Registry #94
Registry #94
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| self.file_path = None | ||
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| def _find_file(self, file_name: str) -> None: | ||
| self.file_name = file_name |
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it would be self.file_id = file_id,
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I don't think so - I decided to have it saved as file_name and don't use file_id anywhere in this class or file.
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are you just asking me to rename it?
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yeah, just renaming it haha. Although, we should keep it consistent through the entire package. I call file name at the literal file name "1XYZ.pdb" for example
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Not saying im perfect, im almost certain I overlooked this somewhere
| if type(plot_result) == str: | ||
| return "Figures created: " + plot_result | ||
| else: | ||
| return "No figures created." | ||
| except ValueError: | ||
| return "No timestep data found in csv file." | ||
| return "File could not be processed." | ||
| except FileNotFoundError: | ||
| return "Issue with CSV file, file not found." |
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Here I usually describe the problem stating that the name/id is not in the path_registry. check again
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that error is caught earlier - I solved this by just returning the error that I raise previously in the code (I explicitly raise the error you are describing)
| @@ -123,6 +123,9 @@ def compute_rmsd(self, selection="backbone", plot=True): | |||
| plt.savefig(f"{self.filename}.png") | |||
| # plt.close() # if you don't want to show the plot in notebooks | |||
| message += f"Plotted RMSD over time. Saved to {self.filename}.png.\n" | |||
| self.path_registry.map_path( | |||
| f"{self.filename}.png", f"{self.filename}.png", message | |||
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Now that i notice, plots are not included in the files yet. Therefore, they don't have an ID. We could include them as records.
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what do you recommend here?
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So far ive been going with a "simple" approach. Anything that comes as an output from the simulation is a record, everything that ends in .pdb is a pdb file, and simulations are saved as scripts.
Also if a file is a "child" of another file, ill just use that as part of the ID to keep it "traceable".
In this case, the plot comes from a Traj file with its time_stamp, so ill just give it an ID like it: REC0_TRAJ123456, where the number is the time stamp from the traj file.
| message = rmsd.calculate_rmsd(rmsd_type, selection, plot) | ||
| except ValueError as e: | ||
| return ( | ||
| f"ValueError: {e}. \nMake sure to provide valid PBD " | ||
| "file and binding site using MDAnalysis selection syntax." | ||
| ) | ||
| except FileNotFoundError as e: | ||
| return str(e) |
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yeah, i like to make this messages to the agent more descriptive.
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I add the description above where I define the filenotfound error message
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overall I like the new structure. Feels way more organized :). I had a couple comments, but I don't think they are critic, except for the ones regarding the files ids for plots. We can either continue with the ID we have so far for the same simulations: REC0,1,2_simid, or make a new one. I would think, that just keeping what we have, and making good descriptions should work :)
most of the description errors you are seeing is because I describe the error when defining it, not when returning it. We can chat soon about the file id |
This PR updates the tools to correctly use path registry and fixes minor bugs