inab / opeb-enrichers

OpenEBench metadata enrichers (citations, GitHub, etc.)
GNU Lesser General Public License v2.1
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Some Wikidata searches fail with syntax error #1

Closed jmfernandez closed 5 years ago

jmfernandez commented 5 years ago

Next generated query:

SELECT  DISTINCT ?internal_id
WHERE {
    {

        SELECT DISTINCT ?internal_id
        WHERE {
            VALUES (?query_pubmed_id) {
                ("29894229")
("19921425")
("27736370")
("18992259")
("18723096")
("18781291")
("25010846")
("29356305")
("20419239")
("28576492")
("25600074")
("21942650")
("20363346")
            }
            ?internal_id wdt:P698 ?query_pubmed_id.
        }

    } UNION {

        SELECT DISTINCT ?internal_id
        WHERE {
            VALUES (?query_doi_id) {
                ("10.1146/ANNUREV-ANCHEM-061417-125811")
("10.1007/S10549-009-0633-5")
("10.1089/NAT.2016.0645")
("10.1016/J.JTBI.2008.09.035")
("10.1016/J.YMPEV.2008.07.019")
("
10.2478/BJMG-2013-0018
")
("10.1007/S00122-008-0870-8")
("10.1016/J.BIOS.2014.06.042")
("10.1111/J.1096-0031.2008.00236.X")
("10.1002/ANIE.201711673")
("10.1039/B922829B")
("10.1016/J.BBRC.2017.05.134")
("10.1111/PBI.12327")
("10.1021/BI201263N")
("10.1016/J.YMPEV.2010.03.036")
            }
            ?internal_id wdt:P356 ?query_doi_id.
        }

    }
}

fails because one of the searched DOIs had a new line from the source. So, the whole code should be sanitized, so this cannot happen

jmfernandez commented 5 years ago

Commits 1a907082d46390b389889821a8552b82261f2c8c and f6a25fa94e31f96364644e728e2f47a967e8222a fixes this case