GSoC - SBML L3V2 models support with some other bug fixes #48

hemilpanchiwala · 2020-06-18T18:12:10Z

Major changes made in SBSCL (from GSoC start):

Before this PR, two PRs have been merged to SBSCL. A complete description of changes made is described in that PRs.
- PR Resolves issues of SBMLTestSuite and FBA #40
- PR Travis fix & JSBML update #37
Absolute as well as Relative tolerances are now fixed for the simulation of SBML models. This has solved the problems of failing test cases of the SBML Test Suite due to small deviations.
Now, SBML models with fbc extensions are simulated using FluxBalanceAnalysis in SBMLTestSuiteTest and SBMLTestRunnerWrapper.
Active objective function variable is added to FluxBalanceAnalysis. And now all the fbc models in the SBML Test Suite pass successfully.
SBML L3V2 models issues solved:
- SBML L3V2 models do not have a fast property which will be handled now.
- SBML L3V2 models now can have constraints, kinetic laws, events, species, rules (assignment rules and rate rules), initial assignments, and any others without math. This has been handled now through this PR in SBSCL.
- Logical operators are now added to compileDouble in ASTNodeValue.
- New functions are added to the ASTNodeInterpreter class. (issue Add functions in ASTNodeInterpreter class for calculating node values of SBML L3V2 models #42)
- Reaction without reactants and products has been solved now. (issue Simulation of models with reaction without reactants and products #41)
- RELATIONAL_GT, RELATIONAL_GEQ, RELATIONAL_EQ, RELATIONAL_NEQ, RELATIONAL_LEQ, and RELATIONAL_LT are now updated to have multiple children.
- SBSCL now supports rateOf csymbol that is newly added in SBML L3V2.
- New variables have been added to RateRuleValue and RuleValue classes.
- A new array changeRate has been added to SBMLinterpreter class that keeps the value of the derivatives at the current time.
- constantHash has also been added to SBMLinterpreter that has key as variables and values are boolean (true if constant else false).
- After making this changes, about 67 SBML L3V2 tests fail excluding the comp tests from the SBML Test Suite.
Many other small issues have been resolved in this PR.

This PR closes #38, closes #41, closes #42, closes #43.
More information about changes made till now in SBSCL can be found at my blog posts [Link].

… ref-issue draeger-lab#43

… ref issue draeger-lab#47 | solves models 1411, 1412, 1414

…t=0 | passes test case 1466 | ref issue draeger-lab#47

…e | passes test cases 1121, 1415, 1419

…s test cases 1642-1644, 1651-1653, 1775-1777 | ref issue draeger-lab#47

…draeger-lab#47

hemilpanchiwala · 2020-07-01T14:16:22Z

Why did subclassing not work? I.e. only overwriting the solve method?

@matthiaskoenig,
It did not work as the new instance of GlpkSolver was made in the solve() method explicitly. We did not have any reference to that class in SBSCL.

Here, the thing is going on as follows:
We make an object of LinearProgramSolver (which is an interface) that is implemented by GLPKSolver class where the solve() method implementation is found. In this solve() method, scpsolver creates an instance of the GlpkSolver class which was creating all the problems and so making that instance (of GlpkSolver) null using deleteProb() solves the issue. But this is all in scpsolver so I made a copy of the GLPKSolver class with making the instance of GlpkSolver null on completing its usage. Once scpsolver makes this change then we can remove this class.

Note: GLPKSolver and GlpkSolver are different classes in scpsolver.

matthiaskoenig

Minor changes requested.
Please add a FluxBalanceAnalysis test which:

takes the ecoli core model, simulates a FBA, compares objective; currently a simple test case for FBA outside of the SBMLTestSuite is missing

matthiaskoenig · 2020-07-03T08:10:30Z

src/main/java/org/simulator/examples/SimulatorExample.java

-    if (solver instanceof AbstractDESSolver) {
-      ((AbstractDESSolver) solver).setIncludeIntermediates(false);
-    }
+        String fileName = "";


Normally one initializes with null. Empty string is always a very risky choice. Change to null.

Updated the code!

matthiaskoenig · 2020-07-03T08:18:37Z

src/main/java/org/simulator/fba/FluxBalanceAnalysis.java

+   * @return
+   */
+  public String getActObjFunc() {
+    return actObjFunc;


Better name is activeObjective. Always write words out. There is code completion which makes larger names easy to use. Also rename functions to getActiveObjective.

matthiaskoenig · 2020-07-03T08:26:32Z

Will merge this as soon as the minor changes & the test case are there.

hemilpanchiwala · 2020-07-03T09:53:00Z

Please add a FluxBalanceAnalysis test which:

takes the ecoli core model, simulates a FBA, compares objective; currently a simple test case for FBA outside of the SBMLTestSuite is missing

@matthiaskoenig, I have updated the changes. And FBA test was there but it was named CobraSolverTest and was ignored by @ignore tag. I have renamed it to FluxBalanceAnalysisTest and also removed the ignore tag.

shalinshah1993

Sorry for the delay here, congratulations @hemilpanchiwala
This is fantastic!

hemilpanchiwala added 28 commits June 6, 2020 14:44

updated deprecated isFast() method to isSetFast() for reaction

70b1960

resolve some SBML L3V2 simulation issues

17cf2a2

format SBMLinterpreter, no code change

37f68f9

fix fast reaction issue

ed49ab0

make tolerances more strict for integrator

b3c0221

add testing with FluxBalanceAnalysis for fbc models

011e216

add log for test case of SBML Test Suite

cd14a3c

add FluxBalanceAnalysis for fbc models in the SBML Test Runner wrapper

7280d2b

small bugfix

88a3817

resolve small issue

4b10ef5

add the logical operator cases to computeDoubleValue for ASTNode

f4ebacb

add active objective function variable in FluxBalanceAnalysis

58020be

change the absTol and relTol for the simulation

69db129

solve issue draeger-lab#42

287abf8

solve issue draeger-lab#41

8667b81

update the calculate nodes method in ASTNodeInterpreter class

03f91b6

update requested changes in commit 287abf8

690a0d9

add rateOf method

33222b1

minor fix

42483ef

minor fix and add comments

5a4aa68

add changeRate variable to SBMLinterpreter class

b73b293

resolve rateOf at time t=0 in issue draeger-lab#43

7fdd3eb

add call computeDerivatives before process rules

ff1aa32

add constantHash to avoid repetitive checking | ref-issue draeger-lab#43

3c680b9

minor fix to only calculate changeRate by ignoring processing rules |…

243cf9f

… ref-issue draeger-lab#43

add delay as paramter for computeDoubleValue in FunctionValue class |…

7380c6d

… ref issue draeger-lab#47 | solves models 1411, 1412, 1414

resolve failed test case 1217, 1218 | ref issue draeger-lab#47

e92ac14

minor changes requested in last commit

cff8ae0

hemilpanchiwala added the gsoc label Jun 18, 2020

hemilpanchiwala requested a review from matthiaskoenig June 18, 2020 18:12

hemilpanchiwala added 6 commits June 27, 2020 23:17

minor updates requested in last commit

8b21f87

update the column_name Time to time in results

7ea3fb9

fix local paths

9fb3726

minor bug fix | rules should be processed after processing events at …

0677654

…t=0 | passes test case 1466 | ref issue draeger-lab#47

made tolerances strict by 0.1 | add delay property to SpeciesReferenc…

73ec69f

…e | passes test cases 1121, 1415, 1419

update conversion factors after processing initialAssignments | passe…

6810ebd

…s test cases 1642-1644, 1651-1653, 1775-1777 | ref issue draeger-lab#47

matthiaskoenig self-requested a review June 28, 2020 22:00

handle FBA tests with no feasible solution

3ca0311

hemilpanchiwala linked an issue Jun 29, 2020 that may be closed by this pull request

Update the SBMLTestSuite Runner for L3V2 #35

Closed

6 tasks

hemilpanchiwala added 2 commits June 30, 2020 01:21

minor fix

665c275

made tolerances more strict by 0.1 | passes test case 1395 | ref issue …

3aecf34

…draeger-lab#47

hemilpanchiwala force-pushed the testrunner branch from 10f4540 to 3aecf34 Compare June 30, 2020 12:24

hemilpanchiwala added 3 commits June 30, 2020 23:16

make event object null if no rules | passes test case 1602 | ref issue …

263b184

…draeger-lab#47

fix GLPK issue

bfa4942

skip failed SBMLTestSuite tests

9774a2a

hemilpanchiwala added 2 commits July 1, 2020 20:02

add reason for adding the NewGLPKSolver class

23377b1

increase timeout for test to 60 seconds in maven

b03756a

hemilpanchiwala linked an issue Jul 2, 2020 that may be closed by this pull request

FBA tests fail on parallel testing #51

Closed

hemilpanchiwala added 2 commits July 2, 2020 16:50

fix small bug while simulating models with fast reactions

5d092d0

update the failed tests array

9939e40

matthiaskoenig approved these changes Jul 3, 2020

View reviewed changes

hemilpanchiwala added 3 commits July 3, 2020 14:53

update changes as requested by @matthiaskoenig

d5b8e9f

minor indentation fix

f0975c1

remove @ignore tag in FluxBalanceAnalysisTest

8d59935

draeger approved these changes Jul 3, 2020

View reviewed changes

draeger merged commit c0d1077 into draeger-lab:master Jul 3, 2020

shalinshah1993 reviewed Jul 3, 2020

View reviewed changes

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GSoC - SBML L3V2 models support with some other bug fixes #48

GSoC - SBML L3V2 models support with some other bug fixes #48

hemilpanchiwala commented Jun 18, 2020

hemilpanchiwala commented Jul 1, 2020 •

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GSoC - SBML L3V2 models support with some other bug fixes #48

GSoC - SBML L3V2 models support with some other bug fixes #48

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hemilpanchiwala commented Jun 18, 2020

Major changes made in SBSCL (from GSoC start):

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