velociraptors / physio_mist Goto Github PK

This project forked from silvermoonnbeam/physio_mist

Java 1.80% C++ 98.20%

physio_mist's Introduction

Physio_MIST
Mark Caral, Sara Cummins, BarbaraJoy Jones

REQUIREMENTS
JDK 6 Update 17: http://java.sun.com/javase/downloads/index.jsp
	The directory containing jvm.dll must be in the user's PATH environment variable.
NUnit: http://www.nunit.org/index.php
Open Physio_MIST.sln in Visual Studio and build the project.

QUERY REQUIREMENTS
MySQL 5.0 and the JDBC: http://dev.mysql.com/downloads/connector/j/5.0.html
Make a database named "fma_owl_3"
Make a MySQL user "fma_test" with the password set to "test" with full privileges on the FMA database.
Unzip the fma3.0.owl.zip file in the QuerySystem directory and run DB_Builder.java
Building the database can take a significant amount of time, but only needs to be done once.

LOADING MODELS
Select File->Load from the main menu.
Browse for the desired file (either an MML text file or an XML file conforming to the Physio_MIST schema) and click the Open button.
A sample model (meal_model.xml) is located in the source directory.

SAVING MODELS
Select File->Save from the main menu.
Enter the desired file name and click the Save button.

EDITING MODELS
Select an item in either the Parameter or Variable tables and click the Edit button. Input must conform to the MML standard, except for the Anatomical Structure and the Description fields.

QUERYING
Select the desired structure in the ontology tree. Right click and select "Find Related Structures..." then select the desired relationship type and click the Run Query button.

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zenophon

physio_mist's Issues

functional test - validate incorrect user input

need to make sure this catches errors

change_structure fails

This test fails, we should figure out why and fix it

functional test - save XML model

test this

functional test - display results of query

need to make sure this works

functional test - creat anatomical query

need to test this

change_value fails

Causes some sort of memory error, need to fix this

functional test - load incorrect file type

make this and run

functional test - load XML anatomical information

make and run this

functional test - validate correct user input

need to make sure this works

functional test - save XML anatomical information

run this

The MML parser strips whitespace as it processes a file. Since if/else/elseif blocks can be delimited by whitespace, the regex won't find those keywords if the block isn't wrapped in parentheses or brackets. For example:
"Y = if (X=0) A+B
else A_C"
becomes "if(X=0)A+BelseA_C" and the validation tries to find a parameter/variable named 'BelseA' and fails.
The alternative is to remove the word boundaries from the regex (or add the keywords to the separators passed to String->Split), but this erroneously strips keywords from variable names. ("x_abs" becomes "x_" and validation fails.)