Model changes to GenomeCoordinates, RepositoryId and ManuallyTyped #71
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manulera
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… extending opencloning_models (#502) * created stubs UploadedFileSource and RepositoryIdSource * next step * next step2 * added rudimentary source/history for local files read in reader/parser and sequences downloaded from genbank. * fixed fields in model * enable higher opencloning-linkml versions * support and test edge case from #488 * starting to work on better serialization * simplify serialization to avoid having to use kwargs, instead define serializer for non-native fields * fix tests (happens because TARGET_MODEL was not behaving properly in SequenceCutSource before) * update notebook output * add some repositories * add the rest of the models * add and test oligonucleotide hybridization * comment Location out * fix existing genbank test and adapt to OpenCloning/OpenCloning_LinkML#71 * update linkml model * update linkml model and drop repository_name field * add location serializer to GenomeCoordinatesSource * update opencloning-linkml to released version * add utility to get coordinates in the format used for the NCBI API * closes #495 * remove TODO comment * genbank: handle source when only one of the edges is provided * use more specific annotation for parsing --------- Co-authored-by: BjornFJohansson <bjornjobb@gmail.com>
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#70