Zenodo server changes require user-agent

[jeffreyhanson]

Hi @eblondel,

Thank you very much for developing this package. I've been using it for a while to access data from Zenodo, and it works brilliantly! Recently, however, I've been encountering errors when trying to query records using DOIs. Specifically, here's a reprex (see end of post for session information).

# note that this example is from the wiki
library(zen4R)
zenodo <- ZenodoManager$new(logger = "INFO")
rec <- zenodo$getRecordByDOI("10.5281/zenodo.3378733")
#> [zen4R][INFO] ZenodoManager - Successfully connected to Zenodo with user token 
#> [zen4R][INFO] ZenodoRequest - Fetching https://zenodo.org/api/records/?q=doi:10.5281//zenodo.3378733&size=10&page=1&all_versions=1 
#> [zen4R][ERROR] ZenodoRequest - Error while executing request 'records/?q=doi:10.5281//zenodo.3378733&size=10&page=1&all_versions=1' 
#> [zen4R][ERROR] ZenodoManager - Error while fetching published records: Internal Server Error 
#> Error in result$doi : $ operator is invalid for atomic vectors

Also, when inspecting the URL (i.e., https://zenodo.org/api/records/?q=doi:10.5281//zenodo.3378733&size=10&page=1&all_versions=1), I see the following text:

{"error_id":"4e8b029ec6d0492d8982730a5c97e74a","message":"Internal Server Error","status":500}

Do you have any ideas on what might be causing this? I've tried both the CRAN and GitHub version, but I receive this error on both versions. I also tried with and without supplying my own personal access token -- in case the issue was due to rate limiting -- but that doesn't appear to fix it either. Please let me know if there's any further information I can provide?

---

Session Information (based on GitHub version)

R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] zen4R_0.6-2    testthat_3.1.4 devtools_2.4.3 usethis_2.1.6 

loaded via a namespace (and not attached):
 [1] xml2_1.3.3        magrittr_2.0.3    pkgload_1.3.0     R6_2.5.1         
 [5] rlang_1.0.4       fastmap_1.1.0     httr_1.4.3        tools_4.2.1      
 [9] pkgbuild_1.3.1    sessioninfo_1.2.2 cli_3.3.0         ellipsis_0.3.2   
[13] remotes_2.4.2     assertthat_0.2.1  lifecycle_1.0.1   crayon_1.5.1     
[17] keyring_1.3.0     brio_1.1.3        processx_3.7.0    purrr_0.3.4      
[21] callr_3.7.0       fs_1.5.2          ps_1.7.1          curl_4.3.2       
[25] memoise_2.0.1     glue_1.6.2        cachem_1.0.6      compiler_4.2.1   
[29] prettyunits_1.1.1 jsonlite_1.8.0   

[jeffreyhanson]

Just an update, when I access the Zenodo URL, in my Google Chrome browser, I now receive a valid JSON response (see below at end of post). But I still see the internal server error when using zen4R.

---

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P. 6434, CH- 1211 Gen\u00e8ve 6, Switzerland","name":"Schuchert, Peter"},{"affiliation":"880 NE 33 rd Street, Boca Raton, Florida, USA","name":"Collins, Richard"}],"custom":{"dwc:collectionCode":["BFLA"],"dwc:eventDate":["2016-04-25","2019-03-04","2019-03-26"],"dwc:family":["Geryoniidae"],"dwc:genus":["Geryonia"],"dwc:kingdom":["Animalia"],"dwc:materialSampleID":["BFLA4029, UF-013448"],"dwc:order":["Limnomedusae"],"dwc:phylum":["Cnidaria"],"dwc:scientificNameAuthorship":["Forsskal"],"dwc:specificEpithet":["proboscidalis"],"dwc:taxonRank":["species"],"dwc:verbatimEventDate":["2016-04-25","2019-03-04","2019-03-26"],"openbiodiv:TaxonomicConceptLabel":["Geryonia proboscidalis (Forsskal, 1775) sec. Schuchert & Collins, 2021"]},"description":"<i>Geryonia proboscidalis</i> (Forssk&aring;l, 1775)   <p>Fig. 61 A-B</p>  <p> <i>Medusa</i> <i>proboscidalis</i> Forssk&aring;l, 1775: 108, pl. 36 fig. 1.</p>   <p> <i>Geryonia hexaphylla</i> P&eacute;ron &amp; Lesueur, 1810: 329. &ndash; Haeckel, 1879: 295, synonym.</p>   <p> <i>Dianaea endrachtensis</i> Quoy &amp; Gaimard, 1824: 566, pl. 84 fig. 2. &ndash; Haeckel, 1879: 295, synonym.</p>   <p> <i>Leuckartiara brevicirrata</i> Haeckel, 1864b: 462. &ndash; Haeckel, 1879: 295, synonym.</p>   <p> <i>Leuckartiara longicirrata</i> Haeckel, 1864b: 463. &ndash; Haeckel, 1879: 295, synonym.</p>   <p> <i>Geryonia umbella</i> Haeckel, 1864b: 464. &ndash; Mayer, 1910: 425, synonym.</p>   <p> <i>Geryonia fungiformis</i> Haeckel, 1864b: 465, new name for <i>Geryonia hexaphylla</i> P&eacute;ron &amp; Lesueur, 1810. &ndash; Mayer, 1910: 425, synonym.</p>   <p> <i>Geryonia conoides</i> Haeckel, 1864b: 466.</p>   <p> <i>Carmarina hastata</i> Haeckel, 1864b: 467, pl. 11 figs 1-10. &ndash; Mayer, 1910: 425, synonym.</p>   <p> <i>Geryones elephas</i> Haeckel, 1879: 294, pl. 18 fig. 7, South Africa.</p>   <p> <i>Geryonia dianaea</i> Haeckel, 1879: 295. &ndash; Mayer, 1910: 425, synonym.</p>   <p> <i>Carmaris umbella</i> Haeckel, 1879: 296. &ndash; Mayer, 1910: 425, synonym.</p>   <p> <i>Carmaris Giltschii</i> Haeckel, 1879: 296, pl. 18 fig. 8. &ndash; Mayer, 1910: 425, synonym.</p>   <p> <i>Geryones mexicana</i> Agassiz &amp; Mayer, 1902: 149, pl. 4 fig. 17. &ndash; Mayer, 1910: 425, synonym.</p>   <p> <i>Carmaris rosea</i> Agassiz &amp; Mayer, 1902: 149, pl. 4 fig. 18. &ndash; Mayer, 1910: 425, synonym.</p>   <p> <i>Geryonia fungiformis. &ndash;</i> Fol, 1873: 471, figs 1-3, pls 24-25, developement.</p>   <p> <i>Geryonia proboscidalis. &ndash;</i> Haeckel, 1879, 295. &ndash; Mayer, 1910: 425, fig. 282, pl. 53 figs 1-3, pl. 43 fig. 10, synonymy. &ndash; Berrill, 1950: 296, development. &ndash; Kramp, 1959a: 192, fig. 292. &ndash; Kramp, 1961: 237. &ndash; Kramp, 1968: 122, fig. 332. &ndash; Horridge, 1969: 348, figs 5-6, statocysts. &ndash; Goy <i>et al.</i>, 1991: 119, fig. 47. &ndash; Bouillon <i>et al</i>., 2004: 237, fig. 150A-C. &ndash; Buecher <i>et al.</i>, 2005: 35.</p>   <p> <b>Examined material:</b> BFLA4029; 1 specimen; 04-MAR-2019; diameter 10 mm; part preserved in formalin (UF-013448) and part in alcohol for DNA extraction; 16S sequence MW528644. &ndash; 26-MAR- 2019; 1 specimen photographed, diameter 20 mm, not collected.</p>   <p>Mediterranean, France, Bay of Villefranche-sur- Mer, 43.6963&deg;N 7.3075&deg;E; 25-APR-2016; diameter 70 mm, photos see DOI: 10.5281/zenodo.53890; whole specimen used for DNA extraction, 16S sequence KX355451.</p>  <p> <b>Description of Florida material:</b> Bell almost hemispherical, 10 to 20 mm wide, jelly thick. Stomach small, on a long conical peduncle, peduncle reaching a length of about twice the bell height (Fig. 61A). Six radial canals, 3-7 centripetal canals betwen pairs of radial canals, ending blindly below apex of subumbrella. Gonads along the six primary radial canals, reaching from circular canal to apex of subumbrella, sheet-like, triangular, pointed end towards circular canal. Two types of tentacles. Six long, perradial tentacles with nematocyst rings, and six short interradial tentacles with adaxial nematocyst clusters, often held upwards adnate to subumbrella (Fig. 61B).</p>   <p> <b>16S Data:</b> The 16S sequence (GMW528644) shows few differences to other published sequences of <i>G. proboscidalis</i> (Table 1). The p-distance to the Mediterranean specimen was 0.17%, and 0.33% to the one from Japan. More differences where found with sequence KT809331 (1.2%) originating from the Sea of Cortez (Bastian Bentlage, pers. com.).</p>   <p> <b>Distribution:</b> Occurs in tropical and subtropical parts of all three oceans, including also the Mediterranean, approximately between 35&deg; and 35&deg;S (Kramp, 1957, 1965). Type locality: Mediterranean Sea (Forssk&aring;l, 1775).</p>   <p> <b>Remarks:</b> With its six radial canals and the two types of tentacles, <i>Geryonia proboscidalis</i> is rather reliably identifiable. It is interesting to note the low 16S sequence divergences observed for the sample from Florida, the Mediterranean, and Japan. <i>Geryonia proboscidalis</i> could thus be a good example of a hydromedusan species with a truely circumglobal distribution.</p>","doi":"10.5281/zenodo.5710656","journal":{"issue":"2","pages":"336-337","title":"Hydromedusae observed during night dives in the Gulf Stream, pp. 237-356 in Revue suisse de Zoologie","volume":"128"},"keywords":["Biodiversity","Taxonomy","Animalia","Cnidaria","Hydrozoa","Limnomedusae","Geryoniidae","Geryonia","Geryonia proboscidalis"],"license":{"id":"CC0-1.0"},"locations":[{"description":"Mediterranean, France, Bay of Villefranche-sur- Mer, 43.6963\u00b0N 7.3075\u00b0E; 25-APR-2016; diameter 70 mm, photos see DOI: 10.5281/zenodo.53890; whole specimen used for DNA extraction, 16S sequence KX355451.","lat":43.6963,"lon":7.3075,"place":"Bay of Villefranche-sur- Mer"}],"notes":"Published as part of <i>Schuchert, Peter &amp; Collins, Richard, 2021, Hydromedusae observed during night dives in the Gulf Stream, pp. 237-356 in Revue suisse de Zoologie 128 (2)</i> on pages 336-337, DOI: 10.35929/RSZ.0049, <a href=\"http://zenodo.org/record/5639938\">http://zenodo.org/record/5639938</a>","publication_date":"2021-10-21","references":["Forsskal P. in: Niebuhr C. E. 1775. Descriptiones animalium avium, amphibiorium, piscium, insectorum, vermium; quae in itinere orientali observavit Petrus Forskal. Post mortem auctoris edidit Carsten Niebuhr. Molleri, KObenhavn, 164 pp. DOI: 10.5962 / bhl. title. 2154","Peron F., Lesueur C. A. 1810. Tableau des caracteres generiques et specifiques de toutes les especes de meduses connues jusqu'a ce jour. Annales du Museum national d'histoire naturelle de Paris 14: 325 - 366. https: // biodiversitylibrary. org / page / 3498981","Haeckel E. 1879. Das System der Medusen. Erster Teil einer Monographie der Medusen. Denkschriften der Medicinisch- Naturwissenschaftlichen Gesellschaft zu Jena 1: I-XX, 1 - 360, 20 pls.","Quoy J. R. C., Gaimard J. P. 1824. Voyage autour du monde ... execute sur les corvettes de S. M. l'Uranie et la Physicienne, pendant les annees 1817 a 1820. Volume 3. In: Freycinet, 1824. Zoologie: iv + 712 pp.","Haeckel E. 1864 b. Die Famile der Russelquallen (Medusae, Geryonidae). Jenaische Zeitschrift fur Medizin und Naturwissenschaften 1: 435 - 461, pls 11 - 12.","Mayer A. G. 1910. Medusae of the world. Hydromedusae, Vols. I & II. Scyphomedusae, Vol III. Carnegie Institution, Washington, pp. 735, plates 1 - 76.","Agassiz A., Mayer A. G. 1902. Medusae. Report of the scientific research expedition to the tropical Pacific. U. S. Fish Comm. St. Albatross, 1899 - 1900. III. Memoirs of the Museum of Comparative Zoology at Harvard College 26: 136 - 176, pls 1 - 14.","Fol H. 1873. Die erste Entwickelung des Geryonideneies. Jenaer Zeitschrift fur Naturwissenschaften 7: 471 - 492, pls 24 - 25.","Berrill N. J. 1950. Development and medusa-bud formation in the hydromedusae. Quarterly Review of Biology 25 (3): 292 - 316.","Kramp P. L. 1959 a. The Hydromedusae of the Atlantic Ocean and adjacent waters. Dana Report 46: 1 - 283.","Kramp P. L. 1961. Synopsis of the medusae of the world. Journal of the Marine Biological Association of the U. K. 40: 1 - 469.","Kramp P. L. 1968. The hydromedusae of the Pacific and Indian oceans. Sections II and III. Dana Report 72: 1 - 200.","Horridge G. A. 1969. Statocysts of medusae and evolution of stereocilia. Tissue & Cell 1: 341 - 353.","Goy J., Lakkis S., Zeidane R. 1991. Les meduses (Cnidaria) des eaux Libanaises. Annales de l'Institut Oceanographique de Paris 67: 99 - 128.","Bouillon J., Medel M. D., Pages F., Gili J. M., Boero B., Gravili C. 2004. Fauna of the Mediterranean Hydrozoa. Scientia Marina 68 (Suppl. 2): 1 - 448.","Buecher E., Goy J., Gibbons M. J. 2005. Hydromedusae of the Agulhas Current. African Invertebrates 46: 27 - 69.","Kramp P. L. 1957. Hydromedusae from the Discovery collections. Discovery Reports 29: 1 - 128.","Kramp P. L. 1965. The hydromedusae of the Pacific and Indian oceans. Dana Report 63: 1 - 162."],"related_identifiers":[{"identifier":"10.35929/RSZ.0049","relation":"isPartOf","resource_type":"publication-article","scheme":"doi"},{"identifier":"http://zenodo.org/record/5639938","relation":"isPartOf","resource_type":"publication-article","scheme":"url"},{"identifier":"http://publication.plazi.org/id/2C28F2045B0C0014FFCFFF96FFDB7820","relation":"isPartOf","resource_type":"publication-article","scheme":"url"},{"identifier":"10.5281/zenodo.5640115","relation":"cites","resource_type":"image-figure","scheme":"doi"},{"identifier":"http://table.plazi.org/id/0CC76BE25B080010FF58FC94FB897B14","relation":"cites","resource_type":"dataset","scheme":"url"},{"identifier":"http://zoobank.org/8382D1CA-7C0E-4B1C-9591-4CEAA2F296FB","relation":"isPartOf","resource_type":"publication-article","scheme":"url"},{"identifier":"10.5281/zenodo.5710655","relation":"isVersionOf","scheme":"doi"}],"relations":{"version":[{"count":1,"index":0,"is_last":true,"last_child":{"pid_type":"recid","pid_value":"5710656"},"parent":{"pid_type":"recid","pid_value":"5710655"}}]},"resource_type":{"subtype":"taxonomictreatment","title":"Taxonomic treatment","type":"publication"},"title":"Geryonia proboscidalis"},"owners":[1161],"revision":5,"stats":{"downloads":0.0,"unique_downloads":0.0,"unique_views":30.0,"version_downloads":0.0,"version_unique_downloads":0.0,"version_unique_views":30.0,"version_views":30.0,"version_volume":0.0,"views":30.0,"volume":0.0},"updated":"2021-11-22T20:03:27.815783+00:00"},{"conceptdoi":"10.5281/zenodo.3467324","conceptrecid":"3467324","created":"2019-11-14T16:49:19.738168+00:00","doi":"10.5281/zenodo.3467325","files":[{"bucket":"bba23aad-8ffb-4acc-8eab-40a32d95310b","checksum":"md5:962d6a74ae0ccf27a7f7e5783a2cce51","key":"Snap-2370.tif","links":{"self":"https://zenodo.org/api/files/bba23aad-8ffb-4acc-8eab-40a32d95310b/Snap-2370.tif"},"size":11173392,"type":"tif"},{"bucket":"bba23aad-8ffb-4acc-8eab-40a32d95310b","checksum":"md5:81d87cdc218c8eefafba8307d1a552c1","key":"SAMERAMASnap-2370.tif","links":{"self":"https://zenodo.org/api/files/bba23aad-8ffb-4acc-8eab-40a32d95310b/SAMERAMASnap-2370.tif"},"size":17690319,"type":"tif"}],"id":3467325,"links":{"badge":"https://zenodo.org/badge/doi/10.5281/zenodo.3467325.svg","bucket":"https://zenodo.org/api/files/bba23aad-8ffb-4acc-8eab-40a32d95310b","conceptbadge":"https://zenodo.org/badge/doi/10.5281/zenodo.3467324.svg","conceptdoi":"https://doi.org/10.5281/zenodo.3467324","doi":"https://doi.org/10.5281/zenodo.3467325","html":"https://zenodo.org/record/3467325","latest":"https://zenodo.org/api/records/3467325","latest_html":"https://zenodo.org/record/3467325","self":"https://zenodo.org/api/records/3467325","thumb250":"https://zenodo.org/api/iiif/v2/bba23aad-8ffb-4acc-8eab-40a32d95310b:bf03fc6e-73e3-484f-997c-760127b2159e:Snap-2370.tif/full/250,/0/default.jpg","thumbs":{"10":"https://zenodo.org/record/3467325/thumb10","100":"https://zenodo.org/record/3467325/thumb100","1200":"https://zenodo.org/record/3467325/thumb1200","250":"https://zenodo.org/record/3467325/thumb250","50":"https://zenodo.org/record/3467325/thumb50","750":"https://zenodo.org/record/3467325/thumb750"}},"metadata":{"access_right":"open","access_right_category":"success","creators":[{"affiliation":"Zenodo","name":"Doe, John"}],"description":"Mark Bredth : 0.2262<br>img. 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Image : 2370<br>L/B ratio : 1.645283019<br>Mark Shape : E<br>Mark Length : 0.5232<br>Note: : <br>Branching : /<br>Intensity Level : <br>","doi":"10.5281/zenodo.3467321","license":{"id":"CC-BY-4.0"},"publication_date":"2019-10-01","related_identifiers":[{"identifier":"10.5281/zenodo.3467320","relation":"isVersionOf","scheme":"doi"}],"relations":{"version":[{"count":1,"index":0,"is_last":true,"last_child":{"pid_type":"recid","pid_value":"3467321"},"parent":{"pid_type":"recid","pid_value":"3467320"}}]},"resource_type":{"subtype":"photo","title":"Photo","type":"image"},"title":"Mark No. 2"},"owners":[77495],"revision":1,"stats":{"downloads":15.0,"unique_downloads":7.0,"unique_views":15.0,"version_downloads":15.0,"version_unique_downloads":7.0,"version_unique_views":15.0,"version_views":18.0,"version_volume":226253223.0,"views":18.0,"volume":226253223.0},"updated":"2019-10-17T10:12:14.156670+00:00"}],"total":2754923},"links":{"next":"https://zenodo.org/api/records/?sort=bestmatch&q=doi%3A10.5281%2F%2Fzenodo.3378733&all_versions=true&page=2&size=10","self":"https://zenodo.org/api/records/?sort=bestmatch&q=doi%3A10.5281%2F%2Fzenodo.3378733&all_versions=true&page=1&size=10"}}

[eblondel]

By evidence, this is due to a change Zenodo server-side. I've seen your new user agent, I will try to create a specific user agent for zen4R as I use to apply for other similar packages.

[eblondel]

@jeffreyhanson I've added a User-Agent systematically to all Zenodo requests.

[eblondel]

i'm going to send a revision to CRAN

[eblondel]

@jeffreyhanson From CRAN: "CRAN submissions will be offline from Jul 22, 2022 to Aug 5, 2022 -CRAN team vacation and maintenance work)" . I will send a revision to CRAN in August

[jeffreyhanson]

Brilliant - thank you very much @eblondel!

[jeffreyhanson]

I'm sorry, I'm trying the latest developmental version on GitHub (version 0.6-2) and I'm still experiencing this issue. Here's the same reprex as before (copied below) and my session information (with the GitHub version of the package). Please let me know if there's any further details I can provide to help resolve this?

library(zen4R)
zenodo <- ZenodoManager$new(logger = "INFO")
rec <- zenodo$getRecordByDOI("10.5281/zenodo.3378733")
#> [zen4R][INFO] ZenodoRequest - Fetching https://zenodo.org/api/records/q=doi:10.5281//zenodo.3378733&size=10&page=1&all_versions=1 
#> [zen4R][ERROR] ZenodoRequest - Error while executing request 'records/q=doi:10.5281//zenodo.3378733&size=10&page=1&all_versions=1' 
#> [zen4R][ERROR] ZenodoManager - Error while fetching published records: Internal Server Error 
Error in result$doi : $ operator is invalid for atomic vectors

---

R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] zen4R_0.6-2    testthat_3.1.4 devtools_2.4.3 usethis_2.1.6 

loaded via a namespace (and not attached):
 [1] xml2_1.3.3        magrittr_2.0.3    pkgload_1.3.0     R6_2.5.1         
 [5] rlang_1.0.4       fastmap_1.1.0     httr_1.4.3        tools_4.2.1      
 [9] pkgbuild_1.3.1    sessioninfo_1.2.2 cli_3.3.0         ellipsis_0.3.2   
[13] remotes_2.4.2     assertthat_0.2.1  lifecycle_1.0.1   crayon_1.5.1     
[17] keyring_1.3.0     brio_1.1.3        processx_3.7.0    purrr_0.3.4      
[21] callr_3.7.0       fs_1.5.2          ps_1.7.1          curl_4.3.2       
[25] memoise_2.0.1     glue_1.6.2        cachem_1.0.6      compiler_4.2.1   
[29] prettyunits_1.1.1 jsonlite_1.8.0   

[eblondel]

Make sure to re-install zen4R from a clean R session, if you use R studio, they are caching issues that prevent from using the latest version. This occurs often if you don't restart R or if you have multiple rstudio open.
I just tried with the same DOI, and it works

[eblondel]

This is what I get

[zen4R][INFO] ZenodoRequest - Fetching https://zenodo.org/api/records/?q=doi:10.5281//zenodo.3378733&size=10&page=1&all_versions=1 
[zen4R][INFO] ZenodoManager - Successfully fetched list of published records - page 1 
[zen4R][INFO] ZenodoManager - Successfully fetched list of published records! 
[zen4R][WARN] ZenodoManager - No record for DOI '10.5281/zenodo.3378733'! 
[zen4R][INFO] ZenodoManager - Try to get deposition by Zenodo specific record id '3378733' 
[zen4R][INFO] ZenodoRequest - Fetching https://zenodo.org/api/records/?q=recid:3378733&size=10&page=1&all_versions=1 
[zen4R][INFO] ZenodoManager - Successfully fetched list of published records - page 1 
[zen4R][INFO] ZenodoManager - Successfully fetched list of published records! 
[zen4R][INFO] ZenodoManager - Successfully fetched record for id '3378733'!

[jeffreyhanson]

Thanks for the suggestion! Although I don't use Rstudio (just plain R from the linux command line), I re-installed the package from GitHub and updated all packages on my system. Unfortunately, I'm still receiving the error. Do you have any other ideas? Would it be possible for me to override the user agent?

[jeffreyhanson]

May I ask what OS you're using? If not Linux, I could submit a PR to add a GitHub Action to enable automatic testing on Ubuntu to help reproduce the error?

[eblondel]

Tests are configured on Ubuntu already. I've added a unit test just know, let's see what we get to help troubleshooting the issue.

[eblondel]

From what I can see, it failed on Ubuntu-latest. I have to dig if it's actually related to the User-Agent, i still suspect Zenodo is experimenting issues and is not fully available.

[eblondel]

@jeffreyhanson I've set-up a browser-like agent to reproduce your tests. I've set-up a unit test that is run on 2 versions of R (latest, devel). The first attempt passed on one dist but not the other. I've re-run the failed job and it passed successfully. All this let me think that Zenodo is actually experimienting issues of availability and unexpectedly you get Internal Server errors.

[jeffreyhanson]

Thank you very much for looking into this further - I really appreciate it! To see if it's just the case that I'm occaisionally getting unexpected Internal server errors, I wrote a short script to try querying the Zenodo API multiple times to see what the success rate would be. If the issue was due to occaisional/unexpected errors, then I would expect to see some success and some failures. After running this script (see below for reference, along with my session Information), I found that none of attempts were succesful out 50 attempts. This would suggest to me that the underlying issue is not due to occaisional failures. What do you think?

# load package
library(zen4R)

# set parameters for testing
## number of times to attempt querying Zenodo API
n_attempts <- 50
## amount of time (number of seconds) to wait between attempts
sleep_duration <- 5

# try querying Zenodo
n_success <- sapply(seq_len(n_attempts), function(x) {
  Sys.sleep(sleep_duration)
  zenodo <- ZenodoManager$new(logger = "INFO")
  result <- try(zenodo$getRecordByDOI("10.5281/zenodo.3378733"), silent = TRUE)
  !inherits(result, "try-error")
})

# compute success rate (as a percentage)
success_rate <- mean(n_success) * 100

# print percentage of times that zen4R worked
# 0% = none of the attempts worked
# 100% = all of the attempts worked
print(success_rate)
#> [1] 0

---

R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] zen4R_0.6-2    testthat_3.1.4 devtools_2.4.4 usethis_2.1.6 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9        compiler_4.2.1    later_1.3.0       urlchecker_1.0.1 
 [5] prettyunits_1.1.1 profvis_0.3.7     remotes_2.4.2     tools_4.2.1      
 [9] digest_0.6.29     pkgbuild_1.3.1    pkgload_1.3.0     jsonlite_1.8.0   
[13] memoise_2.0.1     lifecycle_1.0.1   rlang_1.0.4       shiny_1.7.2      
[17] cli_3.3.0         curl_4.3.2        fastmap_1.1.0     xml2_1.3.3       
[21] stringr_1.4.0     httr_1.4.3        fs_1.5.2          htmlwidgets_1.5.4
[25] glue_1.6.2        R6_2.5.1          processx_3.7.0    sessioninfo_1.2.2
[29] callr_3.7.1       purrr_0.3.4       magrittr_2.0.3    ps_1.7.1         
[33] promises_1.2.0.1  ellipsis_0.3.2    htmltools_0.5.3   assertthat_0.2.1 
[37] mime_0.12         xtable_1.8-4      httpuv_1.6.5      keyring_1.3.0    
[41] stringi_1.7.8     miniUI_0.1.1.1    cachem_1.0.6      crayon_1.5.1     
[45] brio_1.1.3       

[jeffreyhanson]

For comparison, I'll re-run these benchmarks using the PR I posted earlier to what the success rate for that would be given that user agent header. Please give me a while for these runs to complete.

[jeffreyhanson]

Here's the results for running the same code with the PR I posted earlier (see below). Since there's a 100% success rate when using a different user agent header, this would indicate to me that the issue could be resolved by using a different user agent header. It would also further suggest that the issue is unlikely to be due to intermittent/occaissional issues with the Zenodo API. Does that sound right to you? Or maybe I am missing some important detail?

Assuming that I am not misunderstanding something, would it be possible to update the package so that users could manually supply their own user agent header? This would allow me to continue using the official version of the package, since I could supply a user agent header that appears to work on my system. This could potentially be achieved using an environmental variable (similar to ZENODO_PAT), or specifying an option (e.g., something like options(ZENODO_USER_AGENT_HEADER="blah blah blah")). I suppose another fix could be to update the Zenodo manager to allow users to specify this information (e.g., ZenodoManager$new(logger = "INFO", user_agent = "blah blah blah"), but this could be more work? What do you think? I would be happy to prepare a PR that implements any of these options if that would be helpful?

# load package
library(zen4R)

# set parameters for testing
## number of times to attempt querying Zenodo API
n_attempts <- 50
## amount of time (number of seconds) to wait between attempts
sleep_duration <- 5

# try querying Zenodo
n_success <- sapply(seq_len(n_attempts), function(x) {
  Sys.sleep(sleep_duration)
  zenodo <- ZenodoManager$new(logger = "INFO")
  result <- try(zenodo$getRecordByDOI("10.5281/zenodo.3378733"), silent = TRUE)
  !inherits(result, "try-error")
})

# compute success rate (as a percentage)
success_rate <- mean(n_success) * 100

# print percentage of times that zen4R worked
# 0% = none of the attempts worked
# 100% = all of the attempts worked
print(success_rate)
#> [1] 100

---

R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] zen4R_0.6-2    testthat_3.1.4 devtools_2.4.4 usethis_2.1.6 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9        compiler_4.2.1    later_1.3.0       urlchecker_1.0.1 
 [5] prettyunits_1.1.1 profvis_0.3.7     remotes_2.4.2     tools_4.2.1      
 [9] digest_0.6.29     pkgbuild_1.3.1    pkgload_1.3.0     jsonlite_1.8.0   
[13] memoise_2.0.1     lifecycle_1.0.1   rlang_1.0.4       shiny_1.7.2      
[17] cli_3.3.0         curl_4.3.2        fastmap_1.1.0     xml2_1.3.3       
[21] stringr_1.4.0     httr_1.4.3        fs_1.5.2          htmlwidgets_1.5.4
[25] glue_1.6.2        R6_2.5.1          processx_3.7.0    sessioninfo_1.2.2
[29] callr_3.7.1       purrr_0.3.4       magrittr_2.0.3    ps_1.7.1         
[33] promises_1.2.0.1  ellipsis_0.3.2    htmltools_0.5.3   assertthat_0.2.1 
[37] mime_0.12         xtable_1.8-4      httpuv_1.6.5      keyring_1.3.0    
[41] stringi_1.7.8     miniUI_0.1.1.1    cachem_1.0.6      crayon_1.5.1     
[45] brio_1.1.3  

[eblondel]

@jeffreyhanson I've harcoded the same user agent that you put in your PR, but even with this I got Internal server errors randomly through continous integration tests done on R release and devel, without any reproducible pattern. Now the tests appear to pass on Github, but it's because i went there manually to restart the failed tests until they pass. What sounds correct is that now Zenodo requires a user agent, but I can't explain the internal server errors. I will contact Zenodo team and see what they think about it. Meanwhile you can use the current github master which is using the user agent you were suggesting.

[jeffreyhanson]

Awesome - thank you very much, I really appreciate it! I've just tested it now, and it works perfectly for me. Thank you for following up with the Zenodo team as well.