Changes to Data class attributes and TrajectoryData data storage#2422
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Data class attributes and TrajectoryData data storage
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@giovannipizzi and @asle85 I have cleaned Elsa's commits and squashed them into a single one on top of Andreas'. Since this was quite a complicated process due to various merge actions having created duplicate commits, there may have been some changes that have been lost. I doubt it but it would be good if you guys can check if in the changes everything is still there. |
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Methods changed to properties: * `Code.is_hidden` * `RemoteData.is_empty` Name changes: * `ArrayData.iterarrays` to `ArrayData.get_iterarrays` * `Code.full_text_info` to `Code.get_full_text_info` * `Code.is_hidden` to `Code.hidden` * `StructureData._get_cif` to `StructureData.get_cif` * `TrajectoryData._get_aiida_structure` to * `TrajectoryData.get_structure` * `TrajectoryData._get_cif` to `TrajectoryData.get_cif` Data structure storage changes: * Symbols in `TrajectoryData` are now passed as a list instead of * `numpy.ndarray` * Symbols in `TrajectoryData` are now stored as an attribute instead of * an array in the repository * `TrajectoryData.set_trajectory` arguments `stepid` and `cells` are now optional Change `TrajectoryData` to make passing stepids and cells optional. While nothing will be stored for cells if not given a consecutive sequence will be automatically assigned to stepids if missing from the inputs.
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In the previous commit, the ORM for `TrajectoryData` was changed to start storing the `symbols` as a list in the attributes of the node instead of a `numpy` array in the repository, to make it possible to query for the symbols. This requires a data migration which is implemented in this commit. Since it involves the deletion of the data from the repository after it has been copied to the database, the migration is performed in two stages. The first will copy the data from the repository to the attributes on the node and the second will delete the data in the repository. In this way, if an exception occurs during the migration, no data will be lost.
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Fixes #201
Added migrations and tests for TrajectoryData symbols (from numpy array to attribute).
In sqlalchemy migrations and test I used load_node; to discuss if we want to rewrite it to avoid using aiida functionality (e.g. to get and delete numpy arrays).