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Merged
cl117 merged 1 commit into from
Jun 30, 2026
Merged

skip clustering #154

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11 changes: 11 additions & 0 deletions flask/cluster.py
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Original file line number Diff line number Diff line change
Expand Up @@ -115,6 +115,17 @@ def uclust2clusters():

def update_clusters():
logger_.log('------------ Updating clusters ------------', True)

# Re-read config (force a fresh load, not the value cached at import) so a
# flag set at runtime via /config is honored. When skip_clustering is set,
# skip the (very slow) uclust run and keep the clusters from the previous
# run -- update_index will leave the existing clusters_dump untouched.
config_manager._config = None
if config_manager.load_config().get('skip_clustering'):
logger_.log('******** skip_clustering=true: skipping uclust, reusing previous clusters ********', True)
logger_.log('------------ Clustering skipped (previous clusters kept) ------------\n', True)
return None

logger_.log('******** Query for sequences ********', True)
sequences_response = query.query_sparql(sequence_query)
logger_.log('******** Query for sequences complete ********', True)
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14 changes: 1 addition & 13 deletions flask/config.json
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@@ -1,13 +1 @@
{
"uclust_identity": "0.8",
"elasticsearch_index_name": "part",
"pagerank_tolerance": "0.0001",
"elasticsearch_endpoint": "http://localhost:9200/",
"sparql_endpoint": "http://localhost:8890/sparql?",
"last_update_start": "none",
"last_update_end": "none",
"distributed_search": false,
"which_search": "vsearch",
"autoUpdateIndex": false,
"updateTimeInDays": "1"
}
{"uclust_identity": "0.8", "elasticsearch_index_name": "part", "pagerank_tolerance": "0.0001", "elasticsearch_endpoint": "http://localhost:9200/", "sparql_endpoint": "http://localhost:8890/sparql?", "last_update_start": "2026-06-30T15:42:11.762203", "last_update_end": "none", "distributed_search": false, "which_search": "vsearch", "autoUpdateIndex": false, "updateTimeInDays": "1", "skip_clustering": true}
3 changes: 2 additions & 1 deletion flask/explorer.py
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Expand Up @@ -76,7 +76,8 @@ def update_index():
config_manager.save_update_start_time()

clusters = cluster.update_clusters()
data_manager.save_clusters(clusters)
if clusters is not None: # None => skip_clustering, keep existing clusters_dump
data_manager.save_clusters(clusters)

uri2rank = pagerank.update_pagerank()
data_manager.save_uri2rank(uri2rank)
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