diff --git a/mutalyzer/models.py b/mutalyzer/models.py
index 387314ca917869f467acf4437a33af9e34b9614b..24a340fed34dd9a565e3d63c22a23d418607ac1e 100644
--- a/mutalyzer/models.py
+++ b/mutalyzer/models.py
@@ -1,26 +1,14 @@
"""
Collection of serilizable objects used by the SOAP web service. They extend
-from the spyne ClassModel.
+from the Spyne model classes.
-Default attributes for the spyne ClassModel:
-- nillable = True
-- min_occurs = 0
-- max_occurs = 1
-
-Additional attributes values for the spyne String model:
-- min_len = 0
-- max_len = 'unbounded'
-- pattern = None
-
-@todo: Use Mandatory.* models in the ClassModel extensions?
-@todo: See if it improves client code if we use Array(_, nillable=False).
@todo: Move all these models to the mutalyzer.services package and refactor
all uses of them in other places. The SOAP_NAMESPACE variable can then also
be moved there.
"""
-from spyne.model.primitive import String, Integer, Boolean, DateTime, Unicode
+from spyne.model.primitive import Integer, Boolean, DateTime, Unicode
from spyne.model.binary import ByteArray
from spyne.model.complex import ComplexModel, Array
@@ -30,9 +18,8 @@ from mutalyzer import SOAP_NAMESPACE
class Mandatory(object):
"""
This is spyne.model.primitive.Mandatory, but without min_length=1 for
- the String model.
+ the Unicode model.
"""
- String = String(type_name='mandatory_string', min_occurs=1, nillable=False)
Unicode = Unicode(type_name='mandatory_unicode', min_occurs=1, nillable=False)
Integer = Integer(type_name='mandatory_integer', min_occurs=1, nillable=False)
Boolean = Boolean(type_name='mandatory_boolean', min_occurs=1, nillable=False)
@@ -47,8 +34,8 @@ class SoapMessage(ComplexModel):
"""
__namespace__ = SOAP_NAMESPACE
- errorcode = Mandatory.String
- message = Mandatory.String
+ errorcode = Mandatory.Unicode
+ message = Mandatory.Unicode
#SoapMessage
@@ -64,7 +51,7 @@ class Mapping(ComplexModel):
endoffset = Integer
start_g = Integer
end_g = Integer
- mutationType = String
+ mutationType = Unicode
errorcode = Integer
messages = Array(SoapMessage)
#Mapping
@@ -88,8 +75,8 @@ class RawVariant(ComplexModel):
"""
__namespace__ = SOAP_NAMESPACE
- description = Mandatory.String
- visualisation = Mandatory.String
+ description = Mandatory.Unicode
+ visualisation = Mandatory.Unicode
#RawVariant
@@ -104,14 +91,14 @@ class RawVar(ComplexModel):
start_offset = Mandatory.Integer
end = Mandatory.Integer
end_offset = Mandatory.Integer
- type = Mandatory.String
- deleted = Mandatory.String
- inserted = Mandatory.String
+ type = Mandatory.Unicode
+ deleted = Mandatory.Unicode
+ inserted = Mandatory.Unicode
shift = Mandatory.Integer
- startAA = Mandatory.String
- endAA = Mandatory.String
+ startAA = Mandatory.Unicode
+ endAA = Mandatory.Unicode
term = Mandatory.Integer
- hgvs = Mandatory.String
+ hgvs = Mandatory.Unicode
hgvsLength = Mandatory.Integer
#RawVar
@@ -122,7 +109,7 @@ class Allele(ComplexModel):
"""
__namespace__ = SOAP_NAMESPACE
- description = Mandatory.String
+ description = Mandatory.Unicode
allele = Array(RawVar)
#Allele
@@ -133,10 +120,10 @@ class ExonInfo(ComplexModel):
"""
__namespace__ = SOAP_NAMESPACE
- cStart = Mandatory.String
+ cStart = Mandatory.Unicode
gStart = Mandatory.Integer
chromStart = Integer
- cStop = Mandatory.String
+ cStop = Mandatory.Unicode
gStop = Mandatory.Integer
chromStop = Integer
#ExonInfo
@@ -148,34 +135,34 @@ class MutalyzerOutput(ComplexModel):
"""
__namespace__ = SOAP_NAMESPACE
- referenceId = Mandatory.String
- sourceId = Mandatory.String
- sourceAccession = String
- sourceVersion = String
- sourceGi = String
- molecule = Mandatory.String
+ referenceId = Mandatory.Unicode
+ sourceId = Mandatory.Unicode
+ sourceAccession = Unicode
+ sourceVersion = Unicode
+ sourceGi = Unicode
+ molecule = Mandatory.Unicode
- original = String
- mutated = String
+ original = Unicode
+ mutated = Unicode
- origMRNA = String
- mutatedMRNA= String
+ origMRNA = Unicode
+ mutatedMRNA= Unicode
- origCDS = String
- newCDS= String
+ origCDS = Unicode
+ newCDS= Unicode
- origProtein = String
- newProtein = String
- altProtein = String
+ origProtein = Unicode
+ newProtein = Unicode
+ altProtein = Unicode
errors = Integer
warnings = Integer
- summary = String
+ summary = Unicode
- chromDescription = String
- genomicDescription = String
- transcriptDescriptions = Array(String)
- proteinDescriptions = Array(String)
+ chromDescription = Unicode
+ genomicDescription = Unicode
+ transcriptDescriptions = Array(Unicode)
+ proteinDescriptions = Array(Unicode)
exons = Array(ExonInfo)
@@ -191,8 +178,8 @@ class TranscriptNameInfo(ComplexModel):
"""
__namespace__ = SOAP_NAMESPACE
- transcriptName = Mandatory.String
- productName = Mandatory.String
+ transcriptName = Mandatory.Unicode
+ productName = Mandatory.Unicode
#TranscriptNameInfo
@@ -202,9 +189,9 @@ class ProteinTranscript(ComplexModel):
"""
__namespace__ = SOAP_NAMESPACE
- name = Mandatory.String
- id = Mandatory.String
- product = Mandatory.String
+ name = Mandatory.Unicode
+ id = Mandatory.Unicode
+ product = Mandatory.Unicode
#ProteinTranscript
@@ -220,27 +207,27 @@ class TranscriptInfo(ComplexModel):
"""
__namespace__ = SOAP_NAMESPACE
- name = Mandatory.String
- id = Mandatory.String
- product = Mandatory.String
+ name = Mandatory.Unicode
+ id = Mandatory.Unicode
+ product = Mandatory.Unicode
- cTransStart = Mandatory.String
+ cTransStart = Mandatory.Unicode
gTransStart = Mandatory.Integer
chromTransStart = Integer
- cTransEnd = Mandatory.String
+ cTransEnd = Mandatory.Unicode
gTransEnd = Mandatory.Integer
chromTransEnd = Integer
sortableTransEnd = Mandatory.Integer
- cCDSStart = Mandatory.String
+ cCDSStart = Mandatory.Unicode
gCDSStart = Mandatory.Integer
chromCDSStart = Integer
- cCDSStop = Mandatory.String
+ cCDSStop = Mandatory.Unicode
gCDSStop = Mandatory.Integer
chromCDSStop = Integer
- locusTag = Mandatory.String
- linkMethod = Mandatory.String
+ locusTag = Mandatory.Unicode
+ linkMethod = Mandatory.Unicode
exons = Array(ExonInfo)
@@ -254,10 +241,10 @@ class TranscriptMappingInfo(ComplexModel):
"""
__namespace__ = SOAP_NAMESPACE
- name = Mandatory.String
+ name = Mandatory.Unicode
version = Mandatory.Integer
- gene = Mandatory.String
- orientation = Mandatory.String
+ gene = Mandatory.Unicode
+ orientation = Mandatory.Unicode
start = Mandatory.Integer
stop = Mandatory.Integer
@@ -284,15 +271,15 @@ class InfoOutput(ComplexModel):
"""
__namespace__ = SOAP_NAMESPACE
- version = String
- versionParts = Array(String)
- releaseDate = String
- nomenclatureVersion = String
- nomenclatureVersionParts = Array(String)
- serverName = String
- contactEmail = String
- announcement = String
- announcementUrl = String
+ version = Unicode
+ versionParts = Array(Unicode)
+ releaseDate = Unicode
+ nomenclatureVersion = Unicode
+ nomenclatureVersionParts = Array(Unicode)
+ serverName = Unicode
+ contactEmail = Unicode
+ announcement = Unicode
+ announcementUrl = Unicode
#InfoOutput
@@ -302,14 +289,14 @@ class CacheEntry(ComplexModel):
"""
__namespace__ = SOAP_NAMESPACE
- name = Mandatory.String
- gi = String
- hash = Mandatory.String
- chromosomeName = String
+ name = Mandatory.Unicode
+ gi = Unicode
+ hash = Mandatory.Unicode
+ chromosomeName = Unicode
chromosomeStart = Integer
chromosomeStop = Integer
chromosomeOrientation = Integer
- url = String
+ url = Unicode
created = Mandatory.DateTime
- cached = String
+ cached = Unicode
#CacheEntry
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index 9ad68b949688a095f11db601964e45b45f7f415c..ba29c0083360ed1e85c02553c587fbfdeecde370 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -11,7 +11,7 @@ Mutalyzer RPC services.
from spyne.decorator import srpc
from spyne.service import ServiceBase
-from spyne.model.primitive import String, Integer, Boolean, DateTime, Unicode
+from spyne.model.primitive import Integer, Boolean, DateTime, Unicode
from spyne.model.complex import Array
from spyne.model.fault import Fault
import os
@@ -51,7 +51,7 @@ class MutalyzerService(ServiceBase):
super(MutalyzerService, self).__init__(environ)
#__init__
- @srpc(Mandatory.ByteArray, Unicode, Unicode, _returns=String)
+ @srpc(Mandatory.ByteArray, Unicode, Unicode, _returns=Unicode)
def submitBatchJob(data, process='NameChecker', argument=''):
"""
Submit a batch job.
@@ -156,7 +156,7 @@ class MutalyzerService(ServiceBase):
return handle
@srpc(Mandatory.Unicode, Mandatory.Unicode, Mandatory.Integer, Boolean,
- _returns=Array(Mandatory.String))
+ _returns=Array(Mandatory.Unicode))
def getTranscripts(build, chrom, pos, versions=False) :
"""
Get all the transcripts that overlap with a chromosomal position.
@@ -215,7 +215,7 @@ class MutalyzerService(ServiceBase):
return [m.accession for m in mappings]
#getTranscripts
- @srpc(Mandatory.Unicode, Mandatory.Unicode, _returns=Array(Mandatory.String))
+ @srpc(Mandatory.Unicode, Mandatory.Unicode, _returns=Array(Mandatory.Unicode))
def getTranscriptsByGeneName(build, name):
"""
Todo: documentation.
@@ -244,7 +244,7 @@ class MutalyzerService(ServiceBase):
#getTranscriptsByGene
@srpc(Mandatory.Unicode, Mandatory.Unicode, Mandatory.Integer,
- Mandatory.Integer, Mandatory.Integer, _returns=Array(Mandatory.String))
+ Mandatory.Integer, Mandatory.Integer, _returns=Array(Mandatory.Unicode))
def getTranscriptsRange(build, chrom, pos1, pos2, method) :
"""
Get all the transcripts that overlap with a range on a chromosome.
@@ -387,7 +387,7 @@ class MutalyzerService(ServiceBase):
return transcripts
#getTranscriptsMapping
- @srpc(Mandatory.Unicode, Mandatory.Unicode, _returns=Mandatory.String)
+ @srpc(Mandatory.Unicode, Mandatory.Unicode, _returns=Mandatory.Unicode)
def getGeneName(build, accno) :
"""
Find the gene name associated with a transcript.
@@ -536,7 +536,7 @@ class MutalyzerService(ServiceBase):
return T
#transcriptInfo
- @srpc(Mandatory.Unicode, Mandatory.Unicode, _returns=Mandatory.String)
+ @srpc(Mandatory.Unicode, Mandatory.Unicode, _returns=Mandatory.Unicode)
def chromAccession(build, name) :
"""
Get the accession number of a chromosome, given a name.
@@ -574,7 +574,7 @@ class MutalyzerService(ServiceBase):
return chromosome.accession
#chromAccession
- @srpc(Mandatory.Unicode, Mandatory.Unicode, _returns=Mandatory.String)
+ @srpc(Mandatory.Unicode, Mandatory.Unicode, _returns=Mandatory.Unicode)
def chromosomeName(build, accNo) :
"""
Get the name of a chromosome, given a chromosome accession number.
@@ -612,7 +612,7 @@ class MutalyzerService(ServiceBase):
return chromosome.name
#chromosomeName
- @srpc(Mandatory.Unicode, Mandatory.Unicode, _returns=Mandatory.String)
+ @srpc(Mandatory.Unicode, Mandatory.Unicode, _returns=Mandatory.Unicode)
def getchromName(build, acc) :
"""
Get the chromosome name, given a transcript identifier (NM number).
@@ -650,7 +650,7 @@ class MutalyzerService(ServiceBase):
#chromosomeName
@srpc(Mandatory.Unicode, Mandatory.Unicode, Unicode,
- _returns=Array(Mandatory.String))
+ _returns=Array(Mandatory.Unicode))
def numberConversion(build, variant, gene=None):
"""
Converts I{c.} to I{g.} notation or vice versa
@@ -1040,7 +1040,7 @@ class MutalyzerService(ServiceBase):
return transcripts
#getTranscriptsAndInfo
- @srpc(Mandatory.ByteArray, _returns=Mandatory.String)
+ @srpc(Mandatory.ByteArray, _returns=Mandatory.Unicode)
def uploadGenBankLocalFile(data):
"""
Upload a genbank file.
@@ -1081,7 +1081,7 @@ class MutalyzerService(ServiceBase):
return ud
#upLoadGenBankLocalFile
- @srpc(Mandatory.Unicode, _returns=Mandatory.String)
+ @srpc(Mandatory.Unicode, _returns=Mandatory.Unicode)
def uploadGenBankRemoteFile(url) :
"""
Not implemented yet.
@@ -1090,7 +1090,7 @@ class MutalyzerService(ServiceBase):
#upLoadGenBankRemoteFile
@srpc(Mandatory.Unicode, Mandatory.Unicode, Mandatory.Integer,
- Mandatory.Integer, _returns=Mandatory.String)
+ Mandatory.Integer, _returns=Mandatory.Unicode)
def sliceChromosomeByGene(geneSymbol, organism, upStream,
downStream) :
"""
@@ -1119,7 +1119,7 @@ class MutalyzerService(ServiceBase):
#sliceChromosomeByGene
@srpc(Mandatory.Unicode, Mandatory.Integer, Mandatory.Integer,
- Mandatory.Integer, _returns=Mandatory.String)
+ Mandatory.Integer, _returns=Mandatory.Unicode)
def sliceChromosome(chromAccNo, start, end, orientation) :
"""
Todo: documentation, error handling, argument checking, tests.
@@ -1190,7 +1190,7 @@ class MutalyzerService(ServiceBase):
return result
#info
- @srpc(_returns=Mandatory.String)
+ @srpc(_returns=Mandatory.Unicode)
def ping():
"""
Simple function to test the interface.
@@ -1253,7 +1253,7 @@ class MutalyzerService(ServiceBase):
return map(cache_entry_to_soap, cache)
#getCache
- @srpc(Mandatory.Unicode, _returns=Array(Mandatory.String))
+ @srpc(Mandatory.Unicode, _returns=Array(Mandatory.Unicode))
def getdbSNPDescriptions(rs_id):
"""
Lookup HGVS descriptions for a dbSNP rs identifier.