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From: <rv...@us...> - 2010-03-15 01:14:09
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Revision: 578
http://treebase.svn.sourceforge.net/treebase/?rev=578&view=rev
Author: rvos
Date: 2010-03-15 01:14:03 +0000 (Mon, 15 Mar 2010)
Log Message:
-----------
Added getAnnotations() and getLabel() for nexml and rdf serialization.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2010-03-15 01:13:21 UTC (rev 577)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2010-03-15 01:14:03 UTC (rev 578)
@@ -1,5 +1,9 @@
package org.cipres.treebase.domain.taxon;
+import java.net.URI;
+import java.util.List;
+import java.util.Set;
+
import javax.persistence.AttributeOverride;
import javax.persistence.CascadeType;
import javax.persistence.Column;
@@ -10,8 +14,12 @@
import javax.persistence.Table;
import javax.persistence.Transient;
+import org.cipres.treebase.Constants;
+import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.AbstractPersistedObject;
+import org.cipres.treebase.domain.Annotation;
import org.cipres.treebase.domain.TBPersistable;
+import org.cipres.treebase.domain.admin.Person;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.study.Submission;
import org.hibernate.annotations.BatchSize;
@@ -194,4 +202,35 @@
}
return result;
}
+
+ @Transient
+ public List<Annotation> getAnnotations() {
+ List<Annotation> annotations = super.getAnnotations();
+ if ( null != getNcbiTaxID() ) {
+ StringBuilder urlString = new StringBuilder(TreebaseUtil.getPurlDomain());
+ getPhyloWSPath().getPath(urlString).append("NCBI:").append(getNcbiTaxID());
+ annotations.add(new Annotation(Constants.DCTermsURI, "dc:relation", URI.create(urlString.toString())));
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.ncbi", "NCBI:" + getNcbiTaxID()));
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxon", getTaxonVariant().getTaxon().getId()));
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxonLabel", getId()));
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:title.taxon", getTaxonVariant().getTaxon().getName()));
+ }
+ TaxonVariant tv = getTaxonVariant();
+ if ( null != tv ) {
+ if ( null != tv.getNamebankID() ) {
+ StringBuilder urlString = new StringBuilder(TreebaseUtil.getPurlDomain());
+ getPhyloWSPath().getPath(urlString).append("uBio:").append(tv.getNamebankID());
+ annotations.add(new Annotation(Constants.DCTermsURI, "dc:relation", URI.create(urlString.toString())));
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.ubio", "uBio:" + tv.getNamebankID()));
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxonVariant", tv.getId()));
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:title.taxonVariant", tv.getFullName()));
+ }
+ }
+ return annotations;
+ }
+
+ @Transient
+ public String getLabel() {
+ return getTaxonLabel();
+ }
}
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From: <rv...@us...> - 2010-03-16 16:49:25
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Revision: 600
http://treebase.svn.sourceforge.net/treebase/?rev=600&view=rev
Author: rvos
Date: 2010-03-16 16:49:19 +0000 (Tue, 16 Mar 2010)
Log Message:
-----------
Cleaned up annotations, wrapped inside try {} block to be safe.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2010-03-16 16:48:22 UTC (rev 599)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2010-03-16 16:49:19 UTC (rev 600)
@@ -25,6 +25,8 @@
import org.hibernate.annotations.BatchSize;
import org.hibernate.annotations.Cache;
import org.hibernate.annotations.CacheConcurrencyStrategy;
+import org.hibernate.annotations.Fetch;
+import org.hibernate.annotations.FetchMode;
import org.hibernate.annotations.Index;
/**
@@ -134,6 +136,7 @@
*/
@ManyToOne(fetch = FetchType.LAZY, cascade = {CascadeType.MERGE, CascadeType.PERSIST})
@JoinColumn(name = "TAXONVARIANT_ID", nullable = true)
+ @Fetch(FetchMode.JOIN)
public TaxonVariant getTaxonVariant() {
return mTaxonVariant;
}
@@ -153,6 +156,7 @@
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "STUDY_ID", nullable = true)
@Index(name = "TLABEL_STUDY_IDX")
+ @Fetch(FetchMode.JOIN)
public Study getStudy() {
return mStudy;
}
@@ -206,26 +210,29 @@
@Transient
public List<Annotation> getAnnotations() {
List<Annotation> annotations = super.getAnnotations();
- if ( null != getNcbiTaxID() ) {
- StringBuilder urlString = new StringBuilder(TreebaseUtil.getPurlDomain());
- getPhyloWSPath().getPath(urlString).append("NCBI:").append(getNcbiTaxID());
- annotations.add(new Annotation(Constants.DCTermsURI, "dc:relation", URI.create(urlString.toString())));
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.ncbi", "NCBI:" + getNcbiTaxID()));
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxon", getTaxonVariant().getTaxon().getId()));
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxonLabel", getId()));
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:title.taxon", getTaxonVariant().getTaxon().getName()));
+ try {
+ TaxonVariant tv = getTaxonVariant();
+ if ( null != tv ) {
+ if ( null != tv.getNamebankID() ) {
+ annotations.add(new Annotation(Constants.SKOSURI, "skos:closeMatch", URI.create(Constants.uBioBase+tv.getNamebankID())));
+ String fullName = tv.getFullName();
+ if ( ! getLabel().equals(fullName) ) {
+ annotations.add(new Annotation(Constants.SKOSURI, "skos:altLabel",fullName));
+ }
+ if ( null != getNcbiTaxID() ) {
+ annotations.add(new Annotation(Constants.SKOSURI, "skos:closeMatch", URI.create(String.format(Constants.NCBITaxonomyFormat, getNcbiTaxID()))));
+ String taxonName = tv.getTaxon().getLabel();
+ if ( ! fullName.equals(taxonName) ) {
+ annotations.add(new Annotation(Constants.SKOSURI, "skos:prefLabel",taxonName));
+ }
+
+ }
+ }
+ }
}
- TaxonVariant tv = getTaxonVariant();
- if ( null != tv ) {
- if ( null != tv.getNamebankID() ) {
- StringBuilder urlString = new StringBuilder(TreebaseUtil.getPurlDomain());
- getPhyloWSPath().getPath(urlString).append("uBio:").append(tv.getNamebankID());
- annotations.add(new Annotation(Constants.DCTermsURI, "dc:relation", URI.create(urlString.toString())));
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.ubio", "uBio:" + tv.getNamebankID()));
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxonVariant", tv.getId()));
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:title.taxonVariant", tv.getFullName()));
- }
- }
+ catch ( Exception e) {
+ e.printStackTrace();
+ }
return annotations;
}
@@ -233,4 +240,9 @@
public String getLabel() {
return getTaxonLabel();
}
+
+ @Transient
+ public Study getContext() {
+ return getStudy();
+ }
}
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From: <yo...@us...> - 2010-04-08 19:37:15
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Revision: 680
http://treebase.svn.sourceforge.net/treebase/?rev=680&view=rev
Author: youjun
Date: 2010-04-08 19:37:09 +0000 (Thu, 08 Apr 2010)
Log Message:
-----------
avoid using sub_taxonlabel table
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2010-04-07 20:33:07 UTC (rev 679)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2010-04-08 19:37:09 UTC (rev 680)
@@ -58,7 +58,7 @@
private TaxonVariant mTaxonVariant;
private Study mStudy;
- private Submission mSubmission;
+ //private Submission mSubmission;
private Set<TaxonLabelSet> mTaxonLabelSet;
/**
* Constructor.
@@ -174,29 +174,34 @@
}
/**
- * Return the submission this taxonLabel inhabits
- *
- * @return the submission
- * @author mjd 20080929
- * modified by Youjun
- */
- @ManyToOne(cascade = {CascadeType.MERGE, CascadeType.PERSIST, CascadeType.REFRESH})
- @JoinTable(name = "sub_taxonlabel",
- joinColumns = @JoinColumn(name = "taxonlabel_id"),
- inverseJoinColumns = @JoinColumn(name="submission_id")
+ * Return the submission this taxonLabel inhabits
+ *
+ * @return the submission
+ * @author mjd 20080929
+ */
+ @Transient
+ public Submission getSubmission() {
+ Study s = getStudy();
+ return s == null ? null : s.getSubmission();
+ }
+
+ //@ManyToOne(cascade = {CascadeType.MERGE, CascadeType.PERSIST, CascadeType.REFRESH})
+ //@JoinTable(name = "sub_taxonlabel",
+ // joinColumns = @JoinColumn(name = "taxonlabel_id"),
+ // inverseJoinColumns = @JoinColumn(name="submission_id")
- )
- public Submission getSubmission() {
+ //)
+ //public Submission getSubmission() {
- return mSubmission;
- }
+ // return mSubmission;
+ //}
/**
* Set the Submission field.
*/
- public void setSubmission(Submission pNewSubmission) {
- mSubmission = pNewSubmission;
- }
+ //public void setSubmission(Submission pNewSubmission) {
+ // mSubmission = pNewSubmission;
+ //}
/**
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From: <rv...@us...> - 2010-06-04 11:27:38
|
Revision: 715
http://treebase.svn.sourceforge.net/treebase/?rev=715&view=rev
Author: rvos
Date: 2010-06-04 11:27:31 +0000 (Fri, 04 Jun 2010)
Log Message:
-----------
Adding annotations of tb:identifier.taxon.tb1 and tb:identifier.taxonVariants.tb1, if applicable
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2010-06-04 11:26:33 UTC (rev 714)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2010-06-04 11:27:31 UTC (rev 715)
@@ -265,13 +265,19 @@
}
if ( null != getNcbiTaxID() ) {
annotations.add(new Annotation(Constants.SKOSURI, "skos:closeMatch", URI.create(String.format(Constants.NCBITaxonomyFormat, getNcbiTaxID()))));
- String taxonName = tv.getTaxon().getLabel();
+ Taxon taxon = tv.getTaxon();
+ String taxonName = taxon.getLabel();
if ( ! fullName.equals(taxonName) ) {
annotations.add(new Annotation(Constants.SKOSURI, "skos:prefLabel",taxonName));
}
-
+ if ( null != taxon.getTB1LegacyId() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxon.tb1", taxon.getTB1LegacyId()));
+ }
}
}
+ if ( null != tv.getTB1LegacyId() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxonVariant.tb1", tv.getTB1LegacyId()));
+ }
}
}
catch ( Exception e) {
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From: <rv...@us...> - 2011-03-24 11:28:05
|
Revision: 778
http://treebase.svn.sourceforge.net/treebase/?rev=778&view=rev
Author: rvos
Date: 2011-03-24 11:27:59 +0000 (Thu, 24 Mar 2011)
Log Message:
-----------
Added annotations to TaxonLabel to include TaxonVariant and Taxon ID in results.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2011-03-22 17:45:05 UTC (rev 777)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2011-03-24 11:27:59 UTC (rev 778)
@@ -277,7 +277,12 @@
}
if ( null != tv.getTB1LegacyId() ) {
annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxonVariant.tb1", tv.getTB1LegacyId()));
- }
+ }
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxonVariant", tv.getId()));
+ Taxon taxon = tv.getTaxon();
+ if ( null != taxon ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxon", taxon.getId()));
+ }
}
}
catch ( Exception e) {
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From: <rv...@us...> - 2011-04-19 11:16:09
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Revision: 789
http://treebase.svn.sourceforge.net/treebase/?rev=789&view=rev
Author: rvos
Date: 2011-04-19 11:16:03 +0000 (Tue, 19 Apr 2011)
Log Message:
-----------
Now checking to make sure the "legacy" id and the current one aren't the same thing. Only attaching them if they aren't.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2011-04-19 11:10:53 UTC (rev 788)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2011-04-19 11:16:03 UTC (rev 789)
@@ -270,13 +270,15 @@
if ( ! fullName.equals(taxonName) ) {
annotations.add(new Annotation(Constants.SKOSURI, "skos:prefLabel",taxonName));
}
- if ( null != taxon.getTB1LegacyId() ) {
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxon.tb1", taxon.getTB1LegacyId()));
+ Integer tb1LegacyID = taxon.getTB1LegacyId();
+ if ( null != tb1LegacyID && taxon.getId() != tb1LegacyID.longValue() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxon.tb1", tb1LegacyID.longValue()));
}
}
}
- if ( null != tv.getTB1LegacyId() ) {
- annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxonVariant.tb1", tv.getTB1LegacyId()));
+ Integer tb1TvId = tv.getTB1LegacyId();
+ if ( null != tb1TvId && tv.getId() != tb1TvId.longValue() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxonVariant.tb1", tb1TvId.longValue() ));
}
annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxonVariant", tv.getId()));
Taxon taxon = tv.getTaxon();
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From: <rv...@us...> - 2012-02-01 21:03:30
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Revision: 1030
http://treebase.svn.sourceforge.net/treebase/?rev=1030&view=rev
Author: rvos
Date: 2012-02-01 21:03:24 +0000 (Wed, 01 Feb 2012)
Log Message:
-----------
Removed unused imports, trivial commit.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2012-02-01 21:00:31 UTC (rev 1029)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabel.java 2012-02-01 21:03:24 UTC (rev 1030)
@@ -1,7 +1,6 @@
package org.cipres.treebase.domain.taxon;
import java.net.URI;
-import java.util.Collections;
import java.util.List;
import java.util.Set;
@@ -18,11 +17,9 @@
import javax.persistence.Transient;
import org.cipres.treebase.Constants;
-import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.AbstractPersistedObject;
import org.cipres.treebase.domain.Annotation;
import org.cipres.treebase.domain.TBPersistable;
-import org.cipres.treebase.domain.admin.Person;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.study.Submission;
import org.hibernate.annotations.BatchSize;
@@ -31,7 +28,6 @@
import org.hibernate.annotations.Fetch;
import org.hibernate.annotations.FetchMode;
import org.hibernate.annotations.Index;
-import org.hibernate.annotations.IndexColumn;
/**
* TaxonLabel usually associates with one Taxon. If it does not, it usually means the referred
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