Querying RCSB Search via pypdb package has broken

[JatGreer]

According to discussion on pypdb repo here: williamgilpin/pypdb#67, rcsb may have changed their API and broken the pypdb package.

Error:

Querying RCSB Search using the following parameters:
 {"query": {"type": "terminal", "service": "full_text", "parameters": {"value": "F4HvG8"}}, "request_options": {"return_all_hits": true}, "return_type": "entry"} 

[/home/jg/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:267](https://file+.vscode-resource.vscode-cdn.net/home/jg/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:267): UserWarning: It appears request failed with:{
  "timestamp" : 1727439714991,
  "status" : 415,
  "error" : "Unsupported Media Type",
  "path" : "/rcsbsearch/v2/query"
}
  warnings.warn("It appears request failed with:" + response.text)
---------------------------------------------------------------------------
HTTPError                                 Traceback (most recent call last)
Cell In[3], [line 1](vscode-notebook-cell:?execution_count=3&line=1)
----> [1](vscode-notebook-cell:?execution_count=3&line=1) available_only_AF = fetcher.check_db(ONLY_ALPHAFOLD)
      [2](vscode-notebook-cell:?execution_count=3&line=2) available_only_pdb = fetcher.check_db(ONLY_PDB)
      [3](vscode-notebook-cell:?execution_count=3&line=3) available_both = fetcher.check_db(BOTH)

File ~/Software/profet/profet/profet.py:40, in Fetcher.check_db(self, uniprot_id)
     [28](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/Software/profet/profet/profet.py:28) """
     [29](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/Software/profet/profet/profet.py:29) Checks which database contains the searched ID.
     [30](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/Software/profet/profet/profet.py:30) 
   (...)
     [36](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/Software/profet/profet/profet.py:36) 
     [37](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/Software/profet/profet/profet.py:37) """
     [39](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/Software/profet/profet/profet.py:39) available_db = []
---> [40](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/Software/profet/profet/profet.py:40) if self.pdb.check_structure(uniprot_id):
     [41](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/Software/profet/profet/profet.py:41)     available_db.append("pdb")
     [42](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/Software/profet/profet/profet.py:42) if self.alpha.check_structure(uniprot_id):

File ~/Software/profet/profet/pdb.py:35, in PDB_DB.check_structure(self, uniprot_id)
     [33](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/Software/profet/profet/pdb.py:33) search_operator = text_operators.DefaultOperator(value=uniprot_id)
     [34](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/Software/profet/profet/pdb.py:34) try:
---> [35](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/Software/profet/profet/pdb.py:35)     self.results = perform_search(search_operator, self.return_type)
     [36](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/Software/profet/profet/pdb.py:36)     return True
     [37](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/Software/profet/profet/pdb.py:37) except ValueError:

File ~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:185, in perform_search(search_operator, return_type, request_options, return_with_scores, return_raw_json_dict, verbosity)
    [130](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:130) def perform_search(
    [131](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:131)     search_operator: SearchOperator,
    [132](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:132)     return_type: ReturnType = ReturnType.ENTRY,
   (...)
    [136](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:136)     verbosity: bool = True,
    [137](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:137) ) -> Union[List[str], List[ScoredResult], RawJSONDictResponse]:
    [138](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:138)     """Performs search specified by `search_operator`.
    [139](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:139)     Returns entity strings of type `return_type` that match the resulting hits.
    [140](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:140) 
   (...)
    [182](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:182)     ```
    [183](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:183)     """
--> [185](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:185)     return perform_search_with_graph(query_object=search_operator,
    [186](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:186)                                      return_type=return_type,
    [187](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:187)                                      request_options=request_options,
    [188](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:188)                                      return_with_scores=return_with_scores,
    [189](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:189)                                      return_raw_json_dict=return_raw_json_dict,
    [190](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:190)                                      verbosity=verbosity)

File ~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:268, in perform_search_with_graph(query_object, return_type, request_options, return_with_scores, return_raw_json_dict, verbosity)
    [266](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:266) if not response.ok:
    [267](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:267)     warnings.warn("It appears request failed with:" + response.text)
--> [268](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:268)     response.raise_for_status()
    [270](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:270) # If specified, returns raw JSON response from RCSB as Dict
    [271](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:271) # (rather than entity IDs as a string list)
    [272](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/pypdb/clients/search/search_client.py:272) if return_raw_json_dict:

File ~/miniconda3/envs/profet/lib/python3.10/site-packages/requests/models.py:1024, in Response.raise_for_status(self)
   [1019](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/requests/models.py:1019)     http_error_msg = (
   [1020](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/requests/models.py:1020)         f"{self.status_code} Server Error: {reason} for url: {self.url}"
   [1021](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/requests/models.py:1021)     )
   [1023](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/requests/models.py:1023) if http_error_msg:
-> [1024](https://file+.vscode-resource.vscode-cdn.net/home/jg/Downloads/~/miniconda3/envs/profet/lib/python3.10/site-packages/requests/models.py:1024)     raise HTTPError(http_error_msg, response=self)

HTTPError: 415 Client Error:  for url: https://search.rcsb.org/rcsbsearch/v2/query

Reproduce:

import profet

ONLY_ALPHAFOLD = "F4HvG8"
ONLY_PDB = "7U6Q"
BOTH = "A0A023FDY8"

fetcher = profet.Fetcher()
print('Current default database: ', fetcher.get_default_db())

available_only_AF = fetcher.check_db(ONLY_ALPHAFOLD)
available_only_pdb = fetcher.check_db(ONLY_PDB)
available_both = fetcher.check_db(BOTH)

print('Database available for ', ONLY_ALPHAFOLD, ' is ', available_only_AF)
print('Database available for ', ONLY_PDB, ' is ', available_only_pdb)
print('Databases available for ', BOTH, ' are ', available_both)

PDB = fetcher.get_file(ONLY_PDB)
AF = fetcher.get_file(ONLY_ALPHAFOLD)
from_pdb = fetcher.get_file(BOTH)
from_AF = fetcher.get_file(BOTH, db = 'alphafold')