diff --git a/.classpath b/.classpath deleted file mode 100644 index 2c7e14fd..00000000 --- a/.classpath +++ /dev/null @@ -1,26 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/.gitignore b/.gitignore index 76ef4f89..46ff8e91 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,6 @@ dist/ /Error1.txt /ScanReport.xlsx /.classpath +target/ +*.iml +.idea/ diff --git a/.project b/.project index ebaa3b16..1f855c0f 100644 --- a/.project +++ b/.project @@ -1,17 +1,17 @@ - WhiteRabbit + leporidae - org.eclipse.jdt.core.javabuilder + org.eclipse.m2e.core.maven2Builder - org.eclipse.jdt.core.javanature + org.eclipse.m2e.core.maven2Nature diff --git a/.settings/org.eclipse.m2e.core.prefs b/.settings/org.eclipse.m2e.core.prefs new file mode 100644 index 00000000..f897a7f1 --- /dev/null +++ b/.settings/org.eclipse.m2e.core.prefs @@ -0,0 +1,4 @@ +activeProfiles= +eclipse.preferences.version=1 +resolveWorkspaceProjects=true +version=1 diff --git a/README.md b/README.md index defc9b98..51c779f5 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -![alt text](https://github.com/OHDSI/WhiteRabbit/blob/master/src/org/ohdsi/whiteRabbit/WhiteRabbit64.png) WhiteRabbit +![alt text](https://github.com/OHDSI/WhiteRabbit/blob/master/whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit64.png) WhiteRabbit =========== Introduction @@ -35,26 +35,28 @@ White Rabbit and Rabbit in a Hat are pure Java applications. Both applications u System Requirements ============ -Requires Java 1.7 or higher, and read access to the database to be scanned. Java can be downloaded from +Requires Java 1.8 or higher, and read access to the database to be scanned. Java can be downloaded from http://www.java.com. Dependencies ============ - * There are no dependencies. +For the distributable packages, the only requirement is Java 8. For building the package, also Maven is needed. Getting Started =============== WhiteRabbit -1. Under the [Releases](https://github.com/OHDSI/WhiteRabbit/releases) tab, download WhiteRabbit*.zip +1. Under the [Releases](https://github.com/OHDSI/WhiteRabbit/releases) tab, download `WhiteRabbit*.zip` 2. Unzip the download -3. Double-click on WhiteRabbit.jar to start White Rabbit. +3. Double-click on `bin/whiteRabbit.bat` on Windows to start White Rabbit, and `bin/whiteRabbit` on macOS and Linux. (See the [Wiki](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:whiterabbit#running_from_the_command_line) for details on how to run from the command prompt instead) Rabbit-In-A-Hat -1. Using the files downloaded for WhiteRabbit, double-click on RabbitInAHat.jar to start Rabbit-In-A-Hat. +1. Using the files downloaded for WhiteRabbit, double-click on `bin/rabbitInAHat.bat` to start Rabbit-In-A-Hat on Windows, and `bin/rabbitInAHat` on macOS and Linux. + +Note: on releases earlier than version 0.8.0, open the respective `WhiteRabbit.jar` or `RabbitInAHat.jar` files instead. Getting Involved ============= @@ -68,7 +70,9 @@ WhiteRabbit is licensed under Apache License 2.0 Development =========== -White Rabbit and Rabbit in a Hat are being developed in Eclipse. Contributions are welcome. +White Rabbit and Rabbit in a Hat are structured as a Maven package and can be developed in Eclipse. Contributions are welcome. + +To generate the files ready for distribution, run `mvn install`. ### Development status diff --git a/build.xml b/build.xml deleted file mode 100644 index 733c19e9..00000000 --- a/build.xml +++ /dev/null @@ -1,66 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/lib/RedshiftJDBC4-1.1.10.1010.jar b/lib/RedshiftJDBC4-1.1.10.1010.jar deleted file mode 100644 index 52b1cf81..00000000 Binary files a/lib/RedshiftJDBC4-1.1.10.1010.jar and /dev/null differ diff --git a/lib/terajdbc4.jar b/lib/com/teradata/jdbc/terajdbc4/16.0.0.32/terajdbc4-16.0.0.32.jar old mode 100755 new mode 100644 similarity index 100% rename from lib/terajdbc4.jar rename to lib/com/teradata/jdbc/terajdbc4/16.0.0.32/terajdbc4-16.0.0.32.jar diff --git a/lib/com/teradata/jdbc/terajdbc4/16.0.0.32/terajdbc4-16.0.0.32.pom b/lib/com/teradata/jdbc/terajdbc4/16.0.0.32/terajdbc4-16.0.0.32.pom new file mode 100644 index 00000000..19b6b4a2 --- /dev/null +++ b/lib/com/teradata/jdbc/terajdbc4/16.0.0.32/terajdbc4-16.0.0.32.pom @@ -0,0 +1,9 @@ + + + 4.0.0 + com.teradata.jdbc + terajdbc4 + 16.0.0.32 + POM was created from install:install-file + diff --git a/lib/com/teradata/jdbc/terajdbc4/maven-metadata-local.xml b/lib/com/teradata/jdbc/terajdbc4/maven-metadata-local.xml new file mode 100644 index 00000000..61416a7e --- /dev/null +++ b/lib/com/teradata/jdbc/terajdbc4/maven-metadata-local.xml @@ -0,0 +1,12 @@ + + + com.teradata.jdbc + terajdbc4 + + 16.0.0.32 + + 16.0.0.32 + + 20190507142405 + + diff --git a/lib/tdgssconfig.jar b/lib/com/teradata/tdgss/tdgssconfig/16.0.0.0/tdgssconfig-16.0.0.0.jar old mode 100755 new mode 100644 similarity index 100% rename from lib/tdgssconfig.jar rename to lib/com/teradata/tdgss/tdgssconfig/16.0.0.0/tdgssconfig-16.0.0.0.jar diff --git a/lib/com/teradata/tdgss/tdgssconfig/16.0.0.0/tdgssconfig-16.0.0.0.pom b/lib/com/teradata/tdgss/tdgssconfig/16.0.0.0/tdgssconfig-16.0.0.0.pom new file mode 100644 index 00000000..50cfbf09 --- /dev/null +++ b/lib/com/teradata/tdgss/tdgssconfig/16.0.0.0/tdgssconfig-16.0.0.0.pom @@ -0,0 +1,9 @@ + + + 4.0.0 + com.teradata.tdgss + tdgssconfig + 16.0.0.0 + POM was created from install:install-file + diff --git a/lib/com/teradata/tdgss/tdgssconfig/maven-metadata-local.xml b/lib/com/teradata/tdgss/tdgssconfig/maven-metadata-local.xml new file mode 100644 index 00000000..279b440c --- /dev/null +++ b/lib/com/teradata/tdgss/tdgssconfig/maven-metadata-local.xml @@ -0,0 +1,12 @@ + + + com.teradata.tdgss + tdgssconfig + + 16.0.0.0 + + 16.0.0.0 + + 20190507142309 + + diff --git a/lib/commons-csv-1.1.jar b/lib/commons-csv-1.1.jar deleted file mode 100644 index 89bd547f..00000000 Binary files a/lib/commons-csv-1.1.jar and /dev/null differ diff --git a/lib/commons-lang-2.0.jar b/lib/commons-lang-2.0.jar deleted file mode 100644 index c8a28701..00000000 Binary files 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a/lib/poi-ooxml-schemas-3.9-20121203.jar and /dev/null differ diff --git a/lib/postgresql-9.4-1201.jdbc4.jar b/lib/postgresql-9.4-1201.jdbc4.jar deleted file mode 100644 index 0cd5ce20..00000000 Binary files a/lib/postgresql-9.4-1201.jdbc4.jar and /dev/null differ diff --git a/lib/postgresql-9.4-1201.jdbc41.jar b/lib/postgresql-9.4-1201.jdbc41.jar deleted file mode 100644 index a3f19593..00000000 Binary files a/lib/postgresql-9.4-1201.jdbc41.jar and /dev/null differ diff --git a/lib/sqljdbc4.jar b/lib/sqljdbc4.jar deleted file mode 100644 index d6b7f6da..00000000 Binary files a/lib/sqljdbc4.jar and /dev/null differ diff --git a/lib/stax-api-1.0.1.jar b/lib/stax-api-1.0.1.jar deleted file mode 100644 index d9a16651..00000000 Binary files a/lib/stax-api-1.0.1.jar and /dev/null differ diff --git a/lib/ucanaccess-3.0.3.1.jar b/lib/ucanaccess-3.0.3.1.jar deleted file mode 100644 index 3d7ddd51..00000000 Binary files a/lib/ucanaccess-3.0.3.1.jar and /dev/null differ diff --git a/lib/xmlbeans-2.3.0.jar b/lib/xmlbeans-2.3.0.jar deleted file mode 100644 index ccd81634..00000000 Binary files a/lib/xmlbeans-2.3.0.jar and /dev/null differ diff --git a/pom.xml b/pom.xml new file mode 100644 index 00000000..667b9947 --- /dev/null +++ b/pom.xml @@ -0,0 +1,133 @@ + + 4.0.0 + org.ohdsi + leporidae + pom + 0.8.0-SNAPSHOT + + rabbitinahat + whiterabbit + rabbit-core + + Leporidae + https://www.ohdsi.org/analytic-tools/whiterabbit-for-etl-design/ + + + + central + Central Repository + https://repo.maven.apache.org/maven2 + default + + false + + + + clojars + Clojars Repository + http://clojars.org/repo/ + default + + false + + + + icm + ICM Repository + https://maven.ceon.pl/artifactory/ + default + + false + + + + mulesoft + Mulesoft Repository + https://repository.mulesoft.org/nexus/content/repositories/public/ + default + + false + + + + jahia + Geomajas Repository + http://maven.geomajas.org/ + default + + false + + + + local-maven-repo + Local Repository + default + file:///${project.basedir}/../lib + + + + + + central + Central Repository + https://repo.maven.apache.org/maven2 + default + + false + + + never + + + + + + 1.8 + 1.8 + + + + + + + org.codehaus.mojo + appassembler-maven-plugin + 1.10 + + + + + + + jar:jar + + assemble + + + + + + + + + + maven-clean-plugin + 3.1.0 + + + + dist + + ** + + false + + + + + + + diff --git a/rabbit-core/.classpath b/rabbit-core/.classpath new file mode 100644 index 00000000..af1430be --- /dev/null +++ b/rabbit-core/.classpath @@ -0,0 +1,26 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/rabbit-core/.project b/rabbit-core/.project new file mode 100644 index 00000000..8a6ded5e --- /dev/null +++ b/rabbit-core/.project @@ -0,0 +1,23 @@ + + + rabbit-core + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.jdt.core.javanature + org.eclipse.m2e.core.maven2Nature + + diff --git a/rabbit-core/.settings/org.eclipse.jdt.core.prefs b/rabbit-core/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 00000000..714351ae --- /dev/null +++ b/rabbit-core/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,5 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8 +org.eclipse.jdt.core.compiler.compliance=1.8 +org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning +org.eclipse.jdt.core.compiler.source=1.8 diff --git a/rabbit-core/.settings/org.eclipse.m2e.core.prefs b/rabbit-core/.settings/org.eclipse.m2e.core.prefs new file mode 100644 index 00000000..f897a7f1 --- /dev/null +++ b/rabbit-core/.settings/org.eclipse.m2e.core.prefs @@ -0,0 +1,4 @@ +activeProfiles= +eclipse.preferences.version=1 +resolveWorkspaceProjects=true +version=1 diff --git a/rabbit-core/pom.xml b/rabbit-core/pom.xml new file mode 100644 index 00000000..41d29da7 --- /dev/null +++ b/rabbit-core/pom.xml @@ -0,0 +1,122 @@ + + + + leporidae + org.ohdsi + 0.8.0-SNAPSHOT + + 4.0.0 + + rabbit-core + jar + + + + com.oracle.jdbc + ojdbc14 + 10.2.0.1.0 + + + com.microsoft.sqlserver + sqljdbc4 + 4.0 + + + mysql + mysql-connector-java + 5.1.37 + + + dom4j + dom4j + 1.6.1 + + + org.apache.poi + poi + 3.9 + + + org.apache.poi + poi-ooxml + 3.9 + + + org.apache.poi + poi-excelant + 3.9 + + + org.apache.poi + poi-ooxml-schemas + 3.9 + + + stax + stax-api + 1.0.1 + + + org.apache.xmlbeans + xmlbeans + 2.3.0 + + + org.postgresql + postgresql + 9.4-1204-jdbc41 + + + com.cedarsoftware + json-io + 3.0.1 + + + org.apache.commons + commons-csv + 1.1 + + + commons-lang + commons-lang + 2.0 + + + commons-logging + commons-logging + 1.2 + + + org.hsqldb + hsqldb + 2.2.6 + + + com.healthmarketscience.jackcess + jackcess + 2.1.3 + + + net.sf.ucanaccess + ucanaccess + 3.0.3.1 + + + com.amazon.redshift + redshift-jdbc41 + 1.1.10.1010 + + + com.teradata.jdbc + terajdbc4 + 16.0.0.32 + + + com.teradata.tdgss + tdgssconfig + 16.0.0.0 + + + \ No newline at end of file diff --git a/src/org/ohdsi/databases/DBConnector.java b/rabbit-core/src/main/java/org/ohdsi/databases/DBConnector.java similarity index 100% rename from src/org/ohdsi/databases/DBConnector.java rename to rabbit-core/src/main/java/org/ohdsi/databases/DBConnector.java diff --git a/src/org/ohdsi/databases/DbType.java b/rabbit-core/src/main/java/org/ohdsi/databases/DbType.java similarity index 100% rename from src/org/ohdsi/databases/DbType.java rename to rabbit-core/src/main/java/org/ohdsi/databases/DbType.java diff --git a/src/org/ohdsi/databases/RichConnection.java b/rabbit-core/src/main/java/org/ohdsi/databases/RichConnection.java similarity index 100% rename from src/org/ohdsi/databases/RichConnection.java rename to rabbit-core/src/main/java/org/ohdsi/databases/RichConnection.java diff --git a/src/org/ohdsi/ooxml/CustomXWPFDocument.java b/rabbit-core/src/main/java/org/ohdsi/ooxml/CustomXWPFDocument.java similarity index 100% rename from src/org/ohdsi/ooxml/CustomXWPFDocument.java rename to rabbit-core/src/main/java/org/ohdsi/ooxml/CustomXWPFDocument.java diff --git a/src/org/ohdsi/ooxml/ReadXlsxFileWithHeader.java b/rabbit-core/src/main/java/org/ohdsi/ooxml/ReadXlsxFileWithHeader.java similarity index 100% rename from src/org/ohdsi/ooxml/ReadXlsxFileWithHeader.java rename to rabbit-core/src/main/java/org/ohdsi/ooxml/ReadXlsxFileWithHeader.java diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/Database.java b/rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/Database.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/Database.java rename to rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/Database.java diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/Field.java b/rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/Field.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/Field.java rename to rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/Field.java diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/ItemToItemMap.java b/rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/ItemToItemMap.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/ItemToItemMap.java rename to rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/ItemToItemMap.java diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/MappableItem.java b/rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/MappableItem.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/MappableItem.java rename to rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/MappableItem.java diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/Mapping.java b/rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/Mapping.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/Mapping.java rename to rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/Mapping.java diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/Table.java b/rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/Table.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/Table.java rename to rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/Table.java diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/TableCellLongTextRenderer.java b/rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/TableCellLongTextRenderer.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/TableCellLongTextRenderer.java rename to rabbit-core/src/main/java/org/ohdsi/rabbitInAHat/dataModel/TableCellLongTextRenderer.java diff --git a/src/org/ohdsi/utilities/DirectoryUtilities.java b/rabbit-core/src/main/java/org/ohdsi/utilities/DirectoryUtilities.java similarity index 100% rename from src/org/ohdsi/utilities/DirectoryUtilities.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/DirectoryUtilities.java diff --git a/src/org/ohdsi/utilities/RandomUtilities.java b/rabbit-core/src/main/java/org/ohdsi/utilities/RandomUtilities.java similarity index 100% rename from src/org/ohdsi/utilities/RandomUtilities.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/RandomUtilities.java diff --git a/src/org/ohdsi/utilities/SimpleCounter.java b/rabbit-core/src/main/java/org/ohdsi/utilities/SimpleCounter.java similarity index 100% rename from src/org/ohdsi/utilities/SimpleCounter.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/SimpleCounter.java diff --git a/src/org/ohdsi/utilities/StringUtilities.java b/rabbit-core/src/main/java/org/ohdsi/utilities/StringUtilities.java similarity index 100% rename from src/org/ohdsi/utilities/StringUtilities.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/StringUtilities.java diff --git a/src/org/ohdsi/utilities/collections/CountingSet.java b/rabbit-core/src/main/java/org/ohdsi/utilities/collections/CountingSet.java similarity index 100% rename from src/org/ohdsi/utilities/collections/CountingSet.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/collections/CountingSet.java diff --git a/src/org/ohdsi/utilities/collections/IntegerComparator.java b/rabbit-core/src/main/java/org/ohdsi/utilities/collections/IntegerComparator.java similarity index 100% rename from src/org/ohdsi/utilities/collections/IntegerComparator.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/collections/IntegerComparator.java diff --git a/src/org/ohdsi/utilities/collections/LongComparator.java b/rabbit-core/src/main/java/org/ohdsi/utilities/collections/LongComparator.java similarity index 100% rename from src/org/ohdsi/utilities/collections/LongComparator.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/collections/LongComparator.java diff --git a/src/org/ohdsi/utilities/collections/OneToManyList.java b/rabbit-core/src/main/java/org/ohdsi/utilities/collections/OneToManyList.java similarity index 100% rename from src/org/ohdsi/utilities/collections/OneToManyList.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/collections/OneToManyList.java diff --git a/src/org/ohdsi/utilities/collections/OneToManySet.java b/rabbit-core/src/main/java/org/ohdsi/utilities/collections/OneToManySet.java similarity index 100% rename from src/org/ohdsi/utilities/collections/OneToManySet.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/collections/OneToManySet.java diff --git a/src/org/ohdsi/utilities/collections/Pair.java b/rabbit-core/src/main/java/org/ohdsi/utilities/collections/Pair.java similarity index 100% rename from src/org/ohdsi/utilities/collections/Pair.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/collections/Pair.java diff --git a/src/org/ohdsi/utilities/files/IniFile.java b/rabbit-core/src/main/java/org/ohdsi/utilities/files/IniFile.java similarity index 100% rename from src/org/ohdsi/utilities/files/IniFile.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/files/IniFile.java diff --git a/src/org/ohdsi/utilities/files/MultiRowIterator.java b/rabbit-core/src/main/java/org/ohdsi/utilities/files/MultiRowIterator.java similarity index 100% rename from src/org/ohdsi/utilities/files/MultiRowIterator.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/files/MultiRowIterator.java diff --git a/src/org/ohdsi/utilities/files/QuickAndDirtyXlsxReader.java b/rabbit-core/src/main/java/org/ohdsi/utilities/files/QuickAndDirtyXlsxReader.java similarity index 100% rename from src/org/ohdsi/utilities/files/QuickAndDirtyXlsxReader.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/files/QuickAndDirtyXlsxReader.java diff --git a/src/org/ohdsi/utilities/files/ReadTextFile.java b/rabbit-core/src/main/java/org/ohdsi/utilities/files/ReadTextFile.java similarity index 100% rename from src/org/ohdsi/utilities/files/ReadTextFile.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/files/ReadTextFile.java diff --git a/src/org/ohdsi/utilities/files/Row.java b/rabbit-core/src/main/java/org/ohdsi/utilities/files/Row.java similarity index 100% rename from src/org/ohdsi/utilities/files/Row.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/files/Row.java diff --git a/src/org/ohdsi/utilities/files/RowUtilities.java b/rabbit-core/src/main/java/org/ohdsi/utilities/files/RowUtilities.java similarity index 100% rename from src/org/ohdsi/utilities/files/RowUtilities.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/files/RowUtilities.java diff --git a/src/org/ohdsi/utilities/files/StringIdComparator.java b/rabbit-core/src/main/java/org/ohdsi/utilities/files/StringIdComparator.java similarity index 100% rename from src/org/ohdsi/utilities/files/StringIdComparator.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/files/StringIdComparator.java diff --git a/src/org/ohdsi/utilities/files/WriteCSVFileWithHeader.java b/rabbit-core/src/main/java/org/ohdsi/utilities/files/WriteCSVFileWithHeader.java similarity index 100% rename from src/org/ohdsi/utilities/files/WriteCSVFileWithHeader.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/files/WriteCSVFileWithHeader.java diff --git a/src/org/ohdsi/utilities/files/WriteTextFile.java b/rabbit-core/src/main/java/org/ohdsi/utilities/files/WriteTextFile.java similarity index 100% rename from src/org/ohdsi/utilities/files/WriteTextFile.java rename to rabbit-core/src/main/java/org/ohdsi/utilities/files/WriteTextFile.java diff --git a/rabbitinahat/.classpath b/rabbitinahat/.classpath new file mode 100644 index 00000000..6d7587a8 --- /dev/null +++ b/rabbitinahat/.classpath @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/rabbitinahat/.project b/rabbitinahat/.project new file mode 100644 index 00000000..cd9a2bfb --- /dev/null +++ b/rabbitinahat/.project @@ -0,0 +1,23 @@ + + + rabbitinahat + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.jdt.core.javanature + org.eclipse.m2e.core.maven2Nature + + diff --git a/rabbitinahat/.settings/org.eclipse.jdt.core.prefs b/rabbitinahat/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 00000000..714351ae --- /dev/null +++ b/rabbitinahat/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,5 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8 +org.eclipse.jdt.core.compiler.compliance=1.8 +org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning +org.eclipse.jdt.core.compiler.source=1.8 diff --git a/rabbitinahat/.settings/org.eclipse.m2e.core.prefs b/rabbitinahat/.settings/org.eclipse.m2e.core.prefs new file mode 100644 index 00000000..f897a7f1 --- /dev/null +++ b/rabbitinahat/.settings/org.eclipse.m2e.core.prefs @@ -0,0 +1,4 @@ +activeProfiles= +eclipse.preferences.version=1 +resolveWorkspaceProjects=true +version=1 diff --git a/rabbitinahat/pom.xml b/rabbitinahat/pom.xml new file mode 100644 index 00000000..8a302145 --- /dev/null +++ b/rabbitinahat/pom.xml @@ -0,0 +1,42 @@ + + + + leporidae + org.ohdsi + 0.8.0-SNAPSHOT + + 4.0.0 + + rabbitinahat + RabbitInAHat + jar + + + + + org.codehaus.mojo + appassembler-maven-plugin + + ${project.parent.basedir}/dist + -Xmx1200m + + + org.ohdsi.rabbitInAHat.RabbitInAHatMain + rabbitInAHat + + + + + + + + + + org.ohdsi + rabbit-core + ${project.version} + + + \ No newline at end of file diff --git a/src/org/ohdsi/rabbitInAHat/Arrow.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/Arrow.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/Arrow.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/Arrow.java diff --git a/src/org/ohdsi/rabbitInAHat/DescriptionTextArea.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/DescriptionTextArea.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/DescriptionTextArea.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/DescriptionTextArea.java diff --git a/src/org/ohdsi/rabbitInAHat/DetailsListener.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/DetailsListener.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/DetailsListener.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/DetailsListener.java diff --git a/src/org/ohdsi/rabbitInAHat/DetailsPanel.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/DetailsPanel.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/DetailsPanel.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/DetailsPanel.java diff --git a/src/org/ohdsi/rabbitInAHat/ETLMarkupDocumentGenerator.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/ETLMarkupDocumentGenerator.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/ETLMarkupDocumentGenerator.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/ETLMarkupDocumentGenerator.java diff --git a/src/org/ohdsi/rabbitInAHat/ETLTestFrameWorkGenerator.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/ETLTestFrameWorkGenerator.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/ETLTestFrameWorkGenerator.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/ETLTestFrameWorkGenerator.java diff --git a/src/org/ohdsi/rabbitInAHat/ETLWordDocumentGenerator.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/ETLWordDocumentGenerator.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/ETLWordDocumentGenerator.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/ETLWordDocumentGenerator.java diff --git a/src/org/ohdsi/rabbitInAHat/FetchCDMModelFromServer.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/FetchCDMModelFromServer.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/FetchCDMModelFromServer.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/FetchCDMModelFromServer.java diff --git a/src/org/ohdsi/rabbitInAHat/FilterDialog.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/FilterDialog.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/FilterDialog.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/FilterDialog.java diff --git a/src/org/ohdsi/rabbitInAHat/FlexTable.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/FlexTable.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/FlexTable.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/FlexTable.java diff --git a/src/org/ohdsi/rabbitInAHat/LabeledRectangle.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/LabeledRectangle.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/LabeledRectangle.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/LabeledRectangle.java diff --git a/src/org/ohdsi/rabbitInAHat/MappingComponent.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/MappingComponent.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/MappingComponent.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/MappingComponent.java diff --git a/src/org/ohdsi/rabbitInAHat/MappingPanel.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/MappingPanel.java similarity index 96% rename from src/org/ohdsi/rabbitInAHat/MappingPanel.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/MappingPanel.java index 19619884..990405b0 100644 --- a/src/org/ohdsi/rabbitInAHat/MappingPanel.java +++ b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/MappingPanel.java @@ -51,7 +51,6 @@ import org.ohdsi.rabbitInAHat.dataModel.Mapping; import org.ohdsi.rabbitInAHat.dataModel.Table; import org.ohdsi.utilities.collections.IntegerComparator; -import org.ohdsi.whiteRabbit.ObjectExchange; public class MappingPanel extends JPanel implements MouseListener, MouseMotionListener { diff --git a/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/ObjectExchange.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/ObjectExchange.java new file mode 100644 index 00000000..9b6cc374 --- /dev/null +++ b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/ObjectExchange.java @@ -0,0 +1,32 @@ +/******************************************************************************* + * Copyright 2019 Observational Health Data Sciences and Informatics + * + * This file is part of WhiteRabbit + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + ******************************************************************************/ +package org.ohdsi.rabbitInAHat; + +import org.ohdsi.rabbitInAHat.dataModel.ETL; + +import javax.swing.*; + +/** + * This class is used to hold global variables + */ +public final class ObjectExchange { + // utility class + private ObjectExchange() {} + + public static ETL etl; +} diff --git a/src/org/ohdsi/rabbitInAHat/RabbitInAHatMain.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/RabbitInAHatMain.java similarity index 97% rename from src/org/ohdsi/rabbitInAHat/RabbitInAHatMain.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/RabbitInAHatMain.java index 8e9965eb..505abc83 100644 --- a/src/org/ohdsi/rabbitInAHat/RabbitInAHatMain.java +++ b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/RabbitInAHatMain.java @@ -64,7 +64,6 @@ import org.ohdsi.rabbitInAHat.dataModel.MappableItem; import org.ohdsi.rabbitInAHat.dataModel.StemTableAdd; import org.ohdsi.rabbitInAHat.dataModel.Table; -import org.ohdsi.whiteRabbit.ObjectExchange; /** * This is the main class for the RabbitInAHat application diff --git a/src/org/ohdsi/rabbitInAHat/ResizeListener.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/ResizeListener.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/ResizeListener.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/ResizeListener.java diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/ETL.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/dataModel/ETL.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/ETL.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/dataModel/ETL.java diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableAdd.java b/rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/dataModel/StemTableAdd.java similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/StemTableAdd.java rename to rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/dataModel/StemTableAdd.java diff --git a/src/org/ohdsi/rabbitInAHat/RabbitInAHat128.png b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/RabbitInAHat128.png similarity index 100% rename from src/org/ohdsi/rabbitInAHat/RabbitInAHat128.png rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/RabbitInAHat128.png diff --git a/src/org/ohdsi/rabbitInAHat/RabbitInAHat16.png b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/RabbitInAHat16.png similarity index 100% rename from src/org/ohdsi/rabbitInAHat/RabbitInAHat16.png rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/RabbitInAHat16.png diff --git a/src/org/ohdsi/rabbitInAHat/RabbitInAHat256.png b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/RabbitInAHat256.png similarity index 100% rename from src/org/ohdsi/rabbitInAHat/RabbitInAHat256.png rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/RabbitInAHat256.png diff --git a/src/org/ohdsi/rabbitInAHat/RabbitInAHat32.png b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/RabbitInAHat32.png similarity index 100% rename from src/org/ohdsi/rabbitInAHat/RabbitInAHat32.png rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/RabbitInAHat32.png diff --git a/src/org/ohdsi/rabbitInAHat/RabbitInAHat48.png b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/RabbitInAHat48.png similarity index 100% rename from src/org/ohdsi/rabbitInAHat/RabbitInAHat48.png rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/RabbitInAHat48.png diff --git a/src/org/ohdsi/rabbitInAHat/RabbitInAHat64.png b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/RabbitInAHat64.png similarity index 100% rename from src/org/ohdsi/rabbitInAHat/RabbitInAHat64.png rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/RabbitInAHat64.png diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/CDMV4.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV4.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/CDMV4.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV4.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/CDMV5.0.1.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV5.0.1.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/CDMV5.0.1.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV5.0.1.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/CDMV5.1.0.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV5.1.0.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/CDMV5.1.0.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV5.1.0.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/CDMV5.2.0.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV5.2.0.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/CDMV5.2.0.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV5.2.0.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/CDMV5.3.0.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV5.3.0.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/CDMV5.3.0.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV5.3.0.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/CDMV5.3.1.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV5.3.1.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/CDMV5.3.1.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV5.3.1.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/CDMV5.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV5.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/CDMV5.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/CDMV5.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.0.1.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.0.1.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.0.1.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.0.1.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.1.0.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.1.0.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.1.0.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.1.0.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.2.0.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.2.0.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.2.0.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.2.0.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.3.0.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.3.0.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.3.0.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.3.0.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.3.1.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.3.1.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.3.1.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableDefaultMappingV5.3.1.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.0.1.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.0.1.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.0.1.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.0.1.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.1.0.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.1.0.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.1.0.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.1.0.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.2.0.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.2.0.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.2.0.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.2.0.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.3.0.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.3.0.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.3.0.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.3.0.csv diff --git a/src/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.3.1.csv b/rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.3.1.csv similarity index 100% rename from src/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.3.1.csv rename to rabbitinahat/src/main/resources/org/ohdsi/rabbitInAHat/dataModel/StemTableV5.3.1.csv diff --git a/src/org/ohdsi/utilities/RabbitInAHatLauncher.java b/src/org/ohdsi/utilities/RabbitInAHatLauncher.java deleted file mode 100644 index f18fd4d7..00000000 --- a/src/org/ohdsi/utilities/RabbitInAHatLauncher.java +++ /dev/null @@ -1,34 +0,0 @@ -package org.ohdsi.utilities; - -import org.ohdsi.rabbitInAHat.RabbitInAHatMain; - -import java.util.Arrays; -import java.io.File; -import java.util.ArrayList; - -/* Adapted from code found on: - * http://silentdevelopment.blogspot.com/2010/03/how-to-set-or-increase-xmx-heap-memory.html - */ -public class RabbitInAHatLauncher { - private final static int MIN_HEAP = 1200; - - public static void main(String[] args) throws Exception { - - float heapSizeMegs = (Runtime.getRuntime().maxMemory() / 1024) / 1024; - - if (heapSizeMegs > MIN_HEAP) { - System.out.println("Launching with current VM"); - RabbitInAHatMain.main(args); - } else { - System.out.println("Starting new VM"); - String pathToJar = RabbitInAHatMain.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath(); - ArrayList command = new ArrayList(); - command.addAll(Arrays.asList("java", "-Xmx" + MIN_HEAP + "m", "-classpath", pathToJar, "org.ohdsi.rabbitInAHat.RabbitInAHatMain")); - command.addAll(Arrays.asList(args)); - ProcessBuilder pb = new ProcessBuilder(command); - pb.inheritIO(); - pb.redirectError(new File("ErrorStream.txt")); - pb.start(); - } - } -} diff --git a/src/org/ohdsi/utilities/WhiteRabbitLauncher.java b/src/org/ohdsi/utilities/WhiteRabbitLauncher.java deleted file mode 100644 index 05ecdf82..00000000 --- a/src/org/ohdsi/utilities/WhiteRabbitLauncher.java +++ /dev/null @@ -1,29 +0,0 @@ -package org.ohdsi.utilities; - -import java.io.File; - -import org.ohdsi.whiteRabbit.WhiteRabbitMain; - -/* Adapted from code found on: - * http://silentdevelopment.blogspot.com/2010/03/how-to-set-or-increase-xmx-heap-memory.html - */ -public class WhiteRabbitLauncher { - private final static int MIN_HEAP = 1200; - - public static void main(String[] args) throws Exception { - - float heapSizeMegs = (Runtime.getRuntime().maxMemory() / 1024) / 1024; - - if (heapSizeMegs > MIN_HEAP || args.length > 0) { - System.out.println("Launching with current VM"); - WhiteRabbitMain.main(args); - } else { - System.out.println("Starting new VM"); - String pathToJar = WhiteRabbitMain.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath(); - ProcessBuilder pb = new ProcessBuilder("java", "-Xmx" + MIN_HEAP + "m", "-classpath", pathToJar, "org.ohdsi.whiteRabbit.WhiteRabbitMain"); - pb.inheritIO(); - pb.redirectError(new File("ErrorStream.txt")); - pb.start(); - } - } -} diff --git a/whiterabbit/.classpath b/whiterabbit/.classpath new file mode 100644 index 00000000..6d7587a8 --- /dev/null +++ b/whiterabbit/.classpath @@ -0,0 +1,31 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/whiterabbit/.project b/whiterabbit/.project new file mode 100644 index 00000000..1d176399 --- /dev/null +++ b/whiterabbit/.project @@ -0,0 +1,23 @@ + + + whiterabbit + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.jdt.core.javanature + org.eclipse.m2e.core.maven2Nature + + diff --git a/whiterabbit/.settings/org.eclipse.jdt.core.prefs b/whiterabbit/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 00000000..714351ae --- /dev/null +++ b/whiterabbit/.settings/org.eclipse.jdt.core.prefs @@ -0,0 +1,5 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8 +org.eclipse.jdt.core.compiler.compliance=1.8 +org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning +org.eclipse.jdt.core.compiler.source=1.8 diff --git a/whiterabbit/.settings/org.eclipse.m2e.core.prefs b/whiterabbit/.settings/org.eclipse.m2e.core.prefs new file mode 100644 index 00000000..f897a7f1 --- /dev/null +++ b/whiterabbit/.settings/org.eclipse.m2e.core.prefs @@ -0,0 +1,4 @@ +activeProfiles= +eclipse.preferences.version=1 +resolveWorkspaceProjects=true +version=1 diff --git a/whiterabbit/pom.xml b/whiterabbit/pom.xml new file mode 100644 index 00000000..931dff95 --- /dev/null +++ b/whiterabbit/pom.xml @@ -0,0 +1,42 @@ + + + + leporidae + org.ohdsi + 0.8.0-SNAPSHOT + + 4.0.0 + + whiterabbit + WhiteRabbit + jar + + + + + org.codehaus.mojo + appassembler-maven-plugin + + ${project.parent.basedir}/dist + -Xmx1200m + + + org.ohdsi.whiteRabbit.WhiteRabbitMain + whiteRabbit + + + + + + + + + + org.ohdsi + rabbit-core + ${project.version} + + + \ No newline at end of file diff --git a/src/org/ohdsi/whiteRabbit/Console.java b/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/Console.java similarity index 100% rename from src/org/ohdsi/whiteRabbit/Console.java rename to whiterabbit/src/main/java/org/ohdsi/whiteRabbit/Console.java diff --git a/src/org/ohdsi/whiteRabbit/DbSettings.java b/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/DbSettings.java similarity index 100% rename from src/org/ohdsi/whiteRabbit/DbSettings.java rename to whiterabbit/src/main/java/org/ohdsi/whiteRabbit/DbSettings.java diff --git a/src/org/ohdsi/whiteRabbit/ErrorReport.java b/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/ErrorReport.java similarity index 100% rename from src/org/ohdsi/whiteRabbit/ErrorReport.java rename to whiterabbit/src/main/java/org/ohdsi/whiteRabbit/ErrorReport.java diff --git a/src/org/ohdsi/whiteRabbit/ObjectExchange.java b/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/ObjectExchange.java similarity index 87% rename from src/org/ohdsi/whiteRabbit/ObjectExchange.java rename to whiterabbit/src/main/java/org/ohdsi/whiteRabbit/ObjectExchange.java index 2d174bb4..643e87a0 100644 --- a/src/org/ohdsi/whiteRabbit/ObjectExchange.java +++ b/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/ObjectExchange.java @@ -1,14 +1,14 @@ /******************************************************************************* * Copyright 2019 Observational Health Data Sciences and Informatics - * + * * This file is part of WhiteRabbit - * + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * + * * http://www.apache.org/licenses/LICENSE-2.0 - * + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. @@ -19,13 +19,13 @@ import javax.swing.JFrame; -import org.ohdsi.rabbitInAHat.dataModel.ETL; - /** * This class is used to hold global variables */ -public class ObjectExchange { +public final class ObjectExchange { + // utility class + private ObjectExchange() {} + public static JFrame frame; public static Console console; - public static ETL etl; } diff --git a/src/org/ohdsi/whiteRabbit/WhiteRabbitMain.java b/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/WhiteRabbitMain.java similarity index 100% rename from src/org/ohdsi/whiteRabbit/WhiteRabbitMain.java rename to whiterabbit/src/main/java/org/ohdsi/whiteRabbit/WhiteRabbitMain.java diff --git a/src/org/ohdsi/whiteRabbit/fakeDataGenerator/FakeDataGenerator.java b/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/fakeDataGenerator/FakeDataGenerator.java similarity index 100% rename from src/org/ohdsi/whiteRabbit/fakeDataGenerator/FakeDataGenerator.java rename to whiterabbit/src/main/java/org/ohdsi/whiteRabbit/fakeDataGenerator/FakeDataGenerator.java diff --git a/src/org/ohdsi/whiteRabbit/scan/SourceDataScan.java b/whiterabbit/src/main/java/org/ohdsi/whiteRabbit/scan/SourceDataScan.java similarity index 100% rename from src/org/ohdsi/whiteRabbit/scan/SourceDataScan.java rename to whiterabbit/src/main/java/org/ohdsi/whiteRabbit/scan/SourceDataScan.java diff --git a/src/org/ohdsi/whiteRabbit/WhiteRabbit.ico b/whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit.ico similarity index 100% rename from src/org/ohdsi/whiteRabbit/WhiteRabbit.ico rename to whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit.ico diff --git a/src/org/ohdsi/whiteRabbit/WhiteRabbit128.png b/whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit128.png similarity index 100% rename from src/org/ohdsi/whiteRabbit/WhiteRabbit128.png rename to whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit128.png diff --git a/src/org/ohdsi/whiteRabbit/WhiteRabbit16.png b/whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit16.png similarity index 100% rename from src/org/ohdsi/whiteRabbit/WhiteRabbit16.png rename to whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit16.png diff --git a/src/org/ohdsi/whiteRabbit/WhiteRabbit256.png b/whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit256.png similarity index 100% rename from src/org/ohdsi/whiteRabbit/WhiteRabbit256.png rename to whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit256.png diff --git a/src/org/ohdsi/whiteRabbit/WhiteRabbit32.png b/whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit32.png similarity index 100% rename from src/org/ohdsi/whiteRabbit/WhiteRabbit32.png rename to whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit32.png diff --git a/src/org/ohdsi/whiteRabbit/WhiteRabbit48.png b/whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit48.png similarity index 100% rename from src/org/ohdsi/whiteRabbit/WhiteRabbit48.png rename to whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit48.png diff --git a/src/org/ohdsi/whiteRabbit/WhiteRabbit64.png b/whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit64.png similarity index 100% rename from src/org/ohdsi/whiteRabbit/WhiteRabbit64.png rename to whiterabbit/src/main/resources/org/ohdsi/whiteRabbit/WhiteRabbit64.png