From 3e29f29702a188bcffdb7e10a19839d07d64ace9 Mon Sep 17 00:00:00 2001
From: Matej Trojak <trojak@mail.muni.cz>
Date: Wed, 14 Sep 2022 13:58:37 +0200
Subject: [PATCH 1/4] Added config files

---
 tools/parasim/.shed.yml                       | 12 ++++
 tools/parasim/macros.xml                      | 21 ++++++
 tools/parasim/test-data/base.precision.xml    |  5 ++
 tools/parasim/test-data/base.sim_space.xml    |  6 ++
 tools/parasim/test-data/lotkav.model.xml      | 65 +++++++++++++++++++
 .../parasim/test-data/oscil.star.formula.xml  | 57 ++++++++++++++++
 tools/parasim/test-data/params.init_space.xml |  6 ++
 tools/parasim/test-data/result.tsv            | 18 +++++
 8 files changed, 190 insertions(+)
 create mode 100644 tools/parasim/.shed.yml
 create mode 100644 tools/parasim/macros.xml
 create mode 100644 tools/parasim/test-data/base.precision.xml
 create mode 100644 tools/parasim/test-data/base.sim_space.xml
 create mode 100644 tools/parasim/test-data/lotkav.model.xml
 create mode 100644 tools/parasim/test-data/oscil.star.formula.xml
 create mode 100644 tools/parasim/test-data/params.init_space.xml
 create mode 100644 tools/parasim/test-data/result.tsv

diff --git a/tools/parasim/.shed.yml b/tools/parasim/.shed.yml
new file mode 100644
index 0000000..78dfc70
--- /dev/null
+++ b/tools/parasim/.shed.yml
@@ -0,0 +1,12 @@
+owner: sybila
+remote_repository_url: "https://github.com/sybila/galaxytools/tree/main/tools/parasim"
+homepage_url: "https://github.com/sybila/parasim"
+categories:
+  - Systems Biology
+repositories:
+  parasim:
+    description: "Robustness analysis of SBML model with respect to STL property."
+    include:
+      - parasim.xml
+      - test-data
+      - macros.xml
diff --git a/tools/parasim/macros.xml b/tools/parasim/macros.xml
new file mode 100644
index 0000000..00d8d6a
--- /dev/null
+++ b/tools/parasim/macros.xml
@@ -0,0 +1,21 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.2.0</token>
+
+    <xml name="creator">
+        <creator>
+            <person
+                givenName="Martin"
+                familyName="Demko"
+                url="https://github.com/martindemko"/>
+            <person
+                givenName="Matej"
+                familyName="Troják"
+                url="https://github.com/xtrojak"
+                identifier="0000-0003-0841-2707" />
+            <organization
+                url="https://sybila.fi.muni.cz/"
+                email="sybila@fi.muni.cz"
+                name="SYBILA MUNI" />
+        </creator>
+    </xml>
+</macros>
\ No newline at end of file
diff --git a/tools/parasim/test-data/base.precision.xml b/tools/parasim/test-data/base.precision.xml
new file mode 100644
index 0000000..9dd2303
--- /dev/null
+++ b/tools/parasim/test-data/base.precision.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<precision xmlns="http://www.sybila.org/parasim/precision" maxRelativeError="1.0E-8" timeStep="0.1">
+<dimension maxAbsoluteError="1.0E-6"/>
+<dimension maxAbsoluteError="1.0E-6"/>
+</precision>
diff --git a/tools/parasim/test-data/base.sim_space.xml b/tools/parasim/test-data/base.sim_space.xml
new file mode 100644
index 0000000..47366b3
--- /dev/null
+++ b/tools/parasim/test-data/base.sim_space.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<space xmlns="http://www.sybila.org/parasim/space">
+<time max="800.0" min="0.0"/>
+<variable max="200.0" min="0.0" name="predator"/>
+<variable max="200.0" min="0.0" name="prey"/>
+</space>
diff --git a/tools/parasim/test-data/lotkav.model.xml b/tools/parasim/test-data/lotkav.model.xml
new file mode 100644
index 0000000..7d40f65
--- /dev/null
+++ b/tools/parasim/test-data/lotkav.model.xml
@@ -0,0 +1,65 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="1">
+	<model>
+		<listOfCompartments>
+			<compartment id="uVol" size="1"/>
+		</listOfCompartments>
+		<listOfSpecies>
+			<species id="predator" compartment="uVol" initialConcentration="80"/>
+			<species id="prey" compartment="uVol" initialConcentration="40"/>
+		</listOfSpecies>
+		<listOfParameters>
+			<parameter id="natality" value="0.1"/>
+			<parameter id="mortality" value="0.1"/>
+			<parameter id="predation" value="0.002"/>
+		</listOfParameters>
+		<listOfReactions>
+			<reaction id="prey_born" reversible="false">
+				<listOfProducts>
+					<speciesReference species="prey"/>
+				</listOfProducts>
+				<kineticLaw>
+					<math xmlns="http://www.w3.org/1998/Math/MathML">
+						<apply>
+							<times/>
+							<ci> natality </ci>
+							<ci> prey </ci>
+						</apply>
+					</math>
+				</kineticLaw>
+			</reaction>
+			<reaction id="predator_die" reversible="false">
+				<listOfReactants>
+					<speciesReference species="predator"/>
+				</listOfReactants>
+				<kineticLaw>
+					<math xmlns="http://www.w3.org/1998/Math/MathML">
+						<apply>
+							<times/>
+							<ci> mortality </ci>
+							<ci> predator </ci>
+						</apply>
+					</math>
+				</kineticLaw>
+			</reaction>
+			<reaction id="predate" reversible="false">
+				<listOfReactants>
+					<speciesReference species="prey"/>
+				</listOfReactants>
+				<listOfProducts>
+					<speciesReference species="predator"/>
+				</listOfProducts>
+				<kineticLaw>
+					<math xmlns="http://www.w3.org/1998/Math/MathML">
+						<apply>
+							<times/>
+							<ci> predation </ci>
+							<ci> prey </ci>
+							<ci> predator </ci>
+						</apply>
+					</math>
+				</kineticLaw>
+			</reaction>
+		</listOfReactions>
+	</model>
+</sbml>
diff --git a/tools/parasim/test-data/oscil.star.formula.xml b/tools/parasim/test-data/oscil.star.formula.xml
new file mode 100644
index 0000000..0c73dbe
--- /dev/null
+++ b/tools/parasim/test-data/oscil.star.formula.xml
@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<formula xmlns="http://www.sybila.org/parasim/stl-formula">
+	<globally>
+		<interval>
+			<lower type="closed">0</lower>
+			<upper type="closed">300</upper>
+		</interval>
+		<and>
+			<and>
+				<predicate>
+					<variable multiplier="1.0" frozen="0">prey</variable>
+					<greater/>
+					<value>1</value>
+				</predicate>
+				<predicate>
+					<variable multiplier="1.0" frozen="0">predator</variable>
+					<greater/>
+					<value>0</value>
+				</predicate>
+			</and>
+			<future>
+				<interval>
+					<lower type="closed">0</lower>
+					<upper type="closed">50</upper>
+				</interval>
+				<freeze index="1">
+					<and>
+						<future>
+							<interval>
+								<lower type="closed">0</lower>
+								<upper type="closed">75</upper>
+							</interval>
+							<predicate>
+								<variable multiplier="1.0" frozen="1">prey</variable>
+								<variable multiplier="-1.0" frozen="0">prey</variable>
+								<greater/>
+								<value>25</value>
+							</predicate>
+						</future>
+						<future>
+							<interval>
+								<lower type="closed">0</lower>
+								<upper type="closed">75</upper>
+							</interval>
+							<predicate>
+								<variable multiplier="1.0" frozen="0">prey</variable>
+								<variable multiplier="-1.0" frozen="1">prey</variable>
+								<greater/>
+								<value>25</value>
+							</predicate>
+						</future>
+					</and>
+				</freeze>
+			</future>
+		</and>
+	</globally>
+</formula>
diff --git a/tools/parasim/test-data/params.init_space.xml b/tools/parasim/test-data/params.init_space.xml
new file mode 100644
index 0000000..2c53803
--- /dev/null
+++ b/tools/parasim/test-data/params.init_space.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<space xmlns="http://www.sybila.org/parasim/space">
+<time max="0.0" min="0.0"/>
+<parameter max="0.7" min="0.01" name="natality"/>
+<parameter max="0.008" min="1.0E-4" name="predation"/>
+</space>
diff --git a/tools/parasim/test-data/result.tsv b/tools/parasim/test-data/result.tsv
new file mode 100644
index 0000000..83d15b8
--- /dev/null
+++ b/tools/parasim/test-data/result.tsv
@@ -0,0 +1,18 @@
+predator	prey	natality	predation	Robustness
+80.0	40.0	0.01	1.0E-4	-12.5
+80.0	40.0	0.01	0.0012999999	-12.5
+80.0	40.0	0.01	0.0025	-12.5
+80.0	40.0	0.2575	7.0E-4	3.606793
+80.0	40.0	0.2575	0.0012999999	11.5911665
+80.0	40.0	0.2575	0.0018999999	9.342419
+80.0	40.0	0.505	1.0E-4	-12.037555
+80.0	40.0	0.505	7.0E-4	-0.9595153
+80.0	40.0	0.505	0.0012999999	-0.54846215
+80.0	40.0	0.505	0.0018999999	0.5288335
+80.0	40.0	0.505	0.0025	2.125179
+80.0	40.0	0.7525	7.0E-4	-0.9998965
+80.0	40.0	0.7525	0.0012999999	-0.99468964
+80.0	40.0	0.7525	0.0018999999	-0.95502543
+80.0	40.0	1.0	1.0E-4	-12.499986
+80.0	40.0	1.0	0.0012999999	-0.9999726
+80.0	40.0	1.0	0.0025	-0.9955077

From 5e695b315d35192d1b3273eafefff4320f62375e Mon Sep 17 00:00:00 2001
From: Matej Trojak <trojak@mail.muni.cz>
Date: Wed, 14 Sep 2022 13:58:57 +0200
Subject: [PATCH 2/4] Update github path for eBCSgen

---
 tools/ebcsgen/.shed.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ebcsgen/.shed.yml b/tools/ebcsgen/.shed.yml
index a4fcf5f..f6b68b1 100644
--- a/tools/ebcsgen/.shed.yml
+++ b/tools/ebcsgen/.shed.yml
@@ -1,5 +1,5 @@
 owner: sybila
-remote_repository_url: "https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen"
+remote_repository_url: "https://github.com/sybila/galaxytools/tree/main/tools/ebcsgen"
 homepage_url: "https://github.com/sybila/eBCSgen"
 categories:
   - Systems Biology

From b14eb20a15790487a6b223bb9917ad4f84ab027f Mon Sep 17 00:00:00 2001
From: Matej Trojak <trojak@mail.muni.cz>
Date: Wed, 14 Sep 2022 15:46:30 +0200
Subject: [PATCH 3/4] Added structure for parasim tool

---
 tools/parasim/parasim.xml | 77 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100644 tools/parasim/parasim.xml

diff --git a/tools/parasim/parasim.xml b/tools/parasim/parasim.xml
new file mode 100644
index 0000000..b427211
--- /dev/null
+++ b/tools/parasim/parasim.xml
@@ -0,0 +1,77 @@
+<tool id="parasim" name="Parasim" version="@TOOL_VERSION@_galaxy0">
+  <description>for robustness analysis given SBML model and STL property</description>
+
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="creator"/>
+  <requirements>
+    <container type="docker">sybila/parasim:@TOOL_VERSION@</container>
+  </requirements>
+
+  <command detect_errors="exit_code"><![CDATA[
+    sh ${create_experiment} &&
+    export PARASIM_OPTS="-Xmx17179869184" &&
+    #if $full_exploration:
+    /home/galaxy/parasim-full_exploration/bin/parasim
+    #else
+    /home/galaxy/parasim-master-2.2.0/application/build/install/parasim/bin/parasim
+    #end if
+    -e 'experiment' -b -csv '$output' 
+  ]]> </command>
+
+  <configfiles>
+    <configfile name="create_experiment">
+      touch experiment &&
+      echo "sbml.file=$model_file" >> experiment &&
+      echo "stl.file=$property_file" >> experiment &&
+      echo "simulation.precision.file=$precission_file" >> experiment &&
+      echo "space.initial.file=$init_space_file" >> experiment &&
+      echo "space.simulation.file=$simul_space_file" >> experiment &&
+      echo "result.output.file=result.xml" >> experiment &&
+      echo "timeout.amount=$timeHorizon.time" >> experiment &&
+      echo "timeout.unit=$timeHorizon.time_unit" >> experiment &&
+      echo "iteration.limit=$iterations" >> experiment &&
+      echo "Experiment configuration:" &&            
+    </configfile>
+  </configfiles>
+
+  <inputs>
+    <param format="xml" name="model_file" type="data" label="SBML model file"/>
+    <param format="xml" name="property_file" type="data" label="STL property file"/>
+    <param format="xml" name="init_space_file" type="data" label="Initial space file"/>
+    <param format="xml" name="simul_space_file" type="data" label="Simulation space file"/>
+    <param format="xml" name="precission_file" type="data" label="Simulation precission file"/>
+    <param name="full_exploration" type="boolean" checked="false" label="Explore full parameter space (might take significantly more time!)"/>
+    <conditional name="timeHorizon">
+      <param name="time_unit" type="select" label="Time limit until timeout" help="When running simulation exceeds timeout, it terminates.">
+        <option value="SECONDS" >Seconds</option>
+        <option value="MINUTES" selected="true" >Minutes</option>
+        <option value="HOURS" >Hours</option>
+        <option value="DAYS" >Unlimited</option>
+      </param>
+      <when value="DAYS">
+        <param hidden="true" name="time" type="integer" min="1" value="1000" label="Amount of time"/>
+      </when>
+      <when value="HOURS">
+        <param name="time" type="integer" min="1" value="5" label="Amount of time"/>
+      </when>
+      <when value="MINUTES">
+        <param name="time" type="integer" min="1" value="10" label="Amount of time"/>
+      </when>
+      <when value="SECONDS">
+        <param name="time" type="integer" min="1" value="10" label="Amount of time"/>
+      </when>
+    </conditional>
+    <param name="iterations" type="integer" min="1" value="5" label="Iteration limit" help="Limits precision of robustness analysis method. Generally, 10 should be more than sufficient."/>
+  </inputs>
+  <outputs>
+    <data format="tsv" name="output" />
+  </outputs>
+
+  <tests>
+    <test>
+    </test>
+  </tests>
+
+</tool>

From cf2f019b56fd4934db9540f73db16d6a15c10062 Mon Sep 17 00:00:00 2001
From: Matej Trojak <trojak@mail.muni.cz>
Date: Tue, 4 Oct 2022 10:24:58 +0200
Subject: [PATCH 4/4] Add error handling - not fully functional

---
 tools/parasim/macros.xml  |  2 +-
 tools/parasim/parasim.xml | 63 +++++++++++++++++++++++++--------------
 2 files changed, 42 insertions(+), 23 deletions(-)

diff --git a/tools/parasim/macros.xml b/tools/parasim/macros.xml
index 00d8d6a..8b0e664 100644
--- a/tools/parasim/macros.xml
+++ b/tools/parasim/macros.xml
@@ -18,4 +18,4 @@
                 name="SYBILA MUNI" />
         </creator>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
diff --git a/tools/parasim/parasim.xml b/tools/parasim/parasim.xml
index b427211..993809e 100644
--- a/tools/parasim/parasim.xml
+++ b/tools/parasim/parasim.xml
@@ -1,6 +1,5 @@
 <tool id="parasim" name="Parasim" version="@TOOL_VERSION@_galaxy0">
-  <description>for robustness analysis given SBML model and STL property</description>
-
+  <description>robustness analysis of given SBML model and STL property</description>
   <macros>
     <import>macros.xml</import>
   </macros>
@@ -9,30 +8,39 @@
     <container type="docker">sybila/parasim:@TOOL_VERSION@</container>
   </requirements>
 
-  <command detect_errors="exit_code"><![CDATA[
+  <stdio>
+    <regex match="OutOfMemoryError" source="stderr" level="warning" description="Java GC OutOfMemoryError: result data might be incomplete or corrupt!" />
+    <regex match="out of memory" source="stderr" level="warning" description="Java GC OutOfMemoryError: result data might be incomplete or corrupt!" />
+    <regex match="ParseException" source="stderr" level="fatal" description="Error during parsing of input" />
+    <regex match="parse error" source="stderr" level="fatal" description="Error during parsing of input" />
+    <regex match="FormatException" source="stderr" level="fatal" description="Error during parsing of input" />
+    <regex match="IOException" source="stderr" level="fatal" description="IO Exception: Can't load data for experiment." />
+    <regex match="exception" source="stderr" level="fatal" description="Java Exception" />
+    <regex match="error" source="stderr" level="fatal" description="Unknown error" />
+
+    <regex match="nothing to store" level="fatal" description="Nothing to store - no output produced in specified time limit." />
+    <regex match="timeout" level="fatal" description="Computation timeout: result data might be incomplete or corrupt! Increase Time limit until timeout input." />
+    <regex match="killed" level="fatal" description="Out of memory." />
+  </stdio>
+
+  <command><![CDATA[
     sh ${create_experiment} &&
     export PARASIM_OPTS="-Xmx17179869184" &&
-    #if $full_exploration:
-    /home/galaxy/parasim-full_exploration/bin/parasim
-    #else
-    /home/galaxy/parasim-master-2.2.0/application/build/install/parasim/bin/parasim
-    #end if
-    -e 'experiment' -b -csv '$output' 
+    parasim -e 'experiment' -b -csv '$output'
   ]]> </command>
 
   <configfiles>
     <configfile name="create_experiment">
-      touch experiment &&
-      echo "sbml.file=$model_file" >> experiment &&
-      echo "stl.file=$property_file" >> experiment &&
-      echo "simulation.precision.file=$precission_file" >> experiment &&
-      echo "space.initial.file=$init_space_file" >> experiment &&
-      echo "space.simulation.file=$simul_space_file" >> experiment &&
-      echo "result.output.file=result.xml" >> experiment &&
-      echo "timeout.amount=$timeHorizon.time" >> experiment &&
-      echo "timeout.unit=$timeHorizon.time_unit" >> experiment &&
-      echo "iteration.limit=$iterations" >> experiment &&
-      echo "Experiment configuration:" &&            
+      touch experiment
+      echo "sbml.file=$model_file" >> experiment
+      echo "stl.file=$property_file" >> experiment
+      echo "simulation.precision.file=$precission_file" >> experiment
+      echo "space.initial.file=$init_space_file" >> experiment
+      echo "space.simulation.file=$simul_space_file" >> experiment
+      echo "result.output.file=result.xml" >> experiment
+      echo "timeout.amount=$time_horizon.time" >> experiment
+      echo "timeout.unit=$time_horizon.time_unit" >> experiment
+      echo "iteration.limit=$iterations" >> experiment
     </configfile>
   </configfiles>
 
@@ -42,8 +50,7 @@
     <param format="xml" name="init_space_file" type="data" label="Initial space file"/>
     <param format="xml" name="simul_space_file" type="data" label="Simulation space file"/>
     <param format="xml" name="precission_file" type="data" label="Simulation precission file"/>
-    <param name="full_exploration" type="boolean" checked="false" label="Explore full parameter space (might take significantly more time!)"/>
-    <conditional name="timeHorizon">
+    <conditional name="time_horizon">
       <param name="time_unit" type="select" label="Time limit until timeout" help="When running simulation exceeds timeout, it terminates.">
         <option value="SECONDS" >Seconds</option>
         <option value="MINUTES" selected="true" >Minutes</option>
@@ -65,12 +72,24 @@
     </conditional>
     <param name="iterations" type="integer" min="1" value="5" label="Iteration limit" help="Limits precision of robustness analysis method. Generally, 10 should be more than sufficient."/>
   </inputs>
+
   <outputs>
     <data format="tsv" name="output" />
   </outputs>
 
   <tests>
     <test>
+      <param name="model_file" value="lotkav.model.xml" ftype="xml"/>
+      <param name="property_file" value="oscil.star.formula.xml" ftype="xml"/>
+      <param name="init_space_file" value="params.init_space.xml" ftype="xml"/>
+      <param name="simul_space_file" value="base.sim_space.xml" ftype="xml"/>
+      <param name="precission_file" value="base.precision.xml" ftype="xml"/>
+      <section name="time_horizon">
+        <param name="time_unit" value="MINUTES"/>
+        <param name="time" value="30"/>
+      </section>
+      <param name="iterations" value="2"/>
+      <output name="output" value="lotkav.model.xml" ftype="tsv"/>
     </test>
   </tests>