ChristineChichester
commented
10 years ago On Jul 17, 2014, at 9:46 AM, StefanSenger notifications@github.com wrote:
When performing a substructure search with small substructures (e.g. just a pyridine) ring a 504 error is returned EVEN IF a maximum number of hits of only 10, for example, is specified. Here is an example:
Yes for small structures the problem occurs when there is no threshold set. As I understand, even if the number of hits is set for 10, the process still tries to retrieve all and then return the top 10, which ends of giving the error.
I have performed the same search on the RSC chemistry server and everything seems to work fine, so I can only conclude that the issue is caused by the way the Open PHACTS API calls is implemented.
I think that the RSC has a threshold already set in the background. http://ops.rsc.org/JSON.ashx?op=GetSearchResult&rid=08bf1a0e-b5df-48b2-8daf-e94f60af3a40 => [167,69,22,65,17,10,7,4,30,27]
I didn't test it but it is pretty likely that the same problem occurs when performing a similarity search.
Yes, the same thing happens with small molecules, like benzene on the similarity search.
We have a github issue for this, please see: https://github.com/openphacts/GLOBAL/issues/64
An attendee at the community workshop run into this problem and couldn't understand why his substructure search wasn't working. Since people who are new to the API will start with trying simple searches it really is crucial that this is working.
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karapetk
antonisloizou
danidi
valt
When performing a substructure search with small substructures (e.g. just a pyridine) ring a 504 error is returned EVEN IF a maximum number of hits of only 10, for example, is specified. Here is an example:
curl -v -X GET "https://beta.openphacts.org/1.3/structure/substructure?app_id=1853f6fb&app_key=a43c21c1f0b61e99ae5b3d49348f54ae&searchOptions.Molecule=c1cccnc1&searchOptions.MolType=0&resultOptions.Count=10"
I have performed the same search on the RSC chemistry server and everything seems to work fine, so I can only conclude that the issue is caused by the way the Open PHACTS API calls is implemented.
Here is what I got performing the search directly: 1) http://ops.rsc.org/JSON.ashx?op=SubstructureSearch&searchOptions.Molecule=c1cccnc1&resultOptions.Limit=10 => 08bf1a0e-b5df-48b2-8daf-e94f60af3a40 2) http://ops.rsc.org/JSON.ashx?op=GetSearchStatus&rid=08bf1a0e-b5df-48b2-8daf-e94f60af3a40 => {"Count":10,"Elapsed":"PT12M50.843S","Message":"Finished","Progress":1,"Status":6} 3) http://ops.rsc.org/JSON.ashx?op=GetSearchResult&rid=08bf1a0e-b5df-48b2-8daf-e94f60af3a40 => [167,69,22,65,17,10,7,4,30,27]
I didn't test it but it is pretty likely that the same problem occurs when performing a similarity search.
An attendee at the community workshop run into this problem and couldn't understand why his substructure search wasn't working. Since people who are new to the API will start with trying simple searches it really is crucial that this is working.