tooluniverse 1.0.10__py3-none-any.whl → 1.0.11.1__py3-none-any.whl

tooluniverse/tools/geo_get_dataset_info.py

@@ -0,0 +1,46 @@
+"""
+geo_get_dataset_info
+
+Get detailed information about a specific GEO dataset including title, summary, and metadata.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def geo_get_dataset_info(
+    dataset_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get detailed information about a specific GEO dataset including title, summary, and metadata.
+
+    Parameters
+    ----------
+    dataset_id : str
+        GEO dataset ID (e.g., 'GDS1234', 'GSE12345')
+    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": "geo_get_dataset_info", "arguments": {"dataset_id": dataset_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["geo_get_dataset_info"]

tooluniverse/tools/geo_get_sample_info.py

@@ -0,0 +1,46 @@
+"""
+geo_get_sample_info
+
+Get sample information for a GEO dataset including sample characteristics and experimental condit...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def geo_get_sample_info(
+    dataset_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get sample information for a GEO dataset including sample characteristics and experimental condit...
+
+    Parameters
+    ----------
+    dataset_id : str
+        GEO dataset ID (e.g., 'GDS1234', 'GSE12345')
+    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": "geo_get_sample_info", "arguments": {"dataset_id": dataset_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["geo_get_sample_info"]

tooluniverse/tools/geo_search_datasets.py

@@ -0,0 +1,67 @@
+"""
+geo_search_datasets
+
+Search GEO datasets by query terms, organism, study type, or platform. Returns dataset IDs and ba...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def geo_search_datasets(
+    query: Optional[str] = None,
+    organism: Optional[str] = "",
+    study_type: Optional[str] = "",
+    platform: Optional[str] = "",
+    limit: Optional[int] = 50,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search GEO datasets by query terms, organism, study type, or platform. Returns dataset IDs and ba...
+
+    Parameters
+    ----------
+    query : str
+        Search query terms (e.g., 'cancer', 'diabetes', 'microarray')
+    organism : str
+        Organism name (e.g., 'Homo sapiens', 'Mus musculus')
+    study_type : str
+        Type of study (e.g., 'Expression profiling by array', 'Expression profiling b...
+    platform : str
+        Platform used (e.g., 'GPL570', 'GPL96')
+    limit : int
+        Maximum number of results 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": "geo_search_datasets",
+            "arguments": {
+                "query": query,
+                "organism": organism,
+                "study_type": study_type,
+                "platform": platform,
+                "limit": limit,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["geo_search_datasets"]

tooluniverse/tools/gnomad_get_gene_constraints.py

@@ -0,0 +1,49 @@
+"""
+gnomad_get_gene_constraints
+
+Get gene constraint metrics from gnomAD. Returns pLI, LOEUF, and other constraint scores for genes.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gnomad_get_gene_constraints(
+    gene_symbol: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get gene constraint metrics from gnomAD. Returns pLI, LOEUF, and other constraint scores for genes.
+
+    Parameters
+    ----------
+    gene_symbol : str
+        Gene symbol (e.g., 'BRCA1', 'TP53')
+    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": "gnomad_get_gene_constraints",
+            "arguments": {"gene_symbol": gene_symbol},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gnomad_get_gene_constraints"]

tooluniverse/tools/kegg_find_genes.py

@@ -0,0 +1,52 @@
+"""
+kegg_find_genes
+
+Find genes in KEGG database by keyword. Can search across all organisms or within a specific orga...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def kegg_find_genes(
+    keyword: str,
+    organism: Optional[str] = "",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Find genes in KEGG database by keyword. Can search across all organisms or within a specific orga...
+
+    Parameters
+    ----------
+    keyword : str
+        Search keyword for gene names or descriptions
+    organism : str
+        Organism code (e.g., 'hsa' for human, 'mmu' for mouse). Optional - searches a...
+    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": "kegg_find_genes",
+            "arguments": {"keyword": keyword, "organism": organism},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["kegg_find_genes"]

tooluniverse/tools/kegg_get_gene_info.py

@@ -0,0 +1,46 @@
+"""
+kegg_get_gene_info
+
+Get detailed gene information from KEGG by gene ID. Returns gene data including sequence, functio...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def kegg_get_gene_info(
+    gene_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get detailed gene information from KEGG by gene ID. Returns gene data including sequence, functio...
+
+    Parameters
+    ----------
+    gene_id : str
+        KEGG gene identifier (e.g., 'hsa:348', 'hsa:3480')
+    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": "kegg_get_gene_info", "arguments": {"gene_id": gene_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["kegg_get_gene_info"]

tooluniverse/tools/kegg_get_pathway_info.py

@@ -0,0 +1,46 @@
+"""
+kegg_get_pathway_info
+
+Get detailed pathway information from KEGG by pathway ID. Returns pathway data including genes, c...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def kegg_get_pathway_info(
+    pathway_id: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Get detailed pathway information from KEGG by pathway ID. Returns pathway data including genes, c...
+
+    Parameters
+    ----------
+    pathway_id : str
+        KEGG pathway identifier (e.g., 'hsa00010', 'path:hsa00010')
+    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": "kegg_get_pathway_info", "arguments": {"pathway_id": pathway_id}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["kegg_get_pathway_info"]

tooluniverse/tools/kegg_list_organisms.py

@@ -0,0 +1,44 @@
+"""
+kegg_list_organisms
+
+List all available organisms in the KEGG database. Returns organism codes, names, and descriptions.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def kegg_list_organisms(
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    List all available organisms in the KEGG database. Returns organism codes, names, and descriptions.
+
+    Parameters
+    ----------
+    No parameters
+    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": "kegg_list_organisms", "arguments": {}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["kegg_list_organisms"]

tooluniverse/tools/kegg_search_pathway.py

@@ -0,0 +1,46 @@
+"""
+kegg_search_pathway
+
+Search KEGG pathways by keyword. Returns pathway IDs and descriptions matching the search term.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def kegg_search_pathway(
+    keyword: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search KEGG pathways by keyword. Returns pathway IDs and descriptions matching the search term.
+
+    Parameters
+    ----------
+    keyword : str
+        Search keyword for pathway names or descriptions (e.g., 'diabetes', 'metaboli...
+    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": "kegg_search_pathway", "arguments": {"keyword": keyword}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["kegg_search_pathway"]

tooluniverse/tools/ols_find_similar_terms.py

@@ -0,0 +1,63 @@
+"""
+ols_find_similar_terms
+
+Find similar terms using LLM-based similarity
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ols_find_similar_terms(
+    operation: str,
+    term_iri: str,
+    ontology: str,
+    size: Optional[int] = 10,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Find similar terms using LLM-based similarity
+
+    Parameters
+    ----------
+    operation : str
+        The operation to perform (find_similar_terms)
+    term_iri : str
+        The IRI of the term to find similar terms for
+    ontology : str
+        The ontology ID
+    size : int
+        Number of similar terms 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
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "ols_find_similar_terms",
+            "arguments": {
+                "operation": operation,
+                "term_iri": term_iri,
+                "ontology": ontology,
+                "size": size,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ols_find_similar_terms"]

tooluniverse/tools/{get_hyperopt_info.py → ols_get_ontology_info.py}

@@ -1,27 +1,30 @@
 """
-get_hyperopt_info
+ols_get_ontology_info
 
-Get comprehensive information about Hyperopt – distributed hyperparameter optimization
+Get detailed information about an ontology
 """
 
 from typing import Any, Optional, Callable
 from ._shared_client import get_shared_client
 
 
-def get_hyperopt_info(
-    include_examples: bool,
+def ols_get_ontology_info(
+    operation: str,
+    ontology_id: str,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,
     validate: bool = True,
 ) -> Any:
     """
-    Get comprehensive information about Hyperopt – distributed hyperparameter optimization
+    Get detailed information about an ontology
 
     Parameters
     ----------
-    include_examples : bool
-        Whether to include usage examples and quick start guide
+    operation : str
+        The operation to perform (get_ontology_info)
+    ontology_id : str
+        The ID of the ontology to retrieve
     stream_callback : Callable, optional
         Callback for streaming output
     use_cache : bool, default False
@@ -37,8 +40,8 @@ def get_hyperopt_info(
 
     return get_shared_client().run_one_function(
         {
-            "name": "get_hyperopt_info",
-            "arguments": {"include_examples": include_examples},
+            "name": "ols_get_ontology_info",
+            "arguments": {"operation": operation, "ontology_id": ontology_id},
         },
         stream_callback=stream_callback,
         use_cache=use_cache,
@@ -46,4 +49,4 @@ def get_hyperopt_info(
     )
 
 
-__all__ = ["get_hyperopt_info"]
+__all__ = ["ols_get_ontology_info"]

tooluniverse/tools/ols_get_term_ancestors.py

@@ -0,0 +1,67 @@
+"""
+ols_get_term_ancestors
+
+Get ancestor terms of a specific term in an ontology
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ols_get_term_ancestors(
+    operation: str,
+    term_iri: str,
+    ontology: str,
+    include_obsolete: Optional[bool] = False,
+    size: Optional[int] = 20,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get ancestor terms of a specific term in an ontology
+
+    Parameters
+    ----------
+    operation : str
+        The operation to perform (get_term_ancestors)
+    term_iri : str
+        The IRI of the term to retrieve ancestors for
+    ontology : str
+        The ontology ID
+    include_obsolete : bool
+        Include obsolete terms (default: false)
+    size : int
+        Number of results to return (default: 20)
+    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": "ols_get_term_ancestors",
+            "arguments": {
+                "operation": operation,
+                "term_iri": term_iri,
+                "ontology": ontology,
+                "include_obsolete": include_obsolete,
+                "size": size,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ols_get_term_ancestors"]