tooluniverse 1.0.7__py3-none-any.whl → 1.0.8__py3-none-any.whl

tooluniverse/tools/convert_to_markdown.py

@@ -0,0 +1,59 @@
+"""
+convert_to_markdown
+
+Convert a resource described by an http:, https:, file: or data: URI to markdown.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def convert_to_markdown(
+    uri: str,
+    output_path: Optional[str] = None,
+    enable_plugins: Optional[bool] = False,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Convert a resource described by an http:, https:, file: or data: URI to markdown.
+
+    Parameters
+    ----------
+    uri : str
+        URI of the resource to convert (supports http:, https:, file:, data: URIs)
+    output_path : str
+        Optional output file path
+    enable_plugins : bool
+        Enable 3rd-party plugins
+    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": "convert_to_markdown",
+            "arguments": {
+                "uri": uri,
+                "output_path": output_path,
+                "enable_plugins": enable_plugins,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["convert_to_markdown"]

tooluniverse/tools/dbSNP_get_variant_by_rsid.py

@@ -0,0 +1,46 @@
+"""
+dbSNP_get_variant_by_rsid
+
+Fetch dbSNP variant by rsID using NCBI Variation Services (refsnp endpoint).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def dbSNP_get_variant_by_rsid(
+    rsid: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Fetch dbSNP variant by rsID using NCBI Variation Services (refsnp endpoint).
+
+    Parameters
+    ----------
+    rsid : str
+        rsID without 'rs' prefix or with (e.g., rs699 or 699).
+    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": "dbSNP_get_variant_by_rsid", "arguments": {"rsid": rsid}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["dbSNP_get_variant_by_rsid"]

tooluniverse/tools/gnomAD_query_variant.py

@@ -0,0 +1,52 @@
+"""
+gnomAD_query_variant
+
+Query gnomAD GraphQL for a variant in a dataset (returns ID and genome allele counts/frequency).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def gnomAD_query_variant(
+    variant_id: str,
+    dataset: Optional[str] = "gnomad_r4",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Query gnomAD GraphQL for a variant in a dataset (returns ID and genome allele counts/frequency).
+
+    Parameters
+    ----------
+    variant_id : str
+        Variant ID like '1-230710048-A-G'.
+    dataset : str
+        Dataset ID (e.g., gnomad_r4).
+    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_query_variant",
+            "arguments": {"variant_id": variant_id, "dataset": dataset},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["gnomAD_query_variant"]

tooluniverse/tools/openalex_literature_search.py

@@ -10,10 +10,10 @@ from ._shared_client import get_shared_client
 
 def openalex_literature_search(
     search_keywords: str,
-    max_results: int,
-    year_from: int,
-    year_to: int,
-    open_access: bool,
+    max_results: Optional[int] = 10,
+    year_from: Optional[int] = None,
+    year_to: Optional[int] = None,
+    open_access: Optional[bool] = None,
     *,
     stream_callback: Optional[Callable[[str], None]] = None,
     use_cache: bool = False,

tooluniverse/ucsc_tool.py

@@ -0,0 +1,60 @@
+import requests
+from .base_tool import BaseTool
+from .tool_registry import register_tool
+
+
+@register_tool("UCSCTool")
+class UCSCTool(BaseTool):
+    """
+    Local tool wrapper for UCSC Genome Browser track API.
+    Queries knownGene track for genomic regions.
+    """
+
+    def __init__(self, tool_config):
+        super().__init__(tool_config)
+        self.base = "https://api.genome.ucsc.edu/getData/track"
+        self.session = requests.Session()
+
+    def run(self, arguments):
+        genome = arguments.get("genome", "hg38")
+        chrom = arguments.get("chrom")
+        start = arguments.get("start")
+        end = arguments.get("end")
+        track = arguments.get("track", "knownGene")
+
+        if not all([chrom, start is not None, end is not None]):
+            return {"error": "Missing required parameters: chrom, start, end"}
+
+        params = {
+            "genome": genome,
+            "track": track,
+            "chrom": chrom,
+            "start": start,
+            "end": end,
+        }
+
+        resp = self.session.get(self.base, params=params, timeout=30)
+        resp.raise_for_status()
+        data = resp.json()
+
+        features = data.get(track, [])
+        items_returned = len(features)
+
+        # Extract key fields from each feature
+        processed_features = []
+        for feature in features:
+            processed_features.append(
+                {
+                    "name": feature.get("name", ""),
+                    "geneName": feature.get("geneName", ""),
+                    "chrom": feature.get("chrom", ""),
+                    "chromStart": feature.get("chromStart"),
+                    "chromEnd": feature.get("chromEnd"),
+                    "strand": feature.get("strand", ""),
+                }
+            )
+
+        return {
+            "itemsReturned": items_returned,
+            "features": processed_features,
+        }