Merge pull request #320 from microbiomedata/319-remove-obsolete-re-id…

…ing-code

Remove obsolete re-iding code

nmdc_automation/api/__init__.py

@@ -1 +1 @@
-from .nmdcapi import NmdcRuntimeApi, NmdcRuntimeUserApi
+from .nmdcapi import NmdcRuntimeApi

nmdc_automation/api/nmdcapi.py

@@ -396,125 +396,6 @@ def run_query(self, query):
         return resp.json()
 
 
-# TODO - This is deprecated and should be removed along with the re_iding code that uses it
-class NmdcRuntimeUserApi:
-    """
-    Basic Runtime API Client with user/password authentication.
-    """
-    def __init__(self, site_configuration):
-        self.config = UserConfig(site_configuration)
-
-        self.username = self.config.username
-        self.password = self.config.password
-        self.base_url = self.config.base_url
-        self.headers = {}
-        self.token_response = None
-        self.refresh_token_after = None
-
-    def ensure_token(self):
-        if (self.refresh_token_after is None or datetime.now(timezone.utc) >
-                self.refresh_token_after):
-            self.get_token()
-    def get_token(self):
-        token_request_body = {
-            "grant_type": "password",
-            "username": self.username,
-            "password": self.password,
-            "scope": '',
-            "client_id": "",
-            "client_secret": "",
-        }
-        headers = {
-            'accept': 'application/json',
-            'Content-Type': 'application/x-www-form-urlencoded',
-        }
-        rv = requests.post(
-            self.base_url + "token", data=token_request_body
-            )
-        self.token_response = rv.json()
-        if "access_token" not in self.token_response:
-            raise Exception(f"Getting token failed: {self.token_response}")
-
-        self.headers[
-            "Authorization"] = f'Bearer {self.token_response["access_token"]}'
-        self.refresh_token_after = expiry_dt_from_now(
-            **self.token_response["expires"]
-        ) - timedelta(seconds=5)
-
-    def request(self, method, url_path, params_or_json_data=None):
-        self.ensure_token()
-        kwargs = {"url": self.base_url + url_path, "headers": self.headers}
-        if isinstance(params_or_json_data, BaseModel):
-            params_or_json_data = params_or_json_data.dict(exclude_unset=True)
-        if method.upper() == "GET":
-            kwargs["params"] = params_or_json_data
-        else:
-            kwargs["json"] = params_or_json_data
-        rv = requests.request(method, **kwargs)
-        rv.raise_for_status()
-        return rv
-
-    def run_query(self, query: dict):
-        """
-        Function to run a query using the Microbiome Data API.
-        
-        Parameters:
-        query (dict): The query to be run in JSON format.
-        
-        Returns:
-        dict: The response from the API.
-        """
-
-        self.ensure_token()
-        url = f"{self.base_url}queries:run"
-
-        response = requests.post(url, json=query, headers=self.headers)
-        return response.json()
-
-    def validate_record(self, record: dict):
-        """
-        Function to validate a record using the Microbiome Data API.
-
-        Parameters:
-        record (dict): The record to be validated.
-
-        Returns:
-        dict: The response from the API.
-        """
-
-        self.ensure_token()
-        url = f"{self.base_url}metadata/json:validate"
-
-        response = requests.post(url, json=record, headers=self.headers)
-        # check for validation failure
-        if response.status_code == 422:
-            logging.error(f"Validation failed for record: {record}")
-            logging.error(response.json())
-        response.raise_for_status()
-        return response.json()
-
-    def submit_record(self, record: dict):
-        """
-        Function to submit a record using the Microbiome Data API.
-
-        Parameters:
-        record (dict): The record to be submitted.
-
-        Returns:
-        dict: The response from the API.
-        """
-
-        self.ensure_token()
-        url = f"{self.base_url}metadata/json:submit"
-
-        response = requests.post(url, json=record, headers=self.headers)
-        # check if we already have it:
-        if response.status_code == 409:
-            logging.debug(f"Record already exists: {response.json()}")
-            return
-        response.raise_for_status()
-        return response.json()
-
 def jprint(obj):
     print(json.dumps(obj, indent=2))
 

nmdc_automation/jgi_file_staging/models.py

@@ -1,21 +1,21 @@
 from pydantic import BaseModel
 from datetime import datetime
-from typing import Optional
+from typing import Optional, List
 
 
 class Sample(BaseModel):
-    project: str
     apGoldId: str
     studyId: str
-    itsApId: str
+    itsApId: int
+    projects: str
     biosample_id: str
     seq_id: str
     file_name: str
     file_status: str
     file_size: int
     jdp_file_id: str
-    md5sum: Optional[str]
+    md5sum: Optional[str] = None
     analysis_project_id: str
     create_date: datetime = datetime.now()
-    update_date: Optional[datetime]
-    request_id: Optional[str]
+    update_date: Optional[datetime] = None
+    request_id: Optional[str] = None