Update (BASE 2.17.2 API documentation)

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2.17.2: 2011-06-17

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net.sf.basedb.core
Class Update

java.lang.Object
  net.sf.basedb.core.Update

public final class Update
extends Object
extends Object

This class contains static methods used to update items already in the database.

Schema version	Description
1	The original schema as released in RC1.
2	Added `FormulaData`. Added `JobData.getActiveProjectId()` property. The update must set all null values to 0. Added `SchemaVersionData`.
3	Added `ExperimentData.getExperimentalFactors()`. No need to update existing values.
4	Removed unique index for `HelpData.getExternalId()`.
5	Removed the AffyFeatures table and AffyFeatureData item. The table has to be removed manually.
6	Added label and description property to `ParameterValueData` Added `AnyToAnyData`
7	Added `RawBioAssayData.getHasData()`. The update must set all null values to true or false depending on the number of spots. Removed `FileAttachableData` from `RawBioAssayData`. Delete all `FormulaData` with affymetrix raw data type.
8	Added `HardwareData` to BioMaterialEvents and PlateEvents.
9	Added removable property to `HardwareTypeData` The update of existing data is done before the database is initiated.
10	Added `PluginDefinitionData.getSupportsConfigurations()` and `PluginDefinitionData.getRequiresConfiguration()` The update of existing data is done before the database is initiated.
11	Added `AnnotationTypeCategoryData`
12	Fixed incorrect `PlateMapping`:s. The 96-to-384 and 384-to-1536 were wrong. The fix renames and flags the old ones as removed.
13	Added `JobAgentData` and related classes. The update sets the `PluginDefinitionData.isTrusted()` property to true for all existing plugins.
14	Added `PluginPermission` and related classes. The update sets the `PluginDefinitionData.getUsePermissions()` property to true for all existing plugins.
15	Added `JobData.getSendMessage()` and `JobData.getStackTrace()` properties. The update sets the send message to true for all existing jobs.
16	Added `ExtraValueData.getJob()`.
17	Added `MimeTypeData.getFileType()`.
18	Added `ExperimentData.getDirectory()` and `ExperimentData.getTitle()`.
19	Added `PluginConfigurationData.getParameterVersion()` Added `JobData.getParameterVersion()` Changed `PluginConfigurationData.getConfigurationValues()`. The update sets the parameter version for existing jobs and configurations to 1 and copies data from the old table (PluginConfigurationValues) to the new table (VersionedPluginConfigurationValues)
20	Added `FormulaData.getColoring()` Added `ExtraValueTypeData.getColoring()` The update sets all color information to false and null for existing items. The install may later add coloring to some of the formulas.
21	Added `PluginDefinitionData.getAllowImmediateExecution()` The update sets the value to false for all existing plugins with a null value. The installation may later change the value to true for some plugins (ie. export plugins).
22	Added `ProtocolData.getParameters()` Added `AnnotationTypeData.isProtocolParameter()` The update sets the `isProtocolParameter` value to false for all existing annotation types with a null value.
23	Made `BioAssaySetData` and `BioAssayData` annotatable.
24	File parameters are stored as item parameters. The update will move existing file parameter into the ItemValues table.
25	Added `DiskUsageData.getItemType()`. The update will first set all null values to the correct item type by checking the diskconsumable items.
26	Added `AnnotationTypeData.getExternalId()`.
27	Added `ProjectData.getProjectDefaults()`.
28	Added `DataCubeData.getMaxRawMappingsForSpot()`. The update must query the dynamic database and set this value for all existing data cubes.
29	No changes at all except increasing the schema version number. The veryfication of remaining quantity is moved to next update of schema version.
30	No schema change as such, but we need to verify and possibly update the `MeasuredBioMaterialData.getRemainingQuantity()` since a bug may have caused it to have an incorrect value.
31	Added `FileData.isWriteProtected()`. Added `FileData.getLastUpdate()`. The update sets the `isWriteProtected` value to false for all existing files with a null value and `lastUpdate` to the date and time the internal file last was modified for existing files.
32	Added `GroupData.isDefault()`. Added `RoleData.isDefault()`. The update sets the `isDefault` value to false for all existing groups and roles with a null value.
33	Added `JobData.getRemoveJobWhenFinished()`. The update sets the `removeJobWhenFinished` value to false for all existing jobs.
34	Added `ContextData.getItemId()`. The update sets the `itemId` value to 0 for all existing contexts.
35	Check and update the size of File items, since they may be incorrect due to a bug in the File class. The MD5 value in that case also incorrect and is set to null. See ticket http://base.thep.lu.se/ticket/575
36	Added `FormulaData.getAverageMethod()`. Added `ExtraValueTypeData.getAverageMethod()`. The update sets the `averageMethod` to `Formula.AverageMethod.ARITHMETIC_MEAN`. See ticket http://base.thep.lu.se/ticket/648
37	Implement `ExtendableData` to `UserData` Only the schemaVersion number is increased in this class, the real update work is done when the database is re-build.
38	Added `JobData.getExperiment()`. The update sets the experiment for jobs that belong to a single transformation.
39	Remove AnyToAny links created by older versions of the Base1PluginExecuter plug-in.
40	Used to "Change invalid property filter on 'guiContexts.itemType' to '$ctx.itemType'", but since the source problem never was fixed this is now done in 43.
41	Added `MimeTypeData.getAutoCompress()` Added `FileData.isCompressed()`. Added `DirectoryData.getAutoCompress()`. The update sets all values on existing items to false.
42	No longer used.
43	Change invalid property filter on 'guiContexts.itemType' to '$ctx.itemType'". Was originally fixed by 40, but since the source problem never was fixed it must be done again.
44	Added `Platform`, `DataFileType` and a lot of related classes. The update will set a platform for all array designs and raw bioassays. For Affymetrix data it will move the CEL and CDF files from AnyToAny links into FileSet:s.
45	Added `PluginDefinitionData.getUseInternalJobQueue()` The update sets all values on existing items to true (if no job agent has been configured for the plug-in) or false (if a job agent is configured).
46	Made `PluginDefinitionData` and `PluginConfigurationData` annotatable. No special database update is needed. Only increase the schema version.
47	Added `JobData.getSignalTransporter()`. No special database update is needed. Only increase the schema version.
48	Added `ReporterData.getLastSource()`. No special database update is needed. Only increase the schema version.
49	Added `FeatureData.getExternalId()` Added `ArrayDesignData.getFeatureIdentificationMethod()` The update sets the identification method to COORDINATES for all existing array designs, and deletes the unique index on row, column, block on the Features table.
50	Added `DataFileTypeData.getValidatorJarPath()` Added `DataFileTypeData.getMetadataReaderJarPath()` No special database update is needed. Only increase the schema version.
51	External plug-in paths should be relative to the plugins.dir setting in base.config. The update loads all PluginDefinitions with a JAR path and convert the path with `PluginDefinition.convertToRelative(String)`.
52	Added `ArrayDesignData.getNumArrays()`. The update sets the value to 1 for all existing array designs. Added `HybridizationData.getNumArrays()`. The update sets the value to 1 for all existing hybridizations.
53	Added `ArrayDesignBlockData.getFeatureDiameter()`. The update sets the value to 0 for all existing array designs.
54	Added `RawBioAssayData.getJob()`. No special database update is needed. Only increase the schema version.
55	Added `ArrayDesignData.getJob()`. No special database update is needed. Only increase the schema version.
56	Added `ReporterListData.getSize()`. The update needs to calculate the number of reporters in existing lists.
57	Added `JobData.getJobAgentId()`. The update grants `Permission.SELECT_JOBAGENT` to the administrators, power users and job agent roles.
58	Added `DirectoryData.getAutoShare()`. The update sets the value to false for all directories.
59	Added: `BioAssaySetData.getFileSet()`. `BioAssaySetData.getNumFileReporters()`. `BioAssaySetData.getNumFileSpots()`. `BioAssayData.getNumFileSpots()`. `ExtraValueData.getFileSet()`. `ExtraValueData.getNumFileValues()`. The update sets the spot/reporter/value count to 0 for all existing bioassay sets and extra values.
60	Not a schema change as such. We need to update incorrect quota values for experiments. See http://base.thep.lu.se/ticket/1056
61	Added: `JobData.getPluginVersion()`. No special database update is needed. Only increase the schema version.
62	Added: `JobData.getContextItem()`. `JobData.getContextType()`. `JobData.getSubContext()`. No special database update is needed. Only increase the schema version.
63	Added: `JobData.isDryRun()`. The update will set the value for all existing jobs to false.
64	Added: `FileData.getCharacterSet()`. No special database update is needed. Only increase the schema version.
65	Added: `QuantityData`. `UnitData`. `UnitSymbolData`. `AnnotationData.getUnit()`. `AnnotationTypeData.getQuantity()`. No special database update is needed. Only increase the schema version.
66	Added: `BioPlateData`. `BioWellData`. No special database update is needed. Only increase the schema version.
67	Added: `BioMaterialListData`. No special database update is needed. Only increase the schema version.
68	Added: `ProjectData.getAutoPermission()`. The update sets the value for all existing project to 31 (=read, use, write, delete).
69	Added: `RegisteredData`. No special database update is needed. Only increase the schema version.
70	Added: `BioAssaySetData.getIntensityTransform()`. `FormulaData.getSourceIntensityTransform()` `FormulaData.getResultIntensityTransform()` The update sets the values for all existing bioassay sets to 0 (=no transform).
71	Deprecated: `BioAssaySetExporter`. No special database update is needed. Only increase the schema version.
72	Made `Protocol` an `Annotatable` item. No special database update is needed. Only increase the schema version.
73	Added `ChangeHistoryData` and `ChangeHistoryDetailData`. No special update is needed. Only increase the schema version.
74	Added `AnnotationData.getLastUpdate()`. No special update is needed. Only increase the schema version.
75	Added `GroupData.getHiddenMembers()`. The update sets the value for all existing groups to false.
76	Added `AnnotationSetData.getItemId()`. The update sets the value for all existing annotation sets.
77	Added `FormulaData.getValueType()`. The update will set the value for all existing formulas were it is possible to determine the correct type.
78	Added `ProtocolData.getExternalId()`. No special update is needed. Only increase the schema version.
79	Set database column Contexts.sort_property to null if it contains a literal 'null' string. Fix for #1463.
80	Added `BioPlateTypeData`, `BioWellData.getOriginalBioMaterial()`. All existing bio plates are assigned "Storage plate" as their plate type.
81	Added `FileData.getUrl()` and `FileServer`. No special update is needed. Only increase the schema version.
82	Added `PermissionTemplateData` and `ProjectData.getPermissionTemplate()`. No special update is needed. Only increase the schema version.
83	Added `JobData.getExecuteCommand()`. No special update is needed. Only increase the schema version.
84	Added `JobData.getScheduled()`. The update will set the scheduled date to the creation date for all existing jobs that is in WAITING status or higher.
85	Added `TimestampParameterValueData`. The update will change the `DateParameterValueData` to a date-only column type.
86	Fixes a bug in the "recently used settings" handling. The update will remove all settings ending with '.recent' that contains at least one colon (:). See http://base.thep.lu.se/ticket/1517 for more information.
87	Adds `UserData.getSendMessagesAsEmail()`. The update will set the value to FALSE for all existing users.
88	Adds `BioPlateData.isDestroyed()`. The update will set the value to FALSE for all existing bioplates.
89	Adds `BioPlateEventData`, `BioPlateEventTypeData`, `BioPlateEventParticipantData` and `BioMaterialEventData.getBioPlateEventParticipant()`. No special update is needed. Only increase the schema version.
90	Adds `BioPlateData.getFreeWells()`. The update will count the number of free wells on existing bio plates.

Version:: 2.0
Author:: Nicklas
Last modified: $Date: 2011-02-09 14:49:51 +0100 (Wed, 09 Feb 2011) $

Field Summary
`private static Logger`	`log` Log core events.

Constructor Summary
`Update()`

Method Summary
`private static void`	`addPluginPermission(org.hibernate.Session session, int pluginId, Item itemType, int granted, int denied)`
`static void`	`adjustExistingItems(boolean update, ProgressReporter progress, String rootLogin, String rootPassword)` Adjust the existing items in the database to be compatible with the latest mappings.
`private static int`	`getSchemaVersion(org.hibernate.Session session)` Get the current schema version number as it is stored in the database.
`private static void`	`setSchemaVersion(org.hibernate.Session session, int schemaVersion)` Update the database with a new schema version number.
`private static int`	`setSchemaVersionInTransaction(org.hibernate.Session session, int schemaVersion)` Update the schema version version number using a new transaction.
`static void`	`updateDatabase(ProgressReporter progress, String rootLogin, String rootPassword)` Update the database by modifying existing items to follow new requirements.
`private static int`	`updateToSchemaVersion10(SessionControl sc)` Load all plugins and call `PluginDefinition.loadPluginInformation(String, String, boolean)` for each one so that the `PluginDefinition.supportsConfigurations()` and `PluginDefinition.requiresConfiguration()` return correct values.
`private static int`	`updateToSchemaVersion19(org.hibernate.Session session)` Set JobData.getParameterVersion and PluginConfigurationData.getParameterVersion to 1 if they have null values.
`private static int`	`updateToSchemaVersion2(org.hibernate.Session session)` Set Jobs.project_id to 0 for all old jobs with a null value in this column.
`private static int`	`updateToSchemaVersion24(org.hibernate.Session session)` Move FileValues to ItemValues.
`private static int`	`updateToSchemaVersion25(org.hibernate.Session session)` Set the itemType property on all DiskUsageData items.
`private static int`	`updateToSchemaVersion28(SessionControl sc)` Find the number of raw mappings for the spot with the maximum number for each data cube
`private static int`	`updateToSchemaVersion30(org.hibernate.Session session)` Vefify and update the remaining quantity of all biomaterials.
`private static int`	`updateToSchemaVersion31(org.hibernate.Session session)` Set the writeProtected flag on all files with a null value to false.
`private static int`	`updateToSchemaVersion35(org.hibernate.Session session)` Check and update the file size and MD5 on existing file items since they may be incorrect
`private static int`	`updateToSchemaVersion38(org.hibernate.Session session)` Set the experiment for jobs that belong to a single transformation.
`private static int`	`updateToSchemaVersion39(org.hibernate.Session session)` Remove AnyToAny links created by older versions of Base1PluginExecuter
`private static int`	`updateToSchemaVersion4(org.hibernate.Session session)` Find the unique index on HelpTextData.externalId and remove it.
`private static int`	`updateToSchemaVersion42(org.hibernate.Session session)` Has been replaced with `updateToSchemaVersion44(SessionControl)`
`private static int`	`updateToSchemaVersion43(org.hibernate.Session session)` Update property filter on 'guiContexts.itemType' to '$ctx.itemType'
`private static int`	`updateToSchemaVersion44(SessionControl sc)` Set a platform for array designs and raw bioassays Change experiment raw data type if it is "affymetrix" to "platform.affymetrix" Change project default raw data type if it is "affymetrix" to "platform.affymetrix" Move CEL and CDF files into FileSet:s Remove filters on ArrayDesign.isAffyChip property Add READ permission to PLATFORM and DATAFILETYPE for all plug-ins working with ARRAYDESIGN or RAWBIOASSAY
`private static int`	`updateToSchemaVersion45(org.hibernate.Session session)` Update useInternalJobQueue for plug-ins.
`private static int`	`updateToSchemaVersion49(org.hibernate.Session session)` Find the unique index on Feature (row, column and block) and remove it.
`private static int`	`updateToSchemaVersion51(org.hibernate.Session session)` Change all plug-ins with an absolute JAR path to relative paths.
`private static int`	`updateToSchemaVersion56(org.hibernate.Session session)` Count the number of reporters in existing reporter lists.
`private static int`	`updateToSchemaVersion57(org.hibernate.Session session)` Grant `Permission.SELECT_JOBAGENT` permission to administrators, power users and job agent roles.
`private static int`	`updateToSchemaVersion60(org.hibernate.Session session)` Update incorrect quota values for experiments.
`private static int`	`updateToSchemaVersion7(org.hibernate.Session session)` Set RawBioAssays.has_data to true or false depending on the number of spots.
`private static int`	`updateToSchemaVersion76(org.hibernate.Session session, ProgressReporter progress)` Sets the `AnnotationSetData.getItemId()` for all annotation sets with a null value.
`private static int`	`updateToSchemaVersion77(org.hibernate.Session session)` Try to set the value type for as many formulas as possible.
`private static int`	`updateToSchemaVersion79(org.hibernate.Session session)` Set sort_property in Contexts table to null if it contains a literal string 'null'.
`private static int`	`updateToSchemaVersion80(org.hibernate.Session session)` Set the plate type for all existing bio plates to "Storage plate".
`private static int`	`updateToSchemaVersion84(org.hibernate.Session session)` Set the scheduled data for existing jobs.
`private static int`	`updateToSchemaVersion85(org.hibernate.Session session)` Change the date type for the DateValues.values column,.
`private static int`	`updateToSchemaVersion86(org.hibernate.Session session)` Remove all context settings with a name ending with '.recent' that has at least one colon (:) in the value.
`private static int`	`updateToSchemaVersion90(org.hibernate.Session session)` Calculate the value for BioPlateData.getFreeWells() for all existing bioplates.

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Field Detail

log

private static final Logger log

Log core events.

Constructor Detail

Update

public Update()

Method Detail

updateDatabase

public static void updateDatabase(ProgressReporter progress,
                                  String rootLogin,
                                  String rootPassword)
                           throws BaseException

Update the database by modifying existing items to follow new requirements.

Parameters:: progress - An object implementing the ProgressReporter interface; rootLogin - The root user login; rootPassword - The root user password
Throws:: BaseException

getSchemaVersion

private static int getSchemaVersion(org.hibernate.Session session)
                             throws BaseException

Get the current schema version number as it is stored in the database.

Returns:: The schema version number, or 0 if no schem version is found
Throws:: BaseException

setSchemaVersion

private static void setSchemaVersion(org.hibernate.Session session,
                                     int schemaVersion)
                              throws BaseException

Update the database with a new schema version number. This method should be called from an open transaction.

Parameters:: schemaVersion - The new schema version number
Throws:: BaseException

setSchemaVersionInTransaction

private static int setSchemaVersionInTransaction(org.hibernate.Session session,
                                                 int schemaVersion)

Update the schema version version number using a new transaction.

Parameters:: schemaVersion - The new schema version number

updateToSchemaVersion2

private static int updateToSchemaVersion2(org.hibernate.Session session)
                                   throws BaseException

Set Jobs.project_id to 0 for all old jobs with a null value in this column.

Returns:: The new schema version (=2)
Throws:: BaseException

updateToSchemaVersion4

private static int updateToSchemaVersion4(org.hibernate.Session session)
                                   throws BaseException

Find the unique index on HelpTextData.externalId and remove it.

Returns:: The new schema version (=4)
Throws:: BaseException

updateToSchemaVersion7

private static int updateToSchemaVersion7(org.hibernate.Session session)
                                   throws BaseException

Set RawBioAssays.has_data to true or false depending on the number of spots. Delete all Formulas with affymetrix raw data type

Returns:: The new schema version (=7)
Throws:: BaseException

updateToSchemaVersion10

private static int updateToSchemaVersion10(SessionControl sc)
                                    throws BaseException

Load all plugins and call PluginDefinition.loadPluginInformation(String, String, boolean) for each one so that the PluginDefinition.supportsConfigurations() and PluginDefinition.requiresConfiguration() return correct values.

Returns:: The new schema version (=10)
Throws:: BaseException

updateToSchemaVersion19

private static int updateToSchemaVersion19(org.hibernate.Session session)
                                    throws BaseException

Set JobData.getParameterVersion and PluginConfigurationData.getParameterVersion to 1 if they have null values. Copy existing info from PluginConfigurationValues to VersionedPluginConfigurationValues.

Returns:: The new schema version (=19)
Throws:: BaseException

updateToSchemaVersion24

private static int updateToSchemaVersion24(org.hibernate.Session session)
                                    throws BaseException

Move FileValues to ItemValues. Requires setting the ParameterValues.discrimitator to 10 for all parameter with a value of 9 and copying the contents of the FileValues table.

Returns:: The new schema version (=24)
Throws:: BaseException

updateToSchemaVersion25

private static int updateToSchemaVersion25(org.hibernate.Session session)
                                    throws BaseException

Set the itemType property on all DiskUsageData items.

Returns:: The new schema version (=25)
Throws:: BaseException

updateToSchemaVersion28

private static int updateToSchemaVersion28(SessionControl sc)
                                    throws BaseException

Find the number of raw mappings for the spot with the maximum number for each data cube

Returns:: The new schema version (=28)
Throws:: BaseException

updateToSchemaVersion30

private static int updateToSchemaVersion30(org.hibernate.Session session)
                                    throws BaseException

Vefify and update the remaining quantity of all biomaterials.

Returns:: The new schema version (=30)
Throws:: BaseException

updateToSchemaVersion31

private static int updateToSchemaVersion31(org.hibernate.Session session)

Set the writeProtected flag on all files with a null value to false. Set the lastUpdated property on all files with a null value to the last modified time of the internal file.

Returns:: The new schema version (=31)

updateToSchemaVersion35

private static int updateToSchemaVersion35(org.hibernate.Session session)

Check and update the file size and MD5 on existing file items since they may be incorrect

Returns:: The new schema version (=35)

updateToSchemaVersion38

private static int updateToSchemaVersion38(org.hibernate.Session session)

Set the experiment for jobs that belong to a single transformation.

Returns:: The new schema version (=38)

updateToSchemaVersion39

private static int updateToSchemaVersion39(org.hibernate.Session session)

Remove AnyToAny links created by older versions of Base1PluginExecuter

Returns:: The new schema version (=39)

updateToSchemaVersion42

private static int updateToSchemaVersion42(org.hibernate.Session session)

Has been replaced with updateToSchemaVersion44(SessionControl)

Returns:: The new schema version (=42)

updateToSchemaVersion43

private static int updateToSchemaVersion43(org.hibernate.Session session)

Update property filter on 'guiContexts.itemType' to '$ctx.itemType'

Returns:: The new schema version (=43)

updateToSchemaVersion44

private static int updateToSchemaVersion44(SessionControl sc)

Set a platform for array designs and raw bioassays
Change experiment raw data type if it is "affymetrix" to "platform.affymetrix"
Change project default raw data type if it is "affymetrix" to "platform.affymetrix"
Move CEL and CDF files into FileSet:s
Remove filters on ArrayDesign.isAffyChip property
Add READ permission to PLATFORM and DATAFILETYPE for all plug-ins working with ARRAYDESIGN or RAWBIOASSAY

addPluginPermission

private static void addPluginPermission(org.hibernate.Session session,
                                        int pluginId,
                                        Item itemType,
                                        int granted,
                                        int denied)

updateToSchemaVersion45

private static int updateToSchemaVersion45(org.hibernate.Session session)

Update useInternalJobQueue for plug-ins.

Returns:: The new schema version (=45)

updateToSchemaVersion49

private static int updateToSchemaVersion49(org.hibernate.Session session)
                                    throws BaseException

Find the unique index on Feature (row, column and block) and remove it.

Returns:: The new schema version (=49)
Throws:: BaseException

updateToSchemaVersion51

private static int updateToSchemaVersion51(org.hibernate.Session session)
                                    throws BaseException

Change all plug-ins with an absolute JAR path to relative paths.

Returns:: The new schema version (=51)
Throws:: BaseException

updateToSchemaVersion56

private static int updateToSchemaVersion56(org.hibernate.Session session)
                                    throws BaseException

Count the number of reporters in existing reporter lists.

Returns:: The new schema version (=56)
Throws:: BaseException

updateToSchemaVersion57

private static int updateToSchemaVersion57(org.hibernate.Session session)
                                    throws BaseException

Grant Permission.SELECT_JOBAGENT permission to administrators, power users and job agent roles.

Returns:: The new schema version (=57)
Throws:: BaseException

updateToSchemaVersion60

private static int updateToSchemaVersion60(org.hibernate.Session session)
                                    throws BaseException

Update incorrect quota values for experiments.

Returns:: The new schema version (=60)
Throws:: BaseException

updateToSchemaVersion76

private static int updateToSchemaVersion76(org.hibernate.Session session,
                                           ProgressReporter progress)
                                    throws BaseException

Sets the AnnotationSetData.getItemId() for all annotation sets with a null value.

Returns:: The new schema version (=76)
Throws:: BaseException

updateToSchemaVersion77

private static int updateToSchemaVersion77(org.hibernate.Session session)
                                    throws BaseException

Try to set the value type for as many formulas as possible.

Throws:: BaseException

updateToSchemaVersion79

private static int updateToSchemaVersion79(org.hibernate.Session session)
                                    throws BaseException

Set sort_property in Contexts table to null if it contains a literal string 'null'.

Throws:: BaseException

updateToSchemaVersion80

private static int updateToSchemaVersion80(org.hibernate.Session session)
                                    throws BaseException

Set the plate type for all existing bio plates to "Storage plate".

Throws:: BaseException

updateToSchemaVersion84

private static int updateToSchemaVersion84(org.hibernate.Session session)
                                    throws BaseException

Set the scheduled data for existing jobs.

Throws:: BaseException

updateToSchemaVersion85

private static int updateToSchemaVersion85(org.hibernate.Session session)
                                    throws BaseException

Change the date type for the DateValues.values column,.

Throws:: BaseException

updateToSchemaVersion86

private static int updateToSchemaVersion86(org.hibernate.Session session)
                                    throws BaseException

Remove all context settings with a name ending with '.recent' that has at least one colon (:) in the value.

Throws:: BaseException

updateToSchemaVersion90

private static int updateToSchemaVersion90(org.hibernate.Session session)
                                    throws BaseException

Calculate the value for BioPlateData.getFreeWells() for all existing bioplates.

Throws:: BaseException

adjustExistingItems

public static void adjustExistingItems(boolean update,
                                       ProgressReporter progress,
                                       String rootLogin,
                                       String rootPassword)
                                throws BaseException

Adjust the existing items in the database to be compatible with the latest mappings. No update to the schema version should be done here. The code must also consider the case that the update failes at a later stage and that the same update is executed again.

Parameters:: update - FALSE if it is an installation. TRUE if it is an update.; progress - An object implementing the ProgressReporter interface; rootLogin - The root user login; rootPassword - The root user password
Throws:: BaseException