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databaseChangeLog:

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# Application Blocks:    upgrade user to BasicUser
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- changeSet:
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    id:                  1495959628118-1
    author:              matijaobreza (generated)
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    changes:
    - renameTable:
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        newTableName:    userrole
        oldTableName:    user_role
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- changeSet:
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    id:                  1495959628118-3
    author:              matijaobreza (generated)
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    changes:
    - renameColumn:
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        columnDataType:  varchar(255)
        newColumnName:   fullName
        oldColumnName:   name
        remarks:         Full name of user
        tableName:       user
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- changeSet:
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    id:                  1495959628118-5
    author:              matijaobreza (generated)
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    changes:
    - addColumn:
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        tableName:       user
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        columns:
        - column:
            constraints:
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              nullable:  false
            name:        active
            type:        bit
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        - column:
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            name:        createdBy
            type:        bigint
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        - column:
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            name:        lastModifiedBy
            type:        bigint
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        - column:
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            name:        lastModifiedDate
            type:        datetime
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        - column:
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            name:        passwordExpires
            type:        datetime
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        - column:
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            name:        shortName
            type:        varchar(20)
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        - column:
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            name:        version
            type:        integer
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- changeSet:
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    id:                  1495959628118-6
    author:              mobreza
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    changes:
    - sql:
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        comment:         Migrate user.enabled to user.active = user.enabled;
        sql:             update user set active = enabled;
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- changeSet:
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    id:                  1495959628118-7
    author:              matijaobreza (generated)
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    changes:
    - renameColumn:
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        columnDataType:  varchar(20)
        newColumnName:   accountType
        oldColumnName:   loginType
        remarks:         Account type
        tableName:       user
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    - sql:
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        comment:         loginType#PASSWORD is changed to accountType#LOCAL
        sql:             update user set accountType = 'LOCAL' where accountType = 'PASSWORD';
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- changeSet:
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    id:                  1495959628118-8
    author:              mobreza
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    changes:
    - sql:
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        comment:         Assign user.version
        sql:             update user set version = 1 where version is null;
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- changeSet:
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    id:                  1495959628118-9
    author:              matijaobreza (generated)
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    changes:
    - addColumn:
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        tableName:       user
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        columns:
        - column:
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            name:        createdDate
            type:        datetime
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        - column:
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            name:        accountExpires
            type:        datetime
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- changeSet:
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    id:                  1495959628118-10
    author:              matijaobreza (generated)
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    changes:
    - addUniqueConstraint:
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        columnNames:     shortName
        constraintName:  UC_USERSHORTNAME_COL
        tableName:       user
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- changeSet:
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    id:                  1495959628118-11
    author:              matijaobreza (generated)
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    changes:
    - renameColumn:
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        columnDataType:  bigint
        oldColumnName:   user_id
        newColumnName:   userId
        tableName:       userrole
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    - renameColumn:
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        columnDataType:  varchar(50)
        oldColumnName:   user_role
        newColumnName:   role
        tableName:       userrole
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# ClassPK
- changeSet:
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    id:                  1496418311575-1
    author:              matijaobreza
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    changes:
    - renameTable:
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        newTableName:    classpk
        oldTableName:    classname
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- changeSet:
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    id:                  1496418311575-2
    author:              matijaobreza (generated)
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    changes:
    - renameColumn:
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        columnDataType:  varchar(250)
        oldColumnName:   className
        newColumnName:   classname
        tableName:       classpk
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# Country Boundingbox
- changeSet:
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    id:                  1496779094288-1
    author:              matijaobreza (generated)
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    changes:
    - addColumn:
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        tableName:       country
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        columns:
        - column:
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            name:        minLongitude
            type:        double
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        - column:
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            name:        maxLongitude
            type:        double
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        - column:
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            name:        minLatitude
            type:        double
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        - column:
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            name:        maxLatitude
            type:        double

# System accounts
- changeSet:
    id:                  1497558768000-1
    author:              matijaobreza (generated)
    changes:
    - sql:
        comment:         if user#sys==1 convert to accountType#SYSTEM
        sql:             update user set accountType = 'SYSTEM' where sys = 1;
    - dropColumn:
        tableName:       user
        columnName:      sys
    rollback:
    - addColumn:
        tableName:       user
        columnName:      sys
        type:            boolean
    - sql:
        comment:         accountType#SYSTEM to user#sys==1
        sql:             update user set sys = 1 where accountType = 'SYSTEM';
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- changeSet:
    id:                  1497558768000-2
    author:              maxymborodenko (generated)
    changes:
    - addColumn:
        tableName:       accession
        columns:
        - column:
            name:        doi
            type:        varchar(255)
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    rollback:
    - dropColumn:
        tableName:       accession
        columnName:      doi
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- changeSet:
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    id:                  1497558768000-3
    author:              maxymborodenko (generated)
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    changes:
    - addUniqueConstraint:
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        columnNames:     doi
        constraintName:  UQ_accession_doi
        tableName:       accession
    rollback:
    - dropUniqueConstraint:
        tableName:       accession
        constraintName:  UQ_accession_doi
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- changeSet:
    id:                  1497558768000-4
    author:              maxymborodenko (generated)
    changes:
    - addColumn:
        tableName:       accessionhistoric
        columns:
        - column:
            name:        doi
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            type:        varchar(255)
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- changeSet:
    id:                  1505830865186-1
    author:              maxymborodenko (generated)
    changes:
    - addColumn:
        tableName:       user
        columns:
        - column:
            name:        ftpPassword
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            type:        varchar(60)

# file-repository:0.9-SNAPSHOT
- changeSet:
    id:                  1506155384557-1
    author:              mobreza (generated)
    changes:
    - addColumn:
        columns:
        - column:
            constraints:
              nullable:  false
            name:        active
            type:        BIT(1)
        - column:
            constraints:
              nullable:  false
            name:        size
            type:        INT(10)
        - column:
            name:        lastModifiedBy
            type:        BIGINT(19)
        - column:
            name:        createdBy
            type:        BIGINT(19)
        tableName:       repositorydocument
    - addNotNullConstraint:
        columnDataType:  varchar(32)
        columnName:      md5Sum
        tableName:       repositorydocument
    - addNotNullConstraint:
        columnDataType:  varchar(40)
        columnName:      sha1Sum
        tableName:       repositorydocument
    - addUniqueConstraint:
        columnNames:     path, originalFilename
        constraintName:  UK_iubmgqa5xckodr6fbg6vnne0d
        tableName:       repositorydocument
    rollback:
    - dropUniqueConstraint:
        tableName:       repositorydocument
        constraintName:  UK_iubmgqa5xckodr6fbg6vnne0d
    - dropNotNullConstraint:
        tableName:       repositorydocument
        columnName:      sha1Sum
    - dropNotNullConstraint:
        tableName:       repositorydocument
        columnName:      md5Sum
    - dropColumn:
        tableName:       repositorydocument
        columnName:      active
    - dropColumn:
        tableName:       repositorydocument
        columnName:      size
    - dropColumn:
        tableName:       repositorydocument
        columnName:      lastModifiedBy
    - dropColumn:
        tableName:       repositorydocument
        columnName:      createdBy

- changeSet:
    id:                  1506155384557-2
    author:              mobreza (generated)
    changes:
    - addColumn:
        columns:
        - column:
            constraints:
              nullable:  false
            name:        active
            type:        BIT(1)
        - column:
            constraints:
              nullable:  false
            name:        size
            type:        INT(10)
        - column:
            name:        lastModifiedBy
            type:        BIGINT(19)
        - column:
            name:        createdBy
            type:        BIGINT(19)
        tableName:       repositoryfile
    - addNotNullConstraint:
        columnDataType:  varchar(32)
        columnName:      md5Sum
        tableName:       repositoryfile
    - addNotNullConstraint:
        columnDataType:  varchar(40)
        columnName:      sha1Sum
        tableName:       repositoryfile
    - addUniqueConstraint:
        columnNames:     path, originalFilename
        constraintName:  UK_27590ja5w3amn2yj2dryogm6n
        tableName:       repositoryfile
    rollback:
    - dropUniqueConstraint:
        tableName:       repositoryfile
        constraintName:  UK_27590ja5w3amn2yj2dryogm6n
    - dropNotNullConstraint:
        tableName:       repositoryfile
        columnName:      sha1Sum
    - dropNotNullConstraint:
        tableName:       repositoryfile
        columnName:      md5Sum
    - dropColumn:
        tableName:       repositoryfile
        columnName:      active
    - dropColumn:
        tableName:       repositoryfile
        columnName:      size
    - dropColumn:
        tableName:       repositoryfile
        columnName:      lastModifiedBy
    - dropColumn:
        tableName:       repositoryfile
        columnName:      createdBy


- changeSet:
    id:                  1506155384557-3
    author:              mobreza (generated)
    changes:
    - addColumn:
        columns:
        - column:
            constraints:
              nullable:  false
            name:        active
            type:        BIT(1)
        - column:
            name:        createdDate
            type:        DATETIME(19)
        - column:
            name:        createdBy
            type:        BIGINT(19)
        - column:
            name:        lastModifiedDate
            type:        DATETIME(19)
        - column:
            name:        lastModifiedBy
            type:        BIGINT(19)
        tableName:       repositorygallery
    rollback:
    - dropColumn:
        tableName:       repositorygallery
        columnName:      active
    - dropColumn:
        tableName:       repositorygallery
        columnName:      createdDate
    - dropColumn:
        tableName:       repositorygallery
        columnName:      createdBy
    - dropColumn:
        tableName:       repositorygallery
        columnName:      lastModifiedDate
    - dropColumn:
        tableName:       repositorygallery
        columnName:      lastModifiedBy

- changeSet:
    id:                  1506155384557-4
    author:              mobreza (generated)
    changes:
    - addColumn:
        columns:
        - column:
            constraints:
              nullable:  false
            name:        active
            type:        BIT(1)
        - column:
            constraints:
              nullable:  false
            name:        size
            type:        INT(10)
        - column:
            name:        lastModifiedBy
            type:        BIGINT(19)
        - column:
            name:        createdBy
            type:        BIGINT(19)
        tableName:       repositoryimage
    - addNotNullConstraint:
        columnDataType:  varchar(32)
        columnName:      md5Sum
        tableName:       repositoryimage
    - addNotNullConstraint:
        columnDataType:  varchar(40)
        columnName:      sha1Sum
        tableName:       repositoryimage
    - addUniqueConstraint:
        columnNames:     path, originalFilename
        constraintName:  UK_88rxxsqrm09geyh5go9ert6qe
        tableName:       repositoryimage
    rollback:
    - dropUniqueConstraint:
        tableName:       repositoryimage
        constraintName:  UK_88rxxsqrm09geyh5go9ert6qe
    - dropNotNullConstraint:
        tableName:       repositoryimage
        columnName:      sha1Sum
    - dropNotNullConstraint:
        tableName:       repositoryimage
        columnName:      md5Sum
    - dropColumn:
        tableName:       repositoryimage
        columnName:      active
    - dropColumn:
        tableName:       repositoryimage
        columnName:      size
    - dropColumn:
        tableName:       repositoryimage
        columnName:      lastModifiedBy
    - dropColumn:
        tableName:       repositoryimage
        columnName:      createdBy
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- changeSet:
    id:                  1506155384557-5
    author:              mobreza (generated)
    changes:
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    - dropForeignKeyConstraint:
        baseTableName:   repositorygalleryimage
        constraintName:  FK_rl4ttk3kctjy2nedwwlh8os3p
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    - addAutoIncrement:
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        tableName:       repositorygallery
        columnName:      id
        columnDataType:  BIGINT(20)
    - addForeignKeyConstraint:
        constraintName:  FK_rl4ttk3kctjy2nedwwlh8os3p
        baseTableName:   repositorygalleryimage
        baseColumnNames: galleryId
        referencedTableName: repositorygallery
        referencedColumnNames: id
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# OAuth from app-blocks-1.3-SNAPSHOT

- changeSet:
    id:                                1506594404000-2
    author:                            matijaobreza (generated)
    comment:                           naming strategy change for oauthclient
    changes:
    - renameColumn:
        columnDataType:                int
        newColumnName:                 accessTokenValidity
        oldColumnName:                 accessTokenValiditySeconds
        tableName:                     oauthclient
    - renameColumn:
        columnDataType:                int
        newColumnName:                 refreshTokenValidity
        oldColumnName:                 refreshTokenValiditySeconds
        tableName:                     oauthclient
    - renameColumn:
        columnDataType:                varchar(200)
        newColumnName:                 redirect
        oldColumnName:                 redirectUris
        tableName:                     oauthclient
    - renameColumn:
        columnDataType:                varchar(200)
        newColumnName:                 resource
        oldColumnName:                 resourceIds
        tableName:                     oauthclient
    - renameColumn:
        columnDataType:                varchar(200)
        newColumnName:                 scope
        oldColumnName:                 scope
        tableName:                     oauthclient
    - addColumn:
        tableName:                     oauthclient
        columns:
        - column:
            name:                      grants
            type:                      varchar(200)
        - column:
            name:                      autoApprove
            type:                      bit
            constraints:
              nullable:                false
        - column:
            name:                      autoApproveScope
            type:                      varchar(200)
    - dropColumn:
        tableName:                     oauthclient
        columnName:                    additional_information


- changeSet:
    id:                                application-blocks-security-1506594404000-2
    author:                            matijaobreza
    comment:                           Create 'oauthclientrole'
    changes:
    - createTable:
        tableName:                     oauthclientrole
        remarks:                       OAuth Client role list
        columns:
        - column:
            name:                      clientId
            type:                      bigint
            constraints:
              nullable:                false
        - column:
            name:                      oauthclientrole
            type:                      varchar(200)
            constraints:
              nullable:                false
    - addForeignKeyConstraint:
        constraintName:  FK_m2da63y1tfs7mmuv9rht8udt7
        baseTableName:   oauthclientrole
        baseColumnNames: clientId
        referencedTableName: oauthclient
        referencedColumnNames: id
        onDelete: CASCADE
        onUpdate: CASCADE


- changeSet:
    id:                 1507131481000-6
    author:             mobreza
    changes:
    - dropColumn:
        columnName:     grants
        tableName:      oauthclient
    - dropColumn:
        columnName:     authorities
        tableName:      oauthclient
    - renameColumn:
        columnDataType: varchar(200)
        newColumnName:  grants
        oldColumnName:  authorizedGrantTypes
        tableName:      oauthclient
    - sql:
        comment:        Migrate oauthclient , separator to ;
        sql:            update oauthclient set scope = replace(scope, ',', ';'), grants = replace(grants, ',', ';'), redirect = replace(redirect, ',', ';');
    - sql:
        comment:        Create oauthclientrole entries
        sql:            insert into oauthclientrole select id, 'USER' from oauthclient;

- changeSet:
    id:                 1507131481000-7
    author:             mobreza
    changes:
    - sql:
        comment:        Create oauthclientrole entries
        sql:            update oauthclientrole set oauthclientrole='CLIENT' where oauthclientrole='USER';


- changeSet:
    id: 1506605582245-23
    author: auto-generated
    changes:
    - dropTable:
        cascadeConstraints:            true
        tableName:                     oauthaccesstoken
    - createTable:
        columns:
        - column:
            constraints:
              nullable: false
            name: tokenId
            type: VARCHAR(100)
        - column:
            name: authentication
            type: LONGBLOB
        - column:
            name: authenticationId
            type: VARCHAR(100)
        - column:
            name: clientId
            type: VARCHAR(100)
        - column:
            name: refreshToken
            type: VARCHAR(100)
        - column:
            name: token
            type: LONGBLOB
        - column:
            name: username
            type: VARCHAR(100)
        tableName: oauthaccesstoken
    - addPrimaryKey:
        columnNames: tokenId
        constraintName: PRIMARY
        tableName: oauthaccesstoken
    - addUniqueConstraint:
        columnNames: authenticationId
        constraintName: UK_mk5dwyhm8t56m9ood899ec3hx
        tableName: oauthaccesstoken

- changeSet:
    id: 1506605582245-26
    author: auto-generated
    changes:
    - dropTable:
        cascadeConstraints:            true
        tableName:                     oauthrefreshtoken
    - createTable:
        columns:
        - column:
            constraints:
              nullable: false
            name: tokenId
            type: VARCHAR(100)
        - column:
            name: authentication
            type: LONGBLOB
        - column:
            name: token
            type: LONGBLOB
        tableName: oauthrefreshtoken
    - addPrimaryKey:
        columnNames: tokenId
        constraintName: PRIMARY
        tableName: oauthrefreshtoken
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- changeSet:
    id:                                application-blocks-security-1507137884-1
    author:                            matijaobreza
    comment:                           Add refreshToken#clientId
    changes:
    - addColumn:
        tableName:                     oauthrefreshtoken
        columns:
        - column:
            name:                      clientId
            type:                      varchar(100)
            constraints:
              nullable:                false


- changeSet:
    id:                                application-blocks-security-1507137884-2
    author:                            matijaobreza
    comment:                           Extend OAuth Tokens
    changes:
    - addColumn:
        tableName:                     oauthaccesstoken
        columns:
        - column:
            name:                      expiration
            type:                      datetime
    - addColumn:
        tableName:                     oauthrefreshtoken
        columns:
        - column:
            name:                      expiration
            type:                      datetime
        - column:
            name:                      username
            type:                      varchar(100)
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- changeSet:
    id:                   1506155384557-6
    author:               a.lugovskiy (generated)
    changes:
    - addColumn:
        tableName:        article
        columns:
        - column:
            name:         template
            type:         boolean
            defaultValue: false
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- changeSet:
    id:                 1508141056000-1
    author:             mobreza
    comment:            mysql doesn't really like the float type
    changes:
    - renameColumn:
        columnDataType: double
        newColumnName:  seqNo
        oldColumnName:  seqNo
        tableName:      accession
    - renameColumn:
        columnDataType: double
        newColumnName:  seqNo
        oldColumnName:  seqNo
        tableName:      accessionhistoric

- changeSet:
    id:                 1508141056000-2
    author:             mobreza
    comment:            AccessionData extends VersionedModel (adds active)
    changes:
    - addColumn:
        tableName:        accession
        columns:
        - column:
            constraints:
              nullable: false
            defaultValue: true
            name: active
            type: BIT(1)
    - addColumn:
        tableName:        accessionhistoric
        columns:
        - column:
            constraints:
              nullable: false
            defaultValue: true
            name: active
            type: BIT(1)

- changeSet:
    id:                        1508309640296-1
    author:                    mobreza
    comment:                   Add auditlog table
    changes:
    - createTable:
        columns:
        - column:
            autoIncrement:     true
            constraints:
              primaryKey:      true
            name:              id
            type:              BIGINT
        - column:
            constraints:
              nullable:        false
            name:              action
            type:              VARCHAR(10)
        - column:
            name:              createdBy
            type:              BIGINT
        - column:
            name:              entityId
            type:              BIGINT
        - column:
            constraints:
              nullable:        false
            name:              logdate
            type:              datetime(6)
        - column:
            name:              newState
            type:              LONGTEXT
        - column:
            name:              previousState
            type:              LONGTEXT
        - column:
            constraints:
              nullable:        false
            name:              prop
            type:              VARCHAR(50)
        - column:
            constraints:
              nullable:        false
            name:              classPk
            type:              BIGINT
        - column:
            name:              entityClassPk
            type:              BIGINT
        tableName:             auditlog
    - createIndex:
        columns:
        - column:
            name:              classPk
        indexName:             FK_ebwh7n4mlnm1e8ty78h6n279x
        tableName:             auditlog
    - createIndex:
        columns:
        - column:
            name:              entityClassPk
        indexName:             FK_p30btngbfm13fwebfkmklu4wn
        tableName:             auditlog
    - createIndex:
        columns:
        - column:
            name:              entityId
        - column:
            name:              classPk
        - column:
            name:              prop
        indexName:             UK_4jxfygboql2y3pd68nmudrgw
        tableName:             auditlog
    - addForeignKeyConstraint:
        baseColumnNames:       classPk
        baseTableName:         auditlog
        constraintName:        FK_ebwh7n4mlnm1e8ty78h6n279x
        deferrable:            false
        initiallyDeferred:     false
        onDelete:              NO ACTION
        onUpdate:              NO ACTION
        referencedColumnNames: id
        referencedTableName:   classpk
    - addForeignKeyConstraint:
        baseColumnNames:       entityClassPk
        baseTableName:         auditlog
        constraintName:        FK_p30btngbfm13fwebfkmklu4wn
        deferrable:            false
        initiallyDeferred:     false
        onDelete:              NO ACTION
        onUpdate:              NO ACTION
        referencedColumnNames: id
        referencedTableName:   classpk
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- changeSet:
    id:          1508316829948-1
    author:      m.borodenko
    changes:
    - sql:
        comment: if article#slug=='smtp.email-new-password' update to article#slug='smtp-email-new-password'
        sql:     update article set slug = 'smtp-email-new-password' where slug = 'smtp.email-new-password';
    - sql:
        comment: if article#slug=='smtp.email-password' update to article#slug='smtp-email-password'
        sql:     update article set slug = 'smtp-email-password' where slug = 'smtp.email-password';
    - sql:
        comment: if article#slug=='smtp.email-verification' update to article#slug='smtp-email-verification'
        sql:     update article set slug = 'smtp-email-verification' where slug = 'smtp.email-verification';
    - sql:
        comment: if article#slug=='smtp.material-request' update to article#slug='smtp-material-request'
        sql:     update article set slug = 'smtp-material-request' where slug = 'smtp.material-request';
    - sql:
        comment: if article#slug=='smtp.material-confirm-no-pid' update to article#slug='smtp-material-confirm-no-pid'
        sql:     update article set slug = 'smtp-material-confirm-no-pid' where slug = 'smtp.material-confirm-no-pid';
    - sql:
        comment: if article#slug=='smtp.material-confirm' update to article#slug='smtp-material-confirm'
        sql:     update article set slug = 'smtp-material-confirm' where slug = 'smtp.material-confirm';
    - sql:
        comment: if article#slug=='user.password-reset' update to article#slug='user-password-reset'
        sql:     update article set slug = 'user-password-reset' where slug = 'user.password-reset';
    - sql:
        comment: if article#slug=='user.password-reset-email-sent' update to article#slug='user-password-reset-email-sent'
        sql:     update article set slug = 'user-password-reset-email-sent' where slug = 'user.password-reset-email-sent';
    - sql:
        comment: if article#slug=='user.reset-password-instructions' update to article#slug='user-reset-password-instructions'
        sql:     update article set slug = 'user-reset-password-instructions' where slug = 'user.reset-password-instructions';
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# User and OAuthClient extend AclSid
- changeSet:
    id:                        1509390480000-1
    author:                    matijaobreza
    comment:                   Migrate ACL to app-blocks-1.3-SNAPSHOT
    changes:
    - dropForeignKeyConstraint:
        baseTableName:         acl_entry
        constraintName:        FK_fhuoesmjef3mrv0gpja4shvcr
    - dropForeignKeyConstraint:
        baseTableName:         acl_entry
        constraintName:        FK_i6xyfccd4y3wlwhgwpo4a9rm1
    - dropForeignKeyConstraint:
        baseTableName:         acl_object_identity
        constraintName:        FK_nxv5we2ion9fwedbkge7syoc3
    - dropUniqueConstraint:
        tableName:             acl_entry
        constraintName:        UK_gh5egfpe4gaqokya6s0567b0l
    - renameTable:
        oldTableName:          acl_sid
        newTableName:          acl_sid_backup
    - renameTable:
        oldTableName:          acl_entry
        newTableName:          acl_entry_backup
    - createTable:
        columns:
        - column:
            constraints:
              nullable:        true
            name:              type
            type:              INT
        - column:
            autoIncrement:     true
            constraints:
              primaryKey:      true
            name:              id
            type:              BIGINT
        - column:
            constraints:
              nullable:        false
            name:              active
            type:              BIT(1)
            defaultValue:      true
        - column:
            constraints:
              nullable:        false
            name:              version
            type:              INT
        - column:
            name:              createdBy
            type:              BIGINT
        - column:
            name:              createdDate
            type:              datetime(6)
        - column:
            name:              lastModifiedBy
            type:              BIGINT
        - column:
            name:              lastModifiedDate
            type:              datetime(6)
        - column:
            constraints:
              nullable:        false
            name:              principal
            type:              BIT(1)
        - column:
            constraints:
              nullable:        false
            name:              sid
            type:              VARCHAR(100)
        tableName:             acl_sid
    - createTable:
        columns:
        - column:
            autoIncrement:     true
            constraints:
              primaryKey:      true
            name:              id
            type:              BIGINT
        - column:
            constraints:
              nullable:        false
            name:              ace_order
            type:              BIGINT
        - column:
            constraints:
              nullable:        false
            name:              audit_failure
            type:              BIT(1)
        - column:
            constraints:
              nullable:        false
            name:              audit_success
            type:              BIT(1)
        - column:
            constraints:
              nullable:        false
            name:              granting
            type:              BIT(1)
        - column:
            constraints:
              nullable:        false
            name:              mask
            type:              BIGINT
        - column:
            constraints:
              nullable:        false
            name:              acl_object_identity
            type:              BIGINT
        - column:
            constraints:
              nullable:        false
            name:              sid
            type:              BIGINT
        tableName:             acl_entry
    - addUniqueConstraint:
        columnNames:           acl_object_identity, ace_order
        constraintName:        UK_gh5egfpe4gaqokya6s0567b0l
        tableName:             acl_entry
    # Migrate User data to AclSid
    - sql:
        comment:               Migrate all users with their existing IDs to acl_sid
        sql:                   >-
          insert into acl_sid
            (type, id, active, version, createdBy, createdDate, lastModifiedBy,
             lastModifiedDate, principal, sid)
          select
            1, id, active, version, createdBy, createdDate, lastModifiedBy,
            lastModifiedDate, true, uuid
          from user;
    - addForeignKeyConstraint:
        baseColumnNames:       id
        baseTableName:         user
        constraintName:        FK_8qtpnv06elxuryeuv1ac4ximm
        deferrable:            false
        initiallyDeferred:     false
        onDelete:              NO ACTION
        onUpdate:              NO ACTION
        referencedColumnNames: id
        referencedTableName:   acl_sid
    - dropColumn:
        tableName:             user
        columnName:            active
    - dropColumn:
        tableName:             user
        columnName:            version
    - dropColumn:
        tableName:             user
        columnName:            createdBy
    - dropColumn:
        tableName:             user
        columnName:            createdDate
    - dropColumn:
        tableName:             user
        columnName:            lastModifiedBy
    - dropColumn:
        tableName:             user
        columnName:            lastModifiedDate
    # Migrate OAuthClient data to AclSid
    - sql:
        comment:               Migrate OAuthClient to AclSid, they get new IDs, but we can find them with clientId as acl_sid.sid
        sql:                   >-
          insert into acl_sid
            (type, active, version, createdBy, createdDate, lastModifiedBy,
            lastModifiedDate, principal, sid)
          select
            2, active, version, createdBy, createdDate, lastModifiedBy,
            lastModifiedDate, true, clientId
          from oauthclient;
    - sql:
        comment:               Update OAuthClient#id values to their new IDs as per acl_sid
        sql:                   >-
          update oauthclient oa
            join acl_sid sid on sid.sid=oa.clientId
          set oa.id=sid.id
    - addForeignKeyConstraint:
        baseColumnNames:       id
        baseTableName:         oauthclient
        constraintName:        FK_j9t6kj0254t7knyn57orqyaxk
        deferrable:            false
        initiallyDeferred:     false
        onDelete:              NO ACTION
        onUpdate:              NO ACTION
        referencedColumnNames: id
        referencedTableName:   acl_sid
    - dropColumn:
        tableName:             oauthclient
        columnName:            active
    - dropColumn:
        tableName:             oauthclient
        columnName:            version
    - dropColumn:
        tableName:             oauthclient
        columnName:            createdBy
    - dropColumn:
        tableName:             oauthclient
        columnName:            createdDate
    - dropColumn:
        tableName:             oauthclient
        columnName:            lastModifiedBy
    - dropColumn:
        tableName:             oauthclient
        columnName:            lastModifiedDate

    # Migrate acl_object_identity#owner_sid because these have changed
    - sql:
        comment:               Migrate acl_object_identity#owner_sid because these have changed
        sql:                   >-
          update acl_object_identity oid
            join acl_sid_backup oldsid on oldsid.id=oid.owner_sid
            join acl_sid newsid on newsid.sid=oldsid.sid
          set oid.owner_sid=newsid.id
    - addForeignKeyConstraint:
        baseColumnNames:       owner_sid
        baseTableName:         acl_object_identity
        constraintName:        FK_nxv5we2ion9fwedbkge7syoc3
        deferrable:            false
        initiallyDeferred:     false
        onDelete:              NO ACTION
        onUpdate:              NO ACTION
        referencedColumnNames: id
        referencedTableName:   acl_sid
    # Migrate acl_sid_backup data for authorities (roles) -- i.e. everything that has not moved
    - sql:
        comment: Delete invalid authority records from acl_sid_backup (users and oauthclients)
        sql: >-
          delete oldsid from acl_sid_backup oldsid
            inner join acl_sid newsid on newsid.sid=oldsid.sid
          where oldsid.principal = 0;
    - sql:
        comment: Generate new acl_sid for ROLE entries (AclSid.type==0)
        sql: >-
          insert into acl_sid
            (type, active, version, createdBy, createdDate, lastModifiedBy,
            lastModifiedDate, principal, sid)
          select
            0, 1, 0, null, now(), null,
            now(), false, sid
          from acl_sid_backup where principal = 0;
    # Migrate acl_entry data
    - sql:
        comment: Migrate acl_entry_backup data to acl_entry, using new acl_sid#id instead of the old one
        sql: >-
          insert into acl_entry
            (ace_order, audit_failure, audit_success, granting, mask, acl_object_identity, sid)
          select
            e.ace_order, e.audit_failure, e.audit_success, e.granting, e.mask, e.acl_object_identity, newsid.id
          from acl_entry_backup e
            inner join acl_sid_backup oldsid on oldsid.id=e.sid
            inner join acl_sid newsid on newsid.sid=oldsid.sid;
    - dropTable:
        tableName: acl_sid_backup
    - dropTable:
        tableName: acl_entry_backup
    # Activate FK constraints
    - addForeignKeyConstraint:
        baseColumnNames:       acl_object_identity
        baseTableName:         acl_entry
        constraintName:        FK_fhuoesmjef3mrv0gpja4shvcr
        deferrable:            false
        initiallyDeferred:     false
        onDelete:              NO ACTION
        onUpdate:              NO ACTION
        referencedColumnNames: id
        referencedTableName:   acl_object_identity
    - addForeignKeyConstraint:
        baseColumnNames:       sid
        baseTableName:         acl_entry
        constraintName:        FK_i6xyfccd4y3wlwhgwpo4a9rm1
        deferrable:            false
        initiallyDeferred:     false
        onDelete:              NO ACTION
        onUpdate:              NO ACTION
        referencedColumnNames: id
        referencedTableName:   acl_sid
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# Use user#email as acl_sid#sid
- changeSet:
    id:                        1513620354000-1
    author:                    matijaobreza
    comment:                   Use user#email as acl_sid#sid
    changes:
    - sql:
        comment: Inner join acl_sid with user on id and update acl_sid#sid with user#email
        sql: >-
          update acl_sid inner join user on user.id=acl_sid.id
            set acl_sid.sid = user.email;
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# DS2
- changeSet:
    id:                  1525172348000-1
    author:              Matija Obreza
    comment:             Renaming DS2 tables
    changes:
    - renameTable:
        newTableName:    ds2column
        oldTableName:    ds2descriptor
    - renameTable:
        newTableName:    ds2descriptor
        oldTableName:    descriptor
    - renameColumn:
        columnDataType:  BIGINT
        newColumnName:   dsc
        oldColumnName:   dsd
        remarks:         Dataset column
        tableName:       ds2value
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# Upgrade to appliation-blocks:1.4-SNAPSHOT
- changeSet:
    id:            1526423063000-1
    author:        mobreza
    comment:       Add lastLogin to User
    changes:
    - addColumn:
        columns:
        - column:
            name:  lastLogin
            type:  datetime(6)
        tableName: user
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- changeSet:
    id:      1530443149000-2
    author:  mobreza
    comment: Replace blanks with null and delete empty records
    changes:
    - sql:
        sql: update accession set acceUrl = null where acceUrl = '';
    - sql:
        sql: update accession set acqDate = null where acqDate = '';
    - sql:
        sql: update accessionalias set usedBy = null where usedBy = '';
    - sql:
        sql: delete from accessionalias where name = '' and (usedBy is null or instCode is null);
    - sql:
        sql: update accessionbreeding set breederCode = NULL where breederCode = '';
    - sql:
        sql: update accessionbreeding set pedigree = NULL where pedigree = '';
    - sql:
        sql: delete from accessionbreeding where pedigree is null and breederCode is null;
    - sql:
        sql: update accessioncollect set collDate = null where collDate = '';
    - sql:
        sql: update accessioncollect set collSite = null where collSite = '';
    - sql:
        sql: update accessioncollect set collCode = null where collCode = '';
    - sql:
        sql: update accessioncollect set collNumb = null where collNumb = '';
    - sql:
        sql: update accessioncollect set collMissId = null where collMissId = '';
    - sql:
        sql: update accessioncollect set collName = null where collName = '';
    - sql:
        sql: update accessioncollect set collInstAddress = null where collInstAddress = '';
    - sql:
        sql: delete from accessioncollect where collDate = null and collSite = null and collCode = null and collNumb = null and collMissId = null and collName = null and collInstAddress = null and collSrc = null;
    - sql:
        sql: update accessionexchange set acceNumb = null where acceNumb = '';
    - sql:
        sql: update accessionexchange set donorInst = null where donorInst = '';
    - sql:
        sql: update accessionexchange set donorName = null where donorName = '';
    - sql:
        sql: delete from accessionexchange where acceNumb is null and donorInst is null and donorName is null;
    - sql:
        sql: delete from auditlog where classPk = (select id from classpk where classname='org.genesys2.server.model.genesys.PDCI');
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#
# Upgrade Genesys model: relationships flips
#
- changeSet:
    id: 1531216028000-1
    author: mobreza (generated)
    changes:
    - renameTable:
        newTableName:    accession_alias
        oldTableName:    accessionalias
    - renameTable:
        newTableName:    accession_collect
        oldTableName:    accessioncollect
    - renameTable:
        newTableName:    accession_geo
        oldTableName:    accessiongeo
    - renameTable:
        newTableName:    accession_historic
        oldTableName:    accessionhistoric
    - renameTable:
        newTableName:    accession_list
        oldTableName:    accelist
    - renameTable:
        newTableName:    accession_listitem
        oldTableName:    accelistitems
    - renameTable:
        newTableName:    accession_remark
        oldTableName:    accessionremark
    - renameTable:
        newTableName:    grin_taxonomy
        oldTableName:    GrinTaxonomy


- changeSet:
    id: 1531216028024-2
    author: mobreza (generated)
    changes:
    - createTable:
        columns:
        - column:
            constraints:
              nullable: false
            name: accessionId
            type: BIGINT
        - column:
            constraints:
              nullable: false
            name: breederCode
            type: VARCHAR(9)
        tableName: accession_breedercode
    - addPrimaryKey:
        columnNames: accessionId, breederCode
        constraintName: PRIMARY
        tableName: accession_breedercode
    - addForeignKeyConstraint:
        baseColumnNames: accessionId
        baseTableName: accession_breedercode
        constraintName: FK_i24m3cu3iutcu874affqlph62
        deferrable: false
        initiallyDeferred: false
        onDelete: NO ACTION
        onUpdate: NO ACTION
        referencedColumnNames: id
        referencedTableName: acce

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- changeSet:
    id: 1531216028024-2b
    author: mobreza (generated)
    changes:
    - createTable:
        columns:
        - column:
            constraints:
              nullable: false
            name: accessionId
            type: BIGINT
        - column:
            constraints:
              nullable: false
            name: breederName
            type: VARCHAR(250)
        tableName: accession_breedername
    - addPrimaryKey:
        columnNames: accessionId, breederName
        constraintName: PRIMARY
        tableName: accession_breedername
    - addForeignKeyConstraint:
        baseColumnNames: accessionId
        baseTableName: accession_breedername
        constraintName: FK_k4abe2rmtbjbvs1uxv1gv9vyj
        deferrable: false
        initiallyDeferred: false
        onDelete: NO ACTION
        onUpdate: NO ACTION
        referencedColumnNames: id
        referencedTableName: acce

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- changeSet:
    id: 1531216028024-4
    author: mobreza (generated)
    changes:
    - createTable:
        columns:
        - column:
            constraints:
              nullable: false
            name: collectId
            type: BIGINT
        - column:
            constraints:
              nullable: false
            name: collCode
            type: VARCHAR(128)
        tableName: accession_collect_code
    - addPrimaryKey:
        columnNames: collectId, collCode
        constraintName: PRIMARY
        tableName: accession_collect_code
    - addForeignKeyConstraint:
        baseColumnNames: collectId
        baseTableName: accession_collect_code
        constraintName: FK_p16on5ehgaa05ut41f87umkfa
        deferrable: false
        initiallyDeferred: false
        onDelete: NO ACTION
        onUpdate: NO ACTION
        referencedColumnNames: id
        referencedTableName: accession_collect

- changeSet:
    id: 1531216028024-5
    author: mobreza (generated)
    changes:
    - createTable:
        columns:
        - column:
            constraints:
              nullable: false
            name: collectId
            type: BIGINT
        - column:
            constraints:
              nullable: false
            name: collInstAddress
            type: VARCHAR(128)
        tableName: accession_collect_instaddr
    - addPrimaryKey:
        columnNames: collectId, collInstAddress
        constraintName: PRIMARY
        tableName: accession_collect_instaddr
    - addForeignKeyConstraint:
        baseColumnNames: collectId
        baseTableName: accession_collect_instaddr
        constraintName: FK_t9qrwws135bnmm0kh8fywg5j2
        deferrable: false
        initiallyDeferred: false
        onDelete: NO ACTION
        onUpdate: NO ACTION
        referencedColumnNames: id
        referencedTableName: accession_collect


- changeSet:
    id: 1531216028024-6
    author: mobreza (generated)
    changes:
    - createTable:
        columns:
        - column:
            constraints:
              nullable: false
            name: collectId
            type: BIGINT
        - column:
            constraints:
              nullable: false
            name: collName
1408
            type: VARCHAR(250)
Matija Obreza's avatar
Matija Obreza committed
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        tableName: accession_collect_name
    - addPrimaryKey:
        columnNames: collectId, collName
        constraintName: PRIMARY
        tableName: accession_collect_name
    - addForeignKeyConstraint:
        baseColumnNames: collectId
        baseTableName: accession_collect_name
        constraintName: FK_g6h5uuvq16105ljx8r1jjxojr
        deferrable: false
        initiallyDeferred: false
        onDelete: NO ACTION
        onUpdate: NO ACTION
        referencedColumnNames: id
        referencedTableName: accession_collect

- changeSet:
    id: 1531216028024-7
    author: mobreza (generated)
    changes:
    - createTable:
        columns:
        - column:
            constraints:
              nullable: false
            name: accessionId
            type: BIGINT
        - column:
            constraints:
              nullable: false
            name: duplSite
            type: VARCHAR(9)
        tableName: accession_duplsite
    - addPrimaryKey:
        columnNames: accessionId, duplSite
        constraintName: PRIMARY
        tableName: accession_duplsite
    - addForeignKeyConstraint:
        baseColumnNames: accessionId
        baseTableName: accession_duplsite
        constraintName: FK_2se3c4vyb38ci81qch7siopbu
        deferrable: false
        initiallyDeferred: false
        onDelete: NO ACTION
        onUpdate: NO ACTION
        referencedColumnNames: id
        referencedTableName: acce

- changeSet:
    id: 1531216028024-13
    author: mobreza (generated)
    changes:
    - createTable:
        columns:
        - column:
            constraints:
              nullable: false
            name: accessionId
            type: BIGINT
        - column:
            constraints:
              nullable: false
            name: storage
            type: INT
        tableName: accession_storage
    - addPrimaryKey:
        columnNames: accessionId, storage
        constraintName: PRIMARY
        tableName: accession_storage
    - addForeignKeyConstraint:
        baseColumnNames: accessionId
        baseTableName: accession_storage
        constraintName: FK_2lk4y987jla0fka5nafkwmrbq
        deferrable: false
        initiallyDeferred: false
        onDelete: NO ACTION
        onUpdate: NO ACTION
        referencedColumnNames: id
        referencedTableName: acce

- changeSet:
    id:            1531216028024-15
    author:        mobreza
    changes:
    - addColumn:
        tableName: accession
        columns:
        - column:
            # constraints:
            #   nullable: false
            name:  genus
            type:  VARCHAR(100)
        - column:
            name:  ancest
            type:  LONGTEXT
        - column:
            name:  donorCode
            type:  VARCHAR(9)
        - column:
            name:  donorName
            type:  VARCHAR(300)
        - column:
            name:  donorNumb
            type:  VARCHAR(200)
        - column:
            name:  names
            type:  LONGTEXT
        - column:
            name:  otherIds
            type:  LONGTEXT

- changeSet:
    id: 1531216028024-15a
    author: mobreza (generated)
    changes:
    - renameColumn:
        columnDataType:  varchar(100)
        newColumnName:   duplSiteStr
        oldColumnName:   duplSite
        remarks:         MCPD DUPLSITE as string
        tableName:       accession
    - renameColumn:
        columnDataType:  varchar(100)
        newColumnName:   storageStr
        oldColumnName:   storage
        remarks:         MCPD STORAGE as string
        tableName:       accession
    - renameColumn:
        columnDataType:  varchar(3)
        newColumnName:   origCty
        oldColumnName:   orgCty
        remarks:         MCPD storage as string
        tableName:       accession

- changeSet:
    id: 1531216028024-15b
    author: mobreza (generated)
    changes:
    - addColumn:
        tableName: accession_historic
        columns:
        - column:
            # constraints:
            #   nullable: false
            name:  genus
            type:  VARCHAR(100)
        - column:
            name:  ancest
            type:  LONGTEXT
        - column:
            name:  donorCode
            type:  VARCHAR(9)
        - column:
            name:  donorName
            type:  VARCHAR(300)
        - column:
            name:  donorNumb
            type:  VARCHAR(200)
        - column:
            name:  names
            type:  LONGTEXT
        - column:
            name:  otherIds
            type:  LONGTEXT

- changeSet:
    id: 1531216028024-15c
    author: mobreza (generated)
    changes:
    - renameColumn:
        columnDataType:  varchar(100)
        newColumnName:   duplSiteStr
        oldColumnName:   duplSite
        remarks:         MCPD DUPLSITE as string
        tableName:       accession_historic
    - renameColumn:
        columnDataType:  varchar(100)
        newColumnName:   storageStr
        oldColumnName:   storage
        remarks:         MCPD STORAGE as string
        tableName:       accession_historic
    - renameColumn:
        columnDataType:  varchar(3)
        newColumnName:   origCty
        oldColumnName:   orgCty
        remarks:         MCPD storage as string
        tableName:       accession_historic


- changeSet:
    id: 1531216028024-16
    author: mobreza (generated)
    changes:
    - addColumn:
        columns:
        - column:
            name: collId
            type: BIGINT
        - column:
            name: geoId
            type: BIGINT
        - column:
            name: pdciId
            type: BIGINT
        tableName: acce
    - addUniqueConstraint:
        columnNames: collId
        constraintName: UK_8qrr86qim9fyaevm0gmneylnw
        tableName: acce
    - addUniqueConstraint:
        columnNames: geoId
        constraintName: UK_a4cq6l63j6xie0fwv806lfyhu
        tableName: acce
    - addUniqueConstraint:
        columnNames: pdciId
        constraintName: UK_ncmba94f9sebh9h056jqhukum
        tableName: acce

- changeSet:
    id: 1531219203066-4
    author: mobreza (generated)
    changes:
    - createIndex:
        columns:
        - column:
            name: acceNumb
        indexName: IX_acceNumb
        tableName: accession

- changeSet:
    id: 1531219203066-7
    author: mobreza (generated)
    changes:
    - dropForeignKeyConstraint:
        baseTableName: accession_collect
        constraintName: FK_3xjhvjcunn2ievi36gmuvf6nk
    - dropUniqueConstraint:
        constraintName: UK_3xjhvjcunn2ievi36gmuvf6nk
        tableName: accession_collect
    - addForeignKeyConstraint:
        baseColumnNames: collId
        baseTableName: acce
        constraintName: FK_8qrr86qim9fyaevm0gmneylnw
        deferrable: false
        initiallyDeferred: false
        onDelete: NO ACTION
        onUpdate: NO ACTION
        referencedColumnNames: id
        referencedTableName: accession_collect

- changeSet:
    id: 1531219203066-8
    author: mobreza (generated)
    changes:
    - dropForeignKeyConstraint:
        baseTableName: accession_geo
        constraintName: FK_mrtltk1iiohn7x6p6b9saxfee
    - dropUniqueConstraint:
        constraintName: UK_mrtltk1iiohn7x6p6b9saxfee
        tableName: accession_geo
    - addForeignKeyConstraint:
        baseColumnNames: geoId
        baseTableName: acce
        constraintName: FK_a4cq6l63j6xie0fwv806lfyhu
        deferrable: false
        initiallyDeferred: false
        onDelete: NO ACTION
        onUpdate: NO ACTION
        referencedColumnNames: id
        referencedTableName: accession_geo

- changeSet:
    id: 1531219203066-9
    author: mobreza (generated)
    changes:
    - dropForeignKeyConstraint:
        baseTableName: pdci
        constraintName: FK_c3fnk9quh9lou6hd1v5hpanbw
    - dropUniqueConstraint:
        constraintName: UK_offskcy4kgtcg89hcd8w9phmh
        tableName: pdci
    - addForeignKeyConstraint:
        baseColumnNames: pdciId
        baseTableName: acce
        constraintName: FK_ncmba94f9sebh9h056jqhukum
        deferrable: false
        initiallyDeferred: false
        onDelete: NO ACTION
        onUpdate: NO ACTION
        referencedColumnNames: id
        referencedTableName: pdci

- changeSet:
    id: 1531219203066-35
    author: mobreza (generated)
    changes:
    - modifyDataType:
        columnName: datum
        newDataType: varchar(100)
        tableName: accession_geo
    - modifyDataType:
        columnName: method
        newDataType: varchar(100)
        tableName: accession_geo
    - createIndex:
        columns:
        - column:
            name: latitude
        - column:
            name: longitude
        indexName: UK_98cgokk6e16eqowc7iemvshid
        tableName: accession_geo
    - createIndex:
        columns:
        - column:
            name: tileIndex
        indexName: UK_25vrycbl69i8q41ewm4p9m13r
        tableName: accession_geo

- changeSet:
    id: 1531219203066-43
    author: mobreza (generated)
    changes:
    - addNotNullConstraint:
        columnDataType: clob
        columnName: remark
        tableName: accession_remark
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- changeSet:
    id:      1531219203099-1
    author:  mobreza
    comment: Migrate data to new model
    changes:
    - sql:
        sql: >-
          drop table if exists t_collCode;
          create table if not exists t_collCode as
          select
            @num_e := 1 + LENGTH(collCode) - LENGTH(REPLACE(collCode, ';', '')) AS num_e,
            id, collCode,
            SUBSTRING_INDEX(collCode,';',1) as coll1,
            IF(@num_e > 1, SUBSTRING_INDEX(SUBSTRING_INDEX(collCode,';',2),';',-1), null) coll2,
            IF(@num_e > 2, SUBSTRING_INDEX(SUBSTRING_INDEX(collCode,';',3),';',-1), null) coll3,
            IF(@num_e > 3, SUBSTRING_INDEX(SUBSTRING_INDEX(collCode,';',3),';',-1), null) coll4
          from accession_collect where collCode is not null;
          insert into accession_collect_code (collectId,collCode)
            (select distinct id, coll1 from
              (select id, coll1 from t_collCode where coll1 is not null
               union all select id, coll2 from t_collCode where coll2 is not null
               union all select id, coll3 from t_collCode where coll3 is not null
               union all select id, coll4 from t_collCode where coll4 is not null) Q);
          drop table t_collCode;
    - dropColumn:
        columnName: collCode
        tableName: accession_collect

- changeSet:
    id:      1531219203099-2
    author:  mobreza
    comment: Migrate data to new model
    changes:
    - sql:
        sql: >-
          drop table if exists t_collInstAddress;
          create table if not exists t_collInstAddress as
          select
            @num_e := 1 + LENGTH(collInstAddress) - LENGTH(REPLACE(collInstAddress, ';', '')) AS num_e,
            id, collInstAddress,
            SUBSTRING_INDEX(collInstAddress,';',1) as coll1,
            IF(@num_e > 1, SUBSTRING_INDEX(SUBSTRING_INDEX(collInstAddress,';',2),';',-1), null) coll2,
            IF(@num_e > 2, SUBSTRING_INDEX(SUBSTRING_INDEX(collInstAddress,';',3),';',-1), null) coll3,
            IF(@num_e > 3, SUBSTRING_INDEX(SUBSTRING_INDEX(collInstAddress,';',3),';',-1), null) coll4
          from accession_collect where collInstAddress is not null;
          insert into accession_collect_instaddr (collectId,collInstAddress)
            (select distinct id, coll1 from
              (select id, coll1 from t_collInstAddress where coll1 is not null
               union all select id, coll2 from t_collInstAddress where coll2 is not null
               union all select id, coll3 from t_collInstAddress where coll3 is not null
               union all select id, coll4 from t_collInstAddress where coll4 is not null) Q);
          drop table t_collInstAddress;
    - dropColumn:
        columnName: collInstAddress
        tableName: accession_collect

- changeSet:
    id:      1531219203099-3
    author:  mobreza
    comment: Migrate data to new model
    changes:
    - sql:
        sql: >-
          drop table if exists t_collName;
          create table if not exists t_collName as
          select
            @num_e := 1 + LENGTH(collName) - LENGTH(REPLACE(collName, ';', '')) AS num_e,
            id, collName,
            SUBSTRING_INDEX(collName,';',1) as coll1,
            IF(@num_e > 1, SUBSTRING_INDEX(SUBSTRING_INDEX(collName,';',2),';',-1), null) coll2,
            IF(@num_e > 2, SUBSTRING_INDEX(SUBSTRING_INDEX(collName,';',3),';',-1), null) coll3,
            IF(@num_e > 3, SUBSTRING_INDEX(SUBSTRING_INDEX(collName,';',3),';',-1), null) coll4
          from accession_collect where collName is not null;
          insert into accession_collect_name (collectId,collName)
            (select distinct id, coll1 from
              (select id, coll1 from t_collName where coll1 is not null
               union all select id, coll2 from t_collName where coll2 is not null
               union all select id, coll3 from t_collName where coll3 is not null
               union all select id, coll4 from t_collName where coll4 is not null) Q);
          drop table t_collName;
    - dropColumn:
        columnName: collName
        tableName: accession_collect


- changeSet:
    id:      1531219203099-3
    author:  mobreza
    comment: Migrate data to new model
    changes:
    - sql:
        sql: >-
          drop table if exists t_collName;
          create table if not exists t_collName as
          select
            @num_e := 1 + LENGTH(collName) - LENGTH(REPLACE(collName, ';', '')) AS num_e,
            id, collName,
            SUBSTRING_INDEX(collName,';',1) as coll1,
            IF(@num_e > 1, SUBSTRING_INDEX(SUBSTRING_INDEX(collName,';',2),';',-1), null) coll2,
            IF(@num_e > 2, SUBSTRING_INDEX(SUBSTRING_INDEX(collName,';',3),';',-1), null) coll3,
            IF(@num_e > 3, SUBSTRING_INDEX(SUBSTRING_INDEX(collName,';',3),';',-1), null) coll4
          from accession_collect where collName is not null;
          insert into accession_collect_name (collectId,collName)
            (select distinct id, coll1 from
              (select id, coll1 from t_collName where coll1 is not null
               union all select id, coll2 from t_collName where coll2 is not null
               union all select id, coll3 from t_collName where coll3 is not null
               union all select id, coll4 from t_collName where coll4 is not null) Q);
          drop table t_collName;
    - dropColumn:
        columnName: collName
        tableName: accession_collect

- changeSet:
    id: 1531221360983-16
    author: mobreza (generated)
    changes:
    - sql:
        sql: >-
          update accessionbreeding B inner join accession A on A.id = B.accessionId set A.ancest = B.pedigree;
    - sql:
        sql: >-
          update accessionbreeding B inner join accession_historic A on A.id = B.accessionId set A.ancest = B.pedigree;

- changeSet:
    id: 1531221360983-16b
    author: mobreza (generated)
    changes:
    - sql:
        sql: >-
          drop table if exists t_breederCode;
          create table if not exists t_breederCode as
          select
            @num_e := 1 + LENGTH(breederCode) - LENGTH(REPLACE(breederCode, ';', '')) AS num_e,
            accessionId, breederCode,
            SUBSTRING_INDEX(breederCode,';',1) as coll1,
            IF(@num_e > 1, SUBSTRING_INDEX(SUBSTRING_INDEX(breederCode,';',2),';',-1), null) coll2,
            IF(@num_e > 2, SUBSTRING_INDEX(SUBSTRING_INDEX(breederCode,';',3),';',-1), null) coll3,
            IF(@num_e > 3, SUBSTRING_INDEX(SUBSTRING_INDEX(breederCode,';',3),';',-1), null) coll4
          from accessionbreeding where breederCode is not null;
          insert into accession_breedercode (accessionId,breederCode)
            (select distinct accessionId, coll1 from
              (select accessionId, coll1 from t_breederCode where coll1 is not null
               union all select accessionId, coll2 from t_breederCode where coll2 is not null
               union all select accessionId, coll3 from t_breederCode where coll3 is not null
               union all select accessionId, coll4 from t_breederCode where coll4 is not null) Q);
          drop table t_breederCode;
    - dropTable:
        tableName: accessionbreeding


- changeSet:
    id: 1531221360983-37
    author: mobreza (generated)
    changes:
    - sql:
        sql: >-
          update accession a inner join taxonomy2 t on t.id=a.taxonomyId2 set a.genus = t.genus;
    - sql:
        sql: >-
          update accession_historic a inner join taxonomy2 t on t.id=a.taxonomyId2 set a.genus = t.genus;

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# BUG: This kills mariadb when running as non-root in cluster mode
# - changeSet:
#     id: 1531221360983-37a
#     author: mobreza (generated)
#     comment: Move duplicates to accession_historic
#     changes:
#     - sql:
#         sql: >-
#           drop table if exists t_accessiondup;
#           create table t_accessiondup select min(id) minId from accession group by instituteId, genus, acceNumb having count(*) > 1;
#           insert into accession_historic (id, acceNumb, seqNo, acqDate, acqSrc, available, duplSiteStr, inSGSV, inTrust, instCode, mlsStat, origCty, sampStat, storageStr, orgCtyId, instituteId, taxonomyId2, taxGenus, historic, createdDate, lastModifiedDate, createdBy, lastModifiedBy, version, acceurl, cropName, cropId, doi, active, genus, ancest, donorCode, donorName, donorNumb, names, otherIds)
#             select id, acceNumb, seqNo, acqDate, acqSrc, available, duplSiteStr, inSGSV, inTrust, instCode, mlsStat, origCty, sampStat, storageStr, orgCtyId, instituteId, taxonomyId2, taxGenus, historic, createdDate, lastModifiedDate, createdBy, lastModifiedBy, version, acceurl, cropName, cropId, doi, active, genus, ancest, donorCode, donorName, donorNumb, names, otherIds from accession where id in (select minId from t_accessiondup);
#           delete from accession where id in (select minId from t_accessiondup);
#           drop table t_accessiondup;
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- changeSet:
    id:                 1531221360983-37b1
    author:             mobreza (generated)
    changes:
    - dropUniqueConstraint:
        constraintName: UK_975ha8nh9k5itsuvg4bd0853i
        tableName:      accession

- changeSet:
    id:                 1531221360983-37b2
    author:             mobreza (generated)
    changes:
    - dropUniqueConstraint:
        constraintName: UQ_accession_genus_inst
        tableName:      accession

- changeSet:
    id: 1531221360983-37c
    author: mobreza (generated)
    changes:
    - addNotNullConstraint:
        columnDataType: varchar(100)
        columnName: genus
        tableName: accession
    - addUniqueConstraint:
        columnNames: instituteId, genus, acceNumb
        constraintName: UQ_accession_genus_inst
        tableName: accession
    - addNotNullConstraint:
        columnDataType: varchar(100)
        columnName: genus
        tableName: accession_historic
    - dropColumn:
        columnName: taxGenus
        tableName: accession
    - dropColumn:
        columnName: taxGenus
        tableName: accession_historic


- changeSet:
    id: 1531221360983-36
    author: mobreza (generated)
    changes:
    - dropIndex:
        indexName: I_accessionalias_name
        tableName: accession_alias
    - dropColumn:
        columnName: instCode
        tableName: accession_alias

- changeSet:
    id: 1531221360983-29
    author: mobreza (generated)
    changes:
    - sql:
        sql: >-
          update accession_collect C inner join acce A on A.id = C.accessionId set A.collId = C.id;
    - dropColumn:
        columnName: accessionId
        tableName: accession_collect


- changeSet:
    id: 1531221360983-30
    author: mobreza (generated)
    changes:
    - sql:
        sql: >-
          update accession_geo G inner join acce A on A.id = G.accessionId set A.geoId = G.id;
    - dropColumn:
        columnName: accessionId
        tableName: accession_geo

- changeSet:
    id: 1531221360983-31
    author: mobreza (generated)
    changes:
    - sql:
        sql: >-
          update pdci P inner join acce A on A.id = P.accessionId set A.pdciId = P.id;
    - dropColumn:
        columnName: accessionId
        tableName: pdci

- changeSet:
    id: 1531221360983-116
    author: mobreza (generated)
    changes:
    - modifyDataType:
        columnName: uniqueAcceNumbs
        newDataType: boolean
        tableName: faoinstitute
    - addDefaultValue:
        columnDataType: boolean
        columnName: uniqueAcceNumbs
        defaultValueBoolean: false
        tableName: faoinstitute
    - modifyDataType:
        columnName: allowMaterialRequests
        newDataType: boolean
        tableName: faoinstitute
    - addDefaultValue:
        columnDataType: boolean
        columnName: allowMaterialRequests
        defaultValueBoolean: false
        tableName: faoinstitute

- changeSet:
    id: 1531221360983-18
    author: mobreza (generated)
    changes:
    - sql:
        sql: >-
          insert into accession_storage (accessionId, storage) select accessionId, storage from accessionstorage;
          insert into accession_storage (accessionId, storage) select accessionId, storage from accessionstorageh;
    - dropTable:
        tableName: accessionstorage
    - dropTable:
        tableName: accessionstorageh

- changeSet:
    id: 1531221360983-17
    author: mobreza (generated)
    changes:
    - sql:
        sql: >-
          update accessionexchange E inner join accession A on A.id=E.accessionId set A.donorCode=E.donorInst, A.donorName=E.donorName, A.donorNumb=E.acceNumb;
    - sql:
        sql: >-
          update accessionexchange E inner join accession_historic A on A.id=E.accessionId set A.donorCode=E.donorInst, A.donorName=E.donorName, A.donorNumb=E.acceNumb;
    - dropTable:
        tableName: accessionexchange


- changeSet:
    id: 1531221360981-1
    author: mobreza (generated)
    changes:
    - sql:
        sql: >-
          update accession set duplSiteStr = null where duplSiteStr like '%:%';
    - sql:
        sql: >-
          drop table if exists t_duplsite;
          create table if not exists t_duplsite as
          select
            @num_e := 1 + LENGTH(duplSiteStr) - LENGTH(REPLACE(duplSiteStr, ';', '')) AS num_e,
            id, duplSiteStr,
            SUBSTRING_INDEX(duplSiteStr,';',1) as coll1,
            IF(@num_e > 1, SUBSTRING_INDEX(SUBSTRING_INDEX(duplSiteStr,';',2),';',-1), null) coll2,
            IF(@num_e > 2, SUBSTRING_INDEX(SUBSTRING_INDEX(duplSiteStr,';',3),';',-1), null) coll3,
            IF(@num_e > 3, SUBSTRING_INDEX(SUBSTRING_INDEX(duplSiteStr,';',3),';',-1), null) coll4
          from accession where duplSiteStr is not null;
          insert into accession_duplsite (accessionId, duplSite)
            (select distinct id, coll1 from
              (select id, coll1 from t_duplsite where coll1 is not null
               union all select id, coll2 from t_duplsite where coll2 is not null
               union all select id, coll3 from t_duplsite where coll3 is not null
               union all select id, coll4 from t_duplsite where coll4 is not null) Q);
          drop table t_duplsite;


- changeSet:
    id: 1531221360981-2
    author: mobreza (generated)
    changes:
    - sql:
        sql: >-
          update accession_historic set duplSiteStr = null where duplSiteStr like '%:%';
    - sql:
        sql: >-
          drop table if exists t_duplsite;
          create table if not exists t_duplsite as
          select
            @num_e := 1 + LENGTH(duplSiteStr) - LENGTH(REPLACE(duplSiteStr, ';', '')) AS num_e,
            id, duplSiteStr,
            SUBSTRING_INDEX(duplSiteStr,';',1) as coll1,
            IF(@num_e > 1, SUBSTRING_INDEX(SUBSTRING_INDEX(duplSiteStr,';',2),';',-1), null) coll2,
            IF(@num_e > 2, SUBSTRING_INDEX(SUBSTRING_INDEX(duplSiteStr,';',3),';',-1), null) coll3,
            IF(@num_e > 3, SUBSTRING_INDEX(SUBSTRING_INDEX(duplSiteStr,';',3),';',-1), null) coll4
          from accession_historic where duplSiteStr is not null;
          insert into accession_duplsite (accessionId, duplSite)
            (select distinct id, coll1 from
              (select id, coll1 from t_duplsite where coll1 is not null
               union all select id, coll2 from t_duplsite where coll2 is not null
               union all select id, coll3 from t_duplsite where coll3 is not null
               union all select id, coll4 from t_duplsite where coll4 is not null) Q);
          drop table t_duplsite;

- changeSet:
    id:            1531483642000-1
    author:        mobreza
    changes:
    - createIndex:
        columns:
        - column:
            name:  instituteId
        - column:
            name:  seqNo
        indexName: IX_inst_seq
        tableName: accession
    - createIndex:
        columns:
        - column:
            name:  orgCtyId
        - column:
            name:  seqNo
        indexName: IX_cty_seq
        tableName: accession
    - createIndex:
        columns:
        - column:
            name:  taxonomyId2
        - column:
            name:  seqNo
        indexName: IX_taxa_seq
        tableName: accession

- changeSet:
    id:      1531483642000-2
    author:  mobreza
    comment: Remove trailing whitespace in taxonomy2 table
    changes:
    - sql:
        sql: >-
          update taxonomy2 set genus=trim(genus) where genus like '% ';
          update taxonomy2 set species=trim(species) where species like '% ';
          update taxonomy2 set subtaxa=trim(subtaxa) where subtaxa  like '% ';

- changeSet:
    id:      1531483642000-3
    author:  mobreza
    comment: Remove blanks in accession table
    changes:
    - sql:
        sql: >-
          update accession set acqSrc = null where acqSrc = '';

- changeSet:
    id:      1531483642000-4
    author:  mobreza
    comment: Remove blanks in accession table
    changes:
    - sql:
        sql: >-
          update accession set duplSiteStr = null where duplSiteStr = '';
          update accession set storageStr = null where storageStr = '';