def uploaddicom(server, token, dicom_directory):
"""
Create zip archive of dicom files, upload to server. This will check if subject is in server, upload it if not.
Returns parsed xml for dicom object on server. If called on dicom already in server, will return same object as checkdicomexistence.
"""
common.lout('Asked to upload dicom with path '+dicom_directory+' \n')
dicom_image=getfirstdicomfile(dicom_directory)
subject = DicomSubject(dicom_image)
dicom_parsed_xml = checkdicomexistence(server, token, dicom_image.SeriesInstanceUID)
subject_parsed_xml =uploadsubject(server, token, subject)
subject_id = common.get_id_from_parsed_xml(subject_parsed_xml)
if dicom_parsed_xml == None:
common.lout('DICOM with path '+dicom_directory+' not in database, uploading\n')
try :
tmpdname=tempfile.mkdtemp()
dicom_directory_base=os.path.basename(os.path.normpath(dicom_directory))
tmpfname = os.sep.join([tmpdname,dicom_directory_base+'.zip'])
zipfile, dicom_image = zipdicom(dicom_directory,tmpfname)
# so, now, actually do checkin
dicom_doc=dicomdocument(dicom_directory,subject_id,zipfile.filename)
client=poauth.OAuthClient(token)
response=client.post(server+'/object.xml',
data={'object':dicom_doc.toxml()},
files={'file': open(zipfile.filename,'rb')} )
dicom_parsed_xml=common.parse_xml_from_server(response.text)
except Exception as e :
print(e.__repr__())
finally :
shutil.rmtree(tmpdname,ignore_errors=True)
else:
common.lout('DICOM with path '+dicom_directory+' in database, not uploading\n')
return dicom_parsed_xml
def uploadgps(server,token,gps_path,subject_id) :
common.lout('Asked to upload gps with path '+gps_path+' and parent '+subject_id +'\n')
if not os.path.isfile(gps_path) :
raise Exception('Invalid GPS path '+gps_path+ ' given')
gpshash=common.rawfilehash(gps_path)
gps_parsed_xml=checkgpsexistence(server,token,gpshash)
if not gps_parsed_xml is None :
common.lout('gps with path '+gps_path+' in database, not uploading\n')
return gps_parsed_xml
else :
common.lout('gps with path '+gps_path+' not in database, uploading\n')
try :
tmpdname=tempfile.mkdtemp()
zipfilename = os.sep.join([tmpdname,'gps.zip'])
zfile = zipfile.ZipFile(zipfilename, 'w', zipfile.ZIP_DEFLATED)
zfile.write(filename=gps_path,arcname=os.path.basename(gps_path))
zfile.close()
gpsdoc=gpsdocument(gps_path,subject_id,zfile.filename)
client=poauth.OAuthClient(token)
response=client.post(server+'/object.xml',
data={'object':gpsdoc.toxml()},
files={'file': open(zfile.filename,'rb')} )
return common.parse_xml_from_server(response.text)
finally:
shutil.rmtree(tmpdname,ignore_errors=True)
def uploadnii(server,token,nii_path,subject_id) :
# subject_id may be none : in this case, succeed only if nii already in database
common.lout('Asked to upload nii with path '+nii_path+' and parent '+str(subject_id) +'\n')
if not common.determine_file_type(nii_path)=='nii' :
raise Exception('Invalid nii path '+nii_path+' given')
niihashvalue=niihash(nii_path)
nii_parsed_xml=checkniiexistence(server,token,niihashvalue)
if not nii_parsed_xml is None :
common.lout('nii with path '+nii_path+' in database, not uploading')
return nii_parsed_xml
else :
common.lout('nii with path '+nii_path+' not in database, uploading')
try :
tmpdname=tempfile.mkdtemp()
zipfilename=os.sep.join([tmpdname,'nii.zip'])
zfile=zipnii(nii_path,zipfilename)
niidoc=niidocument(nii_path,subject_id,zfile.filename)
client=poauth.OAuthClient(token)
response=client.post(server+'/object.xml',
data={'object':niidoc.toxml()},
files={'file': open(zfile.filename,'rb')} )
return common.parse_xml_from_server(response.text)
finally:
shutil.rmtree(tmpdname,ignore_errors=True)
def uploadsubject(server, token, subject):
common.lout('Asked to upload subject with name '+subject.name+'\n')
subject_parsed_xml=checksubjectexistence(server,token,subject)
if subject_parsed_xml is None :
common.lout('Subject with name '+subject.name+' not in database, uploading\n')
client = poauth.OAuthClient(token)
memoryfile = NamedStringIO(subject.filename, subject.toxml())
response = client.post(''.join([server, '/object.xml']),
data={"object": subject.document.toxml()},
files={"file": memoryfile})
memoryfile.close()
subject_parsed_xml=common.parse_xml_from_server(response.text)
else :
common.lout('Subject with name '+subject.name+' in database, not uploading\n')
return subject_parsed_xml
def uploadlfm(server,token,lfm_hdr_path):
lfmhashval=lfmhash(lfm_hdr_path)
common.lout('Asked to upload lfm with lfmhash '+lfmhashval+'\n')
lfm_parsed_xml=checklfmexistence(server,token,lfm_hdr_path,lfmhashval)
if lfm_parsed_xml is None :
common.lout('lfm with hash ' + lfmhashval+' not in database, uploading\n')
braink_id=find_parent_braink(server,token,lfm_hdr_path)
if braink_id is None :
raise ParentNotFoundException('Parent BrainK run not found on server - you should check it in\n')
try :
tmpdname=tempfile.mkdtemp()
tmpfname = os.sep.join([tmpdname,'lfm.zip'])
zipfile=ziplfm(lfm_hdr_path,tmpfname)
lfmdoc=lfmdocument(lfm_hdr_path,braink_id,zipfile.filename)
lfm_parsed_xml=_uploadzipfile(server,token,lfmdoc,zipfile)
## except Exception as e :
## print e
finally :
shutil.rmtree(tmpdname,ignore_errors=True)
else:
common.lout('lfm with hash ' + lfmhashval+' in database, not uploading\n')
return lfm_parsed_xml
def uploadbraink(server,token,bkstub,recursive_checkin=False):
""" compute hash, check against server, if not found, create zipfile and upload"""
if not isvalidbkstub(bkstub) :
raise Exception('invalid brainkstub')
bkhash=brainkhash(bkstub)
common.lout('Asked to upload braink with stub '+bkstub+' bkhash '+bkhash+'\n')
# how to handle recursive_checkin if MRI,CT,GPS objects do not define subject?
# Grab subject id from MRI, if possible
#
# As of now, code will give not succesfully infer subject if MRI
# is not in the database and if it is not a DICOM file.
#
# It is possible that CT could be dicom, and subject could be
# inferred from CT, but I won't bother to handle this case. To be
# able to deal with this case, the user would need to check in the
# non-DICOM MRI with some tool that associates a subject id.
braink_server_xml=checkbrainkexistence(server,token,bkhash)
if not braink_server_xml is None :
common.lout('braink with hash '+bkhash+' found on server, not uploading\n')
return braink_server_xml
else :
# need to upload
common.lout('braink with hash '+bkhash+' not found on server, uploading\n')
bkparam=parsebkstub(bkstub)
parentdataids={}
subject_id = None
if 'MRI_file' in bkparam :
mri_path = bkparam['MRI_file'][1]
mri_parsed_xml = common.get_database_xml_from_path(server,token,mri_path)
if mri_parsed_xml is None :
if recursive_checkin :
# todo : this should be upload_path, not uploaddicom
# mri image may not be a dicom directory
mri_parsed_xml = dicomobject.upload_image_from_path(server,token,mri_path)
if mri_parsed_xml is None :
raise Exception('Failed to check in image '+mri_path)
else :
raise Exception('MRI at path '+mri_path+' not in database : should check it in')
mri_id = common.get_id_from_parsed_xml(mri_parsed_xml)
subject_id = common.get_parents_from_parsed_xml(mri_parsed_xml)[0]
parentdataids['MRI']=mri_id
if 'CT_file' in bkparam :
ct_path = bkparam['CT_file'][1]
ct_parsed_xml= common.get_database_xml_from_path(server,token,ct_path)
if ct_id is None :
if recursive_checkin :
ct_parsed_xml=dicomobject.upload_image_from_path(server,token,ct_path,parent_id=subject_id)
else:
raise Exception('CT at path '+ct_path+' not in database : should check it in')
ct_id=common.get_id_from_parsed_xml(ct_parsed_xml)
parentdataids['CT']=ct_id
# I have seen parameters of form GPS_sensor_file_(CT_2_MRI),
# I will assume I can find a single key that starts with GPS_sensor_file
GPS_key = [x for x in bkparam.keys() if x.startswith('GPS_sensor_file') and len(bkparam[x])==2]
if len(GPS_key)>1 :
raise Exception('Unexpected number of GPS_sensor_file parameters found')
if len(GPS_key)>0 :
gps_path = bkparam[GPS_key[0]][1]
gps_parsed_xml = common.get_database_xml_from_path(server,token,gps_path)
if gps_parsed_xml is None :
if recursive_checkin :
gps_parsed_xml=gpsobject.uploadgps(server,token,gps_path,subject_id=subject_id)
else :
raise Exception('GPS at path '+gps_path+' not in database : should check it in')
gps_id=common.get_id_from_parsed_xml(gps_parsed_xml)
parentdataids['GPS']=gps_id
# todo :
# similar code for CT_file, GPS_file (or whatever they get called by BrainK)
tmpdname=tempfile.mkdtemp()
bkhead,bktail=os.path.split(bkstub)
zipfilename = os.sep.join([tmpdname,bktail+'-bkout.zip'])
try :
print 'creating braink zipfile',
zfile=zipbkstub(bkstub,zipfilename)
print
brainkdoc=brainkdocument(bkstub,parentdataids,zipfilename)
client=poauth.OAuthClient(token)
response=client.post(server+'/object.xml',
data={'object':brainkdoc.toxml()},
files={'file': open(zfile.filename,'rb')} )
#return etree.fromstring(response.text)
return common.parse_xml_from_server(response.text)
finally :
shutil.rmtree(tmpdname,ignore_errors=True)