116 lines
4.2 KiB
Python
116 lines
4.2 KiB
Python
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import asyncio
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import subprocess
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from pathlib import Path
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from typing import Any
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from .registry import ToolMetadata
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class ToolAdapter:
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def __init__(self, metadata: ToolMetadata, work_dir: str = "/tmp/gene-family"):
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self.metadata = metadata
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self.work_dir = Path(work_dir)
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self.work_dir.mkdir(parents=True, exist_ok=True)
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def execute(self, inputs: dict[str, str], parameters: dict[str, Any]) -> dict:
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cmd = self._build_command(inputs, parameters)
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try:
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result = subprocess.run(
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cmd,
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cwd=str(self.work_dir),
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capture_output=True,
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text=True,
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timeout=self.metadata.timeout,
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)
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return {
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"return_code": result.returncode,
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"stdout": result.stdout,
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"stderr": result.stderr,
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"outputs": self._collect_outputs(),
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}
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except subprocess.TimeoutExpired:
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return {
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"return_code": -1,
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"stdout": "",
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"stderr": f"Tool {self.metadata.id} timed out after {self.metadata.timeout}s",
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"outputs": {},
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}
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except Exception as e:
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return {
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"return_code": -1,
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"stdout": "",
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"stderr": str(e),
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"outputs": {},
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}
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async def aexecute(self, inputs: dict[str, str], parameters: dict[str, Any]) -> dict:
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return await asyncio.to_thread(self.execute, inputs, parameters)
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def _build_command(self, inputs: dict[str, str], parameters: dict[str, Any]) -> list[str]:
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cmd = [self.metadata.executable]
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if self.metadata.id == "hmmsearch":
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cmd.extend([
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"--tblout", str(self.work_dir / "output.tbl"),
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"--domtblout", str(self.work_dir / "dom.tbl"),
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"-E", str(parameters.get("e_value", 1e-5)),
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"--cpu", str(parameters.get("cpu", 4)),
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inputs.get("query", ""),
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inputs.get("target", ""),
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])
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elif self.metadata.id == "blastp":
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cmd.extend([
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"-query", inputs.get("query", ""),
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"-db", inputs.get("db", ""),
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"-evalue", str(parameters.get("e_value", 1e-5)),
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"-max_target_seqs", str(parameters.get("max_target_seqs", 500)),
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"-outfmt", str(parameters.get("outfmt", 6)),
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"-out", str(self.work_dir / "blast_results.txt"),
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])
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elif self.metadata.id == "mafft":
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strategy = parameters.get("strategy", "auto")
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if strategy != "auto":
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cmd.append(f"--{strategy}")
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cmd.extend([
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"--maxiterate", str(parameters.get("maxiterate", 1000)),
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inputs.get("sequences", ""),
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])
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elif self.metadata.id == "iqtree":
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cmd.extend([
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"-s", inputs.get("alignment", ""),
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"-m", parameters.get("model", "MFP"),
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"-bb", str(parameters.get("bootstrap", 1000)),
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"-nt", str(parameters.get("threads", 4)),
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])
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elif self.metadata.id == "meme":
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cmd.extend([
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inputs.get("sequences", ""),
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"-nmotifs", str(parameters.get("nmotifs", 10)),
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"-minw", str(parameters.get("min_width", 6)),
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"-maxw", str(parameters.get("max_width", 200)),
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"-oc", str(self.work_dir / "meme_out"),
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])
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return cmd
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def _collect_outputs(self) -> dict[str, str]:
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outputs = {}
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for output in self.metadata.outputs:
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if output.name == "tblout":
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path = self.work_dir / "output.tbl"
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elif output.name == "domtblout":
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path = self.work_dir / "dom.tbl"
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elif output.name == "tree":
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path = self.work_dir / "*.treefile"
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elif output.name == "alignment":
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path = self.work_dir / "aligned.fasta"
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else:
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continue
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if path.exists():
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outputs[output.name] = str(path)
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return outputs
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