add script for remote exec

llm_semantic_annotator.sh

@@ -0,0 +1,112 @@
+#!/bin/bash
+
+help() {
+    cat << EOF
+Usage: $0 <config_file> <int_commande>
+
+Commands:
+  1. Pseudo workflow [2,4,5,6,7]
+  2. Populate OWL tag embeddings
+  3. Populate abstract embeddings
+  4. Compute similarities between tags and abstract chunks
+  5. Display similarities information
+  6. Build turtle knowledge graph
+  7. Build dataset abstracts annotations CSV file
+
+Details:
+  2: Compute TAG embeddings for all ontologies defined in the populate_owl_tag_embeddings section
+  3: Compute ABSTRACT embeddings (title + sentences) for all abstracts in the dataset
+  4: Compute similarities between TAGS and ABSTRACTS
+  5: Display similarities information on the console
+  6: Generate turtle file with information {score, tag} for each DOI
+  7: Generate CSV file with [doi, tag, pmid, reference_id]
+
+EOF
+}
+
+# Check for help option
+if [[ "$1" == "-h" ]]; then
+    help
+    exit 0
+fi
+
+# Check for correct number of arguments
+if [ "$#" -lt 2 ]; then
+    echo "Error: Not enough arguments."
+    echo "Usage: $0 <config_file> <int_commande> [options]"
+    echo "Use '$0 -h' for more information."
+    exit 1
+fi
+
+config_file=$1
+command=$2
+
+# Validate config file
+if [ ! -f "$config_file" ]; then
+    echo "Error: Config file '$config_file' does not exist."
+    exit 1
+fi
+
+# Validate command is an integer
+if ! [[ "$command" =~ ^[0-9]+$ ]]; then
+    echo "Error: Command must be an integer."
+    exit 1
+fi
+
+venv_name="llm_semantic_annotator_env"
+
+# Fonction pour créer l'environnement virtuel s'il n'existe pas
+create_venv_if_not_exists() {
+    if [ ! -d "$venv_name" ]; then
+        echo "Creating virtual environment..."
+        python3 -m venv "$venv_name"
+        source "$venv_name/bin/activate"
+        pip install -r requirements.txt 
+    else
+        source "$venv_name/bin/activate"
+    fi
+}
+
+run_command() {
+    "$@"
+    local status=$?
+    if [ $status -ne 0 ]; then
+        echo "Error: The command '$*' failed with exit code $status"
+        exit $status
+    fi
+}
+
+execute_command() {
+    case $1 in
+        2) run_command python3 -m llm_semantic_annotator "$config_file" populate_owl_tag_embeddings ;;
+        3) run_command python3 -m llm_semantic_annotator "$config_file" populate_abstract_embeddings ;;
+        4) run_command python3 -m llm_semantic_annotator "$config_file" compute_tag_chunk_similarities ;;
+        5) run_command python3 -m llm_semantic_annotator "$config_file" display_summary ;; 
+        6) run_command python3 -m llm_semantic_annotator "$config_file" build_rdf_graph ;;
+        7) run_command python3 -m llm_semantic_annotator "$config_file" build_dataset_abstracts_annotations ;; 
+        *) echo "Invalid option" ;;
+    esac
+}
+
+# Créer l'environnement virtuel s'il n'existe pas
+create_venv_if_not_exists
+
+case $command in
+    1)
+        run_command python3 -m llm_semantic_annotator "$config_file" populate_owl_tag_embeddings
+        run_command python3 -m llm_semantic_annotator "$config_file" populate_abstract_embeddings
+        run_command python3 -m llm_semantic_annotator "$config_file" compute_tag_chunk_similarities
+        run_command python3 -m llm_semantic_annotator "$config_file" build_rdf_graph
+        run_command python3 -m llm_semantic_annotator "$config_file" display_summary
+        ;;
+    2|3|4|5|6|7)
+        execute_command $command
+        ;;
+    *)
+        echo "Invalid choice"
+        exit 1
+        ;;
+esac
+
+# Désactiver l'environnement virtuel à la fin
+deactivate