fix hasRole

RScripts/libraries.R

@@ -13,5 +13,6 @@ checkAndInstall("univOutl")
 checkAndInstall("simputation")
 checkAndInstall("VIM")
 checkAndInstall("rspa")
+checkAndInstall("SeleMix")
 
 print("Loading libraries...ok ")

RScripts/selemix/IS2_selemix.R

@@ -91,8 +91,12 @@ library("SeleMix")
 
 
 #stima completa
-mlest <- function(workset, y, x=NULL, ...) {
+mlest <- function(workset, s=S,x=X,y=Y,z=Z, ...) {
   #environment check
+   stdout <- vector('character')
+  con <- textConnection('stdout', 'wr', local = TRUE)
+
+
   if(missing(y)) stop('iSS Error: Missing TARGET Variable(s)')
   y <- matrix(as.numeric(workset[,Y]),ncol=length(Y),nrow=nrow(workset))
   if(!missing(x)) x <- matrix(as.numeric(workset[,X]),ncol=length(X),nrow=nrow(workset))
@@ -108,6 +112,7 @@ mlest <- function(workset, y, x=NULL, ...) {
   if(!exists("max.iter"))  max.iter=500
 
   #calcolo funzione
+  print("-------#calcolo funzione")
   est <- ml.est(y=y, x=x, model = model, lambda= as.numeric(lambda),  w= as.numeric(w), lambda.fix=lambda.fix, w.fix=w.fix, eps=as.numeric(eps), max.iter=as.numeric(max.iter), t.outl= as.numeric(t.outl), graph=FALSE)
   if(length(workset)>1) ypred <- matrix(est$ypred,nrow=nrow(workset),ncol=length(Y))
   else ypred <- as.matrix(est$ypred)
@@ -128,7 +133,8 @@ mlest <- function(workset, y, x=NULL, ...) {
   mod <- list(B=est$B, sigma=est$sigma, lambda=est$lambda, w=est$w )
   #setting output roles 
   roles <- list (P= predname, O="outlier", M=names(mod), G=names(report))
-  result <-list( out=data.frame(out,out1), roles= roles, mod=mod, report = report)
+  result <-list( out=data.frame(out,out1), roles= roles, mod=mod, report = report, "log" = stdout)
+
   return(result)
 }
 

db/is2-insert-selemix.sql

@@ -81,7 +81,7 @@ INSERT INTO `is2_step_instance` (`ID`, `METHOD`, `DESCR`, `LABEL`, `APP_SERVICE_
 -- PARAMETER
 -- -----------------------------------------------------
 INSERT INTO `is2_parameter` (`ID`, `NAME`, `DESCR`, `DEFAULT_VAL`, `JSON_TEMPLATE`)  VALUES (101,'MODEL','DATA MODEL',NULL,'{ "data": [], "schema": {"items": {"properties": { "lambda": {"required": true,"title": "Lambda","description":"Estimated value for the variance inflation factor","type": "number", "default":3,"minimum": 0.01,"maximum": 10 },"w": {"required": true,"title": "W","description":"Estimated value for the proportion of contaminated data","type": "number","default":0.05,"minimum": 0.01,"maximum": 1 }, "B": {"required": true,"title": "B","description":"Matrix of estimated regression coefficients","type": "number"}, "sigma": {"required": true,"title": "sigma","description":"Estimated covariance matrix","type": "number"} },"type": "object"},"type": "array" }, "options": {"type": "array","showActionsColumn": false,"hideAddItemsBtn": true }}');
-INSERT INTO `is2_parameter` (`ID`, `NAME`, `DESCR`, `DEFAULT_VAL`, `JSON_TEMPLATE`)  VALUES (102,'INPUT PARAMETERS','INPUT PARAMETERS',NULL,NULL);
+INSERT INTO `is2_parameter` (`ID`, `NAME`, `DESCR`, `DEFAULT_VAL`, `JSON_TEMPLATE`)  VALUES (102,'INPUT PARAMETERS','INPUT PARAMETERS',NULL,'{"data": [],"schema": { "properties": {"graph": {"required": true,"title": "Graph","description": "Activates graphic output","type": "number","default": 0,"minimum": 0.01,"maximum": 10},"model": {"required": true,"title": "Model","description": "Data Distribution: LN lognormal / N Normal","default": "LN"},"tot": {"title": "Tot","description": "Estimates of originals vector for the target variables"},"t.sel": {"title": "t.sel","description": "Optional vector of threshold values for selective edinting on the target variables"},"t.outl": {"required": true,"title": "t.outl","description": "Threshold value for posterior probabilities of identifying outliers","type": "number","default": 0.05,"minimum": 0.01,"maximum": 10},"eps": {"required": true,"title": "eps","description": "Tolerance for the log-likelihood convergence","type": "number","default": 0.0000001,"minimum": 0.0000001,"maximum": 1},"lambda.fix": {"required": true,"title": "lambda.fix","description": "TRUE if w is known","type": "number","default": 0,"maximum": 1 },"w.fix": {"required": true,"title": "w.fix","description": "TRUE if w is known","type": "number","default": 0,"minimum": 0.01,"maximum": 1}},"type": "object" }}');
 INSERT INTO `is2_parameter` (`ID`, `NAME`, `DESCR`, `DEFAULT_VAL`, `JSON_TEMPLATE`)  VALUES (103,'OUTPUT PARAMETERS','OUTPUT PARAMETERS - INFO REPORT',NULL,NULL);
 
 -- -----------------------------------------------------

src/main/java/it/istat/is2/catalogue/relais/service/RelaisService.java

@@ -157,7 +157,7 @@ public class RelaisService {
     }
 
     public Map<?, ?> resultTables(Long idelaborazione, Map<String, ArrayList<String>> ruoliVariabileNome,
-            Map<String, ArrayList<String>> worksetVariabili, Map<String, String> parametriMap) throws Exception {
+            Map<String, ArrayList<String>> worksetIn, Map<String, String> parametriMap) throws Exception {
 
         Map<String, Map<?, ?>> returnOut = new LinkedHashMap<>();
         Map<String, Map<?, ?>> worksetOut = new LinkedHashMap<>();
@@ -184,13 +184,13 @@ public class RelaisService {
             if (codeP_POST.equals(pPostVarname)) {
                 indexItems = 0;
 
-                for (String pPostValue : worksetVariabili.get(pPostVarname)) {
+                for (String pPostValue : worksetIn.get(pPostVarname)) {
                     if (Float.parseFloat(pPostValue) >= Float.parseFloat(paramTU)) {
                         StringBuffer pattern = new StringBuffer();
 
                         for (String ctVarname : ruoliVariabileNome.get(codContengencyTable)) {
                             if (!ctVarname.equals(IS2Const.WORKSET_FREQUENCY)) {
-                                String p = worksetVariabili.get(ctVarname).get(indexItems);
+                                String p = worksetIn.get(ctVarname).get(indexItems);
                                 pattern.append(Double.valueOf(p).intValue());
                             }
                         }
@@ -229,8 +229,8 @@ public class RelaisService {
 
         String firstFiledMA = ruoliVariabileNome.get(codeMatchingA).get(0);
         String firstFiledMB = ruoliVariabileNome.get(codeMatchingB).get(0);
-        int sizeA = worksetVariabili.get(firstFiledMA).size();
-        int sizeB = worksetVariabili.get(firstFiledMB).size();
+        int sizeA = worksetIn.get(firstFiledMA).size();
+        int sizeB = worksetIn.get(firstFiledMB).size();
 
         contingencyService.init(parametriMap.get(params_MatchingVariables));
         variabileNomeListOut.forEach(varname -> {
@@ -243,13 +243,13 @@ public class RelaisService {
             Map<String, String> valuesI = new HashMap<>();
             final Integer innerIA = Integer.valueOf(iA);
             variabileNomeListMA.forEach(varnameMA -> {
-                valuesI.put(varnameMA, worksetVariabili.get(varnameMA).get(innerIA));
+                valuesI.put(varnameMA, worksetIn.get(varnameMA).get(innerIA));
             });
 
             for (int iB = 0; iB < sizeB; iB++) {
                 final Integer innerIB = Integer.valueOf(iB);
                 variabileNomeListMB.forEach(varnameMB -> {
-                    valuesI.put(varnameMB, worksetVariabili.get(varnameMB).get(innerIB));
+                    valuesI.put(varnameMB, worksetIn.get(varnameMB).get(innerIB));
                 });
                 String pattern = contingencyService.getPattern(valuesI);
                 if (patternMatching.contains(pattern)) {

src/main/java/it/istat/is2/workflow/engine/EngineJava.java

@@ -72,9 +72,8 @@ public class EngineJava implements EngineService {
     private StepInstance stepInstance;
     private Map<String, ArrayList<StepRuntime>> dataMap;
     private Map<String, AppRole> ruoliAllMap;
-    private Map<String, ArrayList<String>> worksetVariabili;
+    private Map<String, ArrayList<String>> worksetInput;
     private Map<String, String> parametriMap;
-    private Map<String, ArrayList<String>> modelloMap;
     private Map<String, Map<?, ?>> worksetOut;
     private Map<String, Map<?, ?>> resultOut;
     private LinkedHashMap<String, ArrayList<String>> ruoliVariabileNome;
@@ -109,7 +108,7 @@ public void doAction() throws IllegalAccessException, IllegalArgumentException,
         Class<?>  fnameClass=Class.forName(fnameClassName);
         Method method = ReflectionUtils.findMethod( fnameClass, fname, Long.class, Map.class, Map.class, Map.class);
         Object instance=  context.getBean(fnameClass);
-        resultOut = (Map<String, Map<?, ?>>) method.invoke(instance, dataProcessing.getId(), ruoliVariabileNome, worksetVariabili, parametriMap);
+        resultOut = (Map<String, Map<?, ?>>) method.invoke(instance, dataProcessing.getId(), ruoliVariabileNome, worksetInput, parametriMap);
         worksetOut = (Map<String, Map<?, ?>>) resultOut.get(IS2Const.WF_OUTPUT_WORKSET);
         ruoliOutputStep = (LinkedHashMap<String, ArrayList<String>>) resultOut.get(IS2Const.WF_OUTPUT_ROLES);
         ruoliGruppoOutputStep = (HashMap<String, String>) resultOut.get(IS2Const.WF_OUTPUT_ROLES_GROUP);
@@ -152,11 +151,10 @@ public void prepareEnv() {
         // mappa delle colonne workset <nome campo, oggetto stepv>
         Map<String, ArrayList<StepRuntime>> dataRuoliStepVarMap = Utility.getMapCodiceRuoloStepVariabili(dataList);
         // mappa delle colonne workset <nome,lista valori>
-        worksetVariabili = Utility.getMapWorkSetValuesInRoles(dataMap, new DataTypeCls(IS2Const.DATA_TYPE_VARIABLE), ruoliInputStep.keySet());
+        worksetInput = Utility.getMapWorkSetValuesInRoles(dataMap, new DataTypeCls(IS2Const.DATA_TYPE_VARIABLE), ruoliInputStep.keySet());
 
         // PARAMETRI
         parametriMap = Utility.getMapWorkSetValuesParams(dataMap, new DataTypeCls(IS2Const.DATA_TYPE_PARAMETER));
-        modelloMap = Utility.getMapWorkSetValues(dataMap, new DataTypeCls(IS2Const.DATA_TYPE_MODEL));
         worksetOut = new HashMap<>();
 
         // associo il codice ruolo alla variabile

src/main/java/it/istat/is2/workflow/engine/EngineR.java

@@ -109,7 +109,6 @@ public class EngineR implements EngineService {
 	private Map<String, AppRole> ruoliAllMap;
 	private LinkedHashMap<String, ArrayList<String>> worksetVariabili;
 	private LinkedHashMap<String, ArrayList<String>> parametriMap;
-	private LinkedHashMap<String, ArrayList<String>> modelloMap;
 	private LinkedHashMap<String, ArrayList<String>> ruleset;
 	private LinkedHashMap<String, ArrayList<String>> worksetOut;
 	private HashMap<String, ArrayList<String>> ruoliVariabileNome;
@@ -143,9 +142,7 @@ public void init(DataProcessing dataProcessing, StepInstance stepInstance) throw
 		prepareEnv();
 		createConnection(serverRHost, serverRPort);
 		bindInputColumns(worksetVariabili, EngineR.IS2_WORKSET);
-		// bindInputParams(parametriMap);
-		// bindInputParams(modelloMap);
-		// bindInputParams(ruleset,eng);
+	    bindInputColumns(parametriMap, EngineR.IS2_PARAMETRI);
 		bindInputColumns(ruleset, EngineR.IS2_RULESET);
 		setRuoli(ruoliVariabileNome);
 
@@ -472,7 +469,6 @@ public void prepareEnv() {
 				ruoliInputStep.keySet());
 		// PARAMETRI
 		parametriMap = Utility.getMapWorkSetValues(dataMap, new DataTypeCls(IS2Const.DATA_TYPE_PARAMETER));
-		modelloMap = Utility.getMapWorkSetValues(dataMap, new DataTypeCls(IS2Const.DATA_TYPE_MODEL));
 		ruleset = Utility.getMapWorkSetValues(dataMap, new DataTypeCls(IS2Const.DATA_TYPE_RULESET));
 		worksetOut = new LinkedHashMap<>();
 

src/main/java/it/istat/is2/workflow/service/WorkflowService.java

@@ -78,6 +78,7 @@
 @Service
 public class WorkflowService {
 
+	private final String PATTERN_NAME="\\.|\\s"; 
 	@Autowired
 	private WorkSessionDao workSessionDao;
 	@Autowired
@@ -238,7 +239,7 @@ public void creaAssociazioni(MappingVarsFormBean form, DataProcessing dataProces
 				workset = new Workset();
 				DatasetColumn dscolumn = datasetColumnDao.findById((Long.parseLong(form.getVariable()[i]))).get();
 				workset.setName(
-						dscolumn.getDatasetFile().getFileLabel() + "_" + dscolumn.getName().replaceAll("\\.", "_"));
+						dscolumn.getDatasetFile().getFileLabel() + "_" + dscolumn.getName().replaceAll(PATTERN_NAME, "_"));
 				workset.setContents(dscolumn.getContents());
 				workset.setContentSize(workset.getContents().size());
 			}
@@ -281,7 +282,7 @@ public void updateAssociazione(MappingVarsFormBean form, DataProcessing dataProc
 			workset = new Workset();
 			DatasetColumn dscolumn = datasetColumnDao.findById((Long.parseLong(form.getVariable()[0])))
 					.orElse(new DatasetColumn());
-			workset.setName(dscolumn.getName().replaceAll("\\.", "_"));
+			workset.setName(dscolumn.getName().replaceAll(PATTERN_NAME, "_"));
 			workset.setContents(dscolumn.getContents());
 			workset.setContentSize(workset.getContents().size());
 		}
@@ -345,7 +346,7 @@ public void associaParametri(MappingVarsFormBean form, DataProcessing dataProces
 			stepRuntime.setDataProcessing(dataProcessing);
 			stepRuntime.setAppRole(sxruolo);
 			Workset workset = new Workset();
-			workset.setName(nomeparam);
+			workset.setName(nomeparam.replaceAll(PATTERN_NAME, "_"));
 			stepRuntime.setOrderCode(sxruolo.getOrder());
 			stepRuntime.setDataType(new DataTypeCls(IS2Const.DATA_TYPE_PARAMETER));
 			stepRuntime.setTypeIO(new TypeIO(IS2Const.TYPE_IO_INPUT));
@@ -567,7 +568,7 @@ public void creaAssociazionVarRole(DataProcessing dataProcessing,
 					String nameWorkset = "";
 					if (prefixDataset)
 						nameWorkset = dscolumn.getDatasetFile().getFileLabel() + "_";
-					nameWorkset += dscolumn.getName().replaceAll("\\.", "_");
+					nameWorkset += dscolumn.getName().replaceAll(PATTERN_NAME, "_");
 					workset.setName(nameWorkset);
 					workset.setContents(dscolumn.getContents());
 					workset.setContentSize(workset.getContents().size());

src/main/resources/templates/layout.html

@@ -75,13 +75,13 @@
             <button class="navbar-toggler sidebar-toggler d-md-down-none" type="button" data-toggle="sidebar-lg-show">
                 <span class="navbar-toggler-icon"></span>
             </button>
-            <ul class="nav navbar-nav d-md-down-none">
-                <li class="nav-item px-3" sec:authorize="hasAuthority('ADMIN')" >
+              <ul class="nav navbar-nav d-md-down-none">
+                <li class="nav-item px-3" sec:authorize="hasRole('ADMIN')" >
                     <a class="nav-link" th:href="@{/team}" role="button" aria-haspopup="true" aria-expanded="false">
                         <span th:title="#{Layout.team.link}">Team</span>
                     </a>
                 </li>
-                <li class="nav-item px-3" sec:authorize="hasAuthority('ADMIN')" >
+                <li class="nav-item px-3" sec:authorize="hasRole('ADMIN')" >
                     <a class="nav-link"  data-toggle="dropdown" href="#" role="button" aria-haspopup="true" aria-expanded="false">
                         <span th:title="#{Layout.settings.link}">Settings</span>
                     </a>