Update search parameters of new data point with values from parsed meta data file before submission to proteobot

[viikiid]

Currently the values that are submitted to the public repository are those that users entered in the additional parameters input boxes. As soon as the parsing of the metadatafile is done we will need to change that to the parameters parsed from the meta data file

[RobbinBouwmeester]

@viikiid can you confirm this has been resolved?

[scaramonche]

As far as I understood, this has not been resolved yet, since it is waiting for the parsed meta data to be available in the code.

[viikiid]

This is true, it is not resolved, we need to wait for the parsed metadata file for each search engine

[enryH]

So here metadata refers to the parsed parameters file #101 , e.g. mqpar.xml for MaxQuant.

[scaramonche]

There is a branch use-metadata-params-for-submission where I started this. I have not finalized it because the next step would need to be a unification of the set of parameters and their names that we want to keep and provide on the website. One version is what we have as additional parameters on the website (as defined in webinterface/dda_quant.json) and the other version is the parameters extracted from the meta file and currently defined in proteobench/params/__init__.py.
If I understood correctly, the ones Henry used (params init file) is what we agreed on, but I was not sure if the plan is to use exactly those for the website as well.

[enryH]

We agreed to select and use the names aligned with the SDRF-extended parameters. Some parameters which are needed for a task and are not defined by SDRF-extended will need to be added. See #58 for previous discussion, especially the last comment:
#58 (comment)

[RobbinBouwmeester]

Fixed in #158