pybiolib 1.2.1352__py3-none-any.whl → 1.2.1379__py3-none-any.whl

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

@@ -6,14 +6,17 @@ declare global {
   const biolib: IBioLibGlobals;
 }
 
-/* DEV_DATA_INJECTION */
+// DO NOT MODIFY: Development data files are injected at build time from gui/dev-data/ folder
+const DEV_DATA_FILES: Record<string, string> = {};
 
 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 normalizedPath = path.startsWith('/') ? path.slice(1) : path;
+    
+    if (typeof DEV_DATA_FILES !== 'undefined' && normalizedPath in DEV_DATA_FILES) {
+      const base64Data = DEV_DATA_FILES[normalizedPath];
       const binaryString = atob(base64Data);
       const bytes = new Uint8Array(binaryString.length);
       for (let i = 0; i < binaryString.length; i++) {

biolib/_internal/templates/gui_template/package.json

@@ -14,6 +14,7 @@
   },
   "devDependencies": {
     "@tailwindcss/vite": "4.0.14",
+    "@types/node": "20.17.10",
     "@types/react": "18.3.3",
     "@types/react-dom": "18.3.0",
     "@vitejs/plugin-react": "4.2.1",

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

@@ -1,4 +1,4 @@
-import { Plugin } from 'vite';
+import type { Plugin } from 'vite';
 import fs from 'fs';
 import path from 'path';
 
@@ -32,14 +32,11 @@ export function devDataPlugin(): Plugin {
           
           const devDataJson = JSON.stringify(devDataMap);
           injectedCode = code.replace(
-            '/* DEV_DATA_INJECTION */',
-            `const DEV_DATA_FILES: Record<string, string> = ${devDataJson};`
+            "const DEV_DATA_FILES = {};",
+            `const DEV_DATA_FILES = ${devDataJson};`
           );
         } else {
-          injectedCode = code.replace(
-            '/* DEV_DATA_INJECTION */',
-            '// Dev data not included in production build'
-          );
+          injectedCode = code;
         }
         
         return {

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

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

biolib/app/app.py

@@ -7,6 +7,8 @@ import string
 from pathlib import Path
 
 from biolib import utils
+from biolib._internal.file_utils import path_to_renamed_path
+from biolib._runtime.runtime import Runtime
 from biolib.api.client import ApiClient
 from biolib.biolib_api_client import JobState
 from biolib.biolib_api_client.app_types import App, AppVersion
@@ -20,8 +22,6 @@ from biolib.experiments.experiment import Experiment
 from biolib.jobs.job import Result
 from biolib.typing_utils import Dict, Optional
 from biolib.utils.app_uri import parse_app_uri
-from biolib._runtime.runtime import Runtime
-from biolib._internal.file_utils import path_to_renamed_path
 
 
 class BioLibApp:
@@ -95,7 +95,7 @@ class BioLibApp:
             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)
+                experiment_instance = Experiment(experiment_to_use, _api_client=self._api_client)
             else:
                 experiment_instance = Experiment.get_experiment_in_context()
             experiment_id = experiment_instance.uuid if experiment_instance else None

biolib/experiments/experiment.py

@@ -6,6 +6,7 @@ from biolib import api
 from biolib._internal.types.experiment import DeprecatedExperimentDict, ExperimentDict
 from biolib._internal.types.resource import ResourceDetailedDict
 from biolib._internal.utils import open_browser_window_from_notebook
+from biolib.api.client import ApiClient
 from biolib.biolib_api_client import BiolibApiClient
 from biolib.biolib_errors import BioLibError
 from biolib.jobs.job import Job
@@ -28,7 +29,13 @@ class Experiment:
         }
     )
 
-    def __init__(self, uri: str, _resource_dict: Optional[ResourceDetailedDict] = None):
+    def __init__(
+        self,
+        uri: str,
+        _resource_dict: Optional[ResourceDetailedDict] = None,
+        _api_client: Optional[ApiClient] = None,
+    ):
+        self._api_client = _api_client or api.client
         self._resource_dict: ResourceDetailedDict = _resource_dict or self._get_or_create_resource_dict(uri)
 
     def __enter__(self):
@@ -113,7 +120,7 @@ class Experiment:
             job_id = job
         elif job is None and job_id is None:
             raise BioLibError('A job ID or job object must be provided to add job')
-        api.client.post(
+        self._api_client.post(
             path=f'/experiments/{self.uuid}/jobs/',
             data={'job_uuid': job_id},
         )
@@ -126,7 +133,7 @@ class Experiment:
         else:
             raise BioLibError('A job ID or job object must be provided to remove job')
 
-        api.client.delete(path=f'/experiments/{self.uuid}/jobs/{job_id}/')
+        self._api_client.delete(path=f'/experiments/{self.uuid}/jobs/{job_id}/')
 
     def mount_files(self, mount_path: str) -> None:
         try:
@@ -175,7 +182,7 @@ class Experiment:
 
     # Prints a table listing info about the jobs in this experiment
     def show_jobs(self) -> None:
-        response: JobsPaginatedResponse = api.client.get(
+        response: JobsPaginatedResponse = self._api_client.get(
             path=f'/experiments/{self.uuid}/jobs/',
             params=dict(page_size=10),
         ).json()
@@ -197,11 +204,13 @@ class Experiment:
         if status:
             params['status'] = status
 
-        response: JobsPaginatedResponse = api.client.get(url, params=params).json()
+        response: JobsPaginatedResponse = self._api_client.get(url, params=params).json()
         jobs: List[Job] = [Job(job_dict) for job_dict in response['results']]
 
         for page_number in range(2, response['page_count'] + 1):
-            page_response: JobsPaginatedResponse = api.client.get(url, params=dict(**params, page=page_number)).json()
+            page_response: JobsPaginatedResponse = self._api_client.get(
+                url, params=dict(**params, page=page_number)
+            ).json()
             jobs.extend([Job(job_dict) for job_dict in page_response['results']])
 
         return jobs
@@ -300,21 +309,19 @@ class Experiment:
             )
 
     def rename(self, destination: str) -> None:
-        api.client.patch(f'/resources/{self.uuid}/', data={'uri': destination})
+        self._api_client.patch(f'/resources/{self.uuid}/', data={'uri': destination})
         self._refetch()
 
-    @staticmethod
-    def _get_resource_dict_by_uuid(uuid: str) -> ResourceDetailedDict:
-        resource_dict: ResourceDetailedDict = api.client.get(f'/resources/{uuid}/').json()
+    def _get_resource_dict_by_uuid(self, uuid: str) -> ResourceDetailedDict:
+        resource_dict: ResourceDetailedDict = self._api_client.get(f'/resources/{uuid}/').json()
         if not resource_dict['experiment']:
             raise ValueError('Resource from URI is not an experiment')
 
         return resource_dict
 
-    @staticmethod
-    def _get_or_create_resource_dict(uri: str) -> ResourceDetailedDict:
-        response_dict = api.client.post(path='/experiments/', data={'uri' if '/' in uri else 'name': uri}).json()
-        return Experiment._get_resource_dict_by_uuid(uuid=response_dict['uuid'])
+    def _get_or_create_resource_dict(self, uri: str) -> ResourceDetailedDict:
+        response_dict = self._api_client.post(path='/experiments/', data={'uri' if '/' in uri else 'name': uri}).json()
+        return self._get_resource_dict_by_uuid(uuid=response_dict['uuid'])
 
     def _refetch(self) -> None:
         self._resource_dict = self._get_resource_dict_by_uuid(uuid=self._resource_dict['uuid'])

{pybiolib-1.2.1352.dist-info → pybiolib-1.2.1379.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pybiolib
-Version: 1.2.1352
+Version: 1.2.1379
 Summary: BioLib Python Client
 License: MIT
 License-File: LICENSE

{pybiolib-1.2.1352.dist-info → pybiolib-1.2.1379.dist-info}/RECORD

@@ -30,15 +30,15 @@ biolib/_internal/templates/copilot_template/.github/prompts/biolib_run_apps.prom
 biolib/_internal/templates/gui_template/.yarnrc.yml,sha256=Rz5t74b8A2OBIODAHQyLurCVZ3JWRg-k6nY-XUaX8nA,25
 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/biolib-sdk.ts,sha256=zRN2h4ws7ZuidxYKaRPaurfTxNJN-hX0MdG6POvdxU0,1195
 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/package.json,sha256=4E8pDdnrYYjmKAL8NYFE3OZzBf4-CWdHWEZFAo_zBwg,652
 biolib/_internal/templates/gui_template/tsconfig.json,sha256=T3DJIzeLQ2BL8HLfPHI-IvHtJhnMXdHOoRjkmQlJQAw,541
-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/gui_template/vite-plugin-dev-data.ts,sha256=jLFSl7_DU9W3ScM6fm0aFSCzDhAtzhI9G6zr1exze84,1397
+biolib/_internal/templates/gui_template/vite.config.mts,sha256=5RjRfJHgqLOr-LRydBUnDPr5GrHQuRsviTMC60hvKxU,348
 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
@@ -70,7 +70,7 @@ biolib/_session/session.py,sha256=Ymi9OQW_u_CfYA3JlBakPwRhNaKlb20P2G8SmtJhnzA,18
 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=FjiqT7jCH0pSzKpG_v2Z9ysdUaPhhdPmW5gC-IbnAl0,12230
+biolib/app/app.py,sha256=8k7M8G3HO1TPfBTZrE_iODKX28rxxf-7g-OsUa3x-fY,12260
 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
@@ -143,7 +143,7 @@ biolib/compute_node/webserver/webserver_types.py,sha256=2t8EaFKESnves3BA_NBdnS2y
 biolib/compute_node/webserver/webserver_utils.py,sha256=XWvwYPbWNR3qS0FYbLLp-MDDfVk0QdaAmg3xPrT0H2s,4234
 biolib/compute_node/webserver/worker_thread.py,sha256=7uD9yQPhePYvP2HCJ27EeZ_h6psfIWFgqm1RHZxzobs,12483
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biolib/experiments/experiment.py,sha256=4g1xMYmfp5yzSOdwjf3pUUULF9QjqBJb4uQ25FHrFrk,13688
+biolib/experiments/experiment.py,sha256=ePipnJs6TW84jr9iBfYYRpYuEXUVGIxaD8Z8Jf0FYIA,13909
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
 biolib/jobs/job.py,sha256=X7F_jCwAwtPcI1qu-oLamZNzt1IVSIeOPWlax1ztfAM,29674
 biolib/jobs/job_result.py,sha256=_xqQu9z9BqPQrU6tjqKPuKlQDt5W0Zw5xiQvzEBkDyE,5266
@@ -161,8 +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-1.2.1352.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,,
+pybiolib-1.2.1379.dist-info/METADATA,sha256=K_Bnjzo9XB9Aq5g63v7A6CEKrEc1YC5jh6u0gYMGqCA,1644
+pybiolib-1.2.1379.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+pybiolib-1.2.1379.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.1379.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.1379.dist-info/RECORD,,