Problem after upgrading to OJS 3.2.0-2. Crossref Plugin and another errors

Software Support
1

Hi,
I just upgraded to the current version 3.2.0-1 and then, upgraded to 3.2.0.2.

The Crossref XML Export Plugin is not showing any articles. It keeps running and shows nothing…

05
05810×641 39.6 KB

Chrome Inspect console:

jquery.min.js?v=3.2.0.2:2 GET http://periodicos.ufes.br/geografares/$$$call$$$/grid/pub-ids/pub-id-export-submissions-list-grid/fetch-grid?plugin=crossref&category=importexport&_=1586727566538 500 (Internal Server Error)
send @ jquery.min.js?v=3.2.0.2:2
ajax @ jquery.min.js?v=3.2.0.2:2
w. @ jquery.min.js?v=3.2.0.2:2
a.pkp.controllers.UrlInDivHandler.reload @ pkp.min.js?v=3.2.0.2:202
a.pkp.controllers.UrlInDivHandler @ pkp.min.js?v=3.2.0.2:202
a.pkp.classes.ObjectProxy.parent @ pkp.min.js?v=3.2.0.2:124
b @ pkp.min.js?v=3.2.0.2:122
a.pkp.classes.Helper.objectFactory @ pkp.min.js?v=3.2.0.2:120
(anonymous) @ pkp.min.js?v=3.2.0.2:429
each @ jquery.min.js?v=3.2.0.2:2
each @ jquery.min.js?v=3.2.0.2:2
a.fn.pkpHandler @ pkp.min.js?v=3.2.0.2:429
(anonymous) @ CrossRefExportPlugin:196
l @ jquery.min.js?v=3.2.0.2:2
c @ jquery.min.js?v=3.2.0.2:2
setTimeout (async)
(anonymous) @ jquery.min.js?v=3.2.0.2:2
u @ jquery.min.js?v=3.2.0.2:2
fireWith @ jquery.min.js?v=3.2.0.2:2
fire @ jquery.min.js?v=3.2.0.2:2
u @ jquery.min.js?v=3.2.0.2:2
fireWith @ jquery.min.js?v=3.2.0.2:2
ready @ jquery.min.js?v=3.2.0.2:2
_ @ jquery.min.js?v=3.2.0.2:clock1230:

In httpd error_log file:

Uncaught Error: Call to a member function getData() on null in /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php:215\nStack trace:\n#0 [internal function]: SearchHandler->{closure}(NULL)\n#1 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(216): array_map(Object(Closure), Array)\n#2 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPRouter.inc.php(391): SearchHandler->authors(Array, Object(Request))\n#3 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPPageRouter.inc.php(231): PKPRouter->_authorizeInitializeAndCallRequest(Array, Object(Request), Array, false)\n#4 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/Dispatcher.inc.php(143): PKPPageRouter->route(Object(Request))\n#5 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPApplication.inc.php(278): Dispatcher->dispatch(Object(Request))\n#6 /var/www/ojs-3.2.0-2/index.php(68): PKPApplication->execute()\n#7 {main}\n thrown in /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php on line 215
PHP Fatal error: Uncaught Exception: DB Error: ERROR: column “p.version” must appear in the GROUP BY clause or be used in an aggregate function\nLINHA 1: …sion_id" where “s”.“context_id” in ( $1) order by “p”.“versi…\n ^ Query: select MIN(p.date_published), MAX(p.date_published) from “publications” as “p” left join “submissions” as “s” on “s”.“submission_id” = “p”.“submission_id” where “s”.“context_id” in (?) order by “p”.“version” asc in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php:703\nStack trace:\n#0 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php(103): DAO->handleError(Object(ADODB_postgres8), ‘select MIN(p.da…’)\n#1 /var/www/ojs-3.2.0-2/lib/pkp/classes/services/PKPPublicationService.inc.php(256): DAO->retrieve(‘select MIN(p.da…’, Array)\n#2 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(93): PKP\Services\PKPPublicationService->getDateBoundaries(Array)\n#3 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(146): SearchHandler->_assign in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703
Uncaught Error: Call to a member function getData() on null in /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php:215\nStack trace:\n#0 [internal function]: SearchHandler->{closure}(NULL)\n#1 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(216): array_map(Object(Closure), Array)\n#2 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPRouter.inc.php(391): SearchHandler->authors(Array, Object(Request))\n#3 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPPageRouter.inc.php(231): PKPRouter->_authorizeInitializeAndCallRequest(Array, Object(Request), Array, false)\n#4 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/Dispatcher.inc.php(143): PKPPageRouter->route(Object(Request))\n#5 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPApplication.inc.php(278): Dispatcher->dispatch(Object(Request))\n#6 /var/www/ojs-3.2.0-2/index.php(68): PKPApplication->execute()\n#7 {main}\n thrown in /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php on line 215
PHP Fatal error: Uncaught Exception: DB Error: ERROR: null value in column “submission_id” violates not-null constraint\nDETALHE: Failing row contains (51367, null, 0, marceloaugusti@bol.com.br, 1119, 1, 24779). Query: INSERT INTO authors (email, include_in_browse, publication_id, user_group_id) VALUES (?, ?, ?, ?) in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php:703\nStack trace:\n#0 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php(231): DAO->handleError(Object(ADODB_postgres8), ‘INSERT INTO aut…’)\n#1 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/SchemaDAO.inc.php(79): DAO->update(‘INSERT INTO aut…’, Array)\n#2 /var/www/ojs-3.2.0-2/lib/pkp/classes/submission/form/PKPSubmissionSubmitStep1Form.inc.php(382): SchemaDAO->insertObject(Object(Author))\n#3 /var/www/ojs-3.2.0-2/lib/pkp/pages/submission/PKPSubmissionHandler.inc.php(171): PKPSubmissionSubmitStep1Form->execute()\n#4 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPRouter.inc.php(391): PKPSubmissionHandler->saveStep(Array, Object(Request))\n#5 /var/www/ojs-3.2.0-2/lib/pkp/ in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703, referer: http://periodicos.ufes.br/dimensoes/submission/wizard
PHP Fatal error: Uncaught Exception: DB Error: ERROR: column “p.version” must appear in the GROUP BY clause or be used in an aggregate function\nLINHA 1: …sion_id” where “s”.“context_id” in ( $1) order by “p”.“versi…\n ^ Query: select MIN(p.date_published), MAX(p.date_published) from “publications” as “p” left join “submissions” as “s” on “s”.“submission_id” = “p”.“submission_id” where “s”.“context_id” in (?) order by “p”.“version” asc in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php:703\nStack trace:\n#0 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php(103): DAO->handleError(Object(ADODB_postgres8), ‘select MIN(p.da…’)\n#1 /var/www/ojs-3.2.0-2/lib/pkp/classes/services/PKPPublicationService.inc.php(256): DAO->retrieve(‘select MIN(p.da…’, Array)\n#2 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(93): PKP\Services\PKPPublicationService->getDateBoundaries(Array)\n#3 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(146): SearchHandler->_assign in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703
PHP Fatal error: Uncaught Exception: DB Error: ERROR: column “p.date_published” must appear in the GROUP BY clause or be used in an aggregate function\nLINHA 6: ORDER BY p.date_published DESC, s.submission_id DESC LIMI…\n ^ Query: SELECT\ts.\n\t\t\tFROM\tsubmissions s\n\t\t\t\tLEFT JOIN publications p ON s.current_publication_id = p.publication_id\n\t\t\t\tLEFT JOIN publication_settings ps ON p.publication_id = ps.publication_id LEFT JOIN publication_settings pspidt ON (p.publication_id = pspidt.publication_id) WHERE\ts.status = ?\n\t\t\t\tAND s.context_id = ? AND pspidt.setting_name = ? AND pspidt.setting_value IS NOT NULL GROUP BY s.submission_id\n\t\t\tORDER BY p.date_published DESC, s.submission_id DESC in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php:703\nStack trace:\n#0 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php(197): DAO->handleError(Object(ADODB_postgres8), 'SELECT\ts.\n\t\t\tF…')\n#1 /var/www/ojs-3.2.0-2/lib/pkp/classes/submission/PKPSubmissionDAO.inc.php(388): DAO->retrieveRange('SELECT\ts.\n\t\t\tF. in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703, referer: http://periodicos.ufes.br/geografares/management/importexport/plugin/CrossRefExportPlugin
ojs3: Sem objetos selecionados., referer: http://periodicos.ufes.br/geografares/management/importexport/plugin/CrossRefExportPlugin
PHP Fatal error: Uncaught Exception: DB Error: ERROR: column “p.date_published” must appear in the GROUP BY clause or be used in an aggregate function\nLINHA 6: ORDER BY p.date_published DESC, s.submission_id DESC LIMI…\n ^ Query: SELECT\ts.\n\t\t\tFROM\tsubmissions s\n\t\t\t\tLEFT JOIN publications p ON s.current_publication_id = p.publication_id\n\t\t\t\tLEFT JOIN publication_settings ps ON p.publication_id = ps.publication_id LEFT JOIN publication_settings pspidt ON (p.publication_id = pspidt.publication_id) WHERE\ts.status = ?\n\t\t\t\tAND s.context_id = ? AND pspidt.setting_name = ? AND pspidt.setting_value IS NOT NULL GROUP BY s.submission_id\n\t\t\tORDER BY p.date_published DESC, s.submission_id DESC in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php:703\nStack trace:\n#0 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php(197): DAO->handleError(Object(ADODB_postgres8), 'SELECT\ts.\n\t\t\tF…')\n#1 /var/www/ojs-3.2.0-2/lib/pkp/classes/submission/PKPSubmissionDAO.inc.php(388): DAO->retrieveRange('SELECT\ts.\n\t\t\tF. in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703, referer: http://periodicos.ufes.br/geografares/management/importexport/plugin/CrossRefExportPlugin
ojs3: 404 Not Found, referer: http://publicacoes.ufes.br/
PHP Fatal error: Uncaught Exception: DB Error: ERROR: column “p.version” must appear in the GROUP BY clause or be used in an aggregate function\nLINHA 1: …sion_id” where “s”.“context_id” in ( $1) order by “p”.“versi…\n ^ Query: select MIN(p.date_published), MAX(p.date_published) from “publications” as “p” left join “submissions” as “s” on “s”.“submission_id” = “p”.“submission_id” where “s”.“context_id” in (?) order by “p”.“version” asc in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php:703\nStack trace:\n#0 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php(103): DAO->handleError(Object(ADODB_postgres8), ‘select MIN(p.da…’)\n#1 /var/www/ojs-3.2.0-2/lib/pkp/classes/services/PKPPublicationService.inc.php(256): DAO->retrieve(‘select MIN(p.da…’, Array)\n#2 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(93): PKP\Services\PKPPublicationService->getDateBoundaries(Array)\n#3 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(146): SearchHandler->_assign in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703
ojs3: 404 Not Found
PHP Fatal error: Uncaught Error: Call to a member function getData() on null in /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php:215\nStack trace:\n#0 [internal function]: SearchHandler->{closure}(NULL)\n#1 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(216): array_map(Object(Closure), Array)\n#2 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPRouter.inc.php(391): SearchHandler->authors(Array, Object(Request))\n#3 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPPageRouter.inc.php(231): PKPRouter->_authorizeInitializeAndCallRequest(Array, Object(Request), Array, false)\n#4 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/Dispatcher.inc.php(143): PKPPageRouter->route(Object(Request))\n#5 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPApplication.inc.php(278): Dispatcher->dispatch(Object(Request))\n#6 /var/www/ojs-3.2.0-2/index.php(68): PKPApplication->execute()\n#7 {main}\n thrown in /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php on line 215
PHP Fatal error: Uncaught Exception: DB Error: ERROR: column “p.date_published” must appear in the GROUP BY clause or be used in an aggregate function\nLINE 6: ORDER BY p.date_published DESC, s.submission_id DESC LIMI…\n ^ Query: SELECT\ts.\n\t\t\tFROM\tsubmissions s\n\t\t\t\tLEFT JOIN publications p ON s.current_publication_id = p.publication_id\n\t\t\t\tLEFT JOIN publication_settings ps ON p.publication_id = ps.publication_id LEFT JOIN publication_settings pspidt ON (p.publication_id = pspidt.publication_id) WHERE\ts.status = ?\n\t\t\t\tAND s.context_id = ? AND pspidt.setting_name = ? AND pspidt.setting_value IS NOT NULL GROUP BY s.submission_id\n\t\t\tORDER BY p.date_published DESC, s.submission_id DESC in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php:703\nStack trace:\n#0 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php(197): DAO->handleError(Object(ADODB_postgres8), 'SELECT\ts.\n\t\t\tF…')\n#1 /var/www/ojs-3.2.0-2/lib/pkp/classes/submission/PKPSubmissionDAO.inc.php(388): DAO->retrieveRange('SELECT\ts.*\n\t\t\tF… in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703, referer: http://periodicos.ufes.br/geografares/management/importexport/plugin/CrossRefExportPlugin
HP Fatal error: Uncaught Error: Call to a member function getData() on null in /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php:215\nStack trace:\n#0 [internal function]: SearchHandler->{closure}(NULL)\n#1 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(216): array_map(Object(Closure), Array)\n#2 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPRouter.inc.php(391): SearchHandler->authors(Array, Object(Request))\n#3 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPPageRouter.inc.php(231): PKPRouter->_authorizeInitializeAndCallRequest(Array, Object(Request), Array, false)\n#4 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/Dispatcher.inc.php(143): PKPPageRouter->route(Object(Request))\n#5 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPApplication.inc.php(278): Dispatcher->dispatch(Object(Request))\n#6 /var/www/ojs-3.2.0-2/index.php(68): PKPApplication->execute()\n#7 {main}\n thrown in /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php on line 215
PHP Warning: Division by zero in /var/www/ojs-3.2.0-2/lib/pkp/classes/core/ArrayItemIterator.inc.php on line 134, referer: https://periodicos.ufes.br/argumentum/submissions
PHP Warning: Division by zero in /var/www/ojs-3.2.0-2/lib/pkp/classes/core/ArrayItemIterator.inc.php on line 134, referer: https://periodicos.ufes.br/argumentum/submissions
PHP Warning: Division by zero in /var/www/ojs-3.2.0-2/lib/pkp/classes/core/ArrayItemIterator.inc.php on line 134, referer: https://periodicos.ufes.br/argumentum/workflow/index/27927/3
PHP Warning: Division by zero in /var/www/ojs-3.2.0-2/lib/pkp/classes/core/ArrayItemIterator.inc.php on line 134, referer: https://periodicos.ufes.br/argumentum/workflow/index/27927/3
HP Fatal error: Uncaught Exception: DB Error: ERROR: column “p.version” must appear in the GROUP BY clause or be used in an aggregate function\nLINHA 1: …sion_id” where “s”.“context_id” in ( $1) order by “p”.“versi…\n ^ Query: select MIN(p.date_published), MAX(p.date_published) from “publications” as “p” left join “submissions” as “s” on “s”.“submission_id” = “p”.“submission_id” where “s”.“context_id” in (?) order by “p”.“version” asc in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php:703\nStack trace:\n#0 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php(103): DAO->handleError(Object(ADODB_postgres8), ‘select MIN(p.da…’)\n#1 /var/www/ojs-3.2.0-2/lib/pkp/classes/services/PKPPublicationService.inc.php(256): DAO->retrieve(‘select MIN(p.da…’, Array)\n#2 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(93): PKP\Services\PKPPublicationService->getDateBoundaries(Array)\n#3 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(146): SearchHandler->_assign in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703
HP Fatal error: Uncaught Exception: DB Error: ERROR: column “p.version” must appear in the GROUP BY clause or be used in an aggregate function\nLINHA 1: …sion_id” where “s”.“context_id” in ( $1) order by “p”.“versi…\n ^ Query: select MIN(p.date_published), MAX(p.date_published) from “publications” as “p” left join “submissions” as “s” on “s”.“submission_id” = “p”.“submission_id” where “s”.“context_id” in (?) order by “p”.“version” asc in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php:703\nStack trace:\n#0 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php(103): DAO->handleError(Object(ADODB_postgres8), ‘select MIN(p.da…’)\n#1 /var/www/ojs-3.2.0-2/lib/pkp/classes/services/PKPPublicationService.inc.php(256): DAO->retrieve(‘select MIN(p.da…’, Array)\n#2 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(93): PKP\Services\PKPPublicationService->getDateBoundaries(Array)\n#3 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(146): SearchHandler->_assign in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703
ojs3: 404 Not Found, referer: http://periodicos.ufes.br/machadiana/help/view/editorial/topic/000015
PHP Fatal error: Uncaught Exception: DB Error: ERROR: column “p.version” must appear in the GROUP BY clause or be used in an aggregate function\nLINHA 1: …sion_id” where “s”.“context_id” in ( $1) order by “p”."versi…\n ^ Query: select MIN(p.date_published), MAX(p.date_published) from “publications” as “p” left join “submissions” as “s” on “s”.“submission_id” = “p”.“submission_id” where “s”.“context_id” in (?) order by “p”.“version” asc in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php:703\nStack trace:\n#0 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php(103): DAO->handleError(Object(ADODB_postgres8), ‘select MIN(p.da…’)\n#1 /var/www/ojs-3.2.0-2/lib/pkp/classes/services/PKPPublicationService.inc.php(256): DAO->retrieve(‘select MIN(p.da…’, Array)\n#2 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(93): PKP\Services\PKPPublicationService->getDateBoundaries(Array)\n#3 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(146): SearchHandler->_assign in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703

My system information:

OS platform: Linux
PHP version: 7.2.22
Apache version: Apache/2.4.6 (CentOS) OpenSSL/1.0.2k-fips PHP/7.2.22
Database driver: postgres
Database server version: PostgreSQL 9.2.24 on x86_64-redhat-linux-gnu, compiled by gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-28), 64-bit|

could you help me?

2

Hi @Adriano_Jose,

There are several errors here:

I found two minor PostgreSQL incompatibilties (it seems that some versions of PostgreSQL are more picky than others); these are filed here and there’s a patch: Resolve SQL errors with picky PostgreSQL servers · Issue #5735 · pkp/pkp-lib · GitHub

There may be more happening, but patching that will at least clean up your error log (and should fix the CrossRef export listing).

Regards,
Alec Smecher
Public Knowledge Project Team

1 Like
3

Thanks for your response.
I aplied the pacth and I am now encountering the following error:

HP Fatal error: Uncaught Exception: DB Error: ERROR: operator does not exist: bigint = text\nLINHA 11:JOIN issues i ON (i.issue_id = ps.setting_value)\n ^\nDICA: No operator matches the given name and argument type(s). You might need to add explicit type casts. Query: SELECT\n\t\t\t\to.submission_id,\n\t\t\t\tMAX(s.context_id) AS journal_id,\n\t\t\t\tMAX(i.date_published) AS i_pub,\n\t\t\t\tMAX(p.date_published) AS s_pub,\n\t\t\t\tCOUNT(*) AS count\n\t\t\tFROM\n\t\t\t\tsubmissions s\n\t\t\t\tJOIN publications p ON (p.publication_id = s.current_publication_id)\n\t\t\t\tJOIN publication_settings ps ON (ps.publication_id = p.publication_id AND ps.setting_name=‘issueId’)\n\t\t\t\tJOIN issues i ON (i.issue_id = ps.setting_value)\n\t\t\t\tJOIN submission_search_objects o ON (s.submission_id = o.submission_id)\n\t\t\t\tNATURAL JOIN submission_search_object_keywords o0 NATURAL JOIN submission_search_keyword_list k0\n\t\t\tWHERE\n\t\t\t\ts.status = 3 AND\n\t\t\t\ti.published = 1 AND k0.keyword_text = ? AND (o.type & ?) != 0 AND i.journal_id = ?\n\t\t\tGROUP BY o.s in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703, referer: https://periodicos.ufes.br/contextoslinguisticos/search/search?csrfToken=b800328dd3220ae5191459cd4963c7fd&query=

Regards,
Adriano Moreno

4

Hi @Adriano_Jose,

Phew, yet another of these… You can explicitly add a cast to string for the numeric column by making this change: PostgreSQL "operator does not exist" · Issue #5741 · pkp/pkp-lib · GitHub

Regards,
Alec Smecher
Public Knowledge Project Team

1 Like
5

Hi @asmecher,
I really appreciate what you have been doing and I am very grateful. The resolution of problems is also flowing well, with each step I feel that the system is becoming more stable.

Now I found this error:

[php7: error] [pid 1465] [client 179.252.163.226:539033] PHP Fatal error: Uncaught Exception: DB Error: ERROR: null value in column “submission_id” violates not-null constraint \ n DETAIL: Failing row contains (51723, null, 0, zorayona@gmail.com, 1459, 1, 25128). Query: INSERT INTO authors (email, include_in_browse, publication_id, user_group_id) VALUES (?,?,?,?) In /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc. php: 703 \ nStack trace: \ n # 0 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php(231): DAO-> handleError (Object (ADODB_postgres8) , ‘INSERT INTO aut …’) \ n # 1 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/SchemaDAO.inc.php(79): DAO-> update (’ INSERT INTO aut … ', Array) \ n # 2 /var/www/ojs-3.2.0-2/lib/pkp/classes/submission/form/PKPSubmissionSubmitStep1Form.inc.php(382): SchemaDAO-> insertObject (Object (Author)) \ n # 3 /var/www/ojs-3.2.0-2/lib/pkp/pages/submission/PKPSubmissionHandler.inc.php(171): PKPSubmissionSubmitStep1Form-> execute () \ n # 4 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPRouter.inc.php(391): PKPSubmissionHandler-> saveStep (Array, Object (Request)) \ n # 5 / var / www /ojs-3.2.0-2/lib/pkp/classes in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703, referer: http: / /periodicos.ufes.br/temporalis/submission/wizard

In addition, when I use the Crossref plugin, the following message appears when trying to make a deposit, it shows this message:

Notification
Registration was not fully successful! The DOI registration server returned an error.

The xml file:

48
48877×776 16.3 KB

I don’t know if there is anything related to this, but when we try to publish the article, the contributors are not appearing on the list:

44
441187×543 46.8 KB

but the author made the submission and appears in the first stage:

05
051190×700 134 KB

Do you think this is connected?

6

I found a few more different errors:

[cgi:error] [pid 8953] [client 185.132.53.103:58326] script not found or unable to stat: /var/www/cgi-bin

PHP Fatal error: Uncaught Exception: DB Error: ERROR: operator does not exist: text = bigint\nLINHA 31: …N (ppss.setting_name = $7 AND ppss.setting_value = i.issue_…\n ^\nDICA: No operator matches the given name and argument type(s). You might need to add explicit type casts. Query: SELECT a.*, ug.show_title, p.locale,\n\t\t\t\tCOALESCE(agl.setting_value, agpl.setting_value) AS author_given,\n\t\t\t\tCASE WHEN agl.setting_value <> ‘’ THEN afl.setting_value ELSE afpl.setting_value END AS author_family\n\t\t\tFROM\tauthors a\n\t\t\t\tJOIN user_groups ug ON (a.user_group_id = ug.user_group_id)\n\t\t\t\tJOIN publications p ON (p.publication_id = a.publication_id)\n\t\t\t\tJOIN submissions s ON (s.current_publication_id = p.publication_id)\n\t\t\t\tLEFT JOIN author_settings agl ON (a.author_id = agl.author_id AND agl.setting_name = ? AND agl.locale = ?)\n\t\t\t\tLEFT JOIN author_settings agpl ON (a.author_id = agpl.author_id AND agpl.setting_name = ? AND agpl.locale = p.locale)\n\t\t\t\tLEFT JOIN author_settin in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703

PHP Fatal error: Uncaught Error: Call to a member function getData() on null in /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php:215\nStack trace:\n#0 [internal function]: SearchHandler->{closure}(NULL)\n#1 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(216): array_map(Object(Closure), Array)\n#2 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPRouter.inc.php(391): SearchHandler->authors(Array, Object(Request))\n#3 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPPageRouter.inc.php(231): PKPRouter->_authorizeInitializeAndCallRequest(Array, Object(Request), Array, false)\n#4 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/Dispatcher.inc.php(143): PKPPageRouter->route(Object(Request))\n#5 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPApplication.inc.php(278): Dispatcher->dispatch(Object(Request))\n#6 /var/www/ojs-3.2.0-2/index.php(68): PKPApplication->execute()\n#7 {main}\n thrown in /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php on line 215

PHP Fatal error: Uncaught Exception: DB Error: ERROR: syntax error at or near “AND”\nLINHA 71: AND (LOWER(asf0.setting_value) LIKE LOWER( $8) OR LOWE…\n ^ Query: SELECT a.*, ug.show_title, p.locale,\n\t\t\t\tCOALESCE(agl.setting_value, agpl.setting_value) AS author_given,\n\t\t\t\tCASE WHEN agl.setting_value <> ‘’ THEN afl.setting_value ELSE afpl.setting_value END AS author_family\n\t\t\tFROM\tauthors a\n\t\t\t\tJOIN user_groups ug ON (a.user_group_id = ug.user_group_id)\n\t\t\t\tJOIN publications p ON (p.publication_id = a.publication_id)\n\t\t\t\tJOIN submissions s ON (s.current_publication_id = p.publication_id)\n\t\t\t\tLEFT JOIN author_settings agl ON (a.author_id = agl.author_id AND agl.setting_name = ? AND agl.locale = ?)\n\t\t\t\tLEFT JOIN author_settings agpl ON (a.author_id = agpl.author_id AND agpl.setting_name = ? AND agpl.locale = p.locale)\n\t\t\t\tLEFT JOIN author_settings afl ON (a.author_id = afl.author_id AND afl.setting_name = ? AND afl.locale = ?)\n\t\t\t\tLEFT JOIN author_settings afpl ON (a.author_id = afpl.author_id AND afpl.setti in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703

And there is this that seems to be another problem:

PHP Fatal error: Uncaught Error: Call to a member function getLocalizedFullTitle() on null in /var/www/ojs-3.2.0-2/cache/t_compile/5ab5d9fef2c02a24d6e95c22ce7dbeb486716ddb^504348cc7222e1110a6019067f9a002726c02324_0.plugins-plugins-generic-pdfJsViewer-generic-pdfJsViewer.display.tpl.php:94\nStack trace:\n#0 /var/www/ojs-3.2.0-2/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_resource_base.php(123): content_5e96181fd7ed23_91405111(Object(Smarty_Internal_Template))\n#1 /var/www/ojs-3.2.0-2/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_compiled.php(114): Smarty_Template_Resource_Base->getRenderedTemplateCode(Object(Smarty_Internal_Template))\n#2 /var/www/ojs-3.2.0-2/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php(216): Smarty_Template_Compiled->render(Object(Smarty_Internal_Template))\n#3 /var/www/ojs-3.2.0-2/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php(385): Smarty_Internal_Template->render()\n#4 /var/www/ojs-3.2.0-2/cache/t_compile/5ab5 in /var/www/ojs-3.2.0-2/cache/t_compile/5ab5d9fef2c02a24d6e95c22ce7dbeb486716ddb^504348cc7222e1110a6019067f9a002726c02324_0.plugins-plugins-generic-pdfJsViewer-generic-pdfJsViewer.display.tpl.php on line 94, referer: http://periodicos.ufes.br/agora/index

7

Hi @Adriano_Jose,

For this message…

PHP Fatal error: Uncaught Exception: DB Error: ERROR: operator does not exist: text = bigint\nLINHA 31: …N (ppss.setting_name = $7

…apply pkp/pkp-lib#5741 PostgreSQL operator does not exist error · pkp/ojs@9496c59 · GitHub.

For this message:

PHP Fatal error: Uncaught Error: Call to a member function getData() on null in /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php:215

…can you try the following query to see if you have some orphaned author records?

SELECT author_id FROM authors a LEFT JOIN publications p ON (a.publication_id = p.publication_id) WHERE p.publication_id IS NULL;

For this error:

PHP Fatal error: Uncaught Exception: DB Error: ERROR: syntax error at or near “AND”\nLINHA 71: AND (LOWER(asf0.setting_value) LIKE LOWER( $8) OR LOWE…\n...

…can you describe what you’re doing when you see this?

Regards,
Alec Smecher
Public Knowledge Project Team

1 Like
8

Hi @asmecher,

This select:

SELECT author_id FROM authors a LEFT JOIN publications p ON (a.publication_id = p.publication_id) WHERE p.publication_id IS NULL;

returned 44458 results. I looked for p.publication_id in the Authors table and it’s all NULL.

I migrated from version 2.4.8-5 to 3.1.2-1, and then the other updates. How would this sql in version 2.4.8 be for me to know if it was wrong before the migration? I have a clone before the migration.

The ojs that I manage has more than 80 journals and publishers have reported many errors as difficulty in submitting and DOI deposit, but I do not always know what exactly is the action that caused the error, as in this case … As soon as I gather more accurate information, I send it here.

A new error that appeared in the error log, is this:

 PHP Fatal error:  Uncaught Error: Call to a member function getData() on null in /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php:215\nStack trace:\n#0 [internal function]: SearchHandler->{closure}(NULL)\n#1 /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php(216): array_map(Object(Closure), Array)\n#2 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPRouter.inc.php(391): SearchHandler->authors(Array, Object(Request))\n#3 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPPageRouter.inc.php(231): PKPRouter->_authorizeInitializeAndCallRequest(Array, Object(Request), Array, false)\n#4 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/Dispatcher.inc.php(143): PKPPageRouter->route(Object(Request))\n#5 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPApplication.inc.php(278): Dispatcher->dispatch(Object(Request))\n#6 /var/www/ojs-3.2.0-2/index.php(68): PKPApplication->execute()\n#7 {main}\n  thrown in /var/www/ojs-3.2.0-2/pages/search/SearchHandler.inc.php on line 215

And this:

PHP Fatal error:  Uncaught Error: Call to a member function getLocalizedFullTitle() on null in /var/www/ojs-3.2.0-2/cache/t_compile/5ab5d9fef2c02a24d6e95c22ce7dbeb486716ddb^504348cc7222e1110a6019067f9a002726c02324_0.plugins-plugins-generic-pdfJsViewer-generic-pdfJsViewer.display.tpl.php:94\nStack trace:\n#0 /var/www/ojs-3.2.0-2/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_resource_base.php(123): content_5e96181fd7ed23_91405111(Object(Smarty_Internal_Template))\n#1 /var/www/ojs-3.2.0-2/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_template_compiled.php(114): Smarty_Template_Resource_Base->getRenderedTemplateCode(Object(Smarty_Internal_Template))\n#2 /var/www/ojs-3.2.0-2/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php(216): Smarty_Template_Compiled->render(Object(Smarty_Internal_Template))\n#3 /var/www/ojs-3.2.0-2/lib/pkp/lib/vendor/smarty/smarty/libs/sysplugins/smarty_internal_template.php(385): Smarty_Internal_Template->render()\n#4 /var/www/ojs-3.2.0-2/cache/t_compile/5ab5 in /var/www/ojs-3.2.0-2/cache/t_compile/5ab5d9fef2c02a24d6e95c22ce7dbeb486716ddb^504348cc7222e1110a6019067f9a002726c02324_0.plugins-plugins-generic-pdfJsViewer-generic-pdfJsViewer.display.tpl.php on line 94

Thank you very much for your attention.

Regartds,
Adriano Moreno

9

Hi @Adriano_Jose,

Are you sure your upgrade completed successfully? What do you get for the following query?

SELECT major, minor, revision, build FROM versions WHERE product='ojs2' AND current=1;

Regards,
Alec Smecher
Public Knowledge Project Team

10

Hi @asmecher,
yes, i’m sure the update ended correctly. We kept the name of the ojs2 machine, but updated it correctly, with the message at the end the upgrade that it successfully completed.

This select results:
Capturar

Could this situation not be fixed?

11

Hi @Adriano_Jose,

OK, that’s good news. I’m concerned about the number of author entries that aren’t associated with publications (publication_id), though. Are author listings generally looking correct? Could you look at a sampling of entries in the pre-upgrade database that have the same author_id to see whether they’re associated with submissions (by submission_id)?

Regards,
Alec Smecher
Public Knowledge Project Team

12

Pre-upgrade (2.4.8-5):

SELECT a.author_id, a.submission_id,a.user_group_id,s.stage_id  FROM authors a,submissions s where a.submission_id=s.submission_id and email in ('phellipecunha@hotmail.com','monica.senna20@gmail.com') order by author_id;

Capturar2

Pos-upgrade (3.2.0-2):

SELECT a.author_id, a.submission_id,a.user_group_id,s.stage_id,p.publication_id,p.primary_contact_id  FROM authors a,submissions s, publications p where a.submission_id=s.submission_id and p.submission_id=s.submission_id  and a.email in ('phellipecunha@hotmail.com','monica.senna20@gmail.com') order by author_id;

Capturar3

Is this what you want to see?

regards,
Adriano Moreno

13

Hi @Adriano_Jose,

Are those examples of cases where there is no accompanying entry in publications corresponding to the publication_id in authors after upgrading?

Regards,
Alec Smecher
Public Knowledge Project Team

14

Hi @asmecher,
this select:

select * from publications p where p.submission_id not in (select a.submission_id from authors a);

Returns 541 rows.

this select:

select * from publications p where p.submission_id not in (select s.submission_id from submissions s);

Returns 0 rows.

this select:

select * from submissions s where s.submission_id not in (select a.submission_id from authors a);

Returns 542 rows.

this select:

select * from authors a where a.submission_id not in (select s.submission_id from submissions s);

Returns 34 rows.

In the authors table, the publication_id column is all NULL;

Some submissions do not have authors and some authors do not have submissions, but it does not seem to me much in view of the total, because we have 44458 rows in Authors, 25223 rows in Submissions and 25223 rows in Publications table.

15

Hi @Adriano_Jose,

I would expect the publication_id column of authors to be populated by this query in dbscripts/xml/upgrade/3.2.0_versioning.xml:

UPDATE authors
SET publication_id = s.current_publication_id
FROM submissions s, temp_authors ta
WHERE authors.author_id = ta.author_id AND s.submission_id = ta.submission_id

Just to confirm, what is your driver setting in config.inc.php?

Regards,
Alec Smecher
Public Knowledge Project Team

16

Hi @asmecher
The driver is:
driver = postgres

And my system information:

Capturar4
Capturar41127×349 30 KB

Perhaps the same thing happened when updating email_id, where the data was there, but it just wasn’t copied to the column. So, during the update I ran the script to fill it out.
As I explained here:

Error when updating from 3.1.2-4 to 3.2.0-1 with postgres - #15 by Adriano_Jose

17

Hi @Adriano_Jose,

Hmm, interesting – would it be possible to re-run the upgrade with postgres7 as the driver instead of postgres? [Edit: I’ve added a fix for this for future releases, starting with OJS/OMP 3.2.0-3. See Driver settings of postgres, postgres6, and postgres9 result in missed upgrade steps · Issue #5763 · pkp/pkp-lib · GitHub]

Regards,
Alec Smecher
Public Knowledge Project Team

18

Hi @asmecher,
I did it in production doing a re-upgrade from 3.2.0-2 to 3.2.0-2, but it seems that it didn’t make any difference, because versioning.xml file did not run again.
On a test machine from 3.1.2-4 to 3.2.0-1, versioning.xml file run, but then an error happened::

ERROR: Upgrade failed: DB: ERROR:  duplicate key value violates unique constraint "citations_publication_seq"
DETALHE:  Key (publication_id, seq)=(6114, 3) already exists.

So I took the publication_id column from the authors table on the test machine and copied it to the production machine, as they are clones.
I thought it would work now, but when trying to make a new submission, it presents the following error:

[Sun Apr 19 00:55:38.606588 2020] [php7:error] [pid 9524] [client 172.20.7.116:55391] PHP Fatal error:  Uncaught Exception: DB Error: ERROR:  null value in column "submission_id" violates not-null constraint\nDETALHE:  Failing row contains (51947, null, 0, suporte.periodicos@grupos.ufes.br, 988, 1, 25353). Query: INSERT INTO authors (email, include_in_browse, publication_id, user_group_id) VALUES (?, ?, ?, ?) in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php:703\nStack trace:\n#0 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php(231): DAO->handleError(Object(ADODB_postgres7), 'INSERT INTO aut...')\n#1 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/SchemaDAO.inc.php(79): DAO->update('INSERT INTO aut...', Array)\n#2 /var/www/ojs-3.2.0-2/lib/pkp/classes/submission/form/PKPSubmissionSubmitStep1Form.inc.php(382): SchemaDAO->insertObject(Object(Author))\n#3 /var/www/ojs-3.2.0-2/lib/pkp/pages/submission/PKPSubmissionHandler.inc.php(171): PKPSubmissionSubmitStep1Form->execute()\n#4 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPRouter.inc.php(391): PKPSubmissionHandler->saveStep(Array, Object(Request))\n#5 /var/www/ojs-3.2.0-2/l in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703, referer: http://periodicos.ufes.br/argumentum/submission/wizard

If I do this sql and update the publication_id on authors table, could give any error?

select p.publication_id, a.author_id  
from authors a
inner join  submissions s
on a.submission_id = s.submission_id
inner join publications p
on s.submission_id = p.submission_id
order by a.author_id

so, with the results, in all rows, I do like this:

UPDATE AUTHORS SET PUBLICATION_ID = ... WHERE AUTHOR_ID = ... ; Commit;

Whato do you think about this?

Regards,
Adriano Moreno

19

Hi @Adriano_Jose,

Unfortunately you won’t be able to re-run 3.1.x to 3.2.x steps be re-running the upgrade script again; you’d have to go back to an earlier backup for those scripts to be executed.

Regards,
Alec Smecher
Public Knowledge Project Team

20

Now it worked. I was able to update all the information in the column publication_id in the authors table.
But, when trying to make a new submission, this error keeps showing up and the screen is locked:

[Sun Apr 19 00:55:38.606588 2020] [php7:error] [pid 9524] [client 172.20.7.116:55391] PHP Fatal error: Uncaught Exception: DB Error: ERROR: null value in column "submission_id" violates not-null constraint\nDETALHE: Failing row contains (51947, null, 0, suporte.periodicos@grupos.ufes.br, 988, 1, 25353). Query: INSERT INTO authors (email, include_in_browse, publication_id, user_group_id) VALUES (?, ?, ?, ?) in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php:703\nStack trace:\n#0 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php(231): DAO->handleError(Object(ADODB_postgres7), 'INSERT INTO aut...')\n#1 /var/www/ojs-3.2.0-2/lib/pkp/classes/db/SchemaDAO.inc.php(79): DAO->update('INSERT INTO aut...', Array)\n#2 /var/www/ojs-3.2.0-2/lib/pkp/classes/submission/form/PKPSubmissionSubmitStep1Form.inc.php(382): SchemaDAO->insertObject(Object(Author))\n#3 /var/www/ojs-3.2.0-2/lib/pkp/pages/submission/PKPSubmissionHandler.inc.php(171): PKPSubmissionSubmitStep1Form->execute()\n#4 /var/www/ojs-3.2.0-2/lib/pkp/classes/core/PKPRouter.inc.php(391): PKPSubmissionHandler->saveStep(Array, Object(Request))\n#5 /var/www/ojs-3.2.0-2/l in /var/www/ojs-3.2.0-2/lib/pkp/classes/db/DAO.inc.php on line 703, referer: http://periodicos.ufes.br/argumentum/submission/wizard

I searched the table for the values in the error line and the information is there in the Submissions and Publications tables. What would be the reason for the NULL submission_id information?

select *  from publications where publication_id = 25353  ;

50

select *  from submissions  where submission_id = 29901 ;

34