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neliebineliebi
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Merge pull request #46 from emdb-empiar/RfamToXml
Rfam to xml
2 parents 1de79bb + 86a26db commit 58e4243

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9 files changed

+190
-78
lines changed

9 files changed

+190
-78
lines changed

‎AddedAnnotations.py

Lines changed: 22 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,7 @@
77
from resources.StructureMapping import StructureMapping
88
from resources.PublicationMapping import PublicationMapping, generate_pubmed_dictionary
99
from resources.ProteinTermsMapping import ProteinTermsMapping
10+
from resources.RfamMapping import RfamMapping, generate_rfam_dictionary
1011
from XMLParser import XMLParser
1112
from glob import glob
1213
import logging
@@ -109,6 +110,12 @@ def run(filename):
109110
proteins_map = PT_mapping.execute(uniprot_with_models)
110111
PT_mapping.export_tsv(go_log, interpro_log, pfam_log, cath_log, scop_log, scop2_log, scop2B_log, pdbekb_log)
111112
packed_models["PROTEIN-TERMS"] = proteins_map
113+
if rfam:
114+
rfam_logger = start_logger_if_necessary("rfam_logger", rfam_log_file)
115+
rfam_mapping = RfamMapping(xml.rfams)
116+
rfam_map = rfam_mapping.execute(rfam_dictionary)
117+
rfam_mapping.export_tsv(rfam_logger)
118+
packed_models["RFAM"] = rfam_map
112119

113120
"""
114121
List of things to do:
@@ -127,7 +134,7 @@ def run(filename):
127134
-f '[{"/path/to/EMDB/header/files/folder"}]'
128135
-p '[{"/path/to/PDBe/files/folder"}]'
129136
--uniprot --CPX --component --model --weight --pmc --GO --interpro --pfam --pbdekb
130-
--cath --scop --scop2 --scop2B
137+
--cath --scop --scop2 --scop2B --rfam
131138
"""
132139

133140
parser = argparse.ArgumentParser(prog=prog, usage=usage, add_help=False,
@@ -153,6 +160,7 @@ def run(filename):
153160
parser.add_argument("--scop2", type=bool, nargs='?', const=True, default=False, help="Mapping SCOP2 domains to EMDB entries")
154161
parser.add_argument("--scop2B", type=bool, nargs='?', const=True, default=False, help="Mapping SCOP2B domains to EMDB entries")
155162
parser.add_argument("--pdbekb", type=bool, nargs='?', const=True, default=False, help="Mapping PDBeKB links to EMDB entries")
163+
parser.add_argument("--rfam", type=bool, nargs='?', const=True, default=False, help="Mapping Rfam to EMDB entries")
156164
args = parser.parse_args()
157165

158166
packed_models = {}
@@ -173,6 +181,7 @@ def run(filename):
173181
scop2 = args.scop2
174182
scop2B = args.scop2B
175183
pdbekb = args.pdbekb
184+
rfam = args.rfam
176185
input_json = args.json
177186
uniprot_dictionary = {}
178187

@@ -211,6 +220,8 @@ def run(filename):
211220
if pdbekb:
212221
uniprot = True
213222
db_list.append("pdbekb")
223+
if rfam:
224+
db_list.append("rfam")
214225
if args.all:
215226
uniprot = True
216227
cpx = True
@@ -227,8 +238,9 @@ def run(filename):
227238
scop2 = True
228239
scop2B = True
229240
pdbekb = True
241+
rfam = True
230242
db_list.extend(["pdbe", "uniprot", "chembl", "chebi", "drugbank", "pubmed", "pubmedcentral", "issn",
231-
"orcid", "cpx", "go", "interpro", "pfam", "cath", "scop", "scop2", "scop2B", "pdbekb"])
243+
"orcid", "cpx", "go", "interpro", "pfam", "cath", "scop", "scop2", "scop2B", "pdbekb", "rfam"])
232244

233245
#Get config variables:
234246
config = configparser.ConfigParser()
@@ -315,12 +327,20 @@ def run(filename):
315327
pdbekb_log_file = os.path.join(args.workDir, 'emdb_pdbekb.log')
316328
pdbekb_log = setup_logger('pdbekb_logger', pdbekb_log_file)
317329
pdbekb_log.info("EMDB_ID\tEMDB_SAMPLE_ID\tPDBeKB_ID\tPROVENANCE")
330+
if rfam:
331+
rfam_log_file = os.path.join(args.workDir, 'emdb_rfam.log')
332+
rfam_log = setup_logger('rfam_logger', rfam_log_file)
333+
rfam_log.info("EMDB_ID\tEMDB_SAMPLE_ID\tEMDB_SAMPLE_NAME\tNUMBER_OF_COPIES\tRFAM_ACCESSION\tRFAM_ID\tPROVENANCE")
318334

319335
if uniprot:
320336
uniprot_dictionary, uniprot_with_models = generate_unp_dictionary(uniprot_tab)
321337
if component:
322338
chembl_map, chebi_map, drugbank_map = parseCCD(components_cif)
339+
if rfam:
340+
rfam_dictionary = generate_rfam_dictionary(args.workDir)
341+
323342
pubmed_dict = generate_pubmed_dictionary(args.workDir) if pmc else {}
343+
324344
if input_json:
325345
files = read_json(input_json, args.headerDir)
326346
else:

‎EMICSS/DBVersion.py

Lines changed: 20 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,7 @@ def __init__(self):
2222
self.alphafold = self.__find_afdb_version() # TODO: Version is currently fixed to all entries
2323
self.scop = "1.7.5" # TODO: Create methods to obtain version
2424
self.scop2 = "2.0" # TODO: Create methods to obtain version
25+
self.rfam = self.__find_rfam_version()
2526
self.cpx = None # TODO: Add version
2627
self.scop2b = None # TODO: Add version
2728
self.chebi = None # TODO: Add version
@@ -49,9 +50,27 @@ def get_all_versions(self):
4950
'SCOP': self.scop,
5051
'SCOP2': self.scop2,
5152
'SCOP2B':self.scop2b,
52-
'AlphaFold DB': self.alphafold
53+
'AlphaFold DB': self.alphafold,
54+
'Rfam': self.rfam
5355
}
5456

57+
def __find_rfam_version(self):
58+
url = "https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/README"
59+
try:
60+
response = requests.get(url, timeout=10)
61+
except (requests.exceptions.ConnectTimeout, requests.exceptions.ReadTimeout) as e:
62+
return None
63+
else:
64+
if response.status_code == 200 and response.content:
65+
lines = response.text.split('\n')
66+
# Find the first line containing the word "Release"
67+
for line in lines:
68+
if "Release" in line:
69+
match = re.search(r'Release (\d+\.\d+)', line)
70+
if match:
71+
return match.group(1)
72+
return None
73+
5574
def __find_afdb_version(self):
5675
url = "https://alphafold.ebi.ac.uk/api/prediction/Q5VSL9"
5776
try:

‎EMICSS/EMICSS.py

Lines changed: 18 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
# -*- coding: utf-8 -*-
33

44
#
5-
# Generated Tue Jun 14 21:14:10 2022 by generateDS.py version 2.38.6.
5+
# Generated Thu Aug 1 15:07:22 2024 by generateDS.py version 2.38.6.
66
# Python 3.7.6 (default, Dec 30 2019, 19:38:28) [Clang 11.0.0 (clang-1100.0.33.16)]
77
#
88
# Command line options:
@@ -973,6 +973,7 @@ class provenance_type(str, Enum):
973973
database"""
974974
EMDB='EMDB'
975975
UNI_PROT='UniProt'
976+
UNI_PROT_KB='UniProtKB'
976977
PD_BE='PDBe'
977978
PD_BEKB='PDBe-KB'
978979
ALPHA_FOLDDB='AlphaFold DB'
@@ -993,20 +994,23 @@ class provenance_type(str, Enum):
993994
CATH='CATH'
994995
SCOP='SCOP'
995996
SCOP_2='SCOP2'
997+
SCOP_2_B='SCOP2B'
998+
RFAM='Rfam'
996999

9971000

9981001
class sample_kind(str, Enum):
9991002
COMPLEX='complex'
10001003
PROTEIN='protein'
10011004
LIGAND='ligand'
1005+
RNA='rna'
10021006

10031007

10041008
class emicss(GeneratedsSuper):
10051009
"""EMDB entry idEMICSS schema version"""
10061010
__hash__ = GeneratedsSuper.__hash__
10071011
subclass = None
10081012
superclass = None
1009-
def __init__(self, emdb_id=None, version='0.9.3', schema_location=None, dbs=None, entry_ref_dbs=None, primary_citation=None, weights=None, sample=None, gds_collector_=None, **kwargs_):
1013+
def __init__(self, emdb_id=None, version='0.9.5', schema_location=None, dbs=None, entry_ref_dbs=None, primary_citation=None, weights=None, sample=None, gds_collector_=None, **kwargs_):
10101014
self.gds_collector_ = gds_collector_
10111015
self.gds_elementtree_node_ = None
10121016
self.original_tagname_ = None
@@ -1124,7 +1128,7 @@ def exportAttributes(self, outfile, level, already_processed, namespaceprefix_='
11241128
if self.emdb_id is not None and 'emdb_id' not in already_processed:
11251129
already_processed.add('emdb_id')
11261130
outfile.write(' emdb_id=%s' % (self.gds_encode(self.gds_format_string(quote_attrib(self.emdb_id), input_name='emdb_id')), ))
1127-
if self.version != "0.9.3" and 'version' not in already_processed:
1131+
if self.version != "0.9.5" and 'version' not in already_processed:
11281132
already_processed.add('version')
11291133
outfile.write(' version=%s' % (self.gds_encode(self.gds_format_string(quote_attrib(self.version), input_name='version')), ))
11301134
if self.schema_location is not None and 'schema_location' not in already_processed:
@@ -1295,7 +1299,7 @@ def validate_provenance_type(self, value):
12951299
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
12961300
return False
12971301
value = value
1298-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
1302+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
12991303
if value not in enumerations:
13001304
lineno = self.gds_get_node_lineno_()
13011305
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -1580,7 +1584,7 @@ def validate_provenance_type(self, value):
15801584
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
15811585
return False
15821586
value = value
1583-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
1587+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
15841588
if value not in enumerations:
15851589
lineno = self.gds_get_node_lineno_()
15861590
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -1807,7 +1811,7 @@ def validate_provenance_type(self, value):
18071811
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
18081812
return False
18091813
value = value
1810-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
1814+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
18111815
if value not in enumerations:
18121816
lineno = self.gds_get_node_lineno_()
18131817
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -1952,7 +1956,7 @@ def validate_provenance_type(self, value):
19521956
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
19531957
return False
19541958
value = value
1955-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
1959+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
19561960
if value not in enumerations:
19571961
lineno = self.gds_get_node_lineno_()
19581962
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -2095,7 +2099,7 @@ def validate_provenance_type(self, value):
20952099
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
20962100
return False
20972101
value = value
2098-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
2102+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
20992103
if value not in enumerations:
21002104
lineno = self.gds_get_node_lineno_()
21012105
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -2336,7 +2340,7 @@ def validate_provenance_type(self, value):
23362340
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
23372341
return False
23382342
value = value
2339-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
2343+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
23402344
if value not in enumerations:
23412345
lineno = self.gds_get_node_lineno_()
23422346
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -2590,7 +2594,7 @@ def validate_provenance_type(self, value):
25902594
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
25912595
return False
25922596
value = value
2593-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
2597+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
25942598
if value not in enumerations:
25952599
lineno = self.gds_get_node_lineno_()
25962600
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -3100,7 +3104,7 @@ def validate_sample_kind(self, value):
31003104
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
31013105
return False
31023106
value = value
3103-
enumerations = ['complex', 'protein', 'ligand']
3107+
enumerations = ['complex', 'protein', 'ligand', 'rna']
31043108
if value not in enumerations:
31053109
lineno = self.gds_get_node_lineno_()
31063110
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on sample_kind' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -3113,7 +3117,7 @@ def validate_provenance_type(self, value):
31133117
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
31143118
return False
31153119
value = value
3116-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
3120+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
31173121
if value not in enumerations:
31183122
lineno = self.gds_get_node_lineno_()
31193123
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -3510,7 +3514,7 @@ def validate_sample_kind(self, value):
35103514
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
35113515
return False
35123516
value = value
3513-
enumerations = ['complex', 'protein', 'ligand']
3517+
enumerations = ['complex', 'protein', 'ligand', 'rna']
35143518
if value not in enumerations:
35153519
lineno = self.gds_get_node_lineno_()
35163520
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on sample_kind' % {"value" : encode_str_2_3(value), "lineno": lineno} )
@@ -3523,7 +3527,7 @@ def validate_provenance_type(self, value):
35233527
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s is not of the correct base simple type (str)' % {"value": value, "lineno": lineno, })
35243528
return False
35253529
value = value
3526-
enumerations = ['EMDB', 'UniProt', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2']
3530+
enumerations = ['EMDB', 'UniProt', 'UniProtKB', 'PDBe', 'PDBe-KB', 'AlphaFold DB', 'EMPIAR', 'EuropePMC', 'Complex Portal', 'ChEMBL', 'ChEBI', 'DrugBank', 'PDBe-CCD', 'PubMed', 'PubMed Central', 'ISSN', 'DOI', 'GO', 'InterPro', 'Pfam', 'CATH', 'SCOP', 'SCOP2', 'SCOP2B', 'Rfam']
35273531
if value not in enumerations:
35283532
lineno = self.gds_get_node_lineno_()
35293533
self.gds_collector_.add_message('Value "%(value)s"%(lineno)s does not match xsd enumeration restriction on provenance_type' % {"value" : encode_str_2_3(value), "lineno": lineno} )

‎EMICSS/EMICSSsub.py

Lines changed: 2 additions & 2 deletions
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#!/usr/bin/env python
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#
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# Generated Tue Jun 14 21:14:10 2022 by generateDS.py version 2.38.6.
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# Generated Thu Aug 1 15:07:24 2024 by generateDS.py version 2.38.6.
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# Python 3.7.6 (default, Dec 30 2019, 19:38:28) [Clang 11.0.0 (clang-1100.0.33.16)]
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#
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# Command line options:
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class emicssSub(supermod.emicss):
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def __init__(self, emdb_id=None, version='0.9.3', schema_location=None, dbs=None, entry_ref_dbs=None, primary_citation=None, weights=None, sample=None, **kwargs_):
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def __init__(self, emdb_id=None, version='0.9.5', schema_location=None, dbs=None, entry_ref_dbs=None, primary_citation=None, weights=None, sample=None, **kwargs_):
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super(emicssSub, self).__init__(emdb_id, version, schema_location, dbs, entry_ref_dbs, primary_citation, weights, sample, **kwargs_)
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supermod.emicss.subclass = emicssSub
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# end class emicssSub

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