Changeset 6081
- Timestamp:
- Aug 8, 2012, 10:02:14 AM (11 years ago)
- Location:
- trunk
- Files:
-
- 3 edited
-
config/dist/base.config (modified) (1 diff)
-
doc/src/docbook/admin/installation.xml (modified) (1 diff)
-
doc/src/docbook/appendix/update_warnings.xml (modified) (1 diff)
Legend:
- Unmodified
- Added
- Removed
-
trunk/config/dist/base.config
r5895 r6081 144 144 # ========================= 145 145 146 # Class name of the changelog factory; leave empty to disable the changelog 147 # changelog.factory = net.sf.basedb.core.log.db.DbLogManagerFactory 146 # Change history for items can be logged with the help of extensions. 147 # BASE ships with a built-in extension that log changes to the database. 148 # This is disabled by default, but can be enabled through the web 149 # interface: Adminstrate -> Plug-ins & extensions -> Overview 148 150 149 151 # If the "Change history" tab should be visible in the web interface -
trunk/doc/src/docbook/admin/installation.xml
r6072 r6081 45 45 46 46 <important id="installation.upgrade.important"> 47 <title>Important information for upgrading from BASE 2.17 to BASE 3.0</title> 48 49 <bridgehead>Upgrading is supported from BASE 2.17 only</bridgehead> 47 <title>Important information for upgrading to the current release</title> 50 48 <para> 51 If your BASE is an older 2.x version you'll need to upgrade 52 to BASE 2.17 before an upgrade to BASE 3.0 is possible. 53 </para> 54 55 <warning> 56 <title>Make sure that you have a recent backup of the BASE 2.17 database</title> 57 <para> 58 Before starting the upgrade from BASE 2.17 to BASE 3 ensure that you 59 have a recent backup. If the upgrade fails you must restore the 60 2.17 database before you can try again. The upgrade only changes the 61 'static' part of the database, so you do not have to restore the 62 'dynamic' part or the uploaded files. 63 </para> 64 </warning> 65 66 <bridgehead>Old plug-ins and extensions may not work</bridgehead> 67 <para> 68 The BASE API has changed in several places and it is not certain that 69 plug-ins and extensions developed for BASE 2 works with BASE 3. The 70 upgrade will disable all plug-ins and extensions that are currently installed. 71 Before you upgrade we recommend that you go through all (external) plug-ins 72 and check if there is an updated version. The recommended approach 73 is to first upgrade BASE and then install updated versions of plug-ins 74 and extensions following the instructions in <xref 75 linkend="plugins.installation"/>. 49 This section list some important information that may or may not 50 apply when upgrading from the <emphasis>previous</emphasis> BASE 51 release to the current release (eg. 3.1.x to 3.2.x). If you are 52 upgrading from a BASE installation that is older (eg. 2.x or 3.0.x to 53 3.2.x) you should also read <xref linkend="appendix.update_warnings" />. 76 54 </para> 77 55 56 <bridgehead>Custom logging implementations must be updated</bridgehead> 78 57 <para> 79 If there is no updated version of a specific plug-in you may try 80 a manual re-installation of the old plug-ins. Follow the instructions 81 in <xref linkend="plugins.installation.manual" />. 58 The plug-in functionality for custom logging has been converted 59 to an extension point. The default database logging will continue 60 to function, but custom logging implementations must be converted 61 to an extension. See <xref linkend="appendix.incompatible.3.2" /> and 62 <xref linkend="extensions_developer.logging" /> for more information. 82 63 </para> 83 84 <para> 85 If there is no updated version and the old plug-in doesn't work with 86 BASE 3, you'll need to decide if you really need the plug-in or if 87 the upgrade should wait until a new version of the plug-in 88 has been released. 89 </para> 90 91 <bridgehead>Batch item importer changes</bridgehead> 92 <para> 93 There are several changes to batch item importers that may affect 94 current workflows and file templates used for importing data. 95 </para> 96 97 <itemizedlist> 98 <listitem> 99 <para> 100 Sample and extract importers: The 'pooled' column is no longer used. 101 Instead a 'parent type' column should be used with 102 the parent type as a string value (BIOSOURCE, SAMPLE or EXTRACT). 103 Existing importer configurations and file templates may have to be 104 updated. If no parent type is specified the sample importer assumes 105 a biosource and the extract importer assumes a sample. 106 </para> 107 </listitem> 108 <listitem> 109 <para> 110 Labeled extract importer: This has been deprecated and it is recommended 111 that the <emphasis>Extract importer</emphasis> is used instead. 112 We recommend that existing labeled extract importer configurations are re-created as extract 113 importer configurations. The old labeled extract importer can be 114 re-enabled, but note that the existing configurations still need 115 to be changed due to the 'pooled' column is no longer used. 116 </para> 117 </listitem> 118 <listitem> 119 <para> 120 Hybridization importer: This has been deprecated and we recommend 121 that the <emphasis>Physical bioassay importer</emphasis> is used instead. 122 Existing hybridization importer configurations should be re-created as 123 physical bioassay importer configurations. 124 </para> 125 </listitem> 126 <listitem> 127 <para> 128 Scan importer: This has been deprecated and it is recommended 129 that the <emphasis>Derived bioassay importer</emphasis> is used instead. 130 Existing scan importer configurations should be re-created as derived 131 bioassay importer configurations. 132 </para> 133 </listitem> 134 </itemizedlist> 135 136 <note> 137 The deprecated importers can be re-enabled by an administrator from the 138 <menuchoice> 139 <guimenu>Administrate</guimenu> 140 <guisubmenu>Plug-ins & extensions</guisubmenu> 141 <guimenuitem>Overview</guimenuitem> 142 </menuchoice> page, but they are 143 lacking features that are available in the new importers so this is not 144 something that we recommend. 145 </note> 146 147 <bridgehead>MySQL and PostgreSQL versions</bridgehead> 148 <para> 149 We have only tested BASE 3 with PostgreSQL 9.1. If anyone 150 experiences any issues with earlier PostgreSQL versions, we 151 recommend an upgrade to PostgreSQL 9.1. This is a change since 152 BASE 2 which was tested with PostgreSQL 8.4. Even though BASE 3 153 may work with older PostgreSQL versions, we don't have the resources 154 needed to test and provide support for it. 155 </para> 156 157 <para> 158 We have only tested BASE 3 with MySQL 5.1 (no change since BASE 2). 159 If anyone experiences any issues with earlier (or later) MySQL versions, 160 we recommend an upgrade/downgrade to MySQL 5.1. 161 </para> 162 64 163 65 </important> 164 66 -
trunk/doc/src/docbook/appendix/update_warnings.xml
r5782 r6081 36 36 </para> 37 37 38 <sect1 id="appendix.update_warnings.3.2"> 39 <title>BASE 3.2</title> 40 41 <bridgehead>Custom logging implementations must be updated</bridgehead> 42 <para> 43 The plug-in functionality for custom logging has been converted 44 to an extension point. The default database logging will continue 45 to function, but custom logging implementations must be converted 46 to an extension. See <xref linkend="appendix.incompatible.3.2" /> and 47 <xref linkend="extensions_developer.logging" /> for more information. 48 </para> 49 50 </sect1> 51 52 <sect1 id="appendix.update_warnings.3.0"> 53 <title>BASE 3.0</title> 54 55 <note> 56 <title>Upgrading to BASE 3.0 is supported from BASE 2.17 only</title> 57 <para> 58 If your BASE is an older 2.x version you'll need to upgrade 59 to BASE 2.17 before an upgrade to BASE 3.0 is possible. 60 </para> 61 </note> 62 63 <warning> 64 <title>Make sure that you have a recent backup of the BASE 2.17 database</title> 65 <para> 66 Before starting the upgrade from BASE 2.17 to BASE 3 ensure that you 67 have a recent backup. If the upgrade fails you must restore the 68 2.17 database before you can try again. The upgrade only changes the 69 'static' part of the database, so you do not have to restore the 70 'dynamic' part or the uploaded files. 71 </para> 72 </warning> 73 74 <bridgehead>Old plug-ins and extensions may not work</bridgehead> 75 <para> 76 The BASE API has changed in several places and it is not certain that 77 plug-ins and extensions developed for BASE 2 works with BASE 3. The 78 upgrade will disable all plug-ins and extensions that are currently installed. 79 Before you upgrade we recommend that you go through all (external) plug-ins 80 and check if there is an updated version. The recommended approach 81 is to first upgrade BASE and then install updated versions of plug-ins 82 and extensions following the instructions in <xref 83 linkend="plugins.installation"/>. 84 </para> 85 86 <para> 87 If there is no updated version of a specific plug-in you may try 88 a manual re-installation of the old plug-ins. Follow the instructions 89 in <xref linkend="plugins.installation.manual" />. 90 </para> 91 92 <para> 93 If there is no updated version and the old plug-in doesn't work with 94 BASE 3, you'll need to decide if you really need the plug-in or if 95 the upgrade should wait until a new version of the plug-in 96 has been released. 97 </para> 98 99 <bridgehead>Batch item importer changes</bridgehead> 100 <para> 101 There are several changes to batch item importers that may affect 102 current workflows and file templates used for importing data. 103 </para> 104 105 <itemizedlist> 106 <listitem> 107 <para> 108 Sample and extract importers: The 'pooled' column is no longer used. 109 Instead a 'parent type' column should be used with 110 the parent type as a string value (BIOSOURCE, SAMPLE or EXTRACT). 111 Existing importer configurations and file templates may have to be 112 updated. If no parent type is specified the sample importer assumes 113 a biosource and the extract importer assumes a sample. 114 </para> 115 </listitem> 116 <listitem> 117 <para> 118 Labeled extract importer: This has been deprecated and it is recommended 119 that the <emphasis>Extract importer</emphasis> is used instead. 120 We recommend that existing labeled extract importer configurations are re-created as extract 121 importer configurations. The old labeled extract importer can be 122 re-enabled, but note that the existing configurations still need 123 to be changed due to the 'pooled' column is no longer used. 124 </para> 125 </listitem> 126 <listitem> 127 <para> 128 Hybridization importer: This has been deprecated and we recommend 129 that the <emphasis>Physical bioassay importer</emphasis> is used instead. 130 Existing hybridization importer configurations should be re-created as 131 physical bioassay importer configurations. 132 </para> 133 </listitem> 134 <listitem> 135 <para> 136 Scan importer: This has been deprecated and it is recommended 137 that the <emphasis>Derived bioassay importer</emphasis> is used instead. 138 Existing scan importer configurations should be re-created as derived 139 bioassay importer configurations. 140 </para> 141 </listitem> 142 </itemizedlist> 143 144 <note> 145 The deprecated importers can be re-enabled by an administrator from the 146 <menuchoice> 147 <guimenu>Administrate</guimenu> 148 <guisubmenu>Plug-ins & extensions</guisubmenu> 149 <guimenuitem>Overview</guimenuitem> 150 </menuchoice> page, but they are 151 lacking features that are available in the new importers so this is not 152 something that we recommend. 153 </note> 154 155 <bridgehead>MySQL and PostgreSQL versions</bridgehead> 156 <para> 157 We have only tested BASE 3 with PostgreSQL 9.1. If anyone 158 experiences any issues with earlier PostgreSQL versions, we 159 recommend an upgrade to PostgreSQL 9.1. This is a change since 160 BASE 2 which was tested with PostgreSQL 8.4. Even though BASE 3 161 may work with older PostgreSQL versions, we don't have the resources 162 needed to test and provide support for it. 163 </para> 164 165 <para> 166 We have only tested BASE 3 with MySQL 5.1 (no change since BASE 2). 167 If anyone experiences any issues with earlier (or later) MySQL versions, 168 we recommend an upgrade/downgrade to MySQL 5.1. 169 </para> 170 171 </sect1> 172 38 173 <sect1 id="appendix.update_warnings.2.x"> 39 174 <title>All BASE 2.x releases</title>
Note: See TracChangeset
for help on using the changeset viewer.
