Adding graph node¶

This diagram displays how the GraphWidget responds to user input and adds new nodes to the Ontology. Note that all operations that might change the Ontology pass through the SyntaxController and all operations that read from the loaded Ontologies pass through the IndexAbstractor.

Searching in the index¶

This diagram displays a simple abstraction of how the DocumentationWidget responds to a user search request. Note that it does not include any IndexAbstractor internal operations such as building and maintaining the Index.

Graph widget input loop¶

This diagram displays the activity diagram used by the GraphWidget when a user adds a node to the graph. Of special note is that the parsing of the new graph is done in the background so that the user can still interact with the GraphWidget while it is updating the Ontology.

Text editor input loop¶

This diagram displays the activity diagram used by the TextWidget while the user is typing. Once the user pauses typing, the text editor checks whether the parenthetical syntax is correct, and if it passes a simple syntax check, the text is passed to the parser. The parser then checks syntax and semantics and returns accordingly. If errors occur during parsing, they are displayed in the editor.

Common workflow¶

This diagram displays an abstract view of a common User-interaction with the program. The user starts the program adds a .kif-File, searches in WordNet and finally adds a relation through the GraphWidget. PySUMO automatically converts the relation to kif and appends it to the ontology source.

Exit process¶

This diagram displays an abstract view of the activity diagram when a user wants to exit the program. This is done when the user clicks on the close icon in the title bar of the main window of pySUMO or on ‘Exit’ in the menu ‘File’. The program makes sure that there are no unsaved changes in open ontologies and if there are changes, prompts if they should be saved. If the user doesn’t save them, the modifications will be lost. Note that the program also saves session layouting preferences of the GUI so they can be restored in the next pySUMO session. These preferences include, for example, the position of widgets in the main window.

Module contents¶

The pySUMO library package. This package contains the core functionality of pySUMO. It not only provides the GUI with a feature-rich API, but also validates input and keeps the Ontologies in a consistent state.

Subpackages¶

Submodules¶

pysumo.indexabstractor module¶

This module abstracts all operations on the Ontology index. It is used for every read operation on the Ontology. It eases access to the Ontology and protects the data structures from direct user access.

This module contains:

• IndexAbstractor: The interface to the Ontology index.
• AbstractGraph: An object containing selected graph nodes and relations.
• AbstractGraphNode: A node in a AbstractGraph
• DotGraph: A Graphical representation of an AbstractGraph with DOT

class pysumo.indexabstractor.AbstractGraph(variant, major, minor, root, depth, info)[source]¶

Bases: builtins.object

An abstract representation of a subset of an Ontology as a collection of nodes and relations.

Variables:

• nodes: The list of graph nodes.
• relations: An adjacency matrix of all the paths in the graph.

class pysumo.indexabstractor.AbstractGraphNode(name)[source]¶

Bases: builtins.object

A node in an AbstractGraph. Contains information necessary to recreate an AbstractSyntaxTree from an AbstractGraph.

Varibles:

• name: The name of the AbstractGraphNode.

class pysumo.indexabstractor.IndexAbstractor[source]¶

Bases: builtins.object

The IndexAbstractor provides a high-level index of the AbstractSyntaxTree. Each Ontology is represented by a hashmap, the list of these hashmaps is the index. Average access time is in O(n) where n is the number of loaded Ontologies.

Variables:

• root: The root AbstractSyntaxTree node.
• ontologies: The list of currently active Ontologies.
• index: The index of all terms in the currently active Ontologies.
• wordnet: A reference to the Object containing the SUMO-WordNet mapping.

Methods:

• init_wordnet: Initializes the WordNet mapping.
• update_index: Updates the index.
• search: Searches for a term in the Ontology.
• get_ontology_file: Return an in-memory file object for an Ontology.
• get_completions: Return a list of possible completions for the current index.
• get_graph: Creates an abstract graph containing a view of the Ontology.
• wordnet_locate: Returns information about a term from WordNet.

get_completions()[source]¶

Returns a list of possible completions for the currently loaded ontologies.

get_graph(variant, major=2, minor=1, root=None, depth=None)[source]¶

Returns a hierarchical view of the Ontology.

Arguments:

• variant: The list of terms against which the resulting AbstractGraph matches.
• major: The position of the parent element.
• minor: The position of the child element.
• root: The root node to which all other nodes are related.
• depth: The recursion depth.

Returns:

• AbstractGraph

Raises:

• KeyError

get_ontology_file(ontology)[source]¶

Returns an in-memory file object for the Kif representation of ontology.

init_wordnet()[source]¶

Initializes the SUMO mapping to WordNet.

search(term)[source]¶

Search for term in the in-memory Ontology. Returns all objects that match the search.

Returns:

• {Ontology : (String, int)[]}

update_index(ast)[source]¶

Updates the index with all new AST nodes in ast.

wordnet_locate(term)[source]¶

Use the mapping from SUMO to WordNet to retrieve information about a term.

Arguments:

• term: the term to locate

Returns:

• String[]

Raises:

• KeyError

pysumo.indexabstractor.normalize(term)[source]¶

Normalizes term to aid in searching.

pysumo.wordnet module¶

The interface to WordNet.

This module contains:

• WordNet: An interface to the WordNet online English lexical database.

class pysumo.wordnet.WordNet[source]¶

Bases: builtins.object

An interface to locate and search for items in WordNet. Searches WordNet for information about terms in the Ontology, to find colloquial variations of term names and to find terms that are synonyms of a word.

Methods:

• locate_term: Locates a term in WordNet.
• find_synonym: Finds possibly synonyms for a word.

find_synonym(word)[source]¶

Searches WordNet for possible synonyms for word.

Returns:

• String[]

locate_term(term)[source]¶

Use the mapping from SUMO to WordNet to retrieve information about a term.

Kwargs:

• term: the term to locate

Returns:

• (name : String, type : SSType, gloss : String)[]

pysumo.parser module¶

The pySUMO parsing module. It contains functions to parse and serialize kif-files. It also handles the Ontology’s data structure and parses the mapping of SUMO terms to WordNet.

This module contains:

• AbstractSyntaxTree: The in-memory representation of an Ontology.
• Ontology: Contains basic information about an Ontology.

class pysumo.parser.AbstractSyntaxTree(ontology, parent=None, line=-1)[source]¶

Bases: builtins.object

The AbstractSyntaxTree is a node in the abstract syntax tree. The abstract syntax tree is defined by a root node and its children. The AbstractSyntaxTree is the in-memory representation of the loaded Ontologies for internal purposes only and should never be passed outside of the lib.

Variables:

• parent: The parent node
• children: A list of child nodes.
• name: The name of the AbstractSyntaxTree object.
• element_type: The type of the node element.
• ontology: The Ontology object to which this node corresponds.
• is_indexed: Whether or not this node is indexed.

Methods:

• add_child: Adds a child node.
• remove_child: Removes a child node.

add_child(entry)[source]¶

Adds entry as a child to self.

parse(tokens)[source]¶

remove_child(entry)[source]¶

Removes entry from the node’s children.

exception pysumo.parser.ParseError(line, linenumber)[source]¶

Bases: builtins.Exception

class pysumo.parser.Pos[source]¶

Bases: enum.Enum

class pysumo.parser.SSType[source]¶

Bases: enum.Enum

class pysumo.parser.SUMOConceptWordNetItem(sumo_concept, suffix, synset_offset, lex_filenum, ss_type, synset, ptr_list, frames, gloss)[source]¶

Bases: builtins.object

The object returned from _wtokenize containing info on the SUMO-WordNet mapping.

pysumo.parser.astmerge(trees)[source]¶

Merge two Abstract Syntax Trees

Args:

• trees: a tuple of 2 AST objects

Returns:

• AbstractSyntaxTree

pysumo.parser.kifparse(infile, ontology, ast=None)[source]¶

Parse an ontology and return an AbstractSyntaxTree.

Args:

• ontology: the ontology to parse
• graph: a modified graph of this ontology
• ast: the AST of ontologies which are needed from this ontology
• infile: the file object to parse

Returns:

• AbstractSyntaxTree

pysumo.parser.kifserialize(ast, ontology, out)[source]¶

Writes ontology to disk as kif. Parses ast and writes out all nodes that belong to ontology.

Args:

• ast: the Abstract Syntax Tree
• ontology: The specific ontology with is written to disk
• f: The file object witch written in

Raises:

• OSError

pysumo.parser.wparse(datafiles)[source]¶

Parses the file containing the SUMO-WordNet mapping.

Args:

• path: The path to the SUMO-WordNet mapping files

Returns:

• Dictionary

pysumo.syntaxcontroller module¶

Handles all write accesses to the Ontologies and kif files. The SyntaxController’s main purpose is to act as an intermediary between the user and the Ontology.

This module contains:

• SyntaxController: The interface to the parser/serializer.

class pysumo.syntaxcontroller.Ontology(path, name=None, url=None, lpath=None)[source]¶

Bases: builtins.object

Contains basic information about a KIF file. This class is used to maintain separation between different Ontology-files so the user can choose which are active and where each Ontology should be saved.

Variables:

• name: The name of the Ontology.
• path: The location of the Ontology in the filesystem.
• url: The URL from which the Ontology can be updated.
• active: Whether or not the Ontology is currently loaded.

save()[source]¶

Saves all pending changes in self to self.path.

class pysumo.syntaxcontroller.SyntaxController(index)[source]¶

Bases: builtins.object

The high-level class containing the interface to all parsing/serialization operations. All operations that can modify the Ontology or kif-file are passed through the SyntaxController. The SyntaxController acts as a moderator between user-side widgets and the low-level API ensuring that all requests are correct, that higher objects never gain direct access to internal objects and that all changes to the Ontology are atomic.

Methods:

• parse_partial: Checks a code block for syntax errors.
• parse_patch: Checks a code for correctness and adds it to the Ontology.
• add_ontology: Adds an Ontology to the in-memory Ontology.
• remove_ontology: Removes an Ontology from the in-memory Ontology.
• undo: Undoes the most recent change to the ontology.
• redo: Redoes the most recent change to the ontology.

add_ontology(ontology, newversion=None)[source]¶

Adds ontology to the current in-memory Ontology.

Arguments:

• ontology: the ontology that will be added
• newversion: a string witch represent the new verison of the ontology

Raises:

• ParseError

parse_partial(code_block, ontology=None)[source]¶

Tells self.parser to check code_block for syntactical correctness.

Arguments:

• code_block: the partial code block that will be checked

Raises:

• ParseError

parse_patch(ontology, patch)[source]¶

Apply a patch to the last version of the ontology and parse this new version

Arguments:

• ontology: the ontlogy which is patched
• patch: the patch to add to the ontology

Raises:

• ParseError

redo(ontology)[source]¶

Redoes the last action in ontology

remove_ontology(ontology)[source]¶

Removes ontology from the current in-memory Ontology.

Arguments:

• ontology: the ontology that will be removed

Raises:

• NoSuchOntologyError

undo(ontology)[source]¶

Undoes the last action in ontology

pysumo.syntaxcontroller.get_ontologies(lpath=None)[source]¶

Returns a set of all ontologies provided by pysumo as well as local ontologies.

pysumo.updater module¶

Module which handles updating of Ontologies. It use PycURL to check if any updates are avalible. The URLs for the ontlogies are safe in the ontology so the user can easy add an URL for a new ontlogy.

pysumo.updater.check_for_updates(ontology, function=<function <lambda> at 0x7f4fc7ccde18>)[source]¶

Check if there are updates for ontology. If an update is available, executes function. Function receives the new ontology file as the first positional argument.

Returns:

• Boolean

Raises:

• HTTPError

pysumo.updater.update(ontology, function=<function <lambda> at 0x7f4fc7ccd400>)[source]¶

Checks for updates to ontology and if available downloads them. If the update succeeds, executes function after the download completes. Function receives the path to the downloaded ontology as the first positional argument, and ontology as the second.

Raises:

• HTTPError

Module contents¶

The pySUMO Qt-GUI package. This package contains all classes and widgets needed to display the pySUMO editor. There are also classes created by Qt Designer which are inherited from in the ‘coded’ classes.

Subpackages¶

Submodules¶

pySUMOQt.MainWindow module¶

pySUMOQt.Settings module¶

IndexAbstractor¶

• Delete DotGraph.
• Make root and depth keyword arguments defaulting to None
• Turn index into a simple dict. Makes index access easier and faster.
• Add init_wordnet() to initialize the WordNet mapping
• Add update_index() to build the index
• wordnet_locate() returns a list of strings
• IA now also stores the root AST node and a list of ontologies
• Change get_graph arguments to allow for more complex matching.
• Add normalize method for normalizing string arguments.
• Add function to return list of possible completions.

WordNet¶

• change argument of wparse() from a mapping file to a directory containing the mapping files and the rest of the wordnet database - avoid merging mapping files
• completely get rid of all dependencies on NLToolkit - extending upon it is a nightmare
• locate_term() returns a tuple of String, SSType, String

SyntaxController¶

• Add an optional argument newversion to add_ontology()
• Remove parse_graph(), the user now has to edit the file self
• Remove parse_add(), we can use add_ontology() now
• Moved Ontology to syntaxcontroller module

Logger¶

TextEditor¶

• remove show autocomplete – Qt does this on its own

• Added

  • setTextChanged()
  • _initNumberBar()
  • _updateOntologySelector()
  • _hideLines(lines)
  • _showLines(lines)
  • _zoomOut_()
  • _zoomIn_()
  • showOtherOntology(ontologyname)
  • expandIfBracketRemoved()
  • increaseSize()
  • decreaseSize()
  • expandAll()
  • hideAll()
  • getLayoutWidget()
  • numberbarPaint(number_bar, event)
  • initAutocomplete()
  • searchCompletion()
  • toggleVisibility(line)
  • hideFrom(line)
  • insertCompletion(completion)
  • commit()

Introduce SyntaxHighlightSetting to handle user defined Syntax Highlight Rules

class SyntaxHighlightSetting() __init__( expression, font_weight, font_color, expression_end=’‘) createFormat() get_format() getValues() serialize() deserialize( string)

Introduce class SyntaxHighlighter class SyntaxHighlighter __init__( document) highlightBlock( text)

Introduce Numberbar because Qt does not do this on his own class NumberBar(QWidget) __init__( edit) paintEvent( event) adjustWidth( count) updateContents( rect, scroll) mouseDoubleClickEvent( event)

GraphWidget¶

Komplette Änderung der API, um an pygraphviz anzupassen

MainWindow¶

• Added

  • _showOptionDialog_()
  • _addWidget_(widgetType, widgetMenu)
  • createPySumoWidget(widgetType, widgetMenu)
  • addDeleteWidgetAction(widget)
  • addOrRestoreWidget(widget, menu, directAdd=False)
  • closeEvent(event)
  • createStatusBar()
  • setupStatusConnection()
  • displayLog(socket)
  • _updateStatusbar_(wrappedWidget=None)
  • _deleteWidget_(widget)
  • connectWidget(widget)
  • disconnectWidget(widget, callback=None)
  • getDefaultOutputPath()
  • _newOntology_()
  • _openLocalOntology_()
  • _openRemoteOntology_()
  • addOntology(ontology, newversion=None)
  • notifyOntologyAdded(ontology)
  • _ClearRecentOntologiesHistory_()
  • _deleteOntology_(ontology)
  • _updateOntology_(ontology)
  • _revertOntology_(ontology)
  • _showOntologyProperties_(ontology)
  • _closeOntology(ontology)

• Added quit_handler(signum, frame) to capture SIGINT signal.

• Introduced class PySUMOWidget which wrappes the application widgets.

• Removed class Statusbar, it became useless towards createStatusBar in MainWindow.

• Removed class Menubar, because the menu bar is already created by the designer.

• Removed class Toolbar, because the tool bar is already created by the designer.

• Moved class HelpDialog to module Dialog

Settings¶

• Introduced class LayoutManager.
• Introduced class PySumoSettings.
• Removed class PluginManager.
• Removed class WSettings.
• Moved class OptionDialog to module Dialog.

OptionDialog¶

• Remove createView() and load(path) methods.
• Added other methods to the OptionDialog.

ActionLog¶

• Queue the addition of an ontology to the A0ctionLog * Initialize an ActionLog with an ontology * Modify an ontology and store the changes * Assert that undoing the last action returns the previous state * Assert that undo/redo is invariant * Make sure the queue auto-flushes when exceeding size * Check that addition queue is overwritten when new changes are added and the old changes have not been OK’d. * Assert the invariance of excessive undoes * Assert the invariance of excessive redoes
• Check that ActionLog copes with high workloads

IndexAbstractor¶

• Assert than normalize() normalizes terms correctly.
• Assert that the index is built correctly.
• Test search on various terms
• Test WordNet search and self-initialization.
• Build several AbstractGraphs and check their contents
• Test that get_ontology_file returns the correct kif
• Test that adding multiple ontologies works
• Test that get_completions returns a correct list of terms

Parser¶

SyntaxController¶

• Assert that add_ontology() adds an AST equivalent to the one produced by kifparse()
• Assert the invariance of redundant adds
• Assert that adding and then deleting an ontology is invariant
• Check that adding two ontologies works correctly
• Assert that get_ontologies() lists the correct ontologies
• Assert that modifying the ontology works correctly
• Assert that parsing diffs works correctly
• Assert that undo/redo work correctl

WordNet¶

• Check functionality of locate_term
• Check functionality of find_synonym

Text Editor¶

Texteditor after doing test.

1. Open pySUMO
2. Open TextEditor
3. Open Merge.kif
4. Choose Merge.kif
5. Collapse Line 288
6. Collapse Line 136
7. Collapse Line 134
8. Uncollapse Line 134
9. Uncollapse Line 288
10. Collapse all
11. Expand all

Graphical Settings¶

1. Open pySUMO
2. Open TextEditor
3. Open Merge.kif
4. Choose Merge.kif
5. Open GraphWidget
6. Open DocumentationWidget
7. Open Hierarchy Widget
8. Open TextEdiorWidget

Hierarchy Widget¶

Hierarchywidget after doing test.

Graph Widget¶

Graphwidget after step 6.

Graphwidget after step 11.

1. Open pySUMO
2. Open GraphWidget
3. Open Merge.kif
4. Select instance on Variant selector
5. Select a root node
6. Select a depth (1)
7. Open a new ontology to write temporary content to.
8. Add a node “bla” in Graph Widget
9. Add a node “bla2”
10. Add a node “bla” (error)
11. Add a relation instance between “bla” and “bla2” (error)
12. Change scale
13. Choose a valid selector (there was a messagebox)
14. Add a relation instance between “bla” and “bla2”
15. Undo
16. Redo

Documentation Widget¶

Documentation widget after step 6.

Docwidget after doing test.

1. Open pySUMO
2. Open Merge.kif
3. Open DocumentationWidget
4. Switch to the Ontology tab in the DocumentationWidget
5. Type subrelation into the search field
6. Press Enter
7. Open TextEditor
8. Select Merge.kif in TextEditor
9. Press one of the links listed under “Merge”
10. Switch to the WordNet tab in the DocumentationWidget
11. Search for ‘Object’
12. Search for ‘Table’

MainWindow¶

Widgets ordering.

1. Open pySUMO
2. Open a new Ontology named “Mondial”
3. Open a remote ontology named “Mondial” at location: http://sigmakee.cvs.sourceforge.net/viewvc/sigmakee/KBs/mondial.kif
4. Close the ontology named “Mondial” with save and reopen it as local file.
5. Add Text Editor Widget
6. Add Documentation Widget
7. Add Graph Widget
8. Add Hierarchy Widget
9. Reorder Widgets
10. Make a print preview of the ontology “Mondial” from the Text Editor Widget
11. Delete the Text Editor Widget
12. Make a print preview of the ontology “Mondial” from the Graph Widget
13. Add a node and a relation in Graph widget
14. Delete the Graph Widget
15. Try to update the ontology “Mondial”
16. Open ontology properties dialog for “Mondial” and then close it.
17. Open Option Dialog and then close it
18. Revert the ontology “Mondial”
19. Quit pySUMO