Merge pull request #248 from navis-org/fix_link_types

Fix link types

pymaid/client.py

@@ -609,6 +609,10 @@ def __copy__(self):
     def __deepcopy__(self):
         return self.copy()
 
+    def __hash__(self):
+        """Hash based on server, api_token, http user, http password and project_id."""
+        return hash((self.server, self.api_token, self.http_user, self.http_password, self.project_id))
+
     def copy(self):
         """Returns a copy of this CatmaidInstance. Does not copy cache."""
         return CatmaidInstance(server=self.server,

pymaid/config.py

@@ -16,6 +16,8 @@
 
 import numpy as np
 
+from functools import lru_cache
+
 logger = logging.getLogger('pymaid')
 
 def default_logging():
@@ -116,82 +118,11 @@ def ipywidgets_installed():
     tqdm = tqdm_classic
     trange = trange_classic
 
-# Hard-wired connector types. Use this to check for what's on the server:
-# types = remote_instance.fetch(remote_instance._get_connector_types_url())
-link_types =    [{'name': 'Presynaptic',
-                  'type': 'Synaptic',
-                  'type_id': 'synaptic-connector',
-                  'relation': 'presynaptic_to',
-                  'isreciprocal': False,
-                  'cardinality': 1,
-                  'partner_reference': 'outgoing',
-                  'partner_relation': 'postsynaptic_to',
-                  'relation_id': 14},
-                 {'name': 'Postsynaptic',
-                  'type': 'Synaptic',
-                  'type_id': 'synaptic-connector',
-                  'relation': 'postsynaptic_to',
-                  'isreciprocal': False,
-                  'cardinality': None,
-                  'partner_reference': 'incoming',
-                  'partner_relation': 'presynaptic_to',
-                  'relation_id': 8},
-                 {'name': 'Abutting',
-                  'type': 'Abutting',
-                  'type_id': 'abutting-connector',
-                  'relation': 'abutting',
-                  'isreciprocal': True,
-                  'cardinality': None,
-                  'partner_reference': 'abutting',
-                  'partner_relation': 'abutting',
-                  'relation_id': 54650},
-                 {'name': 'Gap junction',
-                  'type': 'Gap junction',
-                  'type_id': 'gapjunction-connector',
-                  'relation': 'gapjunction_with',
-                  'isreciprocal': True,
-                  'cardinality': 2,
-                  'partner_reference': 'gapjunction',
-                  'partner_relation': 'gapjunction_with',
-                  'relation_id': 686364},
-                 {'name': 'Tight junction',
-                  'type': 'Tight junction',
-                  'type_id': 'tightjunction-connector',
-                  'relation': 'tightjunction_with',
-                  'isreciprocal': True,
-                  'cardinality': 2,
-                  'partner_reference': 'tightjunction',
-                  'partner_relation': 'tightjunction_with',
-                  'relation_id': 10686621},
-                 {'name': 'Desmosome',
-                  'type': 'Desmosome',
-                  'type_id': 'desmosome-connector',
-                  'relation': 'desmosome_with',
-                  'isreciprocal': True,
-                  'cardinality': 2,
-                  'partner_reference': 'desmosome',
-                  'partner_relation': 'desmosome_with',
-                  'relation_id': 10686622},
-                 {'name': 'Attachment',
-                  'type': 'Attachment',
-                  'type_id': 'attachment-connector',
-                  'relation': 'attached_to',
-                  'isreciprocal': False,
-                  'cardinality': None,
-                  'partner_reference': 'attachment',
-                  'partner_relation': 'close_to',
-                  'relation_id': 5989640},
-                 {'name': 'Close to',
-                  'type': 'Spatial',
-                  'type_id': 'spatial-connector',
-                  'relation': 'close_to',
-                  'isreciprocal': True,
-                  'cardinality': None,
-                  'partner_reference': 'close_object',
-                  'partner_relation': 'close_to',
-                  'relation_id': 6216812}]
-
 compact_skeleton_relations = {0: 'presynaptic_to',
                               1: 'postsynaptic_to',
                               2: 'gapjunction_with',
                               3: 'abutting'}
+
+@lru_cache
+def get_link_types(remote_instance):
+    return remote_instance.fetch(remote_instance._get_connector_types_url())

pymaid/fetch/__init__.py

@@ -1225,14 +1225,16 @@ def get_connectors(x, relation_type=None, tags=None, remote_instance=None):
 
     # Map hardwire connector type ID to their type name
     # ATTENTION: "attachment" can be part of any connector type
-    rel_ids = {r['relation_id']: r for r in config.link_types}
+    rel_ids = {r['relation_id']: r for r in config.get_link_types(remote_instance)}
 
     # Get connector type IDs
     cn_ids = {k: v[0][3] for k, v in data['partners'].items()}
 
-    # Map type ID to relation (also note conversion of connector ID to integer)
-    cn_type = {int(k): rel_ids.get(v, {'type': 'unknown'})['type']
-               for k, v in cn_ids.items()}
+    # Map type ID to relation; also note:
+    # 1. Conversion of connector ID to integer)
+    # 2. We're using the "name" field of the relation - this used to be "type" but
+    #    on VFB CATMAID "type" is always "Synaptic" while name can be "Presynaptic" or "Postsynaptic"
+    cn_type = {int(k): rel_ids.get(v, {}).get('name', 'unknown') for k, v in cn_ids.items()}
 
     # Map connector ID to connector type
     df['type'] = df.connector_id.map(cn_type)
@@ -1314,7 +1316,7 @@ def get_connector_links(x, with_tags=False, chunk_size=50,
     df_collection = []
     tags = {}
 
-    link_types = [l['relation'] for l in config.link_types]
+    link_types = [l['relation'] for l in config.get_link_types(remote_instance)]
 
     with config.tqdm(desc='Fetching links', total=len(skids),
                      disable=config.pbar_hide,

pymaid/upload.py

@@ -1336,7 +1336,7 @@ def link_connector(links, remote_instance=None):
                             (node_id, connector_id, 'presynaptic_to') will make node presynaptic to connector
                             (node_id, connector_id, 'postsynaptic_to') will make node postsynaptic to connector
 
-                        See ``pymaid.config.link_types`` for allowed `relation`.
+                        See ``pymaid.config.get_link_types(remote_instance)`` for allowed `relation`.
 
     remote_instance :   CatmaidInstance, optional
                         If not passed directly, will try using global.
@@ -1368,7 +1368,7 @@ def link_connector(links, remote_instance=None):
                          '(node_id, connector_id, relation)')
 
     # Make sure all relations are correct
-    ALLOWED_RELATIONS = [l['relation'] for l in config.link_types]
+    ALLOWED_RELATIONS = [l['relation'] for l in config.get_link_types(remote_instance)]
     if any([l[2] not in ALLOWED_RELATIONS for l in links]):
         raise ValueError('Tuple relationships must be either: {}'.format(', '.join(ALLOWED_RELATIONS)))