Lovd Setup

System logs

What is logged by LOVD

LOVD logs four types of events: authorization events and errors, general events, general errors, and installation and upgrade events. In case the event or error was triggered by an authorized user, the username of this user is also logged.

Authorization events and errors

This list stores both successful and unsuccessful login attempts. When a user's account has been locked, this log shows you from what IP address the login attempts have been made. Also, it shows you if users provide a password or not. Brute-force attempts to hack into LOVD are quickly uncovered using these logs.

Event	Caused by
AuthError	Unsuccessful attempt to log into LOVD. Shows IP address, hostname, username, and the length of the provided password.
AuthLogin	Successful attempt to log into LOVD. Shows IP address, hostname, username, and the length of the provided password.

General events

General events are logged to show a user's activity, to allow collaborating users to track each other's activities or to check what happened to a certain variant or patient entry.

Event	Caused by
ColAdd	A custom column has been added to a variant table or the patient table. In case the column has been added to a variant table, the gene is also displayed.
ColCreate	A new column has been created from the setup area.
ColEdit	A column's display settings or default settings have been edited.
ColRemove	A selected column has been removed from a variant table or the patient table. In case the column has been removed to a variant table, the gene is also displayed.
ColReset	A selected column's display settings are reset to the default settings.
ConfigEdit	Successfully edited LOVD's system settings.
FreeEditFNR	Successfully ran Find & Replace. The column and the selected genes where Find & Replace was performed on are also logged.
GeneCreate	Successfully created a new gene.
GeneDrop	Deleted a gene and it's variants.
GeneEdit	A gene's settings have been edited.
GeneEmpty	All of a gene's variants have been removed.
LinkCreate	A new custom link has been created. If the link also has been added to any columns, this is mentioned in separate log entries.
LinkDrop	A custom link has been deleted.
LinkEdit	A custom link has been edited. If the link also has been removed from or added to any columns, this is mentioned in separate log entries.
ModuleDisable	Successfully disabled a module (turned off).
ModuleEnable	Successfully enabled a module (turned on).
ModuleScan	LOVD scanned for new modules, successfully recognized one and installed it.
ModuleUninstall	Successfully uninstalled (removed) a module.
PatientDrop	A patient and all of it's variants have been deleted.
PatientEdit	A patient has been edited, by an authorized user or a submitter, or submitted changes have been accepted by an authorized user.
SelfEdit	A user has successfully edited him/herself. When a user selects or deselects him/herself as a curator, this is also logged.
SubmitNew	A new submission has been added to LOVD. The gene, internal patient ID and internal variant ID are also displayed. This log entry could also mean that a new variant has been added to an existing patient.
SubmitterAssign	A submitter has been assigned to a patient, or removed from a patient.
SubmitterCreate	A submitter account has been created by an authorized user.
SubmitterDrop	A submitter account has been deleted from the system. This is a non-permanent action.
SubmitterEdit	A submitter account has been edited by an authorized user.
SubmitterPurge	A previously deleted submitter account has been permanently deleted from the system.
SubmitterRegister	A submitter has registered him/herself.
UserBoot	An authorized user that was logged in, has been thrown out of the system by an authorized user with a higher level.
UserCreate	A new authorized user has been created by an authorized user with a higher level. When this user is selected as a curator, this is also logged.
UserDrop	An authorized user has been deleted from the system by an authorized user with a higher level. This is a non-permanent action.
UserEdit	An authorized user has been edited by an authorized user with a higher level. When this user is selected or deselected as a curator, this is also logged.
UserLock	An authorized user has been locked out of the system by an authorized user with a higher level.
UserUnlock	An authorized user's account has been unlocked by an authorized user with a higher level.
VariantDrop	A variant has been dropped from a patient. If this was the patient's only variant, the patient entry is also deleted.
VariantEdit	A variant has been edited by either an authorized user or a submitter who owns the variant's patient entry.
VariantImport	Variant and patient information has been loaded into the database. The number of new patient and variant entries are reported.

General errors

Whenever an unrecoverable error occurs, LOVD logs the error and stops processing. When it's a database error, LOVD tries to log the error to a file.
In principle, during any database event, an error can occur. This is then logged under the name of the event, so any of the above event names can also be found in the error log. In the below table you can find the event names that appear exclusively in the error log. If you find any other event name in the error log, see the above table.

Event	Caused by
CheckUpdate	There was an error while reading the answer of the upstream server to see if there is an update available, or the current version seems newer than the one available.
CURRDB::Lib	An error occurred in a function from the CurrDB class. This is caused by a bug in LOVD.
EmailNotify	An error occurred while sending an email notification to a user who edited his/her own account, a submitter sending in new information, a curator of a gene which has received a new submission, or the database administrator.
HackAttempt	Someone tried to access information or trying to edit or delete information while not being authorized. This error can only be caused if someone is actively modifying the URL to access LOVD.
LibInit	An error occurred in a function from inc-lib-init.php. This is caused by a bug in LOVD.
LibList	An error occurred in a function from inc-lib-list.php. This is caused by a bug in LOVD.
NoCurrDB	The CurrDB class has been initiated without receiving a gene symbol. This is caused by a bug in LOVD.

Installation and upgrade events

During installation of LOVD, a few log entries are added to the Install log to show the progress of the installation. Also, after each upgrade, LOVD will add an entry stating from which version and to which version it has been upgraded.

Event	Caused by
Step2	LOVD has successfully registered the system status, the variant pathogenicities and the variant statuses, and created the database administrator account.
Step3	LOVD successfully stored the system settings.
Step4	LOVD successfully installed the available modules.
Step5	Successfully completed the installation.
Upgrade	LOVD has been upgraded successfully. This entry also reports from which version LOVD was upgraded, which version it has been upgraded to, and how many queries are performed during the upgrade.
UpgradeError	LOVD has found that the database backend is newer than the LOVD files. This can only be caused by retrieving LOVD files from backups without restoring the database. Since this can cause severe problems with the data within LOVD, LOVD will only work if you restore the correct LOVD files.

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