Hi all!
I was wondering whether materials qualitative, string-like metadata are available through MAPI.
By this I mean chemical (e.g. oxide, sulfide, phosphate etc) similarly to the already available crystallographic identification.(e.g. spacegroup symbols)
It appears from MAPI’s docs that this kind of info is not there, or am I missing something?
Hi @acarnevali, you can try looking at the tags data from the provenance endpoint, and the description and condensed_structure fields from the robocrys endpoint in the new API.
– Jason
Hi @munrojm!
I am trying to access the Provenance docs to retrieve tags, but I am facing an error I don’t quite understand.
with MPRester(api_key=key) as mpr:
docs = mpr.provenance.search()
returns
TypeError: __init__() got an unexpected keyword argument 'input_structure'
even though I clearly didn’t pass any keyword arguments. Any idea what’s going on?
This is the traceback, in case it’s needed.
c:\Users\anton\omissis\MP_tags.py in <module>
19 with MPRester(api_key=key) as mpr:
20 print("working on it")
----> 21 docs = mpr.provenance.search()
22 # print(type(docs))
23 # tags = docs.tags
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\mp_api\core\client.py in search(self, num_chunks, chunk_size, all_fields, fields, **kwargs)
784 # documented kwargs.
785
--> 786 return self._get_all_documents(
787 kwargs,
788 all_fields=all_fields,
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\mp_api\core\client.py in _get_all_documents(self, query_params, all_fields, fields, chunk_size, num_chunks)
833 chosen_param = list_entries[0][0] if len(list_entries) > 0 else None
834
--> 835 results = self._query_resource(
836 query_params,
837 fields=fields,
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\mp_api\core\client.py in _query_resource(self, criteria, fields, suburl, use_document_model, parallel_param, num_chunks, chunk_size)
286 url += "/"
287
--> 288 data = self._submit_requests(
289 url=url,
290 criteria=criteria,
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\mp_api\core\client.py in _submit_requests(self, url, criteria, use_document_model, parallel_param, num_chunks, chunk_size)
385 initial_params_list = [{"url": url, "verify": True, "params": copy(crit)} for crit in new_criteria]
386
--> 387 initial_data_tuples = self._multi_thread(use_document_model, initial_params_list)
388
389 for data, subtotal, crit_ind in initial_data_tuples:
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\mp_api\core\client.py in _multi_thread(self, use_document_model, params_list, progress_bar)
585
586 for future in finished:
--> 587 data, subtotal = future.result()
588 if progress_bar is not None:
589 progress_bar.update(len(data["data"]))
c:\Users\anton\miniconda3\envs\mp\lib\concurrent\futures\_base.py in result(self, timeout)
436 raise CancelledError()
437 elif self._state == FINISHED:
--> 438 return self.__get_result()
439
440 self._condition.wait(timeout)
c:\Users\anton\miniconda3\envs\mp\lib\concurrent\futures\_base.py in __get_result(self)
388 if self._exception:
389 try:
--> 390 raise self._exception
391 finally:
392 # Break a reference cycle with the exception in self._exception
c:\Users\anton\miniconda3\envs\mp\lib\concurrent\futures\thread.py in run(self)
50
51 try:
---> 52 result = self.fn(*self.args, **self.kwargs)
53 except BaseException as exc:
54 self.future.set_exception(exc)
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\mp_api\core\client.py in _submit_request_and_process(self, url, verify, params, use_document_model)
624
625 if self.monty_decode:
--> 626 data = json.loads(response.text, cls=MontyDecoder)
627 else:
628 data = json.loads(response.text)
c:\Users\anton\miniconda3\envs\mp\lib\json\__init__.py in loads(s, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)
357 if parse_constant is not None:
358 kw['parse_constant'] = parse_constant
--> 359 return cls(**kw).decode(s)
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\monty\json.py in decode(self, s)
438 """
439 d = json.JSONDecoder.decode(self, s)
--> 440 return self.process_decoded(d)
441
442
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\monty\json.py in process_decoded(self, d)
423 return bson.objectid.ObjectId(d["oid"])
424
--> 425 return {self.process_decoded(k): self.process_decoded(v) for k, v in d.items()}
426
427 if isinstance(d, list):
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\monty\json.py in <dictcomp>(.0)
423 return bson.objectid.ObjectId(d["oid"])
424
--> 425 return {self.process_decoded(k): self.process_decoded(v) for k, v in d.items()}
426
427 if isinstance(d, list):
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\monty\json.py in process_decoded(self, d)
426
427 if isinstance(d, list):
--> 428 return [self.process_decoded(x) for x in d]
429
430 return d
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\monty\json.py in <listcomp>(.0)
426
427 if isinstance(d, list):
--> 428 return [self.process_decoded(x) for x in d]
429
430 return d
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\monty\json.py in process_decoded(self, d)
423 return bson.objectid.ObjectId(d["oid"])
424
--> 425 return {self.process_decoded(k): self.process_decoded(v) for k, v in d.items()}
426
427 if isinstance(d, list):
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\monty\json.py in <dictcomp>(.0)
423 return bson.objectid.ObjectId(d["oid"])
424
--> 425 return {self.process_decoded(k): self.process_decoded(v) for k, v in d.items()}
426
427 if isinstance(d, list):
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\monty\json.py in process_decoded(self, d)
426
427 if isinstance(d, list):
--> 428 return [self.process_decoded(x) for x in d]
429
430 return d
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\monty\json.py in <listcomp>(.0)
426
427 if isinstance(d, list):
--> 428 return [self.process_decoded(x) for x in d]
429
430 return d
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\monty\json.py in process_decoded(self, d)
423 return bson.objectid.ObjectId(d["oid"])
424
--> 425 return {self.process_decoded(k): self.process_decoded(v) for k, v in d.items()}
426
427 if isinstance(d, list):
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\monty\json.py in <dictcomp>(.0)
423 return bson.objectid.ObjectId(d["oid"])
424
--> 425 return {self.process_decoded(k): self.process_decoded(v) for k, v in d.items()}
426
427 if isinstance(d, list):
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\monty\json.py in process_decoded(self, d)
407 data = {k: v for k, v in d.items() if not k.startswith("@")}
408 if hasattr(cls_, "from_dict"):
--> 409 return cls_.from_dict(data)
410 if pydantic is not None and issubclass(cls_, pydantic.BaseModel):
411 return cls_(**data)
c:\Users\anton\miniconda3\envs\mp\lib\site-packages\monty\json.py in from_dict(cls, d)
176 """
177 decoded = {k: MontyDecoder().process_decoded(v) for k, v in d.items() if not k.startswith("@")}
--> 178 return cls(**decoded)
179
180 def to_json(self) -> str:
TypeError: __init__() got an unexpected keyword argument 'input_structure'
Thank you!
I am on mp-api 0.23.3
Hi @acarnevali, okay I can recreate this issue. Not sure why bare calls to search aren’t working. I will look into this, but in the mean time you can get the query to work by explicitly passing pagination parameters (chunk_size=5, num_chunks=2 for example).
– Jason