pyGREAT gives error: AttributeError: 'NoneType' object has no attribute 'text

[MubasherMohammed]

Hi, thanks for developing this great package! I am facing error when executing result = pyGREAT(region_sets, 'hg38', n_cpu=35, _temp_dir = tmp).

File ~/miniconda3/envs/scenicplus/lib/python3.8/site-packages/pycisTopic/pyGREAT.py:79, in pyGREAT(region_sets, species, rule, span, upstream, downstream, two_distance, one_distance, include_curated_reg_doms, bg_choice, tmp_dir, n_cpu, kwargs) 77 ray.init(num_cpus=n_cpu, kwargs) 78 sys.stderr = null ---> 79 pyGREAT_dict = ray.get( 80 [ 81 pyGREAT_oneset_ray.remote( 82 region_sets[key], 83 species, 84 rule, 85 span, 86 upstream, 87 downstream, 88 two_distance, 89 one_distance, 90 include_curated_reg_doms, 91 bg_choice, 92 tmp_dir, 93 ) 94 for key in region_sets.keys() 95 ] 96 ) 97 ray.shutdown() 98 sys.stderr = sys.stderr

File ~/miniconda3/envs/scenicplus/lib/python3.8/site-packages/ray/_private/auto_init_hook.py:22, in wrap_auto_init..auto_init_wrapper(*args, kwargs) 19 @wraps(fn) 20 def auto_init_wrapper(*args, *kwargs): 21 auto_init_ray() ---> 22 return fn(args, kwargs)

File ~/miniconda3/envs/scenicplus/lib/python3.8/site-packages/ray/_private/client_mode_hook.py:103, in client_mode_hook..wrapper(*args, kwargs) 101 if func.name != "init" or is_client_mode_enabled_by_default: 102 return getattr(ray, func.name)(*args, *kwargs) --> 103 return func(args, kwargs)

File ~/miniconda3/envs/scenicplus/lib/python3.8/site-packages/ray/_private/worker.py:2624, in get(object_refs, timeout) 2622 worker.core_worker.dump_object_store_memory_usage() 2623 if isinstance(value, RayTaskError): -> 2624 raise value.as_instanceof_cause() 2625 else: 2626 raise value

RayTaskError(AttributeError): ray::pyGREAT_oneset_ray() (pid=1990234, ip=192.168.0.6) File "/home/mubasher/miniconda3/envs/scenicplus/lib/python3.8/site-packages/pycisTopic/pyGREAT.py", line 174, in pyGREAT_oneset_ray return pyGREAT_oneset( File "/home/mubasher/miniconda3/envs/scenicplus/lib/python3.8/site-packages/pycisTopic/pyGREAT.py", line 278, in pyGREAT_oneset jobId = soup.find("div", attrs={"class": "job_desc_info"}).text AttributeError: 'NoneType' object has no attribute 'text'

I'm not sure exactly how to fix this error. my pycisTopic version '1.0a0' as am still using the old SCENIC+ version. my region_set looks: {'Topic1': +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int64) | (int64) | |--------------+-----------+-----------| | chr1 | 145075000 | 145075500 | | chr1 | 55740500 | 55741000 | | chr1 | 200379000 | 200379500 | | chr1 | 145075500 | 145076000 | | ... | ... | ... | | chrX | 68724500 | 68725000 | | chrX | 46989000 | 46989500 | | chrX | 117250500 | 117251000 | | chrX | 73640000 | 73640500 | +--------------+-----------+-----------+ Unstranded PyRanges object has 482,334 rows and 3 columns from 23 chromosomes. For printing, the PyRanges was sorted on Chromosome., 'Topic2': +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int64) | (int64) | |--------------+-----------+-----------| | chr1 | 244816000 | 244816500 | | chr1 | 110881500 | 110882000 | | chr1 | 17896000 | 17896500 | | chr1 | 160032000 | 160032500 | | ... | ... | ... | | chrX | 39462500 | 39463000 | | chrX | 47510500 | 47511000 | | chrX | 152765500 | 152766000 | | chrX | 52964500 | 52965000 | +--------------+-----------+-----------+ Unstranded PyRanges object has 52,355 rows and 3 columns from 23 chromosomes. For printing, the PyRanges was sorted on Chromosome., 'Topic3': +--------------+-----------+-----------+

any tips will be highly appreciated! thanks..

[SeppeDeWinter]

Hi @MubasherMohammed

Thank you for opening the issue! This function needs to be updated indeed.

I have added it to my todo list and will try to get to it.

Best,

Seppe

[MubasherMohammed]

Thank you @SeppeDeWinter that would be great!