bacdive 1.0.0__tar.gz → 2.0.0__tar.gz

{bacdive-1.0.0 → bacdive-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: bacdive
-Version: 1.0.0
+Version: 2.0.0
 Summary: BacDive-API - Programmatic Access to the BacDive Database
 Home-page: https://bacdive.dsmz.de/
 Author: Julia Koblitz
@@ -13,23 +13,28 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: python-keycloak
 Requires-Dist: requests>=2.25.1
 Requires-Dist: urllib3>=1.26.5
-
-# BacDive API
-
-Using the BacDive API requires registration. Registration is free but the usage of BacDive data is only permitted when in compliance with the BacDive terms of use. See [About BacDive](https://bacdive.dsmz.de/about) for details.
-
-Please register [here](https://api.bacdive.dsmz.de/login).
-
-The Python package can be initialized using your login credentials:
-
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# BacDive API v2
+
+Using the BacDive API does not require registration anymore, but the usage of BacDive data is only permitted when in compliance with the BacDive terms of use. See [About BacDive](https://bacdive.dsmz.de/about) for details.
 
 ```python
 import bacdive
 
-client = bacdive.BacdiveClient('name@mail.example', 'password')
+client = bacdive.BacdiveClient()
 
 # [optional] You may define the search type as one of the following: 
 # 'exact' (default), 'contains', 'startswith', 'endswith'

{bacdive-1.0.0 → bacdive-2.0.0}/README.md

@@ -1,16 +1,11 @@
-# BacDive API
-
-Using the BacDive API requires registration. Registration is free but the usage of BacDive data is only permitted when in compliance with the BacDive terms of use. See [About BacDive](https://bacdive.dsmz.de/about) for details.
-
-Please register [here](https://api.bacdive.dsmz.de/login).
-
-The Python package can be initialized using your login credentials:
+# BacDive API v2
 
+Using the BacDive API does not require registration anymore, but the usage of BacDive data is only permitted when in compliance with the BacDive terms of use. See [About BacDive](https://bacdive.dsmz.de/about) for details.
 
 ```python
 import bacdive
 
-client = bacdive.BacdiveClient('name@mail.example', 'password')
+client = bacdive.BacdiveClient()
 
 # [optional] You may define the search type as one of the following: 
 # 'exact' (default), 'contains', 'startswith', 'endswith'
@@ -119,4 +114,4 @@ client.excludePredictions()
 
 Thanks to [phenolophthaleinum](https://github.com/phenolophthaleinum) for improving the error handling and Joaquim Sardá for improving the BacDive-API and adding new search possibilities.
 
-Examples for search type definitions and array requests are included in the examples above.
+Examples for search type definitions and array requests are included in the examples above.

{bacdive-1.0.0 → bacdive-2.0.0}/bacdive/client.py

@@ -1,13 +1,8 @@
 '''
-Using the BacDive API requires registration. Registrations is free but the 
-usage of BacDive data is only permitted when in compliance with the BacDive 
-terms of use. See https://bacdive.dsmz.de/about for details.
-
-Please register at https://api.bacdive.dsmz.de/login.
+This package is for using the BacDive API V2 (2026-02).
+Registration is not required anymore.
 '''
 
-from keycloak.exceptions import KeycloakAuthenticationError, KeycloakPostError, KeycloakConnectionError
-from keycloak import KeycloakOpenID
 from requests.adapters import HTTPAdapter
 from urllib3.util.retry import Retry
 import requests
@@ -29,7 +24,7 @@ class ReportRetry(Retry):
 
 
 class BacdiveClient():
-    def __init__(self, user, password, public=True, max_retries=10, retry_delay=50, request_timeout=300):
+    def __init__(self, user=None, password=None, public=True, max_retries=10, retry_delay=50, request_timeout=300):
         ''' Initialize client and authenticate on the server '''
         self.result = {}
         self.public = public
@@ -46,32 +41,6 @@ class BacdiveClient():
         else:
             server_url = "https://sso.dmz.dsmz.de/auth/"
 
-        self.keycloak_openid = KeycloakOpenID(
-            server_url=server_url,
-            client_id=client_id,
-            realm_name="dsmz")
-
-        for _ in range(self.max_retries):
-            try:
-                # Get tokens
-                token = self.keycloak_openid.token(user, password)
-                self.access_token = token['access_token']
-                self.refresh_token = token['refresh_token']
-                print("-- Authentication successful --")
-            except KeycloakAuthenticationError as e:
-                print(f"ERROR - Keycloak Authentication failed: {e}\n Retrying in {self.retry_delay} seconds")
-                time.sleep(self.retry_delay)
-            except KeycloakConnectionError as e:
-                print(f"ERROR - Keycloak Connection failed: {e}\n Retrying in {self.retry_delay} seconds")
-                time.sleep(self.retry_delay)
-            except KeycloakPostError as e:
-                print(f"ERROR - Keycloak Connection failed: {e}\n Retrying in {self.retry_delay} seconds")
-                time.sleep(self.retry_delay)
-            else:
-                break # break loop if successful
-        else:
-            print(f"ERROR - Keycloak authentication failed after {self.max_retries} retries.")
-
     def includePredictions(self):
         self.predictions = True
 
@@ -92,9 +61,9 @@ class BacdiveClient():
     def do_api_call(self, url):
         ''' Initialize API call on given URL and returns result as json '''
         if self.public:
-            baseurl = "https://api.bacdive.dsmz.de/"
+            baseurl = "https://api.bacdive.dsmz.de/v2/"
         else:
-            baseurl = "http://api.bacdive-dev.dsmz.local/"
+            baseurl = "http://api.bacdive-dev.dsmz.local/v2/"
         
         if not url.startswith("http"):
             # if base is missing add default:
@@ -107,23 +76,14 @@ class BacdiveClient():
         elif (resp.status_code == 401):
             msg = json.loads(resp.content)
 
-            if msg['message'] == "Expired token":
-                # Access token might have expired (15 minutes life time).
-                # Get new tokens using refresh token and try again.
-                token = self.keycloak_openid.refresh_token(self.refresh_token)
-                self.access_token = token['access_token']
-                self.refresh_token = token['refresh_token']
-                return self.do_api_call(url)
-
             return msg
         else:
             return json.loads(resp.content)
 
     def do_request(self, url):
-        ''' Perform request with authentication '''
+        ''' Perform request'''
         headers = {
             "Accept": "application/json",
-            "Authorization": "Bearer {token}".format(token=self.access_token)
         }
 
         if self.predictions:
@@ -163,7 +123,7 @@ class BacdiveClient():
     def retrieve(self, filter=None):
         ''' Yields all the received entries and does next call if result is incomplete '''
         ids = ";".join([str(i) for i in self.result['results']])
-        entries = self.do_api_call('fetch/'+ids)['results']
+        entries = self.do_api_call('fetch/'+ids)['results'] if ids else []
         for el in entries:
             if isinstance(el, dict):
                 entry = el

{bacdive-1.0.0 → bacdive-2.0.0}/bacdive.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: bacdive
-Version: 1.0.0
+Version: 2.0.0
 Summary: BacDive-API - Programmatic Access to the BacDive Database
 Home-page: https://bacdive.dsmz.de/
 Author: Julia Koblitz
@@ -13,23 +13,28 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: python-keycloak
 Requires-Dist: requests>=2.25.1
 Requires-Dist: urllib3>=1.26.5
-
-# BacDive API
-
-Using the BacDive API requires registration. Registration is free but the usage of BacDive data is only permitted when in compliance with the BacDive terms of use. See [About BacDive](https://bacdive.dsmz.de/about) for details.
-
-Please register [here](https://api.bacdive.dsmz.de/login).
-
-The Python package can be initialized using your login credentials:
-
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# BacDive API v2
+
+Using the BacDive API does not require registration anymore, but the usage of BacDive data is only permitted when in compliance with the BacDive terms of use. See [About BacDive](https://bacdive.dsmz.de/about) for details.
 
 ```python
 import bacdive
 
-client = bacdive.BacdiveClient('name@mail.example', 'password')
+client = bacdive.BacdiveClient()
 
 # [optional] You may define the search type as one of the following: 
 # 'exact' (default), 'contains', 'startswith', 'endswith'

{bacdive-1.0.0 → bacdive-2.0.0}/bacdive.egg-info/requires.txt

@@ -1,3 +1,2 @@
-python-keycloak
 requests>=2.25.1
 urllib3>=1.26.5

{bacdive-1.0.0 → bacdive-2.0.0}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
 
 setuptools.setup(
     name="bacdive",
-    version="1.0.0",
+    version="2.0.0",
     description="BacDive-API - Programmatic Access to the BacDive Database",
     long_description=long_description,
     long_description_content_type="text/markdown",
@@ -22,7 +22,6 @@ setuptools.setup(
     ],
     keywords="microbiology bacteria strains phenotypes",
     install_requires=[
-        "python-keycloak",
         "requests>=2.25.1",
         "urllib3>=1.26.5"
     ]