remove hard-wired link types & use (cached) call to remote instance

navis-org · Aug 30, 2024 · be5ee36 · be5ee36
1 parent 04b5559
commit be5ee36
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Showing 3 changed files with 10 additions and 79 deletions.
diff --git a/pymaid/config.py b/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())
diff --git a/pymaid/fetch/__init__.py b/pymaid/fetch/__init__.py
@@ -1225,7 +1225,7 @@ 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()}
@@ -1314,7 +1314,7 @@ 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,

diff --git a/pymaid/upload.py b/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)))