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specify / specify6

Source Code for Specify 6, Biological Collections Management Platform
https://specifysoftware.org
GNU General Public License v2.0
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Error while updating cache in Data Exporter #390

Closed maxpatiiuk closed 4 years ago

maxpatiiuk commented 4 years ago

Screenshot from 2019-11-08 14-32-16

maxpatiiuk commented 4 years ago

Error while building cache in Data exporter

Specify version: 6.7.0.1 Error: The cache Count not be updated. Error: MysqlDataTruncation (Data truncation: Incorect data value: '2009-00-00' for column 'Fecha_de_identification' at row 1) Database: Botanica Herbario (Costa Rico)

Screenshot from 2019-11-08 14-37-09

maxpatiiuk commented 4 years ago

Tested on Ubuntu 18.04.3 LTS

maxpatiiuk commented 4 years ago

Error fixed in Specify 6.7.04 Issue closed

maxpatiiuk commented 4 years ago

Screenshot from 2019-12-02 09-25-58 Screenshot from 2019-12-02 09-26-29 Screenshot from 2019-12-02 09-26-32 Screenshot from 2019-12-02 09-26-37

./DataExporter 

09:23:37 DEBUG tools.export.ExportPanel:1969 - ********* Current [/home/m001p596/Specify_6_8_00_3/bin/.]
09:23:43 DEBUG ui.db.PropertiesPickListAdapter:292 - Saving PickList
09:23:43 DEBUG ui.db.PropertiesPickListAdapter:296 - [login.databases][specify_6_7_0_4,specify_6_8_00_6]
09:23:43 DEBUG ui.db.PropertiesPickListAdapter:308 - [login.databases_selected][specify_6_8_00_6]
09:23:43 DEBUG ui.db.PropertiesPickListAdapter:292 - Saving PickList
09:23:43 DEBUG ui.db.PropertiesPickListAdapter:296 - [login.servers][localhost]
09:23:43 DEBUG ui.db.PropertiesPickListAdapter:308 - [login.servers_selected][localhost]
09:23:43 DEBUG brc.ui.UIHelper:1640 - try login
09:23:43 DEBUG specify.module.DbLoginCallbackHandler:89 - handle
09:23:43 ERROR ui.db.DatabaseLoginPanel$17:1352 - com.install4j.api.launcher.SplashScreen$ConnectionException: no splash screen available
09:23:45 DEBUG specify.dbsupport.SpecifySchemaUpdateService:317 - appVerNumArg: [6.8.00] dbVersion from XML[2.7] appVersion[6.8.00] schemaVersion[2.7]  spverId[1]  recVerNum[1] 
09:23:45  INFO brc.dbsupport.HibernateUtil:198 - Using database [jdbc:mysql://localhost:3306/specify_6_8_00_6?characterEncoding=UTF-8&autoReconnect=true]
09:23:46 DEBUG brc.ui.UIHelper$1DBListener:1847 - UIHelper.doLogin[DBListener]
09:23:46 DEBUG core.db.DBTableIdMgr:141 - Reading in datamodel file: /home/m001p596/Specify_6_8_00_3/config/specify_datamodel.xml to create and populate DBTableMgr
09:23:46 DEBUG core.db.DBTableIdMgr:311 - Done Reading in datamodel file: /home/m001p596/Specify_6_8_00_3/config/specify_datamodel.xml
09:23:46 DEBUG specify.config.CheckDBAfterLogin:528 - SELECT COUNT(*) FROM specifyuser su INNER JOIN specifyuser_spprincipal ss ON su.SpecifyUserID = ss.SpecifyUserID INNER JOIN spprincipal p ON ss.SpPrincipalID = p.SpPrincipalID LEFT JOIN spprincipal_sppermission pp ON p.SpPrincipalID = pp.SpPrincipalID LEFT OUTER JOIN sppermission pm ON pp.SpPermissionID = pm.SpPermissionID  WHERE p.GroupSubClass = 'edu.ku.brc.af.auth.specify.principal.UserPrincipal' AND p.userGroupScopeID IS NULL
09:23:46 DEBUG specify.config.CheckDBAfterLogin:532 - SELECT COUNT(*) FROM specifyuser su INNER JOIN specifyuser_spprincipal ss ON su.SpecifyUserID = ss.SpecifyUserID INNER JOIN spprincipal p ON ss.SpPrincipalID = p.SpPrincipalID LEFT JOIN spprincipal_sppermission pp ON p.SpPrincipalID = pp.SpPrincipalID LEFT OUTER JOIN sppermission pm ON pp.SpPermissionID = pm.SpPermissionID  WHERE p.GroupSubClass = 'edu.ku.brc.af.auth.specify.principal.UserPrincipal' 
09:23:47 DEBUG ui.forms.ViewSetMgr:373 - /home/m001p596/Specify_6_8_00_3/config/vertpaleo/manager
09:23:47 DEBUG ui.forms.ViewSetMgr:373 - /home/m001p596/Specify_6_8_00_3/config/vertpaleo
09:23:47 DEBUG ui.forms.ViewSetMgr:373 - /home/m001p596/Specify_6_8_00_3/config/common
09:23:47 DEBUG ui.forms.ViewSetMgr:373 - /home/m001p596/Specify_6_8_00_3/config/backstop
09:23:47 DEBUG specify.config.SpecifySchemaI18NService:143 - SELECT cn.Name,splocalecontaineritem.Name,splocalecontaineritem.Format, splocalecontaineritem.IsUIFormatter, splocalecontaineritem.PickListName, splocaleitemstr.Text, splocalecontaineritem.IsHidden, splocalecontaineritem.WebLinkName , splocalecontaineritem.IsRequired  FROM splocalecontainer cn INNER JOIN splocalecontaineritem ON cn.SpLocaleContainerID = splocalecontaineritem.SpLocaleContainerID INNER JOIN splocaleitemstr ON splocalecontaineritem.SpLocaleContainerItemID = splocaleitemstr.SpLocaleContainerItemNameID  where splocaleitemstr.Language = 'en' AND cn.SchemaType = 0 AND cn.DisciplineID = 3 order by cn.Name
09:23:47 DEBUG specify.config.SpecifySchemaI18NService:143 - SELECT cn.Name,splocalecontaineritem.Name,splocalecontaineritem.Format, splocalecontaineritem.IsUIFormatter, splocalecontaineritem.PickListName, splocaleitemstr.Text, splocalecontaineritem.IsHidden, splocalecontaineritem.WebLinkName , splocalecontaineritem.IsRequired  FROM splocalecontainer cn INNER JOIN splocalecontaineritem ON cn.SpLocaleContainerID = splocalecontaineritem.SpLocaleContainerID INNER JOIN splocaleitemstr ON splocalecontaineritem.SpLocaleContainerItemID = splocaleitemstr.SpLocaleContainerItemNameID  where splocaleitemstr.Language = 'en' AND cn.SchemaType = 0 AND cn.DisciplineID = 3 order by cn.Name
09:23:54  WARN specify.tasks.QueryTask:1874 - using current collection's treedef for host taxononmy.
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[Accession] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[AddressOfRecord] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[DNASequence] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[Agent] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[GroupPerson] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[Appraisal] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[Attachment] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[Author] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[Borrow] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[CollectingEvent] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[CollectingTrip] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[CollectionObject] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[CollectionRelationship] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[ConservDescription] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[Container] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[Deaccession] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[DeaccessionPreparation] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[Determination] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[ExchangeIn] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[ExchangeOut] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[Exsiccata] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[ExsiccataItem] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[FieldNotebook] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[FieldNotebookPage] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[FieldNotebookPageSet] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[Geography] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[GeologicTimePeriod] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[Gift] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[GiftPreparation] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[InfoRequest] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[Journal] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[LithoStrat] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[Loan] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[LoanPreparation] to hash
09:23:54 DEBUG specify.tasks.QueryTask:2424 - Adding[LoanReturnPreparation] to hash
09:23:55 DEBUG specify.tasks.QueryTask:2424 - Adding[Locality] to hash
09:23:55 DEBUG specify.tasks.QueryTask:2424 - Adding[MaterialSample] to hash
09:23:55 DEBUG specify.tasks.QueryTask:2424 - Adding[PaleoContext] to hash
09:23:55 DEBUG specify.tasks.QueryTask:2424 - Adding[Permit] to hash
09:23:55 DEBUG specify.tasks.QueryTask:2424 - Adding[Preparation] to hash
09:23:55 DEBUG specify.tasks.QueryTask:2424 - Adding[Project] to hash
09:23:55 DEBUG specify.tasks.QueryTask:2424 - Adding[ReferenceWork] to hash
09:23:55 DEBUG specify.tasks.QueryTask:2424 - Adding[RepositoryAgreement] to hash
09:23:55 DEBUG specify.tasks.QueryTask:2424 - Adding[Shipment] to hash
09:23:55 DEBUG specify.tasks.QueryTask:2424 - Adding[SpAuditLog] to hash
09:23:55 DEBUG specify.tasks.QueryTask:2424 - Adding[Storage] to hash
09:23:55 DEBUG specify.tasks.QueryTask:2424 - Adding[Taxon] to hash
09:23:55 DEBUG specify.tasks.QueryTask:2424 - Adding[TreatmentEvent] to hash
09:23:55 DEBUG specify.dbsupport.RecordTypeCodeBuilder:138 - retrieving TypeCode Fields for edu.ku.brc.specify.datamodel.Locality
09:23:55 DEBUG specify.dbsupport.RecordTypeCodeBuilder:138 - retrieving TypeCode Fields for edu.ku.brc.specify.datamodel.Locality
09:23:55 DEBUG specify.dbsupport.RecordTypeCodeBuilder:138 - retrieving TypeCode Fields for edu.ku.brc.specify.datamodel.Locality
09:23:55 DEBUG specify.dbsupport.RecordTypeCodeBuilder:138 - retrieving TypeCode Fields for edu.ku.brc.specify.datamodel.Locality
09:23:55  INFO subpane.qb.PickListCriteriaCombo:288 - no picklist item found for ''
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55 ERROR subpane.qb.QueryFieldPanel:634 - QueryField is null or ownerQuery is prompt only. Unable to update database object.
09:23:55  INFO subpane.qb.QueryBldrPane:1744 - select distinct co0.collectionObjectId, inst0.termsOfUse, col0.collectionType, co0.catalogNumber, tx0.id, col0.code, geo0.id, geo0.id, geo0.id, col0.description, loc0.latitude1, loc0.longitude1, ce0.startDate, ce0.startDatePrecision, ce0.remarks, tx0.id, tx0.id, loc0.datum, gcd0.geoRefDetDate, geo0.fullName, inst0.code, inst0.altName, tx0.id, inst0.copyright, loc0.localityName, co0.timestampModified, tx0.id, co0.altCatalogNumber, tx0.id, co0.collectionObjectId, ce0.collectingEventId, tx0.fullName, tx0.id, geo0.id, det0.typeStatusName from CollectionObject co0  left join co0.collection col0  left join col0.discipline dsp0  left join dsp0.division dv0  left join dv0.institution inst0  left join co0.determinations det0  left join det0.taxon tx0  left join co0.collectingEvent ce0  left join ce0.locality loc0  left join loc0.geography geo0  left join loc0.geoCoordDetails gcd0  where (det0.isCurrent = true or det0.isCurrent is null) AND (co0.collectionMemberId = 4)
09:23:56 ERROR specify.dbsupport.TaskSemaphoreMgr:968 - Trying to unlock when already unlocked!
09:26:27 ERROR specify.dbsupport.TaskSemaphoreMgr:968 - Trying to unlock when already unlocked!
maxpatiiuk commented 4 years ago

The issue is present in Specify 6.8.00 on Linux in the Vertebrate Paleontology database that was created in this version and has approximately 1 row of data in each table (Collection Objects, Agents, Localities, ...)

When I press Show SQL, here is the resulting code (if it helps in recreation of this issue):

select mapping_1.mapping_1Id as "mapping_1Id", mapping_1.accessRights as "accessRights", mapping_1.basisOfRecord as "basisOfRecord", mapping_1.catalogNumber as "catalogNumber", mapping_1.class as "class", mapping_1.collectionCode as "collectionCode", mapping_1.continent as "continent", mapping_1.country as "country", mapping_1.county as "county", mapping_1.datasetName as "datasetName", mapping_1.decimalLatitude as "decimalLatitude", mapping_1.decimalLongitude as "decimalLongitude", concat(year(mapping_1.eventDate), case when month(mapping_1.eventDate) > 0 then concat('-',lpad(month(mapping_1.eventDate), 2, '0')) else '' end,case when day(mapping_1.eventDate) > 0 then concat('-', lpad(day(mapping_1.eventDate), 2, '0')) else '' end) as "eventDate", mapping_1.eventRemarks as "eventRemarks", mapping_1.family as "family", mapping_1.genus as "genus", mapping_1.geodeticDatum as "geodeticDatum", concat(year(mapping_1.georeferencedDate), case when month(mapping_1.georeferencedDate) > 0 then concat('-',lpad(month(mapping_1.georeferencedDate), 2, '0')) else '' end,case when day(mapping_1.georeferencedDate) > 0 then concat('-', lpad(day(mapping_1.georeferencedDate), 2, '0')) else '' end) as "georeferencedDate", mapping_1.higherGeography as "higherGeography", mapping_1.institutionCode as "institutionCode", mapping_1.institutionID as "institutionID", mapping_1.kingdom as "kingdom", mapping_1.license as "license", mapping_1.locality as "locality", mapping_1.modified as "modified", mapping_1.order as "order", mapping_1.otherCatalogNumbers as "otherCatalogNumbers", mapping_1.phylum as "phylum", mapping_1.preparations as "preparations", mapping_1.recordedBy as "recordedBy", mapping_1.scientificName as "scientificName", mapping_1.specificEpithet as "specificEpithet", mapping_1.stateProvince as "stateProvince", mapping_1.typeStatus as "typeStatus" from mapping_1
maxpatiiuk commented 4 years ago

Export for web portal is successfull. The window that asks for the name and location of Web Portal export has .zip extension set up for a file Screenshot from 2019-12-02 09-29-14

Whereas the regular Export, which results in errors, has All Files instead of an extension. (Maybe a cause of an issue?) Screenshot from 2019-12-02 09-29-32

Here is the successful Web Portal mapping: mapping_web_portal.zip