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Updating rptools from version 6.3.0 to 6.3.2 #152

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merged 4 commits into from
Nov 2, 2023
Merged

Updating rptools from version 6.3.0 to 6.3.2 #152

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0072748
Updating rptools from version 6.3.0 to 6.3.2
guillaume-gricourt Oct 30, 2023
f910a54
Merge branch 'main' into brsynth-rptools
guillaume-gricourt Oct 30, 2023
b9c0cc1
tests(tools): rptools, update
guillaume-gricourt Nov 2, 2023
8fae62e
tests(tools): rptools, update dataset
guillaume-gricourt Nov 2, 2023
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2 changes: 1 addition & 1 deletion tools/rptools/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<macros>
<token name="@TOOL_VERSION@">6.3.0</token>
<token name="@TOOL_VERSION@">6.3.2</token>
<token name="@VERSION_SUFFIX@">0</token>
<xml name="requirements">
<requirements>
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2 changes: 1 addition & 1 deletion tools/rptools/rpextractsink.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
<test>
<!-- test 1: check if identical outputs are produced with iCN718 model input -->
<param name="input" value="iCN718.xml.gz" />
<output name="sink" md5="0a7438b90704bf1ba88e123e6bb54df2" />
<output name="sink" md5="5ff3987609142e828ec8e3c97b8dab12" />
</test>
</tests>
<help><![CDATA[
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6 changes: 3 additions & 3 deletions tools/rptools/rpfba.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,7 @@
<has_text text="5.54302" />
<!--check fba_biomass value-->
<has_text text="1.31359" />
<has_n_lines n="408" />
<has_n_lines n="396" />
</assert_contents>
</output>
</test>
Expand All @@ -92,7 +92,7 @@
<!--check fba_fba value-->
<has_text text="16.47058" />
<not_has_text text="fba_fraction" />
<has_n_lines n="392" />
<has_n_lines n="380" />
</assert_contents>
</output>
</test>
Expand All @@ -110,7 +110,7 @@
<!--check fba_pfba value-->
<has_text text="2623.54248" />
<not_has_text text="fba_fraction" />
<has_n_lines n="392" />
<has_n_lines n="380" />
</assert_contents>
</output>
</test>
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2 changes: 1 addition & 1 deletion tools/rptools/rpthermo.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@
<has_text text="-2308.11630" />
<!--check thermo_dG value-->
<has_text text="-2151.84763" />
<has_n_lines n="483" />
<has_n_lines n="473" />
</assert_contents>
</output>
</test>
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81 changes: 36 additions & 45 deletions tools/rptools/test-data/scored_pathway.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,13 +8,9 @@
<rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>
<rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
<rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
<rdf:li rdf:resource="http://identifiers.org/seed/c"/>
<rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
<rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
<rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
Expand All @@ -23,19 +19,19 @@
</compartment>
</listOfCompartments>
<listOfSpecies>
<species metaid="fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9" id="MNXM97" name="MNXM97" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<species metaid="_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251" id="MNXM13" name="MNXM13" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
<rdf:Description rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
<bqbiol:is>
<rdf:Bag/>
</bqbiol:is>
</rdf:Description>
<rdf:BRSynth rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
<rdf:BRSynth rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
<brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
<brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
<brsynth:inchi value="InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)"/>
<brsynth:inchikey value="COLNVLDHVKWLRT-UHFFFAOYSA-N"/>
<brsynth:smiles value="O=C=O"/>
<brsynth:inchi value="InChI=1S/CO2/c2-1-3"/>
<brsynth:inchikey value="CURLTUGMZLYLDI-UHFFFAOYSA-N"/>
</brsynth:brsynth>
</rdf:BRSynth>
</rdf:RDF>
Expand All @@ -59,73 +55,73 @@
</rdf:RDF>
</annotation>
</species>
<species metaid="_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251" id="MNXM13" name="MNXM13" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<species metaid="_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b" id="MNXM15" name="MNXM15" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
<rdf:Description rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
<bqbiol:is>
<rdf:Bag/>
</bqbiol:is>
</rdf:Description>
<rdf:BRSynth rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
<rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
<brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
<brsynth:smiles value="O=C=O"/>
<brsynth:inchi value="InChI=1S/CO2/c2-1-3"/>
<brsynth:inchikey value="CURLTUGMZLYLDI-UHFFFAOYSA-N"/>
<brsynth:smiles value="N"/>
<brsynth:inchi value="InChI=1S/H3N/h1H3"/>
<brsynth:inchikey value="QGZKDVFQNNGYKY-UHFFFAOYSA-N"/>
</brsynth:brsynth>
</rdf:BRSynth>
</rdf:RDF>
</annotation>
</species>
<species metaid="ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25" id="MNXM1" name="MNXM1" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<species metaid="fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9" id="MNXM97" name="MNXM97" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
<rdf:Description rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
<bqbiol:is>
<rdf:Bag/>
</bqbiol:is>
</rdf:Description>
<rdf:BRSynth rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
<rdf:BRSynth rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
<brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
<brsynth:smiles value="[H+]"/>
<brsynth:inchi value="InChI=1S/p+1"/>
<brsynth:inchikey value="GPRLSGONYQIRFK-UHFFFAOYSA-N"/>
<brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
<brsynth:inchi value="InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)"/>
<brsynth:inchikey value="COLNVLDHVKWLRT-UHFFFAOYSA-N"/>
</brsynth:brsynth>
</rdf:BRSynth>
</rdf:RDF>
</annotation>
</species>
<species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<species metaid="ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25" id="MNXM1" name="MNXM1" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
<rdf:Description rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
<bqbiol:is>
<rdf:Bag/>
</bqbiol:is>
</rdf:Description>
<rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
<rdf:BRSynth rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
<brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
<brsynth:smiles value="[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
<brsynth:inchi value="InChI=1S/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2"/>
<brsynth:inchikey value="PPBRXRYQALVLMV-UHFFFAOYSA-N"/>
<brsynth:smiles value="[H+]"/>
<brsynth:inchi value="InChI=1S/p+1"/>
<brsynth:inchikey value="GPRLSGONYQIRFK-UHFFFAOYSA-N"/>
</brsynth:brsynth>
</rdf:BRSynth>
</rdf:RDF>
</annotation>
</species>
<species metaid="_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b" id="MNXM15" name="MNXM15" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
<rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
<bqbiol:is>
<rdf:Bag/>
</bqbiol:is>
</rdf:Description>
<rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
<rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
<brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
<brsynth:smiles value="N"/>
<brsynth:inchi value="InChI=1S/H3N/h1H3"/>
<brsynth:inchikey value="QGZKDVFQNNGYKY-UHFFFAOYSA-N"/>
<brsynth:smiles value="[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
<brsynth:inchi value="InChI=1S/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2"/>
<brsynth:inchikey value="PPBRXRYQALVLMV-UHFFFAOYSA-N"/>
</brsynth:brsynth>
</rdf:BRSynth>
</rdf:RDF>
Expand All @@ -142,10 +138,7 @@
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.24"/>
<rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.25"/>
</rdf:Bag>
<rdf:Bag/>
</bqbiol:is>
</rdf:Description>
<rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
Expand Down Expand Up @@ -204,9 +197,7 @@
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.102"/>
</rdf:Bag>
<rdf:Bag/>
</bqbiol:is>
</rdf:Description>
<rdf:BRSynth rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
Expand Down Expand Up @@ -326,9 +317,9 @@
</rdf:RDF>
</annotation>
<groups:listOfMembers>
<groups:member groups:idRef="TARGET_0000000001"/>
<groups:member groups:idRef="MNXM97"/>
<groups:member groups:idRef="CMPD_0000000002"/>
<groups:member groups:idRef="MNXM97"/>
<groups:member groups:idRef="TARGET_0000000001"/>
</groups:listOfMembers>
</groups:group>
<groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
Expand All @@ -341,8 +332,8 @@
</annotation>
<groups:listOfMembers>
<groups:member groups:idRef="MNXM13"/>
<groups:member groups:idRef="MNXM1"/>
<groups:member groups:idRef="MNXM15"/>
<groups:member groups:idRef="MNXM1"/>
</groups:listOfMembers>
</groups:group>
<groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
Expand All @@ -355,8 +346,8 @@
</annotation>
<groups:listOfMembers>
<groups:member groups:idRef="MNXM13"/>
<groups:member groups:idRef="MNXM1"/>
<groups:member groups:idRef="MNXM15"/>
<groups:member groups:idRef="MNXM1"/>
<groups:member groups:idRef="MNXM97"/>
</groups:listOfMembers>
</groups:group>
Expand Down