r53901 MediaWiki - Code Review archive

Repository:	MediaWiki
Revision:	< r53900‎ \| r53901 \| r53902 >
Date:	20:58, 28 July 2009
Author:	daniel
Status:	deferred
Tags:
Comment:	consolidate special propery extraction code into WikiWordProperties
Modified paths:	/trunk/WikiWord/WikiWordBuilder4Biography (deleted) (history) /trunk/WikiWord/WikiWordBuilder4LifeScience/src/main/java/de/brightbyte/wikiword/lifescience (deleted) (history) /trunk/WikiWord/WikiWordProperties (added) (history) /trunk/WikiWord/WikiWordProperties/src/main/java/de/brightbyte/wikiword/lifescience (added) (history)

Diff [purge]

Index: trunk/WikiWord/WikiWordProperties/.classpath
—	—	@@ -0,0 +1,10 @@
	2	+<?xml version="1.0" encoding="UTF-8"?>
	3	+<classpath>
	4	+ <classpathentry kind="src" path="src/main/java"/>
	5	+ <classpathentry kind="src" path="src/test/java"/>
	6	+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
	7	+ <classpathentry combineaccessrules="false" kind="src" path="/WikiWord"/>
	8	+ <classpathentry combineaccessrules="false" kind="src" path="/WikiWordBuilder"/>
	9	+ <classpathentry combineaccessrules="false" kind="src" path="/BrightByteUtil"/>
	10	+ <classpathentry kind="output" path="bin"/>
	11	+</classpath>
Index: trunk/WikiWord/WikiWordProperties/.project
—	—	@@ -0,0 +1,17 @@
	2	+<?xml version="1.0" encoding="UTF-8"?>
	3	+<projectDescription>
	4	+ <name>WikiWordBuilder4Biography</name>
	5	+ <comment></comment>
	6	+ <projects>
	7	+ </projects>
	8	+ <buildSpec>
	9	+ <buildCommand>
	10	+ <name>org.eclipse.jdt.core.javabuilder</name>
	11	+ <arguments>
	12	+ </arguments>
	13	+ </buildCommand>
	14	+ </buildSpec>
	15	+ <natures>
	16	+ <nature>org.eclipse.jdt.core.javanature</nature>
	17	+ </natures>
	18	+</projectDescription>
Index: trunk/WikiWord/WikiWordProperties/target/.svnignore
—	—	@@ -0,0 +1,2 @@
	2	+*
	3	+
Property changes on: trunk/WikiWord/WikiWordProperties/target
___________________________________________________________________
Name: svn:ignore
1	4	+ *
Index: trunk/WikiWord/WikiWordProperties/src/main/assembly/src.xml
—	—	@@ -0,0 +1,24 @@
	2	+<assembly>
	3	+ <id>src</id>
	4	+ <formats>
	5	+ <format>tar.gz</format>
	6	+ </formats>
	7	+ <fileSets>
	8	+ <fileSet>
	9	+ <includes>
	10	+ <include>*</include>
	11	+ </includes>
	12	+ <excludes>
	13	+ <exclude>bin</exclude>
	14	+ <exclude>target</exclude>
	15	+ <exclude>local.*</exclude>
	16	+ </excludes>
	17	+ </fileSet>
	18	+ <fileSet>
	19	+ <directory>src</directory>
	20	+ </fileSet>
	21	+ <fileSet>
	22	+ <directory>doc</directory>
	23	+ </fileSet>
	24	+ </fileSets>
	25	+</assembly>
\ No newline at end of file
Index: trunk/WikiWord/WikiWordProperties/src/main/assembly/bin-dep.xml
—	—	@@ -0,0 +1,50 @@
	2	+<assembly>
	3	+ <id>bin-dep</id>
	4	+ <formats>
	5	+ <format>tar.gz</format>
	6	+ </formats>
	7	+ <fileSets>
	8	+ <fileSet>
	9	+ <includes>
	10	+ <include>README*</include>
	11	+ <include>LICENSE*</include>
	12	+ <include>NOTICE*</include>
	13	+ <include>*.properties</include>
	14	+ <include>*.sh</include>
	15	+ <include>*.bat</include>
	16	+ </includes>
	17	+ <excludes>
	18	+ <exclude>debug.*</exclude>
	19	+ <exclude>local.*</exclude>
	20	+ </excludes>
	21	+ </fileSet>
	22	+ <fileSet>
	23	+ <directory>src/main/</directory>
	24	+ <outputDirectory></outputDirectory>
	25	+ <includes>
	26	+ <include>*.rdf</include>
	27	+ </includes>
	28	+ </fileSet>
	29	+ <!--<fileSet>
	30	+ <directory>doc</directory>
	31	+ </fileSet>-->
	32	+ <!--<fileSet>
	33	+ <directory>target</directory>
	34	+ <outputDirectory></outputDirectory>
	35	+ <includes>
	36	+ <include>*.jar</include>
	37	+ </includes>
	38	+ </fileSet>-->
	39	+ </fileSets>
	40	+ <dependencySets>
	41	+ <dependencySet>
	42	+ <outputDirectory>/lib</outputDirectory>
	43	+ <unpack>false</unpack>
	44	+ <scope>runtime</scope>
	45	+ <excludes>
	46	+ <exclude>junit:junit</exclude>
	47	+ <exclude>org.apache.maven.wagon:wagon-ssh</exclude>
	48	+ </excludes>
	49	+ </dependencySet>
	50	+ </dependencySets>
	51	+</assembly>
\ No newline at end of file
Index: trunk/WikiWord/WikiWordProperties/src/main/java/de/brightbyte/wikiword/biography/BiographyConceptType.java
—	—	@@ -0,0 +1,36 @@
	2	+package de.brightbyte.wikiword.biography;
	3	+
	4	+import de.brightbyte.wikiword.ConceptType;
	5	+import de.brightbyte.wikiword.ConceptTypeSet;
	6	+
	7	+/**
	8	+ * Enumeration of concept types; each concept type represents a very broad category of concepts,
	9	+ * which can be used to filter concepts identified in a corpus. The idea is at for some uses,
	10	+ * some kinds of concepts are not usefull, or especially usefull. For example, people and polaces
	11	+ * are not suitable for use in a general dictionary, but very useful for topic tracking.
	12	+ * Each type is associated with a code (for internal use) and a URI (for external use).
	13	+ * The URI is constructed based on {@link RdfEntities.conceptTypeBase}.
	14	+ */
	15	+public class BiographyConceptType extends ConceptType {
	16	+
	17	+ /**
	18	+ * NamespaceSet for the canonical concept types. Loaded from the ConceptTypes.properties
	19	+ * file in this package.
	20	+ */
	21	+ public static final ConceptTypeSet biographyConceptTypes;
	22	+
	23	+ static {
	24	+ try {
	25	+ biographyConceptTypes = getConceptTypes(null, "de.brightbyte.wikiword.biography"); //FIXME: make unmodifiable!
	26	+
	27	+ }
	28	+ catch (NumberFormatException ex) {
	29	+ throw new ExceptionInInitializerError(ex);
	30	+ }
	31	+ }
	32	+
	33	+ public BiographyConceptType(int code, String name) {
	34	+ super(code, name);
	35	+ }
	36	+
	37	+}
Index: trunk/WikiWord/WikiWordProperties/src/main/java/de/brightbyte/wikiword/biography/wikis/WikiConfiguration_enwiki.java
—	—	@@ -0,0 +1,110 @@
	2	+package de.brightbyte.wikiword.biography.wikis;
	3	+
	4	+import java.util.regex.Pattern;
	5	+
	6	+import de.brightbyte.wikiword.ConceptType;
	7	+import de.brightbyte.wikiword.analyzer.WikiConfiguration;
	8	+import de.brightbyte.wikiword.analyzer.extractor.CategoryPatternParameterExtractor;
	9	+import de.brightbyte.wikiword.analyzer.extractor.PagePropertyValueExtractor;
	10	+import de.brightbyte.wikiword.analyzer.extractor.TemplateParameterExtractor;
	11	+import de.brightbyte.wikiword.analyzer.mangler.RegularExpressionMangler;
	12	+import de.brightbyte.wikiword.analyzer.matcher.ExactNameMatcher;
	13	+import de.brightbyte.wikiword.analyzer.matcher.PatternNameMatcher;
	14	+import de.brightbyte.wikiword.analyzer.sensor.HasPropertySensor;
	15	+import de.brightbyte.wikiword.analyzer.template.DefaultTemplateParameterPropertySpec;
	16	+
	17	+public class WikiConfiguration_enwiki extends WikiConfiguration {
	18	+
	19	+ public WikiConfiguration_enwiki() {
	20	+ super();
	21	+
	22	+ stripClutterManglers.add( new RegularExpressionMangler(templatePattern("awd", 1, true), "$1")); //TODO: {{awd\|award\|year\|title\|role\|name}}
	23	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("(Birth\|Death)(Date(AndAge)?\|_date(_and_age)?)", 1, true), " $1") );
	24	+
	25	+ propertyExtractors.add( new CategoryPatternParameterExtractor("^(\\d+s?)_births$", "$1", 0, "person-birth-date") );
	26	+ propertyExtractors.add( new CategoryPatternParameterExtractor("^(\\d+s?)_deaths$", "$1", 0, "person-death-date") );
	27	+
	28	+ propertyExtractors.add( new CategoryPatternParameterExtractor("^(.+)_(artists\|painters\|sculptors)$", "$1", 0, "artist-group") );
	29	+ propertyExtractors.add( new CategoryPatternParameterExtractor("^.*(^\|_)(painter\|sculptor\|photographer)s$", "$2", Pattern.CASE_INSENSITIVE, "artist-group") );
	30	+
	31	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Persondata"),
	32	+ new DefaultTemplateParameterPropertySpec("NAME", "person-sortname").setStripMarkup(true),
	33	+ new DefaultTemplateParameterPropertySpec("NAME", "person-name").setStripMarkup(true),
	34	+ new DefaultTemplateParameterPropertySpec("ALTERNATIV NAMENS", "person-name").setStripMarkup(true)
	35	+ .setSplitPattern(Pattern.compile("\\s[;]\\s")).addNormalizer(Pattern.compile("\$.*?\$"),""),
	36	+ new DefaultTemplateParameterPropertySpec("SHORT DESCRIPTION", "person-occupation").setStripMarkup(true),
	37	+ new DefaultTemplateParameterPropertySpec("DATE OF BIRTH", "person-birth-date").setStripMarkup(true),
	38	+ new DefaultTemplateParameterPropertySpec("PLACE OF BIRTH", "person-birth-place").setStripMarkup(true),
	39	+ new DefaultTemplateParameterPropertySpec("DATE OF DEATH", "person-death-date").setStripMarkup(true),
	40	+ new DefaultTemplateParameterPropertySpec("PLACE OF DEATH", "person-death-place").setStripMarkup(true)
	41	+ ) );
	42	+
	43	+ Pattern defaultSplitPattern = Pattern.compile("[,;/]\\s+\|<br\\s*/?>");
	44	+
	45	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Infobox_Artist"),
	46	+ new DefaultTemplateParameterPropertySpec("name", "person-name").setStripMarkup(true),
	47	+ new DefaultTemplateParameterPropertySpec("birthname", "person-name").setStripMarkup(true),
	48	+ new DefaultTemplateParameterPropertySpec("birthdate", "person-birth-date").setStripMarkup(true),
	49	+ new DefaultTemplateParameterPropertySpec("birthplace", "person-birth-place").setStripMarkup(true),
	50	+ new DefaultTemplateParameterPropertySpec("location", "person-birth-place").setStripMarkup(true),
	51	+ new DefaultTemplateParameterPropertySpec("deathdate", "person-death-date").setStripMarkup(true),
	52	+ new DefaultTemplateParameterPropertySpec("deathplace", "person-death-place").setStripMarkup(true),
	53	+ new DefaultTemplateParameterPropertySpec("nationality", "person-nationality").setStripMarkup(true),
	54	+ new DefaultTemplateParameterPropertySpec("field", "artist-group").setStripMarkup(true).setSplitPattern(defaultSplitPattern),
	55	+ new DefaultTemplateParameterPropertySpec("movement", "artist-group").setStripMarkup(true).setSplitPattern(defaultSplitPattern),
	56	+ new DefaultTemplateParameterPropertySpec("training", "artist-training").setStripMarkup(true),
	57	+ new DefaultTemplateParameterPropertySpec("award", "artist-award").setStripMarkup(true).setSplitPattern(defaultSplitPattern)
	58	+ ) );
	59	+
	60	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("Infobox_(((Medical\|Military)_)?[Pp]erson\|Actor\|Astronaut\|Criminal\|Engineer\|Musical_artist\|Philosopher\|Pope\|ReligiousBio\|Scientist)", 0, true),
	61	+ new DefaultTemplateParameterPropertySpec("name", "person-name").setStripMarkup(true),
	62	+ new DefaultTemplateParameterPropertySpec("other_names", "person-name").setStripMarkup(true),
	63	+ new DefaultTemplateParameterPropertySpec("birth_date", "person-birth-date").setStripMarkup(true),
	64	+ new DefaultTemplateParameterPropertySpec("birth_place", "person-birth-place").setStripMarkup(true),
	65	+ new DefaultTemplateParameterPropertySpec("death_date", "person-death-date").setStripMarkup(true),
	66	+ new DefaultTemplateParameterPropertySpec("death_place", "person-death-place").setStripMarkup(true),
	67	+ new DefaultTemplateParameterPropertySpec("occupation", "person-occupation").setStripMarkup(true),
	68	+ new DefaultTemplateParameterPropertySpec("known_for", "person-known-for").setStripMarkup(true),
	69	+ new DefaultTemplateParameterPropertySpec("nationality", "person-nationality").setStripMarkup(true),
	70	+ new DefaultTemplateParameterPropertySpec("residence", "person-nationality").setStripMarkup(true),
	71	+ new DefaultTemplateParameterPropertySpec("citizenship", "person-nationality").setStripMarkup(true)
	72	+ ) );
	73	+
	74	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("Birth_date\|BrithDate", 0, true),
	75	+ new DefaultTemplateParameterPropertySpec("1", "person-birth-date").setStripMarkup(true)
	76	+ ) );
	77	+
	78	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("Death_date\|DeathDate", 0, true),
	79	+ new DefaultTemplateParameterPropertySpec("1", "person-death-date").setStripMarkup(true)
	80	+ ) );
	81	+
	82	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("Death_date_and_age\|DeathDateAndAge", 0, true),
	83	+ new DefaultTemplateParameterPropertySpec("1", "person-death-date").setStripMarkup(true),
	84	+ new DefaultTemplateParameterPropertySpec("1", "person-birth-date").setStripMarkup(true)
	85	+ ) );
	86	+
	87	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Infobox_Medical_Person"),
	88	+ new DefaultTemplateParameterPropertySpec("profession", "person-occupation").setStripMarkup(true).setSplitPattern(defaultSplitPattern),
	89	+ new DefaultTemplateParameterPropertySpec("profession", "expert-group").setStripMarkup(true).setSplitPattern(defaultSplitPattern),
	90	+ new DefaultTemplateParameterPropertySpec("specialism", "expert-group").setStripMarkup(true).setSplitPattern(defaultSplitPattern),
	91	+ new DefaultTemplateParameterPropertySpec("research_field", "expert-group").setStripMarkup(true).setSplitPattern(defaultSplitPattern),
	92	+ new DefaultTemplateParameterPropertySpec("work_institutions", "person-affiliation").setStripMarkup(true).setSplitPattern(defaultSplitPattern),
	93	+ new DefaultTemplateParameterPropertySpec("prizes", "expert-prize").setStripMarkup(true).setSplitPattern(defaultSplitPattern)
	94	+ ) );
	95	+
	96	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Infobox_Scientist"),
	97	+ new DefaultTemplateParameterPropertySpec("fields", "expert-group").setStripMarkup(true).setSplitPattern(defaultSplitPattern),
	98	+ new DefaultTemplateParameterPropertySpec("alma-mater", "person-education").setStripMarkup(true).setSplitPattern(defaultSplitPattern),
	99	+ new DefaultTemplateParameterPropertySpec("workplaces", "person-affiliation").setStripMarkup(true).setSplitPattern(defaultSplitPattern),
	100	+ new DefaultTemplateParameterPropertySpec("awards", "expert-prize").setStripMarkup(true).setSplitPattern(defaultSplitPattern)
	101	+ ) );
	102	+
	103	+ pageTermExtractors.add( new PagePropertyValueExtractor("person-sortname") );
	104	+ pageTermExtractors.add( new PagePropertyValueExtractor("person-name") );
	105	+
	106	+ conceptTypeSensors.add( new HasPropertySensor<ConceptType>(ConceptType.PERSON, "artist-group"));
	107	+ conceptTypeSensors.add( new HasPropertySensor<ConceptType>(ConceptType.PERSON, "person-name"));
	108	+ conceptTypeSensors.add( new HasPropertySensor<ConceptType>(ConceptType.PERSON, "person-birth-date"));
	109	+ }
	110	+
	111	+}
Index: trunk/WikiWord/WikiWordProperties/src/main/java/de/brightbyte/wikiword/biography/wikis/WikiConfiguration_dewiki.java
—	—	@@ -0,0 +1,55 @@
	2	+package de.brightbyte.wikiword.biography.wikis;
	3	+
	4	+import java.util.regex.Pattern;
	5	+
	6	+import de.brightbyte.wikiword.ConceptType;
	7	+import de.brightbyte.wikiword.analyzer.WikiConfiguration;
	8	+import de.brightbyte.wikiword.analyzer.extractor.CategoryPatternParameterExtractor;
	9	+import de.brightbyte.wikiword.analyzer.extractor.PagePropertyValueExtractor;
	10	+import de.brightbyte.wikiword.analyzer.extractor.TemplateParameterExtractor;
	11	+import de.brightbyte.wikiword.analyzer.matcher.ExactNameMatcher;
	12	+import de.brightbyte.wikiword.analyzer.sensor.HasPropertySensor;
	13	+import de.brightbyte.wikiword.analyzer.template.DefaultTemplateParameterPropertySpec;
	14	+
	15	+public class WikiConfiguration_dewiki extends WikiConfiguration {
	16	+
	17	+ public WikiConfiguration_dewiki() {
	18	+ super();
	19	+
	20	+ propertyExtractors.add( new CategoryPatternParameterExtractor("^Geboren_(\\d+(_v\\._Chr\\.)?)$", "$1", 0, "person-birth-date") );
	21	+ propertyExtractors.add( new CategoryPatternParameterExtractor("^Gestorben_(\\d+(_v\\._Chr\\.)?)$", "$1", 0, "person-death-date") );
	22	+
	23	+ propertyExtractors.add( new CategoryPatternParameterExtractor("^Maler_(der\|des)_(.+)$", "$2", 0, "artist-group") );
	24	+ propertyExtractors.add( new CategoryPatternParameterExtractor("^(Maler\|Bildhauer\|Fotograf)(_\|$).*$", "$1", 0, "artist-group") );
	25	+ propertyExtractors.add( new CategoryPatternParameterExtractor("^.*[^_](maler\|bildhauer\|fotograf)$", "$1", 0, "artist-group").setCapitalize(true) );
	26	+ propertyExtractors.add( new CategoryPatternParameterExtractor("^.*?([-_\\wäöü]+)(maler\|bildhauer\|fotograf)$", "$2", 0, "artist-group") );
	27	+
	28	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Personendaten"),
	29	+ new DefaultTemplateParameterPropertySpec("NAME", "person-sortname").setStripMarkup(true),
	30	+ new DefaultTemplateParameterPropertySpec("NAME", "person-name").setStripMarkup(true),
	31	+ new DefaultTemplateParameterPropertySpec("ALTERNATIVNAMEN", "person-name").setStripMarkup(true)
	32	+ .setSplitPattern(Pattern.compile("\\s[;]\\s")).addNormalizer(Pattern.compile("\$.*?\$"),""),
	33	+ new DefaultTemplateParameterPropertySpec("KURZBESCHREIBUNG", "person-occupation").setStripMarkup(true),
	34	+ new DefaultTemplateParameterPropertySpec("GEBURTSDATUM", "person-birth-date").setStripMarkup(true),
	35	+ new DefaultTemplateParameterPropertySpec("STERBEDATUM", "person-death-date").setStripMarkup(true),
	36	+ new DefaultTemplateParameterPropertySpec("GEBURTSORT", "person-birth-place").setStripMarkup(true),
	37	+ new DefaultTemplateParameterPropertySpec("STERBEORT", "person-death-place").setStripMarkup(true)
	38	+ ) );
	39	+
	40	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("PND"),
	41	+ new DefaultTemplateParameterPropertySpec("1", "ID-PND").setStripMarkup(true) ) );
	42	+
	43	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("LeMO"),
	44	+ new DefaultTemplateParameterPropertySpec("1", "ID-LeMO").setStripMarkup(true) ) );
	45	+
	46	+ //TODO: {{BAM\|Kohl\|Helmut}}
	47	+
	48	+ pageTermExtractors.add( new PagePropertyValueExtractor("person-sortname") );
	49	+ pageTermExtractors.add( new PagePropertyValueExtractor("person-name") );
	50	+
	51	+ conceptTypeSensors.add( new HasPropertySensor<ConceptType>(ConceptType.PERSON, "person-name") );
	52	+ conceptTypeSensors.add( new HasPropertySensor<ConceptType>(ConceptType.PERSON, "person-birth-date") );
	53	+ conceptTypeSensors.add( new HasPropertySensor<ConceptType>(ConceptType.PERSON, "artist-group") );
	54	+ }
	55	+
	56	+}
Index: trunk/WikiWord/WikiWordProperties/src/main/java/de/brightbyte/wikiword/biography/ConceptTypes.properties
Index: trunk/WikiWord/WikiWordProperties/src/main/java/de/brightbyte/wikiword/lifescience/wikis/WikiConfiguration_enwiki.java
—	—	@@ -0,0 +1,668 @@
	2	+package de.brightbyte.wikiword.lifescience.wikis;
	3	+
	4	+import java.util.regex.Matcher;
	5	+import java.util.regex.Pattern;
	6	+
	7	+import de.brightbyte.wikiword.ConceptType;
	8	+import de.brightbyte.wikiword.Namespace;
	9	+import de.brightbyte.wikiword.ResourceType;
	10	+import de.brightbyte.wikiword.analyzer.WikiConfiguration;
	11	+import de.brightbyte.wikiword.analyzer.WikiPage;
	12	+import de.brightbyte.wikiword.analyzer.extractor.CategoryPatternParameterExtractor;
	13	+import de.brightbyte.wikiword.analyzer.extractor.PagePropertyValueExtractor;
	14	+import de.brightbyte.wikiword.analyzer.extractor.PropertyValueExtractor;
	15	+import de.brightbyte.wikiword.analyzer.extractor.TemplateNamePatternParameterExtractor;
	16	+import de.brightbyte.wikiword.analyzer.extractor.TemplateParameterExtractor;
	17	+import de.brightbyte.wikiword.analyzer.extractor.TitlePartExtractor;
	18	+import de.brightbyte.wikiword.analyzer.mangler.RegularExpressionMangler;
	19	+import de.brightbyte.wikiword.analyzer.mangler.TextArmor;
	20	+import de.brightbyte.wikiword.analyzer.matcher.ExactNameMatcher;
	21	+import de.brightbyte.wikiword.analyzer.matcher.PatternNameMatcher;
	22	+import de.brightbyte.wikiword.analyzer.sensor.HasCategoryLikeSensor;
	23	+import de.brightbyte.wikiword.analyzer.sensor.HasCategorySensor;
	24	+import de.brightbyte.wikiword.analyzer.sensor.HasPropertySensor;
	25	+import de.brightbyte.wikiword.analyzer.sensor.HasTemplateLikeSensor;
	26	+import de.brightbyte.wikiword.analyzer.sensor.HasTemplateSensor;
	27	+import de.brightbyte.wikiword.analyzer.sensor.TitleSensor;
	28	+import de.brightbyte.wikiword.analyzer.template.AbstractTemplateParameterPropertySpec;
	29	+import de.brightbyte.wikiword.analyzer.template.DeepTemplateExtractor;
	30	+import de.brightbyte.wikiword.analyzer.template.DefaultTemplateParameterPropertySpec;
	31	+import de.brightbyte.wikiword.analyzer.template.TemplateData;
	32	+import de.brightbyte.wikiword.analyzer.template.TemplateExtractor;
	33	+import de.brightbyte.wikiword.analyzer.template.TemplateParameterPropertySpec;
	34	+import de.brightbyte.wikiword.analyzer.template.TemplateExtractor.Context;
	35	+import de.brightbyte.wikiword.lifescience.LifeScienceConceptType;
	36	+
	37	+public class WikiConfiguration_enwiki extends WikiConfiguration {
	38	+
	39	+ protected static String[] resolveSequence(String s, int max) {
	40	+ int idx = s.indexOf('-');
	41	+ if (idx<0) return new String[] { s };
	42	+
	43	+ return resolveSequence(s.substring(0, idx).trim(), s.substring(idx+1).trim(), max);
	44	+ }
	45	+
	46	+ protected static String[] resolveSequence(String from, String to, int max) {
	47	+ int i = 0;
	48	+ int j = from.length()-1;
	49	+ int k = to.length()-1;
	50	+
	51	+ while (i<from.length() && i<to.length() && from.charAt(i)==to.charAt(i)) {
	52	+ i++;
	53	+ }
	54	+
	55	+ while (j>=i && k>=i && from.charAt(j)==to.charAt(k)) {
	56	+ j--;
	57	+ k--;
	58	+ }
	59	+
	60	+ if (j<i \|\| k<i) return null;
	61	+
	62	+ String f = from.substring(i, j+1);
	63	+ String t = to.substring(i, k+1);
	64	+
	65	+ String prefix = from.substring(0, i);
	66	+ String suffix = from.substring(j+1);
	67	+
	68	+ int a;
	69	+ int b;
	70	+
	71	+ try {
	72	+ a = Integer.parseInt(f);
	73	+ b = Integer.parseInt(t);
	74	+ }
	75	+ catch (NumberFormatException ex) {
	76	+ return null;
	77	+ }
	78	+
	79	+ int c = b-a +1;
	80	+ if (c>max) return null;
	81	+
	82	+ String[] ss = new String[c];
	83	+
	84	+ for (int n=0; n<c; n++) {
	85	+ ss[n] = prefix + (a+n) + suffix;
	86	+ }
	87	+
	88	+ return ss;
	89	+ }
	90	+
	91	+ //FIXME: for some, <br> resp. \n needs to be stripped!
	92	+
	93	+ protected static final String numericChars = "0-9";
	94	+ protected static final String upperAlphabeticChars = "A-Z";
	95	+ protected static final String alphabeticChars = upperAlphabeticChars+"a-z";
	96	+ protected static final String upperAlphaNumericChars = upperAlphabeticChars+numericChars;
	97	+ protected static final String alphaNumericChars = alphabeticChars+numericChars;
	98	+ protected static final String dashChars = "-\u2212\uFE63\u2010-\u2014\uFE58\uFF0D";
	99	+
	100	+ protected static final Pattern identifierSeparatorPattern = Pattern.compile(",\\p{IsZ}+\|[\\p{IsZ};]+\|<br */?>", 0);
	101	+ protected static final Pattern nameSeparatorPattern = Pattern.compile(",\\p{IsZ}+\|[\r\n;]+\|<br */?>", 0);
	102	+ protected static final Pattern badStuffStripPattern = Pattern.compile("[\r\n]+", 0);
	103	+ protected static final Pattern spaceStripPattern = Pattern.compile("\\p{IsZ}+", 0);
	104	+ protected static final Pattern iupacCleanupPattern = Pattern.compile("(?<=["+dashChars+numericChars+"]\|[0-9][a-z])\\p{IsZ}+", 0);
	105	+ protected static final Pattern punctuationStripPattern = Pattern.compile("[\r\n,.;/]+", 0);
	106	+ protected static final Pattern breakStripPattern = Pattern.compile("[\r\n\\p{IsZ}]+", 0);
	107	+
	108	+ private static final String uniProtChars = "["+upperAlphaNumericChars+"]{6,}";
	109	+ private static final String pubChemChars = "["+numericChars+"]+";
	110	+ private static final String pbbChars = "["+numericChars+"]+";
	111	+ private static final String drugBankChars = "["+upperAlphabeticChars+"]{2,}["+numericChars+"]{4,}";
	112	+ private static final String casChars = "["+numericChars+"]+(["+dashChars+"]["+numericChars+"]+)*";
	113	+ private static final String smilesChars = "["+dashChars+"+="+alphaNumericChars+"/\\\\()@#:\\[\\]>.]+"; //FIXME: not greedy enough
	114	+ private static final String atcChars = "["+upperAlphabeticChars+"]{6,}";
	115	+ private static final String diseasesDbChars = "["+numericChars+"]+";
	116	+ private static final String pagesChars = "["+numericChars+"]+(\\s["+dashChars+",]\\s["+numericChars+"]+)*";
	117	+
	118	+ private static final String icd10Chars = "["+upperAlphabeticChars+"]["+numericChars+"]+(\\.["+numericChars+"]*)?"; //FIXME: ranges!
	119	+ private static final String icd9Chars = "["+numericChars+"]+(\\.["+numericChars+"]*)?"; //FIXME: ranges!
	120	+ private static final String icdOChars = "M["+numericChars+"]+(/["+numericChars+"]*)?";
	121	+ private static final String omimChars = "["+numericChars+"]{4,}";
	122	+ private static final String medlinePlusChars = "["+numericChars+"]{6,}";
	123	+ private static final String meshChars = "["+upperAlphabeticChars+"]?["+numericChars+"]+(\\.["+numericChars+"]+)*";
	124	+ private static final String eMedicineChars = "["+alphabeticChars+"]+/["+numericChars+"]+";
	125	+ private static final String chemAbbrevChars = "["+dashChars+alphaNumericChars+"(),]+";
	126	+
	127	+ private static final String inChIChars = "["+dashChars+"+"+alphabeticChars+"\$\$,/]+";
	128	+ private static final String einecsChars = "["+numericChars+"]+(["+dashChars+"]["+numericChars+"]+)*";
	129	+ private static final String ecChemChars = "["+numericChars+"]+(["+dashChars+"]["+numericChars+"]+)*";
	130	+ private static final String uncasnChars = "["+numericChars+"]{4,}";
	131	+ private static final String rtecsChars = "["+upperAlphabeticChars+"]+["+numericChars+"]+";
	132	+ private static final String keggChars = "["+upperAlphabeticChars+"]+["+numericChars+"]+";
	133	+ private static final String chEbiChars = "["+numericChars+"]+";
	134	+ private static final String gmelinChars = "["+numericChars+"]+";
	135	+ private static final String beilsteinChars = "["+numericChars+"]+(["+dashChars+"]["+numericChars+"]+)*";
	136	+ private static final String hgncChars = "["+numericChars+"]+";
	137	+ private static final String hgiChars = "["+numericChars+"]+";
	138	+ private static final String proteinSymbolChars = "["+alphaNumericChars+"]+(["+dashChars+"]["+alphaNumericChars+"]+)(\\.["+numericChars+"]+)";
	139	+ private static final String entrezGeneChars = "["+numericChars+"]+";
	140	+ private static final String refSeqChars = "["+upperAlphabeticChars+"]+_["+numericChars+"]+"; //NOTE: value may contain a decimal point, but we ignore that bit for better matching
	141	+ private static final String pdbChars = "["+upperAlphaNumericChars+"]{4,}";
	142	+
	143	+ private static final String ecEnzymeChars = "["+numericChars+"](\\.["+numericChars+"]+)*";
	144	+ private static final String homoloGeneChars = "["+numericChars+"]+";
	145	+ private static final String mgiChars = "["+numericChars+"]{6,}";
	146	+ private static final String ensemblChars = "["+upperAlphabeticChars+"]{2,}["+numericChars+"]{10,}";
	147	+ private static final String icscChars = "["+numericChars+"]{4,}";
	148	+ private static final String goCodeChars = "["+numericChars+"]{6,}";
	149	+ //private static final String chemFormulaChars = "["+dashChars+"+,\$\$"+alphaNumericChars+"]{3,}";
	150	+ private static final String chemSpiderChars = "["+numericChars+"]+";
	151	+ private static final String threeDMetChars = "["+alphaNumericChars+"]{3,}";
	152	+
	153	+ private static final String dorlandsChars = "["+alphabeticChars+"]+/["+numericChars+"]+";
	154	+ private static final String neuroNamesChars = "["+alphabeticChars+"]+-["+numericChars+"]+";
	155	+
	156	+ //TODO: exclude "Biography"...
	157	+ public static final String lifeScienceJournalPattern = "(^\|[ _])(Chem[a-z]\|Biol?[.a-z]\|Gen[eo][a-z]\|Med[a-z]\|Cell[a-z]\|DNA\|RNA\|Nucleic\|EMBO\|FEBS\|Onco[a-z]\|Blood\|Immono[a-z]\|Cancer\|Virol[a-z]\|Med[a-z]\|Clin[a-z]\|Lancet\|Nature\|PLoS\|Neuro[a-z]\|Zootaxa\|JAMA\|FASEB\|Bacter[a-z]\|Mutat[a-z]\|Mol[a-z]\|Protein\|Dermat[a-z]\|Pathol[a-z]\|Endocr[a-z]\|Microbio[a-z])($\|[_ ])";
	158	+
	159	+
	160	+ protected static DefaultTemplateParameterPropertySpec makeNamePropertySpec(String param, String prop, boolean multi, boolean space) {
	161	+ DefaultTemplateParameterPropertySpec spec = new DefaultTemplateParameterPropertySpec(param, prop);
	162	+
	163	+ if (multi) {
	164	+ if (space) spec.setSplitPattern(nameSeparatorPattern);
	165	+ else spec.setSplitPattern(identifierSeparatorPattern);
	166	+ }
	167	+
	168	+ if (space) spec.addNormalizer(badStuffStripPattern, "");
	169	+ else spec.addNormalizer(spaceStripPattern, "");
	170	+
	171	+ return spec;
	172	+ }
	173	+
	174	+ protected static DefaultTemplateParameterPropertySpec makeIdentifierPropertySpec(String param, String prop, String pattern) {
	175	+ DefaultTemplateParameterPropertySpec spec = new DefaultTemplateParameterPropertySpec(param, prop);
	176	+
	177	+ pattern = "(?<=[^\\w\\d]\|^)("+pattern+")(?=[^\\w\\d]\|$)";
	178	+
	179	+ spec.setFindPattern(Pattern.compile(pattern));
	180	+
	181	+ if (pattern.indexOf('\u2212')>=0) { //XXX: hack for normalizing dashes
	182	+ spec.addNormalizer(Pattern.compile("["+dashChars+"]"), "-");
	183	+ }
	184	+
	185	+ return spec;
	186	+ }
	187	+
	188	+ public WikiConfiguration_enwiki() {
	189	+ super();
	190	+
	191	+ templateExtractorFactory= new TemplateExtractor.Factory() {
	192	+ public TemplateExtractor newTemplateExtractor(Context context, TextArmor armor) {
	193	+ DeepTemplateExtractor extractor = new DeepTemplateExtractor(context, armor);
	194	+ extractor.addContainerField("Protbox", "Codes");
	195	+ extractor.addContainerField("Protbox", "Caption");
	196	+ //FIXME: this needs to accumulate!!!! //FIXME //FIXME //FIXME //FIXME //FIXME //FIXME //FIXME //FIXME //FIXME //FIXME //FIXME //FIXME
	197	+ return extractor;
	198	+ }
	199	+ };
	200	+
	201	+ //NOTE: apply template replacement only when stripping markup, but then before everything else
	202	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("ICD9", 1, true), " $2 ") );
	203	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("ICD10", 3, true), " $2$3.$4 ") ); //XXX: use all 5 params?
	204	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("ICDO", 2, true), " M$2/$3 ") );
	205	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("CAS", 1, true), " $2 ") );
	206	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("ATC", 2, true), " $2$3 ") );
	207	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("DiseasesDB2", 1, true), " $2 ") );
	208	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("OMIM\\d?", 1, true), " $2 ") );
	209	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("SMILES", 1, true), " $2 ") ); //FIXME: named param S= !
	210	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("eMedicine2", 2, true), " $2/$3 ") );
	211	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("MedlinePlus2", 1, true), " $2 ") );
	212	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("PDB", 1, true), " $2 ") );
	213	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("PDB2", 1, true), " $2 ") );
	214	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("PDB3", 1, true), " $2 ") );
	215	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("EC_number", 1, true), " $2 ") );
	216	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("OMIM", 1, true), " $2 ") );
	217	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("EntrezGene", 1, true), " $2 ") );
	218	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("UniProt", 1, true), " $2 ") );
	219	+ stripMarkupManglers.add(0, new RegularExpressionMangler( templatePattern("RefSeq", 1, true), " $2 ") );
	220	+
	221	+ propertyExtractors.add( new TemplateParameterExtractor( new ExactNameMatcher("Cite_journal"),
	222	+ new DefaultTemplateParameterPropertySpec("journal", "journal")
	223	+ .addNormalizer(punctuationStripPattern, "")
	224	+ .setCondition(lifeScienceJournalPattern, 0, false) ) );
	225	+
	226	+ TemplateParameterPropertySpec atcSpec = new AbstractTemplateParameterPropertySpec("ATC") {
	227	+ private Matcher validator = Pattern.compile("["+upperAlphaNumericChars+"]+").matcher("");
	228	+
	229	+ @Override
	230	+ public CharSequence getPropertyValue(WikiPage page, TemplateData params) {
	231	+ CharSequence code= params.getParameter("ATCCode");
	232	+ if (code!=null) {
	233	+ if (code.length()==0) return null;
	234	+ validator.reset(code);
	235	+ if (!validator.matches()) return null;
	236	+ return code;
	237	+ }
	238	+
	239	+ CharSequence pre= params.getParameter("ATC_prefix");
	240	+ CharSequence suf= params.getParameter("ATC_suffix");
	241	+
	242	+ if (pre==null) pre = params.getParameter("ATCCode_prefix");
	243	+ if (suf==null) suf = params.getParameter("ATCCode_suffix");
	244	+
	245	+ if (pre==null \|\| suf==null) return null;
	246	+ if (pre.length()==0 \|\| suf.length()==0) return null;
	247	+
	248	+ validator.reset(pre);
	249	+ if (!validator.matches()) return null;
	250	+
	251	+ validator.reset(suf);
	252	+ if (!validator.matches()) return null;
	253	+
	254	+ return pre+""+suf;
	255	+ }
	256	+ };
	257	+
	258	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Drugbox"),
	259	+ makeNamePropertySpec("IUPAC_name", "IUPAC", false, false).addCleanup(iupacCleanupPattern, ""),
	260	+ makeNamePropertySpec("synonyms", "Name", true, true),
	261	+
	262	+ makeIdentifierPropertySpec("PubChem", "PubChem", pubChemChars),
	263	+ makeIdentifierPropertySpec("DrugBank", "DrugBank", drugBankChars),
	264	+ makeIdentifierPropertySpec("CAS_number", "CAS", casChars),
	265	+
	266	+ makeIdentifierPropertySpec("smiles", "SMILES", smilesChars).addCleanup(breakStripPattern, ""),
	267	+ //makeIdentifierPropertySpec("chemical_formula", "Formula", true, false),
	268	+
	269	+ makeIdentifierPropertySpec("ATC_supplemental", "ATC", atcChars),
	270	+ makeIdentifierPropertySpec("CAS_supplemental", "CAS", casChars),
	271	+ atcSpec
	272	+ ) );
	273	+
	274	+ TemplateParameterPropertySpec eMedSpec = new AbstractTemplateParameterPropertySpec("eMedicine") {
	275	+ private Matcher subjectValidator = Pattern.compile("["+alphaNumericChars+"]+").matcher("");
	276	+ private Matcher topicValidator = Pattern.compile("["+numericChars+"]+").matcher("");
	277	+
	278	+ @Override
	279	+ public CharSequence getPropertyValue(WikiPage page, TemplateData params) {
	280	+ CharSequence pre= params.getParameter("eMedicineSubj");
	281	+ CharSequence suf= params.getParameter("eMedicineTopic");
	282	+ if (pre==null \|\| suf==null) return null;
	283	+ if (pre.length()==0 \|\| suf.length()==0) return null;
	284	+
	285	+ subjectValidator.reset(pre);
	286	+ if (pre.equals("search")) return null;
	287	+ if (!subjectValidator.matches()) return null;
	288	+
	289	+ topicValidator.reset(suf);
	290	+ if (!topicValidator.matches()) return null;
	291	+
	292	+ return pre+"/"+suf;
	293	+ }
	294	+ };
	295	+
	296	+
	297	+ TemplateParameterPropertySpec dorlandsSpec = new AbstractTemplateParameterPropertySpec("Dorlands") {
	298	+ private Matcher preValidator = Pattern.compile("["+alphabeticChars+"]_["+numericChars+"]+").matcher("");
	299	+ private Matcher sufValidator = Pattern.compile("["+numericChars+"]+").matcher("");
	300	+
	301	+ @Override
	302	+ public CharSequence getPropertyValue(WikiPage page, TemplateData params) {
	303	+ CharSequence pre= params.getParameter("DorlandsPre");
	304	+ CharSequence suf= params.getParameter("DorlandsSuf");
	305	+ if (pre==null \|\| suf==null) return null;
	306	+ if (pre.length()==0 \|\| suf.length()==0) return null;
	307	+
	308	+ preValidator.reset(pre);
	309	+ if (!preValidator.matches()) return null;
	310	+
	311	+ sufValidator.reset(suf);
	312	+ if (!sufValidator.matches()) return null;
	313	+
	314	+ return pre+"/"+suf;
	315	+ }
	316	+ };
	317	+
	318	+ TemplateParameterPropertySpec neuroNamesSpec = new AbstractTemplateParameterPropertySpec("NeuroNames") {
	319	+ private Matcher typeValidator = Pattern.compile("["+alphabeticChars+"]+").matcher("");
	320	+ private Matcher numValidator = Pattern.compile("["+numericChars+"]+").matcher("");
	321	+
	322	+ @Override
	323	+ public CharSequence getPropertyValue(WikiPage page, TemplateData params) {
	324	+ CharSequence type= params.getParameter("BrainInfoType");
	325	+ CharSequence num= params.getParameter("BrainInfoNumber");
	326	+ if (type==null \|\| num==null) return null;
	327	+ if (type.length()==0 \|\| num.length()==0) return null;
	328	+
	329	+ typeValidator.reset(type);
	330	+ if (!typeValidator.matches()) return null;
	331	+
	332	+ typeValidator.reset(num);
	333	+ if (!numValidator.matches()) return null;
	334	+
	335	+ return type+"-"+num;
	336	+ }
	337	+ };
	338	+
	339	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("Infobox_Disease\|Infobox_Symptom\|SignSymptom_infobox\|DiseaseDisorder_infobox\|Interventions_infobox", 0, true),
	340	+ makeIdentifierPropertySpec("DiseasesDB", "DiseasesDB", diseasesDbChars),
	341	+ makeIdentifierPropertySpec("ICD10", "ICD10", icd10Chars),
	342	+ makeIdentifierPropertySpec("ICD9", "ICD9", icd9Chars),
	343	+ makeIdentifierPropertySpec("ICDO", "ICDO", icdOChars),
	344	+ makeIdentifierPropertySpec("OMIM", "OMIM", omimChars),
	345	+ makeIdentifierPropertySpec("MedlinePlus", "MedlinePlus", medlinePlusChars),
	346	+ makeIdentifierPropertySpec("MeshID", "MeSH", meshChars), //FIXME: UniqueId vs. TreeNumber
	347	+ makeIdentifierPropertySpec("MeshNumber", "MeSH", meshChars), //FIXME: UniqueId vs. TreeNumber
	348	+ makeNamePropertySpec("MeshName", "MeSHName", true, true),
	349	+ makeIdentifierPropertySpec("OMIM_mult", "OMIM", omimChars),
	350	+ makeIdentifierPropertySpec("DiseasesDB_mult", "DiseasesDB", diseasesDbChars),
	351	+ makeIdentifierPropertySpec("MedlinePlus_mult", "MedlinePlus", medlinePlusChars),
	352	+ makeIdentifierPropertySpec("eMedicine_mult", "eMedicine", eMedicineChars),
	353	+ eMedSpec
	354	+ ) );
	355	+
	356	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Chembox_new"),
	357	+ makeNamePropertySpec("IUPACName", "IUPAC", true, true).addCleanup(iupacCleanupPattern, ""),
	358	+ makeNamePropertySpec("OtherNames", "Name", true, true) //FIXME: often spaced for auto-breaks and separated by <br>
	359	+ ) );
	360	+
	361	+ //TODO: terms from names
	362	+
	363	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("Chembox_[Pp]harmacology", 0, true),
	364	+ makeIdentifierPropertySpec("DrugBank", "DrugBank", drugBankChars),
	365	+ atcSpec
	366	+ ) );
	367	+
	368	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("Chembox_[Hh]azards", 0, true),
	369	+ makeIdentifierPropertySpec("RTECS", "RTECS", rtecsChars)
	370	+ ) );
	371	+
	372	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("Chembox_[Ii]dentifiers", 0, true),
	373	+ makeIdentifierPropertySpec("Abbreviations", "ChemAbbrev", chemAbbrevChars),
	374	+ makeIdentifierPropertySpec("CASNo", "CAS", casChars),
	375	+ makeIdentifierPropertySpec("SMILES", "SMILES", smilesChars).addCleanup(breakStripPattern, ""),
	376	+ makeIdentifierPropertySpec("FullSMILES", "SMILS", smilesChars).addCleanup(breakStripPattern, ""),
	377	+ makeIdentifierPropertySpec("InChI", "InChI", inChIChars).addCleanup(breakStripPattern, ""),
	378	+ makeIdentifierPropertySpec("DrugBank", "DrugBank", drugBankChars),
	379	+ makeIdentifierPropertySpec("EINECS", "EINECS", einecsChars),
	380	+ makeIdentifierPropertySpec("EC-number", "EC/chem", ecChemChars), //NOTE: replaces EINECS and ELINCS; not be confused with the Enzyme Commission EC number for enzymes. makeIdentifierPropertySpec("EINECSCASNO", "CAS", true, false),
	381	+ makeIdentifierPropertySpec("UNNumber", "UNCASN", uncasnChars),
	382	+ makeIdentifierPropertySpec("PubChem", "PubChem", pubChemChars),
	383	+ makeIdentifierPropertySpec("RTECS", "RTECS", rtecsChars),
	384	+ makeIdentifierPropertySpec("KEGG", "KEGG", keggChars),
	385	+ makeNamePropertySpec("MeSHName", "MeSHName", true, true),
	386	+ makeIdentifierPropertySpec("ChEBI", "ChEBI", chEbiChars),
	387	+ makeIdentifierPropertySpec("Beilstein", "Beilstein", beilsteinChars),
	388	+ makeIdentifierPropertySpec("Gmelin", "Gmelin", gmelinChars),
	389	+ makeIdentifierPropertySpec("3DMet", "3DMet", threeDMetChars),
	390	+ makeIdentifierPropertySpec("ChemSpiderID", "ChemSpider", chemSpiderChars),
	391	+ atcSpec
	392	+ ) );
	393	+
	394	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("NatOrganicBox", 0, true),
	395	+ makeNamePropertySpec("name", "IUPAC", false, false).addCleanup(iupacCleanupPattern, ""),
	396	+ makeNamePropertySpec("synonyms", "Name", true, true),
	397	+ makeIdentifierPropertySpec("abbreviations", "ChemAbbrev", chemAbbrevChars),
	398	+ //makeIdentifierPropertySpec("chemical_formula", "Formula", chemFormulaChars),
	399	+
	400	+ makeIdentifierPropertySpec("CAS", "CAS", casChars),
	401	+ makeIdentifierPropertySpec("DrugBank", "DrugBank", drugBankChars), //FIXME: getting "?"
	402	+ makeIdentifierPropertySpec("SMILES", "SMILES", smilesChars).addCleanup(breakStripPattern, ""),
	403	+ makeIdentifierPropertySpec("EINECS", "EINECS", einecsChars),
	404	+ makeIdentifierPropertySpec("PubChem", "PubChem", pubChemChars),
	405	+ atcSpec
	406	+ ) );
	407	+
	408	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("Elementbox", 0, true),
	409	+ makeNamePropertySpec("name", "Name", true, true),
	410	+ makeIdentifierPropertySpec("number", "ElementNumber", "["+numericChars+"]"),
	411	+ makeIdentifierPropertySpec("symbol", "ElementSymbol", "["+alphaNumericChars+"]"),
	412	+
	413	+ makeIdentifierPropertySpec("CAS number", "CAS", casChars),
	414	+ atcSpec
	415	+ ) );
	416	+
	417	+ //TODO: ...as terms
	418	+
	419	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Protbox"),
	420	+ makeNamePropertySpec("Name", "ProteinName", false, true),
	421	+ makeNamePropertySpec("Names", "ProteinName", true, true),
	422	+
	423	+ //makeIdentifierPropertySpec("Gene", "HGNC", hgncChars),
	424	+ makeIdentifierPropertySpec("HGNCid", "HGNC", hgncChars),
	425	+ makeIdentifierPropertySpec("MGIid", "MGI", hgiChars),
	426	+ makeIdentifierPropertySpec("Symbol", "ProteinSymbol", proteinSymbolChars),
	427	+ makeIdentifierPropertySpec("AltSymbols", "ProteinSymbol", proteinSymbolChars),
	428	+
	429	+ makeIdentifierPropertySpec("EntrezGene", "EntrezGene", entrezGeneChars),
	430	+ makeIdentifierPropertySpec("OMIM", "OMIM", omimChars),
	431	+ makeIdentifierPropertySpec("RefSeq", "RefSeq", refSeqChars),
	432	+ makeIdentifierPropertySpec("UniProt", "UniProt", uniProtChars),
	433	+ makeIdentifierPropertySpec("PDB", "PDB", pdbChars),
	434	+ makeIdentifierPropertySpec("ECnumber", "EC/enzyme", ecEnzymeChars)
	435	+ ) );
	436	+
	437	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Taxobox"),
	438	+ makeNamePropertySpec("name", "Name", false, true),
	439	+ makeNamePropertySpec("regnum", "taxo-regnum", true, true),
	440	+ makeNamePropertySpec("divisio", "taxo-divisio", true, true),
	441	+ makeNamePropertySpec("classis", "taxo-classis", true, true),
	442	+ makeNamePropertySpec("ordo", "taxo-ordo", true, true),
	443	+ makeNamePropertySpec("familia", "taxo-familia", true, true),
	444	+ makeNamePropertySpec("genus", "taxo-genus", true, true),
	445	+ makeNamePropertySpec("species", "taxo-species", true, true)
	446	+ ) );
	447	+
	448	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("Enzyme_(links\|references)", 0, true),
	449	+ makeIdentifierPropertySpec("EC_number", "EC/enzyme", ecEnzymeChars)
	450	+ ) );
	451	+
	452	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("GO_code_links"),
	453	+ makeNamePropertySpec("name", "ProteinName", false, true),
	454	+ makeIdentifierPropertySpec("GO_code", "GO_code", goCodeChars)
	455	+ ) );
	456	+
	457	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("CAS_registry"), //XXX: only as identifying element, or also in-context?
	458	+ makeIdentifierPropertySpec("1", "CAS", casChars)
	459	+ ) );
	460	+
	461	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("MSW3_Groves"),
	462	+ makeIdentifierPropertySpec("id", "GrovesId", numericChars),
	463	+ makeIdentifierPropertySpec("pages", "GrovesPages", pagesChars)
	464	+ ) );
	465	+
	466	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Rfam"),
	467	+ makeIdentifierPropertySpec("id", "RNA family", alphaNumericChars),
	468	+ makeNamePropertySpec("name", "Name", false, true)
	469	+ ) );
	470	+
	471	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("Rfam_box", 0, true),
	472	+ makeIdentifierPropertySpec("acc", "RNA family", alphaNumericChars),
	473	+ makeNamePropertySpec("description", "Name", true, true),
	474	+ makeNamePropertySpec("abbreviation", "Name", true, true),
	475	+ makeNamePropertySpec("type", "RNA type", true, true),
	476	+ new DefaultTemplateParameterPropertySpec("journal", "journal")
	477	+ .addNormalizer(punctuationStripPattern, "")
	478	+ .setCondition(lifeScienceJournalPattern, 0, false)
	479	+ ) );
	480	+
	481	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("Infobox_chemical_analysis", 0, true),
	482	+ makeNamePropertySpec("name", "Name", true, true),
	483	+ makeNamePropertySpec("acronym", "Name", true, true),
	484	+ makeNamePropertySpec("classification", "AnalysisClass", true, true),
	485	+ makeNamePropertySpec("analytes", "Analytes", true, true)
	486	+ ) );
	487	+
	488	+ //Stuff from the container field Codes in Protbox:
	489	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Protbox.Codes::OMIM"),
	490	+ makeIdentifierPropertySpec("1", "OMIM", omimChars) ) );
	491	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Protbox.Codes::OMIM2"),
	492	+ makeIdentifierPropertySpec("1", "OMIM", omimChars) ) );
	493	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Protbox.Codes::EntrezGene"),
	494	+ makeIdentifierPropertySpec("1", "EntrezGene", entrezGeneChars) ) );
	495	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Protbox.Codes::UniProt"),
	496	+ makeIdentifierPropertySpec("1", "UniProt", uniProtChars) ) );
	497	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Protbox.Codes::RefSeq"),
	498	+ makeIdentifierPropertySpec("1", "RefSeq", refSeqChars) ) );
	499	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Protbox.Codes::EC_number"),
	500	+ makeIdentifierPropertySpec("1", "EC/enzyme", ecEnzymeChars) ) );
	501	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Protbox.Codes::PDB"),
	502	+ makeIdentifierPropertySpec("1", "PDB", pdbChars) ) );
	503	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Protbox.Caption::PDB"),
	504	+ makeIdentifierPropertySpec("1", "PDB", pdbChars) ) );
	505	+
	506	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Protein"),
	507	+ makeIdentifierPropertySpec("Symbol", "ProteinSymbol", proteinSymbolChars),
	508	+ makeIdentifierPropertySpec("AltSymbols", "ProteinSymbol", proteinSymbolChars),
	509	+ makeIdentifierPropertySpec("CAS_number", "CAS", casChars),
	510	+ makeIdentifierPropertySpec("DrugBank", "DrugBank", drugBankChars), //FIXME: getting "?"
	511	+ makeIdentifierPropertySpec("EntrezGene", "EntrezGene", entrezGeneChars),
	512	+ makeIdentifierPropertySpec("HGNCid", "HGNC", hgncChars),
	513	+ makeIdentifierPropertySpec("MGIid", "MGI", hgiChars),
	514	+ makeIdentifierPropertySpec("OMIM", "OMIM", omimChars),
	515	+ makeIdentifierPropertySpec("PDB", "PDB", pdbChars),
	516	+ makeIdentifierPropertySpec("RefSeq", "RefSeq", refSeqChars),
	517	+ makeIdentifierPropertySpec("UniProt", "UniProt", uniProtChars),
	518	+ makeIdentifierPropertySpec("ECnumber", "EC/enzyme", ecEnzymeChars),
	519	+ makeIdentifierPropertySpec("ATC_supplemental", "ATC", atcChars),
	520	+ makeIdentifierPropertySpec("CAS_supplemental", "CAS", casChars),
	521	+ atcSpec
	522	+ ) );
	523	+
	524	+ //TODO: pull names and symbols as terms!
	525	+
	526	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("GNF_Protein_box"),
	527	+ makeIdentifierPropertySpec("Symbol", "ProteinSymbol", proteinSymbolChars),
	528	+ makeIdentifierPropertySpec("AltSymbols", "ProteinSymbol", proteinSymbolChars),
	529	+ makeIdentifierPropertySpec("HGNCid", "HGNC", hgncChars),
	530	+ makeIdentifierPropertySpec("MGIid", "MGI", hgiChars),
	531	+ makeIdentifierPropertySpec("OMIM", "OMIM", omimChars),
	532	+ makeIdentifierPropertySpec("PDB", "PDB", pdbChars),
	533	+ makeIdentifierPropertySpec("ECnumber", "EC/enzyme", ecEnzymeChars),
	534	+ makeIdentifierPropertySpec("Homologene", "HomoloGene", homoloGeneChars),
	535	+ makeIdentifierPropertySpec("MGIid", "MGI", mgiChars)
	536	+ ) );
	537	+
	538	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("GNF_Ortholog_box"),
	539	+ makeIdentifierPropertySpec("Hs_Uniprot", "UniProt", uniProtChars),
	540	+ makeIdentifierPropertySpec("Mm_Uniprot", "UniProt", uniProtChars),
	541	+ makeIdentifierPropertySpec("Hs_Ensembl", "Ensembl", ensemblChars),
	542	+ makeIdentifierPropertySpec("Mm_Ensembl", "Ensembl", ensemblChars),
	543	+ makeIdentifierPropertySpec("Hs_EntrezGene", "EntrezGene", entrezGeneChars),
	544	+ makeIdentifierPropertySpec("Mm_EntrezGene", "EntrezGene", entrezGeneChars),
	545	+ makeIdentifierPropertySpec("Hs_RefseqProtein", "RefSeq", refSeqChars),
	546	+ makeIdentifierPropertySpec("Mm_RefseqProtein", "RefSeq", refSeqChars),
	547	+ makeIdentifierPropertySpec("Hs_RefseqmRNA", "RefSeq", refSeqChars),
	548	+ makeIdentifierPropertySpec("Mm_RefseqmRNA", "RefSeq", refSeqChars)
	549	+ ) );
	550	+
	551	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Infobox_neuron"),
	552	+ makeNamePropertySpec("neuron_name", "Name", false, true),
	553	+ makeNamePropertySpec("function", "Function", false, true),
	554	+ makeNamePropertySpec("GraySubject", "GraySubject", true, true)
	555	+ ) );
	556	+
	557	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Infobox_neurotransmitter"),
	558	+ makeNamePropertySpec("name", "Name", false, true),
	559	+ makeNamePropertySpec("abbrev", "Name", false, true)
	560	+ ) );
	561	+
	562	+ //TODO: {{MedlinePlus}}...?
	563	+
	564	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("Infobox_(Anatomy\|Artery\|Vein\|Bone\|Brain\|Nerve\|Muscle\|Embryology\|Ligament\|Lymph)", 0, true),
	565	+ makeNamePropertySpec("Name", "Name", true, true),
	566	+ makeNamePropertySpec("Latin", "AnatomyLatin", true, true),
	567	+ makeNamePropertySpec("GraySubject", "GraySubject", true, true),
	568	+ makeNamePropertySpec("MeshName", "MeSHName", true, true),
	569	+ makeIdentifierPropertySpec("MeshNumber", "MeSH", meshChars),
	570	+ makeNamePropertySpec("DorlandsID", "DorlandsName", true, true),
	571	+ makeIdentifierPropertySpec("Dorlands", "Dorlands", dorlandsChars),
	572	+ dorlandsSpec,
	573	+ neuroNamesSpec
	574	+ ) );
	575	+
	576	+ //FIXME: URLDecode for MeshName, etc!
	577	+
	578	+ //TODO: Infobox_(Artery\|Brain\|Bone\|...)
	579	+ // GraySubject, MeSH name&number, DorlandsPre/DorlandsSuf (Elsevier )
	580	+
	581	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("ICSC"),
	582	+ makeIdentifierPropertySpec("1", "ICSC", icscChars)
	583	+ ) );
	584	+
	585	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("PubChem"),
	586	+ makeIdentifierPropertySpec("1", "PubChem", pubChemChars)
	587	+ ) );
	588	+
	589	+
	590	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("PBB"),
	591	+ makeIdentifierPropertySpec("geneid", "_PBB_", pbbChars)
	592	+ ) );
	593	+
	594	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Infobox_abortion_method"),
	595	+ makeNamePropertySpec("name", "Name", false, true),
	596	+ makeNamePropertySpec("AKA/Abbreviation", "Name", true, true),
	597	+ makeNamePropertySpec("Abortion_type", "AbortionType", false, true)
	598	+ ) );
	599	+
	600	+ propertyExtractors.add( new TemplateParameterExtractor(new ExactNameMatcher("Infobox_Birth_control"),
	601	+ makeNamePropertySpec("name", "Name", false, true) //not really interesting, just make the concept show up as relevant for LS
	602	+ ) );
	603	+
	604	+ propertyExtractors.add( new TemplateParameterExtractor(new PatternNameMatcher("Infobox_(((Medical)_)?[Pp]erson\|Scientist)", 0, true),
	605	+ new DefaultTemplateParameterPropertySpec("name", "person-name").setStripMarkup(true),
	606	+ new DefaultTemplateParameterPropertySpec("other_names", "person-name").setStripMarkup(true),
	607	+ new DefaultTemplateParameterPropertySpec("birth_date", "person-birth-date").setStripMarkup(true),
	608	+ new DefaultTemplateParameterPropertySpec("occupation", "person-occupation").setStripMarkup(true),
	609	+ new DefaultTemplateParameterPropertySpec("known_for", "person-known-for").setStripMarkup(true).setSplitPattern(nameSeparatorPattern),
	610	+ new DefaultTemplateParameterPropertySpec("nationality", "person-nationality").setStripMarkup(true)
	611	+ ) );
	612	+
	613	+ propertyExtractors.add(new CategoryPatternParameterExtractor("(_\|$)([Ff]oods\|[Vv]egetables\|[Ff]ruits)", null, 0, "food-group"));
	614	+ propertyExtractors.add(new TemplateNamePatternParameterExtractor("((.+-)?(Med(ical)?\|Treatment\|Pathology\|Anatomy\|Antibiotic\|Disease)(-.+)?)-stub", "$2", 0, "med-stub-group")); //TODO: no limits to this one
	615	+
	616	+ pageTermExtractors.add( new PagePropertyValueExtractor("IUPAC") );
	617	+ pageTermExtractors.add( new PagePropertyValueExtractor("AnatomyLatin") );
	618	+ pageTermExtractors.add( new PagePropertyValueExtractor("ProteinSymbol") );
	619	+ pageTermExtractors.add( new PagePropertyValueExtractor("ProteinName") );
	620	+ pageTermExtractors.add( new PagePropertyValueExtractor("MeSHName") );
	621	+ pageTermExtractors.add( new PagePropertyValueExtractor("Name") );
	622	+ pageTermExtractors.add( new PagePropertyValueExtractor("Symbol") );
	623	+ pageTermExtractors.add( new PagePropertyValueExtractor("DorlandsName") );
	624	+ pageTermExtractors.add( new PagePropertyValueExtractor("person-name") );
	625	+
	626	+ supplementSensors.add( new TitleSensor<ResourceType>(ResourceType.SUPPLEMENT, Namespace.TEMPLATE, "PBB/\\d+", 0));
	627	+
	628	+ supplementNameExtractors.add( new PropertyValueExtractor("_PBB_").setPrefix("Template:PBB/") );
	629	+
	630	+ supplementedConceptExtractors.add( new TitlePartExtractor(Namespace.MAIN, "(.*)_\$data_page\$", 0, "$1") );
	631	+ supplementedConceptExtractors.add( new TitlePartExtractor(Namespace.TEMPLATE, "Infobox_(.*)", 0, "$1")
	632	+ .addCondition( new HasCategorySensor<ResourceType>(ResourceType.SUPPLEMENT, "Periodic_table_infobox_templates") ) );
	633	+
	634	+ conceptTypeSensors.add( new HasCategoryLikeSensor<ConceptType>(LifeScienceConceptType.DRUG, "_(treatments\|therapies)$", 0));
	635	+ conceptTypeSensors.add( new HasTemplateSensor<ConceptType>(LifeScienceConceptType.DRUG, "Drugbox"));
	636	+ conceptTypeSensors.add( new HasTemplateLikeSensor<ConceptType>(LifeScienceConceptType.DRUG, "^Drugs_\|^DrugsNav$", 0));
	637	+ conceptTypeSensors.add( new HasTemplateSensor<ConceptType>(LifeScienceConceptType.DRUG, "Major_Drug_Groups"));
	638	+
	639	+ conceptTypeSensors.add( new HasCategoryLikeSensor<ConceptType>(LifeScienceConceptType.PROTEIN, "EC_\\d+(\\.\\d+)*", 0)); //FIXME: too much meta-stuff!
	640	+ conceptTypeSensors.add( new HasTemplateLikeSensor<ConceptType>(LifeScienceConceptType.PROTEIN, "^(Enzyme_links\|PBB\|Protein\|GNF_.*_box)$", 0) );
	641	+
	642	+ conceptTypeSensors.add( new HasTemplateLikeSensor<ConceptType>(LifeScienceConceptType.CHEMICAL, "^Chembox\|^NatOrganicBox$\|^ICSC$\|^Elementbox\|^(Complex_)?Enzymatic_Reaction", 0));
	643	+ conceptTypeSensors.add( new HasCategorySensor<ConceptType>(LifeScienceConceptType.CHEMICAL, "Chemical_elements"));
	644	+
	645	+ conceptTypeSensors.add( new HasTemplateLikeSensor<ConceptType>(LifeScienceConceptType.DISEASE, "^(Infobox_Disease\|Infobox_Symptom\|SignSymptom_infobox\|DiseaseDisorder_infobox)$", 0));
	646	+ conceptTypeSensors.add( new HasCategoryLikeSensor<ConceptType>(LifeScienceConceptType.DISEASE, "(_diseases\|_disorders)$", 0, false));
	647	+
	648	+ conceptTypeSensors.add( new HasTemplateLikeSensor<ConceptType>(LifeScienceConceptType.ORGAN, "^Infobox_(Brain\|Nerve\|Muscle\|Vein\|Artery\|Bone\|Anatomy\|Ligament\|Lymph)$", 0));
	649	+ conceptTypeSensors.add( new HasTemplateLikeSensor<ConceptType>(LifeScienceConceptType.ORGAN, "_glands$\|^SUNYAnatomy\|^(BUHistology\|AnatomyAtlasesMicroscopic\|Gray's\|Anatomy-stub)$", 0));
	650	+
	651	+ conceptTypeSensors.add( new HasTemplateLikeSensor<ConceptType>(LifeScienceConceptType.FOOD, "Nutritional_value", 0));
	652	+ conceptTypeSensors.add( new HasCategoryLikeSensor<ConceptType>(LifeScienceConceptType.FOOD, "(_\|$)([Ff]oods\|[Vv]egetables\|[Ff]ruits)", 0, false));
	653	+
	654	+ conceptTypeSensors.add( new HasTemplateSensor<ConceptType>(ConceptType.LIFEFORM, "Taxobox"));
	655	+ conceptTypeSensors.add( new HasPropertySensor<ConceptType>(ConceptType.LIFEFORM, "GrovesId"));
	656	+
	657	+ conceptTypeSensors.add( new HasPropertySensor<ConceptType>(ConceptType.PERSON, "person-name"));
	658	+ conceptTypeSensors.add( new HasPropertySensor<ConceptType>(ConceptType.PERSON, "person-birth-date"));
	659	+
	660	+ //TODO; LOTS of anatomy navigation boxes
	661	+
	662	+ //TODO: generic markers, such as {{MedlinePlus}}, {{MeshName}}, {{GPnotebook}}, {{Gene}}, etc, or [[Category:EC_.*]]
	663	+
	664	+ //TODO: terms from properties! (ids, latin name, box caption, etc)
	665	+
	666	+
	667	+ }
	668	+
	669	+}
Index: trunk/WikiWord/WikiWordProperties/src/main/java/de/brightbyte/wikiword/lifescience/LifeScienceConceptType.java
—	—	@@ -0,0 +1,52 @@
	2	+package de.brightbyte.wikiword.lifescience;
	3	+
	4	+import de.brightbyte.wikiword.ConceptType;
	5	+import de.brightbyte.wikiword.ConceptTypeSet;
	6	+
	7	+/**
	8	+ * Enumeration of concept types; each concept type represents a very broad category of concepts,
	9	+ * which can be used to filter concepts identified in a corpus. The idea is at for some uses,
	10	+ * some kinds of concepts are not usefull, or especially usefull. For example, people and polaces
	11	+ * are not suitable for use in a general dictionary, but very useful for topic tracking.
	12	+ * Each type is associated with a code (for internal use) and a URI (for external use).
	13	+ * The URI is constructed based on {@link RdfEntities.conceptTypeBase}.
	14	+ */
	15	+public class LifeScienceConceptType extends ConceptType {
	16	+
	17	+ public static final ConceptType DISEASE;
	18	+ public static final ConceptType DRUG;
	19	+ public static final ConceptType CHEMICAL;
	20	+ public static final ConceptType PROTEIN;
	21	+ public static final ConceptType ORGAN;
	22	+ public static final ConceptType FOOD;
	23	+
	24	+ /**
	25	+ * NamespaceSet for the canonical concept types. Loaded from the ConceptTypes.properties
	26	+ * file in this package.
	27	+ */
	28	+ public static final ConceptTypeSet lifeScienceConceptTypes;
	29	+
	30	+ static {
	31	+ try {
	32	+ lifeScienceConceptTypes = getConceptTypes(null, "de.brightbyte.wikiword.lifescience"); //FIXME: make unmodifiable!
	33	+
	34	+ DISEASE = lifeScienceConceptTypes.getType(1001);
	35	+ //SYMPTOM = wikiProConceptTypes.getType(1002);
	36	+ DRUG = lifeScienceConceptTypes.getType(1003);
	37	+ //TREATMENT = wikiProConceptTypes.getType(1004);
	38	+ CHEMICAL = lifeScienceConceptTypes.getType(1005);
	39	+ PROTEIN = lifeScienceConceptTypes.getType(1006);
	40	+ //GENE = wikiProConceptTypes.getType(1007);
	41	+ ORGAN = lifeScienceConceptTypes.getType(1008);
	42	+ FOOD = lifeScienceConceptTypes.getType(1009);
	43	+ }
	44	+ catch (NumberFormatException ex) {
	45	+ throw new ExceptionInInitializerError(ex);
	46	+ }
	47	+ }
	48	+
	49	+ public LifeScienceConceptType(int code, String name) {
	50	+ super(code, name);
	51	+ }
	52	+
	53	+}
Index: trunk/WikiWord/WikiWordProperties/src/main/java/de/brightbyte/wikiword/lifescience/ConceptTypes.properties
—	—	@@ -0,0 +1,5 @@
	2	+1001=DISEASE
	3	+1003=DRUG
	4	+1005=CHEMICAL
	5	+1006=PROTEIN
	6	+1008=ORGAN
Property changes on: trunk/WikiWord/WikiWordProperties/src/main/java/de/brightbyte/wikiword/lifescience
___________________________________________________________________
Name: svn:mergeinfo
1	7	+
Index: trunk/WikiWord/WikiWordProperties/.svnignore
—	—	@@ -0,0 +1,2 @@
	2	+*.pyc
	3	+
Index: trunk/WikiWord/WikiWordProperties/COPYING
—	—	@@ -0,0 +1,33 @@
	2	+WikiWord is a system for automatically extracting a thesaurus from
	3	+Wikipedia. It was developed by Daniel Kinzler in 2007-2009.
	4	+
	5	+Development started in 2007 as part of a master's thesis at the
	6	+University of Leipzig, see <http://brightbyte.de/page/WikiWord>.
	7	+
	8	+Development was supported since 2009 by Wikimedia Deutschland e.V.
	9	+
	10	+ NOTE: This software is not released as a product. It was designed
	11	+ for Wikimedia Deutschland's own use, and is made public as is, in
	12	+ the hope it may be useful. Wikimedia Deutschland may at any time
	13	+ discontinue developing or supporting this software. There is no
	14	+ guarantee any new versions or even fixes for security issues will
	15	+ be released.
	16	+
	17	+WikiWord was originally licensed under the GPL, with support of the
	18	+University of Leipzig, and was released under the LGPL by its author in
	19	+2009, in coordination with Wikimedia Deutschland. If you want to use it
	20	+under some other license or condition, please contact the author at
	21	+<http://brightbyte.de>.
	22	+
	23	+ This program is free software: you can redistribute it and/or modify
	24	+ it under the terms of the GNU General Public License as published by
	25	+ the Free Software Foundation, either version 3 of the License, or
	26	+ (at your option) any later version.
	27	+
	28	+ This program is distributed in the hope that it will be useful,
	29	+ but WITHOUT ANY WARRANTY; without even the implied warranty of
	30	+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	31	+ GNU General Public License for more details.
	32	+
	33	+ You should have received a copy of the GNU General Public License
	34	+ along with this program. If not, see <http://www.gnu.org/licenses/>.
Property changes on: trunk/WikiWord/WikiWordProperties/bin
___________________________________________________________________
Name: svn:ignore
1	35	+ *
Index: trunk/WikiWord/WikiWordProperties/pom.xml
—	—	@@ -0,0 +1,105 @@
	2	+<project xmlns="http://maven.apache.org/POM/4.0.0"
	3	+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
	4	+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
	5	+
	6	+ <modelVersion>4.0.0</modelVersion>
	7	+ <groupId>de.wikimedia</groupId>
	8	+ <artifactId>WikiWordBuilder4Biography</artifactId>
	9	+ <version>0.3</version>
	10	+
	11	+ <dependencies>
	12	+ <dependency>
	13	+ <groupId>org.wikimedia</groupId>
	14	+ <artifactId>mwdumper</artifactId>
	15	+ <version>1.11</version>
	16	+ <scope>compile</scope>
	17	+ </dependency>
	18	+ <dependency>
	19	+ <groupId>de.brightbyte</groupId>
	20	+ <artifactId>BrightByteUtil</artifactId>
	21	+ <version>0.2</version>
	22	+ <scope>compile</scope>
	23	+ </dependency>
	24	+ <dependency>
	25	+ <groupId>de.brightbyte</groupId>
	26	+ <artifactId>BrightByteDB</artifactId>
	27	+ <version>0.2</version>
	28	+ <scope>compile</scope>
	29	+ </dependency>
	30	+ <dependency>
	31	+ <groupId>de.wikimedia</groupId>
	32	+ <artifactId>WikiWord</artifactId>
	33	+ <version>0.3</version>
	34	+ <scope>compile</scope>
	35	+ </dependency>
	36	+ <dependency>
	37	+ <groupId>de.wikimedia</groupId>
	38	+ <artifactId>WikiWordBuilder</artifactId>
	39	+ <version>0.3</version>
	40	+ <scope>compile</scope>
	41	+ </dependency>
	42	+ <dependency>
	43	+ <groupId>junit</groupId>
	44	+ <artifactId>junit</artifactId>
	45	+ <version>3.8</version>
	46	+ <scope>test</scope>
	47	+ </dependency>
	48	+ </dependencies>
	49	+
	50	+ <build>
	51	+ <plugins>
	52	+ <plugin>
	53	+ <groupId>org.apache.maven.plugins</groupId>
	54	+ <artifactId>maven-compiler-plugin</artifactId>
	55	+ <configuration>
	56	+ <source>1.5</source>
	57	+ <target>1.5</target>
	58	+ </configuration>
	59	+ </plugin>
	60	+ <plugin>
	61	+ <groupId>org.apache.maven.plugins</groupId>
	62	+ <artifactId>maven-javadoc-plugin</artifactId>
	63	+ <executions>
	64	+ <execution>
	65	+ <phase>package</phase>
	66	+ </execution>
	67	+ </executions>
	68	+ </plugin>
	69	+ <plugin>
	70	+ <artifactId>maven-assembly-plugin</artifactId>
	71	+ <configuration>
	72	+ <descriptors>
	73	+ <descriptor>src/main/assembly/bin-dep.xml</descriptor>
	74	+ <descriptor>src/main/assembly/src.xml</descriptor>
	75	+ </descriptors>
	76	+ </configuration>
	77	+ </plugin>
	78	+ </plugins>
	79	+
	80	+ <resources>
	81	+ <resource>
	82	+ <filtering>false</filtering>
	83	+ <directory>src/main/java</directory>
	84	+ <includes>
	85	+ <include>**</include>
	86	+ </includes>
	87	+ <excludes>
	88	+ <exclude>*/.java</exclude>
	89	+ </excludes>
	90	+ </resource>
	91	+ </resources>
	92	+ <testResources>
	93	+ <testResource>
	94	+ <filtering>false</filtering>
	95	+ <directory>src/test/java</directory>
	96	+ <includes>
	97	+ <include>**</include>
	98	+ </includes>
	99	+ <excludes>
	100	+ <exclude>*/.java</exclude>
	101	+ </excludes>
	102	+ </testResource>
	103	+ </testResources>
	104	+ </build>
	105	+
	106	+</project>
Index: trunk/WikiWord/WikiWordProperties/LGPL
—	—	@@ -0,0 +1,165 @@
	2	+ GNU LESSER GENERAL PUBLIC LICENSE
	3	+ Version 3, 29 June 2007
	4	+
	5	+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
	6	+ Everyone is permitted to copy and distribute verbatim copies
	7	+ of this license document, but changing it is not allowed.
	8	+
	9	+
	10	+ This version of the GNU Lesser General Public License incorporates
	11	+the terms and conditions of version 3 of the GNU General Public
	12	+License, supplemented by the additional permissions listed below.
	13	+
	14	+ 0. Additional Definitions.
	15	+
	16	+ As used herein, "this License" refers to version 3 of the GNU Lesser
	17	+General Public License, and the "GNU GPL" refers to version 3 of the GNU
	18	+General Public License.
	19	+
	20	+ "The Library" refers to a covered work governed by this License,
	21	+other than an Application or a Combined Work as defined below.
	22	+
	23	+ An "Application" is any work that makes use of an interface provided
	24	+by the Library, but which is not otherwise based on the Library.
	25	+Defining a subclass of a class defined by the Library is deemed a mode
	26	+of using an interface provided by the Library.
	27	+
	28	+ A "Combined Work" is a work produced by combining or linking an
	29	+Application with the Library. The particular version of the Library
	30	+with which the Combined Work was made is also called the "Linked
	31	+Version".
	32	+
	33	+ The "Minimal Corresponding Source" for a Combined Work means the
	34	+Corresponding Source for the Combined Work, excluding any source code
	35	+for portions of the Combined Work that, considered in isolation, are
	36	+based on the Application, and not on the Linked Version.
	37	+
	38	+ The "Corresponding Application Code" for a Combined Work means the
	39	+object code and/or source code for the Application, including any data
	40	+and utility programs needed for reproducing the Combined Work from the
	41	+Application, but excluding the System Libraries of the Combined Work.
	42	+
	43	+ 1. Exception to Section 3 of the GNU GPL.
	44	+
	45	+ You may convey a covered work under sections 3 and 4 of this License
	46	+without being bound by section 3 of the GNU GPL.
	47	+
	48	+ 2. Conveying Modified Versions.
	49	+
	50	+ If you modify a copy of the Library, and, in your modifications, a
	51	+facility refers to a function or data to be supplied by an Application
	52	+that uses the facility (other than as an argument passed when the
	53	+facility is invoked), then you may convey a copy of the modified
	54	+version:
	55	+
	56	+ a) under this License, provided that you make a good faith effort to
	57	+ ensure that, in the event an Application does not supply the
	58	+ function or data, the facility still operates, and performs
	59	+ whatever part of its purpose remains meaningful, or
	60	+
	61	+ b) under the GNU GPL, with none of the additional permissions of
	62	+ this License applicable to that copy.
	63	+
	64	+ 3. Object Code Incorporating Material from Library Header Files.
	65	+
	66	+ The object code form of an Application may incorporate material from
	67	+a header file that is part of the Library. You may convey such object
	68	+code under terms of your choice, provided that, if the incorporated
	69	+material is not limited to numerical parameters, data structure
	70	+layouts and accessors, or small macros, inline functions and templates
	71	+(ten or fewer lines in length), you do both of the following:
	72	+
	73	+ a) Give prominent notice with each copy of the object code that the
	74	+ Library is used in it and that the Library and its use are
	75	+ covered by this License.
	76	+
	77	+ b) Accompany the object code with a copy of the GNU GPL and this license
	78	+ document.
	79	+
	80	+ 4. Combined Works.
	81	+
	82	+ You may convey a Combined Work under terms of your choice that,
	83	+taken together, effectively do not restrict modification of the
	84	+portions of the Library contained in the Combined Work and reverse
	85	+engineering for debugging such modifications, if you also do each of
	86	+the following:
	87	+
	88	+ a) Give prominent notice with each copy of the Combined Work that
	89	+ the Library is used in it and that the Library and its use are
	90	+ covered by this License.
	91	+
	92	+ b) Accompany the Combined Work with a copy of the GNU GPL and this license
	93	+ document.
	94	+
	95	+ c) For a Combined Work that displays copyright notices during
	96	+ execution, include the copyright notice for the Library among
	97	+ these notices, as well as a reference directing the user to the
	98	+ copies of the GNU GPL and this license document.
	99	+
	100	+ d) Do one of the following:
	101	+
	102	+ 0) Convey the Minimal Corresponding Source under the terms of this
	103	+ License, and the Corresponding Application Code in a form
	104	+ suitable for, and under terms that permit, the user to
	105	+ recombine or relink the Application with a modified version of
	106	+ the Linked Version to produce a modified Combined Work, in the
	107	+ manner specified by section 6 of the GNU GPL for conveying
	108	+ Corresponding Source.
	109	+
	110	+ 1) Use a suitable shared library mechanism for linking with the
	111	+ Library. A suitable mechanism is one that (a) uses at run time
	112	+ a copy of the Library already present on the user's computer
	113	+ system, and (b) will operate properly with a modified version
	114	+ of the Library that is interface-compatible with the Linked
	115	+ Version.
	116	+
	117	+ e) Provide Installation Information, but only if you would otherwise
	118	+ be required to provide such information under section 6 of the
	119	+ GNU GPL, and only to the extent that such information is
	120	+ necessary to install and execute a modified version of the
	121	+ Combined Work produced by recombining or relinking the
	122	+ Application with a modified version of the Linked Version. (If
	123	+ you use option 4d0, the Installation Information must accompany
	124	+ the Minimal Corresponding Source and Corresponding Application
	125	+ Code. If you use option 4d1, you must provide the Installation
	126	+ Information in the manner specified by section 6 of the GNU GPL
	127	+ for conveying Corresponding Source.)
	128	+
	129	+ 5. Combined Libraries.
	130	+
	131	+ You may place library facilities that are a work based on the
	132	+Library side by side in a single library together with other library
	133	+facilities that are not Applications and are not covered by this
	134	+License, and convey such a combined library under terms of your
	135	+choice, if you do both of the following:
	136	+
	137	+ a) Accompany the combined library with a copy of the same work based
	138	+ on the Library, uncombined with any other library facilities,
	139	+ conveyed under the terms of this License.
	140	+
	141	+ b) Give prominent notice with the combined library that part of it
	142	+ is a work based on the Library, and explaining where to find the
	143	+ accompanying uncombined form of the same work.
	144	+
	145	+ 6. Revised Versions of the GNU Lesser General Public License.
	146	+
	147	+ The Free Software Foundation may publish revised and/or new versions
	148	+of the GNU Lesser General Public License from time to time. Such new
	149	+versions will be similar in spirit to the present version, but may
	150	+differ in detail to address new problems or concerns.
	151	+
	152	+ Each version is given a distinguishing version number. If the
	153	+Library as you received it specifies that a certain numbered version
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	155	+applies to it, you have the option of following the terms and
	156	+conditions either of that published version or of any later version
	157	+published by the Free Software Foundation. If the Library as you
	158	+received it does not specify a version number of the GNU Lesser
	159	+General Public License, you may choose any version of the GNU Lesser
	160	+General Public License ever published by the Free Software Foundation.
	161	+
	162	+ If the Library as you received it specifies that a proxy can decide
	163	+whether future versions of the GNU Lesser General Public License shall
	164	+apply, that proxy's public statement of acceptance of any version is
	165	+permanent authorization for you to choose that version for the
	166	+Library.
Index: trunk/WikiWord/WikiWordProperties/build.xml
—	—	@@ -0,0 +1,90 @@
	2	+<?xml version="1.0" encoding="UTF-8"?>
	3	+<project xmlns:artifact="antlib:org.apache.maven.artifact.ant"
	4	+ name="WikiWordBuilder" default="dist" basedir=".">
	5	+ <property name="src" location="src/main/java"/>
	6	+ <property name="build" location="build"/>
	7	+ <property name="dist" location="dist"/>
	8	+
	9	+ <artifact:pom id="maven.project" file="pom.xml">
	10	+ </artifact:pom>
	11	+
	12	+ <artifact:dependencies pathId="compile.classpath" filesetId="compile.fileset" useScope="compile">
	13	+ <artifact:pom refid="maven.project"/>
	14	+ </artifact:dependencies>
	15	+
	16	+ <artifact:dependencies pathId="runtime.classpath" filesetId="runtime.fileset" useScope="runtime">
	17	+ <artifact:pom refid="maven.project"/>
	18	+ </artifact:dependencies>
	19	+
	20	+ <property name="versionedName" value="${maven.project.artifactId}-${maven.project.version}"/>
	21	+
	22	+ <target name="init">
	23	+ <!-- Create the time stamp -->
	24	+ <tstamp/>
	25	+ <!-- Create the build directory structure used by compile -->
	26	+ <mkdir dir="${build}"/>
	27	+ </target>
	28	+
	29	+ <target name="compile" depends="init" description="compile the source " >
	30	+ <!-- Compile the java code from ${src} into ${build} -->
	31	+ <javac srcdir="${src}" destdir="${build}" source="1.5" target="1.5" encoding="UTF-8" debug="true" debuglevel="lines,source,vars">
	32	+ <classpath refid="compile.classpath" />
	33	+ </javac>
	34	+ <copy todir="${build}">
	35	+ <fileset dir="${src}">
	36	+ <exclude name="*/.java"/>
	37	+ </fileset>
	38	+ </copy>
	39	+ </target>
	40	+
	41	+ <target name="dist" depends="compile"
	42	+ description="generate the distribution" >
	43	+ <!-- Create the distribution directory -->
	44	+ <mkdir dir="${dist}/lib"/>
	45	+ <!-- Put everything in ${build} into the MyProject-${DSTAMP}.jar file -->
	46	+ <jar jarfile="${dist}/lib/${versionedName}.jar" basedir="${build}"/>
	47	+ <copy todir="${dist}/lib">
	48	+ <fileset refid="runtime.fileset"/>
	49	+ <mapper type="flatten" />
	50	+ </copy>
	51	+ </target>
	52	+
	53	+ <target name="assemble" depends="dist" description="assemble depolyment package">
	54	+ <mkdir dir="${dist}/unpacked"/>
	55	+ <mkdir dir="${dist}/assembled"/>
	56	+
	57	+ <!-- build jar with all dependencies -->
	58	+ <unjar dest="${dist}/unpacked">
	59	+ <fileset dir="${dist}/lib"/>
	60	+ </unjar>
	61	+
	62	+ <jar jarfile="${dist}/assembled/${versionedName}-with-deps.jar" basedir="${dist}/unpacked"/>
	63	+
	64	+
	65	+ <copy todir="${dist}/assembled/bin">
	66	+ <fileset dir="bin"/>
	67	+ </copy>
	68	+
	69	+ <copy tofile="${dist}/assembled/bin/${maven.project.artifactId}.jar">
	70	+ <fileset file="${dist}/assembled/${versionedName}-with-deps.jar"/>
	71	+ </copy>
	72	+
	73	+ <input addproperty="keystorepass">Enter Keystore Password</input>
	74	+
	75	+ <signjar jar="${dist}/assembled/bin/${maven.project.artifactId}.jar"
	76	+ alias="brightbyte" storepass="${keystorepass}" />
	77	+ </target>
	78	+
	79	+ <target name="install" depends="dist" description="install to local maven repository">
	80	+ <artifact:install file="dist/lib/${versionedName}.jar">
	81	+ <pom refid="maven.project"/>
	82	+ </artifact:install>
	83	+ </target>
	84	+
	85	+ <target name="clean" description="clean up" >
	86	+ <!-- Delete the ${build} and ${dist} directory trees -->
	87	+ <delete dir="${build}"/>
	88	+ <delete dir="${dist}"/>
	89	+ </target>
	90	+
	91	+</project>
Property changes on: trunk/WikiWord/WikiWordProperties
___________________________________________________________________
Name: svn:mergeinfo
1	92	+
Name: svn:ignore
2	93	+ *.pyc

Status & tagging log

18:27, 1 August 2009 😂 (talk | contribs) changed the status of r53901 [removed: new added: deferred]