3657 modular explore

doc/sphinx-guides/source/_static/installation/files/root/external-tools/awesomeTool.json

@@ -1,6 +1,7 @@
 {
   "displayName": "Awesome Tool",
   "description": "The most awesome tool.",
+  "type": "explore",
   "toolUrl": "https://awesometool.com",
   "toolParameters": {
     "queryParameters": [

doc/sphinx-guides/source/_static/installation/files/root/external-tools/dataExplorer.json

@@ -0,0 +1,19 @@
+{
+  "displayName": "Data Explorer",
+  "description": "The Data Explorer provides a GUI which lists the variables in a tabular data file allowing searching, charting and cross tabulation analysis.",
+  "type": "explore",
+  "toolUrl": "https://scholarsportal.github.io/Dataverse-Data-Explorer/",
+  "toolParameters": {
+    "queryParameters": [
+      {
+        "fileId": "{fileId}"
+      },
+      {
+        "siteUrl": "{siteUrl}"
+      },
+      {
+        "key": "{apiToken}"
+      }
+    ]
+  }
+}

doc/sphinx-guides/source/installation/external-tools.rst

@@ -13,10 +13,13 @@ External tools must be expressed in an external tool manifest file, a specific J
 
 .. literalinclude:: ../_static/installation/files/root/external-tools/awesomeTool.json
 
+``type`` is required and must be ``explore`` or ``configure``.
+
 In the example above, a mix of required and optional reserved words appear that can be used to insert dynamic values into tools. The supported values are:
 
 - ``{fileId}`` (required) - The Dataverse database ID of a file the external tool has been launched on.
-- ``{apiToken}`` (optional) - The Dataverse API token of the user launching the external tool.
+- ``{siteUrl}`` (optional) - The URL of the Dataverse installation that hosts the file with the fileId above.
+- ``{apiToken}`` (optional) - The Dataverse API token of the user launching the external tool, if available.
 
 Making an External Tool Available in Dataverse
 ----------------------------------------------

doc/sphinx-guides/source/user/data-exploration/index.rst

@@ -6,6 +6,8 @@
 Data Exploration Guide
 =======================================================
 
+Note that the installation of Dataverse you are using may have additional or different tools configured. Developers interested in creating tools should refer to the :doc:`/installation/external-tools` section of the Installation Guide.
+
 Contents:
 
 .. toctree::

scripts/database/upgrades/upgrade_v4.8.5_to_v4.9.sql

@@ -0,0 +1,2 @@
+ALTER TABLE externaltool ADD COLUMN type character varying(255);
+ALTER TABLE externaltool ALTER COLUMN type SET NOT NULL;

src/main/java/edu/harvard/iq/dataverse/DatasetPage.java

@@ -254,8 +254,10 @@ public enum DisplayMode {
 
     private Boolean hasRsyncScript = false;
 
-    List<ExternalTool> allTools = new ArrayList<>();
-    Map<Long,List<ExternalTool>> queriedFileTools = new HashMap<>(); 
+    List<ExternalTool> configureTools = new ArrayList<>();
+    List<ExternalTool> exploreTools = new ArrayList<>();
+    Map<Long, List<ExternalTool>> configureToolsByFileId = new HashMap<>();
+    Map<Long, List<ExternalTool>> exploreToolsByFileId = new HashMap<>();
 
     public Boolean isHasRsyncScript() {
         return hasRsyncScript;
@@ -1529,9 +1531,10 @@ private String init(boolean initFull) {
                         BundleUtil.getStringFromBundle("file.rsyncUpload.inProgressMessage.details"));
             }
         }
-
-        allTools = externalToolService.findAll();
-
+
+        configureTools = externalToolService.findByType(ExternalTool.Type.CONFIGURE);
+        exploreTools = externalToolService.findByType(ExternalTool.Type.EXPLORE);
+
         return null;
     }
 
@@ -4041,23 +4044,40 @@ public List<DatasetField> getDatasetSummaryFields() {
 
         return DatasetUtil.getDatasetSummaryFields(workingVersion, customFields);
     }
-
-    public List<ExternalTool> getExternalToolsForDataFile(Long fileId) {
-        List<ExternalTool> fileTools = queriedFileTools.get(fileId);
-        if(fileTools != null) { //if already queried before and added to list
-            return fileTools;
+
+    public List<ExternalTool> getConfigureToolsForDataFile(Long fileId) {
+        return getCachedToolsForDataFile(fileId, ExternalTool.Type.CONFIGURE);
+    }
+
+    public List<ExternalTool> getExploreToolsForDataFile(Long fileId) {
+        return getCachedToolsForDataFile(fileId, ExternalTool.Type.EXPLORE);
+    }
+
+    public List<ExternalTool> getCachedToolsForDataFile(Long fileId, ExternalTool.Type type) {
+        Map<Long, List<ExternalTool>> cachedToolsByFileId = new HashMap<>();
+        List<ExternalTool> externalTools = new ArrayList<>();
+        switch (type) {
+            case EXPLORE:
+                cachedToolsByFileId = exploreToolsByFileId;
+                externalTools = exploreTools;
+                break;
+            case CONFIGURE:
+                cachedToolsByFileId = configureToolsByFileId;
+                externalTools = configureTools;
+                break;
+            default:
+                break;
         }
-
-        DataFile dataFile = datafileService.find(fileId);         
-        fileTools = externalToolService.findExternalToolsByFile(allTools, dataFile);
-
-        queriedFileTools.put(fileId, fileTools); //add externalTools to map so we don't have to do the lifting again
-
-        return fileTools;    
+        List<ExternalTool> cachedTools = cachedToolsByFileId.get(fileId);
+        if (cachedTools != null) { //if already queried before and added to list
+            return cachedTools;
+        }
+        DataFile dataFile = datafileService.find(fileId);
+        cachedTools = ExternalToolServiceBean.findExternalToolsByFile(externalTools, dataFile);
+        cachedToolsByFileId.put(fileId, cachedTools); //add to map so we don't have to do the lifting again
+        return cachedTools;
     }
-
 
-
     Boolean thisLatestReleasedVersion = null;
 
     public boolean isThisLatestReleasedVersion() {

src/main/java/edu/harvard/iq/dataverse/FileDownloadHelper.java

@@ -7,7 +7,7 @@
 
 import edu.harvard.iq.dataverse.authorization.Permission;
 import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
-import edu.harvard.iq.dataverse.authorization.users.GuestUser;
+import edu.harvard.iq.dataverse.externaltools.ExternalTool;
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import static edu.harvard.iq.dataverse.util.JsfHelper.JH;
 import java.util.ArrayList;
@@ -260,7 +260,21 @@ public String startExploreDownloadLink(GuestbookResponse guestbookResponse, File
         requestContext.execute("PF('downloadPopup').hide()"); 
         return retVal;
     }
-
+
+     public void explore(GuestbookResponse guestbookResponse, FileMetadata fmd, ExternalTool externalTool) {
+
+         RequestContext requestContext = RequestContext.getCurrentInstance();
+         boolean valid = validateGuestbookResponse(guestbookResponse);
+
+         if (!valid) {
+             return;
+         }
+         // Rather that putting "Explore" in the database, we *could* put externalTool.getDisplayName() for "Data Explorer" or whatever.
+         guestbookResponse.setDownloadtype("Explore");
+         fileDownloadService.explore(guestbookResponse, fmd, externalTool);
+         requestContext.execute("PF('downloadPopup').hide()");
+     }
+
     public String startWorldMapDownloadLink(GuestbookResponse guestbookResponse, FileMetadata fmd){
 
         RequestContext requestContext = RequestContext.getCurrentInstance();

src/main/java/edu/harvard/iq/dataverse/FileDownloadServiceBean.java

@@ -1,14 +1,17 @@
 package edu.harvard.iq.dataverse;
 
+import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
 import edu.harvard.iq.dataverse.authorization.Permission;
+import edu.harvard.iq.dataverse.authorization.users.ApiToken;
 import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
-import edu.harvard.iq.dataverse.dataaccess.SwiftAccessIO;
+import edu.harvard.iq.dataverse.authorization.users.User;
 import edu.harvard.iq.dataverse.datasetutility.TwoRavensHelper;
 import edu.harvard.iq.dataverse.datasetutility.WorldMapPermissionHelper;
-import edu.harvard.iq.dataverse.engine.command.Command;
 import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
 import edu.harvard.iq.dataverse.engine.command.impl.CreateGuestbookResponseCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.RequestAccessCommand;
+import edu.harvard.iq.dataverse.externaltools.ExternalTool;
+import edu.harvard.iq.dataverse.externaltools.ExternalToolHandler;
 import edu.harvard.iq.dataverse.util.FileUtil;
 import java.io.IOException;
 import java.sql.Timestamp;
@@ -19,16 +22,13 @@
 import java.util.logging.Logger;
 import javax.ejb.EJB;
 import javax.ejb.Stateless;
-import javax.faces.context.ExternalContext;
 import javax.faces.context.FacesContext;
-import javax.faces.event.ValueChangeEvent;
 import javax.inject.Inject;
 import javax.inject.Named;
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
 import javax.servlet.ServletOutputStream;
 import javax.servlet.http.HttpServletResponse;
-import org.primefaces.context.RequestContext;
 
 /**
  *
@@ -57,6 +57,8 @@ public class FileDownloadServiceBean implements java.io.Serializable {
     DataverseServiceBean dataverseService;
     @EJB
     UserNotificationServiceBean userNotificationService;
+    @EJB
+    AuthenticationServiceBean authService;
 
     @Inject
     DataverseSession session;
@@ -147,8 +149,50 @@ public void startFileDownload(GuestbookResponse guestbookResponse, FileMetadata
         callDownloadServlet(format, fileMetadata.getDataFile().getId(), recordsWritten);
         logger.fine("issued file download redirect for filemetadata "+fileMetadata.getId()+", datafile "+fileMetadata.getDataFile().getId());
     }
-
-
+
+    public void explore(GuestbookResponse guestbookResponse, FileMetadata fmd, ExternalTool externalTool) {
+        if (externalTool == null) {
+            // Must be from the dataset page.
+            logger.fine("null, must be on dataset page");
+            externalTool = guestbookResponse.getExternalTool();
+        } else {
+            logger.fine("non-null, must be on file page");
+        }
+        ApiToken apiToken = null;
+        User user = session.getUser();
+        if (user instanceof AuthenticatedUser) {
+            AuthenticatedUser authenticatedUser = (AuthenticatedUser) user;
+            apiToken = authService.findApiTokenByUser(authenticatedUser);
+        }
+        DataFile dataFile = null;
+        if (fmd != null) {
+            dataFile = fmd.getDataFile();
+        } else {
+            if (guestbookResponse != null) {
+                dataFile = guestbookResponse.getDataFile();
+            }
+        }
+        // Note that the API token might be null. You can end up with "key=null" or whatever.
+        ExternalToolHandler externalToolHandler = new ExternalToolHandler(externalTool, dataFile, apiToken);
+        String toolUrl = externalToolHandler.getToolUrlWithQueryParams();
+        logger.fine("Exploring with " + toolUrl);
+        try {
+            FacesContext.getCurrentInstance().getExternalContext().redirect(toolUrl);
+        } catch (IOException ex) {
+            logger.info("Problem exploring with " + toolUrl + " - " + ex);
+        }
+        // fmd is null from the popup
+        if (guestbookResponse != null && guestbookResponse.isWriteResponse()
+                && ((fmd != null && fmd.getDataFile() != null) || guestbookResponse.getDataFile() != null)) {
+            if (guestbookResponse.getDataFile() == null && fmd != null) {
+                guestbookResponse.setDataFile(fmd.getDataFile());
+            }
+            if (fmd == null || !fmd.getDatasetVersion().isDraft()) {
+                writeGuestbookResponseRecord(guestbookResponse);
+            }
+        }
+    }
+
     public String startExploreDownloadLink(GuestbookResponse guestbookResponse, FileMetadata fmd){
 
         if (guestbookResponse != null && guestbookResponse.isWriteResponse() 

src/main/java/edu/harvard/iq/dataverse/FilePage.java

@@ -64,7 +64,8 @@ public class FilePage implements java.io.Serializable {
     private Dataset dataset;
     private List<DatasetVersion> datasetVersionsForTab;
     private List<FileMetadata> fileMetadatasForTab;
-    private List<ExternalTool> externalTools;
+    private List<ExternalTool> configureTools;
+    private List<ExternalTool> exploreTools;
 
     @EJB
     DataFileServiceBean datafileService;
@@ -161,10 +162,11 @@ public String init() {
 
           //  this.getFileDownloadHelper().setGuestbookResponse(guestbookResponse);
 
-            List<ExternalTool> allTools = externalToolService.findAll();
-
-            externalTools = externalToolService.findExternalToolsByFile(allTools, file);
-
+            if (file.isTabularData()) {
+                configureTools = externalToolService.findByType(ExternalTool.Type.CONFIGURE);
+                exploreTools = externalToolService.findByType(ExternalTool.Type.EXPLORE);
+            }
+
         } else {
 
             return permissionsWrapper.notFound();
@@ -769,8 +771,12 @@ public String getPublicDownloadUrl() {
         return FileUtil.getPublicDownloadUrl(systemConfig.getDataverseSiteUrl(), fileId);
     }
 
-    public List<ExternalTool> getExternalTools() {
-        return externalTools;
+    public List<ExternalTool> getConfigureTools() {
+        return configureTools;
     }
-
+
+    public List<ExternalTool> getExploreTools() {
+        return exploreTools;
+    }
+
 }

src/main/java/edu/harvard/iq/dataverse/GuestbookResponse.java

@@ -6,6 +6,7 @@
 package edu.harvard.iq.dataverse;
 
 import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
+import edu.harvard.iq.dataverse.externaltools.ExternalTool;
 import java.io.Serializable;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
@@ -81,6 +82,14 @@ public class GuestbookResponse implements Serializable {
     @Transient 
     private boolean writeResponse = true;
 
+    /**
+     * This transient variable is a place to temporarily retrieve the
+     * ExternalTool object from the popup when the popup is required on the
+     * dataset page.
+     */
+    @Transient
+    private ExternalTool externalTool;
+
     public boolean isWriteResponse() {
         return writeResponse;
     }
@@ -106,6 +115,14 @@ public void setFileFormat(String downloadFormat) {
         this.fileFormat = downloadFormat;
     }
 
+    public ExternalTool getExternalTool() {
+        return externalTool;
+    }
+
+    public void setExternalTool(ExternalTool externalTool) {
+        this.externalTool = externalTool;
+    }
+
     public GuestbookResponse(){
 
     }

src/main/java/edu/harvard/iq/dataverse/GuestbookResponseServiceBean.java

@@ -7,8 +7,8 @@
 
 import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
 import edu.harvard.iq.dataverse.authorization.users.User;
+import edu.harvard.iq.dataverse.externaltools.ExternalTool;
 import edu.harvard.iq.dataverse.util.BundleUtil;
-import static edu.harvard.iq.dataverse.util.JsfHelper.JH;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.text.SimpleDateFormat;
@@ -24,8 +24,6 @@
 import javax.ejb.TransactionAttribute;
 import javax.ejb.TransactionAttributeType;
 import javax.faces.application.FacesMessage;
-import javax.faces.component.EditableValueHolder;
-import javax.faces.component.UIComponent;
 import javax.faces.component.UIInput;
 import javax.faces.context.FacesContext;
 import javax.faces.model.SelectItem;
@@ -785,6 +783,26 @@ public GuestbookResponse modifyDatafileAndFormat(GuestbookResponse in, FileMetad
         return in;
     }
 
+    /**
+     * This method was added because on the dataset page when a popup is
+     * required, ExternalTool is null in the poup itself. The
+     * modifyDatafileAndFormat method above was copied and a new argument for
+     * ExternalTool was added.
+     */
+    public GuestbookResponse modifyDatafileAndFormat(GuestbookResponse in, FileMetadata fm, String format, ExternalTool externalTool) {
+        if (in != null && fm.getDataFile() != null) {
+            in.setFileFormat(format);
+            in.setDataFile(fm.getDataFile());
+        }
+        if (in != null && fm.getDatasetVersion() != null && fm.getDatasetVersion().isDraft() ) {
+            in.setWriteResponse(false);
+        }
+        if (in != null && externalTool != null) {
+            in.setExternalTool(externalTool);
+        }
+        return in;
+    }
+
     public Boolean validateGuestbookResponse(GuestbookResponse guestbookResponse, String type) {
 
         boolean valid = true;