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Update pilot6.sql - modifications after curation of first results #1470

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Update pilot6.sql - modifications after curation of first results #1470

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221 changes: 212 additions & 9 deletions ...s/eu/dnetlib/iis/wf/referenceextraction/ukrn/pilot6/main/oozie_app/lib/scripts/pilot6.sql
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
--For testing...
-- attach database "../06.Biomedical06/mydata.db" as d1;
-- cd /storage/eleni/openAIRE/UKNR
-- attach database "/storage/eleni/openAIRE/06.Biomedical06/mydata.db" as d1;
-- create table mydata as select * from (setschema 'docid,text' select * from mydata where
-- docid ='PMC2931525' or docid ='PMC2933899' or
-- docid ='PMC3737084' or docid ='PMC3737070' );
Expand All @@ -13,19 +14,221 @@

create temp table mydata as select * from (setschema 'docid,text' select jsonpath(c1,'$.id', '$.text') from stdinput());

hidden var 'urls' from "www\.animalstudyregistry\.org|aspredicted\.org|www\.anzctr\.org\.au|ensaiosclinicos\.gov\.br|www\.chictr\.org\.cn|cris\.nih\.go\.kr\cris|euclinicaltrials\.eu|ctri\.nic\.in|clinicaltrials\.gov|rpcec\.sld\.cu|www\.onderzoekmetmensen\.nl|www\.clinicaltrialsregister\.eu|drks\.de|trialsearch\.who\.int|inplasy\.com|www\.crd\.york\.ac\.uk\/prospero|www\.isrctn\.com|itmctr\.ccebtcm\.org\.cn|www\.irct\.ir|rctportal\.niph\.go\.jp|www\.clinicaltrials\.jp|rctportal\.niph\.go\.jp|lbctr\.moph\.gov\.lb|osf\.io/search\?resourceType=Registration|pactr\.samrc\.ac\.za|ensayosclinicos-repec\.ins\.gob\.pe|preclinicaltrials\.eu|www\.researchregistry\.com|www\.slctr\.lk|thaiclinicaltrials\.org|ww\.umin\.ac\.jp";
hidden var 'ASR' from "www\.animalstudyregistry\.org|\b10\.17590\/asr\.\d+\b";
hidden var 'AsPredicted' from "aspredicted\.org|\bAsPredicted\s{0,1}#\d+\b";
hidden var 'ANZCTR' from "www\.anzctr\.org\.au|\bACTRN:{0,1}\s{0,1}\d+p{0,1}\b";
hidden var 'ReBec' from "ensaiosclinicos\.gov\.br|\bRBR-\d+[a-z0-9]+\b";
hidden var 'ChiCTR' from "www\.chictr\.org\.cn|\bChiCTR\s{0,1}-{0,1}(?:TRC){0,1}-{0,1}\d+\b";
hidden var 'CRiS' from "cris\.nih\.go\.kr\cris|\bKCT\s{0,1}\d{7}\b";
hidden var 'CTIS' from "euclinicaltrials\.eu|\bEUCT\s{0,1}\d{4}-\d+-\d{2}-\d{2}\b";
hidden var 'CTRI' from "ctri\.nic\.in|\bCTRI/\d{4}/\d{2}/\d+\b";
hidden var 'CT_gov' from "clinicaltrials\.gov|\bNCT\s{0,1}\d+\b";
hidden var 'RPCEC' from "rpcec\.sld\.cu|\bRPCEC\s{0,1}\d+\b";
hidden var 'LTR' from "www\.onderzoekmetmensen\.nl|\bNL\s{0,1}\d+ ; NTR\s{0,1}\d+\b";
hidden var 'EU_CTR' from "www\.clinicaltrialsregister\.eu";
hidden var 'DRKS' from "drks\.de|\bDRKS\s{0,1}\d+\b";
hidden var 'ICTRP' from "trialsearch\.who\.int|\bU\d{4}-\d{4}-\d{4}\b";
hidden var 'INPLASY' from "inplasy\.com|\bINPLASY\s{0,1}\d+\b";
hidden var 'PROSPERO' from "www\.crd\.york\.ac\.uk\/prospero|\bCRD\s{0,1}\d+\b";
hidden var 'ISRCTN' from "www\.isrctn\.com|\bISRCTN\s{0,1}\d+\b";
hidden var 'ITMCTR' from "itmctr\.ccebtcm\.org\.cn|\bITMCTR\s{0,1}\d+\b";
hidden var 'IRCT' from "www\.irct\.ir|\bIRCT\s{0,1}\d+\b";
hidden var 'JMACCT' from "rctportal\.niph\.go\.jp|\bJMA-IIA\s{0,1}\d+\b";
hidden var 'JAPIC' from "www\.clinicaltrials\.jp|\bJapicCTI\s{0,1}-{0,1}\d+\b";
hidden var 'jRCT' from "rctportal\.niph\.go\.jp|\bjRCTs{0,1}\s{0,1}\d+\b";
hidden var 'LBCTR' from "lbctr\.moph\.gov\.lb|\bLBCTR\s{0,1}\d+\b";
hidden var 'OSF' from "osf\.io/search\?resourceType=Registration";
hidden var 'PACTR' from "pactr\.samrc\.ac\.za|\bPACTR\s{0,1}\d+\b";
hidden var 'REPEC' from "ensayosclinicos-repec\.ins\.gob\.pe|\bPER-\d+-\d+\b";
hidden var 'PCT' from "preclinicaltrials\.eu|\bPCTE\s{0,1}\d+\b";
hidden var 'ResearchRegistry' from "www\.researchregistry\.com|\bresearchregistry\s{0,1}\d+\b";
hidden var 'SLCTR' from "www\.slctr\.lk|\bSLCTR/\d{4}/\d+\b";
hidden var 'TCTR' from "thaiclinicaltrials\.org|\bTCTR\s{0,1}\d+\b";
hidden var 'UMIN' from "ww\.umin\.ac\.jp|\bUMIN\s{0,1}\d+\b";

hidden var 'regexstatements' from
"10\.17590\/asr\.\d+|AsPredicted\s{0,1}#\d+|ACTRN:{0,1}\s{0,1}\d+p{0,1}|RBR-\d+[a-z0-9]+|ChiCTR\s{0,1}-{0,1}(?:TRC){0,1}-{0,1}\d+|KCT\s{0,1}\d{7}|EUCT\s{0,1}\d{4}-\d+-\d{2}-\d{2}|CTRI/\d{4}/\d{2}/\d+|NCT\s{0,1}\d+|RPCEC\s{0,1}\d+|NL\s{0,1}\d+ ; NTR\s{0,1}\d+|\d{4}[-–]\d+-\d+|DRKS\s{0,1}\d+|U\d{4}-\d{4}-\d{4}|INPLASY\s{0,1}\d+|CRD\s{0,1}\d+|ISRCTN\s{0,1}\d+|ITMCTR\s{0,1}\d+|IRCT\s{0,1}\d+|JMA-IIA\s{0,1}\d+|JapicCTI\s{0,1}-{0,1}\d+|jRCTs{0,1}\s{0,1}\d+|LBCTR\s{0,1}\d+|PACTR\s{0,1}\d+|PER-\d+-\d+|PCTE\s{0,1}\d+|researchregistry\s{0,1}\d+|SLCTR/\d{4}/\d+|TCTR\s{0,1}\d+|UMIN\s{0,1}\d+";

select jdict('query', 'a', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
select jdict('query', 'ASR', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('urls'))
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('ASR'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'b', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
select jdict('query', 'AsPredicted', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('regexstatements'))
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('AsPredicted'))
from (select docid, text from mydata))
);
)
union all
select jdict('query', 'ANZCTR', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('ANZCTR'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'ReBec', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('ReBec'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'ChiCTR', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('ChiCTR'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'CRiS', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('CRiS'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'CTIS', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('CTIS'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'CTRI', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('CTRI'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'CT_gov', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('CT_gov'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'RPCEC', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('RPCEC'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'LTR', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('LTR'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'EU_CTR', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('EU_CTR'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'DRKS', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('DRKS'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'ICTRP', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('ICTRP'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'INPLASY', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('INPLASY'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'PROSPERO', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('PROSPERO'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'ISRCTN', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('ISRCTN'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'ITMCTR', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('ITMCTR'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'IRCT', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('IRCT'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'JMACCT', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('JMACCT'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'JAPIC', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('JAPIC'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'jRCT', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('jRCT'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'LBCTR', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('LBCTR'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'OSF', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('OSF'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'PACTR', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('PACTR'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'REPEC', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('REPEC'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'PCT', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('PCT'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'ResearchRegistry', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('ResearchRegistry'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'SLCTR', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('SLCTR'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'TCTR', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('TCTR'))
from (select docid, text from mydata))
)
union all
select jdict('query', 'UMIN', 'documentId', docid, 'prev', prev, 'middle', middle, 'next', next)
from ( select docid, prev, middle, next
from (setschema 'docid,prev,middle,next' select docid, textwindow2s(regexpr("\n",text," "), 10, 1, 10, var('UMIN'))
from (select docid, text from mydata))
);