ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2021-05-04T11:48:23+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/204smarty deprecation warnins2021-05-04T11:48:23+02:00Gerald Salingerald.salin@inra.frsmarty deprecation warninsin backend error viewer :
Core: Error handler (FE): PHP Runtime Deprecation Notice: Function create_function() is deprecated in /usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8/ui/nG6/res/smarty/libs/Smarty.class.php line 742
Core: Er...in backend error viewer :
Core: Error handler (FE): PHP Runtime Deprecation Notice: Function create_function() is deprecated in /usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8/ui/nG6/res/smarty/libs/Smarty.class.php line 742
Core: Error handler (FE): PHP User Notice: function call 'assign_by_ref' is unknown or deprecated, use 'assignByRef' in /usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8/ui/nG6/res/smarty/libs/sysplugins/smarty_internal_data.php line 79V3.2.8.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/203Download by URL gives wrong URLs2021-04-30T20:45:23+02:00Gerald Salingerald.salin@inra.frDownload by URL gives wrong URLs![image](/uploads/8ba8b139a78f25f52d2e4ea6538f3916/image.png)
should be https://ng6.toulouse.inra.fr**/fileadmin/dat**a_shortterm/run/XXX/XXXXGMC_L001_R1.fastq.gz![image](/uploads/8ba8b139a78f25f52d2e4ea6538f3916/image.png)
should be https://ng6.toulouse.inra.fr**/fileadmin/dat**a_shortterm/run/XXX/XXXXGMC_L001_R1.fastq.gzV3.2.8.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/202ng6 interface slow2021-04-30T20:13:17+02:00Gerald Salingerald.salin@inra.frng6 interface slowNG6 run view quite long to display clicking on a project in project list view, til we got a blank page
Activating the debug preset in typo3 (https://ng6.toulouse.inra.fr/typo3 > Settings > Configuration Presets > Debug settings > Custom...NG6 run view quite long to display clicking on a project in project list view, til we got a blank page
Activating the debug preset in typo3 (https://ng6.toulouse.inra.fr/typo3 > Settings > Configuration Presets > Debug settings > Custom configuration [Active] : BE=1, FE=1, devIPMask=*, displayErrors=1, systemLogLevel=0
refreshing the view displays the error :
Fatal error: Allowed memory size of 2147483648 bytes exhausted (tried to allocate 1743296768 bytes) in /var/www/html/ng6/typo3conf/ext/typo3db_legacy/Classes/Database/DatabaseConnection.php on line 503
Increasing memory_limit in php.ini solved for some time, but Fatal error: Allowed memory size of 2147483648 bytes exhausted (tried to allocate 1743296768 bytes) in /var/www/html/ng6/typo3conf/ext/typo3db_legacy/Classes/Database/DatabaseConnection.php on line 503
I did not found a way to display sql queries, so I added file_put_contents("/var/www/html/ng6/typo3temp/sql.log", $query."\n",FILE_APPEND);
in /var/www/html/ng6/typo3conf/ext/typo3db_legacy/Classes/Database/DatabaseConnection.php > query function
while refreshing the page, output SQL log :
> nG6_project_analyze.analyze_id WHERE tx_nG6_project.uid=1700
> SELECT * FROM tx_nG6_view_project_run WHERE project_id = 1700
> SELECT * FROM tx_nG6_view_project_run_analyze WHERE project_id = 1700
> SELECT * FROM tx_nG6_view_project_analyze WHERE project_id = 1700
> SELECT project_id , count(*) AS count FROM tx_nG6_view_project_run WHERE project_id = 1700 GROUP BY project_id
> SELECT project_id , count(*) AS count FROM tx_nG6_view_project_run_analyze WHERE project_id = 1700 GROUP BY project_id
> SELECT project_id , count(*) AS count FROM tx_nG6_view_project_analyze WHERE project_id = 1700 GROUP BY project_id
> SELECT * FROM tx_nG6_view_project_user
in phpMyAdmin :
SELECT count(*) FROM tx_nG6_view_project_user > 13619506!!!!!!!!!!!!
SELECT * FROM `fe_rights_levels` > 8911!!! whereas we should only have 3 records
refreshing https://ng6.toulouse.inra.fr/projects?tx_nG6_pi1[project_id]=1700 > 2 more records in fe_rights_levels
DELETE FROM `fe_rights_levels` where uid > 3 : refreshing https://ng6.toulouse.inra.fr/projects?tx_nG6_pi1[project_id]=1700 > the page loading is fast
but 2 more records inserted in fe_rights_levels
![image](/uploads/88e304647f722386078feb20ed52b912/image.png)V3.2.8.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/200allow to display all entries of a datatable in an analysis2021-04-28T16:30:55+02:00Gerald Salingerald.salin@inra.frallow to display all entries of a datatable in an analysisV3.2.8.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/199update links2021-04-28T14:46:19+02:00Gerald Salingerald.salin@inra.frupdate linkswith the new typo3 version, links are human readable :
change the index.php?id=XX&WWWWWWW with the corresponding page slug in the source
and have to create redirects in apache for those who access the old linkswith the new typo3 version, links are human readable :
change the index.php?id=XX&WWWWWWW with the corresponding page slug in the source
and have to create redirects in apache for those who access the old linksV3.2.8.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/160Error when updating a user's email on nG62021-05-04T11:18:53+02:00Romain ThervilleError when updating a user's email on nG6When logged as CTD, on the project "HOLISTIC", I tried to update MAJJ's email, and the new email has been set for CTD instead of MAJJ.
![2020-01-21_113722](/uploads/33afb05071f8d7d0382a0a7743fd2fd8/2020-01-21_113722.png)
Was it because...When logged as CTD, on the project "HOLISTIC", I tried to update MAJJ's email, and the new email has been set for CTD instead of MAJJ.
![2020-01-21_113722](/uploads/33afb05071f8d7d0382a0a7743fd2fd8/2020-01-21_113722.png)
Was it because CTD was on top of the list, or because the logged user was CTD?
Anyway, it's an issue.V3.2.8.1Romain ThervilleRomain Therville