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

fix(lightweight-extension): 环境激活、前缀重命名、数据复制与上传进度

Browse Source 
- service.py: _make_env 用 conda run 激活环境（执行 activate.d，补 PYTHONPATH）
- index_ml.html: 环境下拉框动态加载 + 补传 runtime_env
- runtime_binding.py: 前缀误判修复、放宽 ambiguous、can_rename 判断、子目录数据复制补 mkdir
- api.py: 缺输出目录时友好提示
- main.py + lightWeightExtensionTest.js: run.sh 环境声明 # lightweight-env
- index.html/index_ml.html: 拖拽上传进度条

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
This commit is contained in:
potaser
2026-08-19 20:17:43 +08:00
co-authored by Claude Opus 5
parent fe5f7b9d6e
commit a2e8cbae86
7 changed files with 286 additions and 54 deletions
Download Patch File Download Diff File Expand all files Collapse all files
apps/web/vue3/index.html
+56 -1
View File
@@ -1422,6 +1422,12 @@
placeholder="大文件可直接引用；每行填写一个绝对路径">
</el-input>
</div>
<div v-if="lightweightUploadProgress.active" style="margin-top:9px;">
<el-progress :percentage="lightweightUploadProgress.percent" :stroke-width="8"></el-progress>
<div style="font-size:11px;color:#909399;margin-top:4px;">
{{ lightweightUploadProgress.label }} · {{ formatBytes(lightweightUploadProgress.loaded) }} / {{ formatBytes(lightweightUploadProgress.total) }} · {{ formatBytes(lightweightUploadProgress.speed) }}/s
</div>
</div>
<div style="display:flex; gap:6px; margin-top:9px; align-items:center; justify-content:space-between; flex-wrap:nowrap;">
<el-button
type="primary"
@@ -9148,6 +9154,14 @@ RNA-seq KEGG/fgsea 会优先使用物种级 KEGG gene set；没有物种级缓
statusEvents: []
});
const extensionEnvOptions = ref(['test4py311', 'rnaseq', 'rnaR']);
const lightweightUploadProgress = reactive({
active: false,
percent: 0,
loaded: 0,
total: 0,
speed: 0,
label: '',
});
const lightweightExtensions = ref([]);
const lightweightExtensionConversation = reactive({
cards: [],
@@ -19508,6 +19522,13 @@ compare: [[flesh, peel]]`;
ElMessage.error('上传失败: ' + err.message);
};
const formatBytes = (bytes) => {
if (!Number.isFinite(bytes) || bytes <= 0) return '0 B';
const units = ['B', 'KB', 'MB', 'GB', 'TB'];
const i = Math.min(Math.floor(Math.log(bytes) / Math.log(1024)), units.length - 1);
const v = bytes / Math.pow(1024, i);
return `${v >= 10 || i === 0 ? v.toFixed(0) : v.toFixed(1)} ${units[i]}`;
};
const extensionFileKey = (file) => `${file?.name || ''}::${file?.size || 0}::${file?.lastModified || 0}`;
const extensionUploadPath = (file) => {
const relative = String(file?.lightweightRelativePath || '').trim().replace(/^\/+/, '');
@@ -19623,6 +19644,36 @@ compare: [[flesh, peel]]`;
return port ? `${window.location.protocol}//${host}:${port}${value}` : `${window.location.protocol}//${host}${value}`;
};
const extensionApiFetch = async (path, options = {}) => fetch(extensionApiUrl(path), options);
const uploadExtensionWithProgress = (path, body, label, headers = {}) => {
let lastLoaded = 0, lastTime = Date.now();
const p = lightweightUploadProgress;
p.active = true; p.percent = 0; p.loaded = 0; p.total = 0; p.speed = 0; p.label = label;
return new Promise((resolve, reject) => {
const xhr = new XMLHttpRequest();
xhr.open('POST', extensionApiUrl(path));
Object.entries(headers).forEach(([k, v]) => xhr.setRequestHeader(k, v));
xhr.upload.onprogress = (e) => {
if (!e.lengthComputable) return;
const now = Date.now(), dt = now - lastTime;
if (dt >= 200) { p.speed = (e.loaded - lastLoaded) / (dt / 1000); lastLoaded = e.loaded; lastTime = now; }
p.loaded = e.loaded; p.total = e.total;
p.percent = e.total > 0 ? Math.min(100, Math.round((e.loaded / e.total) * 100)) : 0;
};
xhr.onload = () => {
p.active = false;
resolve({
ok: xhr.status >= 200 && xhr.status < 300,
status: xhr.status,
statusText: xhr.statusText,
json: () => Promise.resolve().then(() => JSON.parse(xhr.responseText)),
text: () => Promise.resolve(xhr.responseText),
});
};
xhr.onerror = () => { p.active = false; reject(new Error('上传失败：网络错误')); };
xhr.onabort = () => { p.active = false; reject(new Error('上传已取消')); };
xhr.send(body);
});
};
const pushExtensionStatus = (message, type = 'info', showDialog = false) => {
const text = String(message || '');
extensionBuild.statusText = text;
@@ -19985,7 +20036,7 @@ compare: [[flesh, peel]]`;
extensionBuild.dataFiles.forEach(file => form.append('raw_data_files', file, extensionUploadPath(file)));
if (hasDataPaths) form.append('raw_data_paths', extensionBuild.dataPaths);
form.append('runtime_env', extensionBuild.runtimeEnv);
const response = await extensionApiFetch('/api/lightweight-extension-stages/upload', { method: 'POST', body: form });
const response = await uploadExtensionWithProgress('/api/lightweight-extension-stages/upload', form, '正在上传拓展包');
if (!response.ok) throw new Error(await extensionApiError(response, '原始包可复现检查提交失败'));
ElMessage.success('文件上传成功，已开始生成并验收');
rememberLightweightOperation(extensionId, 'upload', token, card.card_id);
@@ -23805,6 +23856,7 @@ compare: [[flesh, peel]]`;
uploadedFiles,
extensionBuild,
extensionEnvOptions,
lightweightUploadProgress,
extensionStages,
extensionCompletedStages,
lightweightExtensionConversation,
@@ -23821,6 +23873,7 @@ compare: [[flesh, peel]]`;
cancelExtensionRunParameters,
confirmExtensionRunParameters,
extensionFileKey,
formatBytes,
onExtensionCodeFilesChange,
onExtensionDataFilesChange,
handleLightweightExtensionFolderDrop,
@@ -23971,6 +24024,7 @@ compare: [[flesh, peel]]`;
appendExtensionFiles,
buildLightweightExtensionStage,
lightweightExtensionTestStatus,
uploadExtensionWithProgress,
}, event),
handleLightweightExtensionFolderPick: (event) => window.LightWeightExtensionTest && window.LightWeightExtensionTest.handlePick({
jobInfo,
@@ -23979,6 +24033,7 @@ compare: [[flesh, peel]]`;
appendExtensionFiles,
buildLightweightExtensionStage,
lightweightExtensionTestStatus,
uploadExtensionWithProgress,
}, event),
openLightweightExtensionFolderPicker: () => window.LightWeightExtensionTest && window.LightWeightExtensionTest.openPicker(),
// Working DirectorySelect
apps/web/vue3/index_ml.html
+75 -5
View File
@@ -1397,10 +1397,8 @@
<span>{{ t('名称') }}</span><el-input v-model="extensionBuild.displayName" size="small" placeholder="例如 HMMER hmmsearch"></el-input>
<span>{{ t('原始命令') }}</span><el-input v-model="extensionBuild.command" size="small" placeholder="例如 bash run.sh input.fa"></el-input>
<span>{{ t('环境') }}</span>
<el-select v-model="extensionBuild.runtimeEnv" size="small">
<el-option label="test4py311" value="test4py311"></el-option>
<el-option label="rnaseq" value="rnaseq"></el-option>
<el-option label="rnaR" value="rnaR"></el-option>
<el-select v-model="extensionBuild.runtimeEnv" size="small" filterable>
<el-option v-for="env in extensionEnvOptions" :key="env" :label="env" :value="env"></el-option>
</el-select>
<span>{{ t('原始代码') }}</span><input type="file" multiple @change="onExtensionCodeFilesChange" style="font-size:12px; min-width:0;">
<span v-if="extensionBuild.codeFiles.length"></span>
@@ -1426,6 +1424,12 @@
placeholder="大文件可直接引用；每行填写一个绝对路径">
</el-input>
</div>
<div v-if="lightweightUploadProgress.active" style="margin-top:9px;">
<el-progress :percentage="lightweightUploadProgress.percent" :stroke-width="8"></el-progress>
<div style="font-size:11px;color:#909399;margin-top:4px;">
{{ lightweightUploadProgress.label }} · {{ formatBytes(lightweightUploadProgress.loaded) }} / {{ formatBytes(lightweightUploadProgress.total) }} · {{ formatBytes(lightweightUploadProgress.speed) }}/s
</div>
</div>
<div style="display:flex; gap:6px; margin-top:9px; align-items:center; justify-content:space-between; flex-wrap:nowrap;">
<el-button
type="primary"
@@ -9200,6 +9204,15 @@ RNA-seq KEGG/fgsea 会优先使用物种级 KEGG gene set；没有物种级缓
statusDialogVisible: false,
statusEvents: []
});
const extensionEnvOptions = ref(['test4py311', 'rnaseq', 'rnaR']);
const lightweightUploadProgress = reactive({
active: false,
percent: 0,
loaded: 0,
total: 0,
speed: 0,
label: '',
});
const lightweightExtensions = ref([]);
const lightweightExtensionConversation = reactive({
cards: [],
@@ -9252,6 +9265,18 @@ RNA-seq KEGG/fgsea 会优先使用物种级 KEGG gene set；没有物种级缓
extensionBuild.runtimeEnv = (item.runtime && item.runtime.env) || extensionBuild.runtimeEnv || 'test4py311';
extensionBuild.nlTriggersText = (item.nl_triggers || []).join(', ');
};
const loadExtensionEnvOptions = async () => {
try {
const response = await extensionApiFetch('/api/extension-stages/envs');
if (!response.ok) return;
const data = await response.json();
if (data.success && Array.isArray(data.envs) && data.envs.length) {
extensionEnvOptions.value = data.envs;
}
} catch (err) {
console.warn('[extension env options] load failed', err);
}
};
const extensionRuns = ref([]);
const extensionResultDialogVisible = ref(false);
const extensionRun = reactive({
@@ -19325,6 +19350,13 @@ compare: [[flesh, peel]]`;
ElMessage.error('上传失败: ' + err.message);
};
const formatBytes = (bytes) => {
if (!Number.isFinite(bytes) || bytes <= 0) return '0 B';
const units = ['B', 'KB', 'MB', 'GB', 'TB'];
const i = Math.min(Math.floor(Math.log(bytes) / Math.log(1024)), units.length - 1);
const v = bytes / Math.pow(1024, i);
return `${v >= 10 || i === 0 ? v.toFixed(0) : v.toFixed(1)} ${units[i]}`;
};
const extensionFileKey = (file) => `${file?.name || ''}::${file?.size || 0}::${file?.lastModified || 0}`;
const extensionUploadPath = (file) => {
const relative = String(file?.lightweightRelativePath || '').trim().replace(/^\/+/, '');
@@ -19439,6 +19471,36 @@ compare: [[flesh, peel]]`;
return `${window.location.protocol}//${host}:${window.location.port}${value}`;
};
const extensionApiFetch = async (path, options = {}) => fetch(extensionApiUrl(path), options);
const uploadExtensionWithProgress = (path, body, label, headers = {}) => {
let lastLoaded = 0, lastTime = Date.now();
const p = lightweightUploadProgress;
p.active = true; p.percent = 0; p.loaded = 0; p.total = 0; p.speed = 0; p.label = label;
return new Promise((resolve, reject) => {
const xhr = new XMLHttpRequest();
xhr.open('POST', extensionApiUrl(path));
Object.entries(headers).forEach(([k, v]) => xhr.setRequestHeader(k, v));
xhr.upload.onprogress = (e) => {
if (!e.lengthComputable) return;
const now = Date.now(), dt = now - lastTime;
if (dt >= 200) { p.speed = (e.loaded - lastLoaded) / (dt / 1000); lastLoaded = e.loaded; lastTime = now; }
p.loaded = e.loaded; p.total = e.total;
p.percent = e.total > 0 ? Math.min(100, Math.round((e.loaded / e.total) * 100)) : 0;
};
xhr.onload = () => {
p.active = false;
resolve({
ok: xhr.status >= 200 && xhr.status < 300,
status: xhr.status,
statusText: xhr.statusText,
json: () => Promise.resolve().then(() => JSON.parse(xhr.responseText)),
text: () => Promise.resolve(xhr.responseText),
});
};
xhr.onerror = () => { p.active = false; reject(new Error('上传失败：网络错误')); };
xhr.onabort = () => { p.active = false; reject(new Error('上传已取消')); };
xhr.send(body);
});
};
const pushExtensionStatus = (message, type = 'info', showDialog = false) => {
const text = String(message || '');
extensionBuild.statusText = text;
@@ -19800,7 +19862,8 @@ compare: [[flesh, peel]]`;
extensionBuild.codeFiles.forEach(file => form.append('raw_code_files', file, extensionUploadPath(file)));
extensionBuild.dataFiles.forEach(file => form.append('raw_data_files', file, extensionUploadPath(file)));
if (hasDataPaths) form.append('raw_data_paths', extensionBuild.dataPaths);
const response = await extensionApiFetch('/api/lightweight-extension-stages/upload', { method: 'POST', body: form });
form.append('runtime_env', extensionBuild.runtimeEnv);
const response = await uploadExtensionWithProgress('/api/lightweight-extension-stages/upload', form, '正在上传拓展包');
if (!response.ok) throw new Error(await extensionApiError(response, t('原始包可复现检查提交失败')));
ElMessage.success(t('文件上传成功，已开始生成并验收'));
rememberLightweightOperation(extensionId, 'upload', token, card.card_id);
@@ -23225,6 +23288,7 @@ compare: [[flesh, peel]]`;
startAgentTaskPolling();
startRuntimeMonitor();
loadExtensionStages();
loadExtensionEnvOptions();
loadLightweightExtensionStages();
resumeLightweightOperation();
loadExtensionRuns();
@@ -23556,6 +23620,8 @@ compare: [[flesh, peel]]`;
intentHistory,
uploadedFiles,
extensionBuild,
extensionEnvOptions,
lightweightUploadProgress,
extensionStages,
extensionCompletedStages,
lightweightExtensionConversation,
@@ -23572,6 +23638,7 @@ compare: [[flesh, peel]]`;
cancelExtensionRunParameters,
confirmExtensionRunParameters,
extensionFileKey,
formatBytes,
onExtensionCodeFilesChange,
onExtensionDataFilesChange,
removeExtensionFile,
@@ -23593,6 +23660,7 @@ compare: [[flesh, peel]]`;
validateExtensionStage,
publishExtensionStage,
loadExtensionStages,
loadExtensionEnvOptions,
loadExtensionRuns,
runExtensionStage,
runExtensionStageFromIntent,
@@ -23607,6 +23675,7 @@ compare: [[flesh, peel]]`;
appendExtensionFiles,
buildLightweightExtensionStage,
lightweightExtensionTestStatus,
uploadExtensionWithProgress,
}, event),
handleLightweightExtensionFolderPick: (event) => window.LightWeightExtensionTest && window.LightWeightExtensionTest.handlePick({
jobInfo,
@@ -23615,6 +23684,7 @@ compare: [[flesh, peel]]`;
appendExtensionFiles,
buildLightweightExtensionStage,
lightweightExtensionTestStatus,
uploadExtensionWithProgress,
}, event),
openLightweightExtensionFolderPicker: () => window.LightWeightExtensionTest && window.LightWeightExtensionTest.openPicker(),
methodologyPaperId,
apps/web/vue3/lightWeightExtensionTest.js
+19 -5
View File
@@ -124,6 +124,17 @@
};
}
async function extractEnvDeclaration(files) {
for (const file of files) {
const path = normalizedRelativePath(file).toLowerCase();
if (!path.endsWith('.sh')) continue;
const content = await file.text();
const m = content.match(/^\s*#\s*lightweight-env\s*:\s*([A-Za-z0-9_.-]+)/m);
if (m) return m[1];
}
return null;
}
async function encodeBase64(file) {
const buffer = await file.arrayBuffer();
const bytes = new Uint8Array(buffer);
@@ -146,11 +157,12 @@
payload.files.push(await encodeBase64(file));
payload.relative_paths.push(normalizedRelativePath(file));
}
const response = await fetch('/api/job/import-folder', {
method: 'POST',
headers: { 'Content-Type': 'application/json' },
body: JSON.stringify(payload),
});
const response = await hooks.uploadExtensionWithProgress(
'/api/job/import-folder',
JSON.stringify(payload),
'正在镜像导入 Job',
{ 'Content-Type': 'application/json' },
);
const data = await response.json();
if (!response.ok || !data.success) {
throw new Error(data.detail || data.error || data.message || 'Job 导入失败');
@@ -160,6 +172,8 @@
async function resolveRuntimeEnv(files) {
const dependencies = await extractDependencies(files);
const envDeclaration = await extractEnvDeclaration(files);
if (envDeclaration) dependencies.env_declaration = envDeclaration;
console.log('[lightWeightExtensionTest] 提取的依赖:', JSON.stringify(dependencies), '| 扫描文件数:', files.length);
try {
const response = await fetch('/api/extension-stages/envs/resolve', {
apps/web/vue3/main.py
+19
View File
@@ -8919,6 +8919,7 @@ class ExtensionStageResolveIntentRequest(BaseModel):
class ExtensionStageEnvResolveRequest(BaseModel):
python_imports: List[str] = Field(default_factory=list)
r_packages: List[str] = Field(default_factory=list)
env_declaration: Optional[str] = None
@@ -9015,6 +9016,24 @@ async def _r_packages_for_env(env_name: str) -> set[str]:
@app.post("/api/extension-stages/envs/resolve")
async def resolve_extension_stage_env(req: ExtensionStageEnvResolveRequest):
# 工具显式声明的环境优先（run.sh 里 # lightweight-env: <env>）
if req.env_declaration:
env = req.env_declaration.strip()
proc = await asyncio.create_subprocess_exec(
"conda", "run", "-n", env, "python", "--version",
stdout=asyncio.subprocess.PIPE,
stderr=asyncio.subprocess.PIPE,
)
await proc.communicate()
if proc.returncode == 0:
return {
"success": True,
"runtime_env": env,
"reason": "explicit_env_declaration",
"dependency": env,
"fallback": False,
}
python_imports = _normalized_dependency_names(req.python_imports)
r_packages = _normalized_dependency_names(req.r_packages)
if not python_imports and not r_packages: