fixed code to load knowldge fragment; removed code support access to …

…labkey (that was already broken)
paulopinheiro1234 · Jun 19, 2020 · 1930a77 · 1930a77
1 parent 096b411
commit 1930a77
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Showing 97 changed files with 72 additions and 3,497 deletions.
diff --git a/app/org/hadatac/console/controllers/AuthApplication.java b/app/org/hadatac/console/controllers/AuthApplication.java
@@ -135,8 +135,6 @@ public Result doSignup() {
 	}
 
 	public Result doSignout() {
-		session().remove("LabKeyUserName");
-		session().remove("LabKeyPassword");
 		return this.authenticate.logout();
 	}
 }
diff --git a/app/org/hadatac/console/controllers/Version.java b/app/org/hadatac/console/controllers/Version.java
@@ -13,7 +13,7 @@
 public class Version extends Controller {
 
     public Result index() {
-        String code_version = "1.2.2";
+        String code_version = "1.2.3";
         String base_ontology = ConfigFactory.load().getString("hadatac.community.ont_prefix");
         String loaded_base_ontology = NameSpaces.getInstance().getNameByAbbreviation(base_ontology);
         String loaded_base_ontology_version = Ontology.getVersionFromAbbreviation(base_ontology);

diff --git a/app/org/hadatac/console/controllers/annotator/AutoAnnotator.java b/app/org/hadatac/console/controllers/annotator/AutoAnnotator.java
@@ -21,12 +21,10 @@
 import org.apache.commons.io.IOUtils;
 import org.apache.http.HttpStatus;
 
-import org.hadatac.entity.pojo.Credential;
 import org.hadatac.console.controllers.AuthApplication;
 import org.hadatac.console.controllers.annotator.routes;
 import org.hadatac.console.http.ResumableUpload;
 import org.hadatac.console.models.AssignOptionForm;
-import org.hadatac.console.models.LabKeyLoginForm;
 import org.hadatac.console.models.SysUser;
 import org.hadatac.console.views.html.annotator.*;
 import org.hadatac.console.views.html.triplestore.*;
@@ -41,15 +39,13 @@
 import org.hadatac.entity.pojo.STR;
 import org.hadatac.entity.pojo.ObjectCollection;
 import org.hadatac.entity.pojo.User;
-import org.hadatac.metadata.loader.LabkeyDataHandler;
 import org.hadatac.metadata.loader.URIUtils;
 import org.hadatac.utils.ConfigProp;
 import org.hadatac.utils.Feedback;
 import org.hadatac.utils.FileManager;
 import org.hadatac.utils.NameSpace;
 import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
-import org.labkey.remoteapi.CommandException;
 
 import com.fasterxml.jackson.annotation.JsonTypeInfo.Id;
 import com.typesafe.config.ConfigException.Null;
@@ -293,35 +289,6 @@ public Result postDownloadTemplates(String dir) {
         return postDownloadTemplates(dir);
     }
 
-    @Restrict(@Group(AuthApplication.DATA_MANAGER_ROLE))
-    public Result setLabKeyCredentials() {
-        return ok(syncLabkey.render("init", routes.AutoAnnotator.
-                postSetLabKeyCredentials().url(), ""));
-    }
-
-    @Restrict(@Group(AuthApplication.DATA_MANAGER_ROLE))
-    public Result postSetLabKeyCredentials() {
-        Form<LabKeyLoginForm> form = formFactory.form(LabKeyLoginForm.class).bindFromRequest();
-        String user_name = form.get().getUserName();
-        String password = form.get().getPassword();
-        LabkeyDataHandler loader = new LabkeyDataHandler(
-                ConfigProp.getLabKeySite(), "/", user_name, password);
-        try {
-            loader.checkAuthentication();
-            Credential cred = new Credential();
-            cred.setUserName(user_name);
-            cred.setPassword(password);
-            cred.save();
-        } catch(CommandException e) {
-            if("Unauthorized".equals(e.getMessage())){
-                return ok(syncLabkey.render("login_failed", "", ""));
-            }
-        }
-
-        return ok(main.render("Results", "", 
-                new Html("<h3>Your provided credentials are valid and saved!</h3>")));
-    }
-
     @Restrict(@Group(AuthApplication.DATA_OWNER_ROLE))
     public Result checkAnnotationLog(String dir, String fileId) {
         DataFile dataFile = DataFile.findById(fileId);

diff --git a/app/org/hadatac/console/controllers/annotator/PrepareIngestion.java b/app/org/hadatac/console/controllers/annotator/PrepareIngestion.java
@@ -66,11 +66,6 @@ public Result create(String dir, String fileId, String da_uri) {
 
         // OR create a new DA if the file is not associated with any existing DA
 
-        if (ConfigProp.getLabKeyLoginRequired() && session().get("LabKeyUserName") == null && session().get("LabKeyPassword") == null) {
-            return redirect(org.hadatac.console.controllers.triplestore.routes.LoadKB.logInLabkey(
-                    routes.PrepareIngestion.create(dir, fileId, da_uri).url()));
-        }
-
         String da_label = "";
         String new_da_uri = "";
 
@@ -96,9 +91,6 @@ public Result create(String dir, String fileId, String da_uri) {
         }
 
         da.saveToSolr();
-        if (ConfigProp.getLabKeyLoginRequired()) {
-            da.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-        }
 
         dataFile.setDataAcquisitionUri(da.getUri());
         dataFile.save();
@@ -145,10 +137,6 @@ public Result postRefine(String dir, String fileId, String da_uri, String messag
 
     @Restrict(@Group(AuthApplication.DATA_OWNER_ROLE))
     public Result selectStudy(String dir, String fileId, String da_uri) {
-        if (ConfigProp.getLabKeyLoginRequired() && session().get("LabKeyUserName") == null && session().get("LabKeyPassword") == null) {
-            return redirect(org.hadatac.console.controllers.triplestore.routes.LoadKB.logInLabkey(
-                    routes.PrepareIngestion.selectStudy(dir, fileId, da_uri).url()));
-        }
 
         List<Study> studies = Study.find();
 
@@ -157,10 +145,6 @@ public Result selectStudy(String dir, String fileId, String da_uri) {
 
     @Restrict(@Group(AuthApplication.DATA_OWNER_ROLE))
     public Result selectScope(String dir, String fileId, String da_uri, String std_uri) {
-        if (ConfigProp.getLabKeyLoginRequired() && session().get("LabKeyUserName") == null && session().get("LabKeyPassword") == null) {
-            return redirect(org.hadatac.console.controllers.triplestore.routes.LoadKB.logInLabkey(
-                    routes.PrepareIngestion.selectScope(dir, fileId, da_uri, std_uri).url()));
-        }
 
         String[] fields = null;
         String rowScope = null;
@@ -248,9 +232,6 @@ public Result processSelectStudy(String dir, String fileId, String da_uri) {
             da.setStudyUri(std_uri);
 
             da.saveToSolr();
-            if (ConfigProp.getLabKeyLoginRequired()) {
-                da.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-            }
 
             return ok(prepareIngestion.render(dir, fileId, da, "Updated Stream Specification with deployment information"));
         }
@@ -290,9 +271,6 @@ public Result processSelectScope(String dir, String fileId, String da_uri) {
         da.setCellScopeUri(cellScopeUriList);
 
         da.saveToSolr();
-        if (ConfigProp.getLabKeyLoginRequired()) {
-            da.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-        }
 
         return ok(prepareIngestion.render(dir, fileId, da, "Updated Stream Specification with scope information"));
     }
@@ -322,9 +300,6 @@ public Result processSelectDeployment(String dir, String fileId, String da_uri)
             da.setDeploymentUri(dep_uri);
 
             da.saveToSolr();
-            if (ConfigProp.getLabKeyLoginRequired()) {
-                da.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-            }
 
             return ok(prepareIngestion.render(dir, fileId, da, "Updated Stream Specification with deployment information"));
         }
@@ -358,9 +333,6 @@ public Result processSelectSchema(String dir, String fileId, String da_uri) {
             da.setSchemaUri(das_uri);
 
             da.saveToSolr();
-            if (ConfigProp.getLabKeyLoginRequired()) {
-                da.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-            }
 
             return ok(prepareIngestion.render(dir, fileId, da, "Updated Stream Specification with data acquisition schema information"));
         }
@@ -406,9 +378,6 @@ public Result removeAssociation(String dir, String fileId, String da_uri, String
         }
 
         da.saveToSolr();
-        if (ConfigProp.getLabKeyLoginRequired()) {
-            da.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-        }
 
         message = "Association with " + daComponent + " removed from the Stream Specification.";
         return ok(prepareIngestion.render(dir, fileId, da, message));
@@ -426,9 +395,6 @@ public Result completeDataAcquisition(String dir, String fileId, String da_uri)
         da.setStatus(9999);
 
         da.saveToSolr();
-        if (ConfigProp.getLabKeyLoginRequired()) {
-            da.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-        }
 
         message = "Stream Specification set as complete";
         return ok(prepareIngestion.render(dir, fileId, da, message));

diff --git a/app/org/hadatac/console/controllers/dataacquisitionmanagement/DataAcquisitionManagement.java b/app/org/hadatac/console/controllers/dataacquisitionmanagement/DataAcquisitionManagement.java
@@ -78,11 +78,6 @@ public Result postIndex(int stateId) {
 
     @Restrict(@Group(AuthApplication.DATA_OWNER_ROLE))
     public Result newDataAcquisition() {
-        if (ConfigProp.getLabKeyLoginRequired() && session().get("LabKeyUserName") == null
-                && session().get("LabKeyPassword") == null) {
-            return redirect(org.hadatac.console.controllers.triplestore.routes.LoadKB
-                    .logInLabkey(routes.DataAcquisitionManagement.newDataAcquisition().url()));
-        }
 
         final SysUser sysUser = AuthApplication.getLocalUser(session());
 

diff --git a/app/org/hadatac/console/controllers/dataacquisitionmanagement/DataAcquisitionScope.java b/app/org/hadatac/console/controllers/dataacquisitionmanagement/DataAcquisitionScope.java
@@ -28,10 +28,6 @@ public class DataAcquisitionScope extends Controller {
 
     @Restrict(@Group(AuthApplication.DATA_OWNER_ROLE))
     public Result create(String dir, String fileId, String da_uri) {
-        if (ConfigProp.getLabKeyLoginRequired() && session().get("LabKeyUserName") == null && session().get("LabKeyPassword") == null) {
-            return redirect(org.hadatac.console.controllers.triplestore.routes.LoadKB.logInLabkey(
-                    routes.DataAcquisitionScope.create(dir, fileId, da_uri).url()));
-        }
 
         STR da = null;
         String ownerEmail = AuthApplication.getLocalUser(session()).getEmail();

diff --git a/app/org/hadatac/console/controllers/dataacquisitionmanagement/EditDataAcquisition.java b/app/org/hadatac/console/controllers/dataacquisitionmanagement/EditDataAcquisition.java
@@ -29,7 +29,6 @@
 import org.hadatac.utils.ConfigProp;
 import org.joda.time.format.DateTimeFormat;
 import org.joda.time.format.DateTimeFormatter;
-import org.labkey.remoteapi.CommandException;
 
 import be.objectify.deadbolt.java.actions.Group;
 import be.objectify.deadbolt.java.actions.Restrict;
@@ -41,12 +40,6 @@ public class EditDataAcquisition extends Controller {
 
     @Restrict(@Group(AuthApplication.DATA_OWNER_ROLE))
     public Result index(String dir, String filename, String uri, boolean bChangeParam) {
-        if (ConfigProp.getLabKeyLoginRequired() && 
-                (session().get("LabKeyUserName") == null || session().get("LabKeyPassword") == null)
-                && bChangeParam) {
-            return redirect(org.hadatac.console.controllers.triplestore.routes.LoadKB.logInLabkey(
-                    routes.EditDataAcquisition.index(dir, filename, uri, bChangeParam).url()));
-        }
 
         final SysUser sysUser = AuthApplication.getLocalUser(session());
         try {
@@ -129,13 +122,9 @@ public Result processForm(String dir, String filename, String acquisitionUri, bo
                 }  
 
                 da.saveToSolr();
-                int nRowsAffected = 0;
-                if (ConfigProp.getLabKeyLoginRequired()) {
-                    nRowsAffected = da.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-                }
 
                 return ok(main.render("Results,", "", new Html("<h3>" 
-                        + String.format("%d row(s) have been inserted in Table \"DataAcquisition\"", nRowsAffected) 
+                        + String.format("Content have been inserted in Table \"DataAcquisition\"") 
                         + "</h3>")));
             }
         }

diff --git a/app/org/hadatac/console/controllers/dataacquisitionsearch/Downloader.java b/app/org/hadatac/console/controllers/dataacquisitionsearch/Downloader.java
@@ -24,7 +24,6 @@
 import org.hadatac.entity.pojo.User;
 import org.hadatac.utils.ConfigProp;
 import org.hadatac.utils.Feedback;
-import org.labkey.remoteapi.assay.Run;
 
 import be.objectify.deadbolt.java.actions.Group;
 import be.objectify.deadbolt.java.actions.Restrict;

diff --git a/app/org/hadatac/console/controllers/dataanalysis/NewFunction.java b/app/org/hadatac/console/controllers/dataanalysis/NewFunction.java
@@ -70,14 +70,6 @@ public Result processForm() {
 		// insert the new indicator content inside of the triplestore
 		ind.save();
 
-		// update/create new indicator in LabKey
-		if (ConfigProp.getLabKeyLoginRequired()) {
-		    int nRowsAffected = ind.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-		    if (nRowsAffected <= 0) {
-		        return badRequest("Failed to insert new indicator to LabKey!\n");
-		    }
-		}
-
 		return ok(newFunctionConfirm.render(ind));
     }
 }
diff --git a/app/org/hadatac/console/controllers/deployments/NewDeployment.java b/app/org/hadatac/console/controllers/deployments/NewDeployment.java
@@ -24,7 +24,6 @@
 import org.hadatac.entity.pojo.TriggeringEvent;
 import org.hadatac.metadata.loader.URIUtils;
 import org.hadatac.utils.ConfigProp;
-import org.labkey.remoteapi.CommandException;
 
 import be.objectify.deadbolt.java.actions.Group;
 import be.objectify.deadbolt.java.actions.Restrict;
@@ -57,10 +56,6 @@ public static SparqlQueryResults getQueryResults(String tabName) {
 
     @Restrict(@Group(AuthApplication.DATA_OWNER_ROLE))
     public Result index(String type, String dir, String filename, String da_uri, Integer page) {
-        if (ConfigProp.getLabKeyLoginRequired() && session().get("LabKeyUserName") == null && session().get("LabKeyPassword") == null) {
-            return redirect(org.hadatac.console.controllers.triplestore.routes.LoadKB.logInLabkey(
-                    routes.NewDeployment.index(type, dir, filename, da_uri, page).url()));
-        }
 
         if (type.equalsIgnoreCase("regular")) {
             return ok(newDeployment.render(
@@ -137,16 +132,8 @@ public Result processForm(String dir, String filename, String da_uri, Integer pa
             }
             System.out.println("NewDeployment: Loading existing DA : [" + da_uri + "]");
             da.setDeploymentUri(deployment.getUri());
-            String user_name = session().get("LabKeyUserName");
-            String password = session().get("LabKeyPassword");
-            if (user_name != null && password != null) {
-                if (ConfigProp.getLabKeyLoginRequired()) {
-                    nRowsOfDeployment = deployment.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-                    nRowsOfDA = da.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-                }
-                deployment.saveToTripleStore();
-                da.save();
-            }
+            deployment.saveToTripleStore();
+            da.save();
         } else {
             /* 
              *
@@ -173,16 +160,8 @@ public Result processForm(String dir, String filename, String da_uri, Integer pa
                     param, UserManagement.getUriByEmail(user.getEmail()));
 
             System.out.println("NewDeployment: Showing DA: " + dataAcquisition);
-            String user_name = session().get("LabKeyUserName");
-            String password = session().get("LabKeyPassword");
-            if (user_name != null && password != null) {
-                if (ConfigProp.getLabKeyLoginRequired()) {
-                    nRowsOfDeployment = deployment.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-                    nRowsOfDA = dataAcquisition.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-                }
-                deployment.saveToTripleStore();
-                dataAcquisition.save();
-            }
+            deployment.saveToTripleStore();
+            dataAcquisition.save();
         }
 
         return ok(deploymentConfirm.render("New Deployment created.", data, dir, filename, da_uri, page));

diff --git a/app/org/hadatac/console/controllers/fileviewer/DataDictionaryAnnotator.java b/app/org/hadatac/console/controllers/fileviewer/DataDictionaryAnnotator.java
@@ -32,7 +32,6 @@
 import org.hadatac.entity.pojo.UserGroup;
 import org.hadatac.utils.ConfigProp;
 import org.hadatac.utils.Feedback;
-import org.labkey.remoteapi.assay.Run;
 
 import be.objectify.deadbolt.java.actions.Group;
 import be.objectify.deadbolt.java.actions.Restrict;

diff --git a/app/org/hadatac/console/controllers/indicators/EditIndicator.java b/app/org/hadatac/console/controllers/indicators/EditIndicator.java
@@ -30,10 +30,6 @@ public class EditIndicator extends Controller {
 
 	@Restrict(@Group(AuthApplication.DATA_OWNER_ROLE))
 	public Result index(String ind_uri) {
-		if (ConfigProp.getLabKeyLoginRequired() && session().get("LabKeyUserName") == null && session().get("LabKeyPassword") == null) {
-			return redirect(org.hadatac.console.controllers.triplestore.routes.LoadKB.logInLabkey(
-					routes.EditIndicator.index(ind_uri).url()));
-		}
 
 		Indicator indicator = null;
 
@@ -111,13 +107,6 @@ public Result processForm(String ind_uri) {
 		// insert the new Indicator content inside of the triplestore regardless of any change -- the previous content has already been deleted
 		oldIndicator.save();
 
-		// update/create new Indicator in LabKey
-		if (ConfigProp.getLabKeyLoginRequired()) {
-		    int nRowsAffected = oldIndicator.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-		    if (nRowsAffected <= 0) {
-		        return badRequest("Failed to insert edited Indicator to LabKey!\n");
-		    }
-		}
 
 		return ok(indicatorConfirm.render("Edit Indicator", oldIndicator));
 	}

diff --git a/app/org/hadatac/console/controllers/indicators/NewIndicator.java b/app/org/hadatac/console/controllers/indicators/NewIndicator.java
@@ -27,10 +27,6 @@ public class NewIndicator extends Controller {
 
 	@Restrict(@Group(AuthApplication.DATA_OWNER_ROLE))
 	public Result index() {
-		if (ConfigProp.getLabKeyLoginRequired() && session().get("LabKeyUserName") == null && session().get("LabKeyPassword") == null) {
-			return redirect(org.hadatac.console.controllers.triplestore.routes.LoadKB.logInLabkey(
-					routes.NewIndicator.index().url()));
-		}
 		// may need addressing
 		Indicator indicator = new Indicator();
 
@@ -69,14 +65,6 @@ public Result processForm() {
 		// insert the new indicator content inside of the triplestore
 		ind.save();
 
-		// update/create new indicator in LabKey
-		if (ConfigProp.getLabKeyLoginRequired()) {
-		    int nRowsAffected = ind.saveToLabKey(session().get("LabKeyUserName"), session().get("LabKeyPassword"));
-		    if (nRowsAffected <= 0) {
-		        return badRequest("Failed to insert new indicator to LabKey!\n");
-		    }
-		}
-
 		return ok(newIndicatorConfirm.render(ind));
 	}
 }