pybiolib 1.2.1318__py3-none-any.whl → 1.2.1352__py3-none-any.whl

biolib/_internal/templates/gui_template/App.tsx

@@ -1,16 +1,52 @@
+import { useState, useEffect } from "react";
+import biolib from "./biolib-sdk";
+
 export default function App() {
+  const [outputFileData, setOutputFileData] = useState<Uint8Array | null>(null);
+  const [loading, setLoading] = useState(true);
+
+  const loadOutputData = async () => {
+    setLoading(true);
+    try {
+      const data = await biolib.getOutputFileData("output.json");
+      setOutputFileData(data);
+    } catch (error) {
+      console.error("Error loading output data:", error);
+      setOutputFileData(null);
+    } finally {
+      setLoading(false);
+    }
+  };
+
+  useEffect(() => {
+    loadOutputData();
+  }, []);
+
   return (
     <div className="min-h-screen bg-gray-100 flex items-center justify-center">
-      <div className="text-center">
+      <div className="text-center max-w-2xl mx-auto p-8">
         <h1 className="text-4xl font-bold mb-4">
           Hello, BioLib!
         </h1>
         <p className="text-lg mb-2">
           You have successfully set up your BioLib GUI application.
         </p>
-        <p className="italic">
+        <p className="italic mb-6">
           This is a simple React template with Tailwind CSS styling.
         </p>
+
+        <div className="mt-8 p-4 bg-white rounded-lg shadow">
+          <h2 className="text-xl font-semibold mb-4">Example: Reading Output Files</h2>
+          {loading ? (
+            <p className="text-gray-500">Loading output.json...</p>
+          ) : outputFileData ? (
+            <div className="p-3 bg-gray-50 rounded text-left">
+              <pre className="text-sm">{new TextDecoder().decode(outputFileData)}</pre>
+            </div>
+          ) : (
+            <p className="text-red-500">Failed to load output.json</p>
+          )}
+        </div>
       </div>
     </div>
   );

biolib/_internal/templates/gui_template/biolib-sdk.ts

@@ -0,0 +1,34 @@
+interface IBioLibGlobals {
+  getOutputFileData: (path: string) => Promise<Uint8Array>;
+}
+
+declare global {
+  const biolib: IBioLibGlobals;
+}
+
+/* DEV_DATA_INJECTION */
+
+const devSdkBioLib: IBioLibGlobals = {
+  getOutputFileData: async (path: string): Promise<Uint8Array> => {
+    console.log(`[SDK] getOutputFileData called with path: ${path}`);
+    
+    if (typeof DEV_DATA_FILES !== 'undefined' && path in DEV_DATA_FILES) {
+      const base64Data = DEV_DATA_FILES[path];
+      const binaryString = atob(base64Data);
+      const bytes = new Uint8Array(binaryString.length);
+      for (let i = 0; i < binaryString.length; i++) {
+        bytes[i] = binaryString.charCodeAt(i);
+      }
+      return bytes;
+    }
+    
+    throw new Error(`File not found: ${path}. Add this file to the dev-data/ folder for local development.`);
+  },
+};
+
+const biolib: IBioLibGlobals =
+  process.env.NODE_ENV === "development"
+    ? devSdkBioLib
+    : (window as any).biolib;
+
+export default biolib;

biolib/_internal/templates/gui_template/dev-data/output.json

@@ -0,0 +1,7 @@
+{
+  "message": "Example JSON data for development",
+  "results": [
+    { "id": 1, "value": "Sample result 1" },
+    { "id": 2, "value": "Sample result 2" }
+  ]
+}

biolib/_internal/templates/gui_template/vite-plugin-dev-data.ts

@@ -0,0 +1,52 @@
+import { Plugin } from 'vite';
+import fs from 'fs';
+import path from 'path';
+
+export function devDataPlugin(): Plugin {
+  let isDev = false;
+  
+  return {
+    name: 'dev-data-plugin',
+    configResolved(config) {
+      isDev = config.mode === 'development';
+    },
+    transform(code: string, id: string) {
+      if (id.endsWith('biolib-sdk.ts')) {
+        let injectedCode: string;
+        
+        if (isDev) {
+          const devDataDir = path.join(__dirname, 'dev-data');
+          const devDataMap: Record<string, string> = {};
+          
+          if (fs.existsSync(devDataDir)) {
+            const files = fs.readdirSync(devDataDir);
+            for (const file of files) {
+              const filePath = path.join(devDataDir, file);
+              if (fs.statSync(filePath).isFile()) {
+                const content = fs.readFileSync(filePath);
+                const base64Content = content.toString('base64');
+                devDataMap[file] = base64Content;
+              }
+            }
+          }
+          
+          const devDataJson = JSON.stringify(devDataMap);
+          injectedCode = code.replace(
+            '/* DEV_DATA_INJECTION */',
+            `const DEV_DATA_FILES: Record<string, string> = ${devDataJson};`
+          );
+        } else {
+          injectedCode = code.replace(
+            '/* DEV_DATA_INJECTION */',
+            '// Dev data not included in production build'
+          );
+        }
+        
+        return {
+          code: injectedCode,
+          map: null
+        };
+      }
+    }
+  };
+}

biolib/_internal/templates/gui_template/vite.config.mts

@@ -2,7 +2,8 @@ import { defineConfig } from "vite";
 import react from "@vitejs/plugin-react";
 import tailwindcss from "@tailwindcss/vite";
 import { viteSingleFile } from "vite-plugin-singlefile";
+import { devDataPlugin } from "./vite-plugin-dev-data";
 
 export default defineConfig({
-  plugins: [react(), tailwindcss(), viteSingleFile()],
+  plugins: [react(), tailwindcss(), devDataPlugin(), viteSingleFile()],
 });

biolib/_session/session.py

@@ -5,17 +5,19 @@ from biolib.app import BioLibApp
 
 
 class Session:
-    def __init__(self, _init_dict: ApiClientInitDict) -> None:
+    def __init__(self, _init_dict: ApiClientInitDict, _experiment: Optional[str] = None) -> None:
         self._api = ApiClient(_init_dict=_init_dict)
+        self._experiment = _experiment
 
     @staticmethod
-    def get_session(refresh_token: str, base_url: Optional[str] = None, client_type: Optional[str] = None) -> 'Session':
+    def get_session(refresh_token: str, base_url: Optional[str] = None, client_type: Optional[str] = None, experiment: Optional[str] = None) -> 'Session':
         return Session(
             _init_dict=ApiClientInitDict(
                 refresh_token=refresh_token,
                 base_url=base_url or utils.load_base_url_from_env(),
                 client_type=client_type,
-            )
+            ),
+            _experiment=experiment,
         )
 
     def load(self, uri: str, suppress_version_warning: bool = False) -> BioLibApp:
@@ -39,4 +41,4 @@ class Session:
             >>> app = biolib.load('https://biolib.com/biolib/myapp/')
             >>> result = app.cli('--help')
         """
-        return BioLibApp(uri=uri, _api_client=self._api, suppress_version_warning=suppress_version_warning)
+        return BioLibApp(uri=uri, _api_client=self._api, suppress_version_warning=suppress_version_warning, _experiment=self._experiment)

biolib/app/app.py

@@ -25,8 +25,15 @@ from biolib._internal.file_utils import path_to_renamed_path
 
 
 class BioLibApp:
-    def __init__(self, uri: str, _api_client: Optional[ApiClient] = None, suppress_version_warning: bool = False):
+    def __init__(
+        self,
+        uri: str,
+        _api_client: Optional[ApiClient] = None,
+        suppress_version_warning: bool = False,
+        _experiment: Optional[str] = None,
+    ):
         self._api_client: Optional[ApiClient] = _api_client
+        self._experiment = _experiment
 
         app_response = BiolibAppApi.get_by_uri(uri=uri, api_client=self._api_client)
         self._app: App = app_response['app']
@@ -85,7 +92,12 @@ class BioLibApp:
             raise ValueError('The argument "check" cannot be True when blocking is False')
 
         if not experiment_id:
-            experiment_instance = Experiment(experiment) if experiment else Experiment.get_experiment_in_context()
+            experiment_to_use = experiment if experiment is not None else self._experiment
+            experiment_instance: Optional[Experiment]
+            if experiment_to_use:
+                experiment_instance = Experiment(experiment_to_use)
+            else:
+                experiment_instance = Experiment.get_experiment_in_context()
             experiment_id = experiment_instance.uuid if experiment_instance else None
 
         module_input_serialized = self._get_serialized_module_input(args, stdin, files)

biolib/sdk/__init__.py

@@ -12,8 +12,18 @@ from biolib.app import BioLibApp as _BioLibApp
 Runtime = _Runtime
 
 
-def get_session(refresh_token: str, base_url: Optional[str] = None, client_type: Optional[str] = None) -> _Session:
-    return _Session.get_session(refresh_token=refresh_token, base_url=base_url, client_type=client_type)
+def get_session(
+    refresh_token: str,
+    base_url: Optional[str] = None,
+    client_type: Optional[str] = None,
+    experiment: Optional[str] = None,
+) -> _Session:
+    return _Session.get_session(
+        refresh_token=refresh_token,
+        base_url=base_url,
+        client_type=client_type,
+        experiment=experiment,
+    )
 
 
 def push_app_version(uri: str, path: str) -> _BioLibApp:

{pybiolib-1.2.1318.dist-info → pybiolib-1.2.1352.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pybiolib
-Version: 1.2.1318
+Version: 1.2.1352
 Summary: BioLib Python Client
 License: MIT
 License-File: LICENSE

{pybiolib-1.2.1318.dist-info → pybiolib-1.2.1352.dist-info}/RECORD

@@ -28,14 +28,17 @@ biolib/_internal/templates/copilot_template/.github/prompts/biolib_app_inputs.pr
 biolib/_internal/templates/copilot_template/.github/prompts/biolib_onboard_repo.prompt.md,sha256=BfCkVyafDHFBMu6qcvKlxpnXKJRHNDp5qR_fN4XB9pI,1515
 biolib/_internal/templates/copilot_template/.github/prompts/biolib_run_apps.prompt.md,sha256=-t1bmGr3zEFa6lKHaLcI98yq4Sg1TCMW8xbelNSHaOA,696
 biolib/_internal/templates/gui_template/.yarnrc.yml,sha256=Rz5t74b8A2OBIODAHQyLurCVZ3JWRg-k6nY-XUaX8nA,25
-biolib/_internal/templates/gui_template/App.tsx,sha256=hh_r7P4Pn4HLaE8C1PoECawd81yoC4MfWPu7Op02kWg,509
+biolib/_internal/templates/gui_template/App.tsx,sha256=VfaJO_mxbheRrfO1dU28G9Q4pGsGzeJpPREqtAT4fGE,1692
 biolib/_internal/templates/gui_template/Dockerfile,sha256=nGZQiL7coQBUnH1E2abK2PJ4XRjVS1QXn6HDX9UGpcE,479
+biolib/_internal/templates/gui_template/biolib-sdk.ts,sha256=cplISOz2eUTHXoiF9kftYVMb4qVnEHLkt_wWqdb0HkY,978
+biolib/_internal/templates/gui_template/dev-data/output.json,sha256=wKcJQtN7NGaCJkmEWyRjEbBtTLMHB6pOkqTgWsKmOh8,162
 biolib/_internal/templates/gui_template/index.css,sha256=WYds1xQY2of84ebHhRW9ummbw0Bg9N-EyfmBzJKigck,70
 biolib/_internal/templates/gui_template/index.html,sha256=EM5xzJ9CsJalgzL-jLNkAoP4tgosw0WYExcH5W6DOs8,403
 biolib/_internal/templates/gui_template/index.tsx,sha256=YrdrpcckwLo0kYIA-2egtzlo0OMWigGxnt7mNN4qmlU,234
 biolib/_internal/templates/gui_template/package.json,sha256=iyYYUC0zKGWvZcH8YxN-3w-0N68W5vx-0WPlluMn6Y4,621
 biolib/_internal/templates/gui_template/tsconfig.json,sha256=T3DJIzeLQ2BL8HLfPHI-IvHtJhnMXdHOoRjkmQlJQAw,541
-biolib/_internal/templates/gui_template/vite.config.mts,sha256=Bf1bgRReU3XFsR6rX9yylW2IAxy2cDQI1FHBMjRnyQ4,271
+biolib/_internal/templates/gui_template/vite-plugin-dev-data.ts,sha256=9Fg7kS1xMB5bgUGRExJX8y_AyE2AcVba3k-EfRj352I,1534
+biolib/_internal/templates/gui_template/vite.config.mts,sha256=Pk9T9wkpHowE0WMqOJ_tuLZYhXsslLzLNNkFHYYjHQ4,344
 biolib/_internal/templates/init_template/.biolib/config.yml,sha256=gxMVd1wjbsDvMv4byc8fKEdJFby4qgi6v38mO5qmhoY,453
 biolib/_internal/templates/init_template/.github/workflows/biolib.yml,sha256=sphjoiycV_oc4VbaA8wbUEokSMpnrdB6N-bYju_5Ibo,522
 biolib/_internal/templates/init_template/.gitignore,sha256=dR_jhtT0boUspgk3S5PPUwuO0o8gKGIbdwu8IH638CY,20
@@ -63,11 +66,11 @@ biolib/_internal/utils/__init__.py,sha256=xp1I-lVnu5owV1CW53jiPEZLKmqqHiPUDfauYD
 biolib/_internal/utils/job_url.py,sha256=YpwqCP56BD15M8p2tuSY_Z3O9vWAkG2rJbQu2Z5zqq0,1265
 biolib/_internal/utils/multinode.py,sha256=N7kR49xD1PdkMVlxxzRiSYHfgi9MG-kLCwemcY1rojg,8323
 biolib/_runtime/runtime.py,sha256=9q6Wuo8SBcJIezyScAgq2MDfpT0Pg8lcfbBFmeCWiUE,5974
-biolib/_session/session.py,sha256=US1Y1jfFIAm86-Lq3C7nCXpZXUJXXBVBkND9djMNYxI,1649
+biolib/_session/session.py,sha256=Ymi9OQW_u_CfYA3JlBakPwRhNaKlb20P2G8SmtJhnzA,1824
 biolib/api/__init__.py,sha256=mQ4u8FijqyLzjYMezMUUbbBGNB3iFmkNdjXnWPZ7Jlw,138
 biolib/api/client.py,sha256=2GpKE7QrPgyPdgJgrV7XnZByIJf1n26UCy3aoaHBs1M,7881
 biolib/app/__init__.py,sha256=cdPtcfb_U-bxb9iSL4fCEq2rpD9OjkyY4W-Zw60B0LI,37
-biolib/app/app.py,sha256=Jc2PwNsZDKca9NxvasI_yrnb0q_S9PrJ94lva-y2Zpc,11882
+biolib/app/app.py,sha256=FjiqT7jCH0pSzKpG_v2Z9ysdUaPhhdPmW5gC-IbnAl0,12230
 biolib/app/search_apps.py,sha256=K4a41f5XIWth2BWI7OffASgIsD0ko8elCax8YL2igaY,1470
 biolib/biolib_api_client/__init__.py,sha256=E5EMa19wJoblwSdQPYrxc_BtIeRsAuO0L_jQweWw-Yk,182
 biolib/biolib_api_client/api_client.py,sha256=IONzXeFCHl4wuct6fqOC_7NiTv_zFy6ys0hsAtvLzTA,7578
@@ -147,7 +150,7 @@ biolib/jobs/job_result.py,sha256=_xqQu9z9BqPQrU6tjqKPuKlQDt5W0Zw5xiQvzEBkDyE,526
 biolib/jobs/types.py,sha256=rFs6bQWsNI-nb1Hu9QzOW2zFZ8bOVt7ax4UpGVASxVA,1034
 biolib/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/runtime/__init__.py,sha256=MlRepA11n2H-3plB5rzWyyHK2JmP6PiaP3i6x3vt0mg,506
-biolib/sdk/__init__.py,sha256=Z1S5BgpvM87S2o1libtqkYN1CfYUhn_d4ChEJjwdFKM,2356
+biolib/sdk/__init__.py,sha256=TATbgncVHIzxo_U1zpD1YrdngIIvJkT3S0o2qe3dcg4,2471
 biolib/tables.py,sha256=MmruV-nJLc3HbLVJBAiDuDCgS2-4oaUkpoCLLUNYbxQ,1173
 biolib/typing_utils.py,sha256=ntzrlyTkUaO2OtccLYzCAGztGdca0WT5fikJUmSkT-Y,148
 biolib/user/__init__.py,sha256=Db5wtxLfFz3ID9TULSSTo77csw9tO6RtxMRvV5cqKEE,39
@@ -158,8 +161,8 @@ biolib/utils/cache_state.py,sha256=u256F37QSRIVwqKlbnCyzAX4EMI-kl6Dwu6qwj-Qmag,3
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
 biolib/utils/seq_util.py,sha256=rImaghQGuIqTVWks6b9P2yKuN34uePUYPUFW_Wyoa4A,6737
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.1318.dist-info/METADATA,sha256=Kfin2a-7v8pg6206XqZNFcKTERbw6IVRCvIhR-yb-0E,1644
-pybiolib-1.2.1318.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-pybiolib-1.2.1318.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.1318.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.1318.dist-info/RECORD,,
+pybiolib-1.2.1352.dist-info/METADATA,sha256=XynyBKvX9QaPKQoKAA1I_WX5_XFZDn9X_zjmP2ivUY0,1644
+pybiolib-1.2.1352.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+pybiolib-1.2.1352.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.1352.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.1352.dist-info/RECORD,,