Error transferring Pubmed's articles to Zotero

Ana31770
Hi,

I'm currently having trouble transferring PubMed's articles to Zotero telling me there is ERROR with a file with MEDLINE/nbib and if this file is valid?
But even when I try to do it 1 by 1 file, it's the same error.

ID : 1754722243

Thanks in advance.
  • adamsmith
    could you provide any of the PMIDs for which the nbib doesn't import?
  • Ana31770
    These articles from this link :

    https://pubmed-ncbi-nlm-nih-gov-s.docadis.univ-tlse3.fr/?term=(%22sexual%20orientation*%22%20OR%20%22SO%22%20OR%20%22sexualit*%22%20OR%20%22sexu*%22%20OR%20%22sexual%20histor*%22%20OR%20%22medical%20history%20taking%22%20OR%20%22orientation%20disclos*%22%20OR%20%22gender%20identit*%22%20OR%20%22sex%20behavior*%22%20OR%20%22sexual%20activit*%22%20OR%20%22sexual%20behavior*%22%20OR%20%22Orientation*%20sexuelle*%22%20OR%20%22Sexual%20health%22%20OR%20%22sexual%20identit*%22%20OR%20%22sexual%20preference*%22)%20AND%20(%22recherche%22%20OR%20%22disclos*%22%20OR%20%22discuss*%22%20OR%20%22screen*%22%20OR%20%22abord*%22%20OR%20%22collect*%22%20OR%20%22identif*%22%20OR%20%22aware*%22%20OR%20%22communicat*%22%20OR%20%22understand*%22%20OR%20%22convers*%22%20OR%20%22know*%22%20OR%20%22question*%22%20OR%20%22search*%22)%20AND%20(%22general%20practic*%22%20OR%20%22GP%22%20OR%20%22GPs%22%20OR%20%22primary%20care*%22%20OR%20%22soins%20premiers%22%20OR%20%22family%20physician*%22%20OR%20%22physician*%22%20OR%20%22doctor*%22%20OR%20%22medecin*%20general*%22%20OR%20%22soin*%20ambulatoire*%22%20OR%20%22ambulatory%20care*%22%20OR%20%22outpatient%20care*%22%20OR%20%22Primary%20Healthcare%22%20OR%20%22Primary%20Health%20care%22)%20AND%20(%22LBGT*%22%20OR%20%22men%20who%20have%20sex%20with%20men%22%20OR%20%22lesbian*%22%20OR%20%22transgend*%22%20OR%20%22transsexual*%22%20OR%20%22homosexual*%22%20OR%20%22GLBT*%22%20OR%20%22Non%20Heterosexual*%22%20OR%20%22Non-Heterosexual*%22%20OR%20%22LGBTQ%22%20OR%20%22Sexual%20Minorit*%22%20OR%20%22Gay%22%20OR%20%22gays%22%20OR%20%22Women%20Who%20Have%20Sex%20With%20Women%22%20OR%20%22Bisexual*%22%20OR%20%22Gender%20Minorit*%22)&filter=datesearch.y_10&size=200
  • adamsmith
    Works in general (I tried with the first four items) - have you tried resetting your translators from the Advanced tab of the Zotero preferences?
    Have you opened the .nbib file with a text editor to make sure it looks roughly right?

    @dstillman -- anything in the error report?
  • Ana31770
    Error report :
    [JavaScript Error: "Error: Error(s) encountered during statement execution: FOREIGN KEY constraint failed [QUERY: INSERT OR REPLACE INTO itemTags (itemID, tagID, type) VALUES (?, ?, ?)] [PARAMS: 8698, 6648, 0] [ERROR: FOREIGN KEY constraint failed]" {file: "chrome://zotero/content/xpcom/db.js" line: 680}]

    [JavaScript Error: "Error 413 for item A25A5XT6 in Ma bibliothèque:

    ZoteroObjectUploadError: Abstract field value '[1] Abraham J. Gitlitz Memorial Lecture: Developme…' too long for item '13930963/A25A5XT6'"]

    [JavaScript Error: "Abstract field value '[1] Abraham J. Gitlitz Memorial Lecture: Developme…' too long for item '13930963/A25A5XT6'" {file: "chrome://zotero/content/xpcom/sync/syncEngine.js" line: 1357}]

    [JavaScript Error: "Made no progress during upload -- stopping" {file: "chrome://zotero/content/xpcom/sync/syncEngine.js" line: 1416}]

    [JavaScript Error: "Made no progress during upload -- stopping" {file: "chrome://zotero/content/xpcom/sync/syncEngine.js" line: 1416}]

    [JavaScript Error: "Error 413 for item A25A5XT6 in Ma bibliothèque:

    ZoteroObjectUploadError: Abstract field value '[1] Abraham J. Gitlitz Memorial Lecture: Developme…' too long for item '13930963/A25A5XT6'"]

    [JavaScript Error: "Abstract field value '[1] Abraham J. Gitlitz Memorial Lecture: Developme…' too long for item '13930963/A25A5XT6'" {file: "chrome://zotero/content/xpcom/sync/syncEngine.js" line: 1357}]

    [JavaScript Error: "Made no progress during upload -- stopping" {file: "chrome://zotero/content/xpcom/sync/syncEngine.js" line: 1416}]

    [JavaScript Error: "Made no progress during upload -- stopping" {file: "chrome://zotero/content/xpcom/sync/syncEngine.js" line: 1416}]

    [JavaScript Error: "The connection to wss://stream.zotero.org/ has terminated unexpectedly. Some data may have been transferred." {file: "chrome://zotero/content/xpcom/streamer.js" line: 155}]

    [JavaScript Error: "WebSocket connection closed: 1006 "]

    [JavaScript Error: "The connection to wss://stream.zotero.org/ has terminated unexpectedly. Some data may have been transferred." {file: "chrome://zotero/content/xpcom/streamer.js" line: 155}]

    [JavaScript Error: "WebSocket connection closed: 1006 "]

    [JavaScript Error: "Error 413 for item A25A5XT6 in Ma bibliothèque:

    ZoteroObjectUploadError: Abstract field value '[1] Abraham J. Gitlitz Memorial Lecture: Developme…' too long for item '13930963/A25A5XT6'"]

    [JavaScript Error: "Abstract field value '[1] Abraham J. Gitlitz Memorial Lecture: Developme…' too long for item '13930963/A25A5XT6'" {file: "chrome://zotero/content/xpcom/sync/syncEngine.js" line: 1357}]

    [JavaScript Error: "Made no progress during upload -- stopping" {file: "chrome://zotero/content/xpcom/sync/syncEngine.js" line: 1416}]

    [JavaScript Error: "Made no progress during upload -- stopping" {file: "chrome://zotero/content/xpcom/sync/syncEngine.js" line: 1416}]

    [JavaScript Error: "XML Parsing Error: syntax error
    Location: moz-nullprincipal:{125c7a1d-95e6-8942-8a9f-bdb7141ee323}
    Line Number 1, Column 1:" {file: "moz-nullprincipal:{125c7a1d-95e6-8942-8a9f-bdb7141ee323}" line: 1 column: 1 source: "PMID- 34665380"}]

    [JavaScript Error: "XML Parsing Error: syntax error
    Location: moz-nullprincipal:{15fe6e1d-ddd2-754b-b6ec-c923b2135277}
    Line Number 1, Column 1:" {file: "moz-nullprincipal:{15fe6e1d-ddd2-754b-b6ec-c923b2135277}" line: 1 column: 1 source: "PMID- 34665380"}]

    [JavaScript Error: "XML Parsing Error: syntax error
    Location: moz-nullprincipal:{6e4d8f5d-09cb-4a4a-b4f0-c7716ac86d88}
    Line Number 1, Column 1:" {file: "moz-nullprincipal:{6e4d8f5d-09cb-4a4a-b4f0-c7716ac86d88}" line: 1 column: 1 source: "PMID- 34665380"}]

    [JavaScript Error: "Error(s) encountered during statement execution: FOREIGN KEY constraint failed [QUERY: INSERT OR REPLACE INTO itemTags (itemID, tagID, type) VALUES (?, ?, ?)] [PARAMS: 8699, 6648, 0] [ERROR: FOREIGN KEY constraint failed]" {file: "chrome://zotero/content/xpcom/db.js" line: 680}]

    [JavaScript Error: "Error(s) encountered during statement execution: FOREIGN KEY constraint failed [QUERY: INSERT OR REPLACE INTO itemTags (itemID, tagID, type) VALUES (?, ?, ?)] [PARAMS: 8699, 6648, 0] [ERROR: FOREIGN KEY constraint failed]" {file: "chrome://zotero/content/xpcom/db.js" line: 680}]

    [JavaScript Error: "item.isRegularItem is not a function" {file: "chrome://zotero/content/xpcom/retractions.js" line: 841}]

    [JavaScript Error: "Error(s) encountered during statement execution: no such table: tmpSearchResults_zqXUD5c8 [QUERY: SELECT DISTINCT tagID || ':' || type FROM itemTags JOIN tags USING (tagID) WHERE 1 AND itemID IN (SELECT itemID FROM tmpSearchResults_zqXUD5c8 UNION SELECT itemID FROM itemAnnotations WHERE parentItemID IN (SELECT itemID FROM tmpSearchResults_zqXUD5c8)) ORDER BY name COLLATE NOCASE] [PARAMS: ] [ERROR: no such table: tmpSearchResults_zqXUD5c8]" {file: "chrome://zotero/content/xpcom/db.js" line: 782}]

    [JavaScript Error: "Error: Error(s) encountered during statement execution: FOREIGN KEY constraint failed [QUERY: INSERT OR REPLACE INTO itemTags (itemID, tagID, type) VALUES (?, ?, ?)] [PARAMS: 8699, 6648, 0] [ERROR: FOREIGN KEY constraint failed]" {file: "chrome://zotero/content/xpcom/db.js" line: 680}]

    version => 6.0.26, platform => MacIntel, oscpu => Intel Mac OS X 10.16, locale => fr-FR, appName => Zotero, appVersion => 6.0.26, extensions => Zotero Word for Mac Integration (6.0.6.SA.6.0.26, extension), Zotero LibreOffice Integration (6.0.4.SA.6.0.26, extension)
  • adamsmith
    Have you checked database integrity in the advanced tab of the Zotero preferences? Most of these errors are syncing related, not import-related, but this looks quite off
  • Ana31770
    I've done it again with every words and same results :

    ID : 655081345

    I don't know why it doesn't work, it's the first time.
    May it be because I don't have enough memory ? My Library - 265.1 MB over 300 MB
  • adamsmith
    Nothing to do with storage space. Did you check database integrity? I wasn't clear from your last reply
  • Ana31770
    Hi,

    I've just checked the data base integrity and everything is okay. So I don't understand ?
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