GRAPHICAL USER INTERFACE FOR BULK EDITING OF 3WORLDS ECOLOGICAL MODELS

Transcription

1 RESEARCH SCHOOL OF COMPUTER SCIENCE COLLEGE OF ENGINEERING AND COMPUTER SCIENCE GRAPHICAL USER INTERFACE FOR BULK EDITING OF 3WORLDS ECOLOGICAL MODELS COMP6470 SPECIAL TOPICS IN COMPUTING Supervisors Dr. Shayne Flint & Dr. Ramesh Sankaranarayana Perumal Viravan U

2 Acknowledgements I would take this opportunity to thank my project supervisors Dr. Shayne Flint & Dr. Ramesh Sankaranarayana for giving me an opportunity to work on this project. Their guidance, encouragement and support were very important in helping me complete the project successfully. I would also like to thank Dr. Weifa Liang for his guidance on research and technical writing. Last but not the least, I would like to thank my parents for their moral support and encouragement. 2

3 Abstract 3Worlds is an interdisciplinary research project, which aims to provide simulation and modeling software for ecology and environmental sciences [1]. 3Worlds project database heavily relies on graphs, which can be described using Domain Specific Language (DSL) [3]. In 3Worlds projects, graphs are used to represent ecological models. These graphs are very large in size, some having millions of nodes. This project required bulk editing of node properties, where a set of nodes can be selected using search tools and their common property can to be changed to a particular value. But the current approach to do that was to manually change the DSL and reload it, which keeping in mind the size of these large graphs will be quite impossible to do. As this project is mainly developed to be used by researchers in environmental and life science. It might be a better option to provide them with an easy- to- use graphical user interface that allows them to edit the large graphs, rather than manually changing the DSL files. This project focuses on creating a good interface that allows users to perform edit operations on large graphs more efficiently. The main functionality of this user interface would be to select a set of nodes using search tools and make changes to their common properties. It also provides other graph editing operations like adding nodes, deleting nodes and creating edges between nodes. This interface also provides a spreadsheet view with sorting options, which are useful in graph analysis. 3

4 Table of Contents Acknowledgements 2 Abstract 3 Table of Contents 4 1. Introduction 5 2. Background AOT Graph Database Archetype 7 3. Project Planning Requirements Software Development Process Development Environment 9 4. Implementation Search Feature Node Edge Connection Interface Node Edge Connection Adding a New Node Deleting the selected nodes Node Property Editor Interface Spreadsheet View Tab Property Editor Tab Testing and Evaluation Testing Testing against the archetype Testing whether data updates are in real time Evaluation Conclusions and Future Work Future Work References 21 4

5 1. Introduction 3Worlds is an interdisciplinary research project funded by French Agency of National Research (ANR) [1]. It aims at producing user- friendly software, which provides simulation and modeling for ecological experiments [1]. There are people from various disciplines working on this project, which includes researchers from life, computer and environmental science domains [1]. 3Worlds project's database heavily relies on graphs, which are used to represent the ecological models. In 3Worlds project, nodes in the graphs represent ecological entities like mountains, trees, lakes, etc. Then the edges that connect between nodes are used to represent the relationship between ecological entities. These graphs are very large in size, where some graphs can possibly have millions of nodes and edges. The graphs in 3Worlds project can be described using DSL (Domain Specific Language) files [3]. The 3Worlds project provides various visual representations of graph like spherical view, balloon layout, hyperbolic view, circle layout and many others. But it lacks a user interface that allows editing these large graphs. Recently it was noticed that there were requirements for bulk editing of large graphs in 3Worlds. Where set of nodes can be selected using search tools and common properties of these selected nodes can be changed. For example we select a set of nodes (possibly few thousands) and change value of Property 'p1' to '35' for all the selected nodes. The current approach to edit the graphs is to change the DSL manually and reload, as currently there is no user interface to edit graphs. But it becomes quite impossible to change the DSL manually, as the graphs are very large possibly having millions of nodes and edges. As 3Worlds software is mainly going to be used by researchers in ecology and environmental science domains, it might not be a good idea to expect them to edit large DSL files. Better option would be to provide them with a graphical user interface that allows editing of large graphs more efficiently, even for novice users. This saves the time of those researchers and also simplifies their task. The projects aim was to create a graphical user interface that allows users to edit large graphs. The main functionality of the user interface would be to allow users to select multiple nodes using search tools and edit their common properties. The user interface developed should also allow other editing operations on graphs like creating edges, adding new nodes and deleting nodes. First thought was to build an interface that has graph like structures i.e., nodes with edge connections between them, which can be edited. Where selection tools can be used to select a portion of the graph and we can edit the common properties for the nodes in the selected portion of the graph. Adding nodes can be done by clicking and dragging a node icon into the workspace. Where as edges can be simply created by drawing a line between two nodes. But after initial thoughts and some research, we felt that representing it using graph like structure is not the best solution for this problem. As we are looking at bigger graphs here, graph structures can get messy as the number of nodes and edges increase. Even though you have zoomable interfaces allowing zooming in and 5

6 zooming out to reach various parts of the graph, it might not be very effective. It was preferred to go for a simple interface that can efficiently allow editing of these large graphs. There were basically two interfaces developed i.e., one that allows to select multiple nodes and edit their properties; and other to create edges, add new nodes and delete nodes. This report presents the working of these interfaces and evaluations performed. It also clearly shows how this simple interface is successful in providing a good solution for editing large graphs. 6

7 2. Background This section briefs certain concepts like graph database and Archetypes, which might be important in following the report. 2.1 AOT Graph Database - Graphs in 3Worlds project are based on AOT graph database. In AOT graph database graphs are structured as nodelist, which is a basically a list of connected nodes. These graphs can be described using DSL (As mentioned in the Introduction) [3]. The nodes and edges can have properties associated with them. There are certain basic properties associated with the node namely node name and node label. I. Properties - The nodes in the graph can have properties associated with it. These are name/value pairs i.e., they have a property name and a property value associated with it. II. III. IV. Node Label - As mentioned this is a basic property of the node. The node label can be used to specify which node group the node belongs to i.e., the node group of the node is identified by using the node label. Node Name - It is also a basic property of a node. It specifies the name of the node. Node Edge - The nodes can have edges with other nodes either from the same node group or different node group. These edges can also have properties associated with them, which are also name/value pairs. As mentioned the node has basic properties like node label and node name. The node is identified as <nodelabel:nodename>, for example node:n1, where 'node:' is the node label and 'N1' is the node name. 2.2 Archetype - It is a graph that describes the required structure of other graphs. These archetypes describe the rules for the graph nodes, their properties and connection edges. These archetypes help to make sure that the graph satisfies the requirement for the input process. archetype archetype hasnode reference: "node2:" hasproperty Property1 type: String multiplicity: 1..1 hasproperty Property2 type: Integer multiplicity: 0..1 hasedge hasedge tonode: "node1:" multiplicity: 1..* hasedge hasedge tonode: "node3:" 7

8 multiplicity: 0..1 contd.. hasnode reference: "node3:" Figure 1: Sample Archetype The sample archetype (See Figure 1) mainly shows the rules for the node group with label node2. As per the archetype for all nodes that matches node label "node2:" I. It must have a property named Property1, which is of string type. The multiplicity 1..1 means that these nodes must have only one instance of property named Property1. II. III. IV. It can have a property named Property2, which is of integer type. The multiplicity 0..1 means that these nodes can either have zero or exactly one instance of property named Property2. It can have 1..* edges with nodes that have node label "node1:". It means that it must have at least one edge if not more edges with nodes that matches node label "node1:". It can have 0..1 edge with nodes that have node label "node3:". So it either have no edge or just have one edge with nodes that match node label "node3:". A single archetype can have rules for many node groups, which are specified by their node label. As seen in the example after the rules for "node2:", it is followed by "node3:". The continue symbol means that the archetype contains rules for much more node groups, which might be described similar to rules shown for "node2:". These archetypes are used to specify rules for the different graphs in 3Worlds project, which represent the ecological models. 8

9 3. Project Planning 3.1 Requirements - The main aim of the project was to develop an interface that allows basic editing operation on large graphs. So the following requirements were developed from that. The requirements of the project were stable, while the design of the interface changed a lot during the project. I. REQ1 - The graphical user interface shall allow searching nodes based on various parameters like node name, label and properties. II. III. IV. REQ2- The graphical user interface shall allow editing common properties for a set of nodes. REQ3- The graphical user interface shall allow adding edges for multiple nodes at once. REQ4- The graphical user interface shall allow adding new nodes to the graph. V. REQ5- The graphical user interface shall allow deleting a set of nodes from the graph. VI. REQ6 - The graphical user interface shall provide a spreadsheet view of graph nodes, which shall be used for analysis. 3.2 Software Development Process - This project followed agile software development practices, even though the requirements were clear. This was because the design of the interface changed during the progress of the project. The process was pretty much writing code every day and having discussions at the end of the day with my project supervisor and project users. That discussions will tell us what to do next and what has to be done different from what we are doing now. The final design of the interface was a result of these discussions. Having feedbacks at various stages of the project has helped us develop an interface that efficiently allows editing of large graphs. This process has worked best for us, as deciding a design early on and developing it might have left all the feedback to the end. Which might result in rework or software that does not meet the need of the project users. 3.3 Development Environment - This project is a part of the AOT and 3Worlds project. So it had to be developed using java like its parent projects. The software was developed using Eclipse Helios Version (3.6.1). The project used Maven as a build tool and mercurial as version control system. The operating system used was Mac OS X (Version ). 9

10 4. Implementation There are basically two interfaces that are developed to allow editing of large graphs i.e., Node Edge Connection Interface and Node Property Editor Interface. This section explains about the implementation of these two interfaces and the search feature, which is used across both user interfaces. 4.1 Search Feature As mentioned this search feature is included in both the interfaces i.e., Node Edge Connection Interface and Node Property Editor Interface. This uses the existing search functionality in the graph database and provides a user interface for using it. This search feature basically searches the nodes using a node reference, which will return a list of nodes matching the node reference. The node reference can either contain one node match or collection of node matches. The node match is the search criteria and can contain parameters like node name, node label and properties. It can actually be any combination of these. nodereference ::= <nodematch 1> / <nodematch 2> / <nodematch 3> The above syntax shows a node reference containing three node matches, which are separated by '/'. Figure 2: Graph to explain node reference and node match. When we have multiple node matches in a node reference. Then we evaluate node matches one by one from the left and use the nodes that have out edges from resultant nodes (result of search using previous node match) to evaluate the next node match. For example we evaluate nodematch 1 at first, then evaluate nodematch 2 only for nodes that have out edges from resultant nodes of search conducted using node match 1. 10

11 nodereference :: = node:n1 / node: / node2: The working of evaluation of node reference having multiple node matches could be explained with an example using Figure 2. Above syntax refers to a node reference, which contains 3 node matches. As mentioned earlier the first node match will be evaluated, which in this case will find nodes that have nodelabel = 'node:' and nodename = N1. In the graph (see Figure 2) there is only one node that matches this criteria i.e., node:n1. This node has three out edges i.e., node:n7, node2:n3 and node:n8, now the second node match will be evaluated based on these nodes. The second node match finds nodes that have node label = 'node:', which in this case two nodes out of the three nodes match this criteria i.e., node:n7 and node:n8. These two node have four out edges from them in total i.e., node:n9, node2:n6, node:n4 and node2:n5, now the third node match will be evaluated based on these nodes. The third node match finds out nodes that have node label = 'node2:', which in this case two out of the four nodes match this criteria i.e., node2:n6 and node2:n5. So the final result of the search using that node reference is node2:n6 and node2:n5. The below example shows how nodes are searched using the implemented interface. Figure 3: Search Feature In Figure 3 the node reference searches for nodes with node label "node:" and Property3 = "kkk". It returns a result with node:node1 and node:node6, which match this search criteria. Similarly these three parameters can be used in various combinations to search nodes. The search feature is further strengthened by the recent addition of Groovy, a language to evaluate scripts or expressions [2]. In the case of graph database it allows the users to query the graphs just by typing in java code, which uses the AOT graph query API's. The java code entered can be interpreted by groovy to return the resultant set of nodes. 11

12 This search feature is an important part of these graphical interfaces because it allows users to search for nodes using certain criteria and then edit them. As when we have large graphs it might be quite hard to locate nodes just by going through the complete list of nodes in the graph. 4.2 Node Edge Connection Interface This interface allows adding edges between the nodes, adding new nodes and deleting selected nodes. These features are being explained in this section Node Edge Connection - This feature allows creating edge connections between nodes. Node edge connections can also be created for multiple nodes at the same time using this interface. Figure 4: Node Edge Connection Interface As seen in Figure 4, if we select one node (on the left hand side) it shows all possible connections that the selected node can have (on the right hand side). These possible connection nodes are determined by checking against the archetype for node label of the selected node (in this case for "node1:"), as explained in the Background (Section 2.2). AOT graph database did not have any method that can return all valid nodes that a particular node can have edges with. So a method was created within the archetype class in AOT project that can return all the valid nodes that a particular node can have edges with. By adding this method in the AOT Graph database, it can be used as a standard feature by others using the AOT graph database. It can be seen that on the right hand side (see Figure 4) it shows all the possible connections the selected node can have along with a "Connect" option. By clicking the connect option, it creates an edge between the respective nodes. Then the window is refreshed to show the current possible connection nodes, after checking with the archetype again. As seen in the Background (Section 2.2) the multiplicity can affect how many connections the node can have with nodes from a specific node group. For example if nodes matching node label "node1:" can only have 0..1 connection with nodes matching node label "node2:" and if as of now there are no edges between node1:node1 and any nodes matching node 12

13 label "node2:". This is the case explained in Figure 4. So in the possible connection nodes for node1:node1 (see Figure 4), it shows three nodes matching node label "node2:". Say if we click connect next to node2:node4 (see Figure 4), it creates a edge between node1:node1 and node2:node4. As per the archetype a node matching node label "node1:" can have maximum of one edge with nodes matching "node2:". So when the window refreshes we will only see node3:node3 and node3:node5 as possible connection nodes in the right hand side. This is because the remaining nodes having node label "node2:" are removed, as the multiplicity wont allow them to have any further edges with node1:node1. Figure 5: Node Edge Connection Interface - Multiple Selection This interface also allows creating edges for multiple nodes at the same time. This might be useful in 3Worlds as we are dealing with large graphs, so it can save a lot of time. As seen in Figure 5 when we select multiples nodes, it shows only the common nodes that can have connection with the selected nodes. Again these possible edge connections strictly follow the archetype. By clicking connect next to a node, it creates an edge between that node and each of the selected nodes. For example in Figure 5, if we click Connect next to node2:node2, then it will create the following edges node1:node1 - > node2:node2 node3:node3 - > node2:node2 node3:node5 - > node2:node Adding a New Node: This allows users to add a new node to the graph. As seen in the background the node has certain basic properties like the node name and node label. So when we click "Add New Node" in the Interface (see Figure 5). A dialog box comes up asking for the node label and node name (see Figure 6). 13

14 Figure 6: Adding a New Node The node label can be selected from the drop down menu. The lists of node labels are been extracted from the archetype, which as seen before contains the entire set of node labels and the rules for the nodes belonging to them. After selecting the node label then the user can enter the node name and click ok. If there is no name entered or no label selected it will return with an error. If valid details are entered then the next window will appear prompting the user to enter the values for the properties of the node (see Figure 7). Figure 7: Node Properties Once the node label is selected in the previous window (Figure 6), the archetype will be checked for node properties for nodes matching that selected node label. For this a method was created that gives the entire valid property list for a given node (having a particular node label) and this was added to the archetype class of the AOT Graph Database. Once we enter the values for the properties and click ok, it checks if all property values are valid and adds the new node to the graph Deleting the selected nodes - This feature allows the users to delete the selected nodes. Users can select multiple nodes and delete them by clicking "Delete Selected Nodes". This will delete the selected nodes from the graph and also delete any edges associated with these nodes. 14

15 4.3 Node Property Editor Interface This interface allows editing properties of the nodes and also provides a spreadsheet view of the graph (nodes and properties). This interface has two tabs i.e., Spreadsheet view and Property editor which will be discussed in the following section Spreadsheet View Tab - This basically provides a spreadsheet view of the graph nodes and their properties. The AOT graph database provides various visual representations for the graphs like radial layout, hyperbolic view, spherical view, html view and many others. But it does not have a spreadsheet view of all the nodes and their properties, as even in the html view we can only see information about one node at a time. This spreadsheet view is useful in visualizing large graphs as in the case of 3Worlds project. Figure 8: Node Property Editor - Spreadsheet View. Figure 8 shows the spreadsheet view of the graph nodes and properties. It can be seen from Figure 8 that it allows sorting of columns (Property4 is being sorted in descending order), for both node name and other properties. So it can be very useful to study and analyze big graphs. The cells in the spreadsheet view are editable, unlike the cells in Property editor view. So in the spreadsheet view we can click any cell and edit the respective property, as it can be seen from Figure 8 Property4 of node:node4 is being edited. Then the edited property gets updated in the graph. But this view only allows editing one property at a time, but can be useful sometimes. 15

16 4.3.3 Property Editor Tab - This tab provides the most important feature of this project. This interface allows selecting a set of nodes and editing their common property at once. This is supported by search feature, so the users can search using the search tools and select nodes from the resultant set to edit properties. Figure 9: Node Property Editor Interface - Property Editor. The nodes can be selected by searching or clicking from the table located at the top half, and then the common properties for the selected nodes appear at the bottom half (see Figure 9). After selecting a set of node if we change any property value by entering a new value in the text box next to a property, then it updates that property with the newly entered value for all selected nodes. For example in Figure 9, if we type "123" for Property2, then the Property2 value for Node1, Node4 and Node5 are updated with "123". So in the 3Worlds project it allows users to select a large set of nodes and change a particular property value across all the selected nodes. As in the case of spreadsheet view (Section 4.3.2) this also allows sorting of all columns, it can be useful for selecting nodes to edit properties. The text box next to the property names (in the bottom half) shows if we are editing a single value, different values or null value. I. If a property for all selected nodes have the same value, then the text box next to that property displays the value itself. This indicates that the user is going to edit a property of all selected nodes that have a single value for that property. For example in the Figure 10, node1 and node6 are selected. They both have same value for Property3, so it can be seen in the text box next to Property3 displays 'kkk'. This tells the user that for all selected nodes that particular property has same or single value. 16

17 Figure 10: Node Property Editor Interface - Property Editor - Showing Single Property value. II. III. If a property for the selected nodes has different values, then it is mentioned in the textbox as "..." meaning that the user about to edit a property having different values across the selected nodes. For example in Figure 10 for the selected nodes it can be seen that textbox next to Property1, Property2 and Property4 are displayed as "...". This is because all these properties have different values for the selected nodes. This cautions the user that now he is going to change a property that has different values across selected nodes. If a property for all the selected nodes is null, then it is mentioned in the textbox next to that property as null. This feature is quite useful, as it gives a warning for the user that he is going to edit different values, single value or null value. 17

18 5. Testing and Evaluation Testing and Evaluation are important phases in software development, as it ensures that the software that is going to be delivered is as expected and is useful. 5.1 Testing Testing was a continuous process in this project and it was done it various stages of development. There were different types of testing used in this project like unit testing, integration testing and functional testing. In this project the components were developed individually, before being integrated. This was because to make sure the individual components functioned correctly. For example adding a node, deleting a node, and all such components were developed separately. These components were unit tested to make sure they worked correctly in the context. Then components were integrated and integration testing was performed. Functional Testing was done for the functionalities like editing multiple properties, deleting nodes, searching nodes, adding nodes, creating edges, finding possible edges and few others. This made sure their functional working was correct. Amount of testing performed is not the same for all aspects of the project. Few areas need more testing than the others. Similarly in this project there were few aspects that needed more testing than others. They are discussed in the section below Testing against the archetype: As mentioned before the archetypes describe how the graphs can be structured. So for any change made from the software to the graph, must strictly obey the archetype. There were many places, which required testing for correctness according to the archetype Possible edge connections - It needed to be checked if the suggested connection nodes were according to the archetype. Here the multiplicity had to be looked in with more importance. Properties for new node - The properties suggested for new nodes have to be according to the archetype. The entered properties must also be checked against the multiplicity given for the respective properties. These testing were done by running the software with sample graphs (or sample inputs as required) and checking the output that we get with the expected output. 18

19 5.1.2 Testing whether data updates are in real time - In the case of the property editor, there are two tabs that represent the same data. So updating information in one tab must update the information in the graph and also the other tab. Because if the information are not updated, then users might be editing or working on incorrect data. Updating graph and the data in the interface is also important for the node edge connection interface. For example if we create a new edge using the interface, then the graph must be updated and then the archetype must be checked again to find all possible connection nodes. If this does not happen we might end with invalid edges being created between the nodes, which do not obey the archetype. 5.2 Evaluation This project tries to provide a good interface allowing users to edit large graphs. So it has to be evaluated to see how efficient the interface is in doing so. Graphs of various size were given as an input to the software and seen if they were good for editing the graphs. Mainly they were evaluated to check whether if they were easy to use and did they serve the purpose. This interface was found to be quite useful as it allowed editing of the graph structures using a user interface rather than having to manually change DSL and reload it. There were features like the sorting and deleting of nodes seemed to be very handy. As deleting a node using the DSL file will mean to delete the node and also search for all the associated edges and delete them, but here everything can be done in a click. The sorting of columns along with the search feature helped in analyzing the graph effectively. 19

20 6. Conclusions and Future Work The project was successful in developing a graphical user interface allowing editing of large graphs for the 3Worlds project. It was also seen that a simple user interface provided a good solution for the problem. The project also satisfied the initial requirements and was completed within the given time. Feedback during the entire duration of the project helped to make sure the design of the interface was easy to use and served the purpose. Testing and Evaluation helped to verify the correct working and effectiveness of the project. 6.1 Future Work This was just a first attempt to create a graphical user interface for AOT graph database. So there can be many features that can be included in the future to make editing easier and more effective using these interfaces. I. When editing properties for multiple nodes using this interface, as of now it only allows setting a same value for all the selected nodes. There may be a feature added where it allows to set values based on patterns or algorithms entered using groovy. II. III. The option to delete edges might be a useful feature to add. There might be an option, which allows us to delete either all incoming or all outgoing edges for a selected node. Find and replace can also be a good feature for the node property editor. Where we can find all nodes having a particular property value and replace it with the new entered value. 20

21 7. References 1. 3Worlds 2013, 3Worlds - Overview, viewed 19 May 2013, 2. Groovy 2013, Embedding Groovy, viewed 20 May 2013, 3. Wikepedia 2013, Domain Specific Language, viewed 20 May 2013, specific_language 21