Porgy Documentation
Contents
1. Name Se Glyph 20 Rounded Box NEN Color Add Mo 27 Porgy Documentation Release 2 0 Once validated the new type of portnode will appear in the list as a 2 with a blue background It can then be selected and added to the right of the bridge in the rule tule Attribute Create new portnode Left Click on a source port to start adding a new edge then left click on the destination port Expose 2 2 Linking the portnodes In portgraphs ports are used as means to connect the portnodes together In the rules ports use is twofold they can be used in the left hand or the right hand side indifferently to connect portnodes they can be used to connect elements from the LHS to the RHS to indicate specific ways to reconnect the transformed elements In our example case the two ports are similar so the fashion followed to reconnect the transformed element is quite simple We set each distinct port from the LHS to be corresponding to a unique and distinct port in the RHS To indicate this in the Rule View we will use the same interactor used to add portnodes Click on a port of the red portnode then click on a port of the b ue portnode Repeat the process with the two other ports Navigate in graph 4 9 2 l tule Attribute Expose 2 3 Red edges connecting the LHS to the RHS are created with these operations In our case they w2. Porgy Documentation Release 2 0 Tulip Team December 15 2015 CONTENTS Porgy User Interface 3 IGA cae Behe ee eee ee eo SESS ERRORES URS 59 ES SN d 3 1 2 a UR eue Pob OE A NUR Rode OK eu CURL d 5 led und w eed x S X Guy x 6 Orph Wide se uoo oo ooo ome 7 l5 Derivation tree widget auos e sosa saaat ERR XO Oe SR ORG x 9 4 09 XR REO x 5 god 8 Strategy WIE sibus Ro OREGROROX t3 ROEOR XOR REP x XR ROBAR SEARS SESS 2 EERE 8 9 Presentation of the views 11 deu WE 1 9 38 95 5308 3 2 3 9 HOA eee See PEE 9 9 9 11 22 OPONE so bower eee hea kee eRe hee NOE 8 0 RA 92540429 ee EUR PE 12 23 ice VieW 54422255 14 2 4 Additional trace views 15 Porgy data structure 19 ool ass ook eo hee ye ee Oe ee HOUR OEC ARDEN 19 2 IMG 2564s ewe Bee ARORA 20 Se SANS 2252424 4 549 39 9 2 4173 39 5 39 3 30 4 38 4 9 V S ESE GS 2 34 21 Rewriting in action A tutorial 23 4 1 Import new graph 22 44664 Rex bee be be EOS S 4o oR 4 4 4 bow SEES 23 4 2 sess sesat emer peria OR k X 9 ED 5 3 24 4 3 Applying arule ee ee ee WO CR UR A CRURA UR E e dos OR AUR E UR N
3. rms ee dy camera arx aed TAN J E Er Rules Graphs Derivation trees Lae VH BD Duy s elk LUI n 1 PUMA eei 1 Log widget gn erebi Weni omma abe S BANE ol D Strategies widget Figure 1 1 Overview of the Porgy interface 1 1 Menu File Contains the usual file operations see the Tulip user manual for additional information about this menu New Clear the current session and create a new empty one Open Open a saved session Save Save the current session Save As Save the current session in a new file Exit Quit the software Edit Porgy Documentation Release 2 0 Undo Undo the last operation Redo Redo the last undo operation Copy Copy the selected portnodes and edges from the active view to the clipboard This option is only available if the active view is a Rule view or a graph view Cut Cut the selected portnodes and edges from the active view This option is only available if the active view is a R
4. gt Uu N v v v o SDSLTSAALTAO v 5 Ru Gra Strategies dp Add v Del save Algorithms D Nodes E 2 2 2 2 4 6 6 5 3 4 4 3 3 3 3 2 2 4 4 3 3 2 2 3 3 3 3 Expose Derivation tr as A repeat red blue repeat blue 2yellow repeat 3yellow red 0 9 The graph G 3 at the end of the derivation tree contains one yellow portnode and one red portnode We can thus apply the strategy once more with a drag and drop on G 3 Tulip 4 8 Porgy 3 Graphs Name Small icons Ru Gra Strategies Nodes Algorithms Di an E 2 2 4 6 5 4 3 3 1 3 2 2 4 3 gt wu A N N m 4 Expose Derivation tr dp Add repeat red blue Del save repeat blue 2yellow repeat 3yellow red Three new states are created leaving us with a single red portnode After a final strategy application we end with the following graph 4 4 Strategies 35 Documentation Release 2 0 Tulip 4 8 Porgy File Edit Algorithms Docks Je Name Nod 4 gt S G9 2 2 16 gt S G8 2 2 gt G7 4 gt Q G6 6 gt Y G5 5 5 gt G4 4 4 gt ST G3 3 3 gt lt 7 G2 3 3 17 G18 2 2 gt 17 1 1 gt G16 1 1 gt 4 G15 3 3 G14 2 2 B gt S G13 2 2 G18 2 Lt Small icons Exp 3 3 Ru Gra Derivat
5. 2 4 3 Small multiple View This view allows to visualize the transformations between different graphs using small multiples and or animation User can add intermediate states to emphasize elements present in the P property the LHS and the RHS Small multiples are useful to have an overview of the whole states of the derivation tree The aim of the animation is to interpolate the change each states to show a video of the change You see the film of the transformations Navigation P L I j pP Nas 5 t am m 5 GO G3 G4 _ 611 G18 G19 G20 G21 gt 4 WE e mg G B m e m 2 m 8 B GO Expose 4 4 Figure 2 4 The small multiple and animation view which enable to see the evolution of a branch of a derivation tree Configuration General Intermediate states add the corresponding intermediate states between two states 16 Chapter 2 Presentation of the views Porgy Documentation Release 2 0 Widgets customize the view by selecting the widgets to display Small multiples or Animation Node labels show or hide the node label and scale the label size in function of the node size Animation Animation duration animation duration between two states Rule preview display or hide a preview of the rule involved in the current transformation if the current transformation involve a rule Small multiples Rendering parameters offers to force the labels of
6. 1 4 Graph widget 7 Porgy Documentation Release 2 0 Large icons To display a larger preview hover one of the graphs in the list After a moment a tool tip with a larger preview will appear You can display a visualization edition view for a graph by double clicking on it or by dragging it and dropping it on the workspace More information concerning the Graph view is available in the Graph View section 1 5 Derivation tree widget Derivation Irees x Filter derivation trees Id Name Modes 130 New derivation tree 7 86 New derivation tree 3 10 TraceMain 50 Click on Derivation Trees tab to access to the Derivation Trees management widget Use the text line at the top of the widget to filter derivation trees using names You can display a visualization edition view by double clicking on it or by dragging it and dropping it on the workspace There is several kinds of visualizations see the views section for more information on Porgy views Derivation Tree view This is the general visualization for derivation trees Scatter plot 2D view Histogram view Small multiple view To rename a derivation tree select it and click with the left button on the it s name Input the new name then press return to validate the new name If you press the escape button the edition will be canceled 1 5 1 Contextual menu A right click on the existing derivations will propose the following options Show Create a v
7. Scatter plot 2D View This view allows to create 2d scatter plots of graph nodes from graph properties supported types are Metric and Integer A scatter plot is a type of mathematical diagram using Cartesian coordinates to display values for two variables for a set of data The data 1s displayed as a collection of points each having the value of one variable 2 4 Additional trace views a5 Porgy Documentation Release 2 0 determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis By selecting a set of graph properties a scatter plot matrix will be displayed for each combination of two different properties Each scatter plot can then be displayed individually in a more detailed way A set of interaction tools are bundled with the view to perform selection statistical analysis 2 4 2 Histogram view This view plug in allows to create frequency histograms from graph properties supported types are Metric and Inte ger By selecting a set of graph properties frequency histograms are computed and displayed for values associated to nodes or edges This view also allows to map visual properties colors sizes glyphs of the graph elements with respect to a graph metric in a visual way These operations can be done with the Metric mapping interactor Many interaction tools are also bundled with the view to perform elements selection statistical analysis
8. an application of a strategy or a modification of the P property Set position Select nodes edge 4 9 s G2 Expose LIE Figure 2 3 The Derivation tree view keeps a complete trace of all user operations and can be used to explore the evolution of the graphs after rewriting 2 3 1 Interaction tools You will find in it the following interactors Navigation move rotate and zoom the view Zooming behavior the point under the cursor is moved closer to the center k Get information click an element portnode or edge and Porgy displays all available properties of that element If you hoover an edge it will display the transformation information as a tool tip and it will highlight portnodes involved in this transformation Here is the color code used when highlighting portnodes 14 Chapter 2 Presentation of the views Porgy Documentation Release 2 0 involved in a transformation Simple rule LHS portnodes are in red and RHS are in blue Set position portnodes that are only in the original P property are in red portnodes only in the new P property are in blue and portnodes in both old and new are in green EE Rectangle selection select all elements touching the selection box the previous selection 15 replaced but can be recovered with Undo With Shift the newly selected elements are added to the current selection with Ctrl Alt on Mac the selected elements are remove
9. can be done by selecting a layout in the Ru e View under the tab Rule Attribute 30 Chapter 4 Rewriting in action A tutorial Porgy Documentation Release 2 0 22 Delete portnodesc 4 2 1 Scene gt Porgy GEM Frick GEM Frick Sugiyama OGDF Tree Leaf Layout algorithm to use with this rule none N 4 g D w Vf T UJ Expose Be aware that when visualizing large number of elements redrawing the graph can disturb the mental map of user because of the possible change of each node position In our case we choose the FM 3 layout a force directed layout quick to compute and which gives generally good results We apply this modification to all the rules previously created however the rule blue 2yellow is the one to which it will profit the most 4 3 Applying a rule In Porgy there is two way to apply a rule either by launching it directly from the Rule widget or by using the Strategy widget Both methods are working with drag and drop actions on a graph or onto a node of the derivation tree The application of a rule to a given graph consists in two phases find at least one instance of the left hand side of the rule inside the graph then replace this instance by the right hand side of the rule Let us try to apply the rule red blue on GO First we need to visualize the derivation tree such action can be achieved by double clicking on the current trace call
10. on Mac the selected elements are removed from the current selection IC l Selection edition modify the shape and position Shift click modifies only coordinates Ctrl click modi fies only size Left click outside the selection resets the selection i Edit edge bends click on an edge to select it with this tool then Shift click to add a new bend click a bend to move it or Ctrl click Alt on Mac to remove a bend Add portnodes allow the user to create edit and add portnodes Edges can also be added between ports only by clicking the source node first then the target node Optionally bends may be added by clicking outside of a node X Delete element click a portnode or edge to delete it 2 1 2 Configuration The following options can be customized using the tab on the right side of the view Scene identical to the options available in Tulip allows to customize the view Rule Attribute contains all the specific options of the current rule Layout algorithm select the layout algorithm to perform on the rewritten graph after applying this very rule 2 1 3 Contextual menu Perform a right click Ctrl click Mac to display this menu Center view move the camera the view all the elements Redraw redraw the rule and center the view Take snapshot open the screenshot tool Selection allows you to select specific parts of the rule 2 2 Graph View This 15 the visualization edition view
11. M is used to indicate if the element is transferred into the Position set after the rewriting operation we thus set the property to true Getinformationon 4 Scene Node 14 en E lt gt false false NodeType Center RuleSide Right viewBorderColor D SENE viewBorderWidth 1 viewer viewColor isused true Expose 2 3 Trying to launch the strategy GO now will produce a better but still incomplete result The step explained above must be repeated for each portnode located on the right hand side of each rule 4 4 3 Strategy application Once all those changes are completed we can apply the strategy A to GO To do so proceed similarly to a rule application The Derivation Tree view must be displayed and the graph targeted GO have to be visible Drag and drop the name of the strategy upon GO and wait for the computation to be over You will obtain a derivation tree with eight new states Tulip 4 8 Porgy ile Edit Algorithms Docks Window elp red blue blue 2yel te 1 3yellow red apAdd v repeat red blue repeat blue 2yellow Del repeat 3yellow red i 096 iN The graph G8 contains two red portnodes allowing us to apply the strategy once again By drag and dropping on G6 we obtain five new states 34 Chapter 4 Rewriting in action A tutorial Porgy Documentation Release 2 0 Tulip 4 8 Porgy le Edit ONS v Q m
12. alse i 4 2 1 Rule 1 red to blue One can create a new rule by performing a right click in the Rule widget and selecting Create a new rule in the contextual menu Rules x Small icons m Rules Graphs De Import After having specified the name of the newly created rule we choose to call it red blue a double click on the rule icon in the Rule widget or using a right click and selecting Show will create a new Rule View The view only contains a bridge node for now This element is used to mark the transition between the left hand side and the right hand side We consequently use it as a visual cue indicating the limit between the LHS and the RHS Our rule is supposed to change the color of a node from red to blue we thus have to create a red node on the left a blue node on the right and link the two elements appropriately Red portnode First we must select the interactor allowing to create portnodes Clicking on the name of the interactor display its parameters 4 2 Rule creation 25 Documentation Release 2 0 Add aportnode an 4 9 5 Create new portnode Left Click on a source port to start adding a new edge then left click on the destination port tule Attribute X Expose 2 The interactor lists all the different types of existing portnodes For now the only one available corresponds to the red portnode similar to those existing in GO We will use a slight
13. ansform the red portnode in a blue portnode with red ports A similar treatment can applied to the blue 2yellow rule 5 1 Property Manager 39 Porgy Documentation Release 2 0 for both of the blue ports in the left hand side the viewColor isused property is set to false desactivate the colour matching for those elements for both of the linked ports in the right hand side the viewColor isused property is set to false keep the original colour of the ports matching the rule we obtain the following rewriting result where both ports keep the original colour of their matching correspon dances Expose ES This kind of transformation makes sense when several matching properties are used at the same time but are not relevant in every rule Specifying the local matching properties and whether the value must be passed to the rewritten element allows to rewrite and transform the graph in different ways Please note that this behaviour is only available for ports as they are the sole elements in the right hand side to be linked to other elements in the left hand side 5 2 The Ban property We have mentioned the Position property in the previous tutorial however a second property the Ban property can be used to limit the elements available for the rule application Basically an element can be in the Position set in the Ban set or neither of those neutral When looking for elements during the matching of the LHS f
14. ategies and transform the graph by automatically applying the rules previously created The strategy allows us to choose how we wish to apply each rule In our case no specific behaviour or model is given we thus decide to try applying each rule as many time as possible and see the results obtained As seen before only the rule red blue can be applied in the beginning Applying it once will allow us to launch the blue 2yellow rule afterward but we will then be blocked as the last rule 3yellow red requires three yellow portnodes to be applied If we apply the first two rules three times each we can then apply the last rule two times and obtain two red portnodes 32 Chapter 4 Rewriting in action A tutorial Porgy Documentation Release 2 0 4 4 1 Repeat a rule application The first step is to create a new strategy This can be achieved in the Strategy widget by clicking on the Add button and selecting the option Empty strategy Strategies _ dpAdd v Empty strategy Strategy from derlvation tree Strategy from a file You can rename a strategy by double clicking on it We call our own A for simplicity This first strategy will apply each rule as many times as possible in the logical order red blue blue Zyellow and 3yellow red To do so we can use the repeat command and thus create the strategy as follow repeat red blue repeat blue 2yellow repeat 3yellow red Applying this strategy immediately on GO will not produc
15. ctor to open a widget listing the value of the properties of an element For instance in the case of the rules created in the previous tutorial we take a peek at the values for the properties of the middle yellow portnode in rule 3yellow red tule Attribute Expose 2 3 The selection of the viewColor property in the Property Manager generates a boolean property called view Color isused When set to true the corresponding property is checked for this element during the matching When set to false however the property is still generally checked for the matching but the current element becomes an exception If we set the viewColor isused property value to false for the middle yellow portnode and its ports any chain of three elements with yellow portnodes at its extremities will match Applying the modified 3yellow red rule to G in the derivation tree generated during the tutorial illustrates this perfectly Navigation v 4 Expose G19 is generated with the 3yellow red rule application on G7 7 a result impossible to obtain for the original rule as G only contains 2 yellow portnodes This advanced checking possibility allows further control on the transformations and very fine tuning over the operations we are able to perform 38 Chapter 5 Porgy in details Porgy Documentation Release 2 0 5 1 2 Copying values during rewriting The boolean property isused created after selecting a ma
16. d from the current selection P Zoom box draw a rectangle and zooms on this area Open a new graph view click on a graph and it will be displayed new view a Selection edition modify the shape and position Shift click modifies only coordinates Ctrl click modi fies only size Left click outside the selection resets the selection i Edit edge bends click on an edge to select it with this tool then Shift click to add a new bend click a bend to move it or Ctrl click Alt on Mac to remove a bend 2 3 2 Configuration The following options can be customized using the tab on the right side of the view Parameters Labels choose whether you wish to display the nodes or meta nodes labels Rendering parameters allows you to enable the edge size interpolation or to scale each label size according to their node size 2 3 3 Contextual menu Right click Ctrl click Mac to display this menu Center view move the camera the visualize all the elements in the derivation tree Redraw redraw the derivation tree and center the view Take snapshot open the screenshot tool Show Overview toggle top left overview If a graph is present under the cursor some other options are available Open in a new graph view show the graph under the pointer in a new view Add to Remove from the selection if the graph is present in the current selection remove it else add it 2 4 Additional trace views 2 4 1
17. dge is created by clicking on each port successively when using the interactor tule Attribute Expose 212 This achieve the rule blue 2yellow which is now ready to be used in a rewriting operation 4 2 Rule creation 29 Documentation Release 2 0 4 2 3 Rule 3 yellow to red With the two previous rules achieved this last one will be set in no time We simply want to merge three yellow nodes in a single red one e We create a new rule which we call 3yellow red e All the type of nodes have been created before so we only have to place and connect three yellow nodes on the left of the bridge and a single red one on the right 4 l tule Attribute l i UN 3 lt Pi We then connect the yellow portnodes to the two remaining ports to the red portnode Navigate in graph 4 9 2 f y b HE b 7 D 4 d ule Attribute Expose With the three rules red blue blue Zyellow 3yellow red now ready we focus their application to the graph GO Let us see how we can use each of these rules to transform our initial graph 4 2 4 Layout algorithm Upon rule application and particularly when the number of elements appearing is greater than the number of elements being replaced the layout can become unclear In those case it is advisable to redraw the graph altogether This
18. e appear in the editor on the right From here instructions can be typed to specify in details how the rules can be applied A complete syntax and set of instruction exist and the entire grammar can be consulted in details in the following section 1 7 Log widget This widget will display the information warning and error messages send by porgy 1 7 Log widget 9 Porgy Documentation Release 2 0 10 Chapter 1 Porgy User Interface TWO PRESENTATION OF THE VIEWS You will find here additional information on each of the views available in Porgy 2 1 Rule View This is the visualization edition view for all the rules Navigate in graph EGF E E t 2 4 E lt TR 5 gh 2 E 4 4 lt Expose 1 1 Figure 2 1 The Rule view allows to create customize and visualize rewriting rules 2 1 1 Interaction tools You will find in it the following interactors Navigation move rotate and zoom the view Zooming behavior the point under the cursor is moved closer to the center 2 k Get information click an element portnode or edge and Porgy displays all available properties of that element in the properties widget 11 Porgy Documentation Release 2 0 Rectangle selection select all elements touching the selection box the previous selection 15 replaced but can be recovered with Undo With Shift the newly selected elements are added to the current selection with Ctrl Alt
19. e the expected result as only the first repeat will seem to be executed Before doing so we need to consider the Position and Ban properties 4 4 2 The Position set When creating a rule you can specify whether you want the newly created right elements to be considered afterwards as possible match for rule application More formally at the beginning of a strategy application all the elements of the targeted graph are available for rewriting and thus are in the Position set With each rule application within the strategy the right hand side elements are by default moved out of the Position set where they become no longer available for matching as left hand side elements To use the strategy we must specify for each element in the right hand side of the rules used whether they are put in the Position set for further operation or if they are left out This can can be achieved in the Rule View We present the steps to follow using the red blue rule 2 First select the Get information interactor k Then click in the middle of the b ue portnode and a widget will appear Scene NodeType RuleSide viewBorderColor viewBorderWidth viewColor viewColor isused Expose rir 4 4 Strategies 33 Porgy Documentation Release 2 0 This tool allows you to customize some of the visual properties of the selected element as well as a few others Currently we are interested in the M property initialized at false by default
20. ed TraceMain in the Derivation tree widget using the Show action in the contextual menu appearing with a right click on the trace produces similar result The Derivation Tree view and the thumbnail representing GO have to be visible in the workspace to continue Now in the Rule widget drag the rule red blue on GO A new window will appear in which we set the Maximum number of instances to find at I to only generate one new state Apply rule red blue on model GO Name Rule Name red blue Maximum number of instances to find 1 Property for Position Select a property Property for Ban Select a property 4 3 Applying a rule 31 Porgy Documentation Release 2 0 The application will generate a new graph called G in which the rule red blue has successfully been applied Expose S Because the initial graph GO only contains red portnodes the rules using blue and yellow portnodes cannot successfully be applied on it If we tried to drag one of those rules and drop it we will end up with an invalid state shown as a red thumbnail Navigation Expose Applying the rules by hand allows to test if everything is going according to plans however strategies be used to automatized the process and avoid to perform the transformations manually 4 4 Strategies A strategy is a small script language created to improve the rule rewriting possibilities In this example we will see how to write simple str
21. en one tries to find the instances in at least node of each must be in the Position set It is possible to define more than one set Position Ban similar to Position but with the Ban property If the process works the resulting graph will appear in the derivation tree else a red state will appear 5 4 Strategies A strategy is a small script language created to improve the rule rewriting possibilities 5 4 1 Syntax of the Strategy Language Let L R be port graphs M N positions n 1 0 1 XO m 1 i 1 Let attribute be an attribute label in Vv e Ey a valid expression without variables 5 4 Strategies 41 Porgy Documentation Release 2 0 E af herSels S S ors S repeat SF while S005 ic kt Sis rn y 8 no 8 Rewriting Basics Id Fail Applications A we all T Transformations gt Supt fiction name parameters D AE oneF Ngb F p FU FIFE n FIF Q 0 Comparison F F F F F c isEmpty P Properties Properties Elem Expr Node Edge Por se attribute e True 42 Chapter 5 Porgy in details
22. false viewBorderWidth false 4 viewColor false 5 viewFont false 6 viewFontAwesomelcon false 7 viewFontSize false 8 viewLabel true 9 viewLabelBorderColor false 10 viewLabelBorderWidth false JC Done For instance two portnodes with different names but with a similar number of ports will be considered as similar elements by default If you wish those two elements to be distinguish from each other you can select the property viewLabel containing their respective names in the Property Manager From now on the subgraph matching operation will consider the selected property as an additional condition for the matching to be successful In the screenshot above the state and viewLabel properties have been selected by double clicking in the second column on the appropriate lines doing so makes combo box appear offering to set the value to true or false New properties can be created by clicking the button and outdated ones can be deleted by selecting them and using the button Please remember that the visual properties whose name begin with view are crucial for the visualizations and thus will be restored to their default value if deleted 37 Porgy Documentation Release 2 0 5 1 1 Optional matching Finer control over the selected properties can be achieve when editing each rule allowing for instance to only check the value on specific elements When editing a rule in the Rule View you can use the Get information intera
23. for graphs 2 2 1 Interaction tools You will find in it the following interactors 12 Navigation move rotate and zoom the view Zooming behavior the point under the cursor is moved closer to the center Chapter 2 Presentation of the views Porgy Documentation Release 2 0 1 1 1 2 SHC EGF EGF 2 E 12 2 EGF EGF 2EGFR42EGFR4 8 3 Expose 1 1 Figure 2 2 The Graph view is used to display the different graphs and states of the derivation tree The view also allows first the creation then the edition of the states elements 2 k Get information click an element portnode or edge and Porgy displays all available properties of that element TA Rectangle selection select all elements touching the selection box the previous selection 15 replaced but can be recovered with Undo With Shift the newly selected elements are added to the current selection with Ctrl Alt on Mac the selected elements are removed from the current selection 22 Selection edition modify the shape and position Shift click modifies only coordinates Ctrl click modi fies only size Left click outside the selection resets the selection i Edit edge bends click on an edge to select it with this tool then Shift click to add a new bend click a bend to move it or Ctrl click Alt on Mac to remove a bend Add portnodes and edges allow the user to create edit and add portnodes Edge can also be added by click
24. h handle node types Two possible values 1 for center and 2 for ports 3 2 Rules 2 SHC SHC LHS BRIDGE RHS Figure 3 3 Rewriting rule example A rule is composed of a left hand side LHS a right hand side RHS and a bridge which connects both sides The red edges represent connections of equivalent ports between LHS and RHS For instance the two ports labeled 1 in the LHS EGFR portnode is connected to the RHS EGFR port also labeled 1 These specific edges allow to restore node properties and their connections to the rest of the graph after rewriting All connections between the left hand side and the right hand side must go through a port of the bridge Some additional properties are required to define a rule 20 Chapter 3 Porgy data structure Porgy Documentation Release 2 0 Arity Arity of a LHS port Sometimes a port needs to be connected to some other ports in the graph which are not part of LHS This property is used to indicate the minimum required degree of a port RuleSide for nodes and edges indicates in which part of the rule the element is Integer property There are four possible values 1 for LHS 2 for RHS 3 for the bridge red edges for instance 4 to identify a port of the bridge and 5 to identify specific edges which connect two LHS ports via the bridge The value 4 is used to indicate which node is the center of the bridge It is also used for the edges on either side of the bridge The value 5 is u
25. iew window Help Gives access to this documentation 1 1 1 Toolbar New Clear the current session and create a new empty one 1 e Open Open a saved session ww Save Save the current session w Save As Save the current session under a specific name Undo Undo the last operation e Redo Redo the last undo operation Copy Copy the selected portnodes and edges from the active view to the clipboard This option is only available if the active view is a Rule view or a graph view 4 Chapter 1 Porgy User Interface Porgy Documentation Release 2 0 amp Cut Cut the selected portnodes and edges from the active view This option is only available if the active view is a Rule view or a graph view Paste Paste the portnodes and the edges from the clipboard to the active rule view This option is only available if the active view is a Rule view or a Graph view Snapshot Take a snapshot of the current view F Help Show the help widget 1 2 Workspace Views The workspace is the central place where the visualizations are displayed Every time a graph a rule or a derivation tree is opened its corresponding view will be displayed in this space If one or more views are already present in the workspace the new one will be set in the last position More information concerning the specific views can be found in Presentation of the views Interaction tool para meters Disp
26. ill be used to reconnect the edges attached to the red portnode The red blue rule is now finished and can be directly applied to the graph to start rewriting operations If your are impatient to proceed consult the next section to find out how to apply a rule otherwise there is still two rules to create 28 Chapter 4 Rewriting in action A tutorial Porgy Documentation Release 2 0 4 2 2 Rule 2 blue to yellow Now that the bases have been set we are able to move a bit quicker This second rule have to divide an existing blue node in two yellow nodes As previously seen we start by creating a new rule in the Rule widget right click then Create new called blue 2yellow We add a blue portnode on the left of the bridge We create a new portnode variation with two ports following the steps previously shown for the b ue portnode creation The portnode name is set to 3 and its colour is changed to a light yellow RGB 255 255 127 while its ports receive a primary yellow RGB 255 255 0 We then add two yellow portnodes on the right of the bridge Delete portnodes tule Attribute Expose rA e Deciding how to connect the transformed elements is a bit more specific this time as we divide the blue portnode in two different portnodes We choose to reroute the edges connected to a blue port toward only one yellow port The two yellow portnodes result of the transformation are connected through their unused ports The e
27. ing the source node then the target node You can only add edge between two ports X Delete element click a portnode or edge to delete it 2 2 2 Configuration The following options can be customized using the tab on the right side of the view e Scene identical to the options available in Tulip allows to customize the view 2 2 3 Contextual menu Perform a right click Ctrl click Mac to display this menu 2 2 Graph View 13 Porgy Documentation Release 2 0 Center view move the camera to visualize all the ports in the graph Redraw redraw the graph and center the view You can choose between a force drawing algorithm GEM Frick or a hierarchical drawing algorithm Sugiyama OGDF Take snapshot open the screenshot tool Save selection allow the user to save the current selection in a new local property or in an existing one Click on New property and input the name of the new property to create a new property To erase an existing one just click on the name of the property to replace This is useful to create P and Ban properties Restore selection allow the user to replace the current selection by the selected property 2 3 Derivation Tree view This is the base view for derivation trees Displays the graphs present in a derivation tree as a hierarchy Each edge between two graphs represents the transformation of the source to the destination transformation can be an application of a rule simple rule
28. ion tr Strategies 8 89 db Add repeat red blue repeat blue 2yellow Del repeat 3yellow red T Save 0 No more rules be applied from here leaving us with nineteen states and 2 yellow portnodes 4 5 Afterword Congratulations you have completed this tutorial You now are familiar with the basic inner mechanics of Porgy restart from scratch and create your own rewriting rules and starting graph or open a graph from Tulip and import the rules and start rewriting There is still nonetheless much to see Consult Porgy in details for more information on the advanced possibilities of the platform and discover more on the Property Manager on how to customize the matching and the grammar of the strategy language 36 Chapter 4 Rewriting in action A tutorial CHAPTER FIVE PORGY IN DETAILS In the following section you will find information on the advanced functionalities of Porgy We will consider from here that you have successfully achieved the tutorial presenting how to create rules and apply them We will thus base all the explanations in the direct continuity 5 1 Property Manager The Property Manager is available in the Edit menu The widget will display all the properties existing in the current graph and give you the possibility to select any possible combination of those properties to use as matching criterion Property Manager Property Test for match 1 state true 2 viewBorderColor
29. isualization edition view on the workspace One can also double click on the rule or drag and drop a list element on the workspace to display it Create new Create a new derivation tree based on the graphs selected in the main derivation tree Delete Destruct the selected element One cannot delete the main derivation tree More information concerning the derivation tree view is available in the Derivation Tree view section 1 6 Strategy widget This widget handle all the strategies management actions Add strategy Create an empty strategy 8 Chapter 1 Porgy User Interface Porgy Documentation Release 2 0 Current strategy edition widget Strategies Add strategy dh v swap repeat white1 orelse red1 orelse red2 backToMast Remove strategy Export strategy X test backToMast Layout Algorithm GEM Frick Execute Strategy selection widget Li Layout selection Execute strategy Strategy from derivation tree try to compute the strategy from the selected graph elements in the main derivation tree Import from a file load a strategy from a file The new strategy will have the name of the file loaded without the file extension Remove strategy remove the selected strategy Export strategy save the selected property on the disk 1 6 1 Edition When selecting a strategy by clicking on its name in the widget its cod
30. latform After having launched Porgy choose the item Random Simple PortGraph in the File Import menu Docks Window Help New Ctri N 3 Open Ctri O sel Porgy Tip Import Random Simple PortGraph Random Tree Exit A new window will open allowing you specify the generation options We use the following settings Random Simple PortGraph plugin pa Name nodes 3 edges 3 Connected true Additionnal ports true Same In Out ports true The options nodes edges and Connected are specific to the generator and allow to indicate respectively how many nodes and edges the graph will contain and whether or not the graph have to be connected 23 Porgy Documentation Release 2 0 The two remaining options are specific to Porgy e Additional ports By default each connection to a portnode is achieved using a different port i e if a node is of degree X then it will have X ports one for each in or out coming edge Enabling the Additional ports option will give the exact same number of ports to every portnode while disabling it will reduce the number of ports to one Same In Out ports By default edge orientation is not considered in Porgy setting this option to false differ entiate the existing ports in two distinctive ones labelled n and Out Edges will leave a portnode through an Out port and arrive using an n port Those options are also available when importing a tlp graph A new option is
31. layed graph name Available interaction tools Close view Ee b UN u a E EGFRView parameters Widgets GFR M c p UU ITI ME Move view gt EGF EGF handler ECTS 112 2 EGF EGF Switch to Change Worspace layouts expose mode displayed views 1 2 1 Navigating into the views There is different ways to switch the views displayed in the workspace Change the workspace layout using the control buttons located at the bottom right of the workspace you can change the number of views displayed at a same time Some layouts are only available when enough views are opened simultaneously and the required number of views is reach By default only one view is displayed at once Porgy Documentation Release 2 0 e Switch displayed views the current view can be changed by clicking on the left or right arrow buttons located at the bottom of the workspace Use the Expose mode click on the expose button at the bottom left of the workspace to switch to the Expose mode In this mode each view is represented by a preview and can reordered by drag and dropping Reorder the views in the workspace drag and drop the view using the move view handler located in the top right corner of each view 1 2 2 Configuring a view The list of the configuration widgets for each view appear in as tabs a
32. ly modified version of this portnode double click on the red element to open the customiza tion widget in which we will change the field Name to 1 aportnode an 4 7 2 ES e 2 2 E E 2 3 Expose 2 2 The new variation of the red portnode found in GO is now available and is marked as with a red background Click on it in the list to highlight it and click on the eft of the bridge to create a new portnode in the left hand side of the rule 26 Chapter 4 Rewriting in action A tutorial Blue portnode Create new portnode Left Click on a source port to start adding a new edge then left click on Porgy Documentation Release 2 0 x E lt 9 5 To add the blue variation of the portnode we have to create a new portnode n the Add a portnode interactor parameters click on the button Create a new portnode to display the portnode creator assistant Add portnode an 5 2 G8 Name Color ERR Ports Add Delete a Cancel we can customized new portnode by changing its name colour and number of ports We set the name to 2 and change the default colour to a light blue RGB 0 85 255 Each port can also be personalized by adapting their name shape and colour We add two ports to our portnode and set their shape to be a Rounded Box with a pure blue colour RGB 0 0 255 4 2 Rule creation Add a
33. od qo bos 31 TT aeo e dne RV ROS GRO UK RS ROUEN PUR ee Be dE ee 32 SIO gaa ee aR eR Oe A ER eh SUR OER ES a a 36 Porgy in details 37 Property uu ddr en uk d BU amp EER ERS EEE SE 37 222 Ee DUM plop os 32 9 4 xb wo9 5 E39 CeO eee POP we Box FE web eee ee 40 5 3 Checking a rule application a graph 40 SIDE ION saan nke 4 Xo ea 4 Porgy Documentation Release 2 0 PORGY is an interactive visual environment based on Tulip for modelling complex systems through graphs and graph rewriting rules Graph rewriting systems appear as a powerful formalism to capture and study phenomena occurring in complex systems such as the evolution of bio molecular networks adhoc communication networks or interaction nets CONTENTS 1 Porgy Documentation Release 2 0 20 CONTENTS USER INTERFACE This section describes the Porgy user interface If you need some additional information on an element move the cursor on it and press F1 on Windows or Linux and the help key on Mac to gain access to the help page Menu bar Workspace ELTE 1 1 wire ones Qi H id PORE WI get numm gre naga orar culi kh SEE
34. or each rule at least one of the elements of the left hand side has to be within the Position set for the matching to be valid The matching will be impossible if all of the elements are neutral The Ban set is the exact opposite of the Position set as such the elements banned will be plainly ignored during the matching step The elements in the right hand side of a rule can be send to the Ban set after the rewriting operation by setting the property of each of those elements to true Please note that the Ban property takes priority over the Position property 5 3 Checking a rule application on a graph The application of a rule is made by a drag and drop of a rule to a graph metanode in the derivation tree view If the operation is valid a green square will appear a graph view 40 Chapter 5 Porgy in details Porgy Documentation Release 2 0 Once you drop the rule a parameter configuration widget will appear to configure the rule application Apply rule red blue on model GO Name Rule Name red blue Maximum number of instances to find 1 Property for Position Select a property Property for Ban Select a property Cancel K You can customize these parameters e Rule Name Maximum number of instances to apply the maximum number of matching to compute Position the boolean property that defines a subgraph of the graph This subgraph is used to restrict the search of the instances of the left hand side of the rule Wh
35. sed for edges only when a subgraph of LHS have to be replaced by a single edge The edge is going from a port a of LHS to a port of the bridge then from this latter to another LHS port called 5 Then the rewriting will consist in removing LHS M RHS only When sets to true the element is added to the current position set after rewriting N RHS only When sets to true the element is added to the current ban set after rewriting 3 3 Graphs Graphs have some additional properties to keep a trace of each transformation new Boolean property set to true if the edge or the portnode is new i e it has been created or modified by the last transformation The morphisms between a rule LHS and a graph G are saved as subgraphs of G Each subgraph is the instantiation of a rule LHS and uses some specific properties and graph attributes tag Integer property filled with the Tulip id of the corresponding node or edge in the rule LHS P Property graph attribute which handles the property name used as the position set or NoPosition if positions were not used Ban Property graph attribute which handles the property name used as the ban set or NoBan if ban was not used rulename graph attribute which handles the name of the rule used 3 4 Derivation trees The nodes of the derivation tree are Tulip metanodes associated to each generated graphs There is a black or purple edge between two metanodes a and b if the application of a rule
36. t clicking in the rule widget a menu appear offering the following options Show A rule must be selected to enable this action Displays a visualization edition view for the selected rule One can also double click on the rule or drag and drop the view on the workspace to display it Create new Create a new empty rule Rename Rename the hovered rule Clone A rule must be selected to enable this action Clone the selected rule i e create a copy of the rule with the same port nodes and the same values Delete A rule must be selected to enable this action Delete the rule If the rule is used in an existing graph it cannot be deleted Import Open a file browser window allowing to import one or several rules previously exported files must have the appropriate extension x porgy rule Export Independently save the currently hovered rule for later import More information concerning the Rule view is available in the Rule View section 1 4 Graph widget Graphs x Filter graph ld Mame Nodes ma 128 G47 6 gt 127 G46 6 gt XJ 124 Gas 6 gt 123 G44 5 120 G43 6 7 119 G42 6 2 118 G4l 6 113 640 5 gt 1 112 639 6 2 111 638 6 Small icons v Click on Graphs tab to access to the graphs management widget Use the text line at the top of the widget to filter them using names There is four preview modes No icons Do not display previews Small icons Medium icons
37. t the top right corner of each view To edit those parameters just click on a tab to expand the configuration widget Click on the small cross in the tab to close the opened widget 1 2 3 Changing the current interaction tool To select an interaction tool just click on the icon of the interaction tool you want in the list The current interaction tool button will be updated with the tool name and icon Some interaction tools can be configured by clicking on the interaction tool button at the top left side of the view toolbar The configuration widget will pop up If the interaction tool cannot be configured a short description of the tool will appear To close the configuration widget click again on the current interaction tool button 1 3 Rule widget Rules E rule_5 rule 4 rule 3 rule 2 rule 1 parallel rule 1 rule 1 Small icons Click on Rules tab to access to the Rules management widget Here one can create visualize and destruct rules Use the text line at the top of the widget to filter rules using rule names There is four preview mode List Display the rules in a list without any preview e Small icons Rules are shown using a small preview icon Medium icons Intermediate sized icons Large icons Enlarged rule previews To display an even bigger preview of a rule hover it with your mouse cursor and wait a second 6 Chapter 1 Porgy User Interface Porgy Documentation Release 2 0 1 3 1 Contextual menu By righ
38. tching property the Property Manager can also be modified on the elements of the right hand side This can be used to specify which value to affect during the rewriting process We consider the graph used in the tutorial the rule red blue and the matching property viewColor to illustrate the process e After having selected viewColor in the Property Manager as a matching condition the boolean property view Color isused is created We select both of the blue ports and update their value for viewColor isused to false Get information 4 gt RuleSide viewBorderColor viewBorderWidth tule Attribute viewColor viewColor isused Expose 2 3 e After applying the changed red blue rule we can witness the difference between the normal result G and the modified version in G2 as the ports colours have not changed according to the visual information given by the rule A Navigation When set to true the isused property indicates the value given by the element in the right hand side will be the one rewritten This is the default behaviour thus the ports rewritten are blue like G7 as expressed visually by the corresponding elements in the right hand side However when set to false the value selected is the one obtained from the matching elements corresponding to the linked element of the left hand side As a result the application of the modified rule tr
39. the small multiples to take the whole available space or to have an uniform font size The margin between each preview can also be customised Small multiples layout set the display options for the small multiple view Go for the default layout or force a specific number of lines 2 4 Additional trace views 17 Porgy Documentation Release 2 0 18 Chapter 2 Presentation of the views CHAPTER THREE PORGY DATA STRUCTURE A graph rewriting system is made of these elements Graph the graph being rewritten Rule a transformation rule Derivation tree keeps a trace of each rewrite operation Graph and rules are made with a specific graph structure called a Portgraph To be fully understandable this part of the documentation requires a good knowledge of the Tulip data structure and the latest publication about Porgy see the Porgy web site and the publication at the GRAPHITE 2014 workshop 3 1 Portgraphs Figure 3 1 A portgraph with 5 nodes Nodes of a portgraph have ports and two nodes can be connected by an edge only via ports Internally a portgraph node with 4 ports is made with 5 Tulip nodes and 4 edges connected with a star structure The central node is called e center 19 Porgy Documentation Release 2 0 EGF EGF 1 Figure 3 2 Internal structure of a portgraph node The following Tulip property is used in order to identify correctly each part of a portnode NodeType Integer Property whic
40. then accessible proposing to keep the previously used layout or recompute a new one The graph is generated and imported in the list of graphs as GO see Graph widget You can see that creating this first graph also create TraceMain the main derivation tree The list of available traces is available in the Derivation tree widget If generated using the same parameters your GO should be similar to this one The visual properties of the nodes and ports shapes sizes and colours are using default values We keep them as such for now 4 2 Rule creation With the initial graph imported we can start the rule creation For this tutorial we will create three different rules achieving the following goals change the color of a node from red to blue divide an existing blue node in two yellow nodes and merge three yellow nodes in a single red node The colour will consequently be an important information for our rules and will need to be used as a matching property To enable this we must activate the viewColor property in the Property Manager accessible in the menu Edit gt Property Manager 24 Chapter 4 Rewriting in action A tutorial Porgy Documentation Release 2 0 Property Manager Property st for matc 1 viewBorde false 2 viewBorde false 3 viewColor 4 viewFont false 5 viewFontA false 6 viewFonts false 7 viewLabel false 8 viewLabel false 9 viewLabel false 10 viewLabel f
41. transforms a source graph a into a destination graph b The label of the metanodes on the left side of each node is the name of the graph The result of a strategy is represented by a green edge between the source graph and the result of the strategy A red node indicates a failure i e a rewriting operation was not possible The edges of the derivation tree has many properties which handles all parameters of the rewriting operations Type Integer property which can be 0 to indicate a standard metanode of to indicate that the node 15 a failure node Transformation Ban PropertyName Transformation Instance Transformation PPropertyName Transformation Parallel Information Transformation Rule 3 3 Graphs 21 Porgy Documentation Release 2 0 Figure 3 4 Example of a derivation tree 22 Chapter 3 Porgy data structure FOUR REWRITING IN ACTION A TUTORIAL In the following sections we will explain the guidelines to start working using Porgy We will e start using a random graph create a few different rules using specific properties for the pattern matching apply the rules a few times separately create a strategy for applying the rules in a specific order and finally execute the strategy some times to obtain a few branches on the derivation tree 4 1 Import new graph As a starting point we generate a random simple graph using the appropriate plugin embedded within the p
42. ule view or a graph view Paste Paste the portnodes and the edges from the clipboard to the active rule view This option is only available if the active view is a Rule view or a graph view Select all Clear the selection then add the portnodes and the edges present in the active view Deselect all Clear the selection nvert selection Invert the selection Selected elements become unselected and unselected become selected Delete selection Delete portnodes and edges selected in the active view This option is only available if the active view is a Rule view or a graph view Property manager Allows users to select the properties to use during rewriting operations as match ing parameters for more information consult Property Manager Algorithm Allows the user to compute and apply algorithm Measure Compute and assign a value to the viewMetric property of graph elements For example when running the Portnode s degree algorithm the degree the number of neighbors is computed and stored for each portnode into its viewMetric property Selection Selects nodes and or edges based on advanced criteria Selecting means assigning the viewSelection property General Contains all the base porgy algorithms This menu is made for an advance use of Porgy Docks Allows to show and hide dock widgets in the Porgy user interface Windows Manages the sub windows of the v
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