Upgrade StoragePubMed and Embase .nbib and .ris exports not importing into Zotero
ReportID - 2125938485
I have run a search in PubMed that has generated 900 hits. I have exported the references into an .nbib file, and attempted to import them into Zotero with file > import.
The error message is copied below:
[JavaScript Error: "Error(s) encountered during statement execution: FOREIGN KEY constraint failed [QUERY: INSERT OR REPLACE INTO itemTags (itemID, tagID, type) VALUES (?, ?, ?)] [PARAMS: 11818, 7731, 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: 11818, 7731, 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: Error(s) encountered during statement execution: FOREIGN KEY constraint failed [QUERY: INSERT OR REPLACE INTO itemTags (itemID, tagID, type) VALUES (?, ?, ?)] [PARAMS: 11818, 7731, 0] [ERROR: FOREIGN KEY constraint failed]" {file: "chrome://zotero/content/xpcom/db.js" line: 680}]
[JavaScript Error: "Error: Error(s) encountered during statement execution: FOREIGN KEY constraint failed [QUERY: INSERT OR REPLACE INTO itemTags (itemID, tagID, type) VALUES (?, ?, ?)] [PARAMS: 11818, 7731, 0] [ERROR: FOREIGN KEY constraint failed]" {file: "chrome://zotero/content/xpcom/db.js" line: 680}]
[JavaScript Error: "The connection to wss://stream.zotero.org/ has terminated unexpectedly. Some data may have been transferred."]
[JavaScript Error: "WebSocket connection closed: 1006 "]
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{f594aea5-62ac-4acf-80b0-8bf958470f66}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{f594aea5-62ac-4acf-80b0-8bf958470f66}" line: 1 column: 1 source: "PMID- 35998963"}]
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{3f2370f5-b2e5-4fc7-99ee-327a97bb2000}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{3f2370f5-b2e5-4fc7-99ee-327a97bb2000}" line: 1 column: 1 source: "PMID- 35998963"}]
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{dec76577-3630-4079-9d8b-31b3c62b39a8}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{dec76577-3630-4079-9d8b-31b3c62b39a8}" line: 1 column: 1 source: "PMID- 35998963"}]
[JavaScript Error: "Error(s) encountered during statement execution: FOREIGN KEY constraint failed [QUERY: INSERT OR REPLACE INTO itemTags (itemID, tagID, type) VALUES (?, ?, ?)] [PARAMS: 11819, 6530, 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: 11819, 6530, 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_ZFkjMXVA [QUERY: SELECT DISTINCT tagID || ':' || type FROM itemTags JOIN tags USING (tagID) WHERE 1 AND itemID IN (SELECT itemID FROM tmpSearchResults_ZFkjMXVA UNION SELECT itemID FROM itemAnnotations WHERE parentItemID IN (SELECT itemID FROM tmpSearchResults_ZFkjMXVA)) ORDER BY name COLLATE NOCASE] [PARAMS: ] [ERROR: no such table: tmpSearchResults_ZFkjMXVA]" {file: "chrome://zotero/content/xpcom/db.js" line: 782}]
[JavaScript Error: "Error(s) encountered during statement execution: no such table: tmpSearchResults_ZFkjMXVA [QUERY: SELECT DISTINCT tagID || ':' || type FROM itemTags JOIN tags USING (tagID) WHERE 1 AND itemID IN (SELECT itemID FROM tmpSearchResults_ZFkjMXVA UNION SELECT itemID FROM itemAnnotations WHERE parentItemID IN (SELECT itemID FROM tmpSearchResults_ZFkjMXVA)) AND type IN (?) AND tagID IN (1397, 2347, 2248) ORDER BY name COLLATE NOCASE] [PARAMS: 0] [ERROR: no such table: tmpSearchResults_ZFkjMXVA]" {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: 11819, 6530, 0] [ERROR: FOREIGN KEY constraint failed]" {file: "chrome://zotero/content/xpcom/db.js" line: 680}]
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{8f832e52-8543-4569-b81f-10163ce374de}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{8f832e52-8543-4569-b81f-10163ce374de}" line: 1 column: 1 source: "PMID- 35998963"}]
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{e5f08761-58bb-4d7b-9ddb-205d58d15fd6}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{e5f08761-58bb-4d7b-9ddb-205d58d15fd6}" line: 1 column: 1 source: "PMID- 35998963"}]
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{cc34b86f-bbb5-4bc3-a2ee-036e45327589}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{cc34b86f-bbb5-4bc3-a2ee-036e45327589}" line: 1 column: 1 source: "PMID- 35998963"}]
[JavaScript Error: "Error(s) encountered during statement execution: FOREIGN KEY constraint failed [QUERY: INSERT OR REPLACE INTO itemTags (itemID, tagID, type) VALUES (?, ?, ?)] [PARAMS: 11820, 6530, 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: 11820, 6530, 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_vGvSgZ8t [QUERY: SELECT DISTINCT tagID || ':' || type FROM itemTags JOIN tags USING (tagID) WHERE 1 AND itemID IN (SELECT itemID FROM tmpSearchResults_vGvSgZ8t UNION SELECT itemID FROM itemAnnotations WHERE parentItemID IN (SELECT itemID FROM tmpSearchResults_vGvSgZ8t)) ORDER BY name COLLATE NOCASE] [PARAMS: ] [ERROR: no such table: tmpSearchResults_vGvSgZ8t]" {file: "chrome://zotero/content/xpcom/db.js" line: 782}]
[JavaScript Error: "Error(s) encountered during statement execution: no such table: tmpSearchResults_vGvSgZ8t [QUERY: SELECT DISTINCT tagID || ':' || type FROM itemTags JOIN tags USING (tagID) WHERE 1 AND itemID IN (SELECT itemID FROM tmpSearchResults_vGvSgZ8t UNION SELECT itemID FROM itemAnnotations WHERE parentItemID IN (SELECT itemID FROM tmpSearchResults_vGvSgZ8t)) AND type IN (?) AND tagID IN (1397, 2347, 2248) ORDER BY name COLLATE NOCASE] [PARAMS: 0] [ERROR: no such table: tmpSearchResults_vGvSgZ8t]" {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: 11820, 6530, 0] [ERROR: FOREIGN KEY constraint failed]" {file: "chrome://zotero/content/xpcom/db.js" line: 680}]
version => 6.0.23, platform => Win32, oscpu => Windows NT 10.0; WOW64, locale => en-US, appName => Zotero, appVersion => 6.0.23, extensions => Zotero LibreOffice Integration (6.0.4.SA.6.0.23, extension), Zotero Word for Windows Integration (6.0.3.SA.6.0.23, extension)
I have run a search in PubMed that has generated 900 hits. I have exported the references into an .nbib file, and attempted to import them into Zotero with file > import.
The error message is copied below:
[JavaScript Error: "Error(s) encountered during statement execution: FOREIGN KEY constraint failed [QUERY: INSERT OR REPLACE INTO itemTags (itemID, tagID, type) VALUES (?, ?, ?)] [PARAMS: 11818, 7731, 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: 11818, 7731, 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: Error(s) encountered during statement execution: FOREIGN KEY constraint failed [QUERY: INSERT OR REPLACE INTO itemTags (itemID, tagID, type) VALUES (?, ?, ?)] [PARAMS: 11818, 7731, 0] [ERROR: FOREIGN KEY constraint failed]" {file: "chrome://zotero/content/xpcom/db.js" line: 680}]
[JavaScript Error: "Error: Error(s) encountered during statement execution: FOREIGN KEY constraint failed [QUERY: INSERT OR REPLACE INTO itemTags (itemID, tagID, type) VALUES (?, ?, ?)] [PARAMS: 11818, 7731, 0] [ERROR: FOREIGN KEY constraint failed]" {file: "chrome://zotero/content/xpcom/db.js" line: 680}]
[JavaScript Error: "The connection to wss://stream.zotero.org/ has terminated unexpectedly. Some data may have been transferred."]
[JavaScript Error: "WebSocket connection closed: 1006 "]
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{f594aea5-62ac-4acf-80b0-8bf958470f66}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{f594aea5-62ac-4acf-80b0-8bf958470f66}" line: 1 column: 1 source: "PMID- 35998963"}]
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{3f2370f5-b2e5-4fc7-99ee-327a97bb2000}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{3f2370f5-b2e5-4fc7-99ee-327a97bb2000}" line: 1 column: 1 source: "PMID- 35998963"}]
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{dec76577-3630-4079-9d8b-31b3c62b39a8}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{dec76577-3630-4079-9d8b-31b3c62b39a8}" line: 1 column: 1 source: "PMID- 35998963"}]
[JavaScript Error: "Error(s) encountered during statement execution: FOREIGN KEY constraint failed [QUERY: INSERT OR REPLACE INTO itemTags (itemID, tagID, type) VALUES (?, ?, ?)] [PARAMS: 11819, 6530, 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: 11819, 6530, 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_ZFkjMXVA [QUERY: SELECT DISTINCT tagID || ':' || type FROM itemTags JOIN tags USING (tagID) WHERE 1 AND itemID IN (SELECT itemID FROM tmpSearchResults_ZFkjMXVA UNION SELECT itemID FROM itemAnnotations WHERE parentItemID IN (SELECT itemID FROM tmpSearchResults_ZFkjMXVA)) ORDER BY name COLLATE NOCASE] [PARAMS: ] [ERROR: no such table: tmpSearchResults_ZFkjMXVA]" {file: "chrome://zotero/content/xpcom/db.js" line: 782}]
[JavaScript Error: "Error(s) encountered during statement execution: no such table: tmpSearchResults_ZFkjMXVA [QUERY: SELECT DISTINCT tagID || ':' || type FROM itemTags JOIN tags USING (tagID) WHERE 1 AND itemID IN (SELECT itemID FROM tmpSearchResults_ZFkjMXVA UNION SELECT itemID FROM itemAnnotations WHERE parentItemID IN (SELECT itemID FROM tmpSearchResults_ZFkjMXVA)) AND type IN (?) AND tagID IN (1397, 2347, 2248) ORDER BY name COLLATE NOCASE] [PARAMS: 0] [ERROR: no such table: tmpSearchResults_ZFkjMXVA]" {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: 11819, 6530, 0] [ERROR: FOREIGN KEY constraint failed]" {file: "chrome://zotero/content/xpcom/db.js" line: 680}]
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{8f832e52-8543-4569-b81f-10163ce374de}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{8f832e52-8543-4569-b81f-10163ce374de}" line: 1 column: 1 source: "PMID- 35998963"}]
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{e5f08761-58bb-4d7b-9ddb-205d58d15fd6}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{e5f08761-58bb-4d7b-9ddb-205d58d15fd6}" line: 1 column: 1 source: "PMID- 35998963"}]
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{cc34b86f-bbb5-4bc3-a2ee-036e45327589}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{cc34b86f-bbb5-4bc3-a2ee-036e45327589}" line: 1 column: 1 source: "PMID- 35998963"}]
[JavaScript Error: "Error(s) encountered during statement execution: FOREIGN KEY constraint failed [QUERY: INSERT OR REPLACE INTO itemTags (itemID, tagID, type) VALUES (?, ?, ?)] [PARAMS: 11820, 6530, 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: 11820, 6530, 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_vGvSgZ8t [QUERY: SELECT DISTINCT tagID || ':' || type FROM itemTags JOIN tags USING (tagID) WHERE 1 AND itemID IN (SELECT itemID FROM tmpSearchResults_vGvSgZ8t UNION SELECT itemID FROM itemAnnotations WHERE parentItemID IN (SELECT itemID FROM tmpSearchResults_vGvSgZ8t)) ORDER BY name COLLATE NOCASE] [PARAMS: ] [ERROR: no such table: tmpSearchResults_vGvSgZ8t]" {file: "chrome://zotero/content/xpcom/db.js" line: 782}]
[JavaScript Error: "Error(s) encountered during statement execution: no such table: tmpSearchResults_vGvSgZ8t [QUERY: SELECT DISTINCT tagID || ':' || type FROM itemTags JOIN tags USING (tagID) WHERE 1 AND itemID IN (SELECT itemID FROM tmpSearchResults_vGvSgZ8t UNION SELECT itemID FROM itemAnnotations WHERE parentItemID IN (SELECT itemID FROM tmpSearchResults_vGvSgZ8t)) AND type IN (?) AND tagID IN (1397, 2347, 2248) ORDER BY name COLLATE NOCASE] [PARAMS: 0] [ERROR: no such table: tmpSearchResults_vGvSgZ8t]" {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: 11820, 6530, 0] [ERROR: FOREIGN KEY constraint failed]" {file: "chrome://zotero/content/xpcom/db.js" line: 680}]
version => 6.0.23, platform => Win32, oscpu => Windows NT 10.0; WOW64, locale => en-US, appName => Zotero, appVersion => 6.0.23, extensions => Zotero LibreOffice Integration (6.0.4.SA.6.0.23, extension), Zotero Word for Windows Integration (6.0.3.SA.6.0.23, extension)
and after restarting 2078476288
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{96d5e814-23ab-4c17-a61c-e79fbe7181a8}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{96d5e814-23ab-4c17-a61c-e79fbe7181a8}" line: 1 column: 1 source: "PMID- 37203318"}]
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{821c7f1e-b3a0-4c3f-b48d-5795ddad027c}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{821c7f1e-b3a0-4c3f-b48d-5795ddad027c}" line: 1 column: 1 source: "PMID- 37203318"}]
[JavaScript Error: "XML Parsing Error: syntax error
Location: moz-nullprincipal:{b5067265-5a54-4c22-80e3-89e004e398f4}
Line Number 1, Column 1:" {file: "moz-nullprincipal:{b5067265-5a54-4c22-80e3-89e004e398f4}" line: 1 column: 1 source: "PMID- 37203318"}]
[JavaScript Error: "Item 5629 not found" {file: "chrome://zotero/content/xpcom/data/items.js" line: 804}]
[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_ku28de4H [QUERY: SELECT DISTINCT tagID || ':' || type FROM itemTags JOIN tags USING (tagID) WHERE 1 AND itemID IN (SELECT itemID FROM tmpSearchResults_ku28de4H UNION SELECT itemID FROM itemAnnotations WHERE parentItemID IN (SELECT itemID FROM tmpSearchResults_ku28de4H)) AND type IN (?) AND tagID IN V E R Y L O N G L I S T O F N U M B E R S)
ORDER BY name COLLATE NOCASE] [PARAMS: 0] [ERROR: no such table: tmpSearchResults_ku28de4H]" {file: "chrome://zotero/content/xpcom/db.js" line: 782}]
[JavaScript Error: "Error: Item 5629 not found" {file: "chrome://zotero/content/xpcom/data/items.js" line: 804}]
[JavaScript Error: "operation timed out"]
[JavaScript Error: "operation timed out"]
version => 6.0.26, platform => Win32, oscpu => Windows NT 10.0; WOW64, locale => de, appName => Zotero, appVersion => 6.0.26, extensions => Zotero LibreOffice Integration (6.0.4.SA.6.0.26, extension), Zotero Word for Windows Integration (6.0.3.SA.6.0.26, extension)
https://paperpile.com/t/pmid-to-ris-converter/
Zotero was able to read the resulting RIS document.
If you're trying to save from PubMed or PubMed Central, all you need to do is use the Save to Zotero button in your browser toolbar, as on any other site.
Importing an .nbib or .ris file should also work, and if it's not for you, you should start a new thread and provide a Debug ID for Zotero startup through reproducing that, using the "Restart with Logging Enabled…" option.
Zotero can also import a list of PMIDs — which you can get from PubMed — via its "Add Item by Identifier" tool. I'm not sure anyone has ever asked us for PMCID import. Again, though, there shouldn't be any need for either.