NML RAG

.gitattributes

@@ -38,4 +38,3 @@ openworm.ai_store/docstore.json filter=lfs diff=lfs merge=lfs -text
 openworm.ai_store/graph_store.json filter=lfs diff=lfs merge=lfs -text
 openworm.ai_store/image__vector_store.json filter=lfs diff=lfs merge=lfs -text
 openworm.ai_store/index_store.json filter=lfs diff=lfs merge=lfs -text
-store/embed_openai/default__vector_store.json filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -5,4 +5,3 @@
 /report.Sim_IClamp_GenericMuscleCell.txt
 /report.Sim_IClamp_GenericNeuronCell.txt
 *v.dat
-/copy_latest.sh

app.py

@@ -14,7 +14,7 @@ from openworm_ai.utils.llms import OPENAI_LLMS
 
 import socket
 
-__version__ = "0.6.0"
+__version__ = "0.5.4"
 
 
 def requires_openai_key(llm_ver):

corpus_query.py

@@ -17,8 +17,7 @@ LLM_GPT4o = "GPT4o"
 def print_(text):
     print(text)
 
-from openworm_ai.graphrag.GraphRAG_test import load_index
-'''
+
 def load_index(model):
     OLLAMA_MODEL = model.replace("Ollama:", "") if model is not LLM_GPT4o else None
 
@@ -44,7 +43,7 @@ def load_index(model):
 
     index_reloaded = load_index_from_storage(storage_context)
 
-    return index_reloaded'''
+    return index_reloaded
 
 
 def get_query_engine(index_reloaded, model, similarity_top_k=4):
@@ -132,7 +131,6 @@ def process_query(query, model=llm_ver):
     files_used = []
     for sn in response.source_nodes:
         # print(sn)
-        print(sn.metadata)
         sd = sn.metadata["source document"]
         if "et_al_" in sd:
             sd = sd.replace("WormAtlas Handbook:", "Paper: ")
@@ -184,7 +182,6 @@ if __name__ == "__main__":
     queries = [
         "What are the main types of neurons and muscles in the C. elegans pharynx?",
         "Tell me about the egg laying apparatus",
-        "Tell me about locomotion in C. elegans",
     ]
 
     for query in queries:

{store/embed_openai → openworm.ai_store}/default__vector_store.json

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:7a4ee0a77382438aebe84f4c1d4771af047afdf32a793b6ecad4731b1cacad1c
-size 134107042
+oid sha256:b17d623e2545c0002179e00586be424dbd4f276035c60fdd70b9aa6b5d26f827
+size 13814331

openworm.ai_store/docstore.json

@@ -0,0 +1,3 @@
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+oid sha256:c9aa142d8cefc9eb374dbe6f73074858fa50352249f3444defbfc9900cdb9dca
+size 2296208

openworm.ai_store/graph_store.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8e0a77744010862225c69da83c585f4f8a42fd551b044ce530dbb1eb6e16742c
+size 18

openworm.ai_store/image__vector_store.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d17ed74c1649a438e518a8dc56a7772913dfe1ea7a7605bce069c63872431455
+size 72

openworm.ai_store/index_store.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:02acbe0ae1926e1192c6110b15767773d6f50a61c6d802595be410fc6f67dff4
+size 33511

requirements.txt

@@ -1,5 +1,5 @@
 
-openworm_ai[dev]>=0.5.0
+openworm_ai[dev]>=0.3.1
 openai
 asyncio
 wormneuroatlas

store/embed_openai/graph_store.json

@@ -1 +0,0 @@
-{"graph_dict": {}}

store/embed_openai/image__vector_store.json

@@ -1 +0,0 @@
-{"embedding_dict": {}, "text_id_to_ref_doc_id": {}, "metadata_dict": {}}