def test_addMIRIAMinchiKey(self):
#no inchikeys should be added
rpsbml = rpSBML('test', path=os.path.join('data', 'rpsbml', 'rpsbml.xml'))
self.assertTrue(rpsbml.addMIRIAMinchiKey())
self.assertEqual(rpsbml.readMIRIAMAnnotation(rpsbml.model.getSpecies('MNXM100__64__MNXC3').getAnnotation())['inchikey'][0], 'GVVPGTZRZFNKDS-JXMROGBWSA-K')
#inchikeys are added
gem = rpSBML('test', path=os.path.join('data', 'rpsbml', 'gem.xml'))
self.assertTrue(gem.addMIRIAMinchiKey())
self.assertEqual(gem.readMIRIAMAnnotation(gem.model.getSpecies('M_2pg_c').getAnnotation())['inchikey'][0], 'GXIURPTVHJPJLF-UWTATZPHSA-K')
def test_createMultiFluxObj(self):
#create new group
with tempfile.TemporaryDirectory() as tmp_output_folder:
rpsbml = rpSBML('test', path=os.path.join('data', 'rpsbml', 'rpsbml.xml'))
flux_obj = rpsbml.createMultiFluxObj('test', ['RP1'], [1.0])
self.assertEqual(flux_obj.getId(), 'test')
rpsbml.writeSBML(os.path.join(tmp_output_folder, 'test.xml'))
self.assertEqual(hashlib.md5(open(os.path.join(tmp_output_folder, 'test.xml'), 'rb').read()).hexdigest(), 'c4647ea976dbf1eebbf0e7400af4b65d')
#recover already existing group
rpsbml = rpSBML('test', path=os.path.join('data', 'rpsbml', 'rpsbml.xml'))
flux_obj = rpsbml.createMultiFluxObj('obj_fraction', ['RP1'], [1.0])
self.assertEqual(flux_obj.getId(), 'obj_fraction')
def test_createGroup(self):
#create new group
with tempfile.TemporaryDirectory() as tmp_output_folder:
rpsbml = rpSBML('test', path=os.path.join('data', 'rpsbml', 'rpsbml.xml'))
gro = rpsbml.createGroup('test')
self.assertEqual(gro.getId(), 'test')
rpsbml.writeSBML(os.path.join(tmp_output_folder, 'test.xml'))
self.assertEqual(hashlib.md5(open(os.path.join(tmp_output_folder, 'test.xml'), 'rb').read()).hexdigest(), '19c61349df77d97118210a359710dbbf')
#recover already existing group
rpsbml = rpSBML('test', path=os.path.join('data', 'rpsbml', 'rpsbml.xml'))
gro = rpsbml.createGroup('rp_pathway', 'MNXC3')
self.assertEqual(gro.getId(), 'rp_pathway')
def test_createSpecies(self):
#create new species
with tempfile.TemporaryDirectory() as tmp_output_folder:
rpsbml = rpSBML('test', path=os.path.join('data', 'rpsbml', 'rpsbml.xml'))
spe = rpsbml.createSpecies('test', 'MNXC3')
self.assertEqual(spe.getId(), 'test')
rpsbml.writeSBML(os.path.join(tmp_output_folder, 'test.xml'))
self.assertEqual(hashlib.md5(open(os.path.join(tmp_output_folder, 'test.xml'), 'rb').read()).hexdigest(), '8222edc93f5c1430231d7e16afbf3079')
#recover already existing species
rpsbml = rpSBML('test', path=os.path.join('data', 'rpsbml', 'rpsbml.xml'))
spe = rpsbml.createSpecies('MNXM6', 'MNXC3')
self.assertEqual(spe.getId(), 'MNXM6')
def test_createCompartment(self):
#test with no comp xref
with tempfile.TemporaryDirectory() as tmp_output_folder:
new = rpSBML('test')
new.createModel('test_name', 'test_id')
new.createCompartment('test')
new.writeSBML(os.path.join(tmp_output_folder, 'test.xml'))
self.assertEqual(hashlib.md5(open(os.path.join(tmp_output_folder, 'test.xml'), 'rb').read()).hexdigest(), '87fd0a156f470799bdcf6295decb5faa')
#test with xref
with tempfile.TemporaryDirectory() as tmp_output_folder:
new = rpSBML('test')
new.createModel('test_name', 'test_id')
new.createCompartment('MNXC3')
new.writeSBML(os.path.join(tmp_output_folder, 'test.xml'))
self.assertEqual(hashlib.md5(open(os.path.join(tmp_output_folder, 'test.xml'), 'rb').read()).hexdigest(), 'c27be1b46e4c0f10aaf86362364749e7')
def test_findCreateObjective(self):
#the find part
self.assertEqual(self.rpsbml.findCreateObjective(['RP1_sink'], [1.0]), 'obj_RP1_sink')
#the create part
with tempfile.TemporaryDirectory() as tmp_output_folder:
rpsbml = rpSBML('test', path=os.path.join('data', 'rpsbml', 'rpsbml.xml'))
self.assertEqual(rpsbml.findCreateObjective(['RP2'], [1.0]), 'obj_RP2')
def test_createReturnFluxParameter(self):
#create feature
new = rpSBML('test')
new.createModel('test_name', 'test_id')
param = new.createReturnFluxParameter(8888.0)
self.assertEqual(param.id, 'B_8888_0')
self.assertEqual(param.value, 8888.0)
def test_runCollection(self):
with tempfile.TemporaryDirectory() as tmp_output_folder:
rpFBA.runCollection(os.path.join('data', 'rpfba', 'test.rpcol'),
os.path.join('data', 'rpfba', 'gem.xml'),
os.path.join(tmp_output_folder, 'test.rpcol'),
num_workers=1)
tar = tarfile.open(os.path.join(tmp_output_folder, 'test.rpcol'),
mode='r')
os.mkdir(os.path.join(tmp_output_folder, 'results'))
tar.extractall(os.path.join(tmp_output_folder, 'results'))
self.assertTrue(
len(
glob.glob(
os.path.join(tmp_output_folder, 'results',
'rpsbml_collection', 'models', '*'))) ==
1)
rpsbml = rpSBML(path=glob.glob(
os.path.join(tmp_output_folder, 'results', 'rpsbml_collection',
'models', '*'))[0])
asdict = rpsbml.asDict()
self.assertAlmostEqual(
asdict['pathway']['brsynth']['fba_obj_biomass_restricted']
['value'], 0.6577479108178588)
self.assertAlmostEqual(
asdict['pathway']['brsynth']['fba_obj_fraction']['value'],
0.9438866396863238)
self.assertAlmostEqual(
asdict['pathway']['brsynth']['fba_obj_biomass']['value'],
0.8769972144238116)
def rpPipeline():
with tempfile.TemporaryDirectory() as tmpdir:
params = json.load(request.files['params'])
rp2_file = os.path.join(tmpdir, 'rp2_file.csv')
with open(rp2_file, 'wb') as fo:
fo.write(request.files['rp2_file'].read())
rp2paths_compounds_file = os.path.join(tmpdir,
'rp2paths_compounds_file.csv')
with open(rp2paths_compounds_file, 'wb') as fo:
fo.write(request.files['rp2paths_compounds_file'].read())
rp2paths_pathways_file = os.path.join(tmpdir, 'rp2paths_pathways_file')
with open(rp2paths_pathways_file, 'wb') as fo:
fo.write(request.files['rp2paths_pathways_file'].read())
gem_file = os.path.join(tmpdir, 'gem_file.sbml')
with open(gem_file, 'wb') as fo:
fo.write(request.files['gem_file'].read())
rpcollection_file = os.path.join(tmpdir, 'rpcollection.tar.xz')
rpre_status = rpReader.rp2ToCollection(rp2_file,
rp2paths_compounds_file,
rp2paths_pathways_file,
rpcollection_file,
rpcache=GLOBAL_RPCACHE)
rpeq_status = rpEquilibrator.runCollection(
rpcollection_file,
rpcollection_file,
ph=float(params['ph']),
ionic_strength=float(params['ionic_strength']),
temp_k=float(params['temp_k']),
rpcache=GLOBAL_RPCACHE)
rpfba_status = rpFBA.runCollection(rpcollection_file,
gem_file,
rpcollection_file,
num_workers=params['num_workers'],
keep_merged=params['keep_merged'],
del_sp_pro=params['del_sp_pro'],
del_sp_react=params['del_sp_react'],
rpcache=GLOBAL_RPCACHE)
if params['taxo_id'] == None:
#if you cannot find the annotation then try to recover it from the GEM file
rpsbml_gem = rpSBML(model_name='tmp', path=gem_file)
params['taxo_id'] = rpsbml_gem.readTaxonomy()
rpsel_status = rpSelenzyme.runCollection(
rpcollection_file,
params['taxo_id'],
rpcollection_file,
uniprot_aa_length=SELENZYME_UNIPROT_AA_LENGTH,
data_dir=SELENZYNE_DATA_DIR,
pc=SELENZYME_PC,
rpcache=GLOBAL_RPCACHE)
rpglo_status = rpGlobalScore.runCollection(rpcollection_file,
rpcollection_file,
rpcache=GLOBAL_RPCACHE)
rpcollection_file.seek(0)
return send_file(rpcollection_file,
as_attachment=True,
attachment_filename='rpcollection.tar.xz',
mimetype='application/x-tar')
def test_createUnitDefinition(self):
with tempfile.TemporaryDirectory() as tmp_output_folder:
new = rpSBML('test')
new.createModel('test_name', 'test_id')
unit_def = new.createUnitDefinition('mmol_per_gDW_per_hr')
new.createUnit(unit_def, libsbml.UNIT_KIND_MOLE, 1, -3, 1)
new.createUnit(unit_def, libsbml.UNIT_KIND_GRAM, 1, 0, 1)
new.createUnit(unit_def, libsbml.UNIT_KIND_SECOND, 1, 0, 3600)
new.writeSBML(os.path.join(tmp_output_folder, 'test.xml'))
self.assertEqual(hashlib.md5(open(os.path.join(tmp_output_folder, 'test.xml'), 'rb').read()).hexdigest(), '7e98e6667c2de2fa9078795121203c99')
def test_mergeSBMLFiles(self):
with tempfile.TemporaryDirectory() as tmp_output_folder:
rpMerge.mergeSBMLFiles(
os.path.join('data', 'rpmerge', 'rpsbml.xml'),
os.path.join('data', 'rpmerge', 'gem.xml'),
os.path.join(tmp_output_folder, 'merged.xml'))
rpsbml = rpSBML(path=os.path.join(tmp_output_folder, 'merged.xml'))
reac = rpsbml.model.getReaction('RP1')
self.assertEqual(reac.getId(), 'RP1')
self.assertTrue(
len([i.species for i in reac.getListOfReactants()]) == 1)
spe_id = [i.species for i in reac.getListOfReactants()][0]
self.assertEqual(spe_id, 'M_grdp_c')
self.assertTrue(
len([i.species for i in reac.getListOfProducts()]) == 1)
spe_id = [i.species for i in reac.getListOfProducts()][0]
self.assertEqual(spe_id, 'TARGET_0000000001__64__MNXC3')
def test_createReaction(self):
#TODO: add detection
with tempfile.TemporaryDirectory() as tmp_output_folder:
rpsbml = rpSBML('test', path=os.path.join('data', 'rpsbml', 'rpsbml.xml'))
step = {'rule_id': None,
'left': {'MNXM89557': 1},
'right': {},
'step': None,
'sub_step': None,
'path_id': None,
'transformation_id': None,
'rule_score': None,
'rule_ori_reac': None}
rpsbml.createReaction('test',
999999.0,
0.0,
step,
'MNXC3',
xref={'ec': ['1.1.1.1']})
rpsbml.writeSBML(os.path.join(tmp_output_folder, 'test.xml'))
self.assertEqual(hashlib.md5(open(os.path.join(tmp_output_folder, 'test.xml'), 'rb').read()).hexdigest(), '6c832eb02bb3f1849d2e0b754e44e748')
def test_runCollection(self):
with tempfile.TemporaryDirectory() as tmp_output_folder:
rpEquilibrator.runCollection(
os.path.join('data', 'rpequilibrator', 'test.rpcol'),
os.path.join(tmp_output_folder, 'test.rpcol'))
tar = tarfile.open(os.path.join(tmp_output_folder, 'test.rpcol'),
mode='r')
os.mkdir(os.path.join(tmp_output_folder, 'results'))
tar.extractall(os.path.join(tmp_output_folder, 'results'))
self.assertTrue(
len(
glob.glob(
os.path.join(tmp_output_folder, 'results',
'rpsbml_collection', 'models', '*'))) ==
1)
rpsbml = rpSBML(path=glob.glob(
os.path.join(tmp_output_folder, 'results', 'rpsbml_collection',
'models', '*'))[0])
asdict = rpsbml.asDict()
self.assertAlmostEqual(
asdict['pathway']['brsynth']['dfG_prime_o']['value'],
1784.7384959433493)
def setUpClass(self):
self.gem = rpSBML(path=os.path.join('data', 'rpmerge', 'gem.xml'))
self.rpsbml = rpSBML(
path=os.path.join('data', 'rpmerge', 'rpsbml.xml'))
self.rpmerge = rpMerge(True,
path=os.path.join('data', 'rpmerge', 'gem.xml'))
def setUpClass(self):
#load a rpSBML file
self.rpsbml = rpSBML('test', path=os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', 'rpsbml', 'rpsbml.xml'))
self.gem = rpSBML('gem', path=os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', 'rpsbml', 'gem.xml'))
self.data = json.load(open(os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', 'rpsbml', 'data.json'), 'r'))
self.maxDiff = None #to be able to compare large dict
def rpPipelineService():
with tempfile.TemporaryDirectory() as tmpdir:
########### file in ################
rp2_file = os.path.join(tmpdir, 'rp2_file.csv')
rp2paths_compounds_file = os.path.join(tmpdir,
'rp2paths_compounds_file.csv')
rp2paths_pathways_file = os.path.join(tmpdir, 'rp2paths_pathways_file')
gem_file = os.path.join(tmpdir, 'gem_file.sbml')
try:
with open(rp2_file, 'wb') as fo:
fo.write(request.files['rp2_file'].read())
with open(rp2paths_compounds_file, 'wb') as fo:
fo.write(request.files['rp2paths_compounds_file'].read())
with open(rp2paths_pathways_file, 'wb') as fo:
fo.write(request.files['rp2paths_pathways_file'].read())
with open(gem_file, 'wb') as fo:
fo.write(request.files['gem_file'].read())
except KeyError as e:
app.logger.error('A required file is missing: ' + str(e))
return Response('A required file is missing: ' + str(e),
status=400)
############ parameters ##########
try:
params = json.load(request.files['data'])
except ValueError as e:
app.logger.error('One or more parameters are malformed: ' + str(e))
return Response('One or more parameters are malformed: ' + str(e),
status=400)
except KeyError as e:
app.logger.error('One or more of the parameters are missing: ' +
str(e))
return Response('One or more of the parameters are missing: ' +
str(e),
status=400)
try:
ph = float(params['ph'])
except KeyError:
app.logger.info('No ph passed. Setting to default to 7.5')
ph = 7.5
except ValueError:
app.logger.warning('ph is not recognised. Setting to default 7.5')
ph = 7.5
try:
temp_k = float(params['temp_k'])
except KeyError:
app.logger.info('No temp_k passed. Setting to default to 298.15')
temp_k = 298.15
except ValueError:
app.logger.warning(
'temp_k is not recognised. Setting to default 298.15')
temp_k = 298.15
try:
ionic_strength = float(params['ionic_strength'])
except KeyError:
app.logger.info(
'No ionic_strength passed. Setting to default to 200.0')
ionic_strength = 200.0
except ValueError:
app.logger.warning(
'ionic_strength is not recognised. Setting to default 200.0')
ionic_strength = 200.0
try:
num_workers = int(params['num_workers'])
except KeyError:
app.logger.info('No num_workers passed. Setting to default to 1')
num_workers = 1
except ValueError:
app.logger.warning(
'num_workers is not recognised. Setting to default 1')
num_workers = 1
try:
keep_merged = bool(params['keep_merged'])
except KeyError:
app.logger.info(
'No keep_merged passed. Setting to default to True')
keep_merged = True
except ValueError:
app.logger.warning(
'keep_merged is not recognised. Setting to default True')
keep_merged = True
try:
del_sp_pro = bool(params['del_sp_pro'])
except KeyError:
app.logger.info(
'No del_sp_pro passed. Setting to default to False')
del_sp_pro = False
except ValueError:
app.logger.warning(
'del_sp_pro is not recognised. Setting to default False')
del_sp_pro = False
try:
del_sp_react = bool(params['del_sp_react'])
except KeyError:
app.logger.info(
'No del_sp_react passed. Setting to default to False')
del_sp_react = False
except ValueError:
app.logger.warning(
'del_sp_react is not recognised. Setting to default False')
del_sp_react = False
try:
taxo_id = int(params['taxo_id'])
except KeyError:
app.logger.info(
'No taxo_id passed. Setting to default to None to try and recover from GEM SBML'
)
taxo_id = None
except ValueError:
app.logger.warning(
'taxo_id is not recognised. Setting to default None to try to recover from GEM SBML'
)
taxo_id = None
rpcollection_file = os.path.join(tmpdir, 'rpcollection.tar.xz')
rpre_status = rpReader.rp2ToCollection(rp2_file,
rp2paths_compounds_file,
rp2paths_pathways_file,
rpcollection_file,
rpcache=GLOBAL_RPCACHE)
if not rpre_status:
app.logger.error(
'rpReader has encountered a problem.... please investigate futher'
)
return Response(
'rpReader has encountered a problem.... please investigate futher',
status=400)
rpeq_status = rpEquilibrator.runCollection(
rpcollection_file,
rpcollection_file,
ph=ph,
ionic_strength=ionic_strength,
temp_k=temp_k,
rpcache=GLOBAL_RPCACHE)
if not rpeq_status:
app.logger.error(
'rpEquilibrator has encountered a problem.... please investigate futher'
)
return Response(
'rpEquilibrator has encountered a problem.... please investigate futher',
status=400)
rpfba_status = rpFBA.runCollection(rpcollection_file,
gem_file,
rpcollection_file,
num_workers=num_workers,
keep_merged=keep_merged,
del_sp_pro=del_sp_pro,
del_sp_react=del_sp_react,
rpcache=GLOBAL_RPCACHE)
if not rpfba_status:
app.logger.error(
'rpFBA has encountered a problem.... please investigate futher'
)
return Response(
'rpFBA has encountered a problem.... please investigate futher',
status=400)
if taxo_id == None:
#if you cannot find the annotation then try to recover it from the GEM file
rpsbml_gem = rpSBML(model_name='tmp', path=gem_file)
taxo_id = rpsbml_gem.readTaxonomy()
logging.info('The taxonomy_id is ' + str(taxo_id))
try:
taxo_id = taxo_id[0]
except IndexError:
app.logger.error(
'Could not retreive the taxonomy id and none was passed')
return Response(
'Could not retreive the taxonomy id and none was passed',
status=400)
rpsel_status = rpSelenzyme.runCollection(
rpcollection_file,
taxo_id,
rpcollection_file,
is_cleanup=False,
uniprot_aa_length=SELENZYME_UNIPROT_AA_LENGTH,
data_dir=SELENZYNE_DATA_DIR,
pc=SELENZYME_PC,
rpcache=GLOBAL_RPCACHE)
if not rpsel_status:
app.logger.error(
'rpSelenzyme has encountered a problem.... please investigate futher'
)
return Response(
'rpSelenzyme has encountered a problem.... please investigate futher',
status=400)
rpglo_status = rpGlobalScore.runCollection(rpcollection_file,
rpcollection_file,
rpcache=GLOBAL_RPCACHE)
if not rpglo_status:
app.logger.error(
'rpGlobalScore has encountered a problem.... please investigate futher'
)
return Response(
'rpGlobalScore has encountered a problem.... please investigate futher',
status=400)
#rpcollection_file.seek(0)
return send_file(rpcollection_file,
as_attachment=True,
attachment_filename='rpcollection.tar.xz',
mimetype='application/x-tar')
def test_genericModel(self):
with tempfile.TemporaryDirectory() as tmp_output_folder:
new = rpSBML('test')
new.genericModel('test_name', 'test_id', 'MNXC3')
new.writeSBML(os.path.join(tmp_output_folder, 'test.xml'))
self.assertEqual(hashlib.md5(open(os.path.join(tmp_output_folder, 'test.xml'), 'rb').read()).hexdigest(), 'f1de251a278b40ef0448579e308edf9d')
def test_createModel(self):
with tempfile.TemporaryDirectory() as tmp_output_folder:
new = rpSBML('test')
new.createModel('test_name', 'test_id')
new.writeSBML(os.path.join(tmp_output_folder, 'test.xml'))
self.assertEqual(hashlib.md5(open(os.path.join(tmp_output_folder, 'test.xml'), 'rb').read()).hexdigest(), '79b9063da98b5bd8286afab444f52227')
def test_updateBRSynthPathway(self):
rpsbml = rpSBML('test', path=os.path.join('data', 'rpsbml', 'rpsbml.xml'))
tmp_dict = rpsbml.asDict()
tmp_dict['pathway']['brsynth']['test'] = {'value': 99}
rpsbml.updateBRSynthPathway(tmp_dict)
self.assertEqual(rpsbml.asDict()['pathway']['brsynth']['test']['value'], 99)