doidoost_dismiss #418
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@ -5,8 +5,6 @@ import org.apache.commons.lang3.StringUtils;
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public class DoiCleaningRule {
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public class DoiCleaningRule {
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public static String clean(final String doi) {
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public static String clean(final String doi) {
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return doi
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return doi
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.toLowerCase()
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.toLowerCase()
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@ -15,7 +13,7 @@ public class DoiCleaningRule {
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.replaceFirst(CleaningFunctions.DOI_PREFIX_REGEX, CleaningFunctions.DOI_PREFIX);
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.replaceFirst(CleaningFunctions.DOI_PREFIX_REGEX, CleaningFunctions.DOI_PREFIX);
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}
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}
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public static String normalizeDoi(final String input){
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public static String normalizeDoi(final String input) {
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if (input == null)
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if (input == null)
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return null;
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return null;
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final String replaced = input
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final String replaced = input
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@ -28,7 +26,6 @@ public class DoiCleaningRule {
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if (!replaced.contains("10."))
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if (!replaced.contains("10."))
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return null;
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return null;
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final String ret = replaced.substring(replaced.indexOf("10."));
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final String ret = replaced.substring(replaced.indexOf("10."));
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if (!ret.startsWith(CleaningFunctions.DOI_PREFIX))
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if (!ret.startsWith(CleaningFunctions.DOI_PREFIX))
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@ -0,0 +1,26 @@
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[
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{
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"paramName": "m",
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"paramLongName": "master",
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"paramDescription": "the master name",
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"paramRequired": true
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},
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{
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"paramName": "s",
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"paramLongName": "sourcePath",
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"paramDescription": "The base path of Crossref DUMP",
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"paramRequired": true
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},
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{
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"paramName": "t",
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"paramLongName": "targetPath",
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"paramDescription": "The target path",
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"paramRequired": false
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},
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{
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"paramName": "i",
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"paramLongName": "isLookupUrl",
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"paramDescription": "the Information System Service LookUp URL",
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"paramRequired": true
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}
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]
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@ -0,0 +1,940 @@
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[
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{
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"id": "100007630",
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"uri": "http://dx.doi.org/10.13039/100007630",
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"name": "College of Engineering and Informatics, National University of Ireland, Galway",
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"synonym": []
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},
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{
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"id": "100007731",
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"uri": "http://dx.doi.org/10.13039/100007731",
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"name": "Endo International",
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"synonym": []
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},
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{
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"id": "100008099",
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"uri": "http://dx.doi.org/10.13039/100008099",
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"name": "Food Safety Authority of Ireland",
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"synonym": []
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},
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{
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"id": "100008124",
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"uri": "http://dx.doi.org/10.13039/100008124",
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"name": "Department of Jobs, Enterprise and Innovation",
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"synonym": []
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},
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{
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"id": "100009098",
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"uri": "http://dx.doi.org/10.13039/100009098",
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"name": "Department of Foreign Affairs and Trade, Ireland",
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"synonym": []
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},
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{
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"id": "100009099",
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"uri": "http://dx.doi.org/10.13039/100009099",
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"name": "Irish Aid",
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"synonym": []
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},
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{
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"id": "100009770",
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"uri": "http://dx.doi.org/10.13039/100009770",
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"name": "National University of Ireland",
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"synonym": []
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},
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{
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"id": "100009985",
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"uri": "http://dx.doi.org/10.13039/100009985",
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"name": "Parkinson's Association of Ireland",
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"synonym": []
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},
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{
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"id": "100010399",
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"uri": "http://dx.doi.org/10.13039/100010399",
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"name": "European Society of Cataract and Refractive Surgeons",
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"synonym": []
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},
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{
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"id": "100010414",
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"uri": "http://dx.doi.org/10.13039/100010414",
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"name": "Health Research Board",
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"synonym": [
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"501100001590"
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]
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},
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{
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"id": "100010546",
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"uri": "http://dx.doi.org/10.13039/100010546",
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"name": "Deparment of Children and Youth Affairs, Ireland",
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"synonym": []
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},
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{
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"id": "100010993",
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"uri": "http://dx.doi.org/10.13039/100010993",
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"name": "Irish Nephrology Society",
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"synonym": []
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},
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{
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"id": "100011062",
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"uri": "http://dx.doi.org/10.13039/100011062",
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"name": "Asian Spinal Cord Network",
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"synonym": []
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},
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{
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"id": "100011096",
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"uri": "http://dx.doi.org/10.13039/100011096",
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"name": "Jazz Pharmaceuticals",
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"synonym": []
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},
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{
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"id": "100011396",
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"uri": "http://dx.doi.org/10.13039/100011396",
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"name": "Irish College of General Practitioners",
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"synonym": []
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},
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{
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"id": "100012734",
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"uri": "http://dx.doi.org/10.13039/100012734",
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"name": "Department for Culture, Heritage and the Gaeltacht, Ireland",
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"synonym": []
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},
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{
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"id": "100012754",
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"uri": "http://dx.doi.org/10.13039/100012754",
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"name": "Horizon Pharma",
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"synonym": []
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},
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{
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"id": "100012891",
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"uri": "http://dx.doi.org/10.13039/100012891",
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"name": "Medical Research Charities Group",
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"synonym": []
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},
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{
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"id": "100012919",
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"uri": "http://dx.doi.org/10.13039/100012919",
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"name": "Epilepsy Ireland",
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"synonym": []
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},
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{
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"id": "100012920",
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"uri": "http://dx.doi.org/10.13039/100012920",
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"name": "GLEN",
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"synonym": []
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},
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{
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"id": "100012921",
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"uri": "http://dx.doi.org/10.13039/100012921",
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"name": "Royal College of Surgeons in Ireland",
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"synonym": []
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},
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{
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"id": "100013029",
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"uri": "http://dx.doi.org/10.13039/100013029",
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"name": "Iris O'Brien Foundation",
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"synonym": []
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},
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{
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"id": "100013206",
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"uri": "http://dx.doi.org/10.13039/100013206",
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"name": "Food Institutional Research Measure",
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"synonym": []
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},
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{
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"id": "100013381",
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"uri": "http://dx.doi.org/10.13039/100013381",
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"name": "Irish Phytochemical Food Network",
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"synonym": []
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},
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{
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"id": "100013433",
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"uri": "http://dx.doi.org/10.13039/100013433",
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"name": "Transport Infrastructure Ireland",
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"synonym": []
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},
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{
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"id": "100013461",
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"uri": "http://dx.doi.org/10.13039/100013461",
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"name": "Arts and Disability Ireland",
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"synonym": []
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},
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{
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"id": "100013548",
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"uri": "http://dx.doi.org/10.13039/100013548",
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"name": "Filmbase",
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"synonym": []
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},
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{
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"id": "100013917",
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"uri": "http://dx.doi.org/10.13039/100013917",
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"name": "Society for Musicology in Ireland",
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"synonym": []
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},
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{
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"id": "100014251",
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"uri": "http://dx.doi.org/10.13039/100014251",
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"name": "Humanities in the European Research Area",
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"synonym": []
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},
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{
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"id": "100014364",
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"uri": "http://dx.doi.org/10.13039/100014364",
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"name": "National Children's Research Centre",
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"synonym": []
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},
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{
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"id": "100014384",
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"uri": "http://dx.doi.org/10.13039/100014384",
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"name": "Amarin Corporation",
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"synonym": []
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},
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{
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"id": "100014902",
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"uri": "http://dx.doi.org/10.13039/100014902",
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"name": "Irish Association for Cancer Research",
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"synonym": []
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},
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{
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"id": "100015023",
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"uri": "http://dx.doi.org/10.13039/100015023",
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"name": "Ireland Funds",
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"synonym": []
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},
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{
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"id": "100015037",
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"uri": "http://dx.doi.org/10.13039/100015037",
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"name": "Simon Cumbers Media Fund",
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"synonym": []
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},
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{
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"id": "100015319",
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"uri": "http://dx.doi.org/10.13039/100015319",
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"name": "Sport Ireland Institute",
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"synonym": []
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},
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{
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"id": "100015320",
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"uri": "http://dx.doi.org/10.13039/100015320",
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"name": "Paralympics Ireland",
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"synonym": []
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},
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{
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"id": "100015442",
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"uri": "http://dx.doi.org/10.13039/100015442",
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"name": "Global Brain Health Institute",
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"synonym": []
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},
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{
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"id": "100015776",
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"uri": "http://dx.doi.org/10.13039/100015776",
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"name": "Health and Social Care Board",
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"synonym": []
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},
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{
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"id": "100015992",
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"uri": "http://dx.doi.org/10.13039/100015992",
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"name": "St. Luke's Institute of Cancer Research",
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"synonym": []
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},
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{
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"id": "100017897",
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"uri": "http://dx.doi.org/10.13039/100017897",
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"name": "Friedreich\u2019s Ataxia Research Alliance Ireland",
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"synonym": []
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},
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{
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"id": "100018064",
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"uri": "http://dx.doi.org/10.13039/100018064",
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"name": "Department of Tourism, Culture, Arts, Gaeltacht, Sport and Media",
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"synonym": []
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},
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{
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"id": "100018172",
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"uri": "http://dx.doi.org/10.13039/100018172",
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"name": "Department of the Environment, Climate and Communications",
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"synonym": []
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},
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{
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"id": "100018175",
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"uri": "http://dx.doi.org/10.13039/100018175",
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"name": "Dairy Processing Technology Centre",
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"synonym": []
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},
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{
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||||||
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"id": "100018270",
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"uri": "http://dx.doi.org/10.13039/100018270",
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||||||
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"name": "Health Service Executive",
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||||||
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"synonym": []
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},
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{
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||||||
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"id": "100018529",
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||||||
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"uri": "http://dx.doi.org/10.13039/100018529",
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||||||
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"name": "Alkermes",
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"synonym": []
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},
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{
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||||||
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"id": "100018542",
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||||||
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"uri": "http://dx.doi.org/10.13039/100018542",
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||||||
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"name": "Irish Endocrine Society",
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||||||
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"synonym": []
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||||||
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},
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||||||
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{
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||||||
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"id": "100018754",
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||||||
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"uri": "http://dx.doi.org/10.13039/100018754",
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||||||
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"name": "An Roinn Sl\u00e1inte",
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||||||
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"synonym": []
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},
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{
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||||||
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"id": "100018998",
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||||||
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"uri": "http://dx.doi.org/10.13039/100018998",
|
||||||
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"name": "Irish Research eLibrary",
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||||||
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"synonym": []
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||||||
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},
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||||||
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{
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||||||
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"id": "100019428",
|
||||||
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"uri": "http://dx.doi.org/10.13039/100019428",
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||||||
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"name": "Nabriva Therapeutics",
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||||||
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"synonym": []
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||||||
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},
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||||||
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{
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||||||
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"id": "100019637",
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||||||
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"uri": "http://dx.doi.org/10.13039/100019637",
|
||||||
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"name": "Horizon Therapeutics",
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||||||
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"synonym": []
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||||||
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},
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||||||
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{
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||||||
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"id": "100020174",
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||||||
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"uri": "http://dx.doi.org/10.13039/100020174",
|
||||||
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"name": "Health Research Charities Ireland",
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||||||
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"synonym": []
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||||||
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},
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||||||
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{
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||||||
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"id": "100020202",
|
||||||
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"uri": "http://dx.doi.org/10.13039/100020202",
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||||||
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"name": "UCD Foundation",
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||||||
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"synonym": []
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||||||
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},
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||||||
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{
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||||||
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"id": "100020233",
|
||||||
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"uri": "http://dx.doi.org/10.13039/100020233",
|
||||||
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"name": "Ireland Canada University Foundation",
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||||||
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"synonym": []
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||||||
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},
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||||||
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{
|
||||||
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"id": "100022943",
|
||||||
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"uri": "http://dx.doi.org/10.13039/100022943",
|
||||||
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"name": "National Cancer Registry Ireland",
|
||||||
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"synonym": []
|
||||||
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},
|
||||||
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{
|
||||||
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"id": "501100001581",
|
||||||
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"uri": "http://dx.doi.org/10.13039/501100001581",
|
||||||
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"name": "Arts Council of Ireland",
|
||||||
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"synonym": []
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||||||
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},
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||||||
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{
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||||||
|
"id": "501100001582",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001582",
|
||||||
|
"name": "Centre for Ageing Research and Development in Ireland",
|
||||||
|
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|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001583",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001583",
|
||||||
|
"name": "Cystinosis Foundation Ireland",
|
||||||
|
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|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001584",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001584",
|
||||||
|
"name": "Department of Agriculture, Food and the Marine, Ireland",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001586",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001586",
|
||||||
|
"name": "Department of Education and Skills, Ireland",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001587",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001587",
|
||||||
|
"name": "Economic and Social Research Institute",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001588",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001588",
|
||||||
|
"name": "Enterprise Ireland",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001589",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001589",
|
||||||
|
"name": "Environmental Protection Agency",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001591",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001591",
|
||||||
|
"name": "Heritage Council",
|
||||||
|
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|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001592",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001592",
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||||||
|
"name": "Higher Education Authority",
|
||||||
|
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|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001593",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001593",
|
||||||
|
"name": "Irish Cancer Society",
|
||||||
|
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|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001594",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001594",
|
||||||
|
"name": "Irish Heart Foundation",
|
||||||
|
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|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001595",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001595",
|
||||||
|
"name": "Irish Hospice Foundation",
|
||||||
|
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|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001596",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001596",
|
||||||
|
"name": "Irish Research Council for Science, Engineering and Technology",
|
||||||
|
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|
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|
},
|
||||||
|
{
|
||||||
|
"id": "501100001597",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001597",
|
||||||
|
"name": "Irish Research Council for the Humanities and Social Sciences",
|
||||||
|
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|
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|
},
|
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|
{
|
||||||
|
"id": "501100001598",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001598",
|
||||||
|
"name": "Mental Health Commission",
|
||||||
|
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|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001600",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001600",
|
||||||
|
"name": "Research and Education Foundation, Sligo General Hospital",
|
||||||
|
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|
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|
},
|
||||||
|
{
|
||||||
|
"id": "501100001601",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001601",
|
||||||
|
"name": "Royal Irish Academy",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001603",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001603",
|
||||||
|
"name": "Sustainable Energy Authority of Ireland",
|
||||||
|
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|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001604",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001604",
|
||||||
|
"name": "Teagasc",
|
||||||
|
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|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001627",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001627",
|
||||||
|
"name": "Marine Institute",
|
||||||
|
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|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001628",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001628",
|
||||||
|
"name": "Central Remedial Clinic",
|
||||||
|
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|
||||||
|
},
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||||||
|
{
|
||||||
|
"id": "501100001629",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001629",
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||||||
|
"name": "Royal Dublin Society",
|
||||||
|
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||||||
|
},
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||||||
|
{
|
||||||
|
"id": "501100001630",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001630",
|
||||||
|
"name": "Dublin Institute for Advanced Studies",
|
||||||
|
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|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001631",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001631",
|
||||||
|
"name": "University College Dublin",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001633",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001633",
|
||||||
|
"name": "National University of Ireland, Maynooth",
|
||||||
|
"synonym": []
|
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|
},
|
||||||
|
{
|
||||||
|
"id": "501100001634",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001634",
|
||||||
|
"name": "University of Galway",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001635",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001635",
|
||||||
|
"name": "University of Limerick",
|
||||||
|
"synonym": []
|
||||||
|
},
|
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|
{
|
||||||
|
"id": "501100001636",
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||||||
|
"uri": "http://dx.doi.org/10.13039/501100001636",
|
||||||
|
"name": "University College Cork",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001637",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001637",
|
||||||
|
"name": "Trinity College Dublin",
|
||||||
|
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|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001638",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001638",
|
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|
"name": "Dublin City University",
|
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|
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|
},
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{
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|
"id": "501100002081",
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|
"uri": "http://dx.doi.org/10.13039/501100002081",
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|
"name": "Irish Research Council",
|
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|
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{
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|
"id": "501100002736",
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|
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|
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|
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|
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{
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|
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||||||
|
"uri": "http://dx.doi.org/10.13039/501100002755",
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|
"name": "Brennan and Company",
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|
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{
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|
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|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100002919",
|
||||||
|
"name": "Cork Institute of Technology",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100002959",
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||||||
|
"uri": "http://dx.doi.org/10.13039/501100002959",
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|
"name": "Dublin City Council",
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|
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},
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{
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|
"id": "501100003036",
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|
"uri": "http://dx.doi.org/10.13039/501100003036",
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|
"name": "Perrigo Company Charitable Foundation",
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|
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{
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||||||
|
"id": "501100003037",
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"uri": "http://dx.doi.org/10.13039/501100003037",
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|
"name": "Elan",
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|
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{
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|
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|
"uri": "http://dx.doi.org/10.13039/501100003496",
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|
"name": "HeyStaks Technologies",
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{
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|
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|
"name": "Gaelic Athletic Association",
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|
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{
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|
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"uri": "http://dx.doi.org/10.13039/501100003840",
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|
"name": "Irish Institute of Clinical Neuroscience",
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|
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{
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|
"id": "501100003956",
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||||||
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||||||
|
"name": "Aspect Medical Systems",
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|
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||||||
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|
"name": "Meath Foundation",
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|
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{
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|
"id": "501100004210",
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||||||
|
"uri": "http://dx.doi.org/10.13039/501100004210",
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||||||
|
"name": "Our Lady's Children's Hospital, Crumlin",
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||||||
|
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{
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||||||
|
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||||||
|
"uri": "http://dx.doi.org/10.13039/501100004321",
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||||||
|
"name": "Shire",
|
||||||
|
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},
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|
{
|
||||||
|
"id": "501100004981",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100004981",
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||||||
|
"name": "Athlone Institute of Technology",
|
||||||
|
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||||||
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},
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||||||
|
{
|
||||||
|
"id": "501100006518",
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||||||
|
"uri": "http://dx.doi.org/10.13039/501100006518",
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||||||
|
"name": "Department of Communications, Energy and Natural Resources, Ireland",
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||||||
|
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},
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||||||
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{
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||||||
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||||||
|
"uri": "http://dx.doi.org/10.13039/501100006553",
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||||||
|
"name": "Collaborative Centre for Applied Nanotechnology",
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|
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{
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||||||
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"id": "501100006759",
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||||||
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"uri": "http://dx.doi.org/10.13039/501100006759",
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|
"name": "CLARITY Centre for Sensor Web Technologies",
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{
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||||||
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"uri": "http://dx.doi.org/10.13039/501100009246",
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||||||
|
"name": "Technological University Dublin",
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||||||
|
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},
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||||||
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{
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||||||
|
"id": "501100009269",
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||||||
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||||||
|
"name": "Programme of Competitive Forestry Research for Development",
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||||||
|
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{
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||||||
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"id": "501100009315",
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||||||
|
"uri": "http://dx.doi.org/10.13039/501100009315",
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||||||
|
"name": "Cystinosis Ireland",
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||||||
|
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},
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{
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||||||
|
"id": "501100010808",
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||||||
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"uri": "http://dx.doi.org/10.13039/501100010808",
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||||||
|
"name": "Geological Survey of Ireland",
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{
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||||||
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||||||
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"name": "Alimentary Glycoscience Research Cluster",
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{
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||||||
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},
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{
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"name": "Rann\u00eds",
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{
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||||||
|
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||||||
|
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|
"name": "Inland Fisheries Ireland",
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|
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},
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|
{
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||||||
|
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||||||
|
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"name": "X-Bolt Orthopaedics",
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{
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||||||
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"name": "PrecisionBiotics Group",
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{
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||||||
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||||||
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"name": "Dormant Accounts Fund",
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},
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{
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||||||
|
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||||||
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"uri": "http://dx.doi.org/10.13039/501100016041",
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||||||
|
"name": "St Vincents Anaesthesia Foundation",
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{
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||||||
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||||||
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"uri": "http://dx.doi.org/10.13039/501100017501",
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||||||
|
"name": "FotoNation",
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||||||
|
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||||||
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},
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||||||
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{
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||||||
|
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|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100018641",
|
||||||
|
"name": "Dairy Research Ireland",
|
||||||
|
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||||||
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},
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||||||
|
{
|
||||||
|
"id": "501100018839",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100018839",
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||||||
|
"name": "Irish Centre for High-End Computing",
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|
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},
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{
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||||||
|
"uri": "http://dx.doi.org/10.13039/501100019905",
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||||||
|
"name": "Galway University Foundation",
|
||||||
|
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|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100020036",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100020036",
|
||||||
|
"name": "Dystonia Ireland",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100020221",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100020221",
|
||||||
|
"name": "Irish Motor Neurone Disease Association",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100020270",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100020270",
|
||||||
|
"name": "Advanced Materials and Bioengineering Research",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100020403",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100020403",
|
||||||
|
"name": "Irish Composites Centre",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100020425",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100020425",
|
||||||
|
"name": "Irish Thoracic Society",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100021102",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100021102",
|
||||||
|
"name": "Waterford Institute of Technology",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100021110",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100021110",
|
||||||
|
"name": "Irish MPS Society",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100021525",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100021525",
|
||||||
|
"name": "Insight SFI Research Centre for Data Analytics",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100021694",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100021694",
|
||||||
|
"name": "Elan Pharma International",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100021838",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100021838",
|
||||||
|
"name": "Royal College of Physicians of Ireland",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100022542",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100022542",
|
||||||
|
"name": "Breakthrough Cancer Research",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100022610",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100022610",
|
||||||
|
"name": "Breast Cancer Ireland",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100022728",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100022728",
|
||||||
|
"name": "Munster Technological University",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100022729",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100022729",
|
||||||
|
"name": "Institute of Technology, Tralee",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100023273",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100023273",
|
||||||
|
"name": "HRB Clinical Research Facility Galway",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100023378",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100023378",
|
||||||
|
"name": "Lauritzson Foundation",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100023551",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100023551",
|
||||||
|
"name": "Cystic Fibrosis Ireland",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100023970",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100023970",
|
||||||
|
"name": "Tyndall National Institute",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100024094",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100024094",
|
||||||
|
"name": "Raidi\u00f3 Teilif\u00eds \u00c9ireann",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100024242",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100024242",
|
||||||
|
"name": "Synthesis and Solid State Pharmaceutical Centre",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100024313",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100024313",
|
||||||
|
"name": "Irish Rugby Football Union",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "100007490",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/100007490",
|
||||||
|
"name": "Bausch and Lomb Ireland",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "100007819",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/100007819",
|
||||||
|
"name": "Allergan",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "100010547",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/100010547",
|
||||||
|
"name": "Irish Youth Justice Service",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "100012733",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/100012733",
|
||||||
|
"name": "National Parks and Wildlife Service",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "100015278",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/100015278",
|
||||||
|
"name": "Pfizer Healthcare Ireland",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "100017144",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/100017144",
|
||||||
|
"name": "Shell E and P Ireland",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "100022895",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/100022895",
|
||||||
|
"name": "Health Research Institute, University of Limerick",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100001599",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100001599",
|
||||||
|
"name": "National Council for Forest Research and Development",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100006554",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100006554",
|
||||||
|
"name": "IDA Ireland",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100011626",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100011626",
|
||||||
|
"name": "Energy Policy Research Centre, Economic and Social Research Institute",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100014531",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100014531",
|
||||||
|
"name": "Physical Education and Sport Sciences Department, University of Limerick",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100014745",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100014745",
|
||||||
|
"name": "APC Microbiome Institute",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100014826",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100014826",
|
||||||
|
"name": "ADAPT - Centre for Digital Content Technology",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100020570",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100020570",
|
||||||
|
"name": "College of Medicine, Nursing and Health Sciences, National University of Ireland, Galway",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100020871",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100020871",
|
||||||
|
"name": "Bernal Institute, University of Limerick",
|
||||||
|
"synonym": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"id": "501100023852",
|
||||||
|
"uri": "http://dx.doi.org/10.13039/501100023852",
|
||||||
|
"name": "Moore Institute for Research in the Humanities and Social Studies, University of Galway",
|
||||||
|
"synonym": []
|
||||||
|
}
|
||||||
|
]
|
||||||
|
|
@ -0,0 +1,44 @@
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>jobTracker</name>
|
||||||
|
<value>yarnRM</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>nameNode</name>
|
||||||
|
<value>hdfs://nameservice1</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.use.system.libpath</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.action.sharelib.for.spark</name>
|
||||||
|
<value>spark2</value>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
<property>
|
||||||
|
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
<property>
|
||||||
|
<name>spark2ExtraListeners</name>
|
||||||
|
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
<property>
|
||||||
|
<name>spark2SqlQueryExecutionListeners</name>
|
||||||
|
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2YarnHistoryServerAddress</name>
|
||||||
|
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 </value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2EventLogDir</name>
|
||||||
|
<value>/user/spark/spark2ApplicationHistory</value>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
</configuration>
|
||||||
|
|
@ -0,0 +1,54 @@
|
||||||
|
<workflow-app name="generate_crossref_Datasource" xmlns="uri:oozie:workflow:0.5">
|
||||||
|
<parameters>
|
||||||
|
<property>
|
||||||
|
<name>sourcePath</name>
|
||||||
|
<description>The base path of MAG DUMP CSV Tables</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>targetPath</name>
|
||||||
|
<description>The base path of MAG DUMP CSV Tables</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>isLookupUrl</name>
|
||||||
|
<description>The Information service Lookup URL</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<start to="generateOAF"/>
|
||||||
|
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
<action name="generateOAF">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Crossref TO OAF</name>
|
||||||
|
<class>eu.dnetlib.dhp.collection.crossref.SparkMapDumpIntoOAF</class>
|
||||||
|
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.executor.memoryOverhead=2g
|
||||||
|
--conf spark.sql.shuffle.partitions=3000
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||||
|
<arg>--targetPath</arg><arg>${targetPath}</arg>
|
||||||
|
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||||
|
<arg>--master</arg><arg>yarn</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="End"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<end name="End"/>
|
||||||
|
</workflow-app>
|
||||||
|
|
@ -1,10 +1,17 @@
|
||||||
package eu.dnetlib.dhp.collection.crossref
|
package eu.dnetlib.dhp.collection.crossref
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||||
import eu.dnetlib.dhp.schema.oaf._
|
import eu.dnetlib.dhp.schema.oaf._
|
||||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.{field, qualifier, structuredProperty, subject}
|
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.{field, qualifier, structuredProperty, subject}
|
||||||
import eu.dnetlib.dhp.schema.oaf.utils.{DoiCleaningRule, GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType}
|
import eu.dnetlib.dhp.schema.oaf.utils.{
|
||||||
|
DoiCleaningRule,
|
||||||
|
GraphCleaningFunctions,
|
||||||
|
IdentifierFactory,
|
||||||
|
OafMapperUtils,
|
||||||
|
PidType
|
||||||
|
}
|
||||||
import eu.dnetlib.dhp.utils.DHPUtils
|
import eu.dnetlib.dhp.utils.DHPUtils
|
||||||
import org.apache.commons.lang.StringUtils
|
import org.apache.commons.lang.StringUtils
|
||||||
import org.json4s
|
import org.json4s
|
||||||
|
|
@ -37,18 +44,33 @@ case class funderInfo(id: String, uri: String, name: String, synonym: List[Strin
|
||||||
|
|
||||||
case class mappingFunder(name: String, DOI: Option[String], award: Option[List[String]]) {}
|
case class mappingFunder(name: String, DOI: Option[String], award: Option[List[String]]) {}
|
||||||
|
|
||||||
|
case class CrossrefResult(oafType: String, body: String) {}
|
||||||
|
|
||||||
case object Crossref2Oaf {
|
case object Crossref2Oaf {
|
||||||
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
|
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
|
||||||
|
val mapper = new ObjectMapper
|
||||||
|
|
||||||
val irishFunder: List[funderInfo] = {
|
val irishFunder: List[funderInfo] = {
|
||||||
val s = Source
|
val s = Source
|
||||||
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref/irish_funder.json"))
|
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/irish_funder.json"))
|
||||||
.mkString
|
.mkString
|
||||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||||
lazy val json: org.json4s.JValue = parse(s)
|
lazy val json: org.json4s.JValue = parse(s)
|
||||||
json.extract[List[funderInfo]]
|
json.extract[List[funderInfo]]
|
||||||
}
|
}
|
||||||
|
|
||||||
|
val invalidName = List(
|
||||||
|
",",
|
||||||
|
"none none",
|
||||||
|
"none, none",
|
||||||
|
"none &na;",
|
||||||
|
"(:null)",
|
||||||
|
"test test test",
|
||||||
|
"test test",
|
||||||
|
"test",
|
||||||
|
"&na; &na;"
|
||||||
|
)
|
||||||
|
|
||||||
def getIrishId(doi: String): Option[String] = {
|
def getIrishId(doi: String): Option[String] = {
|
||||||
val id = doi.split("/").last
|
val id = doi.split("/").last
|
||||||
irishFunder
|
irishFunder
|
||||||
|
|
@ -64,8 +86,9 @@ case object Crossref2Oaf {
|
||||||
cf
|
cf
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
def generateDataInfo(): DataInfo = {
|
def generateDataInfo(): DataInfo = {
|
||||||
generateDataInfo("0.9")
|
generateDataInfo("0.91")
|
||||||
}
|
}
|
||||||
|
|
||||||
def generateDataInfo(trust: String): DataInfo = {
|
def generateDataInfo(trust: String): DataInfo = {
|
||||||
|
|
@ -84,6 +107,7 @@ case object Crossref2Oaf {
|
||||||
)
|
)
|
||||||
di
|
di
|
||||||
}
|
}
|
||||||
|
|
||||||
def getOpenAccessQualifier(): AccessRight = {
|
def getOpenAccessQualifier(): AccessRight = {
|
||||||
|
|
||||||
OafMapperUtils.accessRight(
|
OafMapperUtils.accessRight(
|
||||||
|
|
@ -102,6 +126,7 @@ case object Crossref2Oaf {
|
||||||
ModelConstants.DNET_ACCESS_MODES
|
ModelConstants.DNET_ACCESS_MODES
|
||||||
)
|
)
|
||||||
}
|
}
|
||||||
|
|
||||||
def getUnknownQualifier(): AccessRight = {
|
def getUnknownQualifier(): AccessRight = {
|
||||||
OafMapperUtils.accessRight(
|
OafMapperUtils.accessRight(
|
||||||
ModelConstants.UNKNOWN,
|
ModelConstants.UNKNOWN,
|
||||||
|
|
@ -197,14 +222,81 @@ case object Crossref2Oaf {
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
def isValidAuthorName(fullName: String): Boolean = {
|
||||||
|
if (fullName == null || fullName.isEmpty)
|
||||||
|
return false
|
||||||
|
if (invalidName.contains(fullName.toLowerCase.trim))
|
||||||
|
return false
|
||||||
|
true
|
||||||
|
}
|
||||||
|
|
||||||
|
def filterResult(publication: Result): Boolean = {
|
||||||
|
|
||||||
def mappingResult(result: Result, json: JValue, instanceType:Qualifier, originalType: String): Result = {
|
//Case empty publication
|
||||||
|
if (publication == null)
|
||||||
|
return false
|
||||||
|
if (publication.getId == null || publication.getId.isEmpty)
|
||||||
|
return false
|
||||||
|
|
||||||
|
//Case publication with no title
|
||||||
|
if (publication.getTitle == null || publication.getTitle.size == 0)
|
||||||
|
return false
|
||||||
|
|
||||||
|
val s = publication.getTitle.asScala.count(p =>
|
||||||
|
p.getValue != null
|
||||||
|
&& p.getValue.nonEmpty && !p.getValue.equalsIgnoreCase("[NO TITLE AVAILABLE]")
|
||||||
|
)
|
||||||
|
|
||||||
|
if (s == 0)
|
||||||
|
return false
|
||||||
|
|
||||||
|
// fixes #4360 (test publisher)
|
||||||
|
val publisher =
|
||||||
|
if (publication.getPublisher != null) publication.getPublisher.getValue else null
|
||||||
|
|
||||||
|
if (
|
||||||
|
publisher != null && (publisher.equalsIgnoreCase("Test accounts") || publisher
|
||||||
|
.equalsIgnoreCase("CrossRef Test Account"))
|
||||||
|
) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
|
||||||
|
//RELAXED this constraint
|
||||||
|
//Publication with no Author
|
||||||
|
if (publication.getAuthor == null || publication.getAuthor.size() == 0)
|
||||||
|
return true
|
||||||
|
|
||||||
|
//filter invalid author
|
||||||
|
val authors = publication.getAuthor.asScala.map(s => {
|
||||||
|
if (s.getFullname.nonEmpty) {
|
||||||
|
s.getFullname
|
||||||
|
} else
|
||||||
|
s"${s.getName} ${s.getSurname}"
|
||||||
|
})
|
||||||
|
|
||||||
|
val c = authors.count(isValidAuthorName)
|
||||||
|
if (c == 0)
|
||||||
|
return false
|
||||||
|
|
||||||
|
// fixes #4368
|
||||||
|
if (
|
||||||
|
authors.count(s => s.equalsIgnoreCase("Addie Jackson")) > 0 && "Elsevier BV".equalsIgnoreCase(
|
||||||
|
publication.getPublisher.getValue
|
||||||
|
)
|
||||||
|
)
|
||||||
|
return false
|
||||||
|
|
||||||
|
true
|
||||||
|
}
|
||||||
|
|
||||||
|
def mappingResult(result: Result, json: JValue, instanceType: Qualifier, originalType: String): Result = {
|
||||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||||
|
|
||||||
//MAPPING Crossref DOI into PID
|
//MAPPING Crossref DOI into PID
|
||||||
val doi: String = DoiCleaningRule.normalizeDoi((json \ "DOI").extract[String])
|
val doi: String = DoiCleaningRule.normalizeDoi((json \ "DOI").extract[String])
|
||||||
result.setPid(List(structuredProperty(
|
result.setPid(
|
||||||
|
List(
|
||||||
|
structuredProperty(
|
||||||
doi,
|
doi,
|
||||||
qualifier(
|
qualifier(
|
||||||
PidType.doi.toString,
|
PidType.doi.toString,
|
||||||
|
|
@ -213,7 +305,9 @@ case object Crossref2Oaf {
|
||||||
ModelConstants.DNET_PID_TYPES
|
ModelConstants.DNET_PID_TYPES
|
||||||
),
|
),
|
||||||
null
|
null
|
||||||
)).asJava)
|
)
|
||||||
|
).asJava
|
||||||
|
)
|
||||||
|
|
||||||
//MAPPING Crossref DOI into OriginalId
|
//MAPPING Crossref DOI into OriginalId
|
||||||
//and Other Original Identifier of dataset like clinical-trial-number
|
//and Other Original Identifier of dataset like clinical-trial-number
|
||||||
|
|
@ -251,7 +345,9 @@ case object Crossref2Oaf {
|
||||||
val subtitles =
|
val subtitles =
|
||||||
for { JString(title) <- json \ "subtitle" if title.nonEmpty } yield structuredProperty(
|
for { JString(title) <- json \ "subtitle" if title.nonEmpty } yield structuredProperty(
|
||||||
title,
|
title,
|
||||||
ModelConstants.SUBTITLE_QUALIFIER, null)
|
ModelConstants.SUBTITLE_QUALIFIER,
|
||||||
|
null
|
||||||
|
)
|
||||||
result.setTitle((mainTitles ::: originalTitles ::: shortTitles ::: subtitles).asJava)
|
result.setTitle((mainTitles ::: originalTitles ::: shortTitles ::: subtitles).asJava)
|
||||||
|
|
||||||
// DESCRIPTION
|
// DESCRIPTION
|
||||||
|
|
@ -302,9 +398,9 @@ case object Crossref2Oaf {
|
||||||
(json \ "issued" \ "date-parts").extract[List[List[Int]]]
|
(json \ "issued" \ "date-parts").extract[List[List[Int]]]
|
||||||
)
|
)
|
||||||
if (StringUtils.isNotBlank(issuedDate)) {
|
if (StringUtils.isNotBlank(issuedDate)) {
|
||||||
result.setDateofacceptance(field(issuedDate,null))
|
result.setDateofacceptance(field(issuedDate, null))
|
||||||
} else {
|
} else {
|
||||||
result.setDateofacceptance(field(createdDate.getValue,null))
|
result.setDateofacceptance(field(createdDate.getValue, null))
|
||||||
}
|
}
|
||||||
result.setRelevantdate(
|
result.setRelevantdate(
|
||||||
List(createdDate, postedDate, acceptedDate, publishedOnlineDate, publishedPrintDate)
|
List(createdDate, postedDate, acceptedDate, publishedOnlineDate, publishedPrintDate)
|
||||||
|
|
@ -317,7 +413,7 @@ case object Crossref2Oaf {
|
||||||
|
|
||||||
if (subjectList.nonEmpty) {
|
if (subjectList.nonEmpty) {
|
||||||
result.setSubject(
|
result.setSubject(
|
||||||
subjectList.map(s => subject(s,ModelConstants.SUBTITLE_QUALIFIER,null)).asJava
|
subjectList.map(s => subject(s, ModelConstants.SUBTITLE_QUALIFIER, null)).asJava
|
||||||
)
|
)
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -339,7 +435,7 @@ case object Crossref2Oaf {
|
||||||
JObject(license) <- json \ "license"
|
JObject(license) <- json \ "license"
|
||||||
JField("URL", JString(lic)) <- license
|
JField("URL", JString(lic)) <- license
|
||||||
JField("content-version", JString(content_version)) <- license
|
JField("content-version", JString(content_version)) <- license
|
||||||
} yield (field[String](lic,null), content_version)
|
} yield (field[String](lic, null), content_version)
|
||||||
val l = license.filter(d => StringUtils.isNotBlank(d._1.getValue))
|
val l = license.filter(d => StringUtils.isNotBlank(d._1.getValue))
|
||||||
if (l.nonEmpty) {
|
if (l.nonEmpty) {
|
||||||
if (l exists (d => d._2.equals("vor"))) {
|
if (l exists (d => d._2.equals("vor"))) {
|
||||||
|
|
@ -382,9 +478,9 @@ case object Crossref2Oaf {
|
||||||
|
|
||||||
instance.setCollectedfrom(createCrossrefCollectedFrom())
|
instance.setCollectedfrom(createCrossrefCollectedFrom())
|
||||||
if (StringUtils.isNotBlank(issuedDate)) {
|
if (StringUtils.isNotBlank(issuedDate)) {
|
||||||
instance.setDateofacceptance(field(issuedDate,null))
|
instance.setDateofacceptance(field(issuedDate, null))
|
||||||
} else {
|
} else {
|
||||||
instance.setDateofacceptance(field(createdDate.getValue,null))
|
instance.setDateofacceptance(field(createdDate.getValue, null))
|
||||||
}
|
}
|
||||||
val s: List[String] = List("https://doi.org/" + doi)
|
val s: List[String] = List("https://doi.org/" + doi)
|
||||||
// val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null && p.toLowerCase().contains(doi.toLowerCase())).distinct
|
// val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null && p.toLowerCase().contains(doi.toLowerCase())).distinct
|
||||||
|
|
@ -415,6 +511,7 @@ case object Crossref2Oaf {
|
||||||
else
|
else
|
||||||
result
|
result
|
||||||
}
|
}
|
||||||
|
|
||||||
def generateIdentifier(oaf: Result, doi: String): String = {
|
def generateIdentifier(oaf: Result, doi: String): String = {
|
||||||
val id = DHPUtils.md5(doi.toLowerCase)
|
val id = DHPUtils.md5(doi.toLowerCase)
|
||||||
s"50|doiboost____|$id"
|
s"50|doiboost____|$id"
|
||||||
|
|
@ -431,7 +528,12 @@ case object Crossref2Oaf {
|
||||||
List(
|
List(
|
||||||
structuredProperty(
|
structuredProperty(
|
||||||
orcid,
|
orcid,
|
||||||
qualifier( ModelConstants.ORCID_PENDING, ModelConstants.ORCID_PENDING, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES),
|
qualifier(
|
||||||
|
ModelConstants.ORCID_PENDING,
|
||||||
|
ModelConstants.ORCID_PENDING,
|
||||||
|
ModelConstants.DNET_PID_TYPES,
|
||||||
|
ModelConstants.DNET_PID_TYPES
|
||||||
|
),
|
||||||
generateDataInfo()
|
generateDataInfo()
|
||||||
)
|
)
|
||||||
).asJava
|
).asJava
|
||||||
|
|
@ -473,17 +575,16 @@ case object Crossref2Oaf {
|
||||||
null
|
null
|
||||||
}
|
}
|
||||||
|
|
||||||
def convert(input: String, vocabularies: VocabularyGroup): List[Oaf] = {
|
def convert(input: String, vocabularies: VocabularyGroup): List[CrossrefResult] = {
|
||||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||||
lazy val json: json4s.JValue = parse(input)
|
lazy val json: json4s.JValue = parse(input)
|
||||||
|
|
||||||
var resultList: List[Oaf] = List()
|
var resultList: List[CrossrefResult] = List()
|
||||||
|
|
||||||
val objectType = (json \ "type").extractOrElse[String](null)
|
val objectType = (json \ "type").extractOrElse[String](null)
|
||||||
val objectSubType = (json \ "subtype").extractOrElse[String](null)
|
|
||||||
if (objectType == null)
|
if (objectType == null)
|
||||||
return resultList
|
return resultList
|
||||||
val typology =getTypeQualifier(objectType, vocabularies)
|
val typology = getTypeQualifier(objectType, vocabularies)
|
||||||
|
|
||||||
if (typology == null)
|
if (typology == null)
|
||||||
return List()
|
return List()
|
||||||
|
|
@ -507,7 +608,7 @@ case object Crossref2Oaf {
|
||||||
createCrossrefCollectedFrom(),
|
createCrossrefCollectedFrom(),
|
||||||
result.getDataInfo,
|
result.getDataInfo,
|
||||||
result.getLastupdatetimestamp
|
result.getLastupdatetimestamp
|
||||||
)
|
).map(s => CrossrefResult(s.getClass.getSimpleName, mapper.writeValueAsString(s)))
|
||||||
}
|
}
|
||||||
|
|
||||||
result match {
|
result match {
|
||||||
|
|
@ -522,10 +623,15 @@ case object Crossref2Oaf {
|
||||||
|
|
||||||
if (doisReference != null && doisReference.nonEmpty) {
|
if (doisReference != null && doisReference.nonEmpty) {
|
||||||
val citation_relations: List[Relation] = generateCitationRelations(doisReference, result)
|
val citation_relations: List[Relation] = generateCitationRelations(doisReference, result)
|
||||||
resultList = resultList ::: citation_relations
|
resultList = resultList ::: citation_relations.map(s =>
|
||||||
|
CrossrefResult(s.getClass.getSimpleName, mapper.writeValueAsString(s))
|
||||||
|
)
|
||||||
}
|
}
|
||||||
resultList = resultList ::: List(result)
|
if (!filterResult(result))
|
||||||
resultList
|
List()
|
||||||
|
else
|
||||||
|
resultList ::: List(result).map(s => CrossrefResult(s.getClass.getSimpleName, mapper.writeValueAsString(s)))
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
private def createCiteRelation(source: Result, targetPid: String, targetPidType: String): List[Relation] = {
|
private def createCiteRelation(source: Result, targetPid: String, targetPidType: String): List[Relation] = {
|
||||||
|
|
@ -752,10 +858,10 @@ case object Crossref2Oaf {
|
||||||
val source = s"${containerTitles.head} ISBN: ${ISBN.head}"
|
val source = s"${containerTitles.head} ISBN: ${ISBN.head}"
|
||||||
if (publication.getSource != null) {
|
if (publication.getSource != null) {
|
||||||
val l: List[Field[String]] = publication.getSource.asScala.toList
|
val l: List[Field[String]] = publication.getSource.asScala.toList
|
||||||
val ll: List[Field[String]] = l ::: List(field(source,null))
|
val ll: List[Field[String]] = l ::: List(field(source, null))
|
||||||
publication.setSource(ll.asJava)
|
publication.setSource(ll.asJava)
|
||||||
} else
|
} else
|
||||||
publication.setSource(List(field(source,null)).asJava)
|
publication.setSource(List(field(source, null)).asJava)
|
||||||
}
|
}
|
||||||
} else {
|
} else {
|
||||||
// Mapping Journal
|
// Mapping Journal
|
||||||
|
|
@ -823,7 +929,7 @@ case object Crossref2Oaf {
|
||||||
): StructuredProperty = {
|
): StructuredProperty = {
|
||||||
val dp = extractDate(dt, datePart)
|
val dp = extractDate(dt, datePart)
|
||||||
if (StringUtils.isNotBlank(dp))
|
if (StringUtils.isNotBlank(dp))
|
||||||
return structuredProperty(dp, qualifier(classId,classId, schemeId, schemeId),null)
|
return structuredProperty(dp, qualifier(classId, classId, schemeId, schemeId), null)
|
||||||
null
|
null
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -836,12 +942,11 @@ case object Crossref2Oaf {
|
||||||
val item = new Dataset
|
val item = new Dataset
|
||||||
item.setResourcetype(objectType)
|
item.setResourcetype(objectType)
|
||||||
return item
|
return item
|
||||||
}
|
} else if (objectType.getClassid.equalsIgnoreCase("software")) {
|
||||||
else if (objectType.getClassid.equalsIgnoreCase("software")){
|
|
||||||
val item = new Software
|
val item = new Software
|
||||||
item.setResourcetype(objectType)
|
item.setResourcetype(objectType)
|
||||||
return item
|
return item
|
||||||
}else if (objectType.getClassid.equalsIgnoreCase("OtherResearchProduct")){
|
} else if (objectType.getClassid.equalsIgnoreCase("OtherResearchProduct")) {
|
||||||
val item = new OtherResearchProduct
|
val item = new OtherResearchProduct
|
||||||
item.setResourcetype(objectType)
|
item.setResourcetype(objectType)
|
||||||
return item
|
return item
|
||||||
|
|
|
||||||
|
|
@ -1,106 +0,0 @@
|
||||||
package eu.dnetlib.dhp.collection.crossref
|
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
|
||||||
import org.apache.commons.io.IOUtils
|
|
||||||
import org.apache.hadoop.io.{IntWritable, Text}
|
|
||||||
import org.apache.spark.SparkConf
|
|
||||||
import org.apache.spark.sql.expressions.Aggregator
|
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, SaveMode, SparkSession}
|
|
||||||
import org.json4s
|
|
||||||
import org.json4s.DefaultFormats
|
|
||||||
import org.json4s.jackson.JsonMethods.parse
|
|
||||||
import org.slf4j.{Logger, LoggerFactory}
|
|
||||||
|
|
||||||
object CrossrefDataset {
|
|
||||||
|
|
||||||
val logger: Logger = LoggerFactory.getLogger(CrossrefDataset.getClass)
|
|
||||||
|
|
||||||
def to_item(input: String): CrossrefDT = {
|
|
||||||
|
|
||||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
|
||||||
lazy val json: json4s.JValue = parse(input)
|
|
||||||
val ts: Long = (json \ "indexed" \ "timestamp").extract[Long]
|
|
||||||
val doi: String = DoiBoostMappingUtil.normalizeDoi((json \ "DOI").extract[String])
|
|
||||||
CrossrefDT(doi, input, ts)
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
|
||||||
|
|
||||||
val conf: SparkConf = new SparkConf()
|
|
||||||
val parser = new ArgumentApplicationParser(
|
|
||||||
IOUtils.toString(
|
|
||||||
CrossrefDataset.getClass.getResourceAsStream(
|
|
||||||
"/eu/dnetlib/dhp/doiboost/crossref_to_dataset_params.json"
|
|
||||||
)
|
|
||||||
)
|
|
||||||
)
|
|
||||||
parser.parseArgument(args)
|
|
||||||
val spark: SparkSession =
|
|
||||||
SparkSession
|
|
||||||
.builder()
|
|
||||||
.config(conf)
|
|
||||||
.appName(CrossrefDataset.getClass.getSimpleName)
|
|
||||||
.master(parser.get("master"))
|
|
||||||
.getOrCreate()
|
|
||||||
import spark.implicits._
|
|
||||||
|
|
||||||
val crossrefAggregator = new Aggregator[CrossrefDT, CrossrefDT, CrossrefDT] with Serializable {
|
|
||||||
|
|
||||||
override def zero: CrossrefDT = null
|
|
||||||
|
|
||||||
override def reduce(b: CrossrefDT, a: CrossrefDT): CrossrefDT = {
|
|
||||||
if (b == null)
|
|
||||||
return a
|
|
||||||
if (a == null)
|
|
||||||
return b
|
|
||||||
|
|
||||||
if (a.timestamp > b.timestamp) {
|
|
||||||
return a
|
|
||||||
}
|
|
||||||
b
|
|
||||||
}
|
|
||||||
|
|
||||||
override def merge(a: CrossrefDT, b: CrossrefDT): CrossrefDT = {
|
|
||||||
if (b == null)
|
|
||||||
return a
|
|
||||||
if (a == null)
|
|
||||||
return b
|
|
||||||
|
|
||||||
if (a.timestamp > b.timestamp) {
|
|
||||||
return a
|
|
||||||
}
|
|
||||||
b
|
|
||||||
}
|
|
||||||
|
|
||||||
override def bufferEncoder: Encoder[CrossrefDT] = implicitly[Encoder[CrossrefDT]]
|
|
||||||
|
|
||||||
override def outputEncoder: Encoder[CrossrefDT] = implicitly[Encoder[CrossrefDT]]
|
|
||||||
|
|
||||||
override def finish(reduction: CrossrefDT): CrossrefDT = reduction
|
|
||||||
}
|
|
||||||
|
|
||||||
val workingPath: String = parser.get("workingPath")
|
|
||||||
|
|
||||||
val main_ds: Dataset[CrossrefDT] = spark.read.load(s"$workingPath/crossref_ds").as[CrossrefDT]
|
|
||||||
|
|
||||||
val update =
|
|
||||||
spark.createDataset(
|
|
||||||
spark.sparkContext
|
|
||||||
.sequenceFile(s"$workingPath/index_update", classOf[IntWritable], classOf[Text])
|
|
||||||
.map(i => CrossrefImporter.decompressBlob(i._2.toString))
|
|
||||||
.map(i => to_item(i))
|
|
||||||
)
|
|
||||||
|
|
||||||
main_ds
|
|
||||||
.union(update)
|
|
||||||
.groupByKey(_.doi)
|
|
||||||
.agg(crossrefAggregator.toColumn)
|
|
||||||
.map(s => s._2)
|
|
||||||
.write
|
|
||||||
.mode(SaveMode.Overwrite)
|
|
||||||
.save(s"$workingPath/crossref_ds_updated")
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
@ -0,0 +1,61 @@
|
||||||
|
package eu.dnetlib.dhp.collection.crossref
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.AbstractScalaApplication
|
||||||
|
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Dataset => OafDataset}
|
||||||
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory
|
||||||
|
import org.apache.spark.sql._
|
||||||
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
|
class SparkMapDumpIntoOAF(propertyPath: String, args: Array[String], log: Logger)
|
||||||
|
extends AbstractScalaApplication(propertyPath, args, log: Logger) {
|
||||||
|
|
||||||
|
/** Here all the spark applications runs this method
|
||||||
|
* where the whole logic of the spark node is defined
|
||||||
|
*/
|
||||||
|
override def run(): Unit = {
|
||||||
|
val sourcePath = parser.get("sourcePath")
|
||||||
|
log.info("sourcePath: {}", sourcePath)
|
||||||
|
val targetPath = parser.get("targetPath")
|
||||||
|
log.info("targetPath: {}", targetPath)
|
||||||
|
val isLookupUrl: String = parser.get("isLookupUrl")
|
||||||
|
log.info("isLookupUrl: {}", isLookupUrl)
|
||||||
|
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
|
||||||
|
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
|
||||||
|
require(vocabularies != null)
|
||||||
|
transformCrossref(spark, sourcePath, targetPath, vocabularies)
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
def transformCrossref(
|
||||||
|
spark: SparkSession,
|
||||||
|
sourcePath: String,
|
||||||
|
targetPath: String,
|
||||||
|
vocabularies: VocabularyGroup
|
||||||
|
): Unit = {
|
||||||
|
import spark.implicits._
|
||||||
|
val dump = spark.read.text(sourcePath).as[String]
|
||||||
|
dump
|
||||||
|
.flatMap(s => Crossref2Oaf.convert(s, vocabularies))
|
||||||
|
.write
|
||||||
|
.mode(SaveMode.Overwrite)
|
||||||
|
.partitionBy("oafType")
|
||||||
|
.option("compression", "gzip")
|
||||||
|
.text(targetPath)
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
object SparkMapDumpIntoOAF {
|
||||||
|
|
||||||
|
def main(args: Array[String]): Unit = {
|
||||||
|
val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
|
||||||
|
|
||||||
|
new SparkMapDumpIntoOAF(
|
||||||
|
log = logger,
|
||||||
|
args = args,
|
||||||
|
propertyPath = "/eu/dnetlib/dhp/collection/crossref/convert_crossref_dump_to_oaf_params.json"
|
||||||
|
).initialize().run()
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -14,7 +14,6 @@ import scala.collection.JavaConverters._
|
||||||
|
|
||||||
case class MAGPaper(
|
case class MAGPaper(
|
||||||
paperId: Option[Long],
|
paperId: Option[Long],
|
||||||
rank: Option[Int],
|
|
||||||
doi: Option[String],
|
doi: Option[String],
|
||||||
docType: Option[String],
|
docType: Option[String],
|
||||||
paperTitle: Option[String],
|
paperTitle: Option[String],
|
||||||
|
|
@ -29,7 +28,6 @@ case class MAGPaper(
|
||||||
journalName: Option[String],
|
journalName: Option[String],
|
||||||
journalIssn: Option[String],
|
journalIssn: Option[String],
|
||||||
journalPublisher: Option[String],
|
journalPublisher: Option[String],
|
||||||
journalWebpage: Option[String],
|
|
||||||
conferenceSeriesId: Option[Long],
|
conferenceSeriesId: Option[Long],
|
||||||
conferenceInstanceId: Option[Long],
|
conferenceInstanceId: Option[Long],
|
||||||
conferenceName: Option[String],
|
conferenceName: Option[String],
|
||||||
|
|
@ -51,8 +49,6 @@ case class MAGPaper(
|
||||||
abstractText: Option[String],
|
abstractText: Option[String],
|
||||||
// List of authors
|
// List of authors
|
||||||
authors: Option[List[MAGAuthor]],
|
authors: Option[List[MAGAuthor]],
|
||||||
// List of Fields of Study
|
|
||||||
fos: Option[List[MAGFieldOfStudy]],
|
|
||||||
urls: Option[List[String]]
|
urls: Option[List[String]]
|
||||||
)
|
)
|
||||||
|
|
||||||
|
|
@ -65,13 +61,6 @@ case class MAGAuthor(
|
||||||
GridId: Option[String]
|
GridId: Option[String]
|
||||||
)
|
)
|
||||||
|
|
||||||
case class MAGFieldOfStudy(
|
|
||||||
FieldOfStudyId: Option[Long],
|
|
||||||
DisplayName: Option[String],
|
|
||||||
MainType: Option[String],
|
|
||||||
Score: Option[Double]
|
|
||||||
)
|
|
||||||
|
|
||||||
object MagUtility extends Serializable {
|
object MagUtility extends Serializable {
|
||||||
|
|
||||||
val datatypedict = Map(
|
val datatypedict = Map(
|
||||||
|
|
|
||||||
|
|
@ -62,9 +62,7 @@ class SparkCreateMagDenormalizedTable(propertyPath: String, args: Array[String],
|
||||||
//next step we create a table containing
|
//next step we create a table containing
|
||||||
val authors = MagUtility.loadMagEntity(spark, "Authors", magBasePath)
|
val authors = MagUtility.loadMagEntity(spark, "Authors", magBasePath)
|
||||||
val affiliations = MagUtility.loadMagEntity(spark, "Affiliations", magBasePath)
|
val affiliations = MagUtility.loadMagEntity(spark, "Affiliations", magBasePath)
|
||||||
val paaf = MagUtility.loadMagEntity(spark, "PaperAuthorAffiliations", magBasePath)
|
val paperAuthorAffiliations = MagUtility.loadMagEntity(spark, "PaperAuthorAffiliations", magBasePath)
|
||||||
|
|
||||||
val paperAuthorAffiliations = paaf.join(step0, paaf("PaperId") === step0("PaperId"), "leftsemi")
|
|
||||||
|
|
||||||
val j1 = paperAuthorAffiliations
|
val j1 = paperAuthorAffiliations
|
||||||
.join(authors, paperAuthorAffiliations("AuthorId") === authors("AuthorId"), "inner")
|
.join(authors, paperAuthorAffiliations("AuthorId") === authors("AuthorId"), "inner")
|
||||||
|
|
@ -116,26 +114,26 @@ class SparkCreateMagDenormalizedTable(propertyPath: String, args: Array[String],
|
||||||
step2.count()
|
step2.count()
|
||||||
step1.unpersist()
|
step1.unpersist()
|
||||||
|
|
||||||
val fos = MagUtility
|
// val fos = MagUtility
|
||||||
.loadMagEntity(spark, "FieldsOfStudy", magBasePath)
|
// .loadMagEntity(spark, "FieldsOfStudy", magBasePath)
|
||||||
.select($"FieldOfStudyId".alias("fos"), $"DisplayName", $"MainType")
|
// .select($"FieldOfStudyId".alias("fos"), $"DisplayName", $"MainType")
|
||||||
|
//
|
||||||
val paperFieldsOfStudy = MagUtility
|
// val paperFieldsOfStudy = MagUtility
|
||||||
.loadMagEntity(spark, "PaperFieldsOfStudy", magBasePath)
|
// .loadMagEntity(spark, "PaperFieldsOfStudy", magBasePath)
|
||||||
.select($"FieldOfStudyId", $"Score", $"PaperId")
|
// .select($"FieldOfStudyId", $"Score", $"PaperId")
|
||||||
|
//
|
||||||
val paperFoS = paperFieldsOfStudy
|
// val paperFoS = paperFieldsOfStudy
|
||||||
.join(broadcast(fos), fos("fos") === paperFieldsOfStudy("FieldOfStudyId"))
|
// .join(broadcast(fos), fos("fos") === paperFieldsOfStudy("FieldOfStudyId"))
|
||||||
.groupBy("PaperId")
|
// .groupBy("PaperId")
|
||||||
.agg(collect_set(struct("FieldOfStudyId", "DisplayName", "MainType", "Score")).as("FoS"))
|
// .agg(collect_set(struct("FieldOfStudyId", "DisplayName", "MainType", "Score")).as("FoS"))
|
||||||
|
//
|
||||||
val step3 = step2
|
// val step3 = step2
|
||||||
.join(paperFoS, step2("PaperId") === paperFoS("PaperId"), "left")
|
// .join(paperFoS, step2("PaperId") === paperFoS("PaperId"), "left")
|
||||||
.select(step2("*"), paperFoS("FoS"))
|
// .select(step2("*"), paperFoS("FoS"))
|
||||||
.cache()
|
// .cache()
|
||||||
step3.count()
|
// step3.count()
|
||||||
|
//
|
||||||
step2.unpersist()
|
// step2.unpersist()
|
||||||
|
|
||||||
val journals = MagUtility
|
val journals = MagUtility
|
||||||
.loadMagEntity(spark, "Journals", magBasePath)
|
.loadMagEntity(spark, "Journals", magBasePath)
|
||||||
|
|
@ -143,20 +141,18 @@ class SparkCreateMagDenormalizedTable(propertyPath: String, args: Array[String],
|
||||||
$"JournalId",
|
$"JournalId",
|
||||||
$"DisplayName".as("journalName"),
|
$"DisplayName".as("journalName"),
|
||||||
$"Issn".as("journalIssn"),
|
$"Issn".as("journalIssn"),
|
||||||
$"Publisher".as("journalPublisher"),
|
$"Publisher".as("journalPublisher")
|
||||||
$"Webpage".as("journalWebpage")
|
|
||||||
)
|
)
|
||||||
val step4 = step3
|
val step3 = step2
|
||||||
.join(journals, step3("JournalId") === journals("JournalId"), "left")
|
.join(journals, step2("JournalId") === journals("JournalId"), "left")
|
||||||
.select(
|
.select(
|
||||||
step3("*"),
|
step2("*"),
|
||||||
journals("journalName"),
|
journals("journalName"),
|
||||||
journals("journalIssn"),
|
journals("journalIssn"),
|
||||||
journals("journalPublisher"),
|
journals("journalPublisher")
|
||||||
journals("journalWebpage")
|
|
||||||
)
|
)
|
||||||
.cache
|
.cache
|
||||||
step4.count()
|
step3.count()
|
||||||
|
|
||||||
val paper_urls = MagUtility
|
val paper_urls = MagUtility
|
||||||
.loadMagEntity(spark, "PaperUrls", magBasePath)
|
.loadMagEntity(spark, "PaperUrls", magBasePath)
|
||||||
|
|
@ -166,12 +162,11 @@ class SparkCreateMagDenormalizedTable(propertyPath: String, args: Array[String],
|
||||||
|
|
||||||
paper_urls.count
|
paper_urls.count
|
||||||
|
|
||||||
step4
|
step3
|
||||||
.join(paper_urls, step4("PaperId") === paper_urls("PaperId"))
|
.join(paper_urls, step3("PaperId") === paper_urls("PaperId"))
|
||||||
.select(step4("*"), paper_urls("urls"))
|
.select(step3("*"), paper_urls("urls"))
|
||||||
.select(
|
.select(
|
||||||
$"PaperId".as("paperId"),
|
$"PaperId".as("paperId"),
|
||||||
$"Rank".as("rank"),
|
|
||||||
$"Doi".as("doi"),
|
$"Doi".as("doi"),
|
||||||
$"DocType".as("docType"),
|
$"DocType".as("docType"),
|
||||||
$"PaperTitle".as("paperTitle"),
|
$"PaperTitle".as("paperTitle"),
|
||||||
|
|
@ -202,11 +197,9 @@ class SparkCreateMagDenormalizedTable(propertyPath: String, args: Array[String],
|
||||||
$"conferenceLocation".as("conferenceLocation"),
|
$"conferenceLocation".as("conferenceLocation"),
|
||||||
$"conferenceStartDate".as("conferenceStartDate"),
|
$"conferenceStartDate".as("conferenceStartDate"),
|
||||||
$"conferenceEndDate".as("conferenceEndDate"),
|
$"conferenceEndDate".as("conferenceEndDate"),
|
||||||
$"FoS".as("fos"),
|
|
||||||
$"journalName".as("journalName"),
|
$"journalName".as("journalName"),
|
||||||
$"journalIssn".as("journalIssn"),
|
$"journalIssn".as("journalIssn"),
|
||||||
$"journalPublisher".as("journalPublisher"),
|
$"journalPublisher".as("journalPublisher"),
|
||||||
$"journalWebpage".as("journalWebpage"),
|
|
||||||
$"urls"
|
$"urls"
|
||||||
)
|
)
|
||||||
.write
|
.write
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,849 @@
|
||||||
|
{
|
||||||
|
"URL": "http://dx.doi.org/10.1016/j.joca.2019.11.002",
|
||||||
|
"resource": {
|
||||||
|
"primary": {
|
||||||
|
"URL": "https://linkinghub.elsevier.com/retrieve/pii/S106345841931266X"
|
||||||
|
}
|
||||||
|
},
|
||||||
|
"member": "78",
|
||||||
|
"score": 0.0,
|
||||||
|
"created": {
|
||||||
|
"date-parts": [
|
||||||
|
[
|
||||||
|
2019,
|
||||||
|
11,
|
||||||
|
14
|
||||||
|
]
|
||||||
|
],
|
||||||
|
"date-time": "2019-11-14T18:08:38Z",
|
||||||
|
"timestamp": 1573754918000
|
||||||
|
},
|
||||||
|
"update-policy": "http://dx.doi.org/10.1016/elsevier_cm_policy",
|
||||||
|
"license": [
|
||||||
|
{
|
||||||
|
"start": {
|
||||||
|
"date-parts": [
|
||||||
|
[
|
||||||
|
2020,
|
||||||
|
5,
|
||||||
|
1
|
||||||
|
]
|
||||||
|
],
|
||||||
|
"date-time": "2020-05-01T00:00:00Z",
|
||||||
|
"timestamp": 1588291200000
|
||||||
|
},
|
||||||
|
"content-version": "tdm",
|
||||||
|
"delay-in-days": 0,
|
||||||
|
"URL": "https://www.elsevier.com/tdm/userlicense/1.0/"
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"start": {
|
||||||
|
"date-parts": [
|
||||||
|
[
|
||||||
|
2021,
|
||||||
|
5,
|
||||||
|
1
|
||||||
|
]
|
||||||
|
],
|
||||||
|
"date-time": "2021-05-01T00:00:00Z",
|
||||||
|
"timestamp": 1619827200000
|
||||||
|
},
|
||||||
|
"content-version": "vor",
|
||||||
|
"delay-in-days": 365,
|
||||||
|
"URL": "http://www.elsevier.com/open-access/userlicense/1.0/"
|
||||||
|
}
|
||||||
|
],
|
||||||
|
"ISSN": [
|
||||||
|
"1063-4584"
|
||||||
|
],
|
||||||
|
"container-title": [
|
||||||
|
"Osteoarthritis and Cartilage"
|
||||||
|
],
|
||||||
|
"issued": {
|
||||||
|
"date-parts": [
|
||||||
|
[
|
||||||
|
2020,
|
||||||
|
5
|
||||||
|
]
|
||||||
|
]
|
||||||
|
},
|
||||||
|
"issue": "5",
|
||||||
|
"prefix": "10.1016",
|
||||||
|
"reference-count": 50,
|
||||||
|
"indexed": {
|
||||||
|
"date-parts": [
|
||||||
|
[
|
||||||
|
2024,
|
||||||
|
2,
|
||||||
|
27
|
||||||
|
]
|
||||||
|
],
|
||||||
|
"date-time": "2024-02-27T00:38:44Z",
|
||||||
|
"timestamp": 1708994324729
|
||||||
|
},
|
||||||
|
"author": [
|
||||||
|
{
|
||||||
|
"given": "N.",
|
||||||
|
"family": "Sharma",
|
||||||
|
"sequence": "first",
|
||||||
|
"affiliation": []
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"given": "P.",
|
||||||
|
"family": "Drobinski",
|
||||||
|
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|
"name": "copyright",
|
||||||
|
"label": "Copyright"
|
||||||
|
}
|
||||||
|
],
|
||||||
|
"deposited": {
|
||||||
|
"date-parts": [
|
||||||
|
[
|
||||||
|
2022,
|
||||||
|
7,
|
||||||
|
9
|
||||||
|
]
|
||||||
|
],
|
||||||
|
"date-time": "2022-07-09T14:08:02Z",
|
||||||
|
"timestamp": 1657375682000
|
||||||
|
},
|
||||||
|
"language": "en",
|
||||||
|
"page": "658-668",
|
||||||
|
"short-container-title": [
|
||||||
|
"Osteoarthritis and Cartilage"
|
||||||
|
]
|
||||||
|
}
|
||||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,41 @@
|
||||||
|
package eu.dnetlib.dhp.collection.crossref
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper
|
||||||
|
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
|
||||||
|
import org.apache.spark.sql.SparkSession
|
||||||
|
import org.junit.jupiter.api.{BeforeEach, Test}
|
||||||
|
import org.junit.jupiter.api.extension.ExtendWith
|
||||||
|
import org.mockito.junit.jupiter.MockitoExtension
|
||||||
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
|
import scala.io.Source
|
||||||
|
|
||||||
|
@ExtendWith(Array(classOf[MockitoExtension]))
|
||||||
|
class CrossrefMappingTest extends AbstractVocabularyTest {
|
||||||
|
|
||||||
|
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
|
||||||
|
val mapper = new ObjectMapper()
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
def setUp(): Unit = {
|
||||||
|
super.setUpVocabulary()
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
def testMapping(): Unit = {
|
||||||
|
val spark = SparkSession.builder().master("local[*]").appName("TransformCrossref").getOrCreate()
|
||||||
|
|
||||||
|
val s = new SparkMapDumpIntoOAF(null, null, null)
|
||||||
|
import spark.implicits._
|
||||||
|
|
||||||
|
s.transformCrossref(
|
||||||
|
spark,
|
||||||
|
sourcePath = "/home/sandro/Downloads/crossref",
|
||||||
|
targetPath = "/home/sandro/Downloads/crossref_transformed",
|
||||||
|
vocabularies = vocabularies
|
||||||
|
)
|
||||||
|
|
||||||
|
print(spark.read.text("/home/sandro/Downloads/crossref_transformed").count)
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -1,4 +1,4 @@
|
||||||
package eu.dnetlib.doiboost.crossref
|
package eu.dnetlib.doiboost.crossref
|
||||||
|
|
||||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||||
|
|
@ -55,9 +55,7 @@ case object Crossref2Oaf {
|
||||||
.map(f => f.id)
|
.map(f => f.id)
|
||||||
}
|
}
|
||||||
|
|
||||||
|
def mappingResult(result: Result, json: JValue, instanceType: Qualifier, originalType: String): Result = {
|
||||||
|
|
||||||
def mappingResult(result: Result, json: JValue, instanceType:Qualifier, originalType: String): Result = {
|
|
||||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||||
|
|
||||||
//MAPPING Crossref DOI into PID
|
//MAPPING Crossref DOI into PID
|
||||||
|
|
@ -340,7 +338,7 @@ case object Crossref2Oaf {
|
||||||
val objectSubType = (json \ "subtype").extractOrElse[String](null)
|
val objectSubType = (json \ "subtype").extractOrElse[String](null)
|
||||||
if (objectType == null)
|
if (objectType == null)
|
||||||
return resultList
|
return resultList
|
||||||
val typology =getTypeQualifier(objectType, vocabularies)
|
val typology = getTypeQualifier(objectType, vocabularies)
|
||||||
|
|
||||||
if (typology == null)
|
if (typology == null)
|
||||||
return List()
|
return List()
|
||||||
|
|
@ -349,7 +347,6 @@ case object Crossref2Oaf {
|
||||||
if (result == null)
|
if (result == null)
|
||||||
return List()
|
return List()
|
||||||
|
|
||||||
|
|
||||||
mappingResult(result, json, typology._1, typology._3)
|
mappingResult(result, json, typology._1, typology._3)
|
||||||
if (result == null || result.getId == null)
|
if (result == null || result.getId == null)
|
||||||
return List()
|
return List()
|
||||||
|
|
@ -693,12 +690,11 @@ case object Crossref2Oaf {
|
||||||
val item = new Dataset
|
val item = new Dataset
|
||||||
item.setResourcetype(objectType)
|
item.setResourcetype(objectType)
|
||||||
return item
|
return item
|
||||||
}
|
} else if (objectType.getClassid.equalsIgnoreCase("software")) {
|
||||||
else if (objectType.getClassid.equalsIgnoreCase("software")){
|
|
||||||
val item = new Software
|
val item = new Software
|
||||||
item.setResourcetype(objectType)
|
item.setResourcetype(objectType)
|
||||||
return item
|
return item
|
||||||
}else if (objectType.getClassid.equalsIgnoreCase("OtherResearchProduct")){
|
} else if (objectType.getClassid.equalsIgnoreCase("OtherResearchProduct")) {
|
||||||
val item = new OtherResearchProduct
|
val item = new OtherResearchProduct
|
||||||
item.setResourcetype(objectType)
|
item.setResourcetype(objectType)
|
||||||
return item
|
return item
|
||||||
|
|
|
||||||
|
|
@ -48,7 +48,6 @@ object SparkMapDumpIntoOAF {
|
||||||
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
|
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
|
||||||
require(vocabularies != null)
|
require(vocabularies != null)
|
||||||
|
|
||||||
|
|
||||||
spark.read
|
spark.read
|
||||||
.load(parser.get("sourcePath"))
|
.load(parser.get("sourcePath"))
|
||||||
.as[CrossrefDT]
|
.as[CrossrefDT]
|
||||||
|
|
|
||||||
|
|
@ -47,5 +47,4 @@ public abstract class AbstractVocabularyTest {
|
||||||
AbstractVocabularyTest.class.getResourceAsStream("/eu/dnetlib/dhp/doiboost/synonyms.txt")));
|
AbstractVocabularyTest.class.getResourceAsStream("/eu/dnetlib/dhp/doiboost/synonyms.txt")));
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -23,7 +23,7 @@ import scala.io.Source
|
||||||
import scala.util.matching.Regex
|
import scala.util.matching.Regex
|
||||||
|
|
||||||
@ExtendWith(Array(classOf[MockitoExtension]))
|
@ExtendWith(Array(classOf[MockitoExtension]))
|
||||||
class CrossrefMappingTest extends AbstractVocabularyTest{
|
class CrossrefMappingTest extends AbstractVocabularyTest {
|
||||||
|
|
||||||
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
|
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
|
||||||
val mapper = new ObjectMapper()
|
val mapper = new ObjectMapper()
|
||||||
|
|
@ -34,10 +34,15 @@ class CrossrefMappingTest extends AbstractVocabularyTest{
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
def testMissingAuthorParser():Unit = {
|
def testMissingAuthorParser(): Unit = {
|
||||||
val json: String = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/s41567-022-01757-y.json")).mkString
|
val json: String = Source
|
||||||
|
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/s41567-022-01757-y.json"))
|
||||||
|
.mkString
|
||||||
val result = Crossref2Oaf.convert(json, vocabularies)
|
val result = Crossref2Oaf.convert(json, vocabularies)
|
||||||
result.filter(o => o.isInstanceOf[Publication]).map(p=> p.asInstanceOf[Publication]).foreach(p =>assertTrue(p.getAuthor.size()>0))
|
result
|
||||||
|
.filter(o => o.isInstanceOf[Publication])
|
||||||
|
.map(p => p.asInstanceOf[Publication])
|
||||||
|
.foreach(p => assertTrue(p.getAuthor.size() > 0))
|
||||||
}
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
|
|
@ -127,7 +132,6 @@ class CrossrefMappingTest extends AbstractVocabularyTest{
|
||||||
|
|
||||||
val items = resultList.filter(p => p.isInstanceOf[Result])
|
val items = resultList.filter(p => p.isInstanceOf[Result])
|
||||||
|
|
||||||
|
|
||||||
items.foreach(p => println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(p)))
|
items.foreach(p => println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(p)))
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
@ -169,7 +173,6 @@ class CrossrefMappingTest extends AbstractVocabularyTest{
|
||||||
|
|
||||||
assertEquals(doisReference.size, relationList.size)
|
assertEquals(doisReference.size, relationList.size)
|
||||||
|
|
||||||
|
|
||||||
relationList.foreach(p => println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(p)))
|
relationList.foreach(p => println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(p)))
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -190,7 +193,6 @@ class CrossrefMappingTest extends AbstractVocabularyTest{
|
||||||
|
|
||||||
val items = resultList.filter(p => p.isInstanceOf[Result])
|
val items = resultList.filter(p => p.isInstanceOf[Result])
|
||||||
|
|
||||||
|
|
||||||
items.foreach(p => println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(p)))
|
items.foreach(p => println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(p)))
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
@ -646,7 +648,6 @@ class CrossrefMappingTest extends AbstractVocabularyTest{
|
||||||
|
|
||||||
val item: Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result]
|
val item: Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result]
|
||||||
|
|
||||||
|
|
||||||
println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(item))
|
println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(item))
|
||||||
|
|
||||||
assertTrue(
|
assertTrue(
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue