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Create General Structure for Reading FluxML Files #12

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ef95043
First attempt at a fluxml representation and parser
teddygroves Apr 4, 2025
c9ada5e
Fix all ruff linting errors in fluxomics data model
teisnotte Jul 18, 2025
e35f0ff
Added summary function and renamed Pool and Configuration to Metaboli…
teisnotte Jul 25, 2025
2201c09
add FluxML test cases
teisnotte Aug 27, 2025
0c1d4d0
Improved file structure, modified atom_map to include more cases.
teisnotte Aug 28, 2025
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10 changes: 10 additions & 0 deletions .gitignore
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Expand Up @@ -2,3 +2,13 @@
uv.lock
site/
**__pycache__**
.qodo
.aider*
.DS_Store
.ipynb_checkpoints
.claude
.ruff_cache
.vscode/
.venv/
*.egg-info/
*.egg
7 changes: 7 additions & 0 deletions .pre-commit-config.yaml
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Expand Up @@ -3,16 +3,23 @@ repos:
rev: v5.0.0
hooks:
- id: check-yaml
exclude: ^data/
- id: check-json
exclude: ^data/
- id: check-toml
exclude: ^data/
- id: end-of-file-fixer
exclude: ^data/
- id: trailing-whitespace
exclude: ^data/

- repo: https://github.com/astral-sh/ruff-pre-commit
# Ruff version.
rev: v0.8.6
hooks:
# Run the linter.
- id: ruff
exclude: ^data/
# Run the formatter.
- id: ruff-format
exclude: ^data/
114 changes: 114 additions & 0 deletions data/FluxML-Test/antoniewicz_mininetwork.fml
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<?xml version="1.0" encoding="utf-8"?>
<fluxml xmlns="http://www.13cflux.net/fluxml">
<info>
<name>Antoniewicz test network</name>
<version>1.0</version>
<date>2007-10-09 00:00:00</date>
<comment>Network from the EMU paper</comment>
</info>
<reactionnetwork>
<metabolitepools>
<pool atoms="3" id="A"/>
<pool atoms="3" id="B"/>
<pool atoms="2" id="C"/>
<pool atoms="3" id="D"/>
<pool atoms="1" id="E"/>
<pool atoms="3" id="F"/>
<!-- <pool id="X" atoms="4"/> -->
</metabolitepools>
<reaction id="v1">
<reduct cfg="abc" id="A"/>
<rproduct cfg="abc" id="B"/>
</reaction>
<reaction id="v2">
<reduct cfg="abc" id="B"/>
<rproduct cfg="abc" id="D"/>
</reaction>
<reaction id="v3">
<reduct cfg="abc" id="D"/>
<rproduct cfg="abc" id="B"/>
</reaction>
<reaction id="v4">
<reduct cfg="abc" id="B"/>
<rproduct cfg="bc" id="C"/>
<rproduct cfg="a" id="E"/>
</reaction>
<!-- -->
<reaction bidirectional="false" id="v5">
<reduct cfg="abc" id="B"/>
<reduct cfg="de" id="C"/>
<rproduct cfg="bcd" id="D"/>
<rproduct cfg="a" id="E"/>
<rproduct cfg="e" id="E"/>
</reaction>
<!-- -->
<!--
<reaction id="v5_1">
<reduct id="B" cfg="abc"/>
<reduct id="C" cfg="de"/>
<rproduct id="X" cfg="bcda"/>
<rproduct id="E" cfg="e"/>
</reaction>
<reaction id="v5_2">
<reduct id="X" cfg="bcda"/>
<rproduct id="D" cfg="bcd"/>
<rproduct id="E" cfg="a"/>
</reaction>
-->
<reaction bidirectional="false" id="v6">
<reduct cfg="abc" id="D"/>
<rproduct cfg="abc" id="F"/>
</reaction>
<reaction id="efflux_E">
<reduct cfg="a" id="E"/>
</reaction>
<reaction id="efflux_F">
<reduct cfg="abc" id="F"/>
</reaction>
</reactionnetwork>
<configuration name="default">
<comment>Eine Belegung für die Input-Pools</comment>
<input pool="A" type="isotopomer">
<!-- <label cfg="010">1</label> -->
<label cfg="010">1.0</label>
</input>
<constraints>
<net>
<textual>v2 &gt;= v3; v1=100;</textual>
</net>
<xch>
<textual>v2=0; v3=0; v5=0; v6=0; v4=0</textual>
</xch>
</constraints>
<measurement>
<model stationary="true">
<labelingmeasurement>
<group id="m1" scale="one">
<textual>F#M0,1,2,3</textual>
</group>
</labelingmeasurement>
</model>
<data>
<datum id="m1" stddev="0.003" weight="0">0.0001</datum>
<datum id="m1" stddev="0.003" weight="1">0.8008</datum>
<datum id="m1" stddev="0.003" weight="2">0.1983</datum>
<datum id="m1" stddev="0.003" weight="3">0.0009</datum>
</data>
</measurement>
<!-- <simulation type="full" method="cumomer"> -->
<!-- <simulation type="auto" method="cumomer"> -->
<!-- <simulation type="full" method="emu"> -->
<!-- <simulation type="auto" method="emu"> -->
<!-- <simulation type="explicit" method="emu"> -->
<simulation>
<!-- <objects>
<obj pool="F" range="2"/>
</objects> -->
<variables>
<fluxvalue flux="v2" type="net">110</fluxvalue>
<fluxvalue flux="v4" type="net">20</fluxvalue>
</variables>
</simulation>
</configuration>
</fluxml>
<!-- vim:set shiftwidth=2:set expandtab: -->
91 changes: 91 additions & 0 deletions data/FluxML-Test/beispiel.mm
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<?xml version="1.0" encoding="utf-8"?>
<measurement xmlns="http://www.uni-siegen.de/fb11/simtec/13cflux/mm" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.uni-siegen.de/fb11/simtec/13cflux/mm http://www.uni-siegen.de/fb11/simtec/13cflux/mm.xsd">
<mlabel>
<!-- alle Unterelemente optional: -->
<date>2007-05-15 11:11:11</date>
<version>1.0</version>
<comment>kein Kommentar</comment>
<fluxunit>gigamol/year</fluxunit>
<poolsizeunit>gigamol</poolsizeunit>
</mlabel>
<model stationary="false">
<labelingmeasurement>
<MSgroup id="ms_1" spec="Blubb[1-3,5,6]#M0,1,2" times="0.01 0.2 0.3"/>
<MSMSgroup id="msms_1" spec="Bla[1-3:2-3]#M(3,0),(3,1),(3,2)" times="0.2" scale="one"/>
<NMR1Hgroup id="nmr1h_1" spec="Frupp#P1,2" times="0.022 0.033"/>
<NMR13Cgroup id="nmr13c_1" spec="Flapp#S1,T1,3" times="0.9"/>
<group id="gen_1" times="0.1">
<!-- mehrere Zeilen mit Formeln. Jede Zeile nur Ausdrücke der Dimension 1
Alle(!) Typen erlaubt -->
<textual>
0.7*Frup#M3 + Frup#1x0x1 - 1/3*Bla#111x + 1.414213562e-7*Gamma#xxx1 - 3.1415;
Gonzo#1xx - 3*Kermit#xxx * MissPiggy#xxx1
</textual>
</group>
</labelingmeasurement>

<fluxmeasurement>
<!-- times ist hier vorerst immer optional?! -->
<netflux id="fn_1" fluxes="upt1 blupt2" times="10.0"/>
<xchflux id="fx_1" fluxes="upt1 blupt2" times="10.0"/>
</fluxmeasurement>

<poolmeasurement>
<!-- times ist hier vorerst immer optional?! -->
<pgroup id="p_1" pools="Gluc PEP" times="0.1 13"/>
</poolmeasurement>

<fluxratios>
<!-- times ist hier vorerst immer optional?! -->
<netratio id="frn_1" times="0.01 0.2 0.815">(bla/flupp)=(bläh/blubb)</netratio>
<xchratio id="frx_1" times="0.01 0.2">blöd/upt=upt/blubb</xchratio>
</fluxratios>
</model>
<data id="versuch_1">
<dlabel>
<start>2007-05-15 11:11:11</start>
<finish>2007-05-15 11:11:12</finish>
<people>Michael</people>
<strain>Drosophila coli K42</strain>
<comment>blabla bla flupp frupp</comment>
</dlabel>
<!-- MS-Messung ms_1: -->
<datum id="ms_1" time="0.01" stddev="0.1" weight="0">4.321</datum>
<datum id="ms_1" time="0.01" stddev="0.2" weight="1">1.234</datum>
<datum id="ms_1" time="0.01" stddev="0.3" weight="2">1.234</datum>
<datum id="ms_1" time="0.2" stddev="0.4" weight="0">5.432</datum>
<datum id="ms_1" time="0.2" stddev="0.5" weight="1">2.345</datum>
<datum id="ms_1" time="0.2" stddev="0.6" weight="2">2.345</datum>
<datum id="ms_1" time="0.3" stddev="0.7" weight="0">6.543</datum>
<datum id="ms_1" time="0.3" stddev="0.8" weight="1">3.456</datum>
<datum id="ms_1" time="0.3" stddev="0.9" weight="2">3.456</datum>

<!-- MSMS-Messung msms_1: -->
<datum id="msms_1" time="0.2" stddev="0.01" weight="3,0">0.001</datum>
<datum id="msms_1" time="0.2" stddev="0.11" weight="3,1">0.002</datum>
<datum id="msms_1" time="0.2" stddev="0.21" weight="3,2">0.003</datum>

<!-- 1H-NMR-Messung nmr1h_1: -->
<datum id="nmr1h_1" time="0.022" stddev="0.31" pos="1">0.11</datum>
<datum id="nmr1h_1" time="0.022" stddev="0.41" pos="2">0.12</datum>
<datum id="nmr1h_1" time="0.033" stddev="0.51" pos="1">0.13</datum>
<datum id="nmr1h_1" time="0.033" stddev="0.61" pos="2">0.14</datum>

<!-- 13C-NMR-Messung nmr13c_1: -->
<datum id="nmr13c_1" time="0.9" stddev="0.71" pos="1" type="S">0.15</datum>
<datum id="nmr13c_1" time="0.9" stddev="0.81" pos="1" type="T">0.16</datum>
<datum id="nmr13c_1" time="0.9" stddev="0.91" pos="3" type="T">0.17</datum>

<!-- generische Messung gen_1 -->
<datum id="gen_1" row="1" time="0.1" stddev="0.02">0.111111</datum>
<datum id="gen_1" row="2" time="0.1" stddev="0.12">0.222222</datum>

<!-- Flussmessungen fn_1, fx_1: -->
<datum id="fn_1" time="10.0" stddev="0.22">9.81</datum>
<datum id="fx_1" time="10.0" stddev="0.32">3.14</datum>

<!-- Poolmessung p_1: -->
<datum id="p_1" time=".1" stddev="0.42">1.41</datum>
<datum id="p_1" time="13" stddev="0.52">2.82</datum>
</data>
</measurement>
83 changes: 83 additions & 0 deletions data/FluxML-Test/beispiel_stat.mm
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<?xml version="1.0" encoding="utf-8"?>
<measurement xmlns="http://www.uni-siegen.de/fb11/simtec/13cflux/mm" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.uni-siegen.de/fb11/simtec/13cflux/mm http://www.uni-siegen.de/fb11/simtec/13cflux/mm.xsd">
<mlabel>
<!-- alle Unterelemente optional: -->
<date>2007-05-15 11:11:11</date>
<version>1.0</version>
<comment>kein Kommentar</comment>
<fluxunit>gigamol/year</fluxunit>
<poolsizeunit>gigamol</poolsizeunit>
</mlabel>
<model stationary="true">
<labelingmeasurement>
<MSgroup id="ms_1" spec="Blubb[1-3,5,6]#M0,1,2"/>
<MSMSgroup id="msms_1" spec="Bla[1-3:2-3]#M(3,0),(3,1),(3,2)" scale="one"/>
<NMR1Hgroup id="nmr1h_1" spec="Frupp#P1,2"/>
<NMR13Cgroup id="nmr13c_1" spec="Flapp#S1,T1,3"/>
<group id="gen_1">
<!-- mehrere Zeilen mit Formeln. Jede Zeile nur Ausdrücke der Dimension 1
Alle(!) Typen erlaubt -->
<textual>
0.7*Frup#xx01x - 1/3*Bla#111x + 1.414213562e-7*Gamma#xxx1 - 3.1415;
Gonzo#1xx - 3*Kermit#xxx * MissPiggy#xxx1
</textual>
</group>
</labelingmeasurement>

<fluxmeasurement>
<!-- times ist hier vorerst immer optional?! -->
<netflux id="fn_1" fluxes="upt1 blupt2"/>
<xchflux id="fx_1" fluxes="upt1 blupt2"/>
</fluxmeasurement>

<poolmeasurement>
<!-- times ist hier vorerst immer optional?! -->
<pgroup id="p_1" pools="Gluc PEP"/>
</poolmeasurement>

<fluxratios>
<!-- times ist hier vorerst immer optional?! -->
<netratio id="frn_1">(bla/flupp)=(bläh/blubb)</netratio>
<xchratio id="frx_1">blöd/upt=upt/blubb</xchratio>
</fluxratios>
</model>
<data id="versuch_1">
<dlabel>
<start>2007-05-15 11:11:11</start>
<finish>2007-05-15 11:11:12</finish>
<people>Michael</people>
<strain>Drosophila coli K42</strain>
<comment>blabla bla flupp frupp</comment>
</dlabel>
<!-- MS-Messung ms_1: -->
<datum id="ms_1" stddev="0.1" weight="0">4.321</datum>
<datum id="ms_1" stddev="0.2" weight="1">1.234</datum>
<datum id="ms_1" stddev="0.3" weight="2">1.234</datum>

<!-- MSMS-Messung msms_1: -->
<datum id="msms_1" stddev="0.01" weight="3,0">0.001</datum>
<datum id="msms_1" stddev="0.11" weight="3,1">0.002</datum>
<datum id="msms_1" stddev="0.21" weight="3,2">0.003</datum>

<!-- 1H-NMR-Messung nmr1h_1: -->
<datum id="nmr1h_1" stddev="0.31" pos="1">0.11</datum>
<datum id="nmr1h_1" stddev="0.41" pos="2">0.12</datum>

<!-- 13C-NMR-Messung nmr13c_1: -->
<datum id="nmr13c_1" stddev="0.71" pos="1" type="S">0.15</datum>
<datum id="nmr13c_1" stddev="0.81" pos="1" type="T">0.16</datum>
<datum id="nmr13c_1" stddev="0.91" pos="3" type="T">0.17</datum>

<!-- generische Messung gen_1 -->
<datum id="gen_1" row="1" stddev="0.02">0.111111</datum>
<datum id="gen_1" row="2" stddev="0.12">0.222222</datum>

<!-- Flussmessungen fn_1, fx_1: -->
<datum id="fn_1" stddev="0.22">9.81</datum>
<datum id="fx_1" stddev="0.32">3.14</datum>

<!-- Poolmessung p_1: -->
<datum id="p_1" stddev="0.42">1.41</datum>
<datum id="p_1" stddev="0.52">2.82</datum>
</data>
</measurement>
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