For every protein graph that is generated, a file needs to be downloaded from the Uniprot database. For a given protein id, this is always the same file. As these files are saved per run, the same file might be present multiple times in the user data, unnecessarily taking up space. Additionally, if the user is offline and the file was not previously downloaded in the current run, the protein graph cannot be created as the file cannot be downloaded even though, technically, all the necessary data might be present.
The goal is to save the protein files in central location (potentially /user_data/external_data/protein_graph_files/, still up for consideration) so that the above mentioned challenges are resolved.
up for debate
exact structure of directory
save unmodified protein graph files centrally as well?
Acceptance Criteria
[x] each protein file (.txt) should only exist once in a central location
[x] each parsed protein file (_parsed.txt) should only exist once in a central location
[x] runs should use look up protein file in central location, only download & parse if not present
[x] protein graphs can be generated even when offline as long as the protein file is present
[x] unmodified protein graphs should be stored in a central location.
[x] modified protein graph files should be saved per run, not centrally
Issue description
For every protein graph that is generated, a file needs to be downloaded from the Uniprot database. For a given protein id, this is always the same file. As these files are saved per run, the same file might be present multiple times in the user data, unnecessarily taking up space. Additionally, if the user is offline and the file was not previously downloaded in the current run, the protein graph cannot be created as the file cannot be downloaded even though, technically, all the necessary data might be present.
The goal is to save the protein files in central location (potentially/user_data/external_data/protein_graph_files/, still up for consideration) so that the above mentioned challenges are resolved.
up for debate
Acceptance Criteria