Error while extracting a document

[agnesbrnb]

Hi,
I work on an OpenSILEX instance named Siduri. I uploaded a document (CSV file) in an experiment and now I want to download it through the API Python client to use it in the Galaxy API for bioinformatics analysis. The aim is to download various format of document (fastq, fastq.gz, bam, json...).

I managed to authenticate, get the list of documents uploaded in my experiment and get the metadata associated with a document. However, I can't use the function get_document_file from DocumentsApi to download the file as suggested in the documentation. The function returns this error: JSONDecodeError: Unexpected UTF-8 BOM (decode using utf-8-sig): line 1 column 1.

I have a similar JSONDecodeError when trying to use extract_germplasm.

[Isabelle-inrae]

Hi Agnès, it seems client has issue when it need to return other format than Json.
The problem seems to be present in the other services accessing files : export_germplasm, get_data_file.
We are investigating and will come back to you.

[agnesbrnb]

Is it related to #7 ?

[user-123-wq]

Hi,

The bug related to the get_document_file function has already been fixed, and the updated version has been released.

We’ll now focus on the similar JSONDecodeError issue with the extract_germplasm function, which still needs to be addressed.

[agnesbrnb]

Yes I had the information about get_document_file and it works very well thank you.

Is the problem solved for get_data_file?

[niio972]

Hi @agnesbrnb ,

It possible to download datafile. you can adapt the following example:

uri = '{datafile uri}' # str | Datafile URI

data_instance = oCTP.DataApi(pythonClient)
 
try:
    # Get jpg datafile
    datafile = data_instance.get_data_file(uri ) 
    with open("datafile.jpg", "wb") as f:
          f.write(datafile)
except oCTP.rest.ApiException as e:
    print("Exception when calling DocumentsApi->get_document_file: %s\n" % e)

The fix is in the 1.4.9 version of the client. It is know the same behaviour for the document. The client returns bytes object for file.