pybiolib 1.2.1318__tar.gz → 1.2.1352__tar.gz

{pybiolib-1.2.1318 → pybiolib-1.2.1352}/PKG-INFO

@@ -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-1.2.1352/biolib/_internal/templates/gui_template/App.tsx

@@ -0,0 +1,53 @@
+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 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 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>
+  );
+}

pybiolib-1.2.1352/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;

pybiolib-1.2.1352/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" }
+  ]
+}

pybiolib-1.2.1352/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
+        };
+      }
+    }
+  };
+}

{pybiolib-1.2.1318 → pybiolib-1.2.1352}/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()],
 });

{pybiolib-1.2.1318 → pybiolib-1.2.1352}/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)

{pybiolib-1.2.1318 → pybiolib-1.2.1352}/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)

{pybiolib-1.2.1318 → pybiolib-1.2.1352}/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 → pybiolib-1.2.1352}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.1318"
+version = "1.2.1352"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"

pybiolib-1.2.1318/biolib/_internal/templates/gui_template/App.tsx

@@ -1,17 +0,0 @@
-export default function App() {
-  return (
-    <div className="min-h-screen bg-gray-100 flex items-center justify-center">
-      <div className="text-center">
-        <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">
-          This is a simple React template with Tailwind CSS styling.
-        </p>
-      </div>
-    </div>
-  );
-}