| 3 | | * 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]''' |
| 4 | | * 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]''' |
| 5 | | * Remove the `jar_path` column from the `JobAgentSettings` table. '''Done [5621]''' |
| 6 | | * Remove references to `jarPath` property from context filters, sort settings, etc. for `PLUGINDEFINITION` and `PLUGINTYPE`. '''Done [5621]''' |
| 7 | | * Remove four properties for validator and metadata extractor from `DataFileType` and drop the four database columns. '''Done [5624]''' |
| | 3 | * '''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?) |
| | 4 | * '''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. |
| | 5 | * '''Done [5621]'''. Remove the `jar_path` column from the `JobAgentSettings` table. |
| | 6 | * '''Done [5621]'''. Remove references to `jarPath` property from context filters, sort settings, etc. for `PLUGINDEFINITION` and `PLUGINTYPE`. |
| | 7 | * '''Done [5624]'''. Remove four properties for validator and metadata extractor from `DataFileType` and drop the four database columns. |
| | 8 | * '''Done [5703]'''. Copy information in `BioMaterialEventSources` to `BioMaterialEventSources2` so that parent-child linking of biomaterial is retained. Remove the `BioMaterialEventSources` table. |
| | 9 | * '''In progres [5703]'''. Set `BioMaterials.parent_type` column based on information in the `pooled` and `parent_id` column. Remove the `pooled` column. |
| | 10 | * '''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. |
| | 11 | * '''Done [5703]'''. Convert `Label` to `Tag`. Set the subtype on all existing labels. |
| | 12 | * '''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. |
| | 13 | * '''In progress [5703]'''. 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. |
| | 14 | * 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. |
| | 15 | * Drop unique contraint on `FileSetMember` table for `fileset_id` and `datafiletype_id` columns. |
