tooluniverse 1.0.6__py3-none-any.whl → 1.0.8__py3-none-any.whl

tooluniverse/test/test_hpa.py

@@ -1,625 +0,0 @@
-# test_hpa.py
-# Comprehensive test file for all HPA tools including enhanced optimized tools
-
-from tooluniverse import ToolUniverse
-
-
-# Helper function to format dictionary values
-def format_value(value, max_length=800):
-    """Format output values, showing more detail for agent reasoning"""
-    if isinstance(value, dict):
-        formatted = str(value)
-        if len(formatted) > max_length:
-            return formatted[:max_length] + "... (truncated)"
-        return formatted
-    elif isinstance(value, list):
-        if len(value) > 15:  # Show more list items for better context
-            return f"{value[:15]}... (total {len(value)} items)"
-        return value
-    elif isinstance(value, str) and len(value) > max_length:
-        return value[:max_length] + "..."
-    return value
-
-
-# Initialize ToolUniverse and load all tools
-print("🧪 Comprehensive HPA Tools Testing")
-print("=" * 80)
-print("Testing all HPA tools with complete input/output display for agent reasoning")
-print("=" * 80)
-
-tooluni = ToolUniverse()
-tooluni.load_tools()
-
-# Define test genes and parameters with biological context
-VALID_GENE = "TP53"  # Tumor suppressor gene - nuclear protein
-VALID_GENE_2 = "BRCA1"  # Breast cancer susceptibility gene
-VALID_GENE_3 = "EGFR"  # Epidermal growth factor receptor
-VALID_GENE_4 = "ACTB"  # Beta-actin - housekeeping gene
-VALID_GENE_5 = "GFAP"  # Glial fibrillary acidic protein
-VALID_GENE_6 = "INS"  # Insulin - pancreas-specific
-VALID_GENE_7 = "CD3E"  # T-cell surface glycoprotein
-VALID_CELL_LINE = "hela"  # HeLa cervical cancer cell line
-VALID_DISEASE = "breast_cancer"  # Breast cancer
-VALID_ENSEMBL_ID = "ENSG00000134057"  # CCNB1 gene's Ensembl ID
-VALID_ENSEMBL_ID_2 = "ENSG00000141510"  # TP53 gene's Ensembl ID
-VALID_ENSEMBL_ID_3 = "ENSG00000012048"  # BRCA1 gene's Ensembl ID
-VALID_ENSEMBL_ID_4 = "ENSG00000075624"  # ACTB gene's Ensembl ID
-VALID_ENSEMBL_ID_5 = "ENSG00000146648"  # EGFR gene's Ensembl ID
-
-# Comprehensive test cases covering all HPA tools
-comprehensive_test_queries = [
-    # === GENE SEARCH AND BASIC INFO TOOLS ===
-    {
-        "name": "HPA_search_genes_by_query",
-        "arguments": {"search_query": VALID_GENE},
-        "description": "Search for TP53 gene to get Ensembl ID and synonyms",
-        "biological_context": "TP53 is a crucial tumor suppressor gene, mutations cause cancer",
-        "expected_output": "Should return gene name, Ensembl ID, and known synonyms",
-    },
-    {
-        "name": "HPA_search_genes_by_query",
-        "arguments": {"search_query": "BCAS1"},
-        "description": "Search for BCAS1 gene (breast carcinoma amplified sequence 1)",
-        "biological_context": "BCAS1 is involved in breast cancer progression",
-        "expected_output": "Should return ENSG00000064787 as Ensembl ID",
-    },
-    {
-        "name": "HPA_get_gene_basic_info_by_ensembl_id",
-        "arguments": {"ensembl_id": VALID_ENSEMBL_ID_2},
-        "description": "Get basic gene information for TP53 using JSON API",
-        "biological_context": "TP53 basic info should include transcription regulation functions",
-        "expected_output": "Gene name, synonyms, Uniprot ID, biological processes",
-    },
-    # === EXPRESSION ANALYSIS TOOLS ===
-    {
-        "name": "HPA_get_comparative_expression_by_gene_and_cellline",
-        "arguments": {"gene_name": VALID_GENE, "cell_line": VALID_CELL_LINE},
-        "description": "Compare TP53 expression between HeLa cells and healthy tissues",
-        "biological_context": "TP53 is often mutated/dysregulated in cancer cell lines like HeLa",
-        "expected_output": "Cell line expression vs healthy tissue expression with comparison",
-    },
-    {
-        "name": "HPA_get_disease_expression_by_gene_tissue_disease",
-        "arguments": {"gene_name": VALID_GENE_2, "disease_name": VALID_DISEASE},
-        "description": "Compare BRCA1 expression in breast cancer vs healthy breast tissue",
-        "biological_context": "BRCA1 mutations are major risk factor for breast cancer",
-        "expected_output": "Disease vs healthy expression with fold change analysis",
-    },
-    {
-        "name": "HPA_get_rna_expression_in_specific_tissues",
-        "arguments": {
-            "ensembl_id": VALID_ENSEMBL_ID_2,
-            "tissue_names": ["brain", "liver", "heart"],
-        },
-        "description": "Get TP53 RNA expression levels in brain, liver, and heart tissues",
-        "biological_context": "TP53 should be expressed in all tissues as tumor suppressor",
-        "expected_output": "nTPM values for each tissue with expression level categories",
-    },
-    # === NEW OPTIMIZED EXPRESSION TOOLS ===
-    {
-        "name": "HPA_get_rna_expression_by_source",
-        "arguments": {
-            "gene_name": VALID_GENE_4,
-            "source_type": "tissue",
-            "source_name": "brain",
-        },
-        "description": "Get ACTB expression in brain using optimized column-based query",
-        "biological_context": "ACTB is housekeeping gene, should have high expression everywhere",
-        "expected_output": "High nTPM value with 'Very high' or 'High' expression level",
-    },
-    {
-        "name": "HPA_get_rna_expression_by_source",
-        "arguments": {
-            "gene_name": VALID_GENE_6,
-            "source_type": "tissue",
-            "source_name": "pancreas",
-        },
-        "description": "Get insulin expression in pancreas using tissue-specific column",
-        "biological_context": "Insulin is exclusively produced by pancreatic beta cells",
-        "expected_output": "Very high nTPM value showing tissue specificity",
-    },
-    {
-        "name": "HPA_get_rna_expression_by_source",
-        "arguments": {
-            "gene_name": VALID_GENE_5,
-            "source_type": "brain",
-            "source_name": "cerebellum",
-        },
-        "description": "Get GFAP expression in cerebellum using brain region-specific column",
-        "biological_context": "GFAP is astrocyte marker, should be high in brain regions",
-        "expected_output": "High expression indicating glial cell presence",
-    },
-    {
-        "name": "HPA_get_rna_expression_by_source",
-        "arguments": {
-            "gene_name": VALID_GENE_7,
-            "source_type": "blood",
-            "source_name": "t_cell",
-        },
-        "description": "Get CD3E expression in T cells using blood cell-specific column",
-        "biological_context": "CD3E is T cell receptor component, T cell-specific marker",
-        "expected_output": "Very high expression showing T cell specificity",
-    },
-    # === FUNCTIONAL ANALYSIS TOOLS ===
-    {
-        "name": "HPA_get_biological_processes_by_gene",
-        "arguments": {"gene_name": VALID_GENE},
-        "description": "Get biological processes for TP53 with focus on key processes",
-        "biological_context": "TP53 involved in apoptosis, cell cycle, transcription regulation",
-        "expected_output": "List of processes highlighting apoptosis and cell cycle control",
-    },
-    {
-        "name": "HPA_get_contextual_biological_process_analysis",
-        "arguments": {"gene_name": VALID_GENE, "context_name": "brain"},
-        "description": "Analyze TP53 biological functions in brain tissue context",
-        "biological_context": "TP53 protects brain cells from DNA damage and cancer",
-        "expected_output": "Functional relevance assessment based on brain expression",
-    },
-    {
-        "name": "HPA_get_contextual_biological_process_analysis",
-        "arguments": {"gene_name": VALID_GENE_3, "context_name": "hela"},
-        "description": "Analyze EGFR functions in HeLa cell line context",
-        "biological_context": "EGFR drives cell proliferation, often overexpressed in cancer",
-        "expected_output": "High expression with growth/proliferation process relevance",
-    },
-    # === SUBCELLULAR LOCALIZATION TOOLS ===
-    {
-        "name": "HPA_get_subcellular_location",
-        "arguments": {"gene_name": VALID_GENE},
-        "description": "Get TP53 subcellular localization using optimized scml/scal columns",
-        "biological_context": "TP53 is nuclear transcription factor",
-        "expected_output": "Nuclear localization as main location",
-    },
-    {
-        "name": "HPA_get_subcellular_location",
-        "arguments": {"gene_name": VALID_GENE_4},
-        "description": "Get ACTB subcellular localization - cytoskeletal protein",
-        "biological_context": "Actin forms cytoskeletal filaments throughout cytoplasm",
-        "expected_output": "Cytoplasmic/cytoskeletal localization",
-    },
-    {
-        "name": "HPA_get_subcellular_location",
-        "arguments": {"gene_name": VALID_GENE_5},
-        "description": "Get GFAP subcellular localization - intermediate filament protein",
-        "biological_context": "GFAP forms intermediate filaments in astrocyte cytoplasm",
-        "expected_output": "Cytoplasmic intermediate filaments",
-    },
-    # === CANCER AND PROGNOSTICS TOOLS ===
-    {
-        "name": "HPA_get_cancer_prognostics_by_gene",
-        "arguments": {"ensembl_id": VALID_ENSEMBL_ID_2},
-        "description": "Get TP53 prognostic value across cancer types",
-        "biological_context": "TP53 mutations are prognostic markers in many cancers",
-        "expected_output": "Multiple cancer types with prognostic significance",
-    },
-    {
-        "name": "HPA_get_cancer_prognostics_by_gene",
-        "arguments": {"ensembl_id": VALID_ENSEMBL_ID_3},
-        "description": "Get BRCA1 prognostic value in cancers",
-        "biological_context": "BRCA1 mutations affect treatment response and survival",
-        "expected_output": "Breast/ovarian cancer prognostic associations",
-    },
-    # === PROTEIN INTERACTION TOOLS ===
-    {
-        "name": "HPA_get_protein_interactions_by_gene",
-        "arguments": {"gene_name": VALID_GENE_3},
-        "description": "Get EGFR protein-protein interactions",
-        "biological_context": "EGFR interacts with many signaling proteins",
-        "expected_output": "List of interaction partners involved in growth signaling",
-    },
-    {
-        "name": "HPA_get_protein_interactions_by_gene",
-        "arguments": {"gene_name": VALID_GENE},
-        "description": "Get TP53 protein-protein interactions",
-        "biological_context": "TP53 interacts with MDM2, p21, and other cell cycle proteins",
-        "expected_output": "Interaction partners in DNA damage response pathway",
-    },
-    # === COMPREHENSIVE GENE DETAILS (IMAGES) ===
-    {
-        "name": "HPA_get_comprehensive_gene_details_by_ensembl_id",
-        "arguments": {"ensembl_id": "ENSG00000064787"},
-        "description": "Get comprehensive BCAS1 gene details with enhanced XML parsing",
-        "biological_context": "Should include tissue IHC images and subcellular IF images",
-        "expected_output": "Gene info, IHC images, IF images, antibody data, expression summary",
-    },
-    {
-        "name": "HPA_get_comprehensive_gene_details_by_ensembl_id",
-        "arguments": {
-            "ensembl_id": VALID_ENSEMBL_ID_2,
-            "include_images": True,
-            "include_antibodies": True,
-        },
-        "description": "Get comprehensive TP53 details with all data types",
-        "biological_context": "TP53 should have extensive antibody validation and tissue images",
-        "expected_output": "Complete gene profile with images, antibodies, expression data",
-    },
-    # === ERROR HANDLING TESTS ===
-    {
-        "name": "HPA_get_rna_expression_by_source",
-        "arguments": {
-            "gene_name": VALID_GENE,
-            "source_type": "invalid_type",
-            "source_name": "brain",
-        },
-        "description": "Error test: invalid source_type parameter",
-        "biological_context": "Should demonstrate proper error handling",
-        "expected_output": "Error message with available source types listed",
-    },
-    {
-        "name": "HPA_get_subcellular_location",
-        "arguments": {},
-        "description": "Error test: missing required gene_name parameter",
-        "biological_context": "Should demonstrate parameter validation",
-        "expected_output": "Error message indicating gene_name is required",
-    },
-    {
-        "name": "HPA_get_cancer_prognostics_by_gene",
-        "arguments": {"ensembl_id": "INVALID_ENSEMBL_ID"},
-        "description": "Error test: invalid Ensembl ID",
-        "biological_context": "Should handle non-existent gene IDs gracefully",
-        "expected_output": "404 error or no data found message",
-    },
-    # === INTELLIGENT RECOMMENDATION TESTS ===
-    {
-        "name": "HPA_get_rna_expression_by_source",
-        "arguments": {
-            "gene_name": "ACTB",
-            "source_type": "blood",
-            "source_name": "tcell",
-        },
-        "description": "Smart recommendation test: typo in source_name (tcell → t_cell)",
-        "biological_context": "Should provide intelligent suggestions for misspelled parameters",
-        "expected_output": "Error with similar options: ['t_cell'] and complete available list",
-    },
-    {
-        "name": "HPA_get_rna_expression_by_source",
-        "arguments": {
-            "gene_name": "GFAP",
-            "source_type": "brain",
-            "source_name": "cortex",
-        },
-        "description": "Smart recommendation test: partial match (cortex → cerebral_cortex)",
-        "biological_context": "Should find partial matches for brain region names",
-        "expected_output": "Error with similar options suggesting cerebral_cortex",
-    },
-    {
-        "name": "HPA_get_contextual_biological_process_analysis",
-        "arguments": {"gene_name": "TP53", "context_name": "foot"},
-        "description": "Smart recommendation test: invalid tissue name",
-        "biological_context": "Should provide comprehensive tissue and cell line options",
-        "expected_output": "Error with available tissues and cell lines listed",
-    },
-    {
-        "name": "HPA_get_contextual_biological_process_analysis",
-        "arguments": {"gene_name": "EGFR", "context_name": "muscle"},
-        "description": "Smart recommendation test: ambiguous tissue name (muscle → skeletal_muscle)",
-        "biological_context": "Should suggest specific muscle types available",
-        "expected_output": "Error with similar options for muscle-related tissues",
-    },
-    {
-        "name": "HPA_get_comparative_expression_by_gene_and_cellline",
-        "arguments": {"gene_name": "BRCA1", "cell_line": "heLa"},
-        "description": "Smart recommendation test: case sensitivity (heLa → hela)",
-        "biological_context": "Should handle case variations in cell line names",
-        "expected_output": "Error with similar options suggesting hela",
-    },
-    {
-        "name": "HPA_get_comparative_expression_by_gene_and_cellline",
-        "arguments": {"gene_name": "EGFR", "cell_line": "mcf"},
-        "description": "Smart recommendation test: partial cell line name (mcf → mcf7)",
-        "biological_context": "Should suggest complete cell line names",
-        "expected_output": "Error with similar options suggesting mcf7",
-    },
-    {
-        "name": "HPA_get_disease_expression_by_gene_tissue_disease",
-        "arguments": {"gene_name": "BRCA1", "disease_name": "cancer"},
-        "description": "Smart recommendation test: generic disease name",
-        "biological_context": "Should provide specific cancer type options",
-        "expected_output": "Error with specific cancer types like breast_cancer, lung_cancer",
-    },
-    {
-        "name": "HPA_get_disease_expression_by_gene_tissue_disease",
-        "arguments": {"gene_name": "TP53", "disease_name": "colon"},
-        "description": "Smart recommendation test: tissue name as disease (colon → colon_cancer)",
-        "biological_context": "Should suggest adding '_cancer' suffix",
-        "expected_output": "Error with similar options suggesting colon_cancer",
-    },
-    {
-        "name": "HPA_get_rna_expression_by_source",
-        "arguments": {
-            "gene_name": "INS",
-            "source_type": "tissue",
-            "source_name": "islet",
-        },
-        "description": "Smart recommendation test: related but different term (islet → pancreas)",
-        "biological_context": "Should suggest pancreas for insulin-related queries",
-        "expected_output": "Error with pancreas in similar options",
-    },
-    {
-        "name": "HPA_get_rna_expression_by_source",
-        "arguments": {
-            "gene_name": "CD3E",
-            "source_type": "blood",
-            "source_name": "lymphocyte",
-        },
-        "description": "Smart recommendation test: general term (lymphocyte → t_cell, b_cell)",
-        "biological_context": "Should suggest specific lymphocyte subtypes",
-        "expected_output": "Error with t_cell and b_cell in similar options",
-    },
-    # === EDGE CASE RECOMMENDATION TESTS ===
-    {
-        "name": "HPA_get_contextual_biological_process_analysis",
-        "arguments": {"gene_name": "ACTB", "context_name": ""},
-        "description": "Edge case test: empty context_name",
-        "biological_context": "Should require context_name parameter",
-        "expected_output": "Error indicating context_name is required",
-    },
-    {
-        "name": "HPA_get_rna_expression_by_source",
-        "arguments": {
-            "gene_name": "GFAP",
-            "source_type": "tissue",
-            "source_name": "xyz123",
-        },
-        "description": "Edge case test: completely invalid source_name",
-        "biological_context": "Should show no similar options but list all available",
-        "expected_output": "Error with complete tissue list but no similar options",
-    },
-    {
-        "name": "HPA_get_rna_expression_in_specific_tissues",
-        "arguments": {"ensembl_id": VALID_ENSEMBL_ID_2, "tissue_names": "not_a_list"},
-        "description": "Edge case test: wrong parameter type",
-        "biological_context": "Should provide example of correct format",
-        "expected_output": "Error with tissue name examples",
-    },
-]
-
-# Execute all test cases with detailed output
-for idx, query_info in enumerate(comprehensive_test_queries, 1):
-    print(f"\n[{idx}] TOOL: {query_info['name']}")
-    print(f"INPUT ARGUMENTS: {query_info['arguments']}")
-    print(f"DESCRIPTION: {query_info['description']}")
-    print(f"BIOLOGICAL CONTEXT: {query_info['biological_context']}")
-    print(f"EXPECTED OUTPUT: {query_info['expected_output']}")
-    print("-" * 80)
-
-    # Execute the query
-    result = tooluni.run(
-        {"name": query_info["name"], "arguments": query_info["arguments"]}
-    )
-
-    # Display results with complete formatting for agent reasoning
-    if isinstance(result, dict) and "error" in result:
-        print("❌ ERROR RESULT:")
-        print(f"   Error: {result['error']}")
-        if "detail" in result:
-            print(f"   Detail: {result['detail']}")
-
-        # Enhanced interpretation for intelligent recommendation tests
-        error_msg = result["error"]
-        if "Similar options:" in error_msg:
-            print("   🧠 SMART RECOMMENDATION: Tool provided intelligent suggestions!")
-            print("   💡 FUZZY MATCHING: Successfully identified similar valid options")
-            print("   ✨ USER EXPERIENCE: Error message is helpful and actionable")
-        elif "Available" in error_msg and (
-            "tissues:" in error_msg
-            or "cell lines:" in error_msg
-            or "sources:" in error_msg
-        ):
-            print("   📋 COMPREHENSIVE GUIDANCE: Tool provided complete option lists")
-            print("   🎯 PARAMETER VALIDATION: Clear indication of valid inputs")
-        elif "required" in error_msg:
-            print("   ✅ PARAMETER VALIDATION: Proper required field checking")
-        else:
-            print(
-                "   INTERPRETATION: Tool properly handled invalid input with informative error"
-            )
-    else:
-        print("✅ SUCCESS RESULT:")
-
-        if isinstance(result, dict):
-            # Display complete result data
-            print("   COMPLETE OUTPUT DATA:")
-            for key, value in result.items():
-                formatted_value = format_value(value)
-                print(f"     {key}: {formatted_value}")
-
-            # Add biological interpretation
-            print("   BIOLOGICAL INTERPRETATION:")
-
-            # Expression data interpretation
-            if "expression_value" in result:
-                expr_val = result.get("expression_value", "N/A")
-                expr_level = result.get("expression_level", "Unknown")
-                source_type = result.get("source_type", "Unknown")
-                source_name = result.get("source_name", "Unknown")
-                column = result.get("column_queried", "Unknown")
-                gene = result.get("gene_name", "Unknown")
-
-                print(
-                    f"     Gene {gene} shows {expr_level} expression ({expr_val} nTPM)"
-                )
-                print(f"     in {source_name} ({source_type}) via column '{column}'")
-
-                # Biological significance
-                if expr_val != "N/A":
-                    try:
-                        val = float(expr_val)
-                        if val > 50:
-                            print(
-                                "     SIGNIFICANCE: Very high expression suggests major functional role"
-                            )
-                        elif val > 10:
-                            print(
-                                "     SIGNIFICANCE: High expression indicates important function"
-                            )
-                        elif val > 1:
-                            print(
-                                "     SIGNIFICANCE: Moderate expression shows functional presence"
-                            )
-                        else:
-                            print(
-                                "     SIGNIFICANCE: Low expression may indicate limited role"
-                            )
-                    except Exception:
-                        print("     SIGNIFICANCE: Expression level unclear from data")
-
-            # Subcellular location interpretation
-            if "main_locations" in result:
-                main_locs = result.get("main_locations", [])
-                add_locs = result.get("additional_locations", [])
-                total = result.get("total_locations", 0)
-                gene = result.get("gene_name", "Unknown")
-
-                print(f"     Gene {gene} localizes to {total} subcellular compartments")
-                if main_locs:
-                    print(f"     PRIMARY LOCATIONS: {', '.join(main_locs)}")
-                if add_locs:
-                    print(f"     ADDITIONAL LOCATIONS: {', '.join(add_locs)}")
-
-                # Functional implications
-                if any("nuclear" in loc.lower() for loc in main_locs):
-                    print(
-                        "     FUNCTIONAL IMPLICATION: Nuclear localization suggests transcriptional role"
-                    )
-                if any("cytoplasm" in loc.lower() for loc in main_locs):
-                    print(
-                        "     FUNCTIONAL IMPLICATION: Cytoplasmic localization suggests metabolic/structural role"
-                    )
-                if any("membrane" in loc.lower() for loc in main_locs):
-                    print(
-                        "     FUNCTIONAL IMPLICATION: Membrane localization suggests signaling role"
-                    )
-
-            # Cancer prognostics interpretation
-            if "prognostic_cancers_count" in result:
-                count = result.get("prognostic_cancers_count", 0)
-                gene = result.get("gene", "Unknown")
-                prognostics = result.get("prognostic_summary", [])
-
-                print(f"     Gene {gene} has prognostic value in {count} cancer types")
-                if isinstance(prognostics, list) and prognostics:
-                    for prog in prognostics[:3]:  # Show first 3
-                        cancer_type = prog.get("cancer_type", "Unknown")
-                        prog_type = prog.get("prognostic_type", "Unknown")
-                        print(f"     {cancer_type}: {prog_type} prognostic marker")
-                print(
-                    "     CLINICAL SIGNIFICANCE: Can guide treatment decisions and prognosis"
-                )
-
-            # Protein interactions interpretation
-            if "interactor_count" in result:
-                count = result.get("interactor_count", 0)
-                gene = result.get("gene", "Unknown")
-                interactors = result.get("interactors", [])
-
-                print(f"     Gene {gene} interacts with {count} proteins")
-                if interactors and count > 0:
-                    print(
-                        f"     KEY INTERACTORS: {', '.join(interactors[:5])}"
-                    )  # Show first 5
-                    print(
-                        "     NETWORK SIGNIFICANCE: High connectivity suggests central role in pathways"
-                    )
-                else:
-                    print(
-                        "     NETWORK SIGNIFICANCE: Limited interactions or data not available"
-                    )
-
-            # Biological processes interpretation
-            if "total_biological_processes" in result:
-                total_processes = result.get("total_biological_processes", 0)
-                target_processes = result.get("target_process_names", [])
-                gene = result.get("gene_symbol", result.get("gene", "Unknown"))
-
-                print(
-                    f"     Gene {gene} participates in {total_processes} biological processes"
-                )
-                if target_processes:
-                    print(f"     KEY PROCESSES: {', '.join(target_processes)}")
-                    print(
-                        "     FUNCTIONAL SIGNIFICANCE: Involvement in critical cellular processes"
-                    )
-
-            # Comprehensive gene details interpretation
-            if "summary" in result and isinstance(result["summary"], dict):
-                summary = result["summary"]
-                gene = result.get("gene_name", "Unknown")
-
-                print(f"     Gene {gene} comprehensive analysis:")
-                for sum_key, sum_val in summary.items():
-                    print(f"       {sum_key}: {sum_val}")
-
-                ihc_images = summary.get("total_ihc_images", 0)
-                if_images = summary.get("total_if_images", 0)
-                antibodies = summary.get("total_antibodies", 0)
-
-                print(
-                    f"     EXPERIMENTAL EVIDENCE: {ihc_images} tissue images, {if_images} subcellular images, {antibodies} antibodies"
-                )
-                print("     DATA QUALITY: Extensive experimental validation available")
-
-            # Contextual analysis interpretation
-            if "contextual_conclusion" in result:
-                conclusion = result.get("contextual_conclusion", "")
-                context = result.get("context", "Unknown")
-                gene = result.get("gene", "Unknown")
-
-                print(f"     CONTEXTUAL ANALYSIS for {gene} in {context}:")
-                print(f"     {conclusion}")
-
-                relevance = result.get("functional_relevance", "")
-                if relevance:
-                    print(f"     FUNCTIONAL RELEVANCE: {relevance}")
-
-        elif isinstance(result, list):
-            print(f"   LIST RESULT: {len(result)} items")
-            if result:
-                print(f"   FIRST ITEM: {format_value(result[0])}")
-                print("   INTERPRETATION: Multiple data points returned for analysis")
-
-        else:
-            print(f"   RAW RESULT: {format_value(result)}")
-            print("   INTERPRETATION: Direct data output for further processing")
-
-    print("=" * 80)
-
-print("\n🎯 COMPREHENSIVE HPA TOOLS TESTING COMPLETE!")
-print("\n📊 TESTING SUMMARY:")
-print(f"✅ Tested {len(comprehensive_test_queries)} different HPA tools and scenarios")
-print(
-    "✅ Covered all tool categories: search, expression, function, localization, interactions, prognostics"
-)
-print("✅ Included both original and optimized enhanced tools")
-print("✅ Demonstrated error handling and parameter validation")
-print("✅ Added comprehensive intelligent recommendation testing")
-print("✅ Provided complete input/output data for agent reasoning")
-print("✅ Added biological context and functional interpretation")
-
-print("\n🔬 ENHANCED FEATURES DEMONSTRATED:")
-print("✨ Column-based optimized queries for direct data access")
-print("✨ Comprehensive source type mappings (tissue/blood/brain/single_cell)")
-print("✨ Enhanced XML parsing with improved image extraction")
-print("✨ Intelligent error handling with informative messages")
-print("✨ Smart parameter recommendations with fuzzy matching")
-print("✨ Context-aware suggestions for biological terms")
-print("✨ Biological interpretation of results for agent reasoning")
-print("✨ Complete data transparency for downstream analysis")
-
-print("\n🧠 INTELLIGENT RECOMMENDATION FEATURES:")
-print("💡 Typo correction: 'tcell' → suggests 't_cell'")
-print("💡 Partial matching: 'cortex' → suggests 'cerebral_cortex'")
-print("💡 Case handling: 'heLa' → suggests 'hela'")
-print("💡 Context awareness: 'muscle' → suggests 'skeletal_muscle'")
-print("💡 Domain knowledge: 'islet' → suggests 'pancreas' for insulin")
-print("💡 Hierarchical suggestions: 'lymphocyte' → suggests 't_cell', 'b_cell'")
-print("💡 Comprehensive fallback: Shows all available options when no match")
-print("💡 Edge case handling: Empty parameters, wrong types, invalid inputs")
-
-print("\n💡 FOR AGENT USAGE:")
-print("📋 All inputs and outputs are fully displayed")
-print("🧠 Biological context provided for each test")
-print("🔍 Results include functional interpretation")
-print("⚡ Both original and optimized tools available")
-print("🛡️ Error handling demonstrates robustness")
-print("\n" + "=" * 80)

tooluniverse/test/test_humanbase_tool.py

@@ -1,20 +0,0 @@
-from tooluniverse import ToolUniverse
-
-# Step 1: Initialize tool universe
-tooluni = ToolUniverse()
-tooluni.load_tools()
-
-test_queries = [
-    {
-        "name": "humanbase_ppi_analysis",
-        "arguments": {"gene_list": ["TP53", "USP7"], "tissue": "brain"},
-    },
-]
-
-for idx, query in enumerate(test_queries):
-    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))