AttributeError: 'NoneType' object has no attribute 'group' #114

corkdagga · 2024-11-20T08:46:52Z

Hi All,

I am a new mac user and have been slowly setting up the new laptop. I freshly installed cblaster and am running into some problems (see below). I think it could be a python issue. I was using zsh but after installing everything, I changed to bash, then tried to uninstall and reinstall again. I have a feeling this could be there the issue is.

NABI-MAC001:cblaster_test paul$ cblaster search -m remote --rid KV6WEC7B013 -qf myQF_9705.fasta -p test6.html
Importing genomicsqlite failed, falling back to SQLite3
[09:39:43] INFO - Starting cblaster in remote mode
[09:39:43] INFO - Polling NCBI for completion status
[09:39:43] INFO - Checking search status...
[09:39:43] INFO - Search has completed successfully!
[09:39:43] INFO - Retrieving results for search KV6WEC7B013
Traceback (most recent call last):
File "/Users/paul/Library/Python/3.9/bin/cblaster", line 8, in
sys.exit(main())
File "/Users/paul/Library/Python/3.9/lib/python/site-packages/cblaster/main.py", line 432, in main
cblaster(
File "/Users/paul/Library/Python/3.9/lib/python/site-packages/cblaster/main.py", line 318, in cblaster
rid, results = remote.search(
File "/Users/paul/Library/Python/3.9/lib/python/site-packages/cblaster/remote.py", line 371, in search
results = retrieve(rid, hitlist_size=hitlist_size)
File "/Users/paul/Library/Python/3.9/lib/python/site-packages/cblaster/remote.py", line 208, in retrieve
for line in re.search("

(.+?)

", response.text, re.DOTALL)
AttributeError: 'NoneType' object has no attribute 'group'

Any help to get cblaster working would be great! thank you :)

corkdagga · 2024-11-20T11:54:20Z

I also saw some other posts with the same issue, these were either fixed with an updated version or I tried the suggestions but it did not work for me... I am running the latest version.

Clauvio · 2024-11-22T06:02:51Z

Same problem and waiting for someone to help us

FriederikeBiermann · 2024-11-22T17:14:44Z

I think the NCBI API changed its syntax. Try out this PR where I fixed this specific problem: #115

corkdagga · 2024-11-23T07:58:16Z

Thanks! That fix worked for me :)

FriederikeBiermann · 2024-11-23T09:36:25Z

I think this issue should not be closed, as the PR was not merged yet and I expect all users to be affected by this issue. It's really hard to find the connection between the issue and the PR now.

corkdagga · 2024-11-24T16:21:26Z

I think this issue should not be closed, as the PR was not merged yet and I expect all users to be affected by this issue. It's really hard to find the connection between the issue and the PR now.

Sorry about that! Its re-opened.

Dx-wmc · 2024-11-25T06:21:32Z

@FriederikeBiermann According to the PR, I modified the corresponding two lines of code, but the error still occurs.

Traceback (most recent call last):
  File "/home/data/usr/dx/miniconda3/envs/cblaster/bin/cblaster", line 8, in <module>
    sys.exit(main())
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/main.py", line 432, in main
    cblaster(
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/main.py", line 318, in cblaster
    rid, results = remote.search(
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/remote.py", line 373, in search
    results = retrieve(rid, hitlist_size=hitlist_size)
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/remote.py", line 210, in retrieve
    for line in re.search("<PRE>(.+?)</PRE>", response.text, re.DOTALL)
AttributeError: 'NoneType' object has no attribute 'group'

FriederikeBiermann · 2024-11-26T08:36:18Z

@FriederikeBiermann According to the PR, I modified the corresponding two lines of code, but the error still occurs.

Traceback (most recent call last):
  File "/home/data/usr/dx/miniconda3/envs/cblaster/bin/cblaster", line 8, in <module>
    sys.exit(main())
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/main.py", line 432, in main
    cblaster(
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/main.py", line 318, in cblaster
    rid, results = remote.search(
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/remote.py", line 373, in search
    results = retrieve(rid, hitlist_size=hitlist_size)
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/remote.py", line 210, in retrieve
    for line in re.search("<PRE>(.+?)</PRE>", response.text, re.DOTALL)
AttributeError: 'NoneType' object has no attribute 'group'

Did you make sure to install the new version to your conda env or change it directly in the /home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/remote.py?

Dx-wmc · 2024-11-27T10:54:12Z

Yes, I have modified the remote.py and the version of cblaster is latest 1.3.19.

FriederikeBiermann · 2024-11-27T12:58:06Z

Yes, I have modified the remote.py and the version of cblaster is latest 1.3.19.

If you put in a preint statement that prints out the URL it uses to fetch, what does it show?

Dx-wmc · 2024-11-28T03:46:41Z

Hi, this is the output after adding the URL.

[11:35:19] INFO - Starting cblaster in remote mode
[11:35:19] INFO - Launching new search
Request URL (POST): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=PUT&DATABASE=nr&PROGRAM=blastp&FILTER=F&EXPECT=0.01&GAPCOSTS=11+1&MATRIX=BLOSUM62&HITLIST_SIZE=5000&ALIGNMENTS=5000&DESCRIPTIONS=5000&WORD_SIZE=6&COMPOSITION_BASED_STATISTICS=2&THRESHOLD=11
[11:35:23] INFO - Request Identifier (RID): MFT7VWSV013
[11:35:23] INFO - Request Time Of Execution (RTOE): 16s
[11:35:39] INFO - Polling NCBI for completion status
[11:35:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:36:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:37:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:38:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:39:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:40:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:41:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:42:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:43:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:43:40] INFO - Search has completed successfully!
[11:43:40] INFO - Retrieving results for search MFT7VWSV013
Request URL (GET for retrieval): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&ALIGNMENT_VIEW=Tabular&FORMAT_OBJECT=Alignment&HITLIST_SIZE=5000&ALIGNMENTS=5000&DESCRIPTIONS=5000&FORMAT_TYPE=Text
Traceback (most recent call last):
  File "/home/data/usr/dx/miniconda3/envs/cblaster/bin/cblaster", line 8, in <module>
    sys.exit(main())
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/main.py", line 432, in main
    cblaster(
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/main.py", line 318, in cblaster
    rid, results = remote.search(
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/remote.py", line 374, in search
    results = retrieve(rid, hitlist_size=hitlist_size)
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/remote.py", line 211, in retrieve
    for line in re.search("<PRE>(.+?)</PRE>", response.text, re.DOTALL)
AttributeError: 'NoneType' object has no attribute 'group'

FriederikeBiermann · 2024-12-03T07:37:24Z

Hi, this is the output after adding the URL.

[11:35:19] INFO - Starting cblaster in remote mode
[11:35:19] INFO - Launching new search
Request URL (POST): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=PUT&DATABASE=nr&PROGRAM=blastp&FILTER=F&EXPECT=0.01&GAPCOSTS=11+1&MATRIX=BLOSUM62&HITLIST_SIZE=5000&ALIGNMENTS=5000&DESCRIPTIONS=5000&WORD_SIZE=6&COMPOSITION_BASED_STATISTICS=2&THRESHOLD=11
[11:35:23] INFO - Request Identifier (RID): MFT7VWSV013
[11:35:23] INFO - Request Time Of Execution (RTOE): 16s
[11:35:39] INFO - Polling NCBI for completion status
[11:35:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:36:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:37:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:38:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:39:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:40:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:41:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:42:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:43:39] INFO - Checking search status...
Request URL (GET): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&FORMAT_OBJECT=SearchInfo
[11:43:40] INFO - Search has completed successfully!
[11:43:40] INFO - Retrieving results for search MFT7VWSV013
Request URL (GET for retrieval): https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=MFT7VWSV013&ALIGNMENT_VIEW=Tabular&FORMAT_OBJECT=Alignment&HITLIST_SIZE=5000&ALIGNMENTS=5000&DESCRIPTIONS=5000&FORMAT_TYPE=Text
Traceback (most recent call last):
  File "/home/data/usr/dx/miniconda3/envs/cblaster/bin/cblaster", line 8, in <module>
    sys.exit(main())
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/main.py", line 432, in main
    cblaster(
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/main.py", line 318, in cblaster
    rid, results = remote.search(
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/remote.py", line 374, in search
    results = retrieve(rid, hitlist_size=hitlist_size)
  File "/home/data/usr/dx/miniconda3/envs/cblaster/lib/python3.9/site-packages/cblaster/remote.py", line 211, in retrieve
    for line in re.search("<PRE>(.+?)</PRE>", response.text, re.DOTALL)
AttributeError: 'NoneType' object has no attribute 'group'

Interestingly, the retrieve download link now works. Maybe you can also print the response.text?

drboothtj · 2024-12-05T15:14:42Z

There is another issue at play. The API is also preemptively cutting short the result. You can get around this by applying the patch and lowering the -hs or adding some other filter that limits the results.

corkdagga closed this as completed Nov 23, 2024

corkdagga reopened this Nov 24, 2024

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AttributeError: 'NoneType' object has no attribute 'group' #114

AttributeError: 'NoneType' object has no attribute 'group' #114

corkdagga commented Nov 20, 2024

corkdagga commented Nov 20, 2024

Clauvio commented Nov 22, 2024

FriederikeBiermann commented Nov 22, 2024

corkdagga commented Nov 23, 2024

FriederikeBiermann commented Nov 23, 2024

corkdagga commented Nov 24, 2024

Dx-wmc commented Nov 25, 2024

FriederikeBiermann commented Nov 26, 2024

Dx-wmc commented Nov 27, 2024

FriederikeBiermann commented Nov 27, 2024

Dx-wmc commented Nov 28, 2024

FriederikeBiermann commented Dec 3, 2024

drboothtj commented Dec 5, 2024

AttributeError: 'NoneType' object has no attribute 'group' #114

AttributeError: 'NoneType' object has no attribute 'group' #114

Comments

corkdagga commented Nov 20, 2024

corkdagga commented Nov 20, 2024

Clauvio commented Nov 22, 2024

FriederikeBiermann commented Nov 22, 2024

corkdagga commented Nov 23, 2024

FriederikeBiermann commented Nov 23, 2024

corkdagga commented Nov 24, 2024

Dx-wmc commented Nov 25, 2024

FriederikeBiermann commented Nov 26, 2024

Dx-wmc commented Nov 27, 2024

FriederikeBiermann commented Nov 27, 2024

Dx-wmc commented Nov 28, 2024

FriederikeBiermann commented Dec 3, 2024

drboothtj commented Dec 5, 2024