admin/PlantAI-dev
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 1 Wiki Activity

fix(lightweight-extension): 输出前缀绑定、拖拽导入与前端入口修复

Browse Source 
- runtime_binding: 验证时排除输入 sidecar 输出，目录参数跟随输出前缀重命名
- import-folder: 改 multipart 二进制上传，规避大文件 base64 报 Invalid string length
- main: 前端入口切回 index.html，conda 路径兜底

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
This commit is contained in:
potaser
2026-08-24 20:51:22 +08:00
co-authored by Claude Opus 5
parent 4a5fdff6f0
commit dfff8b6c45
3 changed files with 68 additions and 55 deletions
Download Patch File Download Diff File Expand all files Collapse all files
apps/web/vue3/lightWeightExtensionTest.js
+6 -21
View File
@@ -135,33 +135,18 @@
return null;
}
async function encodeBase64(file) {
const buffer = await file.arrayBuffer();
const bytes = new Uint8Array(buffer);
let binary = '';
const chunkSize = 0x8000;
for (let index = 0; index < bytes.length; index += chunkSize) {
binary += String.fromCharCode(...bytes.subarray(index, index + chunkSize));
}
return btoa(binary);
}
async function importFolderToJob(hooks, rootName, files) {
const payload = {
job_id: String(hooks.jobInfo.job_id || '').trim(),
root_name: rootName,
files: [],
relative_paths: [],
};
const form = new FormData();
form.append('job_id', String(hooks.jobInfo.job_id || '').trim());
form.append('root_name', rootName);
for (const file of files) {
payload.files.push(await encodeBase64(file));
payload.relative_paths.push(normalizedRelativePath(file));
form.append('files', file, normalizedRelativePath(file));
form.append('relative_paths', normalizedRelativePath(file));
}
const response = await hooks.uploadExtensionWithProgress(
'/api/job/import-folder',
JSON.stringify(payload),
form,
'正在镜像导入 Job',
{ 'Content-Type': 'application/json' },
);
const data = await response.json();
if (!response.ok || !data.success) {
apps/web/vue3/main.py
+22 -24
View File
@@ -6,7 +6,6 @@ BotanicalBaseAgent - FastAPI Backend
import os
import sys
import json
import base64
import csv
import asyncio
import hashlib
@@ -8830,7 +8829,7 @@ def run_stage_sync(task_id: str, stage: str, job_id: str, params: dict):
async def root():
"""返回Vue3前端页面"""
return FileResponse(
Path(__file__).parent / "index_ml.html",
Path(__file__).parent / "index.html",
headers={
"Cache-Control": "no-cache, no-store, must-revalidate",
"Pragma": "no-cache",
@@ -9059,34 +9058,29 @@ async def upload_file(files: List[UploadFile] = File(...), job_id: str = Form(""
}
class JobImportFolderRequest(BaseModel):
job_id: str
root_name: str = ""
files: List[str] = Field(default_factory=list)
relative_paths: List[str] = Field(default_factory=list)
@app.post("/api/job/import-folder")
async def import_job_folder(req: JobImportFolderRequest):
job_id = str(req.job_id or "").strip()
async def import_job_folder(
job_id: str = Form(...),
root_name: str = Form(""),
files: List[UploadFile] = File(...),
relative_paths: List[str] = Form(...),
):
job_id = str(job_id or "").strip()
if not job_id:
raise HTTPException(status_code=400, detail="job_id is required")
if len(req.files) != len(req.relative_paths):
if len(files) != len(relative_paths):
raise HTTPException(status_code=400, detail="files and relative_paths length mismatch")
root_name = _safe_upload_name(req.root_name or "lightweight_extension_drop")
root_name = _safe_upload_name(root_name or "lightweight_extension_drop")
import_root = INPUT_ROOT / job_id / root_name
import_root.mkdir(parents=True, exist_ok=True)
saved_files: List[str] = []
for encoded, raw_relative in zip(req.files, req.relative_paths):
for upload, raw_relative in zip(files, relative_paths):
relative = Path(str(raw_relative or "").strip())
if not raw_relative or relative.is_absolute() or any(part in {"", ".", ".."} for part in relative.parts):
raise HTTPException(status_code=400, detail=f"invalid relative path: {raw_relative}")
try:
content = base64.b64decode(str(encoded or "").encode("utf-8"), validate=True)
except Exception as exc:
raise HTTPException(status_code=400, detail=f"invalid base64 payload for {raw_relative}: {exc}") from exc
content = await upload.read()
destination = import_root / relative
destination.parent.mkdir(parents=True, exist_ok=True)
destination.write_bytes(content)
@@ -9185,6 +9179,10 @@ class ExtensionStageEnvResolveRequest(BaseModel):
env_declaration: Optional[str] = None
def _conda_exe() -> str:
"""Resolve the conda executable even when it is not on the server process's PATH."""
return shutil.which("conda") or "/home/xzq/miniconda3/bin/conda"
@app.get("/api/extension-stages/envs")
async def list_extension_stage_envs():
@@ -9192,7 +9190,7 @@ async def list_extension_stage_envs():
import json as _json
try:
proc = await asyncio.create_subprocess_exec(
"conda", "env", "list", "--json",
_conda_exe(), "env", "list", "--json",
stdout=asyncio.subprocess.PIPE,
stderr=asyncio.subprocess.PIPE,
)
@@ -9200,7 +9198,7 @@ async def list_extension_stage_envs():
if proc.returncode != 0:
# fallback: try parsing plain-text output
proc2 = await asyncio.create_subprocess_exec(
"conda", "env", "list",
_conda_exe(), "env", "list",
stdout=asyncio.subprocess.PIPE,
stderr=asyncio.subprocess.PIPE,
)
@@ -9249,7 +9247,7 @@ async def _available_extension_env_names() -> List[str]:
async def _python_packages_for_env(env_name: str) -> set[str]:
proc = await asyncio.create_subprocess_exec(
"conda", "run", "-n", env_name, "python", "-c",
_conda_exe(), "run", "-n", env_name, "python", "-c",
"import json, importlib.metadata as m; print(json.dumps(sorted({dist.metadata.get('Name', '') for dist in m.distributions() if dist.metadata.get('Name', '')})))",
stdout=asyncio.subprocess.PIPE,
stderr=asyncio.subprocess.PIPE,
@@ -9266,7 +9264,7 @@ async def _python_packages_for_env(env_name: str) -> set[str]:
async def _r_packages_for_env(env_name: str) -> set[str]:
proc = await asyncio.create_subprocess_exec(
"conda", "run", "-n", env_name, "Rscript", "-e",
_conda_exe(), "run", "-n", env_name, "Rscript", "-e",
"cat(paste(sort(rownames(installed.packages())), collapse='\n'))",
stdout=asyncio.subprocess.PIPE,
stderr=asyncio.subprocess.PIPE,
@@ -9283,7 +9281,7 @@ async def resolve_extension_stage_env(req: ExtensionStageEnvResolveRequest):
if req.env_declaration:
env = req.env_declaration.strip()
proc = await asyncio.create_subprocess_exec(
"conda", "run", "-n", env, "python", "--version",
_conda_exe(), "run", "-n", env, "python", "--version",
stdout=asyncio.subprocess.PIPE,
stderr=asyncio.subprocess.PIPE,
)
@@ -9309,7 +9307,7 @@ async def resolve_extension_stage_env(req: ExtensionStageEnvResolveRequest):
for dep in list(dict.fromkeys(d.lower() for d in python_imports + r_packages)):
proc = await asyncio.create_subprocess_exec(
"conda", "run", "-n", dep, "python", "--version",
_conda_exe(), "run", "-n", dep, "python", "--version",
stdout=asyncio.subprocess.PIPE,
stderr=asyncio.subprocess.PIPE,
)
gfa_core/extension_stage_lightweight/runtime_binding.py
+40 -10
View File
@@ -1004,6 +1004,33 @@ def resolve_runtime_bindings(
binding["original_path"]: binding["runtime_path"]
for binding in input_bindings or []
}
direct_output_fact_ids = {
fact_id
for target in contract.get("patch_targets", [])
if isinstance(target, dict)
and target.get("patch_kind") in {"output_path", "output_reference_path"}
for fact_id in target.get("fact_ids", [])
if isinstance(fact_id, str)
}
# Outputs owned by an input (the input itself or a sidecar like
# ``Pfam-A.WRKY-subset.hmm.h3f`` next to ``Pfam-A.WRKY-subset.hmm``) do not
# belong to the output-prefix namespace; they are renamed via their input
# relationship. Excluding them keeps the shared-prefix derivation from
# being dragged to ``.`` by a top-level sidecar while the remaining outputs
# live under a common directory.
input_owned_paths = {
output["path"]
for output in output_files
if _runtime_input_owned_output(
output["path"],
runtime_by_original,
allow_sidecar=output["fact_id"] not in direct_output_fact_ids,
)
is not None
}
prefix_output_files = [
output for output in output_files if output["path"] not in input_owned_paths
]
participant_options: list[set[tuple[str, str]]] = []
participating_paths: set[str] = set()
for output in output_files:
@@ -1055,11 +1082,11 @@ def resolve_runtime_bindings(
*[{old for old, _new in options} for options in participant_options]
)
if not common_old:
old_prefix = _shared_output_prefix(output_files)
old_prefix = _shared_output_prefix(prefix_output_files)
else:
old_prefix = max(common_old, key=lambda value: (len(value), value))
else:
old_prefix = _shared_output_prefix(output_files)
old_prefix = _shared_output_prefix(prefix_output_files)
if old_prefix is None:
return _blocked_result(
contract,
@@ -1069,14 +1096,6 @@ def resolve_runtime_bindings(
parameter_bindings=parameter_bindings,
)
new_prefix = explicit_prefix or "output"
direct_output_fact_ids = {
fact_id
for target in contract.get("patch_targets", [])
if isinstance(target, dict)
and target.get("patch_kind") in {"output_path", "output_reference_path"}
for fact_id in target.get("fact_ids", [])
if isinstance(fact_id, str)
}
unpatchable_fact_ids = {
fact_id
for target in contract.get("unpatchable_targets", [])
@@ -1412,6 +1431,17 @@ def _binding_replacements(
raise RuntimeBindingError(
"PARAMETER_VALUE_INVALID", f"unsafe runtime parameter: {fact_id}"
)
# 输出目录参数（--outdir / -oc / mkdir -p 的值）跟随输出前缀重命名，
# 否则渲染后的 run.sh 里目录参数与 file 输出路径指向不一致的目录。
if isinstance(prefix, dict):
old_prefix = prefix.get("old_prefix")
new_prefix = prefix.get("new_prefix")
if (
isinstance(old_prefix, str)
and isinstance(new_prefix, str)
and _output_has_prefix(runtime, old_prefix)
):
runtime = _replace_output_prefix(runtime, old_prefix, new_prefix)
add(f"parameter:{fact_id}", original, runtime)
targets_by_key = {