Merge '3747-compute-button-UI' into 2909-3747-swift-compute-button #2909

 #3747

This is a new branch based on 3747-swift-with-derivative-file-support

Conflicts (3747-swift-with-derivative-file-support wins):
doc/sphinx-guides/source/installation/config.rst
src/main/java/edu/harvard/iq/dataverse/dataaccess/DataAccess.java
src/main/java/edu/harvard/iq/dataverse/dataaccess/SwiftAccessIO.java

doc/sphinx-guides/source/installation/config.rst

@@ -637,7 +637,7 @@ The default checksum algorithm used is MD5 and should be sufficient for establis
 :ShibPassiveLoginEnabled
 ++++++++++++++++++++++++
 
-Set ``ShibPassiveLoginEnabled`` to true to enable passive login for Shibboleth. When this feature is enabled, an additional Javascript file (isPassive.js) will be loaded for every page. It will generate a passive login request to your Shibboleth SP when an anonymous user navigates to the site. A cookie named "_check_is_passive_dv" will be created to keep track of whether or not a passive login request has already been made for the user.
+Set ``:ShibPassiveLoginEnabled`` to true to enable passive login for Shibboleth. When this feature is enabled, an additional Javascript file (isPassive.js) will be loaded for every page. It will generate a passive login request to your Shibboleth SP when an anonymous user navigates to the site. A cookie named "_check_is_passive_dv" will be created to keep track of whether or not a passive login request has already been made for the user.
 
 This implementation follows the example on the Shibboleth wiki documentation page for the isPassive feature: https://wiki.shibboleth.net/confluence/display/SHIB2/isPassive
 
@@ -648,3 +648,10 @@ It is recommended that you configure additional error handling for your Service
 You can set the value of "#THIS PAGE#" to the url of your Dataverse homepage, or any other page on your site that is accessible to anonymous users and will have the isPassive.js file loaded.
 
 ``curl -X PUT -d true http://localhost:8080/api/admin/settings/:ShibPassiveLoginEnabled``
+
+:ComputeBaseUrl
++++++++++++++++
+
+Set the base URL for the "Compute" button for a dataset.
+
+``curl -X PUT -d 'https://giji.massopencloud.org/application/dataverse?containerName=' http://localhost:8080/api/admin/settings/:ComputeBaseUrl``

src/main/java/Bundle.properties

@@ -42,6 +42,8 @@ curator=Curator
 explore=Explore
 download=Download
 deaccession=Deaccession
+share=Share
+link=Link
 linked=Linked
 harvested=Harvested
 apply=Apply
@@ -1250,6 +1252,10 @@ file.originalChecksumType=Original File {0}
 file.checksum.exists.tip=A file with this checksum already exists in the dataset.
 file.selectedThumbnail=Thumbnail
 file.selectedThumbnail.tip=The thumbnail for this file is used as the default thumbnail for the dataset. Click 'Advanced Options' button of another file to select that file.
+file.cloudStorageAccess=Cloud Storage Access
+file.cloudStorageAccess.tip=The container name for this dataset needed to access files in cloud storage.
+file.copy=Copy
+file.compute=Compute
 
 file.metaData.dataFile.dataTab.variables=Variables
 file.metaData.dataFile.dataTab.observations=Observations
@@ -1288,6 +1294,7 @@ file.spss-porExtraLabels.title=Upload an additional text file with extra variabl
 file.spss-porExtraLabels.selectToAddBtn=Select File to Add
 file.ingestFailed=Tabular Data Ingest Failed
 file.explore.twoRavens=TwoRavens
+file.map=Map
 file.mapData=Map Data
 file.mapData.worldMap=WorldMap
 file.mapData.unpublished.header=Data Not Published
@@ -1453,7 +1460,7 @@ file.downloadDialog.header=Download File
 file.downloadDialog.tip=Please confirm and/or complete the information needed below in order to download files in this dataset.
 file.downloadDialog.termsTip=I accept these Terms of Use.
 
-file.search.placeholder=Search these data files...
+file.search.placeholder=Search this dataset...
 file.results.btn.sort=Sort
 file.results.btn.sort.option.nameAZ=Name (A-Z)
 file.results.btn.sort.option.nameZA=Name (Z-A)
@@ -1517,7 +1524,7 @@ file.general.metadata.label=General Metadata
 file.description.label=Description
 file.tags.label=Tags
 file.lastupdated.label=Last Updated
-file.DatasetVersion=Dataset Version
+file.DatasetVersion=Version
 
 file.metadataTab.fileMetadata.header=File Metadata
 file.metadataTab.fileMetadata.persistentid.label=Data File Persistent ID

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

@@ -1,6 +1,7 @@
 package edu.harvard.iq.dataverse;
 
 import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
+import edu.harvard.iq.dataverse.dataaccess.SwiftAccessIO;
 import edu.harvard.iq.dataverse.authorization.Permission;
 import edu.harvard.iq.dataverse.authorization.providers.builtin.BuiltinUserServiceBean;
 import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
@@ -369,6 +370,46 @@ public String getDataverseSiteUrl() {
     public void setDataverseSiteUrl(String dataverseSiteUrl) {
         this.dataverseSiteUrl = dataverseSiteUrl;
     }
+
+    public String getSwiftContainerName(){
+        String swiftContainerName = null;
+        String swiftFolderPathSeparator = "-";
+        if (persistentId != null) {
+            dataset = datasetService.findByGlobalId(persistentId); 
+            String authorityNoSlashes = dataset.getAuthority().replace(dataset.getDoiSeparator(), swiftFolderPathSeparator);
+            swiftContainerName = dataset.getProtocol() + swiftFolderPathSeparator + authorityNoSlashes.replace(".", swiftFolderPathSeparator)
+                + swiftFolderPathSeparator + dataset.getIdentifier();
+            logger.info("Swift container name: " + swiftContainerName);
+        }
+
+        return swiftContainerName;
+    }
+
+    //assumes that *ALL* files in ONE specified container are stored in swift backend 
+    //could be changed 
+    //SF 
+    public Boolean isSwiftStorage(){
+        Boolean swiftBool = false;
+        //dataset = datasetService.findByGlobalId(persistentId);
+        Long datasetVersion = workingVersion.getId();
+        if (datasetVersion != null) {
+                int unlimited = 0;
+                int maxResults = unlimited;
+            List<FileMetadata> metadatas = datafileService.findFileMetadataByDatasetVersionId(datasetVersion, maxResults, fileSortField, fileSortOrder);        
+            logger.info("metadatas " + metadatas);
+            if (metadatas != null && metadatas.size() > 0) {
+                if ("swift".equals(System.getProperty("dataverse.files.storage-driver-id")) 
+                    && metadatas.get(0).getDataFile().getStorageIdentifier().startsWith("swift://")) {
+                    swiftBool = true;
+                }
+            }
+        }
+        return swiftBool;
+    }
+
+    public String getComputeUrl() {
+        return settingsService.getValueForKey(SettingsServiceBean.Key.ComputeBaseUrl) + getSwiftContainerName();
+    }
 
     public DataFile getSelectedDownloadFile() {
         return selectedDownloadFile;

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

@@ -225,6 +225,7 @@ public List< String[]> getExporters(){
         return retList;  
     }
 
+
     public String restrictFile(boolean restricted) {
         String fileNames = null;
         String termsOfAccess = this.fileMetadata.getDatasetVersion().getTermsOfUseAndAccess().getTermsOfAccess();        
@@ -542,7 +543,30 @@ public void setSelectedTabIndex(int selectedTabIndex) {
         this.selectedTabIndex = selectedTabIndex;
     }
 
-
+    public Boolean isSwiftStorage () {
+        Boolean swiftBool = false;
+        if (file.getStorageIdentifier().startsWith("swift://")){
+            swiftBool = true;
+        }
+        return swiftBool;
+    }
+
+    public String getSwiftContainerName(){
+        String swiftContainerName = null;
+        String swiftFolderPathSeparator = "-";
+
+        String authorityNoSlashes = file.getOwner().getAuthority().replace(file.getOwner().getDoiSeparator(), swiftFolderPathSeparator);
+        swiftContainerName = file.getOwner().getProtocol() + swiftFolderPathSeparator + authorityNoSlashes.replace(".", swiftFolderPathSeparator)
+            + swiftFolderPathSeparator + file.getOwner().getIdentifier();
+        logger.info("Swift container name: " + swiftContainerName);
+
+        return swiftContainerName;
+    }
+
+    public String getComputeUrl() {
+        return settingsService.getValueForKey(SettingsServiceBean.Key.ComputeBaseUrl) + getSwiftContainerName();
+    }
+
     private List<DataFile> allRelatedFiles() {
         List<DataFile> dataFiles = new ArrayList();
         DataFile dataFileToTest = fileMetadata.getDataFile();

src/main/java/edu/harvard/iq/dataverse/dataaccess/DataAccess.java

@@ -103,7 +103,7 @@ public static DataFileIO createNewDataFileIO(DataFile df, String storageTag, Str
 
         dataFileIO.open(DataAccessOption.WRITE_ACCESS);
         return dataFileIO;
-    }    
-    
+    }
+
 
-}
+}

src/main/java/edu/harvard/iq/dataverse/dataaccess/DataFileIO.java

@@ -146,6 +146,8 @@ public DataFileIO(DataFile dataFile, DataAccessRequest req) {
     private String varHeader;
     private String errorMessage;
 
+    //private String swiftContainerName;
+
     private Boolean isLocalFile = false;
     private Boolean isRemoteAccess = false;
     private Boolean isHttpAccess = false;
@@ -228,6 +230,10 @@ public String getRemoteUrl() {
         return remoteUrl;
     }
 
+    // public String getSwiftContainerName(){
+    //     return swiftContainerName;
+    // }
+
     public GetMethod getHTTPMethod() {
         return method;
     }
@@ -313,6 +319,10 @@ public void setRemoteUrl(String u) {
         remoteUrl = u;
     }
 
+    // public void setSwiftContainerName(String u){
+    //     swiftContainerName = u;
+    // }
+
     public void setHTTPMethod(GetMethod hm) {
         method = hm;
     }

src/main/java/edu/harvard/iq/dataverse/dataaccess/SwiftAccessIO.java

@@ -455,13 +455,14 @@ private StoredObject initializeSwiftFileObject(boolean writeAccess, String auxIt
             swiftEndPoint = p.getProperty("swift.default.endpoint");
 
             //swiftFolderPath = this.getDataFile().getOwner().getDisplayName();
-            String swiftFolderPathSeparator = "_";
+            String swiftFolderPathSeparator = "-";
             String authorityNoSlashes = this.getDataFile().getOwner().getAuthority().replace(this.getDataFile().getOwner().getDoiSeparator(), swiftFolderPathSeparator);
             swiftFolderPath = this.getDataFile().getOwner().getProtocol() + swiftFolderPathSeparator +
                 authorityNoSlashes.replace(".", swiftFolderPathSeparator) +
                 swiftFolderPathSeparator + this.getDataFile().getOwner().getIdentifier();
 
             swiftFileName = storageIdentifier;
+            //setSwiftContainerName(swiftFolderPath);
             //swiftFileName = this.getDataFile().getDisplayName();
             //Storage Identifier is now updated after the object is uploaded on Swift.
             this.getDataFile().setStorageIdentifier("swift://"+swiftEndPoint+":"+swiftFolderPath+":"+swiftFileName);
@@ -589,6 +590,8 @@ Account authenticateWithSwift(String swiftEndPoint) throws IOException {
         String swiftEndPointSecretKey = p.getProperty("swift.password." + swiftEndPoint);
         String swiftEndPointTenantName = p.getProperty("swift.tenant." + swiftEndPoint);
         String swiftEndPointAuthMethod = p.getProperty("swift.auth_type." + swiftEndPoint);
+        String swiftEndPointUrl = p.getProperty("swift.swift_endpoint." + swiftEndPoint);
+        String swiftEndPointTenantId = p.getProperty("swift.tenant_id." + swiftEndPoint);
 
         if (swiftEndPointAuthUrl == null || swiftEndPointUsername == null || swiftEndPointSecretKey == null
                 || "".equals(swiftEndPointAuthUrl) || "".equals(swiftEndPointUsername) || "".equals(swiftEndPointSecretKey)) {
@@ -611,6 +614,7 @@ Account authenticateWithSwift(String swiftEndPoint) throws IOException {
             if (swiftEndPointAuthMethod.equals("keystone")) {
                 account = new AccountFactory()
                         .setTenantName(swiftEndPointTenantName)
+                        // .setTenantId(swiftEndPointTenantId)
                         .setUsername(swiftEndPointUsername)
                         .setPassword(swiftEndPointSecretKey)
                         .setAuthUrl(swiftEndPointAuthUrl)
@@ -662,4 +666,5 @@ private String getSwiftFileURI(StoredObject fileObject) throws IOException {
         return fileUri;
     }
 
+
 }

src/main/java/edu/harvard/iq/dataverse/settings/SettingsServiceBean.java

@@ -33,6 +33,7 @@ public class SettingsServiceBean {
      * So there.
      */
     public enum Key {
+        ComputeBaseUrl,
         IdentifierGenerationStyle,
         OAuth2CallbackUrl,
         DefaultAuthProvider,

src/main/webapp/dataset-license-terms.xhtml

@@ -10,7 +10,7 @@
    <div class="text-right margin-bottom" 
         jsf:rendered="#{dataverseSession.user.authenticated and empty editMode and !widgetWrapper.widgetView
                         and permissionsWrapper.canIssueUpdateDatasetCommand(DatasetPage.dataset)}">
-       <p:commandLink type="button" styleClass="btn btn-default" actionListener="#{DatasetPage.edit('LICENSE')}" 
+       <p:commandLink type="button" styleClass="btn btn-default btn-access" actionListener="#{DatasetPage.edit('LICENSE')}" 
                       update="@form,:messagePanel" oncomplete="javascript:post_edit_terms()" disabled="#{DatasetPage.locked}">
            <f:setPropertyActionListener target="#{DatasetPage.selectedTabIndex}" value="0" />
            <span class="glyphicon glyphicon-briefcase"/> #{bundle['file.dataFilesTab.terms.editTermsBtn']}