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:

• Done [5621]. 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 [5624]. Remove four properties for validator and metadata extractor from DataFileType and drop the four database columns.
• Done [5703]. Copy information in BioMaterialEventSources to BioMaterialEventSources2 so that parent-child linking of biomaterial is retained. Remove the BioMaterialEventSources table.
• Done [5703], [5730]. Set BioMaterials.parent_type and parent_id column based on parent/child information. Remove the pooled column.
• Done [5703]. Convert LabeledExtract to Extract items by updating the BioMaterials.discriminator column. All "soft" relations (eg. item_type+item_id pairs) need to update the item_type column (204->203). Set the subtype on all existing labeled extracts.
• Done [5703]. Convert Label to Tag. Set the subtype on all existing labels.
• Done [5703]. Convert Hybridization to PhysicalBioAssay. Copy information from the Hybridizations table to PhysicalBioAssays. Set new id on BioMaterialEvents.physicalbioassay_id column. Remove BioMaterialEvents.hybridization_id column. All "soft" relations (eg. item_type+item_id pairs) need to update the item_type column (261->267). Set the subtype on all existing hybridizations.
• Done [5703], [5730]. Convert Scan to DerivedBioAssay. Copy information from the Scans table to DerivedBioAssays. Copy information from Images table to FileSetMember. All "soft" relations (eg. item_type+item_id pairs) need to update the item_type column (262->268). Set the subtype on all existing scans.
• Done [5733]. Update RawBioAssay to point to the derived bioassay instead of the scan. Remove scan_id column. Populate extract_id column based on information in the array_num and the positions of biomaterials on the linked hybridization.
• Done [5730]. Drop unique contraint on FileSetMember table for fileset_id and datafiletype_id columns.
• Done [5733]. Set allow_multiple=false for all existing platform file types.
• Done [5703], [5730]. Convert ProtocolType, HardwareType, SoftwareType and FileType to ItemSubtype and make sure all hard and soft references are updated. Drop tables and columns that are no longer used.

[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.

[Nicklas Nordborg]

(In [5703]) References #1591: Upgrade script for BASE 2.17 --> 3.0

Update biomaterials, hybridizations and scans. Still missing some cases for re-linking pooled biomaterials.

Dropping lots of a database columns and tables that are not needed in BASE 3.

[Nicklas Nordborg]

(In [5730]) References #1591: Upgrade script for BASE 2.17 --> 3.0

• Images to files attached to derived bioassays
• Convert software types, hardware types, protocol types and file types to item subtypes.
• Fix biomaterial parent linking

[Nicklas Nordborg]

(In [5733]) References #1591: Upgrade script for BASE 2.17 --> 3.0

• Parent derived bioassay for raw bioassays
• Perent extract for raw bioassays
• Set allow_multiple=false for all existing platform file types