Merge pull request '[graph cleaning] fixed regex behaviour for cleaning ROR and GRID identifiers, added tests' (#315) from pid_cleaning into beta

Reviewed-on: D-Net/dnet-hadoop#315

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/FundRefCleaningRule.java

@@ -6,14 +6,16 @@ import java.util.regex.Pattern;
 
 public class FundRefCleaningRule {
 
-	public static String clean(final String fundrefId) {
+	public static final Pattern PATTERN = Pattern.compile("\\d+");
 
-		String s = fundrefId
+	public static String clean(final String fundRefId) {
+
+		String s = fundRefId
 			.toLowerCase()
 			.replaceAll("\\s", "");
 
-		Matcher m = Pattern.compile("\\d+").matcher(s);
+		Matcher m = PATTERN.matcher(s);
-		if (m.matches()) {
+		if (m.find()) {
 			return m.group();
 		} else {
 			return "";

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GridCleaningRule.java

@@ -6,13 +6,19 @@ import java.util.regex.Pattern;
 
 public class GridCleaningRule {
 
+	public static final Pattern PATTERN = Pattern.compile("(?<grid>\\d{4,6}\\.[0-9a-z]{1,2})");
+
 	public static String clean(String grid) {
 		String s = grid
 			.replaceAll("\\s", "")
 			.toLowerCase();
 
-		Matcher m = Pattern.compile("\\d{4,6}\\.[0-9a-z]{1,2}").matcher(s);
+		Matcher m = PATTERN.matcher(s);
-		return m.matches() ? "grid." + m.group() : "";
+		if (m.find()) {
+			return "grid." + m.group("grid");
+		}
+
+		return "";
 	}
 
 }

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ISNICleaningRule.java

@@ -7,10 +7,12 @@ import java.util.regex.Pattern;
 // https://www.wikidata.org/wiki/Property:P213
 public class ISNICleaningRule {
 
+	public static final Pattern PATTERN = Pattern.compile("([0]{4}) ?([0-9]{4}) ?([0-9]{4}) ?([0-9]{3}[0-9X])");
+
 	public static String clean(final String isni) {
 
-		Matcher m = Pattern.compile("([0]{4}) ?([0-9]{4}) ?([0-9]{4}) ?([0-9]{3}[0-9X])").matcher(isni);
+		Matcher m = PATTERN.matcher(isni);
-		if (m.matches()) {
+		if (m.find()) {
 			return String.join("", m.group(1), m.group(2), m.group(3), m.group(4));
 		} else {
 			return "";

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PICCleaningRule.java

@@ -6,10 +6,12 @@ import java.util.regex.Pattern;
 
 public class PICCleaningRule {
 
+	public static final Pattern PATTERN = Pattern.compile("\\d{9}");
+
 	public static String clean(final String pic) {
 
-		Matcher m = Pattern.compile("\\d{9}").matcher(pic);
+		Matcher m = PATTERN.matcher(pic);
-		if (m.matches()) {
+		if (m.find()) {
 			return m.group();
 		} else {
 			return "";

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PmcCleaningRule.java

@@ -1,13 +1,24 @@
 
 package eu.dnetlib.dhp.schema.oaf.utils;
 
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
 public class PmcCleaningRule {
 
+	public static final Pattern PATTERN = Pattern.compile("PMC\\d{1,8}");
+
 	public static String clean(String pmc) {
 		String s = pmc
 			.replaceAll("\\s", "")
 			.toUpperCase();
-		return s.matches("^PMC\\d{1,8}$") ? s : "";
+
+		final Matcher m = PATTERN.matcher(s);
+
+		if (m.find()) {
+			return m.group();
+		}
+		return "";
 	}
 
 }

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PmidCleaningRule.java

@@ -1,16 +1,25 @@
 
 package eu.dnetlib.dhp.schema.oaf.utils;
 
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
 // https://researchguides.stevens.edu/c.php?g=442331&p=6577176
 public class PmidCleaningRule {
 
+	public static final Pattern PATTERN = Pattern.compile("[1-9]{1,8}");
+
 	public static String clean(String pmid) {
 		String s = pmid
 			.toLowerCase()
-			.replaceAll("\\s", "")
+			.replaceAll("\\s", "");
-			.trim()
+
-			.replaceAll("^0+", "");
+		final Matcher m = PATTERN.matcher(s);
-		return s.matches("^\\d{1,8}$") ? s : "";
+
+		if (m.find()) {
+			return m.group();
+		}
+		return "";
 	}
 
 }

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/RorCleaningRule.java

@@ -7,12 +7,21 @@ import java.util.regex.Pattern;
 // https://ror.readme.io/docs/ror-identifier-pattern
 public class RorCleaningRule {
 
+	public static final String ROR_PREFIX = "https://ror.org/";
+
+	private static final Pattern PATTERN = Pattern.compile("(?<ror>0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2})");
+
 	public static String clean(String ror) {
 		String s = ror
 			.replaceAll("\\s", "")
 			.toLowerCase();
-		Matcher m = Pattern.compile("0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}").matcher(s);
+
-		return m.matches() ? "https://ror.org/" + m.group() : "";
+		Matcher m = PATTERN.matcher(s);
+
+		if (m.find()) {
+			return ROR_PREFIX + m.group("ror");
+		}
+		return "";
 	}
 
 }

dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/GridCleaningRuleTest.java

@@ -0,0 +1,18 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import org.junit.jupiter.api.Test;
+
+class GridCleaningRuleTest {
+
+	@Test
+	void testCleaning() {
+		assertEquals("grid.493784.5", GridCleaningRule.clean("grid.493784.5"));
+		assertEquals("grid.493784.5x", GridCleaningRule.clean("grid.493784.5x"));
+		assertEquals("grid.493784.5x", GridCleaningRule.clean("493784.5x"));
+		assertEquals("", GridCleaningRule.clean("493x784.5x"));
+	}
+
+}

dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/ISNICleaningRuleTest.java

@@ -0,0 +1,19 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import org.junit.jupiter.api.Test;
+
+class ISNICleaningRuleTest {
+
+	@Test
+	void testCleaning() {
+		assertEquals("0000000463436020", ISNICleaningRule.clean("0000 0004 6343 6020"));
+		assertEquals("0000000463436020", ISNICleaningRule.clean("0000000463436020"));
+		assertEquals("", ISNICleaningRule.clean("Q30256598"));
+		assertEquals("0000000493403529", ISNICleaningRule.clean("ISNI:0000000493403529"));
+		assertEquals("000000008614884X", ISNICleaningRule.clean("0000 0000 8614 884X"));
+	}
+
+}

dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/PICCleaningRuleTest.java

@@ -0,0 +1,19 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import org.junit.jupiter.api.Test;
+
+class PICCleaningRuleTest {
+
+	@Test
+	void testCleaning() {
+		assertEquals("887624982", PICCleaningRule.clean("887624982"));
+		assertEquals("", PICCleaningRule.clean("887 624982"));
+		assertEquals("887624982", PICCleaningRule.clean(" 887624982 "));
+		assertEquals("887624982", PICCleaningRule.clean(" 887624982x "));
+		assertEquals("887624982", PICCleaningRule.clean(" 88762498200 "));
+	}
+
+}

dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/PmcCleaningRuleTest.java

@@ -0,0 +1,19 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import org.junit.jupiter.api.Test;
+
+class PmcCleaningRuleTest {
+
+	@Test
+	void testCleaning() {
+		assertEquals("PMC1234", PmcCleaningRule.clean("PMC1234"));
+		assertEquals("PMC1234", PmcCleaningRule.clean(" PMC1234"));
+		assertEquals("PMC12345678", PmcCleaningRule.clean("PMC12345678"));
+		assertEquals("PMC12345678", PmcCleaningRule.clean("PMC123456789"));
+		assertEquals("PMC12345678", PmcCleaningRule.clean("PMC 12345678"));
+	}
+
+}

dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/PmidCleaningRuleTest.java

@@ -0,0 +1,18 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import org.junit.jupiter.api.Test;
+
+class PmidCleaningRuleTest {
+
+	@Test
+	void testCleaning() {
+		assertEquals("1234", PmidCleaningRule.clean("01234"));
+		assertEquals("1234567", PmidCleaningRule.clean("0123 4567"));
+		assertEquals("123", PmidCleaningRule.clean("0123x4567"));
+		assertEquals("", PmidCleaningRule.clean("abc"));
+	}
+
+}

dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/RorCleaningRuleTest.java

@@ -0,0 +1,17 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import org.junit.jupiter.api.Test;
+
+class RorCleaningRuleTest {
+
+	@Test
+	void testCleaning() {
+		assertEquals("https://ror.org/05rpz9w55", RorCleaningRule.clean("https://ror.org/05rpz9w55"));
+		assertEquals("https://ror.org/05rpz9w55", RorCleaningRule.clean("05rpz9w55"));
+		assertEquals("", RorCleaningRule.clean("05rpz9w_55"));
+	}
+
+}