Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.tool_util.locations.dockstore

from urllib.parse import quote

import requests
import yaml

from ..locations import (
    ToolLocationResolver,
)


[docs]class DockStoreResolver(ToolLocationResolver): scheme = "dockstore"
[docs] def get_tool_source_path(self, uri_like): assert uri_like.startswith("dockstore://") tool_id = uri_like[len("dockstore://"):] if ":" in tool_id: tool_id, version = tool_id.split(":", 1) else: tool_id, version = tool_id, "latest" tmp_path = self._temp_path(uri_like + ".cwl") cwl_str = _Ga4ghToolClient().get_tool_cwl(tool_id, version=version, as_string=True) with open(tmp_path, "wb") as f: f.write(cwl_str) return tmp_path
class _Ga4ghToolClient: def __init__(self, base_url="https://www.dockstore.org:8443/api"): self.base_url = base_url def get_tools(self): return self._requests.get("%s/ga4gh/v1/tools" % self.base_url) def get_tool(self, tool_id): url = "{}/ga4gh/v1/tools/{}".format(self.base_url, quote(tool_id, safe='')) return self._requests.get(url) def get_tool_version(self, tool_id, version="latest"): url = "{}/ga4gh/v1/tools/{}/versions/{}".format(self.base_url, quote(tool_id, safe=''), version) return self._requests.get(url) def get_tool_descriptor(self, tool_id, version="latest", tool_type="CWL"): url = "{}/ga4gh/v1/tools/{}/versions/{}/{}/descriptor".format(self.base_url, quote(tool_id, safe=''), version, tool_type) return self._requests.get(url) def get_tool_cwl(self, tool_id, version="latest", as_string=False): tool_type = "CWL" url = "{}/ga4gh/v1/tools/{}/versions/{}/{}/descriptor".format(self.base_url, quote(tool_id, safe=''), version, tool_type) descriptor_response = self._requests.get(url) descriptor_str = descriptor_response.json()["descriptor"] if as_string: return descriptor_str else: return yaml.safe_load(descriptor_str) @property def _requests(self): if requests is None: raise Exception("requests Python library needs to be installed use GA4GH APIs") return requests __all__ = ("DockStoreResolver",)