FileHarvestJob.java: added getScript() and performHarvest() methods
Harvester.java: added stringsToArray(), modified API methods to use it TestFileController.java: implemented preliminary harvest
This commit is contained in:
mbarbier
parent
3804cf4d70
commit
663090318d
3 changed files with 301 additions and 61 deletions
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@ -18,5 +18,17 @@ interface FileHarvestJob {
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* @return null if success, message to be returned to the user if failure
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*/
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String validateUpload(File file);
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/**
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* Gets the console script which can be used to run the harvest job.
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* @return the console script which can be used to run the harvest job
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*/
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String getScript();
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/**
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* Runs a harvest on the files in the specified directory.
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* @param directory the directory containing files to harvest
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*/
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void performHarvest(File directory);
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}
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@ -2,6 +2,8 @@
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package edu.cornell.mannlib.vitro.webapp.controller.harvester;
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import java.util.ArrayList;
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/* //PLEASE SEE JAVADOC COMMENT FOR CLASS BELOW
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import org.vivoweb.harvester.diff.Diff;
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import org.vivoweb.harvester.fetch.CSVtoRDF;
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@ -52,99 +54,135 @@ import org.vivoweb.harvester.util.XPathTool;
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class Harvester {
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/*
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// diff
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public static void runDiff(String ... args) {
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Diff.main(args);
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public static void runDiff(Object ... args) {
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Diff.main(stringsToArray(args));
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}
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// fetch
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public static void runCSVtoRDF(String ... args) {
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CSVtoRDF.main(args);
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public static void runCSVtoRDF(Object ... args) {
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CSVtoRDF.main(stringsToArray(args));
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}
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public static void runD2RMapFetch(String ... args) {
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D2RMapFetch.main(args);
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public static void runD2RMapFetch(Object ... args) {
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D2RMapFetch.main(stringsToArray(args));
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}
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public static void runJDBCFetch(String ... args) {
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JDBCFetch.main(args);
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public static void runJDBCFetch(Object ... args) {
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JDBCFetch.main(stringsToArray(args));
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}
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public static void runNLMJournalFetch(String ... args) {
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NLMJournalFetch.main(args);
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public static void runNLMJournalFetch(Object ... args) {
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NLMJournalFetch.main(stringsToArray(args));
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}
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public static void runOAIFetch(String ... args) {
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OAIFetch.main(args);
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public static void runOAIFetch(Object ... args) {
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OAIFetch.main(stringsToArray(args));
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}
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public static void runPubmedFetch(String ... args) {
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PubmedFetch.main(args);
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public static void runPubmedFetch(Object ... args) {
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PubmedFetch.main(stringsToArray(args));
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}
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public static void runPubmedHTTPFetch(String ... args) {
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PubmedHTTPFetch.main(args);
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public static void runPubmedHTTPFetch(Object ... args) {
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PubmedHTTPFetch.main(stringsToArray(args));
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}
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// qualify
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public static void runChangeNamespace(String ... args) {
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ChangeNamespace.main(args);
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public static void runChangeNamespace(Object ... args) {
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ChangeNamespace.main(stringsToArray(args));
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}
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public static void runQualify(String ... args) {
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Qualify.main(args);
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public static void runQualify(Object ... args) {
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Qualify.main(stringsToArray(args));
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}
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public static void runRenameBlankNodes(String ... args) {
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RenameBlankNodes.main(args);
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public static void runRenameBlankNodes(Object ... args) {
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RenameBlankNodes.main(stringsToArray(args));
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}
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public static void runRenameResources(String ... args) {
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RenameResources.main(args);
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public static void runRenameResources(Object ... args) {
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RenameResources.main(stringsToArray(args));
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}
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public static void runSmush(String ... args) {
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Smush.main(args);
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public static void runSmush(Object ... args) {
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Smush.main(stringsToArray(args));
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}
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public static void runSplitProperty(String ... args) {
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SplitProperty.main(args);
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public static void runSplitProperty(Object ... args) {
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SplitProperty.main(stringsToArray(args));
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}
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// score
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public static void runMatch(String ... args) {
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Match.main(args);
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public static void runMatch(Object ... args) {
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Match.main(stringsToArray(args));
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}
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public static void runPubmedScore(String ... args) {
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PubmedScore.main(args);
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public static void runPubmedScore(Object ... args) {
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PubmedScore.main(stringsToArray(args));
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}
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public static void runScore(String ... args) {
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Score.main(args);
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public static void runScore(Object ... args) {
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Score.main(stringsToArray(args));
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}
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// transfer
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public static void transfer(String ... args) {
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Transfer.main(args);
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public static void runTransfer(Object ... args) {
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Transfer.main(stringsToArray(args));
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}
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// translate
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public static void runGlozeTranslator(String ... args) {
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GlozeTranslator.main(args);
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public static void runGlozeTranslator(Object ... args) {
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GlozeTranslator.main(stringsToArray(args));
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}
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public static void runRunBibutils(String ... args) {
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RunBibutils.main(args);
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public static void runRunBibutils(Object ... args) {
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RunBibutils.main(stringsToArray(args));
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}
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public static void runSanitizeMODSXML(String ... args) {
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SanitizeMODSXML.main(args);
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public static void runSanitizeMODSXML(Object ... args) {
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SanitizeMODSXML.main(stringsToArray(args));
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}
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public static void runSPARQLTranslator(String ... args) {
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SPARQLTranslator.main(args);
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public static void runSPARQLTranslator(Object ... args) {
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SPARQLTranslator.main(stringsToArray(args));
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}
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public static void runXSLTranslator(String ... args) {
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XSLTranslator.main(args);
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public static void runXSLTranslator(Object ... args) {
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XSLTranslator.main(stringsToArray(args));
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}
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// util
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public static void runCSVtoJDBC(String ... args) {
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CSVtoJDBC.main(args);
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public static void runCSVtoJDBC(Object ... args) {
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CSVtoJDBC.main(stringsToArray(args));
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}
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public static void runDatabaseClone(String ... args) {
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DatabaseClone.main(args);
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public static void runDatabaseClone(Object ... args) {
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DatabaseClone.main(stringsToArray(args));
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}
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public static void runMerge(String ... args) {
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Merge.main(args);
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public static void runMerge(Object ... args) {
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Merge.main(stringsToArray(args));
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}
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public static void runXPathTool(String ... args) {
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XPathTool.main(args);
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public static void runXPathTool(Object ... args) {
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XPathTool.main(stringsToArray(args));
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}
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*/
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/**
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* Convenience method to expand the ability to use Java's "..." arg list. Harvester scripts frequently declare sub-macros,
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* so for example you might have:
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*
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* SCOREINPUT="-i $H2MODEL -ImodelName=$MODELNAME -IdbUrl=$MODELDBURL -IcheckEmpty=$CHECKEMPTY"
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* SCOREDATA="-s $H2MODEL -SmodelName=$SCOREDATANAME -SdbUrl=$SCOREDATADBURL -ScheckEmpty=$CHECKEMPTY"
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* SCOREMODELS="$SCOREINPUT -v $VIVOCONFIG -VcheckEmpty=$CHECKEMPTY $SCOREDATA -t $TEMPCOPYDIR -b $SCOREBATCHSIZE"
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* $Score $SCOREMODELS -AGrantNumber=$EQTEST -WGrantNumber=1.0 -FGrantNumber=$GRANTIDNUM -PGrantNumber=$GRANTIDNUM -n ${BASEURI}grant/
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*
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* In order to mimic this functionality for easy use in Java, this method has been created. It takes a "..." arg list of Object
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* objects, and returns an array of Strings. For each object, if it's an array of Strings, each String is added to the output
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* array. Otherwise, its toString() method is called and that value is added to the output array.
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*
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* It is intended to be used with a combination of String and String[] values, in any arbitrary order.
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*
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* All static Harvester methods in this class take an Object arg list rather than a String arg list, and automatically call
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* this method.
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*
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* @param args an array of objects, which ought to be a combination of String and String[] values, in any arbitrary order
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* @return all the strings put together as one array
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*/
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public static String[] stringsToArray(Object ... args) {
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ArrayList<String> allData = new ArrayList<String>();
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for(int i = 0; i < args.length; i++) {
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if(args[i] instanceof String[]) {
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String[] array = (String[])(args[i]);
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for(int j = 0; j < array.length; j++) {
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allData.add(array[j]);
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}
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} else {
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allData.add(args[i].toString());
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}
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}
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return allData.toArray(new String[allData.size()]);
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}
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*/
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}
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@ -2,8 +2,11 @@
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package edu.cornell.mannlib.vitro.webapp.controller.harvester;
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import java.io.BufferedReader;
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import java.io.File;
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import java.io.FileReader;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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@ -235,8 +238,7 @@ public class TestFileController extends FreemarkerHttpServlet {
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@SuppressWarnings("unused")
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private void doHarvest()
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{
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private void doHarvest() {
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/*
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Harvest will entail:
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@ -260,6 +262,8 @@ public class TestFileController extends FreemarkerHttpServlet {
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/**
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* Provides a way of throwing an exception whose message it is OK to display unedited to the user.
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*/
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@ -361,6 +365,192 @@ class CsvHarvestJob implements FileHarvestJob {
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}
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return null;
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}
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@Override
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public String getScript()
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{
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String path = ""; //todo: complete
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File scriptTemplate = new File(path);
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String scriptTemplateContents = readScriptTemplate(scriptTemplate);
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String replacements = performScriptTemplateReplacements(scriptTemplateContents);
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return replacements;
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}
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private String performScriptTemplateReplacements(String scriptTemplateContents) {
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String replacements = scriptTemplateContents;
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/*
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* What needs to be replaced?
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*
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* task directory name
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*/
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//todo: complete
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return replacements;
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}
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private String readScriptTemplate(File scriptTemplate) {
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String scriptTemplateContents = null;
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BufferedReader reader = null;
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try {
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int fileSize = (int)(scriptTemplate.length());
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char[] buffer = new char[fileSize];
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reader = new BufferedReader(new FileReader(scriptTemplate), fileSize);
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reader.read(buffer);
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scriptTemplateContents = new String(buffer);
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} catch (IOException e) {
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log.error(e, e);
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} finally {
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try {
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if(reader != null)
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reader.close();
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} catch(IOException e) {
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log.error(e, e);
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}
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}
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return scriptTemplateContents;
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}
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@Override
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public void performHarvest(File directory) {
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/* //COMMENTED OUT UNTIL HARVESTER INTEGRATION IS WORKING
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String vivoconfig = "config/models/vivo.xml";
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String scorebatchsize = "100";
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String checkempty = "true";
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String namespace = ""; //todo: get namespace
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String h2model = "config/models/h2-sdb.xml";
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String prevharvdburlbase = "jdbc:h2:harvested-data/prevHarvs/";
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String tfrh = "config/recordhandlers/h2-jdbc.xml";
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String harvesterTask = "csv";
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String basedir = "harvested-data/" + harvesterTask;
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String rawrhdir = basedir + "/rh-raw";
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String rdfrhdir = basedir + "/rh-rdf";
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String modeldir = basedir + "/model";
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String scoredatadir = basedir + "/score-data";
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String modeldburl = "jdbc:h2:" + modeldir + "/store";
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String scoredatadburl = "jdbc:h2:" + scoredatadir + "/store";
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String modelname = "csvTempTransfer";
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String scoredataname = "csvScoreData";
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String tempcopydir = basedir + "/temp-copy";
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String[] scoreinput = Harvester.stringsToArray("-i", h2model, "-ImodelName=" + modelname, "-IdbUrl=" + modeldburl, "-IcheckEmpty=" + checkempty);
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String[] scoredata = Harvester.stringsToArray("-s", h2model, "-SmodelName=" + scoredataname, "-SdbUrl=" + scoredatadburl, "-ScheckEmpty=" + checkempty);
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String[] scoremodels = Harvester.stringsToArray(scoreinput, "-v", vivoconfig, "-VcheckEmpty=" + checkempty, scoredata, "-t", tempcopydir, "-b", scorebatchsize);
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String[] cnflags = Harvester.stringsToArray(scoreinput, "-v", vivoconfig, "-n", namespace);
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String eqtest = "org.vivoweb.harvester.score.algorithm.EqualityTest";
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String grantidnum = "http://vivoweb.org/ontology/score#grantID";
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String rdfslabel = "http://www.w3.org/2000/01/rdf-schema#label";
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String personidnum = "http://vivoweb.org/ontology/score#personID";
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String deptidnum = "http://vivoweb.org/ontology/score#deptID";
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String rolein = "http://vivoweb.org/ontology/core#roleIn";
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String piroleof = "http://vivoweb.org/ontology/core#principalInvestigatorRoleOf";
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String copiroleof = "http://vivoweb.org/ontology/core#co-PrincipalInvestigatorRoleOf";
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String datetime = "http://vivoweb.org/ontology/core#dateTime";
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String baseuri = "http://vivoweb.org/harvest/csvfile/";
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//execute fetch
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Harvester.runCSVtoRDF("-o", tfrh, "-O", "fileDir=" + rawrhdir, "-i", "filepath");
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//execute translate
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Harvester.runXSLTranslator("-i", tfrh, "-IfileDir=" + rawrhdir, "-o", tfrh, "-OfileDir=" + rdfrhdir, "-x", "config/datamaps/csv-grant-to-vivo.xsl");
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//execute transfer to import from record handler into local temp model
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Harvester.runTransfer("-o", h2model, "-OmodelName=" + modelname, "-OdbUrl=" + modeldburl, "-h", tfrh, "-HfileDir=" + rdfrhdir, "-n", namespace);
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//smushes in-place(-r) on the Grant id THEN on the person ID then deptID
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Harvester.runSmush(scoreinput, "-P", grantidnum, "-P", personidnum, "-P", deptidnum, "-P", datetime, "-n", baseuri, "-r");
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//scoring of Grants on GrantNumber
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Harvester.runScore(scoremodels, "-AGrantNumber=" + eqtest, "-WGrantNumber=1.0", "-FGrantNumber=" + grantidnum, "-PGrantNumber=" + grantidnum, "-n", baseuri + "grant/");
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//scoring of people on PERSONIDNUM
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Harvester.runScore(scoremodels, "-Aufid=" + eqtest, "-Wufid=1.0", "-Fufid=" + personidnum, "-Pufid=" + personidnum, "-n", baseuri + "person/");
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Harvester.runSmush(scoreinput, "-P", deptidnum, "-n", baseuri + "org/", "-r");
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//scoring of orgs on DeptID
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Harvester.runScore(scoremodels, "-AdeptID=" + eqtest, "-WdeptID=1.0", "-FdeptID=" + deptidnum, "-PdeptID=" + deptidnum, "-n", baseuri + "org/");
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Harvester.runSmush(scoreinput, "-P", rdfslabel, "-n", baseuri + "sponsor/", "-r");
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//scoring sponsors by labels
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Harvester.runScore(scoremodels, "-Alabel=" + eqtest, "-Wlabel=1.0", "-Flabel=" + rdfslabel, "-Plabel=" + rdfslabel, "-n", baseuri + "sponsor/");
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//scoring of PI Roles
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String[] piuri = Harvester.stringsToArray("-Aperson=" + eqtest, "-Wperson=0.5", "-Fperson=" + piroleof, "-Pperson=" + piroleof);
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String[] granturi = Harvester.stringsToArray("-Agrant=" + eqtest, "-Wgrant=0.5", "-Fgrant=" + rolein, "-Pgrant=" + rolein);
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Harvester.runScore(scoremodels, piuri, granturi, "-n", baseuri + "piRole/");
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//scoring of coPI Roles
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String[] copiuri = Harvester.stringsToArray("-Aperson=" + eqtest, "-Wperson=0.5", "-Fperson=" + copiroleof, "-Pperson=" + copiroleof);
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Harvester.runScore(scoremodels, copiuri, granturi, "-n", baseuri + "coPiRole/");
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//find matches using scores and rename nodes to matching uri
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Harvester.runMatch(scoreinput, scoredata, "-b", scorebatchsize, "-t", "1.0", "-r");
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//execute ChangeNamespace to get grants into current namespace
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Harvester.runChangeNamespace(cnflags, "-u", baseuri + "grant/");
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//execute ChangeNamespace to get orgs into current namespace
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Harvester.runChangeNamespace(cnflags, "-u", baseuri + "org/");
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//execute ChangeNamespace to get sponsors into current namespace
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Harvester.runChangeNamespace(cnflags, "-u", baseuri + "sponsor/");
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//execute ChangeNamespace to get people into current namespace
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Harvester.runChangeNamespace(cnflags, "-u", baseuri + "person/");
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//execute ChangeNamespace to get PI roles into current namespace
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Harvester.runChangeNamespace(cnflags, "-u", baseuri + "piRole/");
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//execute ChangeNamespace to get co-PI roles into current namespace
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Harvester.runChangeNamespace(cnflags, "-u", baseuri + "coPiRole/");
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//execute ChangeNamespace to get co-PI roles into current namespace
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Harvester.runChangeNamespace(cnflags, "-u", baseuri + "timeInterval");
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//todo: we probably don't want to do prev harvest stuff for this
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String prevharvestmodel = "http://vivoweb.org/ingest/dsr";
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String addfile = basedir + "/additions.rdf.xml";
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String subfile = basedir + "/subtractions.rdf.xml";
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//find Subtractions
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Harvester.runDiff("-m", h2model, "-MdbUrl=" + prevharvdburlbase + harvesterTask + "/store", "-McheckEmpty=" + checkempty, "-MmodelName=" + prevharvestmodel, "-s", h2model, "-ScheckEmpty=" + checkempty, "-SdbUrl=" + modeldburl, "-SmodelName=" + modelname, "-d", subfile);
|
||||
|
||||
//find Additions
|
||||
Harvester.runDiff("-m", h2model, "-McheckEmpty=" + checkempty, "-MdbUrl=" + modeldburl, "-MmodelName=" + modelname, "-s", h2model, "-ScheckEmpty=" + checkempty, "-SdbUrl=" + prevharvdburlbase + harvesterTask + "/store", "-SmodelName=" + prevharvestmodel, "-d", addfile);
|
||||
|
||||
//apply Subtractions to Previous model
|
||||
Harvester.runTransfer("-o", h2model, "-OdbUrl=" + prevharvdburlbase + harvesterTask + "/store", "-OcheckEmpty=" + checkempty, "-OmodelName=" + prevharvestmodel, "-r", subfile, "-m");
|
||||
|
||||
//apply Additions to Previous model
|
||||
Harvester.runTransfer("-o", h2model, "-OdbUrl=" + prevharvdburlbase + harvesterTask + "/store", "-OcheckEmpty=" + checkempty, "-OmodelName=" + prevharvestmodel, "-r", addfile);
|
||||
|
||||
//apply Subtractions to VIVO
|
||||
Harvester.runTransfer("-o", vivoconfig, "-OcheckEmpty=" + checkempty, "-r", subfile, "-m");
|
||||
|
||||
//apply Additions to VIVO
|
||||
Harvester.runTransfer("-o", vivoconfig, "-OcheckEmpty=" + checkempty, "-r", addfile);
|
||||
*/
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue