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Mathscinet search is not working #10996

Closed TimAlderson closed 7 months ago

TimAlderson commented 8 months ago

JabRef version

5.12 (latest release)

Operating system

Windows

Details on version and operating system

No response

Checked with the latest development build (copy version output from About dialog)

Steps to reproduce the behaviour

Was #10499 closed because it was fixed, or because work is not planned?

Active subscription to Mathscinet confirmed in browser

Perform Web search Mathscinet in Jabref

Appendix

...

Log File Error: org.jabref.logic.importer.FetcherException: An internal parser error occurred while fetching from https://mathscinet.ams.org/mathscinet/api/publications/search?query=algebraic+geometric+codes+basic+notions¤tPage=1&pageSize=100 at org.jabref@5.12.60000/org.jabref.logic.importer.SearchBasedParserFetcher.getBibEntries(Unknown Source) at org.jabref@5.12.60000/org.jabref.logic.importer.SearchBasedParserFetcher.performSearch(Unknown Source) at org.jabref@5.12.60000/org.jabref.logic.importer.SearchBasedFetcher.performSearch(Unknown Source) at org.jabref@5.12.60000/org.jabref.gui.importer.fetcher.WebSearchPaneViewModel.lambda$search$2(Unknown Source) at org.jabref@5.12.60000/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source) at org.jabref@5.12.60000/org.jabref.gui.util.DefaultTaskExecutor$1.call(Unknown Source) at org.jabref.merged.module@5.12.60000/javafx.concurrent.Task$TaskCallable.call(Unknown Source) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source) Caused by: org.jabref.logic.importer.ParseException: Error when parsing entry at org.jabref@5.12.60000/org.jabref.logic.importer.fetcher.MathSciNet.lambda$getParser$0(Unknown Source) ... 13 more Caused by: kong.unirest.json.JSONException: JSONObject["all"] not found. at org.jabref.merged.module@5.12.60000/kong.unirest.json.JSONObject.getProperty(Unknown Source) at org.jabref.merged.module@5.12.60000/kong.unirest.json.JSONObject.getJSONObject(Unknown Source) ... 14 more
TimAlderson commented 8 months ago

Sorry..wrong log file. Here is the file from the most recent :

org.jabref.logic.importer.FetcherException: An internal parser error occurred while fetching from https://mathscinet.ams.org/mathscinet/api/publications/search?query=algebraic+geometric+codes+basic+notions&currentPage=1&pageSize=100 at org.jabref@5.13.233/org.jabref.logic.importer.SearchBasedParserFetcher.getBibEntries(Unknown Source) at org.jabref@5.13.233/org.jabref.logic.importer.SearchBasedParserFetcher.performSearch(Unknown Source) at org.jabref@5.13.233/org.jabref.logic.importer.SearchBasedFetcher.performSearch(Unknown Source) at org.jabref@5.13.233/org.jabref.gui.importer.fetcher.WebSearchPaneViewModel.lambda$search$2(Unknown Source) at org.jabref@5.13.233/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source) at org.jabref@5.13.233/org.jabref.gui.util.DefaultTaskExecutor$1.call(Unknown Source) at org.jabref.merged.module@5.13.233/javafx.concurrent.Task$TaskCallable.call(Unknown Source) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source) Caused by: org.jabref.logic.importer.ParseException: Error when parsing entry at org.jabref@5.13.233/org.jabref.logic.importer.fetcher.MathSciNet.lambda$getParser$0(Unknown Source) ... 13 more Caused by: kong.unirest.json.JSONException: JSONObject["all"] not found. at org.jabref.merged.module@5.13.233/kong.unirest.json.JSONObject.getProperty(Unknown Source) at org.jabref.merged.module@5.13.233/kong.unirest.json.JSONObject.getJSONObject(Unknown Source) ... 14 more

Siedlerchr commented 8 months ago

It would be helpful if you could execute the request in the browser and send/paste us the json file as response so we can look at it. Problem is that we currently don't have a subscription to mathcinet and could not verify this

TimAlderson commented 8 months ago

Thank you for the reply.
I have been searching how to extract a json file using Firefox, but have been unable to figure it out. Any chance of a hint on how to do that?

Siedlerchr commented 8 months ago

It should be possible using the Developer Tools (F12): (It's German, but basically network analysis tab -> then select the request where it shows json -> Right click -> Save answer should give the json

grafik
TimAlderson commented 8 months ago

Thank you. Here are the results from facets and search respectively:

{"authors":[],"journals":[],"entryTypes":[],"itemTypes":[],"reviewStatuses":[],"publicationTypes":[],"primaryClassifications":[],"publicationYears":[],"institutions":[],"statuses":[]}

{"results":[],"total":0} Screenshot 2024-03-10 150108

I performed another search which had more than 0 results (snip below). Is there a file that is more helpful than those above?

Screenshot 2024-03-10 151210

Siedlerchr commented 8 months ago

The json for the search with more than zero results would be nice!

TimAlderson commented 8 months ago

Facets:

{"authors":[{"id":"758603","value":"Alderson, Tim L.","total":27},{"id":"692091","value":"Mellinger, Keith E.","total":9},{"id":"42380","value":"Bruen, Aiden A.","total":4},{"id":"50285","value":"Cohen, Gérard D.","total":1},{"id":"615685","value":"Gács, András","total":1},{"id":"1068150","value":"Huntemann, Svenja","total":1},{"id":"1251963","value":"Neri, Alessandro<sup>1</sup>","total":1},{"id":"149440","value":"Rodier, François","total":1},{"id":"863999","value":"Shi, Minjia","total":1},{"id":"191601","value":"Silverman, Robert","total":1},{"id":"225546","value":"Solé, Patrick","total":1},{"id":"1276838","value":"Zhu, Hongwei<sup>1</sup>","total":1}],"journals":[{"id":"6036","value":"Des. Codes Cryptogr.","total":5},{"id":"2292","value":"IEEE Trans. Inform. Theory","total":3},{"id":"6241","value":"Adv. Math. Commun.","total":2},{"id":"4449","value":"Appl. Algebra Engrg. Comm. Comput.","total":2},{"id":"643","value":"Discrete Math.","total":2},{"id":"5510","value":"Ann. Comb.","total":1},{"id":"6137","value":"Antarct. J. Math.","total":1},{"id":"7425","value":"Atl. Electron. J. Math.","total":1},{"id":"4117","value":"Bull. Inst. Combin. Appl.","total":1},{"id":"615","value":"Discrete Appl. Math.","total":1},{"id":"4633","value":"Electron. J. Combin.","total":1},{"id":"4801","value":"Finite Fields Appl.","total":1},{"id":"6154","value":"Innov. Incidence Geom.","total":1},{"id":"7248","value":"Int. J. Inf. Coding Theory","total":1},{"id":"1833","value":"J. Combin. Theory Ser. A","total":1},{"id":"5169","value":"SIAM J. Discrete Math.","total":1},{"id":"8218","value":"Trans. Comb.","total":1}],"entryTypes":[],"itemTypes":[],"reviewStatuses":[{"id":"Reviewed","value":"Reviewed","total":20},{"id":"Summary","value":"Summary","total":10},{"id":"Indexed","value":"Indexed","total":1}],"publicationTypes":[{"id":"Journal Article","value":"Journal Article","total":26},{"id":"Book Collection","value":"Book Collection","total":2},{"id":"Book Collection Article","value":"Book Collection Article","total":2},{"id":"Thesis","value":"Thesis","total":1}],"primaryClassifications":[{"id":"94","value":"Information and communication theory, circuits","total":26},{"id":"51","value":"Geometry ","total":3},{"id":"11","value":"Number theory","total":1}],"publicationYears":[{"id":"2020","value":"2020","total":1},{"id":"2019","value":"2019","total":4},{"id":"2018","value":"2018","total":1},{"id":"2014","value":"2014","total":1},{"id":"2011","value":"2011","total":1},{"id":"2010","value":"2010","total":3},{"id":"2009","value":"2009","total":2},{"id":"2008","value":"2008","total":8},{"id":"2007","value":"2007","total":5},{"id":"2006","value":"2006","total":2},{"id":"2005","value":"2005","total":2},{"id":"2002","value":"2002","total":1}],"institutions":[{"id":"Department of Mathematics, University of New Brunswick","value":"Department of Mathematics, University of New Brunswick","total":21},{"id":"Department of Mathematics, University of Mary Washington","value":"Department of Mathematics, University of Mary Washington","total":9},{"id":"Department of Electrical and Computer Engineering, University of Calgary","value":"Department of Electrical and Computer Engineering, University of Calgary","total":4},{"id":"Department of Mathematics and Statistics, University of New Brunswick","value":"Department of Mathematics and Statistics, University of New Brunswick","total":4},{"id":"Department of Computer Science, Eötvös Loránd University (ELTE)","value":"Department of Computer Science, Eötvös Loránd University (ELTE)","total":1},{"id":"Department of Mathematics and Statistics, Wright State University","value":"Department of Mathematics and Statistics, Wright State University","total":1},{"id":"Institut de Mathématiques de Luminy, Centre National de la Recherche Scientifique (CNRS)","value":"Institut de Mathématiques de Luminy, Centre National de la Recherche Scientifique (CNRS)","total":1},{"id":"Laboratoire d'Analyse, Géométrie et Applications (LAGA), Université de Paris VIII (Université Paris 8 Vincennes-Saint-Denis)","value":"Laboratoire d'Analyse, Géométrie et Applications (LAGA), Université de Paris VIII (Université Paris 8 Vincennes-Saint-Denis)","total":1},{"id":"Laboratory of Intelligent Computing and Signal Processing, Anhui University","value":"Laboratory of Intelligent Computing and Signal Processing, Anhui University","total":1},{"id":"Mathematisches Institut (I-Math), Universität Zürich","value":"Mathematisches Institut (I-Math), Universität Zürich","total":1},{"id":"School of Mathematics, Anhui University","value":"School of Mathematics, Anhui University","total":1},{"id":"University of New Brunswick","value":"University of New Brunswick","total":1},{"id":"École Nationale Supérieure de Télécommunications (Telecom ParisTech)","value":"École Nationale Supérieure de Télécommunications (Telecom ParisTech)","total":1}],"statuses":[]}

Search:

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Theory"},"volSlash":"N","isbn":null,"elementOrd":null},"translatedIssue":null},"book":null,"reviewer":{"public":true,"reviewers":[{"authId":889610,"rvrCode":85231,"name":"Jitman, Somphong"}]},"paging":{"paging":{"text":"5414--5418"},"translatedPaging":null},"counts":{"cited":2},"itemType":"Reviewed","articleUrl":"https://doi.org/10.1109/TIT.2020.2977319","openURL":{"imageLink":"http://www.lib.unb.ca/img/asin/res20x150.gif","targetLink":"https://unb.on.worldcat.org/atoztitles/link?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&rfr_id=info:sid/ams.org:MathSciNet&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft_id=info:doi/10.1109%2FTIT.2020.2977319&rft.aufirst=Tim&rft.auinit=TL&rft.auinit1=T&rft.auinitm=L&rft.aulast=Alderson&rft.genre=article&rft.issn=00189448&rft.title=Institute of Electrical and Electronics Engineers  Transactions on Information Theory&rft.atitle=On the weights of general MDS codes&rft.stitle=IEEE Trans  Inform  Theory&rft.volume=66&rft.date=2020&rft.spage=5414&rft.epage=5418&rft.pages=5414-5418&rft.issue=9&rft.jtitle=Institute of Electrical and Electronics Engineers  Transactions on Information Theory","textLink":""},"prePubl":null,"public":true},{"mrnumber":4019905,"titles":{"title":"$n$-dimensional optical orthogonal codes, bounds and optimal constructions","translatedTitle":null},"entryType":"J","primaryClass":{"code":"94B65","description":"Bounds on codes"},"authors":[{"id":758603,"name":"Alderson, T. L."}],"issue":{"issue":{"pubYear":2019,"pubYear2":null,"volume":"30","volume2":null,"volume3":null,"number":"5","journal":{"id":4449,"shortTitle":"Appl. Algebra Engrg. Comm. 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L."},{"id":1068150,"name":"Huntemann, Svenja"}],"issue":{"issue":{"pubYear":2014,"pubYear2":null,"volume":"6","volume2":null,"volume3":null,"number":"1","journal":{"id":7425,"shortTitle":"Atl. Electron. J. 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Siedlerchr commented 8 months ago

Thanks a lot, this is really helpful! Judging from the json, we need to add a new parser for the search results Steps for implementation

  1. Add a check if we have key all in response .https://github.com/JabRef/jabref/blob/2a7fc1aa0e2bc3edad3291e96a40087cded4da03/src/main/java/org/jabref/logic/importer/fetcher/MathSciNet.java#L118-L119
  2. Add a new else if for the search result case
  3. Create a new MathSciNetParser + Test using the provided json
  4. Parse the json and return bib entries
koppor commented 8 months ago

Older issue: https://github.com/JabRef/jabref/issues/10499

subhramit commented 8 months ago

Hi, I'd like to work on this. Would be great if I could be assigned!

github-actions[bot] commented 8 months ago

As a general advice for newcomers: check out Contributing for a start. Also, guidelines for setting up a local workspace is worth having a look at.

Feel free to ask here at GitHub, if you have any issue related questions. If you have questions about how to setup your workspace use JabRef's Gitter chat. Try to open a (draft) pull-request early on, so that people can see you are working on the issue and so that they can see the direction the pull request is heading towards. This way, you will likely receive valuable feedback.

subhramit commented 8 months ago

Hi, so I was writing the new parser. This might be a dumb question (I am new to this), but could you clarify to me the difference between facets and results, and whether both are a part of the results? I wasn't able to understand which json format out of the two should be parsed finally.

Siedlerchr commented 8 months ago

Hi, the search json as we use the search endpoint

Facets seem to be filter data, e.g. a list of all authors or journals in the search results you can then refine your search results by (at least on the website).

subhramit commented 8 months ago

@Siedlerchr got it, tysm!

subhramit commented 8 months ago

Another question. In the existing MathSciNet.java lines 121-122 (linked below), the following is present: jabref/src/main/java/org/jabref/logic/importer/fetcher/MathSciNet.java

String bibTexFormat = entriesArray.getJSONObject(i).getString("bibTexFormat");
entries.addAll(bibtexParser.parseEntries(bibTexFormat));

This assumes that there is a "bibTexFormat" field in the JSON object that contains a string representing the complete BibTeX entry. The value of that field is retrieved and parsed using the BibtexParser. However, if the JSON format doesn't include the bibTexFormat field or if the field doesn't contain a valid BibTeX string, these lines would fail to parse the entries correctly. And that is the case with the json for "search" as posted above by @TimAlderson . So correct me if I'm wrong, is a conversion mechanism needed for both the "all" case and the "results" case? Or is there a simpler way?

subhramit commented 8 months ago

(With reference to my last comment) This is one way I've thought of it (an example for "titles" in the json):

else if (element.has("results")) {
    JSONArray entriesArray = element.getJSONArray("results");
    for (int i = 0; i <entriesArray.length(); i++) {
        JsonNode entryNode = entriesArray.getJSONObject(i);
        if (entryNode.has("titles")) {
            String title = entryNode.getObject("titles").getString("title");
            BibEntry bibEntry = new BibEntry();
            bibEntry.setField(StandardField.TITLE, title);
            entries.add(bibEntry);
        }
    }
}

and similarly for the other keys(fields).

Siedlerchr commented 8 months ago

Yes, exactly. You need to write a new Parser/Convert for all fields present I suggest you create it as new Standalone Parser class. you can take some inspiration from CrossRef/BiodiversityLibrary/Lobid They all work with json https://github.com/JabRef/jabref/blob/403b8de60e0623cdafb47a9016f1bdf2dee6c112/src/main/java/org/jabref/logic/importer/fetcher/CrossRef.java#L121

subhramit commented 8 months ago

image I have been able to fix it :) I'll create a pull request soon after reading the formality guidelines. This will be my first one, thank you @Siedlerchr @koppor for the opportunity and help! I'm new into open source and already loving the community.

Siedlerchr commented 8 months ago

@subhramit Yeah! That sounds great! You're welcome! If something is unclear in the guides, just tell us or if you have any questions feel free to ask!