Merge pull request #217 from VirtualFlyBrain/hotfix1

removing white from the random colour selection

src/vfb_connect/cross_server_tools.py

@@ -1416,7 +1416,7 @@ 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: