Package net.sf.basedb.core

Class Update

java.lang.Object
net.sf.basedb.core.Update
public final class Update extends Object
This class contains static methods used to update items already in the database.
Schema version updates
Schema version Description
90 The schema as released in BASE 2.17. For information about schema changes before this check the BASE 2.17 code.
100 The schema as released in BASE 3.0. We don't list all changes here.
101 and 102 Fixes an issue with duplicate FileSetMemberData entries due to a bug in the upgrade program. Make sure that the unique constraint that should prevent duplicates exists.
103 Added ReporterCloneTemplateData and related classes. No special update is required.
104 Make ExperimentData AnnotatableData. No special update is required.
105 Added ItemSubtypeData.getPushAnnotations(). All existing subtypes are set to 'false'.
106 Added BioPlateData.getEntryDate() and BioPlateData.getEventDate(). All existing bioplates get a null value.
107 Added BioPlateTypeData.getStorageType() All existing bioplate types get a null value.
108 Added BioPlateData.getSection(), BioPlateData.getTray() and BioPlateData.getPosition() All existing bioplates get null values.
109 and 110 Added DerivedBioAssayData.getPhysicalBioAssays() and DerivedBioAssayData.getParents() and removed DerivedBioAssayData.getPhysicalBioAssay() and DerivedBioAssayData.getParent(). Existing derived bioassays are updated in a two-step procedure. The first step is to copy existing information to the new tables and the second step is to drop columns that are no longer needed.
111 Not an actual database schema change, but we need to remove annotation sets that have been created without any annotations by the annotation importer and BASE 1->2 migration.
112 Not an actual database schema change, but we need to fix the parent_id and parent_type columns in the BioMaterials table to really reflect what is in the BioMaterialEventSources2 table. For more info see BASE ticket: http://base.thep.lu.se/ticket/1745
113 Made Hardware, Software, Tag and BioMaterialList Annotatable items. No special database update is needed. Only increase the schema version.
114 Added ChangeHistoryDetailData.getOldValue() and ChangeHistoryDetailData.getNewValue(). An update that changes the log format for annotation changes is needed to make log entries using the same format.
115 Added AnnotationTypeData.getDisableLogOfValues(). The update should set the value for all existing annotation types to false.
116 Added JobData.getExternalId() and made JobData a ShareableData item. No special database update is needed. Only increase the schema version.
117 Added FileServerData.getRootPath() and FileServerData.getSshFingerprint(). No special database update is needed. Only increase the schema version.
118 Added SchemaVersionData.getAppId(). The update will set the app id for the current entry to 'net.sf.basedb.core' and the update the schema version.
119 Added AnnotationTypeData.getDisableInheritance(). The update will set the value to FALSE for all existing annotation types.
120 Added ItemListData and removed BioMaterialListData. The update will convert all existing biomaterial lists to item lists and make other changes as are requried to keep things working.
121 No actual schema change, but we need to fix incorrect item lists that has got a '0' member due to ticket http://base.thep.lu.se/ticket/1945.
122 Added RootRawBioAssayData. Existing raw bioassay -- Experiment links are moved over to this item.
123 Remove AnnotationSetData.getInheritedSets(). Existing inherited annotations sets will be converted to inherited annotations.
124 Inherited annotations are moved from the "InheritedAnnotations" table to the "Annotations" table.
125 Experimental factor annotations for an experiment which are found as either primary or inherited annotations on the raw bioassays in the experiment are inherited by the RootRawBioAssayData items. This means that existing experiments will continue to have access to the experimental factors as before.
126 Fixes the conversion formula for Fahrenheit. Existing annotation values that are re-calculated to the corrent result.
127 Added ParameterValueData.isMasked(). All existing parameters are set to false.
128 Added KitData and other things related to it.
129 and 130 Added RemovableData.getRemovedBy() and removed RemovableData.isRemoved(). Existing items that has been flagged for removal are updated by setting the removedBy property to either the owner of the item or, if the item doesn't have an owner, to the root user. In a second step the removed columns are dropped from all tables. Note that this must be done in adjustExistingItems(ProgressReporter, int, String, String) since otherwise the installation will try to create new items in table that still has the 'removed' column but it will not accept 'null' values and the installation will fail.
131 Not an actual database schema change, but we need to fix issues with old date values in the change history table. See http://base.thep.lu.se/ticket/1989 for more information.
132 Not an actual database schema change, but we need to fix issues with annotation entries that have no values. See http://base.thep.lu.se/ticket/1992 for more information.
133 Added SessionData.getAuthenticationMethod(). No special database update is needed. Only increase the schema version.
134 Made Project annotatable. No special database update is needed. Only increase the schema version.
135 Added support for project specific annotations. Added AnnotationTypeData.getProjectAnnotations(). Existing annotation types are set to FALSE. Added AnnotationData.getProjectId() and AnnotationData.getOverrideId(). Existing annotations set both values to 0.
136 Added JobData.getNode() and JobData.getItemSubtype(). Job entries which have a server value containing '[...]' are updated so that the part within '[...]' is moved to the node column.
137 Added FileServerData.getFingerprintType(). File server entries which have a SSH fingerprint value are updated to "MD5".
138 Added NewsData.isSticky(). The update should set the value for all existing news items to false.
139 Added UserDeviceData and related changes in UserData, ClientData and SessionData classes.
140 Added SessionData.getLocation(), SessionData.getLocationLatitude() and SessionData.getLocationLongitude(). No special database update is needed. Only increase the schema version.
141 Added FileServerData.getSshPrivateKey(), FileServerData.getSshPrivateKeyPassword() and FileServerData.getSshPrivateKeyFormat(). No special database update is needed. Only increase the schema version.
142 Added the default password login form. It needs to be disabled by default which is triggered by the schema version update. No actual database change.
143 and 144 Remvoving support for secondary storage. FileData.action has been deleted. The update works in two step and the first step is to set FileData.location=0 (offline) on all files with FileData.location=2 (secondary) and remove filters on the action column The second step is to drop the action column.
145 Added AnnotationTypeData.isIdentifier(). The update will set the value to FALSE for all existing annotation types.
146 and 147 Removed support for spot images:
  • SpotImageCreator plug-in was removed. The entry in the database is marked as disabled.
  • The "SpotImages" table is dropped from the database.
148 Added UserDeviceData.isVerified(). The update will set the value to TRUE for all existing devices.
149 Made File annotatable. No special database update is needed. Only increase the schema version.
150 Added ItemListSyncFilterData.getFilterGroup(), ItemListSyncFilterData.getLastSyncProperties(), ItemListData.getSizeAtLastSync(), ItemListData.getMd5AtLastSync(). The update will set the filterGroup value to 'A+' for all existing filters and generate a lastSyncProperties value from current settings. The update will also set sizeAtLastSync to -1 for existing item lists.
151 Added ChangeHistoryData.getName(). The update will generate a default name for all existing entries based on the registred job, plug-in, client, etc.
152 Added PluginConfiguration.isDisabled(). The update will set the value to FALSE for all existing configurations.
153 Made FileServer annotatable. No special database update is needed. Only increase the schema version.
154 Added: The update will change all contexts with an empty subcontext to "0.0".
Version:
2.0
Author:
Nicklas
Last modified
$Date: 2024-10-29 09:26:17 +0100 (Tue, 29 Oct 2024) $

  • Field Details

    • log

      private static final Logger log
      Log core events.

  • Constructor Details

    • Update

      public Update()

  • Method Details

    • 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

    • verifyRootLoginAndPassword

      static void verifyRootLoginAndPassword(String login, String password)
      Verify the root user login and password. This method is called first in the update procedure, which means that tables, etc. are usually still from the old version.

    • getSchemaVersionInTransaction

      static int getSchemaVersionInTransaction(Session session, String appId) 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

    • getSchemaVersion

      static int getSchemaVersion(Session session, String appId) throws BaseException
      Throws:
      BaseException

    • setSchemaVersion

      static void setSchemaVersion(Session session, String appId, int schemaVersion, int build) 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

    • setSchemaVersion

      private static void setSchemaVersion(Session session, int schemaVersion) throws BaseException
      Throws:
      BaseException

    • setSchemaVersionInTransaction

      private static int setSchemaVersionInTransaction(Session session, int schemaVersion)
      Update the schema version version number using a new transaction.
      Parameters:
      schemaVersion - The new schema version number

    • adjustExistingItems

      public static void adjustExistingItems(ProgressReporter progress, int schemaVersion, 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:
      progress - An object implementing the ProgressReporter interface
      rootLogin - The root user login
      rootPassword - The root user password
      Throws:
      BaseException

    • updateToSchemaVersion101

      private static int updateToSchemaVersion101(Session session) throws BaseException
      Remove duplicate file set members.
      Returns:
      The new schema version (=101)
      Throws:
      BaseException

    • updateToSchemaVersion102

      private static int updateToSchemaVersion102(Session session) throws BaseException
      Add unique index on FileSetMembers(fileset_id,datafiletype_id,file_id)
      Returns:
      The new schema version (=102)
      Throws:
      BaseException

    • updateToSchemaVersion110

      private static int updateToSchemaVersion110(Session session, int currentSchemaVersion) throws BaseException
      Move derived bioassay parent items to different tables. Get rid of old columns in the DerivedBioAssays table.
      Returns:
      The new schema version (=110)
      Throws:
      BaseException

    • updateToSchemaVersion111

      private static int updateToSchemaVersion111(Session session, ProgressReporter progress) throws BaseException
      Remove annotation sets that have no annotation values and no inherited annotations.
      Returns:
      The new schema version (=111)
      Throws:
      BaseException

    • updateToSchemaVersion112

      private static int updateToSchemaVersion112(Session session, ProgressReporter progress) throws BaseException
      Ensure that parent_id and parent_type in BioMaterials table is correct when compared to BioMaterialEventSources2 table.
      Returns:
      The new schema version (=112)
      Throws:
      BaseException

    • updateToSchemaVersion114

      private static int updateToSchemaVersion114(Session session, ProgressReporter progress) throws BaseException
      Ensure that old log entries for annotation changes use the same text format that is used after this update.
      Returns:
      The new schema version (=114)
      Throws:
      BaseException

    • updateToSchemaVersion120

      private static int updateToSchemaVersion120(Session session) throws BaseException
      Transfer existing biomaterial lists to item lists.
      Returns:
      The new schema version (=120)
      Throws:
      BaseException

    • updateToSchemaVersion121

      private static int updateToSchemaVersion121(Session session) throws BaseException
      Remove all '0' members from item lists and decrease the size of the list with 1 where it is found.
      Returns:
      The new schema version (=121)
      Throws:
      BaseException

    • updateToSchemaVersion122

      private static int updateToSchemaVersion122(Session session) throws BaseException
      Move all entries from the "ExperimentRawBioAssays" table to "RootRawBioAssays".
      Returns:
      The new schema version (=122)
      Throws:
      BaseException

    • updateToSchemaVersion123

      private static int updateToSchemaVersion123(Session session) throws BaseException
      Convert all entries from the "InheritedAnnotationSets" table to entries in the "InheritedAnnotations" table.
      Returns:
      The new schema version (=123)
      Throws:
      BaseException

    • updateToSchemaVersion124

      private static int updateToSchemaVersion124(Session session) throws BaseException
      Inherited annotations in the "InheritedAnnotations" table must be converted to entries in the "Annotations" table with source=1 (INHERITED)
      Returns:
      The new schema version (=124)
      Throws:
      BaseException

    • updateToSchemaVersion125

      private static int updateToSchemaVersion125(Session session) throws BaseException
      Experimental factors in existing experiments are inherited to the RootRawBioAssayData items from the RawBioAssayData parents.
      Returns:
      The new schema version (=125)
      Throws:
      BaseException

    • updateToSchemaVersion126

      private static int updateToSchemaVersion126(Session session) throws BaseException
      Fix the conversion formula for Fahrenheit.
      Returns:
      The new schema version (=126)
      Throws:
      BaseException

    • updateToSchemaVersion131

      private static int updateToSchemaVersion131(Session session, ProgressReporter progress) throws BaseException
      Fix the old_values for date annotations in the change history. The fix will scan for all log entries related to DATE annotation types. By ordering the changes by timestamp it should be possible to set the old_value of UPDATE entries to the new_value of the previous entry for the same item and annotation.
      Returns:
      The new schema version (=131)
      Throws:
      BaseException

    • updateToSchemaVersion132

      private static int updateToSchemaVersion132(Session session, ProgressReporter progress) throws BaseException
      Delete annotation entries that have no values.
      Returns:
      The new schema version (=132)
      Throws:
      BaseException

    • updateToSchemaVersion136

      private static int updateToSchemaVersion136(Session session, ProgressReporter progress) throws BaseException
      Update the Jobs table by splitting the server value into a server+node value for all entries that contain '[..]'. That part withing the brackets are removed from the server column and moved to the node column.
      Returns:
      The new schema version (=136)
      Throws:
      BaseException

    • updateToSchemaVersion144

      private static int updateToSchemaVersion144(Session session, int currentSchemaVersion) throws BaseException
      Update the Files table by setting location=0 (offline) on all files with location=2 (secondary), remove the 'action' column and all stored contexts using the 'action' column. Update the QuotaValues table by removing all entries with location=2. Remove the 'secondary_location' column from the QuotaTypes table.
      Returns:
      The new schema version (=144)
      Throws:
      BaseException

    • updateToSchemaVersion147

      private static int updateToSchemaVersion147(Session session, int currentSchemaVersion) throws BaseException
      Returns:
      The new schema version (=147)
      Throws:
      BaseException

    • updateToSchemaVersion151

      private static int updateToSchemaVersion151(Session session, int currentSchemaVersion, ProgressReporter progress) throws BaseException
      Returns:
      The new schema version (=151)
      Throws:
      BaseException

    • updateToSchemaVersion154

      private static int updateToSchemaVersion154(Session session, int currentSchemaVersion, ProgressReporter progress) throws BaseException
      Throws:
      BaseException

    • loadIdToNameMap

      private static Map<Integer,String> loadIdToNameMap(Session session, String sql)

    • recalculateRemainingQuantity

      public static int recalculateRemainingQuantity(ProgressReporter progress) throws BaseException
      Vefify and update the remaining quantity of all biomaterials.
      Returns:
      The number of biomaterial fixed
      Throws:
      BaseException

    • recalculateFreeWells

      public static int recalculateFreeWells(ProgressReporter progress) throws BaseException
      Vefify and update the free wells of all bioplates.
      Returns:
      The number of bioplates fixed
      Throws:
      BaseException

    • convertPresets

      public static void convertPresets(ProgressReporter progress) throws BaseException
      Convert presets to use subtype/subcategories if they have filters that are matching existing configuration.
      Throws:
      BaseException

    • convertSyncFilters

      public static void convertSyncFilters(ProgressReporter progress) throws BaseException
      Convert sync filters to use subtype if they have filters that are matching existing configuration.
      Throws:
      BaseException

    • getTableInfo

      private static TableInfo getTableInfo(Session session, String tableName) throws SQLException
      Throws:
      SQLException

    • dropColumn

      private static void dropColumn(Session session, String tableName, String columnName, ProgressReporter progress) throws SQLException
      Throws:
      SQLException

    • dropIndex

      private static void dropIndex(Session session, boolean unique, String tableName, String... columnNames) throws SQLException
      Throws:
      SQLException

    • createIndex

      private static void createIndex(Session session, boolean unique, String indexName, String tableName, String... columnNames) throws SQLException
      Throws:
      SQLException

    • dropNotNullConstraint

      private static void dropNotNullConstraint(Session session, String tableName, String columnName, String mySqlDataType)

    • dropTable

      private static void dropTable(Session session, String tableName)

    • removeContext

      private static void removeContext(Session session, int itemType)
      Remove context-related information for the given item type.

    • cleanContextFromProperty

      private static void cleanContextFromProperty(Session session, Item itemType, String propertyName, String replacementPropertyName, boolean forceRemoveFilter)

    • replaceInCommaSeparatedList

      private static String replaceInCommaSeparatedList(String list, String find, String replacement)