Couldn't parse Manubot response

[sterding]

Checks

• I have searched the docs, existing issues, and existing discussions for answers first.

Link to your website repo

https://github.com/sterding/donglab.org

Version of Lab Website Template you are using

1.1.6

Description

I got the following error in preview and also after pushing to GitHub. Would you please help?

`Generating citations
Processing source 1 of 42, id: pubmed:37930031
Using Manubot to generate citation## WARNING
Generating csl_item for 'pubmed:37930031' failed due to a SSLError:
HTTPSConnectionPool(host='eutils.ncbi.nlm.nih.gov', port=443): Max retries exceeded with url: /entrez/eutils/efetch.fcgi?db=pubmed&id=37930031&retmode=xml (Caused by SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1123)')))

        Couldn't parse Manubot response

Processing source 2 of 42, id: pubmed:37723137
Using Manubot to generate citation## WARNING
Generating csl_item for 'pubmed:37723137' failed due to a SSLError:
HTTPSConnectionPool(host='eutils.ncbi.nlm.nih.gov', port=443): Max retries exceeded with url: /entrez/eutils/efetch.fcgi?db=pubmed&id=37723137&retmode=xml (Caused by SSLError(SSLEOFError(8, 'EOF occurred in violation of protocol (_ssl.c:1123)')))

        Couldn't parse Manubot response

`

[vincerubinetti]

I don't think you've done anything wrong here. You were rate limited. Unfortunately, having automatic citations necessarily means having a long chain of upstream dependencies (Manubot, CrossRef, eutils, etc) that are live services which can sometimes fail. It looks like your subsequent run was able to cite the problematic pubmed:22955616 source without problems.

[vincerubinetti]

Full error from the failing run for posterity:

Run python _cite/cite.py


--------------------

Compiling sources
Running google-scholar plugin
    Found 0 google-scholar* data file(s)
Running pubmed plugin
    Found 0 pubmed* data file(s)
Running orcid plugin
    Found 0 orcid* data file(s)
Running sources plugin
    Found 1 sources* data file(s)
    Processing data file sources.yaml
        Processing entry 1 of 42, id: pubmed:37930031
        Processing entry 2 of 42, id: pubmed:37723[13](https://github.com/sterding/donglab.org/actions/runs/9902320062/job/27356045949#step:6:14)7
        Processing entry 3 of 42, id: pubmed:37386247
        Processing entry 4 of 42, id: pubmed:36525587
        Processing entry 5 of 42, id: pubmed:35688132
        Processing entry 6 of 42, id: pubmed:35610053
        Processing entry 7 of 42, id: pubmed:35132056
        Processing entry 8 of 42, id: pubmed:34663731
        Processing entry 9 of 42, id: pubmed:34433407
        Processing entry 10 of 42, id: pubmed:34234189
        Processing entry 11 of 42, id: pubmed:34009297
        Processing entry 12 of 42, id: pubmed:33969380
        Processing entry 13 of 42, id: pubmed:33960523
        Processing entry [14](https://github.com/sterding/donglab.org/actions/runs/9902320062/job/27356045949#step:6:15) of 42, id: pubmed:33958783
        Processing entry [15](https://github.com/sterding/donglab.org/actions/runs/9902320062/job/27356045949#step:6:16) of 42, id: pubmed:33884653
        Processing entry [16](https://github.com/sterding/donglab.org/actions/runs/9902320062/job/27356045949#step:6:17) of 42, id: pubmed:33432243
        Processing entry [17](https://github.com/sterding/donglab.org/actions/runs/9902320062/job/27356045949#step:6:18) of 42, id: pubmed:32926651
        Processing entry [18](https://github.com/sterding/donglab.org/actions/runs/9902320062/job/27356045949#step:6:19) of 42, id: pubmed:30482917
        Processing entry [19](https://github.com/sterding/donglab.org/actions/runs/9902320062/job/27356045949#step:6:20) of 42, id: pubmed:30224808
        Processing entry [20](https://github.com/sterding/donglab.org/actions/runs/9902320062/job/27356045949#step:6:21) of 42, id: pubmed:28860381
        Processing entry [21](https://github.com/sterding/donglab.org/actions/runs/9902320062/job/27356045949#step:6:22) of 42, id: pubmed:26636336
        Processing entry [22](https://github.com/sterding/donglab.org/actions/runs/9902320062/job/27356045949#step:6:23) of 42, id: pubmed:26220939
        Processing entry [23](https://github.com/sterding/donglab.org/actions/runs/9902320062/job/27356045949#step:6:24) of 42, id: pubmed:25480889
Processing source 33 of 42, id: pubmed:22196727
## ERROR
Error fetching PubMed metadata for 22196727.
Unsupported XML response from https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=22196727&retmode=xml:
{"error":"API rate limit exceeded","api-key":"172.190.111.146","count":"4","limit":"3"}

## WARNING
Generating csl_item for 'pubmed:22196727' failed due to a ParseError:
not well-formed (invalid token): line 1, column 0
## CRITICAL
Failure: exiting with code 1 due to logged errors
    Using Manubot to generate citation
            Couldn't parse Manubot response
Processing source 34 of 42, id: pubmed:20122234
    Using Manubot to generate citation
Processing source 35 of 42, id: pubmed:19969543
    Using Manubot to generate citation
Processing source 36 of 42, id: pubmed:19698106
    Using Manubot to generate citation
Processing source 37 of 42, id: pubmed:19374772
    Using Manubot to generate citation
Processing source 38 of 42, id: pubmed:184[24](https://github.com/sterding/donglab.org/actions/runs/9902320062/job/27356045949#step:6:25)774
    Using Manubot to generate citation
Processing source 39 of 42, id: pubmed:22955616
## ERROR
Error fetching PubMed metadata for 22955616.
Unsupported XML response from https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=22955616&retmode=xml:
{"error":"API rate limit exceeded","api-key":"172.190.111.146","count":"4","limit":"3"}

## WARNING
Generating csl_item for 'pubmed:22955616' failed due to a ParseError:
not well-formed (invalid token): line 1, column 0
## CRITICAL
Failure: exiting with code 1 due to logged errors
    Using Manubot to generate citation
            Couldn't parse Manubot response
Processing source 40 of 42, id: pubmed:215[26](https://github.com/sterding/donglab.org/actions/runs/9902320062/job/27356045949#step:6:27)222
    Using Manubot to generate citation
Processing source 41 of 42, id: doi:10.1109/mpot.2008.931159
    Using Manubot to generate citation (from cache)
Processing source 42 of 42, id: doi:10.1109/ICBBE.2007.84
    Using Manubot to generate citation (from cache)

--------------------

Saving updated citations
Error(s) occurred above
Error: Process completed with exit code 1.