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tool_util: fold id_util into galaxy.util.tool_version
extract_tool_id_from_xml/extract_tool_id_from_file/build_guid/ is_toolshed_guid had no callers. The one used function, extract_short_id_from_guid, is now short_tool_id next to remove_version_from_guid, and the manual rsplit spellings of the same extraction in the search-doc and populator ontology-id expansions go through the pair as well.
This commit is contained in:
mvdbeek
@@ -1,130 +0,0 @@
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"""
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Utilities for working with tool IDs and GUIDs.
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Tool IDs come in several formats:
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- Short ID: Just the tool identifier (e.g., "bwa", "qiime2__feature_classifier__classify_sklearn")
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- GUID: Full toolshed identifier (e.g., "toolshed.g2.bx.psu.edu/repos/owner/name/tool_id/version")
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This module provides utilities to parse and convert between these formats.
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"""
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import re
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def extract_tool_id_from_xml(xml_content: str, max_read: int = 2000) -> str | None:
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"""
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Extract tool ID from XML content using a simple regex.
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This is a fast extraction method that doesn't require full XML parsing.
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Useful when you need just the ID without macro expansion or validation.
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Args:
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xml_content: The XML content to parse (can be partial).
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max_read: Maximum characters to read from content (default: 2000).
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Returns:
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The tool ID if found, None otherwise.
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Example:
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>>> extract_tool_id_from_xml('<tool id="bwa" version="1.0">')
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'bwa'
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"""
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content = xml_content[:max_read] if len(xml_content) > max_read else xml_content
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match = re.search(r'<tool[^>]+id=["\']([^"\']+)["\']', content)
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return match.group(1) if match else None
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def extract_tool_id_from_file(file_path: str, max_read: int = 2000) -> str | None:
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"""
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Extract tool ID from an XML file.
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Args:
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file_path: Path to the tool XML file.
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max_read: Maximum characters to read from file (default: 2000).
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Returns:
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The tool ID if found, None otherwise.
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"""
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try:
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with open(file_path) as f:
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content = f.read(max_read)
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return extract_tool_id_from_xml(content, max_read=max_read)
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except Exception:
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return None
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def extract_short_id_from_guid(guid: str) -> str | None:
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"""
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Extract the short tool ID from a toolshed GUID.
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GUIDs have the format: toolshed.domain/repos/owner/name/tool_id/version
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This extracts just the tool_id part.
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Args:
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guid: The full toolshed GUID.
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Returns:
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The short tool ID, or the original guid if it's not in the expected format.
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Examples:
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>>> extract_short_id_from_guid("toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.1.0")
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'bwa'
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>>> extract_short_id_from_guid("toolshed.g2.bx.psu.edu/repos/iuc/qiime2__feature_classifier__classify_sklearn/qiime2__feature_classifier__classify_sklearn/2024.5.0+q2galaxy.2024.5.0")
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'qiime2__feature_classifier__classify_sklearn'
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>>> extract_short_id_from_guid("simple_tool")
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'simple_tool'
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"""
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if "/" not in guid:
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# Not a GUID, return as-is
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return guid
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# Split on "/" and extract the second-to-last part
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# Format: toolshed.domain/repos/owner/name/tool_id/version
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# Parts: [domain, "repos", owner, name, tool_id, version]
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parts = guid.split("/")
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if len(parts) >= 2:
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# The tool_id is typically the second-to-last part (before version)
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tool_id = parts[-2]
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return tool_id
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return guid
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def build_guid(tool_shed: str, owner: str, name: str, tool_id: str, version: str) -> str:
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"""
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Build a full toolshed GUID from components.
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Args:
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tool_shed: The toolshed domain (e.g., "toolshed.g2.bx.psu.edu").
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owner: Repository owner.
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name: Repository name.
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tool_id: Tool ID.
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version: Tool version.
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Returns:
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The full GUID string.
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Example:
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>>> build_guid("toolshed.g2.bx.psu.edu", "devteam", "bwa", "bwa", "0.1.0")
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'toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.1.0'
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"""
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return f"{tool_shed}/repos/{owner}/{name}/{tool_id}/{version}"
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def is_toolshed_guid(tool_id: str) -> bool:
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"""
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Check if a tool ID is a toolshed GUID.
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Args:
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tool_id: The tool ID to check.
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Returns:
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True if this looks like a toolshed GUID, False otherwise.
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Examples:
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>>> is_toolshed_guid("toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.1.0")
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True
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>>> is_toolshed_guid("bwa")
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False
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"""
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return "/repos/" in tool_id
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@@ -25,7 +25,6 @@ from galaxy.exceptions import (
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ObjectNotFound,
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RequestParameterInvalidException,
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)
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from galaxy.tool_util.id_util import extract_short_id_from_guid
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from galaxy.tool_util.ontologies.ontology_data import curated_tool_tags
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from galaxy.tool_util.parser import get_tool_source
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from galaxy.tool_util.toolbox.base import (
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@@ -55,7 +54,10 @@ from galaxy.tools.source_store.populator import (
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populate_store_inline,
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)
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from galaxy.util import listify
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from galaxy.util.tool_version import remove_version_from_guid
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from galaxy.util.tool_version import (
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remove_version_from_guid,
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short_tool_id,
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)
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from . import (
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create_tool_from_source,
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ToolBox,
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@@ -238,8 +240,7 @@ class LazyTool:
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def old_id(self) -> str:
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if "old_id" in self._overrides:
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return self._overrides["old_id"]
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short = extract_short_id_from_guid(self._entry.id)
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return short or self._entry.id
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return short_tool_id(self._entry.id)
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@property
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def tool_tags(self) -> list[str]:
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@@ -917,8 +918,8 @@ class LazyToolBox(ToolBox):
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if self._tool_index is None:
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return
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for entry_id in self._tool_index.entries.keys():
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short_id = extract_short_id_from_guid(entry_id)
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if short_id and short_id != entry_id:
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short_id = short_tool_id(entry_id)
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if short_id != entry_id:
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self._shed_short_id_to_guids.setdefault(short_id, set()).add(entry_id)
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# === Override get_tool for lazy loading ===
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@@ -1864,8 +1865,8 @@ class LazyToolBox(ToolBox):
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# resurrects the uninstalled tool via the eager get_tool
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# fall-through. Scrub every object belonging to this guid, but
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# leave sibling installs (other guids, other versions) alone.
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short_id = extract_short_id_from_guid(tool_id)
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if short_id and short_id != tool_id:
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short_id = short_tool_id(tool_id)
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if short_id != tool_id:
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bucket = self._tools_by_old_id.get(short_id)
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if bucket:
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survivors = [
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@@ -94,6 +94,10 @@ from galaxy.tools.source_store.search import (
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from galaxy.util import listify
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from galaxy.util.hash_util import md5_hash_file
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from galaxy.util.properties import load_app_properties
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from galaxy.util.tool_version import (
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remove_version_from_guid,
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short_tool_id,
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)
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from galaxy.util.watcher import (
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EventHandler,
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get_observer_class,
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@@ -473,7 +477,7 @@ def build_index_entry_from_source(
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lowered = tool_id.lower()
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all_ids = [lowered]
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if "/repos/" in lowered:
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all_ids = [lowered, lowered.rsplit("/", 1)[0], lowered.rsplit("/", 2)[-2]]
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all_ids = [lowered, remove_version_from_guid(lowered) or lowered, short_tool_id(lowered)]
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# Same ontology expansion as ``Tool.__init__``: curated EDAM mapping
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# overrides and legacy bio.tools xrefs included.
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ontology_data = expand_ontology_data(tool_source, all_ids, biotools_metadata_source)
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@@ -42,6 +42,10 @@ from galaxy.tools.source_store.index import (
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)
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from galaxy.util import unicodify
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from galaxy.util.hash_util import md5_hash_str
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from galaxy.util.tool_version import (
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remove_version_from_guid,
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short_tool_id,
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)
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log = logging.getLogger(__name__)
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@@ -199,7 +203,7 @@ def _entry_to_doc(entry: ToolIndexEntry, *, include_help: bool = False) -> dict
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tool_id = (entry.id or "").lower()
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all_ids = [tool_id]
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if "/repos/" in tool_id:
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all_ids = [tool_id, tool_id.rsplit("/", 1)[0], tool_id.rsplit("/", 2)[-2]]
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all_ids = [tool_id, remove_version_from_guid(tool_id) or tool_id, short_tool_id(tool_id)]
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if tags := curated_tool_tags(all_ids):
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doc["tool_tags"] = unicodify(",".join(tags))
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if include_help and entry.help_text:
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@@ -6,3 +6,15 @@ def remove_version_from_guid(guid: str) -> str | None:
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return None
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last_slash = guid.rfind("/")
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return guid[:last_slash]
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def short_tool_id(guid: str) -> str:
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"""
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Tool-id segment of a toolshed-derived tool_id(=guid),
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e.g. ``toolshed/repos/owner/name/tool_id/version`` -> ``tool_id``.
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Ids that aren't guids pass through unchanged.
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"""
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versionless = remove_version_from_guid(guid)
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if not versionless or "/" not in versionless:
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return guid
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return versionless.rsplit("/", 1)[-1]
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