[
https://issues.apache.org/jira/browse/CTAKES-484?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Alex Zbarcea updated CTAKES-484:
--------------------------------
Description:
References to resources outside of project:
{code:java}
$ grep --include "*.java" -nRI "C:/"
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java:231:
String keywordsFile = "C:/cTAKES-1.0.5/smoking
status/resources/ss/data/PCS/keywords_PCS_NHGRI.txt";
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java:232:
String stopwordsFile = "C:/cTAKES-1.0.5/smoking
status/resources/ss/data/PCS/stopwords_PCS.txt";
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java:233:
String dataFile = "C:/Temp/SentenceLevelSmokingStatus_PCS.txt";
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java:234:
String libsvmDataFile = "C:/Temp/libsvm_data.txt";
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java:183:
//File tmpFile = new File(textPath); // Note this does not work with
something like "file:/C:/usr/data/MiPACQ/1/xml/0054074073-0.xml"
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java:33:
// Note that on Windows, by default, /sharp-home/assertion/ the same as
C:/sharp-home/assertion/
ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForExampleDrugs.java:53:
File indexDir = new
File("C:/general_workspace/ctakes-dictionary-lookup/resources/lookup/drug_index");//C:/temp/lucene/"
+ "drug-index";
ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForSnomedLikeSample.java:65:
File indexDir = new File("C:/temp/lucene/" + "snomed-like_sample");
// lookup by first_word, results contain UMLS CUIs
ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForSnomedLikeSample.java:66:
File indexDir2 = new File("C:/temp/lucene/" +
"snomed-like_codes_sample"); // for getting snomed codes for a CUI
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java:181:
"C:/Program Files/apache-uima"));
{code}
{code:java}
$ grep --include "*.java" -nRI "\"/home" | sed "s#.*\"\/#\/#g" | sed
"s#\".*##g" | sort -u
/home/dima/i2b2/wiki-index/index_nometa
/home/dima/sharp/cloud/mipacq/xml/all/
/home/dima/sharp/cloud/mipacq/xml/dev/
/home/dima/sharp/cloud/mipacq/xml/test/
/home/dima/sharp/cloud/mipacq/xml/train/
/home/dima/sharp/cloud/share/xml/all/
/home/dima/sharp/cloud/share/xml/dev/
/home/dima/sharp/cloud/share/xml/test/
/home/dima/sharp/cloud/share/xml/train/
/home/dima/sharp/cloud/sharp/xml/all/
/home/dima/sharp/cloud/sharp/xml/dev/
/home/dima/sharp/cloud/sharp/xml/test/
/home/dima/sharp/cloud/sharp/xml/train/
/home/parent/child/someFile
/home/parent/child/someFile.jpg
/home/parent/child/someFile.txt.xmi
/home/subdir/someFile.bsv
/home/subdir/someFile.txt
/home/tmill/Documents/wiki/index_med_5k
/home/tmill/Documents/wiki/index_nometa
/home/tmill/Projects/coref/training/
/home/tmill/Projects/parser/reranker/matrix.txt
/home/tmill/mnt/prv/data/index_vectors_notext
/home/tmill/mnt/rc-pub/odie/gold-pairs/
{code}
was:
References to resources outside of project:
{code:java}
$ grep --include "*.java" -nRI "C:/"
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java:231:
String keywordsFile = "C:/cTAKES-1.0.5/smoking
status/resources/ss/data/PCS/keywords_PCS_NHGRI.txt";
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java:232:
String stopwordsFile = "C:/cTAKES-1.0.5/smoking
status/resources/ss/data/PCS/stopwords_PCS.txt";
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java:233:
String dataFile = "C:/Temp/SentenceLevelSmokingStatus_PCS.txt";
ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java:234:
String libsvmDataFile = "C:/Temp/libsvm_data.txt";
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java:183:
//File tmpFile = new File(textPath); // Note this does not work with
something like "file:/C:/usr/data/MiPACQ/1/xml/0054074073-0.xml"
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java:33:
// Note that on Windows, by default, /sharp-home/assertion/ the same as
C:/sharp-home/assertion/
ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForExampleDrugs.java:53:
File indexDir = new
File("C:/general_workspace/ctakes-dictionary-lookup/resources/lookup/drug_index");//C:/temp/lucene/"
+ "drug-index";
ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForSnomedLikeSample.java:65:
File indexDir = new File("C:/temp/lucene/" + "snomed-like_sample");
// lookup by first_word, results contain UMLS CUIs
ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForSnomedLikeSample.java:66:
File indexDir2 = new File("C:/temp/lucene/" +
"snomed-like_codes_sample"); // for getting snomed codes for a CUI
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java:181:
"C:/Program Files/apache-uima"));
{code}
> Unused or out-of-project references
> -----------------------------------
>
> Key: CTAKES-484
> URL: https://issues.apache.org/jira/browse/CTAKES-484
> Project: cTAKES
> Issue Type: Bug
> Reporter: Alex Zbarcea
> Assignee: Alex Zbarcea
>
> References to resources outside of project:
> {code:java}
> $ grep --include "*.java" -nRI "C:/"
> ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java:231:
> String keywordsFile = "C:/cTAKES-1.0.5/smoking
> status/resources/ss/data/PCS/keywords_PCS_NHGRI.txt";
> ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java:232:
> String stopwordsFile = "C:/cTAKES-1.0.5/smoking
> status/resources/ss/data/PCS/stopwords_PCS.txt";
> ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java:233:
> String dataFile = "C:/Temp/SentenceLevelSmokingStatus_PCS.txt";
> ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/MLutil/GenerateTrainingData.java:234:
> String libsvmDataFile = "C:/Temp/libsvm_data.txt";
> ctakes-assertion/src/main/java/org/apache/ctakes/assertion/cr/MiPACQKnowtatorXMLReader.java:183:
> //File tmpFile = new File(textPath); // Note this does not work
> with something like "file:/C:/usr/data/MiPACQ/1/xml/0054074073-0.xml"
> ctakes-assertion/src/main/java/org/apache/ctakes/assertion/util/AssertionConst.java:33:
> // Note that on Windows, by default, /sharp-home/assertion/ the same as
> C:/sharp-home/assertion/
> ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForExampleDrugs.java:53:
> File indexDir = new
> File("C:/general_workspace/ctakes-dictionary-lookup/resources/lookup/drug_index");//C:/temp/lucene/"
> + "drug-index";
> ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForSnomedLikeSample.java:65:
> File indexDir = new File("C:/temp/lucene/" +
> "snomed-like_sample"); // lookup by first_word, results contain UMLS CUIs
> ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForSnomedLikeSample.java:66:
> File indexDir2 = new File("C:/temp/lucene/" +
> "snomed-like_codes_sample"); // for getting snomed codes for a CUI
> ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java:181:
> "C:/Program Files/apache-uima"));
> {code}
> {code:java}
> $ grep --include "*.java" -nRI "\"/home" | sed "s#.*\"\/#\/#g" | sed
> "s#\".*##g" | sort -u
> /home/dima/i2b2/wiki-index/index_nometa
> /home/dima/sharp/cloud/mipacq/xml/all/
> /home/dima/sharp/cloud/mipacq/xml/dev/
> /home/dima/sharp/cloud/mipacq/xml/test/
> /home/dima/sharp/cloud/mipacq/xml/train/
> /home/dima/sharp/cloud/share/xml/all/
> /home/dima/sharp/cloud/share/xml/dev/
> /home/dima/sharp/cloud/share/xml/test/
> /home/dima/sharp/cloud/share/xml/train/
> /home/dima/sharp/cloud/sharp/xml/all/
> /home/dima/sharp/cloud/sharp/xml/dev/
> /home/dima/sharp/cloud/sharp/xml/test/
> /home/dima/sharp/cloud/sharp/xml/train/
> /home/parent/child/someFile
> /home/parent/child/someFile.jpg
> /home/parent/child/someFile.txt.xmi
> /home/subdir/someFile.bsv
> /home/subdir/someFile.txt
> /home/tmill/Documents/wiki/index_med_5k
> /home/tmill/Documents/wiki/index_nometa
> /home/tmill/Projects/coref/training/
> /home/tmill/Projects/parser/reranker/matrix.txt
> /home/tmill/mnt/prv/data/index_vectors_notext
> /home/tmill/mnt/rc-pub/odie/gold-pairs/
> {code}
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