-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathfix_sbml_validity.py
442 lines (411 loc) · 17.6 KB
/
fix_sbml_validity.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
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 fixBQModelQualifiers(file):
doc = libsbml.readSBMLFromFile(file)
sstr = libsbml.writeSBMLToString(doc)
sstr = sstr.replace("bqmodel:hasProperty", "bqbiol:hasProperty")
sstr = sstr.replace("bqmodel:isEncodedBy", "bqbiol:isEncodedBy")
out = open(file, "w", encoding="utf-8")
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": fixBQModelQualifiers,
"BIOMD0000000648": fixBQModelQualifiers,
"BIOMD0000000652": fixBQModelQualifiers,
"BIOMD0000000653": fixBQModelQualifiers,
"BIOMD0000000654": fixBQModelQualifiers,
"BIOMD0000000655": fixBQModelQualifiers,
"BIOMD0000000656": fixBQModelQualifiers,
"BIOMD0000000657": fixBQModelQualifiers,
"BIOMD0000000755": fixBQModelQualifiers,
"BIOMD0000000953": fixBQModelQualifiers,
"BIOMD0000000989": fixBQModelQualifiers,
"BIOMD0000000994": fixBQModelQualifiers,
"BIOMD0000000995": fixBQModelQualifiers,
"BIOMD0000000996": fixBQModelQualifiers,
"BIOMD0000000997": fixBQModelQualifiers,
"BIOMD0000000998": fixBQModelQualifiers,
"BIOMD0000000999": fixBQModelQualifiers,
"BIOMD0000001000": fixBQModelQualifiers,
"BIOMD0000001001": fixBQModelQualifiers,
"BIOMD0000001002": fixBQModelQualifiers,
"BIOMD0000001003": fixBQModelQualifiers,
"BIOMD0000001006": fixBQModelQualifiers,
"BIOMD0000001007": fixBQModelQualifiers,
"BIOMD0000001009": fixBQModelQualifiers,
"BIOMD0000001010": fixBQModelQualifiers,
"BIOMD0000001019": fixBQModelQualifiers,
"BIOMD0000001020": fixBQModelQualifiers,
"BIOMD0000001026": fixBQModelQualifiers,
"BIOMD0000001027": fixBQModelQualifiers,
"BIOMD0000001028": fixBQModelQualifiers,
"BIOMD0000001029": fixBQModelQualifiers,
"BIOMD0000001039": fixBQModelQualifiers,
"BIOMD0000001044": fixBQModelQualifiers,
"BIOMD0000001045": fixBQModelQualifiers,
"BIOMD0000001077": fixBQModelQualifiers,
"BIOMD0000001078": fixBQModelQualifiers,
"BIOMD0000001079": fixBQModelQualifiers,
"BIOMD0000001080": fixBQModelQualifiers,
}
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")