Bugs

[yosefdroth]

At https://datanator.info/reaction/Potassium%20ferrocyanoferrate(II),O2--%3EUnknown,H2O/Escherichia%20coli click on 'Unknown’ fails
Accessing https://datanator.info/metabolite/2-Hydroxybenzyladenine/Escherichia%20coli generates server error.

[lzy7071]

This is initially caused by a NoneType exception error. There is still an error now because there is no metabolite named 2-Hydroxybenzyladenine in metabolite_meta because the meta collection was built from metabolites in ecmdb and ymdb.

[yosefdroth]

solved in update_metab

[jonrkarr]

The second example still generates a server error
http://localhost:3000/metabolite/2-Hydroxybenzyladenine/Escherichia%20coli

[lzy7071]

The second example still generates a server error
http://localhost:3000/metabolite/2-Hydroxybenzyladenine/Escherichia%20coli

1. I think the URL should have been datanator.info/metabolite/PHKMLSOXANWAKN-UHFFFAOYSA-N/Escherichia%20coli
2. Only link to metabolites with data #222 (comment)

[jonrkarr]

This still displays an error
http://localhost:3000/metabolite/PHKMLSOXANWAKN-UHFFFAOYSA-N/Escherichia%20coli%20E1002

[lzy7071]

This still displays an error
http://localhost:3000/metabolite/PHKMLSOXANWAKN-UHFFFAOYSA-N/Escherichia%20coli%20E1002

That was my bad, the inchikey for 2-hydroxyhexadecanal is BKBDVQVDRVGXKT-UHFFFAOYSA-N. So the actual link should have been https://datanator.info/metabolite/BKBDVQVDRVGXKT-UHFFFAOYSA-N/Escherichia%20coli%20E1002.

It is still giving an error, perhaps the reason being endpoint /metabolites/concentration/?metabolite= https://api.datanator.info/metabolites/concentration/?metabolite=BKBDVQVDRVGXKT-UHFFFAOYSA-N&abstract=true&species=Escherichia%20coli%20E1002 is still being used. The endpoint is obsolete and it takes metabolite name rather than inchikey as the query parameter.

The meta information of the metabolite is being returned using /metabolites/meta/?inchikey= https://api.datanator.info/metabolites/meta/?inchikey=BKBDVQVDRVGXKT-UHFFFAOYSA-N

To retrieve concentration information, one should use /metabolites/concentrations/similar_compounds/ http://api.datanator.info/metabolites/concentrations/similar_compounds/?inchikey=BKBDVQVDRVGXKT-UHFFFAOYSA-N&threshold=0.6&target_species=homo%20sapiens&taxon_distance=false
.

[jonrkarr]

The update_metab branch is using the new endpoint. This isn't integrated into the master branch yet, and deployed.

[jonrkarr]

I think this is now fixed.