v 0.10.2 point release

docs/changelog.md

@@ -2,6 +2,10 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.10.2] - 2024-08-26
+### Fixed
+- add obtaining pephub_path from config file, [#202](https://github.com/pepkit/pipestat/issues/202)
+
 ## [0.10.1] - 2024-08-06
 ### Fixed
 - add pipestat summarize and link for pephub backend

pipestat/_version.py

@@ -1 +1 @@
-__version__ = "0.10.1"
+__version__ = "0.10.2"

pipestat/pipestat.py

@@ -166,7 +166,7 @@ def __init__(
 
         # Load and validate database configuration
         # If results_file_path exists, backend is a file else backend is database.
-        self.cfg["pephub_path"] = pephub_path
+
         self.cfg["config_path"] = select_config(config_file, ENV_VARS["config"])
 
         if config_dict is not None:
@@ -181,6 +181,10 @@ def __init__(
         cfg_schema = load_yaml(CFG_SCHEMA)
         validate(self.cfg[CONFIG_KEY].exp, cfg_schema)
 
+        self.cfg["pephub_path"] = self.cfg[CONFIG_KEY].priority_get(
+            "pephub_path", override=pephub_path
+        )
+
         self.cfg[SCHEMA_PATH] = self.cfg[CONFIG_KEY].priority_get(
             "schema_path", env_var=ENV_VARS["schema"], override=schema_path
         )
@@ -244,8 +248,8 @@ def __init__(
         if self.cfg[FILE_KEY]:
             self.initialize_filebackend(record_identifier, results_file_path, flag_file_dir)
 
-        elif pephub_path:
-            self.initialize_pephubbackend(record_identifier, pephub_path)
+        elif self.cfg["pephub_path"]:
+            self.initialize_pephubbackend(record_identifier, self.cfg["pephub_path"])
         else:
             self.initialize_dbbackend(record_identifier, show_db_logs)
 

tests/conftest.py

@@ -102,6 +102,11 @@ def config_file_path():
     return get_data_file_path("config.yaml")
 
 
+@pytest.fixture
+def config_file_path_pephub():
+    return get_data_file_path("config_pephub_url.yaml")
+
+
 @pytest.fixture
 def config_no_schema_file_path():
     return get_data_file_path("config_no_schema.yaml")

tests/data/config_pephub_url.yaml

@@ -0,0 +1 @@
+pephub_path: "databio/pipestat_demo:default"

tests/test_pipestat.py

@@ -2589,6 +2589,27 @@ def test_pephub_backend_retrieve_one(
 
         assert len(result.keys()) == 6
 
+    @pytest.mark.parametrize(
+        ["rec_id", "val"],
+        [
+            ("test_pipestat_01", {"name_of_something": "test_name"}),
+        ],
+    )
+    def test_pephub_backend_config_file(
+        self,
+        rec_id,
+        val,
+        config_file_path_pephub,
+        schema_file_path,
+    ):
+
+        # Can pipestat obtain pephub url from config file AND successfully retrieve values?
+        psm = PipestatManager(config_file=config_file_path_pephub, schema_path=schema_file_path)
+
+        result = psm.retrieve_one(record_identifier=rec_id)
+
+        assert len(result.keys()) == 6
+
     def test_pephub_backend_retrieve_many(
         self,
         config_file_path,