Merge pull request #23 from willem0boone/dev

updated tests

README.md

@@ -1,32 +1,50 @@
 [![DOI](https://sandbox.zenodo.org/badge/851485026.svg)](https://handle.stage.datacite.org/10.5072/zenodo.109216)
+
 # Edito Resampling datasets
 
 ## About
-This project is part of EDITO-INFRA ([Grant agreement ID: 101101473](https://doi.org/10.3030/101101473)):
-- T7.3: End-to-end demonstrator for aquaculture and maritime industry
+This project is part of EDITO-INFRA 
+([Grant agreement ID: 101101473](https://doi.org/10.3030/101101473)):
+- T7.3: End-to-end demonstrator for aquaculture and maritime industry.
 
 Author: Willem Boone | contact: [[email protected]]([email protected])
 
 ## Goal
 #### Summary of Demonstrator
-The demonstrator use case (DUC) consists of a smartviewer that hosts a model to predict habitat suitability based on environmental living conditions. The smartviewer is maintained in a separate [repository](https://github.com/willem0boone/Edito_model_viewer) and is based on Carbonplan its [seaweed-farming-web](https://carbonplan.org/research/seaweed-farming)/[GitHub](https://github.com/carbonplan/seaweed-farming-web).
-
-In this demonstrator, habitat suitability is calculated using a deterministic model that uses minimum and maximum thresholds on the environmental variables.
+The demonstrator use case (DUC) consists of a smartviewer that hosts a model to 
+predict habitat suitability based on environmental living conditions. The 
+smartviewer is maintained in a separate repository 
+[GitHub - Edito_model_viewer](https://github.com/willem0boone/Edito_model_viewer)
+and is based on Carbonplan its 
+[Mapping seaweed farming potential](https://carbonplan.org/research/seaweed-farming)
+/
+[GitHub - seaweed-farming-web](https://github.com/carbonplan/seaweed-farming-web).
+
+In this demonstrator, habitat suitability is calculated using a deterministic 
+model that uses minimum and maximum thresholds on the environmental variables.
  The environmental parameters that are used are: 
 
-- Sea surface temperature (°C)
-- Sea surface salinity ()
-- Bathymetry (depth in m) 
+- Sea surface temperatur
+- Sea surface salinity
+- Bathymetry
 
-The thresholds for all variables can be adopted using slider widgets. On any changing parameter, the suitability map is updated and rendered in the viewer. Using a time slider, environmental parameters for several future climate scenarios can be accessed and converted in suitability maps.
-This work is available on this [GitHub page](https://github.com/willem0boone/Edito_model_viewer). 
+The thresholds for all variables can be adopted using slider widgets. On any 
+changing parameter, the suitability map is updated and rendered in the viewer. 
+Using a time slider, environmental parameters for several future climate 
+scenarios can be accessed and converted in suitability maps.
 
 #### Data formatting
-The environmental variable dataset used by the smartviewer, need to be provided in a specific format. To create this dataset, different sources and storage from Edito data lake are used. Two pipelines were required: 
-- Downscaling large .zarr datasets to lower resolution. E.g. the bathymetry dataset is around 20GB, which is to large for the demonstrator purpose.
-- Creating pyramids in which each level has increasing resolution (for optimal zooming/rendering).
-
-This work is available on this [GitHub page](https://github.com/willem0boone/Edito_resampling_datasets)
+The environmental variable dataset used by the smartviewer, need to be provided
+in a specific format. To create this dataset, different sources and storage 
+from Edito data lake are used. Two pipelines were required: 
+- Downscaling large .zarr datasets to lower resolution. E.g. the bathymetry 
+- dataset is around 20GB, which is to large for the demonstrator purpose.
+- Creating pyramids in which each level has increasing resolution (for optimal 
+zooming/rendering).
+
+This work is available on
+[GitHub - Edito_resampling_datasets](https://github.com/willem0boone/Edito_resampling_datasets)
+.
 
 ## How to use
 - resampling: package, pip install & documentation will follow. 

docs/source/conf.py

@@ -30,9 +30,10 @@ def extract_version_from_file(file_path):
 # release = '0.1'
 # version = '0.1.0'
 
-codemeta = "../codemeta.json"
+codemeta = "../../codemeta.json"
 version = extract_version_from_file(codemeta)
 
+
 # -- General configuration
 
 extensions = [

docs/source/pyramids.rst

@@ -84,6 +84,7 @@ latitude/longitude as geographical coordinates. On the y axis, coordinates go
 from 1800 (north pole> to 900 (equator> to 0 (south pole>. Notice that this is
 high to low while the plot uses low to high. so the plotting of the map is
 mirrored but it doesn't affect the dataset and pyramid building.
+
 Create pyramid
 ^^^^^^^^^^^^^^
 

docs/source/usage.rst

@@ -4,7 +4,7 @@ Usage
 This page contains examples for both downsampling and creating pyramids. The
 examples are also available in notebooks on the
 `github page <https://github.com/willem0boone/Edito_resampling_datasets/tree/
-main/notebooksL>`_
+main/notebooks>`_.
 
 
 Contents

resampling/config/config.toml

@@ -1,5 +1,7 @@
 endpoint_url='https://minio.lab.dive.edito.eu'
 bucket='oidc-willemboone/EDITO_DUC'
-aws_access_key_id='FDR029N2ZKIUSZHV8GUH'
-aws_secret_access_key='5kAXkWfDpzBm0Beav2sMqcw1zg2FVEtQVhtE19yX'
-aws_session_token="eyJhbGciOiJIUzUxMiIsInR5cCI6IkpXVCJ9.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.y2jahOvyOFyaHBIDXkxHAYbXSHWU9hAkM86c2u9lfu3BOg_FqZD9wU9L_OOijuq2GNzRrfIuyPqAZy_Zo_uqZg"
+aws_access_key_id='CI85QRKB8BMODR4II7Y0'
+aws_secret_access_key='wMjz9Ug6tUFaMHW7tfeUR5L0znlrBzz3eIK9z3mU'
+aws_session_token="eyJhbGciOiJIUzUxMiIsInR5cCI6IkpXVCJ9.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.qR32cJtauR_HbG-fh-BMeMt0_GCm5BzHRWn7yHcmDr9cXtJbAoZ7XjpBITmasTq_WcIoeIf5GNZSYUzkO738LA"
+
+

tests/test_config.py

@@ -3,37 +3,54 @@
 from botocore.exceptions import NoCredentialsError
 from botocore.exceptions import PartialCredentialsError
 from botocore.exceptions import ClientError
-from config import Config
+from resampling.my_store import get_my_store
+import warnings
 
 
-class TestConfig(unittest.TestCase):
-    def test_object(self):
+class TestObjectStore(unittest.TestCase):
+
+    def setUp(self):
+        """ Set up variables shared across tests """
+        self.my_store = None
+
+    def test_get_my_store(self):
+        """ Test to initiate ObjectStore """
         try:
-            config = Config()
+            self.my_store = get_my_store()
         except Exception as e:
-            self.fail(f"Creating Config instance failed with exception: {e}")
+            warnings.warn(
+                f"Initiating Objectstore via get_my_store encountered an "
+                f"error: {e}")
+            self.my_store = None
 
     def test_s3_connection(self):
+        """ Test to check S3 connection, dependent on test_get_my_store """
+        if self.my_store is None:
+            self.skipTest(
+                "Skipping S3 connection test because my_store initialization "
+                "failed.")
+
         try:
-            settings = Config().settings
             # Create an S3 client
             s3_client = boto3.client(
                 's3',
-                endpoint_url=settings.endpoint_url,
-                aws_access_key_id=settings.aws_access_key_id,
-                aws_secret_access_key=settings.aws_secret_access_key,
-                aws_session_token=settings.aws_session_token
+                endpoint_url=self.my_store._endpoint_url,
+                aws_access_key_id=self.my_store._aws_access_key_id,
+                aws_secret_access_key=self.my_store._aws_secret_access_key,
+                aws_session_token=self.my_store._aws_session_token
             )
 
             # Test listing buckets
             response = s3_client.list_buckets()
             self.assertIn('Buckets', response)
 
             # Optionally check if a specific bucket exists
-            bucket_exists = any(bucket['Name'] == settings.bucket for bucket in
-                                response.get('Buckets', []))
+            bucket_exists = any(
+                bucket['Name'] == self.my_store._bucket for bucket in
+                response.get('Buckets', []))
             self.assertTrue(bucket_exists,
-                            f"Bucket {settings.bucket} does not exist.")
+                            f"Bucket {self.my_store._bucket} does not "
+                            f"exist.")
 
         except (NoCredentialsError, PartialCredentialsError) as e:
             self.fail(f"Credentials error: {e}")