multimeric / unipressed Goto Github PK

Hello,

I'd like to use the idmappingclient but I have to get lucky to not end up with the error
UniProt has not yet processed the results, consider using time.sleep() to wait until they are complete.

I have reduced the size of my query lists quite a bit but at some point in my loop, I will get the error. I have added time.sleep() before I call request.each_result() but I don't know how long to set it for to ensure I don't run into the error.

I see there is a "waiting" module but I'm not sure how to incorporate it into this so I can wait indefinitely for the results to be returned.

Thank you for this package.

Dan

Currently we get a lot of the same XXEvidence classes, but many are the same.

Hello there,

I am using the example given in the main README to get the ID mappings:

from unipressed import IdMappingClient
request = IdMappingClient.submit(
    source="UniProtKB_AC-ID", dest="Gene_Name", ids={"A1L190", "A0JP26", "A0PK11"}
)
list(request.each_result())

But I want to check the status before obtaining the results, so I call request.get_status() and obtain the following error:

Traceback (most recent call last):
  File "<stdin>", line 3, in <module>
  File "/usr/local/lib/python3.10/dist-packages/unipressed/id_mapping/core.py", line 52, in get_status
    return requests.get(
KeyError: 'jobStatus'

I hope you can help me to know what I am doing wrong.

See: https://www.uniprot.org/help/id_mapping

The type annotations aren't helpful to those not using an IDE.

Perhaps allow lists, such as [8, '*'] since some users might prefer this.

e.g. html, rdf, fasta, obo, xlsx

https://rest.uniprot.org/docs/?urls.primaryName=uniprotkb#/Miscellaneous/getMappedPublicationsByUniProtAccession

e.g. https://rest.uniprot.org/docs/?urls.primaryName=uniref#/uniref/stream

This will clarify the available download formats

e.g. organism_id is only listed under autoCompleteQueryTerm.

Since this option is only relevant to uniprotkb.

e.g. https://rest.uniprot.org/docs/?urls.primaryName=proteome#/genecentric

In theory we could replace all the TypedDict with pydantic models.

Advantages:

• Could implement advanced validation like regex etc
• Could have low level models for things like ranges

Disadvantages:

• More dependencies, so larger installation
• Much more verbose queries. You would now have to import the appropriate models instead of just using built-in Python constructs

This might be tricky, since each overload depends on the instance variables, so @overload can't be used here. This may require a small API restructure.

There doesn't seem to be a way to add docstrings to Literal, but perhaps they could be converted to enums with docstrings.

The Search dataclass has a include_isoform member variable, but the search method of the UniprotkbClient class does not expose this as a parameter.

Can we add this as a parameter?

This just collects together all the dataset Search subclasses. This could be automated.

It turns out there are OpenAPI docs at https://rest.uniprot.org/docs/. Some info found here can't be found elsewhere.

Documented here: https://www.uniprot.org/help/api_retrieve_entries