modulector-sdk 2.4.0__tar.gz → 2.6.0__tar.gz

{modulector_sdk-2.4.0/src/modulector_sdk.egg-info → modulector_sdk-2.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: modulector-sdk
-Version: 2.4.0
+Version: 2.6.0
 Summary: Typed Python SDK for the Modulector API.
 Author: omicsdatascience
 License-Expression: MIT
@@ -31,10 +31,7 @@ Dynamic: license-file
 
 # Modulector SDK
 
-Typed Python SDK for the Modulector API. The package contains client helpers for
-querying miRNA target interactions, miRNA aliases, methylation sites, disease
-associations, drug associations, and PubMed subscriptions without installing the
-Django backend dependencies.
+Typed Python SDK for the Modulector API. The package contains client helpers for querying predicted and experimentally validated miRNA target interactions, miRNA aliases, methylation sites, disease associations, drug associations, and PubMed subscriptions without installing the Django backend dependencies.
 
 ## Installation
 
@@ -45,7 +42,11 @@ pip install modulector-sdk
 ## Usage
 
 ```python
-from modulector_sdk import get_mirna_details, get_mirna_target_interactions
+from modulector_sdk import (
+    get_mirna_details,
+    get_mirna_target_interactions,
+    get_mirna_target_validations,
+)
 
 details = get_mirna_details("hsa-miR-21-5p")
 interactions = get_mirna_target_interactions(
@@ -53,6 +54,11 @@ interactions = get_mirna_target_interactions(
     gene="PTEN",
     include_pubmeds=True,
 )
+validations = get_mirna_target_validations(
+    mirna="hsa-miR-122-5p",
+    target="SLC7A1",
+    experiment="Western blot",
+)
 ```
 
 Set `MODULECTOR_API_BASE_URL` to target a different Modulector deployment:
@@ -95,11 +101,10 @@ modulector-mcp --transport streamable-http --host 127.0.0.1 --port 8000
 
 Then connect the client to `http://127.0.0.1:8000/mcp`.
 
-The server includes tools for miRNA target interactions, miRNA details and
-aliases, miRNA identifier resolution, methylation site lookup and annotation,
-disease associations, drug associations, and PubMed news subscriptions. Use
-`MODULECTOR_API_BASE_URL` or each tool's `base_url` argument to target a custom
-Modulector deployment.
+The server includes tools for predicted and experimentally validated miRNA target interactions, miRNA details and aliases, miRNA identifier resolution, methylation site lookup and annotation, disease associations, drug associations, and PubMed news subscriptions. Use `MODULECTOR_API_BASE_URL` or each tool's `base_url` argument to target a custom Modulector deployment.
+
+When deployed with the root Docker Compose stack, nginx proxies the MCP
+Streamable HTTP endpoint at `https://<mydomain.com>/mcp`.
 
 ## Development
 

{modulector_sdk-2.4.0 → modulector_sdk-2.6.0}/README.md

@@ -1,9 +1,6 @@
 # Modulector SDK
 
-Typed Python SDK for the Modulector API. The package contains client helpers for
-querying miRNA target interactions, miRNA aliases, methylation sites, disease
-associations, drug associations, and PubMed subscriptions without installing the
-Django backend dependencies.
+Typed Python SDK for the Modulector API. The package contains client helpers for querying predicted and experimentally validated miRNA target interactions, miRNA aliases, methylation sites, disease associations, drug associations, and PubMed subscriptions without installing the Django backend dependencies.
 
 ## Installation
 
@@ -14,7 +11,11 @@ pip install modulector-sdk
 ## Usage
 
 ```python
-from modulector_sdk import get_mirna_details, get_mirna_target_interactions
+from modulector_sdk import (
+    get_mirna_details,
+    get_mirna_target_interactions,
+    get_mirna_target_validations,
+)
 
 details = get_mirna_details("hsa-miR-21-5p")
 interactions = get_mirna_target_interactions(
@@ -22,6 +23,11 @@ interactions = get_mirna_target_interactions(
     gene="PTEN",
     include_pubmeds=True,
 )
+validations = get_mirna_target_validations(
+    mirna="hsa-miR-122-5p",
+    target="SLC7A1",
+    experiment="Western blot",
+)
 ```
 
 Set `MODULECTOR_API_BASE_URL` to target a different Modulector deployment:
@@ -64,11 +70,10 @@ modulector-mcp --transport streamable-http --host 127.0.0.1 --port 8000
 
 Then connect the client to `http://127.0.0.1:8000/mcp`.
 
-The server includes tools for miRNA target interactions, miRNA details and
-aliases, miRNA identifier resolution, methylation site lookup and annotation,
-disease associations, drug associations, and PubMed news subscriptions. Use
-`MODULECTOR_API_BASE_URL` or each tool's `base_url` argument to target a custom
-Modulector deployment.
+The server includes tools for predicted and experimentally validated miRNA target interactions, miRNA details and aliases, miRNA identifier resolution, methylation site lookup and annotation, disease associations, drug associations, and PubMed news subscriptions. Use `MODULECTOR_API_BASE_URL` or each tool's `base_url` argument to target a custom Modulector deployment.
+
+When deployed with the root Docker Compose stack, nginx proxies the MCP
+Streamable HTTP endpoint at `https://<mydomain.com>/mcp`.
 
 ## Development
 

{modulector_sdk-2.4.0 → modulector_sdk-2.6.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "modulector-sdk"
-version = "2.4.0"
+version = "2.6.0"
 description = "Typed Python SDK for the Modulector API."
 readme = "README.md"
 requires-python = ">=3.10"

{modulector_sdk-2.4.0 → modulector_sdk-2.6.0}/src/modulector_sdk/__init__.py

@@ -9,8 +9,10 @@ from .services import (
     MirnaDisease,
     MirnaDrug,
     MirnaTargetInteraction,
+    MirnaTargetValidation,
     SourceLink,
     SubscribePubmedsResponse,
+    SupportType,
     UcscCpgIsland,
     find_methylation_sites,
     find_mirna_codes,
@@ -23,6 +25,7 @@ from .services import (
     get_mirna_codes,
     get_mirna_details,
     get_mirna_target_interactions,
+    get_mirna_target_validations,
     subscribe_pubmeds,
     unsubscribe_pubmeds,
 )
@@ -44,9 +47,11 @@ __all__ = [
     "MirnaDisease",
     "MirnaDrug",
     "MirnaTargetInteraction",
+    "MirnaTargetValidation",
     "PaginatedResponse",
     "SourceLink",
     "SubscribePubmedsResponse",
+    "SupportType",
     "UcscCpgIsland",
     "find_methylation_sites",
     "find_mirna_codes",
@@ -60,6 +65,7 @@ __all__ = [
     "get_mirna_codes",
     "get_mirna_details",
     "get_mirna_target_interactions",
+    "get_mirna_target_validations",
     "get_paginated_response",
     "get_simple_response",
     "iter_paginated_results",

{modulector_sdk-2.4.0 → modulector_sdk-2.6.0}/src/modulector_sdk/mcp_server.py

@@ -3,29 +3,38 @@
 from __future__ import annotations
 
 import argparse
+import os
 from typing import Any, Final, Literal, TypeVar, cast
+from urllib.parse import urlparse
 
 from mcp.server.fastmcp import FastMCP
+from mcp.server.transport_security import TransportSecuritySettings
 
 from . import services
+from .services import SupportType
 from .utils import PaginatedResponse
 
 T = TypeVar("T")
 Transport = Literal["stdio", "sse", "streamable-http"]
 
 SERVER_INSTRUCTIONS: Final[str] = (
-    "Use Modulector to help researchers inspect human miRNA target "
-    "interactions, miRNA aliases, disease and drug associations, and "
+    "Use Modulector to help researchers inspect predicted and experimentally "
+    "validated human miRNA target interactions, miRNA aliases, disease and "
+    "drug associations, and "
     "Illumina methylation site annotations. Prefer finder tools when the "
     "user gives partial or uncertain identifiers, then use the detail or "
     "paginated tools with explicit identifiers. The returned data comes from "
     "the configured Modulector API deployment."
 )
+PUBLIC_BASE_URL: Final[str] = os.getenv(
+    "MODULECTOR_PUBLIC_BASE_URL",
+    services.MODULECTOR_API_BASE_URL,
+)
 
 mcp = FastMCP(
     name="modulector",
     instructions=SERVER_INSTRUCTIONS,
-    website_url=services.MODULECTOR_API_BASE_URL,
+    website_url=PUBLIC_BASE_URL,
 )
 
 
@@ -43,11 +52,13 @@ def about_modulector() -> str:
 
     return (
         "# Modulector\n\n"
-        "Modulector provides programmatic access to curated human miRNA target "
-        "interactions, miRNA aliases, miRNA-disease associations, "
+        "Modulector provides programmatic access to predicted and "
+        "experimentally validated human miRNA target interactions, miRNA "
+        "aliases, miRNA-disease associations, "
         "miRNA-drug associations, and Illumina Infinium MethylationEPIC 2.0 "
         "site annotations.\n\n"
         f"Default API base URL: `{services.MODULECTOR_API_BASE_URL}`\n\n"
+        f"Public website URL: `{PUBLIC_BASE_URL}`\n\n"
         "Use the finder tools for partial identifiers, then query detail or "
         "paginated tools with exact miRNA, gene, disease, drug, or methylation "
         "site filters."
@@ -96,7 +107,7 @@ def get_mirna_target_interactions(
     :param gene: Gene symbol.
     :param score: Minimum MirDIP score between 0 and 1.
     :param include_pubmeds: Whether to include PubMed URLs for interactions.
-    :param ordering: Comma-separated ordering fields, such as ``-score,gene``.
+    :param ordering: Comma-separated ordering fields, such as `-score,gene`.
     :param search: Search term for supported server-side fields.
     :param page: Page number to request.
     :param page_size: Number of records to request.
@@ -121,6 +132,48 @@ def get_mirna_target_interactions(
     )
 
 
+@mcp.tool()
+def get_mirna_target_validations(
+    mirna: str | None = None,
+    target: str | None = None,
+    support_type: SupportType | None = None,
+    experiment: str | None = None,
+    ordering: str | None = None,
+    page: int | None = None,
+    page_size: int | None = None,
+    base_url: str | None = None,
+    timeout: float = 30.0,
+) -> dict[str, Any]:
+    """Return experimentally validated miRNA-target interactions.
+
+    :param mirna: Exact standardized miRNA identifier.
+    :param target: Exact target gene symbol.
+    :param support_type: Exact miRTarBase support classification.
+    :param experiment: Case-insensitive partial experiment name, such as
+        `Western blot`.
+    :param ordering: Comma-separated `mirna` or `gene` ordering fields.
+    :param page: Page number to request.
+    :param page_size: Number of records to request.
+    :param base_url: Optional Modulector API deployment URL.
+    :param timeout: Request timeout in seconds.
+    :return: Paginated miRTarBase validation records.
+    """
+
+    return _page_to_dict(
+        services.get_mirna_target_validations(
+            base_url=_base_url(base_url),
+            mirna=mirna,
+            target=target,
+            support_type=support_type,
+            experiment=experiment,
+            ordering=ordering,
+            page=page,
+            page_size=page_size,
+            timeout=timeout,
+        )
+    )
+
+
 @mcp.tool()
 def get_mirna_details(
     mirna: str,
@@ -135,10 +188,13 @@ def get_mirna_details(
     :return: miRNA detail record.
     """
 
-    return services.get_mirna_details(
-        mirna,
-        base_url=_base_url(base_url),
-        timeout=timeout,
+    return cast(
+        dict[str, Any],
+        services.get_mirna_details(
+            mirna,
+            base_url=_base_url(base_url),
+            timeout=timeout,
+        ),
     )
 
 
@@ -308,10 +364,13 @@ def get_methylation_details(
     :return: Methylation site detail record.
     """
 
-    return services.get_methylation_details(
-        methylation_site,
-        base_url=_base_url(base_url),
-        timeout=timeout,
+    return cast(
+        dict[str, Any],
+        services.get_methylation_details(
+            methylation_site,
+            base_url=_base_url(base_url),
+            timeout=timeout,
+        ),
     )
 
 
@@ -400,6 +459,7 @@ def main() -> None:
         mcp.settings.host = args.host
         mcp.settings.port = args.port
         mcp.settings.json_response = args.json_response
+        _configure_http_transport_security()
     mcp.run(transport=transport)
 
 
@@ -447,6 +507,63 @@ def _base_url(base_url: str | None) -> str:
     return base_url or services.MODULECTOR_API_BASE_URL
 
 
+def _configure_http_transport_security() -> None:
+    """Configure DNS rebinding protection for HTTP MCP transports.
+
+    :return: None.
+    """
+
+    mcp.settings.transport_security = TransportSecuritySettings(
+        allowed_hosts=_allowed_hosts(),
+        allowed_origins=_allowed_origins(),
+    )
+
+
+def _allowed_hosts() -> list[str]:
+    """Return allowed Host headers for the MCP HTTP transport.
+
+    :return: Host header allow-list.
+    """
+
+    configured_hosts = _csv_env("MODULECTOR_MCP_ALLOWED_HOSTS")
+    if configured_hosts:
+        return configured_hosts
+
+    parsed_public_url = urlparse(PUBLIC_BASE_URL)
+    public_host = parsed_public_url.netloc
+    hosts = ["127.0.0.1:*", "localhost:*", "[::1]:*"]
+    if public_host:
+        hosts.append(public_host)
+    return hosts
+
+
+def _allowed_origins() -> list[str]:
+    """Return allowed Origin headers for the MCP HTTP transport.
+
+    :return: Origin header allow-list.
+    """
+
+    configured_origins = _csv_env("MODULECTOR_MCP_ALLOWED_ORIGINS")
+    if configured_origins:
+        return configured_origins
+
+    parsed_public_url = urlparse(PUBLIC_BASE_URL)
+    origins = ["http://127.0.0.1:*", "http://localhost:*", "http://[::1]:*"]
+    if parsed_public_url.scheme and parsed_public_url.netloc:
+        origins.append(f"{parsed_public_url.scheme}://{parsed_public_url.netloc}")
+    return origins
+
+
+def _csv_env(name: str) -> list[str]:
+    """Return comma-separated environment variable values.
+
+    :param name: Environment variable name.
+    :return: Non-empty stripped values.
+    """
+
+    return [value.strip() for value in os.getenv(name, "").split(",") if value.strip()]
+
+
 def _page_to_dict(page: PaginatedResponse[T]) -> dict[str, Any]:
     """Convert a paginated SDK response into a JSON-serializable mapping.
 

{modulector_sdk-2.4.0 → modulector_sdk-2.6.0}/src/modulector_sdk/services.py

@@ -24,6 +24,12 @@ FINDER_LIMIT_MAX: Final[int] = 3000
 
 Ordering = str | Sequence[str]
 ScoreClass = Literal["V", "H", "M", "L"]
+SupportType = Literal[
+    "Functional MTI",
+    "Functional MTI (Weak)",
+    "Non-Functional MTI",
+    "Non-Functional MTI (Weak)",
+]
 
 
 class SourceLink(TypedDict):
@@ -99,6 +105,34 @@ class MirnaTargetInteraction(TypedDict):
     """MirDIP score class for the interaction."""
 
 
+class MirnaTargetValidation(TypedDict):
+    """One experimentally validated miRNA-target interaction record."""
+
+    id: int
+    """Internal record identifier."""
+
+    mirtarbase_id: str
+    """Interaction identifier assigned by miRTarBase."""
+
+    mirna: str
+    """Standardized miRNA identifier."""
+
+    gene: str
+    """Target gene symbol."""
+
+    target_gene_entrez_id: str | None
+    """Entrez identifier for the target gene, when available."""
+
+    experiments: list[str]
+    """Techniques used to validate the miRNA-target interaction."""
+
+    support_type: SupportType
+    """Classification of the experimental support."""
+
+    pmid: str
+    """PubMed identifier for the supporting publication."""
+
+
 class MirnaDisease(TypedDict):
     """One miRNA disease association record."""
 
@@ -208,18 +242,18 @@ def get_mirna_target_interactions(
     :param mirna: miRNA accession ID or miRBase name.
     :param gene: Gene symbol.
     :param score: Minimum mirDIP interaction score. Valid values are between
-        ``0`` and ``1``.
+        `0` and `1`.
     :param include_pubmeds: Whether PubMed links should be included.
     :param ordering: Ordering field or comma-separated fields. Prefix a field
-        with ``-`` for descending order.
+        with `-` for descending order.
     :param search: Search term for supported server-side search fields.
     :param page: Page number to request.
     :param page_size: Number of records per page.
     :param headers: Optional HTTP headers.
     :param timeout: Request timeout in seconds.
-    :param session: Optional ``requests.Session`` to use for the request.
-    :raises ValueError: If neither ``mirna`` nor ``gene`` is provided, or if
-        ``score`` is outside the accepted range.
+    :param session: Optional `requests.Session` to use for the request.
+    :raises ValueError: If neither `mirna` nor `gene` is provided, or if
+        `score` is outside the accepted range.
     :return: Paginated miRNA target interaction records.
     """
 
@@ -248,6 +282,60 @@ def get_mirna_target_interactions(
     return cast(PaginatedResponse[MirnaTargetInteraction], response)
 
 
+def get_mirna_target_validations(
+    base_url: str = MODULECTOR_API_BASE_URL,
+    mirna: str | None = None,
+    target: str | None = None,
+    support_type: SupportType | None = None,
+    experiment: str | None = None,
+    ordering: Ordering | None = None,
+    page: int | None = None,
+    page_size: int | None = None,
+    headers: Headers = None,
+    timeout: float = 30.0,
+    session: requests.Session | None = None,
+) -> PaginatedResponse[MirnaTargetValidation]:
+    """Return experimentally validated miRNA-target interactions.
+
+    :param base_url: Base URL of the Modulector API.
+    :param mirna: Exact standardized miRNA identifier.
+    :param target: Exact target gene symbol.
+    :param support_type: Exact miRTarBase support classification.
+    :param experiment: Case-insensitive partial experiment name.
+    :param ordering: Ordering field or comma-separated fields. Supported fields
+        are `mirna` and `gene`; prefix a field with `-` for descending
+        order.
+    :param page: Page number to request.
+    :param page_size: Number of records per page.
+    :param headers: Optional HTTP headers.
+    :param timeout: Request timeout in seconds.
+    :param session: Optional `requests.Session` to use for the request.
+    :raises ValueError: If neither `mirna` nor `target` is provided.
+    :return: Paginated experimentally validated interaction records.
+    """
+
+    if mirna is None and target is None:
+        raise ValueError("mirna or target is required")
+
+    params = _request_params(
+        mirna=mirna,
+        target=target,
+        support_type=support_type,
+        experiment=experiment,
+        ordering=_format_ordering(ordering),
+    )
+    response = get_paginated_response(
+        _build_url(base_url, "mirna-target-validation"),
+        params=params,
+        page=page,
+        page_size=page_size,
+        headers=headers,
+        timeout=timeout,
+        session=session,
+    )
+    return cast(PaginatedResponse[MirnaTargetValidation], response)
+
+
 def get_mirna_details(
     mirna: str,
     *,
@@ -262,7 +350,7 @@ def get_mirna_details(
     :param base_url: Base URL of the Modulector API.
     :param headers: Optional HTTP headers.
     :param timeout: Request timeout in seconds.
-    :param session: Optional ``requests.Session`` to use for the request.
+    :param session: Optional `requests.Session` to use for the request.
     :return: miRNA aliases, sequence, accession ID, and source links.
     """
 
@@ -298,12 +386,12 @@ def get_mirna_aliases(
     :param previous_mature_mirna: Exact previous mature miRNA filter.
     :param search: Case-insensitive search across identifier fields.
     :param ordering: Ordering field or comma-separated fields. Prefix a field
-        with ``-`` for descending order.
+        with `-` for descending order.
     :param page: Page number to request.
     :param page_size: Number of records per page.
     :param headers: Optional HTTP headers.
     :param timeout: Request timeout in seconds.
-    :param session: Optional ``requests.Session`` to use for the request.
+    :param session: Optional `requests.Session` to use for the request.
     :return: Paginated miRNA alias records.
     """
 
@@ -340,12 +428,12 @@ def find_mirna_codes(
     :param query: miRNA search string.
     :param base_url: Base URL of the Modulector API.
     :param limit: Maximum number of returned values. The API accepts values up
-        to ``3000``.
+        to `3000`.
     :param headers: Optional HTTP headers.
     :param timeout: Request timeout in seconds.
-    :param session: Optional ``requests.Session`` to use for the request.
-    :raises ValueError: If ``limit`` is less than ``1`` or greater than
-        ``3000``.
+    :param session: Optional `requests.Session` to use for the request.
+    :raises ValueError: If `limit` is less than `1` or greater than
+        `3000`.
     :return: Matching miRNA IDs or accession IDs.
     """
 
@@ -374,9 +462,9 @@ def get_mirna_codes(
     :param base_url: Base URL of the Modulector API.
     :param headers: Optional HTTP headers.
     :param timeout: Request timeout in seconds.
-    :param session: Optional ``requests.Session`` to use for the request.
+    :param session: Optional `requests.Session` to use for the request.
     :return: Mapping from each requested identifier to its accession ID, or
-        ``None`` when no accession ID is found.
+        `None` when no accession ID is found.
     """
 
     payload = get_simple_response(
@@ -404,12 +492,12 @@ def find_methylation_sites(
     :param query: Methylation site search string.
     :param base_url: Base URL of the Modulector API.
     :param limit: Maximum number of returned values. The API accepts values up
-        to ``3000``.
+        to `3000`.
     :param headers: Optional HTTP headers.
     :param timeout: Request timeout in seconds.
-    :param session: Optional ``requests.Session`` to use for the request.
-    :raises ValueError: If ``limit`` is less than ``1`` or greater than
-        ``3000``.
+    :param session: Optional `requests.Session` to use for the request.
+    :raises ValueError: If `limit` is less than `1` or greater than
+        `3000`.
     :return: Matching methylation site names.
     """
 
@@ -438,7 +526,7 @@ def get_methylation_sites(
     :param base_url: Base URL of the Modulector API.
     :param headers: Optional HTTP headers.
     :param timeout: Request timeout in seconds.
-    :param session: Optional ``requests.Session`` to use for the request.
+    :param session: Optional `requests.Session` to use for the request.
     :return: Mapping from each requested identifier to matching EPIC 2.0 site
         names.
     """
@@ -468,7 +556,7 @@ def get_methylation_site_genes(
     :param base_url: Base URL of the Modulector API.
     :param headers: Optional HTTP headers.
     :param timeout: Request timeout in seconds.
-    :param session: Optional ``requests.Session`` to use for the request.
+    :param session: Optional `requests.Session` to use for the request.
     :return: Mapping from each requested identifier to associated genes.
     """
 
@@ -498,7 +586,7 @@ def get_methylation_details(
     :param base_url: Base URL of the Modulector API.
     :param headers: Optional HTTP headers.
     :param timeout: Request timeout in seconds.
-    :param session: Optional ``requests.Session`` to use for the request.
+    :param session: Optional `requests.Session` to use for the request.
     :return: Methylation site details, aliases, CpG island relations, and genes.
     """
 
@@ -531,12 +619,12 @@ def get_diseases(
         returned page by page.
     :param search: Case-insensitive search term for disease names.
     :param ordering: Ordering field or comma-separated fields. Prefix a field
-        with ``-`` for descending order.
+        with `-` for descending order.
     :param page: Page number to request.
     :param page_size: Number of records per page.
     :param headers: Optional HTTP headers.
     :param timeout: Request timeout in seconds.
-    :param session: Optional ``requests.Session`` to use for the request.
+    :param session: Optional `requests.Session` to use for the request.
     :return: Paginated miRNA disease association records.
     """
 
@@ -579,12 +667,12 @@ def get_drugs(
     :param search: Case-insensitive search term for condition, small molecule,
         and expression pattern fields.
     :param ordering: Ordering field or comma-separated fields. Prefix a field
-        with ``-`` for descending order.
+        with `-` for descending order.
     :param page: Page number to request.
     :param page_size: Number of records per page.
     :param headers: Optional HTTP headers.
     :param timeout: Request timeout in seconds.
-    :param session: Optional ``requests.Session`` to use for the request.
+    :param session: Optional `requests.Session` to use for the request.
     :return: Paginated miRNA drug association records.
     """
 
@@ -624,7 +712,7 @@ def subscribe_pubmeds(
     :param gene: Optional gene symbol filter for the subscription.
     :param headers: Optional HTTP headers.
     :param timeout: Request timeout in seconds.
-    :param session: Optional ``requests.Session`` to use for the request.
+    :param session: Optional `requests.Session` to use for the request.
     :return: Subscription token response.
     """
 
@@ -648,11 +736,11 @@ def unsubscribe_pubmeds(
 ) -> str:
     """Unsubscribe from PubMed news.
 
-    :param token: Subscription token returned by ``subscribe_pubmeds``.
+    :param token: Subscription token returned by `subscribe_pubmeds`.
     :param base_url: Base URL of the Modulector API.
     :param headers: Optional HTTP headers.
     :param timeout: Request timeout in seconds.
-    :param session: Optional ``requests.Session`` to use for the request.
+    :param session: Optional `requests.Session` to use for the request.
     :return: API confirmation message.
     """
 
@@ -678,10 +766,10 @@ def _build_url(base_url: str, endpoint: str) -> str:
 
 
 def _request_params(**params: Any) -> dict[str, Any]:
-    """Return request parameters without ``None`` values.
+    """Return request parameters without `None` values.
 
     :param params: Query parameters keyed by API parameter name.
-    :return: A dictionary containing only parameters with non-``None`` values.
+    :return: A dictionary containing only parameters with non-`None` values.
     """
 
     return {key: value for key, value in params.items() if value is not None}
@@ -691,7 +779,7 @@ def _bool_param(value: bool | None) -> str | None:
     """Convert an optional boolean to the API's lowercase string form.
 
     :param value: Boolean value to convert.
-    :return: ``"true"``, ``"false"``, or ``None``.
+    :return: `"true"`, `"false"`, or `None`.
     """
 
     if value is None:
@@ -704,7 +792,7 @@ def _format_ordering(ordering: Ordering | None) -> str | None:
 
     :param ordering: A comma-separated ordering string or a sequence of ordering
         fields.
-    :return: A comma-separated ordering string, or ``None``.
+    :return: A comma-separated ordering string, or `None`.
     """
 
     if ordering is None:
@@ -722,8 +810,8 @@ def _validate_limit(limit: int | None) -> None:
     """Validate finder service limit parameters.
 
     :param limit: Limit value to validate.
-    :raises ValueError: If ``limit`` is outside the API's accepted range.
-    :return: ``None``.
+    :raises ValueError: If `limit` is outside the API's accepted range.
+    :return: `None`.
     """
 
     if limit is not None and not 1 <= limit <= FINDER_LIMIT_MAX:
@@ -739,8 +827,10 @@ __all__ = [
     "MirnaDisease",
     "MirnaDrug",
     "MirnaTargetInteraction",
+    "MirnaTargetValidation",
     "SourceLink",
     "SubscribePubmedsResponse",
+    "SupportType",
     "UcscCpgIsland",
     "find_methylation_sites",
     "find_mirna_codes",
@@ -753,6 +843,7 @@ __all__ = [
     "get_mirna_codes",
     "get_mirna_details",
     "get_mirna_target_interactions",
+    "get_mirna_target_validations",
     "subscribe_pubmeds",
     "unsubscribe_pubmeds",
 ]

{modulector_sdk-2.4.0 → modulector_sdk-2.6.0/src/modulector_sdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: modulector-sdk
-Version: 2.4.0
+Version: 2.6.0
 Summary: Typed Python SDK for the Modulector API.
 Author: omicsdatascience
 License-Expression: MIT
@@ -31,10 +31,7 @@ Dynamic: license-file
 
 # Modulector SDK
 
-Typed Python SDK for the Modulector API. The package contains client helpers for
-querying miRNA target interactions, miRNA aliases, methylation sites, disease
-associations, drug associations, and PubMed subscriptions without installing the
-Django backend dependencies.
+Typed Python SDK for the Modulector API. The package contains client helpers for querying predicted and experimentally validated miRNA target interactions, miRNA aliases, methylation sites, disease associations, drug associations, and PubMed subscriptions without installing the Django backend dependencies.
 
 ## Installation
 
@@ -45,7 +42,11 @@ pip install modulector-sdk
 ## Usage
 
 ```python
-from modulector_sdk import get_mirna_details, get_mirna_target_interactions
+from modulector_sdk import (
+    get_mirna_details,
+    get_mirna_target_interactions,
+    get_mirna_target_validations,
+)
 
 details = get_mirna_details("hsa-miR-21-5p")
 interactions = get_mirna_target_interactions(
@@ -53,6 +54,11 @@ interactions = get_mirna_target_interactions(
     gene="PTEN",
     include_pubmeds=True,
 )
+validations = get_mirna_target_validations(
+    mirna="hsa-miR-122-5p",
+    target="SLC7A1",
+    experiment="Western blot",
+)
 ```
 
 Set `MODULECTOR_API_BASE_URL` to target a different Modulector deployment:
@@ -95,11 +101,10 @@ modulector-mcp --transport streamable-http --host 127.0.0.1 --port 8000
 
 Then connect the client to `http://127.0.0.1:8000/mcp`.
 
-The server includes tools for miRNA target interactions, miRNA details and
-aliases, miRNA identifier resolution, methylation site lookup and annotation,
-disease associations, drug associations, and PubMed news subscriptions. Use
-`MODULECTOR_API_BASE_URL` or each tool's `base_url` argument to target a custom
-Modulector deployment.
+The server includes tools for predicted and experimentally validated miRNA target interactions, miRNA details and aliases, miRNA identifier resolution, methylation site lookup and annotation, disease associations, drug associations, and PubMed news subscriptions. Use `MODULECTOR_API_BASE_URL` or each tool's `base_url` argument to target a custom Modulector deployment.
+
+When deployed with the root Docker Compose stack, nginx proxies the MCP
+Streamable HTTP endpoint at `https://<mydomain.com>/mcp`.
 
 ## Development