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[Treebase-guts] SF.net SVN: treebase:[518] trunk/treebase-core/src/main
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From: <vga...@us...> - 2010-02-25 15:32:39
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Revision: 518
http://treebase.svn.sourceforge.net/treebase/?rev=518&view=rev
Author: vgapeyev
Date: 2010-02-25 15:32:32 +0000 (Thu, 25 Feb 2010)
Log Message:
-----------
Fixed run-time errors caused by improper transaction handling.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporterInterface.java
trunk/treebase-core/src/main/resources/applicationContext-standalone.xml
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporter.java 2010-02-24 14:53:46 UTC (rev 517)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporter.java 2010-02-25 15:32:32 UTC (rev 518)
@@ -112,8 +112,8 @@
person.setFirstName(nameParts[1]);
person.setMiddleName("");
person.setEmailAddressString("");
- personHome.save(person);
- personHome.store(person);
+ //personHome.save(person); //-- VG 2010-02-24 These were messing up parent transactions by
+ //personHome.store(person); //-- VG saving too early.
}
warn(person.getLastName());
authors.add(person);
@@ -263,18 +263,136 @@
in = new BufferedReader(
new InputStreamReader(new FileInputStream(inFileName), "UTF8"));
- me.processCitationFile(in, testmode);
+ //me.processCitationFile(in, testmode); //VG-2010-02-25 now deprecated
+ me.processAllCitations(in, testmode);
}
catch ( Exception e ) {
e.printStackTrace();
}
}
+ /** Go through the open citation file and transactionally save each successfully processed citation.
+ * Processing stops on error, with prior transactions committed.
+ * Derived from the deprecated processCitationsFile by factoring out most of the while-loop code
+ * into its own method, so that Spring can make it transactional.
+ */
+ public void processAllCitations(BufferedReader in, boolean testMode) throws NumberFormatException, IOException {
+ String line;
+ while ( ( line = in.readLine()) != null ) {
+ String[] fields = line.split("\t");
+ processOneCitation(fields, testMode);
+ }
+ in.close();
+ }
+
+ /** Process one citation from the file and save the result transactionally.
+ * This method is declared PROPAGATION_REQUIRES_NEW in the bean descriptor.
+ */
+ public void processOneCitation(String[] fields, boolean testMode) throws NumberFormatException, IOException {
+ if ( fields[0].startsWith("*") ) {
+ warn("Line is commented out, skipping");
+ return;
+ }
+ String tb1StudyId = fields[18];
+ Study study = findStudy(tb1StudyId);
+ if ( study == null ) {
+ warn("No such study (TB1 accession): " + tb1StudyId);
+ return;
+ }
+ Citation citationStub = study.getCitation();
+ Citation citation = null;
+ if ( citationStub != null ) {
+ warn("Study "+tb1StudyId+" already associated with a citation "+citationStub.getId());
+// In general, citation stubs already exist for each study. However, these
+// stubs are all of type ArticleCitation, which means that, in the case of
+// BookCitations (for example) we'll get a class cast exception when we try
+// to cast the citation to a book in order to set the editors.
+ //getCitationService().deleteCitation(citationStub);
+ //citation = createCitation(fields[0]);
+ citation = citationStub;
+ }
+ else {
+ warn("No citation stub association with study (TB1 accession) " + tb1StudyId);
+ citation = createCitation(fields[0]);
+ }
+ if ( citation == null ) {
+ warn("No citation was instantiated, skipping this record (TB1 accession) "+tb1StudyId);
+ return;
+ }
+ for ( int i = 0; i < fields.length; i++ ) {
+ if ( ! TreebaseUtil.isEmpty(fields[i]) ) {
+ switch(i) {
+ case 0: citation.setCitationType(fields[i]); break;
+ case 1: setAuthors(citation,fields[i],personHome,false); break;
+ case 2: citation.setPublishYear(Integer.parseInt(fields[i])); break;
+ case 3: if ( citation instanceof BookCitation ) {
+ ((BookCitation)citation).setBookTitle(fields[i]);
+ citation.setTitle(fields[i]);
+ } else {
+ citation.setTitle(fields[i]);
+ } break;
+ case 4: setAuthors(citation,fields[i],personHome,true); break;
+ case 5: if ( citation instanceof ArticleCitation ) {
+ ((ArticleCitation)citation).setJournal(fields[i]);
+ warn("Setting journal name "+fields[i]);
+ } else {
+ warn("Setting book title "+fields[i]);
+ ((BookCitation)citation).setBookTitle(fields[i]);
+ } break;
+ case 6: if ( citation instanceof BookCitation ) {
+ ((BookCitation)citation).setCity(fields[i]);
+ } else {
+ warn("Record has an entry for city, yet it's not a book (TB1 accession) "+tb1StudyId);
+ } break;
+ case 7: if ( citation instanceof BookCitation ) {
+ ((BookCitation)citation).setPublisher(fields[i]);
+ } else {
+ warn("Record has an entry for publisher, yet it's not a book (TB1 accession) "+tb1StudyId);
+ } break;
+ case 8: if ( citation instanceof ArticleCitation ) {
+ ((ArticleCitation)citation).setVolume(fields[i]);
+ } else {
+ warn("Record has an entry for volume, yet it's not an article (TB1 accession) "+tb1StudyId);
+ } break;
+ case 10: if ( citation instanceof ArticleCitation ) {
+ ((ArticleCitation)citation).setIssue(fields[i]);
+ } else {
+ warn("Record has an entry for issue, yet it's not an article (TB1 accession)"+tb1StudyId);
+ } break;
+ case 11: citation.setPages(fields[i]); break;
+ case 15: if ( fields[i].equals("in press") ) {
+ citation.setCitationStatusDescription(CitationStatus.INPRESS);
+ }
+ case 16: citation.setKeywords(fields[i]); break;
+ case 17: citation.setAbstract(checkAbstractLength(fields[i])); break;
+ case 18: citation.setStudy(study); break;
+ case 19: citation.setURL(fields[i]); break;
+ case 20: citation.setDoi(fields[i]); break;
+ default: warn("Empty field expected, found: " + fields[i] + " for line: " + /*was: line */fields.toString()); break;
+ }
+ }
+ }
+ warn("Storing citation "+citation.getId());
+ warn(citation.getAuthorsCitationStyleWithoutHtml());
+ if ( ! testMode ) {
+ study.setCitation(citation);
+ getStudyService().update(study);
+ Long id = study.getCitation().getId();
+ warn("Stored citation at ID " + id);
+ }
+ else {
+ warn("Test run, not saving");
+ }
+ }
+
/**
- *
- *
- * @see org.cipres.treebase.util.CitationDataImporterInterface#processCitationFile(java.io.BufferedReader, boolean)
+ * Deprecated, use processAllCitations() instead.
+ * The programmatic transaction handling via the commit(); beginTransaction(); pair at the end of this method
+ * was leaving an open transaction, leading to an exception. Also, the "-test" command line switch had no effect.
+ * Instead, fine-grained transactions (for each citation) are now achieved by embracing Spring's declarative
+ * transactions: transactions are at boundaries of designated methods. VG-2010-02-25
*/
+ @Deprecated
public void processCitationFile(BufferedReader in, boolean testMode) throws NumberFormatException, IOException {
String line;
Long maxId = new Long(0);
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporterInterface.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporterInterface.java 2010-02-24 14:53:46 UTC (rev 517)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/util/CitationDataImporterInterface.java 2010-02-25 15:32:32 UTC (rev 518)
@@ -24,4 +24,7 @@
public void setCitationHome(CitationHome citationHome);
public void processCitationFile(BufferedReader in, boolean testMode) throws NumberFormatException, IOException;
+ public void processAllCitations(BufferedReader in, boolean testMode) throws NumberFormatException, IOException;
+ public void processOneCitation(String[] fields, boolean testMode) throws NumberFormatException, IOException;
+
}
Modified: trunk/treebase-core/src/main/resources/applicationContext-standalone.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-standalone.xml 2010-02-24 14:53:46 UTC (rev 517)
+++ trunk/treebase-core/src/main/resources/applicationContext-standalone.xml 2010-02-25 15:32:32 UTC (rev 518)
@@ -222,6 +222,8 @@
<property name="transactionAttributes">
<props>
<prop key="processCitationFile">PROPAGATION_REQUIRED</prop>
+ <prop key="processOneCitation">PROPAGATION_REQUIRES_NEW</prop>
+ <prop key="processAllCitations">PROPAGATION_SUPPORTS</prop>
</props>
</property>
</bean>
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