minio-remove-cert (#45)

* removing cert requirement * Edit readme * adding to gitignore * adding to gitignore * Adding example env.yml file
clinical-data-mining · Nov 15, 2024 · ba74977 · ba74977
1 parent 4b1c27e
commit ba74977
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Showing 4 changed files with 22 additions and 21 deletions.
diff --git a/.gitignore b/.gitignore
@@ -8,6 +8,8 @@ docs/source/msk_cdm*.rst
 build
 dist
 *.egg-info
+site/*
+configs/*
 
 # python runtime
 __pycache__/
@@ -22,8 +24,8 @@ __pycache__/
 .DS_Store
 .DS_store
 /credentials.json
-/databricks_env_test.txt
+/configs/databricks_env_test.txt
 /databricks_env.txt
-/certificate_sparky.crt
-/minio_env.txt
+/configs/certificate_sparky.crt
+/configs/minio_env.txt
 /sandbox/
diff --git a/README.md b/README.md
@@ -78,7 +78,7 @@ Run:
 mkdocs serve --dev-addr <Default 127.0.0.1:8000>
 ```
 
-### How to deploy the documentation
+### How to deploy the documentation 
 Run:
 ```
 mkdocs gh-deploy

diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,16 @@
+name: <your-conda-env-example>
+channels:
+  - pytorch
+  - nvidia
+  - conda-forge
+dependencies:
+   - python == 3.10
+   - pandas
+   - pyyaml
+   - minio
+   - requests
+   - ipykernel
+   - conda-build
+   - pip
+   - pip: 
+       - git+https://github.com/clinical-data-mining/msk_cdm.git
diff --git a/src/msk_cdm/minio/_minio_api.py b/src/msk_cdm/minio/_minio_api.py
@@ -23,7 +23,6 @@ def __init__(
         *,
         ACCESS_KEY: Optional[str] = None,
         SECRET_KEY: Optional[str] = None,
-        ca_certs: Optional[str] = None,
         url_port: Optional[str] = "pllimsksparky3:9000", 
         fname_minio_env: Optional[Union[Path, str]] = None,
         bucket: Optional[str] = None,
@@ -39,12 +38,10 @@ def __init__(
         """
         self._ACCESS_KEY = ACCESS_KEY
         self._SECRET_KEY = SECRET_KEY
-        self._ca_certs = ca_certs
         self._url_port = url_port
 
         self._bucket = bucket
         self._client = None
-        self._httpClient = None
 
         if fname_minio_env is not None:
             self._process_env(fname_minio_env)
@@ -245,39 +242,25 @@ def _process_env(self, fname_minio_env):
             self._ACCESS_KEY = dict_config.get("ACCESS_KEY", None)
         if not self._SECRET_KEY:
             self._SECRET_KEY = dict_config.get("SECRET_KEY", None)
-        if not self._ca_certs:
-            self._ca_certs = dict_config.get("CA_CERTS", None)
         if not self._url_port:
             self._url_port = dict_config.get("URL_PORT", None)
         if not self._bucket:
             self._bucket = dict_config.get("BUCKET", None)
 
-        # # Print out for QC
-        # print('Access Key: %s' % self._ACCESS_KEY)
-        # print('Secret Key: %s' % self._SECRET_KEY)
-        # print('CA Cert: %s' % self._ca_certs)
-        # print('URL Port: %s' % self._url_port)
-        # print('Bucket: %s' % self._bucket)
-
         return None
 
     def _connect(self):
         # required for self-signed certs
-        httpClient = urllib3.PoolManager(
-            cert_reqs="CERT_REQUIRED", ca_certs=self._ca_certs
-        )
 
         # Create secure client with access key and secret key
         client = Minio(
             endpoint=self._url_port,
             access_key=self._ACCESS_KEY,
             secret_key=self._SECRET_KEY,
             secure=True,
-            http_client=httpClient,
         )
 
         self._client = client
-        self._httpClient = httpClient
 
         return None