id summary reporter owner description type status priority milestone component version resolution keywords cc 1591 Upgrade script for BASE 2.17 --> 3.0 Nicklas Nordborg 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], [5734]'''. 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. * '''Done [5734]'''. Deprecate and disable batch importers: `LabeledExtractImporter`, `HybridizationImporter`, `ScanImporter`. * '''Done [5803]'''. Project default items are stored as a `ParameterValues` list instead of `AnyToAny` links. * '''Done [5828]'''. Encrypt existing passwords with bcrypt." task closed blocker BASE 3.0 install fixed