tooluniverse 0.2.0__py3-none-any.whl → 1.0.0__py3-none-any.whl

tooluniverse/test/test_fda_drug_labeling.py

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+# === openfda_test_all_tools.py ===
+
+from tooluniverse import ToolUniverse
+
+# Step 1: Initialize tool universe
+tooluni = ToolUniverse()
+tooluni.load_tools()
+
+# Step 2: Define all test queries for all tools
+test_queries = [
+    # # ====== Tests for FAERS_count_reactions_by_drug_event ======
+    # {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "LIPITOR"}},
+    # {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "LIPITOR", "patient.patientsex": "Male", "serious": "Serious"}},
+    # {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "ASPIRIN", "patient.patientagegroup": "Adult"}},
+    # {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "ADVIL", "patient.patientsex": "Female", "patient.patientagegroup": "Elderly", "occurcountry": "US", "serious": "Non-serious"}},
+    # {"name": "FAERS_count_reactions_by_drug_event", "arguments": {"medicinalproduct": "ADVIL", "seriousnessdeath": "Yes"}},
+    # # ====== Tests for FAERS_count_drugs_by_drug_event ======
+    # {"name": "FAERS_count_drugs_by_drug_event", "arguments": {"patient.patientsex": "Female"}},
+    # {"name": "FAERS_count_drugs_by_drug_event", "arguments": {"patient.patientagegroup": "Child"}},
+    # {"name": "FAERS_count_drugs_by_drug_event", "arguments": {"serious": "Serious"}},
+    # {"name": "FAERS_count_drugs_by_drug_event", "arguments": {"occurcountry": "CA", "serious": "Non-serious"}},
+    # # ====== Tests for FAERS_count_country_by_drug_event ======
+    # {"name": "FAERS_count_country_by_drug_event", "arguments": {"medicinalproduct": "METFORMIN"}},
+    # {"name": "FAERS_count_country_by_drug_event", "arguments": {"medicinalproduct": "INSULIN", "patient.patientsex": "Male"}},
+    # {"name": "FAERS_count_country_by_drug_event", "arguments": {"medicinalproduct": "ASPIRIN", "serious": "Serious"}},
+    # {"name": "FAERS_count_country_by_drug_event", "arguments": {"medicinalproduct": "STATIN", "patient.patientsex": "Female", "patient.patientagegroup": "Adult", "serious": "Non-serious"}},
+    # # ====== Tests for FAERS_count_reportercountry_by_drug_event ======
+    # {"name": "FAERS_count_reportercountry_by_drug_event", "arguments": {"medicinalproduct": "LANTUS"}},
+    # {"name": "FAERS_count_reportercountry_by_drug_event", "arguments": {"medicinalproduct": "AMLODIPINE", "patient.patientsex": "Unknown"}},
+    # {"name": "FAERS_count_reportercountry_by_drug_event", "arguments": {"medicinalproduct": "ATORVASTATIN", "patient.patientagegroup": "Elderly"}},
+    # {"name": "FAERS_count_reportercountry_by_drug_event", "arguments": {"medicinalproduct": "GABAPENTIN", "patient.patientsex": "Male", "patient.patientagegroup": "Adult", "serious": "Serious"}},
+    # # ====== Tests for FAERS_count_seriousness_by_drug_event ======
+    # {"name": "FAERS_count_seriousness_by_drug_event", "arguments": {"medicinalproduct": "NAPROXEN"}},
+    # {"name": "FAERS_count_seriousness_by_drug_event", "arguments": {"medicinalproduct": "ALBUTEROL", "patient.patientsex": "Female"}},
+    # {"name": "FAERS_count_seriousness_by_drug_event", "arguments": {"medicinalproduct": "PREDNISONE", "patient.patientagegroup": "Child"}},
+    # {"name": "FAERS_count_seriousness_by_drug_event", "arguments": {"medicinalproduct": "METHOTREXATE", "patient.patientsex": "Male", "patient.patientagegroup": "Adult", "occurcountry": "US"}},
+    # # ====== Tests for FAERS_count_outcomes_by_drug_event ======
+    # {"name": "FAERS_count_outcomes_by_drug_event", "arguments": {"medicinalproduct": "IBUPROFEN"}},
+    # {"name": "FAERS_count_outcomes_by_drug_event", "arguments": {"medicinalproduct": "IBUPROFEN", "patient.patientsex": "Female", "occurcountry": "GB"}},
+    # {"name": "FAERS_count_outcomes_by_drug_event", "arguments": {"medicinalproduct": "IBUPROFEN", "patient.patientsex": "Male", "patient.patientagegroup": "Adolescent"}},
+    # # ====== Tests for FAERS_count_drug_routes_by_event ======
+    # {"name": "FAERS_count_drug_routes_by_event", "arguments": {"medicinalproduct": "INSULIN", "serious": "Serious"}},
+    # {"name": "FAERS_count_drug_routes_by_event", "arguments": {"medicinalproduct": "MORPHINE", "serious": "Non-serious"}},
+    # # ====== Tests for FAERS_count_patient_age_distribution ======
+    # {"name": "FAERS_count_patient_age_distribution", "arguments": {"medicinalproduct": "PENICILLIN"}},
+    # {"name": "FAERS_count_patient_age_distribution", "arguments": {"medicinalproduct": "ACETAMINOPHEN"}},
+    # ====== Tests for FAERS_count_death_related_by_drug ======
+    # {"name": "FAERS_count_death_related_by_drug", "arguments": {"medicinalproduct": "FENTANYL"}},
+    # {"name": "FAERS_count_death_related_by_drug", "arguments": {"medicinalproduct": "WARFARIN"}},
+    # # ====== Tests for FAERS_count_additive_adverse_reactions ======
+    # {"name": "FAERS_count_additive_adverse_reactions", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
+    # {"name": "FAERS_count_additive_adverse_reactions", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "patient.patientsex": "Male"}},
+    # {"name": "FAERS_count_additive_adverse_reactions", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "serious": "Serious"}},
+    # # ====== Tests for FAERS_count_additive_event_reports_by_country ======
+    # {"name": "FAERS_count_additive_event_reports_by_country", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
+    # {"name": "FAERS_count_additive_event_reports_by_country", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "serious": "Non-serious"}},
+    # # ====== Tests for FAERS_count_additive_reports_by_reporter_country ======
+    # {"name": "FAERS_count_additive_reports_by_reporter_country", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
+    # {"name": "FAERS_count_additive_reports_by_reporter_country", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "patient.patientagegroup": "Elderly"}},
+    # # ====== Tests for FAERS_count_additive_seriousness_classification ======
+    # {"name": "FAERS_count_additive_seriousness_classification", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
+    # {"name": "FAERS_count_additive_seriousness_classification", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "occurcountry": "CA"}},
+    # ====== Tests for FAERS_count_additive_reaction_outcomes ======
+    # {"name": "FAERS_count_additive_reaction_outcomes", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
+    # {"name": "FAERS_count_additive_reaction_outcomes", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
+    # ====== Tests for FAERS_count_additive_administration_routes ======
+    # {"name": "FAERS_count_additive_administration_routes", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"]}},
+    # {"name": "FAERS_count_additive_administration_routes", "arguments": {"medicinalproducts": ["LIPITOR", "ASPIRIN"], "serious": "Non-serious"}},
+    #            {'name': 'FAERS_count_additive_seriousness_classification', 'arguments': {'medicinalproducts': ['Dysport'], 'occurcountry': 'US', 'patient.patientagegroup': 'Adult'}},
+    {
+        "name": "FDA_get_drug_names_by_clinical_studies",
+        "arguments": {
+            "clinical_studies": "NSCLC hepatic impairment",
+            "indication": "cardiovascular",
+        },
+    },
+]
+
+# Step 3: Run all test queries
+for idx, query in enumerate(test_queries):
+    try:
+        print(
+            f"\n[{idx+1}] Running tool: {query['name']} with arguments: {query['arguments']}"
+        )
+        result = tooluni.run(query)
+        print("✅ Success. Example output snippet:")
+        print(
+            result if isinstance(result, dict) else str(result)[:500]
+        )  # Print snippet if result is big
+    except Exception as e:
+        print(f"❌ Failed. Error: {str(e)}")

tooluniverse/test/test_gene_ontology_tools.py

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+# test_go.py
+
+from tooluniverse import (
+    ToolUniverse,
+)  # Assuming your ToolUniverse class is in this module
+from typing import Any, Dict, List
+
+# Step 1: Initialize ToolUniverse and load the GO tools
+tooluni = ToolUniverse()
+# This assumes your ToolUniverse is configured to find 'go_tools.json'
+# when the 'go' category is requested.
+tooluni.load_tools(["go"])
+
+# Test GO ID for cell cycle process
+TEST_GO_ID = "GO:0007049"  # cell cycle
+TEST_GENE_NAME = "TP53"  # TP53 gene
+
+test_queries: List[Dict[str, Any]] = [
+    {"name": "GO_search_terms", "arguments": {"query": "cell cycle"}},
+    {"name": "GO_get_term_by_id", "arguments": {"id": TEST_GO_ID}},
+    {"name": "GO_get_term_details", "arguments": {"id": TEST_GO_ID}},
+    {"name": "GO_get_genes_for_term", "arguments": {"id": TEST_GO_ID, "rows": 5}},
+    {"name": "GO_get_annotations_for_gene", "arguments": {"gene_id": TEST_GENE_NAME}},
+]
+
+
+def format_value(value, max_items=5, max_length=200):
+    """Helper function to format output values with more detail"""
+    if isinstance(value, dict):
+        dict_str = str(value)
+        return f"Dict ({len(dict_str)} chars): {dict_str[:500]}{'...' if len(dict_str) > 500 else ''}"
+    elif isinstance(value, list):
+        if not value:
+            return "Empty list"
+        items_to_show = value[:max_items]
+        items_str = "\n  - ".join(
+            [
+                str(item)[:max_length] + ("..." if len(str(item)) > max_length else "")
+                for item in items_to_show
+            ]
+        )
+        remaining = len(value) - max_items
+        return f"List with {len(value)} items:\n  - {items_str}" + (
+            f"\n  ... and {remaining} more items" if remaining > 0 else ""
+        )
+    elif isinstance(value, str):
+        return f"String ({len(value)} chars): {value[:max_length]}{'...' if len(value) > max_length else ''}"
+    else:
+        return f"Type: {type(value)}, Value: {value}"
+
+
+print("--- Starting Gene Ontology (GO) Tool Test ---")
+
+for idx, q in enumerate(test_queries, 1):
+    print(
+        f"\n{'='*80}\n[{idx}] {q['name']}({', '.join([f'{k}={v}' for k, v in q['arguments'].items()])})"
+    )
+    res = tooluni.run(q)
+
+    if isinstance(res, dict) and "error" in res:
+        print(f"ERROR: {res['error']}")
+    else:
+        print(format_value(res))
+    print()
+
+print("\n--- GO Tool Test Completed ---")

tooluniverse/test/test_gwas_tool.py

@@ -0,0 +1,139 @@
+# test_gwas_tool.py
+
+from tooluniverse import ToolUniverse
+
+# Step 1: Initialize ToolUniverse and load all tools (including GWAS tools)
+tooluni = ToolUniverse()
+tooluni.load_tools()
+
+# Step 2: Define test queries for GWAS tools based on the examples
+test_queries = [
+    # Test basic association search (Question 1 from examples)
+    {
+        "name": "gwas_search_associations",
+        "arguments": {"efo_trait": "type 2 diabetes mellitus", "size": 10},
+    },
+    # Test study search (Question 2 from examples)
+    {
+        "name": "gwas_search_studies",
+        "arguments": {"disease_trait": "type 2 diabetes", "cohort": "UKB", "size": 20},
+    },
+    # Test SNP search (Question 3 from examples)
+    {
+        "name": "gwas_search_associations",
+        "arguments": {
+            "rs_id": "rs1050316",
+            "sort": "p_value",
+            "direction": "asc",
+            "size": 10,
+        },
+    },
+    # Test gene-based SNP search (Question 10 from examples)
+    {"name": "gwas_search_snps", "arguments": {"mapped_gene": "HBS1L", "size": 10}},
+    # Test specialized tools
+    {
+        "name": "gwas_get_variants_for_trait",
+        "arguments": {"efo_trait": "type 2 diabetes mellitus", "size": 5},
+    },
+    {
+        "name": "gwas_get_associations_for_trait",
+        "arguments": {"efo_trait": "type 2 diabetes mellitus", "size": 5},
+    },
+    {
+        "name": "gwas_get_associations_for_snp",
+        "arguments": {"rs_id": "rs1050316", "size": 5},
+    },
+    {
+        "name": "gwas_get_studies_for_trait",
+        "arguments": {"efo_trait": "type 2 diabetes mellitus", "size": 5},
+    },
+    {
+        "name": "gwas_get_snps_for_gene",
+        "arguments": {"mapped_gene": "HBS1L", "size": 5},
+    },
+    # Test get by ID tools
+    {"name": "gwas_get_study_by_id", "arguments": {"study_id": "GCST000001"}},
+    {"name": "gwas_get_snp_by_id", "arguments": {"rs_id": "rs429358"}},
+    # Test studies with summary statistics (Question 9 from examples)
+    {
+        "name": "gwas_get_studies_for_trait",
+        "arguments": {
+            "efo_trait": "type 2 diabetes mellitus",
+            "full_pvalue_set": True,
+            "size": 5,
+        },
+    },
+    # Test GxE studies (Question 11 from examples)
+    {
+        "name": "gwas_get_studies_for_trait",
+        "arguments": {
+            "efo_trait": "total blood protein measurement",
+            "gxe": True,
+            "size": 5,
+        },
+    },
+]
+
+
+def format_value(value, max_items=10, max_length=5000):
+    """Helper function to format output values"""
+    if isinstance(value, dict):
+        if "error" in value:
+            return f"ERROR: {value['error']}"
+
+        # Show the structure of the response
+        if "data" in value and "metadata" in value:
+            result = "Response Structure:\n"
+            result += f"  Data: {len(value['data'])} items\n"
+            if value["metadata"]:
+                result += f"  Metadata: {value['metadata']}\n"
+
+            # Show first few data items
+            if value["data"]:
+                result += f"\nFirst {min(max_items, len(value['data']))} data items:\n"
+                for i, item in enumerate(value["data"][:max_items]):
+                    item_str = str(item)
+                    if len(item_str) > max_length:
+                        item_str = item_str[:max_length] + "..."
+                    result += f"  [{i+1}] {item_str}\n"
+
+                if len(value["data"]) > max_items:
+                    result += f"  ... and {len(value['data']) - max_items} more items\n"
+
+            return result
+        else:
+            # Fallback for non-structured responses
+            dict_str = str(value)
+            return f"Dict ({len(dict_str)} chars): {dict_str[:max_length]}{'...' if len(dict_str) > max_length else ''}"
+    elif isinstance(value, list):
+        if not value:
+            return "Empty list"
+        items_to_show = value[:max_items]
+        items_str = "\n  - ".join(
+            [
+                str(item)[:max_length] + ("..." if len(str(item)) > max_length else "")
+                for item in items_to_show
+            ]
+        )
+        remaining = len(value) - max_items
+        return f"List with {len(value)} items:\n  - {items_str}" + (
+            f"\n  ... and {remaining} more items" if remaining > 0 else ""
+        )
+    elif isinstance(value, str):
+        return f"String ({len(value)} chars): {value[:max_length]}{'...' if len(value) > max_length else ''}"
+    else:
+        return f"Type: {type(value)}, Value: {value}"
+
+
+# Step 3: Run all test queries
+for idx, query in enumerate(test_queries, 1):
+    print(
+        f"\n{'='*80}\n[{idx}] Running tool: {query['name']} with arguments: {query['arguments']}"
+    )
+    try:
+        result = tooluni.run(query)
+        print("✅ Success. Output:")
+        print(format_value(result))
+    except (ImportError, AttributeError, KeyError, ValueError) as e:
+        print(f"❌ Failed. Error: {str(e)}")
+    print()