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package eu.dnetlib.functionality.modular.ui.workflows.util;
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import java.io.StringReader;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import javax.annotation.Resource;
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import javax.xml.transform.stream.StreamSource;
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import org.apache.commons.lang.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.dom4j.Document;
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import org.dom4j.Element;
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import org.dom4j.io.SAXReader;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Maps;
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import com.google.common.collect.Sets;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.enabling.tools.ServiceLocator;
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import eu.dnetlib.functionality.modular.ui.workflows.objects.AdvancedMetaWorkflowDescriptor;
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import eu.dnetlib.functionality.modular.ui.workflows.objects.AtomicWorkflowDescriptor;
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import eu.dnetlib.functionality.modular.ui.workflows.objects.MetaWorkflowDescriptor;
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import eu.dnetlib.functionality.modular.ui.workflows.objects.NodeInfo;
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import eu.dnetlib.functionality.modular.ui.workflows.objects.NodeWithUserParams;
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import eu.dnetlib.miscutils.functional.xml.ApplyXslt;
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import eu.dnetlib.msro.workflows.nodes.NodeStatus;
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import eu.dnetlib.msro.workflows.util.WorkflowParam;
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import eu.dnetlib.msro.workflows.util.WorkflowsConstants.WorkflowStatus;
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public class ISLookupClient {
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@Resource(name = "lookupLocator")
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private ServiceLocator<ISLookUpService> lookupLocator;
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private static final Log log = LogFactory.getLog(ISLookupClient.class);
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private static final ApplyXslt metaWorkflowToHTML = new ApplyXslt(new StreamSource(
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ISLookupClient.class.getResourceAsStream("/eu/dnetlib/functionality/modular/workflows/xslt/metawf_profile2html.xslt")));
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public List<String> listSimpleWorflowSections() {
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final String xquery = "distinct-values(//METAWORKFLOW_SECTION/text())";
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try {
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return lookupLocator.getService().quickSearchProfile(xquery);
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} catch (ISLookUpException e) {
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log.error("Error obtaining worflowSections", e);
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return Lists.newArrayList();
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}
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}
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public List<MetaWorkflowDescriptor> listMetaWorflowsForSection(final String name) {
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final String query = queryForMetaWorkflowDescriptor(".//RESOURCE_TYPE/@value='MetaWorkflowDSResourceType' and .//METAWORKFLOW_SECTION='" + name + "'");
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try {
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return Lists.transform(lookupLocator.getService().quickSearchProfile(query), TransformerUtils.toMetaWorkflow);
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} catch (ISLookUpException e) {
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return Lists.newArrayList();
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}
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}
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public AtomicWorkflowDescriptor getAtomicWorkflow(final String id) {
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return TransformerUtils.toAtomicWorkflow.apply(getProfile(id));
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}
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public List<MetaWorkflowDescriptor> listMetaWorflowsForDatasource(final String dsId) {
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final String query = queryForMetaWorkflowDescriptor(".//RESOURCE_TYPE/@value='MetaWorkflowDSResourceType' and .//DATAPROVIDER/@id='" + dsId + "'");
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try {
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return Lists.transform(lookupLocator.getService().quickSearchProfile(query), TransformerUtils.toMetaWorkflow);
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} catch (ISLookUpException e) {
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return Lists.newArrayList();
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}
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}
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private String queryForMetaWorkflowDescriptor(final String cond) {
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return "for $x in /*[" + cond + "] order by $x//METAWORKFLOW_NAME return concat(" + "$x//RESOURCE_IDENTIFIER/@value, ' @@@ ', "
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+ "$x//METAWORKFLOW_NAME, ' @@@ ', " + "$x//METAWORKFLOW_NAME/@family, ' @@@ ', " + "$x//CONFIGURATION/@status)";
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}
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public String getProfile(final String id) {
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try {
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return lookupLocator.getService().getResourceProfile(id);
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} catch (ISLookUpException e) {
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log.error("Error finding profile: " + id, e);
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return null;
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}
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}
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public NodeInfo getNodeInfo(final String wfId, final String nodeName) {
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try {
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final String query = "/*[.//RESOURCE_IDENTIFIER/@value='" + wfId + "']//NODE[@name='" + nodeName + "']";
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final String xml = lookupLocator.getService().getResourceProfileByQuery(query);
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return TransformerUtils.toNodeInfo.apply(xml);
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} catch (Exception e) {
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log.error("Error accessing node " + nodeName + " of wf " + wfId, e);
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return new NodeInfo("", "", new ArrayList<WorkflowParam>());
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}
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}
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public Set<String> getNotConfiguredNodes(final String id) {
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final String query = "for $x in (/*[.//RESOURCE_IDENTIFIER/@value='" + id + "']//NODE) "
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+ "where count($x//PARAM[@required='true' and string-length(normalize-space(.)) = 0]) > 0 " + "return $x/@name/string()";
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try {
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final List<String> list = lookupLocator.getService().quickSearchProfile(query);
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return Sets.newHashSet(list);
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} catch (Exception e) {
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log.error("Error executing xquery: " + query, e);
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return Sets.newHashSet();
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}
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}
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public AdvancedMetaWorkflowDescriptor getMetaWorkflow(final String id) {
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final String xml = getProfile(id);
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final Set<String> innerWfs = Sets.newHashSet();
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try {
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final SAXReader reader = new SAXReader();
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final Document doc = reader.read(new StringReader(xml));
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final String name = doc.valueOf("//METAWORKFLOW_NAME");
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final String family = doc.valueOf("//METAWORKFLOW_NAME/@family");
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final String email = doc.valueOf("//ADMIN_EMAIL");
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final boolean scheduled = Boolean.valueOf(doc.valueOf("//SCHEDULING/@enabled"));;
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final String cronExpression = doc.valueOf("//SCHEDULING/CRON");;
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final int minInterval = Integer.parseInt(doc.valueOf("//SCHEDULING/MININTERVAL"));
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final WorkflowStatus status = WorkflowStatus.valueOf(doc.valueOf("//CONFIGURATION/@status"));
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for (Object o : doc.selectNodes("//WORKFLOW")) {
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final Element wf = (Element) o;
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final String wfId = wf.valueOf("@id");
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innerWfs.add(wfId);
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try {
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final String profile = lookupLocator.getService().getResourceProfile(wfId);
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final Document doc2 = (new SAXReader()).read(new StringReader(profile));
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final String start = doc2.valueOf("//CONFIGURATION/@start");
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final String date = doc2.valueOf("//STATUS/LAST_EXECUTION_DATE");
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wf.addAttribute("start", start);
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if (!StringUtils.isEmpty(date)) {
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wf.addAttribute("date", date);
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}
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if ("disabled".equalsIgnoreCase(start)) {
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wf.addAttribute("disabled", "true");
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}
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if (doc2.selectNodes("//PARAM[@required='true' and string-length(normalize-space(.)) = 0]").isEmpty()) {
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wf.addAttribute("configured", "true");
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} else {
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wf.addAttribute("configured", "false");
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}
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} catch (Exception e) {
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log.error("Error obtaining wf status", e);
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wf.addAttribute("status", NodeStatus.NOT_CONFIGURED.toString());
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}
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}
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// TODO delete this
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ApplyXslt metaWorkflowToHTML = new ApplyXslt(new StreamSource(
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ISLookupClient.class.getResourceAsStream("/eu/dnetlib/functionality/modular/workflows/xslt/metawf_profile2html.xslt")));
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final String html = metaWorkflowToHTML.evaluate(doc.asXML());
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return new AdvancedMetaWorkflowDescriptor(id, name, email, scheduled, cronExpression, minInterval, status, family, innerWfs, html);
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} catch (Exception e) {
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log.error("Error parsing xml: " + xml, e);
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return new AdvancedMetaWorkflowDescriptor("", "", "", false, "", 0, WorkflowStatus.MISSING, "", new HashSet<String>(), "");
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}
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}
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public Map<String, String> listRepoHiWorkflows() {
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final Map<String, String> map = Maps.newHashMap();
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final String query = "for $x in collection('/db/DRIVER/WorkflowDSResources/WorkflowDSResourceType') " + "where $x//WORKFLOW_TYPE='REPO_HI' "
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+ "return concat($x//RESOURCE_IDENTIFIER/@value, ' @@@ ', $x//WORKFLOW_NAME)";
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try {
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for (String s : lookupLocator.getService().quickSearchProfile(query)) {
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String[] arr = s.split("@@@");
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map.put(arr[0].trim(), arr[1].trim());
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}
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} catch (Exception e) {
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log.error("Error executing xquery: " + query, e);
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}
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return map;
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}
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public List<String> listMetaWorflowsForWfId(final String wfId) {
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final String query = "for $x in collection('/db/DRIVER/MetaWorkflowDSResources/MetaWorkflowDSResourceType') where $x//WORKFLOW/@id='" + wfId
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+ "' return $x//RESOURCE_IDENTIFIER/@value/string()";
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try {
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return lookupLocator.getService().quickSearchProfile(query);
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} catch (ISLookUpException e) {
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log.error("Error executing xquery: " + query, e);
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return Lists.newArrayList();
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}
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}
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public boolean isExecutable(final String metaWfId) {
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final String query = "for $x in collection('/db/DRIVER/MetaWorkflowDSResources/MetaWorkflowDSResourceType')[.//RESOURCE_IDENTIFIER/@value = '"
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+ metaWfId
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+ "']//WORKFLOW/@id \n"
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+ "for $y in collection('/db/DRIVER/WorkflowDSResources/WorkflowDSResourceType')[.//RESOURCE_IDENTIFIER/@value = $x]//PARAM[@required='true' and string-length(normalize-space(.)) = 0] \n"
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+ "return $y";
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try {
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return lookupLocator.getService().quickSearchProfile(query).isEmpty();
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} catch (ISLookUpException e) {
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log.error("Error executing xquery: " + query, e);
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return false;
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}
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}
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public List<String> listWfFamilies() {
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final String query = "distinct-values(for $x in collection('/db/DRIVER/MetaWorkflowDSResources/MetaWorkflowDSResourceType') "
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+ "where string-length($x//DATAPROVIDER/@id) > 0 return $x//METAWORKFLOW_NAME/@family/string())";
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try {
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return lookupLocator.getService().quickSearchProfile(query);
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} catch (ISLookUpException e) {
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log.error("Error executing xquery: " + query, e);
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return Lists.newArrayList();
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}
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}
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public String getDatasourceName(final String dsId) {
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final String query = "/*[.//RESOURCE_IDENTIFIER/@value='" + dsId + "']//OFFICIAL_NAME/text()";
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try {
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return lookupLocator.getService().getResourceProfileByQuery(query);
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} catch (ISLookUpException e) {
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log.error("Error executing xquery: " + query, e);
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return "UNKNOWN";
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}
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}
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243
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public List<NodeWithUserParams> listWorkflowUserParams(final String wfId) {
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final List<NodeWithUserParams> res = Lists.newArrayList();
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246
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final String xml = getProfile(wfId);
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try {
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final SAXReader reader = new SAXReader();
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final Document doc = reader.read(new StringReader(xml));
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251
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for (Object o : doc.selectNodes("//NODE[.//PARAM/@managedBy='user']")) {
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final Element node = (Element) o;
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final String name = node.valueOf("@name");
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final String desc = node.valueOf("./DESCRIPTION");
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final List<WorkflowParam> params = Lists.newArrayList();
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for (Object k : node.selectNodes(".//PARAM[@managedBy='user']")) {
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final Element param = (Element) k;
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final String key = param.valueOf("@name");
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final boolean required = "true".equalsIgnoreCase(param.valueOf("@required"));
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final String type = param.valueOf("@type");
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final String function = param.valueOf("@function");
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final String value = param.getText();
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params.add(new WorkflowParam(key, value, required, true, type, function));
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}
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res.add(new NodeWithUserParams(name, desc, params));
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}
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} catch (Exception e) {
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log.error("Error obtaing params of wf: " + wfId, e);
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}
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272
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return res;
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274
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}
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275
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276
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}
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