pybiolib 1.1.1666__py3-none-any.whl → 1.1.1682__py3-none-any.whl

biolib/_internal/http_client.py

@@ -1,6 +1,9 @@
 import json
+import platform
 import time
 import socket
+import ssl
+import subprocess
 import urllib.request
 import urllib.error
 import urllib.parse
@@ -8,6 +11,19 @@ import urllib.parse
 from biolib.biolib_logging import logger_no_user_data
 from biolib.typing_utils import Dict, Optional, Union, Literal, cast
 
+def create_ssl_context():
+    context = ssl.create_default_context()
+    try:
+        if platform.system() == 'Darwin':
+            certificates = subprocess.check_output(
+                "security find-certificate -a -p",
+                shell=True
+            ).decode('utf-8')
+            context.load_verify_locations(cadata=certificates)
+    except BaseException:
+        pass
+    return context
+
 
 class HttpError(urllib.error.HTTPError):
     def __init__(self, http_error: urllib.error.HTTPError):
@@ -39,6 +55,8 @@ class HttpResponse:
 
 
 class HttpClient:
+    ssl_context = None
+
     @staticmethod
     def request(
             url: str,
@@ -47,6 +65,8 @@ class HttpClient:
             headers: Optional[Dict[str, str]] = None,
             retries: int = 0,
     ) -> HttpResponse:
+        if not HttpClient.ssl_context:
+            HttpClient.ssl_context = create_ssl_context()
         headers_to_send = headers or {}
         if isinstance(data, dict):
             headers_to_send['Accept'] = 'application/json'
@@ -66,7 +86,11 @@ class HttpClient:
                 time.sleep(5 * retry_count)
                 logger_no_user_data.debug(f'Retrying HTTP {method} request...')
             try:
-                with urllib.request.urlopen(request, timeout=timeout_in_seconds) as response:
+                with urllib.request.urlopen(
+                    request,
+                    context=HttpClient.ssl_context,
+                    timeout=timeout_in_seconds
+                ) as response:
                     return HttpResponse(response)
 
             except urllib.error.HTTPError as error:

biolib/biolib_api_client/biolib_app_api.py

@@ -1,17 +1,42 @@
+import mimetypes
+import random
 import re
 import os
 import subprocess
 
-import requests
+from requests.exceptions import HTTPError
 
 import biolib.api
 from biolib import biolib_errors
 from biolib.typing_utils import Optional
-from biolib.biolib_api_client.auth import BearerAuth
-from biolib.biolib_api_client import BiolibApiClient, AppGetResponse
-from biolib.biolib_errors import BioLibError
+from biolib.biolib_api_client import AppGetResponse
 from biolib.biolib_logging import logger
 
+def encode_multipart(data, files):
+    boundary = f'----------{random.randint(0, 1000000000)}'
+    line_array = []
+
+    for (key, value) in data.items():
+        if not value is None:
+            line_array.append(f'--{boundary}')
+            line_array.append(f'Content-Disposition: form-data; name="{key}"')
+            line_array.append('')
+            line_array.append(value)
+
+    for (key, (filename, value)) in files.items():
+        line_array.append(f'--{boundary}')
+        line_array.append(f'Content-Disposition: form-data; name="{key}"; filename="{filename}"')
+        line_array.append(f'Content-Type: {mimetypes.guess_type(filename)[0] or "application/octet-stream"}')
+        line_array.append('')
+        line_array.append('')
+        line_array.append(value)
+
+    line_array.append(f'--{boundary}--')
+    line_array.append('')
+
+    data_encoded = b'\r\n'.join([line.encode() if isinstance(line, str) else line for line in line_array])
+    return 'multipart/form-data; boundary={}'.format(boundary), data_encoded
+
 
 def _get_git_branch_name() -> str:
     try:
@@ -51,7 +76,7 @@ class BiolibAppApi:
             app_response: AppGetResponse = response.json()
             return app_response
 
-        except requests.exceptions.HTTPError as error:
+        except HTTPError as error:
             if error.response.status_code == 404:
                 raise biolib_errors.NotFound(f'Application {uri} not found.') from None
 
@@ -69,24 +94,28 @@ class BiolibAppApi:
             set_as_active,
             app_version_id_to_copy_images_from: Optional[str],
     ):
-        response = requests.post(
-            f'{BiolibApiClient.get().base_url}/api/app_versions/',
-            files={
-                'source_files_zip': zip_binary,
-            },
-            data={
-                'app': app_id,
-                'set_as_active': 'true' if set_as_active else 'false',
-                'state': 'published',
-                'app_version_id_to_copy_images_from': app_version_id_to_copy_images_from,
-                'git_branch_name': _get_git_branch_name(),
-                'git_repository_url': _get_git_repository_url(),
-            },
-            auth=BearerAuth(BiolibApiClient.get().access_token)
-        )
-        if not response.ok:
+        try:
+            content_type, data_encoded = encode_multipart(
+                data={
+                    'app': app_id,
+                    'set_as_active': 'true' if set_as_active else 'false',
+                    'state': 'published',
+                    'app_version_id_to_copy_images_from': app_version_id_to_copy_images_from,
+                    'git_branch_name': _get_git_branch_name(),
+                    'git_repository_url': _get_git_repository_url(),
+                },
+                files={
+                    'source_files_zip': ('source_files.zip', zip_binary),
+                }
+            )
+            response = biolib.api.client.post(
+                path='/app_versions/',
+                data=data_encoded,
+                headers={'Content-Type': content_type},
+            )
+        except Exception as error:
             logger.error(f'Push failed for {author}/{app_name}:')
-            raise BioLibError(response.text)
+            raise error
 
         # TODO: When response includes the version number, print the URL for the new app version
         logger.info(f'Initialized new app version for {author}/{app_name}.')

{pybiolib-1.1.1666.dist-info → pybiolib-1.1.1682.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1666
+Version: 1.1.1682
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1666.dist-info → pybiolib-1.1.1682.dist-info}/RECORD

@@ -2,7 +2,7 @@ LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
 README.md,sha256=_IH7pxFiqy2bIAmaVeA-iVTyUwWRjMIlfgtUbYTtmls,368
 biolib/__init__.py,sha256=_ydjlp3Kyqr4iWkT63ZdiiwTbqtHjPS2S51EdU0UTk4,3690
 biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biolib/_internal/http_client.py,sha256=QlOXLeXIHHmgeIQuNMowD4XFzkTq-Pz_67-HyLmFxHM,3042
+biolib/_internal/http_client.py,sha256=TS_TNwAiY73KKkIjlXEvt48JxghUz76C5S76bQ9Kj9Q,3720
 biolib/_internal/push_application.py,sha256=NXQNLPucqkq7eKbNCJQA8OYx4CXYHRJ1CG1ViPAJJH4,10680
 biolib/api/__init__.py,sha256=iIO8ZRdn7YDhY5cR47-Wo1YsNOK8H6RN6jn8yor5WJI,137
 biolib/api/client.py,sha256=jts2QbR-pPU0pAuUaYfWsK4q1O4Nu1nQKv6LYu0T0L0,2754
@@ -14,7 +14,7 @@ biolib/biolib_api_client/api_client.py,sha256=oaLqTb208TLRVW4-h_va734TrVDRD3kLpF
 biolib/biolib_api_client/app_types.py,sha256=vEjkpMwaMfz8MxBBZQfWCkxqT7NXxWocB_Oe9WHjJ_g,2425
 biolib/biolib_api_client/auth.py,sha256=BAXtic6DdaA2QjoDVglnO3PFPoBETQbSraTpIwsZbFc,1267
 biolib/biolib_api_client/biolib_account_api.py,sha256=2Mc6SbmjBSsz8lF2H3iiaZHEm47LyI0B4rjmvzxKHt4,580
-biolib/biolib_api_client/biolib_app_api.py,sha256=naEy1tShrVkL8yCd1n9Q-gNrq6lAcNEAnt7qNl0KJyY,3291
+biolib/biolib_api_client/biolib_app_api.py,sha256=pr52ARrDeB5ioEA7NAjMdmBYb9V2FPy0_URCwdCRZ0A,4397
 biolib/biolib_api_client/biolib_job_api.py,sha256=AvNvflEeCBjG2ZTaFcwvRU-61GdNodFCZQNe50491RM,7823
 biolib/biolib_api_client/biolib_large_file_system_api.py,sha256=5q4UlRw-OB2bRu7CeB14fy-azz2YeSgem5DbvMSaS44,1777
 biolib/biolib_api_client/common_types.py,sha256=RH-1KNHqUF-EkTpfPOSTt5Mq1GPdfju_cqXDesscO1I,123
@@ -101,8 +101,8 @@ biolib/utils/cache_state.py,sha256=BFrZlV4XZIueIFzAFiPidX4hmwADKY5Y5ZuqlerF5l0,3
 biolib/utils/multipart_uploader.py,sha256=PEorMsTNg5f72e3Y-KA3LrI-F6EAnsD9vENV-5EuiX0,9896
 biolib/utils/seq_util.py,sha256=gLnqCr_mcLcxakO44vGBqUn76VI7kLHgXKqyManjd24,4292
 biolib/utils/zip/remote_zip.py,sha256=NCdUnVbGCv7SfXCI-yVU-is_OnyWmLAnVpIdSvo-W4k,23500
-pybiolib-1.1.1666.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1666.dist-info/METADATA,sha256=sFQrMV8cWV9JJsuhP8ZSMPsf6fIDva5Kqbe29B2BSRw,1543
-pybiolib-1.1.1666.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-pybiolib-1.1.1666.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1666.dist-info/RECORD,,
+pybiolib-1.1.1682.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.1682.dist-info/METADATA,sha256=TKjdi5d96iH3SiJWvhNp0joJ-6MI10aT2M3VCa6m0IE,1543
+pybiolib-1.1.1682.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+pybiolib-1.1.1682.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.1682.dist-info/RECORD,,