ref 18096: DataMiner - HTML file does not open in view widget but in a new browser window
https://support.d4science.org/issues/18096 Fixed Content-Type in output files git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@182280 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
parent
b1fcb7a96f
commit
1b1117997e
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@ -1,24 +1,36 @@
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<ReleaseNotes>
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<Changeset component="${groupId}.${artifactId}.1-5-8" date="2019-10-01">
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<Changeset component="org.gcube.dataanalysis.dataminer.1-5-9"
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date="2019-11-20">
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<Change>Fixed Content-Type support for files in the results of
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computations[ticket #18096]</Change>
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</Changeset>
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<Changeset component="org.gcube.dataanalysis.dataminer.1-5-8"
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date="2019-10-01">
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<Change>Fixed https link for output parameter [ticket #17659]</Change>
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</Changeset>
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<Changeset component="${groupId}.${artifactId}.1-5-7" date="2019-03-01">
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<Changeset component="org.gcube.dataanalysis.dataminer.1-5-7"
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date="2019-03-01">
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<Change>Updated https support [ticket #13024]</Change>
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</Changeset>
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<Changeset component="${groupId}.${artifactId}.1-5-6" date="2018-12-13">
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<Changeset component="org.gcube.dataanalysis.dataminer.1-5-6"
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date="2018-12-13">
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<Change>Added https support [ticket #13024]</Change>
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</Changeset>
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<Changeset component="${groupId}.${artifactId}.1-5-2" date="2017-12-13">
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<Changeset component="org.gcube.dataanalysis.dataminer.1-5-2"
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date="2017-12-13">
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<Change>added the right extension on output file</Change>
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<Change>lock file created on execution</Change>
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</Changeset>
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<Changeset component="${groupId}.${artifactId}.1-5-1" date="2017-09-14">
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<Changeset component="org.gcube.dataanalysis.dataminer.1-5-1"
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date="2017-09-14">
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<Change>added accounting on algorithm execution</Change>
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</Changeset>
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<Changeset component="${groupId}.${artifactId}.1-5-0" date="2017-07-31">
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<Changeset component="org.gcube.dataanalysis.dataminer.1-5-0"
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date="2017-07-31">
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<Change>service interface classes moved to wps project</Change>
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</Changeset>
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<Changeset component="${groupId}.${artifactId}.1-1-0" date="2016-10-03">
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<Changeset component="org.gcube.dataanalysis.dataminer.1-1-0"
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date="2016-10-03">
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<Change>First Release</Change>
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</Changeset>
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</ReleaseNotes>
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19
pom.xml
19
pom.xml
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@ -8,7 +8,7 @@
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</parent>
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<groupId>org.gcube.dataanalysis</groupId>
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<artifactId>dataminer</artifactId>
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<version>1.5.8-SNAPSHOT</version>
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<version>1.5.9-SNAPSHOT</version>
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<name>dataminer</name>
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<description>An e-Infrastructure service providing state-of-the art DataMining algorithms and ecological modelling approaches under the Web Processing Service (WPS) standard.</description>
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<scm>
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@ -125,25 +125,14 @@
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<version>4.11</version>
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<scope>test</scope>
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</dependency>
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<!-- <dependency> <groupId>org.gcube.common</groupId> <artifactId>common-authorization</artifactId>
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</dependency> <dependency> <groupId>org.gcube.core</groupId> <artifactId>common-scope</artifactId>
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</dependency> -->
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<dependency>
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<groupId>javassist</groupId>
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<artifactId>javassist</artifactId>
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<version>3.12.1.GA</version>
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</dependency>
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<!-- <dependency>
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<groupId>org.gcube.common</groupId>
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<artifactId>home-library-jcr</artifactId>
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<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
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</dependency>
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<dependency>
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<groupId>org.gcube.common</groupId>
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<artifactId>home-library</artifactId>
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<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
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</dependency> -->
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<dependency >
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<groupId>org.gcube.common</groupId>
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<artifactId>storagehub-client-library</artifactId>
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@ -21,7 +21,7 @@ import org.slf4j.LoggerFactory;
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public class OutputsManager {
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private static Logger LOGGER = LoggerFactory.getLogger(OutputsManager.class);
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private AlgorithmConfiguration config;
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private List<File> generatedFiles = new ArrayList<File>();
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@ -29,7 +29,7 @@ public class OutputsManager {
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private IClient storageclient;
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private String computationsession;
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private List<StoredData> provenanceData = new ArrayList<StoredData>();
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public List<StoredData> getProvenanceData() {
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return provenanceData;
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}
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@ -37,7 +37,7 @@ public class OutputsManager {
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public List<File> getGeneratedData() {
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return generatedFiles;
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}
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public List<File> getGeneratedFiles() {
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return generatedFiles;
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}
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@ -46,12 +46,13 @@ public class OutputsManager {
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return generatedTables;
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}
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public OutputsManager(AlgorithmConfiguration config,String computationsession) {
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public OutputsManager(AlgorithmConfiguration config, String computationsession) {
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this.config = config;
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this.computationsession=computationsession;
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this.computationsession = computationsession;
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}
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public LinkedHashMap<String, Object> createOutput(StatisticalType prioroutput, StatisticalType posterioroutput) throws Exception {
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public LinkedHashMap<String, Object> createOutput(StatisticalType prioroutput, StatisticalType posterioroutput)
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throws Exception {
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LinkedHashMap<String, Object> outputs = new LinkedHashMap<String, Object>();
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@ -66,10 +67,10 @@ public class OutputsManager {
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StatisticalTypeToWPSType postconverter = new StatisticalTypeToWPSType();
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postconverter.convert2WPSType(posterioroutput, false, config);
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generatedFiles.addAll(postconverter.getGeneratedFiles());
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LOGGER.debug("Generated Files "+generatedFiles);
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LOGGER.debug("Generated Files " + generatedFiles);
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generatedTables.addAll(postconverter.getGeneratedTables());
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LOGGER.debug("Generated Tables "+generatedFiles);
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LOGGER.debug("Generated Tables " + generatedFiles);
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LinkedHashMap<String, IOWPSInformation> postOutput = postconverter.outputSet;
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LinkedHashMap<String, IOWPSInformation> ndoutput = new LinkedHashMap<String, IOWPSInformation>();
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@ -102,21 +103,23 @@ public class OutputsManager {
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if (ConfigurationManager.useStorage()) {
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if (postInfo.getLocalMachineContent() != null) {
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// return the url from storage manager
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String storageurl = uploadFileOnStorage(postInfo.getLocalMachineContent(), postInfo.getMimetype());
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String storageurl = uploadFileOnStorage(postInfo.getLocalMachineContent(),
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postInfo.getMimetype());
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postInfo.setContent(storageurl);
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}
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}
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/*
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else if (postInfo.getLocalMachineContent() != null) {
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String url = "<wps:Reference mimeType=\""+postInfo.getMimetype()+"\" xlink:href=\""+postInfo.getContent()+"\" method=\"GET\"/>";
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LOGGER.debug("Reference URL: " + url);
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outputs.put(okey, url);
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}
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else*/
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* else if (postInfo.getLocalMachineContent() != null) { String
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* url = "<wps:Reference mimeType=\""+postInfo.getMimetype()
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* +"\" xlink:href=\""+postInfo.getContent()
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* +"\" method=\"GET\"/>"; LOGGER.debug("Reference URL: " +
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* url); outputs.put(okey, url); } else
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*/
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if (info != null) {
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LOGGER.debug("Found a corresponding output: " + okey);
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outputs.put(okey, postInfo.getContent());
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//add link to the file also among the non deterministic output
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// add link to the file also among the non deterministic
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// output
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if (postInfo.getLocalMachineContent() != null) {
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ndoutput.put(okey, postInfo);
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}
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@ -129,23 +132,23 @@ public class OutputsManager {
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System.gc();
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}
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XmlObject ndxml = generateNonDeterministicOutput(ndoutput);
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outputs.put("non_deterministic_output", ndxml);
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//safety check for declared output, i.e. a priori output
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for (String pkey:priorOutput.keySet()){
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if (outputs.get(pkey)==null){
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LOGGER.debug("Safety check: adding empty string for " + pkey+ " of type "+priorOutput.get(pkey).getClassname());
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// safety check for declared output, i.e. a priori output
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for (String pkey : priorOutput.keySet()) {
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if (outputs.get(pkey) == null) {
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LOGGER.debug("Safety check: adding empty string for " + pkey + " of type "
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+ priorOutput.get(pkey).getClassname());
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outputs.put(pkey, "");
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}
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}
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LOGGER.debug("OutputsManager outputs "+outputs);
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LOGGER.debug("OutputsManager outputs " + outputs);
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return outputs;
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}
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private void saveProvenanceData(IOWPSInformation info){
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private void saveProvenanceData(IOWPSInformation info) {
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String name = info.getName();
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String id = info.getName();
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DataProvenance provenance = DataProvenance.COMPUTED;
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@ -153,59 +156,97 @@ public class OutputsManager {
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String operator = config.getAgent();
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String computationId = computationsession;
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String type = info.getMimetype();
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/* if (info.getLocalMachineContent() != null) {
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type = StoredType.DATA;
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}
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*/
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/*
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* if (info.getLocalMachineContent() != null) { type = StoredType.DATA;
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* }
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*/
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String payload = info.getContent();
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StoredData data = new StoredData(name, info.getAbstractStr(),id, provenance, creationDate, operator, computationId, type,payload,config.getGcubeScope());
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StoredData data = new StoredData(name, info.getAbstractStr(), id, provenance, creationDate, operator,
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computationId, type, payload, config.getGcubeScope());
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provenanceData.add(data);
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}
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private void prepareForStoring() {
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LOGGER.debug("Preparing storage client");
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//String scope = config.getGcubeScope();
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//ScopeProvider.instance.set(scope);
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// String scope = config.getGcubeScope();
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// ScopeProvider.instance.set(scope);
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String serviceClass = "WPS";
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String serviceName = "wps.synch";
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String owner = config.getParam(ConfigurationManager.serviceUserNameParameterVariable);
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storageclient = new StorageClient(serviceClass, serviceName, owner, AccessType.SHARED, MemoryType.VOLATILE).getClient();
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storageclient = new StorageClient(serviceClass, serviceName, owner, AccessType.SHARED, MemoryType.VOLATILE)
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.getClient();
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LOGGER.debug("Storage client ready");
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}
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private String uploadFileOnStorage(String localfile, String mimetype) throws Exception {
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LOGGER.debug("Storing->Start uploading on storage the following file: " + localfile);
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File localFile = new File(localfile);
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String remotef = "/wps_synch_output/" +config.getAgent()+"/"+computationsession+"/"+ localFile.getName();
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storageclient.put(true).LFile(localfile).RFile(remotef);
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String remotef = "/wps_synch_output/" + config.getAgent() + "/" + computationsession + "/"
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+ localFile.getName();
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String contentType=retrieveContentType(localfile);
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LOGGER.debug("Retrieved Content-Type: "+contentType);
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if(contentType==null||contentType.isEmpty()){
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storageclient.put(true).LFile(localfile).RFile(remotef);
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} else {
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storageclient.put(true,contentType).LFile(localfile).RFile(remotef);
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}
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String url = storageclient.getHttpsUrl().RFile(remotef);
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/*
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if (config.getGcubeScope().startsWith("/gcube"))
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url = "http://data-d.d4science.org/uri-resolver/smp?smp-uri=" + url + "&fileName=" + localFile.getName() + "&contentType=" + mimetype;
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else
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url = "http://data.d4science.org/uri-resolver/smp?smp-uri=" + url+ "&fileName=" + localFile.getName() + "&contentType=" + mimetype;
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*/
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* if (config.getGcubeScope().startsWith("/gcube")) url =
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* "http://data-d.d4science.org/uri-resolver/smp?smp-uri=" + url +
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* "&fileName=" + localFile.getName() + "&contentType=" + mimetype; else
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* url = "http://data.d4science.org/uri-resolver/smp?smp-uri=" + url+
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* "&fileName=" + localFile.getName() + "&contentType=" + mimetype;
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*/
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LOGGER.info("Storing->Uploading finished - URL: " + url);
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return url;
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}
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private String retrieveContentType(String fileName) {
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String contentType=null;
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if (fileName != null && !fileName.isEmpty()) {
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String fileNameLowerCase = fileName.toLowerCase();
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if (fileNameLowerCase.endsWith(".html") || fileNameLowerCase.endsWith(".htm")) {
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contentType="text/html";
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} else {
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if (fileNameLowerCase.endsWith(".pdf")) {
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contentType="application/pdf";
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} else {
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if (fileNameLowerCase.endsWith(".log") || fileNameLowerCase.endsWith(".txt")) {
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contentType="text/plain";
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} else {
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if (fileNameLowerCase.endsWith(".json")) {
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contentType="application/json";
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} else {
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}
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}
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}
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}
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}
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return contentType;
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}
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public String cleanTagString(String tag) {
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return tag.replace(" ", "_").replaceAll("[\\]\\[!\"#$%&'()*+,\\./:;<=>?@\\^`{|}~-]", "");
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}
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public XmlObject generateNonDeterministicOutputPlain(LinkedHashMap<String, IOWPSInformation> ndoutput) throws Exception {
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String XMLString = "<gml:featureMember xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">\n" + " <d4science:output fid=\"outputcollection\">\n";
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public XmlObject generateNonDeterministicOutputPlain(LinkedHashMap<String, IOWPSInformation> ndoutput)
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throws Exception {
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String XMLString = "<gml:featureMember xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">\n"
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+ " <d4science:output fid=\"outputcollection\">\n";
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for (String key : ndoutput.keySet()) {
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IOWPSInformation info = ndoutput.get(key);
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String payload = info.getContent();
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String mimetype = info.getMimetype();
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XMLString += " <d4science:k_" + cleanTagString(key) + ">" + " <d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n" + " <d4science:Description><![CDATA[" + (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n" + " <d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + " </d4science:k_" + cleanTagString(key) + ">\n";
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XMLString += " <d4science:k_" + cleanTagString(key) + ">" + " <d4science:Data><![CDATA["
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+ payload + "]]></d4science:Data>\n" + " <d4science:Description><![CDATA["
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+ (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n"
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+ " <d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + " </d4science:k_"
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+ cleanTagString(key) + ">\n";
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}
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XMLString += " </d4science:output>\n" + "</gml:featureMember>\n";
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@ -219,16 +260,21 @@ public class OutputsManager {
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return xmlData;
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}
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public XmlObject generateNonDeterministicOutputCollection(LinkedHashMap<String, IOWPSInformation> ndoutput) throws Exception {
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String XMLString = "<ogr:FeatureCollection xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://ogr.maptools.org/ result_8751.xsd\" xmlns:ogr=\"http://ogr.maptools.org/\" xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">" +
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||||
"\n<gml:featureMember>\n" + " <ogr:Result fid=\"F0\">\n" +
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||||
" <d4science:output fid=\"outputcollection\">\n";
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||||
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||||
public XmlObject generateNonDeterministicOutputCollection(LinkedHashMap<String, IOWPSInformation> ndoutput)
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||||
throws Exception {
|
||||
String XMLString = "<ogr:FeatureCollection xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://ogr.maptools.org/ result_8751.xsd\" xmlns:ogr=\"http://ogr.maptools.org/\" xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">"
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||||
+ "\n<gml:featureMember>\n" + " <ogr:Result fid=\"F0\">\n"
|
||||
+ " <d4science:output fid=\"outputcollection\">\n";
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||||
|
||||
for (String key : ndoutput.keySet()) {
|
||||
IOWPSInformation info = ndoutput.get(key);
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||||
String payload = info.getContent();
|
||||
String mimetype = info.getMimetype();
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XMLString += " <d4science:k_" + cleanTagString(key) + ">" + " <d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n" + " <d4science:Description><![CDATA[" + (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n" + " <d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + " </d4science:k_" + cleanTagString(key) + ">\n";
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XMLString += " <d4science:k_" + cleanTagString(key) + ">" + " <d4science:Data><![CDATA["
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+ payload + "]]></d4science:Data>\n" + " <d4science:Description><![CDATA["
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||||
+ (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n"
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||||
+ " <d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + " </d4science:k_"
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||||
+ cleanTagString(key) + ">\n";
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}
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XMLString += " </d4science:output>\n" + " </ogr:Result>\n</gml:featureMember>\n</ogr:FeatureCollection>";
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||||
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||||
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@ -241,37 +287,46 @@ public class OutputsManager {
|
|||
|
||||
return xmlData;
|
||||
}
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||||
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||||
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||||
public XmlObject generateNonDeterministicOutput(LinkedHashMap<String, IOWPSInformation> ndoutput) throws Exception {
|
||||
|
||||
if (ndoutput.size()==0)
|
||||
|
||||
if (ndoutput.size() == 0)
|
||||
return null;
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||||
|
||||
String XMLString = "<ogr:FeatureCollection xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://ogr.maptools.org/ result_8751.xsd\" xmlns:ogr=\"http://ogr.maptools.org/\" xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">" +
|
||||
"\n<gml:featureMember>\n";
|
||||
|
||||
String XMLString = "<ogr:FeatureCollection xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://ogr.maptools.org/ result_8751.xsd\" xmlns:ogr=\"http://ogr.maptools.org/\" xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">"
|
||||
+ "\n<gml:featureMember>\n";
|
||||
int count = 0;
|
||||
for (String key : ndoutput.keySet()) {
|
||||
IOWPSInformation info = ndoutput.get(key);
|
||||
String payload = info.getContent();
|
||||
String mimetype = info.getMimetype();
|
||||
String abstractStr = info.getAbstractStr();
|
||||
|
||||
LOGGER.debug("IOWPS Information [name="+info.getName()+", abstr="+info.getAbstractStr()+", content="+info.getContent()+", def="+info.getDefaultVal()+"]");
|
||||
|
||||
if ((abstractStr==null || abstractStr.trim().length()==0) && (payload!= null && payload.trim().length()>0))
|
||||
|
||||
LOGGER.debug("IOWPS Information [name=" + info.getName() + ", abstr=" + info.getAbstractStr() + ", content="
|
||||
+ info.getContent() + ", def=" + info.getDefaultVal() + "]");
|
||||
|
||||
if ((abstractStr == null || abstractStr.trim().length() == 0)
|
||||
&& (payload != null && payload.trim().length() > 0))
|
||||
abstractStr = info.getName();
|
||||
else if (abstractStr == null)
|
||||
abstractStr = "";
|
||||
|
||||
//geospatialized
|
||||
// XMLString += " <ogr:Result fid=\"F" + count+ "\">" + "<ogr:geometryProperty><gml:Point><gml:coordinates>0,0</gml:coordinates></gml:Point></ogr:geometryProperty>"+ " <d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n" + " <d4science:Description><![CDATA[" + (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n" + " <d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + " </ogr:Result>\n";
|
||||
XMLString += " <ogr:Result fid=\"F" + count+ "\">" + " <d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n" + " <d4science:Description><![CDATA[" + abstractStr + "]]></d4science:Description>\n" + " <d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + " </ogr:Result>\n";
|
||||
|
||||
// geospatialized
|
||||
// XMLString += " <ogr:Result fid=\"F" + count+ "\">" +
|
||||
// "<ogr:geometryProperty><gml:Point><gml:coordinates>0,0</gml:coordinates></gml:Point></ogr:geometryProperty>"+
|
||||
// " <d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n"
|
||||
// + " <d4science:Description><![CDATA[" + (info.getAbstractStr() !=
|
||||
// null ? info.getAbstractStr() : "") +
|
||||
// "]]></d4science:Description>\n" + " <d4science:MimeType>" +
|
||||
// mimetype + "</d4science:MimeType>\n" + " </ogr:Result>\n";
|
||||
XMLString += " <ogr:Result fid=\"F" + count + "\">" + " <d4science:Data><![CDATA[" + payload
|
||||
+ "]]></d4science:Data>\n" + " <d4science:Description><![CDATA[" + abstractStr
|
||||
+ "]]></d4science:Description>\n" + " <d4science:MimeType>" + mimetype
|
||||
+ "</d4science:MimeType>\n" + " </ogr:Result>\n";
|
||||
count++;
|
||||
}
|
||||
XMLString += " </gml:featureMember>\n</ogr:FeatureCollection>";
|
||||
|
||||
|
||||
|
||||
|
||||
LOGGER.debug("Non deterministic output: " + XMLString);
|
||||
|
||||
XmlObject xmlData = XmlObject.Factory.newInstance();
|
||||
|
|
@ -281,12 +336,12 @@ public class OutputsManager {
|
|||
|
||||
return xmlData;
|
||||
}
|
||||
|
||||
public void shutdown(){
|
||||
try{
|
||||
storageclient.close();
|
||||
}catch(Exception e){
|
||||
|
||||
|
||||
public void shutdown() {
|
||||
try {
|
||||
storageclient.close();
|
||||
} catch (Exception e) {
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue