Sashimi Prepare Corpus not working

Cortext Manager Q&A forum › Category: SASHIMI › Sashimi Prepare Corpus not working
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Dan Kitson asked 4 weeks ago

Hello, I am trying to use Sashimi on a .csv file of abstracts (plus other metadata) from Web of Science. I successfully uploaded the zipped .csv, and the Data Parser seems to have worked correctly. However, when I run the Prepare Corpus script for Sashimi, I get the error below. When I look at the job log, it says “No logs found”. Thanks for your help!

Prepare Corpus did not finish successfully. See the job log for additional information. To obtain help with this 
issue, ask us at the forum and include the following text:

job id: 446924


4 Answers
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aleabdo Staff answered 4 weeks ago

Ni! Hi Dan. There was a mishap in our infrastructure. It should be working now.

Let us know if you still find any issues.

Also, had you been using sashimi before? If so, we’d be interested in hearing what you think about the new “workbook” format that replaced the old HTML tables.

Best!

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Dan Kitson answered 4 weeks ago

Hi Ale! I’ve just recently started working more with Sashimi, so I can’t really comment on the new format. The “prepare corpus” script seems to be working now, though! I was also able to run some domain-topic models. However, when I tried to create a domain map, I got the following error: 

Domain Maps did not finish successfully. See the job log for additional information. To obtain help with this issue, ask us at the forum and include the following text:

job id: 447178




And here is the log:

2025-10-27 16:29:23 INFO : Job store: /srv/local/documents/d740/d7400d37227fc04498e4db2fcb79f8cc/447178
2025-10-27 16:29:23 INFO : 
                           Your choices:
                                                         Container to be used: false
                                                         Whether the method needs network access: false
                                                         SASHIMI method to be called: false
                                                         Title column: Article_Title
                                                         Time column: Publication_Year
                                                         URL field: DOI_Link
                                                         ? "URL template (\"URL field\" \u2192 {})\n"
                                                         : '{}'
                                                         Domain selection: ''
                                                         Add columns to workbook:
                                                         - Article_Title
                           
2025-10-27 16:29:23 INFO : HTTP Request: GET http://10.1.59.221:3000/api/project/256170006910/analysis/5042350006910 "HTTP/1.1 200 OK"
2025-10-27 16:29:23 INFO : Loaded config: /srv/local/documents/86bf/86bf0336827b8133c7849055932845eb/447168
2025-10-27 16:30:33 ERROR : Exit: job failed.
2025-10-27 16:30:33 ERROR : <class 'valueerror'="">: Unknown URL type: nan
2025-10-27 16:30:33 ERROR : Traceback:

 
aleabdo Staff replied 3 weeks ago

Ni! Hi Dan,

I see the problem, there are some cells in your data’s “DOI_Link” column that contain the literal text “nan”, which is not an URL that the XSLX (Excel) format accepts.

We have added a check to make sure this situation no longer causes an error.

If you rerun the analysis you should get the results.

And thanks a lot for reporting the issue.

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Dan Kitson answered 3 weeks ago

Hi Ale,
This worked once yesterday, but I’m trying to run Domain Maps with a different domain-topic model, and it’s getting an error again:

Domain Maps did not finish successfully. See the job log for additional information. To obtain help with this issue, ask us at the forum and include the following text:

job id: 447279


2025-10-28 19:49:44 INFO : Job store: /srv/local/documents/2086/2086e87fcb25a25261e32887100d28b1/447279
2025-10-28 19:49:44 INFO : 
                           Your choices:
                                                         Container to be used: false
                                                         Whether the method needs network access: false
                                                         SASHIMI method to be called: false
                                                         Title column: Article_Title
                                                         Time column: Abstract
                                                         URL field: DOI_Link
                                                         ? "URL template (\"URL field\" \u2192 {})\n"
                                                         : '{}'
                                                         Domain selection: ''
                                                         Add columns to workbook: false
                           
2025-10-28 19:49:45 INFO : HTTP Request: GET http://10.1.59.221:3000/api/project/254780006910/analysis/5043630006910 "HTTP/1.1 200 OK"
2025-10-28 19:49:45 INFO : Loaded config: /srv/local/documents/a902/a9022d6068995bfe7d5fe4ad66e2d095/447275
2025-10-28 19:49:45 ERROR : Exit: job failed.
2025-10-28 19:49:45 ERROR : <class 'typeerror'="">: Method.domain_maps() missing 1 required positional argument: 'extra_cols'
2025-10-28 19:49:45 ERROR : Traceback:


 
0 Vote Up Vote Down
aleabdo Staff answered 3 weeks ago

Ni! Hi Dan,

I see the issue, the application ain’t passing on to the method the default value for the “Add columns to workbook” parameter.

I’ve made sure there is a default value internal to the method, and now it works. That’s a new option, which as you can tell could have been more thoroughly tested 😉

Thanks again for reporting.