There is a Sonar plugin for Jenkins that's pretty rad. Sent from my iPhone
> On May 6, 2015, at 10:57 AM, Masanz, James J. <masanz.ja...@mayo.edu> wrote: > > > Sorry, I wasn't clear, when I said "at build time", I meant the Jenkins > automated build. > > > -----Original Message----- > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > Sent: Wednesday, May 06, 2015 9:52 AM > To: dev@ctakes.apache.org > Subject: RE: build tool suggestion > > Your IDE should have settings that allow custom warnings. Also check out > findbugs -- http://en.wikipedia.org/wiki/FindBugs > > There might be a configurable maven plugin. > > It is a process ... > > -----Original Message----- > From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] > Sent: Tuesday, May 05, 2015 8:01 PM > To: dev@ctakes.apache.org > Subject: build tool suggestion > > > Do you know offhand, would it be easy to have something run at build time > that flags uses of FileReader? > > Related - do we have anything at build time that produces warnings that are > looked at? When I check in a change, I just check whether the next build is > successful or not. I don't look for warnings other than what I see when I > try a compile of my own on my own system. Ideally I think it would be good > to have the use of FileReader cause a meaningful warning. But if there's no > relatively easy way to do that, might we consider having it cause a build > failure? I think the benefits would outweigh the drawbacks. > > -- James > > ________________________________________ > From: Chen, Pei [pei.c...@childrens.harvard.edu] > Sent: Tuesday, May 05, 2015 5:55 PM > To: dev@ctakes.apache.org > Subject: RE: svn commit: r1677903 - in > /ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2: > concept/BsvConceptFactory.java dictionary/BsvRareWordDictionary.java > util/JdbcConnectionFactory.java > > Can we use InputStreamReader instead of FileReader? > That way the resource can also be read from within a jar (potentially from > maven central, etc.) and doesn't have to be fixed to a physical file... > > i.e. > Instead of new BufferedReader(new FileReader(path)) new BufferedReader(new > InputStreamReader(FileLocator.getAsStream(path))) > > --Pei > > -----Original Message----- > From: seanfi...@apache.org [mailto:seanfi...@apache.org] > Sent: Tuesday, May 05, 2015 6:42 PM > To: comm...@ctakes.apache.org > Subject: svn commit: r1677903 - in > /ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2: > concept/BsvConceptFactory.java dictionary/BsvRareWordDictionary.java > util/JdbcConnectionFactory.java > > Author: seanfinan > Date: Tue May 5 22:41:26 2015 > New Revision: 1677903 > > URL: > https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_r1677903&d=BQICaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIag&s=wuwFl1DxU-yGWdGewROupvowHfYFay_u5LYKJUJF2VA&e= > Log: > Use FileLocator to find BSV dictionaries > > Modified: > > ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java > > ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java > > ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java > > Modified: > ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java > URL: > https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Ddictionary-2Dlookup-2Dfast_src_main_java_org_apache_ctakes_dictionary_lookup2_concept_BsvConceptFactory.java-3Frev-3D1677903-26r1-3D1677902-26r2-3D1677903-26view-3Ddiff&d=BQICaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIag&s=N_IOanbEYnXUTZ4ZO3vIjOeYun186kZGjXPKWp-Wi7k&e= > ============================================================================== > --- > ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/concept/BsvConceptFactory.java > (original) > +++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ > +++ ctakes/dictionary/lookup2/concept/BsvConceptFactory.java Tue May 5 > +++ 22:41:26 2015 > @@ -1,5 +1,6 @@ > package org.apache.ctakes.dictionary.lookup2.concept; > > +import org.apache.ctakes.core.resource.FileLocator; > import org.apache.ctakes.dictionary.lookup2.util.CuiCodeUtil; > import org.apache.ctakes.dictionary.lookup2.util.LookupUtil; > import org.apache.ctakes.dictionary.lookup2.util.TuiCodeUtil; > @@ -34,11 +35,12 @@ final public class BsvConceptFactory imp > } > > public BsvConceptFactory( final String name, final String bsvFilePath ) { > - this( name, new File( bsvFilePath ) ); > - } > - > - public BsvConceptFactory( final String name, final File bsvFile ) { > - final Collection<CuiTuiTerm> cuiTuiTerms = parseBsvFile( bsvFile ); > +// this( name, new File( bsvFilePath ) ); > +// } > +// > +// public BsvConceptFactory( final String name, final File bsvFile ) { > +// final Collection<CuiTuiTerm> cuiTuiTerms = parseBsvFile( bsvFile ); > + final Collection<CuiTuiTerm> cuiTuiTerms = parseBsvFile( > +bsvFilePath ); > final Map<Long, Concept> conceptMap = new HashMap<>( cuiTuiTerms.size() > ); > for ( CuiTuiTerm cuiTuiTerm : cuiTuiTerms ) { > final CollectionMap<ConceptCode, String, ? extends > Collection<String>> codes @@ -90,11 +92,21 @@ final public class > BsvConceptFactory imp > * CUI|TUI|Text|PreferredTerm > * </p> > * If the TUI column is omitted then the entityId for the dictionary is > used as the TUI > + * <p/> > + * // * @param bsvFile file containing term rows and bsv columns > * > - * @param bsvFile file containing term rows and bsv columns > + * @param bsvFilePath file containing term rows and bsv columns > * @return collection of all valid terms read from the bsv file > */ > - static private Collection<CuiTuiTerm> parseBsvFile( final File bsvFile ) { > +// static private Collection<CuiTuiTerm> parseBsvFile( final File bsvFile > ) { > + static private Collection<CuiTuiTerm> parseBsvFile( final String > bsvFilePath ) { > + File bsvFile = null; > + try { > + bsvFile = FileLocator.locateFile( bsvFilePath ); > + } catch ( IOException ioE ) { > + ioE.getMessage(); > + return Collections.emptyList(); > + } > final Collection<CuiTuiTerm> cuiTuiTerms = new ArrayList<>(); > try ( final BufferedReader reader = new BufferedReader( new FileReader( > bsvFile ) ) ) { > String line = reader.readLine(); > > Modified: > ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java > URL: > https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Ddictionary-2Dlookup-2Dfast_src_main_java_org_apache_ctakes_dictionary_lookup2_dictionary_BsvRareWordDictionary.java-3Frev-3D1677903-26r1-3D1677902-26r2-3D1677903-26view-3Ddiff&d=BQICaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIag&s=2mhfaak7geaJl8hCTk1LX9lWoSX7h9cRaSwYmnf6w0k&e= > ============================================================================== > --- > ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java > (original) > +++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ > +++ ctakes/dictionary/lookup2/dictionary/BsvRareWordDictionary.java Tue > +++ May 5 22:41:26 2015 > @@ -18,6 +18,7 @@ > */ > package org.apache.ctakes.dictionary.lookup2.dictionary; > > +import org.apache.ctakes.core.resource.FileLocator; > import org.apache.ctakes.dictionary.lookup2.term.RareWordTerm; > import org.apache.ctakes.dictionary.lookup2.util.FastLookupToken; > import org.apache.ctakes.dictionary.lookup2.util.LookupUtil; > @@ -31,6 +32,7 @@ import java.io.FileReader; import java.io.IOException; > import java.util.ArrayList; import java.util.Collection; > +import java.util.Collections; > import java.util.Properties; > > import static > org.apache.ctakes.dictionary.lookup2.dictionary.RareWordTermMapCreator.CuiTerm; > @@ -59,11 +61,12 @@ final public class BsvRareWordDictionary > > > public BsvRareWordDictionary( final String name, final String bsvFilePath > ) { > - this( name, new File( bsvFilePath ) ); > - } > - > - public BsvRareWordDictionary( final String name, final File bsvFile ) { > - final Collection<CuiTerm> cuiTerms = parseBsvFile( bsvFile ); > +// this( name, new File( bsvFilePath ) ); > +// } > +// > +// public BsvRareWordDictionary( final String name, final File bsvFile ) { > +// final Collection<CuiTerm> cuiTerms = parseBsvFile( bsvFile ); > + final Collection<CuiTerm> cuiTerms = parseBsvFile( bsvFilePath ); > final CollectionMap<String, RareWordTerm, ? extends > Collection<RareWordTerm>> rareWordTermMap > = RareWordTermMapCreator.createRareWordTermMap( cuiTerms ); > _delegateDictionary = new MemRareWordDictionary( name, rareWordTermMap > ); @@ -109,11 +112,21 @@ final public class BsvRareWordDictionary > * CUI|TUI|Text|PreferredTerm > * </p> > * If the TUI column is omitted then the entityId for the dictionary is > used as the TUI > + * <p/> > + * // * @param bsvFile file containing term rows and bsv columns > * > - * @param bsvFile file containing term rows and bsv columns > + * @param bsvFilePath path to file containing term rows and bsv > + columns > * @return collection of all valid terms read from the bsv file > */ > - static private Collection<CuiTerm> parseBsvFile( final File bsvFile ) { > +// static private Collection<CuiTerm> parseBsvFile( final File bsvFile ) { > + static private Collection<CuiTerm> parseBsvFile( final String bsvFilePath > ) { > + File bsvFile = null; > + try { > + bsvFile = FileLocator.locateFile( bsvFilePath ); > + } catch ( IOException ioE ) { > + ioE.getMessage(); > + return Collections.emptyList(); > + } > final Collection<CuiTerm> cuiTerms = new ArrayList<>(); > try ( final BufferedReader reader = new BufferedReader( new FileReader( > bsvFile ) ) ) { > String line = reader.readLine(); > > Modified: > ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java > URL: > https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_viewvc_ctakes_trunk_ctakes-2Ddictionary-2Dlookup-2Dfast_src_main_java_org_apache_ctakes_dictionary_lookup2_util_JdbcConnectionFactory.java-3Frev-3D1677903-26r1-3D1677902-26r2-3D1677903-26view-3Ddiff&d=BQICaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=9sLhiql1kiKYdaC8Nx3dTASt89nXQA3uy4kwesnHIag&s=Zojydr1XQ2pr1l6pOrj2iBFd-7iR3__MBP6GNOBDIlQ&e= > ============================================================================== > --- > ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java > (original) > +++ ctakes/trunk/ctakes-dictionary-lookup-fast/src/main/java/org/apache/ > +++ ctakes/dictionary/lookup2/util/JdbcConnectionFactory.java Tue May 5 > +++ 22:41:26 2015 > @@ -21,8 +21,6 @@ import java.util.*; > public enum JdbcConnectionFactory { > INSTANCE; > > - static private final String CTAKES_HOME = "CTAKES_HOME"; > - > static final private Logger LOGGER = Logger.getLogger( > "JdbcConnectionFactory" ); > static final private Logger DOT_LOGGER = Logger.getLogger( > "ProgressAppender" ); > static final private Logger EOL_LOGGER = Logger.getLogger( "ProgressDone" > ); > >
