Merge pull request #81 from SciCatProject/manual_testing

changes from manual testing

resources/config.sample.json

@@ -59,9 +59,15 @@
   "scicat": {
     "host": "https://scicat.host",
     "token": "JWT_TOKEN",
-    "headers": {},
+    "additional_headers": {},
     "timeout": 0,
     "stream": true,
-    "verify": false
+    "verify": false,
+    "api_endpoints": {
+      "datasets": "datasets",
+      "proposals": "proposals",
+      "origdatablocks": "origdatablocks",
+      "instruments": "instruments"
+    }
   }
 }

src/scicat_communication.py

@@ -12,14 +12,14 @@
 def retrieve_value_from_scicat(
     *,
     config: SciCatOptions,
-    variable_url: str,  # It should be already rendered from variable_recipe["url"]
+    scicat_endpoint_url: str,  # It should be already rendered
+    # from variable_recipe["url"]
     field_name: str,  # variable_recipe["field"]
 ) -> str:
-    url = config.host.removesuffix('/') + variable_url
     response: dict = requests.get(
-        url, headers={"token": config.token}, timeout=config.timeout
+        scicat_endpoint_url, headers=config.additional_headers, timeout=config.timeout
     ).json()
-    return response[field_name]
+    return response[field_name] if field_name else response
 
 
 class ScicatDatasetAPIError(Exception):
@@ -52,9 +52,9 @@ def create_scicat_dataset(
     """
     logger.info("Sending POST request to create new dataset")
     response = _post_to_scicat(
-        url=urljoin(config.host, "datasets"),
+        url=config.urls.datasets,
         posting_obj=dataset,
-        headers={"token": config.token, **config.headers},
+        headers=config.additional_headers,
         timeout=config.timeout,
     )
     result: dict = response.json()
@@ -84,9 +84,9 @@ def create_scicat_origdatablock(
     """
     logger.info("Sending POST request to create new origdatablock")
     response = _post_to_scicat(
-        url=urljoin(config.host, "origdatablocks"),
+        url=config.urls.origdatablocks,
         posting_obj=origdatablock,
-        headers={"token": config.token, **config.headers},
+        headers=config.additional_headers,
         timeout=config.timeout,
     )
     result: dict = response.json()
@@ -107,12 +107,24 @@ def create_scicat_origdatablock(
     return result
 
 
+def render_full_url(
+    url: str,
+    config: SciCatOptions,
+) -> str:
+    if not url.startswith("http://") and not url.startswith("https://"):
+        for endpoint in config.urls.keys():
+            if url.startswith(endpoint):
+                url = url.replace(endpoint, config.urls[endpoint])
+                break
+    return url
+
+
 def check_dataset_by_pid(
     pid: str, config: SciCatOptions, logger: logging.Logger
 ) -> bool:
     response = _get_from_scicat(
-        url=urljoin(config.host, f"datasets/{quote(pid)}"),
-        headers=config.headers,
+        url=urljoin(config.host_address, f"datasets/{quote(pid)}"),
+        headers=config.additional_headers,
         timeout=config.timeout,
         stream=config.stream,
         verify=config.verify,
@@ -145,11 +157,11 @@ def check_dataset_by_metadata(
 ) -> bool:
     metadata_dict = {f"scientificMetadata.{metadata_key}.value": metadata_value}
     filter_string = '?filter={"where":' + json.dumps(metadata_dict) + "}"
-    url = urljoin(config.host, "datasets") + filter_string
+    url = urljoin(config.host_address, "datasets") + filter_string
     logger.info("Checking if dataset exists by metadata with url: %s", url)
     response = _get_from_scicat(
         url=url,
-        headers=config.headers,
+        headers=config.additional_headers,
         timeout=config.timeout,
         stream=config.stream,
         verify=config.verify,

src/scicat_configuration.py

@@ -8,6 +8,7 @@
 from pathlib import Path
 from types import MappingProxyType
 from typing import Any, TypeVar, get_origin
+from urllib.parse import urljoin
 
 
 def _load_config(config_file: Path) -> dict:
@@ -231,14 +232,54 @@ class DatasetOptions:
     default_access_groups: list[str] = field(default_factory=default_access_groups)
 
 
+@dataclass(kw_only=True)
+class _ScicatAPIURLs:
+    datasets: str
+    proposals: str
+    origdatablocks: str
+    instruments: str
+
+
+@dataclass(kw_only=True)
+class ScicatEndpoints:
+    datasets: str = "datasets"
+    proposals: str = "proposals"
+    origdatablocks: str = "origdatablocks"
+    instruments: str = "instruments"
+
+
 @dataclass(kw_only=True)
 class SciCatOptions:
     host: str = "https://scicat.host"
     token: str = "JWT_TOKEN"
-    headers: dict = field(default_factory=dict)
+    additional_headers: dict = field(default_factory=dict)
     timeout: int = 0
     stream: bool = True
     verify: bool = False
+    api_endpoints: ScicatEndpoints = field(default_factory=ScicatEndpoints)
+
+    @property
+    def urls(self) -> _ScicatAPIURLs:
+        return _ScicatAPIURLs(
+            datasets=urljoin(self.host_address, self.api_endpoints.datasets),
+            proposals=urljoin(self.host_address, self.api_endpoints.proposals),
+            origdatablocks=urljoin(
+                self.host_address, self.api_endpoints.origdatablocks
+            ),
+            instruments=urljoin(self.host_address, self.api_endpoints.instruments),
+        )
+
+    @property
+    def headers(self) -> dict:
+        return {
+            **self.additional_headers,
+            **{"Authorization": f"Bearer {self.token}"},
+        }
+
+    @property
+    def host_address(self) -> str:
+        """Return the host address ready to be used."""
+        return self.host.removesuffix('/') + "/"
 
 
 @dataclass(kw_only=True)
@@ -330,9 +371,10 @@ def merge_config_and_input_args(
 
 
 def _validate_config_file(target_type: type[T], config_file: Path) -> T:
+    config = {**_load_config(config_file), "config_file": config_file.as_posix()}
     return build_dataclass(
         target_type,
-        {**_load_config(config_file), "config_file": config_file.as_posix()},
+        config,
     )