| 1 | What the update script needs to do
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| 2 | ==========================================================
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| 3 |
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| 4 | 1. Move [Label]:s to [Tag]:s with a subtype
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| 5 | - Make sure the 'Label' subtype exists in the db.
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| 6 | - Copy all labels to tags. Re-use the same id:s if
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| 7 | possible.
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| 8 | - Update all labeled extracts to use the new tags.
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| 9 |
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| 10 | - Soft references: [Item.TAG] should re-use the [Item.LABEL]
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| 11 | id so we don't have to modify anything related to this.
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| 12 | Soft references using 'LABEL' or 'LabelData' must be fixed.
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| 13 | Hopefully the tags can use the same id:s as the labels.
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| 14 |
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| 15 | - Delete the [Labels] table.
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| 16 | - Delete the [BioMaterials.label_id] column.
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| 17 |
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| 18 |
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| 19 | 2. Convert [LabeledExtract]:s into [Extract]:s with a subtype
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| 20 | - Make sure the 'LabeledExtract' subtype exists in the db
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| 21 | - No move of labeled extract data is needed, just change
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| 22 | the discriminator column from 4 to 3.
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| 23 | - Switch from current labels to the new tags.
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| 24 |
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| 25 | - Soft refefecens: The [Item.LABELEDEXTRACT] is removed and
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| 26 | all soft references to it must be changed to [Item.EXTRACT].
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| 27 | Item id:s don't change which is good.
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| 28 |
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| 29 |
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| 30 | 3. Linking biomaterial parents
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| 31 | - Move parent links to the new table for [BioMaterialParent].
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| 32 | It is a one-to-one mapping (except for the 'dummy' column)
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| 33 | and so this should not be difficult.
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| 34 | - Pooled biomaterials with a single parent item should copy
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| 35 | the parent information to [BioMaterials.parent_id] column
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| 36 | and reset the pooled flag.
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| 37 |
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| 38 | - Delete the [BioMaterialSources] table.
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| 39 |
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| 40 | 4. Move [Hybridization]:s to [PhysicalBioAssay]:s
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| 41 | - Make sure the 'Hybridization' subtype exists.
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| 42 | - Copy all data to the new table. It would be good if
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| 43 | we can use the old id:s otherwise keep track of
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| 44 | old vs. new id:s.
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| 45 | - Update [BioMaterialEvents] table to point to the
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| 46 | physical bioassays.
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| 47 |
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| 48 | - Soft references: [Item.PHYSICALBIOASSAY] should re-use the
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| 49 | [Item.HYBRIDIZATION] id so we don't have to modify anything
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| 50 | related to this.
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| 51 | Soft references using 'HYBRIDIZATION' or 'HybridizationData'
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| 52 | must be fixed. Hopefully the bioassays can use the same id:s
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| 53 | as the hybridizations.
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| 54 |
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| 55 | - Delete the [BioMaterialEvents.hybridization_id] column.
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| 56 |
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| 57 | 5. Move [Scan]:s to [DerivedBioAssaySet]
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| 58 | - Make sure the 'Scan' subtype exists
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| 59 | - Copy all data to the new table. Make sure the correct
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| 60 | physical bioassay is linked (easy if they keep the old
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| 61 | id:s).
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| 62 | - Create [DerivedBioAssay] for each array index used on the
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| 63 | hybridization the scan is taken from. Try to link the bioassay
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| 64 | with the extract on that index.
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| 65 | - Move images to [FileSet] for the bioassay set. Image properties
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| 66 | should be added as annotations.
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| 67 |
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| 68 | - Update [RawBioassay]:s created from the scan to use the
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| 69 | derived bioassay instead.
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| 70 |
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| 71 | - Soft references: [Item.DERIVEDBIOASSAYSET] should re-use the
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| 72 | [Item.SCAN] id so we don't have to modify anything
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| 73 | related to this.
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| 74 | Soft references using 'SCAN' or 'ScanData' must be fixed.
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| 75 | Hopefully the bioassay setss can use the same id:s as the
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| 76 | scans.
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| 77 |
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| 78 | - Delete the [RawBioAssays.scan_id] column.
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| 79 | - Delete the [Images] table.
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| 80 | - Delete the [Scans] table.
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| 81 | - Delete the [Hybridizations] table.
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| 82 |
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| 83 | 6. Core plug-ins
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| 84 | Some of the core plug-ins are affected a lot by the changes.
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| 85 | - Labeled extract importer
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| 86 | - Hybridization importer
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| 87 | - Scan importer
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| 88 | - Raw bioassay importer
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| 89 | - Annotation importer?
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| 90 |
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| 91 | I have not yet investigated what the best approach is. One option
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| 92 | is to disable the old plug-ins and create new plug-ins for the new
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| 93 | item types. The other biomaterial importers are also affected, but it
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| 94 | should be possible to update them with new functionality. Eg. work
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| 95 | on specific item subtype and parent/pooled item changes.
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| 96 |
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| 97 |
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| 98 |
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| 99 | Soft item references
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| 100 | --------------------
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| 101 | The database has several places with soft references. This is
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| 102 | typically a two-column reference where one column holds the id
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| 103 | of the item and the other the type of item. In most cases the
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| 104 | type is the integer value from Item.getValue(), but it can also
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| 105 | be the Item.name() value or the Item.getClass().getName() value.
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| 106 | When we move and/or convert between item types we need to update
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| 107 | the soft references.
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| 108 |
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| 109 | So far, I have found the following tables with soft references:
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| 110 |
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| 111 | - AnnotationSets: item_type and item_id
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| 112 | Update the item_type and item_id so that it references the
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| 113 | new/moved item.
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| 114 |
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| 115 | - AnnotationTypeItems: item_type
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| 116 | Update the item_type.
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| 117 |
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| 118 | - AnyToAny: from_id, from_type, to_id, to_type
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| 119 | Update the id:s and type:s so that they references the
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| 120 | new/moved items.
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| 121 |
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| 122 | - BioMaterialLists: member_type
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| 123 | Update the member_type.
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| 124 |
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| 125 | - BioPlateTypes: biomaterial_type
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| 126 | Update the biomaterial_type.
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| 127 |
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| 128 | - ChangeHistoryDetails: item_type and item_id
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| 129 | Update the item_type and item_id so that it references the
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| 130 | new/moved item.
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| 131 |
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| 132 | - Contexts: item_type and item_id
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| 133 |
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| 134 | - ContextSettings: value
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| 135 | Probably has settings related to most recently used
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| 136 | items. I guess it is easiest to simply remove those
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| 137 | settings for affected item types.
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| 138 |
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| 139 | - ItemValues: data_class and data_class_id
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| 140 | Update to the new class and id.
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| 141 |
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| 142 | - Jobs: context_item
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| 143 | Update to the new item type.
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| 144 |
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| 145 | - Keys: item_type
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| 146 | Hmmm... remove/merge/or...???
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| 147 |
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| 148 | - PluginDefinitionGuiContexts: item_type
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| 149 | Remove non-existing contexts and let plug-ins register
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| 150 | for new contexts themself.
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| 151 |
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| 152 | -
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| 153 |
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| 154 |
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| 155 |
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| 156 |
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