Expand ChEMBL resources and standardize webservice output - #455
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Some checks for pubchem (not chembl) kept failing on mac. It seemed this was related to timeout on queries, so I did some refactoring to make the requests more robust. These did not fix the issue at the time. However, the tests pass now, so I'll just merge. We may have to record more tests later. |
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Related to issue #449.
assay,drug_indication,drug_warning,go_slim.chembl_query()withmode = "ws"(web service), webchem retrieves and caches the schema for the requested ChEMBL resource during the session. The schema is then used to standardize the output. For example, if a field is defined as a "string", the returned value is converted to a character vector.NULLor empty lists for missing fields, which complicates downstream processing. Using the schema, these are converted to schema-appropriateNAvalues. This behavior is now hard-coded and cannot be disabled.all.equal()to check whether web service and offline responses match.chembl_query()issues warnings and leaves those fields unchanged.Note, I disabled some CTS tests. It seems to be a webservice issue. I contacted the maintainers.
PR task list:
devtools::document()