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Matthew Stern
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topologic parsing
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‎AUTHORS‎

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All contributors arranged by first commit:
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Matthew Stern
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Benjamin Michalowicz

‎LICENSE‎

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MIT License
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Copyright (c) 2020 Matthew Stern, Benjamin Michalowicz
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎Makefile‎

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# SPDX-License-Identifier: MIT WITH bison-exception WITH swig-exception
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# Copyright © 2020 Matthew Stern, Benjamin Michalowicz
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CC=gcc
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CXX=g++
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MCS=$(MCS)
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LDFLAGS= -lm -lpthread -ltopologic -L. -ltopologic_parse -pthread #-lfl
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CFLAGS=-Wall -Werror -g -fPIC -O2 -ltopologic #-fsanitize=thread
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AR=ar
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BIN=topologic-parse
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FLEX=src/topologic_parser.lex
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BISON=src/topologic_parser.y
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FLEX_C=$(FLEX:.lex=.yy.c)
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BISON_C=$(BISON:.y=.tab.c)
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BISON_H=$(BISON:.y=.tab.h)
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FLEX_OBJ=$(FLEX_C:.c=.o)
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BISON_OBJ=$(BISON_C:.c=.o)
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FLEXPP=src/topologic_parser_cpp.lex
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BISONPP=src/topologic_parser_cpp.ypp
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FLEX_CPP=$(FLEXPP:.lex=.yy.cpp)
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BISON_CPP=$(BISONPP:.ypp=.tab.cpp)
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BISON_HPP=$(BISONPP:.ypp=.tab.hpp)
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FLEX_OBJ_PP=$(FLEX_CPP:.cpp=.o)
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BISON_OBJ_PP=$(BISON_CPP:.cpp=.o)
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TESTS=$(TEST_SRC:.c=)#ADD MORE AS THEY GO
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TEST_SRC=$(wildcard testing/*.c) #ADD MORE IF NEED BE
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TEST_OBJ=$(TEST_SRC:.c=.o)
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TEST_DIR=testing
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all: $(BISON) $(BISON_C) $(BISON_H) $(FLEX) $(FLEX_C) $(BIN) $(TESTS)
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$(FLEX_C):
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flex $(FLEX)
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mv lex.yy.c $(FLEX_C)
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$(CC) -fPIC -g -c $(FLEX_C) -o $(FLEX_OBJ) -lfl -ltopologic
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$(BISON_C): $(BISON)
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bison -d $(BISON) -o $(BISON_C)
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$(CC) -fPIC -g -c $(BISON_C) -o $(BISON_OBJ) -ltopologic
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$(BIN): $(OBJ) $(BISON_OBJ) $(FLEX_OBJ)
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$(AR) rcs libtopologic_parse.a $(OBJ) $(BISON_OBJ) $(FLEX_OBJ)
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$(TESTS): $(BIN) $(TEST_OBJ)
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$(CC) $(CFLAGS) -o $@ libtopologic_parse.a $(TEST_DIR)/$(@F).o $(LDFLAGS)
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cpp: $(BISON_CPP) $(BISON_OBJ_PP) $(BISON_HPP) $(FLEX_CPP) $(FLEX_OBJ_PP)
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$(AR) rcs libtopologic_parse.a $(BISON_OBJ_PP) $(FLEX_OBJ_PP)
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$(FLEX_CPP):
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flex $(FLEXPP)
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mv lex.yy.cc $(FLEX_CPP)
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$(CXX) -fPIC -g -c $(FLEX_CPP) -o $(FLEX_OBJ_PP) -lfl -ltopologic
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$(BISON_CPP): $(BISONPP)
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bison -d $(BISONPP) -o $(BISON_CPP)
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$(CXX) -fPIC -g -c $(BISON_CPP) -o $(BISON_OBJ_PP) -ltopologic
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all:$(BIN)
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.PHONY : clean cpp
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clean:
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rm -f libtopologic_parse.a
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rm -f $(TEST_OBJ) $(TESTS)
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rm -f $(FLEX_C) $(FLEX_OBJ)
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rm -f $(BISON_C) $(BISON_OBJ) $(BISON_H)
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rm -f $(FLEX_CPP) $(FLEX_OBJ_PP)
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rm -f $(BISON_CPP) $(BISON_OBJ_PP) $(BISON_HPP)
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rm -f $(BIN)

‎README.md‎

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# Topologic_Parse
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This is for parsing JSON files for Topologic.
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A library to simulate DFAs and Probabilistic DFAs using context switching. This library provides a way to build and define the behavior of a graph. The client is able to define the function each vertex and edge of the graph make and how the graph transitions from one (the first valid edge) or to many states, as well as which states the graph starts in.
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The library provides a way for the client to define what information is saved localy to each vertex and edge, as well as which information the vertex and edges originating at that edge share. In addition the client can pass information to each initial state that will be passed and modifyable by vertices at each state transition.
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This library can be used to create AI, ML, and simulations (such as of stock options, electron-electron interaction, etc.).
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## Installation
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### Arch Linux
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>yay -S topologic_parse-git
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-To use in program use
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>#include <topologic/topologic_parse.h>
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-Link with
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>gcc ... -ltopologic_parse
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### Manualy
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Build C Library
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>make
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-creates libtopologic.a
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Build C++ Library
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>make cpp
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-creates libtopologic.a
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Clean
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>make clean
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Debug
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>make CFLAGS=-DDEBUG
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## TODO
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# Errata
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## Edge/vertex modification
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Modifying/deleting vertices and edges inside f() not using submit request
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can lead to undefined behavior or dead locks. This is because in CONTEXT
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set to SWITCH or NONE with many starting vertices, can lead to a structure
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being NULL’d with its lock destroyed while another thread is holding that lock
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or two threads trying to modify each other and thus resulting in a dead lock. It
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is up to the client’s discretion to modify directly when in SWITCH or NONE
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with many starting vertices. Although in SINGLE, this should be fine. To
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mitigate this problem, the client should use submit request which will handle
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the requests sequentially with destroying structures last.
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## Graph modification
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Trying to delete the graph while running will result in undefined behav-
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ior. Destroying the graph does not lock any thread and thus will cause race
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conditions. The graph should be deleted only once all threads reach a sink.
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## Parameter Passing
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Parameters passed to edges or vertices functions will be free’d immediately
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after use and therefore will cause an error should they try and be accessed. To
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mitigate the values may be stored in the edge’s or vertex’s global or shared
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variables. Any non standard data type, such as struct, is dependent on the user
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to free its content as the library will only free the pointer to the struct and the
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pointer to the array of variables.
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## Illegal Arguments
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Passing wrong values or wrong number of variables to any function will result
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in failure. A client should be aware of which vertices connect and what edges
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it has and the proper handling required between such connections. Should the
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client choose to dynamically add/remove vertices or edges or even modify while
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running should be aware of the changes that may occur in the graph and the
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resulting change in dependence on proper variable handling.
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## Graph Modification (cont.)
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It is possible to modify the graph while it is running. To do so the client
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should submit request to add a change or pause the graph. Making any changes
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externally may result in undefined behavior if done improperly. Modifying the
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graph directly while running could result in failure.
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Should the number of init vertex args not much the number of vertices in
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the start set the program will result in an error.
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## Data Structure Errata
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Stacks and AVLTree can take non malloc’d data and function normally
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within scope of those non malloc’d data. However, in another scope the memory
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will be unaddressable and thus should be malloc’d memory instead. The stack
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and AVL Tree wll not free the void * data since the void * data structure is
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unknown to them and thus the client should free the memory.
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## SWITCH_UNSAFE
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Should SWITCH_USNAFE be used as the context, then the graph will run like
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how it runs in SWITCH, but the variables shared between the edge and the second vertex
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b will be passed to the edges function. Trying to read the shared variables may lead to a
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race condition in which vertex b or one/some of it's edges are modifying those varibales.
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The client is expected to handle such race conditions, and failing to do so can lead to a possibly
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unsafe execution. Thus this mode is UNSAFE. It is safe to use the shared variables with vertex b
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in context modes NONE and SINGLE since in NONE vertex b cannot also be active, and in SINGLE there
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is no threading.
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‎SECURITY.md‎

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# Security Policy
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## Supported Versions
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Use this section to tell people about which versions of your project are
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currently being supported with security updates.
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| Version | Supported |
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| ------- | ------------------ |
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| 5.1.x | :white_check_mark: |
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| 5.0.x | :x: |
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| 4.0.x | :white_check_mark: |
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| < 4.0 | :x: |
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## Reporting a Vulnerability
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Use this section to tell people how to report a vulnerability.
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Tell them where to go, how often they can expect to get an update on a
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reported vulnerability, what to expect if the vulnerability is accepted or
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declined, etc.

‎Topologic_Design_Document.pdf‎

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‎include/test.h‎

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#ifndef __TOPOLOGIC_TEST__
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#define __TOPOLOGIC_TEST__
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#include <topologic.h>
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#include <assert.h>
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#include <string.h>
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#include <stdio.h>
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#include <stdlib.h>
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#endif

‎refman.pdf‎

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‎src/topologic_parser.lex‎

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/* SPDX-License-Identifier: MIT WITH bison-exception */
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/* Copyright © 2020 Matthew Stern, Benjamin Michalowicz */
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%option noyywrap
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%{
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#include "topologic_parser.tab.h"
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%}
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blanks [ \t\n]+
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%%
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{blanks} { /* IGNORE */ }
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"{" return(L_BRACKET);
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"}" return(R_BRACKET);
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"graph" return(GRAPH);
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":" return(COLON);
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"vertices" return(VERTICES_);
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"edges" return(EDGE_);
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"bi_edges" return(BI_EDGE_);
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"[" return(L_SQUARE);
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"]" return(R_SQUARE);
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"," return(COMMA);
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"max_state" return(MAX_STATE);
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"lvl_verbose" return(LVL_VERBOSE);
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"mem_option" return(MEM_OPT);
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"context" return(LEX_CONTEXT);
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"max_loop" return(MAX_LOOP);
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[0-9]+ {yylval.val = atoi(yytext); return(VALUE);}
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%%

‎src/topologic_parser.y‎

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/* SPDX-License-Identifier: MIT WITH bison-exception */
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/* Copyright © 2020 Matthew Stern, Benjamin Michalowicz */
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%{
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#include <topologic/topologic.h>
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void f(int id, struct graph *graph, struct vertex_result *args, void *glbl, void *edge_vars) {}
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int edge_f(int id, void *args, void *glbl, const void *const edge_vars_a, const void *const edge_vars_b) {return 0;}
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void yyerror(struct graph** graph, const char *s);
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extern FILE *yyin;
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int yylex(void);
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%}
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%union {
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struct graph *graph;
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int val;
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};
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%parse-param {struct graph** graph}
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%token L_BRACKET
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%token R_BRACKET
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%token GRAPH
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%token COLON
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%token VERTICES_
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%token EDGE_
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%token BI_EDGE_
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%token L_SQUARE
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%token R_SQUARE
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%token COMMA
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%token MAX_STATE
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%token LVL_VERBOSE
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%token LEX_CONTEXT
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%token MEM_OPT
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%token MAX_LOOP
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%token <val> VALUE
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%start json
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%%
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json: L_BRACKET GRAPH {*graph = GRAPH_INIT(); if (!(*graph)){fprintf(stderr, "Can't create graph\n"); return -1;}}
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COLON L_BRACKET content R_BRACKET
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R_BRACKET
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;
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content: params g
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| g
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| params
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|
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;
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params: verb COMMA params
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| state COMMA params
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| mem_opt COMMA params
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| context COMMA params
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| max_loop COMMA params
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| verb
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| mem_opt
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| context
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| state
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| max_loop
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|
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;
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state: MAX_STATE COLON VALUE {(*graph)->max_state_changes = $3;}
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;
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verb: LVL_VERBOSE COLON VALUE {(*graph)->lvl_verbose = $3;}
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;
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context: LEX_CONTEXT COLON VALUE {(*graph)->context = $3;}
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;
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mem_opt: MEM_OPT COLON VALUE {(*graph)->mem_option = $3;}
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;
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max_loop: MAX_LOOP COLON VALUE {(*graph)->max_loop = $3;}
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;
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g: vs COMMA es COMMA bes
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| vs COMMA bes COMMA es
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| vs COMMA es
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| vs COMMA bes
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| vs
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;
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vs: VERTICES_ COLON L_SQUARE v R_SQUARE
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;
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v: /* empty */
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| VALUE COMMA {if (create_vertex(*graph, f, $1, NULL) < 0) fprintf(stderr, "Failed To Create Vertex %d\n", $1);}
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v
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| VALUE {if (create_vertex(*graph, f, $1, NULL) < 0) fprintf(stderr, "Failed To Create Vertex %d\n", $1);}
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;
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es: EDGE_ COLON L_BRACKET e R_BRACKET
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;
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e: /* empty */
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| VALUE COLON VALUE COMMA {struct vertex *a = find((*graph)->vertices, $1); struct vertex *b = find((*graph)->vertices, $3); if (a && b) {if (create_edge(a, b, edge_f, NULL) == NULL) fprintf(stderr, "Failed to create Edge Between %d and %d\n", a->id, b->id);} else fprintf(stderr, "Invalid Vertices a:%p b:%p\n", a, b);}
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e
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| VALUE COLON VALUE {struct vertex *a = find((*graph)->vertices, $1); struct vertex *b = find((*graph)->vertices, $3); if (a && b) {if (create_edge(a, b, edge_f, NULL) == NULL) fprintf(stderr, "Failed to create Edge Between %d and %d\n", a->id, b->id);} else fprintf(stderr, "Invalid Vertices a:%p b:%p\n", a, b);}
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;
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bes:BI_EDGE_ COLON L_BRACKET be R_BRACKET
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;
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be: /* empty */
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| VALUE COLON VALUE COMMA {int val = 0; struct vertex *a = find((*graph)->vertices, $1); struct vertex *b = find((*graph)->vertices, $3); if (a && b) { if((val = create_bi_edge(a, b, edge_f, NULL, NULL, NULL) < 0)) fprintf(stderr, "%d: Failed to bi create Edge Between %d and %d\n", val, a->id, b->id);} else fprintf(stderr, "Invalid Vertices a:%p(%d) b:%p(%d)\n", a, $1, b, $3);}
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be
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| VALUE COLON VALUE {int val = 0; struct vertex *a = find((*graph)->vertices, $1); struct vertex *b = find((*graph)->vertices, $3); if (a && b) { if((val = create_bi_edge(a, b, edge_f, NULL, NULL, NULL) < 0)) fprintf(stderr, "%d: Failed to bi create Edge Between %d and %d\n", val, a->id, b->id);} else fprintf(stderr, "Invalid Vertices a:%p(%d) b:%p(%d)\n", a, $1, b, $3);}
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;
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%%
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void yyerror(struct graph** graph, const char *s) {
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fprintf(stderr, "yerror: %s\n", s);
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destroy_graph(*graph);
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*graph = NULL;
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}
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struct graph *parse_json(const char *path) {
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topologic_debug("%s;%s", "parse_json", path);
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FILE *file = fopen(path, "r");
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if (!file) {
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topologic_debug("%s;%s;%p", "parse_json", "invalid file", (void *) NULL);
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return NULL;
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}
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yyin = file;
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struct graph *graph = NULL;
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yyparse(&graph);
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yyin = NULL;
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fclose(file);
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topologic_debug("%s;%s;%p", "parse_json", "success", graph);
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return graph;
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}

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