Merge branch 'master' into synapses

src/vfb_connect/__init__.py

@@ -1,6 +1,6 @@
 from .cross_server_tools import VfbConnect
 
 # Create an instance of VfbConnect and make it available directly
-vfb = VfbConnect()
+vfb = VfbConnect(vfb_launch=True)
 
 __all__ = ['vfb', 'VfbConnect']

src/vfb_connect/cross_server_tools.py

@@ -122,7 +122,7 @@ def __init__(self, neo_endpoint=get_default_servers()['neo_endpoint'],
 
         print("\033[32mSession Established!\033[0m")
         print("")
-        print("\033[33mType \033[35mvfb. \033[33mand press \033[35mtab\033[33m to see available queries. You can run help against any query e.g. \033[35mhelp(vfb.terms)\033[0m")
+        print("\033[33mType \033[35mvfb. \033[33mand press \033[35mtab\033[33m to see available queries. You can run help against any query e.g. \033[35mhelp(vfb.terms)\033[0m") if vfb_launch else None
 
     def __dir__(self):
         return [attr for attr in list(self.__dict__.keys()) if not attr.startswith('_')] + [attr for attr in dir(self.__class__) if not attr.startswith('_') and not attr.startswith('add_')]
@@ -852,6 +852,9 @@ def xref_2_vfb_id(self, acc=None, db='', id_type='', reverse_return=False, retur
                 else:
                     new_acc.append(xref)
             acc = new_acc
+        if isinstance(acc, list) and all(isinstance(x, int) for x in acc):
+            acc = [str(x) for x in acc]
+            print(f"Converted to strings: {acc}") if verbose else None
         if db in VFB_DBS_2_SYMBOLS.keys():
             db = VFB_DBS_2_SYMBOLS[db]
         if db not in self.get_dbs():
@@ -1418,7 +1421,7 @@ def generate_lab_colors(self, num_colors, min_distance=100, verbose=False):
         rgb_colors = []
 
         # Select the first color
-        lab_tree = KDTree([(0, 0, 0)])  # Start tree with black
+        lab_tree = KDTree([(255,255,255),(0, 0, 0)])  # Start tree with black and white
 
         # Pick colors that are far apart from each other and from black
         for lab in lab_colors[0:]:

src/vfb_connect/neo/query_wrapper.py

@@ -4,6 +4,7 @@
 import shutil
 from inspect import getfullargspec
 from string import Template
+from time import sleep
 from xml.sax import saxutils
 import pandas as pd
 import pkg_resources
@@ -609,7 +610,13 @@ def _get_Cached_TermInfo(self, short_forms: iter, summary=True, return_dataframe
             short_forms = list(chain.from_iterable(short_forms)) if any(isinstance(i, list) for i in short_forms) else short_forms
         print(f"Checking cache for results: short_forms={short_forms}") if verbose else None
         print(f"Looking for {len(short_forms)} results.") if verbose else None
-        results = self._serialize_solr_output(vfb_solr.search('*', **{'fl': 'term_info','df': 'id', 'defType': 'edismax', 'q.op': 'OR','rows': len(short_forms)+10,'fq':'{!terms f=id}'+ ','.join(short_forms)}))
+        try:
+            result = vfb_solr.search('*', **{'fl': 'term_info','df': 'id', 'defType': 'edismax', 'q.op': 'OR','rows': len(short_forms)+10,'fq':'{!terms f=id}'+ ','.join(short_forms)})
+        except Exception as e:
+            print(f"\033[33mWarning:\033[0m Cache query failed. Error: {e}")
+            sleep(15) # Sleep for 15 seconds to avoid overloading the server
+            return self._get_Cached_TermInfo(short_forms, summary=summary, return_dataframe=return_dataframe, verbose=verbose)
+        results = self._serialize_solr_output(result)
         print(f"Got {len(results)} results.") if verbose else None
         if len(short_forms) != len(results):
             print(f"Warning: Cache didn't return all results. Got {len(results)} out of {len(short_forms)}") if verbose else None

src/vfb_connect/owl/owlery_query_tools.py

@@ -1,3 +1,4 @@
+from time import sleep
 import requests
 import re
 import json
@@ -70,11 +71,16 @@ def query(self, query_type, return_type,
         if query_by_label:
             query = self.labels_2_ids(query)
         if verbose:
-            print("Running query: " + query) 
+            print("Running query: " + query)
         payload = {'object': query, 'prefixes': json.dumps(self.curies),
                    'direct': direct}
         # print(payload)
-        r = requests.get(url=owl_endpoint, params=payload)
+        try:
+            r = requests.get(url=owl_endpoint, params=payload)
+        except requests.exceptions.RequestException as e:
+            print("\033[31mConnection Error:\033[0m " + str(e))
+            sleep(15)
+            return query(query_type, return_type, query, query_by_label, direct, verbose)
         if verbose:
             print("Query URL: " + r.url)
         if r.status_code == 200:

src/vfb_connect/schema/vfb_term.py

@@ -1572,7 +1572,7 @@ def __init__(self, id=None, term: Optional[Term] = None, related_terms: Optional
         from vfb_connect import vfb
         self.vfb = vfb
         self.debug = verbose
-        self._return_type = self.vfb._return_type # Default to global version but can be set to id, name (list) or full (VFBTerms)
+        self._return_type = self.vfb._return_type if hasattr(self.vfb, '_return_type') else "full"
         if id is not None:
             if isinstance(id, list):
                 id = id[0]
@@ -1681,7 +1681,6 @@ def __init__(self, id=None, term: Optional[Term] = None, related_terms: Optional
             self._instances = None
             self._instances_ids = None
             self._instances_names = None
-            self._return_type = self.vfb._return_type # Default to global version but can be set to id, name (list) or full (VFBTerms)
             self._skeleton = None
             self._mesh = None
             self._volume = None