Upgrade script for BASE 2.17 --> 3.0

[Nicklas Nordborg]

The existing BASE 2.17 database should remain mainly intact, but there may be some things that we need to move around to different tables. We don't know any details yet but we'll probably need some kind of script for this. Here is a list of what we have found so far:

• Remove the affy_chip column from the ArrayDesigns table. This column has not been used for a very long time (BASE 2.5?) Done [5621]
• Remove the jar_path column from the PluginDefinitions and PluginTypes tables. But first copy the filename (not path) to the jar_file column in each table. Done [5621]
• Remove the jar_path column from the JobAgentSettings table. Done [5621]
• Remove references to jarPath property from context filters, sort settings, etc. for PLUGINDEFINITION and PLUGINTYPE. Done [5621]
• Remove four properties for validator and metadata extractor from DataFileType and drop the four database columns. Done [5624]

[Nicklas Nordborg]

(In [5592]) References #1591: Upgrade script for BASE 2.17 --> 3.0

Removed almost everything from Update.java since we will only support upgrading from BASE 2.17.

[Nicklas Nordborg]

(In [5593]) References #1591: Upgrade script for BASE 2.17 --> 3.0

Removed code in Install.java that performs special tasks when updating.

[Nicklas Nordborg]

(In [5621]) References #1591: Upgrade script for BASE 2.17 --> 3.0

Removed unused queries from predefined query xml files. Fixes update for:

• jarPath --> jarFile properties of PluginDefinition, PluginTypes and JobAgentSettings.
• affy_chip column.

[Nicklas Nordborg]

(In [5624]) References #1591: Upgrade script for BASE 2.17 --> 3.0

References #1598: Use the extensions system for data file validators and metadata readers

Update that removes the four columns from the DataFileTypes table and remove all references to the properties from the context settings.