Use metadata params for submission #158
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…h has local dev set to true
…om/Proteobench/ProteoBench into use-metadata-params-for-submission
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| if input_format == "MaxQuant": | ||
| params = maxquant.extract_params(input_file) | ||
| # elif input_format == "AlphaPept": |
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also availabe. Would you like to have a dictionary of extract_params functions in the module preteobench.io.params? Then you could avoid the long block of if/else statements and handle potential key-errros.
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Good point! Will change.
- Many variable names were changed, among others renamed search engine to software - This means that results.json has new entries, see Proteobot/Results_quant_ion_DDA#117 - TODO: still need to adapt the tests and template to the new variable names
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This branch only works if you use the results.json from Proteobot/Results_quant_ion_DDA#117 locally (save it and point to it in DDA_QUANT_RESULTS_PATH and uncomment the two places where it is used in module.py). |
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@RobbinBouwmeester I think it is pretty much done. Tests should work once the results.json in the repo is replaced. Note that the biggest change comes from using |
| @@ -343,6 +359,8 @@ def clone_pr( | |||
| current_datapoint = temporary_datapoints.iloc[-1] | |||
| current_datapoint["is_temporary"] = False | |||
| for k, v in datapoint_params.__dict__.items(): | |||
| if k == "software_name": | |||
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This needs to be removed?
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Indeed, fixed in a (hopefully) more elegant way.
| @@ -380,6 +398,8 @@ def write_json_local_development(self, temporary_datapoints, datapoint_params): | |||
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| # Update parameters based on parsed params | |||
| for k, v in datapoint_params.__dict__.items(): | |||
| if k == "software_name": | |||
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This needs to be removed?
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I think we are good to go. Maybe @enryH can have a final look as an independent observer?
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