tooluniverse 1.0.7__py3-none-any.whl → 1.0.9__py3-none-any.whl

tooluniverse/tools/ClinicalTrialDesignAgent.py

@@ -0,0 +1,63 @@
+"""
+ClinicalTrialDesignAgent
+
+AI agent that designs clinical trial protocols based on preclinical data and regulatory requirements
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ClinicalTrialDesignAgent(
+    drug_name: str,
+    indication: str,
+    preclinical_data: Optional[str] = "",
+    target_population: Optional[str] = "General adult population",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    AI agent that designs clinical trial protocols based on preclinical data and regulatory requirements
+
+    Parameters
+    ----------
+    drug_name : str
+        Name of the drug candidate
+    indication : str
+        Disease indication
+    preclinical_data : str
+        Preclinical efficacy and safety data
+    target_population : str
+        Target patient population
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "ClinicalTrialDesignAgent",
+            "arguments": {
+                "drug_name": drug_name,
+                "indication": indication,
+                "preclinical_data": preclinical_data,
+                "target_population": target_population,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ClinicalTrialDesignAgent"]

tooluniverse/tools/CompoundDiscoveryAgent.py

@@ -0,0 +1,59 @@
+"""
+CompoundDiscoveryAgent
+
+AI agent that analyzes potential drug compounds using multiple strategies and LLM reasoning
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def CompoundDiscoveryAgent(
+    disease_name: str,
+    targets: str,
+    context: Optional[str] = "",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    AI agent that analyzes potential drug compounds using multiple strategies and LLM reasoning
+
+    Parameters
+    ----------
+    disease_name : str
+        Name of the disease
+    targets : str
+        List of therapeutic targets (comma-separated)
+    context : str
+        Additional context or specific requirements
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "CompoundDiscoveryAgent",
+            "arguments": {
+                "disease_name": disease_name,
+                "targets": targets,
+                "context": context,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["CompoundDiscoveryAgent"]

tooluniverse/tools/DOAJ_search_articles.py

@@ -10,8 +10,8 @@ from ._shared_client import get_shared_client
 
 def DOAJ_search_articles(
     query: str,
-    max_results: int,
-    type: str,
+    max_results: Optional[int] = 10,
+    type: Optional[str] = "articles",
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,

tooluniverse/tools/DiseaseAnalyzerAgent.py

@@ -0,0 +1,52 @@
+"""
+DiseaseAnalyzerAgent
+
+AI agent that analyzes disease characteristics and identifies potential therapeutic targets using...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def DiseaseAnalyzerAgent(
+    disease_name: str,
+    context: Optional[str] = "",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    AI agent that analyzes disease characteristics and identifies potential therapeutic targets using...
+
+    Parameters
+    ----------
+    disease_name : str
+        Name of the disease to analyze
+    context : str
+        Additional context or specific focus areas
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "DiseaseAnalyzerAgent",
+            "arguments": {"disease_name": disease_name, "context": context},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["DiseaseAnalyzerAgent"]

tooluniverse/tools/DrugInteractionAnalyzerAgent.py

@@ -0,0 +1,52 @@
+"""
+DrugInteractionAnalyzerAgent
+
+AI agent that analyzes drug-drug interactions and provides clinical recommendations
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def DrugInteractionAnalyzerAgent(
+    compounds: str,
+    patient_context: Optional[str] = "General adult population",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    AI agent that analyzes drug-drug interactions and provides clinical recommendations
+
+    Parameters
+    ----------
+    compounds : str
+        List of compounds to analyze for interactions (comma-separated)
+    patient_context : str
+        Patient context (age, comorbidities, medications, etc.)
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "DrugInteractionAnalyzerAgent",
+            "arguments": {"compounds": compounds, "patient_context": patient_context},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["DrugInteractionAnalyzerAgent"]

tooluniverse/tools/DrugOptimizationAgent.py

@@ -0,0 +1,63 @@
+"""
+DrugOptimizationAgent
+
+AI agent that analyzes drug optimization strategies based on ADMET and efficacy data
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def DrugOptimizationAgent(
+    compounds: str,
+    admet_data: Optional[str] = "",
+    efficacy_data: Optional[str] = "",
+    target_profile: Optional[str] = "",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    AI agent that analyzes drug optimization strategies based on ADMET and efficacy data
+
+    Parameters
+    ----------
+    compounds : str
+        List of compounds to optimize (comma-separated)
+    admet_data : str
+        ADMET properties and issues
+    efficacy_data : str
+        Efficacy and potency data
+    target_profile : str
+        Target profile and requirements
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "DrugOptimizationAgent",
+            "arguments": {
+                "compounds": compounds,
+                "admet_data": admet_data,
+                "efficacy_data": efficacy_data,
+                "target_profile": target_profile,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["DrugOptimizationAgent"]

tooluniverse/tools/Ensembl_lookup_gene_by_symbol.py

@@ -0,0 +1,52 @@
+"""
+Ensembl_lookup_gene_by_symbol
+
+Lookup Ensembl gene by species and gene symbol, returning core metadata and coordinates (uses /xr...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def Ensembl_lookup_gene_by_symbol(
+    symbol: str,
+    species: Optional[str] = "homo_sapiens",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Lookup Ensembl gene by species and gene symbol, returning core metadata and coordinates (uses /xr...
+
+    Parameters
+    ----------
+    species : str
+        Species name (e.g., 'homo_sapiens').
+    symbol : str
+        Gene symbol (e.g., BRCA1).
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "Ensembl_lookup_gene_by_symbol",
+            "arguments": {"species": species, "symbol": symbol},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["Ensembl_lookup_gene_by_symbol"]

tooluniverse/tools/EuropePMC_search_articles.py

@@ -10,7 +10,7 @@ from ._shared_client import get_shared_client
 
 def EuropePMC_search_articles(
     query: str,
-    limit: int,
+    limit: Optional[int] = 5,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,

tooluniverse/tools/GIN_Guidelines_Search.py

@@ -0,0 +1,52 @@
+"""
+GIN_Guidelines_Search
+
+Search Guidelines International Network (GIN) guidelines database. GIN maintains the world's larg...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GIN_Guidelines_Search(
+    query: str,
+    limit: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search Guidelines International Network (GIN) guidelines database. GIN maintains the world's larg...
+
+    Parameters
+    ----------
+    query : str
+        Medical condition, treatment, or clinical topic to search for in GIN guidelin...
+    limit : int
+        Maximum number of guidelines to return (default: 10)
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    list[Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "GIN_Guidelines_Search",
+            "arguments": {"query": query, "limit": limit},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GIN_Guidelines_Search"]

tooluniverse/tools/GWAS_search_associations_by_gene.py

@@ -0,0 +1,52 @@
+"""
+GWAS_search_associations_by_gene
+
+Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def GWAS_search_associations_by_gene(
+    gene_name: str,
+    size: Optional[int] = 5,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search GWAS Catalog associations by gene name (returns strongest risk allele and p-value fields).
+
+    Parameters
+    ----------
+    gene_name : str
+        Gene symbol (e.g., BRCA1).
+    size : int
+        Max associations to return.
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "GWAS_search_associations_by_gene",
+            "arguments": {"gene_name": gene_name, "size": size},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["GWAS_search_associations_by_gene"]

tooluniverse/tools/LiteratureSynthesisAgent.py

@@ -0,0 +1,59 @@
+"""
+LiteratureSynthesisAgent
+
+AI agent that synthesizes literature findings and provides evidence-based insights
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def LiteratureSynthesisAgent(
+    topic: str,
+    literature_data: str,
+    focus_area: Optional[str] = "General",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    AI agent that synthesizes literature findings and provides evidence-based insights
+
+    Parameters
+    ----------
+    topic : str
+        Research topic or question
+    literature_data : str
+        Literature findings or abstracts to synthesize
+    focus_area : str
+        Specific focus area for synthesis
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "LiteratureSynthesisAgent",
+            "arguments": {
+                "topic": topic,
+                "literature_data": literature_data,
+                "focus_area": focus_area,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["LiteratureSynthesisAgent"]

tooluniverse/tools/PMC_search_papers.py

@@ -11,9 +11,9 @@ from ._shared_client import get_shared_client
 def PMC_search_papers(
     query: str,
     limit: int,
-    date_from: str,
-    date_to: str,
-    article_type: str,
+    date_from: Optional[str] = None,
+    date_to: Optional[str] = None,
+    article_type: Optional[str] = None,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,

tooluniverse/tools/PubMed_search_articles.py

@@ -10,8 +10,8 @@ from ._shared_client import get_shared_client
 
 def PubMed_search_articles(
     query: str,
-    limit: int,
-    api_key: str,
+    limit: Optional[int] = 10,
+    api_key: Optional[str] = None,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,

tooluniverse/tools/SemanticScholar_search_papers.py

@@ -11,7 +11,7 @@ from ._shared_client import get_shared_client
 def SemanticScholar_search_papers(
     query: str,
     limit: int,
-    api_key: str,
+    api_key: Optional[str] = None,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,

tooluniverse/tools/UCSC_get_genes_by_region.py

@@ -0,0 +1,67 @@
+"""
+UCSC_get_genes_by_region
+
+Query UCSC Genome Browser track API for knownGene features in a genomic window.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def UCSC_get_genes_by_region(
+    chrom: str,
+    start: int,
+    end: int,
+    genome: Optional[str] = "hg38",
+    track: Optional[str] = "knownGene",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Query UCSC Genome Browser track API for knownGene features in a genomic window.
+
+    Parameters
+    ----------
+    genome : str
+        Genome assembly (e.g., hg38).
+    chrom : str
+        Chromosome (e.g., chr17).
+    start : int
+        Start position (0-based).
+    end : int
+        End position.
+    track : str
+        Track name.
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "UCSC_get_genes_by_region",
+            "arguments": {
+                "genome": genome,
+                "chrom": chrom,
+                "start": start,
+                "end": end,
+                "track": track,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["UCSC_get_genes_by_region"]

tooluniverse/tools/Zenodo_search_records.py

@@ -11,7 +11,7 @@ from ._shared_client import get_shared_client
 def Zenodo_search_records(
     query: str,
     max_results: int,
-    community: str,
+    community: Optional[str] = None,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,