Mercurial > repos > ggricourt > data_manager_bigg
changeset 1:5068c6484606 draft
"planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 8353ca81a49f5c8c7efb00cdf08710f916422a44-dirty"
| author | ggricourt |
|---|---|
| date | Wed, 23 Feb 2022 16:05:27 +0000 |
| parents | 262b8d79bc08 |
| children | 2be543b08426 |
| files | data_manager/bigg_model_sbml_fetcher.py data_manager/bigg_model_sbml_fetcher.xml data_manager/model_sbml_fetcher.py data_manager/model_sbml_fetcher.xml test-data/bigg_model_sbml.json test-data/bigg_model_sbml.loc test-data/e_coli_core.json test-data/e_coli_core.xml test-data/model_sbml.json test-data/model_sbml.loc tool_data_table_conf.xml.test |
| diffstat | 10 files changed, 67 insertions(+), 10031 deletions(-) [+] |
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--- a/data_manager/bigg_model_sbml_fetcher.py Wed Feb 23 14:33:49 2022 +0000 +++ b/data_manager/bigg_model_sbml_fetcher.py Wed Feb 23 16:05:27 2022 +0000 @@ -9,6 +9,56 @@ # Fall back to Python 2 imports from urllib2 import Request, urlopen +BASE_URL = 'http://bigg.ucsd.edu/static/models' +ID2ORG = { + "iCN718": "Acinetobacter baumannii AYE", + "iYO844": "Bacillus subtilis subsp. subtilis str. 168", + "iRC1080": "Chlamydomonas reinhardtii", + "iCN900": "Clostridioides difficile 630", + "iHN637": "Clostridium ljungdahlii DSM 13528", + "iCHOv1_DG44": "Cricetulus griseus", + "iCHOv1": "Cricetulus griseus", + "iAF1260b": "Escherichia coli str. K-12 substr. MG1655", + "iAF1260": "Escherichia coli str. K-12 substr. MG1655", + "iML1515": "Escherichia coli str. K-12 substr. MG1655", + "iJO1366": "Escherichia coli str. K-12 substr. MG1655", + "iJR904": "Escherichia coli str. K-12 substr. MG1655", + "e_coli_core": "Escherichia coli str. K-12 substr. MG1655", + "iAF987": "Geobacter metallireducens GS-15", + "iIT341": "Helicobacter pylori 26695", + "iAT_PLT_636": "Homo sapiens", + "Recon3D": "Homo sapiens", + "iAB_RBC_283": "Homo sapiens", + "RECON1": "Homo sapiens", + "iYL1228": "Klebsiella pneumoniae subsp. pneumoniae MGH 78578", + "iNF517": "Lactococcus lactis subsp. cremoris MG1363", + "iAF692": "Methanosarcina barkeri str. Fusaro", + "iMM1415": "Mus musculus", + "iNJ661": "Mycobacterium tuberculosis H37Rv", + "iEK1008": "Mycobacterium tuberculosis H37Rv", + "iLB1027_lipid": "Phaeodactylum tricornutum CCAP 1055/1", + "iAM_Pb448": "Plasmodium berghei", + "iAM_Pc455": "Plasmodium cynomolgi strain B", + "iAM_Pf480": "Plasmodium falciparum 3D7", + "iAM_Pk459": "Plasmodium knowlesi strain H", + "iAM_Pv461": "Plasmodium vivax Sal-1", + "iJN746": "Pseudomonas putida KT2440", + "iJN1463": "Pseudomonas putida KT2440", + "iND750": "Saccharomyces cerevisiae S288C", + "iMM904": "Saccharomyces cerevisiae S288C", + "STM_v1_0": "Salmonella enterica subsp. enterica serovar Typhimurium str. LT2", + "iYS1720": "Salmonella pan-reactome", + "iSB619": "Staphylococcus aureus subsp. aureus N315", + "iYS854": "Staphylococcus aureus subsp. aureus USA300_TCH1516", + "iJB785": "Synechococcus elongatus PCC 7942", + "iJN678": "Synechocystis sp. PCC 6803", + "iSynCJ816": "Synechocystis sp. PCC 6803", + "iLJ478": "Thermotoga maritima MSB8", + "iIS312": "Trypanosoma cruzi Dm28c", + "iIS312_Trypomastigote": "Trypanosoma cruzi Dm28c", + "iIS312_Epimastigote": "Trypanosoma cruzi Dm28c", + "iIS312_Amastigote": "Trypanosoma cruzi Dm28c" +} def url_download(url, workdir): file_path = os.path.abspath(os.path.join(workdir, os.path.basename(url))) @@ -39,24 +89,24 @@ workdir = params['output_data'][0]['extra_files_path'] os.makedirs(workdir) - file_path = url_download('http://bigg.ucsd.edu/static/models/%s.xml' % (model_id,), workdir) - entry_name = os.path.basename(file_path) - data_manager_json = {"data_tables": {}} + data_manager_json = {'data_tables': {}} + file_path = url_download(BASE_URL + '/' + model_id + '.xml', workdir) + data_manager_entry = {} data_manager_entry['value'] = model_id - data_manager_entry['name'] = entry_name + data_manager_entry['name'] = MODELID2ORG.get(model_id, 'undefined') data_manager_entry['path'] = file_path + data_manager_json['data_tables']['bigg_model_sbml'] = data_manager_entry with open(out_file, 'w') as fh: json.dump(data_manager_json, fh, sort_keys=True) -parser = argparse.ArgumentParser() +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('--out-file', help='JSON output file') + parser.add_argument('--model-id', help='Model BIGG id') + args = parser.parse_args() -parser.add_argument('--model-id', help='Model id') -parser.add_argument('--out-file', help='JSON output file') - -args = parser.parse_args() - -download(args.model_id, args.out_file) + download(args.out_file)
--- a/data_manager/bigg_model_sbml_fetcher.xml Wed Feb 23 14:33:49 2022 +0000 +++ b/data_manager/bigg_model_sbml_fetcher.xml Wed Feb 23 16:05:27 2022 +0000 @@ -9,13 +9,17 @@ --out-file '$out_file' ]]></command> <inputs> - <param name="model_id" type="text" label="Model Id"/> + <param name="model_id" type="select" label="Model Id"> + <option value="iML1515">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option> + </param> </inputs> <outputs> <data name="out_file" format="data_manager_json" /> </outputs> <tests> <test> + <param name="model_id" value="e_coli_core"/> + <output name="out_file" file="e_coli_core.json"/> </test> </tests> <help><![CDATA[
--- a/data_manager/model_sbml_fetcher.py Wed Feb 23 14:33:49 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ -import argparse -import json -import os -import sys -try: - # For Python 3.0 and later - from urllib.request import Request, urlopen -except ImportError: - # Fall back to Python 2 imports - from urllib2 import Request, urlopen - - -def url_download(url, workdir): - file_path = os.path.abspath(os.path.join(workdir, os.path.basename(url))) - src = None - dst = None - try: - req = Request(url) - src = urlopen(req) - with open(file_path, 'wb') as dst: - while True: - chunk = src.read(2**10) - if chunk: - dst.write(chunk) - else: - break - except Exception as e: - sys.exit(str(e)) - finally: - if src: - src.close() - return file_path - - -def download(model_id, out_file): - - with open(out_file) as fh: - params = json.load(fh) - - workdir = params['output_data'][0]['extra_files_path'] - os.makedirs(workdir) - file_path = url_download('http://bigg.ucsd.edu/static/models/%s.xml.gz' % (model_id,), workdir) - entry_name = os.path.basename(file_path) - - data_manager_json = {"data_tables": {}} - data_manager_entry = {} - data_manager_entry['id'] = model_id - data_manager_entry['name'] = entry_name - data_manager_entry['path'] = file_path - - with open(out_file, 'w') as fh: - json.dump(data_manager_json, fh, sort_keys=True) - - -parser = argparse.ArgumentParser() - -parser.add_argument('--model-id', help='Model id') -parser.add_argument('--out-file', help='JSON output file') - -args = parser.parse_args() - -download(args.model_id, args.out_file)
--- a/data_manager/model_sbml_fetcher.xml Wed Feb 23 14:33:49 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -<tool id="model_sbml_fetcher" name="Bigg SBML data manager" tool_type="manage_data" profile="18.09" version="0.0.1"> - <description>Get an SBML model (BiGG)</description> - <requirements> - <requirement type="package" version="3.7">python</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - python '$__tool_directory__/model_sbml_fetcher.py' - --model-id '$model_id' - --out-file '$out_file' - ]]></command> - <inputs> - <param name="model_id" type="text" label="Model Id"/> - </inputs> - <outputs> - <data name="out_file" format="data_manager_json" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help><![CDATA[ -Pick SBML Model -================= - -Download the selected SBML model fromg BiGG database. - - -Version ----------- -0.0.1 - -License -------- - -`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ - - ]]></help> -</tool>
--- a/test-data/bigg_model_sbml.json Wed Feb 23 14:33:49 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"data_tables": {"model_sbml": {"value": "iAF1260", "name": "Escherichia coli str. K-12 substr. MG1655 (iAF1260)", "path": "bigg/model/iAF1260.xml"}}}
--- a/test-data/bigg_model_sbml.loc Wed Feb 23 14:33:49 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -#This file has the format (white space characters are TAB characters): -# -#<model_id> <organism> <file_path> -# -#So, model_smbl.loc could look something like this: -# -#e_coli_core Escherichia coli str. K-12 substr. MG1655 e_coli_core.xml -# -#Your model_sbml.loc file should contain an entry for each individual -#sbml file. -# -e_coli_core Escherichia coli str. K-12 substr. MG1655 ${__HERE__}/e_coli_core.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/e_coli_core.json Wed Feb 23 16:05:27 2022 +0000 @@ -0,0 +1,1 @@ +{"data_tables": {"bigg_model_sbml": {"value": "e_coli_core", "name": "Escherichia coli str. K-12 substr. MG1655", "path": "e_coli_core.xml"}}}
--- a/test-data/e_coli_core.xml Wed Feb 23 14:33:49 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9898 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1" sboTerm="SBO:0000624" fbc:required="false"> - <model fbc:strict="true" id="e_coli_core"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit kind="mole" scale="-3" multiplier="1" exponent="1"/> - <unit kind="gram" scale="0" multiplier="1" exponent="-1"/> - <unit kind="second" scale="0" multiplier="3600" exponent="-1"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <fbc:listOfObjectives fbc:activeObjective="obj"> - <fbc:objective fbc:id="obj" fbc:type="maximize"> - <fbc:listOfFluxObjectives> - <fbc:fluxObjective fbc:reaction="R_BIOMASS_Ecoli_core_w_GAM" fbc:coefficient="1"/> - </fbc:listOfFluxObjectives> - </fbc:objective> - </fbc:listOfObjectives> - <listOfParameters> - <parameter value="-1000" id="cobra_default_lb" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/> - <parameter value="1000" id="cobra_default_ub" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/> - <parameter value="0" id="cobra_0_bound" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/> - <parameter id="R_ATPM_lower_bound" value="8.39" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/> - <parameter id="R_EX_glc__D_e_lower_bound" value="-10" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/> - </listOfParameters> - <listOfCompartments> - <compartment id="e" name="extracellular space" constant="true"/> - <compartment id="c" name="cytosol" constant="true"/> - </listOfCompartments> - <listOfSpecies> - <species id="M_glc__D_e" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="D-Glucose" metaid="M_glc__D_e" sboTerm="SBO:0000247" compartment="e" fbc:charge="0" fbc:chemicalFormula="C6H12O6"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#M_glc__D_e"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/glc__D"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:Glucopyranose"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:12965"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:20999"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:4167"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:17634"/> - <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB00122"/> - <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB06564"/> - <rdf:li rdf:resource="http://identifiers.org/inchi_key/WQZGKKKJIJFFOK-GASJEMHNSA-N"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00031"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.drug/D00009"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM41"/> - <rdf:li rdf:resource="http://identifiers.org/sabiork/1406"/> - <rdf:li rdf:resource="http://identifiers.org/sabiork/1407"/> - <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd26821"/> - <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00027"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - </species> - <species id="M_gln__L_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="L-Glutamine" metaid="M_gln__L_c" sboTerm="SBO:0000247" compartment="c" fbc:charge="0" fbc:chemicalFormula="C5H10N2O3"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#M_gln__L_c"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/gln__L"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLN"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42943"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42899"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32679"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32678"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:58359"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:28300"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42812"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:13110"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:18050"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32666"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:6227"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32665"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:21308"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42814"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:5432"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:24316"/> - <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB00641"/> - <rdf:li rdf:resource="http://identifiers.org/inchi_key/ZDXPYRJPNDTMRX-VKHMYHEASA-N"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00064"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00303"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.drug/D00015"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM37"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.compound/113522"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.compound/212615"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.compound/29472"/> - <rdf:li rdf:resource="http://identifiers.org/sabiork/2011"/> - <rdf:li rdf:resource="http://identifiers.org/sabiork/74"/> - <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00253"/> - <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00053"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - </species> - <species id="M_gln__L_e" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="L-Glutamine" metaid="M_gln__L_e" sboTerm="SBO:0000247" compartment="e" fbc:charge="0" fbc:chemicalFormula="C5H10N2O3"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#M_gln__L_e"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/gln__L"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:GLN"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42943"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42899"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32679"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32678"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:58359"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:28300"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42812"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:13110"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:18050"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32666"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:6227"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:32665"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:21308"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:42814"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:5432"/> - <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:24316"/> - <rdf:li rdf:resource="http://identifiers.org/hmdb/HMDB00641"/> - <rdf:li rdf:resource="http://identifiers.org/inchi_key/ZDXPYRJPNDTMRX-VKHMYHEASA-N"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00064"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00303"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.drug/D00015"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM37"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.compound/113522"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.compound/212615"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.compound/29472"/> - <rdf:li rdf:resource="http://identifiers.org/sabiork/2011"/> - <rdf:li rdf:resource="http://identifiers.org/sabiork/74"/> - <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00253"/> - <rdf:li rdf:resource="http://identifiers.org/seed.compound/cpd00053"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - </species> - <species id="M_glu__L_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="L-Glutamate" metaid="M_glu__L_c" sboTerm="SBO:0000247" compartment="c" fbc:charge="-1" fbc:chemicalFormula="C5H8NO4"> - 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<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_ME2"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ME2"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:MALIC-NADP-RXN"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/1.1.1.40"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00216"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101443"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/18255"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/18256"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/18254"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/18253"/> - <rdf:li rdf:resource="http://identifiers.org/sabiork/142"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00161"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_b2463"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_NADH16" fast="false" reversible="false" name="NADH dehydrogenase (ubiquinone-8 & 3 protons)" metaid="R_NADH16" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_NADH16"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADH16"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.5.3"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101864"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08972"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_h_c" stoichiometry="4" constant="true"/> - <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_q8_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_e" stoichiometry="3" constant="true"/> - <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_q8h2_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_b2276"/> - <fbc:geneProductRef fbc:geneProduct="G_b2277"/> - <fbc:geneProductRef fbc:geneProduct="G_b2278"/> - <fbc:geneProductRef fbc:geneProduct="G_b2279"/> - <fbc:geneProductRef fbc:geneProduct="G_b2280"/> - <fbc:geneProductRef fbc:geneProduct="G_b2281"/> - <fbc:geneProductRef fbc:geneProduct="G_b2282"/> - <fbc:geneProductRef fbc:geneProduct="G_b2283"/> - <fbc:geneProductRef fbc:geneProduct="G_b2284"/> - <fbc:geneProductRef fbc:geneProduct="G_b2285"/> - <fbc:geneProductRef fbc:geneProduct="G_b2286"/> - <fbc:geneProductRef fbc:geneProduct="G_b2287"/> - <fbc:geneProductRef fbc:geneProduct="G_b2288"/> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_NADTRHD" fast="false" reversible="false" name="NAD transhydrogenase" metaid="R_NADTRHD" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_NADTRHD"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NADTRHD"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRNUTRANSHYDROGEN-RXN"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.3"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.2"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/1.6.1.1"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00112"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101898"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/11692"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/11695"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/11694"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/11693"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00083"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_b3962"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_b1602"/> - <fbc:geneProductRef fbc:geneProduct="G_b1603"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_NH4t" fast="false" reversible="true" name="Ammonia reversible transport" metaid="R_NH4t" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_NH4t"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/NH4t"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-206"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:RXN-9615"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-544"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR101950"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-444416"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-444416"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-444416"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-444416"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-444416"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-444416"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-444416"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-444416"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-444416"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-444416"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-444416"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-444416"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-444416"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/28749"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/28748"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/28750"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/28747"/> - <rdf:li rdf:resource="http://identifiers.org/sabiork/11683"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn13364"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09835"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05466"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08987"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08986"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09736"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_nh4_e" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_s0001"/> - <fbc:geneProductRef fbc:geneProduct="G_b0451"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_O2t" fast="false" reversible="true" name="O2 transport diffusion " metaid="R_O2t" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_O2t"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/O2t"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:TRANS-RXN0-474"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102090"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09641"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn05468"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09031"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09032"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09734"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_o2_e" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_s0001"/> - </fbc:geneProductAssociation> - </reaction> - <reaction id="R_PDH" fast="false" reversible="false" name="Pyruvate dehydrogenase" metaid="R_PDH" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound"> - <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> - <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <rdf:Description rdf:about="#R_PDH"> - <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> - <rdf:Bag> - <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/PDH"/> - <rdf:li rdf:resource="http://identifiers.org/biocyc/META:PYRUVDEH-RXN"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/1.8.1.4"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.51"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.4.1"/> - <rdf:li rdf:resource="http://identifiers.org/ec-code/2.3.1.12"/> - <rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00209"/> - <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102425"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-RNO-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-OSA-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-373177"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DME-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-TGU-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-XTR-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CFA-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-BTA-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-HSA-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-GGA-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SPO-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-CEL-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DDI-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-DRE-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SSC-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-SCE-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-ATH-71397"/> - <rdf:li rdf:resource="http://identifiers.org/reactome.reaction/R-MMU-71397"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/28043"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/28045"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/28044"/> - <rdf:li rdf:resource="http://identifiers.org/rhea/28042"/> - <rdf:li rdf:resource="http://identifiers.org/sabiork/523"/> - <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn00154"/> - </rdf:Bag> - </bqbiol:is> - </rdf:Description> - </rdf:RDF> - </sbml:annotation> - <listOfReactants> - <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_b0114"/> - <fbc:geneProductRef fbc:geneProduct="G_b0115"/> - <fbc:geneProductRef fbc:geneProduct="G_b0116"/> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - </listOfReactions> - </model> -</sbml>
--- a/test-data/model_sbml.json Wed Feb 23 14:33:49 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"data_tables": {"bigg_sbml": {"id": "iAF1260", "name": "Escherichia coli str. K-12 substr. MG1655 (iAF1260)", "path": "bigg/model/iAF1260.xml"}}}
--- a/tool_data_table_conf.xml.test Wed Feb 23 14:33:49 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -<tables> - <!-- Location of sbml models --> - <table name="bigg_model_sbml" comment_char="#"> - <columns>value, name, path</columns> - <file path="${__HERE__}/test-data/bigg_model_sbml.loc" /> - </table> -</tables>