save correction

p2m2 · Sep 20, 2024 · 364a7ba · 364a7ba
1 parent ab8157f
commit 364a7ba
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Showing 4 changed files with 39 additions and 11 deletions.
diff --git a/config/1-article.json b/config/1-article.json
@@ -46,12 +46,12 @@
                 }
             },
             "mesh_link" : {
-                "mesh" : {
-                    "url": "https://nlmpubs.nlm.nih.gov/projects/mesh/rdf/mesh.nt",
+                "mesh": {
+                    "filepath" : "data/mesh/2024.ttl",
                     "prefix": "http://id.nlm.nih.gov/mesh/",
-                    "format": "nt",
+                    "format": "turtle",
                     "label" : "<http://www.w3.org/2000/01/rdf-schema#label>",
-                    "properties": ["<http://id.nlm.nih.gov/mesh/vocab#scopeNote>"]
+                    "properties": ["<http://www.w3.org/2000/01/rdf-schema#comment>"]
                 }
             },
             "chemical_link" : {

diff --git a/config/igepp.json b/config/igepp.json
@@ -1,7 +1,7 @@
 {
     "encodeur" : "sentence-transformers/all-MiniLM-L6-v2",
     "threshold_similarity_tag_chunk" : 0.65,
-    "threshold_similarity_tag" : 0.75,
+    "threshold_similarity_tag" : 0.85,
     "batch_size" : 32,
 
     "populate_owl_tag_embeddings" : {

diff --git a/config/mesh_example.json b/config/mesh_example.json
@@ -1,6 +1,6 @@
 {
     "encodeur" : "sentence-transformers/all-MiniLM-L6-v2",
-    "threshold_similarity_tag_chunk" : 0.65,
+    "threshold_similarity_tag_chunk" : 0.40,
     "threshold_similarity_tag" : 0.80,
     "batch_size" : 32,
 

diff --git a/exec.sh b/exec.sh
@@ -11,13 +11,41 @@ run_command() {
     "$@"
     local status=$?
     if [ $status -ne 0 ]; then
-        echo "Erreur: La commande '$*' a échoué avec le code de sortie $status"
+        echo "Error: The command '$*' failed with exit code $status"
         exit $status
     fi
 }
 
-run_command python -m llm_semantic_annotator "$conffile" populate_owl_tag_embeddings
-run_command python -m llm_semantic_annotator "$conffile" populate_ncbi_taxon_tag_embeddings
-run_command python -m llm_semantic_annotator "$conffile" populate_abstract_embeddings
-run_command python -m llm_semantic_annotator "$conffile" compute_tag_chunk_similarities
+execute_command() {
+    case $1 in
+        1) run_command python -m llm_semantic_annotator "$conffile" populate_owl_tag_embeddings ;;
+        2) run_command python -m llm_semantic_annotator "$conffile" populate_ncbi_taxon_tag_embeddings ;;
+        3) run_command python -m llm_semantic_annotator "$conffile" populate_abstract_embeddings ;;
+        4) run_command python -m llm_semantic_annotator "$conffile" compute_tag_chunk_similarities ;;
+        *) echo "Invalid option" ;;
+    esac
+}
+
+echo "What would you like to execute?"
+echo "1. Full workflow"
+echo "2. populate_owl_tag_embeddings"
+echo "3. populate_ncbi_taxon_tag_embeddings"
+echo "4. populate_abstract_embeddings"
+echo "5. compute_tag_chunk_similarities"
+read -p "Enter your choice (1-5): " choice
 
+case $choice in
+    1)
+        run_command python -m llm_semantic_annotator "$conffile" populate_owl_tag_embeddings
+        run_command python -m llm_semantic_annotator "$conffile" populate_ncbi_taxon_tag_embeddings
+        run_command python -m llm_semantic_annotator "$conffile" populate_abstract_embeddings
+        run_command python -m llm_semantic_annotator "$conffile" compute_tag_chunk_similarities
+        ;;
+    2|3|4|5)
+        execute_command $((choice - 1))
+        ;;
+    *)
+        echo "Invalid choice"
+        exit 1
+        ;;
+esac