def __init__(self, uniq, resource, path, **kw):
""" Returns table information """
super(TableExcel, self).__init__(uniq, resource, path, **kw)
if self.t is None:
# try to load the resource binary
b = blob_service.localpath(uniq, resource=resource) or abort (404, 'File not available from blob service')
self.filename = b.path
self.info()
def __init__(self, uniq, resource, path, **kw):
super(PipelineDream3D, self).__init__(uniq, resource, path, **kw)
# try to load the resource binary
b = blob_service.localpath(uniq, resource=resource) or abort (404, 'File not available from blob service')
self.filename = b.path
self.data = {}
raw_pipeline = '{}'
with open(self.filename, 'r') as pipeline_file:
self.data = dream3d_to_json(pipeline_file)
def get_blobs(self, blocking=True):
self.validate()
if self.files is not None:
# dima: do file existence check here
# re-request blob service if unavailable
#log.debug('%s blob from cache'%self.uniq)
return self.files
self.get_resource()
self.files = blob_service.localpath(self.uniq, resource=self.resource, blocking=blocking)
self.ts_files = datetime.now()
return self.files
def __init__(self, uniq, resource, path, **kw):
""" Returns table information """
super(TableHDF, self).__init__(uniq, resource, path, **kw)
if self.t is None:
# try to load the resource binary
b = blob_service.localpath(uniq, resource=resource) or abort (404, 'File not available from blob service')
self.filename = b.path
try:
self.info()
except Exception:
# close any open table
if self.t is not None:
self.t.close()
raise
def __init__(self, uniq, resource, path, **kw):
super(PipelineIJ, self).__init__(uniq, resource, path, **kw)
# allow to initialize with JSON directly
self.filename = None
self.data = kw.get('data', None)
if self.data:
return
# try to load the resource binary
b = blob_service.localpath(uniq, resource=resource) or abort(
404, 'File not available from blob service')
self.filename = b.path
self.data = {}
raw_pipeline = []
with open(self.filename, 'r') as pipeline_file:
self.data = imagej_to_json(pipeline_file)
def fileInfo(relpath, uri, index=0):
xml = data_service.get_resource(uri, view='deep,clean')
if xml is None:
log.warn('skipping unreadable uri %s', uri)
return None
name = xml.get('name')
uniq = xml.get('resource_uniq', None)
# try to figure out a name for the resource
if not name:
name = xml.xpath('./tag[@name="filename"]') or xml.xpath(
'./tag[@name="name"]')
name = name and name[0].get('value')
if not name and uniq:
name = uniq[-4]
if not name:
name = str(index)
path = None
files = None
if uniq is not None:
#del xml.attrib['resource_uniq'] # dima: strip resource_uniq from exported xml
b = blob_service.localpath(uniq)
if b:
files = b.files
if files is not None and len(files) > 0:
path = files[0]
else:
path = b.path
if path and not os.path.exists(path):
path = None
else:
log.warn("Resource %s ( %s ) did not have blob", uniq,
xml.tag)
# if resource is just an XML doc
content = None
if path is None:
content = etree.tostring(xml)
name = '%s_%s' % (name, uniq)
xml = None
# disambiguate file name if present
ext = '' if path is not None else '.xml'
outpath = os.path.join(relpath,
'%s%s' % (name, ext)).replace('\\', '/')
if outpath in fileHash:
fname, ext = os.path.splitext(name)
name = '%s%s%s' % (fname, uniq, ext)
outpath = os.path.join(relpath, '%s%s' % (name, ext)).replace(
'\\', '/')
fileHash[outpath] = name
if files is None or len(files) < 2:
return [{
'xml': xml,
'content': content,
'name': name,
'uniq': uniq,
'path': path,
'relpath': relpath,
'outpath': outpath,
}]
log.debug('fileInfo name: %s, path: %s, relpath: %s, outpath: %s',
name, path, relpath, outpath)
log.debug('fileInfo files: %s', files)
# find minimum relative path
min_length = sys.maxint
for f in files:
min_length = min(min_length, len(os.path.dirname(f)))
minpath = files[0][:min_length + 1]
log.debug('fileInfo minpath: %s', minpath)
# check if file disimbiguation is needed
subpath = files[0][min_length + 1:]
outpath = os.path.join(relpath, name, subpath).replace('\\', '/')
if outpath in fileHash:
name = '%s.%s' % (name, uniq)
outpath = os.path.join(relpath, name,
subpath).replace('\\', '/')
fileHash[outpath] = name
infos = []
first = True
for f in files:
subpath = f[min_length + 1:]
info = {
'name':
os.path.basename(f),
'uniq':
uniq,
'path':
f,
'relpath':
relpath,
'outpath':
os.path.join(relpath, name, subpath).replace('\\', '/'),
'subpath':
subpath.replace('\\', '/'),
}
if first is True:
first = False
info['xml'] = xml
info['content'] = content
infos.append(info)
log.debug('fileInfo infos: %s', infos)
return infos