openphacts / GLOBAL

Global project issues [private for now. owner lee harland]
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Add More (cache-free) tests to testing list #11

Closed leeharland closed 10 years ago

leeharland commented 10 years ago

Here are some of the calls I was running:

https://beta.openphacts.org/1.3/pathway/getTargets?uri=http%3A%2F%2Fidentifiers.org%2Fwikipathways%2FWP673&app_id=15a18100&app_key=528a8272f1cd961d215f318a0315dd3d

by looping over the gene IDs I retrieve from this call, I call I query the counts for each: https://beta.openphacts.org/1.3/target/pharmacology/count?uri=http%3A%2F%2Fidentifiers.org%2Fncbigene%2F2066&app_id=15a18100&app_key=528a8272f1cd961d215f318a0315dd3d&_format=json

From the counts I calculate how often I need to loop over the pharmacology calls with pagesize 250 to get all results, e.g.: https://beta.openphacts.org/1.3/target/pharmacology/pages?uri=http%3A%2F%2Fidentifiers.org%2Fncbigene%2F2066&app_id=15a18100&app_key=528a8272f1cd961d215f318a0315dd3d&_pageSize=250&_format=json&_page=1 with page from 1 to 9

The last two queries start with a gene ID, which needs the IMS to map to a protein URI. To get all data back, I need approx. 600 pharmacology calls.

For all unique Chembl targets I call https://beta.openphacts.org/1.3/target/classifications?uri=http%3A%2F%2Frdf.ebi.ac.uk%2Fresource%2Fchembl%2Ftarget%2FCHEMBL2095942&app_id=15a18100&app_key=528a8272f1cd961d215f318a0315dd3d&tree=go

And for most of the unique Chembl molecules I call https://beta.openphacts.org/1.3/compound/classifications?uri=http%3A%2F%2Frdf.ebi.ac.uk%2Fresource%2Fchembl%2Fmolecule%2FCHEMBL611814&app_id=15a18100&app_key=528a8272f1cd961d215f318a0315dd3d&tree=chebi

The last time I was running this call, I retrieved fewer results than the first time. Was there some problem over night?

For testing, I also ran the smiles in the attached text file with the substructure search:

https://beta.openphacts.org/1.3/structure/substructure?app_id=15a18100&app_key=528a8272f1cd961d215f318a0315dd3d&searchOptions.Molecule=CC%28C%29Nc1ccc%28c%28CC%28%3DO%29NCc2ccc%28cc2%29C%28%3DN%29N%29c1O%29c3ccccc3&resultOptions.Count=200

leeharland commented 10 years ago

Also, must add tests that cover RSC structure searches including EXACT as these went down on 25/4/2014 yet we did not see any alarms