Difference between revisions of "Common Functionality"

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Describe the common functionality provided by any Community Web Portal for searching a collection, browsing the results, managing the content etc.
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==Workspace==
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A workspace represents a collaborative area in which users can exchange and organize information objects (items) according to their specific needs. Because of this, every user of any Virtual Research Environment is provided with this area. Such an area is further organized in workspaces and baskets  as to resemble a classic folder-based file system. The information objects that can be managed via the workspace range from files to D4Science documents, i.e. compound objects comprising metadata, alternative representations and multiple parts. The modality a workspace is populated range from the dragging of D4Science documents (or part of them) to the upload of files from its desktop and the exchange of workspace objects among users.  
  
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== Search ==
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[[Workspace | Click here for more information]]
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Desribe the functionality commonly offered by the Search tab on GridSphere.
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=== Basic Search ===  
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== Login to VO/VRE ==
  
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=== Advanced Search ===
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See [[Log in User Guide]].
  
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=== Collections Browsing ===
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== Search ==
  
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== Result Browsing ==
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See [[Search User Guide]].
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Available functionality for browsing the search results
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=== The Basket ===
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Introduce the notion of the basket. How it is used during result browsing?
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=== Common Browsing Activities ===
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== Annotations ==
 
== Annotations ==
  
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Annotations’ management is performed by Annotation Front-End/ Portlet. This is a graphical user interface which provides an easy and sufficient way to annotate gCube resources. Annotation Front-End can be invoked by selecting to manage the annotations of an object in Results portlet.
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Annotations’ management is performed by the Annotation Portlet. This is a graphical user interface which provides an easy and sufficient way to annotate gCube information objects. Annotation Portlet can be invoked by selecting the “Manage Annotations” action among the actions associated with any item displayed in the Results portlet.
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Then the user is moved to the generic annotation portlet where he is able to see the title, the mimetype, the content of the selected object as well as its generic annotations sorted by their creation date.
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Depending on the mimetype of the annotated object the visualization of its content may differ. For the majority of the objects which are supported from browsers, the content is displayed in a specified part of the portlet. For zip files, its entries are displayed and the user is able to download it. Tiff images are transformed into a displayable format (png), video files are available only for download and the visualization of pdf files depends on the behaviour of the browser (normally a plug-in is required).
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On the other hand, the annotations are shown up as a list where their title, the author’s user name and their creation/ modification date are posted up. The user is able to select which annotations (comments or associations) he wants to see just by clicking on the available checkboxes. The content of the annotations is shown below this list. In the case of associations, the title of the associated object as well as a link to its content is displayed.
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The user may perform three operations. He can add an annotation by clicking on the “Add Annotation” button and afterwards by filling in the title and text field in the case of text annotations or by filling in the title field and selecting an object existing in basket as an associated object in the case of associations. He may also delete or edit an annotation.
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If anchored annotations are supported for the annotated object the user can choose to be moved to the appropriate portlet by clicking on the “Go to anchored mode” button. Three portlets for anchored annotations are provided which are cover images, text and video files.
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[[Image:GenericAnnotationScaled.png|frame|none|Generic Annotation Portlet]]
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In image annotation portlet a user is able to add an annotation to a specific part of the image file. The user selects a space fragment which can be a rectangular area or a specific point (with a pin) and then he fills in the title and text fields. Then the space fragments are shown on the image and by clicking on one of them the content of the annotation is displayed.
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[[Image:ImageAnnotationScaled.png|frame|none|Image Annotation Portlet]]
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In text annotation portlet there is the capability of adding an annotation on a selected text fragment of the file. The selection of the text fragment is done in a very user friendly way as the user has only to choose the part of the text file with his mouse. The text fragments are shown with a different background in order to be distinguishable and by clicking on one of them the content of the annotation is displayed.
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[[Image:TextAnnotationScaled.png|frame|none|Text Annotation Portlet]]
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Then the user is moved to the annotation portlet where s/he is able to see the title, the mimetype, the content of the selected object as well as its  annotations sorted by their creation date and grouped into threads.
  
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In video annotation portlet (still under construction) a user is able to select a time fragment which means a part of the video file that is defined by its starting and ending moment. Video annotation portlet has although some requirements as it needs Java Media Framework installed on the user’s computer.
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Depending on the mimetype of the annotated object, the visualization of its content may differ.  
  
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In most cases, the content is displayed in a specified part of the portlet.
  
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[[Image:VideoAnnotationScaled.png|frame|none|Video Annotation Portlet]]
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For a zip file, its entries are displayed and the user is able to download any of them.  
  
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== Metadata Management ==
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Tiff images are transformed into a displayable format (png); video files are available only for download and the visualization of pdf files depends on the behavior of the browser (normally a plug-in is required).
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View and Edit metadata are the two functionalities that gCube offers to its users concerning the Metadata Management. These are described below.
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=== Metadata Viewing ===
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On the other hand, the annotations are grouped into threads, shown up as a list where the title of each thread is the title of the first contained annotation.
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The user can enter each thread and the annotations of this thread are displayed as a list where the title, their creation/ modification date and the author’s  name are posted up.
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The user is able to select which annotations (comments or associations) s/he wants to see just by clicking on it. The content of the annotations is shown at a pop up window where you can edit it. In the case of associations, the title of the associated object as well as a link to its content is displayed.
  
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The Metadata Viewing Portlet is a graphical user interface that displays the metadata which are associated with a specific information object. This interface displays the object’s metadata in a graphical way which depends on their schema.
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The user can either enter a selected Thread or create a new Thread by clicking on the corresponding buttons. By creating a new Thread a new annotation is actually created.
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After entering a Thread the uses can add an annotation by clicking on the “Add” button and afterwards by filling in the title and text field, in the case of text annotations, or by filling in the title field and selecting an object existing in the basket as an associated object in the case of associations. S/he may also delete or edit an annotation.
  
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Furthermore the portlet provides the ability for each user to change the way the metadata are displayed. If a user wants to manage the layout of the metadata viewing portlet, he may choose one layout of the available. This selection can be done in the user profile editing portlet.
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All the changes made by the user are persisted when s/he presses the "Save Changes" button.
  
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<!--If anchored annotations are supported for the annotated object the user can choose to be moved to the appropriate portlet by clicking on the “Go to anchored mode” button. Three portlets for anchored annotations are provided, namely, cover images, text and video documents.-->
  
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[[Image:MetadataViewingScaled.png|frame|none|Metadata Viewing Portlet]]
 
  
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=== Metadata Editing ===
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[[Image:AnnotViewThreads.png|frame|none|Annotation Portlet]]
  
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Metadata’s editing is performed by Metadata Editing Portlet. This is a graphical user interface which can be invoked by selecting to edit the metadata of an object in Results portlet. Depending on the schema of the metadata different editors can be displayed. There are two visual editors for dc and eiDB schemas and a generic one for the rest. However, for some collections, it is forbidden to change the metadata, something that is stated on screen with a relevant message.
 
  
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The visual metadata editors provide an easy and user friendly way of editing the metadata. Adding, deleting and editing elements can be performed by clicking on the appropriate buttons and filling in text fields. When the user completes his desired changes, he has to apply the changes he has done by clicking on the “Save Changes” button.
 
  
  
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[[Image:MetadataEditingScaled.png|frame|none|Visual Editor]]
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When the object that is annotated is an image the user is able to add an annotation to a specific part of the image file. The user selects a space fragment and then he fills in the title and text fields. Then the space fragments are shown on the image and by clicking on one of them the content of the annotation is displayed.
  
  
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The generic editor provides two options. The first one is to edit the bare xml in a text editor and the second one is to upload an xml file as metadata. However, these options require the user to have sufficient knowledge of XML.
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[[Image:AnnotCreateNew.png|frame|none|New annotation with fragment]]
  
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The user can edit an annotation be selecting the annotation s/he wants to edit and click on the "Edit" button. A pop up window appears with the content of the annotation
  
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[[Image:MetadataEditingGenericScaled.png|frame|none|Generic Editor]]
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[[Image:AnnotEdit.png|frame|none|New annotation with fragment]]
  
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== Index Management ==
 
  
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=== Full Text Index ===
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<!-- In text annotation portlet there is the capability of adding an annotation on a selected text fragment of the textual document (e.g. plain text, xml documents). The selection of the text fragment is done in a very user friendly way as the user has only to choose the part of the text document with his mouse. The text fragments are shown with a different background in order to be distinguishable and by clicking on one of them the content of the annotation is displayed.
  
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After opening the the FullTextManagementPortlet, you will see a screen with an Index Explorer tree on the left side, and an (empty) Index Detail panel on the right. The IndexDetail Panel will be emty as no index resource is currently selected in the Index Explorer tree. The Index Explorer panel however, will always display one or more folder icons when the portlet is ready for use:
 
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[[Image:FullTextPortlet1.png|frame|none|Generic Editor]]
 
  
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The folder icons represent metadata collections available in the VO.
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In video annotation portlet (still under construction) a user will be able to select a time fragment which means a part of the video file that is defined by its starting and ending moment. Video annotation portlet has although some requirements as it needs Java Media Framework installed on the user’s computer. -->
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A big green folder (marked with a [<span style="color:red">1</span>] above) represents a collection name which has one or more related indices.
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A big blue folder (marked [<span style="color:red">2</span>]) represents a collection name which does not have any related indices.
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The single blue folder with a pencil above it and the text "Fake Collections" (marked [<span style="color:red">3</span>]) is the only icon which is certain to be shown (even if no collections exist). This icon represents all collection IDs which are related to one or more indices, but which can not be mapped to a true metadata collections. This is a usual scenario when test indices are created without the need to be connected to a collection, or with a specific need not to be connected to a collection in order to not be used by the rest of the DL infrastructure.  
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A collection name is not necessarily unique, as many collections are allowed to have the same name though not the same ID. Actual metadata collections are represented by a smaller folder icon, along with its collection ID. Collections which have been indexed, are represented by a green folder (marked [<span style="color:red">4</span>]), while collections which have not been indexed are represented by a grey foler (marked [<span style="color:red">5</span>]).
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== Content Viewer ==
  
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==== Full Text Index Information ====
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The content viewer portlet provides the functionality to view a gCube object and all its properties and transform it, if any transformation is available for the object's mime type.
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If you expand the green collection tree items (by clicking on the [+] besides them), one or more Index icons (marked [<span style="color:red">1</span>] bellow) will reveal them selves. These represent Index Managers. If any Index Lookups are connected to the Index Manager, the Index item can be expanded to reveal one or more Index Lookup icons (marked[<span style="color:red">2</span>]):
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[[Image:FullTextPortlet2.png|frame|none|Generic Editor]]
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Using this portlet you can:
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* View the content of the selected object
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* View the available metadata of the object
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* View the aternative representations
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* Transform the main object using any of the available transformation programs (if any) and save the result of the transformation as a new object
  
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If you select either an Index item or an Index Lookup item in the Index Explorer, the Index Detail panel will show a tab panel with information related to the selected resource (WS ResourceProperty values). If an Index item is choosen, the IndexDetail will look similar to the following illustration:
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In order to use this portlet you should select from the results menu the '''Explore Object''' option for the object you would like to explore. After selecting this option you will be redirected to the Content Viewer portlet.<br>
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The main object is displayed as you can see at the image below<br>
  
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[[Image:FullTextPortletDetail1.png|frame|none|Generic Editor]]
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[[File:CVMain.png]]
  
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And if an Index Lookup item is chose, it will look similar to the following:
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When you click on the '''Display''' button the pop-up window with the all the available properties for this object is displayed. You can select any of the available properties to view.
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[[Image:FullTextPortletDetail2.png|frame|none|Generic Editor]]
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For example you can see at the image below the metadata at the FARM_dc schema for this object.<br>
  
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==== Editing the IndexType ====
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[[File:CMDisMetadata.png]]
  
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In order to edit the Index Type of an Index Manager, make sure the correct Index item is selected in the Index Explorer, and select the "Edit" tab in the Index Detail tab panel. This will reveal Index Edit panel:
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To view any of the alternative objects that are related to this object click on them<br>
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[[Image:FullTextPortletDetail3.png|frame|none|Generic Editor]]
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The chosen Index items IndexType is displayed as a list of Index Type Fields with editable checkboxes. The save button will save the IndexType currently shown to the selected Index Management resource.
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If a Index Lookup item was selected, choosing the "Edit" tab will reveal the Index Lookup Edit panel:
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[[File:CVDisAlt.png]]
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[[Image:FullTextPortletDetail4.png|frame|none|Generic Editor]]
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This panel is identical to the Index Edit panel, however only the "Return" checkboxes are enabled. This is due to the fact that the Return Element is the only part of an IndexLookup's index type which is editable. Any other changes will have to be performed towards the Index Management (using the Index Edit panel)
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==== Creating a Full Text Index ====
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=== Transforming the selected object ===
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Creating a new Index can be accomplished by either selecting the "New Index" item (marked [<span style="color:red">1</span>] bellow) or the "New Fake Collection" item (marked [<span style="color:red">2</span>])in the Index Explorer:
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[[Image:FullTextPortlet5.png|frame|none|Generic Editor]]
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Upon selecting one of the two said items, the Index Detail panel will allow you to specify the properties of the new Index. The IndexID property textbox should usually be left empty, in which case the IndexService itself will create a unique ID for the Index. If the "New Fake Collection" item was chosen, you will also need to specify a collection ID (fake - "myTestCollection1" or something to that effect), however if the "New Index" item was chosen, the collection ID will be retrieved from the parent collection item and will not be editable (as in the image above).
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After specifying the properties of the new Index, push the "Create" button in order to create the new Index. Upon success
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Depending on the available transformations programs you can transform the object to a new object and save it.
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[[Image:FullTextPortlet6.png|frame|none|Generic Editor]]
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In the example below the main object can be transformed to a new image with given height and width. <br>
  
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[[Image:FullTextPortlet7.png|frame|none|Generic Editor]]
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[[File:CVTransformMain.png]]
  
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[[Image:FullTextPortlet8.png|frame|none|Generic Editor]]
 
  
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==== Feeding and testing a Full Text Index ====
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=== Search Profile Settings ===
  
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[[Image:FullTextPortlet9.png|frame|none|Generic Editor]]
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The Search Profile portlet can be accessed by all users that have a portal account. Each user has his/her own search profile and he/she can view and/or edit its content through this portlet.
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By editing the search profile's contents you have several options that affect the search results or the presentation of the results and their metadata.
  
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[[Image:FullTextPortlet10.png|frame|none|Generic Editor]]
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<!-- * <b>Personalize the search results:</b>
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** Change the language using the drop-down list. The language in the profile affects the results that will be retrieved. The results will be only contain content in the preferred language.
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** <b>EngineType:</b> InternalEngine
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EngineType element specifies the desired type of the engine that will be
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employed for executing plans produced by the search engine. The value
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type of this element is string. Currently these types are supported:
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  InternalEngine: Search internal execution engine
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  ActiveBPEL: ActiveBPEL engine
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  OSIRIS: OSIRIS execution engine
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* <b>Persistence:</b> false
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Persistence refers to the ability of the execution engine to
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persist its runtime state, in order to perform execution reincarnation,
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multiple executions, execution logging and analysis, etc.
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The value type of this element is boolean (true or false).
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* <b>FaultTolerance: </b>false
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FaultTolerance refers to
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the ability of the execution engine to recover from errors. The value
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type of this element is boolean (true or false).
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<br>
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-->
  
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[[Image:FullTextPortlet11.png|frame|none|Generic Editor]]
 
  
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[[Image:FullTextPortlet12.png|frame|none|Generic Editor]]
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* <b>Personalize the presentation of the results and their metadata:</b>
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** For each available collection you can select any of the available presentable fields that will be used for the presentation of the results from the results portlet when this collection is used in search. If you don't select any field then all the available presentable fields will be displayed.
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** For each available metadata schema you can select one of the available xslts that will be used for the presentation of the metadata. If you don't change anything the default XSLT will be used.
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** A preview is displayed for the current selected schema and XSLT. This helps you to select the desired XSLT.
  
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==== Removing a Full Text Index ====
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In order to apply the changes you need to click on the '''Save profile''' button. A message is displayed to inform you if the profile was successfully updated.
  
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[[Image:FullTextPortletDetail5.png|frame|none|Generic Editor]]
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== Report Management ==
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See [[Report Management]] page.
  
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[[Image:FullTextPortletDetail6.png|frame|none|Generic Editor]]
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== Time Series ==
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[[Time Series | Click here to visit the Time Series portlet guide]]
  
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[[Image:FullTextPortletDetail7.png|frame|none|Generic Editor]]
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== AquaMaps Suite ==
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The AquaMaps suite supports the production of AquaMaps and related data products, i.e. compound objects containing species and biodiversity occurrence predictive maps.  
  
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=== Geo Index ===
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[[AquaMaps | Click here to visit the AquaMaps Suite guide]]
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==== Overview ====
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==== Geo Index Information ====
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==== Editing the GeoIndexType ====
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==== Creating a Geo Index ====
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==== Testing a Geo Index ====
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==== Removing a Geo Index ====
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Latest revision as of 15:23, 8 April 2015

Workspace

A workspace represents a collaborative area in which users can exchange and organize information objects (items) according to their specific needs. Because of this, every user of any Virtual Research Environment is provided with this area. Such an area is further organized in workspaces and baskets as to resemble a classic folder-based file system. The information objects that can be managed via the workspace range from files to D4Science documents, i.e. compound objects comprising metadata, alternative representations and multiple parts. The modality a workspace is populated range from the dragging of D4Science documents (or part of them) to the upload of files from its desktop and the exchange of workspace objects among users.

Click here for more information

Login to VO/VRE

See Log in User Guide.

Search

See Search User Guide.

Annotations

Annotations’ management is performed by the Annotation Portlet. This is a graphical user interface which provides an easy and sufficient way to annotate gCube information objects. Annotation Portlet can be invoked by selecting the “Manage Annotations” action among the actions associated with any item displayed in the Results portlet.

Then the user is moved to the annotation portlet where s/he is able to see the title, the mimetype, the content of the selected object as well as its annotations sorted by their creation date and grouped into threads.

Depending on the mimetype of the annotated object, the visualization of its content may differ.

In most cases, the content is displayed in a specified part of the portlet.

For a zip file, its entries are displayed and the user is able to download any of them.

Tiff images are transformed into a displayable format (png); video files are available only for download and the visualization of pdf files depends on the behavior of the browser (normally a plug-in is required).

On the other hand, the annotations are grouped into threads, shown up as a list where the title of each thread is the title of the first contained annotation. The user can enter each thread and the annotations of this thread are displayed as a list where the title, their creation/ modification date and the author’s name are posted up. The user is able to select which annotations (comments or associations) s/he wants to see just by clicking on it. The content of the annotations is shown at a pop up window where you can edit it. In the case of associations, the title of the associated object as well as a link to its content is displayed.

The user can either enter a selected Thread or create a new Thread by clicking on the corresponding buttons. By creating a new Thread a new annotation is actually created. After entering a Thread the uses can add an annotation by clicking on the “Add” button and afterwards by filling in the title and text field, in the case of text annotations, or by filling in the title field and selecting an object existing in the basket as an associated object in the case of associations. S/he may also delete or edit an annotation.

All the changes made by the user are persisted when s/he presses the "Save Changes" button.


Annotation Portlet



When the object that is annotated is an image the user is able to add an annotation to a specific part of the image file. The user selects a space fragment and then he fills in the title and text fields. Then the space fragments are shown on the image and by clicking on one of them the content of the annotation is displayed.


New annotation with fragment

The user can edit an annotation be selecting the annotation s/he wants to edit and click on the "Edit" button. A pop up window appears with the content of the annotation

New annotation with fragment



Content Viewer

The content viewer portlet provides the functionality to view a gCube object and all its properties and transform it, if any transformation is available for the object's mime type.

Using this portlet you can:

  • View the content of the selected object
  • View the available metadata of the object
  • View the aternative representations
  • Transform the main object using any of the available transformation programs (if any) and save the result of the transformation as a new object

In order to use this portlet you should select from the results menu the Explore Object option for the object you would like to explore. After selecting this option you will be redirected to the Content Viewer portlet.
The main object is displayed as you can see at the image below

CVMain.png

When you click on the Display button the pop-up window with the all the available properties for this object is displayed. You can select any of the available properties to view. For example you can see at the image below the metadata at the FARM_dc schema for this object.

CMDisMetadata.png

To view any of the alternative objects that are related to this object click on them

CVDisAlt.png

Transforming the selected object

Depending on the available transformations programs you can transform the object to a new object and save it. In the example below the main object can be transformed to a new image with given height and width.

CVTransformMain.png


Search Profile Settings

The Search Profile portlet can be accessed by all users that have a portal account. Each user has his/her own search profile and he/she can view and/or edit its content through this portlet. By editing the search profile's contents you have several options that affect the search results or the presentation of the results and their metadata.


  • Personalize the presentation of the results and their metadata:
    • For each available collection you can select any of the available presentable fields that will be used for the presentation of the results from the results portlet when this collection is used in search. If you don't select any field then all the available presentable fields will be displayed.
    • For each available metadata schema you can select one of the available xslts that will be used for the presentation of the metadata. If you don't change anything the default XSLT will be used.
    • A preview is displayed for the current selected schema and XSLT. This helps you to select the desired XSLT.

In order to apply the changes you need to click on the Save profile button. A message is displayed to inform you if the profile was successfully updated.

Report Management

See Report Management page.

Time Series

Click here to visit the Time Series portlet guide

AquaMaps Suite

The AquaMaps suite supports the production of AquaMaps and related data products, i.e. compound objects containing species and biodiversity occurrence predictive maps.

Click here to visit the AquaMaps Suite guide

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