more functions

nmdc_notebook_tools/biosample.py

@@ -12,6 +12,7 @@ def __init__(self):
 
     def get_all_biosamples(self, page_size=25) -> List[Dict]:
         """
+        TODO
         Get all biosamples from the NMDC API.
         params:
             page_size: int
@@ -66,6 +67,36 @@ def find_biosample_by_filter(self, filter: str, page_size=25) -> Dict:
         results = response.json()
         return results
 
+    def find_biosample_by_attribute(
+        self, attribute_name, attribute_value, page_size=25
+    ) -> List[Dict]:
+        """
+        Get a biosample from the NMDC API by its name. Biosamples can be filtered based on their attributes found https://microbiomedata.github.io/nmdc-schema/Biosample/.
+        params:
+            sample_name: str
+                The name of the biosample to query.
+            attribute_name: str
+                The name of the attribute to filter by.
+            attribute_value: str
+                The value of the attribute to filter by.
+            page_size: int
+                The number of results to return per page. Default is 25.
+        """
+        api_client = NMDClient()
+        filter = f"{attribute_name}.search:{attribute_value}"
+
+        # Encode the filter for use in the URL
+        encoded_filter = urllib.parse.quote(filter)
+
+        url = f"{api_client.base_url}/biosamples?filter={encoded_filter}&per_page={page_size}"
+        # get the reponse
+        response = requests.get(url)
+        # check it came back with OK
+        if response.status_code != 200:
+            return (response.status_code, "There was an error.")
+        results = response.json()["results"]
+        return results
+
 
 if __name__ == "__main__":
     pass

nmdc_notebook_tools/study.py

@@ -104,6 +104,23 @@ def find_study_by_pi(self, pi_name: str, page_size=25) -> List[Dict]:
         results = response.json()["results"]
         return results
 
+    def get_study_data_objects(self, study_id: str) -> List[Dict]:
+        """
+        Get the data objects associated with a study.
+        params:
+            study_id: str
+                The id of the study to query.
+        """
+        api_client = NMDClient()
+        url = f"{api_client.base_url}/data_objects/studies/{study_id}"
+        # get the reponse
+        response = requests.get(url)
+        # check it came back with OK
+        if response.status_code != 200:
+            return (response.status_code, "There was an error.")
+        results = response.json()["results"]
+        return results
+
 
 if __name__ == "__main__":
     pass