API doesn't bring out result it should in Exact Search

[lucaxbartek]

When searching for a compound, for example in this case Erythrose, using the SMILES formula obtained from OpenPHACTS (http://ops.rsc.org/OPS1782071), it brings up the error message "Internal server error" with error code 500. @StefanSenger

[ChristineChichester]

Sure. We’ll try take a look before the ttf so we can discuss if necessary.

On Oct 7, 2014, at 4:41 PM, Antonis Loizou notifications@github.com wrote:

OK - Here are the new templates for the 3 methods :

Chemical Structure Search: Similarity http://ops.rsc.org/api/v1/JSON.ashx?op=SimilaritySearch&CSCSearchScopeOptions.RealOnly=true&searchOptions.Molecule={searchOptions.Molecule}

Chemical Structure Search: Substructure http://ops.rsc.org/api/v1/JSON.ashx?op=SubStructureSearch&CSCSearchScopeOptions.RealOnly=true&searchOptions.Molecule={searchOptions.Molecule}

Chemical Structure Search: Exact http://ops.rsc.org/api/v1/JSON.ashx?op=ExactStructureSearch&CSCSearchScopeOptions.RealOnly=true&searchOptions.Molecule={searchOptions.Molecule}

@danidi , @ChristineChichester can we get some testing on this before deploying to OL as a hot patch ?

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[antonisloizou]

Now, what should be done for the 3 " ... to URL methods" ?

[karapetk]

Well, [2] and [3] are seems to be used for Smiles to OPSID conversion. I don't know where you use them on your side. But again, if OPSID is being showed to end user please consider adding "RealOnly" URL parameter to exact search.

[danidi]

I thought SMILES to URL gives the correct result (on 1.4):

"primaryTopic": {
 "_about": "http://ops.rsc.org/OPS1782071",
 "smiles": "C([C@H]([C@H](C=O)O)O)O",

But on develop it returns the wrong one.

[ChristineChichester]

1) test: using a virtual compound smiles string http://ops.rsc.org/api/v1/JSON.ashx?op=ExactStructureSearch&CSCSearchScopeOptions.RealOnly=true&searchOptions.Molecule=CC%28O%29NC1=C%28OC%28=CC1=NC%28N%29N%29C%28O%29=O%29[C@H]%28O%29C%28O%29CO http://ops.rsc.org/JSON.ashx?op=GetSearchResult&rid=60c52a5e-f17f-4bc9-b315-a653f9a9252c http://ops.rsc.org/Compounds/Get/1590655 Result: gives back a virtual compound

2) test http://ops.rsc.org/api/v1/JSON.ashx?op=SubStructureSearch&CSCSearchScopeOptions.RealOnly=true&searchOptions.Molecule=O=C%28O%29c1c%28OC%28=O%29C%29cccc1 http://ops.rsc.org/JSON.ashx?op=GetSearchResult&rid=288a250b-e9ae-41a7-bc12-dc86207efa7a http://ops.rsc.org/Compounds/Get/770050

Result: a virtual compound is found in the results

Conclusion: It doesnt appear that the RealOnly=True is being taken into account.

[karapetk]

I confirm. Will look into it asap.

[danidi]

The erythrose example seems to work correctly now for SMILES to OPSID conversion and exact search on http://ops2.rsc.org/JSON.ashx?

[lucaxbartek]

I confirm it's working!

[danidi]

The chemistry fix is now available from the Open PHACTS API. Luca, can you please retest? If you are happy, we can close this issue. Thank you!

[lucaxbartek]

Daniela, did you mean that it's working on https://dev.openphacts.org/docs/1.4 ? If that's the case, for me it isn't.

C([C@H]([C@H](C=O)O)O)O 

For me this (exactSearch) gives back errorCode404 still. The SMILES to URI call works, gives back http://ops.rsc.org/Compounds/Get/1782071 which in turn has a different SMILES associated, which also doesn't work with the exactSearch.

[danidi]

Ok, it seems the exact search is still not working for this molecule, only SMILES to URL works correctly now. Talking with Ken, it seems to work fine on the rsc API, so we need to check where in between the error occurs.

[danidi]

It also works fine on the OPS Development server. It could be that the exact search still has the filter for certain datasources (erythrose is in chebi only).

[ChristineChichester]

When develop is moved to 1.5, the issue will be solved completely. !.4 will still need a hot fix.