Linting

annotator/auth.py

@@ -13,8 +13,8 @@ def __init__(self, key):
 
 
 class User(object):
-    def __init__(self, id, consumer, is_admin):
-        self.id = id
+    def __init__(self, userid, consumer, is_admin):
+        self.id = userid
         self.consumer = consumer
         self.is_admin = is_admin
 
@@ -108,7 +108,7 @@ def encode_token(token, secret):
 
 def decode_token(token, secret='', ttl=DEFAULT_TTL, verify=True):
     try:
-        if not type(token) is bytes:
+        if not isinstance(token, bytes):
             if six.PY3:
                 token = bytes(token, 'utf-8')
             else:

annotator/document.py

@@ -55,7 +55,7 @@ def _get_all_by_uris(cls, uris):
                                    # index, so ignore this sort instruction if
                                    # 'updated' appears unmapped due to an empty
                                    # index.
-                                   'ignore_unmapped': True,}}]}
+                                   'ignore_unmapped': True}}]}
 
         res = cls.es.conn.search(index=cls.es.index,
                                  doc_type=cls.__type__,

annotator/elasticsearch.py

@@ -1,7 +1,5 @@
 from __future__ import absolute_import
 
-import csv
-import json
 import logging
 import datetime
 
@@ -10,26 +8,26 @@
 import elasticsearch
 from six import iteritems
 from six.moves.urllib.parse import urlparse
-from annotator.atoi import atoi
 
 log = logging.getLogger(__name__)
 
 RESULTS_MAX_SIZE = 200
 RESULTS_DEFAULT_SIZE = 20
 
+
 class ElasticSearch(object):
     """
     Thin wrapper around an ElasticSearch connection to make connection handling
     more convenient.
 
-    Settings for the ES host and index name etcetera can still be changed in the
-    corresponding attributes before the connection (self.conn) is used.
+    Settings for the ES host and index name etcetera can still be changed in
+    the corresponding attributes before the connection (self.conn) is used.
     """
 
     def __init__(self,
-                 host = 'http://127.0.0.1:9200',
-                 index = 'annotator',
-                 authorization_enabled = False):
+                 host='http://127.0.0.1:9200',
+                 index='annotator',
+                 authorization_enabled=False):
         self.host = host
         self.index = index
         self.authorization_enabled = authorization_enabled
@@ -41,7 +39,7 @@ def _connect(self):
         parsed = urlparse(host)
 
         connargs = {
-          'host': parsed.hostname,
+            'host': parsed.hostname,
         }
 
         username = parsed.username
@@ -89,7 +87,7 @@ class _Model(dict):
 
     @classmethod
     def create_all(cls):
-        log.info("Creating index '%s'." % cls.es.index)
+        log.info("Creating index '%s'.", cls.es.index)
         conn = cls.es.conn
         try:
             conn.indices.create(cls.es.index)
@@ -100,7 +98,7 @@ def create_all(cls):
                     or e.error.startswith('InvalidIndexNameException')):
                 log.fatal("Failed to create an Elasticsearch index")
                 raise
-            log.warn("Index creation failed as index appears to already exist.")
+            log.warn("Index creation failed: index appears to already exist.")
         mapping = cls.get_mapping()
         conn.indices.put_mapping(index=cls.es.index,
                                  doc_type=cls.__type__,
@@ -130,13 +128,13 @@ def drop_all(cls):
     # It would be lovely if this were called 'get', but the dict semantics
     # already define that method name.
     @classmethod
-    def fetch(cls, id):
+    def fetch(cls, docid):
         doc = cls.es.conn.get(index=cls.es.index,
                               doc_type=cls.__type__,
                               ignore=404,
-                              id=id)
+                              id=docid)
         if doc.get('found', True):
-            return cls(doc['_source'], id=id)
+            return cls(doc['_source'], id=docid)
 
     @classmethod
     def _build_query(cls, query=None, offset=None, limit=None, sort=None, order=None):
@@ -189,7 +187,7 @@ def search_raw(cls, query=None, params=None, raw_result=False):
     def count(cls, **kwargs):
         """Like search, but only count the number of matches."""
         kwargs.setdefault('params', {})
-        kwargs['params'].update({'search_type':'count'})
+        kwargs['params'].update({'search_type': 'count'})
         res = cls.search(raw_result=True, **kwargs)
         return res['hits']['total']
 

annotator/store.py

@@ -14,6 +14,7 @@
 """
 from __future__ import absolute_import
 
+import csv
 import json
 
 from elasticsearch.exceptions import TransportError
@@ -25,6 +26,7 @@
 
 from annotator.atoi import atoi
 from annotator.annotation import Annotation
+from annotator.elasticsearch import RESULTS_MAX_SIZE
 
 store = Blueprint('store', __name__)
 
@@ -90,7 +92,7 @@ def root():
                 'read': {
                     'method': 'GET',
                     'url': url_for('.read_annotation',
-                                   id=':id',
+                                   docid=':id',
                                    _external=True),
                     'desc': "Get an existing annotation"
                 },
@@ -99,7 +101,7 @@ def root():
                     'url':
                     url_for(
                         '.update_annotation',
-                        id=':id',
+                        docid=':id',
                         _external=True),
                     'query': {
                         'refresh': {
@@ -113,7 +115,7 @@ def root():
                 'delete': {
                     'method': 'DELETE',
                     'url': url_for('.delete_annotation',
-                                   id=':id',
+                                   docid=':id',
                                    _external=True),
                     'desc': "Delete an annotation"
                 }
@@ -173,7 +175,7 @@ def create_annotation():
         refresh = request.args.get('refresh') != 'false'
         annotation.save(refresh=refresh)
 
-        location = url_for('.read_annotation', id=annotation['id'])
+        location = url_for('.read_annotation', docid=annotation['id'])
 
         return jsonify(annotation), 201, {'Location': location}
     else:
@@ -182,9 +184,9 @@ def create_annotation():
 
 
 # READ
-@store.route('/annotations/<id>')
-def read_annotation(id):
-    annotation = g.annotation_class.fetch(id)
+@store.route('/annotations/<docid>')
+def read_annotation(docid):
+    annotation = g.annotation_class.fetch(docid)
     if not annotation:
         return jsonify('Annotation not found!', status=404)
 
@@ -196,9 +198,9 @@ def read_annotation(id):
 
 
 # UPDATE
-@store.route('/annotations/<id>', methods=['POST', 'PUT'])
-def update_annotation(id):
-    annotation = g.annotation_class.fetch(id)
+@store.route('/annotations/<docid>', methods=['POST', 'PUT'])
+def update_annotation(docid):
+    annotation = g.annotation_class.fetch(docid)
     if not annotation:
         return jsonify('Annotation not found! No update performed.',
                        status=404)
@@ -209,7 +211,7 @@ def update_annotation(id):
 
     if request.json is not None:
         updated = _filter_input(request.json, UPDATE_FILTER_FIELDS)
-        updated['id'] = id  # use id from URL, regardless of what arrives in
+        updated['id'] = docid  # use id from URL, regardless of what arrives in
                             # JSON payload
 
         changing_permissions = (
@@ -238,9 +240,9 @@ def update_annotation(id):
 
 
 # DELETE
-@store.route('/annotations/<id>', methods=['DELETE'])
-def delete_annotation(id):
-    annotation = g.annotation_class.fetch(id)
+@store.route('/annotations/<docid>', methods=['DELETE'])
+def delete_annotation(docid):
+    annotation = g.annotation_class.fetch(docid)
 
     if not annotation:
         return jsonify('Annotation not found. No delete performed.',

reindex.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-import sys
 import argparse
 
 from elasticsearch import Elasticsearch
@@ -12,7 +11,8 @@
 WARNING: Documents that are created while reindexing may be lost!
 """
 
-def main(argv):
+
+def main():
     argparser = argparse.ArgumentParser(description=description)
     argparser.add_argument('old_index', help="Index to read from")
     argparser.add_argument('new_index', help="Index to write to")
@@ -39,4 +39,4 @@ def main(argv):
         reindexer.alias(new_index, alias)
 
 if __name__ == '__main__':
-    main(sys.argv)
+    main()

run.py

@@ -34,20 +34,22 @@
 
 here = os.path.dirname(__file__)
 
-def main():
+
+def main(argv):
     app = Flask(__name__)
 
     cfg_file = 'annotator.cfg'
-    if len(sys.argv) == 2:
-        cfg_file = sys.argv[1]
+    if len(argv) == 2:
+        cfg_file = argv[1]
 
     cfg_path = os.path.join(here, cfg_file)
 
     try:
         app.config.from_pyfile(cfg_path)
     except IOError:
         print("Could not find config file %s" % cfg_path, file=sys.stderr)
-        print("Perhaps you need to copy annotator.cfg.example to annotator.cfg", file=sys.stderr)
+        print("Perhaps copy annotator.cfg.example to annotator.cfg",
+              file=sys.stderr)
         sys.exit(1)
 
     if app.config.get('ELASTICSEARCH_HOST') is not None:
@@ -69,10 +71,11 @@ def main():
                 date = time.strftime('%Y-%m-%d')
                 log.fatal("Elasticsearch index mapping is incorrect! Please "
                           "reindex it. You can use reindex.py for this, e.g. "
-                          "python reindex.py --host {0} {1} {1}-{2}".format(
-                              es.host,
-                              es.index,
-                              date))
+                          "python reindex.py --host %s %s %s-%s",
+                          es.host,
+                          es.index,
+                          es.index,
+                          date)
             raise
 
     @app.before_request
@@ -108,4 +111,4 @@ def before_request():
     app.run(host=host, port=port)
 
 if __name__ == '__main__':
-    main()
+    main(sys.argv)

tests/helpers.py

@@ -5,8 +5,8 @@ def __init__(self, key='mockconsumer'):
         self.ttl = 86400
 
 class MockUser(object):
-    def __init__(self, id='alice', consumer=None):
-        self.id = id
+    def __init__(self, userid='alice', consumer=None):
+        self.id = userid
         self.consumer = MockConsumer(consumer if consumer is not None else 'mockconsumer')
         self.is_admin = False
 

tests/test_store.py

@@ -264,7 +264,6 @@ def test_update_ignore_auth_in_payload(self):
         assert_equal(upd['user'], self.user.id, "annotation 'user' field should not be futzable by API")
         assert_equal(upd['consumer'], self.user.consumer.key, "annotation 'consumer' field should not be futzable by API")
 
-
     def test_delete(self):
         kwargs = dict(text=u"Bar", id='456')
         ann = self._create_annotation(**kwargs)