference
                 )
             )
 
-    def __get_resource_metadata__(self, objectId):
+    def _get_resource_metadata(self, objectId):
         """ Return a metadata text object
 
         :param objectId: objectId of the text
@@ -65,7 +70,7 @@ def __get_resource_metadata__(self, objectId):
 
     @property
     def annotations(self):
-        return self.__annotations__
+        return self._annotations
 
     def getResource(self, sha):
         try:
@@ -91,7 +96,7 @@ def getAnnotations(self, targets, wildcard=".", include=None, exclude=None, limi
             else:
                 objectId, subreference = target, None
 
-            ref_in_range = list(self.__getinnerreffs__(
+            ref_in_range = list(self._getinnerreffs(
                 objectId=objectId,
                 subreference=subreference
             ))
@@ -109,7 +114,7 @@ def getAnnotations(self, targets, wildcard=".", include=None, exclude=None, limi
 
         return len(annotations), sorted(annotations, key=lambda x: x.uri)
 
-    def __getinnerreffs__(self, objectId, subreference):
+    def _getinnerreffs(self, objectId, subreference) -> BaseReference:
         """ Resolve the list of urns between in a range
 
         :param text_metadata: Resource Metadata
@@ -121,15 +126,21 @@ def __getinnerreffs__(self, objectId, subreference):
         """
         level = 0
         yield subreference
+
         while level > -1:
-            reffs = self.__nemo__.resolver.getReffs(
-                objectId,
-                subreference=subreference,
-                level=level
-            )
-            if len(reffs) == 0:
+            try:
+                # type == BaseReferenceSet. I removed the explicit typing below since it broke the tests on Python 3.5.
+                reffs = self._nemo.resolver.getReffs(
+                    objectId,
+                    subreference=subreference,
+                    level=level
+                )
+            # This is the new behavior in MyCapytain 3.0.0
+            except CitationDepthError:
                 break
             else:
                 for r in reffs:
-                    yield r
+                    # We only needs the start of the reference here,
+                    # because we specifically want to drop ranges here.
+                    yield r.start
                 level += 1

flask_nemo/query/proto.py

@@ -18,7 +18,7 @@ class QueryPrototype(object):
     MATCH_ALL = "%.%"
 
     def __init__(self, getreffs, **kwargs):
-        self.__getreffs__ = getreffs
+        self._getreffs = getreffs
 
     def getAnnotations(self, targets, wildcard=".", include=None, exclude=None, limit=None, start=1, expand=False,
                        **kwargs):