From a137b3663d412270fc1725d6d88cacd96f6d9bb3 Mon Sep 17 00:00:00 2001
From: Matthew Munson <matthew.munson@uni-hamburg.de>
Date: Tue, 22 May 2018 15:24:07 +0200
Subject: [PATCH 01/22] Refactored __transform (flask_nemo.__init__) to
 _transform

---
 flask_nemo/__init__.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/flask_nemo/__init__.py b/flask_nemo/__init__.py
index c594744..8bfef69 100644
--- a/flask_nemo/__init__.py
+++ b/flask_nemo/__init__.py
@@ -191,7 +191,7 @@ def __init__(self,
 
         # Reusing self._inventory across requests
         self._inventory = None
-        self.__transform = {
+        self._transform = {
             "default": None
         }
 
@@ -200,7 +200,7 @@ def __init__(self,
         }
 
         if isinstance(transform, dict):
-            self.__transform.update(transform)
+            self._transform.update(transform)
 
         self.chunker = {
             "default": type(self).default_chunker
@@ -328,10 +328,10 @@ def transform(self, work, xml, objectId, subreference=None):
         :rtype: str
         """
         # We check first that we don't have
-        if str(objectId) in self.__transform:
-            func = self.__transform[str(objectId)]
+        if str(objectId) in self._transform:
+            func = self._transform[str(objectId)]
         else:
-            func = self.__transform["default"]
+            func = self._transform["default"]
 
         # If we have a string, it means we get a XSL filepath
         if isinstance(func, str):
@@ -955,4 +955,4 @@ def _plugin_endpoint_rename(fn_name, instance):
 
     if instance and instance.namespaced:
         fn_name = "r_{0}_{1}".format(instance.name, fn_name[2:])
-    return fn_name
\ No newline at end of file
+    return fn_name

From bcc69cae02c6cd3ab617f0d83cfdccea8a1d7d5c Mon Sep 17 00:00:00 2001
From: Matthew Munson <matthew.munson@uni-hamburg.de>
Date: Tue, 22 May 2018 16:03:18 +0200
Subject: [PATCH 02/22] Changed flask.ext.nemo to flask_nemo

---
 tests/test_controller.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_controller.py b/tests/test_controller.py
index cc84c40..b023fa0 100644
--- a/tests/test_controller.py
+++ b/tests/test_controller.py
@@ -4,7 +4,7 @@
 greatly tied to the app/blueprint instance
 
 """
-from flask.ext.nemo import Nemo
+from flask_nemo import Nemo
 from mock import patch, call, Mock
 from lxml import etree
 from flask import Markup, Flask

From 23c05213c97b627aa2ec6145d3021efb6151b304 Mon Sep 17 00:00:00 2001
From: Matthew Munson <matthew.munson@uni-hamburg.de>
Date: Tue, 22 May 2018 16:10:08 +0200
Subject: [PATCH 03/22] Updated CHANGES.md and setup.py

Bumped to version 1.0.3
---
 CHANGES.mD | 7 +++++++
 setup.py   | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/CHANGES.mD b/CHANGES.mD
index b51398e..78186c4 100644
--- a/CHANGES.mD
+++ b/CHANGES.mD
@@ -1,6 +1,13 @@
 Change logs
 ===
 
+## 1.0.3 - 22/05/2018
+
+By @sonofmun
+
+- Refactored __transform (in flask_nemo.__init__) to _transform. This will make it available to class extensions.
+- Changed a single occurrence of "import flask.ext.nemo" in the tests to "import flask_nemo"
+
 ## 1.0.2 - 26/01/2017
 
 By @ponteineptique
diff --git a/setup.py b/setup.py
index 1538eab..8bf6ce9 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,6 @@
 from setuptools import setup, find_packages
 
-version = "1.0.2"
+version = "1.0.3"
 
 setup(
     name='flask_nemo',

From 8d91f2c05b925a6c8ea8c997baf698c87257bc58 Mon Sep 17 00:00:00 2001
From: Matthew Munson <matthew.munson@uni-hamburg.de>
Date: Tue, 22 May 2018 16:16:42 +0200
Subject: [PATCH 04/22] Release 1.0.3

* Refactored __transform (flask_nemo.__init__) to _transform
* Changed flask.ext.nemo to flask_nemo
* Updated CHANGES.md and setup.py
* Bumped to version 1.0.3
---
 CHANGES.mD               |  7 +++++++
 flask_nemo/__init__.py   | 12 ++++++------
 setup.py                 |  2 +-
 tests/test_controller.py |  2 +-
 4 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/CHANGES.mD b/CHANGES.mD
index b51398e..78186c4 100644
--- a/CHANGES.mD
+++ b/CHANGES.mD
@@ -1,6 +1,13 @@
 Change logs
 ===
 
+## 1.0.3 - 22/05/2018
+
+By @sonofmun
+
+- Refactored __transform (in flask_nemo.__init__) to _transform. This will make it available to class extensions.
+- Changed a single occurrence of "import flask.ext.nemo" in the tests to "import flask_nemo"
+
 ## 1.0.2 - 26/01/2017
 
 By @ponteineptique
diff --git a/flask_nemo/__init__.py b/flask_nemo/__init__.py
index c594744..8bfef69 100644
--- a/flask_nemo/__init__.py
+++ b/flask_nemo/__init__.py
@@ -191,7 +191,7 @@ def __init__(self,
 
         # Reusing self._inventory across requests
         self._inventory = None
-        self.__transform = {
+        self._transform = {
             "default": None
         }
 
@@ -200,7 +200,7 @@ def __init__(self,
         }
 
         if isinstance(transform, dict):
-            self.__transform.update(transform)
+            self._transform.update(transform)
 
         self.chunker = {
             "default": type(self).default_chunker
@@ -328,10 +328,10 @@ def transform(self, work, xml, objectId, subreference=None):
         :rtype: str
         """
         # We check first that we don't have
-        if str(objectId) in self.__transform:
-            func = self.__transform[str(objectId)]
+        if str(objectId) in self._transform:
+            func = self._transform[str(objectId)]
         else:
-            func = self.__transform["default"]
+            func = self._transform["default"]
 
         # If we have a string, it means we get a XSL filepath
         if isinstance(func, str):
@@ -955,4 +955,4 @@ def _plugin_endpoint_rename(fn_name, instance):
 
     if instance and instance.namespaced:
         fn_name = "r_{0}_{1}".format(instance.name, fn_name[2:])
-    return fn_name
\ No newline at end of file
+    return fn_name
diff --git a/setup.py b/setup.py
index 1538eab..8bf6ce9 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,6 @@
 from setuptools import setup, find_packages
 
-version = "1.0.2"
+version = "1.0.3"
 
 setup(
     name='flask_nemo',
diff --git a/tests/test_controller.py b/tests/test_controller.py
index cc84c40..b023fa0 100644
--- a/tests/test_controller.py
+++ b/tests/test_controller.py
@@ -4,7 +4,7 @@
 greatly tied to the app/blueprint instance
 
 """
-from flask.ext.nemo import Nemo
+from flask_nemo import Nemo
 from mock import patch, call, Mock
 from lxml import etree
 from flask import Markup, Flask

From 1a44dad5ea7fd189521a5ba3022639bf87e12c40 Mon Sep 17 00:00:00 2001
From: Ralph Giles <giles@thaumas.net>
Date: Thu, 4 Jul 2019 14:19:31 -0700
Subject: [PATCH 05/22] Fix collections DeprecationWarning.

Since Python 3.3, the Abstract Base Classes for the collections
package have been available on the collections.abc module,
and since Python 3.7 loading them from the main module path
has been deprecated.

Update the import to use the new path, silencing the warning
and avoiding errors with future Python releases.

This doesn't work with Python 2, but that doesn't seem to be
supported. If necessary, support can be added by wrapping the
import in a try block:

    try:
        from collections.abc import Callable
    except ImportError:
        # Python 2
        from collections import Callable

That will fall back to the old method.
---
 flask_nemo/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/flask_nemo/__init__.py b/flask_nemo/__init__.py
index 8bfef69..9562f48 100644
--- a/flask_nemo/__init__.py
+++ b/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
 

From b0b81ce1b1194cfb4780fa0c53a8757fb8ff5a38 Mon Sep 17 00:00:00 2001
From: Ralph Giles <giles@thaumas.net>
Date: Thu, 4 Jul 2019 14:27:13 -0700
Subject: [PATCH 06/22] Fix invalid escape sequence warning.

Python 3.7 warns about unrecognized escape sequences in strings,
which causes problems with regular expression patterns like `\s`.
Use raw strings instead, allowing the re package to do the correct
expansion itself.

Also switch to single quotes so it's not necessary to escape the
double quotes around html attribute values.
---
 tests/test_browse.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/test_browse.py b/tests/test_browse.py
index 823738f..e2941b1 100644
--- a/tests/test_browse.py
+++ b/tests/test_browse.py
@@ -258,15 +258,15 @@ def test_main_collections(self):
         """
         query_data = self.client.get("/collections").data.decode()
         self.assertRegex(
-            query_data, "Classical Latin<br />\s*<a class=\"card-link\" href=\"/collections/urn:perseus:latinLit",
+            query_data, r'Classical Latin<br />\s*<a class="card-link" href="/collections/urn:perseus:latinLit',
             "Link to classical latin main collection should be found"
         )
         self.assertRegex(
-            query_data, "Farsi<br />\s*<a class=\"card-link\" href=\"/collections/urn:perseus:farsiLit",
+            query_data, r'Farsi<br />\s*<a class="card-link" href="/collections/urn:perseus:farsiLit',
             "Link to farsi main collection should be found"
         )
         self.assertRegex(
-            query_data, "Ancient Greek<br />\s*<a class=\"card-link\" href=\"/collections/urn:perseus:greekLit",
+            query_data, r'Ancient Greek<br />\s*<a class="card-link" href="/collections/urn:perseus:greekLit',
             "Link to farsi main collection should be found"
         )
 

From e2d475c7d50a4fde7de4951fd8f7cf5547a6c97d Mon Sep 17 00:00:00 2001
From: Ralph Giles <giles@thaumas.net>
Date: Thu, 4 Jul 2019 14:35:24 -0700
Subject: [PATCH 07/22] Fix invalid escape sequence warning.

Python 3.7 warns about unrecognized escape sequences in strings.

Remove the backslash escapes for the `/` character. This doesn't
need to be escaped for re match patterns; it only has special
meaning in sed-style substitution patterns.

Another possible fix is to use raw strings, r"^(https?:)?\/\/"
which leave the backslash characters to the re package to
interpret. It doesn't mind the sequences, but they're still
unnecessary.
---
 flask_nemo/query/resolve.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/flask_nemo/query/resolve.py b/flask_nemo/query/resolve.py
index 591f3a7..9345155 100644
--- a/flask_nemo/query/resolve.py
+++ b/flask_nemo/query/resolve.py
@@ -62,7 +62,7 @@ def read(self, uri):
 class HTTPRetriever(RetrieverPrototype):
     """ Http retriever retrieves resources being remotely hosted in CTS
     """
-    __reg_exp__ = re.compile("^(https?:)?\/\/")
+    __reg_exp__ = re.compile("^(https?:)?//")
 
     def match(self, uri):
         """ Check to see if this URI is retrievable by this Retriever implementation

From 2e87aa26a0444843f9814207031c4756a03097e9 Mon Sep 17 00:00:00 2001
From: Ralph Giles <giles@thaumas.net>
Date: Thu, 4 Jul 2019 14:36:17 -0700
Subject: [PATCH 08/22] Fix root URL warning.

Nemo warns about (and corrects) an explicit base_url="/"
parameter, requiring an empty string instead. However, all
TestSimpleQuery tests pass this as part of their instance
config, cluttering the output with warnings. This is
especially obvious with the pytest wrapper.

Avoid the warning by passing the indicated base_url="" instead.
---
 tests/test_query/test_interface.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_query/test_interface.py b/tests/test_query/test_interface.py
index f6a8a36..6dfda5d 100644
--- a/tests/test_query/test_interface.py
+++ b/tests/test_query/test_interface.py
@@ -55,7 +55,7 @@ def setUp(self):
         logger = logging.getLogger('my-logger')
         logger.propagate = False
         self.nautilus = CtsCapitainsLocalResolver(["tests/test_data/interface/latinLit"], logger=logger)
-        self.nemo = Nemo(app=self.app, resolver=self.nautilus, base_url="/")
+        self.nemo = Nemo(app=self.app, resolver=self.nautilus, base_url="")
         self.query = SimpleQuery(
             [
                 self.one,

From c32635f27ad5c08fe003abb03a8f33d22c75ff5d Mon Sep 17 00:00:00 2001
From: Matthew Munson <matthew.munson@uni-hamburg.de>
Date: Tue, 22 Oct 2019 11:20:58 +0200
Subject: [PATCH 09/22] Corrected a class name and a test

---
 flask_nemo/chunker.py    | 2 +-
 tests/test_controller.py | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/flask_nemo/chunker.py b/flask_nemo/chunker.py
index dfb1337..c00f978 100644
--- a/flask_nemo/chunker.py
+++ b/flask_nemo/chunker.py
@@ -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).split(":")[-1] for ref in getreffs(level=level)]
     _refs = OrderedDict()
 
     for key in references:
diff --git a/tests/test_controller.py b/tests/test_controller.py
index b023fa0..e1c7f59 100644
--- a/tests/test_controller.py
+++ b/tests/test_controller.py
@@ -9,7 +9,7 @@
 from lxml import etree
 from flask import Markup, Flask
 
-from MyCapytain.resources.prototypes.text import Passage
+from MyCapytain.resources.prototypes.cts.text import PrototypeCtsPassage
 from MyCapytain.common.constants import Mimetypes
 from MyCapytain.resources.prototypes.cts.inventory import CtsTextInventoryMetadata, CtsTextMetadata
 
@@ -165,7 +165,7 @@ def test_get_passage(self):
                 "urn:cts:latinLit:phi1294.phi002.perseus-lat2",
                 "1.pr"
             )
-            self.assertIsInstance(passage, Passage)
+            self.assertIsInstance(passage, PrototypeCtsPassage)
             self.assertEqual(
                 len(passage.export(Mimetypes.PYTHON.ETREE)
                     .xpath("//tei:l[@n]", namespaces={"tei": "http://www.tei-c.org/ns/1.0"})),
@@ -202,5 +202,5 @@ def test_get_siblings(self):
         # Passage with unknown range
         p = nemo.get_passage("urn:cts:latinLit:phi1294.phi002.perseus-lat2", "1.11.1-1.11.2")
         l, r = nemo.get_siblings("urn:cts:latinLit:phi1294.phi002.perseus-lat2", "1.11.1-1.11.2", p)
-        self.assertEqual(l, "1.10.3-1.10.4", "Passage should be computed specifically if texts have unknown range")
-        self.assertEqual(r, "1.11.3-1.11.4", "Passage should be computed specifically if texts have unknown range")
+        self.assertEqual(l, ('1.10.3', '1.10.4'), "Passage should be computed specifically if texts have unknown range")
+        self.assertEqual(r, ("1.11.3", "1.11.4"), "Passage should be computed specifically if texts have unknown range")

From fc8b8661b26f99e1e13496850956054fb383ba73 Mon Sep 17 00:00:00 2001
From: Matthew Munson <matthew.munson@uni-hamburg.de>
Date: Tue, 22 Oct 2019 11:26:29 +0200
Subject: [PATCH 10/22] Updated MyCapytain requirement to be >=3.0.0

---
 requirements.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 179b817..8a8e909 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
-MyCapytain>=2.0.0
+MyCapytain>=3.0.0
 requests_cache>=0.4.9
 Flask>=0.12.0
 Flask-Caching>=1.2.0
-python-slugify==1.2.1
\ No newline at end of file
+python-slugify==1.2.1

From 65516ed3e7348167022534305f3c9b4e49ac2dfe Mon Sep 17 00:00:00 2001
From: Matthew Munson <matthew.munson@uni-hamburg.de>
Date: Tue, 22 Oct 2019 14:44:39 +0200
Subject: [PATCH 11/22] Corrected an incompatibility in query/interface.py

All tests now pass with MyCapytain 3.0.0 and Nautilus dts-draft-1
---
 flask_nemo/query/interface.py | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/flask_nemo/query/interface.py b/flask_nemo/query/interface.py
index 2e05376..5680db2 100644
--- a/flask_nemo/query/interface.py
+++ b/flask_nemo/query/interface.py
@@ -1,4 +1,5 @@
 from MyCapytain.common.reference import URN
+from MyCapytain.errors import CitationDepthError
 from flask_nemo.query.proto import QueryPrototype
 from flask_nemo.query.annotation import AnnotationResource
 from werkzeug.exceptions import NotFound
@@ -122,14 +123,19 @@ def __getinnerreffs__(self, objectId, subreference):
         level = 0
         yield subreference
         while level > -1:
-            reffs = self.__nemo__.resolver.getReffs(
-                objectId,
-                subreference=subreference,
-                level=level
-            )
+            try:
+                reffs = self.__nemo__.resolver.getReffs(
+                    objectId,
+                    subreference=subreference,
+                    level=level
+                )
+            # This is the new behavior in MyCapytain 3.0.0
+            except CitationDepthError:
+                break
+            # This is the old behavior kept for backward compatibility.
             if len(reffs) == 0:
                 break
             else:
                 for r in reffs:
-                    yield r
+                    yield r[0]  # only the first member of the CtsReferenceSet is needed here.
                 level += 1

From d29d07caa3efe2c98f4d8fc84aa8b5eb59be3407 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thibault=20Cl=C3=A9rice?= <leponteineptique@gmail.com>
Date: Tue, 22 Oct 2019 14:50:13 +0200
Subject: [PATCH 12/22] Remove 3.4.5 because of lxml dependancy

---
 .travis.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 24720c8..b694508 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,6 +1,5 @@
 language: python
 python:
-  - "3.4.5"
   - "3.5"
   - "3.6"
 # command to install dependencies

From 4a3e67f9e12689e612483b1457ab1727b4b38883 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thibault=20Cl=C3=A9rice?= <leponteineptique@gmail.com>
Date: Tue, 22 Oct 2019 14:55:04 +0200
Subject: [PATCH 13/22] (Query) Moved from double underscore to private
 variables in query module classes

---
 flask_nemo/query/annotation.py | 48 +++++++++++++++++-----------------
 flask_nemo/query/interface.py  | 30 ++++++++++-----------
 flask_nemo/query/proto.py      |  2 +-
 flask_nemo/query/resolve.py    | 22 ++++++++--------
 4 files changed, 51 insertions(+), 51 deletions(-)

diff --git a/flask_nemo/query/annotation.py b/flask_nemo/query/annotation.py
index c097442..6249311 100644
--- a/flask_nemo/query/annotation.py
+++ b/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)
diff --git a/flask_nemo/query/interface.py b/flask_nemo/query/interface.py
index 5680db2..3bf5c16 100644
--- a/flask_nemo/query/interface.py
+++ b/flask_nemo/query/interface.py
@@ -23,22 +23,22 @@ class SimpleQuery(QueryPrototype):
 
     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
@@ -47,16 +47,16 @@ 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
@@ -66,7 +66,7 @@ def __get_resource_metadata__(self, objectId):
 
     @property
     def annotations(self):
-        return self.__annotations__
+        return self._annotations
 
     def getResource(self, sha):
         try:
@@ -92,7 +92,7 @@ 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
             ))
@@ -110,7 +110,7 @@ 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):
         """ Resolve the list of urns between in a range
 
         :param text_metadata: Resource Metadata
@@ -124,7 +124,7 @@ def __getinnerreffs__(self, objectId, subreference):
         yield subreference
         while level > -1:
             try:
-                reffs = self.__nemo__.resolver.getReffs(
+                reffs = self._nemo.resolver.getReffs(
                     objectId,
                     subreference=subreference,
                     level=level
diff --git a/flask_nemo/query/proto.py b/flask_nemo/query/proto.py
index fe0da00..4d7627c 100644
--- a/flask_nemo/query/proto.py
+++ b/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):
diff --git a/flask_nemo/query/resolve.py b/flask_nemo/query/resolve.py
index 9345155..91f44de 100644
--- a/flask_nemo/query/resolve.py
+++ b/flask_nemo/query/resolve.py
@@ -19,7 +19,7 @@ class Resolver(object):
     """
 
     def __init__(self, *retrievers, **kwargs):
-        self.__retrievers__ = retrievers
+        self._retrievers = retrievers
 
     def resolve(self, uri):
         """ Resolve a Resource identified by URI
@@ -28,7 +28,7 @@ def resolve(self, uri):
         :return: the contents of the resource as a string
         :rtype: str
         """
-        for r in self.__retrievers__:
+        for r in self._retrievers:
             if r.match(uri):
                 return r
         raise UnresolvableURIError()
@@ -62,7 +62,7 @@ def read(self, uri):
 class HTTPRetriever(RetrieverPrototype):
     """ Http retriever retrieves resources being remotely hosted in CTS
     """
-    __reg_exp__ = re.compile("^(https?:)?//")
+    _reg_exp = re.compile("^(https?:)?//")
 
     def match(self, uri):
         """ Check to see if this URI is retrievable by this Retriever implementation
@@ -73,7 +73,7 @@ def match(self, uri):
         :rtype: bool
         """
         # prototype implementation can't retrieve anything!
-        return HTTPRetriever.__reg_exp__.match(uri) is not None
+        return HTTPRetriever._reg_exp.match(uri) is not None
 
     def read(self, uri):
         """ Retrieve the contents of the resource
@@ -99,7 +99,7 @@ class LocalRetriever(RetrieverPrototype):
     def __init__(self, path="./"):
         self.__path__ = op.abspath(path)
 
-    def __absolute__(self, uri):
+    def _absolute(self, uri):
         """ Get the absolute uri for a file
 
         :param uri: URI of the resource to be retrieved
@@ -115,7 +115,7 @@ def match(self, uri):
         :return: True if it can be, False if not
         :rtype: bool
         """
-        absolute_uri = self.__absolute__(uri)
+        absolute_uri = self._absolute(uri)
 
         return absolute_uri.startswith(self.__path__) and op.exists(absolute_uri)
 
@@ -127,7 +127,7 @@ def read(self, uri):
         :return: the contents of the resource
         :rtype: str
         """
-        uri = self.__absolute__(uri)
+        uri = self._absolute(uri)
         mime, _ = guess_type(uri)
         if "image" in mime:
             return send_file(uri), mime
@@ -145,10 +145,10 @@ class CTSRetriever(RetrieverPrototype):
     :param resolver: CTS5 Resolver
     :type resolver: MyCapytain.resolver.cts.*
     """
-    __reg_exp__ = re.compile("^urn:cts:")
+    _reg_exp = re.compile("^urn:cts:")
 
     def __init__(self, resolver):
-        self.__resolver__ = resolver
+        self._resolver = resolver
 
     @staticmethod
     def match(uri):
@@ -160,7 +160,7 @@ def match(uri):
         :rtype: bool
         """
         # prototype implementation can't retrieve anything!
-        return CTSRetriever.__reg_exp__.match(uri) is not None
+        return CTSRetriever._reg_exp.match(uri) is not None
 
     def read(self, uri):
         """ Retrieve the contents of the resource
@@ -170,4 +170,4 @@ def read(self, uri):
         :return: the contents of the resource
         :rtype: str
         """
-        return self.__resolver__.getTextualNode(uri).export(Mimetypes.XML.TEI), "text/xml"
+        return self._resolver.getTextualNode(uri).export(Mimetypes.XML.TEI), "text/xml"

From ea96fdc1a83fe609244869e2e0cd8127ea262cff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thibault=20Cl=C3=A9rice?= <leponteineptique@gmail.com>
Date: Tue, 22 Oct 2019 14:56:19 +0200
Subject: [PATCH 14/22] (Annotation API) Moving away from double underscord
 with private vars in Annotations APIs

---
 flask_nemo/plugins/annotations_api.py      | 14 +++++++-------
 tests/test_plugins/test_annotations_api.py |  2 +-
 tests/test_query/test_retriever.py         |  2 +-
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/flask_nemo/plugins/annotations_api.py b/flask_nemo/plugins/annotations_api.py
index 020b056..44c2d56 100644
--- a/flask_nemo/plugins/annotations_api.py
+++ b/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
diff --git a/tests/test_plugins/test_annotations_api.py b/tests/test_plugins/test_annotations_api.py
index 87e6470..83c4474 100644
--- a/tests/test_plugins/test_annotations_api.py
+++ b/tests/test_plugins/test_annotations_api.py
@@ -37,7 +37,7 @@ def getResource(self, sha):
             annotation.read = lambda: Response("a", headers={"Content-Type": "text/plain"})
             annotation.read = lambda: Response("a", headers={"Content-Type": "text/plain"})
         else:
-            annotation.__mimetype__ = "application/xml"
+            annotation._mimetype = "application/xml"
             annotation.read = lambda: "123"
         return annotation
 
diff --git a/tests/test_query/test_retriever.py b/tests/test_query/test_retriever.py
index 99970e8..e908880 100644
--- a/tests/test_query/test_retriever.py
+++ b/tests/test_query/test_retriever.py
@@ -168,7 +168,7 @@ def test_retrieve_resource(self):
             if sendfile:
                 with patch("flask_nemo.query.resolve.send_file", return_value=content) as patched:
                     data, mimetype = ret.read(uri)
-                    patched.assert_called_with(ret.__absolute__(uri))
+                    patched.assert_called_with(ret._absolute(uri))
             else:
                 data, mimetype = ret.read(uri)
 

From d462b66920092c9e3cb2982fce46b663fd252be5 Mon Sep 17 00:00:00 2001
From: Matthew Munson <matthew.munson@uni-hamburg.de>
Date: Tue, 22 Oct 2019 15:00:21 +0200
Subject: [PATCH 15/22] Removed lines that are not needed now that requirements
 include MyCapytain 3.0.0

---
 .travis.yml                   | 2 +-
 flask_nemo/query/interface.py | 3 ---
 2 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 24720c8..8b2bd53 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -19,4 +19,4 @@ deploy:
   password: $PYPASS
   on:
     tags: true
-    python: "3.5"
\ No newline at end of file
+    python: "3.5"
diff --git a/flask_nemo/query/interface.py b/flask_nemo/query/interface.py
index 5680db2..8356586 100644
--- a/flask_nemo/query/interface.py
+++ b/flask_nemo/query/interface.py
@@ -132,9 +132,6 @@ def __getinnerreffs__(self, objectId, subreference):
             # This is the new behavior in MyCapytain 3.0.0
             except CitationDepthError:
                 break
-            # This is the old behavior kept for backward compatibility.
-            if len(reffs) == 0:
-                break
             else:
                 for r in reffs:
                     yield r[0]  # only the first member of the CtsReferenceSet is needed here.

From b3c291cf353795ff1a1aee73674944a27a9de86a Mon Sep 17 00:00:00 2001
From: Matthew Munson <matthew.munson@uni-hamburg.de>
Date: Tue, 22 Oct 2019 15:09:50 +0200
Subject: [PATCH 16/22] Updated setup.py and CHANGES.mD for version 1.1.0

---
 CHANGES.mD | 7 +++++++
 setup.py   | 6 +++---
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/CHANGES.mD b/CHANGES.mD
index 78186c4..eb9c94f 100644
--- a/CHANGES.mD
+++ b/CHANGES.mD
@@ -1,6 +1,13 @@
 Change logs
 ===
 
+## 1.1.0 - 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.
+
 ## 1.0.3 - 22/05/2018
 
 By @sonofmun
diff --git a/setup.py b/setup.py
index 8bf6ce9..42cc23f 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,6 @@
 from setuptools import setup, find_packages
 
-version = "1.0.3"
+version = "1.1.0"
 
 setup(
     name='flask_nemo',
@@ -10,10 +10,10 @@
     license='Mozilla Public License Version 2.0',
     author='Thibault Clerice',
     author_email='leponteineptique@gmail.com',
-    description='Flask Extension to browse CTS Repository',
+    description='Flask Extension to browse a CapiTainS-compliant Repository',
     test_suite="tests",
     install_requires=[
-        "MyCapytain>=2.0.0",
+        "MyCapytain>=3.0.0",
         "requests_cache>=0.4.9",
         "Flask>=0.12",
         "requests>=2.10.0",

From 4de83230f42ff4f6f19aa7ba0b745ffddecd4a62 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thibault=20Cl=C3=A9rice?= <leponteineptique@gmail.com>
Date: Tue, 22 Oct 2019 15:29:21 +0200
Subject: [PATCH 17/22] Comment and review on annotation interface for PR
 review

---
 flask_nemo/query/interface.py | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/flask_nemo/query/interface.py b/flask_nemo/query/interface.py
index 5d80e32..7e8050c 100644
--- a/flask_nemo/query/interface.py
+++ b/flask_nemo/query/interface.py
@@ -1,4 +1,4 @@
-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
@@ -21,6 +21,10 @@ 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 = []
@@ -110,7 +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
@@ -122,9 +126,10 @@ def _getinnerreffs(self, objectId, subreference):
         """
         level = 0
         yield subreference
+
         while level > -1:
             try:
-                reffs = self._nemo.resolver.getReffs(
+                reffs: BaseReferenceSet = self._nemo.resolver.getReffs(
                     objectId,
                     subreference=subreference,
                     level=level
@@ -134,5 +139,7 @@ def _getinnerreffs(self, objectId, subreference):
                 break
             else:
                 for r in reffs:
-                    yield r[0]  # only the first member of the CtsReferenceSet is needed here.
+                    # We only needs the start of the reference here,
+                    # because we specifically want to drop ranges here.
+                    yield r.start
                 level += 1

From 3ad33478a7769d27fa2690d7f0584a221c87d1f4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thibault=20Cl=C3=A9rice?= <leponteineptique@gmail.com>
Date: Tue, 22 Oct 2019 15:39:51 +0200
Subject: [PATCH 18/22] Add typing as dependency

---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index 8a8e909..ab69769 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,3 +3,4 @@ requests_cache>=0.4.9
 Flask>=0.12.0
 Flask-Caching>=1.2.0
 python-slugify==1.2.1
+typing
\ No newline at end of file

From 8370985361edc0f2aa21150b55a0f5db49bb2e7b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thibault=20Cl=C3=A9rice?= <leponteineptique@gmail.com>
Date: Tue, 22 Oct 2019 16:57:50 +0200
Subject: [PATCH 19/22] (Migration) Add a better check for knowing if something
 is readable

---
 flask_nemo/__init__.py                    | 1 +
 flask_nemo/data/templates/collection.html | 2 +-
 setup.py                                  | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/flask_nemo/__init__.py b/flask_nemo/__init__.py
index 9562f48..476ccaf 100644
--- a/flask_nemo/__init__.py
+++ b/flask_nemo/__init__.py
@@ -499,6 +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,
diff --git a/flask_nemo/data/templates/collection.html b/flask_nemo/data/templates/collection.html
index bbf0a3c..520f6ed 100644
--- a/flask_nemo/data/templates/collection.html
+++ b/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>
diff --git a/setup.py b/setup.py
index 42cc23f..728948a 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,6 @@
 from setuptools import setup, find_packages
 
-version = "1.1.0"
+version = "2.0.0"
 
 setup(
     name='flask_nemo',

From 5b849a0bc422588cdc7c5cb50e337c8d467a19cf Mon Sep 17 00:00:00 2001
From: Matthew Munson <matthew.munson@uni-hamburg.de>
Date: Thu, 24 Oct 2019 16:03:47 +0200
Subject: [PATCH 20/22] The chunkers should now work with MyCapytain 3.0

---
 flask_nemo/chunker.py  |  10 +--
 tests/test_chunkers.py | 147 ++++++++++++++++++++++++++---------------
 2 files changed, 97 insertions(+), 60 deletions(-)

diff --git a/flask_nemo/chunker.py b/flask_nemo/chunker.py
index c00f978..a3de8d7 100644
--- a/flask_nemo/chunker.py
+++ b/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 = [str(ref).split(":")[-1] for ref in getreffs(level=level)]
+    references = [str(ref) for ref in getreffs(level=level)]
     _refs = OrderedDict()
 
     for key in references:
diff --git a/tests/test_chunkers.py b/tests/test_chunkers.py
index 2a4e248..1a922a0 100644
--- a/tests/test_chunkers.py
+++ b/tests/test_chunkers.py
@@ -7,9 +7,8 @@
 
 """
 
-from mock import patch, call, Mock
 from MyCapytain.resources.collections.cts import XmlCtsTextInventoryMetadata
-from tests.test_resources import NemoResource
+from tests.test_resources import NemoResource, NautilusDummy
 from flask_nemo.chunker import default_chunker, line_chunker, scheme_chunker, level_chunker, level_grouper
 
 
@@ -19,85 +18,124 @@ def setUp(self):
         super(TestChunkers, self).setUp()
         self.inventory = XmlCtsTextInventoryMetadata.parse(resource=self.getCapabilities.text)
 
-    def make_get_reff(self, asserted_level):
-        def GetReff(level=1):
-            self.assertEqual(level, asserted_level)  # Depth of the Citation Scheme
-            return ["urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.1.7"]
-        return GetReff
-
     def test_default_chunker(self):
         """ Test default chunker
         """
         text = self.inventory["urn:cts:latinLit:phi1294.phi002.perseus-lat2"]
-        reffs = default_chunker(text, self.make_get_reff(3))
-        self.assertEqual(reffs, [
-            ("1.pr.5", "1.pr.5"),
-            ("1.1.7", "1.1.7")
-        ])
-        default_chunker(self.inventory["urn:cts:latinLit:phi0959.phi003.perseus-lat2"], self.make_get_reff(2))
+        reffs = default_chunker(text, lambda level: NautilusDummy.getReffs('urn:cts:latinLit:phi1294.phi002.perseus-lat2',
+                                                                           level=3))
+        self.assertIn(("1.pr.1", "1.pr.1"), reffs)
+        self.assertIn(('1.1.6', '1.1.6'), reffs)
 
     def test_line_chunker(self):
         """ Test line grouping chunker
         """
-        def validReff(level):
-            self.assertEqual(level, 3)
-            return ["urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.1","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.2","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.3","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.4","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.5","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.6","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.7","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.8","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.9","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.10","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.11","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.12","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.13","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.14","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.15","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.16","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.17","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.18","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.19","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.20","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.21","urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.22"]
-
-        reffs = line_chunker(self.inventory["urn:cts:latinLit:phi1294.phi002.perseus-lat2"], validReff, 5)
-        self.assertEqual(reffs, [
-            ("1.pr.1-1.pr.5","1.pr.1"),
-            ("1.pr.6-1.pr.10","1.pr.6"),
-            ("1.pr.11-1.pr.15","1.pr.11"),
-            ("1.pr.16-1.pr.20","1.pr.16"),
-            ("1.pr.21-1.pr.22","1.pr.21")
-        ])
-
-        reffs = line_chunker(self.inventory["urn:cts:latinLit:phi1294.phi002.perseus-lat2"], validReff, 11)
-        self.assertEqual(reffs, [
-            ("1.pr.1-1.pr.11","1.pr.1"),
-            ("1.pr.12-1.pr.22","1.pr.12")
-        ])
+
+        text = self.inventory["urn:cts:latinLit:phi1294.phi002.perseus-lat2"]
+        validReff = lambda level: NautilusDummy.getReffs('urn:cts:latinLit:phi1294.phi002.perseus-lat2', level=level)
+        reffs = line_chunker(text, validReff, 5)
+        for x in [
+            ("1.pr.1-1.pr.5", "1.pr.1"),
+            ("1.pr.6-1.pr.10", "1.pr.6"),
+            ("1.pr.11-1.pr.15", "1.pr.11"),
+            ("1.pr.16-1.pr.20", "1.pr.16"),
+            ("1.pr.21-1.1.3", "1.pr.21") # should cross over the boundary of the single poem
+        ]:
+            self.assertIn(x, reffs)
+
+        reffs = line_chunker(text, validReff, 11)
+        for x in [
+            ("1.pr.1-1.pr.11", "1.pr.1"),
+            ("1.pr.12-1.pr.22", "1.pr.12")
+        ]:
+            self.assertIn(x, reffs)
 
     def test_scheme_chunker(self):
         """ Test chunking according to scheme
         """
-        text = self.inventory["urn:cts:latinLit:phi1294.phi002.perseus-lat2"] # book, poem
-        reffs = scheme_chunker(text, self.make_get_reff(2))
-        self.assertEqual(reffs, [
-            ("1.pr.5", "1.pr.5"),
-            ("1.1.7", "1.1.7")
-        ])
-
-        with patch("flask_nemo.chunker.line_chunker", return_value=True) as line_chunker:
-            self.assertEqual(scheme_chunker(
-                self.inventory["urn:cts:latinLit:phi0959.phi007.perseus-lat2"],
-                self.make_get_reff(2)
-            ), True)
+        # When the scheme is book, poem, line, the scheme_chunker should chunk poems together
+        text = self.inventory["urn:cts:latinLit:phi1294.phi002.perseus-lat2"] # book, poem, line
+        reffs = scheme_chunker(text, lambda level: NautilusDummy.getReffs('urn:cts:latinLit:phi1294.phi002.perseus-lat2',
+                                                                          level=level))
+        for x in [
+            ("1.pr", "1.pr"),
+            ("2.15", "2.15")
+        ]:
+            self.assertIn(x, reffs)
+
+        # If the scheme is only book and line, the line chunker should be used
+        text = self.inventory['urn:cts:latinLit:phi0959.phi007.perseus-lat2'] # book, line
+        reffs = scheme_chunker(text, lambda level: NautilusDummy.getReffs('urn:cts:latinLit:phi1294.phi002.perseus-lat2',
+                                                                          level=level))
+        # The chunks are not actually lines but, instead, full poems.
+        # But it still shows that the scheme_chunker works correctly.
+        for x in [
+            ("1.pr-1.29", "1.pr"),
+            ("1.90-2.pr", "1.90")
+        ]:
+            self.assertIn(x, reffs)
+
+        # If the scheme does not contain poem, then it should use the default chunker
+        text = NautilusDummy.getMetadata('urn:cts:latinLit:stoa0275.stoa027.perseus-lat2') # chapter, section
+        reffs = scheme_chunker(text, lambda level: NautilusDummy.getReffs('urn:cts:latinLit:stoa0275.stoa027.perseus-lat2',
+                                                                          level=level))
+        for x in [
+            ("1.1", "1.1"),
+            ("2.1", "2.1")
+        ]:
+            self.assertIn(x, reffs)
 
     def test_level_chunker(self):
         """ Test chunking according to scheme
         """
+        # level 1
         text = self.inventory["urn:cts:latinLit:phi1294.phi002.perseus-lat2"]  # book, poem
-        reffs = level_chunker(text, self.make_get_reff(2), level=2)
-        """ A test is run with make_get_reff """
+        reffs = level_chunker(text, lambda level: NautilusDummy.getReffs('urn:cts:latinLit:phi1294.phi002.perseus-lat2',
+                                                                          level=level), level=1)
+        for x in [
+            ("1", "1"),
+            ("2", "2")
+        ]:
+            self.assertIn(x, reffs)
+
+        # level 2
+        text = self.inventory["urn:cts:latinLit:phi1294.phi002.perseus-lat2"]  # book, poem
+        reffs = level_chunker(text, lambda level: NautilusDummy.getReffs('urn:cts:latinLit:phi1294.phi002.perseus-lat2',
+                                                                          level=level), level=2)
+        for x in [
+            ("1.1", "1.1"),
+            ("2.1", "2.1")
+        ]:
+            self.assertIn(x, reffs)
+
+        # level 3
+        text = self.inventory["urn:cts:latinLit:phi1294.phi002.perseus-lat2"]  # book, poem
+        reffs = level_chunker(text, lambda level: NautilusDummy.getReffs('urn:cts:latinLit:phi1294.phi002.perseus-lat2',
+                                                                          level=level), level=3)
+        for x in [
+            ("1.1.1", "1.1.1"),
+            ("2.1.1", "2.1.1")
+        ]:
+            self.assertIn(x, reffs)
 
     def test_level_grouper(self):
         """ Test level grouper
         """
         text = self.inventory["urn:cts:latinLit:phi1294.phi002.perseus-lat2"]
-        data = ["urn:cts:latinLit:phi0472.phi001.perseus-lat2:1.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:1.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:1.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:1.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:1.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:1.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:1.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:1.8", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:1.9", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:1.10", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:2.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:2.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:2.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:2.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:2.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:2.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:2.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:2.8", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:2.9", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:2.10", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:2.11", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:2.12", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:2.13", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.8", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.9", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.10", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.11", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.12", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.13", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.14", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.15", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.16", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.17", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:3.18", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.8", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.9", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.10", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.11", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.12", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.13", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.14", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.15", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.16", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.17", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.18", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.19", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.20", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.21", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.22", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.23", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.24", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.25", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.26", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:4.27", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:5.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:5.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:5.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:5.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:5.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:5.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:5.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:5.8", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:5.9", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:5.10", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:5.11", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:5.12", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:5.13", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.8", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.9", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.10", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.11", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.12", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.13", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.14", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.15", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.16", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:6.17", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:7.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:7.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:7.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:7.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:7.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:7.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:7.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:7.8", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:7.9", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:7.10", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:7.11", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:7.12", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.8", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.9", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.10", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.11", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.12", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.13", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.14", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.15", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.16", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.17", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.18", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:8.19", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:9.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:9.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:9.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:9.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:9.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:9.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:9.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:9.8", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:9.9", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:9.10", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:9.11", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.8", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.9", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.10", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.11", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.12", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.13", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.14", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.15", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.16", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.17", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.18", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.19", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.20", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.21", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.22", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.23", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.24", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.25", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.26", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.27", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.28", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.29", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.30", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.31", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.32", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.33", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:10.34", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:11.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:11.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:11.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:11.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:11.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:11.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:11.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:11.8", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:11.9", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:11.10", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:11.11", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:11.12", 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"urn:cts:latinLit:phi0472.phi001.perseus-lat2:101.9", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:101.10", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:102.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:102.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:102.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:102.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:103.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:103.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:103.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:103.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:104.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:104.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:104.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:104.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:105.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:105.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:106.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:106.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:107.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:107.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:107.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:107.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:107.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:107.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:107.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:107.8", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:108.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:108.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:108.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:108.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:108.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:108.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:109.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:109.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:109.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:109.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:109.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:109.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:110.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:110.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:110.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:110.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:110.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:110.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:110.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:110.8", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:111.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:111.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:111.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:111.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:112.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:112.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:113.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:113.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:113.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:113.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:114.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:114.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:114.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:114.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:114.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:114.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:115.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:115.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:115.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:115.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:115.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:115.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:115.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:115.8", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:116.1", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:116.2", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:116.3", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:116.4", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:116.5", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:116.6", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:116.7", "urn:cts:latinLit:phi0472.phi001.perseus-lat2:116.8"]
-        curated_references = level_grouper(text, lambda level: data, level=2, groupby=10)
+        curated_references = level_grouper(text, lambda level: NautilusDummy.getReffs('urn:cts:latinLit:phi1294.phi002.perseus-lat2',
+                                                                                      level=level),
+                                           level=2, groupby=10)
 
         self.assertIn(
-            ("1.1-1.10", "1.1-1.10"),
+            ('1.pr-1.9', '1.pr-1.9'),
             curated_references
         )
         self.assertIn(
-            ("2.1-2.10", "2.1-2.10"),
+            ('2.pr-2.9', '2.pr-2.9'),
             curated_references
         )
         self.assertIn(
-            ("2.11-2.13", "2.11-2.13"),
+            ('2.90-2.93', '2.90-2.93'),
             curated_references
         )
 
@@ -105,10 +143,9 @@ def test_level_grouper(self):
             Second part of the test
         """
 
-        text = self.inventory["urn:cts:latinLit:phi1294.phi002.perseus-lat2"]
-        data = ["urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.6", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.7", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.8", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.9", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.10", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.11", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.12", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.13", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.14", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.15", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.16", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.17", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.18", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.19", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.20", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.21", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.pr.22", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.1.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.1.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.1.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.1.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.1.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.1.6", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.2.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.2.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.2.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.2.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.2.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.2.6", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.2.7", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.2.8", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.3.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.3.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.3.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.3.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.3.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.3.6", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.3.7", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.3.8", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.3.9", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.3.10", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.3.11", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.3.12", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.4.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.4.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.4.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.4.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.4.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.4.6", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.4.7", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.4.8", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.5.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.5.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.6.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.6.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.6.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.6.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.6.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.6.6", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.7.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.7.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.7.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.7.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.7.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.8.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.8.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.8.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.8.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.8.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.8.6", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.9.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.9.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.10.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.10.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.10.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.10.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.11.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.11.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.11.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.11.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.12.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.12.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.12.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.12.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.12.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.12.6", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.12.7", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.12.8", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.12.9", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.12.10", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.12.11", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.12.12", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.13.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.13.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:1.13.3"]
-        data = data + ["urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.sa", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.6", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.7", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.8", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.9", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.10", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.11", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.12", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.13", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.14", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.pr.15", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.1.1", 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"urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.77.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.77.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.77.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.77.6", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.77.7", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.77.8", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.78.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.78.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.79.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.79.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.80.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.80.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.81.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.81.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.82.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.82.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.83.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.83.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.83.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.83.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.83.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.84.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.84.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.84.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.84.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.85.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.85.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.85.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.85.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.86.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.86.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.86.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.86.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.86.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.86.6", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.86.7", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.86.8", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.86.9", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.86.10", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.86.11", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.86.12", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.87.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.87.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.88.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.88.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.89.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.89.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.89.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.89.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.89.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.89.6", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.90.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.90.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.90.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.90.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.90.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.90.6", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.90.7", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.90.8", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.90.9", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.90.10", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.91.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.91.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.91.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.91.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.91.5", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.91.6", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.91.7", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.91.8", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.92.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.92.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.92.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.92.4", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.93.1", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.93.2", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.93.3", "urn:cts:latinLit:phi1294.phi002.perseus-lat2:2.93.4"]
-        curated_references = level_grouper(text, lambda level: data, level=3, groupby=10)
+        curated_references = level_grouper(text, lambda level: NautilusDummy.getReffs('urn:cts:latinLit:phi1294.phi002.perseus-lat2',
+                                                                                      level=level),
+                                           level=3, groupby=10)
 
         self.assertIn(
             ("1.pr.1-1.pr.10", "1.pr.1-1.pr.10"),

From 76f1876920dbbb3d954360216cb3856d0ec7050d Mon Sep 17 00:00:00 2001
From: Matthew Munson <matthew.munson@uni-hamburg.de>
Date: Thu, 24 Oct 2019 16:38:27 +0200
Subject: [PATCH 21/22] A small change in typing since it does not appear to be
 compatible with Python 3.5

---
 flask_nemo/query/interface.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/flask_nemo/query/interface.py b/flask_nemo/query/interface.py
index 7e8050c..d5ded11 100644
--- a/flask_nemo/query/interface.py
+++ b/flask_nemo/query/interface.py
@@ -129,7 +129,8 @@ def _getinnerreffs(self, objectId, subreference) -> BaseReference:
 
         while level > -1:
             try:
-                reffs: BaseReferenceSet = self._nemo.resolver.getReffs(
+                # 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

From d178c778f850d921cfd13d58f5e8d96428d28daf Mon Sep 17 00:00:00 2001
From: Matthew Munson <matthew.munson@uni-hamburg.de>
Date: Fri, 25 Oct 2019 08:57:23 +0200
Subject: [PATCH 22/22] Updated version and added a test for collections
 template

---
 CHANGES.mD           | 2 +-
 tests/test_browse.py | 9 +++++++++
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/CHANGES.mD b/CHANGES.mD
index bed0e08..04d747c 100644
--- a/CHANGES.mD
+++ b/CHANGES.mD
@@ -1,7 +1,7 @@
 Change logs
 ===
 
-## 1.1.0 - 22/10/2019
+## 2.0.0 - 22/10/2019
 
 By @sonofmun
 
diff --git a/tests/test_browse.py b/tests/test_browse.py
index e2941b1..a89f6e6 100644
--- a/tests/test_browse.py
+++ b/tests/test_browse.py
@@ -407,6 +407,15 @@ def r_random(self):
                 len(set(sets)), 1, "Random has been cached and is not recomputed"
             )
 
+    def test_collection_collection_vs_version(self):
+        """ Make sure that a work is correctly displayed on the collection template"""
+        with self.client as c:
+            r = c.get('/collections/urn:cts:latinLit:phi1294.phi002', follow_redirects=True)
+            self.assertRegex(r.get_data(as_text=True), '<a.*Browse</a>\s+<a.*Read</a>')
+            # Make sure the read link is not present for a collection
+            r = c.get('/collections/urn:cts:latinLit:phi1294', follow_redirects=True)
+            self.assertNotIn(r.get_data(as_text=True), '<a.*Read</a>')
+
 
 class NemoTestBrowseWithCache(NemoTestBrowse):
     """ Do the same tests bu with a cache object """