You are viewing a plain text version of this content. The canonical link for it is here.
Posted to dev@ctakes.apache.org by "Masanz, James J." <Ma...@mayo.edu> on 2015/05/06 02:00:14 UTC
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.Chen@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: seanfinan@apache.org [mailto:seanfinan@apache.org]
Sent: Tuesday, May 05, 2015 6:42 PM
To: commits@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" );
RE: build tool suggestion
Posted by "Masanz, James J." <Ma...@mayo.edu>.
I was suggesting it only for the Jenkins build, so that people who might not want it as part of their own builds won't see it. But to catch people who might not have their own warning individually defined or who miss it in the warnings of their own build.
-----Original Message-----
From: Kim Ebert [mailto:kim.ebert@perfectsearchcorp.com]
Sent: Wednesday, May 06, 2015 10:13 AM
To: dev@ctakes.apache.org
Subject: Re: build tool suggestion
Would this only be for the Jenkins build?
I would prefer not to have this as part of the regular Maven build.
On Tue, May 5, 2015 at 6:00 PM, Masanz, James J. <Ma...@mayo.edu>
wrote:
>
> 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.Chen@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: seanfinan@apache.org [mailto:seanfinan@apache.org]
> Sent: Tuesday, May 05, 2015 6:42 PM
> To: commits@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" );
>
>
>
Re: build tool suggestion
Posted by Kim Ebert <ki...@perfectsearchcorp.com>.
Would this only be for the Jenkins build?
I would prefer not to have this as part of the regular Maven build.
On Tue, May 5, 2015 at 6:00 PM, Masanz, James J. <Ma...@mayo.edu>
wrote:
>
> 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.Chen@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: seanfinan@apache.org [mailto:seanfinan@apache.org]
> Sent: Tuesday, May 05, 2015 6:42 PM
> To: commits@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" );
>
>
>
RE: build tool suggestion
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
I understood that. I check warnings before checkin. You can do a search for something like https://wiki.jenkins-ci.org/display/JENKINS/Warnings+Plugin
-----Original Message-----
From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
Sent: Wednesday, May 06, 2015 10:58 AM
To: 'dev@ctakes.apache.org'
Subject: RE: build tool suggestion
Sorry, I wasn't clear, when I said "at build time", I meant the Jenkins automated build.
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@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 -- https://urldefense.proofpoint.com/v2/url?u=http-3A__en.wikipedia.org_wiki_FindBugs&d=BQIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=lQlT1hCegc_WtmY10BMmAxiwIIHNxqohrwW7CfGCFq8&s=OQDh6ra47IQjNVh7WZteWKCf_xeSae36jIo_qcjxfS8&e=
There might be a configurable maven plugin.
It is a process ...
-----Original Message-----
From: Masanz, James J. [mailto:Masanz.James@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.Chen@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: seanfinan@apache.org [mailto:seanfinan@apache.org]
Sent: Tuesday, May 05, 2015 6:42 PM
To: commits@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" );
Re: build tool suggestion
Posted by Britt Fitch <br...@wiredinformatics.com>.
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. <Ma...@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.Finan@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.James@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.Chen@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: seanfinan@apache.org [mailto:seanfinan@apache.org]
> Sent: Tuesday, May 05, 2015 6:42 PM
> To: commits@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" );
>
>
RE: build tool suggestion
Posted by "Masanz, James J." <Ma...@mayo.edu>.
Sorry, I wasn't clear, when I said "at build time", I meant the Jenkins automated build.
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@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.James@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.Chen@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: seanfinan@apache.org [mailto:seanfinan@apache.org]
Sent: Tuesday, May 05, 2015 6:42 PM
To: commits@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" );
RE: build tool suggestion
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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.James@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.Chen@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: seanfinan@apache.org [mailto:seanfinan@apache.org]
Sent: Tuesday, May 05, 2015 6:42 PM
To: commits@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" );