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fix_sbml_validity.py
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fix_sbml_validity.py
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import libsbml
import urllib
import pickle
from os import replace
from biosimulators_utils.utils.identifiers_org import validate_identifiers_org_uri
def fixNanoMolar(file):
doc = libsbml.readSBMLFromFile(file)
model = doc.getModel()
for s in range(model.getNumSpecies()):
species = model.getSpecies(s)
if species.getSubstanceUnits() == "nanoMolar":
species.setSubstanceUnits("nanomole")
nm = model.getUnitDefinition("nanoMolar").clone()
nm.setName("nm")
nm.setId("nanomole")
nm.unsetMetaId()
nm.removeUnit(1)
nm.getUnit(0).unsetMetaId()
model.addUnitDefinition(nm)
libsbml.writeSBMLToFile(doc, file)
# The original unit definition, for reference:
"""
<unitDefinition id="nanoMolar" metaid="_476810" name="nM">
<listOfUnits>
<unit kind="mole" metaid="_476822" scale="-9"/>
<unit exponent="-1" kind="litre" metaid="_476834"/>
</listOfUnits>
</unitDefinition>
"""
def fixSBO(file):
doc = libsbml.readSBMLFromFile(file)
model = doc.getModel()
for p in range(model.getNumParameters()):
param = model.getParameter(p)
if param.getSBOTerm() == 345:
param.unsetSBOTerm()
for r in range(model.getNumReactions()):
rxn = model.getReaction(r)
if rxn.getSBOTerm() == 610:
rxn.unsetSBOTerm()
libsbml.writeSBMLToFile(doc, file)
def fixHasProperty(file):
doc = libsbml.readSBMLFromFile(file)
sstr = libsbml.writeSBMLToString(doc)
sstr = sstr.replace("bqmodel:hasProperty", "bqbiol:hasProperty")
out = open(file, "w", encoding="utf8")
out.write(sstr)
out.close()
upgrade_to_l2v4 = ["BIOMD0000000051", "BIOMD0000000060", "BIOMD0000000064", "BIOMD0000000096", "BIOMD0000000097",
"BIOMD0000000164", "BIOMD0000000200", "BIOMD0000000207", "BIOMD0000000425", "BIOMD0000000437",
"BIOMD0000000508", "BIOMD0000000509", "BIOMD0000000584", "BIOMD0000000585", "BIOMD0000000831", ]
make_boundary = {
"BIOMD0000000344": ("MODEL1005280000_moderatestress.xml", "ROS")
}
def changeAssignmentRuleToInitialAssignment(file, identifier):
doc = libsbml.readSBMLFromFile(file)
model = doc.getModel()
rule = model.getRule(identifier)
asnt = rule.getMath()
ia = model.createInitialAssignment()
ia.setSymbol(identifier)
ia.setMath(asnt)
model.removeRule(identifier)
libsbml.writeSBMLToFile(doc, file)
assignment_rule_to_initial_assignment = {
"BIOMD0000000567": ("BIOMD0000000567_url.xml", "A0")
}
particular_fixes = {
"BIOMD0000000439": fixNanoMolar,
"BIOMD0000000479": fixNanoMolar,
"BIOMD0000000631": fixSBO,
"BIOMD0000000647": fixHasProperty,
"BIOMD0000000648": fixHasProperty,
"BIOMD0000000652": fixHasProperty,
"BIOMD0000000653": fixHasProperty,
"BIOMD0000000654": fixHasProperty,
"BIOMD0000000655": fixHasProperty,
"BIOMD0000000656": fixHasProperty,
"BIOMD0000000657": fixHasProperty,
"BIOMD0000000755": fixHasProperty,
"BIOMD0000000953": fixHasProperty,
"BIOMD0000000989": fixHasProperty,
"BIOMD0000000994": fixHasProperty,
"BIOMD0000000995": fixHasProperty,
"BIOMD0000000996": fixHasProperty,
"BIOMD0000000997": fixHasProperty,
"BIOMD0000000998": fixHasProperty,
"BIOMD0000000999": fixHasProperty,
"BIOMD0000001001": fixHasProperty,
"BIOMD0000001002": fixHasProperty,
"BIOMD0000001003": fixHasProperty,
"BIOMD0000001006": fixHasProperty,
"BIOMD0000001007": fixHasProperty,
"BIOMD0000001009": fixHasProperty,
"BIOMD0000001010": fixHasProperty,
"BIOMD0000001019": fixHasProperty,
"BIOMD0000001020": fixHasProperty,
"BIOMD0000001026": fixHasProperty,
"BIOMD0000001027": fixHasProperty,
"BIOMD0000001028": fixHasProperty,
"BIOMD0000001029": fixHasProperty,
"BIOMD0000001039": fixHasProperty,
"BIOMD0000001044": fixHasProperty,
"BIOMD0000001045": fixHasProperty,
}
def fixPubmedId(file, pmid, id):
if int(id[-5:]) > 1044:
raise NotImplementedError("The pubmed ID substitutions have not been checked for biomodels greater than 1044. Unknown id", pmid, "in biomodel", str(id))
pmid2 = ""
if pmid == "[PMID]":
pmid2 = "24354351"
elif "[" in pmid:
pmid2 = pmid.replace("[", "")
pmid2 = pmid2.replace("]", "")
elif "+" in pmid:
pmid2 = pmid.replace("+", "")
elif "PMID:" in pmid:
pmid2 = pmid.replace("PMID:", "")
elif pmid == "---":
pmid2 = "24005054"
else:
#When running in batch, can fail URL checks for a variety of reasons unrelated to it being wrong.
print("Skipping check for PubMed URL", "https://pubmed.ncbi.nlm.nih.gov/" + pmid)
return
#raise NotImplementedError("Unknown problem pubmed ID", pmid)
url = "https://pubmed.ncbi.nlm.nih.gov/" + pmid2
try:
if urllib.request.urlopen(url).getcode() > 400:
raise NotImplementedError("Unknown problem pubmed ID", pmid)
except:
raise NotImplementedError("Unknown problem pubmed ID", pmid)
assert(".xml" in file)
tmpname = file.replace(".xml", ".tmp")
orig = open(file, "r", encoding="utf-8")
new = open(tmpname, "w", encoding="utf-8")
for line in orig:
if pmid + " " in line:
line = line.replace(pmid + " ", pmid2)
if pmid in line:
line = line.replace(pmid, pmid2)
new.write(line)
orig.close()
new.close()
replace(tmpname, file)
def fixIdentifiersNS(file, oldns, id):
newns = ""
if oldns == "obo.go" or oldns == "go.ref":
newns = "go"
elif oldns=="obo.chebi":
newns = "chebi"
elif oldns=="obo.fma" or oldns=="obo.FMA":
newns = "fma"
elif oldns=="obo.pw":
newns = "pw"
elif oldns=="obo.pato":
newns = "pato"
elif oldns=="obo.bto":
newns = "bto"
elif oldns=="biomodels.sbo":
newns = "sbo"
elif oldns=="doi.org":
newns = "doi"
elif oldns=="psimod" or oldns == "psi-mod" or oldns=="obo.psi-mod":
newns = "mod"
else:
INVALID_IDENTIFIERS_NAMESPACES.add(oldns)
return
# raise NotImplementedError("Unknown identifiers wrong ns ", oldns)
assert(newns in VALID_IDENTIFIERS_NAMESPACES or not checkAndAddIdentifiersNamespace(newns))
assert(".xml" in file)
tmpname = file.replace(".xml", ".tmp")
orig = open(file, "r", encoding="utf-8")
new = open(tmpname, "w", encoding="utf-8")
for line in orig:
if "identifiers.org/" + oldns in line:
line = line.replace(oldns, newns)
new.write(line)
orig.close()
new.close()
replace(tmpname, file)
VALID_IDENTIFIERS_NAMESPACES = {'ncbiprotein', 'orphanet', 'unists', '3dmet', 'pubchem.compound', 'meddra', 'eco', 'ido', 'uniprot', 'cco', 'reactome', 'arxiv', 'intact', 'mod', 'narcis', 'ensembl', 'mirbase.mature', 'DOI', 'eo', 'taxonomy', 'unipathway.compound', 'sgd', 'hgnc.symbol', 'ec-code', 'chebi', 'pirsf', 'lipidmaps', 'ecogene', 'kegg.reaction', 'mamo', 'isbn', 'panther.pathway', 'biomodels.teddy', 'kegg.drug', 'brenda', 'kegg.orthology', 'obi', 'pr', 'subtiwiki', 'opb', 'modeldb', 'doi', 'pubmed', 'vario', 'uberon', 'GO', 'kegg.compound', 'insdc', 'doid', 'mirbase', 'cas', 'bto', 'ncit', 'mp', 'biomodels.db', 'neurolex', 't3db', 'hp', 'chembl.compound', 'pdb-ccd', 'tcdb', 'cl', 'pw', 'omit', 'mim', 'unigene', 'ncim', 'envo', 'bao', 'efo', 'pato', 'sbo', 'biomodels.kisao', 'go', 'po', 'kegg.pathway', 'pubchem.substance', 'ncbigene', 'so', 'uniprot.isoform', 'fma', 'kegg.genes', 'icd', 'unipathway.reaction', 'interpro', 'mi'}
INVALID_IDENTIFIERS_NAMESPACES = set()
uri_replacements = {
"bao/274": "bao/0000274",
"bind/130661": "ncbiprotein/NP_011952", #cf Gary Bader's lab
"bind/50058": "ncbiprotein/NP_010550", #cf Gary Bader's lab
"brenda/BTO:0000304": "bto/BTO:0000304",
"bto/00": "bto/BTO:00",
"bto/BTO:000782" : "bto/BTO:0000782",
"bto/BTO:35490": "bto/BTO:0035490", #This doesn't seem to exist.
"bto/BTO::": "bto/BTO:",
"cco/CL:": "cco/CCO:",
"chebi/00": "chebi/CHEBI:00",
"chebi/PATO:": "pato/PATO:",
"doi/doi:%2010.1136/annrheumdis-2014-206295": "doi/doi:10.1136/annrheumdis-2014-206295",
"ensembl/ENSG00000049246.14": "ensembl/ENSG00000049246",
"ensembl/ENSG00000109819.9": "ensembl/ENSG00000109819",
"ensembl/ENSG00000132326.12": "ensembl/ENSG00000132326",
"ensembl/ENSG00000179094.16": "ensembl/ENSG00000179094",
"go/G0": "go/GO",
"go/GI": "go/GO",
"go/GO:000821": "go/GO:0000821",
"go/GO:000828": "go/GO:0000828",
"go/GO:006470": "go/GO:0006470",
"go/SBO:": "sbo/SBO:",
"ido/C101887": "ncit/C101887",
"ido/C171133": "ncit/C171133",
"interpro/P36897": "uniprot/P36897",
"kegg.compound/Cystathionine": "kegg.compound/C02291",
"kegg.genes/K04459": "kegg.orthology/K04459",
"kegg.pathway/2353": "kegg.genes/hsa:2353",
"mamo/MAMO:": "mamo/MAMO_",
"ncit/GO:": "go/GO:",
"ncit/NCIT_C449": "ncit/C449",
"ncit/SBO": "sbo/SBO",
"ncit/c128320": "ncit/C128320",
"ncit/mTORC2": "ncit/C96315",
"ncit/0000511": "ido/0000511",
"ncit/0000514": "ido/0000514",
"ncit/0000597": "ido/0000597",
"ncit/0000621": "ido/0000621",
"ncit/25559": "ncit/C25559",
"neurolex/C25636": "ncit/C25636",
"obi/OBA": "obi/OBI",
"omim/": "mim/",
"omit/OMIT_": "omit/OMIT:",
"pato/00": "pato/PATO:00",
"pato/00": "pato/PATO:00",
"pdb-ccd/26158": "chebi/CHEBI:26158",
"psimi/": "mi/",
"reactome/SBO:0000179": "sbo/SBO:0000179",
"sbo/000": "sbo/SBO:000",
"sbo/GO": "go/GO",
"sbo/degradation": "sbo/SBO:0000179",
"t3db/SBO:": "sbo/SBO:",
"uberon/BTO:0000398": "bto/BTO:0000398",
"unigene/P01730": "uniprot/P01730",
"unipathway.compound/P07333": "uniprot/P07333",
"unipathway.reaction/Q9Z1E3": "uniprot/Q9Z1E3",
"uniprot.isoform/P": "uniprot/P",
"uniprot.isoform/Q": "uniprot/Q",
"uniprot/C21160": "ncit/C21160",
"uniprot/C94967": "ncit/C94967",
"uniprot/GO:0005893": "go/GO:0005893",
"uniprot/PR:000050007": "pr/PR:000050007",
"unists/P00734": "uniprot/P00734",
"org/GO:": "org/go/GO:",
}
def fixURI(uri):
for old in uri_replacements:
if old in uri:
return uri.replace(old, uri_replacements[old])
return None
remaining_bad_uris = []
fixed_uris = {}
def retestAllIdentifiersURIs(file):
bad_uris = []
f = open(file, "r", encoding="utf-8")
for line in f:
if "identifiers.org" in line:
lvec = line.strip().split()
for word in lvec:
if "identifiers.org" in word:
for charstr in word.split('"'):
if "identifiers.org" in charstr:
if "org/GO:" in charstr:
bad_uris.append((file, charstr, "Missing 'go/'"))
# if "omim" in charstr:
# continue
# if "psimi" in charstr:
# continue
try:
validate_identifiers_org_uri(charstr)
except Exception as e:
bad_uris.append((file, charstr, str(e)))
# print(bad_uris[-1])
f.close()
for (file, uri, msg) in bad_uris:
uri2 = fixURI(uri)
# print("new version:", uri2)
if uri2 is not None:
validate_identifiers_org_uri(uri2)
assert(".xml" in file)
tmpname = file.replace(".xml", ".tmp")
orig = open(file, "r", encoding="utf-8")
new = open(tmpname, "w", encoding="utf-8")
for line in orig:
if uri in line:
line = line.replace(uri, uri2)
new.write(line)
orig.close()
new.close()
replace(tmpname, file)
fixed_uris[(file, uri)] = uri2
else:
remaining_bad_uris.append((file, uri))
def checkAndAddIdentifiersNamespace(ns):
url = "https://identifiers.org/" + ns
try:
if urllib.request.urlopen(url).getcode() > 400:
return True
except:
return True
VALID_IDENTIFIERS_NAMESPACES.add(ns)
# print("Current identifiers namespaces:", VALID_IDENTIFIERS_NAMESPACES)
return False
def run(id, sbml_files):
""" Fix invalid SBML
* Fix discovered validation errors in SBML files, including
* unit errors, boundary conditions, and SBO terms.
Args:
id (:obj:`str`): the particular
sbml_files (:obj:`list`): list of SBML files in the directory
"""
if id in upgrade_to_l2v4:
for file in sbml_files:
doc = libsbml.readSBMLFromFile(file)
if doc.getLevel() <= 2 and doc.getVersion() <= 3:
doc.setLevelAndVersion(2, 4, strict=False)
libsbml.writeSBMLToFile(doc, file)
elif id in make_boundary:
(cfile, sid) = make_boundary[id]
for file in sbml_files:
if cfile in file:
doc = libsbml.readSBMLFromFile(file)
species = doc.getModel().getSpecies(sid)
species.setBoundaryCondition(True)
libsbml.writeSBMLToFile(doc, file)
elif id in particular_fixes:
for file in sbml_files:
particular_fixes[id](file)
if id in assignment_rule_to_initial_assignment:
(cfile, sid) = assignment_rule_to_initial_assignment[id]
for file in sbml_files:
if cfile in file:
changeAssignmentRuleToInitialAssignment(file, sid)
#Now fix annotations:
for file in sbml_files:
# print(file)
f = open(file, "r", encoding="utf-8")
bad_pmids = set()
gp_file = open("good_pmids.p", "rb")
good_pmids = pickle.load(gp_file)
pmids_changed = False
gp_file.close()
bad_identifiers_ns = set()
for line in f:
lvec = line.strip().split()
for word in lvec:
if "identifiers.org" in word:
for charstr in word.split('"'):
if "identifiers.org" in charstr:
charvec = charstr.strip("'>/").split("/")
# print(charvec)
for n in range(len(charvec)):
if charvec[n] == "identifiers.org":
if len(charvec) > n+2:
pmid = charvec[n+2]
if charvec[n+1] not in VALID_IDENTIFIERS_NAMESPACES:
# if checkAndAddIdentifiersNamespace(charvec[n+1]):
bad_identifiers_ns.add(charvec[n+1])
assert charvec[n-1] == ""
assert "http" in charvec[n-2]
if charvec[n+1] == "pubmed" and pmid not in good_pmids and pmid not in bad_pmids:
assert(len(pmid)>0)
url = "https://pubmed.ncbi.nlm.nih.gov/" + pmid
try:
if "+" in pmid:
#These make valid URLs, but are invalid URIs: they don't fit the pubmed id pattern.
bad_pmids.add(pmid)
elif urllib.request.urlopen(url).getcode() > 400:
bad_pmids.add(pmid)
else:
good_pmids.add(pmid)
pmids_changed = True
except:
bad_pmids.add(pmid)
f.close()
if pmids_changed:
gp_file = open("good_pmids.p", "wb")
pickle.dump(good_pmids, gp_file)
gp_file.close()
for bad_pmid in bad_pmids:
fixPubmedId(file, bad_pmid, id)
for bad_identifiers_ns in bad_identifiers_ns:
fixIdentifiersNS(file, bad_identifiers_ns, id)
retestAllIdentifiersURIs(file)
# print("Invalid identifiers.org namespaces:")
# print(INVALID_IDENTIFIERS_NAMESPACES)
def writeURIChanges(baduri_filename, changeduri_filename):
f = open(baduri_filename, "w")
for (fname, uri) in remaining_bad_uris:
f.write(fname)
f.write(",")
f.write(uri)
f.write("\n")
f.close()
f = open(changeduri_filename, "w")
for (fname, uri) in fixed_uris:
f.write(fname)
f.write(",")
f.write(uri)
f.write(",")
f.write(fixed_uris[(fname, uri)])
f.write("\n")