Closed BiomedicLJZ closed 2 years ago
Also important to Report that the python env ist completely clean and that the code works in Google colab but i need it to be able to run in local
Thanks, we should have caught this (seems to be coming from a change at the NCBI end though). Can you try pulling from the master branch and retry?
pip install git+https:://github.com/saketkc/pysradb
Works for me, thanks!
Hi. Thanks for fixing this problem. We also encountered it just today and wanted to report this..
Not neccessary at this point anymore. But here's our solution: it seems like xmltodict
0.13.0 is causing the problem. Downgrading it to 0.12.0 solved it for us.
edit: xmltodict 0.13.0 uses dict instead of OrderedDict now (as reported in the issue tracker of xmltodict)
Describe the bug `UnboundLocalError Traceback (most recent call last) Input In [7], in <cell line: 3>() 1 from pysradb import SRAweb 2 db = SRAweb() ----> 3 df = db.sra_metadata('SRP098789') 4 df.head()
File ~\PycharmProjects\Tools\venv\lib\site-packages\pysradb\sraweb.py:516, in SRAweb.sra_metadata(self, srp, sample_attribute, detailed, expand_sample_attributes, output_read_lengths, **kwargs) 514 experiment_record["sample_title"] = exp_sample_name 515 experiment_record["instrument"] = exp_instrument --> 516 experiment_record["instrument_model"] = exp_platform_model 517 experiment_record["instrument_model_desc"] = exp_platform_desc 518 experiment_record["total_spots"] = exp_total_spots
` To Reproduce from pysradb import SRAweb db = SRAweb() df = db.sra_metadata('any data') df.
Desktop (please complete the following information):
Additional context I just used this oackage a week ago with this exact structure and worked fine![imagen_2022-05-24_222235489](https://user-images.githubusercontent.com/99223876/170172995-58f264d3-5140-4d55-8adb-e30a0ac6221a.png)