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Source code for galaxy.tool_util.locations.dockstore

from urllib.parse import quote

import requests
import yaml

from ..locations import (

[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",)